Seed endophytes across cultivars and species, associated compositions, and methods of use thereof

Abstract
Materials and methods for improving plant traits and for providing plant fitness benefits are provided. In some embodiments, the materials, and methods employing the same, can comprise endophytes.
Description
SEQUENCE LISTING

The instant application contains a Sequence Listing with 4957 sequences which has been submitted via EFS-Web and is hereby incorporated by reference in its entirety. Said ASCII copy, created on Jun. 27, 2017, is named 32831US_10035US_Sequence_Listing.txt, and is 21,064,136 bytes in size.


FIELD OF THE INVENTION

Among other things, inventions disclosed herein relate to compositions and methods for improving the cultivation of plants, particularly agricultural plants. In an aspect, inventions described herein relate to beneficial bacteria and fungi that are capable of living in a plant, which may be used to impart improved agronomic traits to the plants. In another aspect, inventions described herein relate to methods of improving plant characteristics by introducing synthetic combinations of such beneficial bacteria and/or fungi to those plants. Further, inventions described herein also provide methods of treating seeds and other plant elements with synthetic combinations of beneficial bacteria and/or fungi that are capable of living within a plant, to impart improved agronomic characteristics to plants, particularly agricultural plants.


BACKGROUND

Agriculture faces numerous challenges that are making it increasingly difficult to provide food, materials, and fuels to the world's population. Population growth and changes in diet associated with rising incomes are increasing global food demand, while many key resources for agriculture are becoming increasingly scarce. By 2050, the FAO projects that total food production must increase by 70% to meet the needs of the growing population, a challenge that is exacerbated by numerous factors, including diminishing freshwater resources, increasing competition for arable land, rising energy prices, increasing input costs, and the likely need for crops to adapt to the pressures of a more extreme global climate. The need to grow nearly twice as much food in more uncertain climates is driving a critical need for new innovations.


Today, crop performance is optimized via of technologies directed towards the interplay between crop genotype (e.g., plant breeding, genetically-modified (GM) crops) and its surrounding environment (e.g., fertilizer, synthetic herbicides, pesticides). While these paradigms have assisted in doubling global food production in the past fifty years, yield growth rates have stalled in many major crops and shifts in the climate have been linked to production declines in important crops such as wheat. In addition to their long development and regulatory timelines, public fears of GM-crops and synthetic chemicals has challenged their use in many key crops and countries, resulting in a complete lack of acceptance for GM traits in wheat and the exclusion of GM crops and many synthetic chemistries from European markets. Thus, there is a significant need for innovative, effective, and publically-acceptable approaches to improving the intrinsic yield and resilience of crops to severe stresses.


SUMMARY OF THE INVENTION

The disclosures of PCT/US2014/044427, filed Jun. 26, 2014, U.S. application Ser. No. 14/316,469, filed Jun. 26, 2014, and PCT/US2014/054160, filed Sep. 4, 2014, are incorporated by reference in their entirety, including the sequence listings containing SEQ ID NOs: 1-1448.


The present invention is based on the discovery that a plant element (e.g., a whole plant, seedling, meristematic tissue, ground tissue, vascular tissue, dermal tissue, seed, leaf, root, shoot, stem, flower, fruit, stolon, bulb, tuber, corm, kelkis, shoot, bud) can be effectively augmented by associating its surface with a single endophyte strain or a plurality of endophytes in an amount that is not normally found on the plant element. Endophytes described herein can be isolated from inside the same plant or a different plant, or from inside a part or tissue of the same plant or different plant. The plant element thus associated with a single endophyte strain or a plurality of endophytes can be used to confer improved agronomic trait or traits to the seed or the plant that is grown or derived from the plant element.


In an embodiment, the invention features a method for improving an agricultural trait in an agricultural plant. In an embodiment, the method includes providing an agricultural plant, seed or tissue thereof; contacting the plant, seed or tissue thereof with a formulation comprising an endophyte that is common to at least two donor plant types that is present in the formulation in an amount effective to colonize the plant; and growing the plants under conditions that allow the endophyte to improve a trait in the plant. In some embodiments, the two donor plants are of the same family. In some embodiments, the two donor plants are of the same genus. In some embodiments, the two donor plants are of the same species. In some embodiments, the agricultural plant tissue, is a seed. In a further embodiment, the population is disposed on the surface of the seed.


In an embodiment, the method for improving an agricultural trait in an agricultural plant includes providing a modern agricultural plant, seed or tissue thereof; contacting the plant, seed, or tissue thereof with a formulation comprising an endophyte derived from an ancestral plant in an amount effective to colonize the plant; and allowing the plant to grow under conditions that allow the endophyte to colonize the plant.


The invention also features a method for preparing a seed comprising an endophyte population. The method comprising applying to an exterior surface of a seed a formulation comprising an endophyte population consisting essentially of an endophyte comprising a 16S rRNA or ITS rRNA nucleic acid sequence at least 95% identical to a nucleic acid sequence selected from the group consisting of SEQ ID NOs: 1-455.


In some embodiments, provided herein is a method for treating seedlings. The method includes contacting foliage or the rhizosphere of a plurality of agricultural plant seedlings with a seed a formulation comprising an endophyte population consisting essentially of an endophyte comprising a 16S rRNA or ITS rRNA nucleic acid sequence at least 95% identical to a nucleic acid sequence selected from the group consisting of SEQ ID NOs: 1-455; and growing the contacted seedlings.


The invention also features a method for modulating a plant trait. The method includes applying to vegetation or an area adjacent the vegetation, a seed a formulation comprising an endophyte population consisting essentially of an endophyte comprising a 16S rRNA or ITS rRNA nucleic acid sequence at least 95% identical to a nucleic acid sequence selected from the group consisting of SEQ ID NOs: 1-455, wherein the formulation is capable of providing a benefit to the vegetation, or to a crop produced from the vegetation.


A method for modulating a plant trait also is featured. The method comprising applying a formulation to soil, the seed a formulation comprising an endophyte population consisting essentially of an endophyte comprising a 16S rRNA or ITS rRNA nucleic acid sequence at least 95% identical to a nucleic acid sequence selected from the group consisting of SEQ ID NOs: 1-455, wherein the formulation is capable of providing a benefit to seeds planted within the soil, or to a crop produced from plants grown in the soil.


In some embodiments, the endophyte comprises a 16S rRNA or ITS rRNA nucleic acid sequence at least 95% identical to a nucleic acid sequence selected from the group consisting of SEQ ID NOs: 1-455. In some embodiments, the endophyte is capable of a function or activity selected from the group consisting of auxin production, nitrogen fixation, production of an antimicrobial compound, mineral phosphate solubilization, siderophore production, cellulase production, chitinase production, xylanase production, and acetoin production. In some embodiments, the endophyte exhibits at least two of: auxin production, nitrogen fixation, production of an antimicrobial compound, mineral phosphate solubilization, siderophore production, cellulase production, chitinase production, xylanase production, and acetoin production.


In some embodiments, the endophyte is capable of metabolizing at least one substrate selected from the group consisting of: a-D-glucose, arabinose, arbutin, b-methyl-D-galactoside, b-methyl-D-glucoside, D-alanine, D-arabitol, D-aspartic acid, D-cellobiose, dextrin, D-fructose, D-galactose, D-gluconic acid, D-glucosamine, dihydroxyacetone, DL-malic acid, D-mannitol, D-mannose, D-melezitose, D-melibiose, D-raffinose, D-ribose, D-serine, D-threonine, D-trehalose, D-xylose, g-amino-N-butyric acid, g-cyclodextrin, gelatin, gentiobiose, glycogen, glycyl-L-aspartic acid, glycyl-L-glutamic acid, glycyl-L-proline, glyoxylic acid, i-erythritol, inosine, L-alanine, L-alanyl-glycine, L-arabinose, L-asparagine, L-aspartic acid, L-galactonic acid-g-lactone, L-glutamic acid, L-glutamine, L-histidine, L-proline, L-rhamnose, L-serine, L-threonine, maltitol, maltose, maltotriose, mannose, N-acetyl-D-glucosamine, oxalic acid, palatinose, pectin, proline, salicin, stachyose, sucrose, trehalose, turanose, tyramine, uridine, and xylose.


In some embodiments, the endophyte is capable of metabolizing at least two substrates selected from the group consisting of: a-D-glucose, arabinose, arbutin, b-methyl-D-galactoside, b-methyl-D-glucoside, D-alanine, D-arabitol, D-aspartic acid, D-cellobiose, dextrin, D-fructose, D-galactose, D-gluconic acid, D-glucosamine, dihydroxyacetone, DL-malic acid, D-mannitol, D-mannose, D-melezitose, D-melibiose, D-raffinose, D-ribose, D-serine, D-threonine, D-trehalose, D-xylose, g-amino-N-butyric acid, g-cyclodextrin, gelatin, gentiobiose, glycogen, glycyl-L-aspartic acid, glycyl-L-glutamic acid, glycyl-L-proline, glyoxylic acid, i-erythritol, inosine, L-alanine, L-alanyl-glycine, L-arabinose, L-asparagine, L-aspartic acid, L-galactonic acid-g-lactone, L-glutamic acid, L-glutamine, L-histidine, L-proline, L-rhamnose, L-serine, L-threonine, maltitol, maltose, maltotriose, mannose, N-acetyl-D-glucosamine, oxalic acid, palatinose, pectin, proline, salicin, stachyose, sucrose, trehalose, turanose, tyramine, uridine, and xylose.


In some embodiments, the endophyte is present at a concentration of at least 102 CFU or spores per seed on the surface of seeds after contacting. In some embodiments, the applying or contacting comprises spraying, immersing, coating, encapsulating, or dusting the seeds or seedlings with the formulation.


In some embodiments, the benefit or agricultural trait is selected from the group consisting of: increased root biomass, increased root length, increased height, increased shoot length, increased leaf number, increased water use efficiency, increased tolerance to low nitrogen stress, increased nitrogen use efficiency, increased overall biomass, increased grain yield, increased photosynthesis rate, increased tolerance to drought, increased heat tolerance, increased salt tolerance, increased resistance to nematode stress, increased resistance to a fungal pathogen, increased resistance to a bacterial pathogen, increased resistance to a viral pathogen, a detectable modulation in the level of a metabolite, a detectable modulation in the transcriptome, and a detectable modulation in the proteome, relative to reference seeds or agricultural plants derived from reference seeds. In some embodiments, the benefit or agricultural trait comprises at least two benefits or agricultural traits selected from the group consisting of: increased root biomass, increased root length, increased height, increased shoot length, increased leaf number, increased water use efficiency, increased tolerance to low nitrogen stress, increased nitrogen use efficiency, increased overall biomass, increased grain yield, increased photosynthesis rate, increased tolerance to drought, increased heat tolerance, increased salt tolerance, increased resistance to nematode stress, increased resistance to a fungal pathogen, increased resistance to a bacterial pathogen, increased resistance to a viral pathogen, a detectable modulation in the level of a metabolite, a detectable modulation in the transcriptome, and a detectable modulation in the proteome, relative to reference seeds or agricultural plants derived from reference seeds. In some embodiments, the benefit is increased tolerance to low nitrogen stress or increased nitrogen use efficiency, and the endophyte is non-diazotrophic.


In some embodiments, the formulation comprises at least one member selected from the group consisting of an agriculturally compatible carrier, a tackifier, a microbial stabilizer, a fungicide, an antibacterial agent, an herbicide, a nematicide, an insecticide, a plant growth regulator, a rodenticide, and a nutrient.


In some embodiments, the endophyte comprises a nucleic acid sequence that is at least 97% identical to a nucleic acid sequence selected from the group consisting of SEQ ID NOs: 1-455, wherein the endophyte is present in the formulation in an amount effective to colonize the mature agricultural plant. In some embodiments, the endophyte comprises a nucleic acid sequence that is at least 99% identical to a nucleic acid sequence selected from the group consisting of SEQ ID NOs: 1-455, wherein the endophyte is present in the formulation in an amount effective to colonize the mature agricultural plant. In some embodiments, the endophyte comprises a nucleic acid sequence that is at least 99.5% identical to a nucleic acid sequence selected from the group consisting of SEQ ID NOs: 1-455, wherein the endophyte is present in the formulation in an amount effective to colonize the mature agricultural plant.


In some embodiments, the plant, seed or tissue thereof is contacted with at least 10 CFU or spores, at least 100 CFU or spores, at least 300 CFU or spores, at least 1,000 CFU or spores, at least 3,000 CFU or spores, at least 10,000 CFU or spores, at least 30,000 CFU or spores, at least 100,000 CFU or spores, at least 300,000 CFU or spores, at least 1,000,000 CFU or spores, or more, of the endophyte.


In some embodiments, the formulation comprises at least two endophytes comprising a nucleic acid sequence that is at least 97% identical, at least 98% identical, at least 99% identical, at least 99.5% identical, or 100% identical, to a nucleic acid sequence selected from the group consisting of SEQ ID NOs: 1-455, wherein the at least two endophytes are present in the formulation in an amount effective to colonize the mature agricultural plant. In some embodiments, the formulation comprises at least two endophytes provided in Table 1, Table 2, Table 7 and Table 8.


In some embodiments, the plant is a monocot. The monocot can be corn, wheat, barley or rice. In some embodiments, the plant is a dicot. The dicot can be a soybean, peanut, canola, cotton, Brassica Napus, cabbage, lettuce, melon, strawberry, turnip, watermelon, tomato or pepper.


In some embodiments, the endophyte is present in the formulation in an amount effective to be detectable within a target tissue of the agricultural plant selected from a fruit, seed, leaf, root or portion thereof.


In some embodiments, the endophyte is detected in an amount of at least 10 CFU or spores, at least 100 CFU or spores, at least 300 CFU or spores, at least 1,000 CFU or spores, at least 3,000 CFU or spores, at least 10,000 CFU or spores, at least 30,000 CFU or spores, at least 100,000 CFU or spores, at least 300,000 CFU or spores, at least 1,000,000 CFU or spores, or more, in the target tissue.


In some embodiments, the endophyte is present in the formulation in an amount effective to increase the biomass and/or yield of the fruit or seed produced by the plant by at least 1%, at least 2%, at least 3%, at least 5%, at least 10%, at least 15%, at least 20%, at least 30%, at least 40%, at least 50%, at least 60%, at least 70%, at least 80%, at least 90%, at least 100%, or more, when compared with the fruit or seed of a reference agricultural plant.


In some embodiments, the endophyte is present in the formulation in an amount effective to detectably increase the biomass of the plant or tissue thereof. In some embodiments, the biomass of the plant, or tissue thereof is detectably increased by at least 1%, at least 2%, at least 3%, at least 5%, at least 10%, at least 15%, at least 20%, at least 30%, at least 40%, at least 50%, at least 60%, at least 70%, at least 80%, at least 90%, at least 100%, or more, when compared with a reference agricultural plant.


In some embodiments, the endophyte is present in the formulation in an amount effective to detectably increase the rate of germination of the seed. In some embodiments, the rate of germination of the seed is increased by at least 0.5%, at least 1%, at least 2%, at least 3%, at least 5%, at least 10%, at least 20%, at least 30%, at least 40%, at least 50%, at least 60%, at least 70%, at least 80%, at least 90%, at least 100% or more, when compared with a reference agricultural plant.


In some embodiments, the endophyte is present in the formulation in an amount effective to detectably induce production of auxin in the plant. In some embodiments, the production of auxin in the plant is increased by at least 1%, at least 2%, at least 3%, at least 5%, at least 10%, at least 20%, at least 30%, at least 40%, at least 50%, at least 60%, at least 70%, at least 80%, at least 90%, at least 100% or more, when compared with a reference agricultural plant.


The invention also features an agricultural plant, or portion of tissue thereof, comprising a formulation comprising an endophyte that is common to at least two donor plant types that is disposed on an exterior surface of the plant or portion of tissue thereof, or within the plant or portion of tissue thereof, in an amount effective to colonize the plant, and in an amount effective to provide a benefit to the modern agricultural plant.


In some embodiments of the agricultural plant, or portion of tissue thereof, the endophyte comprises a nucleic acid sequence that is at least 97% identical to a nucleic acid sequence selected from the group consisting of SEQ ID NOs: 1-455. In some embodiments of the agricultural plant, or portion of tissue thereof, the endophyte comprises a nucleic acid sequence that is at least 99% identical to a nucleic acid sequence selected from the group consisting of SEQ ID NOs: 1-455. In some embodiments of the agricultural plant, or portion of tissue thereof, the endophyte comprises a nucleic acid sequence that is at least 99.5% identical to a nucleic acid sequence selected from the group consisting of SEQ ID NOs: 1-455.


In some embodiments of the agricultural plant, or portion of tissue thereof, the endophyte is capable of a function or activity selected from the group consisting of auxin production, nitrogen fixation, production of an antimicrobial compound, mineral phosphate solubilization, siderophore production, cellulase production, chitinase production, xylanase production, and acetoin production.


In some embodiments of the agricultural plant, or portion of tissue thereof, the endophyte exhibits at least two of: auxin production, nitrogen fixation, production of an antimicrobial compound, mineral phosphate solubilization, siderophore production, cellulase production, chitinase production, xylanase production, and acetoin production.


In some embodiments of the agricultural plant, or portion of tissue thereof, the endophyte is capable of metabolizing at least one substrate selected from the group consisting of: a-D-glucose, arabinose, arbutin, b-methyl-D-galactoside, b-methyl-D-glucoside, D-alanine, D-arabitol, D-aspartic acid, D-cellobiose, dextrin, D-fructose, D-galactose, D-gluconic acid, D-glucosamine, dihydroxyacetone, DL-malic acid, D-mannitol, D-mannose, D-melezitose, D-melibiose, D-raffinose, D-ribose, D-serine, D-threonine, D-trehalose, D-xylose, g-amino-N-butyric acid, g-cyclodextrin, gelatin, gentiobiose, glycogen, glycyl-L-aspartic acid, glycyl-L-glutamic acid, glycyl-L-proline, glyoxylic acid, i-erythritol, inosine, L-alanine, L-alanyl-glycine, L-arabinose, L-asparagine, L-aspartic acid, L-galactonic acid-g-lactone, L-glutamic acid, L-glutamine, L-histidine, L-proline, L-rhamnose, L-serine, L-threonine, maltitol, maltose, maltotriose, mannose, N-acetyl-D-glucosamine, oxalic acid, palatinose, pectin, proline, salicin, stachyose, sucrose, trehalose, turanose, tyramine, uridine, and xylose.


In some embodiments of the agricultural plant, or portion of tissue thereof, the endophyte is capable of metabolizing at least two substrates selected from the group consisting of: a-D-glucose, arabinose, arbutin, b-methyl-D-galactoside, b-methyl-D-glucoside, D-alanine, D-arabitol, D-aspartic acid, D-cellobiose, dextrin, D-fructose, D-galactose, D-gluconic acid, D-glucosamine, dihydroxyacetone, DL-malic acid, D-mannitol, D-mannose, D-melezitose, D-melibiose, D-raffinose, D-ribose, D-serine, D-threonine, D-trehalose, D-xylose, g-amino-N-butyric acid, g-cyclodextrin, gelatin, gentiobiose, glycogen, glycyl-L-aspartic acid, glycyl-L-glutamic acid, glycyl-L-proline, glyoxylic acid, i-erythritol, inosine, L-alanine, L-alanyl-glycine, L-arabinose, L-asparagine, L-aspartic acid, L-galactonic acid-g-lactone, L-glutamic acid, L-glutamine, L-histidine, L-proline, L-rhamnose, L-serine, L-threonine, maltitol, maltose, maltotriose, mannose, N-acetyl-D-glucosamine, oxalic acid, palatinose, pectin, proline, salicin, stachyose, sucrose, trehalose, turanose; tyramine, uridine, and xylose.


In some embodiments of the agricultural plant, or portion of tissue thereof, the formulation is disposed on an exterior surface of the plant or portion of tissue thereof, or within the plant or portion of tissue thereof, by spraying, immersing, coating, encapsulating, or dusting the plant or portion of tissue thereof with the formulation.


In some embodiments, the agricultural plant, or portion of tissue thereof further comprises a formulation that comprises at least one member selected from the group consisting of an agriculturally compatible carrier, a tackifier, a microbial stabilizer, a fungicide, an antibacterial agent, an herbicide, a nematicide, an insecticide, a plant growth regulator, a rodenticide, and a nutrient.


In some embodiments of the agricultural plant, or portion of tissue thereof, the benefit is selected from the group consisting of: increased root biomass, increased root length, increased height, increased shoot length, increased leaf number, increased water use efficiency, increased tolerance to low nitrogen stress, increased nitrogen use efficiency, increased overall biomass, increased yield, increased photosynthesis rate, increased tolerance to drought, increased heat tolerance, increased salt tolerance, increased resistance to nematode stress, increased resistance to a fungal pathogen, increased resistance to a bacterial pathogen, increased resistance to a viral pathogen, increased resistance to herbivory, a detectable modulation in, the level of a metabolite, a detectable modulation in the proteome, and a detectable modulation in the transcriptome, relative to a reference agricultural plant.


In some embodiments of the agricultural plant, or portion of tissue thereof, the benefit comprises at least two benefits selected from the group consisting of increased: root biomass, increased root length, increased height, increased shoot length, increased leaf number, increased water use efficiency, increased tolerance to low nitrogen stress, increased nitrogen use efficiency, increased overall biomass, increased yield, increased photosynthesis rate, increased tolerance to drought, increased heat tolerance, increased salt tolerance, increased resistance to nematode stress, increased resistance to a fungal pathogen, increased resistance to a bacterial pathogen, increased resistance to a viral pathogen, increased resistance to herbivory, a detectable modulation in the level of a metabolite, a detectable modulation in the proteome, and a detectable modulation in the transcriptome, relative to a reference agricultural plant. In some embodiments of the agricultural plant, or portion of tissue thereof, the benefit is increased tolerance to low nitrogen stress or increased nitrogen use efficiency, and the endophyte is non-diazotrophic.


In some embodiments of the agricultural plant, or portion of tissue thereof, the plant or portion of tissue thereof is contacted with at least 10 CFU or spores, at least 100 CFU or spores, at least 300 CFU or spores, at least 1,000 CFU or spores, at least 3,000 CFU or spores, at least 10,000 CFU or spores; at least 30,000 CFU or spores, at least 100,000 CFU or spores, at least 300,000 CFU or spores, at least 1,000,000 CFU or spores, or more, of the endophyte. In some embodiments of the agricultural plant, or portion of tissue thereof, the plant tissue is a seed. In a further embodiment, the endophyte is disposed on the surface of the seed.


In some embodiments, the agricultural plant, or portion of tissue thereof comprises at least two endophytes comprising a nucleic acid sequence that is at least 97% identical, at least 98% identical, at least 99% identical, at least 99.5% identical, or 100% identical, to a nucleic acid sequence selected from the group consisting of SEQ ID NOs: 1-455 in an amount effective to colonize the mature agricultural plant. In some embodiments of the agricultural plant, or portion of tissue thereof, the two endophytes are selected from the groups disclosed in Table 1, Table 2, Table 7 and Table 8.


In some embodiments, the agricultural plant is a monocot. In some embodiments, the portion of tissue thereof is derived from a monocot. The monocot can be corn, wheat, barley or rice.


In some embodiments, the agricultural plant is a dicot. In some embodiments, the portion of tissue thereof is derived from a dicot. The dicot can be a soybean, canola, cotton, Brassica Napus, tomato or pepper.


In some embodiments of the agricultural plant, or portion of tissue thereof, the endophyte is disposed in an amount effective to be detectable within a target tissue of the mature target tissue of the mature agricultural plant selected from a fruit, seed, leaf, root or portion thereof.


In some embodiments of the agricultural plant, or portion of tissue thereof, the population is disposed in an amount effective to increase the rate of germination of the seed. The rate of germination of the seed can be increased by at least 0.5%, at least 1%, at least 2%, at least 3%, at least 5%, at least 10%, at least 20%, at least 30%, at least 40%, at least 50%, at least 60%, at least 70%, at least 80%, at least 90%, at least 100% or more, when compared with a reference agricultural plant.


In some embodiments of the agricultural plant, or portion of tissue thereof, the population is disposed in an amount effective to be detectable within a target tissue of the mature plant. The target tissue can be the root, shoot, leaf, flower, fruit or seed.


In some embodiments of the agricultural plant, or portion of tissue thereof, the population is detected in an amount of at least 10 CFU or spores, at least 100 CFU or spores, at least 300 CFU or spores, at least 1,000 CFU or spores, at least 3,000 CFU or spores, at least 10,000 CFU or spores, at least 30,000 CFU or spores, at least 100,000 CFU or spores, at least 300,000 CFU or spores, at least 1,000,000 CFU or spores, or more, in the plant or target tissue thereof.


In some embodiments of the agricultural plant, or portion of tissue thereof, the population of is disposed in an amount effective to be detectable in the rhizosphere surrounding the plant. The population can be detected in an amount of at least 10 CFU or spores, at least 100 CFU or spores, at least 300 CFU or spores, at least 1,000 CFU or spores, at least 3,000 CFU or spores, at least 10,000 CFU or spores, at least 30,000 CFU or spores, at least 100,000 CFU or spores, at least 300,000 CFU or spores, at least 1,000,000 CFU or spores, or more, in the rhizosphere surrounding the plant.


In some embodiments of the agricultural plant, or portion of tissue thereof, the population is disposed in an amount effective to detectably increase the biomass of the plant. The biomass of the plant can be detectably increased by at least 1%, at least 2%, at least 3%, at least 5%, at least 10%, at least 15%, at least 20%, at least 30%, at least 40%, at least 50%, at least 60%, at least 70%, at least 80%, at least 90%, at least 100%, or more, when compared with a reference agricultural plant.


In some embodiments of the agricultural plant, or portion of tissue thereof, the population is disposed in an amount effective to increase the biomass of a fruit or seed of the plant. The biomass of the fruit or seed of the plant can be detectably increased by at least 1%, at least 2%, at least 3%, at least 5%, at least 10%, at least 15%, at least 20%, at least 30%, at least 40%, at least 50%, at least 60%, at least 70%, at least 80%, at least 90%, at least 100%, or more, when compared with the fruit or seed of a reference agricultural plant.


In some embodiments of the agricultural plant, or portion of tissue thereof, the population is disposed in an amount effective to increase the height of the plant. The height of the plant can be increased by at least 1%, at least 2%, at least 3%, at least 5%, at least 10%, at least 15%, at least 20%, at least 30%, at least 40%, at least 50%, at least 60%, at least 70%, at least 80%, at least 90%, at least 100%, or more, when compared with the height of a reference agricultural plant.


In some embodiments of the agricultural plant, or portion of tissue thereof, the population is disposed in an amount effective to increase production of auxin in the plant. The auxin production of the plant can be increased by at least 1%, at least 2%, at least 3%, at least 5%, at least 10%, at least 15%, at least 20%, at least 30%, at least 40%, at least 50%, at least 60%, at least 70%, at least 80%, at least 90%, at least 100%, or more, when compared with the auxin production of a reference agricultural plant.


In some embodiments of the agricultural plant, or portion of tissue thereof, the population is disposed in an amount effective to increase production of acetoin in the plant. The acetoin production of the plant can be increased by at least 1%, at least 2%, at least 3%, at least 5%, at least 10%, at least 15%, at least 20%, at least 30%, at least 40%, at least 50%, at least 60%, at least 70%, at least 80%, at least 90%, at least 100%, or more, when compared with the acetoin production of a reference agricultural plant.


In some embodiments of the agricultural plant, or portion of tissue thereof, the population is disposed in an amount effective to increase production of siderophore in the plant. The siderophore production of the plant can be increased by at least 1%, at least 2%, at least 3%, at least 5%, at least 10%, at least 15%, at least 20%, at least 30%, at least 40%, at least 50%, at least 60%, at least 70%, at least 80%, at least 90%, at least 100%, or more, when compared with the siderophore production of a reference agricultural plant.


In some embodiments of the agricultural plant, or portion of tissue thereof, the population is disposed in an amount effective to increase resistance to one or more stress conditions selected from the group consisting of a drought stress, heat stress, cold stress, salt stress, and low mineral stress.


In some embodiments of the agricultural plant, or portion of tissue thereof, the population is disposed in an amount effective to effective to increase resistance to one or more biotic stress conditions selected from the group consisting of a nematode stress, insect herbivory stress, fungal pathogen stress, bacterial pathogen stress, and viral pathogen stress.


The invention also features bag comprising at least 1,000 seeds, wherein each seed comprises a formulation comprising an endophyte that is common to at least two donor plant types that is disposed on an exterior surface of the plant or portion of tissue thereof, or within the plant or portion of tissue thereof, in an amount effective to colonize the plant, and in an amount effective to provide a benefit to the modern agricultural plant, wherein each seed is contacted with at least 10 CFU or spores, at least 100 CFU or spores, at least 300 CFU or spores, at least 1,000 CFU or spores, at least 3,000 CFU or spores, at least 10,000 CFU or spores, at least 30,000 CFU or spores, at least 100,000 CFU or spores, at least 300,000 CFU or spores, at least 1,000,000 CFU or spores, or more, of the endophyte, and wherein the bag further comprises a label describing the seeds and/or the population.


In an embodiment, the invention features an agricultural formulation comprising an endophyte comprising a nucleic acid sequence that is at least 97% identical, at least 98% identical, at least 99% identical, at least 99.5% identical, or 100% identical, to a nucleic acid sequence selected from the group consisting of SEQ ID NOs: 1-455 that is present in an amount effective to colonize a mature agricultural plant, wherein the formulation further comprises at least one member selected from the group consisting of an agriculturally compatible carrier, a tackifier, a microbial stabilizer, a fungicide, an antibacterial agent, an herbicide, a nematicide, an insecticide, a plant growth regulator, a rodenticide, and a nutrient.


In some embodiments of the agricultural formulation, the agricultural plant is a monocot. The monocot can be maize, barley, rice, or wheat. In some embodiments of the agricultural formulation, the agricultural plant is a dicot. The dicot can be soybean, canola, cotton, Brassica Napus, tomato, squash, cucumber, pepper, peanut, sunflower, or sugar beet.


In some embodiments of the agricultural formulation, the population consists essentially of an endophyte comprising a nucleic acid sequence that is at least 99% identical to a nucleic acid sequence selected from the group consisting of SEQ ID NOs: 1-455. In some embodiments of the agricultural formulation, the population consists essentially of an endophyte comprising a nucleic acid sequence that is at least 99.5% identical to a nucleic acid sequence selected from the group consisting of SEQ ID NOs: 1-455.


The preparation of claim 87, comprising at least two different endophytes each comprise a nucleic acid sequence that is at least 97% identical, at least 98% identical, at least 99% identical, at least 99.5% identical, or 100% identical, to a nucleic acid sequence selected from the group consisting of SEQ ID NOs: 1-455.


In some embodiments of the agricultural formulation, each of the two different endophytes comprises the nucleic acid sequence disclosed in Table 1, Table 2, Table 7, and Table 8.


In some embodiments of the agricultural formulation, at least 1%, at least 5%, at least 10%, at least 20%, at least 30%, at least 40%, at least 50%, at least 75%, at least 80%, at least 90%, or at least 95% or more, of the population is in spore form.


In some embodiments of the agricultural formulation, the endophytes were adapted to culture on growth medium.


In some embodiments of the agricultural formulation, the preparation is substantially stable at temperatures between about 0° C. and about 50° C. for at least three days. In some embodiments of the agricultural formulation, the preparation is substantially stable at temperatures between about 4° C. and about 37° C. for at least thirty days.


In some embodiments, the agricultural formulation is formulated to provide a population of plants that demonstrates a substantially homogenous growth rate when introduced into agricultural production.


The invention also features a method for making the plant comprising a formulation comprising an endophyte that is common to at least two donor plant types that is disposed on an exterior surface of the plant or portion of tissue thereof, or within the plant or portion of tissue thereof, in an amount effective to colonize the plant, and in an amount effective to provide a benefit to the modern agricultural plant. The method includes providing a modern agricultural plant, and applying to the plant a formulation comprising an endophyte comprising an endophytic microbe comprising a nucleic acid sequence that is at least 97% identical, at least 98% identical, at least 99% identical, at least 99.5% identical, or 100% identical, to a nucleic acid sequence selected from the group consisting of SEQ ID NOs: 1-455 that is present in an amount effective to colonize the plant.


The invention also features a commodity plant product comprising a plant, or a portion or part thereof, comprising a formulation comprising an endophyte that is common to at least two donor plant types that is disposed on an exterior surface of the plant or portion of tissue thereof, or within the plant or portion of tissue thereof, in an amount effective to colonize the plant, and in an amount effective to provide a benefit to the modern agricultural plant. The commodity plant product can be a grain, a flour, a starch, a syrup, a meal, an oil, a film, a packaging, a nutraceutical product, a pulp, an animal feed, a fish fodder, a bulk material for industrial chemicals, a cereal product, a processed human-food product, a sugar or an alcohol and protein.


The invention also features a method of producing a commodity plant product. The method includes obtaining a plant or plant tissue from a plant, progeny or derivative thereof, the plant comprising a formulation comprising an endophyte that is common to at least two donor plant types that is disposed on an exterior surface of the plant or portion of tissue thereof, or within the plant or portion of tissue thereof, in an amount effective to colonize the plant, and in an amount effective to provide a benefit to the modern agricultural plant; and producing the commodity plant product therefrom.


The invention also features a synthetic combination comprising a purified microbial population in association with a plurality of seeds or seedlings of an agricultural plant, wherein the purified microbial population comprises a first endophyte, wherein the first endophyte comprises a 16S rRNA or ITS rRNA nucleic acid sequence at least 97% identical to a nucleic acid sequence selected from the group consisting of SEQ ID NOs: 1-455, and wherein the endophyte is present in the synthetic combination in an amount effective to provide a benefit to the seeds or seedlings or the plants derived from the seeds or seedlings.


In some embodiments of the synthetic combination comprising a purified microbial population, the first endophyte is capable of at least one of: production of an auxin, nitrogen fixation, production of an antimicrobial, production of a siderophore, mineral phosphate solubilization, production of a cellulase, production of a chitinase, production of a xylanase, and production of acetoin, or a combination of two or more thereof.


In some embodiments of the synthetic combination comprising a purified microbial population, the microbial population further comprises a second endophyte. In a further embodiment, the microbial population comprises a second microbial endophyte having an 16S rRNA or ITS rRNA nucleic acid sequence that is less than 95% identical to that of the first microbial endophyte.


In some embodiments of the synthetic combination comprising a purified microbial population, the microbial population further comprises a second endophyte, and wherein the first and second endophytes are independently capable of at least one of production of an auxin, nitrogen fixation, production of an antimicrobial, production of a siderophore, mineral phosphate solubilization, production of a cellulase, production of a chitinase, production of a xylanase, or production of acetoin, or a combination of two or more thereof.


In some embodiments of the synthetic combination comprising a purified microbial population, the first and second endophytes are independently capable of at least one of production of an auxin, nitrogen fixation, production of an antimicrobial, production of a siderophore, mineral phosphate solubilization, production of a cellulase, production of a chitinase, production of a xylanase, or production of acetoin, or a combination of two or more thereof.


In some embodiments of the synthetic combination comprising a purified microbial population, the microbial population further comprises a second endophyte, wherein the first and second endophytes are independently capable of metabolizing at least one substrate selected from the group consisting of: a-D-glucose, arabinose, arbutin, b-methyl-D-galactoside, b-methyl-D-glucoside, D-alanine, D-arabitol, D-aspartic acid, D-cellobiose, dextrin, D-fructose, D-galactose, D-gluconic acid, D-glucosamine, dihydroxyacetone, DL-malic acid, D-mannitol, D-mannose, D-melezitose, D-melibiose, D-raffinose, D-ribose, D-serine, D-threonine, D-trehalose, D-xylose, g-amino-N-butyric acid, g-cyclodextrin, gelatin, gentiobiose, glycogen, glycyl-L-aspartic acid, glycyl-L-glutamic acid, glycyl-L-proline, glyoxylic acid, i-erythritol, inosine, L-alanine, L-alanyl-glycine, L-arabinose, L-asparagine, L-aspartic acid, L-galactonic acid-g-lactone, L-glutamic acid, L-glutamine, L-histidine, L-proline, L-rhamnose, L-serine, L-threonine, maltitol, maltose, maltotriose, mannose, N-acetyl-D-glucosamine, oxalic acid, palatinose, pectin, proline, salicin, stachyose, sucrose, trehalose, turanose, tyramine, uridine, and xylose, or a combination of two or more thereof.


The invention also features a synthetic combination comprising at least two endophytes associated with a seed, wherein at least the first endophyte is heterologous to the seed and wherein the first endophyte comprises a 16S rRNA or ITS rRNA nucleic acid sequence at least 97% identical to a nucleic acid sequence selected from the group consisting of SEQ ID NOs: 1-455, wherein the endophytes are present in the formulation in an amount effective to provide a benefit to the seeds or seedlings or the plants derived from the seeds or seedlings.


In some embodiments of the synthetic combination comprising at least two endophytes, the second endophyte is a bacterial endophyte. In some embodiments of the synthetic combination comprising at least two endophytes, the second endophyte is a fungal endophyte.


In some embodiments of the synthetic combination comprising at least two endophytes, the first endophyte is a fungal endophyte. In some embodiments of the synthetic combination comprising at least two endophytes, the first endophyte is a fungal endophyte and the second endophyte is a fungal endophyte. In some embodiments of the synthetic combination comprising at least two endophytes, the first endophyte is a fungal endophyte and the second endophyte is a bacterial endophyte.


In some embodiments of the synthetic combination comprising at least two endophytes, the first and second endophytes are independently capable of, metabolizing at least one substrate selected from the group consisting of: a-D-glucose, arabinose, arbutin, b-methyl-D-galactoside, b-methyl-D-glucoside, D-alanine, D-arabitol, D-aspartic acid, D-cellobiose, dextrin, D-fructose, D-galactose, D-gluconic acid, D-glucosamine, dihydroxyacetone, DL-malic acid, D-mannitol, D-mannose, D-melezitose, D-melibiose, D-raffinose, D-ribose, D-serine, D-threonine, D-trehalose, D-xylose, g-amino-N-butyric acid, g-cyclodextrin, gelatin, gentiobiose, glycogen, glycyl-L-aspartic acid, glycyl-L-glutamic acid, glycyl-L-proline, glyoxylic acid, i-erythritol, inosine, L-alanine, L-alanyl-glycine, L-arabinose, L-asparagine, L-aspartic acid, L-galactonic acid-g-lactone, L-glutamic acid, L-glutamine, L-histidine, L-proline, L-rhamnose, L-serine, L-threonine, maltitol, maltose, maltotriose, mannose, N-acetyl-D-glucosamine, oxalic acid, palatinose, pectin, proline, salicin, stachyose, sucrose, trehalose, turanose, tyramine, uridine, and xylose, or a combination of two or more thereof.


In some embodiments of any of the synthetic combinations, the first endophyte is capable of metabolizing at least one substrate selected from the group of: a-D-glucose, arabinose, arbutin, b-methyl-D-galactoside, b-methyl-D-glucoside, D-alanine, D-arabitol, D-aspartic acid, D-cellobiose, dextrin, D-fructose, D-galactose, D-gluconic acid, D-glucosamine, dihydroxyacetone, DL-malic acid, D-mannitol, D-mannose, D-melezitose, D-melibiose, D-raffinose, D-ribose, D-serine, D-threonine, D-trehalose, D-xylose, g-amino-N-butyric acid, g-cyclodextrin, gelatin, gentiobiose, glycogen, glycyl-L-aspartic acid, glycyl-L-glutamic acid, glycyl-L-proline, glyoxylic acid, i-erythritol, inosine, L-alanine, L-alanyl-glycine, L-arabinose, L-asparagine, L-aspartic acid, L-galactonic acid-g-lactone, L-glutamic acid, L-glutamine, L-histidine, L-proline, L-rhamnose, L-serine, L-threonine, maltitol, maltose, maltotriose, mannose, N-acetyl-D-glucosamine, oxalic acid, palatinose, pectin, proline, salicin, stachyose, sucrose, trehalose, turanose, tyramine, uridine, and xylose. In some embodiments of the synthetic combination comprising at least two endophytes associated with a seed, both of the endophytes are heterologous to the seed.


In some embodiments of any of the synthetic combinations, the synthetic combination is disposed within a packaging material selected from a bag, box, bin, envelope, carton, or container. In an embodiment of any of the synthetic combinations, the synthetic combination comprises 1000 seed weight amount of seeds, wherein the packaging material optionally comprises a desiccant, and wherein the synthetic combination optionally comprises an anti-fungal agent.


In some embodiments of any of the synthetic combinations, the first endophyte is localized on the surface of the seeds or seedlings. In some embodiments of any of the synthetic combinations, the first endophyte is obtained from a plant species other than the seeds or seedlings of the synthetic combination. In some embodiments of any of the synthetic combinations, the first endophyte is obtained from a plant cultivar different from the cultivar of the seeds or seedlings of the synthetic combination. In some embodiments of any of the synthetic combinations, the first endophyte is obtained from a plant cultivar that is the same as the cultivar of the seeds or seedlings of the synthetic combination.


In some embodiments of any of the synthetic combinations, the first endophyte is a bacterial endophyte.


In some embodiments of any of the synthetic combinations, the first endophyte is capable of at least two of auxin production, nitrogen fixation, production of an antimicrobial compound, mineral phosphate solubilization, siderophore production, cellulase production, chitinase production, xylanase production, and acetoin production.


In some embodiments of any of the synthetic combinations, the first endophyte is capable of metabolizing at least two substrates selected from the group consisting of: a-D-glucose, arabinose, arbutin, b-methyl-D-galactoside, b-methyl-D-glucoside, D-alanine, D-arabitol, D-aspartic acid, D-cellobiose, dextrin, D-fructose, D-galactose, D-gluconic acid, D-glucosamine, dihydroxyacetone, DL-malic acid, D-mannitol, D-mannose, D-melezitose, D-melibiose, D-raffinose, D-ribose, D-serine, D-threonine, D-trehalose, D-xylose, g-amino-N-butyric acid, g-cyclodextrin, gelatin, gentiobiose, glycogen, glycyl-L-aspartic acid, glycyl-L-glutamic acid, glycyl-L-proline, glyoxylic acid, i-erythritol, inosine, L-alanine; L-alanyl-glycine, L-arabinose, L-asparagine, L-aspartic acid, L-galactonic acid-g-lactone, L-glutamic acid, L-glutamine, L-histidine, L-proline, L-rhamnose, L-serine, L-threonine, maltitol, maltose, maltotriose, mannose, N-acetyl-D-glucosamine, oxalic acid, palatinose, pectin, proline, salicin, stachyose, sucrose, trehalose, turanose, tyramine, uridine, and xylose.


In some embodiments of any of the synthetic combinations, the benefit is selected from the group consisting of: increased root biomass, increased root length, increased height, increased shoot length, increased leaf number, increased water use efficiency, increased tolerance to low nitrogen stress, increased nitrogen use efficiency, increased overall biomass, increased grain yield, increased photosynthesis rate, increased tolerance to drought, increased heat tolerance, increased salt tolerance, increased resistance to nematode stress, increased resistance to a fungal pathogen, increased resistance to a bacterial pathogen, increased resistance to a viral pathogen, a detectable modulation in the level of a metabolite, a detectable modulation in the transcriptome, and a detectable modulation in the proteome, relative to reference seeds or agricultural plants derived from reference seeds. In some embodiments, the benefit comprises at least two benefits selected from the group consisting of: increased root biomass, increased root length, increased height, increased shoot length, increased leaf number, increased water use efficiency, increased tolerance to low nitrogen stress, increased nitrogen use efficiency, increased overall biomass, increased grain yield, increased photosynthesis rate, increased tolerance to drought, increased heat tolerance, increased salt tolerance, increased resistance to nematode stress, increased resistance to a fungal pathogen, increased resistance to a bacterial pathogen, increased resistance to a viral pathogen, a detectable modulation in the level of a metabolite, a detectable modulation in the transcriptome, and a detectable modulation in the proteome, relative to reference seeds or agricultural plants derived from reference seeds.


In some embodiments of any of the synthetic combinations, the combination comprises seeds and the first endophyte is associated with the seeds as a coating on the surface of the seeds. In some embodiments of any of the synthetic combinations, the combination comprises seedlings and the first endophyte is contacted with the seedlings as a spray applied to one or more leaves and/or one or more roots of the seedlings. In some embodiments of any of the synthetic combinations, the synthetic combination further comprises one or more additional endophyte species.


In some embodiments of any of the synthetic combinations, the effective amount is at least 1×102 CFU or spores/per seed. In some embodiments of any of the synthetic combinations, the effective amount is at least 1×103 CFU or spores/per seed. In some embodiments of any of the synthetic combinations, the combination comprises seeds and the effective amount is from about 1×102 CFU or spores/per seed to about 1×108 CFU or spores/per seed.


In some embodiments of any of the synthetic combinations, the seed is a seed from an agricultural plant. In some embodiments of any of the synthetic combinations, the seed is a transgenic seed.


In some embodiments of any of the synthetic combinations, the first endophytes are present in an amount of at least 10 CFU or spores, at least 100 CFU or spores, at least 300 CFU or spores, at least 1,000 CFU or spores, at least 3,000 CFU or spores, at least 10,000 CFU or spores, at least 30,000 CFU or spores, at least 100,000 CFU or spores, at least 300,000 CFU or spores, or at least 1,000,000 CFU spores per seed.


In some embodiments, any of the synthetic combinations further comprise one or more of the following: a stabilizer, or a preservative, or a carrier, or a surfactant, an anticomplex agent, or any combination thereof. In some embodiments, any of the synthetic combinations further comprise one or more of the following: fungicide, nematicide, bactericide, insecticide, and herbicide.


The invention also features a plurality of any of the synthetic combinations placed in a medium that promotes plant growth, the medium selected from the group consisting of: soil, hydroponic apparatus, and artificial growth medium. The invention also features a plurality of any of the synthetic combinations, wherein the synthetic combinations are shelf-stable.


The invention also features a plant grown from any of the synthetic combinations disclosed herein, the plant exhibiting an improved phenotype of agronomic interest, selected from the group consisting of: increased root biomass, increased root length, increased height, increased shoot length, increased leaf number, increased water use efficiency, increased tolerance to low nitrogen stress, increased nitrogen use efficiency, increased overall biomass, increased grain yield, increased photosynthesis rate, increased tolerance to drought, increased heat tolerance, increased salt tolerance, increased resistance to nematode stress, increased resistance to a fungal pathogen, increased resistance to a bacterial pathogen, increased resistance to a viral pathogen, a detectable modulation in the level of a metabolite, a detectable modulation in the transcriptome, and a detectable modulation in the proteome.


In some embodiments, the invention features a method for preparing an agricultural seed composition comprising contacting the surface of a plurality of seeds with a formulation comprising a purified microbial population that comprises at least two endophytes that are heterologous to the seed, wherein the first endophyte is capable of metabolizing at least one of a-D-glucose, arabinose, arbutin, b-methyl-D-galactoside, b-methy l-D-glucoside, D-alanine, D-arabitol, D-aspartic acid, D-cellobiose, dextrin, D-fructose, D-galactose, D-gluconic acid, D-glucosamine, dihydroxyacetone, DL-malic acid, D-mannitol, D-mannose, D-melezitose, D-melibiose, D-raffinose, D-ribose, D-serine, D-threonine, D-trehalose, D-xylose, g-amino-N-butyric acid, g-cyclodextrin, gelatin, gentiobiose, glycogen, glycyl-L-aspartic acid, glycyl-L-glutamic acid, glycyl-L-proline, glyoxylic acid, i-erythritol, inosine, L-alanine, L-alanyl-glycine, L-arabinose, L-asparagine, L-aspartic acid, L-galactonic acid-g-lactone, L-glutamic acid, L-glutamine, L-histidine, L-proline, L-rhamnose, L-serine, L-threonine, maltitol, maltose, maltotriose, mannose, N-acetyl-D-glucosamine, oxalic acid, palatinose, pectin, proline, salicin, stachyose, sucrose, trehalose, turanose, tyramine, uridine, and xylose, wherein the endophytes are present in the formulation in an amount capable of modulating a trait of agronomic importance, as compared to isoline plants grown from seeds not contacted with the formulation.


In some embodiments, the invention features a method for preparing an agricultural seed composition, comprising contacting the surface of a plurality of seeds with a formulation comprising a purified microbial population that comprises at least two endophytes that are heterologous to the seed, wherein the first endophyte is capable of at least one function or activity selected from the group consisting of auxin production, nitrogen fixation, production of an antimicrobial compound, mineral phosphate solubilization, siderophore production, cellulase production, chitinase production, xylanase production, and acetoin production, wherein the endophytes are present in the formulation in an amount capable of modulating a trait of agronomic importance, as compared to isoline plants grown from seeds not contacted with the formulation.


In some embodiments, the invention features a method of improving a phenotype during water limited conditions of a plurality of host plants grown from a plurality of seeds, comprising treating the seeds with a formulation comprising at least two endophytes that are heterologous to the seeds, wherein the first endophyte is capable of metabolizing at least one of a-D-glucose, arabinose, arbutin, b-methyl-D-galactoside, b-methyl-D-glucoside, D-alanine, D-arabitol, D-aspartic acid, D-cellobiose, dextrin, D-fructose, D-galactose, D-gluconic acid, D-glucosamine, dihydroxyacetone, DL-malic acid, D-mannitol, D-mannose, D-melezitose, D-melibiose, D-raffinose, D-ribose, D-serine, D-threonine, D-trehalose, D-xylose, g-amino-N-butyric acid, g-cyclodextrin, gelatin, gentiobiose, glycogen, glycyl-L-aspartic acid, glycyl-L-glutamic acid, glycyl-L-proline, glyoxylic acid, i-erythritol, inosine, L-alanine, L-alanyl-glycine, L-arabinose, L-asparagine, L-aspartic acid, L-galactonic acid-g-lactone, L-glutamic acid, L-glutamine, L-histidine, L-proline, L-rhamnose, L-serine, L-threonine, maltitol, maltose, maltotriose, mannose, N-acetyl-D-glucosamine, oxalic acid, palatinose, pectin, proline, salicin, stachyose, sucrose, trehalose, turanose, tyramine, uridine, and xylose, the phenotype improvement selected from the group consisting of: increased root biomass, increased root length, increased height, increased shoot length, increased leaf number, increased water use efficiency, increased tolerance to low nitrogen stress, increased nitrogen use efficiency, increased overall biomass, increased grain yield, increased photosynthesis rate, increased tolerance to drought, increased heat tolerance, increased salt tolerance, increased resistance to nematode stress, increased resistance to a fungal pathogen, increased resistance to a bacterial pathogen, increased resistance to a viral pathogen, a detectable modulation in the level of a metabolite, a detectable modulation in the transcriptome, and a detectable modulation in the proteome.


In some embodiments of the methods, the first endophyte is a bacterial endophyte. In some embodiments of the methods, the first endophyte is a bacterial endophyte and the second endophyte is a bacterial endophyte. In some embodiments of the methods, the first endophyte is a bacterial endophyte and the second endophyte is a fungal endophyte. In some embodiments of the methods, the first endophyte is a fungal endophyte. In some embodiments of the methods, the first endophyte is a fungal endophyte and the second endophyte is a fungal endophyte. In some embodiments of the methods, the first endophyte is a fungal endophyte and the second endophyte is a bacterial endophyte.


In some embodiments of the methods, the first endophyte is capable of metabolizing at least two of a-D-glucose, arabinose, arbutin, b-methyl-D-galactoside, b-methyl-D-glucoside, D-alanine, D-arabitol, D-aspartic acid, D-cellobiose, dextrin, D-fructose, D-galactose, D-gluconic acid, D-glucosamine, dihydroxyacetone, DL-malic acid, D-mannitol, D-mannose, D-melezitose, D-melibiose, D-raffinose, D-ribose, D-serine, D-threonine, D-trehalose, D-xylose, g-amino-N-butyric acid, g-cyclodextrin, gelatin, gentiobiose, glycogen, glycyl-L-aspartic acid, glycyl-L-glutamic acid, glycyl-L-proline, glyoxylic acid, i-erythritol, inosine, L-alanine, L-alanyl-glycine, L-arabinose, L-asparagine, L-aspartic acid, L-galactonic acid-g-lactone, L-glutamic acid, L-glutamine, L-histidine, L-proline, L-rhamnose, L-serine, L-threonine, maltitol, maltose, maltotriose, mannose, N-acetyl-D-glucosamine, oxalic acid, palatinose, pectin, proline, salicin, stachyose, sucrose, trehalose, turanose, tyramine, uridine, and xylose.


In some embodiments of the methods, the second endophyte is capable of metabolizing at least two of a-D-glucose, arabinose, arbutin, b-methyl-D-galactoside, b-methyl-D-glucoside, D-alanine, D-arabitol, D-aspartic acid, D-cellobiose, dextrin, D-fructose, D-galactose, D-gluconic acid, D-glucosamine, dihydroxyacetone, DL-malic acid, D-mannitol, D-mannose, D-melezitose, D-melibiose, D-raffinose, D-ribose, D-serine, D-threonine, D-trehalose, D-xylose, g-amino-N-butyric acid, g-cyclodextrin, gelatin, gentiobiose, glycogen, glycyl-L-aspartic acid, glycyl-L-glutamic acid, glycyl-L-proline, glyoxylic acid, i-erythritol, inosine, L-alanine, L-alanyl-glycine, L-arabinose, L-asparagine, L-aspartic acid, L-galactonic acid-g-lactone, L-glutamic acid, L-glutamine, L-histidine, L-proline, L-rhamnose, L-serine, L-threonine, maltitol, maltose, maltotriose, mannose, N-acetyl-D-glucosamine, oxalic acid, palatinose, pectin, proline, salicin, stachyose, sucrose, trehalose, turanose, tyramine, uridine, and xylose.


In some embodiments of the methods, the formulation comprises the purified microbial population at a concentration of at least about 1×102 CFU/ml or spores/ml in a liquid formulation or about 1×102 CFU/gm or spores/ml in a non-liquid formulation.


In some embodiments of the methods for preparing an agricultural seed composition, the trait of agronomic importance is selected from the group consisting of: increased root biomass, increased root length, increased height, increased shoot length, increased leaf number, increased water use efficiency, increased tolerance to low nitrogen stress, increased nitrogen use efficiency, increased overall biomass, increased grain yield, increased photosynthesis rate, increased tolerance to drought, increased heat tolerance, increased salt tolerance, increased resistance to nematode stress, increased resistance to a fungal pathogen, increased resistance to a bacterial pathogen, increased resistance to a viral pathogen, a detectable modulation in the level of a metabolite, a detectable modulation in the transcriptome, and a detectable modulation in the proteome.


In some embodiments of the methods, at least one of the endophytes is capable of localizing in a plant element of a plant grown from the seed, the plant element selected from the group consisting of: whole plant, seedling, meristematic tissue, ground tissue, vascular tissue, dermal tissue, seed, leaf, root, shoot, stem, flower, fruit, stolon, bulb, tuber, corm, keikis, and bud.


In some embodiments of the methods, at least one of the endophytes is capable of colonizing a plant element of a plant grown from the seed, the plant element selected from the group consisting of: whole plant, seedling, meristematic tissue, ground tissue, vascular tissue, dermal tissue, seed, leaf, root, shoot, stem, flower, fruit, stolon, bulb, tuber, corm, keikis, and bud.


In some embodiments of the methods, the formulation further comprises one or more of the following: a stabilizer, or a preservative, or a carrier, or a surfactant, or an anticomplex agent, or any combination thereof. In some embodiments of the methods, the formulation further comprises one or more of the following: fungicide, nematicide, bactericide, insecticide, and herbicide.


In some embodiments of the methods, the seed is a transgenic seed.


The invention also features a plant derived from one of the methods for preparing an agricultural seed composition, wherein the plant comprises in at least one of its plant elements the endophytes. In some embodiments, the invention also features progeny of the plant derived from one of the methods for preparing an agricultural seed composition wherein the progeny comprises in at least one of its plant elements the endophytes.


In some embodiments of any of the methods, the endophyte expresses one or more genes encoding a protein whose amino acid sequence is at least 95%, at least 96%, at least 97%, at least 98%, at least 99%, or 100% identical to an amino acid sequence selected from the group consisting of SEQ ID NOs: 479, 483, 519, 532, 549, 557, 561, 562, 577, 578, 611, 626, 640, 656, 660, 666, 674, 676, 677, 678, 679, 680, 682, 683, 684; 685, 686, 688, 689, 690, 691, 692, 693, 696, 697, 698, 701, 704, 706, 710, 711, 716, 717, 718, 719, 720, 721, 722, 723, 724, 727, 728, 729, 730, 731, 732, 733, 734, 735, 737, 738, 741, 743, 744, 745, 746, 747, 748, 749, 751, 753, 756, 757, 759, 761, 762, 763, 764, 765, 766, 767, 768, 769, 771, 772, 773, 774, 775, 776, 777, 778, 779, 780, 782, 783, 784, 785, 786, 788, 790, 793, 795, 796, 797, 798, 800, 801, 802, 803, 804, 805, 806, 807, 808, 809, 810, 811, 812, 813, 815, 816, 817, 818, 819, 820, 822, 823, 824, 825, 826, 829, 830, 833, 835, 836, 837, 838, 839, 840, 841, 842, 843, 844, 846, 848, 850, 851, 853, 854, 855, 856, 857, 858, 859, 860, 864, 865, 866, 868, 869, 870, 871, 872, 873, 874, 875, 876, 877, 878, 879, 880, 881, 882, 884, 886, 887, 888, 889, 890, 891, 892, 893, 894, 895, 897, 898, 899, 901, 902, 903, 904, 905, 906, 907, 908, 910, 911, 912, 913, 914, 915, 916, 917, 918, 920, 921, 922, 923, 924, 926, 927, 928, 930, 931, 932, 933, 934, 935, 936, 937, 938, 939, 940, 941, 942, 943, 944, 945, 946, 947, 948, 949, 950, 952, 953, 954, 955, 956, 957, 958, 959, 960, 961, 962, 963, 964, 968, 969, 971, 974, 976, 978, 979, 980, 984, 985, 987, 988, 989, 992, 993, 994, 995, 996, 998, 1000, 1001, 1002, 1003, 1006, 1008, 1010, 1011, 1012, 1014, 1015, 1016, 1017, 1018, 1019, 1021, 1022, 1023, 1024, 1025, 1028, 1029, 1030, 1031, 1032, 1033, 1034, 1036, 1037, 1038, 1040, 1041, 1042, 1043, 1044, 1045, 1046, 1047, 1048, 1049, 1050, 1051, 1055, 1056, 1058, 1059, 1060, 1062, 1064, 1065, 1066, 1068, 1070, 1071, 1072, 1076, 1077, 1079, 1080, 1081, 1083, 1085, 1086, 1087, 1088, 1090, 1091, 1092, 1094, 1095, 1096, 1097, 1098, 1099, 1101, 1102, 1103, 1104, 1106, 1107, 1108, 1110, 1111, 1112, 1113, 1114, 1115, 1116, 1117, 1118, 1119, 1121, 1122, 1123, 1124, 1126, 1127, 1129, 1130, 1131, 1132, 1133, 1134, 1136, 1137, 1138, 1139, 1140, 1142, 1143, 1144, 1145, 1146, 1147, 1148, 1149, 1151, 1153, 1155, 1156, 1157, 1158, 1159, 1160, 1161, 1162, 1163, 1165, 1166, 1167, 1168, 1169, 1170, 1171, 1172, 1174, 1176, 1178, 1179, 1180, 1181, 1182, 1183, 1184, 1185, 1186, 1188, 1189, 1190, 1191, 1192, 1193, 1194, 1196, 1197, 1198, 1199, 1200, 1201, 1203, 1205, 1206, 1207, 1208, 1209, 1210, 1211, 1213, 1214, 1216, 1217, 1218, 1219, 1221, 1222, 1223, 1225, 1226, 1228, 1229, 1230, 1231, 1232, 1233, 1235, 1237, 1238, 1239, 1241, 1242, 1243, 1244, 1245, 1246, 1247, 1248, 1249, 1250, 1251, 1252, 1253, 1255, 1256, 1257, 1258, 1259, 1260, 1261, 1262, 1263, 1264, 1265, 1266, 1267, 1268, 1269, 1270, 1271, 1272, 1273, 1274, 1275, 1276, 1277, 1279, 1280, 1281, 1282, 1283, 1284, 1285, 1286, 1287, 1288, 1290, 1292, 1293, 1296, 1297, 1298, 1300, 1301, 1303, 1304, 1306, 1307, 1308, 1309, 1311, 1312, 1313, 1314, 1317, 1319, 1320, 1321, 1322, 1323, 1324, 1325, 1326, 1327, 1328, 1330, 1331, 1333, 1334, 1335, 1336, 1337, 1338, 1339, 1340, 1341, 1342, 1343, 1344, 1345, 1346, 1347, 1348, 1350, 1351, 1352, 1353, 1355, 1356, 1357, 1358, 1359, 1360, 1361, 1362, 1363, 1364, 1365, 1366, 1368, 1369, 1370, 1371, 1372, 1374, 1375, 1376, 1379, 1380, 1382, 1383, 1384, 1385, 1386, 1388, 1389, 1390, 1391, 1392, 1393, 1396, 1397, 1398, 1399, 1400, 1402, 1403, 1404, 1405, 1406, 1407, 1408, 1409, 1410, 1411, 1412, 1413, 1414, 1415, 1416, 1417, 1418, 1419, 1420, 1421, 1422, 1424, 1425, 1426, 1427, 1428, 1430, 1431, 1432, 1433, 1437, 1438, 1439, 1440, 1441, 1442, 1443, 1444, 1445, 1446, 1447, 1448, 1449, 1450, 1452, 1453, 1456, 1459, 1466, 1467, 1469, 1471, 1478, 1479, 1482, 1483, 1484, 1485, 1487, 1488, 1489, 1490, 1495, 1497, 1498, 1499, 1500, 1501, 1504, 1505, 1506, 1508, 1511, 1513, 1514, 1516, 1520, 1526, 1529, 1534, 1535, 1537, 1538, 1540, 1545, 1547, 1548, 1549, 1550, 1551, 1552, 1553, 1554, 1556, 1559, 1561, 1562, 1565, 1566, 1568, 1569, 1570, 1571, 1573, 1574, 1575, 1576, 1577, 1578, 1579, 1580, 1581, 1582, 1583, 1585, 1588, 1589, 1591, 1592, 1593, 1594, 1595, 1596, 1597, 1598, 1601, 1603, 1604, 1605, 1607, 1608, 1609, 1611, 1612, 1613, 1614, 1615, 1616, 1617, 1618, 1619, 1620, 1622, 1624, 1625, 1626, 1627, 1628, 1629, 1630, 1632, 1633, 1636, 1637, 1638, 1639, 1640, 1641, 1642, 1643, 1644, 1646, 1647, 1648, 1650, 1651, 1652, 1654, 1657, 1659, 1660, 1661, 1664, 1665, 1666, 1667, 1668, 1671, 1673, 1675, 1676, 1678, 1679, 1681, 1684, 1685, 1686, 1689, 1690, 1692, 1693, 1694, 1695, 1696, 1697, 1698, 1701, 1705, 1706, 1707, 1709, 1711, 1712, 1713, 1714, 1716, 1717, 1718, 1720, 1721, 1723, 1724, 1725, 1726, 1728, 1729, 1731, 1732, 1734, 1735, 1736, 1737, 1738, 1739, 1740, 1741, 1743, 1744, 1745, 1746, 1747, 1750, 1751, 1753, 1754, 1755, 1760, 1761, 1762, 1763, 1764, 1765, 1767, 1770, 1771, 1772, 1775, 1776, 1777, 1778, 1779, 1780, 1781, 1782, 1786, 1787, 1788, 1789, 1791, 1792, 1793, 1794, 1795, 1797, 1798, 1799, 1800, 1801, 1803, 1804, 1805, 1806, 1809, 1810, 1811, 1814, 1815, 1818, 1819, 1820, 1821, 1822, 1823, 1824, 1825, 1826, 1828, 1830, 1831, 1833, 1835, 1836, 1837, 1838, 1839, 1840, 1841, 1842, 1843, 1846, 1851, 1852, 1854, 1857, 1858, 1860, 1861, 1862, 1863, 1864, 1866, 1868, 1869, 1870, 1872, 1873, 1874, 1875, 1876, 1878, 1879, 1880, 1881, 1883, 1884, 1885, 1887, 1888, 1892, 1893, 1894, 1896, 1898, 1899, 1900, 1901, 1902, 1903, 1904, 1905, 1906, 1907, 1910, 1911, 1913, 1915, 1916, 1917, 1918, 1920, 1921, 1924, 1925, 1926, 1927, 1928, 1930, 1932, 1933, 1934, 1935, 1938, 1939, 1940, 1942, 1943, 1945, 1946, 1948, 1949, 1950, 1951, 1953, 1954, 1955, 1959, 1960, 1961, 1962, 1963, 1965, 1966, 1967, 1970, 1971, 1973, 1975, 1976, 1977, 1979, 1981, 1982, 1983, 1984, 1985, 1986, 1988, 1990, 1994, 1995, 1996, 1998, 1999, 2000, 2001; 2002, 2003, 2006, 2007, 2008, 2009, 2010, 2011, 2013, 2014, 2015, 2016, 2017, 2018, 2019, 2020, 2021, 2022, 2024, 2025, 2026, 2027, 2028, 2029, 2030, 2031, 2032, 2034, 2035, 2036, 2037, 2038, 2039, 2040, 2041, 2042, 2043, 2044, 2045, 2046, 2047, 2048, 2049, 2050, 2052, 2054, 2055, 2059, 2060, 2062, 2065, 2066, 2067, 2068, 2069, 2070, 2071, 2074, 2076, 2077, 2080, 2081, 2082, 2083, 2085, 2086, 2087, 2088, 2089, 2090, 2091, 2092, 2093, 2095, 2096, 2097, 2098, 2100, 2101, 2102, 2103, 2104, 2105, 2108, 2109, 2110, 2112, 2113, 2115, 2116, 2117, 2118, 2119, 2120, 2121, 2125, 2127, 2128, 2129, 2131, 2132, 2134, 2135, 2136, 2138, 2140, 2141, 2142, 2143, 2145, 2146, 2147, 2148, 2149, 2150, 2153, 2154, 2155, 2156, 2158, 2159, 2160, 2162, 2163, 2165, 2166, 2167, 2168, 2169, 2170, 2171, 2172, 2174, 2176, 2177, 2179; 2180, 2181, 2182, 2183, 2184, 2185, 2186, 2188, 2190, 2191, 2192, 2193, 2194, 2195, 2196, 2197, 2198, 2200, 2202, 2204, 2205, 2206, 2207, 2208, 2210, 2211, 2212, 2214, 2215, 2216, 2217, 2218, 2219, 2220, 2221, 2222, 2223, 2225, 2226, 2227, 2228, 2229, 2230, 2231, 2232, 2233, 2234, 2235, 2236, 2238, 2239, 2241, 2242, 2243, 2244, 2245, 2246, 2248, 2249, 2251, 2253, 2254, 2255, 2257, 2258, 2259, 2261, 2262, 2265, 2267, 2268, 2269, and 2270.


In some embodiments of the methods, protein expression is modulated in response to the first endophyte contacting a plant element. In some embodiments, protein expression is upregulated in response to the first endophyte contacting a plant element. In some embodiments, the amino acid sequence of the upregulated protein is at least 95%, at least 96%, at least 97%, at least 98%, at least 99%, or 100% identical to an amino acid sequence selected from the group consisting of SEQ ID NOs: 549, 640, 656, 676, 684, 690, 937, 1456, 1467, 1479, 1484, 1488, 1490, 1498, 1499, 1500, 1504, 1505, 1508, 1513, 1529, 1534, 1538, 1540, 1547, 1551, 1554, 1561, 1566, 1568, 1570, 1571, 1574, 1578, 1581, 1583, 1591, 1592, 1593, 1597, 1598, 1604, 1605, 1609, 1615, 1616, 1619, 1622, 1624, 1626, 1629, 1630, 1632, 1636, 1638, 1642, 1643, 1647, 1650, 1651, 1652, 1659, 1661, 1664, 1666, 1671, 1675, 1676, 1678, 1684, 1685, 1689, 1692, 1694, 1695, 1696, 1701, 1706, 1709, 1711, 1712, 1718, 1723, 1725, 1728, 1729, 1732, 1737, 1738, 1740, 1741, 1744, 1746, 1747, 1751, 1755, 1761, 1763, 1771, 1772, 1775, 1778, 1779, 1782, 1787, 1788, 1791, 1792, 1797, 1798, 1799, 1800, 1805, 1819, 1824, 1828, 1835, 1840, 1842, 1843, 1846, 1854, 1860, 1862, 1868, 1875, 1892, 1893, 1900, 1901, 1910, 1918, 1924, 1925, 1926, 1928, 1932, 1933, 1934, 1938, 1943, 1946, 1949, 1950, 1953, 1963, 1967, 1971, 1973, 1975, 1985, 1990, 1994, 1998, 2000, 2003, 2006, 2010, 2013, 2016, 2018, 2021, 2025, 2027, 2028, 2030, 2034, 2035, 2036, 2048, 2050, 2052, 2054, 2059, 2062, 2065, 2066, 2067, 2068, 2074, 2080, 2091, 2092, 2093, 2095, 2097, 2098, 2100, 2101, 2104, 2108, 2110, 2112, 2117, 2119, 2125, 2131, 2134, 2135, 2145, 2149, 2150, 2156, 2159, 2162, 2168, 2181, 2185, 2193, 2195, 2196, 2206, 2211, 2216, 2217, 2219, 2220, 2221, 2223, 2231, 2236, 2239, 2242, 2243, 2248, 2255, 2257, 2258, 2259, or 2262.


In some embodiments of the methods, protein expression is repressed in response to the first endophyte contacting a plant element. In some embodiments, the repressed protein amino acid sequence is at least 95%, at least 96%, at least 97%, at least 98%, at least 99%, or 100% identical to a nucleic acid sequence selected from the group consisting of SEQ ID NOs: 479, 483, 519, 532, 557, 626, 674, 678, 680, 683, 685, 688, 690, 696, 697, 701, 704, 706, 710, 711, 717, 720, 722, 723, 724, 728, 729, 730, 732, 733, 734, 737, 741, 744, 745, 748, 749, 751, 753, 756, 757, 761, 764, 766, 768, 769, 772, 773, 774, 778, 779, 782, 783, 784, 788, 790, 793, 795, 796, 797, 800, 802, 803, 806, 807, 808, 810, 812, 817, 818, 819, 820, 822, 825, 826, 833, 836, 837, 839, 841, 846, 848, 851, 853, 854, 855, 856, 857, 860, 864, 865, 866, 870, 872, 874; 876, 878, 879, 880, 881, 882, 884, 886, 887, 890, 891, 893, 894, 895, 898, 901, 903, 905, 907, 908, 910, 911, 912, 913, 915, 917, 918, 921, 924, 926, 927, 928, 933, 934, 935, 936, 937, 938, 940, 942, 944, 945, 946, 947, 950, 952, 954, 955, 957, 960, 961, 962, 963, 964, 968, 971, 976, 978, 979, 985, 987, 989, 992, 1000, 1001, 1002, 1003, 1006, 1008, 1012, 1014, 1018, 1019, 1021, 1022, 1024, 1025, 1028, 1031, 1032, 1034, 1037, 1038, 1040, 1042, 1043, 1046, 1047, 1050, 1051, 1056, 1059, 1064, 1065, 1068, 1070, 1072, 1077, 1079, 1083, 1086, 1087, 1091, 1094, 1095, 1098, 1102, 1103, 1104, 1110, 1111, 1112, 1113, 1114, 1116, 1117, 1118, 1121, 1126, 1130, 1132, 1133, 1134, 1136, 1139, 1143, 1146, 1147, 1151, 1155, 1156, 1158, 1159, 1160, 1162, 1163, 1165, 1168, 1170, 1172, 1174, 1176, 1180, 1182, 1183, 1186, 1188, 1192, 1193, 1194, 1196, 1197, 1198, 1209, 1214, 1217, 1218, 1219, 1221, 1222, 1223, 1225, 1226, 1230, 1237, 1242, 1244, 1249, 1251, 1253, 1256, 1260, 1261, 1262, 1264, 1270, 1272, 1274, 1276, 1279, 1280, 1283, 1284, 1285, 1286, 1288, 1290, 1292, 1298, 1300, 1303, 1307, 1309, 1311, 1312, 1313, 1320, 1321, 1324, 1325, 1328, 1330, 1331, 1333, 1336, 1337, 1339, 1340, 1344, 1346, 1352, 1353, 1355, 1357, 1358, 1359, 1360, 1361, 1363, 1364, 1365, 1370, 1375, 1376, 1379, 1380, 1383, 1384, 1386, 1390, 1391, 1392, 1393, 1396, 1399, 1400, 1402, 1405, 1408, 1411, 1412, 1418, 1420, 1422, 1427, 1428, 1431, 1433, 1438, 1439, 1440, 1442, 1444, 1445, 1449, or 1450.


In some embodiments of the methods, the protein is expressed with at least a two-fold difference, at least a three-fold difference, at least a four-fold difference, at least a five-fold difference, at least a six-fold difference, at least a seven-fold difference, at least an eight-fold difference, at least a nine-fold difference, at least a ten-fold difference or more in expression level as compared to the protein expression level of a reference microorganism. In some embodiments, the difference in expression level of the protein is positive. In some embodiments, the difference in expression level of the protein is negative.


In some embodiments of the methods, the protein is involved in at least one KEGG pathway selected from the group consisting of: endocytosis, purine metabolism, inositol phosphate metabolism, and peroxisome. In some embodiments of the methods, the protein is involved in at least one KEGG pathway selected from the group consisting of: ko00403 (indole diterpene alkaloid biosynthesis), ko00522 (biosynthesis of 12-, 14- and 16-membered macrolides), ko00550 (peptidoglycan biosynthesis), ko00601 (glycosphingolipid biosynthesis—lacto and neolacto series), ko0901 (indole alkaloid biosynthesis), ko01052 (type I polyketide structures), ko010503 (biosynthesis of siderophore group nonribosomal peptides), ko01501 (beta-Lactam resistance), and ko04071 (sphingolipid signaling pathway).


In some embodiments of any of the methods, the plant, crop, seedling, or plant grown from the seed expresses one or more genes whose nucleic acid sequence is at least 95%, at least 96%, at least 97%, at least 98%, at least 99%, or 100% identical to a nucleic acid sequence selected from the group consisting of SEQ ID NOs: 4127, 4128, 4129, 4130, 4131, 4132, 4133, 4134, 4135, 4136, 4137, 4138, 4139, 4140, 4141, 4142, 4143, 4144, 4145, 4146, 4147, 4148, 4149, 4150, 4151, 4152, 4153, 4154, 4155, 4156, 4157, 4158, 4159, 4160, 4161, 4162, 4163, 4164, 4165, 4166, 4167, 4168, 4169, 4170, 4171, 4172, 4173, 4174, 4175, 4176, 4177, 4178, 4179, 4180, 4181, 4182, 4183, 4184, 4185, 4186, 4187, 4188, 4189, 4190, 4191, 4192, 4193, 4194, 4195, 4196, 4197, 4198, 4199, 4200, 4201, 4202, 4203, 4204, 4205, 4206, 4207, 4208, 4209, 4210, 4211, 4212, 4213, 4214, 4215, 4216, 4217, 4218, 4219, 4220, 4221, 4222, 4223, 4224, 4225, 4226, 4227, 4228, 4229, 4230, 4231, 4232, 4233, 4234, 4235, 4236, 4237, 4238, 4239, 4240, 4241, 4242, 4243, 4244, 4245, 4246, 4247, 4248, 4249, 4250, 4251, 4252, 4253, 4254, 4255, 4256, 4257, 4258, 4259, 4260, 4261, 4262, 4263, 4264, 4265, 4266, 4267, 4268, or 4269.


In some embodiments, the one or more plant genes are modulated in response to the first endophyte contacting the plant or plant element as compared to a reference microorganism contacting the plant or plant element. In some embodiments, the one or more plant genes are upregulated in response to the first endophyte contacting a plant element as compared to a reference microorganism contacting the plant or plant element. In some embodiments, the upregulated genes nucleic acid sequence is at least 95%, at least 96%, at least 97%, at least 98%, at least 99%, or 100% identical to a nucleic acid sequence selected from the group consisting of SEQ ID NOs: 4131, 4140, 4142, 4153, 4162, 4167, 4181, 4183, 4184, 4195, 4199, 4201, 4206, 4213, 4222, 4223, 4250, 4253, or 4269.


In some embodiments, the transcription of one or more genes are repressed in response to the first endophyte contacting a plant element as compared to a reference microorganism contacting the plant or plant element. In some embodiments, the repressed genes nucleic acid sequence is at least 95%, at least 96%, at least 97%, at least 98%, at least 99%, or 100% identical to a nucleic acid sequence selected from the group consisting of SEQ ID NOs: 4150.


In some embodiments, the one or more genes are expressed with at least a 0.5-fold difference, at least a 0.6-fold difference, at least a 0.7-fold difference, at least a 0.8-fold difference, at least a 0.9-fold difference, at least a 1.0-fold difference, at least a 1.1-fold difference, at least a 1.2-fold difference, at least a 1.3-fold difference or more in expression level as compared to the gene expression level of a reference microorganism. In some embodiments, the difference in expression level is positive. In some embodiments, the difference in expression level is negative.


In some embodiments, the one or more genes has at least one gene function selected from the group consisting of: cell wall modification, defense response, oxidation-reduction process, biological process, regulation of transcription, metabolic process; glucosinolate biosynthetic process, response to karrikin, protein phosphorylation, protein folding, response to chitin, proteolysis, response to auxin stimulus, DNA-dependent regulation of transcription, N-terminal protein myristoylation, response to oxidative stress, cellular component, leaf senescence, resistance gene-dependent defense response signaling pathway, zinc ion binding, response to cold, malate metabolic process, transport, catalytic activity, response to ozone, VQ motif, regulation of systemic acquired resistance, potassium ion transport, anaerobic respiration, multicellular organismal development, response to heat, methyltransferase activity, response to wounding, oxidation-reduction process, monooxygenase activity, oxidation-reduction process, carbohydrate metabolic process, exocytosis, nuclear-transcribed mRNA poly(A) tail shortening, sodium ion transport, glycerol metabolic process, on willebrand factor A3, response to water deprivation, response to salt stress, and chlorophyll biosynthetic process. In some embodiments, the gene has a gene ontology (GO) identifier selected from the group consisting of: GO:0003824, GO, catalytic activity; GO:0006355, GO, regulation of transcription, DNA-dependent; GO:0009870, GO, defense response signaling pathway, resistance gene-dependent; GO:0008150, GO, biological_process; GO:0010200, GO, response to chitin; GO:0006508, GO, proteolysis; GO:0010193, GO, response to ozone; GO:0006979, GO, response to oxidative stress; and GO:0005975, GO, carbohydrate metabolic process.


In some embodiments, the gene function is selected from the following group: single-stranded DNA specific endodeoxyribonuclease activity, sequence-specific DNA binding transcription factor activity, NAD+ ADP-ribosyltransferase activity, metalloendopeptidase activity, DNA catabolic process, cellular iron ion homeostasis, response to osmotic stress, metallopeptidase activity, zinc ion binding, response to wounding, camalexin biosynthetic process, endoribonuclease activity, producing 5′-phosphomonoesters, cellular response to heat, T/G mismatch-specific endonuclease activity, polyamine oxidase activity, flavin adenine dinucleotide binding, cellular heat acclimation, cellular response to ethylene stimulus, cellular response to nitric oxide, and reactive oxygen species metabolic process.


In some embodiments, the endophyte comprises an ITS rRNA nucleic acid sequence at least 95%, at least 96%, at least 97%, at least 98%, at least 99%, or 100% identical to the nucleic acid sequence of SEQ ID NO: 344.


In some embodiments of any of the methods, the endophyte expresses one or more genes encoding a protein whose amino acid sequence is at least 95%, at least 96%, at least 97%, at least 98%, at least 99%, or 100% identical to an amino acid sequence selected from the group consisting of SEQ ID NOs: 477-501, 505, 514, 518, 521, 528, 530, 531, 550, 566, 567, 572, 579, 580, 581, 587, 593, 600, 602, 614, 623, 630, 635, 643, 645, 652, 657, 661, 662, 667, 670, 672, 673, 4510-4535, 4540, 4541, 4542, 4547, 4555, 4558, 4560, 4569, 4570, 4571, 4572, 4577, 4582, 4592, 4594, 4602, 4608, 4609, 4622, 4626, 4641, 4643, 4653, 4654, 4742-4766, 4734, 4739, 4740, 477, 478, 480, 482, 484, 485, 487, 489, 494, 496, 497, 501, 530, 567, 587, 602, 614, 633, 645, 649, 651, 652, 658, 665, 666, 667, 673, 874, 934, 1013, 1249, 1342, 2252, 2272, 2273, 2281, 2282, 2284, 2285, 2286, 2287, 2289; 2290, 2291, 2292, 2293, 2296, 4510, 4514, 4515, 4518, 4520, 4521, 4525, 4526, 4527, 4529, 4532, 4538, 4539, 4540, 4555, 4559, 4560, 4562, 4569, 4570, 4571, 4572, 4577, 4581, 4582, 4594, 4595, 4597, 4608, 4615, 4618, 4623, 4624, 4626, 4630, 4632, 4635, 4641, 4642, 4646, 4650, 4658, 4659, 4661, 4662, 4663, 4666, 4667, 4668, 4670, 4799, 4801, 4802, 4803, 4804, 4805, 4826, 4827, 4828, 4829, 4830, 4831, 4832, 4833, 4834, 4835, 4836, 4837, 4838, 4839, 4840, 4841, 4863, 4864, 4865, 4866, 4867, 4868, 4869, 4870, 4871, 4872, 4873, 4874, 4875, 4876, 4877, 4878, 4879, 4880, 4881, 4882, 4883, 4884, 4885, 4886, 4887, 4888, 4889, 4890, 4891, 4892, 4893, 4894, 4917, 4918, 4919, 4920, 4921, 4922, 4923, 4924, 4925, 4939, 4940, 4941, 4943, 4947, 4948, 4950, 4951, 4955, 4956, 4957, 2315, 2320, 2322, 2326, 2349, 2350, 2352, 2377, 2382, 2390, 2407, 2422, 2436, 2443, 2457, 2463, 2464, 2470, 2477, 2483, 2721, 2968, 3093, 3185, 4096, 4097, 4098, 4099, 4100, 4101, 4102, 4103, 4104, 4105, 4106, 4107, 4108, 4109, 4110, 4111, 4112, 4113, 4114, 4115, 4116, 4117, 4118, 4119, 4120, 4121, 4122, 4123, 4124, 4125, 4126, 4346, 4353, 4362, 4369, 4386, 4391, 4394, 4408, 4410, 4413, 4415, 4422, 4423, 4432, 4433, 4442, 4469, 4487, 4489, 4491, 4493, 4494, 4495, 4496, 4497, 4498, 4499, 4500, 4501, 4502, 4503, 4504, 4505, 4506, 4507, 4508, 4509, 4343, 4484, 4485, 4486, 4488, 4490, and 4492. In some embodiments of any of the methods, the endophyte expresses one or more genes involved in starch and sucrose metabolism, cell wall degradation, or protection from oxidative stress.


In some embodiments, the protein is expressed with at least a two-fold difference, at least a three-fold difference, at least a four-fold difference, at least a five-fold difference, at least a six-fold difference, at least a seven-fold difference, at least an eight-fold difference, at least a nine-fold difference, at least a ten-fold difference or more in expression level as compared to the protein expression level of a reference microorganism. In some embodiments, the difference in expression level is positive. In some embodiments, the difference in expression level is negative.


In some embodiments, the endophyte comprises an ITS rRNA nucleic acid sequence at least 95%, at least 96%, at least 97%, at least 98%, at least 99%, or 100% identical to a nucleic acid sequence selected from the group consisting of SEQ ID NOs: 344 and 447. In some embodiments, the endophyte comprises a 16S rRNA nucleic acid sequence at least 95%, at least 96%, at least 97%, at least 98%, at least 99%, or 100% identical to a nucleic acid sequence selected from the group consisting of SEQ ID NOs: 439 or 441.


In some embodiments of any of the methods, the endophyte expresses one or more genes encoding a protein whose amino acid sequence is at least 95%, at least 96%, at least 97%, at least 98%, at least 99%, or 100% identical to an amino acid sequence selected from the group consisting of SEQ ID NOs: 479, 483, 519, 532, 549, 557, 561, 562, 577, 578, 611, 626, 640, 656, 660, 666, 674, 676, 677, 678, 679, 680, 682, 683, 684, 685, 686, 688, 689, 690, 691, 692, 693, 696, 697, 698, 701, 704, 706, 710, 711, 716, 717, 718, 719, 720, 721, 722, 723, 724, 727, 728, 729, 730, 731, 732, 733, 734, 735, 737, 738, 741, 743, 744, 745, 746, 747, 748, 749; 751, 753, 756, 757, 759, 761, 762, 763, 764, 765, 766, 767, 768, 769, 771, 772, 773, 774, 775, 776, 777, 778, 779, 780, 782, 783, 784, 785, 786, 788, 790, 793, 795, 796, 797, 798, 800, 801, 802, 803, 804, 805, 806, 807, 808, 809, 810, 811, 812, 813, 815, 816, 817, 818, 819, 820, 822, 823, 824, 825, 826, 829, 830, 833, 835, 836, 837, 838, 839, 840, 841, 842, 843, 844, 846, 848, 850, 851, 853, 854, 855, 856, 857, 858, 859, 860, 864, 865, 866, 868, 869, 870, 871, 872, 873, 874, 875, 876, 877, 878, 879, 880, 881, 882, 884, 886, 887, 888, 889, 890, 891, 892, 893, 894, 895, 897, 898, 899, 901, 902, 903, 904, 905, 906, 907, 908, 910, 911, 912, 913, 914, 915, 916, 917, 918, 920, 921, 922, 923, 924, 926, 927, 928, 930, 931, 932, 933, 934, 935, 936, 937, 938, 939, 940, 941, 942, 943, 944, 945, 946, 947, 948, 949, 950, 952, 953, 954, 955, 956, 957, 958, 959, 960, 961, 962, 963, 964, 968, 969, 971, 974, 976, 978, 979, 980, 984, 985, 987, 988, 989, 992, 993, 994, 995, 996, 998, 1000, 1001, 1002, 1003, 1006, 1008, 1010, 1011, 1012, 1014, 1015, 1016, 1017, 1018, 1019, 1021, 1022, 1023, 1024, 1025, 1028, 1029, 1030, 1031, 1032, 1033, 1034, 1036, 1037, 1038, 1040, 1041, 1042, 1043, 1044, 1045, 1046, 1047, 1048, 1049, 1050, 1051, 1055, 1056, 1058, 1059, 1060, 1062, 1064, 1065, 1066, 1068, 1070, 1071, 1072, 1076, 1077, 1079, 1080, 1081, 1083, 1085, 1086, 1087, 1088, 1090, 1091, 1092, 1094, 1095, 1096, 1097, 1098, 1099, 1101, 1102, 1103, 1104, 1106, 1107, 1108, 1110, 1111, 1112, 1113, 1114, 1115, 1116, 1117, 1118, 1119, 1121, 1122, 1123, 1124, 1126, 1127, 1129, 1130, 1131, 1132, 1133, 1134, 1136, 1137, 1138, 1139, 1140, 1142, 1143, 1144, 1145, 1146, 1147, 1148, 1149, 1151, 1153, 1155, 1156, 1157, 1158, 1159, 1160, 1161, 1162, 1163, 1165, 1166, 1167, 1168, 1169, 1170, 1171, 1172, 1174, 1176, 1178, 1179, 1180, 1181, 1182, 1183, 1184, 1185, 1186, 1188, 1189, 1190, 1191, 1192, 1193, 1194, 1196, 1197, 1198, 1199, 1200, 1201, 1203, 1205, 1206, 1207, 1208, 1209, 1210, 1211, 1213, 1214, 1216, 1217, 1218, 1219, 1221, 1222, 1223, 1225, 1226, 1228, 1229, 1230, 1231, 1232, 1233, 1235, 1237, 1238, 1239, 1241, 1242, 1243, 1244, 1245, 1246, 1247, 1248, 1249, 1250, 1251, 1252, 1253, 1255, 1256, 1257, 1258, 1259, 1260, 1261, 1262, 1263, 1264, 1265, 1266, 1267, 1268, 1269, 1270, 1271, 1272, 1273, 1274, 1275, 1276, 1277, 1279, 1280, 1281, 1282, 1283, 1284, 1285, 1286, 1287, 1288, 1290, 1292, 1293, 1296, 1297, 1298, 1300, 1301, 1303, 1304, 1306, 1307, 1308, 1309, 1311, 1312, 1313, 1314, 1317, 1319, 1320, 1321, 1322, 1323, 1324, 1325, 1326, 1327, 1328, 1330, 1331, 1333, 1334, 1335, 1336, 1337, 1338, 1339, 1340, 1341, 1342, 1343, 1344, 1345, 1346, 1347, 1348, 1350, 1351, 1352, 1353, 1355, 1356, 1357, 1358, 1359, 1360, 1361, 1362, 1363, 1364, 1365, 1366, 1368, 1369, 1370, 1371, 1372, 1374, 1375, 1376, 1379, 1380, 1382, 1383, 1384, 1385, 1386, 1388, 1389, 1390, 1391, 1392, 1393, 1396, 1397, 1398, 1399, 1400, 1402, 1403, 1404, 1405, 1406, 1407, 1408, 1409, 1410, 1411, 1412, 1413, 1414, 1415, 1416, 1417, 1418, 1419, 1420, 1421, 1422, 1424, 1425, 1426, 1427, 1428, 1430, 1431, 1432, 1433, 1437, 1438, 1439, 1440, 1441, 1442, 1443, 1444, 1445, 1446, 1447, 1448, 1449, 1450, 1452, 1453, 1456, 1459, 1466, 1467, 1469, 1471, 1478, 1479, 1482, 1483, 1484, 1485, 1487, 1488, 1489, 1490, 1495, 1497, 1498, 1499, 1500, 1501, 1504, 1505, 1506, 1508, 1511, 1513, 1514, 1516, 1520, 1526, 1529, 1534, 1535, 1537, 1538, 1540, 1545, 1547, 1548, 1549, 1550, 1551, 1552, 1553, 1554, 1556, 1559, 1561, 1562, 1565, 1566, 1568, 1569, 1570, 1571, 1573, 1574, 1575, 1576, 1577, 1578, 1579, 1580, 1581, 1582, 1583, 1585, 1588, 1589, 1591, 1592, 1593, 1594, 1595, 1596, 1597, 1598, 1601, 1603, 1604, 1605, 1607, 1608, 1609, 1611, 1612, 1613, 1614, 1615, 1616, 1617, 1618, 1619, 1620, 1622, 1624, 1625, 1626, 1627, 1628, 1629, 1630, 1632, 1633, 1636, 1637, 1638, 1639, 1640, 1641, 1642, 1643, 1644, 1646, 1647, 1648, 1650, 1651, 1652, 1654, 1657, 1659, 1660, 1661, 1664, 1665, 1666, 1667, 1668, 1671, 1673, 1675, 1676, 1678, 1679, 1681, 1684, 1685, 1686, 1689, 1690, 1692, 1693, 1694, 1695, 1696, 1697, 1698, 1701, 1705, 1706, 1707, 1709, 1711, 1712, 1713, 1714, 1716, 1717, 1718, 1720, 1721, 1723, 1724, 1725, 1726, 1728, 1729, 1731, 1732, 1734, 1735, 1736, 1737, 1738, 1739, 1740, 1741, 1743, 1744, 1745, 1746, 1747, 1750, 1751, 1753, 1754, 1755, 1760, 1761, 1762, 1763, 1764, 1765, 1767, 1770, 1771, 1772, 1775, 1776, 1777, 1778, 1779, 1780, 1781, 1782, 1786, 1787, 1788, 1789, 1791, 1792, 1793, 1794, 1795, 1797, 1798, 1799, 1800, 1801, 1803, 1804, 1805, 1806, 1809, 1810, 1811, 1814, 1815, 1818, 1819, 1820, 1821, 1822, 1823, 1824, 1825, 1826, 1828, 1830, 1831, 1833, 1835, 1836, 1837, 1838, 1839, 1840, 1841, 1842, 1843, 1846, 1851, 1852, 1854, 1857, 1858, 1860, 1861, 1862, 1863, 1864, 1866, 1868, 1869, 1870, 1872, 1873, 1874, 1875, 1876, 1878, 1879, 1880, 1881, 1883, 1884, 1885, 1887, 1888, 1892, 1893, 1894, 1896, 1898, 1899, 1900, 1901, 1902, 1903, 1904, 1905, 1906, 1907, 1910, 1911, 1913, 1915, 1916, 1917, 1918, 1920, 1921, 1924, 1925, 1926, 1927, 1928, 1930, 1932, 1933, 1934, 1935, 1938, 1939, 1940, 1942, 1943, 1945, 1946, 1948, 1949, 1950, 1951, 1953, 1954, 1955, 1959, 1960, 1961, 1962, 1963, 1965, 1966, 1967, 1970, 1971, 1973, 1975, 1976, 1977, 1979, 1981, 1982, 1983, 1984, 1985, 1986, 1988, 1990, 1994, 1995, 1996, 1998, 1999, 2000, 2001, 2002, 2003, 2006, 2007, 2008, 2009, 2010, 2011, 2013, 2014, 2015, 2016, 2017, 2018, 2019, 2020, 2021, 2022, 2024, 2025, 2026, 2027, 2028, 2029, 2030, 2031, 2032, 2034, 2035, 2036, 2037, 2038, 2039, 2040, 2041, 2042, 2043, 2044, 2045, 2046, 2047, 2048, 2049, 2050, 2052, 2054, 2055, 2059, 2060, 2062, 2065, 2066, 2067, 2068, 2069, 2070, 2071, 2074, 2076, 2077, 2080, 2081, 2082, 2083, 2085, 2086, 2087, 2088, 2089, 2090, 2091, 2092, 2093, 2095, 2096, 2097, 2098, 2100, 2101, 2102, 2103, 2104, 2105, 2108, 2109, 2110, 2112, 2113, 2115, 2116, 2117, 2118, 2119, 2120, 2121, 2125, 2127, 2128, 2129, 2131, 2132, 2134, 2135, 2136, 2138, 2140, 2141, 2142, 2143, 2145, 2146, 2147, 2148, 2149, 2150, 2153, 2154, 2155, 2156, 2158, 2159, 2160, 2162, 2163, 2165, 2166, 2167, 2168, 2169, 2170, 2171, 2172, 2174, 2176, 2177, 2179, 2180, 2181, 2182, 2183, 2184, 2185, 2186, 2188, 2190, 2191, 2192, 2193, 2194, 2195, 2196, 2197, 2198, 2200, 2202, 2204, 2205, 2206, 2207, 2208, 2210, 2211, 2212, 2214, 2215, 2216, 2217, 2218, 2219, 2220, 2221, 2222, 2223, 2225, 2226, 2227, 2228, 2229, 2230, 2231, 2232, 2233, 2234, 2235, 2236, 2238, 2239, 2241, 2242, 2243, 2244, 2245, 2246, 2248, 2249, 2251, 2253, 2254, 2255, 2257, 2258, 2259, 2261, 2262, 2265, 2267, 2268, 2269, and 2270.


In some embodiments of any of the methods, expression of the protein is modulated in response to the first endophyte contacting a plant element.


In some embodiments, expression of the protein is upregulated in response to the first endophyte contacting a plant element. In some embodiments, the amino acid sequence of the upregulated protein is at least 95%, at least 96%, at least 97%, at least 98%, at least 99%, or 100% identical to an amino acid sequence selected from the group consisting of SEQ ID NOs: 549, 640, 656, 676, 684, 690, 937, 1456, 1467, 1479, 1484, 1488, 1490, 1498, 1499, 1500, 1504, 1505, 1508, 1513, 1529, 1534, 1538, 1540, 1547, 1551, 1554, 1561, 1566, 1568, 1570, 1571, 1574, 1578, 1581, 1583, 1591, 1592, 1593, 1597, 1598, 1604, 1605, 1609, 1615, 1616, 1619, 1622, 1624, 1626, 1629, 1630, 1632, 1636, 1638, 1642, 1643, 1647, 1650, 1651, 1652, 1659, 1661, 1664, 1666, 1671, 1675, 1676, 1678, 1684, 1685, 1689, 1692, 1694, 1695, 1696, 1701, 1706, 1709, 1711, 1712, 1718, 1723, 1725, 1728, 1729, 1732, 1737, 1738, 1740, 1741, 1744, 1746, 1747, 1751, 1755, 1761, 1763, 1771, 1772, 1775, 1778, 1779, 1782, 1787, 1788, 1791, 1792, 1797, 1798, 1799, 1800, 1805, 1819, 1824, 1828, 1835, 1840, 1842, 1843, 1846, 1854, 1860, 1862, 1868, 1875, 1892, 1893, 1900, 1901, 1910, 1918, 1924, 1925, 1926, 1928, 1932, 1933, 1934, 1938, 1943, 1946, 1949, 1950, 1953, 1963, 1967, 1971, 1973, 1975, 1985, 1990, 1994, 1998, 2000, 2003, 2006, 2010, 2013, 2016, 2018, 2021, 2025, 2027, 2028, 2030, 2034, 2035, 2036, 2048, 2050, 2052, 2054, 2059, 2062, 2065, 2066, 2067, 2068, 2074, 2080, 2091, 2092, 2093, 2095, 2097, 2098, 2100, 2101, 2104, 2108, 2110, 2112, 2117, 2119, 2125, 2131, 2134, 2135, 2145, 2149, 2150, 2156, 2159, 2162, 2168, 2181, 2185, 2193, 2195, 2196, 2206, 2211, 2216, 2217, 2219, 2220, 2221, 2223, 2231, 2236, 2239, 2242, 2243, 2248, 2255, 2257, 2258, 2259, or 2262.


In some embodiments, expression of the protein is repressed in response to the first endophyte contacting a plant element. In some embodiments, the repressed protein amino acid sequence is at least 95%, at least 96%, at least 97%, at least 98%, at least 99%, or 100% identical to a nucleic acid sequence selected from the group consisting of SEQ ID NOs: 479, 483, 519, 532, 557, 626, 674, 678, 680, 683, 685, 688, 690, 696, 697, 701, 704, 706, 710, 711, 717, 720, 722, 723, 724, 728, 729, 730, 732, 733, 734, 737, 741, 744, 745, 748, 749, 751, 753, 756, 757, 761, 764, 766, 768, 769, 772, 773, 774, 778, 779, 782, 783, 784, 788, 790, 793, 795, 796, 797, 800, 802, 803, 806, 807, 808, 810, 812, 817, 818, 819, 820, 822, 825, 826, 833, 836, 837, 839, 841, 846, 848, 851, 853, 854, 855, 856, 857, 860, 864, 865, 866, 870, 872, 874, 876, 878, 879, 880, 881, 882, 884, 886, 887, 890, 891, 893, 894, 895, 898, 901, 903, 905, 907, 908, 910, 911, 912, 913, 915, 917, 918, 921, 924, 926, 927, 928, 933, 934, 935, 936, 937, 938, 940, 942, 944, 945, 946, 947, 950, 952, 954, 955, 957, 960, 961, 962, 963, 964, 968, 971, 976, 978, 979, 985, 987, 989, 992, 1000, 1001, 1002, 1003, 1006, 1008, 1012, 1014, 1018, 1019, 1021, 1022, 1024, 1025, 1028, 1031, 1032, 1034, 1037, 1038, 1040, 1042, 1043, 1046, 1047, 1050, 1051, 1056, 1059, 1064, 1065, 1068, 1070, 1072, 1077, 1079, 1083, 1086, 1087, 1091, 1094, 1095, 1098, 1102, 1103, 1104, 1110, 1111, 1112, 1113, 1114, 1116, 1117, 1118, 1121, 1126, 1130, 1132, 1133, 1134, 1136, 1139, 1143, 1146, 1147, 1151, 1155, 1156, 1158, 1159, 1160, 1162, 1163, 1165, 1168, 1170, 1172, 1174, 1176, 1180, 1182, 1183, 1186, 1188, 1192, 1193, 1194, 1196, 1197, 1198, 1209, 1214, 1217, 1218, 1219, 1221, 1222, 1223, 1225, 1226, 1230, 1237, 1242, 1244, 1249, 1251, 1253, 1256, 1260, 1261, 1262, 1264, 1270, 1272, 1274, 1276, 1279, 1280, 1283, 1284, 1285, 1286, 1288, 1290, 1292, 1298, 1300, 1303, 1307, 1309, 1311, 1312, 1313, 1320, 1321, 1324, 1325, 1328, 1330, 1331, 1333, 1336, 1337, 1339, 1340, 1344, 1346, 1352, 1353, 1355, 1357, 1358, 1359, 1360, 1361, 1363, 1364, 1365, 1370, 1375, 1376, 1379, 1380, 1383, 1384, 1386, 1390, 1391, 1392, 1393, 1396, 1399, 1400, 1402, 1405, 1408, 1411, 1412, 1418, 1420, 1422, 1427, 1428, 1431, 1433, 1438, 1439, 1440, 1442, 1444, 1445, 1449, or 1450.


In some embodiments, the protein is expressed with at least a two-fold difference, at least a three-fold difference, at least a four-fold difference, at least a five-fold difference, at least a six-fold difference, at least a seven-fold difference, at least an eight-fold difference, at least a nine-fold difference, at least a ten-fold difference or more in expression level as compared to the protein expression level of a reference microorganism. In some embodiments of any of the methods, the difference in expression level is positive. In some embodiments, the difference in expression level is negative.


In some embodiments, the protein is involved in at least one KEGG pathway selected from the group consisting of: endocytosis, purine metabolism, inositol phosphate metabolism, and peroxisome. In some embodiments, the protein is involved in at least one KEGG pathway selected from the group consisting of: ko00403 (indole diterpene alkaloid biosynthesis), ko00522 (biosynthesis of 12-, 14- and 16-membered macrolides), ko00550 (peptidoglycan biosynthesis), ko00601 (glycosphingolipid biosynthesis—lacto and neolacto series), ko0901 (indole alkaloid biosynthesis), ko01052 (type I polyketide structures), ko010503 (biosynthesis of siderophore group nonribosomal peptides), ko01501 (beta-Lactam resistance), and ko04071 (sphingolipid signaling pathway).


In some embodiments of any of the plants, formulations, synthetic combinations, or other compositions of the invention, the plant, crop, seedling, or plant grown from the seed expresses one or more genes whose nucleic acid sequence is at least 95%, at least 96%, at least 97%, at least 98%, at least 99%, or 100% identical to a nucleic acid sequence selected from the group consisting of SEQ ID NOs: 4127, 4128, 4129, 4130, 4131, 4132, 4133, 4134, 4135, 4136, 4137, 4138, 4139, 4140, 4141, 4142, 4143, 4144, 4145, 4146, 4147, 4148, 4149, 4150, 4151, 4152, 4153, 4154, 4155, 4156, 4157, 4158, 4159, 4160, 4161, 4162, 4163, 4164, 4165, 4166, 4167, 4168, 4169, 4170, 4171, 4172, 4173, 4174, 4175, 4176, 4177, 4178, 4179, 4180, 4181, 4182, 4183, 4184, 4185, 4186, 4187, 4188, 4189, 4190, 4191, 4192, 4193, 4194, 4195, 4196, 4197, 4198, 4199, 4200, 4201, 4202, 4203, 4204, 4205, 4206, 4207, 4208, 4209, 4210, 4211, 4212, 4213, 4214, 4215, 4216, 4217, 4218, 4219, 4220, 4221, 4222, 4223, 4224, 4225, 4226, 4227, 4228, 4229, 4230, 4231, 4232, 4233, 4234, 4235, 4236, 4237, 4238, 4239, 4240, 4241, 4242, 4243, 4244, 4245, 4246, 4247, 4248, 4249, 4250, 4251, 4252, 4253, 4254, 4255, 4256, 4257, 4258, 4259, 4260, 4261, 4262, 4263, 4264, 4265, 4266, 4267, 4268, or 4269.


In some embodiments, the one or more plant genes are modulated in response to the first endophyte contacting the plant or plant element as compared to a reference microorganism contacting the plant or plant element.


In some embodiments, the one or more plant genes are upregulated in response to the first endophyte contacting a plant element as compared to a reference microorganism contacting the plant or plant element. In some embodiments, the upregulated gene's nucleic acid sequence is at least 95%, at least 96%, at least 97%, at least 98%, at least 99%, or 100% identical to a nucleic acid sequence selected from the group consisting of SEQ ID NOs: 4131, 4140, 4142, 4153, 4162, 4167, 4181, 4183, 4184, 4195, 4199, 4201, 4206, 4213, 4222, 4223, 4250, 4253, or 4269.


In some embodiments, the transcription of one or more genes are repressed in response to the first endophyte contacting a plant element as compared to a reference microorganism contacting the plant or plant element. In some embodiments, the repressed genes nucleic acid sequence is at least 95%, at least 96%, at least 97%, at least 98%, at least 99%, or 100% identical to a nucleic acid sequence selected from the group consisting of SEQ ID NOs: 4150.


In some embodiments, the one or more genes are expressed with at least a 0.5-fold difference, at least a 0.6-fold difference, at least a 0.7-fold difference, at least a 0.8-fold difference, at least a 0.9-fold difference, at least a 1.0-fold difference, at least a 1.1-fold difference, at least a 1.2-fold difference, at least a 1.3-fold difference or more in expression level as compared to the gene expression level of a reference microorganism. In some embodiments, the difference in expression level is positive. In some embodiments, the difference in expression level is negative.


In some embodiments, the one or more genes has at least one gene function selected from the group consisting of: cell wall modification, defense response, oxidation-reduction process, biological process, regulation of transcription, metabolic process, glucosinolate biosynthetic process, response to karrikin, protein phosphorylation, protein folding, response to chitin, proteolysis, response to auxin stimulus, DNA-dependent regulation of transcription, N-terminal protein myristoylation, response to oxidative stress, cellular component, leaf senescence, resistance gene-dependent defense response signaling pathway, zinc ion binding, response to cold, malate metabolic process, transport, catalytic activity, response to ozone, VQ motif, regulation of systemic acquired resistance, potassium ion transport, anaerobic respiration, multicellular organismal development, response to heat, methyltransferase activity, response to wounding, oxidation-reduction process, monooxygenase activity, oxidation-reduction process, carbohydrate metabolic process, exocytosis, nuclear-transcribed mRNA poly(A) tail shortening, sodium ion transport, glycerol metabolic process, on willebrand factor A3, response to water deprivation, response to salt stress, and chlorophyll biosynthetic process. In some embodiments, the gene has a gene ontology (GO) identifier selected from the group consisting of: GO:0003824, GO, catalytic activity; GO:0006355, GO, regulation of transcription, DNA-dependent; GO:0009870, GO, defense response signaling pathway, resistance gene-dependent; GO:0008150, GO, biological_process; GO:0010200, GO, response to chitin; GO:0006508, GO, proteolysis; GO:0010193, GO, response to ozone; GO:0006979, GO, response to oxidative stress; and GO:0005975, GO, carbohydrate metabolic process.


In some embodiments, the gene function is selected from the following group: single-stranded DNA specific endodeoxyribonuclease activity, sequence-specific DNA binding transcription factor activity, NAD+ ADP-ribosyltransferase activity, metalloendopeptidase activity, DNA catabolic process, cellular iron ion homeostasis, response to osmotic stress, metallopeptidase activity, zinc ion binding, response to wounding, camalexin biosynthetic process, endoribonuclease activity, producing 5′-phosphomonoesters, cellular response to heat, T/G mismatch-specific endonuclease activity, polyamine oxidase activity, flavin adenine dinucleotide binding, cellular heat acclimation, cellular response to ethylene stimulus, cellular response to nitric oxide, and reactive oxygen species metabolic process.


In some embodiments, the endophyte comprises an ITS rRNA nucleic acid sequence at least 95%, at least 96%, at least 97%, at least 98%, at least 99%, or 100% identical to the nucleic acid sequence of SEQ ID NO: 344.


In some embodiments of any of the plants, formulations, synthetic combinations, or other compositions of the invention, the endophyte expresses one or more genes encoding a protein whose amino acid sequence is at least 95%, at least 96%, at least 97%, at least 98%, at least 99%, or 100% identical to an amino acid sequence selected from the group consisting of SEQ ID NOs: 477-501, 505, 514, 518, 521, 528, 530, 531, 550, 566, 567, 572, 579, 580, 581, 587, 593, 600, 602, 614, 623, 630, 635, 643, 645, 652, 657, 661, 662, 667, 670, 672, 673, 4510-4535, 4540, 4541, 4542, 4547, 4555, 4558, 4560, 4569, 4570, 4571, 4572, 4577, 4582, 4592, 4594, 4602, 4608, 4609, 4622, 4626, 4641, 4643, 4653, 4654, 4742-4766, 4734, 4739, 4740, 477, 478, 480, 482, 484, 485, 487, 489, 494, 496, 497, 501, 530, 567, 587, 602, 614; 633, 645, 649, 651, 652, 658, 665, 666, 667, 673, 874, 934, 1013, 1249, 1342, 2252, 2272, 2273, 2281, 2282, 2284, 2285, 2286, 2287, 2289, 2290, 2291, 2292, 2293, 2296, 4510, 4514, 4515, 4518, 4520, 4521, 4525, 4526, 4527, 4529, 4532, 4538, 4539, 4540, 4555, 4559, 4560, 4562, 4569, 4570, 4571, 4572, 4577, 4581, 4582, 4594, 4595, 4597, 4608, 4615, 4618, 4623, 4624, 4626, 4630, 4632, 4635, 4641, 4642, 4646, 4650, 4658, 4659, 4661, 4662, 4663, 4666, 4667, 4668, 4670, 4799, 4801, 4802, 4803, 4804, 4805, 4826, 4827, 4828, 4829, 4830, 4831, 4832, 4833, 4834, 4835, 4836, 4837, 4838, 4839, 4840, 4841, 4863, 4864, 4865, 4866, 4867, 4868, 4869, 4870, 4871, 4872, 4873, 4874, 4875, 4876, 4877, 4878, 4879, 4880, 4881, 4882, 4883, 4884, 4885, 4886, 4887, 4888, 4889, 4890, 4891, 4892, 4893, 4894, 4917, 4918, 4919, 4920, 4921, 4922, 4923, 4924, 4925, 4939, 4940, 4941, 4943, 4947, 4948, 4950, 4951, 4955, 4956, 4957, 2315, 2320, 2322, 2326, 2349, 2350, 2352, 2377, 2382, 2390, 2407, 2422, 2436, 2443, 2457, 2463, 2464, 2470, 2477, 2483, 2721, 2968, 3093, 3185, 4096, 4097, 4098, 4099, 4100, 4101, 4102, 4103, 4104, 4105, 4106, 4107, 4108, 4109, 4110, 4111, 4112, 4113, 4114, 4115, 4116, 4117, 4118, 4119, 4120, 4121, 4122, 4123, 4124, 4125, 4126, 4346, 4353, 4362, 4369, 4386, 4391, 4394, 4408, 4410, 4413, 4415, 4422, 4423, 4432, 4433, 4442, 4469, 4487, 4489, 4491, 4493, 4494, 4495, 4496, 4497, 4498, 4499, 4500, 4501, 4502, 4503, 4504, 4505, 4506, 4507, 4508, 4509, 4343, 4484, 4485, 4486, 4488, 4490, and 4492.


In some embodiments of any of the plants, formulations, synthetic combinations, or other compositions of the invention, the endophyte expresses one or more genes involved in starch and sucrose metabolism, cell wall degradation, or protection from oxidative stress. In some embodiments, the protein is expressed with at least a two-fold difference, at least a three-fold difference, at least a four-fold difference, at least a five-fold difference, at least a six-fold difference, at least a seven-fold difference, at least an eight-fold difference, at least a nine-fold difference, at least a ten-fold difference or more in expression level as compared to the protein expression level of a reference microorganism. In some embodiments, the difference in expression level is positive.


In some embodiments, the difference in expression level is negative. In some embodiments, the endophyte comprises an ITS rRNA nucleic acid sequence at least 95%, at least 96%, at least 97%, at least 98%, at least 99%, or 100% identical to a nucleic acid sequence selected from the group consisting of SEQ ID NOs: 344 and 447. In some embodiments, the wherein the endophyte comprises a 16S rRNA nucleic acid sequence at least 95%, at least 96%, at least 97%, at least 98%, at least 99%, or 100% identical to a nucleic acid sequence selected from the group consisting of SEQ ID NOs: 439 or 441.


Therefore, in a first aspect, inventions described herein provide a synthetic combination of a plant element of a first plant and a preparation of an endophyte that is coated onto the surface of the plant element of the first plant such that the endophyte is present at a higher level on the surface of the plant element than is present on the surface of an uncoated reference plant element, wherein the endophyte is isolated from the inside of the plant element of a second plant. In some embodiments, a synthetic combination comprises a plant element of a first plant and a preparation of one or more endophytes. In some embodiments, the one or more endophytes are selected from the group consisting of fungi, bacteria, and combinations thereof. In some embodiments, the one or more endophytes of the synthetic combination are fungi. In some embodiments, at least 1, 2, 3, 4, 5, 6, 7, 8, 9 or 10 or more endophytes of the synthetic combination are fungi. In some embodiments, one or more endophytes of the synthetic combination are bacteria. In some embodiments, at least 1, 2, 3, 4, 5, 6, 7, 8, 9 or 10 or more endophytes of the synthetic combination are bacteria. In some embodiments, one or more endophytes of the synthetic combination comprise both fungi and bacteria. In some embodiments, one or more endophytes of the synthetic combination comprise at least one fungus and at least one bacterium. In some embodiments, one or more endophytes of the synthetic combination comprise at least 1, 2, 3, 4, 5, 6, 7, 8, 9 or 10 or more bacteria, at least 1, 2, 3, 4, 5, 6, 7, 8, 9 or 10 or more fungi, and combinations thereof.


In some embodiments, the endophyte comprises a taxon that is present in at least two species that are selected from cereal, fruit and vegetable, wild grassland and oilseed plants. In some embodiments, the endophyte comprises a nucleic acid that is at least 97% identical, for example, at least 98% identical, at least 99% identical, at least 99.5% identical, or 100% identical to the nucleic acid sequence selected from the groups provided in Table 1, Table 2, Table 7, and Table 8.


In some embodiments, the isolated endophyte is cultured, for example, prior to being coated onto the surface of the plant element. The endophyte can be cultured in a synthetic or semi-synthetic medium.


The isolated endophyte can be associated with the surface of the seed of the first plant. In some embodiments, the endophyte is not associated with the surface of the plant element of the first plant.


The present invention contemplates a synthetic combination in which the first plant and the second plant are the same species. In a particular embodiment, the first plant and the second plant are the same cultivar. The synthetic combination may also make use of an endophyte that is isolated from a plant that is a different species from the first plant.


In some embodiments, the plant element of the first plant is from a monocotyledonous plant. For example, the plant element of the first plant is from a cereal plant. The plant element of the first plant can be selected from the group consisting of maize, wheat, barley, onion, rice, or sorghum. In an alternative embodiment, the seed of the first plant is from a dicotyledonous plant. The plant element of the first plant can be selected from the group consisting of cotton, Brassica napus, tomato, pepper, cabbage, lettuce, melon, strawberry, turnip, watermelon, peanut or soybean. In a particular embodiment, the plant is not a cotton plant. In still another embodiment, the plant is not a soybean. In another embodiment, the plant is not maize. In yet another embodiment, the plant is not wheat.


In some embodiments, the plant element of the first plant can be from a genetically modified plant. In another embodiment, the plant element of the first plant can be a hybrid plant element.


The synthetic combination can comprise a plant element of the first plant that is surface-sterilized prior to combining with the endophytes.


As stated above, the endophyte used in the synthetic combination is derived from within the plant element of a second plant. In some embodiments, the second plant is a monocotyledonous plant or tissue thereof. In a particular embodiment, the second plant is a cereal plant or tissue thereof. In some embodiments, the second plant is selected from the group consisting of a maize plant, a barley plant, a wheat plant, an onion plant, a rice plant, or a sorghum plant. In some embodiments, the plant element is a seed that is a naked grain (i.e., without hulls or fruit cases). In an alternative embodiment, the second plant is a dicotyledonous plant. For example, the second plant can be selected from the group consisting of a cotton plant, a Brassica Napus plant, a tomato plant, a pepper plant, a cabbage plant, a lettuce plant, a melon plant, a strawberry plant, a turnip plant, a watermelon plant, a peanut plant or a soybean plant.


In some embodiments, the endophyte is coated on the surface of the plant element of the first plant in an amount effective to confer in the plant element or resulting plant thereof an improved agronomic trait. For example, in one embodiment, the agronomic trait is selected from the group consisting of: improved leaf biomass, improved vigor, improved fruit mass, improved grain yield, improved root mass, increased flower number, increased plant height, earlier flowering, and enhanced germination rate. Alternatively, or in addition, the agronomic trait is selected from the group consisting of: improved resistance to drought, improved water use efficiency, improved nitrogen use efficiency, improved nitrogen uptake, improved resistance to salt stress, improved resistance to heat, improved resistance to cold, improved metal tolerance, and improved nutritional content, improved uptake of micronutrients including metal ions, improved uptake of phosphorus and improved uptake of potassium. In some embodiments, the agronomic trait is selected from the group consisting of: improved nematode resistance, improved fungal pathogen resistance, improved pathogen resistance, improved herbivore resistance, improved viral pathogen resistance.


In some embodiments, the seed of the first plant is coated with at least 1 CFU or spores of the endophyte per seed, for example, at least 2 CFU or spores, at least 5 CFU or spores, at least 10 CFU or spores, at least 30 CFU or spores, at least 100 CFU or spores, at least 300 CFU or spores, at least 1,000 CFU or spores, at least 3,000 CFU or spores, at least 10,000 CFU or spores, at least 30,000 CFU or spores or more per seed.


The synthetic combination can additionally comprise a seed coating composition. The seed coating composition can comprise an agent selected from the group consisting of: a fungicide, an antibacterial agent, an herbicide, a nematicide, an insecticide, a plant growth regulator, a rodenticide, a nutrient, and combinations thereof. The seed coating composition can further comprise an agent selected from the group consisting of an agriculturally acceptable carrier, a tackifier, a microbial stabilizer, and combinations thereof. In some embodiments, the seed coating composition can contain a second microbial preparation, including but not limited to a rhizobial bacterial preparation.


The present invention contemplates the use of endophytes that are unmodified, as well as those that are modified. In some embodiments, the endophyte is a recombinant endophyte. In one particular embodiment, the endophyte is modified prior to coating onto the surface of the seed such that it has enhanced compatibility with an antimicrobial agent when compared with the unmodified. For example, the endophyte can be modified such that it has enhanced compatibility with an antibacterial agent. In an alternative embodiment, the endophyte has enhanced compatibility with an antifungal agent. The endophyte can be modified such that it exhibits at least 3 fold greater, for example, at least 5 fold greater, at least 10 fold greater, at least 20 fold greater, at least 30 fold greater or more resistance to an antimicrobial agent when compared with the unmodified endophyte. The endophyte can be substantially purified from any other microbial entity. In one embodiment, the antimicrobial agent is an antibacterial agent. In another embodiment, the antimicrobial agent is an antifungal agent.


In one particular embodiment, the antimicrobial agent is glyphosate. For example, the modified endophyte exhibits at least 3 fold greater, for example, at least 5 fold greater, at least 10 fold greater, at least 20 fold greater, at least 30 fold greater or more resistance to the antimicrobial agent when compared with the unmodified endophyte. In the alternative, the modified endophyte has a doubling time in growth medium containing at least 1 mM glyphosate, for example, at least 2 mM glyphosate, at least 5 mM glyphosate, at least 10 mM glyphosate, at least 15 mM glyphosate or more, that is no more than 250%, for example, no more than 200%, no more than 175%, no more than 150%, or no more than 125%, of the doubling time of the endophyte in the same growth medium containing no glyphosate. In still another embodiment, the modified endophyte has a doubling time in a plant tissue containing at least 10 ppm glyphosate, for example, at least 15 ppm glyphosate, at least 20 ppm glyphosate, at least 30 ppm glyphosate, at least 40 ppm glyphosate or more, that is no more than 250%, for example, no more than 200%, no more than 175%, no more than 150%, or no more than 125%, of the doubling time of the unmodified endophyte in a reference plant tissue containing no glyphosate.


The present invention also contemplates the use of multiple endophytes. For example, in some embodiments, the synthetic combination described above can comprise a plurality of purified endophytes, for example, 2, 3, 4 or more different types of endophytes.


In another aspect, the present invention provides for a method for improving a trait in an agricultural plant, the method comprising: Providing an agricultural plant, contacting the plant with a formulation comprising a endophytic microbial entity comprising a nucleic acid sequence that is at least 97% identical, at least 98% identical, at least 99% identical, at least 99.5% identical, or 100% identical, to the nucleic acid sequence selected from the groups provided in Table 1, Table 2, Table 7, and Table 8 that is present in the formulation in an amount effective to colonize the plant and allowing the plant to grow under conditions that allow the endophytic microbial entity to colonize the plant.


Also described herein are preparations comprising a population of isolated modified endophytes described above. Preparations described herein further comprise an agriculturally acceptable carrier, and the preparation comprises an amount of endophytes sufficient to improve an agronomic trait of the population of seeds. For example, in one embodiment, the agronomic trait is selected from the group consisting of: improved leaf biomass, improved vigor, improved fruit mass, improved grain yield, improved root mass, increased flower number, increased plant height, earlier flowering, enhanced germination rate and combinations thereof. Alternatively, or in addition, the agronomic trait is selected from the group consisting of: improved resistance to drought, improved water use efficiency, improved nitrogen use efficiency, improved nitrogen uptake, improved resistance to salt stress, improved resistance to heat, improved resistance to cold, improved metal tolerance, improved nutritional content, improved uptake of micronutrients including metal ions, improved uptake of phosphorus, improved uptake of potassium and combinations thereof. In some embodiments, the agronomic trait is selected from the group consisting of: improved nematode resistance, improved fungal pathogen resistance, improved pathogen resistance, improved herbivore resistance, improved viral pathogen resistance, and combinations thereof. In some embodiments, the preparation is substantially stable at temperatures between about 2° C. and about 45° C. for at least about thirty days.


Preparations can be conveniently formulated to provide the ideal number of endophytes onto a seed to produce synthetic combinations described above. In some embodiments, a preparation is formulated to provide at least 100 endophytes, for example, at least 300 endophyte, 1,000 endophytes, 3,000 endophytes, 10,000 endophytes or more per seed. In some embodiments, a preparation is formulated to provide a population of plants that demonstrates a substantially homogenous growth rate when introduced into agricultural production. Inventions described herein also contemplate a preparation comprising two or more different purified endophytes.


Also described herein are commodity plant products comprising a plant or part of a plant (including a seed) and further comprising the modified endophyte described above that is present in a detectable level, for example, as detected by the presence of its nucleic acid by PCR.


In another aspect of the present invention, a seed comprising synthetic combinations described herein is provided. In still another aspect, disclosed is a substantially uniform population of seeds comprising a plurality of such seeds. In one embodiment, at least 10%, at least 20%, at least 30%, at least 40%, at least 50%, at least 60%, at least 70%, at least 75%, at least 80%, at least 90%, at least 95% or more of the seeds in the population, contains a viable endophyte or endophytes disposed on the surface of the seeds. In a particular embodiment, at least 10%, at least 20%, at least 30%, at least 40%, at least 50%, at least 60%, at least 70%, at least 75%, at least 80%, at least 90%, at least 95% or more of the seeds in the population contains at least 10 CFU or spores, for example, at least 30 CFU or spores, at least 100 CFU or spores, at least 300 CFU or spores, at least 1,000 CFU or spores, at least 3,000 CFU or spores, at least 10,000 CFU or spores or more, of the endophyte or endophytes coated onto the surface of the seed.


In still another aspect, the present invention discloses a substantially uniform population of plants produced by growing the population of seeds described above. In one embodiment, at least 75%, at least 80%, at least 90%, at least 95% or more of the plants comprise in one or more tissues an effective amount of the endophyte or endophytes. In another embodiment, at least 10%, 20%, 30%, 40%, 50%, 60%, 70%, 75%, at least 80%, at least 90%, at least 95% or more of the plants comprise a microbe population that is substantially similar.


In another aspect, described herein is an agricultural field, including a greenhouse comprising the population of plants described above. In on embodiment, the agricultural field comprises at least 100 plants. In another embodiment, the population occupies at least about 100 square feet of space, wherein at least about 10%, 20%, 30%, 40%, 50%, 60%, 70%, 80%, 90% or more than 90% of the population comprises an effective amount of the microbe. In another embodiment, the population occupies at least about 100 square feet of space, wherein at least about 10%, 20%, 30%, 40%, 50%, 60%, 70%, 80%, 90% or more than 90% of the population comprises the microbe in reproductive tissue. In still another embodiment, the population occupies at least about 100 square feet of space, wherein at least about 10%, 20%, 30%, 40%, 50%, 60%, 70%, 80%, 90% or more than 90% of the population comprises at least 10 CFUs or spores, 100 CFUs or spores, 1,000 CFUs or spores, 10,000 CFUs or spores or more of the microbe. In yet another embodiment, the population occupies at least about 100 square feet of space, wherein at least about 10%, 20%, 30%, 40%, 50%, 60%, 70%, 80%, 90% or more than 90% of the population comprises an exogenous microbe (i.e., the endophyte) of monoclonal origin.


In another aspect, disclosed is a method of producing a commodity plant product, comprising obtaining a plant or plant tissue from the synthetic combination described above, and producing the commodity plant product therefrom. The commodity plant product can be produced from the seed, or the plant (or a part of the plant) grown from the seed. The commodity plant product can also be produced from the progeny of such plant or plant part. The commodity plant product can be is selected from the group consisting of grain, flour, starch, seed oil, syrup, meal, flour, oil, film, packaging, nutraceutical product, an animal feed, a fish fodder, a cereal product, a processed human-food product, a sugar or an alcohol and protein.





BRIEF DESCRIPTION OF THE DRAWINGS

The drawings are for illustration purposes only not for limitation.



FIG. 1 depicts an exemplary schematic of a KEGG pathway for Glycolysis/Gluconeogenesis. The secreted proteome of a beneficial and neutral Agrobacterium were contrasted, and KEGG IDs that were enriched are depicted. 5AY represents beneficial SYM01004 (SEQ ID NO: 441). 5BY represents neutral SYM00091 (SEQ ID NO: 427). Light grey ovals represent proteins corresponding to 5AY. Dark grey ovals represent proteins corresponding to 5BY. Medium grey ovals represent proteins corresponding with both 5AY and 5BY. P-value=1.36e−8



FIG. 2 depicts an exemplary schematic of a KEGG pathway for starch and sucrose metabolism. The secreted proteome of a beneficial and neutral bacteria and fungi were contrasted, and KEGG IDs that were enriched are depicted.





DETAILED DESCRIPTION
Definitions

In order for the present invention to be more readily understood, certain terms are first defined below. Additional definitions for the following terms and other terms are set forth throughout the specification.


As used herein, an “agricultural seed” is a seed used to grow a plant typically used in agriculture (an “agricultural plant”). The seed may be of a monocot or dicot plant, and may w be planted for the production of an agricultural product, for example grain, food, feed, fiber, fuel, etc. As used herein, an agricultural seed is a seed that is prepared for planting, for example, in farms for growing.


An “endophyte” or “endophytic entity” or “endophytic microbe” is a symbiotic organism (e.g., a microorganism, e.g., a bacterium, e.g., a fungi) capable of living within a plant or is otherwise associated therewith, and does not cause disease or harm the plant otherwise, and confers one or more beneficial properties to the host plant. In some embodiments, an endophyte is a microorganism. In some embodiments, an endophyte is a microorganism that is associated with one or more host plant tissues and is in a symbiotic, e.g., beneficial relationship with said host plant tissues. In some embodiments, an endophyte is a microorganism, e.g., a bacterial or fungal organism, that confers an increase in yield, an increase in biomass, an increase in stress resistance, an increase in fitness, or combinations thereof, in its host plant. Endophytes may occupy the intracellular or extracellular spaces of plant tissue, including the leaves, stems, flowers, fruits, seeds, roots and combinations thereof. As used herein, the term “endophytic component” refers to a composition and/or structure that is part of the endophyte.


As used herein, the term “microbe” or “microorganism” refers to any species or taxon of microorganism, including, but not limited to, archaea, bacteria, microalgae, fungi (including mold and yeast species), mycoplasmas, microspores, nanobacteria, oomycetes, and protozoa. In some embodiments, a microbe or microorganism is an endophyte. In some embodiments, a microbe is an endophyte. In some embodiments, a microbe or microorganism encompasses individual cells (e.g., unicellular microorganisms) or more than one cell (e.g., multi-cellular microorganism). A “population of microorganisms” may thus refer to a multiple cells of a single microorganism, in which the cells share common genetic derivation. As used herein, the term “neutral” microbe or “neutral” microorganism refers to a microorganism that is both non-beneficial and non-pathogenic to a host plant.


As used herein, the term “bacteria” or “bacterium” refers in general to any prokaryotic organism, and may reference an organism from either Kingdom Eubacteria (Bacteria), Kingdom Archaebacteria (Archae), or both.


As used herein, the term “fungus” or “fungi” refers in general to any organism from Kingdom Fungi.


A “spore” or a population of “spores” refers to bacteria or fungi that are generally viable, more resistant to environmental influences such as heat and bactericidal or fungicidal agents than other forms of the same bacteria or fungi, and typically capable of germination and out-growth. Bacteria and fungi that are “capable of forming spores” are those bacteria and fungi comprising the genes and other necessary abilities to produce spores under suitable environmental conditions.


“Internal Transcribed Spacer” (ITS) refers to the spacer DNA (non-coding DNA) situated between the small-subunit ribosomal RNA (rRNA) and large-subunit rRNA genes in the chromosome or the corresponding transcribed region in the polycistronic rRNA precursor transcript.


A “plurality of endophytes” means two or more types of endophyte entities, e.g., of simple bacteria or simple fungi, complex fungi, or combinations thereof. In some embodiments, the two or more types of endophyte entities are two or more strains of endophytes. In other embodiments, the two or more types of endophyte entities are two or more species of endophytes. In yet other embodiments, the two or more types of endophyte entities are two or more genera of endophytes. In yet other embodiments, the two or more types of endophyte entities are two or more families of endophytes. In yet other embodiments, the two or more types of endophyte entities are two or more orders of endophytes.


A “population” of endophytes refers to a plurality of cells of a single endophyte, in which the cells share common genetic derivation.


A “complex network” means a plurality of endophytes co-localized in an environment, such as on or within an agricultural plant. Preferably, a complex network includes two or more types of endophyte entities that synergistically interact, such synergistic endophytic populations capable of providing a benefit to the agricultural seed, seedling, or plant derived thereby.


The terms “pathogen” and “pathogenic” in reference to a bacterium or fungus includes any such organism that is capable of causing or affecting a disease, disorder or condition of a host comprising the organism.


A “spore” or a population of “spores” refers to bacteria or fungi that are generally viable, more resistant to environmental influences such as heat and bactericidal or fungicidal agents than other forms of the same bacteria or fungi, and typically, capable of germination and out-growth. Bacteria and fungi that are “capable of forming spores” are those bacteria and fungi comprising the genes and other necessary abilities to produce spores under suitable environmental conditions.


As used herein, a “colony-forming unit” (“CFU”) is used as a measure of viable microorganisms in a sample. A CFU is an individual viable cell capable of forming on a solid medium a visible colony whose individual cells are derived by cell division from one parental cell.


The term “isolated” is intended to specifically reference an organism, cell, tissue, polynucleotide, or polypeptide that is removed from its original source and purified from additional components with which it was originally associated. For example, an endophyte may be considered isolated from a seed if it is removed from that seed source and purified so that it is isolated from any additional components with which it was originally associated. Similarly, an endophyte may be removed and purified from a plant or plant element so that it is isolated and no longer associated with its source plant or plant element.


As used herein, an isolated strain of a microbe is a strain that has been removed from its natural milieu. “Pure cultures” or “isolated cultures” are cultures in which the organisms present are only of one strain of a particular genus and species. This is in contrast to “mixed cultures,” which are cultures in which more than one genus and/or species of microorganism are present. As such, the term “isolated” does not necessarily reflect the extent to which the microbe has been purified. A “substantially pure culture” of the strain of microbe refers to a culture which contains substantially no other microbes than the desired strain or strains of microbe. In other words, a substantially pure culture of a strain of microbe is substantially free of other contaminants, which can include microbial contaminants. Further, as used herein, a “biologically pure” strain is intended to mean the strain separated from materials with which it is normally associated in nature. A strain associated with other strains, or with compounds or materials that it is not normally wound with in nature, is still defined as “biologically pure.” A monoculture of a particular strain is, of course, “biologically pure.” As used herein, the term “enriched culture” of an isolated microbial strain refers to a microbial culture that contains more that 50%, 60%, 70%, 80%, 90%, or 95% of the isolated strain.


A “plant element” is intended to generically reference either a whole plant or a plant component, including but not limited to plant tissues, parts, and cell types. A plant element is preferably one of the following: whole plant, seedling, meristematic tissue, ground tissue, vascular tissue, dermal tissue, seed, leaf, root, shoot, stem, flower, fruit, stolon, bulb, tuber, corm, kelkis, shoot, bud. As used herein, a “plant element” is synonymous to a “portion” of a plant, and refers to any part of the plant, and can include distinct tissues and/or organs, and may be used interchangeably with the term “tissue” throughout.


Similarly, a “plant reproductive element” is intended to generically reference any part of a plant that is able to initiate other plants via either sexual or asexual reproduction of that plant, for example but not limited to: seed, seedling, root, shoot, stolon, bulb, tuber, corm, keikis, or bud.


A “population” of plants, as used herein, refers to a plurality of plants that are of the same taxonomic category, typically of the same species, and will also typically share a common genetic derivation.


As used herein, an “agricultural seed” is a seed used to grow a plant typically used in agriculture (an “agricultural plant”). The seed may be of a monocot or dicot plant, and may be planted for the production of an agricultural product, for example feed, food, fiber, fuel, etc. As used herein, an agricultural seed is a seed that is prepared for planting, for example, in farms for growing.


“Agricultural plants”, or “plants of agronomic importance”, include plants that are cultivated by humans for food, feed, fiber, and fuel purposes. Agricultural plants include monocotyledonous species such as: maize (Zea mays), common wheat (Triticum aestivum), spelt (Triticum spelta), einkorn wheat (Triticum monococcum), emmer wheat (Triticum dicoccum), durum wheat (Triticum durum), Asian rice (Oryza sativa), African rice (Oryza glabaerreima), wild rice (Zizania aquatica, Zizania latifolia, Zizania palustris, Zizania texana), barley (Hordeum vulgare), Sorghum (Sorghum bicolor), Finger millet (Eleusine coracana), Proso millet (Panicum miliaceum), Pearl millet (Pennisetum glaucum), Foxtail millet (Setaria italica), Oat (Avena sativa), Triticale (Triticosecale), rye (Secale cereal), Russian wild rye (Psathyrostachys juncea), bamboo (Bambuseae), or sugarcane (e.g., Saccharum arundinaceum, Saccharum barberi, Saccharum bengalense, Saccharum edule, Saccharum munja, Saccharum officinarum, Saccharum procerum, Saccharum ravennae, Saccharum robustum, Saccharum sinense, or Saccharum spontaneum); as well as dicotyledonous species such as: soybean (Glycine max), canola and rapeseed cultivars (Brassica napus), cotton (genus Gossypium), alfalfa (Medicago sativa), cassava (genus Manihot), potato (Solanum tuberosum), tomato (Solanum lycopersicum), pea (Pisum sativum), chick pea (Cicer arietinum), lentil (Lens culinaris), flax (Linum usitatissimum), peanut (Arachis hypogaea) and many varieties of vegetables.


A “host plant” includes any plant, particularly a plant of agronomic importance, which an endophyte can colonize. As used herein, an endophyte is said to “colonize” a plant or plant element when it can be stably detected within the plant or plant element over a period time; such as one or more days, weeks, months or years, in other words, a colonizing entity is not transiently associated with the plant or plant element. Such host plants are preferably plants of agronomic importance.


A “non-host target” means an organism or chemical compound that is altered in some way after contacting a host plant or host fungus that comprises an endophyte, as a result of a property conferred to the host plant or host fungus by the endophyte.


As used herein, a “hybrid plant” refers generally refers to a plant that is the product of a cross between two genetically different parental plants. A hybrid plant is generated by either a natural or artificial process of hybridization whereby the entire genome of one species, variety cultivar, breeding line or individual plant is combined intra- or interspecifically into the genome of species, variety or cultivar or line, breeding line or individual plant by crossing.


An “inbred plant”, as used herein, refers to a plant or plant line that has been repeatedly crossed or inbred to achieve a high degree of genetic uniformity, and low heterozygosity, as is known in the art.


The term “isoline” is a comparative term, and references organisms that are genetically identical, but may differ in treatment. In one example, two genetically identical maize plant embryos may be separated into two different groups, one receiving a treatment (such as transformation with a heterologous polynucleotide, to create a genetically modified plant) and one control that does not receive such treatment. Any phenotypic differences between the two groups may thus be attributed solely to the treatment and not to any inherency of the plant's genetic makeup. In another example, two genetically identical seeds may be treated with a formulation that introduces an endophyte composition. Any phenotypic differences between the plants derived from those seeds may be attributed to the treatment, thus forming an isoline comparison.


Similarly, by the terms “reference plant”, “reference agricultural plant” or “reference seed”, it is meant an agricultural plant or seed of the same species, strain, or cultivar to which a treatment, formulation, composition or endophyte preparation as described herein is not administered/contacted. A reference agricultural plant or seed, therefore, is identical to the treated plant with the exception of the presence of the endophyte and can serve as a control for detecting the effects of the endophyte that is conferred to the plant.


A “reference environment” refers to the environment, treatment or condition of the plant in which a measurement is made. For example, production of a compound in a plant associated with an endophyte can be measured in a reference environment of drought stress, and compared with the levels of the compound in a reference agricultural plant under the same conditions of drought stress. Alternatively, the levels of a compound in plant associated with an endophyte and reference agricultural plant can be measured under identical conditions of no stress.


A “population” of plants refers to more than one plant, that are of the same taxonomic category, typically be of the same species, and will also typically share a common genetic derivation.


In some embodiments, the invention contemplates the use of microbes that are “exogenous” to a seed or plant. As used herein, a microbe is considered exogenous to the seed or plant if the plant element that is unmodified (e.g., a plant element that is not treated with the plurality of endophytes described herein) does not contain the microbe.


In some embodiments, a microbe can be “endogenous” to a seed or plant. As used herein, a microbe is considered “endogenous” to a plant or seed, if the endophyte or endophyte component is derived from, or is otherwise found in, a plant element of the plant specimen from which it is sourced. In embodiments in which an endogenous endophyte is applied, the endogenous microbe is applied in an amount that differs from the levels typically found in the plant.


In some embodiments, the present invention contemplates the synthetic compositions comprising the combination of a plant element, seedling, or whole plants and an endophyte population, in which the endophyte population is “heterologously disposed”.


In some aspects, “heterologously disposed” means that the plant element, seedling, or plant does not contain detectable levels of the microbe in that same plant element, seedling, or plant. For example if said plant element or seedling or plant does not naturally have the endophyte associated with it and the endophyte is applied, the endophyte would be considered to be heterologously disposed. In some aspects, “heterologously disposed” means that the endophyte is being applied to a different plant element than that with which the endophyte is naturally associated. For example, if said plant element or seedling or plant has the endophyte normally found in the root tissue but not in the leaf tissue, and the endophyte is applied to the leaf, the endophyte would be considered to be heterologously disposed. In some aspects, “heterologously disposed” means that the endophyte being applied to a different tissue or cell layer of the plant element than that in which the microbe is naturally found. For example, if endophyte is naturally found in the mesophyll layer of leaf tissue but is being applied to the epithelial layer, the endophyte would be considered to be heterologously disposed. In some aspects, “heterologously disposed” means that the endophyte being applied is at a greater concentration, number, or amount of the plant element, seedling, or plant, than that which is naturally found in said plant element, seedling, or plant. For example, an endophyte concentration that is being applied is at least 1.5 times, between 1.5 and 2 times, 2 times, between 2 and 3 times, 3 times, between 3 and 5 times, 5 times, between 5 and 7 times, 7 times, between 7 and 10 times, 10 times greater, or even greater than 10 times higher number, amount, or concentration than that which is naturally present, the endophyte would be considered to be heterologously disposed. In some aspects, “heterologously disposed” means that the endophyte is applied to a developmental stage of the plant element, seedling, or plant in which said endophyte is not naturally associated, but may be associated at other stages. For example, if an endophyte is normally found at the flowering stage of a plant and no other stage, an endophyte applied at the seedling stage may be considered to be heterologously disposed. For the avoidance of doubt, “heterologously disposed” contemplates use of microbes that are “exogenous” to a seed or plant.


In some cases, the present invention contemplates the use of microbes that are “compatible” with agricultural chemicals, including but not limited to, a fungicide, an anti-complex compound, a bactericide, a virucide, an herbicide, a nematicide, a parasiticide, a pesticide, or any other agent widely used in agricultural which has the effect of killing or otherwise interfering with optimal growth of another organism. As used herein, a microbe is “compatible” with an agricultural chemical, when the microbe is modified, such as by genetic modification, e.g., contains a transgene that confers resistance to an herbicide, or otherwise adapted to grow in, or otherwise survive, the concentration of the agricultural chemical used in agriculture. For example, a microbe disposed on the surface of plant element is compatible with the fungicide metalaxyl if it is able to survive the concentrations that are applied on the plant element surface.


“Biomass” means the total mass or weight (fresh or dry), at a given time, of a plant tissue, plant tissues, an entire plant, or population of plants, usually given as weight per unit area. The term may also refer to all the plants or species in the community (community biomass).


Some of the compositions and methods described herein involve single endophyte strains or plurality of endophytes in an amount effective to colonize a plant. As used herein, a microbe is said to “colonize” a plant or seed when it can exist in an endophytic relationship with the plant in the plant environment, for example inside the plant or a part or tissue thereof, including the seed.


The compositions and methods herein may provide for an improved “agronomic trait” or “trait of agronomic importance” to a host plant, which may include, but not be limited to, the following: altered oil content, altered protein content, altered seed carbohydrate composition, altered seed oil composition, and altered seed protein composition, chemical tolerance, cold tolerance, delayed senescence, disease resistance, drought tolerance, ear weight, growth improvement, health enhancement, heat tolerance, herbicide tolerance, herbivore resistance, improved nitrogen fixation, improved nitrogen utilization, improved root architecture, improved water use efficiency, increased biomass, increased root length, increased seed weight, increased shoot length, increased yield, increased yield under water-limited conditions, kernel mass, kernel moisture content, metal tolerance, number of ears, number of kernels per ear, number of pods, nutrition enhancement, pathogen resistance, pest resistance, photosynthetic capability improvement, salinity tolerance, stay-green, vigor improvement, increased dry weight of mature seeds, increased fresh weight of mature seeds, increased number of mature seeds per plant, increased chlorophyll content, increased number of pods per plant, increased length of pods per plant, reduced number of wilted leaves per plant, reduced number of severely wilted leaves per plant, and increased number of non-wilted leaves per plant, a detectable modulation in the level of a metabolite, a detectable modulation in the level of a transcript, and a detectable modulation in the proteome, compared to an isoline plant grown from a seed without said seed treatment formulation.


Additionally, “altered metabolic function” or “altered enzymatic function” may include, but not be limited to, the following: altered production of an auxin, altered nitrogen fixation, altered production of an antimicrobial compound, altered production of a siderophore, altered mineral phosphate solubilization, altered production of a cellulase, altered production of a chitinase, altered production of a xylanase, altered production of acetoin and altered ability to metabolize a carbon source.


An “increased yield” can refer to any increase in biomass or seed or fruit weight, seed size, seed number per plant, seed number per unit area, bushels per acre, tons per acre, kilo per hectare, or carbohydrate yield. Typically, the particular characteristic is designated when referring to increased yield, e.g., increased grain yield or increased seed size.


“Agronomic trait potential” is intended to mean a capability of a plant element for exhibiting a phenotype, preferably an improved agronomic trait, at some point during its life cycle, or conveying said phenotype to another plant element with which it is associated in the same plant. For example, a plant element may comprise an endophyte that will provide benefit to leaf tissue of a plant from which the plant element is grown; in such case, the plant element comprising such endophyte has the agronomic trait potential for a particular phenotype (for example, increased biomass in the plant) even if the seed itself does not display said phenotype.


By the term “capable of metabolizing” a particular carbon substrate, it is meant that the endophyte is able to utilize that carbon substrate as an energy source.


The term “synthetic combination” means a plurality of elements associated by human endeavor, in which said association is not found in nature. In some embodiments, “synthetic combination” is used to refer to a treatment formulation associated with a plant element. In some aspects of the present invention, “synthetic combination” refers to a purified population of endophytes in a treatment formulation comprising additional compositions with which said endophytes are not found associated in nature. The combination may be achieved, for example, by coating the surface of the seed of a plant, such as an agricultural plant, or host plant elements with an endophyte. In some embodiments of the present invention, “synthetic combination” refers to one or more plant elements in association with an isolated, purified population of endophytes in a treatment formulation comprising additional compositions with which said endophytes are not found associated in nature.


A “treatment formulation” refers to a mixture of chemicals that facilitate the stability, storage, and/or application of the endophyte composition(s). In some embodiments, an agriculturally compatible carrier can be used to formulate an agricultural formulation or other composition that includes a purified endophyte preparation. As used herein an “agriculturally compatible carrier” refers to any material, other than water, that can be added to a plant element without causing or having an adverse effect on the plant element (e.g., reducing seed germination) or the plant that grows from the plant element, or the like.


In some cases, the present invention contemplates the use of compositions that are “compatible” with agricultural chemicals, for example, a fungicide, an anti-complex compound, or any other agent widely used in agricultural which has the effect of killing or otherwise interfering with optimal growth of another organism.


Some compositions described herein contemplate the use of an agriculturally compatible carrier. As used herein an “agriculturally compatible carrier” is intended to refer to any material, other than water, which can be added to a seed or a seedling without causing/having an adverse effect on the seed, the plant that grows from the seed, seed germination, or the like.


As used herein, a nucleic acid has “homology” or is “homologous” to a second nucleic acid if the nucleic acid sequence has a similar sequence to the second, nucleic acid sequence. The terms “identity”, “percent sequence identity” or “identical” in the context of nucleic acid sequences refer to the residues in the two sequences that are the same when aligned for maximum correspondence. There are a number of different algorithms known in the art that can be used to measure nucleotide sequence identity. For instance, polynucleotide sequences can be compared using FASTA, Gap or Bestfit, which are programs in Wisconsin Package Version 10.0, Genetics Computer Group (GCG), Madison, Wis. FASTA provides alignments and percent sequence identity of the regions of the best overlap between the query and search sequences. In some embodiments, sequences can be compared using Geneious (Biomatters, Ltd., Auckland, New Zealand). In other embodiments, polynucleotide sequences can be compared using the multiple sequence alignment algorithm MUSCLE. In some embodiments the nucleic acid sequence to be aligned is a complete gene. In some embodiments, the nucleic acid sequence to be aligned is a gene fragment. In some embodiments, if the nucleic acid sequence to be aligned is a gene fragment, the percent identity to a second nucleic acid sequence is considered X % identical if the two sequences are X % identical the length of the shortest sequence.


The term “substantial homology” or “substantial similarity,” when referring to a nucleic acid or fragment thereof, indicates that, when optimally aligned with appropriate nucleotide insertions or deletions with another nucleic acid (or its complementary strand), there is nucleotide sequence identity in at least about 76%, 80%, 85%, or at least about 90%, or at least about 95%, 96%, 97%, 98% or 99% of the nucleotide bases, as measured by any well-known algorithm of sequence identity, such as FASTA, BLAST, MUSCLE or Gap, as discussed above.


As used herein, the terms “operational taxonomic unit,” “OTU,” “taxon,” “hierarchical cluster,” and “cluster” are used interchangeably. An operational taxon unit (OTU) refers to a group of one or more organisms that comprises a node in a clustering tree. The level of a cluster is determined by its hierarchical order. In some embodiments, an OTU is a group tentatively assumed to be a valid taxon for purposes of phylogenetic analysis. In other embodiments, an OTU is any of the extant taxonomic units under study. In yet another embodiment, an OTU is given a name and a rank. For example, an OTU can represent a domain, a sub-domain, a kingdom, a sub-kingdom, a phylum, a sub-phylum, a class, a sub-class, an order, a sub-order, a family, a subfamily, a genus, a subgenus, or a species. In some embodiments, OTUs can represent one or more organisms from the kingdoms eubacteria, protista, or fungi at any level of a hierarchal order. In some embodiments, an OTU represents a prokaryotic or fungal order.


As used herein, the terms “water-limited condition”, “water stress condition” and “drought condition”, or “water-limited”, “water stress”, and “drought”, may be used interchangeably. For example, a method or composition for improving a plant's ability to grow under drought conditions means the same as the ability to grow under water-limited conditions. In such cases, the plant can be further said to display improved tolerance to drought stress.


The terms “decreased”, “fewer”, “slower” and “increased” “faster” “enhanced” “greater” as used herein refers to a decrease or increase in a characteristic of the endophyte treated seed or resulting plant compared to an untreated seed or resulting plant. For example, a decrease in a characteristic may be at least 1%, at least 2%, at least 3%, at least 4%, at least 5%, at least 10%, at least 15%, at least 20%, at least 25%, at least 30%, at least 35%, at least 40%, at least 45%, at least 50%, at least about 60%, at least 75%, at least about 80%, at least about 90%, at least 100%, at least 200%, at least about 300%, at least about 400% or more lower than the untreated control. For example, a decrease may be between 1% and 5%, or between 5% and 10%, or between 10% and 15%, or between 15% and 20%, or between 20% and 25%, or between 25% and 30%, or between 30% and 35%, or between 35% and 40%, or between 45% and 50% lower than the untreated control or the formulation control. An increase may be at least 1%, at least 2%, at least 3%, at least 4%, at least 5%, at least 10%, at least 15%, at least 20%, at least 25%, at least 30%, at least 35%, at least 40%, at least 45%, at least 50%, at least about 60%, at least 75%, at least about 80%, at least about 90%, at least 100%, at least 200%, at least about 300%, at least about 400% or more higher than the untreated control. For example, an increase may be between 1% and 5%, or between 5% and 10%, or between 10% and 15%, or between 15% and 20%, or between 20% and 25%, or between 25% and 30%, or between 30% and 35%, or between 35% and 40%, or between 45% and 50% higher than the untreated control or the formulation control.


Endophytes


Agricultural plants appear to associate with symbiotic microorganisms termed endophytes, particularly bacteria and fungi, that may have been important during evolution and may contribute to plant survival and performance. However, modern agricultural processes may have perturbed this relationship, resulting in increased crop losses, diminished stress resilience, biodiversity losses, and increasing dependence on external chemicals, fertilizers, and other unsustainable agricultural practices. There is a need for novel methods for generating plants with novel microbiome properties that can sustainably increase yield, stress resilience, and decrease fertilizer and chemical use.


The inventors have undertaken a systematic comparison of the microbial communities that reside within a wide diversity of plants. As such, the endophytic microbes useful for the invention generally relate to endophytic microbes that are present in agricultural plants.


In part, the present invention describes preparations of novel endophytes, and the creation of synthetic combinations of agricultural seeds and/or seedlings with heterologous endophytes and formulations containing the synthetic combinations, as well as the recognition that such synthetic combinations display a diversity of beneficial properties present in the agricultural plants and the associated endophyte populations newly created by the present inventors. Such beneficial properties include metabolism, transcript expression, proteome alterations, morphology, and the resilience to a variety of environmental stresses, and the combination of a plurality of such properties.


Provided are novel compositions, methods, and products related our invention's ability to overcome the limitations of the prior art in order to provide reliable increases in crop yield, biomass, germination, vigor, stress resilience, and other properties to agricultural crops.


We find that beneficial microbes can be robustly derived from plant elements, optionally cultured, administered heterologously to agricultural plant elements such as seeds, and colonize the resulting plant tissues with high efficiency to confer multiple beneficial properties.


We find that microbes can confer beneficial properties across a range of concentrations.


We find that endophytes can be heterologously disposed onto seedlings of a distinct cultivar, species, or crop type and confer benefits to those new recipients. For example, endophytes from corn cultivars are heterologously provided to wheat cultivars to confer a benefit. This is surprising given the observations of distinct microbiome preferences in distinct plant and mammalian hosts and, in particular, the likelihood that microbes derived from seeds have been co-evolved to be specialized to a particular host.


We further find that combinations of heterologously disposed endophytes confer additive advantages to plants, including multiple functional properties and resulting in seed, seedling, and plant hosts that display single or multiple improved agronomic properties.


Endophytes are microbes that grow inside a plant. Recent appreciation that endophytes can confer remarkable traits upon the host plant is the basis for the present invention. The inventors have developed a method to introduce isolated endophytes to another plant by coating the microbes onto the surface of a seed of a plant. By combining an endophyte sourced from one plant, it is possible to transfer the beneficial agronomic trait onto an agricultural plant, and therefore holds great promise for increasing agricultural productivity.


Combining a selected plant species, OTU, strain or cultivar with one or more types of endophytes thus provides mechanisms by which, alone or in parallel with plant breeding and transgenic technologies, is provided improved yield from crops and generation of products thereof. Therefore, in a first aspect, the present invention provides a synthetic combination comprising the combination of a plant element, seedling, or whole plants and a single endophyte strain or a plurality of endophytes, in which the single endophyte strain or a plurality of endophytes are “heterologously disposed.”


Synthetic Compositions of Plant Elements and Endophytes


The present invention contemplates a synthetic combination of a plant element of a plant that is coated with an endophyte on its surface. The plant element can be any agricultural plant element, for example an agricultural seed. In one embodiment, the plant element of the first plant is from a monocotyledonous plant. For example, the plant element of the first plant is from a cereal plant. The plant element of the first plant can be selected from the group consisting of a maize plant, a wheat plant, a barley plant, an onion plant, a sorghum plant, or a rice plant. In an alternative embodiment, the plant element of the first plant is from a dicotyledonous plant. The plant element of the first plant can be selected from the group consisting of a cotton plant, a Brassica napus plant, a tomato plant, a pepper plant, a cabbage plant, a lettuce plant, a melon plant, a strawberry plant, a turnip plant, a watermelon plant, a peanut plant, or a soybean plant. In a particular embodiment, the plant is not a cotton plant. In still another embodiment, the seed of the first plant can be from a genetically modified plant. In another embodiment, the seed of the first plant can be a hybrid seed.


The synthetic combination can comprise a plant element of the first plant that is surface-sterilized prior to combining with the endophytes. Such pre-treatment prior to coating the plant element with endophytes removes the presence of other microbes that may interfere with the optimal colonization, growth and/or function of the endophyte. Surface sterilization of plant elements can be accomplished without killing the plant elements as described herein elsewhere (see, for example, the section Isolation of endophytes).


Sources of Endophytes


As described herein, endophytes can be derived from heterologous, homologous, or engineered sources, optionally cultured, administered heterologously as a single endophyte strain or a plurality of endophytes to plant elements, and, as a result of the administration, confer multiple beneficial properties. In some embodiments, endophytes are derived from plant elements or soil. In some embodiments, the plant element from which the endophyte is derived is a monocotyledonous plant. In a particular embodiment, the plant is a cereal plant or tissue thereof. In yet another embodiment, plant is selected from the group consisting of a maize plant, a barley plant, a wheat plant, a sugarcane plant, a sorghum plant, or a rice plant. In some embodiments, the plant element is a naked grain (i.e., without hulls or fruit cases). In an alternative embodiment, the plant element from which the endophyte is derived is a W dicotyledonous plant. For example, a plant can be selected from the group consisting of a cotton plant, a Brassica napus plant, a tomato plant, a pepper plant, a cabbage plant, a lettuce plant, a melon plant, a strawberry plant, a turnip plant, a watermelon plant, a peanut plant, or a soybean plant.


In some embodiments, the endophytes can be obtained from a plant element of the same or different crop, and can be from the same or different cultivar or variety as the plant element to which the composition is heterologously associated. For example, endophytes from a particular corn variety can be isolated and coated onto the surface of a corn seed of the same variety. In other embodiments, the endophytes can be isolated from a related species (e.g., an endophyte isolated from Triticum monococcum (einkorn wheat) can be coated onto the surface of a T. aestivum (common wheat) plant element; or, an endophyte from Hordeum vulgare (barley) can be isolated and coated onto the plant element of another member of the Triticeae family, for example, plant elements of the rye plant, Secale cereale). In still another embodiment, the endophytes can be isolated from a plant part of a plant that is distantly related to the plant element onto which the endophyte is to be coated. For example, tomato-derived endophytes are isolated and coated onto a rice plant element. In still another embodiment, endophytes used in a composition or used to make a synthetic composition can be obtained from a plant element of a plant that is distantly related to the plant element onto which the endophyte is to be coated. For example, a tomato-derived endophyte can be isolated and coated onto a rice plant element.


In some embodiments, the present invention contemplates the use of endophytes that can confer a beneficial agronomic trait upon the seed or resulting plant onto which it is coated. In another embodiment, the seed endophytes useful for the present invention can also be isolated from seeds of plants adapted to a particular environment, including, but not limited to, an environment with water deficiency, salinity, acute and/or chronic heat stress, acute and/or chronic cold stress, nutrient deprived soils including, but not limited to, micronutrient deprived soils, macronutrient (e.g., potassium, phosphate, nitrogen) deprived soils, pathogen stress, including fungal, nematode, insect, viral, bacterial pathogen stress. In one example, the endophyte is isolated from the seed of a plant that grows in a water deficient environment.


The synthetic combination of the present invention contemplates the presence of an endophyte on the surface of the seed of the first plant. In one embodiment, the seed of the to first plant is coated with at least 10 CFU or spores of the endophyte per seed, for example, at least 20 CFU or spores, at least 50 CFU or spores, at least 100 CFU or spores, at least 200 CFU or spores, at least 300 CFU or spores, at least 500 CFU or spores, at least 1,000 CFU or spores, at least 3,000 CFU or spores, at least 10,000 CFU or spores, at least 30,000 CFU or spores or more per plant element. In another embodiment, the plant element is coated with at least 10, for example, at least 20, at least 50, at least 100, at least 200, at least 300, at least 500, at least 1,000, at least 3,000, at least 10,000, at least 30,000, at least 100,000, at least 300,000, at least 1,000,000 or more of the endophyte as detected by the number of copies of a particular endophyte gene detected, for example, by quantitative PCR.


The endophyte useful for the present invention can be a fungus. In another embodiment, the endophyte can be a bacterium. In one embodiment, the endophyte is not an Agrobacterium. In another embodiment, the endophyte is not capable of nitrogen fixation (for example, from the genus Rhizobium). In still another embodiment, the endophyte is not from the genus Acetobacter. In yet another embodiment, the endophyte is not from the genus Bacillus. In a particular embodiment, the endophyte is not Bacillus mojavensis. In yet another embodiment, the endophyte is not from the genus Neotyphodium.


Historical taxonomic classification of fungi has been according to morphological presentation. Beginning in the mid-1800's, it was recognized that some fungi have a pleomorphic life cycle, and that different nomenclature designations were being used for different forms of the same fungus. In 1981, the Sydney Congress of the International Mycological Association laid out rules for the naming of fungi according to their status as anamorph, teleomorph, or holomorph. With the development of genomic sequencing, it became evident that taxonomic classification based on molecular phylogenetics did not align with morphological-based nomenclature. As a result, in 2011 the International Botanical Congress adopted a resolution approving the International Code of Nomenclature for Algae, Fungi, and Plants (Melbourne Code) (2012), with the stated outcome of designating “One Fungus=One Name”. However, systematics experts have not aligned on common nomenclature for all fungi, nor are all existing databases and information resources inclusive of updated taxonomies. As such, many fungi referenced herein may be described by their anamorph form but it is understood that based on identical genomic sequencing, any pleomorphic state of that fungus may be considered to be the same organism. For example, the genus Alternaria is the anamorph form of the teleomorph genus Lewia, ergo both would be understood to be the same organism with the same DNA sequence.


Exogenous Endophytes


In one embodiment, the endophyte is an endophytic microbe that was isolated from a different plant than the inoculated plant. For example, in one embodiment, the endophyte can be an endophyte isolated from a different plant of the same species as the inoculated plant. In some cases, the endophyte can be isolated from a species related to the inoculated plant.


The breeding of plants for agriculture, as well as cultural practices used to combat microbial pathogens, may have resulted in the loss in modern cultivars of the endophytes present in their wild ancestors or other wild plants, or such practices may have inadvertently promoted other novel or rare plant-endophyte interactions, or otherwise altered the microbial) population. The former is the case in maize and its phylogenetically confirmed, direct wild ancestor, Parviglumis teosinte (Zea mays ssp. Parviglumis). Although both species have seeds that appear to contain a common core of endophytic bacterial species, the relative abundance of certain groups is higher in seeds of teosinte than modern corn. It is possible that this higher diversity and titer of endophytes in the ancestor is correlated with an equally wide range of physiological responses derived from the symbiosis that allow the plant to better adapt to the environment and tolerate stress. In order to survey plant groups for potentially useful endophytes, seeds of their wild ancestors, wild relatives, primitive landraces, modern landraces, modern breeding lines, and elite modern agronomic varieties can be screened for microbial endophytes by culture and culture independent methods as described herein. In addition, microbial endophytes can be isolated from other wild plants, such as grassland plants.


In some cases, plants are inoculated with endophytes that are exogenous to the seed of the inoculated plant. In one embodiment, the endophyte is derived from a plant of another species. For example, an endophyte that is normally found in dicots is applied to a monocot plant (e.g., inoculating corn with a soy bean-derived endophyte), or vice versa. In other cases, the endophyte to be inoculated onto a plant can be derived from a related species of the plant that is being inoculated. In one embodiment, the endophyte can be derived from a related taxon, for example, from a related species. The plant of another species can be an agricultural plant. For example, an endophyte derived from Hordeum irregulare can be used to inoculate a Hordeum vulgare L., plant. Alternatively, it can be derived from a ‘wild’ plant (i.e., a non-agricultural plant). For example, endophytes normally associated with the wild cotton Gossypium klotzschianum can be used to inoculate commercial varieties of Gossypium hirsutum plants. Endophytes normally associated with a wild turnip plant or a wild watermelon plant can be used to inoculate commercial varieties of turnip or watermelon plants, respectively. As an alternative example of deriving an endophyte from a ‘wild’ plant, endophytic bacteria isolated from the South East Asian jungle orchid, Cymbidium eburneum, as can be isolated and testing for their capacity to benefit seedling development and survival of agricultural crops such as wheat, maize, soy and others. In another example, endophytes may be isolated from wild grassland plants. In other cases, the endophyte can be isolated from an ancestral species of the inoculated plant. For example, an endophyte derived from Zea diploperennis can be used to inoculate a commercial variety of modern corn, or Zea mays.


Selection of Plant Species from Desired Habitats for Isolation of Microbial Endophytes


Different environments can contain significantly different populations of endophytes. For example, geographically isolated soils from different parts of the Americas have been shown to differ in 96% of the bacterial species they contain. Soils containing different microbial populations can strongly influence the endophytic bacterial population observed inside Arabidopsis illustrating that the environment can at least partially alter a plant's associated microbial population. This suggests that plants growing and especially thriving in choice environments are colonized by different and perhaps beneficial endophytes, whose isolation and inoculation onto crop plants may aid these plants to better survive in the same choice environment or to better resist certain stresses encountered in a normal agricultural environment. For instance, at least some of the bacteria isolated from plants growing in arid environments are expected to confer drought tolerance to host plants they are transplanted onto. Additionally, novel endophtytes may be found in related crop varieties grown in the choice environment. Once a choice environment is selected, seeds of choice plants to be sampled will be identified by their healthy and/or robust growth, and will then be sampled at least 5 at a time by excavating the entire plants plus small root ball including roots and associated soil and any seeds or fruit present on the plant. These will be placed in a cool (4° C. environment) for storage and prompt transport back to the lab for extraction of endophytes and DNA using methods described herein. Identification of choice environments or ecosystems for bioprospecting of plant associated endophytes from either wild plants or crop plants growing in the choice environments or ecosystems follows protocols described herein.


In one embodiment, the endophyte-associated plant is harvested from a soil type different than the normal soil type that the crop plant is grown on, for example from a gelisol (soils with permafrost within 2 m of the surface), for example from a histosol (organic soil), for example from a spodosol (acid forest soils with a subsurface accumulation of metal-humus complexes), for example from an andisol (soils formed in volcanic ash), for example from a oxisol (intensely weathered soils of tropical and subtropical environments), for example from a vertisol (clayey soils with high shrink/swell capacity), for example from an aridisol (CaCO3-containing soils of arid environments with subsurface horizon development), for example from a ultisol (strongly leached soils with a subsurface zone of clay accumulation and <35% base saturation), for example from a mollisol (grassland soils with high base status), for example from an alfisol (moderately leached soils with a so subsurface zone of clay accumulation and >35% base saturation), for example from a inceptisol (soils with weakly developed subsurface horizons), for example from a entisol (soils with little or no morphological development).


In another embodiment, the endophyte-associated plant is harvested from an ecosystem where the agricultural plant is not normally found, for example a tundra ecosystem as opposed to a temperate agricultural farm, for example from tropical and subtropical moist broadleaf forests (tropical and subtropical, humid), for example from tropical and subtropical dry broadleaf forests (tropical and subtropical, semihumid), for example from tropical and subtropical coniferous forests (tropical and subtropical, semihumid), for example from temperate broadleaf and mixed forests (temperate, humid), for example from temperate coniferous forests (temperate, humid to semihumid), from for example from boreal forests/taiga (subarctic, humid), for example from tropical and subtropical grasslands, savannas, and shrublands (tropical and subtropical, semiarid), for example from temperate grasslands, savannas, and shrublands (temperate, semiarid), for example from flooded grasslands and savannas (temperate to tropical, fresh or brackish water inundated), for example from montane grasslands and shrublands (alpine or montane climate), for example from Mediterranean forests, woodlands, and scrub or sclerophyll forests (temperate warm, semihumid to semiarid with winter rainfall), for example from mangrove forests, and for example from deserts and xeric shrublands (temperate to tropical, arid).


In another embodiment, the endophyte-associated plant is harvested from a soil with an average pH range that is different from the optimal soil pH range of the crop plant, for example the plant may be harvested from an ultra acidic soil (<3.5), from an extreme acid soil (3.5-4.4), from a very strong acid soil (4.5-5.0), from a strong acid soil (5.1-5.5), from a moderate acid soil (5.6-6.0), from an slight acid soil (6.1-6.5), from an neutral soil (6.6-7.3), from an slightly alkaline soil (7.4-7.8), from an moderately alkaline soil (7.9-8.4), from a strongly alkaline soil (8.5-9.0), or from an very strongly alkaline soil (>9.0).


In one embodiment, the endophyte-associated plant is harvested from an environment with average air temperatures lower than the normal growing temperature of the crop plant, for example 2-5° C. colder than average, for example, at least 5-10° C. colder, at least 10-15° C. colder, at least at least 15-20° C. colder, at least 20-25° C. colder, at least 25-30° C. colder, at least 30-35° C. colder, at least 35-40° C. colder, at least 40-45° C. colder, at least 45-50° C. colder, at least 50-55° C. colder or more, when compared with crop plants grown under normal conditions during an average growing season.


In one embodiment, the endophyte-associated plant is harvested from an environment with average air temperatures higher than the normal growing temperature of the crop plant, for example 2-5° C. hotter than average, for example, at least 5-10° C. hotter, at least 10-15° C. hotter, at least at least 15-20° C. hotter, at least 20-25° C. hotter, at least 25-30° C. hotter, at least 30-35° C. hotter, at least 35-40° C. hotter, at least 40-45° C. hotter, at least 45-50° C. hotter, at least 50-55° C. hotter or more, when compared with crop plants grown under normal conditions during an average growing season.


In another embodiment, the endophyte-associated plant is harvested from an environment with average rainfall lower than the optimal average rainfall received by the crop plant, for example 2-5% less rainfall than average, for example, at least 5-10% less rainfall, at least 10-15% less rainfall, at least 15-20% less rainfall, at least 20-25% less rainfall, at least 25-30% less rainfall, at least 30-35% less rainfall, at least 35-40% less rainfall, at least 40-45% less rainfall, at least 45-50% less rainfall, at least 50-55% less rainfall, at least 55-60% less rainfall, at least 60-65% less rainfall, at least 65-70% less rainfall, at least 70-75% less rainfall, at least 80-85% less rainfall, at least 85-90% less rainfall, at least 90-95% less rainfall, or less, when compared with crop plants grown under normal conditions during an average growing season.


In one embodiment, the endophyte-associated plant is harvested from an environment with average rainfall higher than the optimal average rainfall of the crop plant, for example 2-5% more rainfall than average, for example, at least 5-10% more rainfall, at least 10-15% more rainfall, at least 15-20% more rainfall, at least 20-25% more rainfall, at least 25-30% more rainfall, at least 30-35% more rainfall, at least 35-40% more rainfall, at least 40-45% more rainfall, at least 45-50% more rainfall, at least 50-55% more rainfall, at least 55-60% more rainfall, at least 60-65% more rainfall, at least 65-70% more rainfall, at least 70-75% more rainfall, at least 80-85% more rainfall, at least 85-90% more rainfall, at least 90-95% more rainfall, at least 95-100% more rainfall, or even greater than 100% more rainfall, or even greater than 200% more rainfall, or even greater than 300% more rainfall, or even greater than 400% more rainfall, or even greater than 500% more rainfall, when compared with crop plants grown under normal conditions during an average growing season.


In another embodiment, the endophyte-associated plant is harvested from a soil type with different soil moisture classification than the normal soil type that the crop plant is grown on, for example from an aquic soil (soil is saturated with water and virtually free of gaseous oxygen for sufficient periods of time, such that there is evidence of poor aeration), for example from an udic soil (soil moisture is sufficiently high year-round in most years to meet plant requirement), for example from an ustic soil (soil moisture is intermediate between udic and aridic regimes; generally, plant-available moisture during the growing season, but severe periods of drought may occur), for example from an aridic soil (soil is dry for at least half of the growing season and moist for less than 90 consecutive days), for example from a xeric soil (soil moisture regime is found in Mediterranean-type climates, with cool, moist winters and warm, dry summers).


In one embodiment, the endophyte-associated plant is harvested from an environment with average rainfall lower than the optimal average rainfall of the crop plant, for example 2-95% less rainfall than average, for example, at least 5-90% less rainfall, at least 10-85% less rainfall, at least 15-80% less rainfall, at least 20-75% less rainfall, at least 25-70% less rainfall, at least 30-65% less rainfall, at least 35-60% less rainfall, at least 40-55% less rainfall, at least 45-50% less rainfall, when compared with crop plants grown under normal conditions during an average growing season.


In one embodiment, the endophyte-associated plant is harvested from an environment with average rainfall higher than the optimal average rainfall of the crop plant, for example 2-5% more rainfall than average, for example, at least 5-10% more rainfall, at least 10-15% more rainfall, at least 15-20% more rainfall, at least 20-25% more rainfall, at least 25-30% more rainfall, at least 30-35% more rainfall, at least 35-40% more rainfall, at least 40-45% more rainfall, at least 45-50% more rainfall, at least 50-55% more rainfall, at least 55-60% more rainfall, at least 60-65% more rainfall, at least 65-70% more rainfall, at least 70-75% more rainfall, at least 80-85% more rainfall, at least 85-90% more rainfall, at least 90-95% more rainfall, at least 95-100% more rainfall, or even greater than 100% more rainfall, or even greater than 200% more rainfall, or even greater than 300% more rainfall, or even greater than 400% more rainfall, or even greater than 500% more rainfall, when compared with crop plants grown under normal conditions during an average growing season.


In another embodiment, the endophyte-associated plant is harvested from an agricultural environment with a crop yield lower than the average crop yield expected from the crop plant grown under average cultivation practices on normal agricultural land, for example 2-5% lower yield than average, for example, at least 5-10% lower yield, at least 10-15% lower yield, at least 15-20% lower yield, at least 20-25% lower yield, at least 25-30% lower yield, at least 30-35% lower yield, at least 35-40% lower yield, at least 40-45% lower yield, at least 45-50% lower yield, at least 50-55% lower yield, at least 55-60% lower yield, at least 60-65% lower yield, at least 65-70% lower yield, at least 70-75% lower yield, at least 80-85% lower yield, at least 85-90% lower yield, at least 90-95% lower yield, or less, when compared with crop plants grown under normal conditions during an average growing season.


In a related embodiment, the endophyte-associated plant is harvested from an agricultural environment with a crop yield lower than the average crop yield expected from the crop plant grown under average cultivation practices on normal agricultural land, for example 2-95% lower yield than average, for example, at least 5-90% lower yield, at least 10-85% lower yield, at least 15-80% lower yield, at least 20-75% lower yield, at least 25-70% lower yield, at least 30-65% lower yield, at least 35-60% lower yield, at least 40-55% lower yield, at least 45-50% lower yield, when compared with crop plants grown under normal conditions during an average growing season.


In one embodiment, the endophyte-associated plant is harvested from an environment with average crop yield higher than the optimal average crop yield of the crop plant, for example 2-5% more yield than average, for example, at least 5-10% more yield, at least 10-15% more yield, at least 15-20% more yield, at least 20-25% more yield, at least 25-30% more yield, at least 30-35% more yield, at least 35-40% more yield, at least 40-45% more yield, at least 45-50% more yield, at least 50-55% more yield, at least 55-60% more yield, at least 60-65% more yield, at least 65-70% more yield, at least 70-75% more yield, at least 80-85% more yield, at least 85-90% more yield, at least 90-95% more yield, at least 95-100% more yield, or even greater than 100% more yield, or even greater than 200% more yield, or even greater than 300% more yield, or even greater than 400% more yield, or even greater than 500% more yield, when compared with crop plants grown under normal conditions during an average growing season.


In a related embodiment, the endophyte-associated plant is harvested from an environment with average crop yield higher than the optimal average crop yield of the crop plant, 2-500% more yield than average, 2-400% more yield than average, 2-300% more yield than average, 2-200% more yield than average, 2-95% more yield than average, for example, at least 5-90% more yield, at least 10-85% more yield, at least 15-80% more yield, at least 20-75% more yield, at least 25-70% more yield, at least 30-65% more yield, at least 35-60% more yield, at least 40-55% more yield, at least 45-50% more yield, when compared with crop plants grown under normal conditions during an average growing season.


In another embodiment, the endophyte-associated plant is harvested from a environment where soil contains lower total nitrogen than the optimum levels recommended in order to achieve average crop yields for a plant grown under average cultivation practices on normal agricultural land, for example 2-5% less nitrogen than average, for example, at least 5-10% less nitrogen, at least 10-15% less nitrogen, at least 15-20% less nitrogen, at least 20-25% less nitrogen, at least 25-30% less nitrogen, at least 30-35% less nitrogen, at least 35-40% less nitrogen, at least 40-45% less nitrogen, at least 45-50% less nitrogen, at least 50-55% less nitrogen, at least 55-60% less nitrogen, at least 60-65% less nitrogen, at least 65-70% less nitrogen, at least 70-75% less nitrogen, at least 80-85% less nitrogen, at least 85-90% less nitrogen, at least 90-95% less nitrogen, or less, when compared with crop plants grown under normal conditions during an average growing season.


In another embodiment, the endophyte-associated plant is harvested from a environment where soil contains higher total nitrogen than the optimum levels recommended in order to achieve average crop yields for a plant grown under average cultivation practices on normal agricultural land, for example 2-5% more nitrogen than average, for example, at least 5-10% more nitrogen, at least 10-15% more nitrogen, at least 15-20% more nitrogen, at least 20-25% more nitrogen, at least 25-30% more nitrogen, at least 30-35% more nitrogen, at least 35-40% more nitrogen, at least 40-45% more nitrogen, at least 45-50% more nitrogen, at least 50-55% more nitrogen, at least 55-60% more nitrogen, at least 60-65% more nitrogen, at least 65-70% more nitrogen, at least 70-75% more nitrogen, at least 80-85% more nitrogen, at least 85-90% more nitrogen, at least 90-95% more nitrogen, at least 95-100% more nitrogen, or even greater than 100% more nitrogen, or even greater than 200% more nitrogen, or even greater than 300% more nitrogen, or even greater than 400% more nitrogen, or even greater than 500% more nitrogen, when compared with crop plants grown under normal conditions during an average growing season.


In another embodiment, the endophyte-associated plant is harvested from a environment where soil contains lower total phosphorus than the optimum levels recommended in order to achieve average crop yields for a plant grown under average cultivation practices on normal agricultural land, for example 2-5% less phosphorus than average, for example, at least 5-10% less phosphorus, at least 10-15% less phosphorus, at least 15-20% less phosphorus, at least 20-25% less phosphorus, at least 25-30% less phosphorus, at least 30-35% less phosphorus, at least 35-40% less phosphorus, at least 40-45% less phosphorus, at least 45-50% less phosphorus, at least 50-55% less phosphorus, at least 55-60% less phosphorus, at least 60-65% less phosphorus, at least 65-70% less phosphorus, at least 70-75% less phosphorus, at least 80-85% less phosphorus, at least 85-90% less phosphorus, at least 90-95% less phosphorus, or less, when compared with crop plants grown under normal conditions during an average growing season.


In another embodiment, the endophyte-associated plant is harvested from a environment where soil contains higher total phosphorus than the optimum levels recommended in order to achieve average crop yields for a plant grown under average cultivation practices on normal agricultural land, for example 2-5% more phosphorus than average, for example, at least 5-10% more phosphorus, at least 10-15% more phosphorus, at least 15-20% more phosphorus, at least 20-25% more phosphorus, at least 25-30% more phosphorus, at least 30-35% more phosphorus, at least 35-40% more phosphorus, at least 40-45% more phosphorus, at least 45-50% more phosphorus, at least 50-55% more phosphorus, at least 55-60% more phosphorus, at least 60-65% more phosphorus, at least 65-70% more phosphorus, at least 70-75% more phosphorus, at least 80-85% more phosphorus, at least 85-90% more phosphorus, at least 90-95% more phosphorus, at least 95-100% more phosphorus, or even greater than 100% more phosphorus, or even greater than 200% more phosphorus, or even greater than 300% more phosphorus, or even greater than 400% more phosphorus, or even greater than 500% more phosphorus, when compared with crop plants grown under normal conditions during an average growing season.


In another embodiment, the endophyte-associated plant is harvested from a environment where soil contains lower total potassium than the optimum levels recommended in order to achieve average crop yields for a plant grown under average cultivation practices on normal agricultural land, for example 2-5% less potassium than average, for example, at least 5-10% less potassium, at least 10-15% less potassium, at least 15-20% less potassium, at least 20-25% less potassium, at least 25-30% less potassium, at least 30-35% less potassium, at least 35-40% less potassium, at least 40-45% less potassium, at least 45-50% less potassium, at least 50-55% less potassium, at least 55-60% less potassium, at least 60-65% less potassium, at least 65-70% less potassium, at least 70-75% less potassium, at least 80-85% less potassium, at least 85-90% less potassium, at least 90-95% less potassium, or less, when compared with crop plants grown under normal conditions during an average growing season.


In another embodiment, the endophyte-associated plant is harvested from a environment where soil contains higher total potassium than the optimum levels recommended in order to achieve average crop yields for a plant grown under average cultivation practices on normal agricultural land, for example 2-5% more potassium than average, for example, at least 5-10% more potassium, at least 10-15% more potassium, at least 15-20% more potassium, at least 20-25% more potassium, at least 25-30% more potassium, at least 30-35% more potassium, at least 35-40% more potassium, at least 40-45% more potassium, at least 45-50% more potassium, at least 50-55% more potassium, at least 55-60% more potassium, at least 60-65% more potassium, at least 65-70% more potassium, at least 70-75% more potassium, at least 80-85% more potassium, at least 85-90% more potassium, at least 90-95% more potassium, at least 95-100% more potassium, or even greater than 100% more potassium, or even greater than 200% more potassium, or even greater than 300% more potassium, or even greater than 400% more potassium, or even greater than 500% more potassium, when compared with crop plants grown under normal conditions during an average growing season.


In another embodiment, the endophyte-associated plant is harvested from a environment where soil contains lower total sulfur than the optimum levels recommended in order to achieve average crop yields for a plant grown under average cultivation practices on normal agricultural land, for example 2-5% less sulfur than average, for example, at least 5-10% less sulfur, at least 10-15% less sulfur, at least 15-20% less sulfur, at least 20-25% less sulfur, at least 25-30% less sulfur, at least 30-35% less sulfur, at least 35-40% less sulfur, at least 40-45% less sulfur, at least 45-50% less sulfur, at least 50-55% less sulfur, at least 55-60% less sulfur, at least 60-65% less sulfur, at least 65-70% less sulfur, at least 70-75% less sulfur, at least 80-85% less sulfur, at least 85-90% less sulfur, at least 90-95% less sulfur, or less, when compared with crop plants grown under normal conditions during an average growing season.


In another embodiment, the endophyte-associated plant is harvested from a environment where soil contains higher total sulfur than the optimum levels recommended in order to achieve average crop yields for a plant grown under average cultivation practices on normal agricultural land, for example 2-5% more sulfur than average, for example, at least 5-10% more sulfur, at least 10-15% more sulfur, at least 15-20% more sulfur, at least 20-25% more sulfur, at least 25-30% more sulfur, at least 30-35% more sulfur, at least 35-40% more sulfur, at least 40-45% more sulfur, at least 45-50% more sulfur, at least 50-55% more sulfur, at least 55-60% more sulfur, at least 60-65% more sulfur, at least 65-70% more sulfur, at least 70-75% more sulfur, at least 80-85% more sulfur, at least 85-90% more sulfur, at least 90-95% more sulfur, at least 95-100% more sulfur, or even greater than 100% more sulfur, or even greater than 200% more sulfur, or even greater than 300% more sulfur, or even greater than 400% more sulfur, or even greater than 500% more sulfur, when compared with crop plants grown under normal conditions during an average growing season.


In another embodiment, the endophyte-associated plant is harvested from a environment where soil contains lower total calcium than the optimum levels recommended in order to achieve average crop yields for a plant grown under average cultivation practices on normal agricultural land, for example 2-5% less calcium than average, for example, at least 5-10% less calcium, at least 10-15% less calcium, at least 15-20% less calcium, at least 20-25% less calcium, at least 25-30% less calcium, at least 30-35% less calcium, at least 35-40% less calcium, at least 40-45% less calcium, at least 45-50% less calcium, at least 50-55% less calcium, at least 55-60% less calcium, at least 60-65% less calcium, at least 65-70% less calcium, at least 7.0-75% less calcium, at least 80-85% less calcium, at least 85-90% less calcium, at least 90-95% less calcium, or less, when compared with crop plants grown under normal conditions during an average growing season.


In another embodiment, the endophyte-associated plant is harvested from a environment where soil contains lower total magnesium than the optimum levels recommended in order to achieve average crop yields for a plant grown under average cultivation practices on normal agricultural land, for example 2-5% less magnesium than average, for example, at least 5-10% less magnesium, at least 10-15% less magnesium, at least 15-20% less magnesium, at least 20-25% less magnesium, at least 25-30% less magnesium, at least 30-35% less magnesium, at least 35-40% less magnesium, at least 40-45% less magnesium, at least 45-50% less magnesium, at least 50-55% less magnesium, at least 55-60% less magnesium, at least 60-65% less magnesium, at least 65-70% less magnesium, at least 70-75% less magnesium, at least 80-85% less magnesium, at least 85-90% less magnesium, at least 90-95% less magnesium, or less, when compared with crop plants grown under normal conditions during an average growing season.


In another embodiment, the endophyte-associated plant is harvested from a environment where soil contains higher total sodium chloride (salt) than the optimum levels recommended in order to achieve average crop yields for a plant grown under average cultivation practices on normal agricultural land, for example 2-5% more salt than average, for example, at least 5-10% more salt, at least 10-15% more salt, at least 15-20% more salt, at least 20-25% more salt, at least 25-30% more salt, at least 30-35% more salt, at least 35-40% more salt, at least 40-45% more salt, at least 45-50% more salt, at least 50-55% more salt, at least 55-60% more salt, at least 60-65% more salt, at least 65-70% more salt, at least 70-75% more salt, at least 80-85% more salt, at least 85-90% more salt, at least 90-95% more salt, at least 95-100% more salt, or even greater than 100% more salt, or even greater than 200% more salt, or even greater than 300% more salt, or even greater than 400% more salt, or even greater than 500% more salt, when compared with crop plants grown under normal conditions during an average growing season.


Relocalization of Endophytes


In some embodiments, a single endophyte strain or a plurality of endophytes that are used to treat a plant element are capable of localizing to a different tissue of the plant, regardless of the original source of the endophyte. For example, the endophyte can be capable of localizing to any one of the tissues in the plant, including: the root, adventitious root, seminal root, root hair, shoot, leaf, flower, bud, tassel, meristem, pollen, pistil, ovaries, stamen, fruit, stolon, rhizome, nodule, tuber, trichome, guard cells, hydathode, petal, sepal, glume, rachis, vascular cambium, phloem, and xylem. In one embodiment, the endophyte is capable of localizing to the root and/or the root hair of the plant. In another embodiment, the endophyte is capable of localizing to the photosynthetic tissues, for example, leaves and shoots of the plant. In other cases, the endophyte is localized to the vascular tissues of the plant, for example, in the xylem and phloem. In still another embodiment, the endophyte is capable of localizing to the reproductive tissues (flower, pollen, pistil, ovaries, stamen, fruit) of the plant. In another embodiment, the endophyte is capable of localizing to the root, shoots, leaves and reproductive tissues of the plant. In still another embodiment, the endophyte colonizes a fruit or seed tissue of the plant. In still another embodiment, the endophyte is able to colonize the plant such that it is present in the surface of the plant (i.e., its presence is detectably present on the plant exterior, or the episphere of the plant). In still other embodiments, the endophyte is capable of localizing to substantially all, or all, tissues of the plant. In certain embodiments, the endophyte is not localized to the root of a plant. In other cases, the endophyte is not localized to the photosynthetic tissues of the plant.


Endophytes Capable of Altering the Metabolome, Epigenome, or Transcriptome of Plants


The endophytes useful for the invention can also be classified according to the changes conferred upon the plant. For example, the endophyte can alter the hormone status or levels of hormone production in the plant, which in turn can affect many physiological parameters, including flowering time, water efficiency, apical dominance and/or lateral shoot branching, increase in root hair, and alteration in fruit ripening. The endophyte may also introduce other changes to the plant, including biochemical, metabolomic, proteomic, genomic, epigenomic and/or transcriptomic profiles of endophyte-associated plants can be compared with reference agricultural plants under the same conditions.


Metabolomic differences between the plants can be detected using methods known in the art. For example, a biological sample (whole tissue, exudate, phloem sap, xylem sap, root exudate, etc.) from the endophyte-associated and reference agricultural plants can be analyzed essentially as described in Fiehn et al., (2000) Nature Biotechnol., 18, 1157-1161, or Roessner et al., (2001) Plant Cell, 13, 11-29. Such metabolomic methods can be used to detect differences in levels in hormone, nutrients, secondary metabolites, root exudates, phloem sap content, xylem sap content, heavy metal content, and the like. Such methods are also useful for detecting alterations in microbial content and status; for example, the presence and levels of bacterial/fungal signaling molecules (e.g., autoinducers and pheromones), which can indicate the status of group-based behavior of endophytes based on, for example, population of endophyte-associated and reference agricultural plants can also be performed to detect changes in expression of at least one transcript, or a set or network of genes upon endophyte association. Similarly, epigenetic changes can be detected using methylated DNA immunoprecipitation followed by high-throughput sequencing.


Combinations of Endophytes


Combinations of endophytes can be selected by any one or more of several criteria. In one embodiment, compatible endophytes are selected. As used herein, “compatibility” refers to endophyte populations that do not significantly interfere with the growth, propagation, and/or production of beneficial substances of the other. Incompatible endophyte populations can arise, for example, where one of the populations produces or secrets a compound that is toxic or deleterious to the growth of the other population(s). Incompatibility arising from production of deleterious compounds/agents can be detected using methods known in the art, and as described herein elsewhere. Similarly, the distinct populations can compete for limited resources in a way that makes co-existence difficult.


In another embodiment, combinations are selected on the basis of compounds produced by each population of endophytes. For example, the first population is capable of producing siderophores, and another population is capable of producing anti-fungal compounds. In an embodiment, the first population of endophytes or endophytic components is capable of a function selected from the group consisting of auxin production, nitrogen fixation, and production of an antimicrobial compound, siderophore production, mineral phosphate solubilization, cellulase production, chitinase production, xylanase production, and acetoin production, carbon source utilization, and combinations thereof. In another embodiment, the second population of endophytes or endophytic component is capable of a function selected from the group consisting of auxin production, nitrogen fixation, production of an antimicrobial compound, siderophore production, mineral phosphate solubilization, cellulase production, chitinase production, xylanase production, and acetoin production, and combinations thereof. In still another embodiment, the first and second populations are capable of at least one different function.


In still another embodiment, the combinations of endophytes are selected for their distinct localization in the plant after colonization. For example, the first population of endophytes or endophytic components can colonize, and in some cases preferentially colonize, the root tissue, while a second population can be selected on the basis of its preferential colonization of the aerial parts of the agricultural plant. Therefore, in an embodiment, the first population is capable of colonizing one or more of the tissues selected from the group consisting of a root, shoot, leaf, flower, and seed. In another embodiment, the second population is capable of colonizing one or more tissues selected from the group consisting of root, shoot, leaf, flower, and seed. In still another embodiment, the first and second populations are capable of colonizing a different tissue within the agricultural plant.


In some embodiments, combinations of endophytes are selected for their ability to confer a benefit to the host plant at different points in the life cycle of said host plant. In one example, one endophyte can be selected to impart improved seedling vigor, and a second endophyte can be selected to improve soil nutrient acquisition by roots of the mature plant.


In still another embodiment, combinations of endophytes are selected for their ability to confer one or more distinct fitness traits on the inoculated agricultural plant, either individually or in synergistic association with other endophytes. In another embodiment, one endophyte may induce the colonization of a second endophyte. Alternatively, two or more endophytes may induce the colonization of a third endophyte. For example, the first population of endophytes or endophytic components is selected on the basis that it confers significant increase in biomass, while the second population promotes increased drought tolerance on the inoculated agricultural plant. Therefore, in one embodiment, the first population is capable of conferring at least one trait selected from the group consisting of thermal tolerance, herbicide tolerance, drought resistance, insect resistance, fungus resistance, virus resistance, bacteria resistance, male sterility, cold tolerance, salt tolerance, increased yield, enhanced nutrient use efficiency, increased nitrogen use efficiency, increased fermentable carbohydrate content, reduced lignin content, increased antioxidant content, enhanced water use efficiency, increased vigor, increased germination efficiency, earlier or increased flowering, increased biomass, altered root-to-shoot biomass ratio, enhanced soil water retention, or a combination thereof. In another embodiment, the second population is capable of conferring a trait selected from the group consisting of thermal tolerance, herbicide tolerance, drought resistance, insect resistance, fungus resistance, virus resistance, bacteria resistance, male sterility, cold tolerance, salt tolerance, increased yield, enhanced nutrient use efficiency, increased nitrogen use efficiency, increased fermentable carbohydrate content, reduced lignin content, increased antioxidant content, enhanced water use efficiency, increased vigor, increased germination efficiency, earlier or increased flowering, increased biomass, altered root-to-shoot biomass ratio, and enhanced soil water retention. In still another embodiment, each of the first and second population is capable of conferring a different trait selected from the group consisting of thermal tolerance, herbicide tolerance, drought resistance, insect resistance, fungus resistance, virus resistance, bacteria resistance, male sterility, cold tolerance, salt tolerance, increased yield, enhanced nutrient use efficiency, increased nitrogen use efficiency, increased fermentable carbohydrate content, reduced lignin content, increased antioxidant content, enhanced water use efficiency, increased vigor, increased germination efficiency, earlier or increased flowering, increased biomass, altered root-to-shoot biomass ratio, and enhanced soil water retention.


The combinations of endophytes can also be selected based on combinations of the above criteria. For example, the first population of endophytes can be selected on the basis of the compound it produces (e.g., its ability to fix nitrogen, thus providing a potential nitrogen source to the plant), while the second population can be selected on the basis of its ability to confer increased resistance of the plant to a pathogen (e.g., a fungal pathogen).


In some embodiments of the present invention, it is contemplated that combinations of endophytes can provide an increased benefit to the host plant, as compared to that conferred by a single endophyte, by virtue of additive effects. For example, one endophyte strain that induces a benefit in the host plant may induce such benefit equally well in a plant that is also colonized with a different endophyte strain that also induces the same benefit in the host plant. The host plant thus exhibits the same total benefit from the combination of different endophyte strains as the additive benefit to individual plants colonized with each individual endophyte of the combination. In one example, a plant is colonized with two different endophyte strains: one provides a 1× increase in biomass when associated with the plant, and the other provides a 2× increase in biomass when associated with a different plant. When both endophyte strains are associated with the same plant, that plant would experience a 3× (additive of 1×+2× single effects) increase in auxin biomass. Additive effects are a surprising embodiment of the present invention, as non-compatibility of endophytes may result in a cancellation of the beneficial effects of both endophytes.


In some embodiments of the present invention, it is contemplated that a combination of endophytes can provide an increased benefit to the host plant, as compared to that conferred by a single endophyte, by virtue of synergistic effects. For example, one endophyte strain that induces a benefit in the host plant may induce such benefit beyond additive effects in a plant that is also colonized with a different endophyte strain that also induces that benefit in the host plant. The host plant thus exhibits the greater total benefit from the combination of different endophyte strains than could be seen from the additive benefit of individual plants colonized with each individual endophyte of the combination. In one example, a plant is colonized with two different endophyte strains: one provides a 1× increase in biomass when associated with a plant, and the other provides a 2× increase in biomass when associated with a different plant. When both endophyte strains are associated with the same plant, that plant would experience a 5× (greater than an additive of 1×+2× single effects) increase in biomass. Synergistic effects are a surprising embodiment of the present invention.


Inoculation with Multiple Endophytes


In another embodiment, the present invention contemplates methods of coating a plant element, e.g., a seed of a plant, with a plurality of endophytes, as well as synthetic compositions comprising a plurality of endophytes on and/or in the plant element. The methods according to this embodiment can be performed in a manner similar to those described herein for single endophyte coating. In one example, multiple endophytes can be prepared in a single preparation that is coated onto the plant element, e.g., a seed. The endophytes can be from a common origin (i.e., a same plant). Alternatively, the endophytes can be from different plants.


Where multiple endophytes are coated onto a plant element, each endophyte can be a bacterium. In the alternative, each endophyte can be a fungus. In still another embodiment, a plurality of bacterial and fungal endophytes can be coated onto the surface of a plant element.


Where a plurality of endophytes are coated onto the plant element, any or all of the endophytes may be capable of conferring a beneficial trait onto the host plant. In some cases, all of the endophytes are capable of conferring a beneficial trait onto the host plant. The trait conferred by each of the endophytes may be the same (e.g., both improve the host plant's tolerance to a particular biotic stress), or may be distinct (e.g., one improves the host plant's tolerance to drought, while another improves phosphate utilization). In other cases the conferred trait may be the result of interactions between the endophytes.


In one embodiment, an agricultural plant is contacted with a formulation comprising at least two endophytic microbial entities. Specific examples of pairs of endophytic microbial entities that can be applied to an agricultural plant include, for example, a pair of endophytic microbes containing nucleic acid sequences that are each at least 97% identical to the nucleic acid sequence selected from the groups provided in Table 1, Table 2, Table 7 and Table 8.


Isolation of Endophytes


According to the present invention, endophytes are isolated from a plant element, e.g., a seed of a plant. Because endophytes are capable of living and/or residing within the plant, or portion of the plant (including the seed), the endophytic nature of a microbe can distinguished from surface associated microbes by its resistance to surface sterilization techniques. Therefore, in one embodiment, endophytes are isolated from plant elements after the surface of the plant element is sterilized by contacting with non-specific antimicrobial agents such as sodium hypochlorite, hydrogen peroxide, copper oxychloride, copper hydroxide, copper sulfate, chlorothalonil, cuprous oxide, streptomycin, copper ammonium carbonate, copper diammonia diacetate complex, copper octanoate, oxytetracycline, fosetyl-AL or chloropicrin, in an aqueous solution and also optionally including detergents such as SDS, triton X-100, tween 20, can be used. In addition, dried seeds can be soaked in organic solvents such as ethanol, for example 50%-90% ethanol. Antibacterial or antifungal agents (e.g., captan, maneb, thiram, fludioxonil, etc.), particularly those that do not penetrate into the plant element, can also be used. In general, plant elements are soaked in an aqueous solution or commercial formulation containing one or more of these compounds for 30 seconds to 12 hours in a plastic container. After surface sterilization, the plant element is removed from the antibacterial formulation and washed 3-5 times with sterile distilled water. In an alternative embodiment where the plant element is a seed, the seed coat can be removed under sterile conditions, and the microbes inside the seed isolated and characterized.


Once surface-residing microbes are removed, the surviving microbes present in the plant element are generally considered endophytes. Such endophytes can be a bacterium or fungus, and can be isolated by homogenizing the surface sterilized seeds, and placing the homogenate under conditions allowing growth of the microbe. Therefore, the loss of microbe viability upon surface sterilization indicates that the microbes are almost exclusively located on the seed surface. In contrast, resistance of the microbe population to such plant element sterilization methods indicates an internal localization of the microbes. Alternatively, the presence of microbial DNA after surface sterilization with agents that cross-link or otherwise destroy DNA can be detected using sensitive detection methods such as PCR to establish the presence of the microbe within the plant element.


Growth of Endophytes


Viability of the microbe can be tested after plant element surface sterilization, or after removal of the seed coat, by homogenizing the plant element and placing the homogenate under conditions that promote growth of the microbe. In the alternative, the presence of microbes can be detected visually or microscopically if the microbes can form a colony that is visible by such inspection. Reagents are also available for the detection of microbes: the stain aniline blue can be used for detecting hyphae, other assays are known in the art.


Endophytes may require special conditions to allow for growth in isolation. A number of different growth media can be used to grow the endophytes. Additional details of endophyte growth are described within the examples sections.


Functional Attributes of Endophytes


In some cases, a single endophyte strain, a plurality of endophytes, or each individual type of endophytes of that plurality, may produce one or more compounds and/or have one or more activities, e.g., one or more of the following: production of a metabolite, production of a phytohormone such as auxin, production of acetoin, production of an antimicrobial compound, production of a siderophore, production of a cellulase, production of a pectinase, production of a chitinase, production of a xylanase, nitrogen fixation, or mineral phosphate solubilization. For example, an endophyte can produce a phytohormone selected from the group consisting of an auxin, a cytokinin, a gibberellin, ethylene, a brassinosteroid, and abscisic acid. In some embodiments, the endophyte produces auxin (e.g., indole-3-acetic acid (IAA)). Production of auxin can be assayed as described herein. Many of the microbes described herein are capable of producing the plant hormone auxin indole-3-acetic acid (IAA) when grown in culture. Auxin plays a key role in altering the physiology of the plant, including the extent of root growth. Therefore, in other embodiments, endophytes are disposed on the surface or within a tissue of the plant element in an amount effective to detectably increase production of auxin in the agricultural plant when compared with a reference agricultural plant. In some embodiments, the increased auxin production can be detected in a tissue type selected from the group consisting of the root, shoot, leaves, and flowers.


In some embodiments, a single endophyte strain, a plurality of endophytes, or each individual type of endophytes of that plurality, can produce a compound with antimicrobial properties. For example, the compound can have antibacterial properties, as determined by the growth assays provided herein. In some embodiments, the compound with antibacterial properties shows bacteriostatic or bactericidal activity against E. coli and/or Bacillus sp. In other embodiments, the endophyte produces a compound with antifungal properties, for example, fungicidal or fungistatic activity against S. cerevisiae and/or Rhizoctonia.


In some embodiments, a single endophyte strain, a plurality of endophytes, or each individual type of endophytes of that plurality, is capable of nitrogen fixation, and is thus capable of producing ammonium from atmospheric nitrogen. The ability of endophytes to fix nitrogen can be confirmed by testing for growth of the fungus in nitrogen-free growth media, for example, LGI media, as described herein.


In some embodiments, a single endophyte strain, a plurality of endophytes, or each individual type of endophytes of that plurality, can produce a compound that increases the solubility of mineral phosphate in the medium, i.e., mineral phosphate solubilization, for example, using growth assays known in the art. In some embodiments, the endophytes produce a compound that allows the bacterium to grow in growth media comprising Ca3HPO4 as the sole phosphate source.


In some embodiments, a single endophyte strain, a plurality of endophytes, or each individual type of endophytes of that plurality, can produce a siderophore. Siderophores are small high-affinity iron chelating agents secreted by microorganisms that increase the bioavailability of iron. Siderophore production by the endophytes can be detected, for example, using methods known in the art.


In some embodiments, a single endophyte strain, a plurality of endophytes, or each individual type of endophytes of that plurality, can produce a hydrolytic enzyme. For example, in some embodiments, an endophytes can produce a hydrolytic enzyme selected from the group consisting of a cellulase, a pectinase, a chitinase and a xylanase. Hydrolytic enzymes can be detected using the methods known in the art.


Selection of Endophytes Conferring Beneficial Traits


The present invention contemplates inoculation of plants with microbes. As described earlier, the microbes can be derived from many different plants species, from different parts of the plants, and from plants isolated across different environments. Once a microbe is isolated, it can be tested for its ability to confer a beneficial trait. Numerous tests can be performed both in vitro and in vivo to assess what benefits, if any, are conferred upon the plant. In one embodiment, a microbe is tested in vitro for an activity selected from the group consisting of: liberation of complexed phosphates, liberation of complexed iron (e.g., through secretion of siderophores), production of phytohormones, production of antibacterial compounds, production of antifungal compounds, production of insecticidal compounds, production of nematicidal compounds, production and/or secretion of ACC deaminase, production and/or secretion of acetoin, production and/or secretion of pectinase, production and/or secretion of cellulase, and production and/or secretion of RNAse. Exemplary in vitro methods for the above can be found in the Examples sections below.


It is noted that the initial test for the activities listed above can also be performed using a mixture of microbes, for example, a community of microbes isolated from a single plant. A positive activity readout using such mixture can be followed with the isolation of individual microbes within that population and repeating the in vitro tests for the activities to isolate the microbe responsible for the particular activity. Once validated using a single microbe isolate, then the plant can be inoculated with a microbe, and the test performed in vivo, either in growth chamber or greenhouse conditions, and comparing with a control plant that was not inoculated with the microbe.


Endophyte Preparations


Also described herein is a preparation comprising one or more isolated modified endophytes described above. The preparation further comprises an agriculturally acceptable carrier, and the preparation comprises an amount of endophytes sufficient to improve an agronomic trait of the population of seeds. In one embodiment, the isolated endophyte is cultured, for example, on semi-synthetic or synthetic growth medium. In one embodiment, the endophyte is provided as a powder, for example, a lyophilized powder. In another embodiment, the endophyte is applied in suspension at a suitable concentration. The preparation of microbes can be an aqueous solution, an oil-in-water emulsion or water-in-oil emulsion containing a minimum concentration of a microbe. Microbes are present as live cells, viable cells, spores, or mycelia. Typically, the concentration is at least 104 CFU/ml or spores/ml, for example at least 3×104 CFU/mL or spores/ml, at least 105 CFU/mL or spores/ml, at least 3×105 CFU/mL or spores/ml, at least 106 CFU/mL or spores/ml, at least 3×106 CFU/mL or spores/ml, at least 107 CFU/ml or spores/ml, at least 3×107 CFU/mL or spores/ml, at least 108 CFU/mL or spores/ml, 109 CFU/mL or spores/ml, or more. In one embodiment, the preparation is a solution containing a microbe at a concentration between about 105 CFU/mL or spores/ml and about 109 CFU/mL or spores/ml. In another embodiment, the preparation contains a microbe at a concentration between about 106 CFU/mL or spores/ml and about 108 CFU/mL or spores/ml.


The synthetic preparation can also contain any number of other components. In one embodiment, the synthetic preparation may contain growth media or constituents required for the growth and propagation of the microbe. In one embodiment, the growth medium is selected from the group provided in the table below.









TABLE 100







Exemplary growth medium









Microbe




Type
Media
Organisms





Bacteria
Nutrient Peptone Agar
Heterotrophic bacteria



MacConkey Agar + myo-inositol +

Klebsiella Sp.




Carbenicillin



J agar

Bacillus sp. and other





firmicutes



N-poor Medium (LGT)
Aerobic heterotrophic N2-




fixing bacteria



Yeast Mannitol Agar

Rhizobium sp.




King's B medium

Pseudomonas sp.




SC medium
Fastidious bacteria



R2A agar
Oligotrophic bacteria



Tryptic Soy Agar
Heterotrophic bacteria


Fungi
Cornmeal agar
Fungi



Glucose-Yeast extract agar +
Selective enumeration of



tetracycline
yeasts and molds.



Potato-Dextrose agar (PDA)
Yeasts and molds



Potato-Dextrose broth (PDB)
Yeast and molds



Sabouraud Agar
Yeasts, molds and aciduric




microorganisms



V8 Agar
Fungi



Malt Dextrose Agar
Identification of yeasts and




moulds



Czapek's medium
Fungi and Mold



SPT agar

Verticillium sp.










The synthetic preparation can be of a defined pH range. In one embodiment, the pH of the preparation can be between pH 5.5-6.0, pH 5.75-6.25, pH 6.0-6.5, pH 6.25-6.75, pH 6.5-7.0, pH 6.75-7.25, and pH 7.0-7.5. The pH of the medium can be adjusted using any biologically compatible buffering agent.


The synthetic preparation can also comprise a carrier, such as diatomaceous earth, clay, or chitin, which act to complex with chemical agents, such as control agents.


The synthetic preparation can also comprise an adherent. Such agents are useful for combining the microbes of the invention with carriers that can contain other compounds (e.g., control agents that are not biologic), to yield a coating composition. Such compositions help create coatings around the plant or seed to maintain contact between the microbe and other agents with the plant or plant part. In one embodiment, adherents are selected from the group consisting of: alginate, gums, starches, lecithins, formononetin, polyvinyl alcohol, alkali formononetinate, hesperetin, polyvinyl acetate, cephalins, Gum Arabic, Xanthan Gum, Mineral Oil, Polyethylene Glycol (PEG), Polyvinyl pyrrolidone (PVP), Arabino-galactan, Methyl Cellulose, PEG 400, Chitosan, Polyacrylamide, Polyacrylate, Polyacrylonitrile, Glycerol, Triethylene glycol, Vinyl Acetate, Gellan Gum, Polystyrene, Polyvinyl, Carboxymethyl cellulose, Gum Ghatti, and polyoxyethylene-polyoxybutylene block copolymers. Other examples of adherent compositions that can be used in the synthetic preparation include those described in EP 0818135, CA 1229497, WO 2013090628, EP 0192342, WO 2008103422 and CA 1041788, each of which is incorporated by reference in its entirety.


The synthetic preparation can also contain one or more reagents that promote internalization of the microbe into the plant, and can include any one of the following classes of compounds: a surfactant, an abrasive, an osmoticum, and a plant signaling molecule.


The preparation can also contain a surfactant. Non-limiting examples of surfactants include nitrogen-surfactant blends such as Prefer 28 (Cenex), Surf-N (US), Inhance (Brandt), P-28 (Wilfarm) and Patrol (Helena); esterified seed oils include Sun-It II (AmCy), MSO (UAP), Scoil (Agsco), Hasten (Wilfarm) and Mes-100 (Drexel); and organo-silicone surfactants include Silwet L77 (UAP), Silikin (Terra), Dyne-Amic (Helena), Kinetic (Helena), Sylgard 309 (Wilbur-Ellis) and Century (Precision). In one embodiment, the surfactant is present at a concentration of between 0.01% v/v to 10% v/v. In another embodiment, the surfactant is present at a concentration of between 0.1% v/v to 1% v/v.


The synthetic preparation of a defined osmolality can also be used. In one embodiment, the synthetic preparation has an osmolality of less than about 100 mOsm, for example less than about 75 mOsm, less than about 50 mOsm, or less than about 25 mOsm. In another embodiment, the synthetic preparation has an osmolality of at least 250 mOsm, for example at least 300 mOsm, at least 400 mOsm, at least 500 mOsm, at least 600 mOsm, at least 700 mOsm, at least 800 mOsm, 900 mOsm or greater. The osmolality of the preparation can be adjusted by addition of an osmoticum: the osmoticum can be any commonly used osmoticum, and can selected from the group consisting of: mannitol, sorbitol, NaCl, KCl, CaCl2, MgSO4, sucrose, or any combination thereof.


The endophyte can be obtained from growth in culture, for example, using semi-synthetic or synthetic growth medium. In addition, the microbe can be cultured on solid media, for example on petri dishes, scraped off and suspended into the preparation. Microbes at different growth phases can be used. For example, microbes at lag phase, early-log phase, mid-log phase, late-log phase, stationary phase, early death phase, or death phase can be used.


For certain microbes that exist as mycelia or mycelia-like structures, pre-treatment of the microbes with enzymes (including, but not limited to, driselase, gluculase, cellulase, beta-glucanase, lysozyme, zymolyase) can be used to generate protoplasts in order to provide a suspension of microbes. After generation of protoplasts, the microbes can be allowed to partially regenerate the cell walls by leaving the protoplasts in a growth medium or solution with relatively high osmolarity for a short time (typically less than about 12 hours at room temperature) to prevent bursting of protoplasts.


Detection and Quantitation of Endophytes and Other Microbes


The presence of the endophyte or other microbes can be detected and its localization in or on the host plant (including the seed) can be determined using a number of different methodologies. The presence of the microbe in the embryo or endosperm, as well as its localization with respect to the plant cells, can be determined using methods known in the art, including immunofluorescence microscopy using microbe specific antibodies, or fluorescence in situ hybridization. The presence and quantity of other microbes can be established by the FISH, immunofluorescence and PCR methods using probes that are specific for the microbe. Alternatively, degenerate probes recognizing conserved sequences from many bacteria and/or fungi can be employed to amplify a region, after which the identity of the microbes present in the tested tissue/cell can be determined by sequencing.


Therefore, in one embodiment, where the endophyte is coated onto the surface of a plant element of a first plant such that the endophyte is present at a higher level on the surface of the plant element than is present on the surface of an uncoated reference plant element, the level of the endophyte present on the surface of the uncoated reference plant element is determined by culturing microbes that are present on the surface of the plant element. In another embodiment, the level of the endophyte present on the surface of the uncoated reference plant element is determined by PCR.


Uniformity of Seeds and Plants


In another aspect, the seeds according to the present invention provide a substantially uniform population of seeds with a uniform endophyte composition. The uniform population of seeds can be of a predefined weight. For example, a substantially uniform population of seeds containing at least 100 g seeds, for example at least 1 kg seeds, at least 5 kg seeds, at least 10 kg seeds, can be provided by the method according to the present invention that contains—as a whole product—more than 1%, for example more than 5%, more than 10%, more than 20%, more than 30%, more than 40%, especially more than 50%, of the endophytic microorganism, i.e., the strain that is coated onto the surface of the seeds. According to a preferred embodiment, the present invention provides a marketable seed product containing at least 100 g seeds, for example, at least 1 kg seeds, for example at least 5 kg seeds, at least 10 kg seeds, wherein—as a whole product—more than 50%, for example, more than 60%, more than 70%, more than 80%, more than 90%, more than 95%, more than 99%, or 100% of the seeds contain the microbe, i.e., the inoculant strain. Each of the seeds can also contain a uniform number of microbes (for example, viable endophytes): for example, at least 50% of the seeds, for example at least 60%, at least 70%, at least 80%, at least 90%, at least 95%, at least 99%, or more of the seeds in the population can contain at least 100 CFU or spores, at least 300 CFU or spores, at least 1,000 CFU or spores, at least 3,000 CFU or spores, at least 10,000 CFU or spores, at least 30,000 CFU or spores or more, of the endophytic microorganism. In some embodiments, at least 50% of the seeds, for example at least 60%, at least 70%, at least 80%, at least 90%, at least 95%, at least 99%, or more of the seeds in the population contains a single endophyte or a plurality of endophytes at a concentration between about 100 CFU or spores and about 30,000 CFU or spores, between about 100 CFU or spores and about 300 CFU or spores, between about 100 CFU or spores and about 1,000 CFU or spores, between about 100 CFU or spores and about 3,000 CFU or spores, between about 100 CFU or spores and about 10,00 CFU or spores, between about 100 CFU or spores and about 30,000 CFU or spores, between about 300 CFU or spores and about 1,000 CFU or spores, between about 300 CFU or spores and about 3,000 CFU or spores, between about 300 CFU or spores and about 10,00 CFU or spores, between about 300 CFU or spores and about 30,000 CFU or spores, between about 1,000 CFU or spores and about 3,000 CFU or spores, between about 1,000 CFU or spores and about 10,00 CFU or spores, between about 1,000 CFU or spores and about 30,00 CFU or spores, between about 3,000 CFU or spores and about 10,000 CFU or spores, between about 3,000 CFU or spores and about 30,00 CFU or spores, or between about 10,000 CFU or spores and about 30,000 CFU or spores. The endophyte can also be quantitated using other means, for example, using quantitative PCR, to detect the total number of endophyte present on each seed.


The uniformity of the microbes within the seed population can be measured in several different ways. In one embodiment, a substantial portion of the population of seeds, for example at least 10%, at least 20%, at least 30%, at least 40%, at least 50%, at least 60%, at least 70%, at least 75%, at least 80%, at least 90%, at least 95% or more of the seeds in a population, contains a viable endophyte on its surface. In another embodiment, a substantial portion of the population of seeds, for example at least 10%, at least 20%, at least 30%, at least 40%, at least 50%, at least 60%, at least 70%, at least 75%, at least 80%, at least 90%, at least 95% or more of the seeds in a population contain on its surface a threshold number of viable microbe that is at least 1 CFU or spore per seed, at least 10 CFU or spores per seed, for example, at least 100 CFU or spores, at least 300 CFU or spores, at least 1,000 CFU or spores, at least 3,000 CFU or spores, or more, of the microbe per seed. In some embodiments, a substantial portion of the population of seeds, for example at least 10%, at least 20%, at least 30%, at least 40%, at least 50%, at least 60%, at least 70%, at least 75%, at least 80%, at least 90%, at least 95% or more of the seeds in a population contain on its surface a threshold number of viable microbe that is between 1 CFU or spore per seed and about 3,000 CFU or spores per seed, between 1 CFU or spore per seed and about 10 CFU or spores per seed, between 1 CFU or spore per seed and about 100 CFU or spores per seed, between 1 CFU or spore per seed and about 300 CFU or spores per seed, between 1 CFU or spore per seed and about 1,000 CFU or spores per seed, between 1 CFU or spore per seed and about 3,000 CFU or spores per seed, between about 10 CFU or spore per seed and about 100 CFU or spores per seed, between about 10 CFU or spore per seed and about 300 CFU or spores per seed, between about 10 CFU or spore per seed and about 1,000 CFU or spores per seed, between about 10 CFU or spore per seed and about 3,000 CFU or spores per seed, between about 100 CFU or spore per seed and about 300 CFU or spores per seed, between about 100 CFU or spore per seed and about 1,000 CFU or spores per seed, between about 100 CFU or spore per seed and about 3,000 CFU or spores per seed, between about 300 CFU or spore per seed and about 1,000 CFU or spores per seed, between about 300 CFU or spore per seed and about 3,000 CFU or spores per seed, or between about 1,000 CFU or spore per seed and about 3,000 CFU or spores per seed.


In still another aspect, the present invention discloses a substantially uniform population of plants produced by growing the population of seeds described above. In one embodiment, at least 75%, at least 80%, at least 90%, at least 95% or more of the plants comprise in one or more tissues an effective amount of the endophyte or endophytes. In another embodiment, at least 1%, between 1% and 10%, for example, at least 10%, between 10% and 20%, at least 20%, between 20% and 30%, at least 30%, between 30% and 40%, at least 40%, between 40% and 50%, at least 50%, between 50% and 60%, at least 60%, between 60% and 70%, at least 70%, between 70% and 75%, at least 75%, between 75% and 80%, at least 80%, between 80% and 90%, at least 90%, between 90% and 95%, at least 95% or more of the plants comprise a microbe population that is substantially similar.


In some cases, a substantial portion of the population of plants or seeds, for example, at least 1%, between 1% and 10%, for example, at least 10%, between 10% and 20%, at least 20%, between 20% and 30%, at least 30%, between 30% and 40%, at least 40%, between 40% and 50%, at least 50%, between 50% and 60%, at least 60%, between 60% and 70%, at least 70%, between 70% and 75%, at least 75%, between 75% and 80%, at least 80%, between 80% and 90%, at least 90%, between 90% and 95%, at least 95% or more of the seeds in a population, is coated with an endophyte that is able to perform one of the following functions, including: to stimulate plant growth, grow on nitrogen-free media, solubilize phosphate, sequester iron, secrete RNAse, antagonize pathogens, catabolize the precursor of ethylene, produce auxin and acetoin/butanediol. In some cases, a substantial portion of the population of seeds, for example, at least 1%, between 1% and 10%, for example, at least 10%, between 10% and 20%, at least 20%, between 20% and 30%, at least 30%, between 30% and 40%, at least 40%, between 40% and 50%, at least 50%, between 50% and 60%, at least 60%, between 60% and 70%, at least 70%, between 70% and 75%, at least 75%, between 75% and 80%, at least 80%, between 80% and 90%, at least 90%, between 90% and 95%, at least 95% or more of the seeds in a population, exhibits at least one of the endophyte community attributes listed in herein (e.g., total CFUs, presence of a taxa, absence of a taxa, spatial distribution, intercellular colonization, functional properties of endophytes; presence of monoclonal strain, presence of conserved subset of microbial plasmid repertoire, microbe isolated from habitat that is distinct from the location of seed production, etc.).


Increased uniformity of microbes in plants or seeds can also be detected by measuring the presence of non-genomic nucleic acids present in the microbes. For examples, where the microbe that is inoculated into the plant is known to harbor a plasmid or episome, the presence of the plasmid or episome can be detected in individual plants or seeds by using conventional methods of nucleic acid detection. Therefore, in one embodiment, a substantial portion of the population of seeds, for example at least example at least 1%, between 1% and 10%, for example, at least 10%, between 10% and 20%, at least 20%, between 20% and 30%, at least 30%, between 30% and 40%, at least 40%, between 40% and 50%, at least 50%, between 50% and 60%, at least 60%, between 60% and 70%, at least 70%, between 70% and 75%, at least 75%, between 75% and 80%, at least 80%, between 80% and 90%, at least 90%, between 90% and 95%, at least 95% or more of the seeds in a population, has a detectable presence of the microbial plasmid or episome.


Increased uniformity of the microbes' epigenetic status can also be used to detect increased uniformity of a population of seeds or plants derived from such seeds. For example, where a microbe that has been inoculated by a plant is also present in the plant (for example, in a different tissue or portion of the plant), or where the introduced microbe is sufficiently similar to a microbe that is present in some of the plants (or portion of the plant, including seeds), it is still possible to distinguish between the inoculated microbe and the native microbe, for example, by distinguishing between the two microbe types on the basis of their epigenetic status. Therefore, in one embodiment, the epigenetic status is detected in microbes across individual seeds or the plants that grow from such seeds.


It is also known that certain viruses are associated with endophytic fungi (such as the Curvularia thermal tolerance virus (CThTV) described in Márquez, L. M., et al., (2007). Science 315: 513-515). Therefore, the presence and quantity of a virus can be used to measure uniformity of seeds or plants containing the endophyte. For example, where the inoculated microbe is known to be associated with a virus, the presence of that virus can be used as a surrogate indicator of uniformity. Therefore, in one embodiment, a substantial portion of the seeds, for example at least 1%, between 1% and 10%, for example, at least 10%, between 10% and 20%, at least 20%, between 20% and 30%, at least 30%, between 30% and 40%, at least 40%, between 40% and 50%, at least 50%, between 50% and 60%, at least 60%, between 60% and 70%, at least 70%, between 70% and 75%, at least 75%, between 75% and 80%, at least 80%, between 80% and 90%, at least 90%, between 90% and 95%, at least 95% or more of the seeds, contain the virus. In other embodiments, where one or more of the endogenous microbes contain associated viruses which are not found in, and not compatible with the inoculated microbe, the loss (i.e., absence) of the virus can be used to measure uniformity of the seed population. As such, in another embodiment, a substantial portion of the seeds, for example at least 1%, between 1% and 10%, for example, at least 10%, between 10% and 20%, at least 20%, between 20% and 30%, at least 30%, between 30% and 40%, at least 40%, between 40% and 50%, at least 50%, between 50% and 60%, at least 60%, between 60% and 70%, at least 70%, between 70% and 75%, at least 75%, between 75% and 80%, at least 80%, between 80% and 90%, at least 90%, between 90% and 95%, at least 95% or more of the seeds, do not contain the virus. In other cases, the genetic sequence of the virus can be used to measure the genetic similarity of the virus within a population. In one embodiment, a substantial proportion of the seeds, for example, at least 10%, for example at least 20%, at least 30%, at least 40%, at least 50%, at least 60%, at least 70%, at least 80%, at least 90%, at least 95% or more of the seeds contain the same virus, for example, as determined by sequence analysis.


Such uniformity in microbial composition is unique and is extremely advantageous for high-tech and/or industrial agriculture. It allows significant standardization with respect to qualitative endophyte load of seed products. Suitable volumes or weights are those that are currently used for plant seeds (e.g., the at least 100 g, at least 1, 5 or 10 kg; but also 25 or more, 40 or more, 50 kg or more, even 100 kg or more, 500 kg or more, 1 ton or more, etc.). Suitable containers or packages are those traditionally used in plant seed commercialization: however, also other containers with more sophisticated storage capabilities (e.g., with microbiologically tight wrappings or with gas- or water-proof containments) can be used. The amount of endophytes (qualitatively and quantitatively) contained in the seeds or in the marketable seed product as a whole can be determined by standard techniques in microbiology readily available to any person skilled in the art of plant endophyte analysis.


In some cases, a sub-population of agricultural seeds can be further selected on the basis of increased uniformity, for example, on the basis of uniformity of microbial population. For example, individual seeds of pools collected from individual cobs, individual plants, individual plots (representing plants inoculated on the same day) or individual fields can be tested for uniformity of microbial density, and only those pools meeting specifications (e.g., at least 80% of tested seeds have minimum density, as determined by quantitative methods described elsewhere) are combined to provide the agricultural seed sub-population.


The methods described herein can also comprise a validating step. The validating step can entail, for example, growing some seeds collected from the inoculated plants into mature agricultural plants, and testing those individual plants for uniformity. Such validating step can be performed on individual seeds collected from cobs, individual plants, individual plots (representing plants inoculated on the same day) or individual fields, and tested as described above to identify pools meeting the required specifications.


Agricultural Field


In another aspect, described herein is an agricultural field, including a greenhouse, comprising the population of plants described above. In one embodiment, the agricultural field comprises at least 100 plants. In another embodiment, the population occupies at least about 100 square feet of space, wherein at least about 10%, 20%, 30%, 40%, 50%, 60%, 70%, 80%, 90% or more than 90% of the population comprises an effective amount of the microbe. In another embodiment, the population occupies at least about 100 square feet of space, wherein at least 1%, between 1% and 10%, for example, at least 10%, between 10% and 20%, at least 20%, between 20% and 30%, at least 30%, between 30% and 40%, at least 40%, between 40% and 50%, at least 50%, between 50% and 60%, at least 60%, between 60% and 70%, at least 70%, between 70% and 75%, at least 75%, between 75% and 80%, at least 80%, between 80% and 90%, at least 90%, between 90% and 95%, at least 95% or more of the population comprises the microbe in reproductive tissue. In still another embodiment, the population occupies at least about 100 square feet of space, wherein at least about 10%, 20%, 30%, 40%, 50%, 60%, 70%, 80%, 90% or more than 90% of the population comprises at least 10 CFUs or spores, 100 CFUs or spores, 1,000 CFUs or spores, 10,000 CFUs or spores or more of the microbe. In still another embodiment, the population occupies at least about 100 square feet of space, wherein at least 1%, between 1% and 10%, for example, at least 10%, between 10% and 20%, at least 20%, between 20% and 30%, at least 30%, between 30% and 40%, at least 40%, between 40% and 50%, at least 50%, between 50% and 60%, at least 60%, between 60% and 70%, at least 70%, between 70% and 75%, at least 75%, between 75% and 80%, at least 80%, between 80% and 90%, at least 90%, between 90% and 95%, at least 95% or more of the population comprises between about 10 CFU or spores and about 10,000 CFU or spores, between about 10 CFU or spores and about 100 CFU or spores, between about 10 CFU or spores and about 1,000 CFU or spores, between about 100 CFU or spores and about 1,000 CFU or spores, between about 100 CFU or spores and about 10,00 CFU or spores, or between about 1,000 CFU or spores and about 10,000 CFU or spores. In yet another embodiment, the population occupies at least about 100 square feet of space, wherein at least 1%, between 1% and 10%, for example, at least 10%, between 10% and 20%, at least 20%, between 20% and 30%, at least 30%, between 30% and 40%, at least 40%, between 40% and 50%, at least 50%, between 50% and 60%, at least 60%, between 60% and 70%, at least 70%, between 70% and 75%, at least 75%, between 75% and 80%, at least 80%, between 80% and 90%, at least 90%, between 90% and 95%, at least 95% or more of the population comprises a exogenous microbe (i.e., the endophyte) of monoclonal origin.


Plants can be grown individually from the seeds coated with the endophytes to propagate the desired microbes in indoor or outdoor settings. An advantage of the present invention is that it allows multiple plants harboring endophytes to be grown under agricultural methods as a means of providing improved uniformity of microbe-derived benefits to farmers.


Therefore, in another aspect, provided herein are indoor arrangements of populations (e.g., greenhouse) of plants generated from the methods of the present invention. Such arrangements can include at least a defined number of plants of the present invention, such as at least 1, at least 2, at least 3, between 3 and 5, at least 5, between 5 and 10, at least 10, between 10 and 15, at least 15, between 15 and 20, at least 20, between 20 and 30, at least 30, between 30 and 50, at least 50, between 50 and 100, at least 100, between 100 and 200, at least 200, between 200 and 500, at least 500, between 500 and 1000, at least 1000, between 1000 and 5000, at least 5000, between 5000 and 10000, at least 10000 or more plants.


Also provided herein are agricultural fields that contain population of plants generated from the seeds of the present invention. Agricultural fields can occupy as little as 100 square feet or less, or can occupy hundreds or thousands of acres. Area of field containing a population of microbe-associated plants can be measured in square feet, such as at least 100, 500, 1000, 5000, 10,000, 50,000 or greater than 50,000 square feet, or can be measured in acres, such as least 1, at least 2, at least 3, between 3 and 5, at least 5, between 5 and 10, at least 10, between 10 and 15, at least 15, between 15 and 20, at least 20, between 20 and 30, at least 30, between 30 and 50, at least 50, between 50 and 100, at least 100, between 100 and 200, at least 200, between 200 and 500, at least 500, between 500 and 1000, at least 1000, between 1000 and 5000, at least 5000, between 5000 and 10000, at least 10000, between 10000 and 50000, at least 50000 or greater acres. The field can also be measured in hectares, for example at least 1, at least 2, at least 3, between 3 and 5, at least 5, between 5 and 10, at least 10, between 10 and 15, at least 15, between 15 and 20, at least 20, between 20 and 30, at least 30, between 30 and 50, at least 50, between 50 and 100, at least 100, between 100 and 200, at least 200, between 200 and 500, at least 500, between 500 and 1000, at least 1000, between 1000 and 5000, at least 5000, between 5000 and 10000, at least 10000 or more hectares. Additionally, a field containing a population of microbe-associated plants can be characterized by the number of plants in the population, generally a field is at least two, such as at least 3, between 3 and 5, at least 5, between 5 and 10, at least 10, between 10 and 15, at least 15, between 15 and 20, at least 20, between 20 and 30, at least 30, between 30 and 50, at least 50, between 50 and 100, at least 100, between 100 and 200, at least 200, between 200 and 500, at least 500, between 500 and 1000, at least 1000, between 1000 and 5000, at least 5000, between 5000 and 10000, at least 10000, between 10000 and 25000, at least 250000, between 25000 and 50000, at least 500000, between 50000 and 75000, at least 750000, between 75000 and 100000, at least 1000000 or more plants. A field is generally a contiguous area but may be separated by geographical features such as roads, waterways, buildings, fences, and the like known to those skilled in the art. Because the microbe-associated plants described herein benefit from an increased level of uniformity of germination and other characteristics, it is desirable to maximize the percentage of plants containing microbes. For example, at least 10% (e.g., between 10% and 20%, at least 20%, between 20% and 30%, at least 30%, between 30% and 40%, at least 40%, between 40% and 50%, at least 50%, between 50% and 60%, at least 60%, between 60% and 70%, at least 70%, between 70% and 75%, at least 75%, between 75% and 80%, at least 80%, between 80% and 90%, at least 90%, between 90% and 95%, between 95% and 99%, at least 99% or more) of the plants contain the microbes.


Endophytes Compatible with Agrichemicals


In certain embodiments, the endophyte is selected on the basis of its compatibility with commonly used agrichemicals. As mentioned earlier, plants, particularly agricultural plants, can be treated with a vast array of agrichemicals, including fungicides, biocides (anti-bacterial agents), herbicides, insecticides, nematicides, rodenticides, fertilizers, and other agents.


In some cases, it can be important for the endophyte to be compatible with agrichemicals, particularly those with fungicidal or antibacterial properties, in order to persist in the plant although, as mentioned earlier, there are many such fungicidal or antibacterial agents that do not penetrate the plant, at least at a concentration sufficient to interfere with the endophyte. Therefore, where a systemic fungicide or antibacterial agent is used in the plant, compatibility of the endophyte to be inoculated with such agents will be an important criterion.


In one embodiment, natural isolates of endophytes that are compatible with agrichemicals can be used to inoculate the plants according to the methods described herein. For example, fungal endophytes which are compatible with agriculturally employed fungicides can be isolated by plating a culture of the endophytes, on a petri dish containing an effective concentration of the fungicide, and isolating colonies of the endophyte that are compatible with the fungicide. In another embodiment, an endophyte that is compatible with a fungicide is used for the methods described herein. Fungicide compatible endophytes can also be isolated by selection on liquid medium. The culture of endophytes can be plated on petri dishes without any forms of mutagenesis; alternatively, the endophytes can be mutagenized using any means known in the art. For example, microbial cultures can be exposed to UV light, gamma-irradiation, or chemical mutagens such as ethylmethanesulfonate (EMS) prior to selection on fungicide containing media. Finally, where the mechanism of action of a particular fungicide is known, the target gene can be specifically mutated (either by gene deletion, gene replacement, site-directed mutagenesis, etc.) to generate an endophyte that is resilient against that particular fungicide. It is noted that the above-described methods can be used to isolate fungi that are compatible with both fungistatic and fungicidal compounds.


It will also be appreciated by one skilled in the art that a plant may be exposed to multiple types of fungicides or antibacterial compounds, either simultaneously or in succession, for example at different stages of plant growth. Where the target plant is likely to be exposed to multiple fungicidal and/or antibacterial agents, an endophyte that is compatible with many or all of these agrichemicals can be used to inoculate the plant. An endophyte that is compatible with several fungicidal agents can be isolated, for example, by serial selection. An endophyte that is compatible with the first fungicidal agent is isolated as described above (with or without prior mutagenesis). A culture of the resulting endophyte can then be selected for the ability to grow on liquid or solid media containing the second antifungal compound (again, with or without prior mutagenesis). Colonies isolated from the second selection are then tested to confirm its compatibility to both antifungal compounds.


Likewise, bacterial endophytes that are compatible to biocides (including herbicides such as glyphosate or antibacterial compounds, whether bacteriostatic or bactericidal) that are agriculturally employed can be isolated using methods similar to those described for isolating fungicide compatible endophytes. In one embodiment, mutagenesis of the microbial population can be performed prior to selection with an antibacterial agent. In another embodiment, selection is performed on the microbial population without prior mutagenesis. In still another embodiment, serial selection is performed on an endophyte: the endophyte is first selected for compatibility to a first antibacterial agent. The isolated compatible endophyte is then cultured and selected for compatibility to the second antibacterial agent. Any colony thus isolated is tested for compatibility to each, or both antibacterial agents to confirm compatibility with these two agents.


Resistance, or compatibility with an antimicrobial agent can be determined by a number of means known in the art, including the comparison of the minimal inhibitory concentration (MIC) of the unmodified and modified endophyte. Therefore, in one embodiment, the present invention discloses an isolated modified endophyte derived from an endophyte isolated from within a plant or tissue thereof, wherein the endophyte is modified such that it exhibits at least 3 fold greater, for example, at least 5 fold greater, at least 10 fold greater, at least 20 fold greater, at least 30 fold greater or more MIC to an antimicrobial agent when compared with the unmodified endophyte.


In one particular aspect, disclosed herein are bacterial endophytes with enhanced resistance to the herbicide glyphosate. In one embodiment, the bacterial endophyte has a doubling time in growth medium containing at least 1 mM glyphosate, for example, at least 2 mM glyphosate, at least 5 mM glyphosate, at least 10 mM glyphosate, at least 15 mM glyphosate or more, that is no more than 250%, for example, no more than 200%, no more than 175%, no more than 150%, or no more than 125%, of the doubling time of the endophyte in the same growth medium containing no glyphosate. In one particular embodiment, the bacterial endophyte has a doubling time in growth medium containing 5 mM glyphosate that is no more than 150% the doubling time of the endophyte in the same growth medium containing no glyphosate.


In another embodiment, the bacterial endophyte has a doubling time in a plant tissue containing at least 10 ppm glyphosate, for example, at least 15 ppm glyphosate, at least 20 ppm glyphosate, at least 30 ppm glyphosate, at least 40 ppm glyphosate or more, that is no more than 250%, for example, no more than 200%, no more than 175%, no more than 150%, or no more than 125%, of the doubling time of the endophyte in a reference plant tissue containing no glyphosate. In one particular embodiment, the bacterial endophyte has a doubling time in a plant tissue containing 40 ppm glyphosate that is no more than 150% the doubling time of the endophyte in a reference plant tissue containing no glyphosate.


The selection process described above can be repeated to identify isolates of the endophyte that are compatible with a multitude of antifungal or antibacterial agents.


Candidate isolates can be tested to ensure that the selection for agrichemical compatibility did not result in loss of a desired microbial bioactivity. Isolates of the endophyte that are compatible with commonly employed fungicides can be selected as described above. The resulting compatible endophyte can be compared with the parental endophyte on plants in its ability to promote germination.


The agrichemical compatible endophytes generated as described above can be detected in samples. For example, where a transgene was introduced to render the endophyte resistant to the agrichemical(s), the transgene can be used as a target gene for amplification and detection by PCR. In addition, where point mutations or deletions to a portion of a specific gene or a number of genes results in compatibility with the agrichemical(s), the unique point mutations can likewise be detected by PCR or other means known in the art. Such methods allow the detection of the microbe even if it is no longer viable. Thus, commodity plant products produced using the agrichemical compatible microbes described herein can readily be identified by employing these and related methods of nucleic acid detection.


Improved Traits Conferred by the Endophyte


The present invention contemplates the establishment of a microbial symbiont in a plant. In one embodiment, the microbial association results in a detectable change to the seed or plant. The detectable change can be an improvement in a number of agronomic traits (e.g., improved general health, increased response to biotic or abiotic stresses, or enhanced properties of the plant or a plant part, including fruits and grains). Alternatively, the detectable change can be a physiological or biological change that can be measured by methods known in the art. The detectable changes are described in more detail in the sections below. As used herein, an endophyte is considered to have conferred an improved agricultural trait whether or not the improved trait arose from the plant, the endophyte, or the concerted action between the plant and endophyte. Therefore, for example, whether a beneficial hormone or chemical is produced by the plant or endophyte, for purposes of the present invention, the endophyte will be considered to have conferred an improved agronomic trait upon the host plant.


In some embodiments, plant-endophyte combinations confer an agronomic benefit in agricultural plants. In some embodiments, the agronomic trait is selected from the group consisting of altered oil content, altered protein content, altered seed carbohydrate composition, altered seed oil composition, and altered seed protein composition, chemical tolerance, cold tolerance, delayed senescence, disease resistance, drought tolerance, ear weight, growth improvement, health enhancement, heat tolerance, herbicide tolerance, herbivore resistance, improved nitrogen fixation, improved nitrogen utilization, improved root architecture, improved water use efficiency, increased biomass, increased root length, increased seed weight, increased shoot length, increased yield, increased yield under water-limited conditions, kernel mass, kernel moisture content, metal tolerance, number of ears, number of kernels per ear, number of pods, nutrition enhancement, pathogen resistance, pest resistance, photosynthetic capability improvement, salinity tolerance, stay-green, vigor improvement, increased dry weight of mature seeds, increased fresh weight of mature seeds, increased number of mature seeds per plant, increased chlorophyll content, increased number of pods per plant, increased length of pods per plant, reduced number of wilted leaves per plant, reduced number of severely wilted leaves per plant, and increased number of non-wilted leaves per plant, a detectable modulation in the level of a metabolite, a detectable modulation in the level of a transcript, and a detectable modulation in the proteome relative to a reference plant. In other embodiments, at least two agronomic traits are improved in the agricultural plant.


For example, the endophyte may provide an improved benefit or tolerance to a plant that is of at least 3%, between 3% and 5%, at least 5%, between 5% and 10%, least 10%, between 10% and 15%, for example at least 15%, between 15% and 20%, at least 20%, between 20% and 30%, at least 30%, between 30% and 40%, at least 40%, between 40% and 50%, at least 50%, between 50% and 60%, at least 60%, between 60% and 75%, at least 75%, between 75% and 100%, at least 100%, between 100% and 150%, at least 150%, between 150% and 200%, at least 200%, between 200% and 300%, or at least 300% or more, when compared with uninoculated plants grown under the same conditions.


In some aspects, provided herein, are methods for producing a seed of a plant with a heritably altered trait. The trait of the plant can be altered without known genetic modification of the plant genome, and comprises the following steps. First, a preparation of an isolated endophyte that is exogenous to the seed of the plant is provided, and optionally processed to produce a microbial preparation. The microbial preparation is then contacted with the plant. The plants are then allowed to go to seed, and the seeds, which contain the endophytes on and/or in the seed are collected. The endophytes contained within the seed are viably incorporated into the seed.


The method of the present invention can facilitate crop productivity by enhancing germination, seedling vigor and biomass in comparison with a non-treated control. Moreover, the introduction of the beneficial microorganisms to within the seed instead of by, e.g., seed coating, makes the endophytes less susceptible to environmental perturbation and more compatible with chemical seed coatings (e.g., pesticides and herbicides). Using endophyte colonized seeds, the plant growth and biomass increases are statistically similar to those obtained using conventional inoculation methods e.g., exogenous seed soaking and soil inoculation (that are more laborious and less practicable in certain circumstances).


Improved General Health


Also described herein are plants, and fields of plants, that are associated with beneficial endophytes, such that the overall fitness, productivity or health of the plant or a portion thereof, is maintained, increased and/or improved over a period of time. Improvement in overall plant health can be assessed using numerous physiological parameters including, but not limited to, height, overall biomass, root and/or shoot biomass, seed germination, seedling survival, photosynthetic efficiency, transpiration rate, seed/fruit number or mass, plant grain or fruit yield, leaf chlorophyll content, photosynthetic rate, root length, or any combination thereof. Improved plant health, or improved field health, can also be demonstrated through improved resistance or response to a given stress, either biotic or abiotic stress, or a combination of one or more abiotic stresses, as provided herein.


Other Abiotic Stresses


Disclosed herein are endophyte-associated plants with increased resistance to an abiotic stress. Exemplary abiotic stresses include, but are not limited to: drought, salt, high metal content, low nutrients, cold stress, and heat stress.


Drought and Heat Tolerance


When soil water is depleted or if water is not available during periods of drought, crop yields are restricted. Plant water deficit develops if transpiration from leaves exceeds the supply of water from the roots. The available water supply is related to the amount of water held in the soil and the ability of the plant to reach that water with its root system. Transpiration of water from leaves is linked to the fixation of carbon dioxide by photosynthesis through the stomata. The two processes are positively correlated so that high carbon dioxide influx through photosynthesis is closely linked to water loss by transpiration. As water transpires from the leaf, leaf water potential is reduced and the stomata tend to close in a hydraulic process limiting the amount of photosynthesis. Since crop yield is dependent on the fixation of carbon dioxide in photosynthesis, water uptake and transpiration are contributing factors to crop yield: Plants which are able to use less water to fix the same amount of carbon dioxide or which are able to function normally at a lower water potential have the potential to conduct more photosynthesis and thereby to produce more biomass and economic yield in many agricultural systems.


In some cases, a plant resulting from seeds or other plant elements treated with a single endophyte strain or a plurality of endophytes can exhibit a physiological change, such as a compensation of the stress-induced reduction in photosynthetic activity (expressed, for example, as ΔFv/Fm) after exposure to heat shock or drought conditions as compared to a corresponding control, genetically identical plant that does not contain the endophytes grown in the same conditions. In some cases, the endophyte-associated plant as disclosed herein can exhibit an increased change in photosynthetic activity ΔFv(ΔFv/Fm) after heat-shock or drought stress treatment, for example 1, 2, 3, 4, 5, 6, 7 days or more after the heat-shock or drought stress treatment, or until photosynthesis ceases, as compared with corresponding control plant of similar developmental stage but not comprising the endophytes. For example, a plant having a plurality of the endophytes able to confer heat and/or drought-tolerance can exhibit a ΔFv/Fm of from about 0.1 to about 0.8 after exposure to heat-shock or drought stress or a ΔFv/Fm range of from about 0.03 to about 0.8 under one day, or 1, 2, 3, 4, 5, 6, 7, or over 7 days post heat-shock or drought stress treatment, or until photosynthesis ceases. In some embodiments, stress-induced reductions in photosynthetic activity can be compensated by at least about 0.25% (for example, at least about 0.5%, between 0.5% and 1%, at least about 1%, between 1% and 2%, at least about 2%, between 2% and 3%, at least about 3%, between 3% and 5%, at least about 5%, between 5% and 10%, at least about 8%, at least about 10%, between 10% and 15%, at least about 15%, between 15% and 20%, at least about 20%, between 20$ and 25%, at least about 25%, between 25% and 30%, at least about 30%, between 30% and 40%, at least about 40%, between 40% and 50%, at least about 50%, between 50% and 60%, at least about 60%, between 60% and 75%, at least about 75%; between 75% and 80%, at least about 80%, between 80% and 85%, at least about 85%, between 85% and 90%, at least about 90%, between 90% and 95%, at least about 95%, between 95% and 99%, at least about 99%, between 99% and 100%, or at least 100%) as compared to the photosynthetic activity decrease in a corresponding reference agricultural plant following heat shock conditions. Significance of the difference between endophyte-associated and reference agricultural plants can be established upon demonstrating statistical significance, for example at p<0.05 with an appropriate parametric or non-parametric statistic, e.g., Chi-square test, Student's t-test, Mann-Whitney test, or F-test based on the assumption or known facts that the endophyte-associated plant and reference agricultural plant have identical or near identical genomes (isoline comparison).


In selecting traits for improving crops, a decrease in water use, without a change in growth would have particular merit in an irrigated agricultural system where the water input costs were high. An increase in growth without a corresponding jump in water use would have applicability to all agricultural systems. In many agricultural systems where water supply is not limiting, an increase in growth, even if it came at the expense of an increase in water use also increases yield. Water use efficiency (WUE) is a parameter often correlated with drought tolerance, and is the CO2 assimilation rate per water transpired by the plant. An increased water use efficiency of the plant relates in some cases to an increased fruit/kernel size or number. Therefore, in some embodiments, the plants described herein exhibit an increased water use efficiency when compared with a reference agricultural plant grown under the same conditions. For example, the plants grown from the plant elements comprising the plurality of endophytes can have at least 3%, between 3% and 5%, at least 5%, between 5% and 10%, least 10%, between 10% and 15%, for example at least 15%, between 15% and 20%, at least 20%, between 20% and 30%, at least 30%, between 30% and 40%, at least 40%, between 40% and 50%, at least 50%, between 50% and 60%, at least 60%, between 60% and 75%, at least 75%, between 75% and 100%, or at least 100% higher WUE than a reference agricultural plant grown under the same conditions. Such an increase in WUE can occur under conditions without water deficit, or under conditions of water to deficit, for example, when the soil water content is less than or equal to 60% of water saturated soil, for example, less than or equal to 50%, less than or equal to 40%, less than or equal to 30%, less than or equal to 20%, less than or equal to 10% of water saturated soil on a weight basis. In a related embodiment, the plant comprising the plurality of endophytes can have at least. 10% higher relative water content (RWC), for example, at least 3%, between 3% and 5%, at least 5%, between 5% and 10%, least 10%, between 10% and 15%, for example at least 15%, between 15% and 20%, at least 20%, between 20% and 30%, at least 30%, between 30% and 40%, at least 40%, between 40% and 50%, at least 50%, between 50% and 60%, at least 60%, between 60% and 75%, at least 75%, between 75% and 100%, or at least 100% higher RWC than a reference agricultural plant grown under the same conditions.


In some embodiments, the plants comprise a single endophyte strain or a plurality of endophytes able to increase heat and/or drought-tolerance in sufficient quantity, such that increased growth or improved recovery from wilting under conditions of heat or drought stress is observed. For example, a plurality of endophyte populations described herein can be present in sufficient quantity in a plant, resulting in increased growth as compared to a plant that does not contain endophytes, when grown under drought conditions or heat shock conditions, or following such conditions. Increased heat and/or drought tolerance can be assessed with physiological parameters including, but not limited to, increased height, overall biomass, root and/or shoot biomass, seed germination, seedling survival, photosynthetic efficiency, transpiration rate, seed/fruit number or mass, plant grain or fruit yield, leaf chlorophyll content, photosynthetic rate, root length, wilt recovery, turgor pressure, or any combination thereof, as compared to a reference agricultural plant grown under similar conditions. For example, the endophyte may provide an improved benefit or tolerance to a plant that is of at least 3%, between 3% and 5%, at least 5%, between 5% and 10%, least 10%, between 10% and 15%, for example at least 15%, between 15% and 20%, at least 20%, between 20% and 30%, at least 30%, between 30% and 40%, at least 40%, between 40% and 50%, at least 50%, between 50% and 60%, at least 60%, between 60% and 75%, at least 75%, between 75% and 100%, or at least 100%, when compared with uninoculated plants grown under the same conditions.


In various embodiments, a a single endophyte strain or plurality of endophytes introduced into altered seed microbiota can confer in the resulting plant thermal tolerance, herbicide tolerance, drought resistance, insect resistance, fungus resistance, virus resistance, bacteria resistance, male sterility, cold tolerance, salt tolerance, increased yield, enhanced nutrient use efficiency, increased nitrogen use efficiency, increased protein content, increased fermentable carbohydrate content, reduced lignin content, increased antioxidant content, enhanced water use efficiency, increased vigor, increased germination efficiency, earlier or increased flowering, increased biomass, altered root-to-shoot biomass ratio, enhanced soil water retention, or a combination thereof. A difference between the endophyte-associated plant and a reference agricultural plant can also be measured using other methods known in the art.


Salt Stress


In other embodiments, a a single endophyte strain or plurality of endophytes able to confer increased tolerance to salinity stress can be introduced into plants. The resulting plants comprising endophytes can exhibit increased resistance to salt stress, whether measured in terms of survival under saline conditions, or overall growth during, or following salt stress. The physiological parameters of plant health recited above, including height, overall biomass, root and/or shoot biomass, seed germination, seedling survival, photosynthetic efficiency, transpiration rate, seed/fruit number or mass, plant grain or fruit yield, leaf chlorophyll content, photosynthetic rate, root length, or any combination thereof, can be used to measure growth, and compared with the growth rate of reference agricultural plants (e.g., isogenic plants without the endophytes) grown under identical conditions. For example, the endophyte may provide an improved benefit or tolerance to a plant that is of at least 3%, between 3% and 5%, at least 5%, between 5% and 10%, least 10%, between 10% and 15%, for example at least 15%, between 15% and 20%, at least 20%, between 20% and 30%, at least 30%, between 30% and 40%, at least 40%, between 40% and 50%, at least 50%, between 50% and 60%, at least 60%, between 60% and 75%, at least 75%, between 75% and 100%, or at least 100%, when compared with uninoculated plants grown under the same conditions.


In other instances, endophyte-associated plants and reference agricultural plants can be grown in soil or growth media containing different concentration of sodium to establish the inhibitory concentration of sodium (expressed, for example, as the concentration in which growth of the plant is inhibited by 50% when compared with plants grown under no sodium stress). Therefore, in another embodiment, a plant resulting from seeds containing an endophyte able to confer salt tolerance described herein exhibits an increase in the inhibitory sodium concentration by at least 10 mM, for example at least 15 mM, at least 20 mM, at least 30 mM, at least 40 mM, at least 50 mM, at least 60 mM, at least 70 mM, at least 80 mM, at least 90 mM, at least 100 mM or more, when compared with the reference agricultural plants.


High Metal Content


Plants are sessile organisms and therefore must contend with the environment in which they are placed. While plants have adapted many mechanisms to deal with chemicals and substances that may be deleterious to their health, heavy metals represent a class of toxins which are highly relevant for plant growth and agriculture. Plants use a number of mechanisms to cope with toxic levels of heavy metals (for example, nickel, cadmium, lead, mercury, arsenic, or aluminum) in the soil, including excretion and internal sequestration. For agricultural purposes, it is important to have plants that are able to tolerate otherwise hostile conditions, for example soils containing elevated levels of toxic heavy metals. Endophytes that are able to confer increased heavy metal tolerance may do so by enhancing sequestration of the metal in certain compartments. Use of such endophytes in a plant would allow the development of novel plant-endophyte combinations for purposes of environmental remediation (also known as phytoremediation). Therefore, in one embodiment, the plant containing the endophyte able to confer increased metal tolerance exhibits a difference in a physiological parameter that is at least about 5% greater, for example at least about 5%, at least about 8%, at least about 10%, at least about 15%, at least about 20%, at least about 25%, at least about 30%, at least about 40%, at least about 50%, at least about 60%, at least about 75%, at least about 80%, at least about 80%, at least about 90%, or at least 100%, at least about 200%, at least about 300%, at least about 400% or greater than a reference agricultural plant grown under the same heavy metal concentration in the soil.


Alternatively, the inhibitory concentration of the heavy metal can be determined for the endophyte-associated plant and compared with a reference agricultural plant under the same conditions. Therefore, in one embodiment, the plants resulting from seeds containing an endophyte able to confer heavy metal tolerance described herein exhibit an increase in the inhibitory sodium concentration by at least 0.1 mM, for example at least 0.3 mM, at least 0.5 mM, at least 1 mM, at least 2 mM, at least 5 mM, at least 10 mM, at least 15 mM, at least 20 mM, at least 30 mM, at least 50 mM or more, when compared with the reference agricultural plants.


Finally, plants inoculated with endophytes that are able to confer increased metal tolerance exhibits an increase in overall metal accumulation by at least 10%, for example at least 15%, at least 20%, at least 30%, at least 40%, at least 50%, at least 60%, at least 75%, at least 100%, at least 150%, at least 200%, at least 300% or more, when compared with uninoculated plants grown under the same conditions.


Low Nutrient Stress


A single endophyte strain or a plurality of endophytes described herein may also confer to the plant an increased ability to grow in nutrient limiting conditions, for example by solubilizing or otherwise making available to the plants macronutrients or micronutrients that are complexed, insoluble, or otherwise in an unavailable form. In some embodiments, a plant is inoculated with a plurality of endophytes that confer increased ability to liberate and/or otherwise provide to the plant with nutrients selected from the group consisting of phosphate, nitrogen, potassium, iron, manganese, calcium, molybdenum, vitamins, or other micronutrients. Such a plant can exhibit increased growth in soil comprising limiting amounts of such nutrients when compared with reference agricultural plant. Differences between the endophyte-associated plant and reference agricultural plant can be measured by comparing the biomass of the two plant types grown under limiting conditions, or by measuring the physical parameters described above. Therefore, in some embodiments, the plant comprising endophytes shows increased tolerance to nutrient limiting conditions as compared to a reference agricultural plant grown under the same nutrient limited concentration in the soil, as measured for example by increased biomass or seed yield of at least 3%, between 3% and 5%, at least 5%, between 5% and 10%, least 10%, between 10% and 15%, for example at least 15%, between 15% and 20%, at least 20%, between 20% and 30%, at least 30%, between 30% and 40%, at least 40%, between 40% and 50%, at least 50%, between 50% and 60%, at least 60%, between 60% and 75%, at least 75%, between 75% and 100%, or at least 100%, when compared with uninoculated plants grown under the same conditions. In other embodiments, the plant containing the plurality of endophytes is able to grown under nutrient stress conditions while exhibiting no difference in the physiological parameter compared to a plant that is grown without nutrient stress. In some embodiments, such a plant will exhibit no difference in the physiological parameter when grown with 2-5% less nitrogen than average cultivation practices on normal agricultural land, for example, at least 10%, between 10% and 15%, for example at least 15%, between 15% and 20%, at least 20%, between 20% and 30%, at least 30%, between 30% and 40%, at least 40%, between 40% and 50%, at least 50%, between 50% and 60%, at least 60%, between 60% and 75%, at least 75%, or between 75% and 100%, less nitrogen, when compared with crop plants grown under normal conditions during an average growing season. In some embodiments, the microbe capable of providing nitrogen-stress tolerance to a plant is diazotrophic. In other embodiments, the microbe capable of providing nitrogen-stress tolerance to a plant is non-diazotrophic.


Cold Stress


In some cases, endophytes can confer to the plant the ability to tolerate cold stress. Many known methods exist for the measurement of a plant's tolerance to cold stress (as reviewed, for example, in Thomashow (2001) Plant Physiol. 125: 89-93, and Gilmour et al. (2000) Plant Physiol. 124: 1854-1865, both of which are incorporated herein by reference in their entirety). As used herein, cold stress refers to both the stress induced by chilling (0° C.-15° C.) and freezing (<0° C.). Some cultivars of agricultural plants can be particularly sensitive to cold stress, but cold tolerance traits may be multigenic, making the breeding process difficult. Endophytes able to confer cold tolerance would potentially reduce the damage suffered by farmers on an annual basis. Improved response to cold stress can be measured by survival of plants, the amount of necrosis of parts of the plant, or a change in crop yield loss, as well as the physiological parameters used in other examples. Therefore, in one embodiment, the plant containing the endophyte able to confer increased cold tolerance exhibits a difference in a physiological parameter that is at least about 5% greater, for example at least about 5%, at least about 8%, at least about 10%, at least about 15%, at least about 20%, at least about 25%, at least about 30%, at least about 40%, at least about 50%, at least about 60%, at least about 75%, at least about 80%, at least about 80%, at least about 90%, or at least 100%, at least about 200%, at least about 300%, at least about 400% or greater than a reference agricultural plant grown under the same conditions of cold stress.


Biotic Stress


In other embodiments, a single endophyte strain or plurality of endophytes protects the plant from a biotic stress, for example, insect infestation, nematode infestation, complex infection, fungal infection, oomycete infection, protozoal infection, viral infection, and herbivore grazing, or a combination thereof. For example, the endophyte may provide an improved benefit or tolerance to a plant that is of at least 3%, between 3% and 5%, at least 5%, between 5% and 10%, least 10%, between 10% and 15%, for example at least 15%, between 15% and 20%, at least 20%, between 20% and 30%, at least 30%, between 30% and 40%, at least 40%, between 40% and 50%, at least 50%, between 50% and 60%, at least 60%, between 60% and 75%, at least 75%, between 75% and 100%, or at least 100%, when compared with uninoculated plants grown under the same conditions.


Insect Herbivory


There are an abundance of insect pest species that can infect or infest a wide variety of plants. Pest infestation can lead to significant damage. Insect pests that infest plant species are particularly problematic in agriculture as they can cause serious damage to crops and significantly reduce plant yields. A wide variety of different types of plant are susceptible to pest infestation including commercial crops such as cotton, soybean, wheat, barley, and corn.


In some embodiments, endophytes described herein confer upon the host plant the ability to repel insect herbivores. In other cases, the endophytes may produce, or induce the production in the plant of, compounds which are insecticidal or insect repellant. The insect may be any one of the common pathogenic insects affecting plants, particularly agricultural plants. Examples include, but are not limited to: Leptinotarsa spp. (e.g., L. decemlineata (Colorado potato beetle), L. juncta (false potato beetle), or L. texana (Texan false potato beetle)); Nilaparvata spp. (e.g., N. lugens (brown planthopper)); Laode/phax spp. (e.g., L. striatellus (small brown planthopper)); Nephotettix spp. (e.g., N. virescens or N. cincticeps (green leafhopper), or N. nigropictus (rice leafhopper)); Sogatella spp. (e.g., S. furcifera (white-backed planthopper)); Chilo spp. (e.g., C. suppressalis (rice striped stem borer), C. auricilius (gold-fringed stem borer), or C. polychrysus (dark-headed stem borer)); Sesamia spp. (e.g., S. inferens (pink rice borer)); Tryporyza spp. (e.g., T. innotata (white rice borer), or T. incertulas (yellow rice borer)); Anthonomus spp. (e.g., A. grandis (boll weevil)); Phaedon spp. (e.g., P. cochleariae (mustard leaf beetle)); Epilachna spp. (e.g., E. varivetis (Mexican bean beetle)); Tribolium spp. (e.g., T. castaneum (red floor beetle)); Diabrotica spp. (e.g., D. virgifera. (western corn rootworm), D. barberi (northern corn rootworm), D. undecimpunctata howardi (southern corn rootworm), D. virgifera zeae (Mexican corn rootworm); Ostrinia spp. (e.g., O. nubilalis (European corn borer)); Anaphothrips spp. (e.g., A. obscrurus (grass thrips)); Pectinophora spp. (e.g., P. gossypiella (pink bollworm)); Heliothis spp. (e.g., H. virescens (tobacco budworm)); Trialeurodes spp. (e.g., T. abutiloneus (banded-winged whitefly) T. vaporariorum (greenhouse whitefly)); Bemisia spp. (e.g., B. argentifolii (silverleaf whitefly)); Aphis spp. (e.g., A. gossypii (cotton aphid)); Lygus spp. (e.g., L. lineolaris (tarnished plant bug) or L. hesperus (western tarnished plant bug)); Euschistus spp. (e.g., E. conspersus (consperse stink bug)); Chlorochroa spp. (e.g., C. sayi (Say stinkbug)); Nezara spp. (e.g., N. viridula (southern green stinkbug)); Thrips spp. (e.g., T. tabaci (onion thrips)); Frankliniella spp. (e.g., F. fusca (tobacco thrips), or F. occidentalis (western flower thrips)); Acheta spp. (e.g., A. domesticus (house cricket)); Myzus spp. (e.g., M. persicae (green peach aphid)); Macrosiphum spp. (e.g., M. euphorbiae (potato aphid)); Blissus spp. (e.g., B. leucopterus (chinch bug)); Acrostemum spp. (e.g., A. hilare (green stink bug)); Chilotraea spp. (e.g., C. polychrysa (rice stalk borer)); Lissorhoptrus spp. (e.g., L. oryzophilus (rice water weevil)); Rhopalosiphum spp. (e.g., R. maidis (corn leaf aphid)); Anuraphis spp. (e.g., A. maidiradicis (corn root aphid)), and combinations thereof.


The endophyte-associated plant can be tested for its ability to resist, or otherwise repel, pathogenic insects by measuring, for example, insect load, overall plant biomass, biomass of the fruit or grain, percentage of intact leaves, or other physiological parameters described herein, and comparing with a reference agricultural plant. In some embodiments, the endophyte-associated plant exhibits increased biomass as compared to a reference agricultural plant grown under the same conditions (e.g., grown side-by-side, or adjacent to, endophyte-associated plants). In other embodiments, the endophyte-associated plant exhibits increased fruit or grain yield as compared to a reference agricultural plant grown under the same conditions (e.g., grown side-by-side, or adjacent to, endophyte-associated plants). In any of the above, the endophyte may provide an improved benefit or tolerance to a plant that is of at least 3%, between 3% and 5%, at least 5%, between 5% and 10%, least 10%, between 10% and 15%, for example at least 15%, between 15% and 20%, at least 20%, between 20% and 30%, at least 30%, between 30% and 40%, at least 40%, between 40% and 50%, at least 50%, between 50% and 60%, at least 60%, between 60% and 75%, at least 75%, between 75% and 100%, or at least 100%, when compared with uninoculated plants grown under the same conditions.


Nematodes


Nematodes are microscopic roundworms that feed on the roots, fluids, leaves and stems of more than 2,000 row crops, vegetables, fruits, and ornamental plants, causing an estimated $100 billion crop loss worldwide and accounting for 13% of global crop losses due to disease. A variety of parasitic nematode species infect crop plants, including root-knot nematodes (RKN), cyst- and lesion-forming nematodes. Root-knot nematodes, which are characterized by causing root gall formation at feeding sites, have a relatively broad host range and are therefore parasitic on a large number of crop species. The cyst- and lesion-forming nematode species have a more limited host range, but still cause considerable losses in susceptible crops.


Signs of nematode damage include stunting and yellowing of leaves, and wilting of the plants during hot periods. Nematode infestation, however, can cause significant yield losses without any obvious above-ground disease symptoms. The primary causes of yield reduction are due to underground root damage. Roots infected by SCN are dwarfed or stunted. Nematode infestation also can decrease the number of nitrogen-fixing nodules on the roots, and may make the roots more susceptible to attacks by other soil-borne plant nematodes.


In some embodiments, the endophyte-associated plant has an increased resistance to a nematode when compared with a reference agricultural plant. As before with insect herbivores, biomass of the plant or a portion of the plant, or any of the other physiological parameters mentioned elsewhere, can be compared with the reference agricultural plant grown under the same conditions. Particularly useful measurements include overall plant biomass, biomass and/or size of the fruit or grain, and root biomass. In some embodiments, the endophyte-associated plant exhibits increased biomass as compared to a reference agricultural plant grown under the same conditions (e.g., grown side-by-side, or adjacent to, the endophyte-associated plants, under conditions of nematode challenge). In other embodiments, the endophyte-associated plant exhibits increased root biomass as compared to a reference agricultural plant grown under the same conditions (e.g., grown side-by-side, or adjacent to, the endophyte-associated plants, under conditions of nematode challenge). In still another embodiment, the endophyte-associated plant exhibits increased fruit or grain yield as compared to a reference agricultural plant grown under the same conditions (e.g., grown side-by-side, or adjacent to, the endophyte-associated plants, under conditions of nematode challenge). In any of the above, the endophyte may provide an improved benefit or tolerance to a plant that is of at least 3%, between 3% and 5%, at least 5%, between 5% and 10%, least 10%, between 10% and 15%, for example at least 15%, between 15% and 20%, at least 20%, between 20% and 30%, at least 30%, between 30% and 40%, at least 40%, between 40% and 50%, at least 50%, between 50% and 60%, at least 60%, between 60% and 75%, at least 75%, between 75% and 100%, or at least 100%, when compared with uninoculated plants grown under the same conditions.


Fungal Pathogens


Fungal diseases are responsible for yearly losses of over $10 Billion on agricultural crops in the US, represent 42% of global crop losses due to disease, and are caused by a large variety of biologically diverse pathogens. Different strategies have traditionally been used to control them. Resistance traits have been bred into agriculturally important varieties, thus providing various levels of resistance against either a narrow range of pathogen isolates or races, or against a broader range. However, this involves the long and labor intensive process of introducing desirable traits into commercial lines by genetic crosses and, due to the risk of pests evolving to overcome natural plant resistance, a constant effort to breed new resistance traits into commercial lines is required. Alternatively, fungal diseases have been controlled by the application of chemical fungicides. This strategy usually results in efficient control, but is also associated with the possible development of resistant pathogens and can be associated with a negative impact on the environment. Moreover, in certain crops, such as barley and wheat, the control of fungal pathogens by chemical fungicides is difficult or impractical.


The present invention contemplates the use a single endophyte strain or of a plurality of endophytes that is able to confer resistance to fungal pathogens to the host plant. Increased resistance to fungal inoculation can be measured, for example, using any of the physiological parameters presented above, by comparing with reference agricultural plants. In some embodiments, the endophyte-associated plant exhibits increased biomass and/or less pronounced disease symptoms as compared to a reference agricultural plant grown under the same conditions (e.g., grown side-by-side, or adjacent to, the endophyte-associated plants, infected with the fungal pathogen). In still another embodiment, the endophyte-associated plant exhibits increased fruit or grain yield as compared to a reference agricultural plant grown under the same conditions (e.g., grown side-by-side, or adjacent to, the endophyte-associated plants, infected with the fungal pathogen). In other embodiments, the endophyte-associated plant exhibits decreased hyphal growth as compared to a reference agricultural plant grown under the same conditions (e.g., grown side-by-side, or adjacent to, the endophyte-associated plants, infected with the fungal pathogen). In any of the above, the endophyte may provide an improved benefit or tolerance to a plant that is of at least 3%, between 3% and 5%, at least 5%, between 5% and 10%, least 10%, between 10% and 15%, for example at least 15%, between 15% and 20%, at least 20%, between 20% and 30%, at least 30%, between 30% and 40%, at least 40%, between 40% and 50%, at least 50%, between 50% and 60%, at least 60%, between 60% and 75%, at least 75%, between 75% and 100%, or at least 100%, when compared with uninoculated plants grown under the same conditions.


Viral Pathogens


Plant viruses are estimated to account for 18% of global crop losses due to disease. There are numerous examples of viral pathogens affecting agricultural productivity. Examples include the American wheat striate mosaic virus (AWSMV) (wheat striate mosaic), Barley stripe mosaic virus (BSMV), Barley yellow dwarf virus (BYDV), Brome mosaic virus (BMV), Cereal chlorotic mottle virus (CCMV), Corn chlorotic vein banding virus (CCVBV), Brazilian maize mosaic virus, Corn lethal necrosis Virus complex from Maize chlorotic mottle virus, (MCMV), Maize dwarf mosaic virus (MDMV), A or B Wheat streak mosaic virus (WSMV), Cucumber mosaic virus (CMV), Cynodon chlorotic streak virus (CCSV), Johnsongrass mosaic virus (JGMV), Maize bushy stunt Mycoplasma-like organism (MLO) associated virus, Maize chlorotic dwarf Maize chlorotic dwarf virus (MCDV), Maize chlorotic mottle virus (MCMV), Maize dwarf mosaic virus (MDMV), strains A, D, E and F, Maize leaf fleck virus (MLFV), Maize line virus (MLV), Maize mosaic (corn leaf stripe, Maize mosaic virus (MMV), enanismo rayado), Maize mottle and chlorotic stunt virus, Maize pellucid ringspot virus (MPRV), Maize raya gruesa virus (MRGV), Maize rayado fino (fine striping) virus (MRFV), Maize red stripe virus (MRSV), Maize ring mottle virus (MRMV), Maize rio cuarto virus (MRCV), Maize rough dwarf virus (MRDV), Cereal tillering disease virus, Maize sterile stunt virus, barley yellow striate virus, Maize streak virus (MSV), Maize stripe virus, Maize chloroticstripe virus, maize hoja blanca virus, Maize stunting virus; Maize tassel abortion virus (MTAV), Maize vein enation virus (MVEV), Maize wallaby ear virus (MWEV), Maize white leaf virus, Maize white line mosaic virus (MWLMV), Millet red leaf virus (MRLV), Northern cereal mosaic virus (NCMV), Oat pseudorosette virus, (zakuklivanie), Oat sterile dwarf virus (OSDV), Rice black-streaked dwarf virus (RBSDV), Rice stripe virus (RSV), Sorghum mosaic virus (SrMV), Sugarcane mosaic virus (SCMV) strains H, I and M, Sugarcane Fiji disease virus (FDV), Sugarcane mosaic virus (SCMV) strains A, B, D, E, SC, BC, Sabi and MB (formerly MDMV-B), and Wheat spot mosaic virus (WSMV). In one embodiment, the endophyte-associated plant provides protection against viral pathogens such that there is at least 5% greater biomass, for example, at least 10%, at least 15%, at least 20%, at least 30%, at least 40%, at least 50%, at least 75%, at least 100% or more biomass, than the reference agricultural plant grown under the same conditions. In still another embodiment, the endophyte-associated plant exhibits at least 5% greater fruit or grain yield, for example, at least 10%, at least 15%, at least 20%, at least 30%, at least 40%, at least 50%, at least 75%, at least 100% or more fruit or grain yield when challenged with a virus, as compared to a reference agricultural plant grown under the same conditions. In yet another embodiment, the endophyte-associated plant exhibits at least 5% lower viral titer, for example, at least 10%, at least 15%; at least 20%, at least 30%, at least 40%, at least 50%, at least 75%, at least 100% lower viral titer when challenged with a virus, as compared to a reference agricultural plant grown under the same conditions.


Bacterial Pathogens


Likewise, bacterial pathogens are a significant problem negatively affecting agricultural productivity and accounting for 27% of global crop losses due to plant disease. In one embodiment, the endophyte-associated plant described herein provides protection against bacterial pathogens such that there is at least 5% greater biomass, for example, at least 10%, at least 15%, at least 20%, at least 30%, at least 40%, at least 50%, at least 75%, at least 100% or more biomass, than the reference agricultural plant grown under the same conditions. In still another embodiment, the endophyte-associated plant exhibits at least 5% greater fruit or grain yield, for example, at least 10%, at least 15%, at least 20%, at least 30%, at least 40%, at least 50%, at least 75%, at least 100% or more fruit or grain yield when challenged with a bacterial pathogen, than the reference agricultural plant grown under the same conditions. In yet another embodiment, the endophyte-associated plant exhibits at least 5% lower bacterial count, for example, at least 10%, at least 15%, at least 20%, at least 30%, at least 40%, at least 50%, at least 75%, at least 100% lower bacterial count when challenged with a bacteria, as compared to a reference agricultural plant grown under the same conditions.


Yield and Biomass Improvement


In other embodiments, the improved trait can be an increase in overall biomass of the plant or a part of the plant, including its fruit or seed. In some embodiments, a single endophyte strain or a plurality of endophytes is disposed on the surface or within a tissue of the plant element in an amount effective to increase the biomass of the plant, or a part or tissue of the plant grown from the plant element. The increased biomass is useful in the production of commodity products derived from the plant. Such commodity products include an animal feed, a fish fodder, a cereal product, a processed human-food product, a sugar or an alcohol. Such products may be a fermentation product or a fermentable product, one such exemplary product is a biofuel. The increase in biomass can occur in a part of the plant (e.g., the root tissue, shoots, leaves, etc.), or can be an increase in overall biomass. Increased biomass production, such an increase meaning at at least 3%, between 3% and 5%, at least 5%, between 5% and 10%, least 10%, between 10% and 15%, for example at least 15%, between 15% and 20%, at least 20%, between 20% and 30%, at least 30%, between 30% and 40%, at least 40%, between 40% and 50%, at least 50%, between 50% and 60%, at least 60%, between 60% and 75%, at least 75%, between 75% and 100%, or at least 100%, when compared with uninoculated plants grown under the same conditions. Such increase in overall biomass can be under relatively stress-free conditions. In other cases, the increase in biomass can be in plants grown under any number of abiotic or biotic stresses, including drought stress, salt stress, heat stress, cold stress, low nutrient stress, nematode stress, insect herbivory stress, fungal pathogen stress, bacterial pathogen stress, and viral pathogen stress. In some embodiments, a plurality of endophytes is disposed in an amount effective to increase root biomass by at least 3%, between 3% and 5%, at least 5%, between 5% and 10%, least 10%, between 10% and 15%, for example at least 15%, between 15% and 20%, at least 20%, between 20% and 30%, at least 30%, between 30% and 40%, at least 40%, between 40% and 50%, at least 50%, between 50% and 60%, at least 60%, between 60% and 75%, at least 75%, between 75% and 100%, or at least 100%, when compared with uninoculated plants grown under the same conditions, when compared with a reference agricultural plant. In other cases, a plurality of endophytes is disposed on the plant element in an amount effective to increase the average biomass of the fruit or cob from the resulting plant at least 3%, between 3% and 5%, at least 5%, between 5% and 10%, least 10%, between 10% and 15%, for example at least 15%, between 15% and 20%, at least 20%, between 20% and 30%, at least 30%, between 30% and 40%, at least 40%, between 40% and 50%, at least 50%, between 50% and 60%, at least 60%, between 60% and 75%, at least 75%, between 75% and 100%, or at least 100%, when compared with uninoculated plants grown under the same conditions.


Increase in Plant Growth Hormones


Many of the microbes described herein are capable of producing the plant hormone auxin indole-3-acetic acid (IAA) when grown in culture. Auxin may play a key role in altering the physiology of the plant, including the extent of root growth. Therefore, in other embodiments, a single endophyte strain or a plurality of endophytes is disposed on the surface or within a tissue of the plant element in an amount effective to detectably induce production of auxin in the agricultural plant. For example, the increase in auxin production can be at least 2%, at least 3%, at least 4%, at least 5%, at least 6%, at least 7%, at least 8%, at least 9%, at least 10%, at least 15%, for example, at least 20%, at least 30%, at least 40%, at least 50%, at least 60%, at least 75%, at least 100%, or more, when compared with a reference agricultural plant. In some embodiments, the increased auxin production can be detected in a tissue type selected from the group consisting of the root, shoot, leaves, and flowers.


Improvement of Other Traits.


In other embodiments, a single endophyte strain or a plurality of endophytes can confer other beneficial traits to the plant. Improved traits can include an improved nutritional content of the plant or plant element used for human consumption. In some embodiments, the endophyte-associated plant is able to produce a detectable change in the content of at least one nutrient. Examples of such nutrients include amino acid, protein, oil (including any one of Oleic acid, Linoleic acid, Alpha-linoleic acid, Saturated fatty acids, Palmitic acid, Stearic acid and Trans fats), carbohydrate (including sugars such as sucrose, glucose and fructose, starch, or dietary fiber), Vitamin A, Thiamine (vit. B1), Riboflavin (vit. B2), Niacin (vit. B3), Pantothenic acid (B5), Vitamin B6, Folate (vit. B9), Choline, Vitamin C, Vitamin E, Vitamin K, Calcium, Iron, Magnesium, Manganese, Phosphorus, Potassium, Sodium, Zinc. In some embodiments, the endophyte-associated plant or part thereof contains at least one increased nutrient when compared with reference agricultural plants.


In other cases, the improved trait can include reduced content of a harmful or undesirable substance when compared with reference agricultural plants. Such compounds include those which are harmful when ingested in large quantities or are bitter tasting (for example, oxalic acid, amygdalin, certain alkaloids such as solanine, caffeine, nicotine, quinine and morphine, tannins, cyanide). As such, in some embodiments, the endophyte-associated plant or part thereof contains less of the undesirable substance when compared with reference agricultural plant. In a related embodiment, the improved trait can include improved taste of the plant or a part of the plant, including the fruit or seed. In a related embodiment, the improved trait can include reduction of undesirable compounds produced by other endophytes in plants, such as degradation of Fusarium-produced deoxynivalenol (also known as vomitoxin and a virulence factor involved in Fusarium head blight of maize and wheat) in a part of the plant, including the fruit or seed.


The endophyte-associated plant can also have an altered hormone status or altered levels of hormone production when compared with a reference agricultural plant. An alteration in hormonal status may affect many physiological parameters, including flowering time, water efficiency, apical dominance and/or lateral shoot branching, increase in root hair, and alteration in fruit ripening.


The association between the endophytes and the plant can also be detected using other methods known in the art. For example, the biochemical, genomic, epigenomic, transcriptomic, metabolomics, and/or proteomic profiles of endophyte-associated plants can be compared with reference agricultural plants under the same conditions.


Transcriptome analysis of endophyte-associated and reference agricultural plants can also be performed to detect changes in expression of at least one transcript, or a set or network of genes upon endophyte association. Similarly, epigenetic changes can be detected using methylated DNA immunoprecipitation followed by high-throughput sequencing.


Metabolomic or proteomic differences between the plants can be detected using methods known in the art. The metabolites, proteins, or other compounds described herein can be detected using any suitable method including, but not limited to gel electrophoresis, liquid and gas phase chromatography, either alone or coupled to mass spectrometry, NMR, immunoassays (enzyme-linked immunosorbent assays (ELISA)), chemical assays, spectroscopy and the like. In some embodiments, commercial systems for chromatography and NMR analysis are utilized. Such metabolomic methods can be used to detect differences in levels in hormone, nutrients, secondary metabolites, root exudates, phloem sap content, xylem sap content, heavy metal content, and the like. Such methods are also useful for detecting alterations in endophyte content and status; for example, the presence and levels of signaling molecules (e.g., autoinducers and pheromones), which can indicate the status of group-based behavior of endophytes based on, for example, population density. In some embodiments, a biological sample (whole tissue, exudate, phloem sap, xylem sap, root exudate, etc.) from endophyte-associated and reference agricultural plants can be analyzed essentially as known in the art.


In some embodiments, metabolites in plants can be modulated by making synthetic combinations of plants with pluralities of endophytes. For example, a plurality of endophytes can cause a detectable modulation (e.g., an increase or decrease) in the level of various metabolites, e.g., indole-3-carboxylic acid, trans-zeatin, abscisic acid, phaseic acid, indole-3-acetic acid, indole-3-butyric acid, indole-3-acrylic acid, jasmonic acid, jasmonic acid methyl ester, dihydrophaseic acid, gibberellin A3, salicylic acid, upon colonization of a plant.


In some embodiments, a single endophyte strain or a plurality of endophytes modulates the level of the metabolite directly (e.g., the microbes produces the metabolite, resulting in an overall increase in the level of the metabolite found in the plant). In other cases, the agricultural plant, as a result of the association with the plurality of endophytes, exhibits a modulated level of the metabolite (e.g., the plant reduces the expression of a biosynthetic enzyme responsible for production of the metabolite as a result of the microbe inoculation). In still other cases, the modulation in the level of the metabolite is a consequence of the activity of both the microbe and the plant (e.g., the plant produces increased amounts of the metabolite when compared with a reference agricultural plant, and the endophyte also produces the metabolite). Therefore, as used herein, a modulation in the level of a metabolite can be an alteration in the metabolite level through the actions of the microbe and/or the inoculated plant.


The levels of a metabolite can be measured in an agricultural plant, and compared with the levels of the metabolite in a reference agricultural plant, and grown under the same conditions as the inoculated plant. The uninoculated plant that is used as a reference agricultural plant is a plant that has not been applied with a formulation with the plurality of endophytes (e.g., a formulation comprising a plurality of populations of purified endophytes). The uninoculated plant used as the reference agricultural plant is generally the same species and cultivar as, and is isogenic to, the inoculated plant.


The metabolite whose levels are modulated (e.g., increased or decreased) in the endophyte-associated plant may serve as a primary nutrient (i.e., it provides nutrition for the humans and/or animals who consume the plant, plant tissue, or the commodity plant product derived therefrom, including, but not limited to, a sugar, a starch, a carbohydrate, a protein, an oil, a fatty acid, or a vitamin). The metabolite can be a compound that is important for plant growth, development or homeostasis (for example, a phytohormone such as an auxin, cytokinin, gibberellin, a brassinosteroid, ethylene, or abscisic acid, a signaling molecule, or an antioxidant). In other embodiments, the metabolite can have other functions. For example, in some embodiments, a metabolite can have bacteriostatic, bactericidal, fungistatic, fungicidal or antiviral properties. In other embodiments, the metabolite can have insect-repelling, insecticidal, nematode-repelling, or nematicidal properties. In still other embodiments, the metabolite can serve a role in protecting the plant from stresses, may help improve plant vigor or the general health of the plant. In yet another embodiment, the metabolite can be a useful compound for industrial production. For example, the metabolite may itself be a useful compound that is extracted for industrial use, or serve as an intermediate for the synthesis of other compounds used in industry. In a particular embodiment, the level of the metabolite is increased within the agricultural plant or a portion thereof such that it is present at a concentration of at least 0.1 ug/g dry weight, for example, at least 0.3 ug/g dry weight, between 0.3 ug/g and 1.0 ug/g dry weight, at least 1.0 ug/g dry weight, between 1.0 ug/g and 3.0 ug/g dry weight, at least 3.0 ug/g dry weight, between 3.0 ug/g and 10 ug/g dry weight, at least 10 ug/g dry weight, between 10 ug/g and 30 ug/g dry to weight, at least 30 ug/g dry weight, between 30 ug/g and 100 ug/g dry weight, at least 100 ug/g dry weight, between 100 ug/g and 300 ug/g dry weight, at least 300 ug/g dry weight, between 300 ug/g and 1 mg/g dry weight, or more than 1 mg/g dry weight, of the plant or portion thereof.


Likewise, the modulation can be a decrease in the level of a metabolite. The reduction can be in a metabolite affecting the taste of a plant or a commodity plant product derived from a plant (for example, a bitter tasting compound), or in a metabolite which makes a plant or the resulting commodity plant product otherwise less valuable (for example, reduction of oxalate content in certain plants, or compounds which are deleterious to human and/or animal health). The metabolite whose level is to be reduced can be a compound that affects quality of a commodity plant product (e.g., reduction of lignin levels).


Commodity Plant Product


The present invention provides a commodity plant product, as well as methods for producing a commodity plant product, that is derived from a plant of the present invention. As used herein, a “commodity plant product” refers to any composition or product that is comprised of material derived from a plant, seed, plant cell, or plant part of the present invention. Commodity plant products may be sold to consumers and can be viable or nonviable. Nonviable commodity products include but are not limited to nonviable seeds and grains; processed seeds, seed parts, and plant parts; dehydrated plant tissue, frozen plant tissue, and processed plant tissue; seeds and plant parts processed for animal feed for terrestrial and/or aquatic animal consumption, oil, meal, flour, flakes, bran, fiber, paper, tea, coffee, silage, crushed of whole grain, and any other food for human or animal consumption; and biomasses and fuel products; and raw material in industry. Industrial uses of oils derived from the agricultural plants described herein include ingredients for paints, plastics, fibers, detergents, cosmetics, lubricants, and biodiesel fuel. Soybean oil may be split, inter-esterified, sulfurized, epoxidized, polymerized, ethoxylated, or cleaved. Designing and producing soybean oil derivatives with improved functionality and improved oliochemistry is a rapidly growing field. The typical mixture of triglycerides is usually split and separated into pure fatty acids, which are then combined with petroleum-derived alcohols or acids, nitrogen, sulfonates, chlorine, or with fatty alcohols derived from fats and oils to produce the desired type of oil or fat. Commodity plant products also include industrial compounds, such as a wide variety of resins used in the formulation of adhesives, films, plastics, paints, coatings and foams.


In some cases, commodity plant products derived from the plants, or using the methods of the present invention can be identified readily. In some cases, for example, the presence of viable endophytes can be detected using the methods described herein elsewhere. In other cases, particularly where there are no viable endophytes, the commodity plant product may still contain at least a detectable amount of the specific and unique DNA corresponding to the microbes described herein. Any standard method of detection for polynucleotide molecules may be used, including methods of detection disclosed herein.


Formulations for Agricultural Use


The present invention contemplates a synthetic combination of a plant element that is associated with a single endophyte strain or a plurality of endophytes to confer an improved trait of agronomic importance to the host plant, or an improved agronomic trait potential to a plant element associated with the endophytes, that upon and after germination will confer said benefit to the resultant host plant.


In some embodiments, the plant element is associated with a single endophyte strain or a plurality of endophytes on its surface. Such association is contemplated to be via a mechanism selected from the group consisting of: spraying, immersion, coating, encapsulating, dusting, dripping, aerosolizing, seed treatment, root wash, seedling soak, foliar application, soil inocula, in-furrow application, sidedress application, soil pre-treatement, wound inoculation, drip tape irrigation, vector-mediation via a pollinator, injection, osmopriming, hydroponics, aquaponics, and aeroponics.


In some embodiments, the plant element is a leaf, and the synthetic combination is formulated for application as a foliar treatment.


In some embodiments, the plant element is a seed, and the synthetic combination is formulated for application as a seed coating.


In some embodiments, the plant element is a root, and the synthetic combination is formulated for application as a root treatment.


In certain embodiments, the plant element becomes associated with a plurality of endophytes through delayed exposure. For example, the soil in which a plant element is to be introduced is first treated with a composition comprising a plurality of endophytes. In another example, the area around the plant or plant element is exposed to a formulation comprising a plurality of endophytes, and the plant element becomes subsequently associated with the endophytes due to movement of soil, air, water, insects, mammals, human intervention, or other methods.


The plant element can be obtained from any agricultural plant. In some embodiments, the plant element of the first plant is from a monocotyledonous plant. For example, the plant element of the first plant is from a cereal plant. The plant element of the first plant can be selected from the group consisting of a maize seed, a wheat seed, a barley seed, a rice seed, a sugarcane seed, a maize root, a wheat root, a barley root, a sugarcane root, a rice root, a maize leaf, a wheat leaf, a barley leaf, a sugarcane leaf, or a rice leaf. In an alternative embodiment, the plant element of the first plant is from a dicotyledonous plant. The plant element of the first plant can be selected from the group consisting of a cotton seed, a tomato seed, a canola seed, a pepper seed, a soybean seed, a cotton root, a tomato root, a canola root, a pepper root, a soybean root, a cotton leaf, a tomato leaf, a canola leaf, a pepper leaf, or a soybean leaf. In still another embodiment, the plant element of the first plant can be from a genetically modified plant. In other embodiments, the plant element of the first plant can be a hybrid plant element.


The synthetic combination can comprise a plant element of the first plant which is surface-sterilized prior to combining with a plurality of endophytes. Such pre-treatment prior to coating the seed with endophytes removes the presence of other microbes which may interfere with the optimal colonization, growth and/or function of the endophytes. Surface sterilization of seeds can be accomplished without killing the seeds as described herein.


A single endophyte strain or a plurality of endophytes is intended to be useful in the improvement of agricultural plants, and as such, may be formulated with other compositions as part of an agriculturally compatible carrier. It is contemplated that such carriers can include, but not be limited to: seed treatment, root treatment, foliar treatment, soil treatment. The carrier composition with a plurality of endophytes, may be prepared for agricultural application as a liquid, a solid, or a gas formulation. Application to the plant may be achieved, for example, as a powder for surface deposition onto plant leaves, as a spray to the whole plant or selected plant element, as part of a drip to the soil or the roots, or as a coating onto the seed prior to planting. Such examples are meant to be illustrative and not limiting to the scope of the invention.


In some embodiments, the present invention contemplates plant elements comprising a single endophyte strain or a plurality of endophytes, and further comprising a formulation. The formulation useful for these embodiments generally comprises at least one member selected from the group consisting of an agriculturally compatible carrier, a tackifier, a microbial stabilizer, a fungicide, an antibacterial agent, an herbicide, a nematicide, an insecticide, a plant growth regulator, a rodenticide, and a nutrient.


In some cases, a single endophyte strain or a plurality of endophytes is mixed with an agriculturally compatible carrier. The carrier can be a solid carrier or liquid carrier. The carrier may be any one or more of a number of carriers that confer a variety of properties, such as increased stability, wettability, or dispersability. Wetting agents such as natural or synthetic surfactants, which can be nonionic or ionic surfactants, or a combination thereof can be included in a composition of the invention. Water-in-oil emulsions can also be used to formulate a composition that includes a plurality of endophytes. Suitable formulations that may be prepared include wettable powders, granules, gels, agar strips or pellets, thickeners, and the like, microencapsulated particles, and the like, liquids such as aqueous flowables, aqueous suspensions, water-in-oil emulsions, etc. The formulation may include grain or legume products, for example, ground grain or beans, broth or flour derived from grain or beans, starch, sugar, or oil.


In some embodiments, the agricultural carrier may be soil or plant growth medium. Other agricultural carriers that may be used include fertilizers, plant-based oils, humectants, or combinations thereof. Alternatively, the agricultural carrier may be a solid, such as diatomaceous earth, loam, silica, alginate, clay, bentonite, vermiculite, seed cases, other plant and animal products, or combinations, including granules, pellets, or suspensions. Mixtures of any of the aforementioned ingredients are also contemplated as carriers, such as but not limited to, pesta (flour and kaolin clay), agar or flour-based pellets in loam, sand, or clay, etc. Formulations may include food sources for the cultured organisms, such as barley, rice, or other biological materials such as seed, leaf, root, plant elements, sugar cane bagasse, hulls or stalks from grain processing, ground plant material or wood from building site refuse, sawdust or small fibers from recycling of paper, fabric, or wood. Other suitable formulations will be known to those skilled in the art.


In some embodiments, the formulation can comprise a tackifier or adherent. Such agents are useful for combining the microbial population of the invention with carriers that can contain other compounds (e.g., control agents that are not biologic), to yield a coating composition. Such compositions help create coatings around the plant or plant element to maintain contact between the microbe and other agents with the plant or plant part. In some embodiments, adherents are selected from the group consisting of: alginate, gums, starches, lecithins, formononetin, polyvinyl alcohol, alkali formononetinate, hesperetin, polyvinyl acetate, cephalins, Gum Arabic, Xanthan Gum, carragennan, PGA, other biopolymers, Mineral Oil, Polyethylene Glycol (PEG), Polyvinyl pyrrolidone (PVP), Arabino-galactan, Methyl Cellulose, PEG 400, Chitosan, Polyacrylamide, Polyacrylate, Polyacrylonitrile, Glycerol, Triethylene glycol, Vinyl Acetate, Gellan Gum, Polystyrene, Polyvinyl, Carboxymethyl cellulose, Gum Ghatti, and polyoxyethylene-polyoxybutylene block copolymers. Other examples of adherent compositions that can be used in the synthetic preparation include those described in EP 0818135, CA 1229497, WO 2013090628, EP 0192342, WO 2008103422 and CA 1041788, each of which is incorporated herein by reference in its entirety.


It is also contemplated that the formulation may further comprise an anti-caking agent.


The formulation can also contain a surfactant, wetting agent, emulsifier, stabilizer, or anti-foaming agent. Non-limiting examples of surfactants include nitrogen-surfactant blends such as Prefer 28 (Cenex), Surf-N (US), Inhance (Brandt), P-28 (Wilfarm) and Patrol (Helena); esterified seed oils include Sun-It II (AmCy), MSO (UAP), Scoil (Agsco), Hasten (Wilfarm) and Mes-100 (Drexel); and organo-silicone surfactants include Silwet L77 (UAP), Silikin (Terra), Dyne-Auric (Helena), Kinetic (Helena), Sylgard 309 (Wilbur-Ellis) and Century (Precision), polysorbate 20, polysorbate 80, Tween 20, Tween 80, Scattics, Alktest TW20, Canarcel, Peogabsorb 80, Triton X-100, Conco NI, Dowfax 9N, Igebapl CO, Makon, Neutronyx 600, Nonipol NO, Plytergent B, Renex 600, Solar NO, Sterox, Serfonic N, T-DET-N, Tergitol NP, Triton N, IGEPAL CA-630, Nonident P-40, and Pluronic. In some embodiments, the surfactant is present at a concentration of between 0.01% v/v to 10% v/v. In other embodiments, the surfactant is present at a concentration of between 0.1% v/v to 1% v/v. An example of an anti-foaming agent is Antifoam-C.


In certain cases, the formulation includes a microbial stabilizer. Such an agent can include a desiccant. As used herein, a “desiccant” can include any compound or mixture of compounds that can be classified as a desiccant regardless of whether the compound or compounds are used in such concentrations that they in fact have a desiccating effect on the liquid inoculant. Such desiccants are ideally compatible with the endophytes used, and should promote the ability of the microbial population to survive application on the plant elements and to survive desiccation. Examples of suitable desiccants include one or more of trehalose, sucrose, glycerol, and Methylene glycol. Other suitable desiccants include, but are not limited to, non-reducing sugars and sugar alcohols (e.g., mannitol or sorbitol). The amount of desiccant introduced into the formulation can range from about 5% to about 50% by weight/volume, for example, between about 10% to about 40%, between about 15% and about 35%, or between about 20% and about 30%.


In some cases, it is advantageous for the formulation to contain agents such as a fungicide, an antibacterial agent, an herbicide, a nematicide, an insecticide, a plant growth regulator, a rodenticide, a bactericide, a virucide, and a nutrient. Such agents are ideally compatible with the agricultural plant element or seedling onto which the formulation is applied (e.g., it should not be deleterious to the growth or health of the plant). Furthermore, the agent is ideally one which does not cause safety concerns for human, animal or industrial use (e.g., no safety issues, or the compound is sufficiently labile that the commodity plant product derived from the plant contains negligible amounts of the compound).


In the liquid form, for example, solutions or suspensions, a plurality of endophytes can be mixed or suspended in aqueous solutions. Suitable liquid diluents or carriers include aqueous solutions, petroleum distillates, or other liquid carriers.


Solid compositions can be prepared by dispersing a plurality of endophytes of the invention in and on an appropriately divided solid carrier, such as peat, wheat, bran, vermiculite, clay, talc, bentonite, diatomaceous earth, fuller's earth, pasteurized soil, and the like. When such formulations are used as wettable powders, biologically compatible dispersing agents such as non-ionic, anionic, amphoteric, or cationic dispersing and emulsifying agents can be used.


The solid carriers used upon formulation include, for example, mineral carriers such as kaolin clay, pyrophyllite, bentonite, montmorillonite, diatomaceous earth, acid white soil, vermiculite, and pearlite, and inorganic salts such as ammonium sulfate, ammonium phosphate, ammonium nitrate, urea, ammonium chloride, and calcium carbonate. Also, organic fine powders such as wheat flour, wheat bran, and rice bran may be used. The liquid carriers include vegetable oils such as soybean oil and cottonseed oil, glycerol, ethylene glycol, polyethylene glycol, propylene glycol, polypropylene glycol, etc.


In some embodiments, the formulation is ideally suited for coating of a plurality of endophytes onto plant elements. The plurality of endophytes is capable of conferring many agronomic benefits to the host plants. The ability to confer such benefits by coating the plurality of endophytes on the surface of plant elements has many potential advantages, particularly when used in a commercial (agricultural) scale.


A single endophyte strain or a plurality of endophytes can be combined with one or more of the agents described above to yield a formulation suitable for combining with an agricultural plant element or seedling. The plurality of endophytes can be obtained from growth in culture, for example, using a synthetic growth medium. In addition, the microbe can be cultured on solid media, for example on petri dishes, scraped off and suspended into the preparation. Microbes at different growth phases can be used. For example, microbes at lag phase, early-log phase, mid-log phase, late-log phase, stationary phase, early death phase, or death phase can be used. Endophytic spores may be used for the present invention, for example but not limited to: arthospores, sporangispores, conidia, chlamadospores, pycnidiospores, endospores, zoospores.


The formulations comprising a plurality of endophytes of the present invention typically contains between about 0.1 to 95% by weight, for example, between about 1% and 90%, between about 3% and 75%, between about 5% and 60%, between about 10% and 50% in wet weight of a plurality of endophytes. In some embodiments, the formulation contains at least about 10{circumflex over ( )}2 per ml of formulation, at least about 10{circumflex over ( )}3 per ml of formulation, for example, at least about 10{circumflex over ( )}4, at least about 10{circumflex over ( )}5, at least about 10{circumflex over ( )}6, at least about 10{circumflex over ( )}7 CFU or spores, at least about 10{circumflex over ( )}3 CFU or spores per ml of formulation. In some embodiments, the formulation be applied to the plant element at about 10{circumflex over ( )}2 CFU/seed, between 10{circumflex over ( )}2 and 10{circumflex over ( )}3 CFU, at least about 10{circumflex over ( )}3 CFU, between 10{circumflex over ( )}3 and 10{circumflex over ( )}4 CFU, at least about 10{circumflex over ( )}4 CFU, between 10{circumflex over ( )}4 and 10{circumflex over ( )}5 CFU, at least about 10{circumflex over ( )}5 CFU, between 10{circumflex over ( )}5 and 10{circumflex over ( )}6 CFU, at least about 10{circumflex over ( )}6 CFU, between 10{circumflex over ( )}6 and 10{circumflex over ( )}7 CFU, at least about 10{circumflex over ( )}7 CFU, between 10{circumflex over ( )}7 and 10{circumflex over ( )}8 CFU, or even greater than 10{circumflex over ( )}8 CFU per seed.


The compositions provided herein are preferably stable. The endophyte may be shelf-stable, where at least 0.01%, of the CFU or spores are viable after storage in desiccated form (i.e., moisture content of 30% or less) for 1, 2, 3, 4, 5, 6, 7, 8, 9, 10 or greater than 10 weeks at 4° C. or at room temperature. Optionally, a shelf-stable formulation is in a dry formulation, a powder formulation, or a lyophilized formulation. In some embodiments, the formulation is formulated to provide stability for the population of endophytes. In one embodiment, the formulation is substantially stable at temperatures between about −20° C. and about 50° C. for at least about 1, 2, 3, 4, 5, or 6 days, or 1, 2, 3 or 4 weeks, or 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11 or 12 months, or one or more years. In another embodiment, the formulation is substantially stable at temperatures between about 4° C. and about 37° C. for at least about 5, 10, 15, 20, 25, 30 or greater than 30 days.


As described above, in certain embodiments, the present invention contemplates the use of a single endophyte strain or a plurality of endophytes heterologously disposed on the plant, for example, the plant element. In certain cases, the agricultural plant may contain bacteria that are substantially similar to, or even genetically indistinguishable from, the bacteria that are being applied to the plant. It is noted that, in many cases, the bacteria that are being applied is substantially different from the bacteria already present in several significant ways. First, the bacteria that are being applied to the agricultural plant have been adapted to culture, or adapted to be able to grow on growth media in isolation from the plant. Second, in many cases, the bacteria that are being applied are derived from a clonal origin, rather than from a heterologous origin and, as such, can be distinguished from the bacteria that are already present in the agricultural plant by the clonal similarity. For example, where a microbe that has been inoculated by a plant is also present in the plant (for example, in a different tissue or portion of the plant), or where the introduced microbe is sufficiently similar to a microbe that is present in some of the plants (or portion of the plant, including plant elements), it is still possible to distinguish between the inoculated microbe and the native microbe by distinguishing between the two microbe types on the basis of their epigenetic status (e.g., the bacteria that are applied, as well as their progeny, would be expected to have a much more uniform and similar pattern of cytosine methylation of its genome, with respect to the extent and/or location of methylation).


It is, of course, also possible to provide a coating with additional microorganisms (either the same or different as the endophyte that was inoculated). Therefore, according to another embodiment of the present invention, the obtained plant seed containing microorganisms is therefore subjected to a further seed impregnation step.


Once coated with the endophyte formulation, the seeds can be mixed and allowed to dry before germination occurs.


Endophytes Compatible with Agrichemicals


In certain embodiments, the single endophyte strain or the plurality of endophytes is selected on the basis of its compatibility with commonly used agrichemicals. As mentioned earlier, plants, particularly agricultural plants, can be treated with a vast array of agrichemicals, including fungicides, biocides (anti-complex agents), herbicides, insecticides, nematicides, rodenticides, fertilizers, and other agents.


In some cases, it can be important for the single endophyte strain or the plurality of endophytes to be compatible with agrichemicals, particularly those with anticomplex properties, in order to persist in the plant although, as mentioned earlier, there are many such anticomplex agents that do not penetrate the plant, at least at a concentration sufficient to interfere with the endophytes. Therefore, where a systemic anticomplex agent is used in the plant, compatibility of the endophytes to be inoculated with such agents will be an important criterion.


Fungicides


In some embodiments, the control agent is a fungicide. As used herein, a fungicide is any compound or agent (whether chemical or biological) that can either inhibit the growth of a fungus or kill a fungus. In that sense, a “fungicide”, as used herein, encompasses compounds that may be fungistatic or fungicidal. As used herein, the fungicide can be a protectant, or agents that are effective predominantly on the seed surface, providing protection against seed surface-borne pathogens and providing some level of control of soil-borne pathogens. Non-limiting examples of protectant fungicides include captan, maneb, thiram, or fludioxonil.


The fungicide can be a systemic fungicide, which can be absorbed into the emerging seedling and inhibit or kill the fungus inside host plant tissues. Systemic fungicides used for seed treatment include, but are not limited to the following: azoxystrobin, carboxin, mefenoxam, metalaxyl, thiabendazole, trifloxystrobin, and various triazole fungicides, including difenoconazole, ipconazole, tebuconazole, and triticonazole. Mefenoxam and metalaxyl are primarily used to target the water mold fungi Pythium and Phytophthora. Some fungicides are preferred over others, depending on the plant species, either because of subtle differences in sensitivity of the pathogenic fungal species, or because of the differences in the fungicide distribution or sensitivity of the plants. In some embodiments, the endophyte is compatible with at least one of the fungicides selected from the group consisting of: 2-(thiocyanatomethylthio)-benzothiazole, 2-phenylphenol, 8-hydroxyquinoline sulfate, ametoctradin, amisulbrom, antimycin, Ampelomyces quisqualis, azaconazole, azoxystrobin, Bacillus subtilis, benalaxyl, benomyl, benthiavalicarb-isopropyl, benzylaminobenzene-sulfonate (BABS) salt, bicarbonates, biphenyl, bismerthiazol, bitertanol, bixafen, blasticidin-S, borax, Bordeaux mixture, boscalid, bromuconazole, bupirimate, calcium polysulfide, captafol, captan, carbendazim, carboxin, carpropamid, carvone, chloroneb, chlorothalonil, chlozolinate, Coniothyrium minitans, copper hydroxide, copper octanoate, copper oxychloride, copper sulfate, copper sulfate (tribasic), cuprous oxide, cyazofamid, cyflufenamid, cymoxanil, cyproconazole, cyprodinil, dazomet, debacarb, diammonium ethylenebis-(dithiocarbamate), dichlofluanid, dichlorophen, diclocymet, diclomezine, dichloran, diethofencarb, difenoconazole, difenzoquat ion, diflumetorim, dimethomorph, dimoxystrobin, diniconazole, diniconazole-M, dinobuton, dinocap, diphenylamine, dithianon, dodemorph, dodemorph acetate, dodine, dodine free base, edifenphos, enestrobin, epoxiconazole, ethaboxam, ethoxyquin, etridiazole, famoxadone, fenamidone, fenarimol, fenbuconazole, fenfuram, fenhexamid, fenoxanil, fenpiclonil, fenpropidin, fenpropimorph, fentin, fentin acetate, fentin hydroxide, ferbam, ferimzone, fluazinam, fludioxonil, flumorph, fluopicolide, fluopyram, fluoroimide, fluoxastrobin, fluquinconazole, flusilazole, flusulfamide, flutianil, flutolanil, flutriafol, fluxapyroxad, folpet, formaldehyde, fosetyl, fosetyl-aluminium, fuberidazole, furalaxyl, furametpyr, guazatine, guazatine acetates, GY-81, hexachlorobenzene, hexaconazole, hymexazol, imazalil, imazalil sulfate, imibenconazole, iminoctadine, iminoctadine triacetate, iminoctadine tris(albesilate), ipconazole, iprobenfos, iprodione, iprovalicarb, isoprothiolane, isopyrazam, isotianil, kasugamycin, kasugamycin hydrochloride hydrate, kresoxim-methyl, mancopper, mancozeb, mandipropamid, maneb, mepanipyrim, mepronil, mercuric chloride, mercuric oxide, mercurous chloride, metalaxyl, mefenoxam, metalaxyl-M, metam, metam-ammonium, metam-potassium, metam-sodium, metconazole, methasulfocarb, methyl iodide, methyl isothiocyanate, metiram, metominostrobin, metrafenone, mildiomycin, myclobutanil, nabam, nitrothal-isopropyl, nuarimol, octhilinone, ofurace, oleic acid (fatty acids), orysastrobin, oxadixyl, oxine-copper, oxpoconazole fumarate, oxycarboxin, pefurazoate, penconazole, pencycuron, penflufen, pentachlorophenol, pentachlorophenyl laurate, penthiopyrad, phenylmercury acetate, phosphonic acid, phthalide, picoxystrobin, polyoxin B, polyoxins, polyoxorim, potassium bicarbonate, potassium hydroxyquinoline sulfate, probenazole, prochloraz, procymidone, propamocarb, propamocarb hydrochloride, propiconazole, propineb, proquinazid, prothioconazole, pyraclostrobin, pyrametostrobin, pyraoxystrobin, pyrazophos, pyribencarb, pyributicarb, pyrifenox, pyrimethanil, pyroquilon, quinoclamine, quinoxyfen, quintozene, Reynoutria sachalinensis extract, sedaxane, silthiofam, simeconazole, sodium 2-phenylphenoxide, sodium bicarbonate, sodium pentachlorophenoxide, spiroxamine, sulfur, SYP-Z071, SYP-Z048, tar oils, tebuconazole, tebufloquin, tecnazene, tetraconazole, thiabendazole, thifluzamide, thiophanate-methyl, thiram, tiadinil, tolclofos-methyl, tolylfluanid, triadimefon, triadimenol, triazoxide, tricyclazole, tridemorph, trifloxystrobin, triflumizole, triforine, triticonazole, validamycin, valifenalate, valiphenal, vinclozolin, zineb, ziram, zoxamide, Candida oleophila, Fusarium oxysporum, Gliocladium spp., Phlebiopsis gigantea, Streptomyces griseoviridis, Trichoderma spp., (RS)—N-(3,5-dichlorophenyl)-2-(methoxymethyl)-succinimide, 1,2-dichloropropane, 1,3-dichloro-1,1,3,3-tetrafluoroacetone hydrate, 1-chloro-2,4-dinitronaphthalene, 1-chloro-2-nitropropane, 2-(2-heptadecyl-2-imidazolin-1-yl)ethanol, 2,3-dihydro-5-phenyl-1,4-dithi-ine 1,1,4,4-tetraoxide, 2-methoxyethylmercury acetate, 2-methoxyethylmercury chloride, 2-methoxyethylmercury silicate, 3-(4-chlorophenyl)-5-methylrhodanine, 4-(2-nitroprop-1-enyl)phenyl thiocyanateme, ampropylfos, anilazine, azithiram, barium polysulfide, Bayer 32394, benodanil, benquinox, bentaluron, benzamacril; benzamacril-isobutyl, benzamorf, binapacryl, bis(methylmercury) sulfate, bis(tributyltin) oxide, buthiobate, cadmium calcium copper zinc chromate sulfate, carbamorph, CECA, chlobenthiazone, chloraniformethan, chlorfenazole, chlorquinox, climbazole, cyclafuramid, cypendazole, cyprofuram, decafentin, dichlone, dichlozoline, diclobutrazol, dimethirimol, dinocton, dinosulfon, dinoterbon, dipyrithione, ditalimfos, dodicin, drazoxolon, EBP, ESBP, etaconazole, etem, ethirim, fenaminosulf, fenapanil, fenitropan, 5-fluorocytosine and profungicides thereof, fluotrimazole, furcarbanil, furconazole, furconazole-cis, furmecyclox, furophanate, glyodine, griseofulvin, halacrinate, Hercules 3944, hexylthiofos, ICIA0858, isopamphos, isovaledione, mebenil, mecarbinzid, metazoxolon, methfuroxam, methylmercury dicyandiamide, metsulfovax, milneb, mucochloric anhydride, myclozolin, N-3,5-dichlorophenyl-succinimide, N-3-nitrophenylitaconimide, natamycin, N-ethylmercurio-4-toluenesulfonanilide, nickel bis(dimethyldithiocarbamate), OCH, phenylmercury dimethyldithiocarbamate, phenylmercury nitrate, phosdiphen, picolinamide UK-2A and derivatives thereof, prothiocarb; prothiocarb hydrochloride, pyracarbolid, pyridinitril, pyroxychlor, pyroxyfur, quinacetol; quinacetol sulfate, quinazamid, quinconazole, rabenzazole, salicylanilide, SSF-109, sultropen, tecoram, thiadifluor, thicyofen, thiochlorfenphim, thiophanate, thioquinox, tioxymid, triamiphos, triarimol, triazbutil, trichlamide, urbacid, XRD-563, and zarilamide, IK-1140. In still another embodiment, an endophyte that is compatible with an antibacterial compound is used for the methods described herein. For example, the endophyte is compatible with at least one of the antibiotics selected from the group consisting of: Amikacin, Gentamicin, Kanamycin, Neomycin, Netilmicin, Tobramycin, Paromomycin, Spectinomycin, Geldanamycin, Herbimycin, Rifaximin, streptomycin, Loracarbef, Ertapenem, Doripenem, Imipenem/Cilastatin, Meropenem, Cefadroxil, Cefazolin, Cefalotin or Cefalothin, Cefalexin, Cefaclor, Cefamandole, Cefoxitin, Cefprozil, Cefuroxime, Cefixime, Cefdinir, Cefditoren, Cefoperazone, Cefotaxime, Cefpodoxime, Ceftazidime, Ceftibuten, Ceftizoxime, Ceftriaxone, Cefepime, Ceftaroline fosamil, Ceftobiprole, Teicoplanin, Vancomycin, Telavancin, Clindamycin, Lincomycin, Daptomycin, Azithromycin, Clarithromycin, Dirithromycin, Erythromycin, Roxithromycin, Troleandomycin, Telithromycin, Spiramycin, Aztreonam, Furazolidone, Nitrofurantoin, Linezolid, Posizolid, Radezolid, Torezolid, Amoxicillin, Ampicillin, Azlocillin, Carbenicillin, Cloxacillin, Dicloxacillin, Flucloxacillin, Mezlocillin, Methicillin, Nafcillin, Oxacillin, Penicillin G, Penicillin V, Piperacillin, Penicillin G, Temocillin, Ticarcillin, Amoxicillin/clavulanate, Ampicillin/sulbactam, Piperacillin/tazobactam, Ticarcillin/clavulanate, Bacitracin, Colistin, Polymyxin B, Ciprofloxacin, Enoxacin, Gatifloxacin, Levofloxacin, Lomefloxacin, Moxifloxacin, Nalidixic acid, Norfloxacin, Ofloxacin, Trovafloxacin, Grepafloxacin, Sparfloxacin, Temafloxacin, Mafenide, Sulfacetamide, Sulfadiazine, Silver sulfadiazine, Sulfadimethoxine, Sulfamethizole, Sulfamethoxazole, Sulfanilimide (archaic), Sulfasalazine, Sulfisoxazole, Trimethoprim-Sulfamethoxazole (Co-trimoxazole) (TMP-SMX), Sulfonamidochrysoidine (archaic), Demeclocycline, Doxycycline, Minocycline, Oxytetracycline, Tetracycline, Clofazimine, Dapsone, Capreomycin, Cycloserine, Ethambutol, Ethionamide, Isoniazid, Pyrazinamide, Rifampicin (Rifampin in US), Rifabutin, Rifapentine, Streptomycin, Arsphenamine, Chloramphenicol, Fosfomycin, Fusidic acid, Metronidazole, Mupirocin, Platensimycin, Quinupristin/Dalfopristin, Thiamphenicol, Tigecycline, Tinidazole, and Trimethoprim.


A fungicide can be a biological control agent, such as a bacterium or fungus. Such organisms may be parasitic to the pathogenic fungi, or secrete toxins or other substances which can kill or otherwise prevent the growth of fungi. Any type of fungicide, particularly ones that are commonly used on plants, can be used as a control agent in a seed composition.


Antibacterial Agents


In some cases, the seed coating composition comprises a control agent which has antibacterial properties. In some embodiments, the control agent with antibacterial properties is selected from the compounds described herein elsewhere. In other embodiments, the compound is Streptomycin, oxytetracycline, oxolinic acid, or gentamicin.


Plant Growth Regulators


The seed coat composition can further comprise a plant growth regulator. In some embodiments, the plant growth regulator is selected from the group consisting of: Abscisic acid, amidochlor, ancymidol, 6-benzylaminopurine, brassinolide, butralin, chlormequat (chlormequat chloride), choline chloride, cyclanilide, daminozide, dikegulac, dimethipin, 2,6-dimethylpuridine, ethephon, flumetralin, flurprimidol, fluthiacet, forchlorfenuron, gibberellic acid, inabenfide, indole-3-acetic acid, maleic hydrazide, mefluidide, mepiquat (mepiquat chloride), naphthaleneacetic acid, N-6-benzyladenine, paclobutrazol, prohexadione (prohexadione—calcium), prohydrojasmon, thidiazuron, triapenthenol, tributyl phosphorotrithioate, 2,3,5-tri-iodobenzoic acid, trinexapac-ethyl and uniconazole. Other examples of antibacterial compounds which can be used as part of a seed coating composition include those based on dichlorophene and benzylalcohol hemi formal (Proxel® from ICI or Acticide® RS from Thor Chemie and Kathon® MK from Rohm & Haas) and isothiazolinone derivatives such as alkylisothiazolinones and benzisothiazolinones (Acticide® MBS from Thor Chemie). Other plant growth regulators that can be incorporated seed coating compositions are described in US 2012/0108431, which is incorporated by reference in its entirety.


Nematicides


Preferred nematode-antagonistic biocontrol agents include ARF18; Arthrobotrys spp.; Chaetomium spp.; Cylindrocarpon spp.; Exophilia spp.; Fusarium spp.; Gliocladium spp.; Hirsutella spp.; Lecanicillium spp.; Monacrosporium spp.; Myrothecium spp.; Neocosmospora spp.; Paecilomyces spp.; Pochonia spp.; Stagonospora spp.; vesicular-arbuscular mycorrhizal fungi, Burkholderia spp.; Pasteuria spp., Brevibacillus spp.; Pseudomonas spp.; and Rhizobacteria. Particularly preferred nematode-antagonistic biocontrol agents include ARF18, Arthrobotrys oligospora, Arthrobotrys dactyloides, Chaetomium globosum, Cylindrocarpon heteronema, Exophilia jeanselmei, Exophilia pisciphila, Fusarium aspergilus, Fusarium solani, Gliocladium catenulatum, Gliocladium roseum, Gliocladium virens, Hirsutella rhossiliensis, Hirsutella minnesotensis, Lecanicillium lecanii, Monacrosporium drechsleri, Monacrosporium gephyropagum, Myrotehcium verrucaria, Neocosmospora vasinfecta, Paecilomyces lilacinus, Pochonia chlamydosporia, Stagonospora heteroderae, Stagonospora phaseoli, vesicular-arbuscular mycorrhizal fungi, Burkholderia cepacia, Pasteuria penetrans, Pasteuria thornei, Pasteuria nishizawae, Pasteuria ramosa, Pastrueia usage, Brevibacillus laterosporus strain G4, Pseudomonas fluorescens and Rhizobacteria.


Nutrients


In other embodiments, the seed coating composition can comprise a nutrient. The nutrient can be selected from the group consisting of a nitrogen fertilizer including, but not limited to Urea, Ammonium nitrate, Ammonium sulfate, Non-pressure nitrogen solutions, Aqua ammonia, Anhydrous ammonia, Ammonium thiosulfate, Sulfur-coated urea, Urea-formaldehydes, IBDU, Polymer-coated urea, Calcium nitrate, Ureaform, and Methylene urea, phosphorous fertilizers such as Diammonium phosphate, Monoammonium phosphate, Ammonium polyphosphate, Concentrated superphosphate and Triple superphosphate, and potassium fertilizers such as Potassium chloride, Potassium sulfate, Potassium-magnesium sulfate, Potassium nitrate. Such compositions can exist as free salts or ions within the seed coat composition. Alternatively, nutrients/fertilizers can be complexed or chelated to provide sustained release over time.


Rodenticides


Rodents such as mice and rats cause considerable economical damage by eating and soiling planted or stored seeds. Moreover, mice and rats transmit a large number of infectious diseases such as plague, typhoid, leptospirosis, trichinosis and salmonellosis. Anticoagulants such as coumarin and indandione derivatives play an important role in the control of rodents. These active ingredients are simple to handle, relatively harmless to humans and have the advantage that, as the result of the delayed onset of the activity, the animals being controlled identify no connection with the bait that they have ingested, therefore do not avoid it. This is an important aspect in particular in social animals such as rats, where individuals act as tasters. In some embodiments, the seed coating composition comprises a rodenticide selected from the group of substances consisting of 2-isovalerylindan-1,3-dione, 4-(quinoxalin-2-ylamino)benzenesulfonamide, alpha-chlorohydrin, aluminum phosphide, antu, arsenous oxide, barium carbonate, bisthiosemi, brodifacoum, bromadiolone, bromethalin, calcium cyanide, chloralose, chlorophacinone, cholecalciferol, coumachlor, coumafuryl, coumatetralyl, crimidine, difenacoum, difethialone, diphacinone, ergocalciferol, flocoumafen, fluoroacetamide, flupropadine, flupropadine hydrochloride, hydrogen cyanide, iodomethane, lindane, magnesium phosphide, methyl bromide, norbormide, phosacetim, phosphine, phosphorus, pindone, potassium arsenite, pyrinuron, scilliroside, sodium arsenite, sodium cyanide, sodium fluoroacetate, strychnine, thallium sulfate, warfarin and zinc phosphide.


Compatibility


In some embodiments, a single endophyte strain or a plurality of endophytes that are compatible with agrichemicals can be used to inoculate the plants according to the methods described herein. In each case below, each single endophyte strain or each type of endophyte used in a plurality of endophytes can be tested for compatibility on their own or as the plurality. Endophytes that are compatible with agriculturally employed anticomplex agents can be isolated by plating a culture of endophytes on a petri dish comprising an effective concentration of the anticomplex agent, and isolating colonies of endophytes that are compatible with the anticomplex agent. In other embodiments, a plurality of endophytes that are compatible with an anticomplex agent are used for the methods described herein.


In some embodiments, the endophytes of the present invention display tolerance to an agrichemical selected from the group consisting of: Aeris®, Avicta® DuoCot 202, Cruiser®, Syntenta CCB® (A), Clariva®, Albaugh, Dynasty®, Apron®, Maxim®, Gaucho®, Provoke® ST, Syngenta CCB®, Trilex®, WG Purple, WG Silver, Azoxystrobin, Carboxin, Difenoconazole, Fludioxonil, fluxapyroxad, Ipconazole, Mefenoxam, Metalaxyl, Myclobutanil, Penflufen, pyraclostrobin, Sedaxane, TCMTB, Tebuconazole, Thiram, Triadimenol (Baytan®), Trifloxystrobin, Triticonazole, Tolclofos-methyl, PCNB, Abamectin, Chlorpyrifos, Clothianidin, Imidacloprid, Thiamethoxam, and Thiodicarb.


Bactericide-compatible endophytes can also be isolated by selection on liquid medium. The culture of endophytes can be plated on petri dishes without any forms of mutagenesis; alternatively, endophytes can be mutagenized using any means known in the art. For example, endophyte cultures can be exposed to UV light, gamma-irradiation, or chemical mutagens such as ethylmethanesulfonate (EMS), ethidium bromide (EtBr) dichlovos (DDVP, methyl methane sulphonale (MMS), triethylphosphate (TEP), trimethylphosphate (TMP), nitrous acid, or DNA base analogs, prior to selection on fungicide comprising media. Finally, where the mechanism of action of a particular bactericide is known, the target gene can be specifically mutated (either by gene deletion, gene replacement, site-directed mutagenesis, etc.) to generate a plurality of endophytes that are resilient against that particular chemical. It is noted that the above-described methods can be used to isolate endophytes that are compatible with both bacteriostatic and bactericidal compounds.


It will also be appreciated by one skilled in the art that a plant may be exposed to multiple types of anticomplex compounds, either simultaneously or in succession, for example at different stages of plant growth. Where the target plant is likely to be exposed to multiple anticomplex agents, a plurality of endophytes that are compatible with many or all of these agrichemicals can be used to inoculate the plant. Endophytes that are compatible with several agents can be isolated, for example, by serial selection. Endophytes that are compatible with the first agent can be isolated as described above (with or without prior mutagenesis). A culture of the resulting endophytes can then be selected for the ability to grow on liquid or solid media comprising the second agent (again, with or without prior mutagenesis). Colonies isolated from the second selection are then tested to confirm its compatibility to both agents.


Likewise, endophytes that are compatible to biocides (including herbicides such as glyphosate or anticomplex compounds, whether bacteriostatic or bactericidal) that are agriculturally employed can be isolated using methods similar to those described for isolating compatible endophytes. In some embodiments, mutagenesis of the endophytes can be performed prior to selection with an anticomplex agent. In other embodiments, selection is performed on the endophytes without prior mutagenesis. In still another embodiment, serial selection is performed on endophytes: the endophytes are first selected for compatibility to a first anticomplex agent. The isolated compatible endophytes are then cultured and selected for compatibility to the second anticomplex agent. Any colony thus isolated is tested for compatibility to each, or both anticomplex agents to confirm compatibility with these two agents.


Compatibility with an antimicrobial agent can be determined by a number of means known in the art, including the comparison of the minimal inhibitory concentration (MIC) of the unmodified and modified endophytes. Therefore, in some embodiments, the present invention discloses modified endophytes, wherein the endophytes are modified such that they exhibits at least 3 fold greater, for example, at least 5 fold greater, between 5 and 10 fold greater, at least 10 fold greater, between 10 and 20 fold greater, at least 20 fold greater, between 20 and 30 fold greater, at least 30 fold greater or more MIC to an antimicrobial agent when compared with the unmodified endophytes.


In some embodiments, disclosed herein are endophytes with enhanced compatibility to the herbicide glyphosate. In some embodiments, the endophytes have a doubling time in growth medium comprising least 1 mM glyphosate, for example, between 1 mM and 2 mM glyphosate, at least 2 mM glyphosate, between 2 mM and 5 mM glyphosate, at least 5 mM glyphosate, between 5 mM and 10 mM glyphosate, at least 10 mM glyphosate, between 10 mM and 15 mM glyphosate, at least 15 mM glyphosate or more, that is no more than 250%, between 250% and 100%, for example, no more than 200%, between 200% and 175%, no more than 175%, between 175% and 150%, no more than 150%, between 150% and 125%, or no more than 125%, of the doubling time of the endophytes in the same growth medium comprising no glyphosate. In some embodiments, the endophytes have a doubling time in growth medium comprising 5 mM glyphosate that is no more than 150% the doubling time of the endophytes in the same growth medium comprising no glyphosate.


In other embodiments, the endophytes have a doubling time in a plant tissue comprising at least 10 ppm glyphosate, for example, between 10 and 15 ppm, at least 15 ppm glyphosate, between 15 and 10 ppm, at least 20 ppm glyphosate, between 20 and 30 ppm, at least 30 ppm glyphosate, between 30 and 40 ppm, at least 40 ppm glyphosate or more, that is no more than 250%, between 250% and 200%, for example, no more than 200%, between 200% and 175%, no more than 175%, between 175% and 150%, no more than 150%, between 150% and 125%, of the doubling time of the endophytes in a reference plant tissue comprising no glyphosate. In some embodiments, the endophytes have a doubling time in a plant tissue comprising 40 ppm glyphosate that is no more than 150% the doubling time of the endophytes in a reference plant tissue comprising no glyphosate.


The selection process described above can be repeated to identify isolates of endophytes that are compatible with a multitude of agents.


Candidate isolates can be tested to ensure that the selection for agrichemical compatibility did not result in loss of a desired bioactivity. Isolates of endophytes that are compatible with commonly employed agents can be selected as described above. The resulting compatible endophytes can be compared with the parental endophytes on plants in its ability to promote germination.


The agrichemical compatible endophytes generated as described above can be detected in samples. For example, where a transgene was introduced to render the endophytes compatible with the agrichemical(s), the transgene can be used as a target gene for amplification and detection by PCR. In addition, where point mutations or deletions to a portion of a specific gene or a number of genes results in compatibility with the agrichemical(s), the unique point mutations can likewise be detected by PCR or other means known in the art. Such methods allow the detection of the endophytes even if they is no longer viable. Thus, commodity plant products produced using the agrichemical compatible endophytes described herein can readily be identified by employing these and related methods of nucleic acid detection.


Populations of Plant Elements


The synthetic combinations of the present invention may be confined within an object selected from the group consisting of: bottle, jar, ampule, package, vessel, bag, box, bin, envelope, carton, container, silo, shipping container, truck bed, and case. In a particular embodiment, the population of plant elements is packaged in a bag or container suitable for commercial sale. For example, a bag contains a unit weight or count of the plant elements comprising a plurality of endophytes as described herein, and further comprises a label. In one embodiment, the bag or container contains at least 100 plant elements, between 100 and 1,000 plant elements, 1,000 plant elements, between 1,000 and 5,000 plant elements, for example, at least 5,000 plant elements, between 5,000 and 10,000 plant elements, at least 10,000 plant elements, between 10,000 and 20,000 plant elements, at least 20,000 plant elements, between 20,000 and 30,000 plant elements, at least 30,000 plant elements, between 30,000 and 50,000 plant elements, at least 50,000 plant elements, between 50,000 and 70,000 plant elements, at least 70,000 plant elements, between 70,000 and 80,000 plant elements, at least 80,000 plant elements, between 80,000 and 90,000, at least 90,000 plant elements or more. In another embodiment, the bag or container can comprise a discrete weight of plant elements, for example, at least 1 lb, between 1 and 2 lbs, at least 2 lbs, between 2 and 5 lbs, at least 5 lbs, between 5 and 10 lbs, at least 10 lbs, between 10 and 30 lbs, at least 30 lbs, between 30 and 50 lbs, at least 50 lbs, between 50 and 70 lmbs, at least 70 lbs or more. The label can contain additional information, for example, the information selected from the group consisting of: net weight, lot number, geographic origin of the plant elements, test date, germination rate, inert matter content, and the amount of noxious weeds, if any. Suitable containers or packages include those traditionally used in plant plant element commercialization. The invention also contemplates other containers with more sophisticated storage capabilities (e.g., with microbiologically tight wrappings or with gas- or water-proof containments).


In some cases, a sub-population of plant elements comprising a plurality of endophytes is further selected on the basis of increased uniformity, for example, on the basis of uniformity of microbial population. For example, individual plant elements of pools collected from individual cobs, individual plants, individual plots (representing plants inoculated on the same day) or individual fields can be tested for uniformity of microbial density, and only those pools meeting specifications (e.g., at least 80% of tested plant elements have minimum density, as determined by quantitative methods described elsewhere) are combined to provide the agricultural plant element sub-population.


The methods described herein can also comprise a validating step. The validating step can entail, for example, growing some plant elements collected from the inoculated plants into mature agricultural plants, and testing those individual plants for uniformity. Such validating step can be performed on individual plant elements collected from cobs, individual plants, individual plots (representing plants inoculated on the same day) or individual fields, and tested as described above to identify pools meeting the required specifications.


In some embodiments, methods described herein include planting a synthetic composition described herein. Suitable planters include an air seeder and/or fertilizer apparatus used in agricultural operations to apply particulate materials including one or more of the following, seed, fertilizer and/or inoculants, into soil during the planting operation. Seeder/fertilizer devices can include a tool bar having ground-engaging openers thereon, behind which is towed a wheeled cart that includes one or more containment tanks or bins and associated metering means to respectively contain and meter therefrom particulate materials.


In certain embodiments, a composition described herein may be in the form of a liquid, a slurry, a solid, or a powder (wettable powder or dry powder). In another embodiment, a composition may be in the form of a seed coating. Compositions in liquid, slurry, or powder (e.g., wettable powder) form may be suitable for coating plant elements. When used to coat plant elements, the composition may be applied to the plant elements and allowed to dry. In embodiments wherein the composition is a powder (e.g., a wettable powder), a liquid, such as water, may need to be added to the powder before application to a seed.


In still another embodiment, the methods can include introducing into the soil an inoculum of one or more of the endophyte populations described herein. Such methods can include introducing into the soil one or more of the compositions described herein. The inoculum(s) or compositions may be introduced into the soil according to methods known to those skilled in the art. Non-limiting examples include in-furrow introduction, spraying, coating seeds, foliar introduction, etc. In a particular embodiment, the introducing step comprises in-furrow introduction of the inoculum or compositions described herein.


In one embodiment, plant elements may be treated with composition(s) described herein in several ways but preferably via spraying or dripping. Spray and drip treatment may be conducted by formulating compositions described herein and spraying or dripping the composition(s) onto a seed(s) via a continuous treating system (which is calibrated to apply treatment at a predefined rate in proportion to the continuous flow of seed), such as a drum-type of treater. Batch systems, in which a predetermined batch size of seed and composition(s) as described herein are delivered into a mixer, may also be employed.


In another embodiment, the treatment entails coating plant elements. One such process involves coating the inside wall of a round container with the composition(s) described herein, adding plant elements, then rotating the container to cause the plant elements to contact the wall and the composition(s), a process known in the art as “container coating”. Plant elements can be coated by combinations of coating methods. Soaking typically entails using liquid forms of the compositions described. For example, plant elements can be soaked for about 1 minute to about 24 hours (e.g., for at least 1 min, between 1 and 5 min, 5 min, between 5 and 10 min, 10 min, between 10 and 20 min, 20 min, between 20 and 40 min, 40 min, between 40 and 80 min, 80 min, between 80 min and 3 hrs, 3 hrs, between 3 hrs and 6 hrs, 6 hr, between 6 hrs and 12 hrs, 12 hr, between 12 hrs and 24 hrs, or at least 24 hrs).


Throughout the specification, the word “comprise,” or variations such as “comprises” or “comprising,” will be understood to imply the inclusion of a stated integer or group of integers but not the exclusion of any other integer or group of integers.


Although the present invention has been described in detail with reference to examples below, it is understood that various modifications can be made without departing from the spirit of the invention. For instance, while the particular examples below may illustrate the methods and embodiments described herein using a specific plant, the principles in these examples may be applied to any agricultural crop. Therefore, it will be appreciated that the scope of this invention is encompassed by the embodiments of the inventions recited herein and the specification rather than the specific examples that are exemplified below.


EXAMPLES
Example 1: Cultivation-Independent Analysis of Microbial Taxa in Agriculturally Relevant Seed Communities Based on Marker Gene High-Throughput Sequencing

Example Description


Microbial taxa found in agriculturally relevant communities were identified using high-throughput marker gene sequencing across several crops and numerous varieties of seeds.


Experimental Description


To identify core (i.e. ubiquitous) microbial taxa across seeds, we used high-throughput sequencing of marker genes for bacteria, archaea, and fungi.


Cereals


2 inbred, 10 landrace, 4 teosinte corn seeds, and 4 modern and 4 wild wheat seeds were obtained. Accessions were categorized into landrace, wild, and inbred varieties based on their assessment of improvement status. In order to extract microbial DNA, the seeds were first sterilized in one of four different manners. Some of the seeds were surface sterilized using 95% ethanol to reduce superficial contaminant microbes, then rinsed in water. Others were first soaked in sterile, DNA-free water for 48 hours to soften them, and they were surface sterilized using 95% ethanol to reduce superficial contaminant microbes, then rinsed in water. Others were rinsed in deionized water, immersed in 95% ethanol for 5 seconds, 0.5% NaOCl for 2 minutes, 70% ethanol for 2 minutes, and then washed three times in deionized water for 1 minute each.


Grasslands


To identify microbial taxa from seeds of wild grassland plants, we used high-throughput sequencing of marker genes for bacteria, archaea, and fungi. Seeds from the following wild grassland species were obtained: Big bluestem, Side oats grama, Bicknell's sedge, Short beak sedge, Canada wild rye, Virginia wild rye, June grass, Leafy satin grass, Switch grass, Little bluestem, Prairie cord grass, Prairie dropseed, Nodding wild onion, Meadow/Canada anemone, Common milkweed, Butterfly weed, Whorled milkweed, New England aster, False boneset, Tall coreopsis, Shooting star, Pale purple coneflower, Rattlesnake master, Tall boneset, Purple joe pye weed, Biennial gaure, Prairie smoke, False sunflower, Rough blazing star, Wild bergamot, Horse mint, Common evening primrose, Wild quinine, Beardtongue, Yellow coneflower, Black-eyed Susan, Sweet black-eyed susan, Compass plant, Prairie dock, Stiff goldenrod, Showy goldenrod, Hairy aster, Hoary vervain, Culver's root, Golden alexanders, Dogtooth daisy, Wild blue iris, Pointed broom sedge, Dark green bulrush, and Blue vervain. In order to extract microbial DNA, the seeds were first soaked in sterile, DNA-free water for 48 h to soften them, and they were surface sterilized using 95% ethanol to reduce superficial contaminant microbes, then rinsed in water.


Fruits and Vegetables


Seeds from 22 different varieties of cabbage were obtained, including broccoli, cauliflower, and collards. In addition, seeds from 8 different varieties of lettuce, 9 varieties of melon (including cantaloupe and honeydew), 7 varieties of onions (including cippolini, shallots, and vidalia), 4 varieties of tomatoes, one variety of toria, 4 varieties of turnip, 7 varieties of watermelon, and one variety of yellow sarcon were obtained. For strawberries, the seeds or runner plant tissue of 9 varieties were obtained. For sterilization, the seeds were first soaked in sterile, DNA-free water for 48 h to soften them, and they were surface sterilized using 95% ethanol to reduce superficial contaminant microbes, then rinsed in water. Strawberry tissue was surface sterilized using 95% ethanol, then rinsed in water.


Oilseed


Seeds from 1 wild and 3 modern cultivars of Brassica Napus were also obtained. In order to extract microbial DNA, the seeds were first soaked in sterile, DNA-free water for 48 h to soften them, and they were surface sterilized using 95% ethanol to reduce superficial contaminant microbes, then rinsed in water.


The seeds or tissues from all of the plants described above were then ground using a mortar and pestle treated with 95% ethanol and RNAse Away (Life Technologies, Inc., Grand Island, N.Y.) to remove contaminant DNA. DNA was extracted from the ground seeds using the PowerPlant Pro DNA extraction kit (Mo Bio Laboratories, Inc., Carlsbad, Calif.) according to the manufacturer's instructions. The surface wash off from certain sterilization treatments of cereal seeds was also collected and DNA was extracted as above.


Marker genes were amplified and sequenced from the extracted DNA. For the bacterial and archaeal analyses, the V4 hypervariable region of the 16S rRNA gene was targeted (primers 515f/806r), and for fungi, the first internal transcribed spacer (ITS1) region of the rRNA operon (primers ITS1f/ITS2r) was targeted. The two marker genes were PCR amplified separately using 35 cycles, and error-correcting 12-bp barcoded primers specific to each sample were used to facilitate combining of samples. To reduce the amplification of chloroplast and mitochondrial DNA, PNA clamps specific to the rRNA genes in these organelles were used. PCR reactions to amplify 16S rRNA genes followed the protocol of (Lundberg et al. 2013), and those to amplify ITS regions followed the protocol of (Fierer et al. 2012). PCR products were quantified using the PicoGreen assay (Life Technologies, Inc., Grand Island, N.Y.), pooled in equimolar concentrations, and cleaned using the UltraClean kit (Mo Bio Laboratories, Inc., Carlsbad, Calif.). Cleaned DNA pools were sequenced on an Illumina MiSeq instrument at the University of Colorado Next Generation Sequencing Facility.


OTU Assignment


For both 16S rRNA and ITS1 sequences, the raw sequence data were reassigned to distinct samples using a custom Python script, and quality filtering and OTU (i.e. operational taxonomic unit) clustering was conducted using the UPARSE pipeline (Edgar 2013). Briefly, a de novo sequence database with representative sequences for each OTU was created using a 97% similarity threshold, and raw reads were mapped to this database to calculate sequence counts per OTU per sample. Prior to creating the database, sequences were quality filtered using an expected error frequency threshold of 0.5 errors per sequence. In addition, sequences were dereplicated and singletons were removed prior to creating the database. OTUs were provided taxonomic classifications using the RDP classifier (Wang et al. 2007) trained with the Greengenes (McDonald et al. 2012) and UNITE (Abarenkov et al. 2010) databases for 16S rRNA and ITS sequences, respectively. To account for differences in the variable number of sequences per sample, each sample was rarefied to 1000 16S rRNA and 1000 ITS sequences per sample. OTUs classified as chloroplasts or mitochondria were discarded prior to rarefaction.


Overall differences in bacterial community composition between the control and inoculated plants were evaluated using non-metric multidimensional scaling based on Bray-Curtis dissimilarities in order to visualize pairwise differences between sample communities. Permutational analysis of variance (PERMANOVA) was used to statistically test the significance of these differences. Analyses were conducted using the vegan package in R (R Core Team 2013). To determine the OTUs contributing to overall differences among crop types, mean relative abundances were calculated for each OTU within each crop type. Only OTUs with a mean relative abundance of 0.1% in either group were included in this analysis.


Results


Across seeds from all plants analyzed herein, a total of 144 bacterial and 145 fungal OTUs were detected and evaluated (Table 3 and Table 4) following stringent sequence quality filtering approach. Among all OTUs, 28 bacterial OTUs and 20 fungal OTUs were found to be core taxa within seeds across plants (Table 1 and Table 2).









TABLE 3







Exemplary bacterial endophytes present in all plants.















SEQ









ID


OTU_ID
NO
Phylum
Class
Order
Family
Genus
Species

















OTU_558
1
OD1
ABY1

















OTU_762
2
Actinobacteria
Actinobacteria
Actinomycetales
Microbacteriaceae














OTU_136
3
Actinobacteria
Actinobacteria
Actinomycetales
Streptomycetaceae

Streptomyces



OTU_161
4
Actinobacteria
Actinobacteria
Actinomycetales
Corynebacteriaceae

Corynebacterium



OTU_309
5
Actinobacteria
Actinobacteria
Actinomycetales
Corynebacteriaceae

Corynebacterium














OTU_63
6
Actinobacteria
Actinobacteria
Actinomycetales
Geodermatophilaceae














OTU_67
7
Actinobacteria
Actinobacteria
Actinomycetales
Sanguibacteraceae

Sanguibacter















OTU_1203
8
Actinobacteria
Actinobacteria
Actinomycetales
Microbacteriaceae

Rathayibacter


caricis



OTU_364
9
Actinobacteria
Actinobacteria
Actinomycetales
Micrococcaceae

Microbispora


rosea



OTU_130
10
Actinobacteria
Actinobacteria
Actinomycetales
Nocardiaceae

Rhodococcus


fascians



OTU_74
11
Actinobacteria
Actinobacteria
Actinomycetales
Kineosporiaceae

Kineococcus














OTU_41
12
Actinobacteria
Actinobacteria
Actinomycetales
Microbacteriaceae



OTU_24
13
Actinobacteria
Actinobacteria
Actinomycetales
Microbacteriaceae


OTU_1230
14
Proteobacteria
Alphaproteobacteria
Sphingomonadales
Sphingomonadaceae














OTU_30
15
Proteobacteria
Alphaproteobacteria
Caulobacterales
Caulobacteraceae

Mycoplana















OTU_799
16
Proteobacteria
Alphaproteobacteria
Rhizobiales
Rhizobiaceae

Agrobacterium














OTU_101
17
Proteobacteria
Alphaproteobacteria
Rhizobiales
Aurantimonadaceae














OTU_572
18
Proteobacteria
Alphaproteobacteria
Rhizobiales
Phyllobacteriaceae

Mesorhizobium















OTU_153
19
Proteobacteria
Alphaproteobacteria
Rhizobiales
Hyphomicrobiaceae

Devosia















OTU_140
20
Proteobacteria
Alphaproteobacteria
Sphingomonadales
Sphingomonadaceae

Sphingomonas














OTU_194
21
Proteobacteria
Alphaproteobacteria
Rhizobiales
Methylocystaceae



OTU_158
22
Proteobacteria
Alphaproteobacteria
Caulobacterales
Caulobacteraceae














OTU_124
23
Proteobacteria
Alphaproteobacteria
Sphingomonadales
Sphingomonadaceae

Sphingomonas


wittichii














OTU_188
24
Proteobacteria
Alphaproteobacteria
Rhodospirillales
Acetobacteraceae














OTU_1287
25
Proteobacteria
Alphaproteobacteria
Sphingomonadales
Sphingomonadaceae

Novosphingobium



OTU_971
26
Proteobacteria
Alphaproteobacteria
Rhodobacterales
Rhodobacteraceae

Rhodobacter














OTU_20
27
Proteobacteria
Alphaproteobacteria
Rhizobiales
Aurantimonadaceae














OTU_57
28
Proteobacteria
Alphaproteobacteria
Sphingomonadales
Sphingomonadaceae

Novosphingobium














OTU_49
29
Proteobacteria
Alphaproteobacteria
Rhizobiales
Methylobacteriaceae














OTU_1222
30
Proteobacteria
Alphaproteobacteria
Sphingomonadales
Sphingomonadaceae

Sphingomonas



OTU_80
31
Proteobacteria
Alphaproteobacteria
Sphingomonadales
Sphingomonadaceae

Sphingomonas



OTU_436
32
Proteobacteria
Alphaproteobacteria
Sphingomonadales
Sphingomonadaceae

Sphingomonas















OTU_1077
33
Proteobacteria
Alphaproteobacteria
Rhizobiales
Methylobacteriaceae

Methylobacterium


adhaesivum














OTU_510
34
Proteobacteria
Alphaproteobacteria
Rhodospirillales
Rhodospirillaceae

Azospirillum















OTU_43
35
Proteobacteria
Alphaproteobacteria
Rhizobiales
Methylobacteriaceae

Methylobacterium


adhaesivum














OTU_65
36
Proteobacteria
Alphaproteobacteria
Rhodospirillales
Acetobacteraceae















OTU_64
37
Proteobacteria
Alphaproteobacteria
Sphingomonadales
Sphingomonadaceae

Sphingomonas


wittichii














OTU_27
38
Proteobacteria
Alphaproteobacteria
Sphingomonadales
Sphingomonadaceae

Sphingomonas



OTU_47
39
Proteobacteria
Alphaproteobacteria
Rhizobiales
Methylobacteriaceae

Methylobacterium



OTU_15
40
Proteobacteria
Alphaproteobacteria
Rhizobiales
Rhizobiaceae

Agrobacterium















OTU_956
41
Proteobacteria
Alphaproteobacteria
Rhizobiales
Methylobacteriaceae

Methylobacterium


adhaesivum














OTU_21
42
Proteobacteria
Alphaproteobacteria
Rhizobiales
Methylobacteriaceae

Methylobacterium



OTU_14
43
Proteobacteria
Alphaproteobacteria
Sphingomonadales
Sphingomonadaceae

Sphingomonas



OTU_6
44
Proteobacteria
Alphaproteobacteria
Sphingomonadales
Sphingomonadaceae

Sphingomonas



OTU_1436
45
Proteobacteria
Alphaproteobacteria
Sphingomonadales
Sphingomonadaceae

Sphingomonas



OTU_61
46
Firmicutes
Bacilli
Bacillales
Paenibacillaceae

Paenibacillus















OTU_77
47
Firmicutes
Bacilli
Lactobacillales
Leuconostocaceae

Leuconostoc




OTU_358
48
Firmicutes
Bacilli
Bacillales
Bacillaceae

Bacillus


badius














OTU_353
49
Firmicutes
Bacilli
Bacillales
Paenibacillaceae

Paenibacillus















OTU_1250
50
Firmicutes
Bacilli
Bacillales
Planococcaceae

Sporosarcina


ginsengi



OTU_84
51
Firmicutes
Bacilli
Bacillales
Bacillaceae


OTU_34
52
Firmicutes
Bacilli
Bacillales
Bacillaceae

Bacillus


cereus














OTU_98
53
Firmicutes
Bacilli
Bacillales
Paenibacillaceae

Paenibacillus



OTU_152
54
Firmicutes
Bacilli
Bacillales
Paenibacillaceae

Paenibacillus



OTU_1178
55
Firmicutes
Bacilli
Bacillales
Planococcaceae

Planomicrobium















OTU_299
56
Firmicutes
Bacilli
Lactobacillales
Leuconostocaceae

Leuconostoc















OTU_241
57
Firmicutes
Bacilli
Lactobacillales
Carnobacteriaceae

Carnobacterium















OTU_203
58
Firmicutes
Bacilli
Lactobacillales
Streptococcaceae

Lactococcus















OTU_25
59
Firmicutes
Bacilli
Bacillales
Paenibacillaceae















OTU_17
60
Firmicutes
Bacilli
Bacillales
Bacillaceae

Bacillus















OTU_330
61
Firmicutes
Bacilli
Lactobacillales
Lactobacillaceae














OTU_211
62
Firmicutes
Bacilli
Lactobacillales
Enterococcaceae

Enterococcus



OTU_108
63
Firmicutes
Bacilli
Bacillales
Staphylococcaceae

Staphylococcus















OTU_19
64
Firmicutes
Bacilli
Bacillales
Paenibacillaceae

Paenibacillus


amylolyticus














OTU_16
65
Firmicutes
Bacilli
Bacillales
[Exiguobacteraceae]

Exiguobacterium















OTU_372
66
Firmicutes
Bacilli
Bacillales
Sporolactobacillaceae

Bacillus


racemilacticus



OTU_222
67
Firmicutes
Bacilli
Bacillales
Bacillaceae

Geobacillus



OTU_653
68
Firmicutes
Bacilli
Bacillales
Bacillaceae

Bacillus


endophyticus














OTU_11
69
Firmicutes
Bacilli
Bacillales
Paenibacillaceae

Paenibacillus















OTU_71
70
Firmicutes
Bacilli
Bacillales
Paenibacillaceae

Saccharibacillus


kuerlensis



OTU_13
71
Firmicutes
Bacilli
Bacillales
Bacillaceae

Bacillus


flexus



OTU_10
72
Firmicutes
Bacilli
Bacillales
Planococcaceae

Sporosarcina


ginsengi














OTU_118
73
Proteobacteria
Betaproteobacteria
Burkholderiales
Comamonadaceae

Comamonas



OTU_676
74
Proteobacteria
Betaproteobacteria
Burkholderiales
Comamonadaceae

Limnohabitans



OTU_1014
75
Proteobacteria
Betaproteobacteria
Burkholderiales
Oxalobacteraceae

Janthinobacterium














OTU_26
76
Proteobacteria
Betaproteobacteria
Burkholderiales
Oxalobacteraceae














OTU_182
77
Proteobacteria
Betaproteobacteria
Burkholderiales
Alcaligenaceae

Pigmentiphaga















OTU_980
78
Proteobacteria
Betaproteobacteria
Burkholderiales
Oxalobacteraceae

Janthinobacterium


lividum














OTU_35
79
Proteobacteria
Betaproteobacteria
Burkholderiales
Comamonadaceae

Polaromonas














OTU_1226
80
Proteobacteria
Betaproteobacteria
Burkholderiales
Comamonadaceae



OTU_1068
81
Proteobacteria
Betaproteobacteria
Burkholderiales
Oxalobacteraceae


OTU_1252
82
Proteobacteria
Betaproteobacteria
Burkholderiales
Comamonadaceae













OTU_113
83
Proteobacteria
Betaproteobacteria
Burkholderiales
Oxalobacteraceae

Janthinobacterium














OTU_39
84
Proteobacteria
Betaproteobacteria
Burkholderiales
Comamonadaceae















OTU_345
85
Proteobacteria
Betaproteobacteria
Burkholderiales
Oxalobacteraceae

Ralstonia















OTU_168
86
Proteobacteria
Betaproteobacteria
Burkholderiales
Comamonadaceae














OTU_7
87
Proteobacteria
Betaproteobacteria
Burkholderiales
Oxalobacteraceae

Janthinobacterium














OTU_1344
88
Proteobacteria
Betaproteobacteria
Burkholderiales
Oxalobacteraceae















OTU_87
89
Firmicutes
Clostridia
Clostridiales
Clostridiaceae

Clostridium


butyricum



OTU_206
90
Firmicutes
Clostridia
Clostridiales
Clostridiaceae

Clostridium


intestinale














OTU_258
91
Firmicutes
Clostridia
Clostridiales
Clostridiaceae















OTU_342
92
Firmicutes
Clostridia
Clostridiales
Clostridiaceae

Thermoanaero-


saccharolyticum










bacterium



OTU_259
93
Firmicutes
Clostridia
Thermoanaero-
Caldicell-

Caldicellulosiruptor


saccharolyticus







bacterales
ulosiruptoraceae













OTU_428
94
Firmicutes
Clostridia
Thermoanaero-
Carboxydocellaceae

Carboxydocella







bacterales


OTU_485
95
Bacteroidetes
Cytophagia
Cytophagales
Cytophagaceae

Hymenobacter



OTU_1306
96
Bacteroidetes
Cytophagia
Cytophagales
Cytophagaceae

Hymenobacter



OTU_735
97
Bacteroidetes
Cytophasia
Cytophagales
Cytophagaceae

Hymenobacter



OTU_37
98
Bacteroidetes
Cytophagia
Cytophagales
Cytophagaceae

Hymenobacter



OTU_775
99
Bacteroidetes
Cytophagia
Cytophagales
Cytophagaceae

Hymenobacter



OTU_141
100
Bacteroidetes
Cytophagia
Cytophagales
Cytophagaceae

Hymenobacter














OTU_149
101
Proteobacteria
Deltaproteobacteria
Myxococcales
Cystobacterineae














OTU_70
102
Bacteroidetes
Flavobacteriia
Flavobacteriales
[Weeksellaceae]

Chryseobacterium



OTU_23
103
Bacteroidetes
Flavobacteriia
Flavobacteriales
[Weeksellaceae]

Chryseobacterium



OTU_236
104
Bacteroidetes
Flavobacteriia
Flavobacteriales
[Weeksellaceae]

Chryseobacterium



OTU_148
105
Bacteroidetes
Flavobacteriia
Flavobacteriales
[Weeksellaceae]

Chryseobacterium



OTU_181
106
Bacteroidetes
Flavobacteriia
Flavobacteriales
[Weeksellaceae]

Chryseobacterium














OTU_347
107
Proteobacteria
Gammaproteobacteria
Enterobacteriales
Enterobacteriaceae















OTU_1190
108
Proteobacteria
Gammaproteobacteria
Enterobacteriales
Enterobacteriaceae

Yersinia




OTU_1201
109
Proteobacteria
Gammaproteobacteria
Enterobacteriales
Enterobacteriaceae

Enterobacter


hormaechei



OTU_679
110
Proteobacteria
Gammaproteobacteria
Pseudomonadales
Pseudomonadaceae

Pseudomonas


fragi














OTU_234
111
Proteobacteria
Gammaproteobacteria
Pseudomonadales
Pseudomonadaceae















OTU_46
112
Proteobacteria
Gammaproteobacteria
Pseudomonadales
Moraxellaceae

Acinetobacter


lwoffii



OTU_1274
113
Proteobacteria
Gammaproteobacteria
Xanthomonadales
Xanthomonadaceae

Stenotrophomonas


maltophilia














OTU_1303
114
Proteobacteria
Gammaproteobacteria
Enterobacteriales
Enterobacteriaceae



OTU_401
115
Proteobacteria
Gammaproteobacteria
Enterobacteriales
Enterobacteriaceae


OTU_1261
116
Proteobacteria
Gammaproteobacteria
Enterobacteriales
Enterobacteriaceae













OTU_548
117
Proteobacteria
Gammaproteobacteria
Xanthomonadales
Xanthomonadaceae

Stenotrophomonas















OTU_132
118
Proteobacteria
Gammaproteobacteria
Pseudomonadales
Pseudomonadaceae

Pseudomonas


veronii














OTU_1343
119
Proteobacteria
Gammaproteobacteria
Pseudomonadales
Pseudomonadaceae



OTU_22
120
Proteobacteria
Gammaproteobacteria
Pseudomonadales
Pseudomonadaceae













OTU_163
121
Proteobacteria
Gammaproteobacteria
Xanthomonadales
Xanthomonadaceae

Stenotrophomonas



OTU_771
122
Proteobacteria
Gammaproteobacteria
Pseudomonadales
Pseudomonadaceae

Pseudomonas



OTU_826
123
Proteobacteria
Gammaproteobacteria
Pseudomonadales
Pseudomonadaceae

Pseudomonas



OTU_166
124
Proteobacteria
Gammaproteobacteria
Xanthomonadales
Xanthomonadaceae

Xanthomonas














OTU_1441
125
Proteobacteria
Gammaproteobacteria
Enterobacteriales
Enterobacteriaceae















OTU_1158
126
Proteobacteria
Gammaproteobacteria
Enterobacteriales
Enterobacteriaceae

Serratia


marcescens














OTU_1083
127
Proteobacteria
Gammaproteobacteria
Pseudomonadales
Pseudomonadaceae



OTU_8
128
Proteobacteria
Gammaproteobacteria
Pseudomonadales
Pseudomonadaceae














OTU_18
129
Proteobacteria
Gammaproteobacteria
Xanthomonadales
Xanthomonadaceae

Xanthomonas


axonopodis



OTU_51
130
Proteobacteria
Gammaproteobacteria
Oceanospirillales
Halomonadaceae

Halomonas



OTU_72
131
Proteobacteria
Gammaproteobacteria
Pseudomonadales
Pseudomonadaceae

Pseudomonas


viridiflava














OTU_9
132
Proteobacteria
Gammaproteobacteria
Pseudomonadales
Pseudomonadaceae

Pseudomonas















OTU_696
133
Proteobacteria
Gammaproteobacteria
Enterobacteriales
Enterobacteriaceae

Escherichia


coli














OTU_53
134
Proteobacteria
Gammaproteobacteria
Enterobacteriales
Enterobacteriaceae

Enterobacter















OTU_4
135
Proteobacteria
Gammaproteobacteria
Enterobacteriales
Enterobacteriaceae

Pantoea


agglomeraris














OTU_220
136
Tenericutes
Mollicutes
Anaeroplasmatales
Anaeroplasmataceae

Asteroleplasma














OTU_343
137
Bacteroidetes
Sphingobacteriia
Sphingobacteriales
Sphingobacteriaceae















OTU_82
138
Bacteroidetes
Sphingobacteriia
Sphingobacteriales
Sphingobacteriaceae

Pedobacter















OTU_69
139
Bacteroidetes
Sphingobacteriia
Sphingobacteriales
Sphingobacteriaceae















OTU_36
140
Bacteroidetes
Sphingobacteriia
Sphingobacteriales
Sphingobacteriaceae

Pedobacter




OTU_1386
141
Bacteroidetes
Sphingobacteriia
Sphingobacteriales
Sphingobacteriaceae

Pedobacter



OTU_1165
142
Bacteroidetes
Sphingobacteriia
Sphingobacteriales
Sphingobacteriaceae

Pedobacter


cryoconitis



OTU_368
143
Bacteroidetes
Sphingobacteriia
Sphingobacteriales
Sphingobacteriaceae

Pedobacter



OTU_91
144
Cyanobacteria
















TABLE 4







Exemplary fungal endophytes present in all plants















SEQ









ID


OTU_ID
NO
Phylum
Class
Order
Family
Genus
Species

















OTU_288
145
Basidiomycota
Agaricomycetes
Corticiales
Corticiaceae

Waitea


circinata var











circinata



OTU_327
146
Basidiomycota
Agaricomycetes
Cantharellales
Ceratobasidiaceae

Thanatephorus


cucumeris



OTU_1
147
Ascomycota
Dothideomycetes
Pleosporales
Pleosporaceae

Alternaria

sp MY_2011


OTU_2
148
Ascomycota
Dothideomycetes
Capnodiales
Mycosphaerellaceae

Cladosporium



OTU_12
149
Ascomycota
Dothideomycetes
Capnodiales
Davidiellaceae

Davidiella


tassiana



OTU_9
150
Ascomycota
Dothideomycetes
Pleosporales
Pleosporaceae

Lewia


infectoria



OTU_29
151
Ascomycota
Dothideomycetes
Pleosporales
Pleosporaceae

Epicoccum


nigrum



OTU_15
152
Ascomycota
Dothideomycetes
Pleosporales
Pleosporaceae

Ulocladium



OTU_55
153
Ascomycota
Dothideomycetes
Capnodiales
Davidiellaceae

Cladosporium



OTU_10
154
Ascomycota
Dothideomycetes
Pleosporales
Incertae sedis

Phoma

sp P48E5


OTU_133
155
Ascomycota
Dothideomycetes
Capnodiales
Davidiellaceae

Cladosporium

sp ascomyc1


OTU_26
156
Ascomycota
Dothideomycetes
Pleosporales
Phaeosphaeriaceae
unidentified
Phaeosphaeriaceae









sp MJ23


OTU_47
157
Ascomycota
Dothideomycetes


OTU_24
158
Ascomycota
Dothideomycetes
Pleosporales
Phaeosphaeriaceae


OTU_522
159
Ascomycota
Dothideomycetes
Pleosporales
Phaeosphaeriaceae

Ampelomyces


quisqualis



OTU_66
160
Ascomycota
Dothideomycetes
Pleosporales
Pleosporaceae

Dendryphiella


arenaria



OTU_23
161
Ascomycota
Dothideomycetes
Capnodiales
Mycosphaerellaceae

Septoria


phalaridis



OTU_71
162
Ascomycota
Dothideomycetes
Pleosporales


OTU_27
163
Ascomycota
Dothideomycetes
Pleosporales
Incertae sedis


OTU_32
164
Ascomycota
Dothideomycetes
Dothideales
Dothioraceae

Aureobasidium



OTU_20
165
Ascomycota
Dothideomycetes
Pleosporales
Phaeosphaeriaceae
unidentified
Phaeosphaeriaceae









sp MJ23


OTU_16
166
Ascomycota
Dothideomycetes
Pleosporales
Incertae sedis

Phoma



OTU_44
167
Ascomycota
Dothideomycetes
Capnodiales
Davidiellaceae

Cladosporium

sp 234B


OTU_38
168
Ascomycota
Dothideomycetes
Pleosporales
Phaeosphaeriaceae


OTU_104
169
Ascomycota
Dothideomycetes
Pleosporales
Pleosporaceae

Alternaria


brassicicola



OTU_1123
170
Ascomycota
Dothideomycetes
Pleosporales
Phaeosphaeriaceae
unidentified
Phaeosphaeriaceae









sp MJ23


OTU_90
171
Ascomycota
Dothideomycetes
Pleosporales
Phaeosphaeriaceae

Ampelomyces


quisqualis



OTU_48
172
Ascomycota
Dothideomycetes
Incertae sedis
Incertae sedis

Leptospora


rubella



OTU_73
173
Ascomycota
Dothideomycetes
Pleosporales
Incertae sedis

Phoma


rhei



OTU_1432
174
Ascomycota
Dothideomycetes
Pleosporales
Leptosphaeriaceae
unidentified
uncultured










Epicoccum



OTU_1095
175
Ascomycota
Dothideomycetes
Pleosporales
Pleosporaceae

Lewia


infectoria



OTU_486
176
Ascomycota
Dothideomycetes
Pleosporales
Phaeosphaeriaceae

Parastagonospora


caricis



OTU_110
177
Ascomycota
Dothideomycetes
Capnodiales
Davidiellaceae

Cladosporium

sp ascomyc1


OTU_78
178
Ascomycota
Dothideomycetes
Pleosporales
Phaeosphaeriaceae

Phaeosphaeria



OTU_83
179
Ascomycota
Dothideomycetes
unidentified
unidentified
unidentified
Dothideomycetes sp


OTU_815
180
Ascomycota
Dothideomycetes
Pleosporales
Pleosporaceae

Alternaria

sp MY_2011


OTU_244
181
Ascomycota
Dothideomycetes
Capnodiales
Davidiellaceae

Cladosporium


sphaerospermum



OTU_775
182
Ascomycota
Dothideomycetes
Pleosporales
Pleosporaceae

Alternaria

sp MY_2011


OTU_259
183
Ascomycota
Dothideomycetes
Pleosporales
Pleosporaceae

Lewia


infectoria



OTU_447
184
Ascomycota
Dothideomycetes
Pleosporales
Incertae sedis

Phoma


macrostoma



OTU_1429
185
Ascomycota
Dothideomycetes
Pleosporales
Incertae sedis

Phoma

sp P48E5


OTU_122
186
Ascomycota
Dothideomycetes
Pleosporales
Incertae sedis

Phoma


macrostoma



OTU_82
187
Ascomycota
Dothideomycetes
Pleosporales
Phaeosphaeriaceae
unidentified
Phaeosphaeriaceae sp


OTU_324
188
Ascomycota
Dothideomycetes
Pleosporales
Pleosporaceae

Lewia


infectoria



OTU_60
189
Ascomycota
Dothideomycetes
Pleosporales
Pleosporaceae

Cochliobolus



OTU_142
190
Ascomycota
Dothideomycetes
Incertae sedis
Pseudeurotiaceae

Pseudeurotium



OTU_92
191
Ascomycota
Dothideomycetes
Capnodiales
Mycosphaerellaceae

Cercospora


nicotianae



OTU_87
192
Ascomycota
Dothideomycetes
Capnodiales
Mycosphaerellaceae

Mycosphaerella


punctiformis



OTU_99
193
Ascomycota
Dothideomycetes
Pleosporales
Leptosphaeriaceae


OTU_1316
194
Ascomycota
Dothideomycetes
Pleosporales
Incertae sedis

Phoma



OTU_138
195
Ascomycota
Dothideomycetes
Capnodiales
Davidiellaceae

Cladosporium



OTU_992
196
Ascomycota
Dothideomycetes
Dothideales
Dothioraceae

Aureobasidium


pullulans



OTU_378
197
Ascomycota
Dothideomycetes
Pleosporales
Incertae sedis

Phoma



OTU_353
198
Ascomycota
Dothideomycetes
Pleosporales
Incertae sedis

Phoma



OTU_227
199
Ascomycota
Dothideomycetes
Pleosporales
Incertae sedis


OTU_68
200
Ascomycota
Dothideomycetes
Pleosporales
Incertae sedis

Phoma


paspali



OTU_680
201
Ascomycota
Dothideomycetes


OTU_97
202
Ascomycota
Dothideomycetes
Pleosporales
Phaeosphaeriaceae
unidentified
Phaeosphaeriaceae









sp MJ23


OTU_115
203
Ascomycota
Dothideomycetes
Pleosporales
Phaeosphaeriaceae

Phaeosphaeria



OTU_22
204
Ascomycota
Eurotiomycetes
Eurotiales
Trichocomaceae

Penicillium



OTU_262
205
Ascomycota
Eurotiomycetes
Eurotiales
Trichocomaceae

Penicillium


citrinum



OTU_17
206
Ascomycota
Eurotiomycetes
Eurotiales
Trichocomaceae

Aspergillus


niger



OTU_28
207
Ascomycota
Eurotiomycetes
Eurotiales
Trichocomaceae

Penicillium


bialowiezense



OTU_21
208
Ascomycota
Eurotiomycetes
Eurotiales
Trichocomaceae
unidentified
uncultured










Eurotium



OTU_938
209
Ascomycota
Eurotiomycetes
Eurotiales
Trichocomaceae

Penicillium



OTU_64
210
Ascomycota
Eurotiomycetes
Eurotiales
Trichocomaceae

Penicillium


spinulosum



OTU_105
211
Ascomycota
Eurotiomycetes
Eurotiales
Trichocomaceae

Emericella


nidulans



OTU_527
212
Ascomycota
Eurotiomycetes
Eurotiales
Trichocomaceae

Penicillium


bialowiezense



OTU_121
213
Ascomycota
Eurotiomycetes
Eurotiales
Trichocomaceae

Penicillium



OTU_77
214
Ascomycota
Eurotiomycetes
Eurotiales
Trichocomaceae

Aspergillus


flavus



OTU_340
215
Ascomycota
Eurotiomycetes
Eurotiales
Trichocomaceae

Penicillium



OTU_186
216
Ascomycota
Eurotiomycetes
Eurotiales
Trichocomaceae

Talaromyces



OTU_131
217
Ascomycota
Eurotiomycetes
Eurotiales
Trichocomaceae

Emericella


nidulans



OTU_18
218
Zygomycota
Incertae sedis
Mucorales
Rhizopodaceae

Rhizopus


oryzae



OTU_6
219
Ascomycota
Leotiomycetes
Helotiales
Helotiaceae


OTU_42
220
Ascomycota
Leotiomycetes
Erysiphales
Erysiphaceae

Erysiphe


cruciferarum



OTU_125
221
Ascomycota
Leotiomycetes
Helotiales
Sclerotiniaceae

Botrytis

sp CID95


OTU_50
222
Basidiomycota
Microbotryomycetes
Sporidiobolales
Incertae sedis

Sporobolomyces


oryzicola



OTU_37
223
Basidiomycota
Microbotryomycetes
Sporidiobolales
Incertae sedis

Sporobolomyces


roseus



OTU_1406
224
Basidiomycota
Microbotryomycetes
Sporidiobolales
Incertae sedis

Sporobolomyces



OTU_72
225
Basidiomycota
Microbotryomycetes
Sporidiobolales
Incertae sedis

Sporobolomyces


ruberrimus



OTU_1184
226
Basidiomycota
Microbotryomycetes
Sporidiobolales
Incertae sedis

Sporobolomyces


roseus



OTU_70
227
Basidiomycota
Microbotryomycetes
Sporidiobolales
Incertae sedis
unidentified
Sporidiobolales sp


OTU_65
228
Basidiomycota
Microbotryomycetes
Sporidiobolales
Incertae sedis

Rhodosporidium


diobovatum



OTU_103
229
Basidiomycota
Microbotryomycetes
Sporidiobolales
Incertae sedis

Sporobolomyces


symmetricus



OTU_53
230
Ascomycota
Saccharomycetes
Saccharomycetales
Pichiaceae

Pichia


fermentans



OTU_94
231
Ascomycota
Saccharomycetes
Saccharomycetales
Saccharomycodaceae

Hanseniaspora


uvarum



OTU_86
232
Ascomycota
Saccharomycetes
Saccharomycetales
Saccharomycodaceae

Hanseniaspora


thailandica



OTU_5
233
Ascomycota
Sordariomycetes
Hypocreales
Nectriaceae

Fusarium



OTU_11
234
Ascomycota
Sordariomycetes
Xylariales
Incertae sedis

Monographella

sp 68


OTU_13
235
Ascomycota
Sordariomycetes
Hypocreales
Nectriaceae

Fusarium


culmorum



OTU_25
236
Ascomycota
Sordariomycetes
Sordariales


OTU_120
237
Ascomycota
Sordariomycetes
Hypocreales
Incertae sedis

Acremonium

sp 2 J12


OTU_1072
238
Ascomycota
Sordariomycetes
Hypocreales
Nectriaceae

Gibberella


intricans



OTU_58
239
Ascomycota
Sordariomycetes
Hypocreales
Nectriaceae

Gibberella


intricans



OTU_62
240
Ascomycota
Sordariomycetes
Hypocreales


OTU_30
241
Ascomycota
Sordariomycetes
Hypocreales
Nectriaceae

Gibberella


baccata



OTU_56
242
Ascomycota
Sordariomycetes
Hypocreales
Incertae sedis

Acremonium

sp 4053


OTU_209
243
Ascomycota
Sordariomycetes
Hypocreales
Nectriaceae

Fusarium


petroliphilum



OTU_34
244
Ascomycota
Sordariomycetes
Incertae sedis
Plectosphaerellaceae

Gibellulopsis

sp YH_2012


OTU_45
245
Ascomycota
Sordariomycetes
Xylariales
Incertae sedis

Monographella


cucumerina



OTU_100
246
Ascomycota
Sordariomycetes
Hypocreales
unidentified
unidentified


OTU_877
247
Ascomycota
Sordariomycetes
Hypocreales
Nectriaceae

Fusarium


sporotrichioides



OTU_682
248
Ascomycota
Sordariomycetes
Hypocreales
Nectriaceae


OTU_81
249
Ascomycota
Sordariomycetes
Diaporthales
Diaporthaceae

Phomopsis

sp MAFF 239532


OTU_238
250
Ascomycota
Sordariomycetes
Sordariales
Lasiosphaeriaceae
unidentified
Lasiosphaeriaceae sp


OTU_85
251
Ascomycota
Sordariomycetes
Sordariales
Chaetomiaceae

Chaetomium


globosum



OTU_525
252
Ascomycota
Sordariomycetes


OTU_106
253
Ascomycota
Sordariomycetes
Incertae sedis
Glomerellaceae

Colletotrichum


acutatum



OTU_150
254
Ascomycota
Sordariomycetes
Hypocreales
Incertae sedis

Acremonium


dichromosporum



OTU_1278
255
Ascomycota
Sordariomycetes
Hypocreales
Nectriaceae

Fusarium


sporotrichioides



OTU_1403
256
Ascomycota
Sordariomycetes
Xylariales
Incertae sedis

Monographella

sp 68


OTU_160
257
Ascomycota
Sordariomycetes
Incertae sedis
Plectosphaerellaceae

Lectera


longa



OTU_1214
258
Ascomycota
Sordariomycetes
Hypocreales
Nectriaceae

Gibberella


intricans



OTU_181
259
Ascomycota
Sordariomycetes
Hypocreales
Cordycipitaceae

Engyodontium


album



OTU_172
260
Ascomycota
Sordariomycetes
Hypocreales
Nectriaceae

Fusarium


poae



OTU_19
261
Basidiomycota
Tremellomycetes
unidentified
unidentified
unidentified
uncultured










Cryptococcus



OTU_40
262
Basidiomycota
Tremellomycetes
Filobasidiales
Filobasidiaceae

Cryptococcus



OTU_74
263
Basidiomycota
Tremellomycetes
Tremellales
Incertae sedis

Cryptococcus


victoriae



OTU_163
264
Basidiomycota
Tremellomycetes
Tremellales
unidentified
unidentified
Tremellales sp TG05


OTU_52
265
Basidiomycota
Tremellomycetes
Tremellales
Incertae sedis

Cryptococcus


victoriae



OTU_325
266
Basidiomycota
Tremellomycetes
Tremellales
Incertae sedis

Hannaella



OTU_128
267
Basidiomycota
Tremellomycetes
Filobasidiales
Filobasidiaceae

Cryptococcus


wieringae



OTU_180
268
Basidiomycota
Tremellomycetes
Tremellales
Incertae sedis

Cryptococcus


laurentii



OTU_46
269
Basidiomycota
Tremellomycetes
Filobasidiales
Filobasidiaceae

Cryptococcus


oeirensis



OTU_174
270
Basidiomycota
Tremellomycetes
Tremellales
Incertae sedis

Cryptococcus

sp VP_2009b


OTU_69
271
Basidiomycota
Tremellomycetes
Filobasidiales
Filobasidiaceae

Cryptococcus


oeirensis



OTU_80
272
Basidiomycota
Tremellomycetes
Cystofilobasidiales
Cystofilobasidiaceae

Udeniomyces


puniceus



OTU_96
273
Basidiomycota
Tremellomycetes
Cystofilobasidiales
Cystofilobasidiaceae

Udeniomyces


pyricola



OTU_51
274
Basidiomycota
Tremellomycetes
Tremellales
Incertae sedis

Bullera


Bullera unica



OTU_109
275
Basidiomycota
Tremellomycetes
Tremellales
Incertae sedis

Dioszegia


fristingensis



OTU_222
276
Basidiomycota
Tremellomycetes
Cystofilobasidiales
Cystofilobasidiaceae

Cystofilobasidium


infirmominiatum



OTU_1054
277
Basidiomycota
Tremellomycetes
Filobasidiales
Filobasidiaceae

Cryptococcus


oeirensis



OTU_971
278
Basidiomycota
Tremellomycetes
unidentified
unidentified
unidentified
Tremellomycetes sp


OTU_79
279
Basidiomycota
Tremellomycetes
Tremellales
Incertae sedis

Hannaella


luteola



OTU_135
280
Basidiomycota
Tremellomycetes
Filobasidiales
Filobasidiaceae

Cryptococcus


albidus



OTU_166
281
Basidiomycota
Tremellomycetes
Tremellales
Incertae sedis

Cryptococcus


victoriae



OTU_111
282
Basidiomycota
Tremellomycetes
unidentified
unidentified
unidentified
Tremellomycetes sp


OTU_158
283
Basidiomycota
Tremellomycetes
unidentified
unidentified
unidentified
Tremellomycetes sp


OTU_91
284
Basidiomycota
Tremellomycetes
Filobasidiales
Filobasidiaceae

Cryptococcus


albidus



OTU_127
285
Basidiomycota
Tremellomycetes
Tremellales
Incertae sedis

Hannaella



OTU_1103
286
Basidiomycota
Wallemiomycetes
Wallemiales
Wallemiaceae

Wallemia


sebi



OTU_54
287
Basidiomycota
Wallemiomycetes
Wallemiales
Wallemiaceae

Wallemia


muriae



OTU_114
288
Basidiomycota
Wallemiomycetes
Wallemiales
Wallemiaceae

Wallemia


sebi



OTU_1326
289
Basidiomycota
Wallemiomycetes
Wallemiales
Wallemiaceae

Wallemia


muriae

















TABLE 1







Exemplary core bacterial endophytes















SEQ









ID


OTU_ID
NO
Phylum
Class
Order
Family
Genus
Species

















OTU_47
39

Alphaproteobacteria
Rhizobiales
Methylobacteriaceae

Methylobacterium




OTU_14
43

Alphaproteobacteria
Sphingomonadales
Sphingomonadaceae

Sphingomonas



OTU_6
44

Alphaproteobacteria
Sphingomonadales
Sphingomonadaceae

Sphingomonas



OTU_25
59

Bacilli
Bacillales
Paenibacillaceae


OTU_19
64

Bacilli
Bacillales
Paenibacillaceae

Paenibacillus


amylolyticus



OTU_16
65

Bacilli
Bacillales
[Exiguobacteraceae]

Exiguobacterium



OTU_222
67

Bacilli
Bacillales
Bacillaceae

Geobacillus



OTU_653
68

Bacilli
Bacillales
Bacillaceae

Bacillus


endophyticus



OTU_11
69

Bacilli
Bacillales
Paenibacillaceae

Paenibacillus



OTU_71
70

Bacilli
Bacillales
Paenibacillaceae

Saccharibacillus


kuerlensis



OTU_13
71

Bacilli
Bacillales
Bacillaceae

Bacillus


flexus



OTU_1014
75

Betaproteobacteria
Burkholderiales
Oxalobacteraceae

Janthinobacterium



OTU_168
86

Betaproteobacteria
Burkholderiales
Comamonadaceae


OTU_7
87

Betaproteobacteria
Burkholderiales
Oxalobacteraceae

Janthinobacterium



OTU_1344
88

Betaproteobacteria
Burkholderiales
Oxalobacteraceae


OTU_1303
114

Gammaproteobacteria
Enterobacteriales
Enterobacteriaceae


OTU_401
115

Gammaproteobacteria
Enterobacteriales
Enterobacteriaceae


OTU_1261
116

Gammaproteobacteria
Enterobacteriales
Enterobacteriaceae


OTU_771
122

Gammaproteobacteria
Pseudomonadales
Pseudomonadaceae

Pseudomonas



OTU_1441
125

Gammaproteobacteria
Enterobacteriales
Enterobacteriaceae


OTU_1158
126

Gammaproteobacteria
Enterobacteriales
Enterobacteriaceae

Serratia


marcescens



OTU_8
128

Gammaproteobacteria
Pseudomonadales
Pseudomonadaceae


OTU_18
129

Gammaproteobacteria
Xanthomonadales
Xanthomonadaceae

Xanthomonas


axonopodis



OTU_51
130

Gammaproteobacteria
Oceanospirillales
Halomonadaceae

Halomonas



OTU_9
132

Gammaproteobacteria
Pseudomonadales
Pseudomonadaceae

Pseudomonas



OTU_696
133

Gammaproteobacteria
Enterobacteriales
Enterobacteriaceae

Escherichia


coli



OTU_53
134

Gammaproteobacteria
Enterobacteriales
Enterobacteriaceae

Enterobacter



OTU_4
135

Gammaproteobacteria
Enterobacteriales
Enterobacteriaceae

Pantoea


agglomerans

















TABLE 2







Exemplary core fungal endophytes














OTU_ID
SEQ ID NO
Phylum
Class
Order
Family
Genus
Species

















OTU_1
147

Dothideomycetes
Pleosporales
Pleosporaceae

Alternaria

sp MY_2011


OTU_2
148

Dothideomycetes
Capnodiales
Mycosphaerellaceae
unidentified
uncultured










Cladosporium



OTU_12
149

Dothideomycetes
Capnodiales
Davidiellaceae

Davidiella


tassiana



OTU_9
150

Dothideomycetes
Pleosporales
Pleosporaceae

Lewia


infectoria



OTU_815
180

Dothideomycetes
Pleosporales
Pleosporaceae

Alternaria

sp MY_2011


OTU_775
182

Dothideomycetes
Pleosporales
Pleosporaceae

Alternaria

sp MY_2011


OTU_22
204

Eurotiomycetes
Eurotiales
Trichocomaceae

Penicillium



OTU_6
219

Leotiomycetes
Helotiales
Helotiaceae


OTU_50
222

Microbotryomycetes
Sporidiobolales
Incertae sedis

Sporobolomyces


oryzicola



OTU_37
223

Microbotryomycetes
Sporidiobolales
Incertae sedis

Sporobolomyces


roseus



OTU_1406
224

Microbotryomycetes
Sporidiobolales
Incertae sedis

Sporobolomyces



OTU_1184
226

Microbotryomycetes
Sporidiobolales
Incertae sedis

Sporobolomyces


roseus



OTU_5
233

Sordariomycetes
Hypocreales
Nectriaceae

Fusarium



OTU_1072
238

Sordariomycetes
Hypocreales
Nectriaceae

Gibberella


intricans



OTU_58
239

Sordariomycetes
Hypocreales
Nectriaceae

Gibberella


intricans



OTU_682
248

Sordariomycetes
Hypocreales
Nectriaceae


OTU_19
261

Tremellomycetes
unidentified
unidentified
unidentified
uncultured










Cryptococcus



OTU_40
262

Tremellomycetes
Filobasidiales
Filobasidiaceae

Cryptococcus



OTU_52
265

Tremellomycetes
Tremellales
Incertae sedis

Cryptococcus


victoriae



OTU_166
281

Tremellomycetes
Tremellales
Incertae sedis

Cryptococcus


victoriae










Example 2—Identification and Characterization of Culturable Bacterial and Fungal Endophytes Belonging to Core OTUs

In order to better understand the role played by core seed-derived endophytic microbes in improving the vigor, general health and stress resilience of agricultural plants, we initiated a systematic screen to isolate and characterize endophytic microbes from seeds and tissues of commercially significant agricultural plants.


Seeds from diverse types of cereals, fruits, vegetables, grasses, oilseed, and other seeds were acquired and screened for cultivatable microbes, as described below. Culturable microbes (i.e., SYM strains) belonging to the same OTUs as the core OTUs described in Table 1 and Table 2 were isolated and identified.


Isolation of Bacteria and Fungi from the Interior of Seeds


Isolation of fungi and bacteria (including endophytes) from the interior of surface-sterilized seeds was performed using techniques known in the art. Surface sterilized seeds were ground, diluted in liquid media, and the suspension used to inoculate solid media plates. These were incubated under different conditions at room temperature.


Experiment Description

Approximately fifty surface-sterilized seeds were transferred aseptically to a sterile blender and ground. The ground seeds were resuspended in 50 mL of sterile R2A broth, and incubated for 4 h at room temperature. Ten 1 mL aliquots of the seed homogenates were collected and centrifuged, their supernatants discarded and the pellets gently resuspended in 1 mL of sterile 0.05 phosphate buffer; 0.5 mL of 50% glycerol is added to each of five tubes. These were stored at −80 C for further characterization. The remaining aliquots were diluted down twice in hundred-fold dilutions to 10−4. 100 microliters of the 1, 10−2, and 10−4 dilutions were used to inoculate three Petri dishes containing the following media in order to isolate of bacteria and/or fungi:

    • 1. Tryptic Soy agar
    • 2. R2A agar
    • 3. Potato dextrose agar
    • 4. Sabouraud Agar
    • 5. Other media depending on target microorganism


The plates were divided into three sets comprising each media type and incubated in different environments. The first set was incubated aerobically, the second under anaerobic conditions, and the third under microaerophilic conditions and all were inspected daily for up to 5 days. 1-2 individual colonies per morphotype were isolated and streaked for purity onto fresh plates of the same media/environment from which the microorganism was isolated. Plates were incubated at room temperature for 2-5 days. After an isolate grew it was streaked once more onto a fresh plate of the same media to ensure purity and incubated under the same environmental conditions.


From the second streaked plate, isolates were stored in Tryptic soy broth +15% glycerol at −80° C. for further characterization, by first scraping 2-3 colonies (about 10 μL) from the plate into a cryogenic tube containing 1.5 mL of the above-mentioned media and gently resuspending the cells. Alternatively, isolates were propagated in specialized media as recommended for the particular taxon of microorganism. The microbes obtained represent those that live in the seeds of the plant accession.


Isolation of Bacteria and Fungi from Plant Interior Tissues


Isolation of fungi and bacteria (including endophytes) from surface-sterilized plant tissues was performed using techniques known in the art. Surface sterilized plant tissues were ground, diluted in liquid media, and then this suspension was used to inoculate solid media plates. These were incubated under different environmental conditions at room temperature.


Experiment Description

Approximately fifty grams of surface-sterilized plant tissue were transferred aseptically to a sterile blender and ground. The ground tissue was resuspended in 50 mL of sterile R2A broth, and incubated for 4 h at room temperature. Ten 1 mL aliquots of the plant tissue homogenates were collected and centrifuged, their supernatants discarded and the pellets gently resuspended in 1 mL of sterile 0.05 phosphate buffer. 0.5 mL of 50% Glycerol was added to each of five tubes. These were stored at −80° C. for possible further characterization. The remaining aliquots were diluted down twice in hundred-fold dilutions to 10−4. One hundred microliters of the 1, 10−2, and 10−4 dilutions were used to inoculate three Petri dishes containing the following media in order to isolate of bacteria and/or fungi:

    • 1. Tryptic Soy agar
    • 2. R2A agar
    • 3. Potato dextrose agar
    • 4. Sabouraud Agar
    • 5. Other media depending on target microorganism


Plates were divided into three sets comprising each media type and incubated in different environments. The first set was incubated aerobically, the second under anaerobic conditions, and the third under microaerophilic conditions and all were inspected daily for up to 5 days. 1-2 individual colonies per morphotype were isolated and streaked for purity onto fresh plates of the same media/environment from which the microorganism was isolated. Plates were incubated at room temperature for 2-5 days. After an isolate grew it was streaked once more onto a fresh plate of the same media to ensure purity and incubated under the same environmental conditions.


From the second streaked plate, isolates were stored in Tryptic soy broth +15% glycerol at −80° C. for further characterization, by first scraping 2-3 colonies (about 10 μL) from the plate into a cryogenic tube containing 1.5 mL of the above-mentioned media and gently resuspending the cells. Alternatively, isolates were propagated in specialized media as recommended for the particular taxon of microorganism.


Isolation of Bacteria and Fungi from Plant or Seed Surfaces


To collect phyllosphere, rhizosphere, or spermosphere material for culturing of microbes, unwashed shoot, roots or seeds were shaken free/cleaned of any attached soil and stuffed into sterile 50 mL Falcon tubes. To these, 10 mL of sterile 0.1 M sodium phosphate buffer was added and shaken, followed by 5 minutes of sonication to dislodge microbes from plant surfaces, with the resulting cloudy or muddy wash collected in a separate 15 mL Falcon tube. 100 μL of this microbe filled wash was directly spread onto agar plates or nutrient broth for culturing and enrichment, or it was further diluted with sterile 0.1 M sodium phosphate buffer by 10×, 100×, 1,000×, 10,000× and even 100,000×, before microbial culturing on agar plates or nutrient broth. Glycerol stock preparations of the plant surface wash solution were made at this point by mixing 1 mL of the soil wash solution and 0.5 mL of sterile, 80% glycerol, flash freezing the preparation in a cryotube dipped in liquid nitrogen, and storing at −80° C. Nutrient broth inoculated with a mixture of plant surface bacteria forms a stable, mixed community of microbes which was used in plant inoculation experiments described herein, subcultured in subsequent broth incubations, or spread on agar plates and separated into individual colonies which were tested via methods described herein.


Characterization of Fungal and Bacterial Isolates


Characterization of fungi and bacteria isolated from surface-sterilized or non-sterilized plant or seed tissues was performed using techniques known in the art. These techniques take advantage of differential staining of microorganisms, morphological characteristics of cells, spores, or colonies, biochemical reactions that provide differential characterization, and DNA amplification and sequencing of diagnostic regions of genes, among other methods.


Experimental Description


Isolates of bacteria and/or fungi isolated as described herein (including endophytic bacteria and fungi) were categorized into three types: bacterial isolates, fungal isolates, and unknown isolates (since yeast colonies can resemble bacterial colonies in some cases) based on colony morphology, formation of visible mycelia, and/or formation of spores. To determine if an unknown isolate was bacterial or fungal, microscopic analysis of the isolates was performed. Some of the analyses known to the art to differentiate microorganisms include, but are not limited to: the 10% KOH test, positive staining with Lactophenol cotton blue, Gram staining, and growth on media with selective agents. The distinguishing features observed by these tests are relative cell size (yeast size is much larger than bacterial size), formation of hyphae and spores (filamentous bacteria form smaller hyphae than fungi, and do not form structures containing spores), or growth under selection agents (most bacteria can grow in the presence of antifungal compounds like nystatin, while most fungi cannot; likewise, most fungi are unaffected by the presence of broad-spectrum antibiotics like chloramphenicol and spectinomycin).


To identify the isolates, DNA sequence analysis of conserved genomic regions like the ribosomal DNA loci was performed. To obtain DNA to perform PCR amplifications, some cellular growth from solid media (approximately 5-10 μL) was resuspended in 30 μL of sterile Tris/EDTA buffer (pH 8.0). Samples were heated to 98° C. for 10 minutes followed by cooling down to 4° C. for 1 minute in a thermocycler. This cycle was repeated twice. Samples were then centrifuged at ˜13,000 RCF for 1-5 minutes and used as DNA template for PCR reactions. Below is a series of exemplary primer combinations used to identify isolates to a genus level.









TABLE 5







Exemplary primer combinations for isolate identification at a genus level









Primer 1
Primer 2
Target





V4_515F (5′-
V4_806R (5′-
The 4th Variable region of the


GTGCCAGCMGCCGCGGTAA-
GGACTACHVGGGTWTCTAAT-3′)
bacterial 16S rDNA


3′) (SEQ ID NO: 453)
(SEQ ID NO: 454)






27F (5′-
1492R (5′-
Full length of the bacterial 16S


AGAGTTTGATCCTGGCTCAG-
GGTTACCTTGTTACGACTTT-3′)
rDNA, from position 8-1507.


3′) (SEQ ID NO: 455)
(SEQ ID NO: 456)






ITS1 (5′-
ITS2 (5′-
~240 bp ITS1 region of fungal


TCCGTAGGTGAACCTGCGG-
GCTGCGTTCTTCATCGATGC-3′)
genome


3′) (SEQ ID NO: 457)
(SEQ ID NO: 458)






SR1R (5′-
SR6 (5′-TGTTACGACTTTTACTT-
Small subunit (18s) of the


TACCTGGTTGATQCTGCCAGT-
3′) (SEQ ID NO: 460)
fungal rDNA gene


3′) (SEQ ID NO: 459)







ITS1F (5′-
ITS4 (5′-
~600-1000 bp ITS region of


CTTGGTCATTTAGAGGAAGTA
TCCTCCGCTTATTGATATGC-3′)
fungal genomes


A-3′) (SEQ ID NO: 461)
(SEQ ID NO: 462)






ITS5 (Universal) (5′-
ITS4Asco (Ascomycota-specific): 5′
~500 bp fragment from


GGAAGTAAAAGTCGTAACAA
CGTTACTRRGGCAATCCCTGTTG3′
different fungal Phyla


GG-3′) (SEQ ID NO: 463)
(SEQ ID NO: 464) or




ITS4Basidio (Basidiomycota-




specific): 5′




GCRCGGAARACGCTTCTC3′ (SEQ




ID NO: 465); or




ITS4Chytrid (Chytridiomycota-




specific): 5′




TTTTCCCGTTTCATTCGCCA3′




(SEQ ID NO: 466); or




ITS4Oo (Oomycota-specific): 5′




ATAGACTACAATTCGCC 3′ (SEQ




ID NO: 467); or




ITS4Zygo (Zygomycota-specific): 5′




AAAACGTWTCTTCAAA 3′ (SEQ




ID NO: 468)






SSUmAf-(equimolar mix of 2
LSUmAr (equimolar mix of 4
1000-1600 bp fragment of the


degenerate primers) and SSUmCf
degenerate primers) and LSUmBr
Glomerycota (arbuscular


equimolar mix of 3 degenerate
(equimolar mix of 5 degenerate
mycorrhizae) genome


primers)
primers)
comprising partial SSU, whole




internal transcribed spacer




(ITS) rDNA region and partial




LSU.





Arch 340F (5′-
Arch 1000R (5′-
~660 bp product of the 18S


CCCTAYGGGGYGCASCAG-3′)
GAGARGWRGTGCATGGCC-3′)
from Archaea


(SEQ ID NO: 469)
(SEQ ID NO: 470)






27F-Degen (5′-
27F-Degen (5′-
Full length of the bacterial 16S


AGRRTTYGATYMTGGYTYAG-
HGGHTACCTTGTTACGACTT-3′)
rDNA, from position 8-1507.


3′) (SEQ ID NO: 471)
(SEQ ID NO: 472)



and 799f (5′-




AACMGGATTAGATACCCKG-




3′) (SEQ ID NO: 473)









To decrease background noise due to the non-specific binding of primers to DNA, the thermocycler was programmed for a touchdown-PCR, which increased specificity of the reaction at higher temperatures and increased the efficiency towards the end by lowering the annealing temperature. Exemplary conditions for performing Touchdown PCR are shown in Table 6.









TABLE 6







Exemplary conditions for performing Touchdown PCR










Step #
Cycle
Temperature
Time














1
Initial Denaturalization
98° C.*
5
m


2
Denaturalization
98° C.*
30
s


3
Annealing
Predicted optimal Tm for
30
s




the primer set +10° C.,




minus 1° C./cycle










4
Elongation
72° C.*
1 m/1 Kb











5
GoTo Step 2 × 10 times





6
Denaturalization
98° C.*
30
s


7
Annealing
Predicted optimal Tm
30
s




for the primer set










8
Elongation
72° C.*
1 m/1 Kb











9
GoTo Step 6 × 20 times





10
Final Elongation
72° C.*
5
m


11
Cool Down
4° C.
5
m





*Or the temperature specified by the DNA polymerase manufacturer for this step.






PCR reactions were purified to remove primers, dNTPs, and other components by methods known in the art, for example by the use of commercially available PCR clean-up kits.


The resulting sequences were aligned as query sequences with the publicly available databases GenBank nucleotide, RDP, UNITE and PlutoF. RDP was specifically compiled and used for bacterial 16s classification. UNITE and PlutoF were specifically compiled and used for identification of fungi. In all the cases, the strains were identified to species level if their sequences were more than 95% similar to any identified accession from all databases analyzed. When the similarity percentage was between 90-97%, the strain was classified at genus, family, order, class, subdivision or phylum level depending on the information displayed in databases used. Isolates with lower similarity values (from 30-90%) were classified as “unknown” or “uncultured” depending on the information displayed after BLAST analysis. To compliment the molecular identification, fungal taxa were confirmed by inducing sporulation on PDA or V8 agar plates and using reported morphological criteria for identification of fruiting bodies structure and shape. Bacterial taxa were confirmed by using reported morphological criteria in specialized differential media for the particular taxon, or by biochemical differentiation tests, as described by the Bergey's Manual of Systematic Microbiology (Whitman, William B., et al., eds. Bergey's Manual® of systematic bacteriology. Vols. 1-5. Springer, 2012).


Culture-Independent Characterization of Fungal and Bacterial Communities in Seeds or Plants


To understand the diversity of culturable and unculturable microbial (e.g., bacterial and fungal) taxa that reside inside of seeds or plants of agriculturally-relevant cultivars, landraces, and ancestral wild varieties, microbial DNA was extracted from surface sterilized seed or plant parts, as described herein, followed by amplification of conserved genomic regions, for example the ribosomal DNA loci. Amplified DNA represented a “snapshot” of the full microbial community inside seeds or plants.


Experimental Description

To obtain microbial DNA from seeds, plants or plant parts, the seeds, plants or plant parts were surface sterilized under aseptic conditions as described herein. Microbial DNA from seeds, plants, or plant parts was extracted using methods known in the art, for example using commercially available Seed-DNA or plant DNA extraction kits, or the following method.

    • 1. A sample of each kind of seed or plant tissue is placed in a cold-resistant container and 10-50 mL of liquid nitrogen is applied. The seeds or plant tissues are then macerated to a powder.
    • 2. Genomic DNA is extracted from each seed or plant tissue preparation, following a chloroform:isoamyl alcohol 24:1 protocol (Sambrook et al. 1989).


Fungal-specific primers were used to amplify the ITS (Internal Transcribed Spacer) region of nuclear ribosomal DNA. Bacterial specific primers were used to amplify region of the 16s rDNA gene of the bacterial genome. Sequences obtained through NGS platforms were analyzed against databases, such as the ones mentioned herein.


Exemplary primer pairs used for this analysis are listed in Table 5.


As an alternative to next generation sequencing, Terminal Restriction Fragment Length Polymorphism, (TRFLP) can be performed. Group specific, fluorescently labeled primers are used to amplify diagnostic regions of genes in the microbial population. This fluorescently labeled PCR product is cut by a restriction enzyme chosen for heterogeneous distribution in the PCR product population. The enzyme cut mixture of fluorescently labeled and unlabeled DNA fragments is then submitted for sequence analysis on a Sanger sequence platform such as the Applied Biosystems 3730 DNA Analyzer.


Determination of the Plant Pathogenic Potential of Microbial Isolates


Since a microbe that confers positive traits to one cultivar might be a pathogenic agent in a different plant species, a general assay was used to determine the pathogenic potential of microbial isolates. Surface and interior-sterilized seeds are germinated in water agar, and once the plant develops its first set of leaves, are inoculated with the isolate. Alternatively, the plants are inoculated as seeds. For inoculation the microbial isolate is grown on solid media, and inoculated into a plant or onto a seed via any of the methods described herein. Plants are allowed to grow under ideal conditions for 2-3 weeks and any pathogenic effect of the introduced microbe is evaluated against uninoculated control plants.


Identification of Culturable Microbial Isolates that Correspond to Core OTUs


To accurately characterize the isolated microbial endophytes, colonies were submitted for marker gene sequencing, and the sequences were analyzed to provide taxonomic classifications. Among the cultured microbes (SYM strains), those with at least 97% 16S or ITS sequence similarity to OTUs of Table 1 and Table 2 were identified. Exemplary isolated microbes that correspond to core OTUs are listed in Table 7 (bacteria) and Table 8 (fungi).









TABLE 7







Exemplary bacterial endophytes









SEQ




ID


NO
SYM
Taxonomic Classification












290
SYM00003
Bacteria; Proteobacteria; Betaproteobacteria; Burkholderiales;




Oxalobacteraceae; Ralstonia pickettii


291
SYM00009
Bacteria; Proteobacteria; Betaproteobacteria; Burkholderiales;




Oxalobacteraceae; Ralstonia pickettii


292
SYM00013
Bacteria; Proteobacteria; Gammaproteobacteria; Pseudomonadales;




Pseudomonadaceae; Pseudomonas oryzihabitans


293
SYM00017A
Bacteria; Proteobacteria; Alphaproteobacteria; Rhizobiales;




Rhizobiaceae; Agrobacterium larrymoorei


294
SYM00018
Bacteria; Proteobacteria; Gammaproteobacteria; Enterobacteriales;




Enterobacteriaceae; Pantoea dispersa


295
SYM00020
Bacteria; Proteobacteria; Gammaproteobacteria; Enterobacteriales;




Enterobacteriaceae; Pantoea dispersa


296
SYM00021b
Bacteria; Proteobacteria; Gammaproteobacteria; Enterobacteriales;




Enterobacteriaceae; Escherichia hermannii


297
SYM00025
Bacteria; Proteobacteria; Gammaproteobacteria; Enterobacteriales;




Enterobacteriaceae; Pantoea dispersa


298
SYM00033
Bacteria; Proteobacteria; Gammaproteobacteria; Enterobacteriales;




Enterobacteriaceae; Enterobacter ludwigii


300
SYM00043
Bacteria; Proteobacteria; Gammaproteobacteria; Enterobacteriales;




Enterobacteriaceae; Pantoea dispersa


301
SYM00044
Bacteria; Proteobacteria; Gammaproteobacteria; Enterobacteriales;




Enterobacteriaceae; Enterobacter hormaechei


302
SYM00050
Bacteria; Proteobacteria; Gammaproteobacteria; Enterobacteriales;




Enterobacteriaceae; Enterobacter cloacae


303
SYM00053
Bacteria; Proteobacteria; Gammaproteobacteria; Enterobacteriales;




Enterobacteriaceae; Escherichia hermannii


305
SYM00062c
Bacteria; Firmicutes; Bacilli; Bacillales; Paenibacillaceae;





Saccharibacillus kuerlensis



306
SYM00065
Bacteria; Proteobacteria; Alphaproteobacteria; Sphingomonadales;




Sphingomonadaceae; Sphingomonas sanguinis


308
SYM00068
Bacteria; Proteobacteria; Gammaproteobacteria; Pseudomonadales;




Pseudomonadaceae; Pseudomonas psychrotolerans


309
SYM00070
Bacteria; Proteobacteria; Gammaproteobacteria; Enterobacteriales;




Enterobacteriaceae; Pantoea agglomerans


310
SYM00074
Bacteria; Proteobacteria; Gammaproteobacteria; Enterobacteriales;




Enterobacteriaceae; Enterobacter cloacae


311
SYM00103
Bacteria; Proteobacteria; Betaproteobacteria; Burkholderiales;




Oxalobacteraceae; Ralstonia pickettii


321
SYM00170
Bacteria; Firmicutes; Bacilli; Bacillales; Paenibacillaceae;





Paenibacillus hunanensis



322
SYM00183
Bacteria; Proteobacteria; Gammaproteobacteria; Xanthomonadales;




Xanthomonadaceae; Stenotrophomonas maltophilia


323
SYM00184
Bacteria; Proteobacteria; Gammaproteobacteria; Xanthomonadales;




Xanthomonadaceae; Stenotrophomonas maltophilia


324
SYM00207
Bacteria; Firmicutes; Bacilli; Bacillales; Bacillaceae; Bacillus





pumilus



325
SYM00212
Bacteria; Firmicutes; Bacilli; Bacillales; Bacillaceae; Bacillus sp.


326
SYM00219
Bacteria; Firmicutes; Bacilli; Bacillales; Bacillaceae; Bacillus sp.


327
SYM00234
Bacteria; Firmicutes; Bacilli; Bacillales; Paenibacillaceae;





Paenibacillus sp.



328
SYM00236
Bacteria; Proteobacteria; Alphaproteobacteria; Rhizobiales;




Methylobacteriaceae; Methylobacterium sp.


329
SYM00248
Bacteria; Proteobacteria; Gammaproteobacteria; Enterobacteriales;




Enterobacteriaceae; Pantoea sp.


330
SYM00249
Bacteria; Firmicutes; Bacilli; Bacillales; Bacillaceae; Bacillus sp.


331
SYM00506c
Bacteria; Firmicutes; Bacilli; Bacillales; Paenibacillaceae;





Paenibacillus sp.



332
SYM00507
Bacteria; Firmicutes; Bacilli; Bacillales; Bacillaceae; Bacillus sp.


333
SYM00508
Bacteria; Proteobacteria; Gammaproteobacteria; Enterobacteriales;




Enterobacteriaceae; Enterobacter asburiae


334
SYM00525
Bacteria; Actinobacteria; incertae sedis; Actinomycetales;




Microbacteriaceae; Curtobacterium sp.


335
SYM00538A
Bacteria; Proteobacteria; Alphaproteobacteria; Sphingomonadales;




Sphingomonadaceae; Sphingomonas aquatilis


336
SYM00538B
Bacteria; Firmicutes; Bacilli; Bacillales; Paenibacillaceae;





Paenibacillus sp.



337
SYM00538i
Bacteria; Bacteroidetes; Flavobacteriia; Flavobacteriales;




[Weeksellaceae]; Chryseobacterium sp.


338
SYM00543
Bacteria; Firmicutes; Bacilli; Bacillales; Bacillaceae; Bacillus sp.


339
SYM00545
Bacteria; Firmicutes; Bacilli; Bacillales; Paenibacillaceae;





Paenibacillus sp.



340
SYM00549
Bacteria; Firmicutes; Bacilli; Bacillales; Paenibacillaceae;





Paenibacillus sp.



341
SYM00563
Bacteria; Firmicutes; Bacilli; Bacillales; Bacillaceae; Bacillus sp.


343
SYM00574
Bacteria; Proteobacteria; Betaproteobacteria; Burkholderiales;




Burkholderiaceae; Burkholderia gladioli


347
SYM00617
Bacteria; Firmicutes; Bacilli; Bacillales; Bacillaceae; Bacillus sp.


348
SYM00620
Bacteria; Proteobacteria; Gammaproteobacteria; Enterobacteriales;




Enterobacteriaceae; Enterobacter sp.


350
SYM00627
Bacteria; Proteobacteria; Gammaproteobacteria; Enterobacteriales;




Enterobacteriaceae; Enterobacter sp.


351
SYM00628
Bacteria; Proteobacteria; Gammaproteobacteria; Enterobacteriales;




Enterobacteriaceae; Enterobacter sp.


353
SYM00646
Bacteria; Proteobacteria; Gammaproteobacteria; Pseudomonadales;




Pseudomonadaceae; Pseudomonas sp.


354
SYM00650
Bacteria; Proteobacteria; Gammaproteobacteria; Pseudomonadales;




Pseudomonadaceae; Pseudomonas sp.


355
SYM00662
Bacteria; Proteobacteria; Gammaproteobacteria; Pseudomonadales;




Pseudomonadaceae; Pseudomonas putida


358
SYM00714
Bacteria; Proteobacteria; Alphaproteobacteria; Rhizobiales;




Rhizobiaceae; Agrobacterium sp.


365
SYM00905
Bacteria; Proteobacteria; Gammaproteobacteria; Xanthomonadales;




Xanthomonadaceae; Stenotrophomonas sp.


366
SYM00924
Bacteria; Proteobacteria; Alphaproteobacteria; Rhizobiales;




Methylobacteriaceae; Methylobacterium sp.


367
SYM00963
Bacteria; Proteobacteria; Gammaproteobacteria; Enterobacteriales;




Enterobacteriaceae; Escherichia coli


368
SYM00982
Bacteria; Bacteroidetes; Flavobacteriia; Flavobacteriales;




[Weeksellaceae]; Chryseobacterium sp.


369
SYM00987
Bacteria; Proteobacteria; Gammaproteobacteria; Enterobacteriales;




Enterobacteriaceae; Escherichia coli


370
SYM00978
Bacteria; Proteobacteria; Alphaproteobacteria; Rhizobiales;




Methylobacteriaceae; Methylobacterium aquaticum


371
SYM00991
Bacteria; Proteobacteria; Beta Proteobacteria; Burkholderiales;




Comamonadaceae; Acidovorax avenae


372
SYM00999
Bacteria; Proteobacteria; Alphaproteobacteria; Rhizobiales;




Methylobacteriaceae; Methylobacterium sp.


373
SYM01049
Bacteria; Proteobacteria; Gammaproteobacteria; Enterobacteriales;




Enterobacteriaceae; Enterobacter sp.


426
SYM00057B
Bacteria; Proteobacteria; Betaproteobacteria; Burkholderiales;




Burkholderiaceae; Burkholderia caledonica


427
SYM00091
Bacteria; Proteobacteria; Alphaproteobacteria; Rhizobiales;




Rhizobiaceae; Rhizobium sp.


428
SYM00092D
Bacteria; Proteobacteria; Alphaproteobacteria; Caulobacterales;




Caulobacteraceae; Brevundimonas sp.


430
SYM00290
Bacteria; Proteobacteria; Gammaproteobacteria; Pseudomonadales;




Moraxellaceae; Acinetobacter lwoffii


433
SYM00576
Bacteria; Proteobacteria; Gammaproteobacteria; Enterobacteriales;




Enterobacteriaceae; Pantoea dispersa


434
SYM00607
Bacteria; Proteobacteria; Gammaproteobacteria; Enterobacteriales;




Enterobacteriaceae; Pantoea stewartii


435
SYM00619
Bacteria; Firmicutes; Bacilli; Bacillales; [Exiguobacteraceae];





Exiguobacterium acetylicum



436
SYM00786
Bacteria; Proteobacteria; Gammaproteobacteria; Enterobacteriales;




Enterobacteriaceae; Pantoea dispersa


437
SYM00879
Bacteria; Proteobacteria; Alphaproteobacteria; Rhizobiales;




Methylobacteriaceae; Methylobacterium populi


438
SYM00879B
Bacteria; Proteobacteria; Alphaproteobacteria; Sphingomonadales;




Sphingomonadaceae; Sphingomonas aquatilis


439
SYM00906
Bacteria; Proteobacteria; Gammaproteobacteria; Xanthmonadales;




Xanthomonadaceae; Stenotrophomonas rhizophila


440
SYM00965
Bacteria; Proteobacteria; Alphaproteobacteria; Sphingomonadales;




Erythrobacteraceae; Luteibacter yeojuensis


441
SYM01004
Bacteria; Proteobacteria; Alphaproteobacteria; Rhizobiales;




Rhizobiaceae; Agrobacterium larrymoorei


442
SYM01022
Bacteria; Actinobacteria; incertae sedis; Actinomycetales;




Microbacteriaceae; Curtobacterium flaccumfaciens;


451
SYM00865
Bacteria; Proteobacteria; Gammaproteobacteria; Xanthomonadales;




Xanthomonadaceae; Stenotrophomonas rhizophila


452
SYM01158
Bacteria; Proteobacteria; Gammaproteobacteria; Enterobacteriales;




Enterobacteriaceae; Pantoea agglomerans
















TABLE 8







Exemplary fungal endophytes









SEQ




ID


NO
SYM
Taxonomic Classification












299
SYM00034
Fungi; Ascomycota; Sordariomycetes; Hypocreales; Incertae sedis;





Acremonium zeae



304
SYM00061A
Fungi; Ascomycota; Sordariomycetes; Hypocreales; Incertae sedis;





Acremonium zeae



307
SYM00066
Fungi; Ascomycota; Sordariomycetes; Hypocreales; Incertae sedis;





Acremonium zeae



312
SYM00120
Fungi; Ascomycota; Dothideomycetes; Pleosporales; Pleosporaceae;





Alternaria alternata



313
SYM00122
Fungi; Ascomycota; Dothideomycetes; Pleosporales; Pleosporaceae;





Epicoccum nigrum



314
SYM00123
Fungi; Ascomycota; Dothideomycetes; Pleosporales; Pleosporaceae;





Epicoccum nigrum



315
SYM00124
Fungi; Ascomycota; Sordariomycetes; Hypocreales; Nectriaceae;





Fusarium graminearum



316
SYM00129
Fungi; Ascomycota; Sordariomycetes; Hypocreales; Nectriaceae;





Fusarium proliferatum



317
SYM00135
Fungi; Ascomycota; Sordariomycetes; Hypocreales; Nectriaceae;





Fusarium proliferatum



318
SYM00136
Fungi; Ascomycota; Sordariomycetes; Hypocreales; Nectriaceae;





Fusarium proliferatum



319
SYM00151
Fungi; Ascomycota; Sordariomycetes; Hypocreales; Nectriaceae;





Fusarium proliferatum



320
SYM00154
Fungi; Ascomycota; Sordariomycetes; Hypocreales; Nectriaceae;





Fusarium sp.



342
SYM00566B
Fungi; Ascomycota; Sordariomycetes; Hypocreales; Incertae sedis;





Acremonium zeae



344
SYM00577
Fungi; Ascomycota; Sordariomycetes; Hypocreales; Incertae sedis;





Acremonium zeae



345
SYM00590
Fungi; Ascomycota; Sordariomycetes; Hypocreales; Incertae sedis;





Acremonium zeae



346
SYM00603
Fungi; Ascomycota; Sordariomycetes; Hypocreales; Incertae sedis;





Acremonium zeae



349
SYM00622
Fungi; Ascomycota; Sordariomycetes; Hypocreales; Incertae sedis;





Acremonium strictum



352
SYM00629
Fungi; Ascomycota; Sordariomycetes; Hypocreales; Incertae sedis;





Acremonium strictum



356
SYM00663
Fungi; Ascomycota; Dothideomycetes; Pleosporales; Pleosporaceae;





Alternaria alternata



357
SYM00696
Fungi; Ascomycota; Dothideomycetes; Pleosporales; Pleosporaceae;





Alternaria tenuissima



359
SYM00741a
Fungi; Ascomycota; Dothideomycetes; Pleosporales; Incertae sedis;





Phoma herbarum



360
SYM00741b
Fungi; Ascomycota; Dothideomycetes; Capnodiales; Davidiellaceae;





Cladosporium tenuissimum



361
SYM00793
Fungi; Ascomycota; Sordariomycetes; Hypocreales; Nectriaceae;





Fusarium verticillioides



362
SYM00795
Fungi; Ascomycota; Sordariomycetes; Hypocreales; Incertae sedis;





Acremonium zeae



363
SYM00854
Fungi; Ascomycota; Dothideomycetes; Pleosporales; Pleosporaceae;





Epicoccum sorghinum



364
SYM00880
Fungi; Ascomycota; Dothideomycetes; Pleosporales; Pleosporaceae;





Alternaria tenuissima



374
SYM01300
Fungi; Ascomycota; Sordariomycetes; Hypocreales; Incertae sedis;





Acremonium zeae



375
SYM01303
Fungi; Ascomycota; Sordariomycetes; Hypocreales; Nectriaceae;





Fusarium sp.



376
SYM01310
Fungi; Ascomycota; Sordariomycetes; Hypocreales; Nectriaceae;





Fusarium proliferatum



377
SYM01311
Fungi; Ascomycota; Sordariomycetes; Hypocreales; Nectriaceae;





Fusarium sp.



378
SYM01314
Fungi; Ascomycota; Sordariomycetes; Hypocreales; Incertae sedis;





Acremonium zeae



379
SYM01315
Fungi; Ascomycota; Dothideomycetes; Capnodiales; Davidiellaceae;





Cladosporium sp.



380
SYM01325
Fungi; Ascomycota; Dothideomycetes; Pleosporales; Pleosporaceae;





Alternaria sp.



381
SYM01326
Fungi; Ascomycota; Dothideomycetes; Pleosporales; Pleosporaceae;





Alternaria alternata



382
SYM01327
Fungi; Ascomycota; Dothideomycetes; Capnodiales; Davidiellaceae;





Cladosporium sp.



383
SYM01328
Fungi; Ascomycota; Dothideomycetes; Pleosporales; Pleosporaceae;





Alternaria sp.



384
SYM01333
Fungi; Ascomycota; Dothideomycetes; Pleosporales; Pleosporaceae;





Alternaria infectoria



385
SYM15811
Fungi; Ascomycota; Dothideomycetes; Pleosporales; Pleosporaceae;





Alternaria sp.



386
SYM15820
Fungi; Ascomycota; Sordariomycetes; Trichosphaeriales; incertae




sedis; Nigrospora oryzae


387
SYM15821
Fungi; Ascomycota; Sordariomycetes; Trichosphaeriales; incertae




sedis; Nigrospora oryzae


388
SYM15825
Fungi; Ascomycota; Sordariomycetes; Hypocreales; Nectriaceae;





Fusarium sp.



389
SYM15828
Fungi; Ascomycota; Sordariomycetes; Hypocreales; Nectriaceae;





Fusarium sp.



390
SYM15831
Fungi; Ascomycota; Sordariomycetes; Hypocreales; Nectriaceae;





Fusarium sp.



391
SYM15837
Fungi; Ascomycota; Sordariomycetes; Hypocreales; Nectriaceae;





Fusarium sp.



392
SYM15839
Fungi; Ascomycota; Sordariomycetes; Hypocreales; Nectriaceae;





Fusarium sp.



393
SYM15847
Fungi; Ascomycota; Sordariomycetes; Hypocreales; Nectriaceae;





Fusarium udum



394
SYM15870
Fungi; Ascomycota; Sordariomycetes; Hypocreales; Nectriaceae;





Fusarium sp.



395
SYM15872
Fungi; Ascomycota; Sordariomycetes; Hypocreales; Nectriaceae;





Fusarium sp.



396
SYM15890
Fungi; Ascomycota; Dothideomycetes; Capnodiales; Davidiellaceae;





Cladosporium sp.



397
SYM15901
Fungi; Ascomycota; Sordariomycetes; Hypocreales; Nectriaceae;





Fusarium sp.



398
SYM15920
Fungi; Ascomycota; Sordariomycetes; Hypocreales; Nectriaceae;





Fusarium equiseti



399
SYM15926
Fungi; Ascomycota; Dothideomycetes; Pleosporales; Pleosporaceae;





Alternaria sp.



400
SYM15928
Fungi; Ascomycota; Dothideomycetes; Pleosporales; Pleosporaceae;





Alternaria sp.



401
SYM15932
Fungi; Ascomycota; Sordariomycetes; Hypocreales; Nectriaceae;





Fusarium sp.



402
SYM15939
Fungi; Ascomycota; Sordariomycetes; Hypocreales; Nectriaceae;





Fusarium sp.



429
SYM00157
Fungi; Ascomycota; Dothideomycetes; incertae sedis; incertae sedis;





Leptosphaerulina chartarum



431
SYM00299
Fungi; Ascomycota; Dothideomycetes; Capnodiales; Davidiellaceae;





Cladosporium tenuissimum



432
SYM00301
Fungi; Ascomycota; Eurotiomycetes; Eurotiales; Trichocomaceae;





Penicillium chrysogenum



443
SYM01324
Fungi; Ascomycota; Eurotiomycetes; Eurotiales; Trichocomaceae;





Aspergillus pseudoglaucus



444
SYM01329
Fungi; Ascomycota; Dothideomycetes; Pleosporales; Didymellaceae;





Peyronellaea glomerata



445
SYM01330
Fungi; Zygomycota; incertae sedis; Mucorales; Rhizopodaceae;





Rhizopus oryzae



446
SYM12462
Fungi; Ascomycota; Dothideomycetes; Capnodiales; Davidiellaceae;





Cladosporium sphaerospermum



447
SYM15774
Fungi; Ascomycota; Dothideomycetes; Pleosporales; Incertae sedis;





Phoma medicaginis



448
SYM15783
Fungi; Ascomycota; Dothideomycetes; Pleosporales; Pleosporaceae;





Alternaria macrospora



449
SYM00300
Fungi; Ascomycota; Sordariomycetes; Hypocreales; Incertae sedis;





Acremonium strictum



450
SYM01331
Fungi; Ascomycota; Dothideomycetes; Pleosporales; Incertae sedis;





Phoma pedeiae



453
SYM15810
Fungi; Ascomycota; Sordariomycetes; Hypocreales; Nectriaceae;





Fusarium sp.



454
SYM15879
Fungi; Ascomycota; Sordariomycetes; Hypocreales; Nectriaceae;





Fusarium torulosum



455
SYM15880
Fungi; Ascomycota; Eurotiomycetes; Eurotiales; Trichocomaceae;





Penicillium chrysogenum



299
SYM00034
Fungi; Ascomycota; Sordariomycetes; Hypocreales; Incertae sedis;





Acremonium zeae










Example 2: Synthetic Compositions Comprising Plant Seeds and a Single Endophyte Strain or a Plurality of Endophytes Confer Benefits to Agricultural Plants

This example describes the ability of synthetic compositions comprising plant seeds and a single endophyte strain or a plurality of endophyte strains described herein, to confer one or more benefits to a host plant. Among other things, this Example describe the ability of endophytes (e.g., bacterial and fungal endophytes described herein) to confer beneficial traits on a variety of host plants, including but not limited to, dicots (e.g., soy, peanut) and monocots (e.g., corn, soy, wheat, cotton, sorghum), and combinations thereof. Endophyte-inoculated seeds (e.g., seeds described herein) were tested under water-limited conditions (e.g., drought stress) in seed germination assays and seedling root, vigor assays to test whether one or more endophytes confer an increase in tolerance to these stresses. These growth tests were performed using growth assays (e.g., germination assays and seedling root vigor assays) on sterile filter papers. Seeds were treated either with a single bacterial or fungal strain, or with a combination of two bacterial or two fungal strains. In some embodiments, seeds were treated with a combination of at least one bacterial and at least one fungal strain.


Experimental Description

Growth & Scale-Up of Bacteria for Inoculation


Each bacterial endophyte was streaked out onto 20% Tryptic Soy Agar, forming a lawn on regular Petri dishes (9 cm in diameter). Once the bacteria grew to high density, which happened after one or two days depending on the bacterial growth rate, a plate per bacterial strain was scraped with the aid of a sterile loop (filling the entire hole of the loop and producing a droplet of bacterial biomass of about 20 mg). The bacteria collected in this way were transferred into 1 ml of sterile 50 mM Phosphate Buffer Saline (PBS) in a microcentrifuge tube and fully resuspended by vortexing for ˜20 sec at maximum speed. This method achieves highly concentrated (˜0.5-1 optical density, corresponding to about 108 CFU/mL) and viable bacteria pre-adapted to live coating a surface.


Growth & Scale-Up of Fungi for Inoculation


Fungal isolates were grown from a frozen stock on Petri dishes containing potato dextrose agar and the plates were incubated at room temperature for about a week. After mycelia and spore development, four agar plugs (1 cm in diameter) were used to inoculate erlenmeyers containing 150 ml of potato dextrose broth. Liquid cultures were grown at room temperature and agitation on an orbital shaker at 115 rpm for 4 days. Then, the cultures were transferred to 50 ml sterile test tubes with conical bottoms. Mycelium mats were disrupted by pulse sonication at 75% setting and 3 pulses of 20 seconds each, using a Fisher Scientific sonicator (Model FB120) with a manual probe (CL-18). The sonicated cultures were used in the same manner as the bacterial suspensions for seed inoculation.


Surface Sterilization of Seeds


Un-treated seeds (e.g., soy seeds or wheat seeds) were sterilized overnight with chlorine gas as follows: 200 g of seeds were weighed and placed in a 250 mL glass bottle. The opened bottle and its cap were placed in a dessicator jar in a fume hood. A beaker containing 100 mL of commercial bleach (8.25% sodium hypochlorite) was placed in the dessicator jar. Immediately prior to sealing the jar, 3 mL of concentrated hydrochloric acid (34-37.5%) were carefully added to the bleach. The sterilization was left to proceed for 17-24 h. After sterilization, the bottle was closed with its sterilized cap, and reopened in a sterile flow hood. The opened bottle was left in the sterile hood for a couple hours to air out the seeds and remove chlorine gas leftover. The bottle was then closed and the seeds stored at room temperature in the dark until use.


Preparation of Synthetic Compositions Comprising Plant Seeds and Endophytes


The following procedure was used to coat seeds with a plurality of fungal endophyte inocula for planting in greenhouse and field trials. First, 3% Sodium alginate (SA) was prepared and autoclaved in the following manner. Erlenmeyer flasks were filled with the appropriate amount of deionized water and warmed to about 50 degrees. C on a heat plate with agitation using a stirring bar. SA powder was poured slowly into the water until it all dissolved. The solution was autoclaved (121° C. @15PSI for 30 minutes). Talcum powder was autoclaved in dry cycle (121° C. @15PSI for 30 minutes) and aliquoted in Ziploc bags or 50 ml falcon tubes at a ratio of 15 g per kg of seed to be treated for formulation controls and 10 g per kg of seed for actual treatments.


The next day, seeds were treated with either powdered or liquid formulations.


For powdered formulations, 10 g per kg of seed was allocated to the seeds to be treated, according to the following procedure. Seeds were placed in large plastic container. 16.6 ml of 2% SA per Kg of seeds to be treated were poured on the seeds. The container was covered and shaken slowly in orbital motion for about 20 seconds to disperse the SA. Endophyte powder was mixed with an equal amount of talcum powder. The mix of endophytes and talc was added on top of the seeds, trying to disperse it evenly. The container was covered and seeds are shaken slowly in orbital motion for about 20 seconds. 13.3 ml of Flo-rite per kg of seed to be treated was poured on the seeds. Seeds were shaken again, slowly and in orbital motion.


For liquid formulations, 8.5 mL per seed was allocated to the seeds to be treated, according to the following procedure. Seeds were placed in large plastic container. 8.3 ml of 2% SA per kg of seed and the same amount of bacterial culture (8.3 ml per kg of seed) was poured on the seeds. The container was covered and shaken slowly in orbital motion for about 20 seconds to disperse the SA. 15 g of talcum powder per kg of seed was added, trying to disperse it evenly. The container was covered and seeds were shaken slowly in orbital motion for about 20 seconds. 13.3 ml of Flo-rite per kg of seed to be treated are poured on the seeds. Seeds were shaken again, slowly and in orbital motion. For soy seeds, 10 μL of sodium alginate and inoculum were applied for every one gram of seeds. For wheat seeds, the amount of SA and bacterial suspension or fungal inoculum was adjusted to 15 ml/kg to account for the larger surface to volume ratio of these small seeds.


Testing for Germination Enhancement Under Drought Stress


Polyethylene glycol (PEG) is an inert, water-binding polymer with a non-ionic and virtually impermeable long chain that accurately mimics drought stress under dry-soil conditions. The higher the concentration of PEG, the lower the water potential achieved, thus inducing higher water stress in a watery medium. To determine germination enhancement in seeds, the interiors of which are colonized by microbial strains, the effect of osmotic potential on germination is tested at a range of water potential representative of drought conditions following Perez-Fernandez et al. [J. Environ. Biol. 27: 669-685 (2006)]. The range of water potentials simulates those that are known to cause drought stress in a range of cultivars and wild plants, (−0.05 MPa to −5 MPa). The appropriate concentration of polyethylene glycol (6000) required to achieve a particular water potential was determined following Michel and Kaufmann (Plant Physiol., 51: 914-916 (1973)) and further modifications by Hardegree and Emmerich (Plant Physiol., 92, 462-466 (1990)). The final equation used to determine amounts of PEG is: Ψ=0.130 [PEG]2 T-13.7 [PEG]2; where the osmotic potential (Ψ) is a function of temperature (T).


Soy Seedling Germination Assay in Drought Conditions


For each SYM tested in the germination assay, ten (10) SYM-coated soy seeds were placed on a 150 mm Petri plate that contained a single heavy germination paper (SD5-1/4 76# heavy weight seed germination paper, Anchor Paper Co., St. Paul, Minn.). To each petri plate, 10 mL 8% polyethylene glycol (PEG 6000) was added for germination screening assays in drought conditions. Plates were covered and incubated at in the dark at 22° Celcius and 60% relative humidity for four days for bacterial SYM strains) or five days for fungal SYM strains. All experiments were done in triplicate under sterile conditions. Seedlings were scored based on germination percentage relative to formulation only and non-treated seedling controls at the end of the incubation period. Exemplary soy germination results under drought conditions are shown in Table A.









TABLE A







Soy germination assay results














Ave (%



Crop
SYM1
SYM2
toNT)
Type














soy
SYM00057B

155.83
bacteria


soy
SYM00074

283.33
bacteria


soy
SYM00091
SYM00092D
120.00
bacterial plurality


soy
SYM00092D

175.83
bacteria


soy
SYM00590

141.18
bacteria


soy
SYM00603

135.29
bacteria


soy
SYM00607
SYM00091
115.00
bacterial plurality


soy
SYM00607
SYM00092D
135.00
bacterial plurality


soy
SYM00619

212.50
bacteria


soy
SYM00092D
SYM15879
140.00
Bacterium-Fungus






plurality


soy
SYM00092D
SYM15880
115.00
Bacterium-Fungus






plurality


soy
SYM00092D
SYM15934
115.00
Bacterium-Fungus






plurarlity


soy
SYM00299

115.51
fungi


soy
SYM00301

123.02
fungi


soy
SYM00577

141.18
fungi


soy
SYM01310

135.29
fungi


soy
SYM01311

135.29
fungi


soy
SYM01314

135.29
fungi


soy
SYM01330

325.00
fungi


soy
SYM15774

115.98
fungi


soy
SYM15783

141.18
fungi


soy
SYM15879
SYM15934
110.00
fungal plurality


soy
SYM15880
SYM15884
158.82
fungal plurality










Soy Seedling Root Vigor Assay in Drought Conditions


For each SYM tested in the root vigor assay, ten (10) soy seeds were placed equidistant to each other on moistened heavy weight germination paper sandwiches. Each layer of the germination paper was pre-soaked in 25 mL of sterile distilled water. The germination paper sandwich was rolled, taped using surgical tape, placed in glass bottles and incubated at 22° Celcius with 60% relative humidity in dark for four (4) days to allow seed germination. On day five (5), bottle lids were removed and seed samples were placed in a growth chamber set to 25° Celcius, 70% RH, 250-300 microEinsten light for 12 hours and 18° Celcius, 60% RH dark 12 hours for five (5) days. Placement of bottles were randomized daily to reduce any positional effect throughout the incubation period. At the end of the experiment, each soy seedling was measured for total root length and compared relative to formulation only and non-treated seedling controls. Exemplary soy root vigor results under drought conditions are shown in Table B.









TABLE B







Soy root vigor assay results















Ave(%
SE(%



Crop
SYM1
SYM2
toNT)
toNT)
Type















soy
SYM00057B

98.0
11.9
bacteria


soy
SYM00074

99.0
10.8
bacteria


soy
SYM00091
SYM00092D
96.7
5.9
bacterial plurality


soy
SYM00092D

87.9
12.9
bacteria


soy
SYM00590

100.6
11.8
bacteria


soy
SYM00603

118.2
9.3
bacteria


soy
SYM00607
SYM00091
82.3
5.1
bacterial plurality


soy
SYM00607
SYM00092D
92.1
8.1
bacterial plurality


soy
SYM00619

99.0
12.4
bacteria


soy
SYM00092D
SYM15879
72.6
8.7
Bacterium -







Fungus plurality


soy
SYM00092D
SYM15880
111.2
2.2
Bacterium -







Fungus plurality


soy
SYM00092D
SYM15934
82.8
9.7
Bacterium -







fungus plurality


soy
SYM00299

92.5
10.0
fungi


soy
SYM00301

111.3
8.5
fungi


soy
SYM00577

132.4
3.3
fungi


soy
SYM01310

91.2
15.7
fungi


soy
SYM01311

97.6
12.3
fungi


soy
SYM01314

107.1
12.3
fungi


soy
SYM01330

97.6
16.0
fungi


soy
SYM15774

153.7
7.6
fungi


soy
SYM15783

137.1
7.6
fungi


soy
SYM15879
SYM15934
95.0
12.3
fungal plurality


soy
SYM15880
SYM15884
104.7
12.3
fungal plurality










Wheat Seedling Germination Assay in Drought Conditions


For each SYM tested, 25 uL of sonicated, 7-day old fungal culture or 3-day old bacteria culture was added into 15 mL of semi-solid solution [12.5% polyethylene glycol (PEG 6000) and 0.3% of agar] pre-aliquoted in a 90 mm deep well petri dish. After adding the SYM biomass, the petri dishes were horizontally shaken for even distribution of SYM biomass. Fifteen (15) surface-steriled wheat seeds were placed onto each petri dish. Plates were covered and incubated in the dark at 24° Celcius and 60% relative humidity for three days in a Conviron chamber. All experiments were done in triplicate under sterile conditions. Seedlings were scored by counting the number of germinated seedlings per dish and the performance of each SYM normalized as germination percentage relative to formulation only and non-treated seedling controls at the end of the incubation period. Exemplary wheat germination results under drought conditions are shown in Table C.









TABLE C







Wheat germination assay results















Ave(%
SE(%



Crop
SYM1
SYM2
toNT)
toNT)
Type















wheat
SYM00044

126.9
5.5
bacteria


wheat
SYM00044
SYM00021B
150.0
0.0
bacterial plurality


wheat
SYM00044
SYM00074
136.4
7.9
bacterial plurality


wheat
SYM00044
SYM00879
145.5
18.2
bacterial plurality


wheat
SYM00044
SYM00879B
136.4
7.9
bacterial plurality


wheat
SYM00057B

107.4
11.5
bacteria


wheat
SYM00057B
SYM00906
154.5
16.4
bacterial plurality


wheat
SYM00057B
SYM01004
136.4
20.8
bacterial plurality


wheat
SYM00074

109.4
11.0
bacteria


wheat
SYM00074
SYM00092D
131.8
9.1
bacterial plurality


wheat
SYM00074
SYM00290
131.8
12.0
bacterial plurality


wheat
SYM00074
SYM00879
131.8
12.0
bacterial plurality


wheat
SYM00074
SYM01004
136.4
7.9
bacterial plurality


wheat
SYM00074
SYM01022
154.5
16.4
bacterial plurality


wheat
SYM00092D

118.6
7.4
bacteria


wheat
SYM00092D
SYM00021B
136.4
13.6
bacterial plurality


wheat
SYM00092D
SYM00865
135.0
8.7
bacterial plurality


wheat
SYM00092D
SYM00965
150.0
17.3
bacterial plurality


wheat
SYM00212

157.9
0.0
bacteria


wheat
SYM00290

119.6
6.8
bacteria


wheat
SYM00290
SYM00906
131.8
27.6
bacterial plurality


wheat
SYM00290
SYM01022
145.5
24.1
bacterial plurality


wheat
SYM00696

108.3
10.1
bacteria


wheat
SYM00786
SYM00865
140.0
18.0
bacterial plurality


wheat
SYM00879

111.4
7.2
bacteria


wheat
SYM00879
SYM01004
172.7
4.5
bacterial plurality


wheat
SYM00879B

105.2
17.3
bacteria


wheat
SYM00906

125.0
7.2
bacteria


wheat
SYM00906
SYM01004
136.4
7.9
bacterial plurality


wheat
SYM00965
SYM00865
150.0
17.3
bacterial plurality


wheat
SYM01004

115.2
12.5
bacteria


wheat
SYM01004
SYM01022
140.9
16.4
bacterial plurality


wheat
SYM01022

115.5
9.3
bacteria


wheat
SYM01158

142.1
24.1
bacteria


wheat
SYM01326

103.8
8.5
bacteria


wheat
SYM00157

115.6
10.1
fungi


wheat
SYM00157
SYM15783
141.7
11.0
fungal plurality


wheat
SYM00299

121.4
10.6
fungi


wheat
SYM00299
SYM00696
145.8
11.0
fungal plurality


wheat
SYM00299
SYM01324
133.3
25.3
fungal plurality


wheat
SYM00299
SYM15783
137.5
0.0
fungal plurality


wheat
SYM00301

112.7
10.1
fungi


wheat
SYM00301
SYM01326
133.3
15.0
fungal plurality


wheat
SYM00301
SYM15774
145.8
11.0
fungal plurality


wheat
SYM01324

114.2
8.8
fungi


wheat
SYM01326
SYM12462
129.2
11.0
fungal plurality


wheat
SYM12462
SYM15774
133.3
18.2
fungal plurality


wheat
SYM12462
SYM15783
141.7
16.7
fungal plurality


wheat
SYM15774

122.4
9.5
fungi


wheat
SYM15774
SYM01324
137.5
12.5
fungal plurality


wheat
SYM15783

120.0
5.4
fungi


wheat
SYM15783
SYM01324
129.2
8.3
fungal plurality


wheat
SYM15879

99.4
8.5
fungi


wheat
SYM15880
SYM15888
159.1
12.0
fungal plurality










Wheat Seedling Root Vigor Assay in Drought Conditions


For each SYM tested, twelve (12) SYM-coated wheat seeds were placed onto a 125 mm filter paper pre-wet with 5 mL of 12.5% polyethylene glycol (PEG 6000). The seeds were arranged in a circular formation and with embryo facing toward the center of the filter paper. Plates were covered and incubated in the dark at 24° Celcius and 60% relative humidity for three days in a Conviron chamber. All experiments were done in triplicate under sterile conditions. At the end of the incubation period, images were taken for each plate and root length were measured (in pixel) on the images using ImageJ and the pixel was finally converted into cm based on an internal standard. The performance of each SYM was normalized as root length percentage relative to formulation only and non-treated seedling controls. Exemplary wheat root vigor results under drought conditions are shown in Table D.









TABLE D







Wheat root vigor assay results












Crop
SYM1
SYM2
Ave (% to NT)
SE (% to NT)
Type















wheat
SYM00021B

104.0
4.4
bacteria


wheat
SYM00044

101.4
4.0
bacteria


wheat
SYM00044
SYM00021B
111.7
3.7
bacterial







plurality


wheat
SYM00044
SYM00074
101.9
5.1
bacterial







plurality


wheat
SYM00044
SYM00879
105.4
4.6
bacterial







plurality


wheat
SYM00044
SYM00879B
107.6
5.0
bacterial







plurality


wheat
SYM00057B

102.8
4.6
bacteria


wheat
SYM00057B
SYM00906
118.7
5.4
bacterial







plurality


wheat
SYM00057B
SYM01004
104.1
4.8
bacterial







plurality


wheat
SYM00074

111.2
5.6
bacteria


wheat
SYM00074
SYM00092D
99.5
4.4
bacterial







plurality


wheat
SYM00074
SYM00290
103.5
4.3
bacterial







plurality


wheat
SYM00074
SYM00879
107.8
4.6
bacterial







plurality


wheat
SYM00074
SYM01004
110.8
4.7
bacterial







plurality


wheat
SYM00074
SYM01022
102.9
4.7
bacterial







plurality


wheat
SYM00092D

112.1
3.8
bacteria


wheat
SYM00092D
SYM00021B
103.5
5.8
bacterial







plurality


wheat
SYM00092D
SYM00865
105.2
5.5
bacterial







plurality


wheat
SYM00092D
SYM00965
119.2
4.5
bacterial







plurality


wheat
SYM00212

117.7
5.6
bacteria


wheat
SYM00290

103.2
6.3
bacteria


wheat
SYM00290
SYM00906
103.1
5.5
bacterial







plurality


wheat
SYM00290
SYM01022
112.7
4.0
bacterial







plurality


wheat
SYM00696

162.0
19.6
bacteria


wheat
SYM00786
SYM00865
111.3
4.3
bacterial







plurality


wheat
SYM00879

102.0
4.9
bacteria


wheat
SYM00879
SYM01004
111.5
5.3
bacterial







plurality


wheat
SYM00879B

102.3
5.8
bacteria


wheat
SYM00906

118.3
5.2
bacteria


wheat
SYM00906
SYM01004
111.1
5.3
bacterial







plurality


wheat
SYM00965
SYM00865
111.3
5.5
bacterial







plurality


wheat
SYM01004

111.6
4.9
bacteria


wheat
SYM01004
SYM01022
108.2
5.6
bacterial







plurality


wheat
SYM01022

102.1
6.3
bacteria


wheat
SYM01158

117.0
5.6
bacteria


wheat
SYM00157

128.1
17.9
fungi


wheat
SYM00157
SYM15783
234.4
13.5
fungal plurality


wheat
SYM00299

140.3
11.2
fungi


wheat
SYM00299
SYM00696
47.4
11.5
fungal plurality


wheat
SYM00299
SYM01324
72.6
15.9
fungal plurality


wheat
SYM00299
SYM15783
90.2
14.2
fungal plurality


wheat
SYM00301

183.7
17.0
fungi


wheat
SYM00301
SYM01326
28.9
8.2
fungal plurality


wheat
SYM00301
SYM15774
226.9
17.2
fungal plurality


wheat
SYM01324

181.9
18.5
fungi


wheat
SYM01326

62.4
14.1
fungi


wheat
SYM01326
SYM12462
60.4
10.6
fungal plurality


wheat
SYM01329

195.7
15.0
fungi


wheat
SYM01330

102.7
8.2
fungi


wheat
SYM12462

96.3
15.7
fungi


wheat
SYM12462
SYM15774
17.6
7.8
fungal plurality


wheat
SYM12462
SYM15783
198.2
16.3
fungal plurality


wheat
SYM15774

143.4
5.2
fungi


wheat
SYM15774
SYM01324
102.5
16.2
fungal plurality


wheat
SYM15783

119.0
14.8
fungi


wheat
SYM15783
SYM01324
61.5
13.2
fungal plurality


wheat
SYM15879

158.9
15.2
fungi


wheat
SYM15880
SYM15888
148.6
13.3
fungal plurality









Discussion

Plant vigor and improved stress resilience are important components of providing fitness to a plant in an agricultural setting. These were measured in germination assays and seedling root vigor assays to test the improvement on plant phenotype as conferred by microbial inoculation. The collection of seed-derived endophytes produced a measurable response in soy and wheat when inoculated as compared to non-inoculated controls, as shown in Table A, Table B, Table C and Table D. For example, most of the strains tested were found to produce a favorable phenotype in any of the measured multiple parameters such as germination efficiency, root length, or shoot length, suggesting that the strains play an intimate role modulating and improving plant vigor and conferring stress resilience to the host plant. The stress responses in the strain collection can be seen by the ability of a subgroup to confer a beneficial response under different conditions such as water stress. These can be applicable to products for arid and marginal lands. In a large proportion of cases for the tested strains, the beneficial effect was measurable in several crops. In one aspect of the invention, it is understood that beneficial strains described herein are capable of colonizing multiple varieties and plant species.


Example 3: Synthetic Compositions Comprising Plant Seeds and a Single Endophyte Strain or a Plurality of Endophyte Strains Confer Benefits to Agricultural Plants

This Example describes the ability of synthetic compositions comprising plant seeds and a single endophyte strain or a plurality of endophyte strains described herein, to confer beneficial traits to a host plant. Among other things, this Example describe the ability of endophytes (e.g., bacterial and fungal endophytes described herein) to confer beneficial traits on a variety of host plants, including but not limited to, dicots (e.g., soy, peanuts) and monocots (e.g., corn, soy, wheat, cotton, sorghum), and combinations thereof. Endophyte-inoculated seeds (e.g., seeds described herein) are tested under normal conditions, biotic stress, heat stress, cold stress, high salt stress, soil with high metal content, and combinations thereof, in seed germination assays and seedling root vigor assays to test whether one or more endophytes confer an increase in tolerance to one or more stresses. Growth tests are performed using growth assays (e.g., germination assays and seedling root vigor assays) on sterile filter papers. In some embodiments, seeds are treated either with a single bacterial or fungal strain, or with a combination of two bacterial or two fungal strains. In some embodiments, seeds are treated with two or more bacterial or fungal strains. In some embodiments, seeds are treated with a combination of at least one bacterial and at least one fungal strain.


Growth and scale-up of bacteria and fungi for inoculation, surface sterilization of seeds, and seed coating are performed as described herein.


Testing for Germination Enhancement in Normal Conditions


Standard Germination Tests are used to assess the ability of the endophyte to enhance the seeds' germination and early growth. Briefly, 400 seeds (e.g., seeds described herein) are coated with one or more endophytes described herein, and are placed in between wet brown paper towels (8 replicates with 50 seeds each). An equal number of seeds are treated with formulation only. Paper towels are placed on top of 1×2 feet plastic trays and maintained in a growth chamber set at 25° C. and 70% humidity for 7 days. Seedlings are scored based on germination percentage relative to formulation only and non-treated seedling controls


Testing for Germination Enhancement Under Biotic Stress


A modification of the method developed by Hodgson [Am. Potato. J. 38: 259-264 (1961)] is used to test germination enhancement in microbe-colonized seeds under biotic stress. Biotic stress is understood as a concentration of inocula in the form of cell (bacteria) or spore suspensions (fungus) of a known pathogen for a particular crop (e.g., Pantoea stewartii or Fusarium graminearum for Zea mays L.). Briefly, for each level of biotic stress, 400 seeds (e.g., seeds described herein), the interiors of which are colonized by microbial strains, and 400 seed controls (lacking the microbial strains), are placed in between brown paper towels: 8 replicates with 50 seeds each for each treatment (microbe-colonized and control). Each one of the replicates is placed inside a large petri dish (150 mm in diameter). The towels are then soaked with 10 mL of pathogen cell or spore suspension at a concentration of 104 to 108 cells/spores per mL. Each level corresponds with an order of magnitude increment in concentration (thus, 5 levels). The petri dishes are maintained in a growth chamber set at 25° C. and 70% humidity for 7 days. The proportion of seeds that germinate successfully is compared between the seeds coming from microbe-colonized plants with those coming from controls for each level of biotic stress.


Testing for Germination Enhancement in Heat Conditions


Standard Germination Tests are used to determine if a microbe colonizing the interior of a seed protects maize against heat stress during germination. Briefly, 400 seeds (e.g, seeds described herein), the interiors of which are colonized by microbial strains are placed in between wet brown paper towels (8 replicates with 50 seeds each). An equal number of seeds obtained from control plants that lack the microbe is treated in the same way. The paper towels are placed on top of 1×2 ft plastic trays and maintained in a growth chamber set at 16:8 hour light:dark cycle, 70% humidity, and at least 120 μE/m2/s light intensity for 7 days. A range of high temperatures (from 35° C. to 45° C., with increments of 2 degrees per assay) is tested to assess the germination of microbe-colonized seeds at each temperature. The proportion of seeds that germinate successfully is compared between the seeds coming from microbe-colonized plants and those coming from controls.


Testing for Germination Enhancement in Cold Conditions


Standard Germination Tests are used to determine if a microbe colonizing the interior of a seed protects maize against cold stress during germination. Briefly, 400 seeds (e.g., seeds described herein), the interiors of which are colonized by microbial strains are placed in between wet brown paper towels (8 replicates with 50 seeds each). An equal number of seeds obtained from control plants that lack the microbe is treated in the same way. The paper towels are placed on top of 1×2 ft plastic trays and maintained in a growth chamber set at 16:8 hour light:dark cycle, 70% humidity, and at least 120 μE/m2/s light intensity for 7 days. A range of low temperatures (from 0° C. to 10° C., with increments of 2 degrees per assay) is tested to assess the germination of microbe-colonized seeds at each temperature. The proportion of seeds that germinate successfully is compared between the seeds coming from microbe-colonized plants and those coming from controls.


Testing for Germination Enhancement in High Salt Concentrations


Germination experiments are conducted in 90 mm diameter petri dishes. Replicates consist of a Petri dish, watered with 10 mL of the appropriate solution and 20 seeds floating in the solution. 400 seeds (e.g., seeds described herein), the interiors of which are colonized by microbial strains, and 400 seed controls (lacking the microbial strains) are tested in this way (40 petri dishes total). To prevent large variations in salt concentration due to evaporation, dishes are sealed with parafilm and the saline solutions are renewed weekly by pouring out the existing saline solution in the petri dish and adding the same amount of fresh solution. A range of saline solutions (100-500 mM NaCl) is tested for to assess the germination of microbe-colonized seeds at varying salt levels. Petri dishes are maintained in a growth chamber set at 25° C., 16:8 hour light:dark cycle, 70% humidity, and at least 120 μE/m2/s light intensity. The proportion of seeds that germinates successfully after two weeks is compared between the seeds coming from inoculated plants and those coming from controls.


Testing for Germination Enhancement in Soils with High Metal Content


Standard Germination Tests are used to determine if a microbe colonizing the interior of a seed protects maize against stress due to high soil metal content during germination. Briefly, 400 seeds (e.g., seeds described herein), the interiors of which are colonized by microbial strains, are placed in between wet brown paper towels (8 replicates with 50 seeds each). An equal number of seeds obtained from control plants that lack the microbe (microbe-free) is treated in the same way. The paper towels are placed on top of 1×2 ft plastic trays with holes to allow water drainage. The paper towels are covered with an inch of sterile sand. For each metal to be tested, the sand needs to be treated appropriately to ensure the release and bioavailability of the metal. For example, in the case of aluminum, the sand is watered with pH 4.0+˜1 g/Kg soil Al+3 (−621 uM). The trays are maintained in a growth chamber set at 25° C. and 70% humidity for 7 days. The proportion of seeds that germinates successfully is compared between the seeds coming from microbe-colonized plants and those coming from controls.


Testing for Growth Promotion in Growth Chamber in Normal Conditions


Soil is made from a mixture of 60% Sunshine Mix #5 (Sun Gro; Bellevue, Wash., USA) and 40% vermiculite. To determine if a particular microbe colonizing the interior of seeds is capable of promoting plant growth under normal conditions, 24 pots are prepared in two 12-pot no-hole flat trays with 28 grams of dry soil in each pot, and 2 L of filtered water is added to each tray. The water is allowed to soak into the soil and the soil surface is misted before seeding. For each seed-microbe combination, 12 pots are seeded with 3-5 seeds colonized by the microbe and 12 pots are seeded with 3-5 seeds lacking the microbe (microbe-free plants). The seeded pots are covered with a humidity dome and kept in the dark for 3 days, after which the pots are transferred to a growth chamber set at 25° C., 16:8 hour light:dark cycle, 70% humidity, and at least 120 μE/m2/s light intensity. The humidity domes are removed on day 5, or when cotyledons are fully expanded. After removal of the domes, each pot is irrigated to saturation with 0.5× Hoagland's solution, then allowing the excess solution to drain. Seedlings are then thinned to 1 per pot. In the following days, the pots are irrigated to saturation with filtered water, allowing the excess water to drain after about 30 minutes of soaking, and the weight of each 12-pot flat tray is recorded weekly. Canopy area is measured at weekly intervals. Terminal plant height, average leaf area and average leaf length are measured at the end of the flowering stage. The plants are allowed to dry and seed weight is measured. Significance of difference in growth between microbe-colonized plants and controls lacking the microbe is assessed with the appropriate statistical test depending on the distribution of the data at p<0.05.


Testing for Growth Promotion in Growth Chamber Under Biotic Stress


Soil is made from a mixture of 60% Sunshine Mix #5 (Sun Gro; Bellevue, Wash., USA) and 40% vermiculite. To determine if a particular microbe colonizing the interior of seeds is capable of promoting plant growth in the presence of biotic stress, 24 pots are prepared in two 12-pot no-hole flat trays with 28 grams of dry soil in each pot, and 2 L of filtered water is added to each tray. The water is allowed to soak into the soil before planting. For each seed-microbe combination test, 12 pots are seeded with 3-5 seeds colonized by the microbe and 12 pots are seeded with 3-5 seeds lacking the microbe (microbe-free plants). The seeded pots are covered with a humidity dome and kept in the dark for 3 days, after which the pots are transferred to a growth chamber set at 25° C., 16:8 hour light:dark cycle, 70% humidity, and at least 120 μE/m2/s light intensity. The humidity domes are removed on day 5, or when cotyledons are fully expanded. After removal of the domes, each pot is irrigated to saturation with 0.5× Hoagland's solution, allowing the excess solution to drain. Seedlings are then thinned to 1 per pot. In the following days, the pots are irrigated to saturation with filtered water, allowing the excess water to drain after about 30 minutes of soaking.


Several methods of inoculation are used depending on the lifestyle of the pathogen. For leaf pathogens (e.g., Pseudomonas syringeae or Colletotrichum graminicola), a suspension of cells for bacteria (108 cell/mL) or spores for fungi (107 spores/mL) is applied with an applicator on the adaxial surface of each of the youngest fully expanded leaves. Alternatively for fungal pathogens that do not form conidia easily, two agar plugs containing mycelium (˜4 mm in diameter) are attached to the adaxial surface of each of the youngest leaves on each side of the central vein. For vascular pathogens (e.g., Pantoea stewartii or Fusarium moniliforme), the suspension of cells or spores is directly introduced into the vasculature (5-10 μL) through a minor injury inflected with a sterile blade. Alternatively, the seedlings can be grown hydroponically in the cell/spore or mycelium suspension. To test the resilience of the plant-microbe combination against insect stresses, such as thrips or aphids, plants are transferred to a specially-designated growth chamber containing the insects. Soil-borne insect or nematode pathogens are mixed into or applied topically to the potting soil. In all cases, care is taken to contain the fungal, insect, nematode or other pathogen and prevent release outside of the immediate testing area.


The weight of each 12-pot flat tray is recorded weekly. Canopy area is measured at weekly intervals. Terminal plant height, average leaf area and average leaf length are measured at the cease of flowering. The plants are allowed to dry and seed weight is measured. Significance of difference in growth between microbe-colonized plants and controls lacking the microbe is assessed with the appropriate statistical test depending on the distribution of the data at p<0.05.


Example 4—Functional Characterization of Endophytes

Auxin Production Assay


Auxin is an important plant hormone, which can promote cell enlargement and inhibit branch development (meristem activity) in above ground plant tissues, while below ground it has the opposite effect, promoting root branching and growth. Interestingly, plant auxin is manufactured above ground and transported to the roots. It thus follows that plant, and especially root inhabiting microbes which produce significant amounts of auxin, will be able to promote root branching and development even under conditions where the plant reduces its own production of auxin. Such conditions can exist for example when soil is flooded and roots encounter an anoxic environment.


Indole containing IAA is able to generate a pinkish chromophore under acidic conditions in the presence of ferric chloride. For auxin measurement, 1 μl of overnight-grown cultures of endophytic bacterial strains were inoculated into 750 μl of R2A broth supplemented with L-TRP (5 mM) in 2-mL 96 well culture plates. The plates were sealed with a breathable membrane and incubated at 23° C. with constant shaking at 200 rpm for 4 days. To measure auxin production by fungal strains, 3 μl of 5-day old liquid fungal cultures were inoculated into 1 ml R2A broth supplemented with L-TRP (5 mM) in 24-well culture plates. The plates were sealed with breathable tape and incubated at 23° C. with constant shaking at 130 rpm for 4 days. After 4 days, 100 μL of each culture was transferred to a 96 well plate. 25 μL of Salkowski reagent (1 mL of FeCl3 0.5 M solution to 50 mL of 35% HClO4) was added into each well and the plates were incubated in the dark for 30 minutes before taking picture and measuring 540 nm absorption using the SpectraMax M5 plate reader (Molecular Devices). Dark pink halos around colonies are visualized in the membrane by background illumination using a light table.


Endophytes were screened for their ability to produce auxins as possible root, growth promoting agents. Four replicates were performed for each strain assayed. Exemplary auxin production results for endophytes belonging to core OTUs are presented below in Table E, Table F, and Table G.


Acetoin and Diacetyl Production Assay


For acetoin measurements, microbial strains were cultured as described above in R2A broth supplemented with 5% glucose. After 4 days, 100 μL of each culture was transferred to a 96 well plate and mixed with 25 μL Barritt's Reagents A and B and 525 nm absorption was measured. Barritt's Reagents A and B were prepared by mixing 5 g/L creatine mixed 3:1 (v/v) with freshly prepared alpha-naphthol (75 g/L in 2.5 M sodium hydroxide). After 15 minutes, plates are scored for red or pink colouration against a copper coloured negative control. Four replicates were performed for each strain assayed. Exemplary acetoin production results for endophytes belonging to core OTUs are presented below in Table E, Table F, and Table G.


Siderophore Production Assay


To ensure no contaminating iron is carried over from previous experiments, all glassware is deferrated with 6 M HCl and water prior to media preparation. For siderophore measurements, microbial strains were cultured as described above in R2A broth. After 3 days of incubation at 25° C., plates are overlaid with 0-CAS overlay. Again using the cleaned glassware, 1 liter of 0-CAS overlay is made by mixing 60.5 mg of Chrome azurol S (CAS), 72.9 mg of hexadecyltrimethyl ammonium bromide (HDTMA), 30.24 g of finely crushed Piperazine-1,4-bis-2-ethanesulfonic acid (PIPES) with 10 mL of 1 mM FeCl3.6H2O in 10 mM HCl solvent. The PIPES had to be finely powdered and mixed gently with stirring (not shaking) to avoid producing bubbles, until a dark blue colour is achieved. Melted 1% agarose is then added to pre-warmed O-CAS just prior pouring the overlay in a proportion of 1:3 (v/v). After 15 minutes, colour change is scored by looking for purple halos (catechol type siderophores) or orange colonies (hydroxamate siderophores). Four replicates were performed for each strain assayed.


In many environments, iron is a limiting nutrient for growth. A coping mechanism which many microbes have developed is to produce and secrete iron chelating compounds called siderophores which often only that particular species or strain has the means to re-uptake and interact with to release the bound iron, making it available for metabolism. A fringe effect of siderophore production and secretion is that a siderophore secreting microbes can remove all the bio-available iron in its environment, making it difficult for a competing species to invade and grow in that micro-environment.


Siderophore production by microbes on a plant surface or inside a plant may both show that a microbe is equipped to grow in a nutrient limited environment, and perhaps protect the plant environment from invasion by other, perhaps undesirable microbes. Exemplary siderophore production results for endophytes belonging to core OTUs are presented below in Table E, Table F, and Table G.









TABLE E







Auxin, siderophore, and acetoin production by bacterial


endophytes belonging to core OTUs;












SEQ ID
Secretes
Produces
Produces


Strain
NO.
siderophores
Auxin/Indoles
Acetoin














SYM00003
290
2
1
0


SYM00009
291
1
1
0


SYM00013
292
0
1
0


SYM00017A
293
1
3
0


SYM00018
294
0
3
2


SYM00020
295
0
2
2


SYM00021b
296
0
2
3


SYM00025
297
1
3
2


SYM00043
300
1
3
2


SYM00044
301
1
1
3


SYM00050
302
1
2
3


SYM00053
303
1
1
2


SYM00062C
305
1
2
1


SYM00068
308
2
2
0


SYM00070
309
2
2
0


SYM00074
310
2
3
0


SYM00103
311
2
2
2


SYM00183
322
0
2
1


SYM00184
323
0
2
0


SYM00207
324
1
2
2


SYM00212
325
2
2
3


SYM00219
326
3
2
3


SYM00234
327
2
2
2


SYM00236
328
0
2
0


SYM00248
329
1
2
0


SYM00249
330
2
2
2


SYM00506c
331
0
2
2


SYM00507
332
1
2
2


SYM00508
333
0
3
2


SYM00525
525
2
2
3


SYM00538A
335
3
2
3


SYM00538B
336
2
2
2


SYM00538i
337
0
1
0


SYM00543
338
0
3
1


SYM00545
339
2
2
2


SYM00549
340
2
2
2


SYM00563
341
2
2
1


SYM00574
343
3
1
0


SYM00617
347
1
3
1


SYM00620
348
1
3
0


SYM00627
350
0
1
3


SYM00628
351
2
2
3


SYM00646
353
3
2
3


SYM00650
354
2
2
0


SYM00662
355
1
1
1


SYM00714
358
1
2
2


SYM00905
365
3
2
2


SYM00924
366
2
2
2


SYM00963
367
2
2
1


SYM00978
370
2
2
1


SYM00982
368
0
2
3


SYM00987
369
1
3
2


SYM00991
371
1
2
2


SYM00999
372
1
1
3


SYM01049
373
1
1
0





Legend:


0 = no production;


1 = low production;


2 = medium production;


3 = high production













TABLE F







Auxin, siderophore, and acetoin production by fungal


endophytes belonging to core OTUs;












SEQ ID
Secretes
Produces
Produces


Strain
NO.
siderophores
Auxin/Indoles
Acetoin














SYM00034
299
1
0
0


SYM00061A
304
1
0
2


SYM00066
307
1
0
0


SYM00120
312
1
0
0


SYM00122
313
0
0
0


SYM00123
314
1
0
3


SYM00124
315
1
1
0


SYM00129
316
0
1
0


SYM00135
317
0
1
0


SYM00136
318
0
0
1


SYM00151
319
1
1
0


SYM00154
320
0
0
0


SYM00566B
342
3
0
0


SYM00577
344
0
0
1


SYM00590
345
0
1
2


SYM00603
346
2
1
0


SYM00622
349
1
0
2


SYM00629
352
0
1
2


SYM00663
356
2
1
2


SYM00696
357
2
0
0


SYM00741b
360
0
0
0


SYM00793
361
1
0
0


SYM00795
362
1
0
1


SYM00854
363
2
0
2


SYM00880
364
2
1
2


SYM01300
374
2
1
0


SYM01310
376
0
2
0


SYM01311
377
0
0
0


SYM01314
378
2
1
0


SYM01315
379
0
0
0


SYM01325
380
0
0
2


SYM01326
381
0
0
2


SYM01327
382
2
1
2


SYM01328
383
1
0
0


SYM01333
384
0
0
0


SYM15811
385
3
1
0


SYM15820
386
1
0
0


SYM15821
387
1
0
0


SYM15825
388
0
0
2


SYM15828
389
0
0
2


SYM15831
390
2
1
2


SYM15837
391
1
0
0


SYM15839
392
2
0
0


SYM15847
393
0
0
0


SYM15870
394
0
0
0


SYM15872
395
0
0
1


SYM15890
396
0
0
2


SYM15901
397
0
0
2


SYM15920
398
2
0
2


SYM15926
399
1
2
0


SYM15928
400
0
0
0


SYM15932
401
0
0
0


SYM15939
402
0
1
0





Legend:


0 = no production;


1 = low production;


2 = medium production;


3 = high production













TABLE G







Exemplary siderophore, auxin, and acetoin production of microbial endophytes


belonging to core OTUs;
















SEQ ID
Secretes
Produces
Produces


SYM
Taxonomy
Type
NO.
siderophores
Auxin/Indoles
Acetoin
















SYM00021B

Escherichia sp.

bacteria
296
1
1
3


SYM00044

Escherichia sp.

bacteria
301
1
1
3


SYM00057b

Burkholderia sp.

bacteria
426
1
2
3


SYM00074

Enterobacter sp.

bacteria
310
0
3
0


SYM00091

Agrobacterium sp.

bacteria
427
2
2
0


SYM00092D

Brevundimonas sp.

bacteria
428
3
3
3


SYM00157

Leptosphaerulina sp.

fungi
429
3
1
0


SYM00212

Bacillus sp.

bacteria
325
0
0
3


SYM00290

Acinetobacter sp.

bacteria
430
1
0
0


SYM00300

Acremonium sp.

fungi
449
2
0
2


SYM00301

Penicillium sp.

fungi
432
0
0
2


SYM00577

Acremonium sp.

fungi
344
0
0
0


SYM00619

Exiguobacterium sp.

bacteria
435
0
0
0


SYM00865

Stenotrophomonas sp.

bacteria
451
2
1
1


SYM00879

Methylobacterium sp.

bacteria
437
0
0
0


SYM00879B

Sphingomonas sp.

bacteria
438
3
1
0


SYM00906

Stenotrophomonas sp.

bacteria
439
1
1
1


SYM00965

Luteibacter sp.

bacteria
440
2
3
3


SYM01004

Agrobacterium sp.

bacteria
441
1
2
2


SYM01022

Curtobacterium sp.

bacteria
442
3
2
3


SYM01158

Pantoea sp.

bacteria
452
1
1
1


SYM01314

Fusarium sp.

fungi
378
2
1
0


SYM01324

Aspergillus sp.

fungi
443
2
1
0


SYM01326

Alternaria sp.

fungi
381
0
0
0


SYM01329

Phoma sp.

fungi
444
1
0
2


SYM01330

Rhizopus sp.

fungi
445
0
0
0


SYM01331

Phoma sp.

fungi
450
0
0
1


SYM12462

Cladosporium sp.

fungi
446
0
0
2


SYM15774

Phoma sp.

fungi
447
0
0
1


SYM15783

Alternaria sp.

fungi
448
0
0
2


SYM15810

Fusarium sp.

fungi
453
0
2
1


SYM15879

Fusarium sp.

fungi
454
0
0
0


SYM15880

Penicillium sp.

fungi
455
0
0
1





Legend:


0 = no production;


1 = low production;


2 = medium production;


3 = high production






Assay for Growth on Nitrogen Free LGI Media


All glassware is cleaned with 6 M HCl before media preparation. A new 96 deep-well plate (2 mL well volume) is filled with 250 ul/well of sterile LGI broth [per. L, 50 g Sucrose, 0.01 g FeCl3-6H2O, 0.8 g K3PO4, 0.2 g MgSO4-7H2O, 0.002 g Na2MoO4-2H2O, pH 7.5]. Microbes are inoculated into the 96 wells simultaneously with a flame-sterilized 96 pin replicator. The plate is sealed with a breathable membrane, incubated at 28° C. without shaking for 3 days, and OD600 readings taken with a 96 well plate reader.


A nitrogen fixing plant associated bacterium is able theoretically to add to the host's nitrogen metabolism, and the most famous beneficial plant associated bacteria, rhizobia, are able to do this within specially adapted organs leguminous plant grows for them to be able to do this. In some embodiments, seed associated microbes described herein are, able to fix nitrogen in association with developing seedling, regardless of whether they colonize the plant's surfaces or interior, and thereby add to the plant's nitrogen nutrition.


ACC Deaminase Activity Assay


Microbes are assayed for growth with ACC as their sole source of nitrogen. Prior to media preparation all glassware is cleaned with 6 M HCl. A 2 M filter sterilized solution of ACC (#1373A, Research Organics, USA) is prepared in water. 1 μl/mL of this is added to autoclaved LGI broth (see above), and 1 mL aliquots are placed in a new 96 well plate. The plate is sealed with a breathable membrane, incubated at 25° C. with gentle shaking for 5 days, and OD600 readings taken. Only wells that are significantly more turbid than their corresponding nitrogen free LGI wells are considered to display ACC deaminase activity.


Plant stress reactions are strongly impacted by the plant's own production and overproduction of the gaseous hormone ethylene. Ethylene is metabolized from its precursor 1-aminocyclopropane-1-carboxylate (ACC) which can be diverted from ethylene metabolism by microbial and plant enzymes having ACC deaminase activity. As the name implies, ACC deaminase removes molecular nitrogen from the ethylene precursor, removing it as a substrate for production of the plant stress hormone and providing for the microbe a source of valuable nitrogen nutrition.


Mineral Phosphate Solubilization Assay


Microbes are plated on tricalcium phosphate media. This is prepared as follows: 10 g/L glucose, 0.373 g/L NH4NO3, 0.41 g/L MgSO4, 0.295 g/L NaCl, 0.003 FeCl3, 0.7 g/L Ca3HPO4 and 20 g/L Agar, pH 6, then autoclaved and poured into 150 mm plates. After 3 days of growth at 25° C. in darkness, clear halos are measured around colonies able to solubilize the tricalcium phosphate.


RNAse Activity Assay


1.5 g of torula yeast RNA (# R6625, Sigma) is dissolved in 1 mL of 0.1 M Na2HPO4 at pH 8, filter sterilized and added to 250 mL of autoclaved R2A agar media which is poured into 150 mm plates. The bacteria from a glycerol stock plate are inoculated using a flame-sterilized 96 pin replicator, and incubated at 25° C. for 3 days. On day three, plates are flooded with 70% perchloric acid (#311421, Sigma) for 15 minutes and scored for clear halo production around colonies.


Pectinase Activity Assay


Adapting a previous protocol 0.2% (w/v) of citrus pectin (#76280, Sigma) and 0.1% triton X-100 are added to R2A media, autoclaved and poured into 150 mm plates. Bacteria are inoculated using a 96 pin plate replicator. After 3 days of culturing in the darkness at 25° C., pectinase activity is visualized by flooding the plate with Gram's iodine. Positive colonies are surrounded by clear halos.


Cellulase Activity Assay


Adapting a previous protocol, 0.2% carboxymethylcellulose (CMC) sodium salt (# C5678, Sigma) and 0.1% triton X-100 are added to R2A media, autoclaved and poured into 150 mm plates. Bacteria are inoculated using a 96 pin plate replicator. After 3 days of culturing in the darkness at 25° C., cellulose activity is visualized by flooding the plate with Gram's iodine. Positive colonies are surrounded by clear halos.


Antibiosis Assay


Bacteria or fungi are inoculated using a 96 pin plate replicator onto 150 mm Petri dishes containing R2A agar, then grown for 3 days at 25° C. At this time, colonies of either E. coli DH5α (gram negative tester), Bacillus subtillus ssp. Subtilis (gram positive tester), or yeast strain AH109 (fungal tester) are resuspended in 1 mL of 50 mM Na2HPO4 buffer to an OD600 of 0.2, and 30 μl of this is mixed with 30 mL of warm LB agar. This is quickly poured completely over a microbe array plate, allowed to solidify and incubated at 37° C. for 16 hours. Antibiosis is scored by looking for clear halos around microbial colonies.


BIOLOG Characterization of Endophyte Substrate Metabolism


In addition to the auxin, acetoin, and siderophore assays described above, endophytes described herein were characterized for their ability to metabolize a variety of carbon substrates. Liquid cultures of microbe were first sonicated to achieve homogeneity. 1 mL culture of each strain was harvested by centrifugation for 10 minutes at 4500 RPM and subsequently washed three times with sterile distilled water to remove any traces of residual media. Microbial samples were resuspended in sterile distilled water to a final OD590 of 0.2. Measurements of absorbance were taken using a SpectraMax M microplate reader (Molecular Devices, Sunnyvale, Calif.).


Sole carbon substrate assays were done using BIOLOG Phenotype MicroArray (PM) 1 and 2A MicroPlates (Hayward, Calif.). An aliquot of each bacterial cell culture (2.32 mL) were inoculated into 20 mL sterile IF-0a GN/GP Base inoculating fluid (IF-0), 0.24 mL 100× Dye F obtained from BIOLOG, and brought to a final volume of 24 mL with sterile distilled water. Negative control PM1 and PM2A assays were also made similarly minus bacterial cells to detect abiotic reactions. An aliquot of fungal culture (0.05 mL) of each strain were inoculated into 23.95 mL FF-1F medium obtained from BIOLOG. Microbial cell suspensions were stirred in order to achieve uniformity. One hundred microliters of the microbial cell suspension was added per well using a multichannel pipettor to the 96-well BIOLOG PM1 and PM2A MicroPlates that each contained 95 carbon sources and one water-only (negative control) well.


MicroPlates were sealed in paper surgical tape (Dynarex, Orangeburg, N.Y.) to prevent plate edge effects, and incubated stationary at 24° C. in an enclosed container for 70 hours. Absorbance at 590 nm was measured for all MicroPlates at the end of the incubation period to determine carbon substrate utilization for each strain and normalized relative to the negative control (water only) well of each plate (Garland and Mills, 1991; Barua et al., 2010; Siemens et al., 2012; Blumenstein et al., 2015). The bacterial assays were also calibrated against the negative control (no cells) PM1 and PM2A MicroPlates data to correct for any biases introduced by media on the colorimetric analysis (Borglin et al., 2012). Corrected absorbance values that were negative were considered as zero for subsequent analysis (Garland and Mills, 1991; Blumenstein et al., 2015) and a threshold value of 0.1 and above was used to indicate the ability of a particular microbial strain to use a given carbon substrate (Barua et al., 2010; Blumenstein et al., 2015). Additionally, bacterial MicroPlates were visually examined for the irreversible formation of violet color in wells indicating the reduction of the tetrazolium redox dye to formazan that result from cell respiration (Garland and Mills, 1991). Fungal PM tests were measured as growth assays and visual observation of mycelial growth in each well was made. Exemplary BIOLOG substrate utilization by endophytes described herein are presented in Table H, Table I, Table J, Table K, Table L, Table M, Table N, Table O, Table P, Table Q, Table R, Table S, Table T, and Table U.









TABLE H





Substrate utilization as determined by BIOLOG PM1 MicroPlates by bacterial


endophytes belonging to OTUs present in landrace and wild corn and wheat seeds that are


present in lower levels in modern corn and wheat seeds.

















Strain/Substrate














SYM00013
SYM00018
SYM00183
SYM00184
SYM00219
SYM00043





D-Serine
NO
NO
NO
NO
NO
NO


D-Glucose-6-Phosphate
NO
NO
NO
NO
NO
YES


L-Asparagine
NO
NO
NO
NO
NO
NO


L-glutamine
NO
NO
NO
NO
NO
NO


Glycyl-L-Aspartic acid
YES
NO
NO
NO
NO
YES


Glycyl-L-Glutamic acid
NO
NO
YES
YES
NO
NO


Glycyl-L-Proline
NO
NO
YES
YES
NO
NO


L-Arabinose
YES
YES
NO
YES
NO
YES


D-Sorbitol
NO
NO
NO
YES
NO
NO


D-Galactonic acid-?-lactone
YES
YES
NO
NO
YES
YES


D-Aspartic acid
NO
NO
NO
NO
NO
NO


m-Tartaric acid
YES
YES
NO
NO
NO
YES


Citric acid
NO
NO
NO
NO
NO
NO


Tricarballylic acid
NO
NO
NO
NO
NO
NO


p-Hydroxy Phenyl acetic acid
NO
NO
NO
NO
NO
NO


N-Acetyl-D-Glucosamine
YES
YES
YES
YES
YES
YES


Glycerol
NO
NO
NO
NO
NO
YES


D-L-Malic acid
NO
NO
NO
YES
NO
YES


D-Glucosaminic acid
NO
YES
NO
NO
NO
YES


D-Glucose-1-Phosphate
NO
YES
NO
NO
NO
YES


m-Inositol
NO
YES
NO
YES
NO
YES


L-Serine
NO
NO
NO
NO
NO
NO


m-Hydroxy Phenyl Acetic acid
NO
NO
NO
NO
NO
NO


D-Saccharic acid
NO
NO
NO
YES
NO
YES


L-Fucose
NO
NO
NO
NO
NO
NO


D-Ribose
NO
YES
YES
YES
NO
YES


1,2-Propanediol
NO
NO
NO
NO
NO
NO


D-Fructose-6-Phosphate
NO
YES
NO
NO
NO
NO


D-Threonine
NO
NO
NO
NO
NO
NO


L-Threonine
NO
NO
NO
NO
NO
NO


Tyramine
YES
YES
YES
NO
YES
NO


Succinic acid
NO
NO
NO
NO
NO
NO


D-Glucuronic acid
NO
NO
NO
NO
NO
NO


Tween 20
NO
NO
NO
YES
NO
NO


Tween 40
NO
NO
NO
NO
NO
YES


Tween 80
NO
NO
YES
YES
NO
NO


Fumaric acid
NO
NO
NO
NO
NO
NO


L-Alanine
YES
YES
YES
YES
YES
YES


D-Psicose
NO
YES
NO
NO
NO
YES


D-Galactose
YES
YES
NO
YES
YES
YES


D-Gluconic acid
NO
YES
NO
NO
NO
YES


L-Rhamnose
NO
YES
NO
NO
YES
YES


a-Keto-Glutaric acid
NO
NO
YES
NO
NO
NO


a-Hydroxy Glutaric acid-?-lactone
YES
NO
NO
YES
NO
NO


Bromo succinic acid
NO
NO
NO
NO
NO
NO


L-Alanyl-Glycine
YES
YES
YES
YES
NO
NO


L-Lyxose
NO
YES
NO
NO
NO
YES


L-Aspartic acid
NO
NO
YES
NO
NO
NO


D-L-a-Glycerol phosphate
NO
NO
NO
NO
NO
NO


D-Fructose
NO
NO
NO
YES
NO
YES


a-Keto-Butyric acid
NO
NO
NO
NO
NO
NO


a-Hydroxy Butyric acid
NO
NO
NO
NO
NO
NO


Propionic acid
NO
YES
NO
NO
NO
NO


Acetoacetic acid
NO
NO
NO
NO
NO
NO


Glucuronamide
NO
NO
NO
NO
NO
NO


L-Proline
NO
YES
YES
NO
NO
NO


D-Xylose
YES
YES
YES
YES
NO
YES


Acetic acid
NO
YES
NO
YES
NO
YES


a-Methyl-D-Galactoside
NO
NO
NO
NO
YES
NO


β-Methyl-D-glucoside
NO
YES
NO
YES
YES
YES


Mucic acid
YES
YES
YES
NO
NO
YES


N-acetyl-β-D-Mannosamine
NO
NO
NO
NO
NO
NO


Pyruvic acid
NO
YES
YES
YES
YES
YES


D-Alanine
YES
YES
YES
YES
YES
NO


L-Lactic acid
NO
NO
NO
NO
NO
YES


a-D-Glucose
NO
YES
YES
YES
NO
YES


a-D-Lactose
NO
NO
YES
YES
NO
NO


Adonitol
NO
YES
YES
NO
NO
NO


Glycolic acid
NO
NO
NO
NO
NO
NO


Mono Methyl Succinate
NO
NO
NO
NO
NO
NO


L-Galactonic-acid-?-lactone
NO
YES
YES
YES
YES
YES


D-Trehalose
NO
NO
NO
NO
NO
YES


Formic acid
NO
YES
NO
NO
NO
YES


Maltose
NO
YES
YES
YES
YES
YES


Lactulose
NO
NO
YES
YES
NO
NO


Maltotriose
NO
YES
YES
YES
YES
YES


Glyoxylic acid
NO
NO
NO
NO
NO
NO


Methyl Pyruvate
NO
NO
NO
NO
NO
NO


D-Galacturonic acid
NO
NO
YES
NO
NO
YES


D-Mannose
NO
YES
YES
YES
NO
YES


D-Mannitol
NO
YES
NO
YES
NO
YES


D-Melibiose
NO
YES
YES
YES
YES
YES


Sucrose
NO
NO
YES
YES
NO
YES


2-Deoxy adenosine
NO
YES
NO
NO
NO
YES


D-Cellobiose
NO
YES
YES
YES
YES
YES


D-Malic acid
NO
NO
NO
NO
NO
NO


Phenylethyl-amine
NO
NO
NO
NO
NO
NO


Dulcitol
NO
NO
NO
NO
YES
YES


L-Glutamic acid
NO
NO
NO
NO
NO
NO


Thymidine
NO
YES
NO
NO
NO
YES


Uridine
YES
YES
YES
YES
NO
NO


Adenosine
NO
YES
NO
NO
YES
YES


Inosine
NO
NO
NO
YES
NO
NO


L-Malic acid
NO
NO
NO
NO
NO
NO


2-Aminoethanol
NO
YES
YES
YES
NO
NO












Strain/Substrate














SYM00050
SYM00508
SYM00617
SYM00620
SYM00068
SYM00905





D-Serine
YES
NO
NO
NO
NO
NO


D-Glucose-6-Phosphate
YES
YES
NO
YES
NO
NO


L-Asparagine
NO
NO
NO
NO
NO
NO


L-glutamine
NO
NO
NO
NO
NO
NO


Glycyl-L-Aspartic acid
YES
NO
NO
NO
NO
NO


Glycyl-L-Glutamic acid
NO
NO
NO
NO
YES
NO


Glycyl-L-Proline
YES
NO
NO
NO
YES
YES


L-Arabinose
YES
NO
NO
NO
YES
NO


D-Sorbitol
YES
NO
NO
NO
NO
NO


D-Galactonic acid-?-lactone
NO
NO
NO
NO
NO
NO


D-Aspartic acid
NO
NO
NO
NO
NO
NO


m-Tartaric acid
NO
NO
NO
NO
NO
NO


Citric acid
NO
NO
NO
NO
YES
NO


Tricarballylic acid
NO
NO
NO
NO
NO
NO


p-Hydroxy Phenyl acetic acid
YES
NO
NO
NO
NO
NO


N-Acetyl-D-Glucosamine
YES
NO
NO
NO
NO
NO


Glycerol
YES
NO
NO
NO
NO
NO


D-L-Malic acid
NO
YES
YES
NO
YES
NO


D-Glucosaminic acid
NO
YES
NO
NO
NO
NO


D-Glucose-1-Phosphate
YES
YES
NO
NO
NO
NO


m-Inositol
YES
NO
NO
NO
NO
NO


L-Serine
NO
NO
NO
NO
NO
NO


m-Hydroxy Phenyl Acetic acid
YES
NO
NO
YES
NO
NO


D-Saccharic acid
YES
YES
NO
NO
NO
NO


L-Fucose
NO
NO
NO
NO
NO
NO


D-Ribose
NO
NO
NO
NO
YES
NO


1,2-Propanediol
NO
NO
NO
NO
NO
NO


D-Fructose-6-Phosphate
YES
YES
NO
YES
NO
NO


D-Threonine
NO
NO
NO
NO
NO
NO


L-Threonine
NO
NO
NO
NO
NO
NO


Tyramine
NO
NO
NO
NO
YES
NO


Succinic acid
NO
NO
NO
NO
NO
NO


D-Glucuronic acid
YES
NO
NO
NO
NO
NO


Tween 20
NO
NO
NO
NO
NO
NO


Tween 40
NO
NO
NO
NO
NO
NO


Tween 80
NO
NO
NO
NO
NO
YES


Fumaric acid
NO
NO
NO
NO
NO
NO


L-Alanine
YES
NO
NO
YES
YES
YES


D-Psicose
NO
NO
NO
NO
NO
NO


D-Galactose
YES
YES
NO
NO
NO
NO


D-Gluconic acid
YES
YES
NO
YES
NO
NO


L-Rhamnose
YES
YES
YES
YES
YES
NO


a-Keto-Glutaric acid
YES
NO
NO
NO
YES
NO


a-Hydroxy Glutaric acid-?-lactone
YES
NO
NO
NO
YES
NO


Bromo succinic acid
NO
NO
NO
NO
NO
NO


L-Alanyl-Glycine
YES
NO
NO
NO
YES
NO


L-Lyxose
YES
YES
NO
NO
YES
NO


L-Aspartic acid
YES
YES
NO
NO
NO
NO


D-L-a-Glycerol phosphate
NO
NO
NO
NO
NO
NO


D-Fructose
YES
NO
NO
NO
YES
NO


a-Keto-Butyric acid
NO
NO
NO
NO
NO
NO


a-Hydroxy Butyric acid
NO
NO
NO
NO
NO
NO


Propionic acid
NO
NO
NO
NO
YES
NO


Acetoacetic acid
NO
NO
NO
NO
NO
NO


Glucuronamide
NO
NO
NO
NO
NO
NO


L-Proline
NO
NO
NO
NO
YES
NO


D-Xylose
YES
NO
NO
NO
YES
NO


Acetic acid
NO
NO
NO
NO
NO
NO


a-Methyl-D-Galactoside
YES
NO
NO
YES
NO
NO


β-Methyl-D-glucoside
YES
YES
NO
NO
NO
NO


Mucic acid
YES
YES
NO
NO
YES
NO


N-acetyl-β-D-Mannosamine
YES
NO
YES
NO
NO
NO


Pyruvic acid
YES
YES
NO
NO
YES
NO


D-Alanine
NO
NO
NO
NO
NO
NO


L-Lactic acid
YES
NO
NO
NO
NO
NO


a-D-Glucose
YES
NO
YES
NO
NO
NO


a-D-Lactose
NO
NO
NO
NO
NO
NO


Adonitol
NO
NO
NO
NO
NO
NO


Glycolic acid
NO
NO
NO
NO
NO
NO


Mono Methyl Succinate
NO
NO
NO
NO
NO
NO


L-Galactonic-acid-?-lactone
YES
YES
NO
YES
YES
NO


D-Trehalose
YES
NO
NO
NO
NO
NO


Formic acid
NO
NO
NO
NO
NO
NO


Maltose
YES
YES
YES
NO
NO
YES


Lactulose
NO
NO
NO
NO
NO
NO


Maltotriose
YES
YES
YES
NO
NO
YES


Glyoxylic acid
NO
NO
NO
NO
NO
NO


Methyl Pyruvate
YES
YES
NO
NO
YES
NO


D-Galacturonic acid
YES
NO
NO
YES
NO
NO


D-Mannose
YES
NO
NO
NO
NO
YES


D-Mannitol
YES
NO
NO
NO
NO
NO


D-Melibiose
YES
NO
YES
NO
NO
NO


Sucrose
YES
NO
NO
NO
NO
NO


2-Deoxy adenosine
YES
YES
NO
YES
NO
NO


D-Cellobiose
YES
YES
YES
NO
NO
YES


D-Malic acid
NO
NO
NO
NO
YES
NO


Phenylethyl-amine
NO
NO
NO
NO
NO
NO


Dulcitol
NO
NO
YES
NO
NO
NO


L-Glutamic acid
YES
NO
NO
NO
NO
NO


Thymidine
YES
YES
NO
NO
NO
NO


Uridine
YES
YES
NO
NO
NO
NO


Adenosine
NO
YES
NO
YES
NO
NO


Inosine
NO
NO
NO
NO
NO
NO


L-Malic acid
NO
NO
NO
NO
NO
NO


2-Aminoethanol
NO
NO
NO
NO
NO
NO
















TABLE I





Substrate utilization as determined by BIOLOG PM2A MicroPlates by bacterial


endophytes belonging to OTUs present in landrace and wild corn and wheat seeds that are


present in lower levels in modern corn and wheat seeds.

















Strain/Substrate














SYM00013
SYM00018
SYM00183
SYM00184
SYM00219
SYM00043





N-acetyl-D-Galactosamine
NO
NO
YES
YES
NO
NO


Gentiobiose
NO
YES
YES
YES
YES
YES


D-Raffinose
NO
NO
NO
NO
YES
NO


Capric acid
NO
NO
NO
NO
NO
NO


D-lactic acid methyl ester
NO
NO
NO
NO
NO
NO


Acetamide
NO
NO
NO
NO
NO
NO


L-Ornithine
YES
YES
NO
YES
YES
NO


Chondrointin sulfate C
NO
NO
NO
NO
NO
NO


N-acetyl-neuraminic acid
NO
NO
NO
NO
NO
NO


L-glucose
NO
NO
NO
NO
NO
NO


Salicin
NO
NO
YES
YES
YES
NO


Caproic acid
NO
NO
NO
NO
NO
NO


Malonic acid
NO
NO
NO
NO
NO
NO


L-Alaninamide
NO
NO
YES
YES
NO
NO


L-Phenylalanine
YES
NO
NO
NO
NO
NO


a-Cyclodextrin
NO
NO
NO
NO
NO
NO


β-D-allose
NO
NO
NO
NO
NO
NO


Lactitol
NO
NO
YES
YES
NO
NO


Sedoheptulosan
NO
NO
NO
NO
NO
NO


Citraconic acid
YES
NO
NO
NO
NO
NO


Melibionic acid
NO
NO
NO
NO
YES
NO


N-Acetyl-L-Glutamic acid
NO
NO
NO
YES
NO
NO


L-Pyroglutamic acid
YES
YES
YES
YES
YES
NO


β-Cyclodextrin
NO
NO
NO
NO
YES
NO


Amygdalin
NO
NO
YES
YES
NO
NO


D-Melezitose
NO
NO
NO
NO
NO
NO


L-Sorbose
NO
NO
NO
NO
NO
NO


Citramalic acid
NO
NO
NO
NO
NO
NO


Oxalic acid
NO
NO
NO
NO
NO
NO


L-Arginine
NO
NO
NO
NO
NO
NO


L-Valine
YES
YES
NO
YES
YES
NO


γ-Cyclodextrin
NO
NO
NO
NO
YES
NO


D-arabinose
NO
NO
NO
NO
NO
NO


Maltitol
NO
NO
YES
YES
NO
NO


Stachyose
NO
NO
NO
NO
NO
NO


D-Glucosamine
YES
YES
YES
YES
YES
YES


Oxalomalic acid
YES
YES
YES
YES
NO
YES


Glycine
NO
NO
NO
NO
NO
NO


D,L-Carnitine
YES
YES
NO
NO
NO
NO


Dextrin
NO
NO
NO
YES
YES
NO


D-arabitol
NO
NO
NO
NO
NO
NO


a-Methyl-D-Glucoside
NO
NO
NO
NO
NO
NO


D-Tagatose
NO
NO
NO
NO
NO
NO


2-Hydroxy benzoic acid
NO
NO
NO
NO
NO
NO


Quinic acid
NO
NO
NO
NO
NO
NO


L-Histidine
NO
NO
NO
NO
NO
YES


Sec-Butylamine
NO
NO
NO
NO
NO
NO


Gelatin
NO
NO
YES
YES
NO
NO


L-arabitol
NO
NO
NO
NO
NO
NO


D-Methyl-D-Galactoside
NO
NO
NO
YES
NO
NO


Turanose
NO
NO
YES
YES
NO
NO


4-Hydroxy benzoic acid
NO
NO
NO
NO
NO
NO


D-Ribono-1,4-Lactone
NO
NO
NO
NO
NO
NO


L-Homoserine
NO
NO
NO
NO
NO
NO


D,L-Octopamine
YES
YES
YES
YES
YES
NO


Glycogen
NO
NO
NO
NO
NO
NO


Arbutin
NO
NO
YES
YES
YES
NO


3-Methyl Glucose
NO
NO
NO
NO
NO
NO


Xylitol
NO
NO
NO
YES
NO
NO


β-Hydroxy butyric acid
NO
NO
NO
NO
NO
NO


Sebacic acid
NO
NO
NO
NO
NO
NO


Hydroxy-L-Proline
NO
NO
NO
NO
NO
NO


Putrescine
NO
YES
NO
NO
NO
NO


Inulin
NO
NO
YES
YES
YES
YES


2-Deoxy-D-Ribose
NO
NO
NO
NO
NO
NO


β-Methyl-D-Glucuronic acid
NO
NO
NO
NO
NO
NO


N-Acetyl-D-glucosaminitol
NO
NO
NO
NO
NO
NO


γ-Hydroxy butyric acid
NO
NO
NO
NO
NO
NO


Sorbic acid
NO
NO
NO
NO
NO
NO


L-Isoleucine
YES
NO
NO
NO
NO
NO


Dihydroxy acetone
NO
NO
NO
YES
NO
NO


Laminarin
NO
NO
NO
NO
NO
NO


i-Erythritol
NO
NO
NO
NO
NO
NO


a-Methyl-D-Mannoside
NO
NO
NO
NO
NO
NO


γ-amino butyric acid
YES
YES
NO
NO
NO
YES


a-Keto-valeric acid
NO
NO
NO
NO
NO
NO


Succinamic acid
NO
NO
NO
NO
NO
NO


L-Leucine
YES
NO
NO
NO
NO
NO


2,3-Butanediol
YES
NO
NO
NO
NO
NO


Mannan
NO
NO
NO
NO
NO
NO


D-Fucose
NO
NO
NO
NO
NO
NO


β-Methyl-D-Xyloside
NO
NO
NO
NO
NO
NO


d-amino valeric acid
NO
NO
NO
NO
NO
NO


Itaconic acid
NO
NO
NO
NO
NO
NO


D-Tartaric acid
NO
NO
NO
NO
NO
NO


L-Lysine
NO
NO
NO
NO
NO
NO


2,3-Butanone
NO
NO
NO
NO
NO
NO


Pectin
NO
NO
NO
NO
NO
NO


3-0-β-D-Galactopyranosyl-D-
NO
NO
NO
NO
NO
NO


arabinose


Palatinose
NO
NO
YES
YES
YES
NO


Butyric acid
NO
NO
NO
NO
NO
NO


5-Keto-D-Gluconic acid
NO
YES
NO
NO
NO
YES


L-Tartaric acid
YES
YES
NO
NO
NO
YES


L-Methionine
NO
NO
NO
NO
NO
NO


3-Hydroxy 2-Butanone
NO
NO
NO
NO
NO
NO












Strain/Substrate














SYM00050
SYM00508
SYM00617
SYM00620
SYM00068
SYM00905





N-acetyl-D-Galactosamine
YES
NO
NO
NO
NO
YES


Gentiobiose
YES
YES
YES
YES
NO
YES


D-Raffinose
YES
NO
NO
YES
NO
NO


Capric acid
NO
NO
NO
NO
NO
NO


D-lactic acid methyl ester
YES
NO
NO
NO
NO
NO


Acetamide
NO
NO
NO
NO
YES
NO


L-Ornithine
YES
NO
NO
NO
YES
NO


Chondrointin sulfate C
NO
NO
NO
NO
NO
NO


N-acetyl-neuraminic acid
NO
NO
NO
YES
NO
NO


L-glucose
NO
NO
NO
NO
NO
NO


Salicin
YES
YES
YES
NO
NO
YES


Caproic acid
NO
YES
NO
NO
NO
NO


Malonic acid
NO
NO
NO
NO
NO
NO


L-Alaninamide
NO
NO
NO
NO
NO
YES


L-Phenylalanine
NO
NO
NO
NO
YES
NO


a-Cyclodextrin
NO
NO
NO
NO
NO
NO


β-D-allose
NO
NO
NO
NO
NO
NO


Lactitol
NO
NO
NO
NO
NO
YES


Sedoheptulosan
NO
NO
NO
NO
NO
NO


Citraconic acid
NO
NO
NO
NO
YES
NO


Melibionic acid
YES
NO
NO
YES
YES
NO


N-Acetyl-L-Glutamic acid
YES
NO
NO
NO
NO
NO


L-Pyroglutamic acid
NO
YES
NO
NO
YES
NO


β-Cyclodextrin
NO
NO
NO
NO
NO
NO


Amygdalin
NO
NO
YES
NO
NO
NO


D-Melezitose
NO
NO
YES
NO
NO
NO


L-Sorbose
NO
NO
NO
NO
NO
NO


Citramalic acid
NO
NO
NO
NO
NO
NO


Oxalic acid
NO
NO
NO
NO
NO
NO


L-Arginine
NO
NO
NO
NO
NO
NO


L-Valine
NO
NO
NO
NO
YES
NO


γ-Cyclodextrin
NO
NO
NO
NO
NO
NO


D-arabinose
NO
YES
NO
NO
NO
NO


Maltitol
NO
NO
NO
NO
NO
YES


Stachyose
NO
NO
NO
NO
NO
NO


D-Glucosamine
YES
YES
YES
NO
YES
YES


Oxalomalic acid
NO
NO
YES
NO
YES
YES


Glycine
NO
NO
NO
NO
NO
NO


D,L-Carnitine
NO
NO
NO
NO
NO
NO


Dextrin
NO
YES
YES
YES
NO
NO


D-arabitol
NO
YES
NO
NO
NO
NO


a-Methyl-D-Glucoside
NO
NO
NO
NO
NO
NO


D-Tagatose
NO
YES
NO
NO
NO
NO


2-Hydroxy benzoic acid
NO
NO
NO
NO
NO
NO


Quinic acid
NO
NO
NO
NO
NO
NO


L-Histidine
NO
NO
NO
YES
NO
NO


Sec-Butylamine
NO
NO
NO
NO
NO
NO


Gelatin
NO
NO
NO
NO
NO
YES


L-arabitol
NO
NO
NO
NO
NO
NO


D-Methyl-D-Galactoside
NO
YES
NO
YES
NO
NO


Turanose
NO
NO
NO
NO
NO
NO


4-Hydroxy benzoic acid
NO
NO
NO
NO
NO
NO


D-Ribono-1,4-Lactone
NO
NO
NO
NO
NO
NO


L-Homoserine
NO
NO
NO
NO
NO
NO


D,L-Octopamine
NO
NO
YES
NO
YES
YES


Glycogen
NO
YES
NO
NO
NO
NO


Arbutin
YES
YES
YES
NO
NO
YES


3-Methyl Glucose
NO
YES
NO
NO
NO
NO


Xylitol
NO
NO
NO
NO
NO
NO


β-Hydroxy butyric acid
YES
YES
NO
NO
NO
NO


Sebacic acid
NO
NO
NO
NO
NO
NO


Hydroxy-L-Proline
YES
NO
NO
NO
NO
NO


Putrescine
YES
NO
NO
NO
NO
NO


Inulin
NO
NO
NO
NO
NO
NO


2-Deoxy-D-Ribose
NO
YES
NO
YES
NO
NO


β-Methyl-D-Glucuronic acid
NO
NO
NO
NO
NO
NO


N-Acetyl-D-glucosaminitol
NO
NO
NO
NO
NO
NO


γ-Hydroxy butyric acid
NO
NO
NO
NO
NO
NO


Sorbic acid
NO
NO
NO
NO
NO
NO


L-Isoleucine
NO
YES
NO
NO
YES
NO


Dihydroxy acetone
YES
YES
NO
NO
NO
NO


Laminarin
NO
NO
NO
NO
NO
NO


i-Erythritol
NO
NO
NO
NO
NO
NO


a-Methyl-D-Mannoside
NO
NO
NO
NO
NO
NO


γ-amino butyric acid
NO
NO
NO
NO
NO
NO


a-Keto-valeric acid
NO
NO
NO
NO
NO
NO


Succinamic acid
NO
NO
NO
NO
NO
NO


L-Leucine
NO
NO
NO
NO
NO
NO


2,3-Butanediol
NO
NO
NO
NO
NO
NO


Mannan
NO
NO
NO
NO
NO
NO


D-Fucose
NO
NO
NO
NO
NO
NO


β-Methyl-D-Xyloside
NO
NO
NO
NO
NO
NO


d-amino valeric acid
NO
NO
NO
NO
NO
NO


Itaconic acid
YES
YES
NO
NO
NO
NO


D-Tartaric acid
NO
NO
NO
NO
NO
NO


L-Lysine
NO
NO
NO
NO
NO
NO


2,3-Butanone
NO
NO
NO
NO
NO
NO


Pectin
NO
YES
NO
NO
NO
NO


3-0-β-D-Galactopyranosyl-D-
NO
NO
NO
NO
NO
NO


arabinose


Palatinose
NO
NO
NO
NO
NO
YES


Butyric acid
NO
NO
NO
NO
NO
NO


5-Keto-D-Gluconic acid
NO
YES
NO
NO
NO
NO


L-Tartaric acid
NO
YES
NO
NO
NO
NO


L-Methionine
NO
NO
NO
NO
NO
NO


3-Hydroxy 2-Butanone
NO
NO
NO
NO
NO
NO









Twelve SYM strains of culturable bacteria belonging to OTUs present in landrace and wild corn and wheat seeds that are present in lower levels in modern corn and wheat seeds were tested for sole carbon substrate utilization using BIOLOG PM1 and PM2A MicroPlates. The most utilized substrates by these strains are L-alanine, L-galactonic-acid-γ-lactone, maltose, maltotriose, D-cellobiose, gentiobiose, and D-glucosamine. The least utilized substrates by these strains are L-asparagine, L-glutamine, D-aspartic acid, tricarballylic acid, L-serine, L-fucose, 1,2-propanediol, D-threonine, L-threonine, succinic acid, fumaric acid, bromo succinic acid, D-L-a-glycerol phosphate, a-keto-butyric acid, a-hydroxy butyric acid, acetoacetic acid, glucuronamide, glycolic acid, mono methyl succinate, glyoxylic acid, phenylethyl-amine, and L-malic acid.


The substrates most utilized by a large number of the culturable bacteria belonging to core OTUs are mucic acid, L-arabinose, L-galactonic-acid-γ-lactone, N-acetyl-D-glucosamine, maltose, maltotriose, and D-cellobiose. These core bacteria did not utilize sedoheptulosan, oxalic acid, 2-hydroxy benzoic acid, quinic acid, mannan, L-methionine, N-acetyl-D-glucosaminitol, sorbic acid, 2,3-butanone, succinic acid, phenylethyl-amine, and 3-hydroxy 2-butanone as sole carbon sources. Results for the culturable fungi belonging to core OTUs indicate that D-sorbitol, L-arabinose, N-acetyl-D-glucosamine, glycerol, tween 40, tween 80, D-gluconic acid, L-proline, a-D-glucose, D-trehalose, maltose, lactulose, D-mannose, D-mannitol, sucrose, D-cellobiose, L-glutamic acid, L-ornithine, and L-pyroglutamic acid are carbon substrates that are utilized by a large number of the endophyte strains examined here. The carbon substrate that seemed to be not utilized by fungi in these assays is 2-deoxy-D-ribose. All other substrates could be utilized as a sole carbon nutrient by at least one fungal SYM strain.









TABLE J





Substrate utilization as determined by BIOLOG PM1 MicroPlates by bacterial


endophytes belonging to core OTUs.

















Strain/Substrate
















SYM00103
SYM01049
SYM00013
SYM00017A
SYM00018
SYM00183
SYM00184
SYM00020





D-Serine
NO
NO
NO
NO
NO
NO
NO
NO


D-Glucose-6-Phosphate
NO
NO
NO
YES
NO
NO
NO
NO


L-Asparagine
NO
NO
NO
YES
NO
NO
NO
NO


L-glutamine
NO
NO
NO
NO
NO
NO
NO
NO


Glycyl-L-Aspartic acid
NO
YES
YES
NO
NO
NO
NO
NO


Glycyl-L-Glutamic acid
YES
NO
NO
NO
NO
YES
YES
NO


Glycyl-L-Proline
NO
NO
NO
NO
NO
YES
YES
NO


L-Arabinose
NO
YES
YES
YES
YES
NO
YES
YES


D-Sorbitol
NO
NO
NO
YES
NO
NO
YES
NO


D-Galactonic acid-?-lactone
NO
YES
YES
NO
YES
NO
NO
YES


D-Aspartic acid
NO
NO
NO
NO
NO
NO
NO
NO


m-Tartaric acid
NO
YES
YES
NO
YES
NO
NO
YES


Citric acid
NO
NO
NO
NO
NO
NO
NO
NO


Tricarballylic acid
NO
NO
NO
NO
NO
NO
NO
NO


p-Hydroxy Phenyl acetic acid
NO
NO
NO
YES
NO
NO
NO
NO


N-Acetyl-D-Glucosamine
NO
NO
YES
YES
YES
YES
YES
YES


Glycerol
NO
NO
NO
YES
NO
NO
NO
NO


D-L-Malic acid
NO
NO
NO
YES
NO
NO
YES
NO


D-Glucosaminic acid
NO
NO
NO
YES
YES
NO
NO
YES


D-Glucose-1-Phosphate
NO
NO
NO
YES
YES
NO
NO
YES


m-Inositol
NO
NO
NO
YES
YES
NO
YES
YES


L-Serine
NO
NO
NO
NO
NO
NO
NO
NO


m-Hydroxy Phenyl Acetic acid
NO
NO
NO
NO
NO
NO
NO
NO


D-Saccharic acid
NO
NO
NO
YES
NO
NO
YES
NO


L-Fucose
NO
NO
NO
YES
NO
NO
NO
NO


D-Ribose
NO
YES
NO
YES
YES
YES
YES
NO


1,2-Propanediol
NO
NO
NO
NO
NO
NO
NO
NO


D-Fructose-6-Phosphate
NO
NO
NO
YES
YES
NO
NO
NO


D-Threonine
NO
NO
NO
NO
NO
NO
NO
NO


L-Threonine
NO
NO
NO
NO
NO
NO
NO
NO


Tyramine
NO
NO
YES
YES
YES
YES
NO
YES


Succinic acid
NO
NO
NO
NO
NO
NO
NO
NO


D-Glucuronic acid
NO
NO
NO
NO
NO
NO
NO
NO


Tween 20
NO
NO
NO
NO
NO
NO
YES
NO


Tween 40
NO
NO
NO
NO
NO
NO
NO
NO


Tween 80
YES
YES
NO
NO
NO
YES
YES
NO


Fumaric acid
NO
NO
NO
NO
NO
NO
NO
NO


L-Alanine
YES
NO
YES
YES
YES
YES
YES
YES


D-Psicose
NO
NO
NO
YES
YES
NO
NO
YES


D-Galactose
NO
YES
YES
YES
YES
NO
YES
YES


D-Gluconic acid
YES
NO
NO
NO
YES
NO
NO
NO


L-Rhamnose
NO
NO
NO
YES
YES
NO
NO
YES


a-Keto-Glutaric acid
YES
NO
NO
YES
NO
YES
NO
NO


a-Hydroxy Glutaric acid-?-
NO
NO
YES
YES
NO
NO
YES
NO


lactone


Bromo succinic acid
NO
NO
NO
NO
NO
NO
NO
NO


L-Alanyl-Glycine
YES
NO
YES
YES
YES
YES
YES
YES


L-Lyxose
NO
NO
NO
NO
YES
NO
NO
YES


L-Aspartic acid
YES
NO
NO
NO
NO
YES
NO
NO


D-L-a-Glycerol phosphate
NO
NO
NO
NO
NO
NO
NO
NO


D-Fructose
NO
NO
NO
YES
NO
NO
YES
YES


a-Keto-Butyric acid
NO
NO
NO
NO
NO
NO
NO
NO


a-Hydroxy Butyric acid
NO
NO
NO
NO
NO
NO
NO
NO


Propionic acid
NO
NO
NO
YES
YES
NO
NO
NO


Acetoacetic acid
NO
NO
NO
NO
NO
NO
NO
NO


Glucuronamide
NO
NO
NO
NO
NO
NO
NO
NO


L-Proline
NO
NO
NO
NO
YES
YES
NO
NO


D-Xylose
YES
YES
YES
YES
YES
YES
YES
YES


Acetic acid
NO
NO
NO
YES
YES
NO
YES
NO


a-Methyl-D-Galactoside
NO
NO
NO
YES
NO
NO
NO
NO


β-Methyl-D-glucoside
NO
NO
NO
YES
YES
NO
YES
YES


Mucic acid
YES
YES
YES
YES
YES
YES
NO
YES


N-acetyl-β-D-Mannosamine
NO
NO
NO
NO
NO
NO
NO
NO


Pyruvic acid
NO
YES
NO
YES
YES
YES
YES
YES


D-Alanine
YES
NO
YES
YES
YES
YES
YES
YES


L-Lactic acid
NO
NO
NO
NO
NO
NO
NO
NO


a-D-Glucose
NO
YES
NO
YES
YES
YES
YES
NO


a-D-Lactose
NO
NO
NO
NO
NO
YES
YES
NO


Adonitol
NO
NO
NO
YES
YES
YES
NO
NO


Glycolic acid
YES
NO
NO
NO
NO
NO
NO
NO


Mono Methyl Succinate
NO
YES
NO
NO
NO
NO
NO
NO


L-Galactonic-acid-?-lactone
YES
YES
NO
YES
YES
YES
YES
YES


D-Trehalose
YES
NO
NO
YES
NO
NO
NO
NO


Formic acid
NO
NO
NO
NO
YES
NO
NO
YES


Maltose
NO
YES
NO
YES
YES
YES
YES
YES


Lactulose
NO
NO
NO
YES
NO
YES
YES
NO


Maltotriose
NO
NO
NO
YES
YES
YES
YES
YES


Glyoxylic acid
NO
NO
NO
NO
NO
NO
NO
NO


Methyl Pyruvate
NO
NO
NO
NO
NO
NO
NO
NO


D-Galacturonic acid
YES
NO
NO
YES
NO
YES
NO
NO


D-Mannose
NO
YES
NO
YES
YES
YES
YES
NO


D-Mannitol
NO
NO
NO
YES
YES
NO
YES
NO


D-Melibiose
NO
NO
NO
YES
YES
YES
YES
NO


Sucrose
NO
NO
NO
YES
NO
YES
YES
NO


2-Deoxy adenosine
NO
NO
NO
NO
YES
NO
NO
NO


D-Cellobiose
NO
YES
NO
YES
YES
YES
YES
YES


D-Malic acid
NO
YES
NO
NO
NO
NO
NO
NO


Phenylethyl-amine
NO
NO
NO
NO
NO
NO
NO
NO


Dulcitol
NO
NO
NO
NO
NO
NO
NO
NO


L-Glutamic acid
NO
NO
NO
NO
NO
NO
NO
NO


Thymidine
NO
NO
NO
NO
YES
NO
NO
NO


Uridine
YES
NO
YES
YES
YES
YES
YES
NO


Adenosine
YES
NO
NO
YES
YES
NO
NO
NO


Inosine
NO
NO
NO
NO
NO
NO
YES
NO


L-Malic acid
NO
NO
NO
NO
NO
NO
NO
NO


2-Aminoethanol
YES
NO
NO
YES
YES
YES
YES
NO












Strain/Substrate
















SYM00207
SYM00212
SYM00219
SYM00234
SYM00236
SYM00248
SYM00249
SYM00260





D-Serine
NO
NO
NO
NO
NO
YES
NO
NO


D-Glucose-6-Phosphate
NO
YES
NO
NO
NO
YES
YES
NO


L-Asparagine
NO
NO
NO
NO
NO
NO
YES
YES


L-glutamine
NO
NO
NO
NO
NO
NO
YES
NO


Glycyl-L-Aspartic acid
NO
YES
NO
NO
NO
NO
NO
NO


Glycyl-L-Glutamic acid
YES
YES
NO
NO
NO
NO
NO
YES


Glycyl-L-Proline
NO
NO
NO
NO
NO
NO
NO
NO


L-Arabinose
NO
YES
NO
YES
YES
YES
YES
YES


D-Sorbitol
NO
NO
NO
NO
NO
NO
NO
NO


D-Galactonic acid-?-lactone
NO
NO
YES
NO
NO
NO
NO
NO


D-Aspartic acid
NO
YES
NO
NO
NO
NO
NO
NO


m-Tartaric acid
NO
YES
NO
NO
NO
NO
NO
NO


Citric acid
NO
NO
NO
NO
NO
NO
YES
YES


Tricarballylic acid
NO
YES
NO
NO
NO
NO
NO
NO


p-Hydroxy Phenyl acetic acid
NO
NO
NO
NO
NO
NO
NO
NO


N-Acetyl-D-Glucosamine
YES
YES
YES
YES
NO
YES
YES
NO


Glycerol
NO
YES
NO
YES
NO
YES
NO
YES


D-L-Malic acid
YES
YES
NO
YES
NO
NO
NO
YES


D-Glucosaminic acid
NO
NO
NO
NO
NO
NO
NO
NO


D-Glucose-1-Phosphate
NO
YES
NO
NO
NO
NO
YES
NO


m-Inositol
NO
YES
NO
NO
NO
YES
YES
YES


L-Serine
NO
NO
NO
NO
NO
NO
NO
YES


m-Hydroxy Phenyl Acetic acid
YES
NO
NO
NO
NO
NO
NO
NO


D-Saccharic acid
NO
YES
NO
NO
NO
NO
NO
YES


L-Fucose
NO
YES
NO
NO
NO
NO
NO
NO


D-Ribose
NO
YES
NO
NO
NO
YES
YES
NO


1,2-Propanediol
NO
YES
NO
NO
NO
NO
NO
YES


D-Fructose-6-Phosphate
NO
YES
NO
NO
NO
NO
YES
NO


D-Threonine
NO
NO
NO
NO
NO
NO
NO
NO


L-Threonine
YES
NO
NO
NO
NO
NO
NO
YES


Tyramine
YES
YES
YES
YES
NO
YES
YES
NO


Succinic acid
NO
NO
NO
NO
NO
NO
NO
NO


D-Glucuronic acid
NO
NO
NO
NO
NO
NO
YES
NO


Tween 20
NO
NO
NO
NO
NO
NO
NO
YES


Tween 40
NO
NO
NO
NO
NO
NO
NO
YES


Tween 80
NO
NO
NO
NO
NO
NO
NO
YES


Fumaric acid
NO
YES
NO
NO
NO
NO
NO
YES


L-Alanine
YES
YES
YES
YES
YES
YES
NO
YES


D-Psicose
NO
NO
NO
NO
NO
NO
NO
NO


D-Galactose
NO
NO
YES
NO
NO
YES
YES
NO


D-Gluconic acid
NO
YES
NO
YES
NO
NO
NO
YES


L-Rhamnose
NO
YES
YES
YES
NO
YES
YES
NO


a-Keto-Glutaric acid
YES
YES
NO
NO
YES
NO
NO
YES


a-Hydroxy Glutaric acid-?-
NO
YES
NO
NO
YES
NO
NO
YES


lactone


Bromo succinic acid
NO
NO
NO
NO
NO
NO
NO
YES


L-Alanyl-Glycine
YES
YES
NO
YES
NO
YES
NO
YES


L-Lyxose
NO
NO
NO
NO
NO
YES
NO
NO


L-Aspartic acid
YES
NO
NO
NO
YES
YES
YES
YES


D-L-a-Glycerol phosphate
NO
NO
NO
NO
NO
NO
NO
YES


D-Fructose
NO
YES
NO
YES
NO
YES
NO
NO


a-Keto-Butyric acid
YES
YES
NO
NO
NO
NO
NO
NO


a-Hydroxy Butyric acid
NO
YES
NO
NO
NO
NO
NO
YES


Propionic acid
YES
YES
NO
NO
NO
NO
NO
YES


Acetoacetic acid
NO
NO
NO
NO
NO
NO
NO
YES


Glucuronamide
NO
NO
NO
NO
NO
NO
NO
NO


L-Proline
YES
YES
NO
YES
YES
YES
NO
YES


D-Xylose
NO
YES
NO
YES
YES
YES
NO
YES


Acetic acid
YES
YES
NO
YES
YES
NO
NO
YES


a-Methyl-D-Galactoside
NO
YES
YES
YES
NO
YES
NO
NO


β-Methyl-D-glucoside
NO
YES
YES
YES
NO
YES
YES
YES


Mucic acid
YES
YES
NO
YES
NO
YES
NO
YES


N-acetyl-β-D-Mannosamine
NO
NO
NO
YES
NO
NO
NO
YES


Pyruvic acid
YES
YES
YES
YES
NO
NO
YES
YES


D-Alanine
NO
NO
YES
NO
NO
NO
YES
NO


L-Lactic acid
NO
NO
NO
NO
NO
NO
NO
YES


a-D-Glucose
NO
YES
NO
YES
NO
YES
NO
NO


a-D-Lactose
NO
YES
NO
YES
NO
YES
NO
NO


Adonitol
YES
NO
NO
YES
NO
NO
NO
NO


Glycolic acid
YES
YES
NO
NO
NO
NO
NO
YES


Mono Methyl Succinate
YES
NO
NO
YES
NO
NO
NO
YES


L-Galactonic-acid-?-lactone
YES
YES
YES
YES
NO
NO
NO
YES


D-Trehalose
NO
NO
NO
YES
NO
YES
NO
NO


Formic acid
NO
NO
NO
NO
NO
YES
NO
YES


Maltose
NO
YES
YES
YES
NO
YES
YES
YES


Lactulose
NO
YES
NO
YES
NO
NO
NO
NO


Maltotriose
NO
YES
YES
YES
NO
YES
YES
YES


Glyoxylic acid
NO
NO
NO
NO
NO
NO
NO
YES


Methyl Pyruvate
NO
YES
NO
YES
NO
NO
NO
YES


D-Galacturonic acid
YES
NO
NO
NO
NO
NO
NO
YES


D-Mannose
NO
NO
NO
YES
NO
YES
NO
NO


D-Mannitol
NO
NO
NO
YES
NO
YES
YES
YES


D-Melibiose
NO
YES
YES
YES
NO
YES
NO
NO


Sucrose
NO
NO
NO
YES
NO
NO
YES
NO


2-Deoxy adenosine
NO
NO
NO
NO
NO
YES
NO
YES


D-Cellobiose
YES
YES
YES
YES
NO
YES
YES
YES


D-Malic acid
NO
NO
NO
NO
NO
YES
NO
YES


Phenylethyl-amine
NO
NO
NO
NO
NO
NO
NO
NO


Dulcitol
NO
NO
YES
NO
NO
NO
NO
NO


L-Glutamic acid
NO
NO
NO
NO
NO
NO
NO
NO


Thymidine
YES
YES
NO
YES
NO
NO
YES
YES


Uridine
YES
YES
NO
YES
NO
NO
YES
YES


Adenosine
NO
YES
YES
YES
NO
YES
NO
YES


Inosine
YES
NO
NO
YES
NO
NO
NO
NO


L-Malic acid
YES
NO
NO
NO
NO
NO
NO
YES


2-Aminoethanol
NO
NO
NO
YES
NO
NO
NO
YES
















TABLE K





Substrate utilization as determined by BIOLOG PM1 MicroPlates by bacterial


endophytes belonging to core OTUs.

















Strain/Substrate

















SYM00290
SYM00292
SYM00003
SYM00043
SYM00050
SYM05066
SYM00508
SYM00525
SYM00053





D-Serine
NO
YES
NO
NO
YES
NO
NO
NO
YES


D-Glucose-6-
NO
NO
NO
YES
YES
NO
YES
NO
YES


Phosphate


L-Asparagine
NO
NO
NO
NO
NO
NO
NO
NO
NO


L-glutamine
NO
NO
NO
NO
NO
NO
NO
NO
NO


Glycyl-L-Aspartic
NO
NO
NO
YES
YES
NO
NO
NO
YES


acid


Glycyl-L-
NO
NO
NO
NO
NO
NO
NO
NO
NO


Glutamic acid


Glycyl-L-Proline
NO
NO
NO
NO
YES
NO
NO
NO
YES


L-Arabinose
YES
YES
YES
YES
YES
NO
NO
NO
YES


D-Sorbitol
NO
NO
NO
NO
YES
NO
NO
YES
YES


D-Galactonic
NO
NO
NO
YES
NO
NO
NO
NO
NO


acid-?-lactone


D-Aspartic acid
NO
NO
NO
NO
NO
NO
NO
NO
NO


m-Tartaric acid
NO
NO
NO
YES
NO
NO
NO
NO
NO


Citric acid
NO
YES
NO
NO
NO
NO
NO
NO
NO


Tricarballylic
NO
NO
NO
NO
NO
NO
NO
NO
NO


acid


p-Hydroxy
NO
NO
NO
NO
YES
NO
NO
NO
NO


Phenyl acetic acid


N-Acetyl-D-
YES
YES
YES
YES
YES
NO
NO
YES
YES


Glucosamine


Glycerol
YES
YES
NO
YES
YES
NO
NO
NO
NO


D-L-Malic acid
YES
YES
NO
YES
NO
NO
YES
YES
NO


D-Glucosaminic
NO
NO
YES
YES
NO
NO
YES
NO
NO


acid


D-Glucose-1-
NO
NO
NO
YES
YES
NO
YES
NO
NO


Phosphate


m-Inositol
NO
YES
NO
YES
YES
NO
NO
YES
YES


L-Serine
NO
NO
NO
NO
NO
NO
NO
NO
NO


m-Hydroxy
NO
NO
NO
NO
YES
NO
NO
NO
YES


Phenyl Acetic


acid


D-Saccharic acid
NO
YES
NO
YES
YES
NO
YES
NO
NO


L-Fucose
YES
NO
NO
NO
NO
NO
NO
NO
NO


D-Ribose
YES
YES
YES
YES
NO
NO
NO
YES
NO


1,2-Propanediol
YES
NO
NO
NO
NO
NO
NO
NO
NO


D-Fructose-6-
NO
NO
NO
NO
YES
NO
YES
NO
YES


Phosphate


D-Threonine
YES
NO
NO
NO
NO
NO
NO
NO
NO


L-Threonine
YES
NO
NO
NO
NO
NO
NO
NO
NO


Tyramine
NO
YES
YES
NO
NO
NO
NO
NO
NO


Succinic acid
NO
NO
NO
NO
NO
NO
NO
NO
NO


D-Glucuronic
NO
NO
NO
NO
YES
NO
NO
NO
NO


acid


Tween 20
YES
NO
NO
NO
NO
NO
NO
NO
NO


Tween 40
YES
NO
NO
YES
NO
NO
NO
NO
NO


Tween 80
YES
NO
NO
NO
NO
NO
NO
NO
NO


Fumaric acid
YES
YES
NO
NO
NO
NO
NO
NO
NO


L-Alanine
YES
YES
YES
YES
YES
NO
NO
YES
YES


D-Psicose
NO
NO
NO
YES
NO
NO
NO
NO
NO


D-Galactose
YES
YES
NO
YES
YES
NO
YES
YES
NO


D-Gluconic acid
YES
YES
NO
YES
YES
NO
YES
NO
YES


L-Rhamnose
YES
YES
NO
YES
YES
NO
YES
YES
YES


a-Keto-Glutaric
NO
YES
NO
NO
YES
NO
NO
NO
YES


acid


a-Hydroxy
NO
NO
NO
NO
YES
NO
NO
NO
NO


Glutaric acid-?-


lactone


Bromo succinic
NO
YES
NO
NO
NO
NO
NO
NO
NO


acid


L-Alanyl-Glycine
YES
YES
YES
NO
YES
NO
NO
YES
NO


L-Lyxose
NO
NO
NO
YES
YES
NO
YES
NO
NO


L-Aspartic acid
NO
YES
NO
NO
YES
NO
YES
YES
NO


D-L-a-Glycerol
NO
NO
NO
NO
NO
NO
NO
NO
NO


phosphate


D-Fructose
YES
YES
NO
YES
YES
NO
NO
YES
YES


a-Keto-Butyric
NO
NO
NO
NO
NO
NO
NO
NO
NO


acid


a-Hydroxy
YES
NO
NO
NO
NO
NO
NO
NO
NO


Butyric acid


Propionic acid
YES
YES
YES
NO
NO
NO
NO
NO
NO


Acetoacetic acid
YES
YES
NO
NO
NO
NO
NO
NO
NO


Glucuronamide
YES
NO
NO
NO
NO
NO
NO
NO
NO


L-Proline
NO
YES
NO
NO
NO
NO
NO
NO
NO


D-Xylose
YES
YES
YES
YES
YES
NO
NO
NO
YES


Acetic acid
YES
YES
NO
YES
NO
NO
NO
YES
NO


a-Methyl-D-
YES
YES
NO
NO
YES
NO
NO
NO
YES


Galactoside


β-Methyl-D-
YES
YES
NO
YES
YES
NO
YES
YES
YES


glucoside


Mucic acid
NO
YES
YES
YES
YES
NO
YES
YES
YES


N-acetyl-β-D-
YES
YES
NO
NO
YES
NO
NO
NO
YES


Mannosamine


Pyruvic acid
YES
YES
YES
YES
YES
NO
YES
NO
NO


D-Alanine
YES
NO
NO
NO
NO
NO
NO
NO
NO


L-Lactic acid
NO
YES
NO
YES
YES
NO
NO
NO
YES


a-D-Glucose
YES
YES
NO
YES
YES
NO
NO
NO
YES


a-D-Lactose
YES
YES
NO
NO
NO
NO
NO
YES
NO


Adonitol
NO
NO
NO
NO
NO
NO
NO
NO
NO


Glycolic acid
NO
NO
NO
NO
NO
NO
NO
NO
NO


Mono Methyl
YES
YES
NO
NO
NO
NO
NO
NO
NO


Succinate


L-Galactonic-
YES
YES
YES
YES
YES
NO
YES
YES
YES


acid-?-lactone


D-Trehalose
YES
YES
NO
YES
YES
NO
NO
NO
YES


Formic acid
NO
YES
NO
YES
NO
NO
NO
NO
NO


Maltose
YES
YES
NO
YES
YES
NO
YES
YES
YES


Lactulose
YES
YES
NO
NO
NO
NO
NO
YES
NO


Maltotriose
YES
YES
NO
YES
YES
NO
YES
YES
YES


Glyoxylic acid
NO
YES
YES
NO
NO
NO
NO
NO
NO


Methyl Pyruvate
YES
YES
NO
NO
YES
NO
YES
NO
NO


D-Galacturonic
NO
YES
NO
YES
YES
NO
NO
NO
NO


acid


D-Mannose
NO
YES
NO
YES
YES
NO
NO
NO
YES


D-Mannitol
YES
YES
NO
YES
YES
NO
NO
YES
YES


D-Melibiose
YES
YES
NO
YES
YES
NO
NO
YES
YES


Sucrose
YES
YES
NO
YES
YES
NO
NO
YES
YES


2-Deoxy
NO
YES
NO
YES
YES
NO
YES
NO
YES


adenosine


D-Cellobiose
YES
YES
NO
YES
YES
NO
YES
YES
YES


D-Malic acid
NO
YES
NO
NO
NO
NO
NO
NO
NO


Phenylethyl-
NO
NO
NO
NO
NO
NO
NO
NO
NO


amine


Dulcitol
YES
NO
NO
YES
NO
NO
NO
NO
NO


L-Glutamic acid
NO
NO
NO
NO
YES
NO
NO
NO
NO


Thymidine
YES
YES
NO
YES
YES
NO
YES
NO
YES


Uridine
YES
YES
YES
NO
YES
NO
YES
YES
YES


Adenosine
YES
YES
YES
YES
NO
NO
YES
NO
NO


Inosine
NO
YES
NO
NO
NO
NO
NO
NO
NO


L-Malic acid
NO
YES
NO
NO
NO
NO
NO
NO
NO


2-Aminoethanol
NO
NO
NO
NO
NO
NO
NO
NO
NO












Strain/Substrate


















SYM00538A
SYM00538B
SYM00538i
SYM00543
SYM00563
SYM00574
SYM00057B
SYM00617







D-Serine
NO
NO
NO
YES
NO
NO
NO
NO



D-Glucose-6-
NO
NO
NO
YES
NO
NO
NO
NO



Phosphate



L-Asparagine
NO
NO
NO
YES
NO
NO
NO
NO



L-glutamine
NO
NO
NO
NO
NO
NO
NO
NO



Glycyl-L-Aspartic
NO
NO
NO
NO
NO
NO
NO
NO



acid



Glycyl-L-
NO
NO
NO
YES
NO
YES
NO
NO



Glutamic acid



Glycyl-L-Proline
NO
NO
NO
NO
NO
NO
YES
NO



L-Arabinose
NO
YES
YES
YES
YES
YES
YES
NO



D-Sorbitol
NO
NO
NO
NO
NO
NO
NO
NO



D-Galactonic
NO
NO
NO
NO
NO
NO
NO
NO



acid-?-lactone



D-Aspartic acid
NO
NO
NO
NO
NO
NO
NO
NO



m-Tartaric acid
NO
NO
NO
NO
NO
NO
NO
NO



Citric acid
NO
NO
YES
YES
NO
YES
NO
NO



Tricarballylic
NO
NO
NO
NO
NO
NO
NO
NO



acid



p-Hydroxy
NO
NO
NO
NO
NO
NO
NO
NO



Phenyl acetic acid



N-Acetyl-D-
YES
YES
YES
YES
NO
YES
NO
NO



Glucosamine



Glycerol
NO
YES
NO
YES
NO
YES
NO
NO



D-L-Malic acid
YES
YES
YES
YES
NO
YES
NO
YES



D-Glucosaminic
NO
NO
NO
NO
NO
NO
NO
NO



acid



D-Glucose-1-
NO
NO
NO
NO
NO
NO
NO
NO



Phosphate



m-Inositol
NO
YES
YES
YES
NO
YES
NO
NO



L-Serine
NO
NO
NO
YES
NO
YES
NO
NO



m-Hydroxy
NO
NO
NO
NO
NO
NO
YES
NO



Phenyl Acetic



acid



D-Saccharic acid
NO
NO
YES
YES
NO
YES
NO
NO



L-Fucose
NO
NO
NO
YES
NO
NO
YES
NO



D-Ribose
NO
NO
NO
YES
NO
NO
NO
NO



1,2-Propanediol
NO
NO
NO
NO
NO
YES
NO
NO



D-Fructose-6-
NO
NO
NO
NO
NO
NO
NO
NO



Phosphate



D-Threonine
NO
NO
NO
NO
NO
NO
NO
NO



L-Threonine
NO
NO
NO
YES
NO
YES
NO
NO



Tyramine
NO
NO
NO
YES
NO
NO
NO
NO



Succinic acid
NO
NO
NO
NO
NO
NO
NO
NO



D-Glucuronic
NO
NO
NO
NO
NO
NO
NO
NO



acid



Tween 20
NO
YES
NO
NO
NO
YES
YES
NO



Tween 40
NO
NO
NO
NO
NO
YES
NO
NO



Tween 80
NO
NO
NO
YES
NO
YES
NO
NO



Fumaric acid
NO
NO
NO
NO
NO
YES
NO
NO



L-Alanine
NO
NO
NO
YES
NO
YES
NO
NO



D-Psicose
NO
NO
NO
NO
NO
NO
NO
NO



D-Galactose
NO
YES
NO
NO
NO
NO
YES
NO



D-Gluconic acid
NO
YES
NO
YES
NO
YES
NO
NO



L-Rhamnose
NO
YES
NO
NO
YES
NO
YES
YES



a-Keto-Glutaric
YES
YES
YES
YES
NO
YES
NO
NO



acid



a-Hydroxy
NO
NO
YES
NO
NO
YES
NO
NO



Glutaric acid-?-



lactone



Bromo succinic
NO
NO
NO
YES
NO
YES
NO
NO



acid



L-Alanyl-Glycine
YES
YES
YES
YES
NO
YES
NO
NO



L-Lyxose
NO
NO
NO
NO
NO
NO
NO
NO



L-Aspartic acid
NO
YES
YES
YES
NO
YES
NO
NO



D-L-a-Glycerol
NO
NO
NO
NO
NO
YES
NO
NO



phosphate



D-Fructose
NO
YES
NO
YES
NO
NO
NO
NO



a-Keto-Butyric
NO
NO
NO
NO
NO
NO
NO
NO



acid



a-Hydroxy
NO
NO
NO
NO
NO
YES
NO
NO



Butyric acid



Propionic acid
NO
NO
YES
NO
NO
YES
NO
NO



Acetoacetic acid
NO
NO
NO
YES
NO
YES
NO
NO



Glucuronamide
NO
NO
NO
NO
NO
NO
NO
NO



L-Proline
YES
NO
YES
NO
NO
YES
NO
NO



D-Xylose
NO
YES
NO
NO
NO
YES
NO
NO



Acetic acid
NO
YES
YES
YES
NO
YES
YES
NO



a-Methyl-D-
NO
YES
NO
NO
NO
NO
NO
NO



Galactoside



β-Methyl-D-
NO
YES
NO
YES
NO
YES
NO
NO



glucoside



Mucic acid
NO
NO
YES
YES
NO
YES
YES
NO



N-acetyl-β-D-
NO
YES
NO
NO
NO
YES
NO
YES



Mannosamine



Pyruvic acid
NO
YES
NO
YES
NO
YES
NO
NO



D-Alanine
NO
NO
NO
NO
NO
NO
YES
NO



L-Lactic acid
NO
NO
NO
YES
NO
YES
NO
NO



a-D-Glucose
NO
YES
NO
YES
NO
NO
YES
YES



a-D-Lactose
NO
YES
NO
NO
NO
NO
NO
NO



Adonitol
NO
NO
NO
NO
NO
NO
NO
NO



Glycolic acid
NO
NO
NO
NO
NO
YES
NO
NO



Mono Methyl
NO
YES
NO
NO
NO
YES
NO
NO



Succinate



L-Galactonic-
YES
NO
YES
NO
NO
YES
NO
NO



acid-?-lactone



D-Trehalose
NO
YES
NO
NO
NO
NO
NO
NO



Formic acid
NO
YES
NO
YES
NO
YES
YES
NO



Maltose
YES
YES
NO
YES
YES
YES
NO
YES



Lactulose
NO
YES
NO
NO
NO
NO
NO
NO



Maltotriose
YES
YES
NO
YES
YES
YES
NO
YES



Glyoxylic acid
NO
NO
NO
NO
NO
YES
NO
NO



Methyl Pyruvate
YES
YES
NO
YES
NO
YES
NO
NO



D-Galacturonic
NO
YES
YES
NO
NO
YES
NO
NO



acid



D-Mannose
YES
YES
NO
NO
YES
NO
NO
NO



D-Mannitol
NO
YES
YES
NO
NO
YES
NO
NO



D-Melibiose
NO
YES
NO
NO
NO
NO
NO
YES



Sucrose
NO
YES
YES
NO
NO
NO
NO
NO



2-Deoxy
NO
NO
NO
YES
NO
YES
NO
NO



adenosine



D-Cellobiose
NO
YES
NO
YES
YES
YES
NO
YES



D-Malic acid
NO
NO
NO
NO
NO
YES
NO
NO



Phenylethyl-
NO
NO
NO
NO
NO
NO
NO
NO



amine



Dulcitol
NO
NO
NO
NO
NO
NO
NO
YES



L-Glutamic acid
NO
NO
NO
NO
NO
NO
NO
NO



Thymidine
NO
YES
NO
YES
NO
YES
NO
NO



Uridine
NO
YES
YES
YES
NO
YES
NO
NO



Adenosine
NO
YES
NO
YES
NO
YES
NO
NO



Inosine
YES
YES
NO
YES
NO
NO
NO
NO



L-Malic acid
NO
NO
NO
YES
NO
YES
NO
NO



2-Aminoethanol
NO
YES
YES
NO
NO
YES
NO
NO

















TABLE L





Substrate utilization as determined by BIOLOG PM1 MicroPlates by bacterial


endophytes belonging to core OTUs.

















Strain/Substrate














SYM00620
SYM00627
SYM00628
SYM00062C
SYM00650
SYM00068





D-Serine
NO
NO
YES
NO
NO
NO


D-Glucose-6-Phosphate
YES
YES
YES
NO
NO
NO


L-Asparagine
NO
NO
NO
NO
NO
NO


L-glutamine
NO
NO
NO
NO
NO
NO


Glycyl-L-Aspartic acid
NO
NO
NO
NO
YES
NO


Glycyl-L-Glutamic acid
NO
NO
NO
NO
NO
YES


Glycyl-L-Proline
NO
NO
NO
NO
NO
YES


L-Arabinose
NO
NO
YES
NO
YES
YES


D-Sorbitol
NO
NO
NO
NO
NO
NO


D-Galactonic acid-?-lactone
NO
YES
YES
NO
NO
NO


D-Aspartic acid
NO
NO
NO
NO
NO
NO


m-Tartaric acid
NO
NO
NO
NO
NO
NO


Citric acid
NO
NO
NO
NO
NO
YES


Tricarballylic acid
NO
NO
NO
NO
NO
NO


p-Hydroxy Phenyl acetic acid
NO
NO
NO
NO
NO
NO


N-Acetyl-D-Glucosamine
NO
YES
YES
NO
NO
NO


Glycerol
NO
NO
NO
NO
NO
NO


D-L-Malic acid
NO
NO
NO
NO
NO
YES


D-Glucosaminic acid
NO
NO
NO
NO
NO
NO


D-Glucose-1-Phosphate
NO
NO
NO
NO
NO
NO


m-Inositol
NO
NO
YES
NO
NO
NO


L-Serine
NO
NO
NO
NO
NO
NO


m-Hydroxy Phenyl Acetic acid
YES
NO
YES
NO
NO
NO


D-Saccharic acid
NO
NO
NO
NO
NO
NO


L-Fucose
NO
NO
YES
NO
NO
NO


D-Ribose
NO
NO
NO
NO
NO
YES


1,2-Propanediol
NO
NO
NO
NO
NO
NO


D-Fructose-6-Phosphate
YES
YES
YES
NO
NO
NO


D-Threonine
NO
NO
NO
NO
NO
NO


L-Threonine
NO
NO
NO
NO
NO
NO


Tyramine
NO
NO
NO
NO
NO
YES


Succinic acid
NO
NO
NO
NO
NO
NO


D-Glucuronic acid
NO
NO
NO
NO
NO
NO


Tween 20
NO
NO
NO
NO
NO
NO


Tween 40
NO
NO
NO
NO
NO
NO


Tween 80
NO
NO
NO
NO
NO
NO


Fumaric acid
NO
NO
NO
NO
NO
NO


L-Alanine
YES
NO
YES
NO
NO
YES


D-Psicose
NO
NO
NO
NO
NO
NO


D-Galactose
NO
NO
YES
NO
NO
NO


D-Gluconic acid
YES
YES
NO
NO
NO
NO


L-Rhamnose
YES
YES
YES
NO
YES
YES


a-Keto-Glutaric acid
NO
NO
NO
NO
NO
YES


a-Hydroxy Glutaric acid-?-
NO
NO
NO
NO
NO
YES


lactone


Bromo succinic acid
NO
NO
NO
NO
NO
NO


L-Alanyl-Glycine
NO
NO
NO
NO
NO
YES


L-Lyxose
NO
NO
NO
NO
NO
YES


L-Aspartic acid
NO
NO
NO
NO
NO
NO


D-L-a-Glycerol phosphate
NO
NO
NO
NO
NO
NO


D-Fructose
NO
NO
NO
NO
NO
YES


a-Keto-Butyric acid
NO
NO
NO
NO
NO
NO


a-Hydroxy Butyric acid
NO
NO
NO
NO
NO
NO


Propionic acid
NO
NO
NO
NO
NO
YES


Acetoacetic acid
NO
NO
NO
NO
NO
NO


Glucuronamide
NO
NO
NO
NO
NO
NO


L-Proline
NO
NO
YES
NO
NO
YES


D-Xylose
NO
YES
YES
NO
YES
YES


Acetic acid
NO
NO
NO
NO
NO
NO


a-Methyl-D-Galactoside
YES
YES
YES
NO
NO
NO


β-Methyl-D-glucoside
NO
YES
YES
NO
NO
NO


Mucic acid
NO
YES
YES
NO
YES
YES


N-acetyl-β-D-Mannosamine
NO
NO
YES
NO
NO
NO


Pyruvic acid
NO
YES
NO
NO
NO
YES


D-Alanine
NO
NO
YES
NO
NO
NO


L-Lactic acid
NO
NO
NO
NO
NO
NO


a-D-Glucose
NO
NO
NO
NO
YES
NO


a-D-Lactose
NO
NO
NO
YES
NO
NO


Adonitol
NO
NO
NO
NO
NO
NO


Glycolic acid
NO
NO
NO
NO
NO
NO


Mono Methyl Succinate
NO
NO
NO
NO
YES
NO


L-Galactonic-acid-?-lactone
YES
YES
YES
NO
NO
YES


D-Trehalose
NO
NO
NO
NO
YES
NO


Formic acid
NO
YES
NO
NO
NO
NO


Maltose
NO
YES
YES
YES
YES
NO


Lactulose
NO
NO
NO
YES
NO
NO


Maltotriose
NO
YES
YES
NO
NO
NO


Glyoxylic acid
NO
NO
NO
NO
NO
NO


Methyl Pyruvate
NO
NO
NO
NO
NO
YES


D-Galacturonic acid
YES
NO
NO
NO
NO
NO


D-Mannose
NO
NO
NO
NO
NO
NO


D-Mannitol
NO
NO
NO
NO
NO
NO


D-Melibiose
NO
YES
YES
YES
NO
NO


Sucrose
NO
YES
NO
NO
NO
NO


2-Deoxy adenosine
YES
YES
YES
NO
NO
NO


D-Cellobiose
NO
YES
YES
NO
NO
NO


D-Malic acid
NO
NO
NO
NO
YES
YES


Phenylethyl-amine
NO
NO
NO
NO
NO
NO


Dulcitol
NO
YES
NO
YES
NO
NO


L-Glutamic acid
NO
NO
NO
NO
NO
NO


Thymidine
NO
YES
YES
YES
NO
NO


Uridine
NO
NO
YES
NO
NO
NO


Adenosine
YES
NO
YES
NO
NO
NO


Inosine
NO
NO
NO
NO
NO
NO


L-Malic acid
NO
NO
NO
NO
NO
NO


2-Aminoethanol
NO
NO
NO
NO
NO
NO












Strain/Substrate














SYM00070
SYM00714
SYM00009
SYM00905
SYM00924
SYM00963





D-Serine
NO
NO
NO
NO
NO
NO


D-Glucose-6-Phosphate
NO
YES
NO
NO
NO
NO


L-Asparagine
NO
NO
NO
NO
NO
NO


L-glutamine
NO
NO
NO
NO
NO
NO


Glycyl-L-Aspartic acid
NO
NO
NO
NO
NO
NO


Glycyl-L-Glutamic acid
NO
NO
NO
NO
NO
NO


Glycyl-L-Proline
NO
NO
NO
YES
NO
NO


L-Arabinose
YES
YES
YES
NO
NO
NO


D-Sorbitol
NO
YES
NO
NO
NO
NO


D-Galactonic acid-?-lactone
NO
YES
NO
NO
NO
NO


D-Aspartic acid
NO
NO
NO
NO
NO
NO


m-Tartaric acid
NO
NO
NO
NO
NO
NO


Citric acid
NO
NO
NO
NO
NO
NO


Tricarballylic acid
NO
NO
NO
NO
NO
NO


p-Hydroxy Phenyl acetic acid
NO
NO
NO
NO
NO
NO


N-Acetyl-D-Glucosamine
YES
YES
NO
NO
NO
NO


Glycerol
YES
YES
NO
NO
NO
NO


D-L-Malic acid
YES
YES
NO
NO
NO
NO


D-Glucosaminic acid
NO
NO
YES
NO
NO
NO


D-Glucose-1-Phosphate
NO
YES
NO
NO
NO
NO


m-Inositol
NO
YES
NO
NO
NO
NO


L-Serine
NO
YES
NO
NO
NO
NO


m-Hydroxy Phenyl Acetic acid
NO
NO
NO
NO
NO
NO


D-Saccharic acid
YES
YES
NO
NO
NO
NO


L-Fucose
YES
YES
NO
NO
NO
YES


D-Ribose
YES
NO
NO
NO
NO
NO


1,2-Propanediol
NO
NO
NO
NO
NO
NO


D-Fructose-6-Phosphate
YES
YES
NO
NO
YES
NO


D-Threonine
NO
NO
NO
NO
NO
NO


L-Threonine
NO
NO
NO
NO
NO
NO


Tyramine
YES
NO
NO
NO
NO
NO


Succinic acid
NO
NO
NO
NO
NO
NO


D-Glucuronic acid
NO
NO
NO
NO
NO
NO


Tween 20
NO
NO
NO
NO
NO
NO


Tween 40
NO
NO
NO
NO
NO
NO


Tween 80
NO
NO
YES
YES
NO
YES


Fumaric acid
NO
NO
NO
NO
NO
NO


L-Alanine
YES
YES
NO
YES
NO
NO


D-Psicose
NO
YES
NO
NO
NO
NO


D-Galactose
YES
NO
NO
NO
NO
NO


D-Gluconic acid
NO
YES
NO
NO
NO
NO


L-Rhamnose
YES
YES
NO
NO
NO
NO


a-Keto-Glutaric acid
YES
YES
NO
NO
NO
NO


a-Hydroxy Glutaric acid-?-
YES
YES
NO
NO
NO
NO


lactone


Bromo succinic acid
NO
NO
NO
NO
NO
NO


L-Alanyl-Glycine
YES
NO
NO
NO
NO
NO


L-Lyxose
YES
YES
NO
NO
NO
NO


L-Aspartic acid
YES
YES
NO
NO
YES
NO


D-L-a-Glycerol phosphate
NO
NO
NO
NO
NO
NO


D-Fructose
YES
YES
NO
NO
NO
NO


a-Keto-Butyric acid
NO
NO
NO
NO
NO
NO


a-Hydroxy Butyric acid
NO
NO
NO
NO
NO
NO


Propionic acid
NO
YES
NO
NO
NO
YES


Acetoacetic acid
NO
NO
NO
NO
NO
NO


Glucuronamide
NO
NO
NO
NO
NO
NO


L-Proline
YES
NO
NO
NO
NO
NO


D-Xylose
YES
YES
YES
NO
NO
NO


Acetic acid
YES
YES
NO
NO
NO
NO


a-Methyl-D-Galactoside
NO
YES
NO
NO
NO
YES


β-Methyl-D-glucoside
YES
YES
NO
NO
NO
NO


Mucic acid
YES
YES
YES
NO
NO
YES


N-acetyl-β-D-Mannosamine
NO
NO
NO
NO
NO
NO


Pyruvic acid
NO
NO
NO
NO
NO
NO


D-Alanine
YES
NO
NO
NO
NO
NO


L-Lactic acid
NO
YES
NO
NO
NO
NO


a-D-Glucose
YES
YES
NO
NO
NO
NO


a-D-Lactose
NO
YES
NO
NO
NO
YES


Adonitol
YES
YES
NO
NO
NO
NO


Glycolic acid
NO
NO
NO
NO
NO
NO


Mono Methyl Succinate
NO
NO
NO
NO
YES
NO


L-Galactonic-acid-?-lactone
YES
YES
YES
NO
NO
NO


D-Trehalose
NO
YES
NO
NO
NO
NO


Formic acid
YES
YES
NO
NO
NO
NO


Maltose
YES
YES
NO
YES
NO
YES


Lactulose
NO
YES
NO
NO
NO
YES


Maltotriose
YES
YES
NO
YES
NO
YES


Glyoxylic acid
NO
NO
NO
NO
YES
NO


Methyl Pyruvate
NO
NO
NO
NO
NO
YES


D-Galacturonic acid
NO
YES
NO
NO
NO
NO


D-Mannose
NO
YES
NO
YES
NO
NO


D-Mannitol
NO
YES
NO
NO
NO
NO


D-Melibiose
YES
YES
NO
NO
NO
NO


Sucrose
NO
NO
NO
NO
NO
NO


2-Deoxy adenosine
YES
NO
NO
NO
NO
NO


D-Cellobiose
NO
YES
NO
YES
NO
NO


D-Malic acid
NO
YES
NO
NO
NO
YES


Phenylethyl-amine
NO
NO
NO
NO
NO
NO


Dulcitol
NO
NO
NO
NO
NO
YES


L-Glutamic acid
NO
NO
NO
NO
NO
NO


Thymidine
NO
NO
NO
NO
NO
YES


Uridine
YES
NO
YES
NO
NO
NO


Adenosine
NO
NO
NO
NO
NO
NO


Inosine
NO
YES
NO
NO
NO
NO


L-Malic acid
NO
YES
NO
NO
NO
NO


2-Aminoethanol
NO
NO
NO
NO
NO
NO












Strain/Substrate















SYM00978
SYM00982
SYM00987
SYM00991
SYM00999







D-Serine
YES
NO
NO
YES
NO



D-Glucose-6-Phosphate
NO
NO
NO
YES
NO



L-Asparagine
NO
NO
NO
NO
NO



L-glutamine
NO
NO
NO
NO
NO



Glycyl-L-Aspartic acid
NO
NO
NO
NO
NO



Glycyl-L-Glutamic acid
NO
NO
NO
NO
NO



Glycyl-L-Proline
NO
NO
NO
NO
NO



L-Arabinose
NO
NO
YES
NO
YES



D-Sorbitol
NO
NO
NO
NO
NO



D-Galactonic acid-?-lactone
NO
NO
NO
NO
NO



D-Aspartic acid
NO
NO
NO
NO
NO



m-Tartaric acid
NO
NO
NO
NO
NO



Citric acid
NO
NO
NO
NO
NO



Tricarballylic acid
NO
NO
NO
NO
NO



p-Hydroxy Phenyl acetic acid
NO
NO
YES
NO
NO



N-Acetyl-D-Glucosamine
NO
NO
YES
NO
NO



Glycerol
NO
NO
NO
NO
NO



D-L-Malic acid
NO
YES
NO
NO
NO



D-Glucosaminic acid
NO
NO
NO
NO
NO



D-Glucose-1-Phosphate
NO
NO
NO
NO
NO



m-Inositol
NO
NO
NO
NO
NO



L-Serine
NO
NO
NO
NO
NO



m-Hydroxy Phenyl Acetic acid
NO
NO
NO
NO
NO



D-Saccharic acid
NO
NO
YES
NO
YES



L-Fucose
YES
NO
NO
NO
NO



D-Ribose
NO
NO
NO
NO
NO



1,2-Propanediol
NO
NO
NO
NO
NO



D-Fructose-6-Phosphate
NO
NO
NO
YES
NO



D-Threonine
NO
NO
NO
NO
NO



L-Threonine
NO
NO
NO
NO
NO



Tyramine
NO
NO
NO
NO
NO



Succinic acid
NO
NO
NO
NO
NO



D-Glucuronic acid
NO
NO
NO
NO
NO



Tween 20
NO
NO
NO
NO
NO



Tween 40
NO
NO
NO
NO
NO



Tween 80
NO
NO
YES
NO
NO



Fumaric acid
NO
NO
NO
NO
NO



L-Alanine
NO
NO
NO
NO
NO



D-Psicose
NO
NO
NO
NO
NO



D-Galactose
NO
NO
NO
NO
NO



D-Gluconic acid
NO
NO
NO
NO
NO



L-Rhamnose
NO
NO
NO
NO
NO



a-Keto-Glutaric acid
NO
YES
NO
NO
NO



a-Hydroxy Glutaric acid-?-
NO
NO
NO
NO
NO



lactone



Bromo succinic acid
NO
NO
NO
NO
NO



L-Alanyl-Glycine
NO
NO
NO
NO
NO



L-Lyxose
NO
NO
NO
NO
NO



L-Aspartic acid
NO
NO
NO
NO
NO



D-L-a-Glycerol phosphate
NO
NO
NO
NO
NO



D-Fructose
NO
NO
NO
NO
NO



a-Keto-Butyric acid
NO
NO
NO
NO
NO



a-Hydroxy Butyric acid
NO
NO
NO
NO
NO



Propionic acid
NO
NO
NO
NO
NO



Acetoacetic acid
NO
NO
NO
NO
NO



Glucuronamide
NO
NO
NO
NO
NO



L-Proline
NO
NO
NO
NO
NO



D-Xylose
NO
NO
NO
NO
NO



Acetic acid
NO
YES
NO
NO
NO



a-Methyl-D-Galactoside
NO
NO
NO
NO
NO



β-Methyl-D-glucoside
NO
NO
NO
NO
NO



Mucic acid
NO
NO
YES
NO
YES



N-acetyl-β-D-Mannosamine
YES
NO
NO
YES
NO



Pyruvic acid
NO
NO
NO
NO
NO



D-Alanine
NO
NO
NO
NO
NO



L-Lactic acid
NO
NO
YES
NO
NO



a-D-Glucose
NO
NO
YES
YES
NO



a-D-Lactose
NO
NO
NO
NO
NO



Adonitol
NO
NO
NO
NO
NO



Glycolic acid
NO
NO
NO
NO
NO



Mono Methyl Succinate
NO
NO
NO
NO
YES



L-Galactonic-acid-?-lactone
NO
NO
YES
NO
NO



D-Trehalose
NO
NO
NO
NO
NO



Formic acid
NO
NO
NO
NO
NO



Maltose
NO
NO
NO
YES
NO



Lactulose
NO
NO
YES
NO
NO



Maltotriose
NO
NO
NO
NO
NO



Glyoxylic acid
NO
NO
NO
NO
YES



Methyl Pyruvate
NO
NO
NO
NO
YES



D-Galacturonic acid
NO
NO
NO
NO
NO



D-Mannose
NO
NO
NO
NO
NO



D-Mannitol
NO
NO
NO
NO
NO



D-Melibiose
NO
NO
NO
NO
NO



Sucrose
NO
NO
YES
YES
NO



2-Deoxy adenosine
NO
NO
NO
NO
NO



D-Cellobiose
NO
NO
NO
NO
NO



D-Malic acid
NO
NO
NO
NO
NO



Phenylethyl-amine
NO
NO
NO
NO
NO



Dulcitol
NO
NO
NO
NO
NO



L-Glutamic acid
NO
NO
NO
NO
NO



Thymidine
NO
NO
NO
NO
NO



Uridine
NO
NO
NO
NO
NO



Adenosine
NO
NO
NO
NO
NO



Inosine
NO
NO
NO
NO
NO



L-Malic acid
NO
NO
NO
NO
NO



2-Aminoethanol
NO
NO
NO
NO
NO

















TABLE M





Substrate utilization as determined by BIOLOG PM2A MicroPlates by bacterial


endophytes belonging to core OTUs.

















Strain/Substrate
















SYM00103
SYM01049
SYM00013
SYM00017A
SYM00018
SYM00183
SYM00184
SYM00020





N-acetyl-D-Galactosamine
NO
NO
NO
YES
NO
YES
YES
NO


Gentiobiose
NO
NO
NO
YES
YES
YES
YES
YES


D-Raffinose
NO
NO
NO
YES
NO
NO
NO
NO


Capric acid
NO
NO
NO
NO
NO
NO
NO
NO


D-lactic acid methyl ester
NO
NO
NO
NO
NO
NO
NO
NO


Acetamide
NO
NO
NO
NO
NO
NO
NO
NO


L-Ornithine
YES
NO
YES
YES
YES
NO
YES
YES


Chondrointin sulfate C
NO
NO
NO
NO
NO
NO
NO
NO


N-acetyl-neuraminic acid
NO
NO
NO
NO
NO
NO
NO
NO


L-glucose
NO
NO
NO
NO
NO
NO
NO
NO


Salicin
NO
NO
NO
YES
NO
YES
YES
NO


Caproic acid
NO
NO
NO
NO
NO
NO
NO
NO


Malonic acid
NO
NO
NO
NO
NO
NO
NO
NO


L-Alaninamide
NO
NO
NO
NO
NO
YES
YES
NO


L-Phenylalanine
NO
NO
YES
NO
NO
NO
NO
NO


a-Cyclodextrin
NO
NO
NO
NO
NO
NO
NO
NO


β-D-allose
NO
NO
NO
YES
NO
NO
NO
NO


Lactitol
NO
NO
NO
YES
NO
YES
YES
NO


Sedoheptulosan
NO
NO
NO
NO
NO
NO
NO
NO


Citraconic acid
NO
NO
YES
NO
NO
NO
NO
NO


Melibionic acid
NO
NO
NO
YES
NO
NO
NO
NO


N-Acetyl-L-Glutamic acid
YES
NO
NO
YES
NO
NO
YES
NO


L-Pyroglutamic acid
YES
NO
YES
YES
YES
YES
YES
YES


β-Cyclodextrin
NO
NO
NO
NO
NO
NO
NO
NO


Amygdalin
NO
NO
NO
NO
NO
YES
YES
NO


D-Melezitose
NO
NO
NO
NO
NO
NO
NO
NO


L-Sorbose
NO
NO
NO
NO
NO
NO
NO
NO


Citramalic acid
NO
NO
NO
NO
NO
NO
NO
NO


Oxalic acid
NO
NO
NO
NO
NO
NO
NO
NO


L-Arginine
NO
NO
NO
YES
NO
NO
NO
NO


L-Valine
YES
NO
YES
YES
YES
NO
YES
YES


γ-Cyclodextrin
NO
NO
NO
NO
NO
NO
NO
NO


D-arabinose
NO
NO
NO
NO
NO
NO
NO
NO


Maltitol
NO
NO
NO
YES
NO
YES
YES
NO


Stachyose
NO
NO
NO
NO
NO
NO
NO
NO


D-Glucosamine
YES
YES
YES
YES
YES
YES
YES
YES


Oxalomalic acid
YES
NO
YES
YES
YES
YES
YES
YES


Glycine
NO
NO
NO
NO
NO
NO
NO
NO


D,L-Carnitine
YES
YES
YES
YES
YES
NO
NO
NO


Dextrin
NO
NO
NO
NO
NO
NO
YES
NO


D-arabitol
NO
NO
NO
NO
NO
NO
NO
NO


a-Methyl-D-Glucoside
NO
NO
NO
NO
NO
NO
NO
NO


D-Tagatose
NO
NO
NO
NO
NO
NO
NO
NO


2-Hydroxy benzoic acid
NO
NO
NO
NO
NO
NO
NO
NO


Quinic acid
NO
NO
NO
NO
NO
NO
NO
NO


L-Histidine
NO
YES
NO
NO
NO
NO
NO
NO


Sec-Butylamine
NO
NO
NO
NO
NO
NO
NO
NO


Gelatin
NO
NO
NO
NO
NO
YES
YES
NO


L-arabitol
NO
NO
NO
NO
NO
NO
NO
NO


β-Methyl-D-Galactoside
NO
NO
NO
YES
NO
NO
YES
NO


Turanose
NO
YES
NO
YES
NO
YES
YES
NO


4-Hydroxy benzoic acid
NO
NO
NO
NO
NO
NO
NO
NO


D-Ribono-1,4-Lactone
NO
NO
NO
YES
NO
NO
NO
NO


L-Homoserine
NO
NO
NO
NO
NO
NO
NO
NO


D,L-Octopamine
YES
NO
YES
YES
YES
YES
YES
YES


Glycogen
NO
NO
NO
NO
NO
NO
NO
NO


Arbutin
NO
NO
NO
YES
NO
YES
YES
NO


3-Methyl Glucose
NO
NO
NO
NO
NO
NO
NO
NO


Xylitol
NO
NO
NO
NO
NO
NO
YES
NO


β-Hydroxy butyric acid
NO
NO
NO
NO
NO
NO
NO
NO


Sebacic acid
YES
NO
NO
NO
NO
NO
NO
NO


Hydroxy-L-Proline
NO
NO
NO
NO
NO
NO
NO
NO


Putrescine
YES
NO
NO
YES
YES
NO
NO
NO


Inulin
NO
NO
NO
YES
NO
YES
YES
NO


2-Deoxy-D-Ribose
NO
NO
NO
NO
NO
NO
NO
NO


β-Methyl-D-Glucuronic acid
NO
NO
NO
NO
NO
NO
NO
NO


N-Acetyl-D-glucosaminitol
NO
NO
NO
NO
NO
NO
NO
NO


γ-Hydroxy butyric acid
NO
NO
NO
NO
NO
NO
NO
NO


Sorbic acid
NO
NO
NO
NO
NO
NO
NO
NO


L-Isoleucine
YES
NO
YES
YES
NO
NO
NO
NO


Dihydroxy acetone
NO
YES
NO
NO
NO
NO
YES
NO


Laminarin
NO
NO
NO
NO
NO
NO
NO
NO


i-Erythritol
NO
NO
NO
NO
NO
NO
NO
NO


a-Methyl-D-Mannoside
NO
NO
NO
NO
NO
NO
NO
NO


γ-amino butyric acid
YES
YES
YES
YES
YES
NO
NO
NO


a-Keto-valeric acid
NO
NO
NO
NO
NO
NO
NO
NO


Succinamic acid
NO
YES
NO
NO
NO
NO
NO
NO


L-Leucine
YES
NO
YES
YES
NO
NO
NO
NO


2,3-Butanediol
NO
NO
YES
NO
NO
NO
NO
NO


Mannan
NO
NO
NO
NO
NO
NO
NO
NO


D-Fucose
NO
NO
NO
NO
NO
NO
NO
NO


β-Methyl-D-Xyloside
NO
NO
NO
YES
NO
NO
NO
NO


d-amino valeric acid
NO
NO
NO
NO
NO
NO
NO
NO


Itaconic acid
NO
NO
NO
NO
NO
NO
NO
NO


D-Tartaric acid
NO
NO
NO
NO
NO
NO
NO
NO


L-Lysine
NO
NO
NO
NO
NO
NO
NO
NO


2,3-Butanone
NO
NO
NO
NO
NO
NO
NO
NO


Pectin
NO
NO
NO
NO
NO
NO
NO
NO


3-0-β-D-Galactopyranosyl-D-
NO
NO
NO
NO
NO
NO
NO
NO


arabinose


Palatinose
NO
NO
NO
YES
NO
YES
YES
NO


Butyric acid
NO
NO
NO
NO
NO
NO
NO
NO


5-Keto-D-Gluconic acid
NO
NO
NO
NO
YES
NO
NO
YES


L-Tartaric acid
YES
NO
YES
NO
YES
NO
NO
YES


L-Methionine
NO
NO
NO
NO
NO
NO
NO
NO


3-Hydroxy 2-Butanone
NO
NO
NO
NO
NO
NO
NO
NO












Strain/Substrate

















SYM00207
SYM00212
SYM00219
SYM00234
SYM00236
SYM00248
SYM00249







N-acetyl-D-Galactosamine
NO
NO
NO
NO
NO
NO
NO



Gentiobiose
NO
YES
YES
YES
NO
YES
YES



D-Raffinose
NO
YES
YES
YES
NO
YES
YES



Capric acid
YES
NO
NO
NO
NO
NO
NO



D-lactic acid methyl ester
NO
NO
NO
NO
NO
NO
NO



Acetamide
NO
NO
NO
NO
NO
NO
NO



L-Ornithine
YES
YES
YES
YES
YES
NO
NO



Chondrointin sulfate C
NO
NO
NO
NO
NO
NO
NO



N-acetyl-neuraminic acid
NO
NO
NO
NO
NO
NO
NO



L-glucose
NO
NO
NO
NO
NO
YES
NO



Salicin
NO
YES
YES
YES
NO
NO
YES



Caproic acid
YES
NO
NO
NO
NO
NO
NO



Malonic acid
NO
NO
NO
NO
NO
NO
NO



L-Alaninamide
NO
NO
NO
NO
YES
NO
YES



L-Phenylalanine
NO
NO
NO
NO
NO
NO
NO



a-Cyclodextrin
NO
YES
NO
YES
NO
NO
NO



β-D-allose
NO
NO
NO
NO
NO
NO
NO



Lactitol
NO
NO
NO
YES
NO
YES
NO



Sedoheptulosan
NO
NO
NO
NO
NO
NO
NO



Citraconic acid
NO
NO
NO
NO
NO
NO
NO



Melibionic acid
NO
YES
YES
NO
NO
YES
NO



N-Acetyl-L-Glutamic acid
NO
NO
NO
YES
NO
NO
NO



L-Pyroglutamic acid
YES
YES
YES
YES
YES
YES
NO



β-Cyclodextrin
NO
NO
YES
YES
NO
NO
YES



Amygdalin
NO
YES
NO
YES
NO
YES
YES



D-Melezitose
NO
YES
NO
YES
NO
YES
YES



L-Sorbose
NO
NO
NO
NO
NO
NO
NO



Citramalic acid
NO
NO
NO
NO
NO
NO
NO



Oxalic acid
NO
NO
NO
NO
NO
NO
NO



L-Arginine
NO
NO
NO
NO
NO
NO
NO



L-Valine
NO
YES
YES
YES
NO
NO
NO



γ-Cyclodextrin
NO
NO
YES
YES
NO
NO
NO



D-arabinose
NO
NO
NO
NO
NO
NO
NO



Maltitol
NO
YES
NO
YES
NO
YES
YES



Stachyose
NO
YES
NO
YES
NO
NO
NO



D-Glucosamine
NO
YES
YES
YES
YES
YES
YES



Oxalomalic acid
NO
NO
NO
YES
YES
YES
YES



Glycine
NO
NO
NO
NO
NO
NO
YES



D,L-Carnitine
NO
NO
NO
YES
NO
NO
YES



Dextrin
NO
NO
YES
YES
NO
NO
NO



D-arabitol
YES
NO
NO
NO
NO
NO
NO



a-Methyl-D-Glucoside
NO
NO
NO
YES
YES
NO
YES



D-Tagatose
NO
NO
NO
NO
NO
NO
YES



2-Hydroxy benzoic acid
NO
NO
NO
NO
NO
NO
NO



Quinic acid
NO
NO
NO
NO
NO
NO
NO



L-Histidine
YES
YES
NO
NO
NO
NO
NO



Sec-Butylamine
NO
NO
NO
NO
NO
NO
YES



Gelatin
YES
NO
NO
YES
NO
NO
YES



L-arabitol
NO
NO
NO
NO
NO
NO
NO



β-Methyl-D-Galactoside
NO
NO
NO
YES
NO
NO
NO



Turanose
NO
YES
NO
YES
NO
NO
YES



4-Hydroxy benzoic acid
NO
NO
NO
NO
NO
NO
NO



D-Ribono-1,4-Lactone
NO
NO
NO
NO
NO
NO
NO



L-Homoserine
YES
NO
NO
NO
NO
NO
NO



D,L-Octopamine
NO
NO
YES
YES
YES
NO
NO



Glycogen
NO
NO
NO
YES
NO
NO
NO



Arbutin
NO
YES
YES
YES
NO
YES
YES



3-Methyl Glucose
NO
NO
NO
NO
NO
NO
NO



Xylitol
NO
NO
NO
YES
NO
NO
NO



β-Hydroxy butyric acid
NO
NO
NO
NO
NO
NO
NO



Sebacic acid
NO
NO
NO
NO
YES
NO
NO



Hydroxy-L-Proline
NO
NO
NO
NO
YES
NO
YES



Putrescine
NO
YES
NO
NO
NO
NO
NO



Inulin
NO
NO
YES
NO
NO
YES
YES



2-Deoxy-D-Ribose
NO
NO
NO
NO
NO
NO
NO



β-Methyl-D-Glucuronic acid
NO
NO
NO
NO
NO
NO
NO



N-Acetyl-D-glucosaminitol
NO
NO
NO
NO
NO
NO
NO



γ-Hydroxy butyric acid
NO
NO
NO
NO
NO
NO
NO



Sorbic acid
NO
NO
NO
NO
NO
NO
NO



L-Isoleucine
YES
YES
NO
YES
NO
NO
NO



Dihydroxy acetone
NO
NO
NO
NO
NO
NO
NO



Laminarin
NO
NO
NO
YES
NO
NO
NO



i-Erythritol
YES
NO
NO
NO
NO
NO
NO



a-Methyl-D-Mannoside
NO
NO
NO
NO
NO
NO
NO



γ-amino butyric acid
NO
NO
NO
YES
NO
NO
YES



a-Keto-valeric acid
NO
NO
NO
NO
NO
NO
NO



Succinamic acid
NO
YES
NO
NO
NO
NO
NO



L-Leucine
YES
NO
NO
YES
NO
NO
NO



2,3-Butanediol
NO
NO
NO
YES
NO
NO
NO



Mannan
NO
NO
NO
NO
NO
NO
NO



D-Fucose
NO
NO
NO
NO
NO
NO
NO



β-Methyl-D-Xyloside
NO
NO
NO
YES
NO
NO
NO



d-amino valeric acid
NO
NO
NO
NO
YES
NO
NO



Itaconic acid
YES
YES
NO
NO
NO
NO
NO



D-Tartaric acid
NO
NO
NO
NO
NO
NO
NO



L-Lysine
NO
NO
NO
NO
NO
NO
NO



2,3-Butanone
NO
NO
NO
NO
NO
NO
NO



Pectin
NO
NO
NO
YES
NO
NO
NO



3-0-β-D-Galactopyranosyl-D-
NO
NO
NO
YES
NO
NO
NO



arabinose



Palatinose
NO
YES
YES
YES
NO
NO
NO



Butyric acid
YES
NO
NO
NO
NO
NO
NO



5-Keto-D-Gluconic acid
NO
NO
NO
NO
NO
NO
NO



L-Tartaric acid
NO
NO
NO
NO
NO
NO
NO



L-Methionine
NO
NO
NO
NO
NO
NO
NO



3-Hydroxy 2-Butanone
NO
NO
NO
NO
NO
NO
NO

















TABLE N





Substrate utilization as determined by BIOLOG PM2A MicroPlates by bacterial


endophytes belonging to core OTUs.

















Strain/Substrate
















SYM00260
SYM00290
SYM00292
SYM00003
SYM00043
SYM00050
SYM05066
SYM00508





N-acetyl-D-Galactosamine
NO
NO
NO
NO
NO
YES
NO
NO


Gentiobiose
YES
YES
YES
NO
YES
YES
NO
YES


D-Raffinose
YES
YES
YES
NO
NO
YES
NO
NO


Capric acid
NO
NO
NO
NO
NO
NO
NO
NO


D-laclic acid methyl ester
NO
NO
NO
NO
NO
YES
NO
NO


Acetamide
NO
NO
NO
NO
NO
NO
NO
NO


L-Ornithine
YES
NO
NO
YES
NO
YES
NO
NO


Chondrointin sulfate C
YES
NO
NO
NO
NO
NO
NO
NO


N-acetyl-neuraminic acid
NO
NO
NO
NO
NO
NO
NO
NO


L-glucose
NO
NO
NO
NO
NO
NO
NO
NO


Salicin
YES
YES
YES
NO
NO
YES
NO
YES


Caproic acid
YES
NO
YES
NO
NO
NO
NO
YES


Malonic acid
YES
NO
NO
NO
NO
NO
NO
NO


L-Alaninamide
NO
YES
NO
NO
NO
NO
NO
NO


L-Phenylalanine
YES
NO
NO
YES
NO
NO
NO
NO


a-Cyclodextrin
NO
YES
YES
NO
NO
NO
NO
NO


β-D-allose
NO
NO
YES
NO
NO
NO
NO
NO


Lactitol
NO
YES
YES
NO
NO
NO
NO
NO


Sedoheptulosan
NO
NO
NO
NO
NO
NO
NO
NO


Citraconic acid
NO
NO
NO
YES
NO
NO
NO
NO


Melibionic acid
YES
NO
NO
NO
NO
YES
NO
NO


N-Acetyl-L-Glutamic acid
YES
NO
YES
NO
NO
YES
NO
NO


L-Pyroglutamic acid
YES
NO
YES
YES
NO
NO
NO
YES


β-Cyclodextrin
NO
YES
YES
NO
NO
NO
NO
NO


Amygdalin
NO
YES
YES
NO
NO
NO
NO
NO


D-Melezitose
NO
YES
YES
NO
NO
NO
NO
NO


L-Sorbose
NO
NO
NO
NO
NO
NO
NO
NO


Citramalic acid
YES
NO
YES
NO
NO
NO
NO
NO


Oxalic acid
NO
NO
NO
NO
NO
NO
NO
NO


L-Arginine
YES
NO
NO
NO
NO
NO
NO
NO


L-Valine
YES
NO
YES
YES
NO
NO
NO
NO


γ-Cyclodextrin
NO
YES
YES
NO
NO
NO
NO
NO


D-arabinose
NO
YES
YES
NO
NO
NO
NO
YES


Maltitol
NO
YES
YES
NO
NO
NO
NO
NO


Stachyose
YES
YES
YES
NO
NO
NO
NO
NO


D-Glucosamine
YES
YES
YES
YES
YES
YES
NO
YES


Oxalomalic acid
YES
YES
YES
YES
YES
NO
YES
NO


Glycine
NO
NO
NO
NO
NO
NO
NO
NO


D,L-Carnitine
NO
NO
NO
YES
NO
NO
NO
NO


Dextrin
YES
YES
YES
NO
NO
NO
NO
YES


D-arabitol
NO
NO
YES
NO
NO
NO
NO
YES


a-Methyl-D-Glucoside
NO
YES
YES
NO
NO
NO
NO
NO


D-Tagatose
NO
YES
NO
NO
NO
NO
NO
YES


2-Hydroxy benzoic acid
NO
NO
NO
NO
NO
NO
NO
NO


Quinic acid
NO
NO
NO
NO
NO
NO
NO
NO


L-Histidine
YES
YES
NO
NO
YES
NO
NO
NO


Sec-Butylamine
NO
NO
NO
NO
NO
NO
NO
NO


Gelatin
YES
YES
YES
NO
NO
NO
NO
NO


L-arabitol
NO
NO
NO
NO
NO
NO
NO
NO


β-Methyl-D-Galactoside
NO
YES
YES
NO
NO
NO
NO
YES


Turanose
NO
YES
YES
NO
NO
NO
NO
NO


4-Hydroxy benzoic acid
NO
NO
NO
NO
NO
NO
NO
NO


D-Ribono-1,4-Lactone
NO
NO
NO
NO
NO
NO
NO
NO


L-Homoserine
NO
NO
NO
NO
NO
NO
NO
NO


D,L-Octopamine
NO
NO
NO
YES
NO
NO
YES
NO


Glycogen
YES
YES
YES
NO
NO
NO
NO
YES


Arbutin
NO
YES
YES
NO
NO
YES
NO
YES


3-Methyl Glucose
NO
NO
YES
NO
NO
NO
NO
YES


Xylitol
NO
NO
YES
NO
NO
NO
NO
NO


β-Hydroxy butyric acid
YES
NO
NO
NO
NO
YES
NO
YES


Sebacic acid
YES
NO
NO
NO
NO
NO
NO
NO


Hydroxy-L-Proline
YES
NO
YES
NO
NO
YES
NO
NO


Putrescine
YES
NO
NO
NO
NO
YES
NO
NO


Inulin
YES
YES
YES
YES
YES
NO
NO
NO


2-Deoxy-D-Ribose
NO
NO
YES
NO
NO
NO
NO
YES


β-Methyl-D-Glucuronic acid
NO
NO
YES
NO
NO
NO
NO
NO


N-Acetyl-D-glucosaminitol
NO
NO
NO
NO
NO
NO
NO
NO


γ-Hydroxy butyric acid
YES
NO
NO
NO
NO
NO
NO
NO


Sorbic acid
NO
NO
NO
NO
NO
NO
NO
NO


L-Isoleucine
YES
NO
YES
YES
NO
NO
NO
YES


Dihydroxy acetone
NO
NO
YES
NO
NO
YES
NO
YES


Laminarin
NO
YES
YES
NO
NO
NO
NO
NO


i-Erythritol
NO
NO
NO
NO
NO
NO
NO
NO


a-Methyl-D-Mannoside
NO
NO
NO
NO
NO
NO
NO
NO


γ-amino butyric acid
YES
NO
NO
YES
YES
NO
NO
NO


a-Keto-valeric acid
YES
NO
NO
NO
NO
NO
NO
NO


Succinamic acid
NO
NO
NO
NO
NO
NO
NO
NO


L-Leucine
NO
NO
YES
YES
NO
NO
NO
NO


2,3-Butanediol
YES
NO
NO
NO
NO
NO
NO
NO


Mannan
NO
NO
NO
NO
NO
NO
NO
NO


D-Fucose
NO
NO
NO
NO
NO
NO
NO
NO


β-Methyl-D-Xyloside
NO
YES
YES
NO
NO
NO
NO
NO


d-amino valeric acid
YES
NO
NO
NO
NO
NO
NO
NO


Itaconic acid
YES
NO
YES
NO
NO
YES
NO
YES


D-Tartaric acid
NO
NO
NO
NO
NO
NO
NO
NO


L-Lysine
YES
NO
NO
NO
NO
NO
NO
NO


2,3-Butanone
NO
NO
NO
NO
NO
NO
NO
NO


Pectin
NO
YES
YES
NO
NO
NO
NO
YES


3-0-β-D-Galactopyranosyl-D-
NO
NO
YES
NO
NO
NO
NO
NO


arabinose


Palatinose
NO
YES
YES
NO
NO
NO
NO
NO


Butyric acid
YES
NO
NO
YES
NO
NO
NO
NO


5-Keto-D-Gluconic acid
NO
NO
NO
NO
YES
NO
NO
YES


L-Tartaric acid
NO
NO
NO
NO
YES
NO
NO
YES


L-Methionine
NO
NO
NO
NO
NO
NO
NO
NO


3-Hydroxy 2-Butanone
NO
NO
NO
NO
NO
NO
NO
NO












Strain/Substrate


















SYM00525
SYM00053
SYM00538A
SYM00538B
SYM00538i
SYM00543
SYM00563
SYM00574







N-acetyl-D-Galactosamine
NO
YES
NO
NO
NO
NO
NO
NO



Gentiobiose
YES
YES
NO
YES
YES
NO
YES
NO



D-Raffinose
NO
YES
NO
YES
NO
NO
NO
NO



Capric acid
NO
NO
NO
NO
NO
NO
NO
NO



D-laclic acid methyl ester
NO
YES
NO
NO
NO
NO
NO
NO



Acetamide
NO
NO
NO
NO
NO
NO
NO
YES



L-Ornithine
NO
NO
NO
NO
NO
NO
NO
NO



Chondrointin sulfate C
NO
NO
NO
NO
NO
NO
NO
NO



N-acetyl-neuraminic acid
NO
NO
NO
NO
NO
NO
NO
NO



L-glucose
NO
NO
NO
NO
NO
NO
NO
NO



Salicin
YES
YES
NO
YES
YES
NO
YES
NO



Caproic acid
NO
NO
NO
NO
NO
NO
NO
NO



Malonic acid
YES
NO
NO
NO
NO
NO
NO
NO



L-Alaninamide
YES
NO
YES
NO
YES
NO
NO
YES



L-Phenylalanine
NO
NO
NO
NO
NO
NO
NO
YES



a-Cyclodextrin
NO
NO
YES
NO
NO
YES
NO
NO



β-D-allose
NO
NO
NO
NO
NO
NO
NO
NO



Lactitol
YES
NO
NO
YES
NO
NO
NO
NO



Sedoheptulosan
NO
NO
NO
NO
NO
NO
NO
NO



Citraconic acid
NO
NO
NO
NO
NO
NO
NO
YES



Melibionic acid
NO
YES
NO
NO
NO
NO
NO
NO



N-Acetyl-L-Glutamic acid
NO
YES
NO
NO
YES
NO
NO
NO



L-Pyroglutamic acid
YES
NO
YES
NO
YES
YES
NO
YES



β-Cyclodextrin
NO
NO
YES
YES
NO
NO
NO
NO



Amygdalin
YES
NO
NO
YES
YES
NO
YES
NO



D-Melezitose
YES
NO
NO
YES
NO
NO
NO
NO



L-Sorbose
NO
NO
NO
NO
NO
NO
NO
NO



Citramalic acid
NO
NO
NO
NO
NO
NO
NO
NO



Oxalic acid
NO
NO
NO
NO
NO
NO
NO
NO



L-Arginine
NO
NO
NO
NO
NO
YES
NO
YES



L-Valine
NO
NO
NO
NO
NO
NO
NO
NO



γ-Cyclodextrin
NO
NO
YES
YES
NO
NO
NO
NO



D-arabinose
NO
NO
NO
NO
NO
NO
NO
YES



Maltitol
YES
NO
NO
YES
NO
NO
NO
NO



Stachyose
YES
NO
NO
YES
NO
NO
NO
NO



D-Glucosamine
YES
YES
YES
YES
YES
YES
YES
YES



Oxalomalic acid
YES
NO
YES
YES
YES
YES
YES
YES



Glycine
NO
NO
NO
NO
NO
NO
NO
NO



D,L-Carnitine
NO
NO
NO
NO
NO
NO
NO
YES



Dextrin
YES
NO
YES
YES
NO
YES
NO
NO



D-arabitol
NO
NO
NO
NO
NO
NO
NO
NO



a-Methyl-D-Glucoside
NO
NO
NO
YES
NO
NO
NO
NO



D-Tagatose
NO
NO
NO
NO
NO
NO
NO
NO



2-Hydroxy benzoic acid
NO
NO
NO
NO
NO
NO
NO
NO



Quinic acid
NO
NO
NO
NO
NO
NO
NO
NO



L-Histidine
NO
NO
NO
NO
NO
YES
NO
YES



Sec-Butylamine
NO
NO
NO
NO
NO
NO
NO
NO



Gelatin
NO
NO
YES
NO
YES
YES
NO
NO



L-arabitol
NO
NO
NO
NO
NO
NO
NO
NO



β-Methyl-D-Galactoside
YES
NO
NO
YES
NO
NO
NO
YES



Turanose
YES
NO
NO
YES
NO
NO
NO
NO



4-Hydroxy benzoic acid
NO
NO
NO
NO
NO
NO
NO
YES



D-Ribono-1,4-Lactone
NO
NO
NO
NO
NO
NO
NO
YES



L-Homoserine
NO
NO
NO
NO
NO
NO
NO
YES



D,L-Octopamine
NO
NO
NO
NO
NO
NO
NO
NO



Glycogen
NO
NO
NO
YES
NO
YES
NO
NO



Arbutin
YES
YES
YES
NO
YES
NO
YES
NO



3-Methyl Glucose
NO
NO
NO
NO
NO
NO
NO
NO



Xylitol
YES
NO
NO
NO
NO
NO
NO
YES



β-Hydroxy butyric acid
NO
YES
NO
NO
NO
NO
NO
YES



Sebacic acid
NO
NO
NO
NO
NO
NO
NO
YES



Hydroxy-L-Proline
YES
YES
NO
NO
NO
YES
NO
YES



Putrescine
NO
YES
NO
NO
NO
NO
NO
NO



Inulin
NO
NO
YES
YES
YES
NO
NO
YES



2-Deoxy-D-Ribose
NO
NO
NO
NO
NO
NO
NO
NO



β-Methyl-D-Glucuronic acid
YES
NO
NO
NO
NO
NO
NO
NO



N-Acetyl-D-glucosaminitol
NO
NO
NO
NO
NO
NO
NO
NO



γ-Hydroxy butyric acid
NO
NO
NO
NO
NO
NO
NO
NO



Sorbic acid
NO
NO
NO
NO
NO
NO
NO
NO



L-Isoleucine
NO
NO
NO
NO
NO
NO
NO
NO



Dihydroxy acetone
NO
YES
NO
NO
NO
NO
NO
YES



Laminarin
NO
NO
NO
YES
NO
NO
NO
YES



i-Erythritol
NO
NO
NO
NO
NO
NO
NO
NO



a-Methyl-D-Mannoside
YES
NO
NO
NO
NO
NO
NO
NO



γ-amino butyric acid
NO
NO
NO
NO
NO
NO
NO
YES



a-Keto-valeric acid
NO
NO
NO
NO
NO
NO
NO
NO



Succinamic acid
NO
NO
NO
NO
NO
NO
NO
NO



L-Leucine
NO
NO
NO
NO
NO
NO
NO
NO



2,3-Butanediol
NO
NO
NO
YES
NO
NO
NO
NO



Mannan
NO
NO
NO
NO
NO
NO
NO
NO



D-Fucose
NO
NO
NO
NO
NO
NO
NO
NO



β-Methyl-D-Xyloside
NO
NO
NO
YES
NO
NO
NO
NO



d-amino valeric acid
NO
NO
NO
NO
NO
NO
NO
NO



Itaconic acid
NO
YES
NO
NO
NO
NO
NO
NO



D-Tartaric acid
NO
NO
NO
NO
NO
NO
NO
YES



L-Lysine
NO
NO
NO
NO
NO
NO
NO
NO



2,3-Butanone
NO
NO
NO
NO
NO
NO
NO
NO



Pectin
NO
NO
NO
YES
NO
NO
NO
NO



3-0-β-D-Galactopyranosyl-D-
NO
NO
NO
YES
NO
NO
NO
NO



arabinose



Palatinose
YES
NO
NO
YES
NO
NO
NO
NO



Butyric acid
NO
NO
NO
NO
NO
NO
NO
NO



5-Keto-D-Gluconic acid
NO
NO
NO
NO
NO
NO
NO
YES



L-Tartaric acid
NO
NO
NO
NO
NO
NO
NO
YES



L-Methionine
NO
NO
NO
NO
NO
NO
NO
NO



3-Hydroxy 2-Butanone
NO
NO
NO
NO
NO
NO
NO
NO

















TABLE O





Substrate utilization as determined by BIOLOG PM2A MicroPlates by bacterial


endophytes belonging to core OTUs.

















Strain/Substrate















SYM00057B
SYM00617
SYM00620
SYM00627
SYM00628
SYM00062C
SYM00650





N-acetyl-D-Galactosamine
NO
NO
NO
NO
YES
NO
NO


Gentiobiose
NO
YES
YES
YES
YES
YES
NO


D-Raffinose
NO
NO
YES
YES
YES
YES
NO


Capric acid
NO
NO
NO
NO
NO
NO
NO


D-lactic acid methyl ester
NO
NO
NO
NO
NO
NO
NO


Acetamide
NO
NO
NO
NO
NO
NO
NO


L-Ornithine
NO
NO
NO
NO
NO
NO
NO


Chondrointin sulfate C
NO
NO
NO
NO
NO
NO
NO


N-acetyl-neuraminic acid
NO
NO
YES
NO
NO
NO
NO


L-glucose
NO
NO
NO
NO
NO
NO
NO


Salicin
NO
YES
NO
YES
YES
YES
NO


Caproic acid
NO
NO
NO
NO
NO
NO
NO


Malonic acid
NO
NO
NO
NO
NO
NO
NO


L-Alaninamide
NO
NO
NO
NO
NO
NO
NO


L-Phenylalanine
NO
NO
NO
NO
NO
NO
NO


a-Cyclodextrin
NO
NO
NO
NO
NO
NO
NO


β-D-allose
NO
NO
NO
NO
NO
NO
NO


Lactitol
NO
NO
NO
NO
NO
YES
NO


Sedoheptulosan
NO
NO
NO
NO
NO
NO
NO


Citraconic acid
NO
NO
NO
NO
NO
NO
NO


Melibionic acid
NO
NO
YES
YES
YES
NO
NO


N-Acetyl-L-Glutamic acid
NO
NO
NO
NO
NO
YES
NO


L-Pyroglutamic acid
NO
NO
NO
NO
NO
YES
NO


β-Cyclodextrin
NO
NO
NO
NO
NO
NO
NO


Amygdalin
NO
YES
NO
NO
NO
YES
NO


D-Melezitose
NO
YES
NO
NO
NO
YES
NO


L-Sorbose
NO
NO
NO
NO
NO
NO
NO


Citramalic acid
NO
NO
NO
NO
NO
NO
NO


Oxalic acid
NO
NO
NO
NO
NO
NO
NO


L-Arginine
NO
NO
NO
NO
NO
NO
NO


L-Valine
NO
NO
NO
NO
NO
NO
NO


γ-Cyclodextrin
NO
NO
NO
NO
NO
NO
NO


D-arabinose
NO
NO
NO
NO
YES
NO
YES


Maltitol
NO
NO
NO
YES
YES
NO
NO


Stachyose
NO
NO
NO
NO
NO
YES
NO


D-Glucosamine
YES
YES
NO
YES
YES
YES
NO


Oxalomalic acid
YES
YES
NO
NO
NO
YES
NO


Glycine
NO
NO
NO
NO
NO
NO
NO


D,L-Carnitine
NO
NO
NO
NO
NO
NO
NO


Dextrin
NO
YES
YES
NO
NO
YES
NO


D-arabitol
NO
NO
NO
NO
NO
NO
NO


a-Methyl-D-Glucoside
NO
NO
NO
YES
YES
NO
NO


D-Tagatose
NO
NO
NO
NO
NO
NO
NO


2-Hydroxy benzoic acid
NO
NO
NO
NO
NO
NO
NO


Quinic acid
NO
NO
NO
NO
NO
NO
NO


L-Histidine
YES
NO
YES
NO
NO
NO
YES


Sec-Butylamine
NO
NO
NO
NO
NO
NO
NO


Gelatin
NO
NO
NO
NO
NO
NO
NO


L-arabitol
NO
NO
NO
NO
NO
NO
NO


β-Methyl-D-Galactoside
NO
NO
YES
YES
YES
YES
NO


Turanose
NO
NO
NO
YES
NO
YES
NO


4-Hydroxy benzoic acid
NO
NO
NO
NO
NO
NO
NO


D-Ribono-1,4-Lactone
NO
NO
NO
NO
NO
NO
NO


L-Homoserine
YES
NO
NO
NO
NO
NO
NO


D,L-Octopamine
NO
YES
NO
NO
NO
YES
NO


Glycogen
NO
NO
NO
NO
NO
NO
NO


Arbutin
NO
YES
NO
YES
YES
YES
NO


3-Methyl Glucose
NO
NO
NO
NO
YES
NO
NO


Xylitol
YES
NO
NO
NO
NO
NO
NO


β-Hydroxy butyric acid
NO
NO
NO
NO
NO
NO
NO


Sebacic acid
YES
NO
NO
NO
NO
NO
NO


Hydroxy-L-Proline
NO
NO
NO
NO
NO
NO
YES


Putrescine
NO
NO
NO
NO
YES
NO
NO


Inulin
YES
NO
NO
NO
NO
YES
NO


2-Deoxy-D-Ribose
NO
NO
YES
NO
NO
NO
YES


β-Methyl-D-Glucuronic acid
NO
NO
NO
NO
NO
NO
NO


N-Acetyl-D-glucosaminitol
NO
NO
NO
NO
NO
NO
NO


γ-Hydroxy butyric acid
NO
NO
NO
NO
NO
NO
NO


Sorbic acid
NO
NO
NO
NO
NO
NO
NO


L-Isoleucine
NO
NO
NO
NO
NO
YES
NO


Dihydroxy acetone
YES
NO
NO
YES
YES
NO
YES


Laminarin
NO
NO
NO
NO
NO
NO
NO


i-Erythritol
NO
NO
NO
NO
NO
NO
NO


a-Methyl-D-Mannoside
NO
NO
NO
NO
NO
NO
NO


γ-amino butyric acid
YES
NO
NO
NO
NO
NO
YES


a-Keto-valeric acid
NO
NO
NO
NO
NO
NO
NO


Succinamic acid
NO
NO
NO
NO
NO
NO
NO


L-Leucine
YES
NO
NO
NO
NO
NO
NO


2,3-Butanediol
NO
NO
NO
NO
NO
YES
NO


Mannan
NO
NO
NO
NO
NO
NO
NO


D-Fucose
NO
NO
NO
NO
NO
NO
NO


β-Methyl-D-Xyloside
NO
NO
NO
NO
NO
YES
NO


d-amino valeric acid
NO
NO
NO
NO
NO
NO
NO


Itaconic acid
NO
NO
NO
NO
NO
NO
NO


D-Tartaric acid
YES
NO
NO
NO
NO
NO
NO


L-Lysine
NO
NO
NO
NO
NO
NO
NO


2,3-Butanone
NO
NO
NO
NO
NO
NO
NO


Pectin
NO
NO
NO
NO
NO
NO
NO


3-0-β-D-Galactopyranosyl-
NO
NO
NO
NO
YES
NO
NO


D-arabinose


Palatinose
NO
NO
NO
YES
YES
YES
NO


Butyric acid
NO
NO
NO
NO
NO
NO
NO


5-Keto-D-Gluconic acid
NO
NO
NO
NO
NO
NO
NO


L-Tartaric acid
NO
NO
NO
NO
NO
NO
NO


L-Methionine
NO
NO
NO
NO
NO
NO
NO


3-Hydroxy 2-Butanone
NO
NO
NO
NO
NO
NO
NO












Strain/Substrate















SYM00068
SYM00070
SYM00714
SYM00009
SYM00905
SYM00924
SYM00963





N-acetyl-D-Galactosamine
NO
NO
YES
NO
YES
NO
NO


Gentiobiose
NO
NO
YES
NO
YES
NO
NO


D-Raffinose
NO
NO
YES
NO
NO
NO
NO


Capric acid
NO
NO
NO
NO
NO
NO
NO


D-lactic acid methyl ester
NO
NO
NO
NO
NO
NO
NO


Acetamide
YES
NO
NO
NO
NO
NO
NO


L-Ornithine
YES
YES
NO
YES
NO
NO
NO


Chondrointin sulfate C
NO
NO
NO
NO
NO
NO
NO


N-acetyl-neuraminic acid
NO
NO
NO
NO
NO
NO
NO


L-glucose
NO
NO
NO
NO
NO
NO
NO


Salicin
NO
NO
YES
NO
YES
NO
NO


Caproic acid
NO
NO
NO
NO
NO
NO
NO


Malonic acid
NO
NO
NO
NO
NO
NO
NO


L-Alaninamide
NO
NO
YES
NO
YES
YES
NO


L-Phenylalanine
YES
NO
NO
YES
NO
NO
NO


a-Cyclodextrin
NO
NO
NO
NO
NO
NO
NO


β-D-allose
NO
NO
YES
NO
NO
NO
NO


Lactitol
NO
NO
YES
NO
YES
NO
NO


Sedoheptulosan
NO
NO
NO
NO
NO
NO
NO


Citraconic acid
YES
NO
NO
YES
NO
YES
NO


Melibionic acid
YES
NO
YES
NO
NO
NO
NO


N-Acetyl-L-Glutamic acid
NO
NO
NO
NO
NO
NO
NO


L-Pyroglutamic acid
YES
YES
YES
YES
NO
NO
NO


β-Cyclodextrin
NO
NO
NO
NO
NO
NO
NO


Amygdalin
NO
NO
NO
NO
NO
NO
NO


D-Melezitose
NO
NO
YES
NO
NO
NO
YES


L-Sorbose
NO
NO
NO
NO
NO
NO
YES


Citramalic acid
NO
NO
NO
NO
NO
NO
NO


Oxalic acid
NO
NO
NO
NO
NO
NO
NO


L-Arginine
NO
NO
YES
NO
NO
NO
NO


L-Valine
YES
YES
YES
YES
NO
NO
NO


γ-Cyclodextrin
NO
NO
NO
NO
NO
NO
NO


D-arabinose
NO
NO
YES
NO
NO
YES
YES


Maltitol
NO
NO
YES
NO
YES
NO
YES


Stachyose
NO
NO
NO
NO
NO
NO
YES


D-Glucosamine
YES
YES
YES
YES
YES
NO
NO


Oxalomalic acid
YES
YES
YES
YES
YES
NO
NO


Glycine
NO
NO
NO
NO
NO
NO
NO


D,L-Carnitine
NO
YES
NO
YES
NO
NO
NO


Dextrin
NO
NO
NO
NO
NO
NO
NO


D-arabitol
NO
NO
NO
NO
NO
NO
NO


a-Methyl-D-Glucoside
NO
NO
YES
NO
NO
NO
YES


D-Tagatose
NO
NO
NO
NO
NO
NO
NO


2-Hydroxy benzoic acid
NO
NO
NO
NO
NO
NO
NO


Quinic acid
NO
NO
NO
NO
NO
NO
NO


L-Histidine
NO
YES
YES
NO
NO
NO
NO


Sec-Butylamine
NO
NO
NO
NO
NO
NO
NO


Gelatin
NO
NO
NO
NO
YES
NO
NO


L-arabitol
NO
NO
NO
NO
NO
NO
NO


β-Methyl-D-Galactoside
NO
NO
YES
NO
NO
NO
YES


Turanose
NO
NO
YES
NO
NO
NO
YES


4-Hydroxy benzoic acid
NO
NO
NO
NO
NO
NO
NO


D-Ribono-1,4-Lactone
NO
NO
YES
NO
NO
NO
NO


L-Homoserine
NO
NO
NO
NO
NO
NO
NO


D,L-Octopamine
YES
YES
NO
YES
YES
NO
YES


Glycogen
NO
NO
NO
NO
NO
NO
NO


Arbutin
NO
YES
YES
NO
YES
NO
NO


3-Methyl Glucose
NO
NO
NO
NO
NO
NO
NO


Xylitol
NO
YES
YES
YES
NO
NO
NO


β-Hydroxy butyric acid
NO
NO
NO
NO
NO
NO
NO


Sebacic acid
NO
NO
NO
NO
NO
NO
NO


Hydroxy-L-Proline
NO
NO
NO
NO
NO
NO
NO


Putrescine
NO
YES
NO
NO
NO
NO
NO


Inulin
NO
NO
NO
NO
NO
NO
NO


2-Deoxy-D-Ribose
NO
NO
NO
NO
NO
YES
NO


β-Methyl-D-Glucuronic acid
NO
NO
NO
NO
NO
NO
NO


N-Acetyl-D-glucosaminitol
NO
NO
NO
NO
NO
NO
NO


γ-Hydroxy butyric acid
NO
NO
NO
NO
NO
YES
NO


Sorbic acid
NO
NO
NO
NO
NO
NO
NO


L-Isoleucine
YES
YES
YES
YES
NO
NO
NO


Dihydroxy acetone
NO
NO
NO
NO
NO
YES
YES


Laminarin
NO
NO
NO
NO
NO
NO
NO


i-Erythritol
NO
NO
NO
NO
NO
NO
NO


a-Methyl-D-Mannoside
NO
NO
NO
NO
NO
NO
NO


γ-amino butyric acid
NO
YES
YES
NO
NO
NO
NO


a-Keto-valeric acid
NO
NO
NO
NO
NO
NO
NO


Succinamic acid
NO
NO
NO
NO
NO
YES
NO


L-Leucine
NO
NO
YES
YES
NO
NO
NO


2,3-Butanediol
NO
NO
NO
NO
NO
NO
NO


Mannan
NO
NO
NO
NO
NO
NO
NO


D-Fucose
NO
NO
YES
NO
NO
NO
NO


β-Methyl-D-Xyloside
NO
NO
YES
NO
NO
NO
NO


d-amino valeric acid
NO
NO
NO
NO
NO
NO
NO


Itaconic acid
NO
NO
NO
NO
NO
NO
NO


D-Tartaric acid
NO
NO
NO
NO
NO
NO
NO


L-Lysine
NO
NO
NO
NO
NO
NO
NO


2,3-Butanone
NO
NO
NO
NO
NO
NO
NO


Pectin
NO
NO
NO
NO
NO
NO
NO


3-0-β-D-Galactopyranosyl-
NO
NO
NO
NO
NO
NO
NO


D-arabinose


Palatinose
NO
NO
YES
NO
YES
NO
YES


Butyric acid
NO
NO
NO
NO
NO
NO
NO


5-Keto-D-Gluconic acid
NO
NO
NO
NO
NO
NO
NO


L-Tartaric acid
NO
YES
NO
YES
NO
NO
NO


L-Methionine
NO
NO
NO
NO
NO
NO
NO


3-Hydroxy 2-Butanone
NO
NO
NO
NO
NO
NO
NO












Strain/Substrate















SYM00978
SYM00982
SYM00987
SYM00991
SYM00999







N-acetyl-D-Galactosamine
NO
NO
NO
YES
NO



Gentiobiose
NO
NO
NO
NO
NO



D-Raffinose
NO
NO
NO
YES
NO



Capric acid
NO
NO
NO
NO
NO



D-lactic acid methyl ester
NO
NO
NO
NO
NO



Acetamide
NO
NO
NO
NO
NO



L-Ornithine
NO
NO
NO
NO
NO



Chondrointin sulfate C
NO
NO
NO
NO
NO



N-acetyl-neuraminic acid
NO
NO
NO
NO
NO



L-glucose
NO
NO
NO
NO
NO



Salicin
NO
NO
NO
YES
NO



Caproic acid
NO
NO
NO
NO
NO



Malonic acid
NO
NO
NO
NO
NO



L-Alaninamide
NO
NO
NO
NO
NO



L-Phenylalanine
NO
NO
NO
NO
NO



a-Cyclodextrin
NO
YES
NO
NO
NO



β-D-allose
NO
NO
NO
NO
NO



Lactitol
NO
NO
NO
NO
NO



Sedoheptulosan
NO
NO
NO
NO
NO



Citraconic acid
NO
NO
NO
NO
NO



Melibionic acid
YES
NO
NO
NO
NO



N-Acetyl-L-Glutamic acid
NO
NO
YES
NO
NO



L-Pyroglutamic acid
NO
YES
YES
NO
NO



β-Cyclodextrin
NO
YES
NO
NO
NO



Amygdalin
NO
NO
NO
YES
NO



D-Melezitose
NO
NO
YES
NO
NO



L-Sorbose
NO
NO
YES
NO
NO



Citramalic acid
NO
NO
NO
NO
NO



Oxalic acid
NO
NO
NO
NO
NO



L-Arginine
NO
NO
NO
NO
NO



L-Valine
NO
NO
NO
NO
NO



γ-Cyclodextrin
NO
NO
NO
NO
NO



D-arabinose
NO
NO
NO
NO
NO



Maltitol
NO
NO
NO
NO
NO



Stachyose
NO
NO
NO
NO
NO



D-Glucosamine
YES
NO
YES
YES
YES



Oxalomalic acid
YES
NO
YES
NO
YES



Glycine
NO
NO
NO
NO
NO



D,L-Carnitine
NO
NO
NO
NO
NO



Dextrin
NO
NO
NO
YES
NO



D-arabitol
NO
NO
NO
NO
NO



a-Methyl-D-Glucoside
NO
NO
NO
NO
NO



D-Tagatose
NO
NO
NO
NO
NO



2-Hydroxy benzoic acid
NO
NO
NO
NO
NO



Quinic acid
NO
NO
NO
NO
NO



L-Histidine
NO
NO
NO
NO
NO



Sec-Butylamine
NO
NO
NO
NO
NO



Gelatin
NO
YES
NO
NO
NO



L-arabitol
NO
NO
NO
NO
NO



β-Methyl-D-Galactoside
YES
NO
YES
NO
NO



Turanose
NO
NO
YES
NO
NO



4-Hydroxy benzoic acid
NO
NO
NO
NO
NO



D-Ribono-1,4-Lactone
NO
NO
NO
NO
NO



L-Homoserine
NO
NO
NO
NO
NO



D,L-Octopamine
NO
NO
YES
YES
NO



Glycogen
NO
NO
NO
NO
NO



Arbutin
YES
NO
NO
YES
NO



3-Methyl Glucose
NO
NO
NO
NO
NO



Xylitol
NO
NO
NO
NO
NO



β-Hydroxy butyric acid
NO
NO
NO
NO
NO



Sebacic acid
YES
NO
NO
NO
NO



Hydroxy-L-Proline
NO
NO
YES
YES
YES



Putrescine
NO
NO
NO
NO
NO



Inulin
NO
NO
YES
NO
YES



2-Deoxy-D-Ribose
NO
NO
NO
NO
NO



β-Methyl-D-Glucuronic acid
NO
NO
NO
NO
NO



N-Acetyl-D-glucosaminitol
NO
NO
NO
NO
NO



γ-Hydroxy butyric acid
NO
NO
NO
NO
NO



Sorbic acid
NO
NO
NO
NO
NO



L-Isoleucine
NO
NO
NO
NO
NO



Dihydroxy acetone
NO
NO
YES
NO
NO



Laminarin
NO
YES
NO
NO
NO



i-Erythritol
NO
NO
NO
NO
NO



a-Methyl-D-Mannoside
NO
NO
NO
NO
NO



γ-amino butyric acid
NO
NO
NO
NO
NO



a-Keto-valeric acid
NO
NO
NO
NO
NO



Succinamic acid
NO
NO
NO
NO
NO



L-Leucine
NO
NO
NO
NO
NO



2,3-Butanediol
NO
NO
NO
NO
NO



Mannan
NO
NO
NO
NO
NO



D-Fucose
NO
NO
NO
NO
NO



β-Methyl-D-Xyloside
NO
NO
NO
NO
NO



d-amino valeric acid
NO
NO
NO
NO
NO



Itaconic acid
NO
NO
NO
YES
NO



D-Tartaric acid
NO
NO
NO
NO
NO



L-Lysine
NO
NO
NO
NO
NO



2,3-Butanone
NO
NO
NO
NO
NO



Pectin
NO
NO
NO
YES
NO



3-0-β-D-Galactopyranosyl-
NO
NO
YES
NO
NO



D-arabinose



Palatinose
YES
NO
YES
NO
NO



Butyric acid
NO
NO
NO
NO
NO



5-Keto-D-Gluconic acid
NO
NO
NO
NO
NO



L-Tartaric acid
NO
NO
NO
NO
NO



L-Methionine
NO
NO
NO
NO
NO



3-Hydroxy 2-Butanone
NO
NO
NO
NO
NO

















TABLE P





Substrate utilization as determined by BIOLOG PM1 MicroPlates by fungal


endophytes belonging to core OTUs.





















Strain/Substrate
SYM00120
SYM00122
SYM00123
SYM00124
SYM00129
SYM01300





D-Serine
NO
NO
YES
YES
NO
NO


D-Glucose-6-Phosphate
NO
NO
NO
YES
YES
NO


L-Asparagine
NO
NO
NO
YES
NO
YES


L-glutamine
NO
NO
NO
YES
YES
YES


Glycyl-L-Aspartic acid
NO
NO
NO
NO
NO
YES


Glycyl-L-Glutamic acid
NO
NO
NO
YES
NO
YES


Glycyl-L-Proline
NO
NO
NO
YES
NO
YES


L-Arabinose
YES
NO
NO
NO
YES
NO


D-Sorbitol
NO
NO
YES
YES
YES
YES


D-Galactonic acid-?-lactone
NO
NO
NO
NO
NO
YES


D-Aspartic acid
NO
NO
YES
YES
NO
NO


m-Tartaric acid
NO
NO
NO
YES
NO
YES


Citric acid
NO
NO
NO
YES
NO
YES


Tricarballylic acid
NO
NO
NO
YES
NO
YES


p-Hydroxy Phenyl acetic acid
NO
NO
NO
YES
NO
NO


N-Acetyl-D-Glucosamine
NO
NO
YES
YES
YES
YES


Glycerol
YES
NO
NO
YES
YES
YES


D-L-Malic acid
NO
NO
NO
YES
NO
YES


D-Glucosaminic acid
NO
NO
NO
YES
NO
YES


D-Glucose-1-Phosphate
NO
NO
YES
YES
NO
YES


m-Inositol
NO
NO
NO
YES
NO
YES


L-Serine
NO
NO
NO
YES
NO
YES


m-Hydroxy Phenyl Acetic acid
NO
NO
NO
YES
NO
YES


D-Saccharic acid
NO
NO
NO
YES
NO
YES


L-Fucose
NO
NO
NO
YES
NO
YES


D-Ribose
NO
NO
YES
YES
YES
YES


1,2-Propanediol
NO
NO
NO
YES
NO
NO


D-Fructose-6-Phosphate
NO
NO
NO
NO
NO
NO


D-Threonine
NO
NO
YES
YES
NO
NO


L-Threonine
NO
YES
NO
YES
NO
YES


Tyramine
YES
NO
NO
YES
NO
YES


Succinic acid
NO
NO
NO
YES
NO
YES


D-Glucuronic acid
NO
NO
YES
YES
YES
YES


Tween 20
NO
NO
NO
YES
YES
YES


Tween 40
NO
NO
YES
YES
YES
YES


Tween 80
NO
NO
YES
NO
YES
YES


Fumaric acid
NO
NO
YES
NO
NO
YES


L-Alanine
NO
NO
NO
YES
NO
YES


D-Psicose
NO
NO
NO
YES
NO
NO


D-Galactose
YES
NO
YES
YES
NO
YES


D-Gluconic acid
NO
NO
NO
YES
YES
YES


L-Rhamnose
NO
NO
NO
YES
YES
YES


a-Keto-Glutaric acid
NO
NO
NO
YES
NO
YES


a-Hydroxy Glutaric acid-?-
NO
NO
YES
YES
NO
YES


lactone


Bromo succinic acid
NO
NO
YES
YES
NO
YES


L-Alanyl-Glycine
NO
NO
YES
YES
NO
YES


L-Lyxose
NO
NO
NO
YES
NO
NO


L-Aspartic acid
NO
NO
YES
YES
NO
YES


D-L-a-Glycerol phosphate
NO
NO
NO
YES
NO
NO


D-Fructose
NO
NO
NO
YES
YES
YES


a-Keto-Butyric acid
NO
NO
NO
YES
NO
NO


a-Hydroxy Butyric acid
NO
NO
NO
YES
NO
NO


Propionic acid
NO
NO
YES
YES
NO
YES


Acetoacetic acid
NO
NO
NO
YES
NO
NO


Glucuronamide
NO
NO
NO
NO
NO
NO


L-Proline
NO
NO
NO
YES
NO
YES


D-Xylose
YES
NO
NO
YES
YES
YES


Acetic acid
NO
NO
YES
YES
NO
NO


a-Methyl-D-Galactoside
NO
NO
NO
YES
YES
NO


β-Methyl-D-glucoside
NO
NO
YES
YES
YES
YES


Mucic acid
NO
NO
NO
YES
YES
YES


N-acetyl-β-D-Mannosamine
NO
NO
YES
YES
NO
NO


Pyruvic acid
NO
NO
YES
YES
YES
YES


D-Alanine
NO
NO
YES
YES
NO
YES


L-Lactic acid
NO
NO
YES
NO
NO
YES


a-D-Glucose
NO
NO
NO
YES
YES
YES


a-D-Lactose
NO
NO
YES
YES
YES
YES


Adonitol
NO
NO
NO
YES
NO
YES


Glycolic acid
NO
NO
YES
YES
NO
NO


Mono Methyl Succinate
NO
NO
NO
YES
NO
YES


L-Galactonic-acid-?-lactone
NO
NO
NO
NO
NO
YES


D-Trehalose
NO
NO
NO
YES
YES
YES


Formic acid
NO
NO
NO
YES
NO
NO


Maltose
YES
NO
YES
YES
YES
YES


Lactulose
YES
NO
NO
YES
NO
YES


Maltotriose
NO
NO
YES
YES
YES
YES


Glyoxylic acid
NO
NO
YES
YES
NO
NO


Methyl Pyruvate
NO
NO
YES
YES
NO
YES


D-Galacturonic acid
NO
NO
YES
YES
YES
YES


D-Mannose
NO
NO
YES
YES
YES
YES


D-Mannitol
NO
NO
YES
YES
YES
YES


D-Melibiose
NO
NO
YES
YES
YES
YES


Sucrose
NO
NO
YES
YES
YES
YES


2-Deoxy adenosine
NO
NO
NO
NO
NO
NO


D-Cellobiose
NO
NO
YES
YES
NO
YES


D-Malic acid
NO
NO
NO
YES
NO
YES


Phenylethyl-amine
NO
NO
NO
NO
NO
NO


Dulcitol
NO
NO
YES
YES
YES
YES


L-Glutamic acid
NO
NO
YES
YES
NO
YES


Thymidine
NO
NO
NO
YES
NO
NO


Uridine
NO
NO
YES
YES
NO
YES


Adenosine
NO
NO
YES
YES
NO
YES


Inosine
NO
NO
NO
YES
YES
YES


L-Malic acid
YES
NO
NO
YES
NO
YES


2-Aminoethanol
NO
NO
YES
YES
NO
YES





Strain/Substrate
SYM01310
SYM01311
SYM01314
SYM01315
SYM01325
SYM01326





D-Serine
NO
YES
NO
YES
NO
NO


D-Glucose-6-Phosphate
NO
NO
YES
NO
NO
NO


L-Asparagine
YES
YES
YES
NO
YES
YES


L-glutamine
YES
YES
YES
NO
YES
YES


Glycyl-L-Aspartic acid
NO
YES
NO
YES
NO
YES


Glycyl-L-Glutamic acid
YES
YES
YES
YES
NO
NO


Glycyl-L-Proline
NO
YES
YES
NO
NO
YES


L-Arabinose
YES
YES
YES
YES
YES
YES


D-Sorbitol
YES
YES
YES
YES
YES
YES


D-Galactonic acid-?-lactone
NO
NO
YES
NO
NO
NO


D-Aspartic acid
NO
YES
NO
NO
NO
NO


m-Tartaric acid
NO
YES
YES
YES
NO
NO


Citric acid
YES
YES
YES
YES
NO
YES


Tricarballylic acid
NO
YES
YES
NO
YES
NO


p-Hydroxy Phenyl acetic acid
NO
NO
YES
NO
NO
YES


N-Acetyl-D-Glucosamine
YES
YES
YES
YES
YES
YES


Glycerol
YES
YES
NO
YES
YES
NO


D-L-Malic acid
YES
YES
YES
YES
NO
NO


D-Glucosaminic acid
NO
NO
YES
NO
NO
YES


D-Glucose-1-Phosphate
NO
NO
YES
NO
NO
NO


m-Inositol
YES
YES
YES
YES
YES
YES


L-Serine
YES
YES
YES
NO
NO
YES


m-Hydroxy Phenyl Acetic acid
NO
NO
NO
YES
NO
NO


D-Saccharic acid
YES
YES
YES
YES
YES
YES


L-Fucose
NO
YES
YES
YES
NO
NO


D-Ribose
YES
YES
NO
YES
YES
YES


1,2-Propanediol
NO
NO
NO
NO
NO
NO


D-Fructose-6-Phosphate
NO
NO
NO
NO
NO
NO


D-Threonine
NO
YES
NO
NO
NO
NO


L-Threonine
NO
YES
NO
NO
NO
YES


Tyramine
YES
YES
YES
YES
NO
YES


Succinic acid
YES
YES
NO
NO
NO
YES


D-Glucuronic acid
YES
YES
YES
YES
NO
YES


Tween 20
YES
YES
YES
YES
NO
YES


Tween 40
NO
YES
YES
YES
YES
YES


Tween 80
YES
YES
YES
YES
YES
YES


Fumaric acid
YES
YES
YES
YES
YES
YES


L-Alanine
YES
YES
YES
YES
YES
YES


D-Psicose
NO
NO
NO
NO
NO
NO


D-Galactose
YES
YES
YES
YES
YES
YES


D-Gluconic acid
YES
YES
YES
NO
YES
YES


L-Rhamnose
NO
YES
YES
YES
YES
NO


a-Keto-Glutaric acid
YES
YES
YES
NO
NO
YES


a-Hydroxy Glutaric acid-?-
YES
YES
YES
NO
NO
NO


lactone


Bromo succinic acid
YES
YES
YES
NO
YES
YES


L-Alanyl-Glycine
YES
YES
YES
NO
NO
YES


L-Lyxose
NO
NO
NO
NO
NO
NO


L-Aspartic acid
YES
YES
YES
YES
NO
YES


D-L-a-Glycerol phosphate
YES
NO
YES
YES
NO
NO


D-Fructose
YES
YES
YES
YES
YES
YES


a-Keto-Butyric acid
NO
YES
NO
YES
NO
NO


a-Hydroxy Butyric acid
NO
YES
NO
NO
NO
NO


Propionic acid
YES
YES
YES
NO
NO
NO


Acetoacetic acid
NO
NO
NO
YES
NO
NO


Glucuronamide
NO
NO
NO
NO
NO
NO


L-Proline
YES
YES
YES
YES
YES
NO


D-Xylose
YES
YES
YES
NO
YES
NO


Acetic acid
NO
YES
NO
NO
NO
NO


a-Methyl-D-Galactoside
YES
YES
NO
NO
YES
YES


β-Methyl-D-glucoside
YES
YES
YES
NO
YES
YES


Mucic acid
YES
YES
YES
YES
NO
YES


N-acetyl-β-D-Mannosamine
NO
NO
NO
YES
NO
NO


Pyruvic acid
YES
YES
YES
NO
NO
YES


D-Alanine
YES
YES
YES
NO
NO
YES


L-Lactic acid
YES
YES
YES
YES
NO
YES


a-D-Glucose
YES
YES
YES
YES
YES
YES


a-D-Lactose
NO
YES
YES
NO
NO
YES


Adonitol
YES
YES
YES
YES
YES
NO


Glycolic acid
NO
NO
NO
NO
NO
NO


Mono Methyl Succinate
NO
YES
YES
NO
NO
NO


L-Galactonic-acid-?-lactone
YES
YES
YES
NO
YES
YES


D-Trehalose
YES
YES
YES
YES
YES
YES


Formic acid
NO
NO
NO
YES
NO
NO


Maltose
YES
YES
YES
NO
YES
YES


Lactulose
NO
YES
NO
YES
NO
NO


Maltotriose
NO
YES
YES
YES
YES
YES


Glyoxylic acid
NO
NO
NO
NO
NO
NO


Methyl Pyruvate
YES
YES
NO
NO
NO
YES


D-Galacturonic acid
YES
YES
YES
NO
NO
YES


D-Mannose
YES
YES
YES
NO
YES
YES


D-Mannitol
YES
YES
YES
YES
YES
YES


D-Melibiose
YES
YES
NO
NO
YES
NO


Sucrose
YES
YES
YES
NO
YES
YES


2-Deoxy adenosine
NO
YES
NO
NO
NO
NO


D-Cellobiose
YES
YES
YES
NO
YES
YES


D-Malic acid
YES
YES
YES
NO
NO
NO


Phenylethyl-amine
NO
NO
NO
NO
NO
NO


Dulcitol
NO
YES
NO
NO
NO
NO


L-Glutamic acid
YES
YES
YES
YES
YES
YES


Thymidine
NO
NO
NO
NO
NO
NO


Uridine
YES
YES
YES
NO
NO
YES


Adenosine
NO
NO
YES
YES
NO
NO


Inosine
YES
YES
YES
YES
NO
YES


L-Malic acid
YES
YES
YES
YES
YES
YES


2-Aminoethanol
YES
YES
YES
NO
YES
NO

















Strain/Substrate
SYM01327
SYM01328
SYM01333
SYM0135
SYM0136







D-Serine
NO
NO
NO
NO
NO



D-Glucose-6-Phosphate
YES
YES
NO
NO
NO



L-Asparagine
YES
YES
YES
NO
NO



L-glutamine
YES
NO
YES
YES
NO



Glycyl-L-Aspartic acid
n/a
NO
NO
NO
NO



Glycyl-L-Glutamic acid
YES
YES
NO
NO
NO



Glycyl-L-Proline
YES
YES
NO
NO
NO



L-Arabinose
YES
YES
YES
YES
YES



D-Sorbitol
YES
YES
YES
YES
YES



D-Galactonic acid-?-lactone
YES
NO
YES
NO
NO



D-Aspartic acid
NO
NO
NO
NO
NO



m-Tartaric acid
NO
NO
NO
NO
NO



Citric acid
n/a
NO
YES
NO
NO



Tricarballylic acid
YES
YES
NO
YES
NO



p-Hydroxy Phenyl acetic acid
YES
NO
NO
NO
NO



N-Acetyl-D-Glucosamine
YES
NO
YES
YES
YES



Glycerol
YES
YES
YES
NO
NO



D-L-Malic acid
YES
YES
YES
NO
NO



D-Glucosaminic acid
YES
NO
NO
NO
NO



D-Glucose-1-Phosphate
YES
NO
NO
NO
NO



m-Inositol
n/a
NO
YES
NO
NO



L-Serine
YES
NO
YES
NO
NO



m-Hydroxy Phenyl Acetic acid
NO
YES
NO
NO
NO



D-Saccharic acid
YES
NO
YES
NO
NO



L-Fucose
YES
NO
NO
NO
NO



D-Ribose
YES
YES
NO
YES
NO



1,2-Propanediol
NO
NO
NO
NO
NO



D-Fructose-6-Phosphate
NO
NO
NO
NO
NO



D-Threonine
n/a
YES
NO
NO
NO



L-Threonine
NO
YES
NO
NO
NO



Tyramine
YES
NO
YES
NO
NO



Succinic acid
YES
NO
YES
NO
NO



D-Glucuronic acid
YES
YES
YES
YES
NO



Tween 20
YES
NO
YES
YES
YES



Tween 40
YES
YES
YES
YES
YES



Tween 80
YES
YES
YES
YES
YES



Fumaric acid
n/a
YES
YES
NO
NO



L-Alanine
YES
YES
YES
NO
NO



D-Psicose
NO
YES
NO
NO
NO



D-Galactose
YES
YES
YES
YES
YES



D-Gluconic acid
YES
YES
YES
YES
YES



L-Rhamnose
YES
NO
NO
NO
NO



a-Keto-Glutaric acid
YES
YES
YES
NO
NO



a-Hydroxy Glutaric acid-?-
YES
YES
YES
NO
NO



lactone



Bromo succinic acid
n/a
NO
NO
NO
NO



L-Alanyl-Glycine
YES
YES
YES
NO
NO



L-Lyxose
NO
NO
NO
NO
NO



L-Aspartic acid
YES
YES
YES
NO
NO



D-L-a-Glycerol phosphate
YES
NO
NO
NO
NO



D-Fructose
YES
YES
YES
YES
NO



a-Keto-Butyric acid
YES
NO
NO
NO
NO



a-Hydroxy Butyric acid
NO
NO
NO
NO
NO



Propionic acid
n/a
NO
NO
NO
NO



Acetoacetic acid
NO
NO
NO
NO
NO



Glucuronamide
NO
NO
NO
NO
NO



L-Proline
YES
YES
YES
YES
NO



D-Xylose
YES
NO
YES
YES
NO



Acetic acid
YES
NO
NO
NO
NO



a-Methyl-D-Galactoside
YES
YES
NO
YES
YES



β-Methyl-D-glucoside
NO
YES
NO
YES
YES



Mucic acid
n/a
YES
YES
NO
NO



N-acetyl-β-D-Mannosamine
NO
YES
NO
NO
NO



Pyruvic acid
YES
NO
YES
NO
NO



D-Alanine
YES
NO
YES
NO
NO



L-Lactic acid
YES
NO
YES
NO
NO



a-D-Glucose
YES
YES
YES
YES
YES



a-D-Lactose
YES
YES
YES
NO
NO



Adonitol
YES
NO
YES
NO
NO



Glycolic acid
n/a
NO
NO
NO
NO



Mono Methyl Succinate
YES
NO
NO
NO
NO



L-Galactonic-acid-?-lactone
YES
NO
YES
YES
NO



D-Trehalose
YES
NO
YES
YES
NO



Formic acid
NO
YES
NO
NO
NO



Maltose
YES
YES
YES
YES
YES



Lactulose
YES
YES
NO
NO
NO



Maltotriose
YES
YES
NO
YES
YES



Glyoxylic acid
n/a
NO
NO
NO
NO



Methyl Pyruvate
YES
NO
NO
NO
NO



D-Galacturonic acid
YES
NO
YES
NO
NO



D-Mannose
YES
YES
YES
YES
YES



D-Mannitol
YES
NO
YES
YES
YES



D-Melibiose
YES
YES
NO
YES
YES



Sucrose
YES
YES
YES
YES
YES



2-Deoxy adenosine
NO
NO
NO
NO
NO



D-Cellobiose
n/a
YES
NO
YES
NO



D-Malic acid
YES
NO
NO
NO
NO



Phenylethyl-amine
NO
NO
NO
NO
NO



Dulcitol
NO
YES
NO
NO
NO



L-Glutamic acid
YES
NO
YES
YES
YES



Thymidine
YES
YES
NO
NO
NO



Uridine
YES
NO
YES
NO
YES



Adenosine
YES
NO
YES
NO
NO



Inosine
n/a
NO
YES
NO
NO



L-Malic acid
YES
NO
YES
NO
NO



2-Aminoethanol
YES
NO
YES
NO
NO

















TABLE Q





Substrate utilization as determined by BIOLOG PM1 MicroPlates by fungal


endophytes belonging to core OTUs.























Strain/Substrate
SYM00151
SYM00154
SYM015811
SYM15820
SYM15825
SYM15828
SYM15831
SYM15837





D-Serine
NO
NO
NO
NO
YES
NO
NO
NO


D-Glucose-6-Phosphate
YES
YES
NO
NO
NO
NO
NO
NO


L-Asparagine
YES
NO
YES
YES
YES
YES
YES
YES


L-glutamine
YES
NO
NO
YES
YES
YES
YES
YES


Glycyl-L-Aspartic acid
NO
YES
YES
YES
YES
YES
NO
NO


Glycyl-L-Glutamic acid
NO
YES
NO
YES
YES
YES
NO
YES


Glycyl-L-Proline
YES
YES
NO
YES
YES
YES
YES
NO


L-Arabinose
YES
YES
NO
YES
YES
YES
YES
YES


D-Sorbitol
YES
YES
YES
YES
YES
YES
YES
YES


D-Galactonic acid-?-lactone
NO
YES
YES
YES
NO
NO
NO
YES


D-Aspartic acid
NO
YES
NO
NO
NO
NO
NO
YES


m-Tartaric acid
YES
NO
NO
NO
YES
NO
YES
NO


Citric acid
YES
YES
YES
YES
YES
YES
YES
YES


Tricarballylic acid
YES
NO
NO
NO
YES
NO
NO
YES


p-Hydroxy Phenyl acetic acid
YES
YES
YES
YES
NO
YES
NO
YES


N-Acetyl-D-Glucosamine
YES
YES
NO
YES
YES
YES
YES
NO


Glycerol
YES
YES
YES
YES
YES
YES
YES
NO


D-L-Malic acid
NO
YES
NO
YES
YES
YES
NO
YES


D-Glucosaminic acid
NO
YES
YES
NO
NO
NO
NO
NO


D-Glucose-1-Phosphate
NO
NO
NO
NO
NO
NO
NO
NO


m-Inositol
YES
YES
NO
YES
YES
YES
NO
YES


L-Serine
NO
NO
NO
YES
YES
YES
NO
YES


m-Hydroxy Phenyl Acetic acid
NO
NO
NO
NO
NO
NO
NO
NO


D-Saccharic acid
YES
NO
NO
YES
YES
YES
YES
YES


L-Fucose
NO
YES
NO
NO
NO
YES
YES
NO


D-Ribose
YES
YES
NO
YES
YES
YES
YES
YES


1,2-Propanediol
NO
YES
NO
NO
NO
YES
NO
NO


D-Fructose-6-Phosphate
NO
YES
NO
NO
NO
NO
NO
NO


D-Threonine
NO
NO
NO
NO
NO
NO
NO
YES


L-Threonine
NO
NO
YES
YES
YES
NO
NO
YES


Tyramine
YES
YES
NO
NO
YES
YES
NO
YES


Succinic acid
YES
YES
NO
YES
YES
YES
NO
YES


D-Glucuronic acid
NO
YES
NO
YES
YES
YES
NO
NO


Tween 20
YES
YES
YES
YES
YES
YES
YES
YES


Tween 40
YES
YES
YES
YES
YES
YES
YES
YES


Tween 80
YES
YES
NO
YES
YES
YES
YES
YES


Fumaric acid
NO
NO
YES
YES
YES
YES
YES
NO


L-Alanine
YES
NO
YES
YES
YES
YES
YES
NO


D-Psicose
NO
YES
NO
NO
NO
NO
NO
NO


D-Galactose
YES
YES
NO
YES
YES
YES
YES
YES


D-Gluconic acid
YES
YES
YES
YES
YES
YES
YES
YES


L-Rhamnose
YES
YES
NO
NO
YES
NO
NO
YES


a-Keto-Glutaric acid
NO
NO
YES
YES
NO
YES
NO
NO


a-Hydroxy Glutaric acid-?-
NO
YES
NO
YES
NO
YES
NO
YES


lactone


Bromo succinic acid
NO
YES
NO
NO
YES
YES
NO
NO


L-Alanyl-Glycine
YES
YES
YES
YES
YES
YES
YES
YES


L-Lyxose
NO
NO
NO
NO
NO
NO
NO
NO


L-Aspartic acid
YES
NO
NO
YES
YES
YES
YES
YES


D-L-a-Glycerol phosphate
NO
YES
YES
YES
NO
YES
NO
YES


D-Fructose
YES
YES
YES
YES
YES
YES
YES
YES


a-Keto-Butyric acid
NO
YES
NO
NO
YES
NO
NO
NO


a-Hydroxy Butyric acid
NO
YES
NO
NO
YES
NO
NO
NO


Propionic acid
NO
YES
NO
NO
YES
YES
YES
YES


Acetoacetic acid
NO
NO
NO
NO
NO
NO
NO
NO


Glucuronamide
NO
NO
YES
NO
NO
NO
NO
YES


L-Proline
YES
YES
NO
YES
YES
YES
YES
YES


D-Xylose
YES
NO
NO
YES
YES
YES
YES
YES


Acetic acid
YES
YES
NO
YES
YES
YES
YES
YES


a-Methyl-D-Galactoside
YES
NO
NO
NO
YES
YES
YES
YES


β-Methyl-D-glucoside
YES
YES
NO
NO
YES
NO
YES
YES


Mucic acid
YES
YES
NO
YES
YES
YES
YES
YES


N-acetyl-β-D-Mannosamine
NO
YES
NO
NO
NO
YES
NO
YES


Pyruvic acid
YES
YES
NO
YES
YES
YES
YES
NO


D-Alanine
YES
NO
YES
YES
NO
YES
YES
YES


L-Lactic acid
YES
NO
NO
YES
YES
YES
YES
NO


a-D-Glucose
YES
YES
YES
YES
YES
YES
YES
YES


a-D-Lactose
YES
NO
NO
NO
YES
NO
NO
YES


Adonitol
YES
YES
YES
YES
YES
YES
NO
YES


Glycolic acid
NO
YES
NO
NO
YES
NO
NO
NO


Mono Methyl Succinate
YES
NO
NO
NO
YES
NO
YES
NO


L-Galactonic-acid-?-lactone
YES
YES
NO
YES
YES
YES
YES
YES


D-Trehalose
YES
YES
NO
YES
YES
YES
YES
YES


Formic acid
YES
NO
NO
NO
YES
NO
NO
NO


Maltose
YES
YES
NO
YES
YES
NO
YES
YES


Lactulose
YES
YES
NO
NO
YES
NO
YES
YES


Maltotriose
YES
NO
NO
YES
YES
YES
YES
YES


Glyoxylic acid
NO
YES
NO
NO
YES
NO
NO
NO


Methyl Pyruvate
YES
NO
NO
YES
YES
YES
YES
YES


D-Galacturonic acid
YES
YES
YES
YES
YES
YES
YES
YES


D-Mannose
YES
YES
NO
YES
YES
YES
YES
YES


D-Mannitol
YES
YES
YES
YES
YES
YES
YES
YES


D-Melibiose
YES
NO
YES
YES
YES
YES
YES
YES


Sucrose
YES
YES
NO
YES
YES
YES
YES
YES


2-Deoxy adenosine
YES
NO
NO
NO
YES
NO
NO
NO


D-Cellobiose
YES
YES
NO
YES
YES
NO
YES
YES


D-Malic acid
YES
YES
YES
NO
YES
NO
NO
YES


Phenylethyl-amine
NO
NO
NO
NO
NO
NO
NO
NO


Dulcitol
YES
YES
NO
NO
YES
NO
YES
YES


L-Glutamic acid
YES
YES
YES
YES
YES
YES
YES
YES


Thymidine
NO
YES
NO
NO
YES
NO
YES
NO


Uridine
YES
YES
YES
YES
YES
NO
YES
YES


Adenosine
NO
YES
YES
YES
NO
YES
YES
YES


Inosine
YES
NO
YES
YES
NO
YES
YES
YES


L-Malic acid
YES
YES
NO
YES
NO
YES
YES
NO


2-Aminoethanol
YES
YES
NO
YES
YES
YES
NO
YES





Strain/Substrate
SYM15839
SYM15847
SYM15872
SYM15890
SYM15901
SYM15920
SYM15926
SYM15928





D-Serine
YES
YES
NO
NO
NO
YES
NO
NO


D-Glucose-6-Phosphate
NO
NO
NO
NO
NO
NO
NO
NO


L-Asparagine
NO
YES
YES
NO
YES
YES
YES
YES


L-glutamine
YES
YES
YES
YES
YES
YES
NO
NO


Glycyl-L-Aspartic acid
NO
NO
NO
NO
NO
YES
NO
NO


Glycyl-L-Glutamic acid
NO
YES
YES
YES
YES
YES
NO
NO


Glycyl-L-Proline
NO
YES
YES
NO
YES
YES
NO
YES


L-Arabinose
YES
YES
YES
YES
YES
YES
NO
YES


D-Sorbitol
YES
YES
YES
YES
YES
YES
NO
YES


D-Galactonic acid-?-lactone
YES
NO
NO
NO
NO
YES
YES
NO


D-Aspartic acid
NO
NO
NO
NO
NO
YES
NO
YES


m-Tartaric acid
YES
NO
YES
NO
YES
YES
NO
NO


Citric acid
NO
YES
NO
YES
NO
NO
NO
NO


Tricarballylic acid
YES
YES
YES
YES
YES
YES
NO
NO


p-Hydroxy Phenyl acetic acid
YES
NO
NO
NO
NO
YES
NO
NO


N-Acetyl-D-Glucosamine
YES
YES
YES
YES
YES
YES
YES
YES


Glycerol
YES
YES
YES
YES
YES
YES
YES
YES


D-L-Malic acid
YES
NO
YES
YES
YES
YES
NO
NO


D-Glucosaminic acid
NO
NO
NO
YES
NO
NO
NO
NO


D-Glucose-1-Phosphate
NO
NO
NO
NO
NO
NO
NO
NO


m-Inositol
YES
YES
YES
YES
YES
YES
NO
NO


L-Serine
NO
NO
YES
NO
YES
YES
NO
NO


m-Hydroxy Phenyl Acetic acid
NO
NO
NO
NO
NO
NO
NO
NO


D-Saccharic acid
YES
NO
YES
YES
YES
YES
NO
YES


L-Fucose
NO
NO
NO
NO
NO
NO
NO
NO


D-Ribose
YES
YES
YES
NO
YES
YES
NO
YES


1,2-Propanediol
NO
NO
NO
NO
NO
NO
NO
NO


D-Fructose-6-Phosphate
NO
NO
NO
NO
NO
NO
NO
NO


D-Threonine
NO
NO
NO
NO
NO
YES
NO
NO


L-Threonine
NO
NO
YES
NO
YES
YES
NO
NO


Tyramine
YES
YES
YES
NO
YES
YES
YES
NO


Succinic acid
NO
NO
NO
YES
YES
YES
NO
NO


D-Glucuronic acid
NO
YES
YES
YES
YES
YES
YES
YES


Tween 20
YES
YES
YES
NO
YES
YES
YES
YES


Tween 40
YES
NO
YES
YES
YES
YES
NO
YES


Tween 80
YES
YES
YES
YES
YES
YES
NO
YES


Fumaric acid
NO
NO
YES
NO
YES
YES
NO
YES


L-Alanine
NO
YES
YES
YES
YES
YES
YES
NO


D-Psicose
NO
NO
NO
NO
NO
NO
NO
NO


D-Galactose
YES
YES
YES
NO
YES
YES
YES
NO


D-Gluconic acid
YES
YES
YES
YES
YES
YES
NO
YES


L-Rhamnose
YES
YES
YES
NO
YES
YES
NO
NO


a-Keto-Glutaric acid
NO
NO
YES
YES
NO
NO
NO
NO


a-Hydroxy Glutaric acid-?-
NO
NO
NO
NO
NO
NO
NO
NO


lactone


Bromo succinic acid
YES
YES
YES
NO
YES
YES
NO
NO


L-Alanyl-Glycine
YES
YES
YES
YES
YES
YES
NO
YES


L-Lyxose
NO
NO
NO
NO
NO
YES
YES
NO


L-Aspartic acid
NO
YES
YES
YES
YES
YES
NO
YES


D-L-a-Glycerol phosphate
YES
NO
YES
NO
NO
NO
YES
NO


D-Fructose
YES
YES
YES
YES
YES
YES
NO
NO


a-Keto-Butyric acid
NO
YES
YES
NO
NO
NO
NO
NO


a-Hydroxy Butyric acid
NO
NO
NO
NO
NO
NO
NO
NO


Propionic acid
YES
NO
NO
YES
YES
YES
NO
NO


Acetoacetic acid
NO
NO
NO
NO
NO
YES
NO
NO


Glucuronamide
NO
NO
NO
NO
NO
NO
NO
NO


L-Proline
YES
YES
YES
YES
YES
YES
YES
YES


D-Xylose
YES
YES
YES
NO
YES
YES
NO
YES


Acetic acid
YES
YES
YES
NO
YES
YES
YES
NO


a-Methyl-D-Galactoside
YES
YES
YES
NO
YES
YES
NO
NO


β-Methyl-D-glucoside
YES
YES
YES
NO
YES
YES
NO
YES


Mucic acid
YES
YES
YES
YES
YES
YES
NO
NO


N-acetyl-β-D-Mannosamine
NO
NO
NO
NO
NO
NO
NO
NO


Pyruvic acid
YES
YES
YES
YES
YES
YES
NO
YES


D-Alanine
NO
NO
NO
NO
NO
YES
YES
NO


L-Lactic acid
YES
YES
YES
NO
YES
YES
NO
YES


a-D-Glucose
YES
YES
YES
YES
YES
YES
YES
YES


a-D-Lactose
NO
YES
YES
NO
YES
YES
NO
NO


Adonitol
NO
NO
YES
NO
YES
YES
NO
NO


Glycolic acid
NO
NO
NO
NO
NO
NO
NO
NO


Mono Methyl Succinate
NO
NO
NO
YES
NO
NO
NO
YES


L-Galactonic-acid-?-lactone
YES
YES
YES
YES
YES
YES
YES
YES


D-Trehalose
YES
YES
YES
YES
YES
YES
NO
YES


Formic acid
NO
NO
YES
YES
YES
NO
NO
NO


Maltose
YES
YES
YES
YES
YES
YES
YES
YES


Lactulose
NO
NO
YES
NO
YES
YES
NO
NO


Maltotriose
YES
YES
YES
NO
YES
YES
YES
YES


Glyoxylic acid
NO
NO
YES
NO
YES
NO
NO
NO


Methyl Pyruvate
YES
YES
YES
YES
YES
YES
NO
YES


D-Galacturonic acid
YES
YES
YES
NO
YES
YES
YES
NO


D-Mannose
YES
YES
YES
YES
YES
YES
NO
YES


D-Mannitol
YES
YES
YES
NO
YES
YES
NO
YES


D-Melibiose
YES
YES
YES
NO
YES
YES
NO
YES


Sucrose
YES
YES
YES
YES
YES
YES
NO
YES


2-Deoxy adenosine
YES
NO
YES
NO
YES
NO
NO
NO


D-Cellobiose
YES
YES
YES
YES
YES
YES
NO
YES


D-Malic acid
YES
NO
YES
NO
YES
YES
NO
NO


Phenylethyl-amine
NO
NO
NO
NO
NO
NO
NO
NO


Dulcitol
YES
YES
YES
NO
YES
YES
NO
YES


L-Glutamic acid
YES
YES
YES
YES
YES
YES
NO
NO


Thymidine
NO
NO
YES
NO
YES
NO
NO
NO


Uridine
NO
YES
YES
YES
YES
NO
NO
NO


Adenosine
NO
YES
YES
NO
YES
NO
NO
NO


Inosine
NO
NO
NO
YES
YES
YES
YES
NO


L-Malic acid
NO
YES
YES
NO
YES
YES
NO
YES


2-Aminoethanol
NO
YES
YES
NO
YES
YES
YES
YES
















TABLE R





Substrate utilization as determined by BIOLOG PM1 MicroPlates by fungal


endophytes belonging to core OTUs.





















Strain/Substrate
SYM15932
SYM00160
SYM00034
SYM00566B
SYM00577
SYM00590





D-Serine
NO
NO
NO
NO
NO
NO


D-Glucose-6-Phosphate
NO
NO
NO
NO
NO
NO


L-Asparagine
NO
NO
YES
NO
YES
YES


L-glutamine
NO
YES
YES
YES
YES
NO


Glycyl-L-Aspartic acid
NO
NO
YES
NO
NO
NO


Glycyl-L-Glutamic acid
NO
NO
NO
NO
NO
NO


Glycyl-L-Proline
NO
YES
NO
YES
YES
NO


L-Arabinose
YES
NO
YES
NO
YES
YES


D-Sorbitol
NO
NO
YES
NO
YES
YES


D-Galactonic acid-?-lactone
NO
NO
NO
YES
NO
NO


D-Aspartic acid
NO
NO
NO
NO
NO
NO


m-Tartaric acid
NO
NO
NO
YES
YES
NO


Citric acid
NO
NO
NO
YES
YES
NO


Tricarballylic acid
NO
NO
NO
NO
NO
NO


p-Hydroxy Phenyl acetic acid
NO
NO
NO
YES
YES
NO


N-Acetyl-D-Glucosamine
NO
NO
YES
YES
YES
YES


Glycerol
NO
NO
YES
YES
NO
NO


D-L-Malic acid
NO
YES
NO
NO
YES
NO


D-Glucosaminic acid
NO
NO
YES
YES
NO
NO


D-Glucose-1-Phosphate
NO
NO
NO
NO
NO
NO


m-Inositol
NO
NO
NO
YES
YES
NO


L-Serine
NO
NO
NO
YES
YES
NO


m-Hydroxy Phenyl Acetic acid
NO
NO
NO
NO
NO
NO


D-Saccharic acid
NO
NO
NO
YES
YES
NO


L-Fucose
NO
NO
NO
NO
NO
NO


D-Ribose
NO
NO
YES
YES
YES
YES


1,2-Propanediol
NO
NO
NO
NO
NO
NO


D-Fructose-6-Phosphate
NO
NO
NO
YES
NO
NO


D-Threonine
NO
NO
NO
NO
NO
NO


L-Threonine
NO
NO
NO
NO
YES
NO


Tyramine
YES
NO
NO
NO
YES
NO


Succinic acid
NO
NO
YES
NO
NO
NO


D-Glucuronic acid
YES
NO
NO
NO
YES
NO


Tween 20
NO
NO
YES
NO
YES
YES


Tween 40
NO
YES
YES
YES
YES
NO


Twecn 80
NO
NO
YES
YES
YES
NO


Fumaric acid
NO
YES
YES
YES
NO
NO


L-Alanine
NO
NO
NO
NO
YES
YES


D-Psicose
NO
NO
NO
NO
NO
NO


D-Galactose
NO
NO
YES
NO
YES
NO


D-Gluconic acid
NO
NO
NO
YES
YES
YES


L-Rhamnose
NO
NO
YES
NO
YES
NO


a-Keto-Glutaric acid
NO
NO
YES
NO
NO
NO


a-Hydroxy Glutaric acid-?-
NO
NO
NO
YES
YES
NO


lactone


Bromo succinic acid
NO
NO
YES
NO
NO
NO


L-Alanyl-Glycine
NO
NO
NO
NO
NO
NO


L-Lyxose
NO
YES
NO
NO
NO
NO


L-Aspartic acid
NO
NO
YES
YES
YES
NO


D-L-a-Glycerol phosphate
NO
NO
NO
YES
NO
NO


D-Fructose
YES
YES
YES
YES
YES
YES


a-Keto-Butyric acid
NO
NO
NO
NO
NO
NO


a-Hydroxy Butyric acid
NO
NO
NO
NO
NO
NO


Propionic acid
NO
NO
NO
NO
NO
NO


Acetoacetic acid
NO
NO
NO
NO
NO
NO


Glucuronamide
NO
NO
NO
NO
NO
NO


L-Proline
NO
NO
YES
NO
YES
NO


D-Xylose
NO
NO
NO
YES
YES
NO


Acetic acid
NO
NO
NO
NO
NO
NO


a-Methyl-D-Galactoside
YES
NO
NO
NO
YES
NO


β-Methyl-D-glucoside
YES
YES
YES
YES
YES
YES


Mucic acid
NO
NO
NO
YES
YES
NO


N-acetyl-β-D-Mannosamine
NO
NO
NO
NO
NO
NO


Pyruvic acid
NO
NO
NO
NO
YES
NO


D-Alanine
NO
NO
NO
YES
YES
NO


L-Lactic acid
NO
NO
NO
NO
NO
NO


a-D-Glucose
YES
YES
YES
YES
YES
YES


a-D-Lactose
NO
NO
NO
NO
NO
NO


Adonitol
NO
NO
NO
NO
YES
NO


Glycolic acid
NO
NO
NO
NO
NO
NO


Mono Methyl Succinate
YES
NO
NO
NO
YES
NO


L-Galaclonic-acid-?-lactone
NO
NO
NO
NO
YES
NO


D-Trehalose
YES
NO
YES
YES
YES
YES


Formic acid
NO
NO
NO
NO
NO
NO


Maltose
YES
YES
YES
NO
YES
YES


Lactulose
NO
NO
NO
NO
NO
NO


Maltotriose
YES
YES
YES
NO
YES
YES


Glyoxylic acid
NO
NO
NO
NO
NO
NO


Methyl Pyruvate
NO
YES
NO
NO
NO
NO


D-Galacturonic acid
NO
NO
NO
NO
YES
YES


D-Mannose
YES
YES
YES
YES
YES
NO


D-Mannitol
YES
NO
YES
YES
YES
YES


D-Melibiose
NO
NO
NO
NO
YES
NO


Sucrose
YES
YES
YES
YES
YES
NO


2-Deoxy adenosine
NO
NO
NO
NO
YES
NO


D-Cellobiose
YES
YES
YES
NO
YES
YES


D-Malic acid
NO
NO
NO
NO
YES
NO


Phenylethyl-amine
NO
NO
NO
NO
NO
NO


Dulcitol
NO
NO
YES
YES
YES
YES


L-Glutamic acid
NO
NO
YES
NO
NO
NO


Thymidine
NO
NO
NO
NO
NO
NO


Uridine
NO
NO
NO
NO
YES
NO


Adenosine
NO
YES
NO
NO
NO
NO


Inosine
NO
NO
NO
YES
YES
NO


L-Malic acid
NO
NO
YES
NO
YES
YES


2-Aminoethanol
NO
NO
NO
NO
YES
NO





Strain/Substrate
SYM00603
SYM00061A
SYM00622
SYM00629
SYM00066
SYM00663





D-Serine
NO
YES
NO
NO
NO
NO


D-Glucose-6-Phosphate
NO
NO
NO
NO
NO
NO


L-Asparagine
YES
YES
YES
YES
NO
YES


L-glutamine
YES
YES
YES
YES
NO
YES


Glycyl-L-Aspartic acid
NO
YES
NO
NO
NO
NO


Glycyl-L-Glutamic acid
YES
YES
NO
NO
YES
NO


Glycyl-L-Proline
YES
YES
NO
NO
NO
NO


L-Arabinose
YES
YES
YES
NO
NO
NO


D-Sorbitol
YES
YES
YES
YES
NO
NO


D-Galactonic acid-?-lactone
YES
NO
YES
NO
NO
NO


D-Aspartic acid
NO
NO
NO
NO
NO
YES


m-Tartaric acid
NO
YES
NO
NO
NO
NO


Citric acid
YES
YES
YES
YES
NO
YES


Tricarballylic acid
NO
NO
NO
NO
NO
NO


p-Hydroxy Phenyl acetic acid
YES
NO
NO
NO
YES
NO


N-Acetyl-D-Glucosamine
YES
YES
YES
YES
NO
YES


Glycerol
YES
YES
NO
YES
YES
YES


D-L-Malic acid
YES
YES
YES
YES
NO
YES


D-Glucosaminic acid
YES
NO
NO
NO
YES
NO


D-Glucose-1-Phosphate
NO
NO
NO
NO
YES
NO


m-Inositol
YES
YES
YES
YES
NO
NO


L-Serine
YES
YES
YES
NO
NO
YES


m-Hydroxy Phenyl Acetic acid
NO
NO
NO
NO
YES
NO


D-Saccharic acid
YES
YES
YES
NO
NO
NO


L-Fucose
NO
NO
NO
NO
NO
NO


D-Ribose
YES
YES
YES
YES
NO
NO


1,2-Propanediol
NO
NO
NO
NO
YES
NO


D-Fructose-6-Phosphate
NO
NO
NO
NO
NO
NO


D-Threonine
NO
YES
NO
NO
NO
NO


L-Threonine
NO
YES
NO
NO
NO
NO


Tyramine
YES
NO
YES
YES
NO
NO


Succinic acid
YES
YES
YES
YES
YES
NO


D-Glucuronic acid
YES
YES
YES
YES
NO
YES


Tween 20
YES
YES
NO
YES
NO
NO


Tween 40
YES
YES
YES
YES
NO
YES


Twecn 80
YES
YES
YES
YES
YES
YES


Fumaric acid
YES
YES
YES
YES
NO
NO


L-Alanine
YES
YES
YES
NO
YES
YES


D-Psicose
NO
YES
NO
NO
YES
NO


D-Galactose
YES
YES
YES
NO
NO
NO


D-Gluconic acid
YES
YES
YES
YES
NO
NO


L-Rhamnose
NO
YES
NO
NO
NO
NO


a-Keto-Glutaric acid
YES
NO
NO
YES
NO
YES


a-Hydroxy Glutaric acid-?-
YES
YES
YES
NO
NO
NO


lactone


Bromo succinic acid
YES
YES
NO
NO
NO
NO


L-Alanyl-Glycine
YES
YES
YES
YES
NO
YES


L-Lyxose
NO
YES
NO
NO
NO
NO


L-Aspartic acid
YES
YES
YES
YES
NO
YES


D-L-a-Glycerol phosphate
YES
NO
YES
YES
NO
YES


D-Fructose
YES
YES
YES
YES
NO
YES


a-Keto-Butyric acid
NO
YES
NO
NO
NO
NO


a-Hydroxy Butyric acid
NO
NO
NO
YES
NO
NO


Propionic acid
YES
NO
NO
NO
NO
YES


Acetoacetic acid
NO
NO
NO
NO
NO
NO


Glucuronamide
NO
NO
NO
NO
NO
NO


L-Proline
YES
YES
YES
YES
NO
YES


D-Xylose
YES
YES
YES
YES
NO
NO


Acetic acid
NO
NO
NO
NO
NO
NO


a-Methyl-D-Galactoside
NO
YES
NO
NO
NO
NO


β-Methyl-D-glucoside
NO
YES
NO
NO
YES
NO


Mucic acid
YES
YES
YES
YES
NO
YES


N-acetyl-β-D-Mannosamine
NO
YES
NO
NO
NO
NO


Pyruvic acid
NO
YES
NO
NO
NO
YES


D-Alanine
YES
YES
YES
YES
NO
NO


L-Lactic acid
YES
YES
YES
NO
NO
YES


a-D-Glucose
YES
YES
YES
YES
YES
YES


a-D-Lactose
NO
YES
NO
NO
NO
YES


Adonitol
YES
YES
YES
YES
NO
YES


Glycolic acid
NO
NO
NO
NO
NO
NO


Mono Methyl Succinate
NO
YES
NO
NO
NO
NO


L-Galaclonic-acid-?-lactone
YES
YES
NO
YES
NO
NO


D-Trehalose
YES
YES
YES
YES
NO
NO


Formic acid
NO
NO
NO
NO
NO
NO


Maltose
NO
YES
NO
NO
YES
YES


Lactulose
NO
YES
NO
NO
NO
YES


Maltotriose
NO
YES
NO
NO
YES
YES


Glyoxylic acid
NO
NO
NO
NO
NO
NO


Methyl Pyruvate
NO
YES
NO
YES
NO
YES


D-Galacturonic acid
YES
YES
YES
YES
YES
NO


D-Mannose
YES
YES
YES
NO
NO
YES


D-Mannitol
YES
YES
NO
YES
YES
NO


D-Melibiose
NO
YES
NO
NO
YES
NO


Sucrose
YES
YES
YES
YES
NO
YES


2-Deoxy adenosine
NO
YES
NO
NO
NO
NO


D-Cellobiose
NO
YES
YES
NO
YES
YES


D-Malic acid
YES
YES
NO
YES
NO
NO


Phenylethyl-amine
NO
NO
NO
NO
NO
NO


Dulcitol
NO
YES
NO
NO
YES
NO


L-Glutamic acid
YES
YES
YES
YES
NO
YES


Thymidine
NO
NO
NO
NO
NO
NO


Uridine
YES
YES
YES
YES
NO
NO


Adenosine
YES
NO
YES
YES
NO
NO


Inosine
YES
YES
YES
YES
NO
YES


L-Malic acid
YES
YES
YES
NO
NO
YES


2-Aminoethanol
YES
YES
YES
YES
NO
NO

















Strain/Substrate
SYM00696
SYM00741A
SYM00741B
SYM00854
SYM00880







D-Serine
NO
NO
NO
NO
NO



D-Glucose-6-Phosphate
NO
NO
NO
NO
NO



L-Asparagine
YES
YES
YES
YES
YES



L-glutamine
YES
YES
YES
YES
NO



Glycyl-L-Aspartic acid
NO
NO
NO
NO
NO



Glycyl-L-Glutamic acid
NO
NO
YES
NO
NO



Glycyl-L-Proline
NO
NO
YES
NO
NO



L-Arabinose
YES
NO
YES
YES
NO



D-Sorbitol
NO
YES
YES
NO
NO



D-Galactonic acid-?-lactone
NO
NO
YES
NO
NO



D-Aspartic acid
NO
NO
NO
YES
NO



m-Tartaric acid
NO
NO
NO
NO
NO



Citric acid
NO
YES
YES
YES
NO



Tricarballylic acid
NO
NO
NO
NO
NO



p-Hydroxy Phenyl acetic acid
NO
NO
YES
NO
NO



N-Acetyl-D-Glucosamine
NO
NO
YES
YES
NO



Glycerol
YES
YES
YES
NO
NO



D-L-Malic acid
NO
NO
YES
YES
YES



D-Glucosaminic acid
NO
NO
YES
NO
NO



D-Glucose-1-Phosphate
NO
NO
NO
NO
NO



m-Inositol
NO
NO
YES
NO
NO



L-Serine
NO
YES
YES
YES
NO



m-Hydroxy Phenyl Acetic acid
NO
NO
NO
NO
NO



D-Saccharic acid
YES
NO
YES
YES
NO



L-Fucose
NO
NO
NO
NO
NO



D-Ribose
NO
NO
YES
NO
NO



1,2-Propanediol
NO
NO
NO
NO
NO



D-Fructose-6-Phosphate
NO
NO
NO
NO
NO



D-Threonine
NO
NO
NO
NO
NO



L-Threonine
NO
NO
NO
NO
NO



Tyramine
NO
NO
NO
NO
NO



Succinic acid
NO
NO
YES
YES
NO



D-Glucuronic acid
NO
YES
YES
NO
NO



Tween 20
NO
NO
YES
YES
NO



Tween 40
NO
NO
YES
YES
NO



Twecn 80
NO
NO
YES
YES
NO



Fumaric acid
NO
YES
YES
YES
NO



L-Alanine
YES
YES
YES
YES
NO



D-Psicose
NO
NO
NO
NO
NO



D-Galactose
YES
NO
YES
YES
NO



D-Gluconic acid
NO
YES
YES
YES
NO



L-Rhamnose
NO
NO
NO
YES
NO



a-Keto-Glutaric acid
NO
YES
YES
YES
NO



a-Hydroxy Glutaric acid-?-
NO
NO
YES
NO
NO



lactone



Bromo succinic acid
NO
NO
YES
YES
NO



L-Alanyl-Glycine
NO
NO
YES
YES
NO



L-Lyxose
NO
NO
NO
YES
NO



L-Aspartic acid
NO
NO
YES
YES
NO



D-L-a-Glycerol phosphate
NO
NO
YES
NO
NO



D-Fructose
YES
NO
YES
YES
NO



a-Keto-Butyric acid
NO
NO
NO
NO
NO



a-Hydroxy Butyric acid
NO
NO
NO
NO
NO



Propionic acid
NO
NO
YES
NO
NO



Acetoacetic acid
NO
NO
NO
NO
NO



Glucuronamide
NO
NO
NO
NO
NO



L-Proline
YES
YES
YES
YES
NO



D-Xylose
YES
NO
YES
YES
NO



Acetic acid
NO
NO
YES
NO
NO



a-Methyl-D-Galactoside
NO
NO
NO
NO
NO



β-Methyl-D-glucoside
YES
NO
NO
YES
YES



Mucic acid
NO
YES
YES
YES
NO



N-acetyl-β-D-Mannosamine
NO
NO
NO
NO
NO



Pyruvic acid
NO
NO
YES
NO
NO



D-Alanine
NO
NO
YES
YES
NO



L-Lactic acid
YES
NO
YES
NO
NO



a-D-Glucose
YES
YES
YES
YES
NO



a-D-Lactose
YES
NO
NO
YES
NO



Adonitol
NO
NO
YES
YES
NO



Glycolic acid
NO
NO
NO
NO
NO



Mono Methyl Succinate
YES
NO
NO
YES
NO



L-Galaclonic-acid-?-lactone
YES
NO
YES
YES
NO



D-Trehalose
YES
YES
YES
YES
NO



Formic acid
NO
NO
NO
NO
NO



Maltose
YES
YES
NO
YES
YES



Lactulose
YES
NO
NO
YES
NO



Maltotriose
YES
NO
NO
YES
YES



Glyoxylic acid
NO
NO
NO
NO
NO



Methyl Pyruvate
NO
NO
YES
NO
NO



D-Galacturonic acid
YES
NO
YES
YES
NO



D-Mannose
YES
NO
YES
YES
NO



D-Mannitol
NO
NO
YES
YES
NO



D-Melibiose
YES
NO
NO
YES
NO



Sucrose
YES
YES
YES
YES
YES



2-Deoxy adenosine
NO
NO
NO
NO
NO



D-Cellobiose
YES
YES
NO
YES
YES



D-Malic acid
NO
NO
NO
YES
NO



Phenylethyl-amine
NO
NO
NO
NO
NO



Dulcitol
YES
NO
NO
YES
NO



L-Glutamic acid
YES
NO
YES
YES
NO



Thymidine
NO
NO
NO
NO
NO



Uridine
NO
NO
YES
YES
NO



Adenosine
NO
NO
YES
NO
NO



Inosine
YES
NO
YES
NO
NO



L-Malic acid
YES
YES
YES
YES
NO



2-Aminoethanol
NO
NO
YES
NO
NO

















TABLE S





Substrate utilization as determined by BIOLOG PM2A MicroPlates by fungal


endophytes belonging to core OTUs.























Strain/Substrate
SYM00120
SYM00122
SYM00123
SYM00124
SYM00129
SYM01300
SYM01310
SYM01311





N-acetyl-D-Galactosamine
NO
NO
YES
NO
NO
YES
NO
NO


Gentiobiose
NO
NO
YES
YES
YES
NO
NO
YES


D-Raffinose
NO
NO
YES
YES
YES
NO
NO
YES


Capric acid
NO
NO
NO
NO
NO
YES
NO
NO


D-lactic acid methyl ester
NO
YES
YES
NO
NO
NO
NO
NO


Acetamide
NO
NO
YES
NO
NO
NO
NO
NO


L-Ornithine
NO
YES
YES
YES
YES
YES
YES
YES


Chondrointin sulfate C
NO
NO
YES
NO
NO
NO
NO
NO


N-acetyl-neuraminic acid
NO
YES
YES
NO
NO
YES
NO
NO


L-glucose
NO
YES
NO
NO
NO
NO
NO
NO


Salicin
YES
NO
NO
YES
NO
NO
NO
YES


Caproic acid
NO
NO
NO
NO
NO
YES
NO
NO


Malonic acid
NO
NO
YES
YES
NO
YES
NO
NO


L-Alaninamide
NO
NO
YES
NO
NO
YES
NO
NO


L-Phenylalanine
YES
NO
NO
NO
NO
YES
NO
YES


a-Cyclodextrin
YES
YES
YES
YES
YES
YES
YES
YES


β-D-allose
NO
NO
YES
NO
NO
NO
NO
NO


Lactitol
NO
NO
NO
NO
NO
NO
NO
NO


Sedoheptulosan
YES
YES
NO
YES
NO
NO
NO
NO


Citraconic acid
NO
YES
YES
NO
NO
NO
NO
NO


Melibionic acid
NO
NO
NO
NO
NO
NO
NO
NO


N-Acetyl-L-Glutamic acid
NO
NO
NO
NO
NO
YES
YES
NO


L-Pyroglutamic acid
NO
NO
YES
NO
NO
YES
YES
YES


β-Cyclodextrin
NO
YES
YES
NO
NO
NO
NO
NO


Amygdalin
NO
NO
NO
YES
NO
NO
NO
YES


D-Melezitose
NO
YES
YES
NO
YES
NO
NO
YES


L-Sorbose
NO
NO
YES
NO
YES
NO
NO
NO


Citramalic acid
YES
NO
NO
NO
NO
NO
NO
NO


Oxalic acid
NO
NO
YES
YES
NO
NO
NO
NO


L-Arginine
NO
NO
NO
YES
NO
YES
YES
YES


L-Valine
NO
YES
YES
NO
NO
YES
YES
YES


γ-Cyclodextrin
NO
NO
YES
YES
NO
NO
NO
NO


D-arabinose
NO
NO
NO
YES
NO
NO
NO
NO


Maltitol
NO
NO
YES
YES
YES
NO
NO
YES


Stachyose
NO
NO
NO
YES
NO
NO
NO
YES


D-Glucosamine
NO
NO
NO
NO
NO
YES
NO
NO


Oxalomalic acid
NO
NO
YES
YES
NO
NO
NO
NO


Glycine
NO
NO
NO
YES
NO
NO
NO
NO


D,L-Carnitine
NO
YES
NO
NO
NO
YES
NO
NO


Dextrin
NO
NO
YES
NO
YES
NO
NO
YES


D-arabitol
NO
YES
NO
YES
NO
NO
NO
YES


a-Methyl-D-Glucoside
NO
NO
NO
NO
NO
NO
NO
NO


D-Tagatose
NO
NO
NO
YES
NO
NO
NO
NO


2-Hydroxy benzoic acid
NO
YES
NO
NO
NO
NO
NO
NO


Quinic acid
NO
NO
NO
NO
NO
YES
NO
YES


L-Histidine
NO
NO
NO
NO
YES
YES
YES
YES


Sec-Butylamine
NO
NO
NO
NO
NO
NO
NO
NO


Gelatin
YES
YES
YES
YES
NO
YES
YES
YES


L-arabitol
NO
YES
YES
NO
NO
NO
NO
NO


β-Methyl-D-Galactoside
NO
NO
YES
NO
NO
NO
NO
YES


Turanose
NO
YES
YES
YES
YES
NO
YES
YES


4-Hydroxy benzoic acid
NO
NO
YES
NO
NO
NO
NO
NO


D-Ribono-1,4-Lactone
NO
YES
YES
NO
NO
NO
NO
NO


L-Homoserine
NO
NO
NO
NO
NO
NO
NO
NO


D,L-Octopamine
NO
NO
YES
NO
NO
YES
YES
YES


Glycogen
YES
YES
YES
YES
NO
YES
NO
YES


Arbutin
NO
NO
YES
YES
NO
NO
NO
YES


3-Methyl Glucose
YES
NO
NO
NO
NO
NO
NO
NO


Xylitol
NO
NO
YES
NO
NO
NO
NO
NO


β-Hydroxy butyric acid
NO
NO
YES
NO
NO
YES
NO
YES


Sebacic acid
YES
YES
YES
NO
NO
YES
NO
NO


Hydroxy-L-Proline
NO
NO
NO
YES
NO
YES
YES
YES


Putrescine
NO
YES
NO
YES
YES
YES
YES
YES


Inulin
NO
YES
YES
NO
NO
NO
NO
NO


2-Deoxy-D-Ribose
NO
NO
NO
NO
NO
NO
NO
NO


β-Methyl-D-Glucuronic acid
YES
YES
NO
NO
NO
NO
NO
NO


N-Acetyl-D-glucosaminitol
NO
YES
YES
NO
NO
NO
NO
NO


γ-Hydroxy butyric acid
NO
YES
YES
NO
NO
NO
NO
NO


Sorbic acid
NO
NO
YES
NO
NO
NO
NO
NO


L-Isoleucine
NO
NO
NO
YES
YES
YES
YES
YES


Dihydroxy acetone
NO
NO
YES
NO
NO
NO
NO
NO


Laminarin
NO
NO
NO
NO
NO
NO
NO
NO


i-Erythritol
NO
NO
YES
NO
NO
NO
YES
NO


a-Methyl-D-Mannoside
NO
NO
YES
NO
NO
NO
NO
NO


γ-amino butyric acid
NO
YES
NO
NO
YES
YES
YES
YES


a-Keto-valeric acid
NO
NO
YES
NO
NO
NO
NO
NO


Succinamic acid
NO
NO
YES
NO
NO
YES
NO
NO


L-Leucine
NO
NO
NO
YES
NO
YES
YES
YES


2,3-Butanediol
YES
NO
YES
NO
NO
NO
NO
NO


Mannan
NO
NO
YES
NO
NO
NO
NO
NO


D-Fucose
NO
NO
NO
NO
NO
NO
NO
NO


β-Methyl-D-Xyloside
NO
YES
NO
NO
NO
NO
NO
NO


d-amino valeric acid
NO
YES
YES
NO
NO
NO
NO
YES


Itaconic acid
NO
NO
YES
NO
NO
NO
NO
NO


D-Tartaric acid
NO
YES
NO
NO
NO
NO
NO
NO


L-Lysine
NO
NO
YES
NO
NO
NO
NO
YES


2,3-Butanone
NO
NO
YES
NO
NO
NO
NO
NO


Pectin
NO
YES
NO
YES
NO
NO
NO
YES


3-0-β-D-Galactopyranosyl-D-
NO
NO
YES
NO
NO
NO
YES
NO


arabinose


Palatinose
NO
NO
YES
YES
YES
NO
NO
YES


Butyric acid
NO
YES
NO
NO
NO
NO
YES
NO


5-Keto-D-Gluconic acid
NO
NO
NO
NO
NO
NO
NO
YES


L-Tartaric acid
NO
NO
YES
NO
NO
NO
NO
YES


L-Methionine
NO
YES
NO
NO
NO
NO
NO
NO


3-Hydroxy 2-Butanone
NO
NO
NO
NO
NO
NO
NO
NO



















Strain/Substrate
SYM01314
SYM01315
SYM01324
SYM01325
SYM01326
SYM01327
SYM01333







N-acetyl-D-Galactosamine
YES
YES
NO
NO
NO
YES
NO



Gentiobiose
NO
YES
YES
YES
NO
NO
NO



D-Raffinose
NO
NO
NO
YES
YES
NO
NO



Capric acid
YES
NO
NO
NO
YES
YES
YES



D-lactic acid methyl ester
NO
NO
NO
NO
NO
NO
NO



Acetamide
NO
NO
NO
NO
NO
NO
NO



L-Ornithine
YES
YES
NO
YES
YES
YES
YES



Chondrointin sulfate C
NO
YES
NO
NO
NO
NO
NO



N-acetyl-neuraminic acid
YES
NO
NO
NO
NO
YES
NO



L-glucose
NO
NO
NO
NO
NO
NO
NO



Salicin
NO
NO
NO
YES
YES
NO
NO



Caproic acid
NO
NO
NO
NO
YES
NO
NO



Malonic acid
NO
NO
NO
NO
NO
NO
NO



L-Alaninamide
YES
NO
NO
YES
YES
YES
YES



L-Phenylalanine
YES
NO
NO
NO
NO
YES
NO



a-Cyclodextrin
YES
YES
YES
YES
YES
YES
YES



β-D-allose
NO
YES
NO
NO
NO
NO
NO



Lactitol
NO
YES
YES
NO
NO
NO
NO



Sedoheptulosan
NO
NO
NO
NO
NO
NO
NO



Citraconic acid
NO
YES
NO
NO
NO
NO
NO



Melibionic acid
YES
YES
NO
NO
NO
NO
NO



N-Acetyl-L-Glutamic acid
YES
NO
NO
NO
YES
YES
YES



L-Pyroglutamic acid
YES
YES
NO
YES
YES
YES
YES



β-Cyclodextrin
NO
NO
NO
NO
NO
NO
NO



Amygdalin
NO
NO
NO
YES
NO
NO
NO



D-Melezitose
NO
NO
YES
YES
NO
NO
NO



L-Sorbose
NO
NO
NO
NO
NO
NO
NO



Citramalic acid
NO
NO
NO
NO
NO
YES
NO



Oxalic acid
NO
NO
NO
NO
NO
NO
NO



L-Arginine
YES
YES
NO
YES
YES
YES
YES



L-Valine
YES
NO
NO
YES
YES
YES
YES



γ-Cyclodextrin
NO
YES
NO
YES
NO
NO
YES



D-arabinose
NO
YES
NO
NO
NO
NO
NO



Maltitol
NO
NO
YES
NO
NO
NO
NO



Stachyose
NO
NO
YES
YES
NO
NO
NO



D-Glucosamine
YES
NO
NO
NO
NO
YES
NO



Oxalomalic acid
NO
YES
NO
NO
NO
NO
NO



Glycine
NO
NO
NO
NO
NO
YES
NO



D,L-Carnitine
YES
NO
NO
NO
YES
YES
NO



Dextrin
NO
YES
NO
YES
NO
NO
NO



D-arabitol
NO
YES
YES
YES
NO
NO
YES



a-Methyl-D-Glucoside
NO
NO
YES
NO
NO
NO
NO



D-Tagatose
NO
NO
NO
NO
NO
NO
NO



2-Hydroxy benzoic acid
YES
YES
NO
NO
YES
NO
NO



Quinic acid
YES
NO
YES
YES
NO
NO
NO



L-Histidine
YES
YES
YES
NO
YES
YES
YES



Sec-Butylamine
NO
NO
NO
NO
NO
NO
NO



Gelatin
YES
YES
YES
YES
YES
YES
YES



L-arabitol
NO
YES
NO
NO
NO
NO
NO



β-Methyl-D-Galactoside
NO
NO
NO
NO
NO
NO
NO



Turanose
NO
NO
NO
NO
NO
NO
NO



4-Hydroxy benzoic acid
NO
YES
NO
NO
NO
NO
NO



D-Ribono-1,4-Lactone
NO
YES
NO
NO
YES
NO
NO



L-Homoserine
NO
NO
NO
NO
NO
NO
NO



D,L-Octopamine
YES
NO
NO
NO
YES
YES
YES



Glycogen
NO
YES
YES
YES
YES
NO
NO



Arbutin
NO
YES
YES
YES
NO
NO
NO



3-Methyl Glucose
NO
NO
NO
NO
NO
NO
NO



Xylitol
NO
YES
NO
NO
NO
NO
NO



β-Hydroxy butyric acid
NO
YES
YES
YES
NO
YES
YES



Sebacic acid
NO
YES
NO
NO
NO
NO
NO



Hydroxy-L-Proline
YES
YES
NO
YES
YES
YES
YES



Putrescine
NO
YES
NO
YES
NO
NO
NO



Inulin
NO
YES
NO
NO
YES
NO
NO



2-Deoxy-D-Ribose
NO
NO
NO
NO
NO
NO
NO



β-Methyl-D-Glucuronic acid
NO
YES
NO
NO
NO
NO
NO



N-Acetyl-D-glucosaminitol
NO
NO
NO
NO
NO
NO
NO



γ-Hydroxy butyric acid
NO
YES
NO
NO
NO
NO
NO



Sorbic acid
NO
NO
NO
NO
NO
NO
NO



L-Isoleucine
YES
NO
NO
YES
YES
YES
YES



Dihydroxy acetone
NO
NO
NO
NO
NO
NO
NO



Laminarin
NO
NO
NO
YES
NO
NO
NO



i-Erythritol
NO
YES
NO
NO
NO
NO
YES



a-Methyl-D-Mannoside
NO
YES
NO
NO
NO
NO
NO



γ-amino butyric acid
YES
YES
YES
YES
YES
YES
YES



a-Keto-valeric acid
NO
YES
NO
NO
NO
NO
NO



Succinamic acid
YES
YES
NO
YES
YES
YES
NO



L-Leucine
YES
YES
NO
NO
YES
YES
YES



2,3-Butanediol
NO
NO
NO
NO
NO
NO
NO



Mannan
NO
NO
NO
NO
NO
NO
NO



D-Fucose
NO
NO
NO
NO
NO
NO
NO



β-Methyl-D-Xyloside
NO
YES
NO
NO
NO
NO
NO



d-amino valeric acid
NO
YES
NO
NO
NO
NO
NO



Itaconic acid
NO
YES
NO
NO
NO
NO
NO



D-Tartaric acid
NO
YES
NO
NO
NO
NO
NO



L-Lysine
NO
YES
NO
YES
NO
NO
NO



2,3-Butanone
NO
YES
NO
NO
NO
NO
NO



Pectin
NO
YES
NO
NO
NO
NO
NO



3-0-β-D-Galactopyranosyl-D-
NO
YES
YES
NO
NO
NO
YES



arabinose



Palatinose
NO
YES
YES
YES
NO
NO
NO



Butyric acid
NO
NO
NO
NO
NO
NO
NO



5-Keto-D-Gluconic acid
NO
YES
NO
YES
NO
NO
NO



L-Tartaric acid
NO
NO
NO
NO
NO
NO
NO



L-Methionine
NO
NO
NO
NO
NO
NO
NO



3-Hydroxy 2-Butanone
NO
YES
NO
NO
NO
NO
NO

















TABLE T





Substrate utilization as determined by BIOLOG PM2A MicroPlates by fungal


endophytes belonging to core OTUs.





















Strain/Substrate
SYM00135
SYM00136
SYM00151
SYM00154
SYM15811
SYM15820





N-acetyl-D-Galactosamine
NO
NO
NO
NO
NO
NO


Gentiobiose
NO
YES
YES
NO
NO
NO


D-Raffinose
YES
YES
YES
YES
YES
NO


Capric acid
NO
NO
NO
NO
YES
NO


D-lactic acid methyl ester
NO
NO
NO
NO
YES
NO


Acetamide
NO
NO
NO
NO
NO
NO


L-Ornithine
YES
NO
YES
NO
NO
YES


Chondrointin sulfate C
NO
NO
NO
NO
NO
NO


N-acetyl-neuraminic acid
NO
NO
NO
NO
NO
NO


L-glucose
NO
NO
NO
NO
NO
NO


Salicin
NO
NO
YES
NO
YES
NO


Caproic acid
NO
NO
NO
NO
YES
NO


Malonic acid
NO
NO
YES
NO
NO
NO


L-Alaninamide
NO
NO
YES
NO
YES
NO


L-Phenylalanine
NO
NO
YES
NO
NO
NO


a-Cyclodextrin
YES
YES
YES
YES
YES
NO


β-D-allose
NO
NO
NO
NO
NO
NO


Lactitol
NO
NO
NO
NO
YES
NO


Sedoheptulosan
NO
NO
NO
NO
NO
NO


Citraconic acid
NO
NO
NO
NO
NO
NO


Melibionic acid
NO
NO
NO
NO
NO
NO


N-Acetyl-L-Glutamic acid
NO
NO
NO
NO
NO
YES


L-Pyroglutamic acid
NO
YES
YES
NO
YES
YES


β-Cyclodextrin
NO
NO
NO
NO
NO
NO


Amygdalin
NO
NO
YES
NO
NO
NO


D-Melezitose
YES
YES
YES
NO
YES
NO


L-Sorbose
NO
YES
YES
NO
NO
NO


Citramalic acid
NO
NO
NO
NO
NO
NO


Oxalic acid
NO
YES
NO
NO
NO
NO


L-Arginine
NO
NO
YES
NO
NO
YES


L-Valine
NO
NO
NO
NO
NO
YES


γ-Cyclodextrin
NO
YES
NO
NO
NO
NO


D-arabinose
NO
NO
NO
NO
NO
NO


Maltitol
NO
YES
YES
NO
NO
NO


Stachyose
YES
YES
YES
NO
NO
NO


D-Glucosamine
NO
NO
NO
NO
NO
NO


Oxalomalic acid
NO
NO
NO
NO
NO
NO


Glycine
NO
NO
NO
NO
YES
NO


D,L-Carnitine
NO
NO
NO
NO
NO
NO


Dextrin
YES
NO
YES
NO
YES
NO


D-arabitol
YES
NO
YES
NO
NO
NO


a-Methyl-D-Glucoside
NO
NO
NO
NO
NO
NO


D-Tagatose
NO
NO
NO
NO
NO
NO


2-Hydroxy benzoic acid
NO
NO
NO
NO
NO
NO


Quinic acid
NO
NO
YES
NO
YES
NO


L-Histidine
NO
YES
NO
NO
YES
YES


Sec-Butylamine
NO
NO
NO
NO
NO
NO


Gelatin
NO
NO
YES
NO
NO
YES


L-arabitol
NO
NO
NO
NO
NO
NO


β-Methyl-D-Galactoside
NO
YES
NO
NO
NO
NO


Turanose
YES
YES
YES
YES
NO
NO


4-Hydroxy benzoic acid
NO
NO
NO
NO
NO
NO


D-Ribono-1,4-Lactone
NO
NO
NO
NO
YES
NO


L-Homoserine
NO
NO
NO
NO
NO
NO


D,L-Octopamine
NO
NO
NO
NO
YES
YES


Glycogen
NO
YES
YES
NO
NO
NO


Arbutin
NO
YES
YES
NO
NO
NO


3-Methyl Glucose
NO
NO
NO
NO
NO
NO


Xylitol
NO
NO
NO
NO
YES
NO


β-Hydroxy butyric acid
NO
NO
YES
NO
NO
NO


Sebacic acid
NO
NO
NO
NO
NO
NO


Hydroxy-L-Proline
NO
NO
YES
NO
YES
YES


Putrescine
YES
YES
YES
NO
NO
NO


Inulin
NO
NO
NO
NO
NO
NO


2-Deoxy-D-Ribose
NO
NO
NO
NO
NO
NO


β-Methyl-D-Glucuronic acid
NO
NO
NO
NO
NO
NO


N-Acetyl-D-glucosaminitol
NO
NO
NO
NO
NO
NO


γ-Hydroxy butyric acid
NO
NO
NO
NO
YES
NO


Sorbic acid
NO
NO
NO
NO
NO
NO


L-Isoleucine
NO
NO
YES
NO
NO
YES


Dihydroxy acetone
NO
NO
NO
NO
NO
NO


Laminarin
NO
NO
YES
NO
NO
NO


i-Erythritol
NO
NO
NO
NO
NO
NO


a-Methyl-D-Mannoside
NO
NO
NO
NO
NO
NO


γ-amino butyric acid
NO
YES
YES
NO
YES
NO


a-Keto-valeric acid
NO
NO
NO
NO
NO
NO


Succinamic acid
NO
NO
NO
NO
NO
NO


L-Leucine
NO
NO
YES
YES
NO
NO


2,3-Butanediol
NO
NO
NO
NO
NO
NO


Mannan
NO
NO
NO
NO
NO
NO


D-Fucose
NO
NO
NO
NO
NO
NO


β-Methyl-D-Xyloside
NO
NO
NO
NO
NO
NO


d-amino valeric acid
NO
NO
NO
NO
NO
NO


Itaconic acid
NO
NO
NO
NO
YES
NO


D-Tartaric acid
NO
NO
NO
NO
NO
NO


L-Lysine
NO
NO
YES
NO
NO
NO


2,3-Butanone
NO
NO
NO
NO
NO
NO


Pectin
NO
NO
YES
NO
NO
NO


3-0-β-D-Galactopyranosyl-D-
NO
NO
NO
NO
NO
NO


arabinose


Palatinose
YES
YES
YES
NO
YES
NO


Butyric acid
NO
NO
NO
NO
YES
NO


5-Keto-D-Gluconic acid
NO
NO
NO
NO
NO
NO


L-Tartaric acid
NO
NO
YES
NO
YES
NO


L-Methionine
NO
NO
NO
NO
NO
NO


3-Hydroxy 2-Butanone
NO
NO
NO
NO
NO
NO





Strain/Substrate
SYM15825
SYM15828
SYM15831
SYM15837
SYM15839
SYM15847





N-acetyl-D-Galactosamine
NO
NO
NO
NO
NO
NO


Gentiobiose
YES
NO
NO
NO
YES
YES


D-Raffinose
YES
NO
YES
YES
YES
YES


Capric acid
NO
NO
NO
NO
NO
NO


D-lactic acid methyl ester
NO
NO
NO
NO
NO
NO


Acetamide
NO
NO
NO
NO
NO
NO


L-Ornithine
YES
YES
YES
YES
YES
YES


Chondrointin sulfate C
NO
NO
NO
NO
NO
NO


N-acetyl-neuraminic acid
NO
NO
NO
NO
NO
NO


L-glucose
NO
NO
NO
NO
NO
NO


Salicin
YES
NO
YES
NO
YES
YES


Caproic acid
NO
NO
NO
NO
NO
NO


Malonic acid
YES
NO
NO
YES
NO
NO


L-Alaninamide
YES
NO
NO
NO
NO
YES


L-Phenylalanine
YES
NO
NO
NO
YES
YES


a-Cyclodextrin
NO
YES
YES
YES
YES
YES


β-D-allose
NO
NO
NO
NO
NO
NO


Lactitol
NO
NO
NO
NO
NO
NO


Sedoheptulosan
NO
NO
NO
NO
NO
YES


Citraconic acid
NO
NO
NO
NO
NO
NO


Melibionic acid
NO
NO
NO
NO
NO
NO


N-Acetyl-L-Glutamic acid
NO
YES
NO
YES
NO
NO


L-Pyroglutamic acid
YES
YES
YES
YES
YES
YES


β-Cyclodextrin
NO
NO
NO
NO
NO
NO


Amygdalin
YES
NO
NO
YES
YES
YES


D-Melezitose
YES
NO
YES
YES
YES
YES


L-Sorbose
NO
NO
NO
YES
YES
NO


Citramalic acid
NO
NO
NO
NO
NO
NO


Oxalic acid
NO
NO
NO
NO
NO
NO


L-Arginine
YES
YES
YES
YES
YES
YES


L-Valine
YES
YES
NO
YES
YES
NO


γ-Cyclodextrin
YES
NO
NO
NO
YES
NO


D-arabinose
NO
NO
NO
NO
NO
NO


Maltitol
YES
NO
NO
NO
NO
NO


Stachyose
YES
NO
YES
YES
YES
YES


D-Glucosamine
NO
NO
YES
YES
YES
NO


Oxalomalic acid
NO
NO
NO
NO
NO
NO


Glycine
YES
NO
NO
NO
NO
YES


D,L-Carnitine
NO
NO
YES
YES
NO
NO


Dextrin
YES
NO
YES
YES
YES
NO


D-arabitol
YES
NO
NO
NO
NO
NO


a-Methyl-D-Glucoside
NO
NO
NO
NO
YES
NO


D-Tagatose
NO
NO
NO
NO
NO
NO


2-Hydroxy benzoic acid
NO
NO
NO
NO
NO
NO


Quinic acid
YES
NO
NO
NO
YES
NO


L-Histidine
YES
YES
NO
NO
YES
NO


Sec-Butylamine
NO
NO
NO
NO
NO
NO


Gelatin
YES
YES
NO
YES
YES
YES


L-arabitol
NO
NO
NO
NO
NO
NO


β-Methyl-D-Galactoside
NO
NO
NO
YES
NO
NO


Turanose
YES
NO
YES
YES
YES
YES


4-Hydroxy benzoic acid
NO
NO
NO
NO
NO
NO


D-Ribono-1,4-Lactone
NO
NO
NO
NO
NO
NO


L-Homoserine
NO
NO
NO
NO
NO
NO


D,L-Octopamine
NO
YES
NO
YES
NO
NO


Glycogen
YES
NO
YES
YES
YES
YES


Arbutin
YES
NO
NO
YES
YES
YES


3-Methyl Glucose
NO
NO
NO
NO
NO
NO


Xylitol
NO
NO
NO
NO
NO
NO


β-Hydroxy butyric acid
NO
NO
NO
NO
NO
NO


Sebacic acid
YES
NO
NO
YES
NO
NO


Hydroxy-L-Proline
YES
YES
YES
YES
YES
YES


Putrescine
YES
YES
NO
NO
YES
YES


Inulin
NO
NO
NO
YES
NO
NO


2-Deoxy-D-Ribose
NO
NO
NO
NO
NO
NO


β-Methyl-D-Glucuronic acid
NO
NO
NO
NO
NO
NO


N-Acetyl-D-glucosaminitol
NO
NO
NO
NO
NO
NO


γ-Hydroxy butyric acid
NO
NO
NO
NO
NO
NO


Sorbic acid
NO
NO
NO
NO
NO
NO


L-Isoleucine
YES
YES
YES
YES
YES
YES


Dihydroxy acetone
NO
NO
NO
NO
NO
NO


Laminarin
NO
NO
NO
NO
YES
NO


i-Erythritol
NO
NO
NO
YES
NO
NO


a-Methyl-D-Mannoside
NO
NO
NO
NO
NO
NO


γ-amino butyric acid
YES
NO
YES
YES
YES
YES


a-Keto-valeric acid
NO
NO
NO
YES
NO
NO


Succinamic acid
YES
NO
NO
YES
NO
YES


L-Leucine
YES
NO
NO
YES
YES
YES


2,3-Butanediol
NO
NO
NO
NO
NO
NO


Mannan
NO
NO
NO
NO
NO
NO


D-Fucose
NO
NO
NO
NO
NO
NO


β-Methyl-D-Xyloside
NO
NO
NO
NO
NO
NO


d-amino valeric acid
NO
NO
NO
NO
NO
YES


Itaconic acid
NO
NO
NO
YES
NO
NO


D-Tartaric acid
NO
NO
NO
NO
NO
NO


L-Lysine
YES
NO
YES
YES
NO
YES


2,3-Butanone
NO
NO
NO
NO
NO
NO


Pectin
YES
YES
YES
YES
YES
NO


3-0-β-D-Galactopyranosyl-D-
YES
NO
NO
NO
NO
NO


arabinose


Palatinose
YES
NO
YES
YES
YES
YES


Butyric acid
YES
YES
NO
YES
NO
NO


5-Keto-D-Gluconic acid
NO
NO
NO
NO
NO
NO


L-Tartaric acid
YES
NO
NO
NO
NO
NO


L-Methionine
NO
NO
NO
NO
NO
NO


3-Hydroxy 2-Butanone
NO
NO
NO
NO
NO
NO

















Strain/Substrate
SYM15872
SYM15890
SYM15901
SYM15920
SYM15926







N-acetyl-D-Galactosamine
NO
NO
NO
NO
NO



Gentiobiose
YES
NO
YES
YES
NO



D-Raffinose
YES
NO
YES
YES
NO



Capric acid
NO
NO
NO
NO
NO



D-lactic acid methyl ester
NO
NO
NO
NO
NO



Acetamide
NO
NO
NO
NO
NO



L-Ornithine
YES
YES
YES
YES
YES



Chondrointin sulfate C
YES
NO
NO
NO
NO



N-acetyl-neuraminic acid
NO
NO
NO
NO
NO



L-glucose
NO
NO
NO
NO
NO



Salicin
YES
NO
YES
YES
NO



Caproic acid
NO
NO
NO
NO
NO



Malonic acid
YES
NO
NO
NO
NO



L-Alaninamide
YES
NO
NO
NO
NO



L-Phenylalanine
YES
NO
YES
YES
NO



a-Cyclodextrin
YES
YES
YES
YES
YES



β-D-allose
NO
NO
NO
NO
NO



Lactitol
NO
NO
NO
NO
NO



Sedoheptulosan
YES
NO
NO
NO
NO



Citraconic acid
NO
NO
NO
NO
NO



Melibionic acid
NO
NO
NO
NO
NO



N-Acetyl-L-Glutamic acid
NO
NO
NO
NO
YES



L-Pyroglutamic acid
YES
YES
YES
YES
NO



β-Cyclodextrin
NO
NO
NO
NO
NO



Amygdalin
YES
NO
YES
YES
NO



D-Melezitose
YES
NO
YES
YES
NO



L-Sorbose
NO
NO
YES
NO
NO



Citramalic acid
NO
NO
NO
NO
NO



Oxalic acid
YES
NO
NO
NO
YES



L-Arginine
YES
NO
YES
YES
NO



L-Valine
YES
NO
YES
YES
YES



γ-Cyclodextrin
YES
NO
YES
YES
NO



D-arabinose
YES
NO
NO
NO
NO



Maltitol
YES
NO
YES
YES
YES



Stachyose
YES
NO
YES
YES
NO



D-Glucosamine
NO
NO
NO
NO
NO



Oxalomalic acid
NO
NO
NO
NO
NO



Glycine
YES
NO
YES
NO
NO



D,L-Carnitine
NO
NO
NO
NO
NO



Dextrin
YES
NO
YES
YES
YES



D-arabitol
YES
NO
YES
YES
NO



a-Methyl-D-Glucoside
YES
NO
NO
YES
NO



D-Tagatose
NO
NO
NO
NO
NO



2-Hydroxy benzoic acid
NO
NO
NO
NO
NO



Quinic acid
YES
NO
NO
YES
NO



L-Histidine
YES
NO
YES
YES
YES



Sec-Butylamine
NO
NO
YES
NO
NO



Gelatin
YES
YES
YES
YES
YES



L-arabitol
YES
NO
NO
NO
NO



β-Methyl-D-Galactoside
YES
NO
NO
NO
NO



Turanose
YES
NO
YES
YES
NO



4-Hydroxy benzoic acid
YES
NO
NO
NO
NO



D-Ribono-1,4-Lactone
NO
NO
NO
NO
NO



L-Homoserine
NO
NO
NO
NO
NO



D,L-Octopamine
YES
YES
NO
NO
NO



Glycogen
YES
NO
YES
YES
NO



Arbutin
YES
NO
YES
YES
NO



3-Methyl Glucose
NO
NO
NO
NO
NO



Xylitol
YES
NO
NO
NO
NO



β-Hydroxy butyric acid
NO
YES
YES
YES
NO



Sebacic acid
YES
NO
NO
NO
NO



Hydroxy-L-Proline
YES
YES
YES
YES
YES



Putrescine
YES
NO
YES
YES
NO



Inulin
NO
YES
NO
NO
NO



2-Deoxy-D-Ribose
NO
NO
NO
NO
NO



β-Methyl-D-Glucuronic acid
YES
NO
NO
NO
YES



N-Acetyl-D-glucosaminitol
NO
NO
NO
NO
NO



γ-Hydroxy butyric acid
NO
NO
NO
NO
NO



Sorbic acid
NO
NO
NO
NO
NO



L-Isoleucine
YES
NO
YES
YES
NO



Dihydroxy acetone
NO
NO
NO
NO
NO



Laminarin
NO
YES
NO
YES
NO



i-Erythritol
NO
NO
NO
NO
NO



a-Methyl-D-Mannoside
NO
NO
NO
NO
NO



γ-amino butyric acid
YES
NO
YES
YES
YES



a-Keto-valeric acid
YES
YES
NO
NO
NO



Succinamic acid
YES
NO
YES
NO
NO



L-Leucine
YES
NO
YES
YES
NO



2,3-Butanediol
YES
NO
NO
NO
NO



Mannan
NO
NO
NO
NO
NO



D-Fucose
NO
NO
NO
NO
NO



β-Methyl-D-Xyloside
NO
NO
NO
NO
NO



d-amino valeric acid
YES
NO
YES
NO
YES



Itaconic acid
NO
NO
NO
NO
YES



D-Tartaric acid
NO
NO
NO
NO
NO



L-Lysine
YES
NO
YES
NO
NO



2,3-Butanone
NO
NO
NO
NO
NO



Pectin
YES
NO
YES
YES
YES



3-0-β-D-Galactopyranosyl-D-
YES
NO
NO
NO
NO



arabinose



Palatinose
YES
YES
YES
YES
NO



Butyric acid
YES
NO
YES
YES
NO



5-Keto-D-Gluconic acid
NO
NO
YES
NO
NO



L-Tartaric acid
YES
NO
YES
YES
NO



L-Methionine
NO
NO
NO
NO
NO



3-Hydroxy 2-Butanone
NO
NO
NO
NO
NO

















TABLE U





Substrate utilization as determined by BIOLOG PM2A MicroPlates by fungal


endophytes belonging to core OTUs.





















Strain/Substrate
SYM15928
SYM15932
SYM00160
SYM00034
SYM00566B
SYM00577





N-acetyl-D-Galactosamine
NO
NO
NO
NO
NO
NO


Gentiobiose
YES
YES
YES
YES
NO
YES


D-Raffinose
YES
YES
YES
NO
NO
YES


Capric acid
NO
NO
NO
NO
NO
NO


D-lactic acid methyl ester
NO
NO
NO
NO
NO
NO


Acetamide
NO
NO
NO
NO
NO
NO


L-Ornithine
YES
YES
NO
YES
NO
YES


Chondrointin sulfate C
NO
YES
NO
NO
NO
NO


N-acetyl-neuraminic acid
NO
NO
NO
NO
NO
NO


L-glucose
NO
NO
NO
NO
NO
NO


Salicin
YES
YES
YES
YES
NO
YES


Caproic acid
NO
NO
NO
NO
NO
NO


Malonic acid
NO
NO
NO
NO
YES
NO


L-Alaninamide
NO
NO
NO
YES
NO
YES


L-Phenylalanine
NO
NO
NO
NO
NO
YES


a-Cyclodextrin
YES
YES
YES
YES
YES
NO


β-D-allose
YES
NO
NO
NO
NO
NO


Lactitol
NO
NO
NO
NO
NO
NO


Sedoheptulosan
NO
NO
NO
NO
NO
NO


Citraconic acid
NO
NO
NO
NO
NO
NO


Melibionic acid
NO
NO
NO
NO
NO
YES


N-Acetyl-L-Glutamic acid
NO
NO
NO
NO
NO
NO


L-Pyroglutamic acid
YES
NO
NO
YES
YES
YES


β-Cyclodextrin
NO
YES
YES
NO
NO
NO


Amygdalin
NO
YES
NO
YES
NO
YES


D-Melezitose
YES
YES
YES
YES
NO
YES


L-Sorbose
NO
NO
NO
NO
NO
YES


Citramalic acid
NO
NO
NO
NO
NO
NO


Oxalic acid
NO
YES
NO
NO
NO
NO


L-Arginine
YES
YES
NO
YES
NO
YES


L-Valine
NO
NO
NO
YES
NO
YES


γ-Cyclodextrin
YES
YES
YES
NO
NO
YES


D-arabinose
NO
NO
NO
NO
NO
NO


Maltitol
YES
YES
YES
NO
NO
YES


Stachyose
YES
YES
YES
NO
NO
YES


D-Glucosamine
NO
NO
NO
YES
NO
YES


Oxalomalic acid
NO
NO
NO
NO
NO
NO


Glycine
NO
NO
NO
NO
NO
NO


D,L-Carnitine
NO
NO
NO
NO
NO
NO


Dextrin
YES
YES
YES
YES
NO
YES


D-arabitol
YES
NO
NO
YES
NO
YES


a-Methyl-D-Glucoside
YES
NO
YES
NO
NO
NO


D-Tagatose
NO
NO
NO
NO
NO
NO


2-Hydroxy benzoic acid
NO
NO
NO
NO
NO
NO


Quinic acid
NO
YES
NO
YES
NO
NO


L-Histidine
NO
NO
NO
NO
YES
YES


Sec-Butylamine
NO
NO
NO
NO
NO
NO


Gelatin
YES
YES
NO
YES
NO
YES


L-arabitol
NO
YES
NO
NO
NO
NO


β-Methyl-D-Galactoside
NO
YES
NO
YES
NO
NO


Turanose
YES
YES
YES
YES
NO
YES


4-Hydroxy benzoic acid
NO
NO
NO
NO
NO
NO


D-Ribono-1,4-Lactone
NO
NO
NO
NO
NO
NO


L-Homoserine
NO
NO
NO
NO
NO
NO


D,L-Octopamine
NO
NO
NO
NO
NO
YES


Glycogen
YES
YES
YES
YES
NO
YES


Arbutin
YES
YES
YES
YES
NO
YES


3-Methyl Glucose
NO
NO
NO
NO
NO
NO


Xylitol
NO
NO
YES
NO
YES
NO


β-Hydroxy butyric acid
YES
NO
NO
NO
YES
YES


Sebacic acid
NO
NO
NO
NO
NO
NO


Hydroxy-L-Proline
NO
NO
NO
NO
YES
YES


Putrescine
YES
NO
NO
YES
NO
YES


Inulin
YES
NO
NO
NO
NO
NO


2-Deoxy-D-Ribose
NO
NO
NO
NO
NO
NO


β-Methyl-D-Glucuronic acid
NO
YES
NO
NO
NO
NO


N-Acetyl-D-glucosaminitol
NO
NO
NO
NO
NO
NO


γ-Hydroxy butyric acid
NO
NO
NO
NO
NO
NO


Sorbic acid
NO
NO
NO
NO
YES
NO


L-Isoleucine
NO
YES
NO
YES
NO
YES


Dihydroxy acetone
NO
NO
NO
NO
NO
NO


Laminarin
NO
NO
NO
YES
NO
NO


i-Erythritol
YES
NO
NO
YES
NO
NO


a-Methyl-D-Mannoside
NO
NO
NO
NO
NO
NO


γ-amino butyric acid
YES
NO
NO
YES
NO
YES


a-Keto-valeric acid
NO
YES
NO
NO
YES
NO


Succinamic acid
NO
NO
NO
YES
NO
NO


L-Leucine
NO
NO
NO
YES
NO
YES


2,3-Butanediol
NO
NO
NO
NO
NO
NO


Mannan
NO
NO
NO
NO
NO
NO


D-Fucose
NO
YES
NO
NO
NO
NO


β-Methyl-D-Xyloside
NO
NO
NO
NO
NO
NO


d-amino valeric acid
NO
NO
NO
NO
NO
YES


Itaconic acid
NO
NO
NO
NO
NO
NO


D-Tartaric acid
NO
NO
NO
NO
NO
NO


L-Lysine
NO
NO
NO
YES
YES
NO


2,3-Butanone
NO
NO
NO
NO
NO
NO


Pectin
YES
YES
YES
YES
NO
YES


3-0-β-D-Galactopyranosyl-D-
NO
NO
NO
NO
NO
YES


arabinose


Palatinose
YES
YES
YES
YES
NO
YES


Butyric acid
NO
NO
NO
NO
NO
NO


5-Keto-D-Gluconic acid
NO
NO
NO
NO
NO
NO


L-Tartaric acid
NO
YES
NO
NO
NO
YES


L-Methionine
NO
NO
YES
NO
NO
NO


3-Hydroxy 2-Butanone
NO
NO
NO
NO
NO
NO





Strain/Substrate
SYM00590
SYM00603
SYM00061A
SYM00622
SYM00629
SYM00066





N-acetyl-D-Galactosamine
NO
NO
NO
NO
NO
NO


Gentiobiose
YES
NO
YES
NO
NO
NO


D-Raffinose
NO
NO
YES
NO
NO
YES


Capric acid
NO
YES
NO
NO
NO
NO


D-lactic acid methyl ester
NO
NO
NO
NO
NO
NO


Acetamide
NO
NO
NO
NO
NO
NO


L-Ornithine
YES
YES
YES
YES
YES
NO


Chondrointin sulfate C
NO
NO
NO
NO
NO
NO


N-acetyl-neuraminic acid
NO
NO
NO
NO
NO
NO


L-glucose
NO
NO
NO
NO
NO
NO


Salicin
YES
NO
YES
NO
NO
NO


Caproic acid
NO
NO
NO
NO
NO
NO


Malonic acid
NO
NO
YES
NO
NO
NO


L-Alaninamide
NO
YES
YES
NO
NO
NO


L-Phenylalanine
NO
YES
NO
NO
NO
NO


a-Cyclodextrin
NO
YES
YES
YES
NO
YES


β-D-allose
NO
NO
NO
NO
NO
NO


Lactitol
NO
NO
YES
NO
NO
NO


Sedoheptulosan
NO
NO
NO
NO
NO
NO


Citraconic acid
NO
NO
NO
NO
NO
NO


Melibionic acid
NO
NO
YES
NO
NO
NO


N-Acetyl-L-Glutamic acid
NO
YES
NO
YES
YES
NO


L-Pyroglutamic acid
NO
YES
YES
YES
NO
NO


β-Cyclodextrin
NO
NO
NO
NO
NO
NO


Amygdalin
NO
NO
NO
NO
NO
NO


D-Melezitose
NO
NO
YES
NO
NO
NO


L-Sorbose
NO
NO
NO
NO
NO
NO


Citramalic acid
NO
NO
NO
NO
NO
NO


Oxalic acid
NO
NO
NO
NO
NO
NO


L-Arginine
NO
YES
YES
YES
YES
NO


L-Valine
NO
YES
NO
YES
YES
NO


γ-Cyclodextrin
NO
NO
YES
NO
NO
NO


D-arabinose
NO
NO
NO
NO
NO
NO


Maltitol
NO
NO
YES
NO
NO
NO


Stachyose
NO
NO
YES
NO
NO
NO


D-Glucosamine
NO
YES
NO
YES
NO
NO


Oxalomalic acid
NO
NO
NO
NO
NO
NO


Glycine
NO
NO
NO
NO
NO
NO


D,L-Carnitine
NO
YES
NO
YES
NO
NO


Dextrin
NO
NO
YES
NO
NO
NO


D-arabitol
NO
NO
YES
NO
YES
NO


a-Methyl-D-Glucoside
NO
NO
NO
NO
NO
NO


D-Tagatose
NO
NO
NO
NO
NO
NO


2-Hydroxy benzoic acid
NO
NO
NO
NO
NO
NO


Quinic acid
NO
YES
NO
NO
NO
NO


L-Histidine
NO
YES
YES
YES
NO
NO


Sec-Butylamine
NO
NO
NO
NO
NO
NO


Gelatin
YES
NO
YES
NO
NO
NO


L-arabitol
NO
NO
YES
NO
NO
NO


β-Methyl-D-Galactoside
NO
NO
YES
NO
NO
NO


Turanose
NO
NO
YES
NO
NO
NO


4-Hydroxy benzoic acid
NO
NO
YES
NO
NO
NO


D-Ribono-1,4-Lactone
NO
NO
NO
NO
NO
NO


L-Homoserine
NO
NO
YES
NO
NO
NO


D,L-Octopamine
NO
YES
YES
YES
YES
NO


Glycogen
YES
NO
YES
YES
NO
NO


Arbutin
YES
NO
YES
NO
NO
NO


3-Methyl Glucose
NO
NO
NO
NO
NO
NO


Xylitol
NO
NO
NO
NO
NO
NO


β-Hydroxy butyric acid
NO
NO
NO
NO
NO
NO


Sebacic acid
NO
NO
YES
YES
NO
NO


Hydroxy-L-Proline
YES
YES
YES
YES
YES
NO


Putrescine
NO
YES
YES
NO
NO
NO


Inulin
YES
NO
NO
YES
YES
NO


2-Deoxy-D-Ribose
NO
NO
NO
NO
NO
NO


β-Methyl-D-Glucuronic acid
NO
NO
YES
NO
NO
NO


N-Acetyl-D-glucosaminitol
NO
NO
NO
NO
NO
NO


γ-Hydroxy butyric acid
NO
NO
YES
NO
NO
NO


Sorbic acid
NO
NO
YES
NO
NO
NO


L-Isoleucine
NO
YES
NO
YES
YES
NO


Dihydroxy acetone
NO
NO
NO
NO
NO
NO


Laminarin
NO
NO
YES
NO
NO
NO


i-Erythritol
YES
NO
NO
NO
YES
NO


a-Methyl-D-Mannoside
NO
NO
NO
NO
NO
NO


γ-amino butyric acid
YES
YES
YES
YES
YES
NO


a-Keto-valeric acid
NO
NO
YES
NO
NO
NO


Succinamic acid
NO
NO
YES
NO
NO
NO


L-Leucine
NO
YES
NO
YES
YES
NO


2,3-Butanediol
NO
NO
YES
NO
NO
NO


Mannan
NO
NO
NO
NO
NO
NO


D-Fucose
NO
NO
NO
NO
NO
NO


β-Methyl-D-Xyloside
NO
NO
NO
NO
NO
NO


d-amino valeric acid
NO
NO
YES
NO
NO
NO


Itaconic acid
NO
NO
NO
NO
NO
NO


D-Tartaric acid
NO
NO
NO
NO
NO
NO


L-Lysine
NO
NO
YES
NO
NO
NO


2,3-Butanone
NO
NO
NO
NO
NO
NO


Pectin
NO
NO
YES
NO
NO
NO


3-0-β-D-Galactopyranosyl-D-
NO
NO
NO
NO
NO
NO


arabinose


Palatinose
YES
NO
NO
NO
NO
NO


Butyric acid
NO
NO
YES
NO
NO
NO


5-Keto-D-Gluconic acid
NO
NO
NO
NO
NO
NO


L-Tartaric acid
NO
NO
YES
NO
NO
NO


L-Methionine
NO
NO
NO
NO
NO
NO


3-Hydroxy 2-Butanone
NO
NO
NO
NO
NO
NO





Strain/Substrate
SYM00663
SYM00696
SYM00741A
SYM00741B
SYM00854
SYM00880





N-acetyl-D-Galactosamine
NO
NO
NO
NO
NO
YES


Gentiobiose
NO
YES
YES
NO
NO
NO


D-Raffinose
NO
YES
YES
NO
YES
NO


Capric acid
NO
NO
NO
NO
NO
NO


D-lactic acid methyl ester
NO
NO
NO
NO
NO
NO


Acetamide
NO
YES
NO
NO
NO
YES


L-Ornithine
YES
YES
YES
YES
NO
NO


Chondrointin sulfate C
NO
YES
YES
NO
NO
NO


N-acetyl-neuraminic acid
NO
NO
NO
NO
NO
YES


L-glucose
NO
NO
YES
NO
NO
NO


Salicin
NO
YES
NO
NO
NO
NO


Caproic acid
NO
YES
NO
NO
NO
NO


Malonic acid
NO
NO
NO
NO
NO
NO


L-Alaninamide
NO
YES
NO
YES
NO
YES


L-Phenylalanine
NO
NO
YES
NO
NO
NO


a-Cyclodextrin
NO
NO
NO
YES
NO
YES


β-D-allose
NO
YES
NO
NO
NO
YES


Lactitol
NO
YES
YES
NO
NO
YES


Sedoheptulosan
NO
NO
YES
NO
NO
YES


Citraconic acid
NO
YES
NO
NO
NO
YES


Melibionic acid
NO
NO
YES
NO
NO
NO


N-Acetyl-L-Glutamic acid
NO
YES
NO
YES
NO
YES


L-Pyroglutamic acid
YES
NO
YES
YES
YES
YES


β-Cyclodextrin
NO
NO
YES
NO
NO
YES


Amygdalin
NO
NO
YES
NO
YES
YES


D-Melezitose
NO
YES
YES
NO
NO
YES


L-Sorbose
NO
NO
YES
NO
NO
NO


Citramalic acid
NO
NO
NO
NO
NO
YES


Oxalic acid
NO
YES
NO
NO
NO
YES


L-Arginine
YES
YES
YES
YES
YES
YES


L-Valine
NO
YES
YES
YES
NO
YES


γ-Cyclodextrin
NO
YES
NO
NO
YES
NO


D-arabinose
NO
YES
NO
NO
NO
NO


Maltitol
NO
YES
YES
NO
YES
YES


Stachyose
NO
YES
YES
NO
YES
YES


D-Glucosamine
NO
NO
NO
NO
NO
NO


Oxalomalic acid
NO
NO
NO
NO
NO
NO


Glycine
NO
YES
YES
NO
NO
YES


D,L-Carnitine
NO
NO
NO
YES
NO
NO


Dextrin
NO
YES
YES
NO
YES
YES


D-arabitol
NO
YES
YES
NO
YES
NO


a-Methyl-D-Glucoside
NO
NO
YES
NO
NO
NO


D-Tagatose
YES
NO
NO
NO
NO
NO


2-Hydroxy benzoic acid
NO
YES
YES
NO
NO
NO


Quinic acid
NO
YES
NO
NO
NO
YES


L-Histidine
NO
YES
NO
YES
NO
NO


Sec-Butylamine
NO
NO
NO
NO
NO
NO


Gelatin
NO
YES
YES
YES
YES
NO


L-arabitol
NO
YES
NO
NO
NO
YES


β-Methyl-D-Galactoside
NO
YES
NO
NO
NO
NO


Turanose
NO
YES
NO
NO
YES
YES


4-Hydroxy benzoic acid
NO
YES
NO
NO
NO
YES


D-Ribono-1,4-Lactone
YES
YES
NO
NO
YES
YES


L-Homoserine
NO
NO
NO
NO
NO
NO


D,L-Octopamine
NO
NO
YES
YES
YES
NO


Glycogen
YES
YES
YES
NO
YES
YES


Arbutin
NO
YES
YES
YES
YES
YES


3-Methyl Glucose
NO
NO
YES
NO
NO
NO


Xylitol
NO
NO
NO
NO
NO
YES


β-Hydroxy butyric acid
NO
YES
YES
NO
NO
NO


Sebacic acid
NO
NO
NO
NO
NO
NO


Hydroxy-L-Proline
YES
NO
YES
YES
YES
YES


Putrescine
NO
YES
YES
NO
NO
YES


Inulin
NO
YES
YES
YES
NO
YES


2-Deoxy-D-Ribose
NO
NO
NO
NO
NO
NO


β-Methyl-D-Glucuronic acid
NO
YES
NO
NO
NO
NO


N-Acetyl-D-glucosaminitol
NO
YES
NO
NO
NO
YES


γ-Hydroxy butyric acid
NO
YES
NO
NO
NO
NO


Sorbic acid
NO
NO
NO
NO
NO
NO


L-Isoleucine
NO
YES
YES
YES
NO
YES


Dihydroxy acetone
NO
NO
NO
NO
NO
NO


Laminarin
NO
NO
NO
NO
NO
NO


i-Erythritol
NO
YES
NO
YES
YES
NO


a-Methyl-D-Mannoside
NO
YES
NO
NO
NO
NO


γ-amino butyric acid
NO
YES
YES
YES
YES
YES


a-Keto-valeric acid
NO
YES
NO
NO
NO
YES


Succinamic acid
NO
YES
YES
NO
YES
YES


L-Leucine
NO
NO
YES
YES
NO
NO


2,3-Butanediol
NO
YES
NO
NO
NO
YES


Mannan
NO
YES
NO
NO
NO
YES


D-Fucose
NO
YES
NO
NO
NO
YES


β-Methyl-D-Xyloside
NO
NO
NO
NO
NO
NO


d-amino valeric acid
NO
NO
NO
NO
NO
NO


Itaconic acid
NO
YES
NO
NO
NO
NO


D-Tartaric acid
NO
YES
NO
NO
NO
NO


L-Lysine
NO
YES
YES
NO
NO
YES


2,3-Butanone
NO
NO
NO
NO
NO
NO


Pectin
NO
YES
YES
NO
YES
YES


3-0-β-D-Galactopyranosyl-D-
NO
YES
YES
YES
NO
YES


arabinose


Palatinose
YES
YES
YES
NO
YES
YES


Butyric acid
NO
NO
NO
NO
YES
NO


5-Keto-D-Gluconic acid
NO
YES
NO
NO
NO
NO


L-Tartaric acid
NO
NO
NO
NO
NO
NO


L-Methionine
NO
NO
NO
NO
NO
NO


3-Hydroxy 2-Butanone
YES
NO
NO
NO
NO
NO










Characterization of Culturable Microbes: Substrate Use


Additional BIOLOG analyses were performed. For additional biolog analyses, microbes were cultivated in three biological replicates for each strain. Each bacterium was initially streaked on Reasoner's 2A (R2A) agar, distinct CFUs selected and cultured in 6 mL R2A broth for 4 days. Fungal strains were streaked on potato dextrose (PD) agar and individual plugs containing spores and mycelial tissues were used to initiate growth in 6 mL PD broth for 6 days. All strains were grown with agitation at room temperature. One mL liquid cultures of each sample were harvested by centrifugation for 15 minutes at 4500 RPM and subsequently washed at least four times with sterile distilled water to remove any traces of residual media. Additionally, fungal cultures were first sonicated to achieve homogeneity after the growth period. Microbes were resuspended in 500 μL sterile distilled water and measurements of absorbance were taken using a SpectraMax M microplate reader (Molecular Devices, Sunnyvale, Calif.).


Sole carbon substrate assays were done using BIOLOG Phenotype MicroArray (PM) 1 and 2A MicroPlates (Hayward, Calif.). An aliquot of each bacterial cell culture corresponding to a final absorbance of 0.2 were inoculated into 20 mL sterile IF-0a GN/GP Base inoculating fluid (IF-0), 0.24 mL 100× Dye B obtained from BIOLOG, and brought to a final volume of 24 mL with sterile distilled water in 50 mL Falcon tubes. Negative control PM1 and PM2A assays were done similarly for each dye minus bacterial cells to detect abiotic reactions. Fungal culture of each strain with a final absorbance of 0.2 (˜63% turbidity) was brought to a final volume of 24 mL with the FF-1F medium (BIOLOG). Microbial cell suspensions in tubes were gently shaken to achieve uniformity. One hundred microliters of the microbial cell suspension was added per well using a multichannel pipettor to the 96-well BIOLOG PM1 and PM2A MicroPlates that each contained 95 carbon sources and one water-only (negative control) well. All steps were performed under sterile conditions using biosafety cabinets.


MicroPlates were sealed in paper surgical tape (Dynarex, Orangeburg, N.Y.) to minimize plate edge effects, and incubated stationary at 24° C. in an enclosed container for a minimum of 72 hours. Absorbance at 590 nm was measured for all MicroPlates at least every 24 hours or at a defined interval (72 hours post-assay) to determine carbon substrate utilization for each strain. Measurements were normalized relative to the negative control (water only) well of each plate (Garland and Mills, 1991; Barua et al., 2010; Siemens et al., 2012; Blumenstein et al., 2015). Bacterial MicroPlates were also visually examined for the irreversible formation of violet color in wells indicating the reduction of the tetrazolium redox dye to formazan that result from cell respiration (Garland and Mills, 1991), and assessed against the negative control (no cells) PM1 and PM2A MicroPlates to detect any abiotic color changes potentially introduced by the medium and/or dyes (Borglin et al., 2012). Normalized absorbance values that were negative were considered as zero for subsequent analysis (Garland and Mills, 1991; Blumenstein et al., 2015) and a threshold value of 0.1 and above was used to indicate the ability of a particular microbial strain to use a given carbon substrate (Barua et al., 2010; Blumenstein et al., 2015). Fungal PM tests were measured as growth assays and visual observation of mycelial growth in each well was made.









TABLE V





Substrate utilization as determined by BIOLOG PM1 MicroPlates by bacterial


endophytes belonging to OTUs present in cereal seeds, fruit seeds, vegetable seeds, and oil seeds.





















Strain/Substrate
SYM00021b
SYM00044
SYM00057b
SYM00074
SYM00091
SYM00092d





1,2-Propanediol
NO
NO
NO
NO
NO
NO


2-Aminoethanol
NO
NO
NO
NO
NO
NO


2′-Deoxyadenosine
YES
YES
YES
YES
YES
YES


a-D-Glucose
YES
YES
YES
YES
YES
YES


a-D-Lactose
YES
YES
YES
YES
YES
YES


a-Hydroxybutyric acid
NO
NO
NO
NO
YES
NO


a-Hydroxyglutaric acid-g-
NO
NO
NO
NO
YES
NO


Lactone


a-Ketobutyric acid
NO
NO
NO
NO
YES
NO


a-Ketoglutaric acid
YES
NO
NO
NO
YES
NO


a-Methyl-D-Galactoside
YES
YES
YES
YES
YES
NO


Acetic acid
YES
YES
YES
YES
YES
YES


Acetoacetic acid
NO
NO
NO
NO
NO
NO


Adenosine
YES
YES
YES
YES
YES
YES


Adonitol
YES
YES
YES
YES
YES
NO


Ala-Gly
YES
YES
YES
YES
YES
YES


b-Methyl-D-Glucoside
YES
YES
YES
YES
YES
YES


Bromosuccinic acid
NO
NO
NO
YES
YES
YES


Citric acid
YES
YES
YES
YES
YES
YES


D-Alanine
YES
YES
YES
YES
YES
YES


D-Aspartic acid
NO
NO
NO
NO
NO
NO


D-Cellobiose
YES
YES
YES
YES
YES
YES


D-Fructose
YES
YES
YES
YES
YES
YES


D-Fructose-6-Phosphate
YES
YES
YES
YES
YES
YES


D-Galactonic acid-g-
YES
YES
YES
YES
YES
YES


Lactone


D-Galactose
YES
YES
YES
YES
YES
YES


D-Galacturonic acid
YES
YES
YES
YES
YES
YES


D-Gluconic acid
YES
YES
YES
YES
YES
YES


D-Glucosaminic acid
YES
YES
YES
NO
YES
YES


D-Glucose-1-Phosphate
YES
YES
YES
YES
YES
YES


D-Glucose-6-Phosphate
YES
YES
YES
YES
YES
YES


D-Glucuronic acid
YES
YES
YES
YES
YES
YES


D-Malic acid
NO
NO
NO
NO
YES
NO


D-Mannitol
YES
YES
YES
YES
YES
YES


D-Mannose
YES
YES
YES
YES
YES
YES


D-Melibiose
YES
YES
YES
YES
YES
YES


D-Psicose
YES
NO
NO
NO
YES
YES


D-Ribose
YES
YES
YES
YES
YES
YES


D-Saccharic acid
YES
YES
YES
YES
YES
YES


D-Serine
NO
NO
NO
NO
NO
NO


D-Sorbitol
YES
YES
YES
YES
YES
NO


D-Threonine
NO
NO
NO
NO
NO
NO


D-Trehalose
YES
YES
YES
YES
YES
YES


D-Xylose
YES
YES
YES
YES
YES
YES


DL-a-Glycerol Phosphate
YES
YES
YES
YES
YES
YES


DL-Malic acid
YES
YES
YES
YES
YES
YES


Dulcitol
YES
YES
YES
YES
NO
YES


Formic acid
YES
YES
YES
NO
YES
YES


Fumaric acid
YES
YES
YES
YES
YES
YES


Glucuronamide
NO
NO
NO
YES
NO
NO


Gly-Asp
NO
YES
YES
YES
NO
YES


Gly-Glu
NO
YES
YES
YES
NO
YES


Gly-Pro
NO
YES
YES
YES
YES
YES


Glycerol
YES
YES
YES
YES
YES
YES


Glycolic acid
NO
NO
NO
NO
YES
NO


Glyoxylic acid
NO
YES
YES
NO
NO
NO


Inosine
YES
YES
YES
YES
YES
YES


L-Alanine
YES
YES
YES
YES
YES
YES


L-Arabinose
YES
YES
YES
YES
YES
YES


L-Asparagine
YES
YES
YES
YES
YES
YES


L-Aspartic acid
YES
YES
YES
YES
YES
YES


L-Fucose
NO
NO
NO
NO
YES
NO


L-Galactonic acid-g-
YES
YES
YES
YES
YES
YES


Lactone


L-Glutamic acid
YES
YES
YES
YES
YES
YES


L-Glutamine
YES
YES
YES
YES
YES
YES


L-Lactic acid
YES
YES
YES
YES
YES
YES


L-Lyxose
NO
NO
NO
YES
YES
YES


L-Malic acid
YES
YES
YES
YES
YES
YES


L-Proline
YES
YES
YES
YES
YES
YES


L-Rhamnose
YES
YES
YES
YES
YES
YES


L-Serine
YES
YES
YES
YES
YES
YES


L-Threonine
NO
NO
NO
YES
YES
NO


Lactulose
NO
NO
NO
NO
YES
YES


m-Hydroxyphenyl Acetic
NO
YES
YES
YES
NO
NO


acid


m-Inositol
YES
NO
NO
NO
YES
YES


m-Tartaric acid
YES
NO
NO
NO
YES
YES


Maltose
YES
YES
YES
YES
YES
YES


Maltotriose
YES
YES
YES
YES
YES
YES


Methylpyruvate
YES
YES
YES
YES
YES
YES


Mono-Methylsuccinate
NO
NO
NO
NO
YES
NO


Mucic acid
YES
YES
YES
YES
YES
YES


N-Acetyl-D-Glucosamine
YES
YES
YES
YES
YES
YES


N-Acetyl-D-
NO
NO
NO
NO
NO
NO


Mannosamine


Negative Control
NO
NO
NO
NO
NO
NO


p-Hydroxyphenyl Acetic
NO
YES
YES
YES
YES
NO


acid


Phenylethylamine
NO
NO
NO
NO
NO
NO


Propionic acid
NO
NO
NO
NO
YES
NO


Pyruvic acid
YES
YES
YES
YES
YES
YES


Succinic acid
YES
YES
YES
YES
YES
YES


Sucrose
YES
YES
YES
YES
YES
YES


Thymidine
YES
YES
YES
YES
NO
YES


Tricarballylic acid
NO
NO
NO
NO
NO
NO


Tween 20
NO
NO
NO
YES
YES
YES


Tween 40
YES
NO
NO
YES
YES
YES


Tween 80
YES
NO
NO
YES
YES
YES


Tyramine
NO
NO
NO
NO
NO
NO


Uridine
NO
NO
NO
YES
YES
YES





Strain/Substrate
SYM00212
SYM00290
SYM00619
SYM00865
SYM00879
SYM00879b





1,2-Propanediol
NO
NO
NO
NO
NO
NO


2-Aminoethanol
NO
NO
NO
NO
NO
NO


2′-Deoxyadenosine
YES
NO
YES
YES
NO
YES


a-D-Glucose
YES
NO
YES
YES
YES
YES


a-D-Lactose
YES
NO
NO
YES
YES
YES


a-Hydroxybutyric acid
NO
YES
NO
NO
NO
YES


a-Hydroxyglutaric acid-g-
NO
NO
YES
YES
NO
YES


Lactone


a-Ketobutyric acid
NO
YES
YES
NO
NO
YES


a-Ketoglutaric acid
NO
NO
YES
YES
YES
YES


a-Methyl-D-Galactoside
YES
NO
NO
YES
YES
YES


Acetic acid
YES
YES
YES
YES
YES
YES


Acetoacetic acid
NO
NO
NO
NO
NO
NO


Adenosine
YES
NO
YES
YES
NO
YES


Adonitol
YES
NO
YES
YES
NO
YES


Ala-Gly
YES
NO
YES
YES
NO
YES


b-Methyl-D-Glucoside
YES
YES
YES
YES
YES
YES


Bromosuccinic acid
YES
YES
YES
YES
YES
YES


Citric acid
NO
NO
YES
YES
YES
YES


D-Alanine
YES
YES
YES
YES
NO
YES


D-Aspartic acid
NO
NO
NO
NO
NO
NO


D-Cellobiose
YES
NO
YES
YES
YES
YES


D-Fructose
YES
YES
YES
YES
YES
YES


D-Fructose-6-Phosphate
YES
NO
NO
YES
NO
YES


D-Galactonic acid-g-
NO
NO
NO
NO
NO
NO


Lactone


D-Galactose
YES
YES
NO
YES
NO
YES


D-Galacturonic acid
YES
NO
YES
YES
YES
YES


D-Gluconic acid
YES
YES
YES
YES
NO
YES


D-Glucosaminic acid
NO
NO
YES
YES
NO
YES


D-Glucose-1-Phosphate
YES
NO
NO
YES
NO
YES


D-Glucose-6-Phosphate
YES
YES
NO
YES
YES
YES


D-Glucuronic acid
YES
NO
YES
YES
NO
YES


D-Malic acid
NO
YES
YES
YES
NO
YES


D-Mannitol
YES
NO
YES
YES
YES
YES


D-Mannose
YES
YES
NO
YES
YES
YES


D-Melibiose
YES
NO
NO
YES
NO
YES


D-Psicose
NO
NO
NO
YES
NO
YES


D-Ribose
YES
YES
YES
YES
YES
YES


D-Saccharic acid
YES
YES
NO
YES
YES
YES


D-Serine
NO
NO
NO
NO
NO
NO


D-Sorbitol
NO
NO
NO
NO
NO
NO


D-Threonine
NO
NO
NO
NO
NO
NO


D-Trehalose
YES
YES
YES
YES
YES
YES


D-Xylose
YES
YES
YES
YES
NO
YES


DL-a-Glycerol Phosphate
YES
YES
YES
YES
NO
YES


DL-Malic acid
YES
YES
YES
YES
YES
YES


Dulcitol
NO
YES
NO
YES
NO
YES


Formic acid
NO
NO
NO
YES
YES
YES


Fumaric acid
YES
YES
YES
YES
YES
YES


Glucuronamide
NO
NO
NO
NO
NO
NO


Gly-Asp
YES
NO
NO
YES
NO
YES


Gly-Glu
YES
YES
YES
YES
YES
YES


Gly-Pro
YES
NO
YES
YES
YES
YES


Glycerol
YES
YES
YES
YES
NO
YES


Glycolic acid
NO
NO
NO
NO
NO
YES


Glyoxylic acid
NO
NO
NO
NO
NO
NO


Inosine
YES
NO
YES
YES
NO
YES


L-Alanine
YES
YES
NO
YES
NO
YES


L-Arabinose
YES
YES
YES
YES
YES
YES


L-Asparagine
YES
YES
YES
YES
NO
YES


L-Aspartic acid
YES
YES
YES
YES
YES
YES


L-Fucose
NO
NO
YES
NO
NO
YES


L-Galactonic acid-g-
YES
YES
YES
YES
YES
YES


Lactone


L-Glutamic acid
YES
YES
YES
YES
NO
YES


L-Glutamine
YES
YES
YES
YES
YES
YES


L-Lactic acid
YES
YES
YES
YES
YES
YES


L-Lyxose
YES
YES
NO
NO
YES
NO


L-Malic acid
YES
YES
YES
YES
YES
YES


L-Proline
YES
YES
YES
YES
YES
YES


L-Rhamnose
YES
NO
NO
NO
NO
YES


L-Serine
YES
NO
YES
YES
NO
YES


L-Threonine
NO
NO
NO
YES
NO
NO


Lactulose
YES
NO
YES
YES
YES
YES


m-Hydroxyphenyl Acetic
YES
NO
YES
YES
NO
YES


acid


m-Inositol
NO
NO
NO
YES
NO
YES


m-Tartaric acid
NO
NO
NO
YES
NO
YES


Maltose
YES
NO
YES
YES
YES
YES


Maltotriose
YES
NO
YES
YES
YES
YES


Methylpyruvate
YES
YES
YES
YES
YES
YES


Mono-Methylsuccinate
NO
YES
YES
YES
NO
YES


Mucic acid
NO
YES
NO
YES
NO
YES


N-Acetyl-D-Glucosamine
YES
YES
YES
YES
YES
YES


N-Acetyl-D-
YES
NO
NO
NO
NO
NO


Mannosamine


Negative Control
NO
NO
NO
NO
NO
NO


p-Hydroxyphenyl Acetic
YES
NO
YES
NO
NO
YES


acid


Phenylethylamine
NO
NO
NO
NO
NO
NO


Propionic acid
NO
NO
NO
YES
YES
YES


Pyruvic acid
YES
YES
YES
YES
YES
YES


Succinic acid
YES
YES
YES
YES
YES
YES


Sucrose
YES
NO
YES
YES
YES
YES


Thymidine
YES
NO
NO
YES
NO
YES


Tricarballylic acid
NO
NO
YES
NO
NO
YES


Tween 20
NO
YES
YES
YES
YES
YES


Tween 40
YES
YES
YES
YES
YES
YES


Tween 80
YES
YES
YES
YES
YES
YES


Tyramine
NO
NO
NO
NO
NO
NO


Uridine
YES
YES
YES
YES
YES
YES

















Strain/Substrate
SYM00906
SYM00965
SYM01004
SYM01022
SYM01158







1,2-Propanediol
NO
NO
YES
NO
NO



2-Aminoethanol
NO
NO
YES
NO
YES



2′-Deoxyadenosine
YES
YES
YES
YES
NO



a-D-Glucose
YES
YES
YES
YES
YES



a-D-Lactose
YES
YES
YES
YES
NO



a-Hydroxybutyric acid
YES
YES
NO
NO
YES



a-Hydroxyglutaric acid-g-
NO
YES
YES
YES
NO



Lactone



a-Ketobutyric acid
YES
YES
NO
NO
YES



a-Ketoglutaric acid
YES
YES
YES
YES
YES



a-Methyl-D-Galactoside
YES
YES
YES
YES
NO



Acetic acid
YES
YES
YES
YES
YES



Acetoacetic acid
NO
NO
NO
NO
NO



Adenosine
YES
YES
YES
YES
NO



Adonitol
NO
YES
YES
NO
YES



Ala-Gly
YES
YES
YES
YES
YES



b-Methyl-D-Glucoside
YES
YES
YES
YES
NO



Bromosuccinic acid
YES
YES
YES
YES
YES



Citric acid
YES
YES
YES
YES
YES



D-Alanine
YES
YES
YES
YES
YES



D-Aspartic acid
NO
NO
NO
NO
NO



D-Cellobiose
YES
YES
YES
YES
YES



D-Fructose
YES
YES
YES
YES
YES



D-Fructose-6-Phosphate
YES
YES
YES
YES
NO



D-Galactonic acid-g-
NO
YES
YES
YES
YES



Lactone



D-Galactose
YES
YES
YES
YES
YES



D-Galacturonic acid
NO
YES
YES
YES
NO



D-Gluconic acid
YES
YES
YES
YES
YES



D-Glucosaminic acid
NO
YES
YES
YES
YES



D-Glucose-1-Phosphate
NO
YES
YES
YES
NO



D-Glucose-6-Phosphate
NO
YES
YES
YES
NO



D-Glucuronic acid
YES
YES
YES
YES
YES



D-Malic acid
NO
YES
YES
YES
YES



D-Mannitol
YES
YES
YES
YES
NO



D-Mannose
YES
YES
YES
YES
YES



D-Melibiose
YES
YES
YES
YES
NO



D-Psicose
YES
YES
YES
YES
NO



D-Ribose
YES
YES
YES
YES
YES



D-Saccharic acid
NO
YES
YES
YES
NO



D-Serine
NO
NO
NO
NO
NO



D-Sorbitol
YES
YES
YES
YES
NO



D-Threonine
NO
NO
NO
NO
NO



D-Trehalose
YES
YES
YES
YES
YES



D-Xylose
YES
YES
YES
YES
YES



DL-a-Glycerol Phosphate
YES
YES
YES
YES
NO



DL-Malic acid
YES
YES
YES
YES
YES



Dulcitol
NO
YES
YES
NO
YES



Formic acid
NO
YES
YES
YES
NO



Fumaric acid
YES
YES
YES
YES
YES



Glucuronamide
NO
NO
NO
NO
NO



Gly-Asp
NO
YES
YES
NO
YES



Gly-Glu
YES
YES
YES
YES
YES



Gly-Pro
YES
YES
YES
YES
YES



Glycerol
YES
YES
YES
YES
NO



Glycolic acid
NO
YES
NO
YES
YES



Glyoxylic acid
NO
YES
NO
NO
NO



Inosine
YES
YES
YES
YES
NO



L-Alanine
YES
YES
YES
YES
YES



L-Arabinose
YES
YES
YES
YES
YES



L-Asparagine
YES
YES
YES
YES
YES



L-Aspartic acid
YES
YES
YES
YES
YES



L-Fucose
YES
YES
YES
YES
YES



L-Galactonic acid-g-
YES
YES
YES
YES
YES



Lactone



L-Glutamic acid
YES
YES
YES
YES
YES



L-Glutamine
YES
YES
YES
YES
YES



L-Lactic acid
YES
YES
YES
YES
YES



L-Lyxose
YES
YES
YES
NO
NO



L-Malic acid
YES
YES
YES
YES
YES



L-Proline
YES
YES
YES
YES
YES



L-Rhamnose
NO
YES
YES
NO
YES



L-Serine
YES
YES
YES
YES
YES



L-Threonine
YES
YES
YES
NO
NO



Lactulose
YES
YES
YES
YES
NO



m-Hydroxyphenyl Acetic
YES
YES
YES
YES
NO



acid



m-Inositol
NO
YES
YES
YES
YES



m-Tartaric acid
NO
YES
YES
YES
NO



Maltose
NO
YES
YES
YES
YES



Maltotriose
YES
YES
YES
YES
YES



Methylpyruvate
YES
YES
YES
YES
YES



Mono-Methylsuccinate
YES
YES
YES
YES
NO



Mucic acid
NO
YES
YES
YES
NO



N-Acetyl-D-Glucosamine
YES
YES
YES
YES
YES



N-Acetyl-D-
NO
NO
YES
NO
NO



Mannosamine



Negative Control
NO
NO
NO
NO
NO



p-Hydroxyphenyl Acetic
YES
YES
NO
YES
NO



acid



Phenylethylamine
NO
YES
NO
YES
NO



Propionic acid
YES
YES
YES
YES
YES



Pyruvic acid
YES
YES
YES
YES
YES



Succinic acid
YES
YES
YES
YES
YES



Sucrose
YES
YES
YES
YES
YES



Thymidine
NO
YES
NO
YES
NO



Tricarballylic acid
NO
YES
NO
YES
NO



Tween 20
YES
YES
YES
YES
NO



Tween 40
YES
YES
YES
YES
NO



Tween 80
YES
YES
YES
YES
YES



Tyramine
NO
YES
NO
NO
NO



Uridine
YES
YES
YES
YES
YES

















TABLE W





Substrate utilization as determined by BIOLOG PM1 MicroPlates by fungal


endophytes belonging to OTUs present in cereal seeds, fruit seeds, vegetable seeds, and oil seeds.
























SYM00157
SYM00300
SYM00301
SYM00577
SYM01314
SYM01324
SYM01326
SYM01329





1,2-Propanediol
YES
YES
NO
YES
YES
NO
NO
YES


2-Aminoethanol
YES
YES
YES
YES
YES
YES
YES
NO


2′-Deoxyadenosine
YES
YES
YES
YES
YES
YES
YES
YES


a-D-Glucose
YES
YES
YES
YES
YES
YES
YES
YES


a-D-Lactose
YES
YES
YES
YES
YES
YES
YES
YES


a-Hydroxybutyric acid
NO
YES
YES
NO
YES
YES
NO
NO


a-Hydroxyglutaric acid-g-Lactone
YES
NO
NO
NO
YES
YES
YES
NO


a-Ketobutyric acid
YES
YES
YES
YES
YES
YES
YES
NO


a-Ketoglutaric acid
YES
YES
YES
YES
YES
YES
YES
YES


a-Methyl-D-Galactoside
YES
YES
YES
YES
YES
YES
YES
YES


Acetic acid
YES
YES
YES
YES
YES
YES
YES
YES


Acetoacetic acid
YES
NO
YES
NO
YES
NO
YES
NO


Adenosine
YES
YES
YES
YES
YES
YES
YES
NO


Adonitol
YES
YES
YES
YES
YES
YES
YES
YES


Ala-Gly
YES
YES
YES
YES
YES
YES
YES
YES


b-Methyl-D-Glucoside
YES
YES
YES
YES
YES
YES
YES
YES


Bromosuccinic acid
YES
YES
YES
YES
YES
YES
YES
NO


Citric acid
YES
YES
YES
YES
YES
YES
YES
YES


D-Alanine
YES
YES
YES
YES
YES
NO
YES
NO


D-Aspartic acid
NO
YES
NO
NO
YES
YES
YES
YES


D-Cellobiose
YES
YES
YES
YES
YES
YES
YES
YES


D-Fructose
YES
YES
YES
YES
YES
YES
YES
YES


D-Fructose-6-Phosphate
NO
YES
NO
NO
YES
NO
YES
YES


D-Galactonic acid-g-Lactone
NO
NO
NO
NO
NO
NO
NO
NO


D-Galactose
YES
YES
YES
YES
YES
YES
YES
YES


D-Galacturonic acid
YES
YES
YES
YES
YES
YES
YES
YES


D-Gluconic acid
YES
NO
YES
NO
YES
YES
YES
YES


D-Glucosaminic acid
YES
YES
YES
YES
YES
YES
YES
YES


D-Glucose-1-Phosphate
NO
YES
NO
NO
NO
NO
NO
NO


D-Glucose-6-Phosphate
NO
YES
NO
NO
YES
NO
YES
NO


D-Glucuronic acid
YES
YES
YES
YES
YES
YES
YES
YES


D-Malic acid
NO
YES
YES
YES
YES
YES
YES
YES


D-Mannitol
YES
YES
YES
YES
YES
YES
YES
YES


D-Mannose
YES
YES
YES
YES
YES
YES
YES
YES


D-Melibiose
YES
YES
YES
YES
YES
YES
YES
YES


D-Psicose
YES
YES
YES
NO
NO
YES
YES
YES


D-Ribose
YES
YES
YES
YES
YES
YES
YES
YES


D-Saccharic acid
YES
YES
YES
NO
YES
YES
NO
YES


D-Serine
YES
YES
YES
YES
YES
YES
YES
NO


D-Sorbitol
YES
YES
YES
YES
YES
YES
YES
YES


D-Threonine
YES
NO
NO
NO
YES
NO
YES
YES


D-Trehalose
YES
YES
YES
YES
YES
YES
YES
YES


D-Xylose
YES
YES
YES
YES
YES
YES
YES
NO


DL-a-Glycerol Phosphate
NO
NO
NO
NO
YES
NO
YES
NO


DL-Malic acid
YES
YES
YES
YES
YES
YES
YES
YES


Dulcitol
YES
YES
YES
YES
YES
YES
YES
YES


Formic acid
YES
NO
YES
NO
YES
YES
YES
NO


Fumaric acid
YES
YES
YES
YES
YES
YES
YES
YES


Glucuronamide
NO
NO
NO
NO
NO
NO
YES
NO


Gly-Asp
YES
YES
YES
YES
YES
YES
YES
YES


Gly-Glu
YES
YES
YES
YES
YES
YES
YES
YES


Gly-Pro
YES
YES
YES
YES
YES
YES
YES
YES


Glycerol
YES
YES
YES
YES
YES
YES
YES
NO


Glycolic acid
NO
NO
NO
NO
YES
YES
NO
NO


Glyoxylic acid
YES
NO
NO
NO
YES
YES
NO
NO


Inosine
YES
YES
YES
NO
YES
YES
YES
NO


L-Alanine
YES
YES
YES
YES
YES
YES
YES
YES


L-Arabinose
YES
YES
YES
YES
YES
YES
YES
YES


L-Asparagine
YES
YES
YES
YES
YES
YES
YES
NO


L-Aspartic acid
YES
YES
YES
YES
YES
YES
YES
NO


L-Fucose
YES
YES
YES
YES
YES
YES
YES
YES


L-Galactonic acid-g-Lactone
YES
YES
YES
YES
YES
YES
YES
YES


L-Glulamic acid
YES
YES
YES
YES
YES
YES
YES
YES


L-Glutamine
YES
YES
YES
YES
YES
YES
YES
YES


L-Lactic acid
YES
YES
YES
YES
YES
YES
YES
NO


L-Lyxose
YES
YES
YES
YES
YES
NO
YES
NO


L-Malic acid
YES
YES
YES
YES
YES
YES
YES
YES


L-Proline
YES
YES
YES
YES
YES
YES
YES
YES


L-Rhamnose
YES
YES
YES
YES
YES
YES
YES
YES


L-Serine
YES
YES
YES
YES
YES
YES
YES
YES


L-Threonine
YES
YES
YES
YES
YES
YES
YES
YES


Lactulose
YES
YES
YES
YES
YES
YES
YES
YES


m-Hydroxyphenyl Acetic acid
YES
YES
YES
NO
YES
YES
NO
YES


m-Inositol
YES
YES
YES
YES
YES
YES
YES
YES


m-Tartaric acid
YES
YES
YES
NO
YES
YES
YES
YES


Maltose
YES
YES
YES
YES
YES
YES
YES
YES


Maltotriose
YES
YES
YES
YES
YES
YES
YES
YES


Methylpyruvate
YES
YES
YES
YES
YES
YES
YES
NO


Mono-Methylsuccinate
YES
YES
YES
YES
YES
YES
YES
NO


Mucic acid
YES
YES
YES
NO
YES
YES
NO
YES


N-Acetyl-D-Glucosamine
YES
YES
YES
YES
YES
YES
YES
YES


N-Acetyl-D-Mannosamine
NO
YES
NO
NO
YES
NO
YES
NO


Negative Control
NO
NO
NO
NO
NO
NO
NO
NO


p-Hydroxyphenyl Acetic acid
YES
NO
YES
YES
YES
YES
NO
NO


Phenylethylamine
NO
NO
NO
NO
YES
NO
YES
NO


Propionic acid
YES
YES
YES
YES
YES
YES
YES
NO


Pyruvic acid
YES
YES
YES
YES
YES
YES
YES
YES


Succinic acid
YES
YES
YES
YES
YES
YES
YES
YES


Sucrose
YES
YES
YES
YES
YES
YES
YES
YES


Thymidine
YES
NO
NO
NO
NO
YES
YES
NO


Tricarballylic acid
NO
NO
YES
YES
YES
YES
NO
NO


Tween 20
YES
YES
YES
YES
YES
YES
YES
NO


Tween 40
YES
YES
YES
YES
YES
YES
YES
YES


Tween 80
YES
YES
YES
YES
YES
YES
YES
YES


Tyramine
YES
YES
YES
YES
YES
YES
YES
YES


Uridine
YES
NO
YES
YES
YES
NO
YES
YES






SYM01330
SYM01331
SYM12462
SYM15774
SYM15783
SYM15810
SYM15879
SYM15880





1,2-Propanediol
NO
NO
YES
NO
NO
YES
YES
NO


2-Aminoethanol
NO
NO
NO
NO
YES
YES
YES
YES


2′-Deoxyadenosine
NO
NO
NO
YES
YES
YES
YES
YES


a-D-Glucose
YES
YES
YES
YES
YES
YES
YES
YES


a-D-Lactose
YES
YES
YES
YES
YES
YES
YES
YES


a-Hydroxybutyric acid
YES
NO
NO
NO
YES
YES
YES
NO


a-Hydroxyglutaric acid-g-Lactone
YES
NO
YES
YES
YES
NO
YES
NO


a-Ketobutyric acid
YES
NO
YES
YES
YES
YES
YES
YES


a-Ketoglutaric acid
YES
YES
YES
NO
YES
YES
YES
YES


a-Methyl-D-Galactoside
NO
YES
YES
YES
YES
YES
YES
YES


Acetic acid
NO
YES
YES
NO
YES
YES
YES
YES


Acetoacetic acid
NO
NO
YES
YES
YES
NO
YES
NO


Adenosine
NO
YES
YES
NO
YES
YES
YES
YES


Adonitol
NO
YES
YES
YES
YES
YES
YES
YES


Ala-Gly
YES
YES
YES
YES
YES
YES
YES
YES


b-Methyl-D-Glucoside
YES
YES
YES
YES
YES
YES
YES
YES


Bromosuccinic acid
YES
YES
YES
YES
YES
YES
YES
YES


Citric acid
YES
NO
YES
NO
YES
NO
YES
YES


D-Alanine
NO
NO
NO
NO
NO
YES
YES
YES


D-Aspartic acid
NO
YES
YES
YES
YES
YES
YES
NO


D-Cellobiose
YES
YES
YES
YES
YES
YES
YES
YES


D-Fructose
YES
YES
YES
YES
YES
YES
YES
YES


D-Fructose-6-Phosphate
YES
NO
NO
YES
NO
YES
YES
NO


D-Galactonic acid-g-Lactone
NO
NO
YES
NO
NO
NO
YES
NO


D-Galactose
YES
YES
YES
YES
YES
YES
YES
YES


D-Galacturonic acid
YES
YES
YES
YES
YES
YES
YES
YES


D-Gluconic acid
YES
YES
YES
YES
YES
YES
YES
YES


D-Glucosaminic acid
NO
NO
YES
YES
YES
NO
NO
NO


D-Glucose-1-Phosphate
YES
NO
YES
YES
NO
NO
NO
NO


D-Glucose-6-Phosphate
YES
NO
YES
YES
YES
YES
YES
NO


D-Glucuronic acid
YES
YES
YES
YES
YES
YES
YES
YES


D-Malic acid
NO
YES
NO
NO
YES
YES
YES
YES


D-Mannitol
YES
YES
YES
NO
YES
YES
YES
YES


D-Mannose
YES
YES
YES
YES
YES
YES
YES
YES


D-Melibiose
YES
YES
YES
YES
YES
YES
YES
YES


D-Psicose
NO
YES
NO
NO
YES
YES
YES
YES


D-Ribose
YES
YES
YES
YES
YES
YES
YES
YES


D-Saccharic acid
YES
YES
YES
NO
YES
YES
YES
YES


D-Serine
NO
NO
NO
NO
YES
YES
YES
NO


D-Sorbitol
YES
YES
YES
NO
YES
YES
YES
YES


D-Threonine
NO
YES
YES
YES
YES
NO
YES
NO


D-Trehalose
YES
YES
YES
YES
YES
YES
YES
YES


D-Xylose
YES
YES
YES
NO
YES
YES
YES
YES


DL-a-Glycerol Phosphate
YES
NO
NO
YES
YES
YES
YES
YES


DL-Malic acid
NO
YES
YES
YES
YES
YES
YES
YES


Dulcitol
NO
YES
YES
NO
YES
YES
YES
YES


Formic acid
NO
NO
NO
YES
NO
YES
YES
NO


Fumaric acid
NO
YES
YES
YES
YES
YES
YES
YES


Glucuronamide
NO
NO
NO
NO
NO
NO
YES
NO


Gly-Asp
NO
YES
YES
YES
YES
YES
YES
YES


Gly-Glu
YES
YES
YES
YES
YES
YES
YES
YES


Gly-Pro
YES
YES
YES
YES
YES
YES
YES
YES


Glycerol
YES
NO
YES
YES
YES
YES
YES
YES


Glycolic acid
YES
NO
NO
YES
YES
YES
NO
YES


Glyoxylic acid
NO
NO
YES
NO
YES
YES
YES
YES


Inosine
NO
YES
YES
NO
NO
YES
YES
YES


L-Alanine
YES
YES
YES
YES
YES
YES
YES
YES


L-Arabinose
YES
YES
YES
NO
YES
YES
YES
YES


L-Asparagine
YES
YES
YES
YES
YES
YES
YES
YES


L-Aspartic acid
NO
YES
YES
YES
YES
YES
YES
YES


L-Fucose
YES
YES
NO
YES
NO
YES
YES
NO


L-Galactonic acid-g-Lactone
YES
YES
YES
YES
YES
YES
YES
YES


L-Glulamic acid
NO
YES
YES
YES
YES
YES
YES
YES


L-Glutamine
YES
YES
YES
YES
YES
YES
YES
YES


L-Lactic acid
NO
YES
YES
YES
YES
YES
YES
YES


L-Lyxose
YES
YES
NO
NO
YES
YES
YES
YES


L-Malic acid
YES
YES
YES
YES
YES
YES
YES
YES


L-Proline
YES
YES
YES
NO
YES
YES
YES
YES


L-Rhamnose
YES
YES
YES
YES
YES
YES
YES
YES


L-Serine
YES
YES
YES
YES
YES
YES
YES
YES


L-Threonine
NO
NO
YES
YES
YES
YES
YES
YES


Lactulose
NO
YES
YES
YES
YES
YES
YES
NO


m-Hydroxyphenyl Acetic acid
NO
NO
YES
YES
YES
NO
NO
YES


m-Inositol
NO
YES
YES
YES
YES
YES
YES
YES


m-Tartaric acid
NO
YES
NO
NO
YES
YES
YES
NO


Maltose
YES
YES
YES
YES
YES
YES
YES
YES


Maltotriose
YES
YES
YES
YES
YES
YES
YES
YES


Methylpyruvate
YES
YES
YES
YES
YES
YES
YES
YES


Mono-Methylsuccinate
YES
YES
YES
YES
YES
YES
YES
YES


Mucic acid
NO
YES
YES
YES
YES
YES
YES
YES


N-Acetyl-D-Glucosamine
YES
YES
YES
YES
YES
YES
YES
YES


N-Acetyl-D-Mannosamine
YES
NO
NO
YES
YES
NO
NO
NO


Negative Control
NO
NO
NO
NO
NO
NO
NO
NO


p-Hydroxyphenyl Acetic acid
YES
YES
YES
NO
YES
YES
YES
YES


Phenylethylamine
NO
NO
NO
NO
NO
NO
NO
YES


Propionic acid
NO
NO
YES
YES
YES
YES
YES
YES


Pyruvic acid
NO
YES
YES
YES
YES
YES
YES
YES


Succinic acid
NO
YES
YES
YES
YES
YES
YES
YES


Sucrose
YES
YES
YES
YES
YES
YES
YES
YES


Thymidine
NO
NO
YES
NO
NO
YES
YES
NO


Tricarballylic acid
NO
NO
NO
YES
YES
YES
NO
NO


Tween 20
YES
YES
YES
YES
YES
YES
YES
YES


Tween 40
YES
YES
YES
YES
YES
YES
YES
YES


Tween 80
YES
YES
YES
YES
YES
YES
YES
YES


Tyramine
NO
YES
YES
NO
YES
YES
YES
YES


Uridine
NO
NO
NO
NO
NO
YES
YES
YES
















TABLE X





Substrate utilization as determined by BIOLOG PM2 MicroPlates by bacterial endophytes


belonging to OTUs present in cereal seeds, fruit seeds, vegetable seeds, and oil seeds.

















Substrate
















Strain
SYM00021b
SYM00044
SYM00057b
SYM00074
SYM00091
SYM00092d
SYM00212
SYM00290
SYM00619





2-Deoxy-D-Ribose
NO
YES
YES
YES
YES
NO
YES
YES
YES


2-Hydroxybenzoic
NO
NO
NO
NO
NO
NO
NO
NO
NO


acid


2,3-Butanediol
YES
NO
NO
NO
NO
NO
NO
NO
NO


2,3-Butanedione
NO
NO
NO
NO
NO
NO
NO
NO
NO


3-Hydroxy-2-
NO
NO
NO
YES
NO
NO
NO
NO
NO


butanone


3-Methylglucose
NO
NO
NO
NO
NO
YES
NO
NO
NO


3-O-b-D-
YES
YES
YES
YES
YES
YES
NO
YES
NO


Galactopyranosyl-


D-Arabinose


4-Hydroxybenzoic
NO
NO
NO
NO
YES
NO
NO
NO
NO


acid


5-Keto-D-Gluconic
YES
YES
YES
NO
NO
YES
YES
YES
NO


acid


a-Cyclodextrin
NO
NO
NO
YES
YES
YES
NO
NO
YES


a-Keto-Valeric acid
NO
NO
NO
NO
NO
NO
NO
YES
NO


a-Methyl-D-
NO
NO
NO
NO
YES
YES
NO
NO
YES


Glucoside


a-Methyl-D-
NO
NO
NO
NO
NO
NO
NO
NO
NO


Mannoside


Acetamide
YES
NO
NO
NO
NO
NO
NO
NO
NO


Amygdalin
YES
YES
YES
YES
YES
YES
NO
YES
YES


Arbutin
YES
YES
YES
YES
YES
YES
YES
NO
NO


b-Cyclodextrin
NO
NO
NO
NO
YES
YES
NO
YES
YES


b-D-Allose
NO
NO
NO
NO
NO
NO
NO
NO
NO


b-Hydroxybutyric
YES
NO
NO
NO
YES
NO
NO
YES
NO


acid


b-Methyl-D-
YES
YES
YES
YES
YES
YES
YES
NO
YES


Galactoside


b-Methyl-D-
NO
NO
NO
YES
NO
NO
NO
NO
NO


Glucuronic acid


b-Methyl-D-
NO
NO
NO
NO
NO
NO
NO
NO
NO


Xyloside


Butyric acid
NO
NO
NO
YES
NO
NO
NO
YES
NO


Capric acid
NO
NO
NO
NO
NO
NO
NO
NO
NO


Caproic acid
NO
NO
NO
NO
NO
NO
NO
YES
NO


Chondroitin Sulfate
YES
NO
NO
YES
YES
NO
NO
NO
NO


C


Citraconic acid
NO
NO
NO
NO
NO
YES
NO
NO
NO


Citramalic acid
YES
NO
NO
NO
NO
NO
NO
NO
NO


d-Amino Valeric
NO
NO
NO
NO
YES
NO
NO
NO
NO


acid


D-Arabinose
NO
NO
NO
NO
YES
YES
YES
YES
NO


D-Arabitol
YES
YES
YES
YES
YES
YES
YES
NO
YES


D-Fucose
YES
YES
YES
NO
YES
YES
NO
NO
NO


D-Glucosamine
YES
YES
YES
YES
YES
YES
YES
YES
YES


D-Lactic acid
NO
NO
NO
YES
NO
NO
NO
YES
NO


Methyl Ester


D-Lactitol
NO
NO
NO
YES
YES
NO
NO
NO
NO


D-Melezitose
NO
NO
NO
NO
NO
NO
YES
NO
NO


D-Raffinose
YES
YES
YES
YES
YES
NO
YES
NO
NO


D-Ribono-1,4-
YES
NO
NO
NO
NO
YES
NO
NO
NO


Lactone


D-Tagatose
NO
NO
NO
NO
NO
NO
NO
NO
NO


D-Tartaric acid
YES
NO
NO
YES
NO
NO
NO
NO
NO


D,L-Carnitine
NO
NO
NO
NO
YES
NO
NO
NO
NO


D,L-Octopamine
NO
NO
NO
NO
NO
NO
NO
NO
NO


Dextrin
YES
YES
YES
YES
YES
YES
YES
YES
YES


Dihydroxyacetone
NO
NO
NO
YES
YES
YES
YES
YES
YES


g-Amino-N-Butyric
YES
NO
NO
NO
YES
YES
NO
NO
NO


acid


g-Cyclodextrin
NO
NO
NO
NO
NO
NO
NO
NO
NO


g-Hydroxybutyric
NO
NO
NO
NO
NO
NO
NO
NO
NO


acid


Gelatin
NO
NO
NO
YES
YES
NO
NO
YES
NO


Gentiobiose
YES
YES
YES
YES
YES
YES
YES
NO
YES


Glycine
NO
NO
NO
YES
NO
NO
NO
NO
NO


Glycogen
NO
YES
YES
YES
NO
YES
YES
YES
YES


Hydroxy-L-Proline
NO
NO
NO
NO
YES
NO
NO
NO
NO


i-Erythritol
YES
NO
NO
NO
YES
YES
YES
NO
NO


Inulin
NO
NO
NO
NO
NO
NO
NO
NO
NO


Itaconic acid
NO
NO
NO
NO
YES
NO
NO
NO
NO


L-Alaninamide
YES
NO
NO
YES
YES
YES
NO
YES
NO


L-Arabitol
NO
NO
NO
NO
YES
YES
NO
NO
NO


L-Arginine
YES
YES
YES
YES
YES
YES
NO
NO
NO


L-Glucose
NO
NO
NO
NO
NO
NO
NO
NO
NO


L-Histidine
YES
NO
NO
YES
YES
YES
YES
NO
NO


L-Homoserine
NO
NO
NO
NO
NO
NO
NO
NO
NO


L-Isoleucine
NO
NO
NO
NO
YES
NO
NO
NO
NO


L-Leucine
YES
NO
NO
NO
NO
NO
NO
NO
NO


L-Lysine
NO
NO
NO
NO
YES
NO
NO
NO
NO


L-Methionine
NO
NO
NO
NO
NO
YES
NO
NO
NO


L-Ornithine
YES
YES
YES
YES
YES
YES
YES
YES
NO


L-Phenylalanine
YES
NO
NO
YES
NO
NO
YES
NO
NO


L-Pyroglutamic acid
YES
NO
NO
YES
NO
YES
NO
NO
NO


L-Sorbose
NO
NO
NO
NO
NO
NO
NO
NO
NO


L-Tartaric acid
YES
YES
YES
NO
NO
YES
YES
NO
NO


L-Valine
NO
NO
NO
NO
NO
NO
NO
NO
NO


Laminarin
NO
NO
NO
NO
YES
NO
NO
YES
NO


Malonic acid
YES
NO
NO
YES
NO
NO
YES
NO
NO


Maltitol
YES
NO
NO
NO
YES
NO
NO
NO
NO


Mannan
NO
NO
NO
YES
NO
YES
YES
YES
NO


Melibionic acid
YES
YES
YES
YES
YES
NO
NO
YES
NO


N-Acetyl-D-
YES
NO
NO
NO
NO
NO
NO
NO
NO


Galactosamine


N-Acetyl-D-
NO
NO
NO
NO
NO
NO
NO
NO
NO


Glucosaminitol


N-Acetyl-L-
NO
NO
NO
YES
NO
YES
NO
NO
NO


Glutamic acid


N-Acetyl-
NO
YES
YES
YES
NO
NO
YES
NO
NO


Neuraminic acid


Negative Control. 1
NO
NO
NO
NO
NO
NO
NO
NO
NO


Oxalic acid
NO
NO
NO
NO
NO
NO
NO
NO
NO


Oxalomalic acid
NO
NO
NO
NO
YES
YES
NO
YES
NO


Palatinose
YES
NO
NO
NO
YES
NO
NO
NO
YES


Pectin
YES
YES
YES
YES
YES
YES
YES
YES
NO


Putrescine
YES
NO
NO
YES
NO
NO
NO
NO
NO


Quinic acid
YES
NO
NO
NO
YES
YES
NO
NO
NO


Salicin
YES
YES
YES
YES
YES
YES
YES
NO
YES


Sebacic acid
YES
NO
NO
NO
NO
NO
NO
YES
YES


sec-Butylamine
NO
NO
NO
NO
NO
NO
NO
NO
NO


Sedoheptulosan
NO
NO
NO
NO
NO
NO
NO
NO
NO


Sorbic acid
NO
NO
NO
NO
NO
NO
NO
YES
NO


Stachyose
NO
NO
NO
NO
YES
NO
NO
NO
NO


Succinamic acid
YES
YES
YES
YES
YES
YES
YES
YES
NO


Turanose
YES
NO
NO
NO
YES
YES
NO
NO
YES


Xylitol
NO
NO
NO
NO
YES
NO
NO
NO
NO












Substrate

















Strain
SYM00865
SYM00879
SYM00879b
SYM00906
SYM00965
SYM01004
SYM01022
SYM01158







2-Deoxy-D-Ribose
YES
YES
YES
YES
YES
NO
YES
YES



2-Hydroxybenzoic
NO
NO
NO
NO
NO
NO
NO
NO



acid



2,3-Butanediol
NO
NO
YES
NO
YES
YES
NO
YES



2,3-Butanedione
NO
NO
NO
NO
NO
NO
NO
NO



3-Hydroxy-2-
NO
NO
NO
NO
NO
NO
YES
YES



butanone



3-Methylglucose
NO
NO
YES
NO
YES
YES
YES
YES



3-O-b-D-
YES
YES
YES
YES
YES
YES
YES
YES



Galactopyranosyl-



D-Arabinose



4-Hydroxybenzoic
NO
NO
NO
NO
NO
YES
NO
YES



acid



5-Keto-D-Gluconic
YES
YES
YES
NO
YES
YES
YES
YES



acid



a-Cyclodextrin
YES
NO
YES
NO
YES
YES
YES
NO



a-Keto-Valeric acid
NO
NO
NO
NO
YES
NO
YES
YES



a-Methyl-D-
NO
NO
NO
YES
YES
YES
YES
YES



Glucoside



a-Methyl-D-
NO
NO
YES
NO
NO
NO
NO
NO



Mannoside



Acetamide
NO
YES
NO
NO
YES
NO
NO
NO



Amygdalin
YES
YES
YES
YES
YES
YES
YES
YES



Arbutin
YES
YES
YES
YES
YES
YES
YES
YES



b-Cyclodextrin
NO
NO
YES
NO
YES
YES
YES
NO



b-D-Allose
NO
NO
NO
NO
YES
NO
NO
NO



b-Hydroxybutyric
NO
YES
YES
YES
YES
YES
YES
YES



acid



b-Methyl-D-
YES
YES
YES
YES
YES
YES
YES
YES



Galactoside



b-Methyl-D-
NO
NO
NO
NO
NO
NO
YES
YES



Glucuronic acid



b-Methyl-D-
NO
NO
YES
NO
YES
YES
NO
YES



Xyloside



Butyric acid
YES
YES
YES
YES
YES
YES
YES
YES



Capric acid
NO
NO
NO
NO
NO
NO
NO
NO



Caproic acid
NO
NO
NO
NO
NO
NO
NO
YES



Chondroitin Sulfate
YES
YES
YES
YES
YES
NO
YES
YES



C



Citraconic acid
NO
NO
YES
NO
YES
YES
NO
YES



Citramalic acid
NO
NO
YES
NO
YES
YES
YES
YES



d-Amino Valeric
NO
NO
NO
NO
YES
NO
YES
YES



acid



D-Arabinose
NO
YES
YES
YES
YES
YES
NO
YES



D-Arabitol
YES
NO
YES
NO
YES
YES
YES
YES



D-Fucose
NO
NO
NO
NO
YES
YES
NO
YES



D-Glucosamine
YES
YES
YES
YES
YES
YES
YES
YES



D-Lactic acid
YES
YES
NO
NO
NO
YES
YES
YES



Methyl Ester



D-Lactitol
YES
YES
NO
YES
YES
YES
YES
YES



D-Melezitose
NO
NO
YES
YES
YES
YES
YES
YES



D-Raffinose
YES
NO
YES
YES
YES
YES
YES
YES



D-Ribono-1,4-
NO
NO
YES
YES
YES
YES
NO
YES



Lactone



D-Tagatose
YES
NO
YES
NO
YES
YES
NO
YES



D-Tartaric acid
NO
NO
NO
NO
NO
YES
NO
YES



D,L-Carnitine
NO
NO
NO
NO
YES
YES
NO
YES



D,L-Octopamine
NO
NO
NO
NO
NO
NO
YES
NO



Dextrin
YES
YES
YES
YES
YES
YES
YES
YES



Dihydroxyacetone
YES
YES
YES
YES
YES
YES
YES
YES



g-Amino-N-Butyric
YES
NO
YES
NO
YES
YES
YES
YES



acid



g-Cyclodextrin
YES
NO
YES
NO
YES
NO
YES
YES



g-Hydroxybutyric
NO
YES
YES
NO
YES
YES
YES
YES



acid



Gelatin
YES
YES
YES
YES
YES
YES
YES
YES



Gentiobiose
YES
YES
YES
YES
YES
YES
YES
YES



Glycine
NO
NO
NO
NO
YES
NO
YES
YES



Glycogen
YES
NO
YES
YES
YES
YES
YES
YES



Hydroxy-L-Proline
YES
NO
YES
NO
YES
YES
YES
YES



i-Erythritol
NO
YES
NO
NO
YES
YES
NO
YES



Inulin
YES
NO
NO
NO
NO
NO
YES
YES



Itaconic acid
NO
NO
YES
YES
YES
NO
YES
YES



L-Alaninamide
YES
YES
YES
YES
YES
NO
YES
YES



L-Arabitol
NO
NO
YES
NO
YES
YES
NO
YES



L-Arginine
YES
NO
YES
NO
YES
YES
YES
YES



L-Glucose
NO
NO
NO
NO
NO
NO
NO
NO



L-Histidine
YES
NO
YES
YES
YES
YES
YES
YES



L-Homoserine
NO
NO
NO
NO
YES
NO
YES
NO



L-Isoleucine
YES
NO
YES
YES
YES
YES
YES
YES



L-Leucine
YES
YES
YES
YES
YES
YES
YES
YES



L-Lysine
YES
NO
YES
NO
YES
YES
YES
YES



L-Methionine
NO
NO
NO
NO
NO
NO
NO
NO



L-Ornithine
YES
NO
YES
YES
YES
YES
YES
YES



L-Phenylalanine
YES
NO
YES
YES
YES
NO
YES
NO



L-Pyroglutamic acid
NO
NO
YES
YES
YES
YES
YES
YES



L-Sorbose
NO
NO
NO
NO
NO
NO
NO
NO



L-Tartaric acid
NO
YES
NO
NO
NO
NO
YES
YES



L-Valine
YES
NO
YES
YES
YES
NO
YES
YES



Laminarin
YES
YES
YES
YES
YES
YES
YES
YES



Malonic acid
YES
YES
NO
YES
YES
YES
NO
YES



Maltitol
YES
YES
NO
YES
YES
YES
YES
YES



Mannan
NO
NO
NO
YES
YES
YES
NO
YES



Melibionic acid
YES
NO
YES
NO
YES
YES
YES
YES



N-Acetyl-D-
YES
YES
YES
YES
YES
YES
YES
YES



Galactosamine



N-Acetyl-D-
NO
NO
NO
NO
NO
NO
NO
YES



Glucosaminitol



N-Acetyl-L-
YES
NO
YES
YES
YES
NO
YES
YES



Glutamic acid



N-Acetyl-
NO
NO
YES
YES
YES
NO
NO
YES



Neuraminic acid



Negative Control. 1
NO
NO
NO
NO
NO
NO
NO
NO



Oxalic acid
NO
YES
NO
NO
NO
YES
NO
NO



Oxalomalic acid
YES
YES
YES
YES
YES
YES
YES
YES



Palatinose
YES
YES
YES
YES
YES
YES
YES
YES



Pectin
YES
YES
YES
YES
YES
YES
YES
YES



Putrescine
NO
NO
YES
YES
YES
YES
YES
YES



Quinic acid
YES
NO
YES
NO
YES
YES
YES
YES



Salicin
YES
YES
YES
YES
YES
YES
YES
YES



Sebacic acid
NO
NO
YES
NO
YES
NO
YES
YES



sec-Butylamine
NO
NO
NO
NO
NO
NO
NO
NO



Sedoheptulosan
NO
NO
NO
NO
NO
NO
NO
NO



Sorbic acid
YES
NO
YES
YES
YES
NO
YES
YES



Stachyose
NO
NO
NO
NO
YES
YES
YES
YES



Succinamic acid
YES
YES
YES
YES
YES
YES
YES
YES



Turanose
YES
YES
YES
YES
YES
YES
YES
YES



Xylitol
NO
NO
YES
NO
YES
YES
NO
NO

















TABLE Y





Substrate utilization as determined by BIOLOG PM2 MicroPlates by fungal endophytes belonging


to OTUs present in cereal seeds, fruit seeds, vegetable seeds, and oil seeds.

















Substrate















Strain
SYM00157
SYM00300
SYM00301
SYM00577
SYM01314
SYM01324
SYM01326
SYM01329





2-Deoxy-D-Ribose
YES
NO
NO
NO
YES
NO
NO
NO


2-Hydroxybenzoic acid
YES
YES
YES
YES
YES
YES
YES
NO


2,3-Butanediol
NO
NO
YES
NO
NO
YES
NO
NO


2,3-Butanedione
NO
NO
YES
NO
NO
YES
NO
NO


3-Hydroxy-2-butanone
NO
NO
NO
NO
NO
YES
NO
NO


3-Methylglucose
YES
NO
YES
YES
NO
NO
NO
YES


3-O-b-D-
YES
YES
YES
YES
YES
YES
NO
YES


Galactopyranosyl-D-


Arabinose


4-Hydroxybenzoic acid
YES
YES
YES
YES
YES
YES
YES
YES


5-Keto-D-Gluconic acid
NO
NO
YES
NO
YES
YES
YES
NO


a-Cyclodextrin
YES
YES
YES
YES
YES
YES
YES
YES


a-Keto-Valeric acid
YES
YES
YES
YES
YES
YES
YES
YES


a-Methyl-D-Glucoside
YES
YES
YES
YES
YES
YES
YES
YES


a-Methyl-D-Mannoside
YES
NO
YES
NO
NO
YES
YES
NO


Acetamide
YES
YES
YES
NO
NO
NO
NO
NO


Amygdalin
YES
YES
YES
YES
YES
YES
YES
YES


Arbutin
YES
YES
YES
YES
YES
YES
YES
YES


b-Cyclodextrin
YES
YES
YES
NO
NO
YES
YES
NO


b-D-Allose
NO
NO
YES
NO
NO
NO
YES
NO


b-Hydroxybutyric acid
YES
YES
YES
YES
YES
YES
YES
YES


b-Methyl-D-Galactoside
YES
YES
YES
YES
YES
YES
YES
YES


b-Methyl-D-Glucuronic
YES
NO
NO
NO
YES
NO
NO
NO


acid


b-Methyl-D-Xyloside
NO
NO
YES
NO
YES
YES
YES
NO


Butyric acid
YES
YES
YES
YES
YES
YES
YES
YES


Capric acid
NO
NO
NO
NO
NO
NO
NO
NO


Caproic acid
NO
YES
YES
YES
YES
YES
YES
NO


Chondroitin Sulfate C
YES
NO
YES
NO
YES
YES
NO
NO


Citraconic acid
YES
NO
YES
NO
YES
YES
NO
NO


Citramalic acid
YES
NO
NO
NO
YES
YES
NO
YES


d-Amino Valeric acid
NO
YES
YES
YES
YES
YES
YES
NO


D-Arabinose
YES
YES
YES
YES
YES
YES
YES
YES


D-Arabitol
YES
YES
YES
YES
YES
YES
YES
YES


D-Fucose
YES
NO
YES
NO
YES
YES
NO
NO


D-Glucosamine
YES
YES
YES
YES
YES
YES
YES
NO


D-Lactic acid Methyl
YES
NO
YES
NO
NO
NO
NO
NO


Ester


D-Lactitol
YES
YES
YES
YES
NO
NO
YES
YES


D-Melezitose
YES
YES
YES
YES
YES
YES
YES
YES


D-Raffinose
YES
YES
YES
YES
YES
YES
YES
YES


D-Ribono-1,4-Lactone
YES
NO
YES
YES
YES
NO
YES
NO


D-Tagatose
NO
YES
YES
NO
YES
NO
YES
NO


D-Tartaric acid
YES
NO
NO
NO
YES
NO
NO
NO


D,L-Carnitine
YES
NO
YES
NO
NO
NO
NO
NO


D,L-Octopamine
YES
NO
YES
NO
YES
YES
NO
NO


Dextrin
YES
YES
YES
YES
YES
YES
YES
YES


Dihydroxyacetone
YES
YES
YES
YES
YES
YES
YES
NO


g-Amino-N-Butyric acid
YES
YES
YES
YES
YES
YES
YES
YES


g-Cyclodextrin
YES
YES
YES
YES
YES
YES
YES
YES


g-Hydroxybutyric acid
YES
YES
YES
YES
YES
YES
YES
YES


Gelatin
YES
YES
YES
YES
YES
YES
YES
YES


Gentiobiose
YES
YES
YES
YES
YES
YES
YES
YES


Glycine
YES
YES
YES
YES
YES
YES
YES
NO


Glycogen
YES
YES
YES
YES
YES
YES
YES
YES


Hydroxy-L-Proline
YES
YES
YES
YES
YES
YES
YES
NO


i-Erythritol
YES
YES
YES
YES
YES
YES
YES
YES


Inulin
YES
YES
YES
YES
YES
NO
NO
NO


Itaconic acid
NO
NO
YES
NO
NO
NO
NO
YES


L-Alaninamide
YES
YES
YES
YES
YES
YES
YES
YES


L-Arabitol
YES
YES
YES
YES
YES
YES
YES
YES


L-Arginine
YES
YES
YES
YES
YES
YES
YES
YES


L-Glucose
NO
NO
YES
NO
NO
NO
YES
NO


L-Histidine
YES
YES
YES
YES
YES
YES
YES
NO


L-Homoserine
YES
YES
YES
YES
NO
YES
YES
NO


L-Isoleucine
YES
YES
YES
YES
YES
YES
YES
YES


L-Leucine
YES
YES
YES
YES
YES
YES
YES
NO


L-Lysine
YES
YES
YES
YES
YES
YES
YES
NO


L-Methionine
NO
NO
NO
NO
NO
NO
NO
NO


L-Ornithine
YES
YES
YES
YES
YES
YES
YES
YES


L-Phenylalanine
YES
YES
YES
YES
YES
YES
YES
NO


L-Pyroglutamic acid
YES
YES
YES
YES
YES
YES
YES
YES


L-Sorbose
NO
YES
YES
YES
YES
YES
YES
NO


L-Tartaric acid
YES
NO
YES
NO
YES
YES
YES
YES


L-Valine
YES
YES
YES
YES
YES
YES
YES
YES


Laminarin
YES
YES
YES
YES
YES
YES
YES
NO


Malonic acid
YES
NO
YES
YES
YES
YES
YES
NO


Maltitol
YES
YES
YES
YES
YES
YES
YES
YES


Mannan
YES
NO
YES
NO
YES
NO
NO
NO


Melibionic acid
YES
NO
YES
YES
YES
YES
YES
NO


N-Acetyl-D-
YES
NO
NO
NO
NO
NO
YES
NO


Galactosamine


N-Acetyl-D-
NO
NO
NO
NO
YES
YES
NO
YES


Glucosaminitol


N-Acetyl-L-Glutamic
NO
NO
YES
NO
NO
YES
NO
NO


acid


N-Acetyl-Neuraminic
NO
NO
NO
NO
NO
NO
NO
NO


acid


Negative Control. 1
NO
NO
NO
NO
NO
NO
NO
NO


Oxalic acid
YES
YES
YES
YES
YES
YES
YES
NO


Oxalomalic acid
NO
NO
NO
NO
YES
NO
NO
NO


Palatinose
YES
YES
YES
YES
YES
YES
YES
YES


Pectin
YES
NO
YES
NO
YES
YES
YES
YES


Putrescine
YES
YES
YES
YES
YES
YES
YES
YES


Quinic acid
YES
YES
YES
YES
YES
YES
YES
YES


Salicin
YES
YES
YES
YES
YES
YES
YES
YES


Sebacic acid
YES
YES
YES
YES
YES
YES
YES
NO


sec-Butylamine
NO
YES
YES
NO
NO
NO
NO
NO


Sedoheptulosan
YES
YES
NO
NO
YES
YES
YES
YES


Sorbic acid
YES
YES
YES
YES
YES
YES
YES
NO


Stachyose
YES
YES
YES
YES
YES
YES
YES
YES


Succinamic acid
YES
YES
YES
YES
YES
YES
NO
YES


Turanose
YES
YES
YES
YES
YES
YES
YES
YES


Xylitol
YES
YES
YES
YES
YES
YES
YES
YES












Substrate

















Strain
SYM01330
SYM01331
SYM12462
SYM15774
SYM15783
SYM15810
SYM15879
SYM15880







2-Deoxy-D-Ribose
NO
NO
NO
NO
YES
YES
YES
NO



2-Hydroxybenzoic acid
YES
YES
YES
YES
YES
YES
YES
YES



2,3-Butanediol
YES
YES
NO
YES
NO
YES
NO
NO



2,3-Butanedione
YES
YES
NO
NO
NO
YES
NO
NO



3-Hydroxy-2-butanone
YES
NO
NO
NO
NO
NO
NO
NO



3-Methylglucose
YES
YES
NO
NO
YES
NO
YES
NO



3-O-b-D-
NO
YES
YES
YES
YES
YES
NO
YES



Galactopyranosyl-D-



Arabinose



4-Hydroxybenzoic acid
YES
YES
NO
YES
YES
YES
YES
YES



5-Keto-D-Gluconic acid
YES
YES
YES
YES
YES
YES
YES
YES



a-Cyclodextrin
YES
YES
YES
YES
YES
YES
YES
YES



a-Keto-Valeric acid
YES
YES
YES
YES
YES
YES
YES
YES



a-Methyl-D-Glucoside
YES
YES
NO
YES
YES
YES
YES
YES



a-Methyl-D-Mannoside
YES
YES
NO
NO
YES
YES
YES
NO



Acetamide
YES
YES
NO
YES
NO
NO
NO
NO



Amygdalin
YES
YES
YES
YES
YES
YES
YES
YES



Arbutin
YES
YES
YES
YES
YES
YES
YES
YES



b-Cyclodextrin
NO
YES
YES
YES
YES
YES
YES
YES



b-D-Allose
NO
NO
NO
YES
YES
YES
YES
YES



b-Hydroxybutyric acid
YES
YES
YES
YES
YES
YES
YES
NO



b-Methyl-D-Galactoside
YES
YES
YES
YES
YES
YES
YES
YES



b-Methyl-D-Glucuronic
YES
NO
NO
NO
NO
NO
YES
NO



acid



b-Methyl-D-Xyloside
NO
NO
NO
NO
YES
YES
NO
NO



Butyric acid
YES
YES
NO
NO
YES
YES
YES
YES



Capric acid
NO
NO
NO
NO
NO
NO
NO
NO



Caproic acid
NO
YES
NO
NO
YES
YES
YES
YES



Chondroitin Sulfate C
YES
YES
YES
NO
NO
YES
YES
NO



Citraconic acid
YES
YES
YES
NO
YES
YES
NO
NO



Citramalic acid
YES
YES
NO
NO
YES
YES
YES
YES



d-Amino Valeric acid
YES
YES
YES
NO
YES
YES
YES
YES



D-Arabinose
NO
YES
YES
YES
YES
YES
YES
YES



D-Arabitol
YES
YES
YES
YES
YES
YES
YES
YES



D-Fucose
NO
YES
NO
YES
YES
YES
YES
YES



D-Glucosamine
YES
YES
NO
NO
NO
YES
YES
YES



D-Lactic acid Methyl
YES
NO
YES
NO
NO
YES
NO
NO



Ester



D-Lactitol
NO
YES
YES
YES
YES
YES
YES
NO



D-Melezitose
YES
YES
YES
YES
YES
YES
YES
YES



D-Raffinose
YES
YES
YES
YES
YES
YES
YES
YES



D-Ribono-1,4-Lactone
YES
YES
NO
NO
YES
NO
NO
YES



D-Tagatose
YES
NO
NO
NO
YES
YES
YES
YES



D-Tartaric acid
YES
NO
NO
YES
YES
NO
YES
NO



D,L-Carnitine
YES
YES
YES
NO
NO
NO
NO
NO



D,L-Octopamine
NO
YES
NO
YES
YES
YES
YES
NO



Dextrin
YES
YES
YES
YES
YES
YES
YES
YES



Dihydroxyacetone
YES
YES
NO
NO
YES
YES
YES
NO



g-Amino-N-Butyric acid
YES
YES
YES
NO
YES
YES
YES
YES



g-Cyclodextrin
YES
YES
YES
YES
YES
YES
YES
YES



g-Hydroxybutyric acid
YES
YES
YES
YES
YES
YES
NO
NO



Gelatin
YES
YES
YES
YES
YES
YES
YES
NO



Gentiobiose
YES
YES
YES
YES
YES
YES
YES
YES



Glycine
YES
YES
YES
NO
YES
YES
YES
YES



Glycogen
YES
YES
YES
YES
YES
YES
YES
YES



Hydroxy-L-Proline
YES
YES
YES
NO
YES
YES
YES
YES



i-Erythritol
YES
YES
YES
NO
YES
YES
NO
YES



Inulin
YES
NO
YES
YES
NO
YES
YES
YES



Itaconic acid
NO
YES
NO
NO
NO
NO
NO
NO



L-Alaninamide
YES
YES
YES
YES
YES
YES
YES
NO



L-Arabitol
YES
YES
YES
NO
YES
YES
YES
YES



L-Arginine
YES
YES
YES
YES
YES
YES
YES
YES



L-Glucose
NO
YES
NO
NO
YES
YES
YES
NO



L-Histidine
YES
NO
YES
YES
YES
YES
YES
YES



L-Homoserine
NO
YES
NO
NO
YES
NO
YES
NO



L-Isoleucine
YES
YES
YES
YES
YES
YES
YES
YES



L-Leucine
YES
YES
NO
YES
YES
YES
YES
NO



L-Lysine
YES
YES
YES
YES
YES
YES
YES
YES



L-Methionine
NO
NO
NO
YES
YES
NO
NO
NO



L-Ornithine
YES
YES
YES
YES
YES
YES
YES
YES



L-Phenylalanine
YES
YES
YES
YES
YES
YES
YES
YES



L-Pyroglutamic acid
YES
YES
YES
YES
NO
YES
YES
YES



L-Sorbose
YES
NO
YES
NO
YES
YES
YES
YES



L-Tartaric acid
NO
YES
NO
YES
NO
YES
YES
NO



L-Valine
YES
YES
NO
NO
YES
YES
YES
YES



Laminarin
NO
YES
YES
YES
YES
YES
YES
NO



Malonic acid
YES
YES
NO
YES
YES
YES
YES
NO



Maltitol
YES
YES
NO
YES
YES
YES
YES
YES



Mannan
YES
NO
YES
YES
NO
NO
NO
NO



Melibionic acid
YES
YES
YES
YES
NO
YES
YES
NO



N-Acetyl-D-
YES
NO
NO
YES
NO
YES
NO
NO



Galactosamine



N-Acetyl-D-
NO
NO
NO
NO
NO
YES
YES
NO



Glucosaminitol



N-Acetyl-L-Glutamic
YES
YES
NO
YES
NO
NO
NO
NO



acid



N-Acetyl-Neuraminic
NO
NO
NO
NO
NO
NO
NO
NO



acid



Negative Control. 1
NO
NO
NO
NO
NO
NO
NO
NO



Oxalic acid
YES
YES
YES
NO
YES
YES
YES
NO



Oxalomalic acid
YES
NO
NO
NO
YES
YES
YES
NO



Palatinose
YES
YES
YES
YES
YES
YES
YES
YES



Pectin
YES
YES
YES
YES
YES
YES
YES
YES



Putrescine
YES
YES
YES
NO
YES
YES
YES
YES



Quinic acid
YES
YES
NO
YES
YES
YES
YES
YES



Salicin
YES
YES
YES
YES
YES
YES
YES
YES



Sebacic acid
YES
YES
YES
NO
YES
YES
YES
YES



sec-Butylamine
NO
NO
NO
NO
NO
NO
NO
NO



Sedoheptulosan
YES
YES
YES
YES
YES
YES
YES
YES



Sorbic acid
YES
YES
NO
NO
YES
YES
YES
NO



Stachyose
YES
YES
YES
YES
YES
YES
YES
YES



Succinamic acid
YES
YES
YES
YES
YES
YES
YES
NO



Turanose
YES
YES
YES
YES
YES
YES
YES
YES



Xylitol
YES
YES
YES
YES
YES
YES
YES
YES










Seventeen (17) bacterial SYM strains and sixteen (16) fungal SYM strains were tested in biological triplicate for sole carbon substrate utilization using BIOLOG PM1 and PM2A MicroPlates. The most utilized substrates overall by these strains are a-D-Glucose, Arbutin, b-Methyl-D-Galactoside, b-Methyl-D-Glucoside, D-Arabitol, D-Cellobiose, Dextrin, D-Fructose, D-Galactose, D-Gluconic acid, D-Glucosamine, Dihydroxyacetone, DL-Malic acid, D-Mannitol, D-Mannose, D-Melezitose, D-Melibiose, D-Raffinose, D-Ribose, D-Trehalose, D-Xylose, g-Amino-N-Butyric acid, g-Cyclodextrin, Gelatin, Gentiobiose, Glycogen, i-Erythritol, L-Alanine, L-Arabinose, L-Galactonic acid-g-Lactone, L-Histidine, L-Proline, L-Rhamnose, Maltitol, Maltose, Maltotriose, N-Acetyl-D-Glucosamine, Palatinose, Pectin, Salicin, Stachyose, Sucrose, and Turanose. Overall, these strains did not utilize 2,3-Butanediol, 2,3-Butanedione, b-Methyl-D-Glucuronic acid, b-Methyl-D-Xyloside, Capric acid, D,L-Carnitine, Glucuronamide, Itaconic acid, L-Methionine, N-Acetyl-D-Glucosaminitol, N-Acetyl-Neuraminic acid, Phenylethylamine, or sec-Butylamine as sole carbon sources.


The most utilized substrates by these seventeen bacterial endophytes are 2-Deoxy-D-Ribose, a-D-Glucose, a-Methyl-D-Galactoside, Arbutin, b-Methyl-D-Galactoside, b-Methyl-D-Glucoside, D-Arabitol, D-Cellobiose, Dextrin, D-Fructose, D-Galactose, D-Galacturonic acid, D-Gluconic acid, D-Glucosamine, Dihydroxyacetone, DL-Malic acid, D-Mannitol, D-Mannose, D-Melibiose, D-Raffinose, D-Ribose, D-Trehalose, D-Xylose, Gelatin, Gentiobiose, L-Arabinose, L-Aspartic acid, L-Galactonic acid-g-Lactone, L-Glutamic acid, L-Glutamine, L-Histidine, L-Ornithine, L-Proline, Maltose, Maltotriose, N-Acetyl-D-Glucosamine, Pyruvic acid, Salicin, Sucrose, and Turanose. These bacterial endophytes did not utilize 1,2-Propanediol, 2,3-Butanediol, 2,3-Butanedione, 2-Aminoethanol, 2-Hydroxybenzoic acid, 3-Hydroxy-2-butanone, 3-Methylglucose, 4-Hydroxybenzoic acid, Acetamide, Acetoacetic acid, a-Hydroxybutyric acid, a-Hydroxyglutaric acid-g-Lactone, a-Ketobutyric acid, a-Keto-Valeric acid, a-Methyl-D-Glucoside, a-Methyl-D-Mannoside, b-D-Allose, b-Methyl-D-Glucuronic acid, b-Methyl-D-Xyloside, Capric acid, Caproic acid, Citraconic acid, Citramalic acid, D,L-Carnitine, D,L-Octopamine, d-Amino Valeric acid, D-Aspartic acid, D-Melezitose, D-Serine, D-Tagatose, D-Tartaric acid, D-Threonine, g-Cyclodextrin, g-Hydroxybutyric acid, Glucuronamide, Glycine, Glycolic acid, Glyoxylic acid, Hydroxy-L-Proline, i-Erythritol, Inulin, Itaconic acid, L-Arabitol, L-Fucose, L-Glucose, L-Homoserine, L-Methionine, L-Sorbose, L-Threonine, L-Valine, m-Tartaric acid, N-Acetyl-D-Glucosaminitol, N-Acetyl-D-Mannosamine, N-Acetyl-Neuraminic acid, Oxalic acid, Phenylethylamine, Sebacic acid, sec-Butylamine, Sedoheptulosan, Stachyose, Tricarballylic acid, Tyramine, or Xylitol as sole carbon sources.


The most utilized substrates by these sixteen fungal endophytes are a-D-Glucose, a-Methyl-D-Glucoside, Amygdalin, Arbutin, b-Methyl-D-Galactoside, b-Methyl-D-Glucoside, D-Arabitol, D-Cellobiose, Dextrin, D-Fructose, D-Galactose, D-Mannitol, D-Mannose, D-Melezitose, D-Melibiose, D-Raffinose, D-Trehalose, D-Xylose, g-Amino-N-Butyric acid, g-Cyclodextrin, Gentiobiose, Glycogen, i-Erythritol, L-Alanine, L-Arabinose, L-Arginine, L-Ornithine, L-Rhamnose, Maltitol, Maltose, Maltotriose, N-Acetyl-D-Glucosamine, Palatinose, Pectin, Putrescine, Quinic acid, Salicin, Stachyose, Sucrose, and Turanose. These fungal endophytes did not utilize 2,3-Butanediol, 2,3-Butanedione, 2-Deoxy-D-Ribose, b-Methyl-D-Glucuronic acid, b-Methyl-D-Xyloside, Capric acid, D,L-Carnitine, D-Galactonic acid-g-Lactone, D-Glucose-1-Phosphate, Glucuronamide, Itaconic acid, L-Methionine, N-Acetyl-D-Galactosamine, N-Acetyl-D-Glucosaminitol, N-Acetyl-L-Glutamic acid, N-Acetyl-Neuraminic acid, Phenylethylamine, or sec-Butylamine as sole carbon sources.


Example 5: Transcriptomic Characterization of Host Plant Response to Synthetic Compositions Comprising Plant Seeds and an Endophyte (Soy RNA-SEQ Experiments)

This Example describes the ability of synthetic compositions comprising plant seeds a single endophyte strain or a plurality of endophyte strains described herein, to confer beneficial traits to a host plant. Among other things, this Example describe the ability of endophytes (e.g., endophytes described herein) to confer beneficial traits on a variety of host plants by modulating the transcriptome of the host plant. In some embodiments, host plants include, but are not limited to, dicots (e.g., soy, peanuts) and monocots (e.g., plants described herein, e.g., corn, soy, wheat, cotton, sorghum), and combinations thereof.


Among other things, this Example describes surprising and unexpected modulations in the transcriptome of a host plant in response to synthetic compositions comprising plant seeds and a beneficial fungal endophyte strain, compared to a neutral fungal strain of the same genus.


Plant Seedling


Untreated soy seeds were surface sterilized using chlorine fumes. Briefly, Erlenmyer flasks containing seeds and a bottle with 100 mL of fresh bleach solution were placed in a desiccation jar located in a fume hood. Immediately prior to closing the lid of the desiccation jar, 3 mL hydrochloric acid was carefully pipetted into the bleach. Sterilization was done for 17 hours, and upon completion the flasks with seeds were removed, sealed in sterile foil, and opened in a sterile biosafety cabinet or laminar flow hood for subsequent work.


Soy Seedling Assay


Seeds were first coated with 3% sodium alginate, and gently shaken to obtain homogenous coverage. SYM strain fungal inoculum grown as described previously was added to the sodium alginate coated seeds and gently mixed. For every one gram of seeds, 10 μL of sodium alginate and inoculum were applied. Formulation only soybean seeds were coated with 3% sodium alginate and fresh PDB.


Ten seeds were placed on a 150 mm Petri plate that contained a single heavy germination paper (SD5-1/4 76# heavy weight seed germination paper, Anchor Paper Co., St. Paul, Minn.) added with 10 mL 8% polyethylene glycol (PEG 6000). Plates were incubated at 22° Celsius in dark and 60% relative humidity for five days. Seedlings were harvested at the end of the incubation period and stored in −80° C. until total RNA isolation using standard extraction method using TriReagent (Sigma-Aldrich, St. Louis, Mo., USA) and purification with RNeasy Mini Kit (Qiagen, Hilden, Germany). All experiments (beneficial, neural, formulation) were done in triplicate under sterile conditions resulting in a total of nine samples.


Soy RNA-SEQ


Initial quality control was performed using Agilent Bioanalyzer and Tapestation.


PolyA cDNA Preparation


For each of the 9 soybean RNAs, polyA cDNA was prepared using a Clontech cDNA synthesis kit. Briefly, after initial QC passed, 500 ng of total RNA was used to generate 1-2 ug of cDNA using Clontech SMARTer PCR cDNA kit (Clontech Laboratories, Inc., Mountain View, Calif. USA, catalog #634925). Manufacturer's instructions were strictly followed to perform polyA cDNA construction; 14 PCR cycles were performed.


Fragmentation


Briefly, cDNA was fragmented using Bioruptor (Diagenode, Inc., Denville, N.J. USA). Fragmented cDNAs were tested for size distribution and concentration using an Agilent Bioanalyzer 2100 or Tapestation 2200 and Nanodrop.


DNA Library Construction


For each the 9 soybean samples, Illumina libraries were made from qualified fragmented cDNA using Beckman Coulter SPRIworks HT Reagent Kit (Beckman. Coulter, Inc. Indianapolis, Ind. USA, catalog # B06938) on the Biomek FXp liquid handler.


Beckman Biomek FXp (Biomek 6000, Beckman Coulter) fully automatic workstation and a Beckman HT library kit were used to generate fragment libraries. The instructions were strictly followed to perform library construction. Briefly, after fragmentation the ends were repaired and ‘A’ bases were added to the 3′ end of the fragments. Adapters were then ligated to both ends. The adaptor-ligated templates were further purified using Agencourt AMPure SPRI beads. The adaptor-ligated library was amplified by ligation-mediated PCR which consisted of 10 cycles of amplification, and the PCR product was purified using Agencourt AMPure SPRI beads again. After the library construction procedure was completed, QC was performed using a Nanodrop and Agilent Bioanalyzer to ensure the library quality and quantity.


RNA Sequencing


Sequencing was performed on an Illumina HiSeq 2500, using Rapid run v2.0 chemistry which generated paired-end reads of 106 nucleotides (nt.) according to Illumina manufacturer's instructions. The initial data analysis was started directly on the HiSeq 2500 System during the run. The HiSeq Control Software 2.2.58 in combination with RTA 1.18.64 (real time analysis) performed the initial image analysis and base calling. In addition, bcl2fastq1.8.4 generated and reported run statistics. Data was analyzed using FASTQC (Babraham Institute, Cambridge, UK) comprising the sequence information which was used for all subsequent bioinformatics analyses. Sequences were de-multiplexed according to the 6 bp index code with 1 mismatch allowed.


Analysis


Differential analysis of the soy transcriptome in the presence of neutral vs beneficial fungi was performed using standard RNA-seq analysis methods. Briefly, mapped reads overlapping with exon features were counted and aggregated by gene. These gene-level counts were analyzed with the DESeq2 R package, available through the Bioconductor software repository. All possible comparisons of the three groups (control, neutral, beneficial) were performed, and the false discovery rate method was used to adjust p-values for multiple testing. High- and low-confidence differential gene lists were created using false discovery rate thresholds of 0.1 and 0.05, and log 2 fold-change thresholds of 1 and 2, respectively. Set differences were extracted, e.g., genes differentially expressed in beneficial vs control but not in neutral vs control. Gene Ontology (GO) enrichment analysis was performed for all differential gene lists.









TABLE 500







This table shows the genes that are up-regulated (negative log FC) or down-regulated (positive log FC)


in soybean as a result of treatment with a beneficial endophyte, as compared to formulation control.













SEQ




Median Exp.
Median Exp.


ID
Gene
Annotation
log FC
Adj. p-value
Beneficial
Formulation
















4127
GLYMA01G31730
GO:0006952, GO, defense response
−1.369956983
3.89E−08
12.63236736
3.673553109


4128
GLYMA01G31921
NA
−1.238022219
1.45E−06
8.528180493
2.738466863


4129
GLYMA01G38630
GO:0055114, GO, oxidation-reduction
−1.099323189
0.000263359
4.903703783
1.347924708




process


4130
GLYMA01G41070
GO:0008150, GO, biological_process
−1.568722399
1.04E−14
13.25341979
3.395530442


4131
GLYMA01G43420
GO:0006355, GO, regulation of
−1.253171009
1.81E−09
22.27987154
8.177409896




transcription, DNA-dependent


4132
GLYMA01G44660
GO:0008150, GO, biological_process
−1.163160876
1.25E−05
7.245224059
1.797232944


4133
GLYMA02G01400
GO:0008152, GO, metabolic process
−1.1051522
1.17E−05
5.985185092
2.156679533


4134
GLYMA02G03420
GO:0019761, GO, glucosinolate
−1.015176361
4.96E−05
24.06891956
9.008550154




biosynthetic process


4135
GLYMA02G04000
GO:0080167, GO, response to karrikin
−1.070349401
8.30E−10
27.49585031
12.58063061


4136
GLYMA02G06150
GO:0008150, GO, biological_process
−1.034377122
2.01E−05
49.3568446
19.85942403


4137
GLYMA02G09750
GO:0006468, GO, protein
−1.109501892
1.06E−05
18.65539483
5.75161279




phosphorylation


4138
GLYMA02G14260
GO:0008150, GO, biological_process
−1.251479824
4.10E−10
30.38164301
12.49076896


4139
GLYMA02G36700
GO:0006457, GO, protein folding
1.234514786
1.70E−08
5.983985525
17.25483837


4140
GLYMA02G40990
GO:0010200, GO, response to chitin
−1.627009953
7.37E−22
34.59243212
10.33408943


4141
GLYMA02G42251
NA
−1.411718736
9.82E−18
83.37686498
28.48614217


4142
GLYMA02G45420
GO:0006508, GO, proteolysis
−1.424759326
7.78E−14
51.01901733
15.27648003


4143
GLYMA03G00540
GO:0006468, GO, protein
−1.349391458
2.98E−07
9.405290859
1.803380617




phosphorylation


4144
GLYMA03G01820
GO:0008150, GO, biological_process
−1.012023704
0.000952197
3.464573325
0.988478119


4145
GLYMA03G01835
NA
−1.259097901
1.11E−08
22.70628056
8.626718132


4146
GLYMA03G01840
GO:0008150, GO, biological_process
−1.407747152
6.51E−15
50.47616829
19.58983909


4147
GLYMA03G03480
GO:0009733, GO, response to auxin
−1.008891294
3.93E−06
14.00695871
5.543723171




stimulus


4148
GLYMA03G05220
GO:0006355, GO, regulation of
−1.368776464
5.33E−08
11.67294705
3.873928733




transcription, DNA-dependent


4149
GLYMA03G30410
GO:0006499, GO, N-terminal protein
−1.076960853
0.000354785
4.230130817
1.068669995




myristoylation


4150
GLYMA03G34780
GO:0006979, GO, response to oxidative
1.536202396
9.85E−09
0.576235643
3.953912477




stress


4151
GLYMA03G35950
GO:0005575, GO, cellular_component
−1.037941628
6.65E−05
5.718030613
2.27092374


4152
GLYMA03G35980
GO:0010150, GO, leaf senescence
−1.093799446
2.45E−08
27.18357532
9.618029959


4153
GLYMA03G36330
GO:0009870, GO, defense response
−1.456183569
7.05E−14
14.35544394
3.606761235




signaling pathway, resistance gene-




dependent


4154
GLYMA03G42390
GO:0008270, GO, zinc ion binding
−1.155489867
7.37E−09
20.94734334
7.6919159


4155
GLYMA04G00490
GO:0008150, GO, biological_process
−1.066752001
0.000134501
5.490016192
2.066817886


4156
GLYMA04G00890
GO:0009409, GO, response to cold
−1.23197541
1.83E−05
2.97009185
0.667918747


4157
GLYMA04G02280
GO:0008150, GO, biological_process
−1.129891407
1.65E−07
27.07697307
12.08932932


4158
GLYMA04G04760
GO:0006979, GO, response to oxidative
−1.145087639
1.78E−13
110.3884138
47.53681137




stress


4159
GLYMA04G09110
GO:0006108, GO, malate metabolic
−1.023288707
6.87E−08
62.46892211
27.71861586




process


4160
GLYMA04G09770
GO:0006810, GO, transport
−1.067742926
9.20E−06
7.225108449
2.785711064


4161
GLYMA04G11140
GO:0006810, GO, transport
−1.034043016
0.000731927
3.411272197
0.667918747


4162
GLYMA04G12600
GO:0003824, GO, catalytic activity
−1.311303393
8.14E−10
40.34895396
12.12689444


4163
GLYMA04G12610
GO:0003824, GO, catalytic activity
−1.283734962
9.78E−06
1.652334971
0


4164
GLYMA04G17650
GO:0010193, GO, response to ozone
−1.384727165
3.29E−11
12.87039802
3.594465888


4165
GLYMA04G37530
GO:0008150, GO, biological_process
1.196382319
7.27E−06
2.216290935
8.800660535


4166
GLYMA04G40700
NA
−1.056299293
8.46E−11
67.64119934
32.350193


4167
GLYMA04G40710
GO:0008150, GO, biological_process
−1.564590555
2.15E−18
24.55650356
7.278793424


4168
GLYMA04G40861
NA
−1.006211746
7.60E−06
19.61481513
7.146730595


4169
GLYMA04G41701
NA
−1.201080148
1.28E−05
5.170209424
1.247337714


4170
GLYMA05G03243
NA
−1.226133282
7.41E−08
14.53544951
5.476933727


4171
GLYMA05G22760
PF05678, PFAM, VQ motif
−1.058133573
0.000138289
7.995169212
2.217489269


4172
GLYMA05G25920
GO:0008150, GO, biological_process
−1.461542925
7.05E−14
22.86618395
7.368655071


4173
GLYMA05G33340
GO:0008150, GO, biological_process
1.371586716
5.70E−09
2.475076542
8.038398599


4174
GLYMA05G34760
GO:0010112, GO, regulation of systemic
−1.093610202
3.89E−08
18.28228693
8.348984339




acquired resistance


4175
GLYMA05G37690
GO:0006813, GO, potassium ion transport
−1.152485783
4.56E−13
64.84867276
29.1151737


4176
GLYMA06G02340
GO:0008150, GO, biological_process
−1.000797368
1.73E−07
50.90257732
23.63361322


4177
GLYMA06G10450
GO:0008150, GO, biological_process
−1.442423906
2.55E−11
10.54954485
2.771861586


4178
GLYMA06G10580
GO:0008150, GO, biological_process
−1.333680454
9.34E−11
13.65235216
3.774189183


4179
GLYMA06G13090
GO:0006355, GO, regulation of
−1.099137285
0.000134501
7.195652291
2.938842487




transcription, DNA-dependent


4180
GLYMA06G14090
GO:0008150, GO, biological_process
−1.147251562
5.98E−13
143.6465402
58.94924057


4181
GLYMA06G45020
NA
−1.262217964
3.80E−15
53.83413936
18.7100657


4182
GLYMA06G45043
NA
1.138574305
3.09E−10
3928.774615
8118.418788


4183
GLYMA07G06320
GO:0006355, GO, regulation of
−1.006619206
2.17E−07
33.46599312
13.89270994




transcription, DNA-dependent


4184
GLYMA07G11960
GO:0010200, GO, response to chitin
−1.161974193
8.23E−07
43.02133043
12.67049226


4185
GLYMA07G15800
GO:0008150, GO, biological_process
1.009903371
2.03E−06
5127.965314
11633.54157


4186
GLYMA07G29730
GO:0006499, GO, N-terminal protein
−1.193477886
7.29E−05
2.437920029
0.400751248




myristoylation


4187
GLYMA08G01900
GO:0006813, GO, potassium ion transport
−1.203154273
2.80E−12
62.30901873
28.12669558


4188
GLYMA08G02580
GO:0006355, GO, regulation of
−1.102088699
1.08E−07
59.11095104
27.85221176




transcription, DNA-dependent


4189
GLYMA08G08360
GO:0006952, GO, defense response
−1.107144375
4.96E−05
6.556038754
1.870172492


4190
GLYMA08G10435
NA
1.27926219
6.52E−06
1.305040358
4.642868156


4191
GLYMA08G11260
GO:0008150, GO, biological_process
−1.031833196
3.58E−09
51.55092715
23.63361322


4192
GLYMA08G16810
GO:0009061, GO, anaerobic respiration
−1.153355774
1.13E−09
32.75678002
14.02629369


4193
GLYMA08G17140
GO:0007275, GO, multicellular organismal
1.013378053
0.001635642
0.479710153
1.803380617




development


4194
GLYMA08G22630
GO:0009408, GO, response to heat
1.167051089
1.64E−05
1.950336023
6.144852474


4195
GLYMA09G00720
GO:0008150, GO, biological_process
−1.297617667
9.76E−07
6.023027473
1.335837494


4196
GLYMA09G06840
NA
1.043842712
0.000230515
1.980061233
6.236688568


4197
GLYMA09G12440
GO:0008168, GO, methyltransferase
−1.110391457
0.000138289
4.637198143
0.868294371




activity


4198
GLYMA09G21040
NA
−1.129686949
0.000191718
3.015093242
0.449308236


4199
GLYMA09G30250
GO:0010200, GO, response to chitin
−1.480411528
3.22E−16
37.95040319
10.04799825


4200
GLYMA09G38930
GO:0009611, GO, response to wounding
−1.114614822
3.43E−05
5.809822961
2.00959965


4201
GLYMA09G41670
GO:0006355, GO, regulation of
−1.282700181
1.93E−09
17.21626437
5.127943934




transcription, DNA-dependent


4202
GLYMA10G04210
GO:0006355, GO, regulation of
−1.021042996
1.99E−05
9.380998542
4.672805655




transcription, DNA-dependent


4203
GLYMA10G22100
GO:0055114, GO, oxidation-reduction
−1.184360983
7.75E−05
1.595729473
0.179723294




process


4204
GLYMA10G37920
GO:0004497, GO, monooxygenase activity
−1.440645295
3.88E−10
13.27198089
3.339593736


4205
GLYMA10G39971
NA
−1.199223405
2.01E−05
5.223510552
1.87100657


4206
GLYMA10G44160
GO:0006355, GO, regulation of
−1.469325378
1.70E−11
28.40950127
8.549359964




transcription, DNA-dependent


4207
GLYMA11G06660
GO:0055114, GO, oxidation-reduction
−1.013056688
6.65E−05
40.40225509
14.96137994




process


4208
GLYMA11G13290
NA
−1.186249968
1.08E−06
34.87607854
13.47924708


4209
GLYMA11G13800
GO:0005975, GO, carbohydrate metabolic
−1.212845405
8.71E−11
32.35378475
12.62366432




process


4210
GLYMA11G13810
GO:0005975, GO, carbohydrate metabolic
−1.025842415
0.000230184
5.330112808
2.204131866




process


4211
GLYMA11G16120
NA
−1.343091922
6.61E−11
16.52334971
4.313359066


4212
GLYMA11G21250
GO:0006468, GO, protein
−1.06809702
0.000495067
2.77165866
0.718893178




phosphorylation


4213
GLYMA11G25670
GO:0010193, GO, response to ozone
−1.137836997
1.03E−05
8.634782749
2.695849416


4214
GLYMA11G33450
GO:0010200, GO, response to chitin
−1.387745046
4.11E−19
57.82678829
19.16926804


4215
GLYMA12G00460
GO:0006468, GO, protein
−1.042089407
1.75E−09
35.01739678
15.63592661




phosphorylation


4216
GLYMA12G00780
GO:0005975, GO, carbohydrate metabolic
1.075138028
0.000616457
0.443258187
1.536213118




process


4217
GLYMA12G01420
GO:0006952, GO, defense response
−1.02645451
1.87E−07
30.36318581
14.73731014


4218
GLYMA12G05770
GO:0005975, GO, carbohydrate metabolic
1.235797291
3.38E−07
9.663028477
25.91524739




process


4219
GLYMA12G05800
GO:0005975, GO, carbohydrate metabolic
−1.014997151
7.90E−06
29.83592268
13.15799932




process


4220
GLYMA12G08020
GO:0006887, GO, exocytosis
−1.088877462
8.78E−06
7.18078263
2.494675427


4221
GLYMA12G09830
GO:0000289, GO, nuclear-transcribed
−1.038592224
5.61E−09
269.4683333
120.4146073




mRNA poly(A) tail shortening


4222
GLYMA12G12260
NA
−1.305617284
9.36E−18
48.29082204
15.69609056


4223
GLYMA12G15620
GO:0005975, GO, carbohydrate metabolic
−1.21921729
2.12E−08
28.83591029
10.41953246




process


4224
GLYMA12G36310
GO:0006814, GO, sodium ion transport
−1.417198792
1.03E−07
6.076328601
1.335837494


4225
GLYMA13G09690
GO:0006071, GO, glycerol metabolic
−1.091584652
1.88E−07
29.58212608
11.0874512




process


4226
GLYMA13G09840
GO:0006071, GO, glycerol metabolic
−1.048336234
2.07E−07
45.73236789
20.63868929




process


4227
GLYMA13G10010
GO:0006468, GO, protein
−1.18204335
2.97E−06
7.515459059
2.286785808




phosphorylation


4228
GLYMA13G19560
GO:0006355, GO, regulation of
−1.2382138
5.37E−07
6.870501899
2.078896189




transcription, DNA-dependent


4229
GLYMA13G22540
NA
−1.055564007
1.97E−08
31.66087008
13.47924708


4230
GLYMA13G35320
GO:0006952, GO, defense response
1.440915562
2.97E−12
52.07520214
149.0804727


4231
GLYMA13G35710
GO:0008150, GO, biological_process
1.011655056
0.000625306
0.045001392
1.61750965


4232
GLYMA14G05710
PTHR10499:SF51, Panther, VON
−1.079821764
0.000308777
1.935059842
0.138593079




WILLEBRAND FACTOR A3


4233
GLYMA14G06640
GO:0006979, GO, response to oxidative
−1.215771987
1.16E−08
20.25689915
6.791060885




stress


4234
GLYMA14G06900
GO:0009408, GO, response to heat
1.019854223
0.00021457
3.195098808
9.684821834


4235
GLYMA14G09571
NA
−1.007062495
0.001249681
2.925090458
0.868294371


4236
GLYMA14G32430
GO:0009414, GO, response to water
1.002316095
1.01E−06
10.62032843
22.59067192




deprivation


4237
GLYMA14G39300
GO:0010200, GO, response to chitin
−1.134859314
4.96E−09
71.15700599
29.02531205


4238
GLYMA14G39950
GO:0008150, GO, biological_process
−1.057047859
1.33E−08
19.72141739
7.553322821


4239
GLYMA15G11140
GO:0009651, GO, response to salt stress
−1.008285337
1.31E−05
28.83591029
14.15987744


4240
GLYMA15G13510
GO:0006979, GO, response to oxidative
−1.4392098
9.46E−11
19.88132077
5.543723171




stress


4241
GLYMA16G06520
GO:0008150, GO, biological_process
−1.436684015
1.57E−08
5.625173959
0.988478119


4242
GLYMA16G31401
NA
−1.106530815
1.52E−05
9.270286684
3.118344284


4243
GLYMA17G01530
GO:0008150, GO, biological_process
−1.037614878
0.001129298
1.773032748
0.400751248


4244
GLYMA17G03340
GO:0006952, GO, defense response
−1.220260866
1.01E−10
372.1615091
135.9882569


4245
GLYMA17G05240
GO:0006355, GO, regulation of
−1.407526282
2.79E−13
17.00305986
5.8108931




transcription, DNA-dependent


4246
GLYMA17G11340
GO:0008150, GO, biological_process
−1.27822077
1.25E−09
20.03527005
7.368655071


4247
GLYMA17G11490
GO:0008150, GO, biological_process
−1.298456505
3.81E−06
3.411272197
0.623668857


4248
GLYMA17G35430
GO:0006979, GO, response to oxidative
−1.083557924
1.71E−10
130.7740442
53.1082335




stress


4249
GLYMA18G03066
NA
−1.022521386
2.16E−08
84.85539591
34.95618076


4250
GLYMA18G04770
GO:0010200, GO, response to chitin
−1.328972157
1.26E−22
78.45926054
28.58692238


4251
GLYMA18G20470
GO:0010193, GO, response to ozone
−1.03304461
0.000267522
6.875845522
2.137339991


4252
GLYMA18G28830
GO:0015995, GO, chlorophyll biosynthetic
−1.360956021
6.62E−07
4.850402655
1.001878121




process


4253
GLYMA18G44030
GO:0006355, GO, regulation of
−1.121912469
5.61E−06
14.60450909
5.682316251




transcription, DNA-dependent


4254
GLYMA18G49158
NA
−1.354034842
4.58E−07
4.635143342
0.801502497


4255
GLYMA18G50691
NA
−1.039325485
9.07E−05
6.715942138
2.40450749


4256
GLYMA18G53250
GO:0008150, GO, biological_process
1.250925416
2.68E−08
2.878260916
9.255749663


4257
GLYMA19G01440
GO:0009408, GO, response to heat
1.091071017
3.48E−13
33.43603401
78.48045279


4258
GLYMA19G34490
NA
−1.064397801
0.000164104
5.265162825
1.536213118


4259
GLYMA19G35740
GO:0006355, GO, regulation of
−1.062085765
4.69E−05
7.225108449
2.516126122




transcription, DNA-dependent


4260
GLYMA19G37161
NA
−1.105970011
0.000101771
3.89098235
1.078339767


4261
GLYMA19G38570
GO:0010150, GO, leaf senescence
−1.11397824
4.23E−09
34.91223889
14.4677252


4262
GLYMA19G38590
GO:0010150, GO, leaf senescence
−1.295108361
8.98E−07
5.540727338
1.707371297


4263
GLYMA19G41410
GO:0005975, GO, carbohydrate metabolic
1.336821707
2.59E−06
0.132977456
2.003756241




process


4264
GLYMA20G01170
GO:0006499, GO, N-terminal protein
−1.124709392
4.41E−06
6.715942138
2.156679533




myristoylation


4265
GLYMA20G03850
NA
−1.027846502
0.000691549
4.05012525
1.247337714


4266
GLYMA20G25990
GO:0006499, GO, N-terminal protein
−1.110406177
1.18E−09
60.21186205
26.50918593




myristoylation


4267
GLYMA20G26600
GO:0006952, GO, defense response
−1.008944076
7.29E−07
46.74508933
17.03192805


4268
GLYMA20G27020
GO:0008150, GO, biological_process
−1.092005979
2.85E−10
42.46413432
18.10059805


4269
GLYMA20G35180
GO:0006355, GO, regulation of
−1.034170042
9.83E−09
21.94128026
9.751613708




transcription, DNA-dependent


4270
GLYMA03G37400
GO:0042545, GO, cell wall modification
1.646163821
2.88E−09
0.213204512
2.426264


4271
GLYMA03G38840
GO:0005975, GO, carbohydrate metabolic
2.018195916
1.64E−15
0.576235643
5.391699




process


4272
GLYMA07G15380
GO:0009693, GO, ethylene biosynthetic
1.14033694
9.07E−05
0.900027833
4.133636




process


4273
GLYMA08G46450
GO:0005975, GO, carbohydrate metabolic
2.028493959
7.27E−15
0.310280731
3.684328




process


4274
GLYMA09G35840
GO:0005975, GO, carbohydrate metabolic
3.395302467
6.40E−68
1.152471286
24.89168




process


4275
GLYMA10G30340
GO:0008150, GO, biological_process
−2.087505841
1.42E−27
35.23204566
5.032252


4276
GLYMA11G02350
GO:0005975, GO, carbohydrate metabolic
2.628824882
2.44E−30
1.012721434
13.47925




process


4277
GLYMA12G01510
GO:0005975, GO, carbohydrate metabolic
3.161170918
8.63E−48
0.5400167
13.1198




process


4278
GLYMA13G30440
GO:0008150, GO, biological_process
−2.347970113
7.37E−22
7.195652291
0.467543


4279
GLYMA15G07700
PF00264, PFAM, Common central domain
0.824086029
0.018602054
3.102807309
19.05067




of tyrosinase


4281
GLYMA17G08400
GO:0006032, GO, chitin catabolic process
−2.054291387
1.57E−22
16.26757546
2.066818


4283
GLYMA17G14890
GO:0006869, GO, lipid transport
1.278386816
1.57E−08
25.8419523
62.159


4284
GLYMA18G47390
GO:0009611, GO, response to wounding
−2.306445262
6.24E−19
3.900672046
0.089862


4285
GLYMA18G53440
GO:0008150, GO, biological_process
0.105360923
0.992007499
16.84315647
19.54162










The genes described in this table show significant (fdr adjusted p-value <=0.05) differences in expression in soybean seedlings treated with a Acremonium zea sp. with beneficial effects on soybean growth and soybean seedlings treated with a formulation (“Beneficial v Formulation”). “Median Exp. Beneficial” and “Median Exp. Formulation” represent the median expression value in cpm across biological replicates of soy seedlings treated with the beneficial Acremonium and formulation, respectively. “Log FC” represents the estimate of the log 2-fold-change of the contrast. “Adj. p-value” represents the false discovery rate (Benjamini & Hochberg, 1995) adjusted p-values.









TABLE 501







This table shows the genes that are up-regulated (positive log FC) or down-regulated (negative log FC) in soybean as


a result of treatment with a beneficial endophyte, as compared to a soybean treated with a reference microorganism.


















Median Exp.
Median Exp.


SEQ ID
Gene
Annotation
log FC
Adj. p-value
Neutral
Beneficial
















4162
GLYMA04G12600
GO:0003824, GO, catalytic activity
1.206357
9.85E−08
13.26698
40.34895


4201
GLYMA09G41670
GO:0006355, GO, regulation of transcription, DNA-
1.221864
1.58E−06
5.909453
17.21626




dependent


4153
GLYMA03G36330
GO:0009870, GO, defense response signaling pathway,
0.856536
0.000672
6.648135
14.35544




resistance gene-dependent


4253
GLYMA18G44030
GO:0006355, GO, regulation of transcription, DNA-
0.998764
0.001135
5.793248
14.60451




dependent


4181
GLYMA06G45020
NA
0.657628
0.003708
31.22163
53.83414


4195
GLYMA09G00720
GO:0008150, GO, biological_process
0.90306
0.003708
2.788204
6.023027


4206
GLYMA10G44160
GO:0006355, GO, regulation of transcription, DNA-
0.819527
0.009033
13.67119
28.4095




dependent


4269
GLYMA20G35180
GO:0006355, GO, regulation of transcription, DNA-
0.663267
0.009033
13.62622
21.94128




dependent


4167
GLYMA04G40710
GO:0008150, GO, biological_process
0.829353
0.010992
12.55759
24.5565


4140
GLYMA02G40990
GO:0010200, GO, response to chitin
0.795223
0.01505
17.04244
34.59243


4183
GLYMA07G06320
GO:0006355, GO, regulation of transcription, DNA-
0.748416
0.015784
18.20323
33.46599




dependent


4142
GLYMA02G45420
GO:0006508, GO, proteolysis
0.894101
0.016107
21.73835
51.01902


4199
GLYMA09G30250
GO:0010200, GO, response to chitin
0.819331
0.017054
15.30126
37.9504


4250
GLYMA18G04770
GO:0010200, GO, response to chitin
0.787911
0.019874
39.88881
78.45926


4213
GLYMA11G25670
GO:0010193, GO, response to ozone
0.897841
0.02031
3.00749
8.634783


4150
GLYMA03G34780
GO:0006979, GO, response to oxidative stress
−0.91553
0.022156
2.078494
0.576236


4222
GLYMA12G12260
NA
0.730565
0.02231
26.27596
48.29082


4184
GLYMA07G11960
GO:0010200, GO, response to chitin
0.881315
0.026957
16.19823
43.02133


4131
GLYMA01G43420
GO:0006355, GO, regulation of transcription, DNA-
0.792195
0.0384
11.50233
22.27987




dependent


4223
GLYMA12G15620
GO:0005975, GO, carbohydrate metabolic process
0.802313
0.040823
13.75344
28.83591


4270
GLYMA03G37400
GO:0042545, GO, cell wall modification
0.166032
NA
0.052762975
0.213204512


4271
GLYMA03G38840
GO:0005975, GO, carbohydrate metabolic process
−0.91714
0.022324
1.793941164
0.576235643


4272
GLYMA07G15380
GO:0009693, GO, ethylene biosynthetic process
0.727432
0.132533
0.265339603
0.900027833


4273
GLYMA08G46450
GO:0005975, GO, carbohydrate metabolic process
−0.44339
0.684951
0.844207607
0.310280731


4274
GLYMA09G35840
GO:0005975, GO, carbohydrate metabolic process
−1.28626
1.70E−05
4.047392811
1.152471286


4275
GLYMA10G30340
GO:0008150, GO, biological_process
0.531076
0.317217
17.04402084
35.23204566


4276
GLYMA11G02350
GO:0005975, GO, carbohydrate metabolic process
−0.39592
0.826706
1.636260886
1.012721434


4277
GLYMA12G01510
GO:0005975, GO, carbohydrate metabolic process
−0.84175
0.059336
1.503591084
0.5400167


4278
GLYMA13G30440
GO:0008150, GO, biological_process
0.559495
0.472633
2.564949496
7.195652291


4279
GLYMA15G07700
PF00264, PFAM, Common central domain of tyrosinase
0.458456
0.694846
1.618957124
3.102807309


4280
GLYMA15G12600
GO:0006869, GO, lipid transport
0.833553
0.064382
3.165778525
12.27825178


4281
GLYMA17G08400
GO:0006032, GO, chitin catabolic process
0.945666
0.000294
6.191257405
16.26757546


4282
GLYMA17G14860
GO:0006869, GO, lipid transport
0.776484
0.105214
5.711320967
15.77999146


4283
GLYMA17G14890
GO:0006869, GO, lipid transport
0.617561
0.305278
10.76364699
25.8419523


4284
GLYMA18G47390
GO:0009611, GO, response to wounding
1.018065
0.000747
1.618957124
3.900672046


4285
GLYMA18G53440
GO:0008150, GO, biological_process
−2.04965
6.81E−35
91.12165855
16.84315647










This table describes soybean genes differentially expressed in soybean seedlings treated with an Acremonium zea sp. with neutral effects on soybean growth and soybean seedlings treated with an Acremonium zea sp. with beneficial effects on soybean growth. “Median Exp. Neutral” and “Median Exp. Beneficial” represent the median expression value in cpm across biological replicates of soy seedlings treated with the neutral Acremonium and beneficial Acremonium, respectively. “Log FC” represents the estimate of the log 2-fold-change of the contrast. “Adj. p-value” represents the false discovery rate (Benjamini & Hochberg, 1995) adjusted p-values.









TABLE 502







This table describes gene ontology terms which are significantly enriched or depleted in the set of genes differently


expressed between soybean seedlings treated with an Acremonium zea sp. with neutral effects on soybean


growth and soybean seedlings treated with a Acremonium zea sp. with beneficial effects on soybean growth.










GO ID
GO Description
Gene ID
SEQ ID





GO: 0000014
single-stranded
GLYMA15G07430, GLYMA15G07430
4286; 4286



DNA specific



endodeoxyribonuclease



activity


GO: 0003700
sequence-specific
GLYMA03G34730, GLYMA03G41750, GLYMA05G32040,
4288; 4295; 4292; 4296; 4297; 4201;



DNA binding
GLYMA06G11700, GLYMA08G16190, GLYMA09G41670,
4298; 4299; 4300; 4301; 4302; 4303;



transcription factor
GLYMA13G21350, GLYMA19G37410, GLYMA19G40650,
4304; 4305; 4288; 4306; 4292; 4307;



activity
GLYMA0041S00350, GLYMA01G41520, GLYMA01G44230,
4308; 4297; 4309; 4310; 4298; 4311;




GLYMA02G00290, GLYMA03G33070, GLYMA03G34730,
4312; 4313; 4314; 4299; 4131; 4148;




GLYMA04G35380, GLYMA05G32040, GLYMA06G20400,
4305; 4158; 4174; 4315; 4316; 4179;




GLYMA08G14320, GLYMA08G16190, GLYMA08G18470,
4183; 4188; 4308; 4193; 4317; 4201;




GLYMA13G18400, GLYMA13G21350, GLYMA15G00570,
4318; 4202; 4206; 4319; 4310; 4228;




GLYMA17G06610, GLYMA18G43580, GLYMA19G34740,
4311; 4320; 4245; 4248; 4253; 4259;




GLYMA19G37410, GLYMA01G43420, GLYMA03G05220,
4321; 4269




GLYMA03G33070, GLYMA04G04760, GLYMA05G34760,




GLYMA05G36970, GLYMA06G04840, GLYMA06G13090,




GLYMA07G06320, GLYMA08G02580, GLYMA08G14320,




GLYMA08G17140, GLYMA09G08330, GLYMA09G41670,




GLYMA10G04190, GLYMA10G04210, GLYMA10G44160,




GLYMA13G17250, GLYMA13G18400, GLYMA13G19560,




GLYMA15G00570, GLYMA15G19910, GLYMA17G05240,




GLYMA17G35430, GLYMA18G44030, GLYMA19G35740,




GLYMA19G35770, GLYMA20G35180


GO: 0003950
NAD+ ADP-
GLYMA04G35560
4289



ribosyltransferase



activity


GO: 0004222
metalloendopeptidase
GLYMA01G41750, GLYMA01G04350
4290; 4287



activity


GO: 0006308
DNA catabolic
GLYMA15G07430, GLYMA01G20900, GLYMA15G07430,
4286; 4322; 4286; 4322



process
GLYMA01G20900


GO: 0006879
cellular iron ion
GLYMA13G27300, GLYMA13G27300
4291; 4291



homeostasis


GO: 0006970
response to osmotic
GLYMA05G32040, GLYMA09G41670, GLYMA05G32040,
4292; 4201; 4292; 4148; 4201; 4253



stress
GLYMA03G05220, GLYMA09G41670, GLYMA18G44030


GO: 0008237
metallopeptidase
GLYMA01G41750, GLYMA01G04350
4290; 4287



activity


GO: 0008270
zinc ion binding
GLYMA01G41750, GLYMA01G04350, GLYMA03G33070,
4290; 4287; 4305; 4335; 4305; 4154;




GLYMA09G26100, GLYMA03G33070, GLYMA03G42390,
4158; 4159; 4316; 4206; 4228; 4248;




GLYMA04G04760, GLYMA04G09110, GLYMA06G04840,
4259; 4321




GLYMA10G44160, GLYMA13G19560, GLYMA17G35430,




GLYMA19G35740, GLYMA19G35770


GO: 0009611
response to
GLYMA06G45240, GLYMA06G45280, GLYMA06G45370,
4293; 4323; 4324; 4325; 4326; 4327;



wounding
GLYMA06G45410, GLYMA12G32750, GLYMA13G37720,
4328; 4284; 4329; 4293; 4324; 4325;




GLYMA13G37770, GLYMA18G47390, GLYMA01G41290,
4326; 4330; 4331; 4332; 4327; 4333;




GLYMA06G45240, GLYMA06G45370, GLYMA06G45410,
4328; 4311; 4334; 4284; 4158; 4316;




GLYMA12G32750, GLYMA13G23680, GLYMA13G35820,
4200; 4221; 4311; 4248; 4284




GLYMA13G35850, GLYMA13G37720, GLYMA13G37750,




GLYMA13G37770, GLYMA15G00570, GLYMA18G06810,




GLYMA18G47390, GLYMA04G04760, GLYMA06G04840,




GLYMA09G38930, GLYMA12G09830, GLYMA15G00570,




GLYMA17G35430, GLYMA18G47390


GO: 0010120
camalexin
GLYMA03G05220, GLYMA09G41670, GLYMA18G44030
4148; 4201; 4253



biosynthetic process


GO: 0016891
endoribonuclease
GLYMA15G07430, GLYMA15G07430
4286; 4286



activity, producing



5′-



phosphomonoesters


GO: 0034605
cellular response to
GLYMA03G05220, GLYMA09G41670, GLYMA18G44030
4148; 4201; 4253



heat


GO: 0043765
T/G mismatch-
GLYMA15G07430, GLYMA15G07430
4286; 4286



specific



endonuclease



activity


GO: 0046592
polyamine oxidase
GLYMA10G11700, GLYMA10G11700
4294; 4294



activity


GO: 0050660
flavin adenine
GLYMA04G12600, GLYMA10G11700, GLYMA10G11700,
4162; 4294; 4294; 4336; 4162; 4163; 4336



dinucleotide binding
GLYMA19G44870, GLYMA04G12600, GLYMA04G12610,




GLYMA19G44870


GO: 0070370
cellular heat
GLYMA03G05220, GLYMA09G41670, GLYMA18G44030
4148; 4201; 4253



acclimation


GO: 0071369
cellular response to
GLYMA13G27300, GLYMA13G27300
4291; 4291



ethylene stimulus


GO: 0071732
cellular response to
GLYMA13G27300, GLYMA13G27300
4291; 4291



nitric oxide


GO: 0072593
reactive oxygen
GLYMA04G35560
4289



species metabolic



process










“Genome count” represents the number of genes associated with the GO term that were found in the soybean genome. “Observed DEG count” represents the number of genes associated with the GO term that were differentially expressed in the Neutral v Beneficial contrast. “Expected DEG count” represents the number of genes associated with the GO term that are expected to be found by chance in a random set selection of that number of genes. “Status” represents whether genes with the GO term are over or under-represented in the set of DEGs. “Adj. p-value” represents the false discovery rate (Benjamini & Hochberg, 1995) adjusted p-values.


Genes that are modulated in soybean in response to treatment with a beneficial endophyte include those involved in a variety of plant processes, such as plant defense (including responses to chitin and wounding), stress responses (including salt stress, water deprivation, cold, ozone, heat, osmotic), defense against oxidative stress (oxidation-reduction process, monooxygenase activity, oxidation-reduction process, ion binding, nitric oxide). For example, expression of genes involved in the following processes were modulated: cell wall modification, defense response, oxidation-reduction process, biological process, regulation of transcription, metabolic process, glucosinolate biosynthetic process, response to karrikin, protein phosphorylation, protein folding, response to chitin, proteolysis, response to auxin stimulus, DNA-dependent regulation of transcription, N-terminal protein myristoylation, response to oxidative stress, cellular component, leaf senescence, resistance gene-dependent defense response signaling pathway, zinc ion binding, response to cold, malate metabolic process, transport, catalytic activity, response to ozone, VQ motif, regulation of systemic acquired resistance, potassium ion transport, anaerobic respiration, multicellular organismal development, response to heat, methyltransferase activity, response to wounding, oxidation-reduction process, monooxygenase activity, oxidation-reduction process, carbohydrate metabolic process, exocytosis, nuclear-transcribed mRNA poly(A) tail shortening, sodium ion transport, glycerol metabolic process, response to water deprivation, response to salt stress, and chlorophyll biosynthetic process.


Example 6: Functional Characterization of Endophytes (Microbe RNA-SEQ Experiments)

This Example describes the ability of synthetic compositions comprising plant seeds and a single endophyte strain or a plurality of endophyte strains described herein, to confer beneficial traits to a host plant. Among other things, this Example provides exemplary characterization of modulations in a beneficial endophyte's transcriptome in response to host plant interactions, as compared to transcriptome changes in the transcriptome of a neutral (e.g., non-beneficial and non-pathogenic) microbe of the same genus.


RNA sequencing was used to explore differences in mRNA expression of genes common to the two strains of Acremonium zeae.


Among other things, this Example describe the ability of host plants (e.g., host plants described herein, e.g., dicots, e.g., soy, peanuts, and monocots, e.g., corn, soy, wheat, cotton, sorghum) to differentially modulate the transcriptome of a beneficial endophyte as compared to the transcriptome of a neutral microbe of the same genus. This Example describes surprising and unexpected modulations in the transcriptome of a beneficial endophyte in response to whole plant homogenate, compared to a neutral fungal strain of the same genus.


In particular, this Example describes an exemplary transcriptomic comparison between the functional capacity of a beneficial fungal endophyte genome and the genome of a neutral fungal microbe of the same genus. Briefly, each set of microbial predicted genes was annotated with pathway and orthologous group information from the KEGG database. Pathways and ortholog groups appearing in one genome but not the other were extracted and manually explored for biological relevance to the phenotype differences.


Fungal Biomass


Beneficial (SYM00577) and neutral (SYM00300) fungal strains of Acremonium zeae were initially streaked onto PD agar and incubated at room temperature until colony formation. Distinct plugs consisting of spores and mycelia were used to inoculate 125 mL PD broth and cultured for 5 days at room temperature with agitation (200 RPM). Each strain was grown in three biological replicates in duplicates totaling 12 flasks.


On day 5 of culture, 1 mL of total plant homogenate obtained from 6 day old soybean seedlings extracted with 50 mM Phosphate-buffered saline (PBS) at a ratio of 2 mL buffer/gram plant mass was added to the fungi. The plant homogenate solution was prepared in three replicates, and each replicate was applied to the corresponding beneficial and neutral fungal cultures. One mL of PBS solution was applied to each fungal biological replicate as the negative control.


Fungal biomass was harvested 24 hours after the addition of either the plant homogenate or PBS only solutions by centrifuging at 4500 RPM for 20 minutes in 50 mL Falcon tubes to allow culture separation prior to the removal of supernatant. Fungal tissues were stored immediately in −80° C. until total RNA isolation using standard extraction method using TriReagent (Sigma-Aldrich, St. Louis, Mo., USA) and purification with RNeasy Mini Kit (Qiagen, Hilden, Germany).


Fungal RNA-SEQ


Initial quality control was performed using Agilent Bioanalyzer and Tapestation.


rRNA Depletion


1 μg of total RNA was subjected to rRNA depletion using the RiboZero Yeast kit (Epicentre Biotechnologies, Illumina.com, catalog # MRZY1306). Manufacturer's instructions were strictly followed to perform rRNA depletion.


Stranded cDNA Preparation


After rRNA depletion, depletedRNA was used to generate 1-2 ug of cDNA using: Illumina TruSeq Stranded Total RNA LT kit (Illumina.com, catalog # RS-122-2201). Manufacturer's instructions were strictly followed to perform cDNA construction; and library construction.


RNA Sequencing


Sequencing was performed on an Illumina HiSeq 2500, using Rapid run v2.0 chemistry which generated paired-end reads of 106 nucleotides according to Illumina manufacturer's instructions. The initial data analysis was started directly on the HiSeq 2500 System during the run. The HiSeq Control Software 2.2.58 in combination with RTA 1.18.64 (real time analysis) performed the initial image analysis and base calling. In addition, bcl2fastq1.8.4 generated and reported run statistics. Data was analyzed using FASTQC (Babraham Institute, Cambridge, UK) comprising the sequence information which was used for all subsequent bioinformatics analyses. Sequences were de-multiplexed according to the 6 bp index code with 1 mismatch allowed.


Analysis


Expression levels for each gene were quantified as transcripts per million (TPM) using Cufflinks. The Blast Best Reciprocal Hits (BRH) method was used to define orthologous groups for similar gene pairs across species. Expression was mapped directly to BRH groups to create an expression matrix and the limma method was used to uncover genes (1) differentially expressed with vs without plant homogenate within each species, (2) differentially expressed across species within each plant homogenate condition, and (3) responding differently to plant homogenate in the different species. The false discovery rate method was used to adjust p-values for multiple testing. In each case, significance was defined as adjusted p-value less than 0.05 and absolute log 2 fold change greater than 2.


Functional and Comparative Genomics


Prior to applying differential expression analysis, the functional capabilities of a beneficial and neutral Acremonium zeae, i.e., SYM00577 (beneficial) and SYM00300 (neutral), were contrasted at the gene function (GO) and pathway level. A shared goal of both the genome comparison and the transcriptome analyses was the construction of orthologous groups. In the case of comparative genomics, annotations of these orthologs provided an overview of shared capabilities, while for RNA-seq they provided anchors for comparison of expression data; i.e. rows in the expression matrix.


Differential KEGG Orthology Groups


The unique and shared orthology group (OG) terms were counted for SYM00577 and SYM00300. Most KO terms were shared by both strains, with 62 terms found in SYM00300 only, and 207 terms found in SYM00577 only, with 2,676 KO terms overlapping between both strains. This process was repeated for KEGG Pathways, and the total and shared number of pathways was again similar, with 324 of the pathways shared between strains. Unique pathways in SYM00577 that were not present in SYM00300, include, but are not limited to, indole diterpene alkaloid biosynthesis, biosynthesis of 12-, 14- and 16-membered macrolides, peptidoglycan biosynthesis, glycosphingolipid biosynthesis—lacto and neolacto series, indole alkaloid biosynthesis, type I polyketide structures, biosynthesis of siderophore group nonribosomal peptides, beta-Lactam resistance, sphingolipid signaling pathway, Vibrio cholera pathogenic cycle, central carbon metabolism in cancer, choline metabolism in cancer, and nicotinate and nicotinamide metabolism. Exemplary KEGG Pathway differences for SYM00577 are illustrated below in Table 600.









TABLE 600







Exemplary KEGG Pathways present in SYM0577,


but absent in SYM0300













Number



KEGG Term
KEGG Term Description
of Genes















ko00403
Indole diterpene alkaloid biosynthesis
1



ko00522
Biosynthesis of 12-, 14- and
1




16-memebered macrolides



ko00550
Peptidoglycan biosynthesis
2



ko00601
Glycosphingolipid biosynthesis -
1




lacto and neolacto series



ko00901
Indole alkaloid biosynthesis
1



ko01052
Type I polyketide structures
1



ko01053
Biosynthesis of siderophore
2




group nonribosomal peptides



ko01501
Beta-Lactam resistance
7



ko04071
Sphingolipid signaling pathway
46



ko05111
Vibrio cholera pathogenic cycle
1



ko05230
Central carbon metabolism in cancer
29



ko05231
Choline metabolism in cancer
30











In the above example, the Sphingolipid signaling pathway included 46 genes. To determine whether all of the genes (i.e., orthologous groups) in the pathway were unique to only SYM00577, a query was performed to determine which of the Sphingolipid pathway genes in SYM00577 do not share any KEGG OG terms with SYM00300 genes.


Interestingly, even though the Sphingolipid Signaling Pathway annotation is attached to 46 genes in SYM00577 but no genes in SYM00300, only one orthologous group from that pathway (sphingomyelin phosphodiesterase, annotating 4 genes) is not present in SYM300.


Unique pathways in SYM00300 that were not present in SYM00577, include, but are not limited to, beta-Lactam resistance, DDT degradation, Flavone and flavonol biosynthesis, and ECM-receptor interaction. Exemplary KEGG Pathway differences for SYM00300 are illustrated below in Table 700.









TABLE 601







Exemplary KEGG Pathways present in SYM0300,


but absent in SYM0577









KEGG Term
KEGG Term Description
Number of Genes





ko00312
Beta-Lactam resistance
4


ko00351
DDT degradation
3


ko00944
Flavone and flavonol biosynthesis
1


ko04512
ECM-receptor interaction
2









Blast Best Reciprocal Hits (BBRH)


The NCBI Blast+ software was installed and used to build blast databases from each set of amino acid sequences, then each transcriptome was blasted against the database created from the other. Best Reciprocal Hits (BRH) were calculated by filtering for high percent identity, gathering the best hits, and joining the targets from one output with the queries from the other. The result was a query-target-reciprocal trio, which was filtered for trios where the query was the same as its reciprocal. The e-value and bitscores from the two blast outputs were averaged (since they are asymmetric) for the BRH pairs, and an ortholog group identifier was created.


Calculation of in-Paralogs


In-paralogs are paralogs that are the result of speciation first, then duplication of the genes later. In-paralogs are more likely to retain the same function as the ortholog than out-paralogs, which represent duplication, followed by speciation. Considering the high proportion of SYM00300 genes that have BRH orthologs, along with the realization that SYM00577 has nearly twice as many transcripts, we considered the possibility of a major genome duplication event somewhere in the phylogenetic history of SYM00577, and extended the orthologous groups to include in-paralogs.


An important step after BRH is, for each orthologous pair, to include same-species genes more similar to each member of the pair than the cross-species ortholog similarity. This was accomplished using all-versus-all Blast within the same species, to expand our orthologous groups.


Another approach to building ortholog groups was to apply a threshold to the same-species hits for each member of the ortholog pairs. To find the best threshold, we explored the distribution of scores in these BRH/same-species tables described above, normalizing by the ortholog score.


RNA-SEQ Cross-Species Comparison


RNA-seq cufflinks FPKM values were generated for two species of fungus (Acremonium zeae), with three biological replicates each. An expression matrix was built using orthologouos groups, to explore the structure of the data, characterize data quality, and to elucidate pathway-level expression differences between SYM00577 and SYM00300.



















TABLE 602










Median
Median






SEQ ID
SYM577
SEQ ID
SYM300

Exp.
Exp.


t-
Adj. p-


SYM00577
gene
SYM00300
gene
Description
SYM00577
SYM00300
Log FC
B-statistic
statistic
value

























694
g3058.t1
2499
g1604.t1

0
5.625962
5.651891
7.35527
14.19007
8.51E−06


695
g3790.t1
2501
g2628.t1
K12486: SMAP
0
6.121031
5.983809
6.039604
11.33524
1.91E−05


681
g4581.t1
3296
g4123.t1
K00574: E2.1.1.79, cfa
0.511902
7.31261
7.115847
5.836125
10.97939
2.24E−05


682
g9772.t1
3297
g936.t1
K06874: K06874
1.832874
7.06298
5.150347
5.58339
10.56106
2.71E−05


1454
g3066.t1
2510
g11773.t1

0
4.229364
4.33707
5.111231
9.840967
4.33E−05


1455
g2768.t1
3298
g9143.t1
K03937: NDUFS4
0
3.159447
3.192054
5.100931
9.826062
4.35E−05


1456
g21086.t1
2530
g6575.t1

6.213302
0
−6.32587
4.86651
−9.49529
5.53E−05


1457
g13116.t1
2518
g7771.t1

0
4.229765
4.831879
4.862002
9.489083
5.54E−05


1458
g900.t1
3299
g9375.t1

0
2.925165
2.991998
4.824313
9.437402
5.73E−05


693
g2076.t1
2498
g2520.t1

3.957232
13.01167
9.729519
4.68583
9.250787
6.67E−05


1459
g5141.t1
3300
g3839.t1
K06662: HRAD17,
1.158624
7.175348
6.392146
4.57545
9.105599
7.49E−05






RAD24


1460
g10898.t1
2515
g5903.t1

0
2.733166
2.603795
4.241238
8.683922
0.000107


1461
g19933.t1
3301
g3124.t1
K10885: XRCC5, KU80,
0
2.454643
2.568635
4.162803
8.588628
0.000116






G22P2


685
g6380.t1
2492
g764.t1
K05857: PLCD
3.201415
9.359327
5.628694
3.892588
8.270189
0.000152


689
g849.t1
2496
g9453.t1
K06997: K06997
2.698993
7.96329
5.067599
3.750578
8.108628
0.000171


1462
g156.t1
3302
g5221.t1

0
2.981748
2.98057
3.513183
7.846843
0.000215


1463
g10541.t1
3303
g6687.t1
K17862: PPOC
0
2.880335
2.956642
3.496903
7.829254
0.000219


1464
g15671.t1
3304
g6482.t1
K11771: SWI1, ADR6
0
2.123699
2.319853
3.367017
7.690534
0.000246


1465
g5602.t1
2531
g7524.t1
K14774: UTP25, DEF
0
4.214818
5.146089
3.215759
7.532472
0.000282


1466
g4223.t1
3305
g1757.t1

2.289499
7.236816
5.448174
3.206971
7.523401
0.000284


684
g2536.t1
3306
g3569.t1

9.671862
2.518007
−7.85736
3.098463
−7.41238
0.000316


1467
g8228.t1
3307
g10052.t1
K01674: cah
5.638975
1.15932
−4.58017
2.941341
−7.25475
0.000366


1468
g10616.t1
3308
g4156.t1
K15562: BUR1, SGV1
0
4.260933
4.233331
2.939239
7.252662
0.000366


1469
g10359.t1
3309
g7715.t1

2.199706
9.30437
7.40778
2.907247
7.221016
0.000378


1470
g12048.t1
3310
g810.t1

0.205106
6.22836
5.696498
2.79987
7.11586
0.000412


1471
g7057.t1
3311
g6310.t1
K05610: UCHL5, UCH37
2.367427
6.390825
4.178102
2.772937
7.089735
0.000422


680
g1340.t1
2553
g523.t1

0
5.30819
5.122003
2.739527
7.057466
0.000434


1472
g5411.t1
3312
g8610.t1

0
5.724304
5.482331
2.691237
7.011091
0.000454


1474
g2755.t1
3314
g9155.t1
K13106: BUD13,
0
2.648734
2.611976
2.63723
6.959594
0.000475






CWC26


1473
g9212.t1
3313
g11325.t1
K03380: E1.14.13.7
0.695829
8.890455
7.737352
2.638623
6.960917
0.000475


1475
g7541.t1
3315
g7266.t1
K01230: MAN1
0.593738
3.991249
3.523245
2.589692
6.914582
0.000494


1476
g10543.t1
3316
g6689.t1
K11866: STAMBP,
0
2.512821
2.348519
2.557397
6.88417
0.000506






AMSH


1477
g1098.t1
3317
g4042.t1

0
8.363912
7.407417
2.550651
6.877834
0.000509


1478
g5757.t1
3318
g5200.t1
K16261: YAT
2.629263
6.731656
4.004055
2.491406
6.822441
0.000533


1479
g6616.t1
3319
g11275.t1
K00128: E1.2.1.3
14.15644
4.764987
−7.9496
2.391867
−6.73036
0.000579


676
g7741.t1
2557
g7091.t1

7.176506
3.981694
−3.40286
2.312767
−6.65805
0.000618


1480
g3094.t1
3320
g11797.t1
K02155: ATPeV0C,
0.181741
4.905207
4.139345
2.177837
6.536419
0.000699






ATP6L


1481
g4793.t1
3321
g3693.t1

0.802943
6.094219
5.125954
2.035034
6.409958
0.00079


1482
g4553.t1
3322
g4081.t1

1.09266
4.629
3.630404
1.987031
6.367956
0.000827


1483
g2790.t1
3323
g5023.t1

2.621767
6.913986
4.339207
1.945501
6.331819
0.000856


1484
g12353.t1
3324
g12077.t1

7.044527
1.163008
−6.15638
1.883313
−6.27805
0.0009


1485
g9391.t1
2535
g3643.t1
K12821: PRPF40, PRP40
3.337644
7.951706
4.079618
1.87347
6.269579
0.000908


1486
g501.t1
2522
g5516.t1
K11713: PGTB1
0.17786
7.158208
5.970183
1.860221
6.25819
0.000918


1487
g4315.t1
3325
g1973.t1
K00507: SCD, desC
2.439884
8.285639
5.723788
1.809797
6.215014
0.000956


1488
g9843.t1
3326
g9771.t1
K00799: GST, gst
8.277156
1.535981
−6.40337
1.808206
−6.21366
0.000956


1489
g11092.t1
3327
g7982.t1

2.025136
6.798845
4.871183
1.802892
6.209122
0.000958


1490
g11703.t1
3328
g6616.t1
K01785: galM, GALM
5.853172
0.587191
−5.06599
1.752712
−6.16645
0.001006


1491
g11062.t1
3329
g1580.t1

0
8.467134
6.867295
1.691984
6.115148
0.001064


1492
g13143.t1
3330
g4290.t1
K10878: SPO11
0
2.383986
2.169112
1.68932
6.112906
0.001065


1493
g10366.t1
2548
g5460.t1

0
4.099839
3.972778
1.675269
6.101093
0.001078


1494
g9622.t1
3331
g7240.t1
K01648: ACLY
0
2.029549
2.402941
1.580259
6.02172
0.00118


677
g13489.t1
2556
g8733.t1

4.049293
1.53096
−2.39019
1.568038
−6.01157
0.001191


1495
g11681.t1
3332
g10864.t1
K01081: E3.1.3.5
2.030435
5.800198
3.546964
1.557877
6.003149
0.001197


1496
g13112.t1
3333
g7720.t1

0
2.5721
2.197403
1.547012
5.99415
0.001208


1497
g6237.t1
2500
g7135.t1

4.217621
11.98228
7.390343
1.524373
5.975438
0.00123


1498
g5325.t1
2546
g2235.t1
K17794: TIM23
5.393638
9.737867
4.665515
1.490748
5.947736
0.001262


1499
g7356.t1
3334
g10411.t1

5.363476
2.004245
−4.00808
1.46351
−5.92537
0.001296


1500
g502.t1
2516
g5517.t1

6.13678
0.881592
−5.04567
1.401059
−5.87436
0.001355


1501
g8003.t1
3335
g3392.t1

1.075006
6.028587
4.451645
1.395621
5.869934
0.001362


691
g5563.t1
2493
g7478.t1

4.683265
9.926473
4.734657
1.388209
5.863907
0.00137


1502
g973.t1
3336
g8044.t1
K12733: PPIL1
0
4.446627
4.444962
1.37841
5.855946
0.001379


1503
g9616.t1
3337
g7246.t1

0
3.761644
3.227741
1.346391
5.829996
0.001416


1504
g2349.t1
3338
g9226.t1
K10865: MRE11
5.092776
8.748668
3.95033
1.335801
5.821433
0.001427


1505
g2683.t1
2507
g4140.t1

5.881648
1.482684
−3.92467
1.322012
−5.8103
0.001445


1506
g3045.t1
2533
g1615.t1

3.526626
10.01023
6.461973
1.267461
5.766418
0.00152


1507
g2056.t1
3339
g2541.t1

0
2.16783
2.561107
1.216459
5.725628
0.001583


521
g11059.t1
2317
g2900.t1
K01074: PPT
0
3.417929
3.812645
1.160246
5.680931
0.001668


1508
g7593.t1
3340
g7644.t1
K10577: UBE2I, UBC9
5.000466
0
−4.49434
1.150461
−5.67318
0.001683


1509
g1121.t1
3341
g220.t1

0.238182
9.960466
8.035072
1.140622
5.665391
0.00169


1510
g13554.t1
3342
g4591.t1

0
7.155818
7.18618
1.13793
5.663262
0.001694


1511
g10068.t1
3343
g4260.t1

3.254602
6.373357
2.860288
1.096613
5.630659
0.001757


1512
g3061.t1
3344
g11768.t1

0
2.736145
2.449758
1.082316
5.619411
0.001776


1513
g7120.t1
3345
g5585.t1
K01537: E3.6.3.8
6.177509
2.088352
−4.42526
1.079268
−5.61702
0.001776


1514
g1980.t1
3346
g6240.t1

4.780929
1.696677
−3.47296
1.055478
−5.59834
0.001816


1515
g15450.t1
3347
g6505.t1

0
3.663174
4.662175
1.041385
5.587303
0.001837


1516
g10937.t1
3348
g9861.t1

3.34381
8.292693
5.149782
1.007277
5.560652
0.001901


1517
g2104.t1
3349
g2481.t1

0
8.858449
6.876201
0.947423
5.514113
0.00201


1518
g1101.t1
3350
g4046.t1

0
4.4026
5.770884
0.936128
5.505363
0.002025


678
g2539.t1
2558
g3572.t1

2.326788
6.873537
4.818842
0.882431
5.463904
0.002121


1519
g3140.t1
3351
g5042.t1

0
2.321166
2.269216
0.871446
5.45545
0.002145


1520
g5369.t1
3352
g9557.t1

3.908588
6.910264
3.013639
0.855938
5.443533
0.002178


1521
g12261.t1
3353
g7374.t1
K00480: E1.14.13.1
0
8.154209
8.090694
0.846077
5.435964
0.002195


1522
g9519.t1
3354
g6593.t1
K03126: TAF12
0
9.766076
7.663496
0.828036
5.422137
0.002231


686
g857.t1
2491
g9451.t1
K01950: E6.3.5.1,
3.88692
0.53345
−3.15682
0.77121
−5.37875
0.002339






NADSYN1, QNS1, nadE


1523
g8434.t1
2550
g10211.t1

0
5.304746
5.464585
0.750938
5.363328
0.002378


1524
g6597.t1
3355
g10126.t1

0
4.518563
5.208532
0.74287
5.3572
0.002397


1525
g5093.t1
3356
g2950.t1
K14688: SLC30A1, ZNT1
0
2.409393
2.458919
0.737239
5.352927
0.0024


1526
g823.t1
3357
g8190.t1

3.431051
7.673807
3.935357
0.734868
5.351128
0.002404


1527
g839.t1
3358
g9466.t1

0
4.219241
4.683516
0.682084
5.311188
0.002522


1528
g13121.t1
3359
g11183.t1

0
6.54144
6.317655
0.656359
5.291798
0.002581


1529
g847.t1
3360
g9458.t1

8.023071
3.66916
−3.61918
0.631424
−5.27305
0.002636


1530
g4627.t1
3361
g6024.t1

0.792826
6.42714
5.759738
0.630803
5.272583
0.002636


1531
g10595.t1
3362
g10624.t1
K17987: NBR1
0
2.09236
2.123128
0.620131
5.264574
0.00266


1532
g12318.t1
3363
g7423.t1
K00166: BCKDHA,
0
2.598413
2.602354
0.593035
5.244275
0.002723






bkdA1


1533
g12695.t1
3364
g8902.t1
K10842: MNAT1
0
3.108472
2.951239
0.560072
5.219651
0.002803


1534
g14294.t1
3365
g4038.t1
K02980: RP-S29e,
5.882987
3.465017
−2.42606
0.543504
−5.2073
0.002847






RPS29


1535
g7862.t1
3366
g10519.t1
K13690: CMT1
4.585103
6.930322
2.588027
0.531605
5.198448
0.002873


1536
g2863.t1
3367
g11267.t1

0.167864
4.829719
5.552288
0.513015
5.184633
0.002917


1537
g1455.t1
2542
g6968.t1

4.374836
10.80524
6.455862
0.511076
5.183194
0.00292


1538
g2438.t1
3368
g6704.t1

9.091153
1.287615
−7.87656
0.465153
−5.14918
0.003038


1539
g667.t1
3369
g2708.t1
K10256: FAD2
0.327373
4.952806
4.589933
0.444695
5.134069
0.003073


1540
g4890.t1
3370
g4524.t1
K01530: E3.6.3.1
5.691668
0.913041
−4.25594
0.443497
−5.13319
0.003074


1542
g2756.t1
3372
g9154.t1

0
2.205609
2.199562
0.441939
5.132036
0.003074


1541
g20204.t1
3371
g9206.t1
K00274: MAO, aofH
0
6.517404
6.487337
0.442311
5.132311
0.003074


1543
g2398.t1
3373
g9298.t1

0
5.749657
5.429453
0.437917
5.12907
0.003085


1544
g9984.t1
3374
g9679.t1

0
7.061175
7.03614
0.33213
5.051456
0.003396


1545
g15304.t1
3375
g10452.t1

1.631174
5.484335
3.961905
0.302009
5.029495
0.00348


1547
g1470.t1
3377
g6945.t1

6.211143
0.601353
−6.20846
0.295485
−5.02475
0.003494


1546
g11003.t1
3376
g1982.t1

0
6.436399
5.197988
0.296732
5.025654
0.003494


1548
g142.t1
3378
g5823.t1
K09051: SKO1, ATF1,
2.033429
6.991069
5.119512
0.271682
5.007443
0.003566






PCR1


1549
g39.t1
3379
g2832.t1
K04450: ATF2, CREBP1
2.082302
6.377889
3.852174
0.21306
4.964987
0.003764


1550
g8675.t1
3380
g10949.t1

4.582792
1.158136
−3.14557
0.202072
−4.95705
0.003807


1551
g1012.t1
3381
g8081.t1
K01027: OXCT
5.414227
8.052451
2.663064
0.177006
4.938984
0.003878


1552
g2399.t1
3382
g9299.t1

1.458025
7.000976
4.992111
0.176335
4.938501
0.003878


1553
g6515.t1
3383
g2075.t1
K02950: RP-S12,
1.845883
4.922544
2.936732
0.153955
4.922403
0.003952






MRPS12, rpsL


1554
g6586.t1
2539
g10115.t1

5.631067
0.472025
−4.60323
0.143733
−4.91506
0.003983


1555
g8523.t1
3384
g6295.t1

0
7.66857
6.377663
0.128487
4.904122
0.004038


1556
g6667.t1
3385
g2221.t1

2.68424
6.205712
2.966025
0.118613
4.897045
0.00407


1557
g12827.t1
3386
g7851.t1

0
4.848962
3.8249
0.081084
4.870203
0.004213


1558
g5681.t1
3387
g2305.t1

0
5.574437
5.607999
0.076246
4.866749
0.004223


1559
g8598.t1
3388
g11593.t1

3.906492
6.364882
2.414039
0.063154
4.857409
0.004267


1560
g14604.t1
3389
g6507.t1

0.987454
5.421424
4.548644
0.028742
4.83291
0.004395


1561
g3926.t1
2519
g3966.t1

5.357872
3.212704
−2.19688
−0.01172
−4.8042
0.00456


1562
g3438.t1
3390
g4707.t1

1.724857
6.502863
4.96045
−0.02749
4.793029
0.004613


1563
g1922.t1
3391
g6158.t1
K08334: BECN1, VPS30,
0.398499
5.785388
4.960056
−0.03595
4.787047
0.004637






ATG6


1564
g3435.t1
3392
g4711.t1

0
8.300404
6.565756
−0.04588
4.780026
0.004676


1565
g11568.t1
3393
g4160.t1
K11322: EPC
2.908649
5.395163
2.502674
−0.05175
4.775878
0.004698


1566
g4022.t1
3394
g3195.t1

6.571337
1.444687
−5.93348
−0.05319
−4.77486
0.004702


1567
g1119.t1
3395
g218.t1
K15161: CCNC, SSN8
0
4.698233
4.08668
−0.05414
4.774192
0.004703


1568
g5372.t1
3396
g9560.t1

5.009004
0.930924
−4.29137
−0.05628
−4.77268
0.00471


1569
g8513.t1
3397
g6303.t1
K01417: E3.4.24.—
2.66779
6.304272
3.371495
−0.06746
4.764793
0.004752


1570
g10723.t1
3398
g4265.t1
K15078: SLX1
6.249677
1.09824
−5.32732
−0.07338
−4.76062
0.004767


1571
g7955.t1
3399
g10265.t1

7.449289
0.568709
−6.91497
−0.08661
−4.7513
0.004818


1572
g8436.t1
3400
g7726.t1
K08257: E3.2.1.101
0
5.100303
5.10056
−0.1098
4.73499
0.004903


1573
g1465.t1
3401
g6950.t1

4.476144
0.61942
−4.17994
−0.11145
−4.73383
0.004908


1574
g2407.t1
3402
g9484.t1
K13127: RNF113A,
7.768564
2.987939
−3.79401
−0.11976
−4.728
0.00494






CWC24


1575
g2487.t1
3403
g3514.t1
K15192: BTAF1, MOT1
3.532261
7.801782
4.747107
−0.1259
4.723684
0.00496


1576
g6309.t1
3404
g3004.t1

2.982283
6.81987
3.754204
−0.13074
4.720289
0.004976


1577
g1705.t1
3405
g4639.t1

1.748524
7.933591
6.241738
−0.13773
4.715388
0.005007


1578
g6321.t1
3406
g3017.t1

9.8442
5.01489
−4.79374
−0.14476
−4.71045
0.005035


1579
g4284.t1
3407
g1936.t1
K18174: COA2
1.986154
6.571374
4.216021
−0.15159
4.705676
0.005055


1580
g20937.t1
3408
g7417.t1
K01266: dmpA
1.071718
4.362008
3.114427
−0.16727
4.694696
0.005126


1581
g6962.t1
3409
g6429.t1

5.332152
0.25936
−5.40138
−0.16906
−4.69345
0.005132


1582
g18713.t1
3410
g4630.t1
K03083: GSK3B
1.333651
4.783178
4.745248
−0.17254
4.69101
0.005148


1583
g8296.t1
3411
g5088.t1

5.102827
0.74787
−5.06033
−0.17731
−4.68768
0.005171


1584
g1028.t1
3412
g8097.t1
K10352: MYH
0
5.91366
5.909517
−0.18093
4.685146
0.005187


1585
g7984.t1
3413
g10232.t1

4.17451
0
−3.96717
−0.18723
−4.68075
0.005215


1586
g2260.t1
3414
g10672.t1

0
11.59719
8.078404
−0.20485
4.668452
0.005296


1587
g2057.t1
3415
g2540.t1

0
3.495725
2.912854
−0.21761
4.659559
0.005358


1265
g16176.t1
2509
g5232.t1

4.464184
8.046322
3.412183
−0.22053
4.657525
0.005368


1588
g710.t1
3416
g9945.t1

3.004512
5.305027
3.457727
−0.26143
4.629086
0.005573


1589
g11909.t1
3417
g11960.t1
K00967: PCYT2
4.581714
0.355634
−4.34247
−0.2642
−4.62716
0.005582


1590
g133.t1
3418
g5828.t1

0
6.458979
5.351051
−0.2661
4.625846
0.005584


1591
g16811.t1
3419
g6747.t1

5.812564
0.429992
−4.86386
−0.27492
−4.61972
0.005629


1592
g1007.t1
3420
g8077.t1

8.250805
2.385735
−4.65062
−0.27955
−4.61651
0.005649


1593
g2691.t1
3421
g3101.t1

6.59247
0.374474
−6.18721
−0.28128
−4.61531
0.005656


1594
g941.t1
3422
g9318.t1
K01067: E3.1.2.1, ACH1
1.499245
7.499861
6.073538
−0.318
4.5899
0.005824


1595
g4067.t1
3423
g3251.t1

3.814933
6.244839
2.600899
−0.32454
4.585383
0.005862


1596
g7999.t1
3424
g3379.t1

3.95884
1.293984
−3.01927
−0.36383
−4.55828
0.006086


1597
g6280.t1
3425
g12254.t1
K13719: OTU1, YOD1
10.87548
3.850161
−7.09783
−0.38264
−4.54533
0.006175


1598
g2441.t1
3426
g6710.t1

7.528783
1.563904
−5.0227
−0.39468
−4.53706
0.006224


1599
g6940.t1
3427
g6448.t1

0
6.016039
5.937675
−0.41441
4.523508
0.006341


1601
g5186.t1
3429
g3777.t1
K02934: RP-L6e, RPL6
4.28578
0
−4.72311
−0.41768
−4.52127
0.006349


1600
g3254.t1
3428
g8225.t1

0
5.869262
5.544325
−0.41746
4.521417
0.006349


1602
g2757.t1
3430
g9153.t1
K15053: CHMP7
0
2.528581
2.167777
−0.42072
4.519182
0.006365


1603
g8191.t1
3431
g9716.t1

2.640244
5.393849
2.932616
−0.42423
4.51677
0.006385


1604
g41.t1
2544
g2830.t1
K10740: RPA3
5.456896
1.684193
−3.50612
−0.43149
−4.5118
0.006426


1605
g7930.t1
3432
g2853.t1
K01077: E3.1.3.1, phoA,
5.436852
2.710109
−4.15755
−0.43376
−4.51024
0.006432






phoB


1606
g9899.t1
3433
g3476.t1

0
5.790708
5.501572
−0.43434
4.509842
0.006432


1607
g6747.t1
3434
g4361.t1
K08793: STK32, YANK
1.640577
7.804707
6.025167
−0.43912
4.506569
0.006449


1609
g3450.t1
3436
g4695.t1
K11319: ING3
7.793056
1.832762
−5.3581
−0.44607
−4.50182
0.006476


1608
g13903.t1
3435
g687.t1
K01426: E3.5.1.4, amiE
2.308161
5.757553
3.146851
−0.44596
4.501889
0.006476


1610
g4174.t1
3437
g1802.t1
K03164: TOP2
0
4.461914
4.257824
−0.44926
4.499626
0.006485


1611
g1817.t1
3438
g1704.t1
K13941: folKP
1.569971
6.747653
4.234672
−0.45137
4.498183
0.00649


1612
g16037.t1
3439
g4108.t1
K01744: aspA
4.664569
6.76341
2.175875
−0.45455
4.496007
0.006508


1613
g10914.t1
3440
g5925.t1

1.756741
4.535424
3.244364
−0.46789
4.486892
0.006589


1614
g138.t1
3441
g3729.t1

4.847226
0.925828
−5.03041
−0.47101
−4.48476
0.006598


1615
g2936.t1
3442
g5964.t1

8.044894
0.248534
−6.73944
−0.47284
−4.4835
0.006601


1616
g8866.t1
3443
g2108.t1
K13339: PEX6, PXAAA1
11.8966
2.107495
−8.86497
−0.48781
−4.47329
0.006671


1617
g4740.t1
3444
g2014.t1
K02606: ORC4
4.269663
1.432791
−2.74295
−0.48799
−4.47317
0.006671


1618
g17490.t1
3445
g10534.t1
K10777: LIG4, DNL4
1.37437
7.556488
5.810689
−0.48948
4.472145
0.006674


1619
g6095.t1
3446
g7353.t1

10.01399
0.524763
−9.03171
−0.51858
−4.45231
0.006833


1620
g1092.t1
3447
g4035.t1

1.619955
5.721483
3.640435
−0.53362
4.442078
0.006907


1621
g12252.t1
3448
g235.t1

0.132439
3.243255
3.821541
−0.53381
4.441948
0.006907


1622
g6796.t1
3449
g4421.t1
K03680: EIF2B4
5.126406
0.843849
−4.22061
−0.54287
−4.43579
0.006966


1623
g797.t1
3450
g8161.t1

0
3.053206
2.866046
−0.55063
4.430521
0.007005


1624
g5647.t1
3451
g1105.t1

5.271321
0.695521
−5.99485
−0.556
−4.42687
0.007028


1625
g15866.t1
3452
g9844.t1

2.040941
8.117785
5.437517
−0.57127
4.416512
0.007114


1626
g6617.t1
3453
g11274.t1
K13953: adhP
9.164416
5.669006
−3.74273
−0.57468
−4.41419
0.007135


1628
g6780.t1
3455
g4396.t1

4.325036
1.1994
−3.75976
−0.57681
−4.41275
0.007142


1627
g5153.t1
3454
g3822.t1

1.244336
5.595008
3.814632
−0.57638
4.413043
0.007142


1629
g5834.t1
3456
g1171.t1
K04393: CDC42
5.842709
0.801203
−4.48638
−0.5775
−4.41229
0.007142


1630
g5375.t1
3457
g9563.t1

6.246832
2.775505
−3.21809
−0.59214
−4.40237
0.007231


1631
g10368.t1
3458
g5462.t1
K00826: E2.6.1.42, ilvE
0.323199
4.887494
4.532182
−0.59353
4.401421
0.007232


1632
g2826.t1
3459
g9093.t1

5.715948
1.969325
−4.3438
−0.60813
−4.39154
0.007312


1633
g8263.t1
3460
g10014.t1
K09540: SEC63
1.178199
4.647047
3.105882
−0.60945
4.390652
0.007317


1634
g1996.t1
3461
g6244.t1

0
2.161944
2.537016
−0.61338
4.387995
0.007343


1636
g565.t1
3463
g3893.t1

7.212095
4.016141
−3.8261
−0.62616
−4.37935
0.007416


1635
g10532.t1
3462
g6657.t1

0
6.423209
4.950366
−0.62535
4.379902
0.007416


1637
g9223.t1
3464
g6550.t1
K14402: CPSF2, CFT2
4.757601
1.422654
−3.02304
−0.63182
−4.37553
0.007456


1638
g4375.t1
3465
g2132.t1
K17777: TIM9
6.581887
2.288969
−5.04428
−0.64088
−4.36942
0.007514


1639
g3924.t1
3466
g3968.t1
K03854: KTR
4.507947
8.80016
3.527047
−0.64187
4.368744
0.007517


1640
g5877.t1
3467
g10964.t1

1.237514
5.716716
4.577402
−0.65497
4.359912
0.007609


1641
g7244.t1
3468
g10768.t1

1.270272
6.454926
4.671181
−0.66639
4.35221
0.007694


1642
g3215.t1
3469
g6111.t1

6.28213
1.918338
−4.18097
−0.67385
−4.34719
0.007746


1643
g2744.t1
3470
g8873.t1

12.4437
4.004642
−6.34323
−0.67665
−4.3453
0.007764


1644
g10172.t1
3471
g8453.t1

1.719814
6.975262
4.867858
−0.67848
4.34407
0.007769


1646
g11998.t1
3473
g2455.t1
K01792: E5.1.3.15
4.113876
1.68217
−2.91764
−0.68435
−4.34012
0.007808


1645
g9935.t1
3472
g6028.t1

0
5.001669
5.050202
−0.68376
4.340518
0.007808


1647
g9810.t1
3474
g10828.t1

6.142355
2.944412
−3.12615
−0.68611
−4.33894
0.007817


1648
g2585.t1
3475
g1533.t1

1.186682
5.314928
4.416457
−0.70324
4.327418
0.007953


1649
g5812.t1
3476
g7683.t1

0.086084
5.755875
5.49766
−0.70639
4.3253
0.00797


1650
g7613.t1
3477
g7623.t1
K12177: COPS3, CSN3
6.832706
1.20583
−6.6405
−0.71007
−4.32283
0.007995


1651
g21752.t1
3478
g11785.t1

9.138517
2.10622
−5.18056
−0.71052
−4.32253
0.007995


1652
g8125.t1
3479
g7937.t1
K14829: IPI3
5.635984
8.165687
3.420929
−0.71501
4.319512
0.008023


1653
g1265.t1
3480
g446.t1

0
2.255216
2.515104
−0.72389
4.313556
0.008084


1654
g1851.t1
3481
g1893.t1
K14806: DDX31, DBP7
4.180789
6.833176
3.613285
−0.72476
4.312968
0.008086


1655
g5970.t1
3482
g7911.t1

0.787727
4.745143
3.037594
−0.72641
4.311862
0.00809


1656
g9210.t1
3483
g432.t1

0
5.395553
4.999741
−0.72979
4.309594
0.008103


1657
g4885.t1
3484
g5284.t1
K00451: HGD, hmgA
2.711021
9.250394
4.936597
−0.75813
4.290601
0.008322


1658
g9727.t1
3485
g1208.t1

0
2.707059
2.656284
−0.77155
4.281622
0.008405


1659
g1852.t1
3486
g1892.t1

9.129284
5.622142
−2.9499
−0.77281
−4.28078
0.008408


1661
g4708.t1
3488
g2052.t1

5.134526
2.604627
−2.75857
−0.77636
−4.27841
0.008419


1662
g1264.t1
3489
g447.t1
K07975: K07975
0
3.433264
3.424199
−0.77691
4.27804
0.008419


1660
g9176.t1
3487
g6513.t1

1.38307
7.023037
5.604965
−0.77564
4.27889
0.008419


1663
g10978.t1
3490
g5642.t1

0
9.109111
6.49256
−0.77811
4.277239
0.00842


1664
g7775.t1
3491
g849.t1

5.558934
1.67851
−5.74356
−0.78625
−4.2718
0.008488


1665
g10472.t1
3492
g2156.t1

1.835908
10.72995
8.679924
−0.80576
4.258766
0.008642


1666
g11361.t1
3493
g11673.t1
K01613: psd, PISD
5.614261
0.835332
−3.65067
−0.81024
−4.25578
0.008666


1667
g5499.t1
3494
g4955.t1

4.580901
7.497146
2.894342
−0.81895
4.249973
0.008726


1668
g8184.t1
3495
g5029.t1
K05607: AUH
3.031275
0
−3.53658
−0.84752
−4.23094
0.008935


1669
g9878.t1
3496
g11628.t1
K05755: ARPC4
0
8.072633
7.232249
−0.84945
4.229652
0.008948


1670
g10675.t1
3497
g8521.t1
K00688: E2.4.1.1, glgP,
0.169628
5.781937
5.478988
−0.85152
4.228278
0.008956






PYG


1671
g9232.t1
3498
g3432.t1
K00545: COMT
7.296935
0.411124
−6.22613
−0.8545
−4.2263
0.00898


1672
g9988.t1
3499
g9675.t1
K00130: betB, gbsA
0
2.553591
3.110324
−0.86233
4.221089
0.009044


1673
g1414.t1
3500
g6284.t1

2.311758
6.717528
4.69322
−0.86385
4.220079
0.009053


1674
g6733.t1
3501
g4345.t1
K09043: AP1F
0
5.001212
4.248888
−0.86816
4.217209
0.00909


1675
g7043.t1
3502
g6332.t1

5.859345
10.2543
4.890605
−0.88033
4.209124
0.009187


1676
g2705.t1
3503
g8367.t1
K00528: E1.18.1.2, fpr
7.551805
3.162022
−5.08662
−0.88328
−4.20717
0.009204


1677
g10342.t1
3504
g51.t1

0
5.678545
5.567869
−0.88506
4.205988
0.00921


1678
g5928.t1
3505
g11021.t1
K09885: AQPF
5.755454
0.419682
−5.37723
−0.89503
−4.19937
0.009274


1679
g8175.t1
3506
g7987.t1

1.51165
7.320745
5.975986
−0.89646
4.198423
0.009275


1680
g8032.t1
3507
g4282.t1

0
4.127275
3.299567
−0.91209
4.188055
0.009398


1681
g9814.t1
3508
g10824.t1
K03062: PSMC1, RPT2
1.362902
5.056672
3.336585
−0.91516
4.186022
0.009415


1682
g11969.t1
3509
g7462.t1

0.489568
5.568038
4.427228
−0.91543
4.185844
0.009415


1683
g10790.t1
3510
g10663.t1

0.828146
4.846815
3.562604
−0.92472
4.179692
0.009497


1684
g4805.t1
3511
g1632.t1

8.950015
5.163246
−3.59682
−0.93185
−4.17497
0.009558


1685
g6554.t1
3512
g10090.t1
K15565: CTK3
5.222663
0.144855
−4.83662
−0.93476
−4.17304
0.009576


1686
g1116.t1
3513
g4063.t1

1.005429
5.625694
3.855418
−0.94482
4.16639
0.009663


1687
g8449.t1
3514
g2682.t1
K05954: FNTB
0
5.399599
4.115948
−0.95049
4.162638
0.009697


1689
g6525.t1
3516
g2064.t1
K09493: CCT1, TCP1
9.538137
1.667123
−6.73424
−0.95515
−4.15956
0.009725


1690
g5857.t1
3517
g1146.t1
K02320: POLA1
3.021693
6.891883
4.04023
−0.95542
4.159376
0.009725


1688
g1274.t1
3515
g460.t1

0
6.05494
9.515249
−0.95514
4.159568
0.009725


1691
g12431.t1
3518
g10686.t1
K07127: uraH, pucM,
0
5.825339
4.833292
−0.95677
4.158489
0.009733






hiuH


1692
g5322.t1
3519
g2238.t1
K03426: E3.6.1.22,
5.48509
2.765673
−3.98262
−0.95893
−4.15706
0.009743






NUDT12, nudC


1693
g10361.t1
3520
g7713.t1

2.118062
5.477606
3.633039
−0.96411
4.153638
0.009765


1694
g2712.t1
3521
g8360.t1

6.902933
0.496994
−4.89563
−0.97385
−4.1472
0.009833


1695
g6927.t1
3522
g6460.t1
K00485: FMO
9.696666
1.489752
−6.7401
−0.98605
−4.13915
0.009945


1696
g6520.t1
3523
g2069.t1

7.419005
0.788997
−5.06498
−0.98929
−4.13702
0.009974


1697
g15004.t1
3524
g3115.t1

4.410253
0.439607
−3.37848
−0.99169
−4.13543
0.009991


1698
g13717.t1
3525
g9904.t1
K01426: E3.5.1.4, amiE
2.122753
4.721599
2.459777
−0.99262
4.134823
0.009991


1699
g11731.t1
3526
g5851.t1
K00804: GGPS1
0.641201
8.014106
6.275604
−0.99873
4.130792
0.010032


1700
g12319.t1
3527
g7427.t1
K06127: COQ5
0
3.18054
4.279183
−1.0114
4.122445
0.010158


1037
g11120.t1
2520
g739.t1
K11309: RTT109, KAT11
4.245031
0.362852
−4.44703
−1.02232
−4.11525
0.010262


1701
g10208.t1
3528
g11172.t1
K08737: MSH6
5.231935
0.620193
−4.43745
−1.02255
−4.11511
0.010262


1702
g4510.t1
3529
g10815.t1

0.110413
4.81464
3.815621
−1.03144
4.109255
0.010342


1703
g10697.t1
3530
g8542.t1
K01702: LEU1
0.263634
7.912518
6.023521
−1.04447
4.100686
0.010463


1704
g15805.t1
3531
g2331.t1
K02154: ATPeV0A,
0
2.888609
4.034147
−1.04529
4.100149
0.010465






ATP6N


1705
g5031.t1
3532
g9002.t1
K02830: HRAD1, RAD17
3.089916
5.598348
2.991585
−1.04815
4.098268
0.010485


1706
g5436.t1
3533
g3139.t1
K16261: YAT
5.060429
1.262422
−4.0977
−1.04901
−4.0977
0.010485


1707
g4238.t1
3534
g1742.t1

1.066099
4.155929
2.917914
−1.053
4.09508
0.010521


1708
g10868.t1
3535
g125.t1

0
3.653087
3.440687
−1.05442
4.094146
0.01053


1709
g6783.t1
3536
g4399.t1

6.220556
1.013936
−4.77542
−1.0556
−4.09337
0.010537


1710
g3062.t1
3537
g11769.t1

0
2.560725
2.204735
−1.06092
4.089879
0.010585


1711
g10221.t1
3538
g11208.t1

6.889613
0.40438
−7.11534
−1.06965
−4.08415
0.010672


1712
g1829.t1
3539
g1715.t1

5.791735
1.495617
−4.17043
−1.08999
−4.07081
0.010861


1713
g8326.t1
3540
g5128.t1
K00505: TYR
3.610494
6.260581
3.534926
−1.09636
4.066632
0.010911


1714
g3155.t1
3541
g4991.t1

3.59858
7.647083
3.797219
−1.11173
4.056562
0.011074


1715
g2222.t1
3542
g11603.t1

0.225549
4.813511
4.351037
−1.12206
4.049805
0.011164


1716
g11759.t1
3543
g10216.t1

3.685926
0
−4.53515
−1.12292
−4.04924
0.011168


1717
g8206.t1
3544
g8502.t1

3.420719
10.03021
6.493771
−1.1248
4.048012
0.011183


679
g4287.t1
2759
g1939.t1
K00275: pdxH, PNPO
0.807563
3.090838
2.176492
−1.13595
4.040719
0.011299


690
g7926.t1
2497
g8597.t1

6.166677
8.61834
2.778981
−1.13847
4.039073
0.011322


1718
g4064.t1
3545
g3254.t1
K00002: AKR1A1, adh
6.100438
1.079083
−4.91125
−1.15384
−4.02903
0.01147


1720
g5795.t1
3547
g4862.t1
K00451: HGD, hmgA
3.591089
6.8767
2.956306
−1.15712
4.026889
0.011485


1719
g5609.t1
3546
g7533.t1

0.882686
5.320606
3.796705
−1.15678
4.027112
0.011485


1721
g19766.t1
3548
g11689.t1
K08272: CAB39, MO25
4.724331
1.509326
−3.78959
−1.16405
−4.02236
0.011549


1722
g7985.t1
3549
g10231.t1

0
4.06043
3.846952
−1.16466
4.021964
0.01155


1723
g4377.t1
3550
g2134.t1

14.14762
6.168036
−7.54239
−1.1682
−4.01966
0.01158


1724
g10842.t1
3551
g9831.t1
K15283: SLC35E1
3.417746
7.907833
4.552081
−1.17777
4.013415
0.011665


1725
g3810.t1
3552
g5153.t1
K01539: ATP1A
5.831954
9.975934
4.809042
−1.1815
4.010981
0.011698


1726
g4351.t1
3553
g2123.t1

2.978188
5.643247
2.777696
−1.19302
4.003473
0.011817


1727
g12887.t1
3554
g7811.t1
K03868: RBX1, ROC1
0
6.027624
4.370298
−1.19414
4.002739
0.011824


1728
g13707.t1
3555
g7796.t1
K04706: PIAS1
6.517298
4.766243
−2.04941
−1.20773
−3.99389
0.011956


1729
g16831.t1
3556
g10344.t1

6.338633
1.444662
−4.08292
−1.20964
−3.99265
0.011974


1731
g3916.t1
3558
g3976.t1

4.817018
0.75673
−4.65895
−1.22292
−3.98401
0.012097


1730
g5660.t1
3557
g1082.t1

0
4.671882
3.638252
−1.22213
3.984518
0.012097


1732
g9151.t1
3559
g6484.t1

6.278283
0.8931
−5.76977
−1.23184
−3.9782
0.012199


1733
g12202.t1
3560
g9295.t1

0.672484
4.169208
2.907439
−1.23665
3.975077
0.012241


1734
g5282.t1
3561
g2288.t1

4.202468
0.654126
−3.30483
−1.23744
−3.97457
0.012244


1735
g7572.t1
3562
g7669.t1

3.978653
7.606234
3.70123
−1.2385
3.973875
0.012244


1736
g3235.t1
3563
g8210.t1

4.470468
8.184527
5.15127
−1.24494
3.969692
0.012307


697
g852.t1
2502
g9454.t1
K11824: AP2A
4.880882
7.286171
2.290375
−1.24576
3.969158
0.012307


1737
g6716.t1
3564
g4321.t1

9.948221
2.821953
−6.95531
−1.25354
−3.9641
0.012386


1738
g2067.t1
3565
g2530.t1

7.69826
4.922109
−3.56419
−1.26788
−3.95479
0.012535


1739
g7743.t1
3566
g7093.t1

2.175372
4.617996
2.642137
−1.27196
3.95215
0.0125706


1740
g5491.t1
3567
g9819.t1

9.301085
2.365816
−5.52656
−1.27566
−3.94974
0.012619


1741
g10936.t1
3568
g2319.t1

8.259645
1.32013
−5.22157
−1.27719
−3.94876
0.012632


939
g4598.t1
2528
g6014.t1

4.80428
1.524453
−3.6354
−1.2848
−3.94382
0.012715


1742
g10549.t1
3569
g6695.t1

0
1.785939
2.000492
−1.29585
3.936658
0.012829


527
g4985.t1
2324
g8953.t1

0.777528
7.11879
6.4966
−1.30752
3.929102
0.012948


578
g8174.t1
2376
g7986.t1

1.469754
6.185503
4.308101
−1.31185
3.926293
0.012985


1743
g2143.t1
3570
g11929.t1
K00772: E2.4.2.28,
4.8374
0.969878
−3.56778
−1.3345
−3.91164
0.013284






mtaP


1744
g9848.t1
3571
g9777.t1
K06970: rlmF
9.547112
5.371618
−3.97134
−1.34065
−3.90767
0.013349


1745
g12220.t1
3572
g11110.t1
K07870: RHOT1, ARHT1
3.884302
6.478847
3.518086
−1.34423
3.905351
0.013393


1746
g2291.t1
3573
g10709.t1

5.385805
9.526471
4.775916
−1.34937
3.902029
0.013444


1747
g2147.t1
3574
g11880.t1
K14789: NOP6
6.507448
1.977499
−4.68012
−1.35307
−3.89964
0.013467


1748
g6355.t1
3575
g794.t1
K00236: SDHC, SDH3
0.536878
6.254053
4.787495
−1.36034
3.894946
0.013558


1749
g2869.t1
3576
g11261.t1

0.327373
6.340001
4.80532
−1.36591
3.891347
0.013632


1750
g2360.t1
3577
g9254.t1
K12200: PDCD6IP, ALIX,
3.801939
1.686361
−2.17748
−1.36819
−3.88988
0.013658






RIM20


1751
g3560.t1
3578
g3325.t1

6.818439
0.789095
−4.92675
−1.37135
−3.88784
0.013689


1752
g10589.t1
3579
g7032.t1

0
2.526539
3.338928
−1.37427
3.885952
0.013716


1753
g16530.t1
3580
g8785.t1

4.610888
0.254363
−4.08665
−1.38154
−3.88126
0.013816


1754
g5177.t1
3581
g3786.t1
K03321: TC.SULP
4.026352
0.667334
−3.40117
−1.38727
−3.87757
0.013878


1755
g9386.t1
3582
g3647.t1
K01082: E3.1.3.7, cysQ,
7.430096
4.382531
−3.00795
−1.38737
−3.8775
0.013878






MET22, BPNT1


1756
g6130.t1
3583
g7316.t1
K08657: TASP1
0.095949
5.575509
5.53383
−1.38749
3.87743
0.013878


1757
g8530.t1
3584
g6289.t1
K05532: MNN11
0
5.816826
4.892278
−1.38966
3.876025
0.013899


1758
g21699.t1
3585
g5541.t1
K03448: FEN2, LIZ1
0.735044
3.625342
2.870907
−1.39176
3.874673
0.013906


1759
g9934.t1
3586
g6029.t1
K16575: ACTR1, ARP1
0
5.832405
5.597162
−1.39893
3.870056
0.013978


1760
g4777.t1
3587
g3680.t1

3.32587
5.729749
2.411959
−1.4021
3.868009
0.014015


1761
g11542.t1
3588
g4184.t1

7.517977
2.707186
−4.47011
−1.41398
−3.86036
0.014171


1762
g2157.t1
3589
g11896.t1

3.702226
7.226007
3.353898
−1.41467
3.859914
0.014174


1763
g16189.t1
3590
g1458.t1
K14454: GOT1
10.63207
6.499538
−6.07526
−1.41542
−3.85943
0.014178


1764
g8348.t1
3591
g5159.t1

4.264457
6.507615
2.242904
−1.41809
3.857714
0.014202


1765
g1259.t1
3592
g452.t1

2.440869
6.057593
3.423879
−1.42343
3.854274
0.01426


1766
g2764.t1
3593
g9147.t1
K10745: RNASEH2C
0
2.695204
3.586065
−1.42688
3.852056
0.014297


1767
g7927.t1
3594
g8596.t1

4.918651
7.912131
3.059833
−1.4292
3.850562
0.014312


1768
g2676.t1
3595
g4133.t1
K00294: E1.2.1.88
0.612742
5.41036
4.447987
−1.4294
3.850434
0.014312


1769
g7548.t1
3596
g7259.t1

0.649867
5.412471
4.266032
−1.43441
3.847211
0.014366


1771
g5182.t1
3598
g3781.t1

9.026587
2.801517
−6.79697
−1.43708
−3.84549
0.014391


1770
g7942.t1
3597
g9703.t1

2.085423
7.573442
5.338061
−1.43698
3.845559
0.014391


1772
g4091.t1
3599
g3293.t1
K01687: ilvD
6.303323
0.815929
−5.63696
−1.43932
−3.84405
0.014418


1773
g12310.t1
3600
g7399.t1

0
7.275303
5.468252
−1.44443
3.840765
0.014489


1774
g3831.t1
3601
g2596.t1
K07005: K07005
0
4.871672
3.653881
−1.4486
3.838085
0.014546


1776
g3521.t1
3603
g2212.t1
K10666: RNF5
4.087847
5.915388
2.294451
−1.45392
3.834664
0.014606


1775
g22438.t1
3602
g4987.t1

5.797361
8.454162
3.989287
−1.45372
3.834797
0.014606


1777
g4129.t1
3604
g1851.t1

3.118092
5.15901
2.22408
−1.45469
3.834169
0.01461


1778
g12080.t1
3605
g7812.t1

5.157342
0.417205
−5.18316
−1.4566
−3.83294
0.014632


1779
g18095.t1
3606
g931.t1

5.760364
1.160199
−6.11966
−1.45925
−3.83124
0.014666


1780
g2261.t1
3607
g10673.t1

4.246251
8.170102
5.158696
−1.46304
3.828806
0.014718


1781
g2951.t1
3608
g5953.t1
K11129: NHP2, NOLA2
4.43109
0.997175
−3.38379
−1.46821
−3.82548
0.014759


1782
g2355.t1
3609
g9249.t1
K07192: FLOT
6.819585
1.646734
−5.57734
−1.47687
−3.81992
0.014873


1783
g3075.t1
3610
g11781.t1

0
4.238844
3.140408
−1.48663
3.813664
0.014988


1784
g9642.t1
3611
g6905.t1

0
4.384934
5.279139
−1.48909
3.812083
0.015012


1786
g7748.t1
3613
g7098.t1
K12815: DHX38, PRP16
1.598146
5.454032
3.568819
−1.49259
3.809836
0.015052


1785
g10300.t1
3612
g22.t1

0
4.950892
4.957814
−1.49227
3.810047
0.015052


1787
g1381.t1
3614
g8684.t1

6.537476
0
−5.14045
−1.49524
−3.80814
0.01508


1788
g3923.t1
3615
g3970.t1

5.651846
0.874231
−4.49336
−1.49537
−3.80806
0.01508


1789
g2286.t1
3616
g10703.t1
K11362: HFI1, ADA1
1.780691
5.389549
3.610777
−1.50303
3.803144
0.015181


692
g5169.t1
2506
g3798.t1

4.28203
6.198144
2.254081
−1.50534
3.801665
0.01521


1790
g5917.t1
3617
g11006.t1

0.479676
3.343978
2.923854
−1.5088
3.799443
0.01525


1791
g6287.t1
3618
g8349.t1
K11366: USP22_27_51,
7.027226
0
−6.44608
−1.51412
−3.79604
0.01533






UBP8


1792
g6643.t1
3619
g10197.t1

5.091815
1.733439
−3.47331
−1.51828
−3.79337
0.01539


1793
g12218.t1
3620
g11102.t1

2.315098
5.094179
2.505163
−1.52401
3.789702
0.015468


1794
g7936.t1
3621
g11228.t1
K00232: E1.3.3.6,
4.459893
9.555022
5.227644
−1.52659
3.788048
0.015503






ACOX1, ACOX3


1795
g5748.t1
3622
g5250.t1

1.632799
4.080474
2.918063
−1.52796
3.787172
0.015518


1796
g9069.t1
3623
g8579.t1

0
6.161139
6.446955
−1.53152
3.784889
0.01556


1797
g6312.t1
3624
g3007.t1
K05236: COPA
5.253098
7.43545
2.144029
−1.54263
3.77778
0.0157


1799
g8177.t1
3626
g7989.t1

9.520565
3.609284
−4.61836
−1.54631
−3.77543
0.015742


1798
g14196.t1
3625
g5807.t1
K01754: E4.3.1.19, ilvA,
5.027436
7.101036
2.225321
−1.54586
3.775716
0.015742






tdcB


1800
g6471.t1
3627
g5309.t1
K11237: BEM1
8.657428
1.580264
−5.3132
−1.54781
−3.77447
0.015759


1801
g8179.t1
3628
g7991.t1
K15450: TYW3
1.394748
4.160609
2.833287
−1.55061
3.772678
0.015798


1802
g6447.t1
3629
g5339.t1

0.745984
4.49131
3.550615
−1.55175
3.771949
0.015808


1803
g4305.t1
3630
g1960.t1
K07179: RIOK2
2.332881
9.808031
7.49955
−1.56836
3.761323
0.016051


1804
g10921.t1
3631
g2051.t1

3.554471
15.34968
12.40633
−1.5698
3.760406
0.016067


1805
g7453.t1
3632
g6882.t1
K11230: SSK2
6.592207
0.47792
−6.24926
−1.57242
−3.75873
0.016095


1806
g4994.t1
3633
g8965.t1

4.95489
0.379021
−5.0321
−1.57389
−3.75779
0.016103


1807
g13512.t1
3634
g8777.t1
K07047: K07047
0
1.953187
2.809714
−1.57688
3.75588
0.016146


1808
g13145.t1
3635
g4288.t1
K12795: SUGT1, SGT1
0
3.863111
4.262765
−1.57792
3.755218
0.016156


1809
g2403.t1
3636
g9304.t1

3.466706
5.880267
2.766617
−1.58819
3.748658
0.0163


1810
g11546.t1
3637
g4179.t1

2.95634
4.859952
2.334894
−1.59077
3.747012
0.016337


1811
g6245.t1
2545
g7144.t1

3.519044
0.986255
−2.56971
−1.59307
−3.74554
0.016351


1812
g20527.t1
3638
g9499.t1

0
2.423781
3.298103
−1.5938
3.745074
0.016355


1814
g485.t1
3640
g5481.t1

3.211934
0.513195
−3.05545
−1.59982
−3.74123
0.016427


1813
g9589.t1
3639
g6640.t1
K14564: NOP56
0
4.752235
3.463157
−1.59979
3.741252
0.016427


1815
g17338.t1
3641
g4825.t1

3.253347
11.98725
6.42899
−1.60143
3.74021
0.016446


1816
g5556.t1
3642
g7468.t1

0.321853
8.712554
6.936626
−1.60594
3.737329
0.0165


683
g9852.t1
3089
g9791.t1

0.93993
4.257415
3.235897
−1.61117
3.733993
0.016567


1817
g9592.t1
3643
g6324.t1

0
3.24119
4.466041
−1.61236
3.733234
0.01657


1818
g9909.t1
3644
g3464.t1

4.899061
0.389899
−4.4519
−1.61774
−3.7298
0.016649


1819
g347.t1
3645
g8852.t1
K01619: deoC, DERA
5.001834
2.638493
−2.09583
−1.61831
−3.72944
0.01665


1820
g3024.t1
3646
g8280.t1
K15183: ELL
4.940617
6.802739
2.356057
−1.62092
3.727777
0.016675


1821
g3400.t1
3647
g10340.t1

4.574834
8.898182
4.895081
−1.62268
3.726654
0.016684


1822
g5059.t1
3648
g8329.t1
K15544: SSU72
3.885616
1.04666
−3.67463
−1.62812
−3.72318
0.016767


1823
g13701.t1
3649
g7800.t1
K00227: SC5DL, ERG3
3.52458
8.32101
6.721913
−1.62826
3.723097
0.016767


1824
g7883.t1
3650
g8666.t1
K17871: ndh1
8.978821
4.745077
−4.2343
−1.62992
−3.72204
0.016789


1825
g9357.t1
3651
g4026.t1

1.461054
4.608619
3.269834
−1.64365
3.713291
0.017021


1826
g6504.t1
3652
g10649.t1
K01487: E3.5.4.3, guaD
3.115047
5.480797
3.226369
−1.64905
3.709853
0.017102


1827
g996.t1
3653
g8065.t1
K03859: PIGC, GPI2
0
5.164011
5.152798
−1.65445
3.70641
0.017175


1828
g12072.t1
3654
g7819.t1

7.465114
4.358481
−4.43566
−1.66028
−3.7027
0.017256


1829
g8430.t1
3655
g6112.t1

0
3.595832
4.134153
−1.664
3.700333
0.017293


1830
g1011.t1
3656
g8080.t1

1.836426
5.321783
3.474028
−1.66832
3.697583
0.01736


1831
g7418.t1
2549
g7203.t1
K17497: PMM
4.250746
0.725203
−3.91923
−1.6743
−3.69378
0.017427


1832
g9496.t1
3657
g5757.t1

0.783088
6.487481
4.380159
−1.67836
3.691201
0.017484


1833
g9186.t1
3658
g6518.t1

4.151632
10.48721
6.043581
−1.68184
3.688985
0.017532


1834
g7004.t1
3659
g6378.t1
K11229: BCK1
0
2.324218
2.253785
−1.68839
3.684823
0.017638


1836
g8143.t1
3661
g7948.t1

4.054206
0.695466
−3.66885
−1.6899
−3.68386
0.017639


1835
g11752.t1
3660
g9854.t1
K11086: SNRPB, SMB
5.274986
2.280814
−3.12018
−1.6896
−3.68405
0.017639


1837
g17537.t1
3662
g9665.t1

4.57235
8.898002
4.283534
−1.69297
3.681912
0.017688


1838
g5667.t1
3663
g1075.t1

4.489128
2.536094
−2.39358
−1.70341
−3.67528
0.017868


1839
g6664.t1
3664
g2224.t1
K13525: VCP, CDC48
2.105221
5.652047
4.78303
−1.70384
3.675005
0.017868


1840
g2801.t1
3665
g9129.t1

7.466543
0.556432
−6.6491
−1.70804
−3.67233
0.017928


1841
g4812.t1
3666
g9598.t1

4.049291
6.42879
2.167629
−1.70915
3.671628
0.017928


1843
g2466.t1
3668
g6718.t1

5.98403
0
−5.16123
−1.7182
−3.66588
0.018067


1842
g249.t1
3667
g11056.t1
K00276: AOC3, AOC2,
5.423135
1.39377
−3.95337
−1.71813
−3.66593
0.018067






tynA


1844
g13312.t1
3669
g4520.t1
K018GO: maiA, GSTZ1
0
2:734484
3.220496
−1.71843
3.665736
0.018067


1845
g9893.t1
3670
g3483.t1

0
6.706192
4.9767S9
−1.71907
3.665331
0.01807


1846
g17202.t1
3671
g3078.t1

5.68592
2.231786
−3.83595
−1.72034
−3.66452
0.018076


1847
g5069.t1
3672
g8336.t1
K14521: NAT10, KRE33
0
3.583017
3.343135
−1.72847
3.659364
0.018188


1848
g7275.t1
3673
g11843.t1

0.251195
5.321335
4.264195
−1.7299
3.658459
0.018207


1849
g4877.t1
3674
g4496.t1

0.134441
10.17863
6.723251
−1.73151
3.657431
0.018229


1850
g12737.t1
3675
g5715.t1

0
3.366893
5.496972
−1.7331
3.656428
0.018251


1851
g3173.t1
3676
g11661.t1

3.672536
1.077381
−2.65537
−1.73393
−3.6559
0.018258


1852
g4631.t1
3677
g2422.t1

2.311883
4.745023
2.541357
−1.73959
3.652307
0.018351


1853
g601.t1
3678
g3857.t1

0
4.551928
4.659305
−1.74334
3.649928
0.018406


1854
g4634.t1
3679
g2419.t1

5.63215
7.748538
2.895179
−1.74706
3.647572
0.018445


1855
g13170.t1
3680
g1290.t1
K01620: ItaE
0
1.960601
3.162229
−1.74722
3.647467
0.018445


1856
g3136.t1
3681
g5050.t1

0
2.474936
2.012582
−1.75162
3.644677
0.018519


1857
g14953.t1
3682
g1391.t1

3.334724
6.021478
2.572465
−1.75216
3.644334
0.018519


1858
g11237.t1
3683
g1362.t1

2.76252
5.104646
2.123089
−1.76267
3.637676
0.018659


1859
g1833.t1
3684
g1913.t1
K03248: EIF3G
0
3.706133
3.037564
−1.76489
3.636266
0.018694


1860
g6040.t1
3685
g11728.t1
K16368: DGK1
9.681271
2.587529
−5.33304
−1.7661
−3.6355
0.018707


1861
g11936.t1
3686
g10365.t1

4.454058
0.327662
−3.42743
−1.76646
−3.63527
0.018707


1862
g4010.t1
3687
g8176.t1
K15427: SIT4, PPH1
5.918167
1.131513
−3.97297
−1.77022
−3.63289
0.018745


1864
g3458.t1
3689
g4687.t1

2.234014
5.975139
2.819321
−1.77233
3.631552
0.018756


1865
g4936.t1
3690
g4576.t1

0.924146
3.716899
3.064721
−1.77306
3.631089
0.018756


1866
g1815.t1
3691
g1702.t1

2.685797
6.479459
3.431879
−1.77314
3.63104
0.018756


1863
g7697.t1
3688
g11510.t1

1.950115
6.128154
4.639048
−1.77179
3.631893
0.018756


1867
g1592.t1
3692
g12245.t1

0
4.518156
4.414945
−1.7816
3.62568
0.01888


1868
g9431.t1
3693
g10302.t1

5.228093
0.705484
−5.82699
−1.78382
−3.62428
0.018915


1869
g10761.t1
3694
g12006.t1
K15082: RAD7
3.567408
6.390408
2.846424
−1.7985
3.614981
0.01914


1870
g6898.t1
3695
g1355.t1

2.604143
5.101685
2.991821
−1.80118
3.613286
0.019185


1871
g13109.t1
3696
g9757.t1
K01620: ItaE
0
2.071355
2.163561
−1.80694
3.609643
0.019256


1872
g1060.t1
3697
g8133.t1

4.616756
0.514584
−3.57327
−1.81051
−3.60738
0.019301


1873
g7618.t1
3698
g7618.t1

2.193329
5.285081
3.154401
−1.81683
3.603386
0.019394


1874
g1395.t1
3699
g6218.t1

3.913913
7.425386
3.628307
−1.82293
3.599533
0.019503


1875
g1934.t1
3700
g10921.t1

6.270225
2.041068
−5.92102
−1.82531
−3.59803
0.01953


1876
g10864.t1
3701
g114.t1

1.463031
4.938665
3.973683
−1.82564
3.59782
0.01953


1877
g10895.t1
3702
g5900.t1

0
4.186104
3.125415
−1.8289
3.595755
0.019562


1878
g5532.t1
3703
g11340.t1

1.931855
7.130479
5.020293
−1.83514
3.591812
0.019672


1879
g7251.t1
3704
g10776.t1

4.989318
0.254069
−3.57371
−1.85053
−3.58209
0.019932


1880
g3894.t1
3705
g3998.t1
K00846: KHK
2.877684
5.230358
3.413778
−1.86007
3.576066
0.020088


1881
g819.t1
3706
g8183.t1

3.722054
7.412978
4.05158
−1.86516
3.572854
0.020168


1882
g5100.t1
3707
g2942.t1
K06688: UBE2C, UBC11
0
1.914572
2.214387
−1.86814
3.570972
0.020216


1883
g5175.t1
3708
g3792.t1
K11498: CENPE
3.281173
0.222331
−4.74201
−1.88553
−3.56
0.020535


1884
g6483.t1
3709
g5291.t1
K13728: MAD2L2
1.918177
10.9648
7.40681
−1.89484
3.554125
0.020681


1885
g8029.t1
3710
g4279.t1
K01464: DPYS, dht,
3.138026
5.812027
3.152124
−1.89915
3.551408
0.020756






hydA


1888
g1840.t1
3713
g1902.t1

4.350369
6.555403
3.614501
−1.90291
3.549042
0.020781


1886
g5081.t1
3711
g8569.t1
K00505: TYR
0
4.71171
4.573953
−1.9019
3.549673
0.020781


1887
g1692.t1
3712
g4651.t1

1.082713
6.142533
4.604924
−1.90263
3.549214
0.020781


1889
g11007.t1
3714
g8699.t1

0
1.587767
2.088946
−1.90951
3.544881
0.020897


1890
g1760.t1
3715
g1200.t1

0
3.246854
2.445799
−1.91563
3.541022
0.021005


1891
g10371.t1
3716
g10538.t1

0
4.965362
5.078563
−1.91874
3.539065
0.021065


1892
g7221.t1
3717
g5890.t1

5.661483
1.072226
−3.76681
−1.93127
−3.53117
0.021281


1893
g6375.t1
3718
g771.t1

8.208151
3.648937
−4.25444
−1.93282
−3.53019
0.021294


1896
g2909.t1
3721
g6002.t1

1.238494
4.449583
3.244239
−1.93586
3.52828
0.021322


1894
g5154.t1
3719
g3823.t1
K17095: ANXA7_11
3.505958
9.283634
4.528734
−1.93535
3.528604
0.021322


1895
g20345.t1
3720
g7516.t1

0
4.951177
4.852188
−1.93559
3.528453
0.021322


1897
g12606.t1
3722
g1144.t1

0
2.337207
2.424768
−1.94189
3.524487
0.02143


1898
g7465.t1
3723
g6869.t1

3.054874
8.104242
4.242867
−1.94419
3.52304
0.021452


1899
g5267.t1
3724
g9694.t1

1.826832
5.783242
3.837809
−1.9491
3.519947
0.021535


1900
g4664.t1
3725
g2382.t1

5.504862
1.603502
−4.21381
−1.95339
−3.51725
0.021593


1901
g17749.t1
2523
g12099.t1

7.598291
9.839638
2.512479
−1.95532
3.516031
0.021628


1902
g6418.t1
3726
g5371.t1
K03778: ldhA
2.853999
4.669676
2.946243
−1.95976
3.513237
0.021721


1903
g10763.t1
3727
g12010.t1
K01209: E3.2.1.55, abfA
2.945033
0
−3.29535
−1.96318
−3.51109
0.02177


1904
g666.t1
3728
g9881.t1

4.362664
0.664419
−3.76077
−1.96699
−3.50869
0.021838


1906
g1908.t1
3730
g8731.t1

2.211455
0
−3.68585
−1.97784
−3.50187
0.022044


1907
g3413.t1
3731
g4733.t1
K06902: UMF1
2.141863
7.189473
4.094946
−1.97792
3.501818
0.022044


1905
g9155.t1
3729
g6487.t1
K02324: POLE1
4.234902
8.900666
4.422793
−1.97738
3.502159
0.022044


1908
g10394.t1
3732
g10563.t1

0
5.322562
4.509387
−1.9801
3.50045
0.022075


1909
g7696.t1
3733
g11509.t1

0.601935
3.107555
2.748423
−1.98765
3.495705
0.022202


1910
g2535.t1
3734
g3567.t1
K05758: ARPC2
11.15766
3.882187
−7.40548
−1.99331
−3.49215
0.022306


1911
g8186.t1
3735
g7993.t1
K01079: serB, PSPH
4.063757
0.499721
−4.16492
−1.99443
−3.49144
0.022322


1912
g4471.t1
3736
g6834.t1

0.878562
4.743026
3.759323
−1.99869
3.488764
0.022414


1913
g8237.t1
3737
g10043.t1

3.086194
5.293821
2.302039
−1.99973
3.488113
0.022418


1914
g9619.t1
3738
g7243.t1
K11339: MORF4L1,
0
2.363574
3.497394
−2.00042
3.487675
0.022424






MRG15, EAF3


1915
g1911.t1
3739
g6147.t1
K08334: BECN1, VPS30,
4.443069
1.325402
−4.48934
−2.0025
−3.48637
0.022458






ATG6


1916
g7540.t1
3740
g7267.t1
K01179: E3.2.1.4
3.106323
7.044516
4.718377
−2.0027
3.486247
0.022458


1917
g2857.t1
3741
g9061.t1

4.958463
1.63825
−3.2435
−2.00585
−3.48427
0.022502


1918
g5306.t1
3742
g2255.t1

5.053243
1.769587
−3.06328
−2.00736
−3.48332
0.022507


1919
g4916.t1
3743
g4552.t1
K13950: pabAB
0
4.100904
3.309752
−2.00896
3.482311
0.022524


1920
g7255.t1
3744
g10781.t1

1.044041
5.343757
3.456906
−2.0128
3.479902
0.022607


1921
g5468.t1
3745
g8430.t1

4.014859
1.728033
−2.2011
−2.02184
−3.47423
0.022807


1922
g10379.t1
3746
g10546.t1
K03507: DPB11
0
2.887983
2.329258
−2.02243
3.473857
0.02281


1923
g2332.t1
3747
g9197.t1
K09484: QUIB, qa-3
0.359609
4.730422
6.455702
−2.04055
3.462484
0.023216


640
g12554.t1
2440
g3576.t1
K02953: RP-S13e,
6.593986
3.286592
−3.5936
−2.0451
−3.45963
0.023319






RPS13


1924
g134.t1
3748
g5827.t1

6.48267
2.73113
−3.87561
−2.04641
−3.4588
0.023339


1925
g6562.t1
3749
g10098.t1
K04627: STE3
6.840025
3.508287
−3.0943
−2.04677
−3.45858
0.023339


1926
g835.t1
3750
g8204.t1

5.9061
3.739419
−2.89332
−2.05738
−3.45193
0.023574


1927
g3961.t1
3751
g3929.t1
K15631: ABA3
4.682251
0.610791
−4.20667
−2.05917
−3.4508
0.023606


1928
g9090.t1
3752
g8544.t1

9.042656
3.394564
−4.42541
−2.06054
−3.44994
0.023622


1929
g8220.t1
3753
g10063.t1
K11380: NTO1
0.981794
5.762532
4.770402
−2.06314
3.448316
0.023659


1930
g1688.t1
3754
g4655.t1

3.67154
6.41277
3.431308
−2.06707
3.445853
0.02371


1931
g10593.t1
3755
g7036.t1

0
1.637191
2.310481
−2.06843
3.444999
0.023734


1932
g7454.t1
3756
g6881.t1
K13237: DECR2
7.244054
3.351771
−4.66071
−2.07246
−3.44247
0.023826


1933
g1006.t1
3757
g8076.t1

5.641821
1.01679
−5.33245
−2.07757
−3.43927
0.023924


1934
g558.t1
3758
g6454.t1

5.468701
2.998081
−3.81423
−2.07899
−3.43838
0.02395


1935
g8492.t1
3759
g3364.t1

2.17787
5.143839
3.198935
−2.08565
3.434206
0.024077


1936
g3284.t1
3760
g8263.t1
K04567: KARS, lysS
0
3.096837
2.750146
−2.09247
3.429933
0.024176


1937
g10375.t1
3761
g10542.t1
K18163: NDUFAF6
0
3.09048
3.372823
−2.09383
3.429081
0.024189


1938
g9651.t1
3762
g6914.t1

8.216351
3.957187
−3.97535
−2.09941
−3.42558
0.02429


1939
g6236.t1
3763
g7134.t1

1.92867
9.554801
7.372855
−2.10264
3.423559
0.024364


1940
g5143.t1
3764
g3836.t1

2.580565
8.674743
4.091749
−2.1038
3.422838
0.024383


1941
g11455.t1
3765
g7021.t1

0.596448
5.043975
4.462447
−2.10687
3.420916
0.024452


1942
g5389.t1
3766
g2429.t1

4.873893
0
−5.94573
−2.11075
−3.41849
0.024543


1943
g6232.t1
3767
g7130.t1

6.918168
0.488136
−5.39134
−2.11243
−3.41743
0.024569


1944
g13866.t1
3768
g4613.t1
K15115: SLC25A32,
0.791928
5.833256
4.134026
−2.11257
3.417341
0.024569






MFT


1945
g7546.t1
3769
g7261.t1
K06113: abnA_B
1.693461
6.005734
3.98049
−2.11746
3.414282
0.024676


1946
g10144.t1
3770
g8474.t1
K17086: TM9SF2_4
6.358648
2.274685
−5.01733
−2.12573
−3.40911
0.024862


1947
g8973.t1
3771
g11361.t1
K08496: GOSR2, BOS1
0
3.168015
2.664668
−2.12811
3.407616
0.024915


1948
g5708.t1
3772
g2670.t1

3.903218
6.617966
3.389449
−2.13389
3.403997
0.025048


1950
g6963.t1
3774
g6427.t1
K14408: CSTF3, RNA14
6.941008
0
−5.14398
−2.13547
−3.40301
0.025067


1949
g15819.t1
3773
g6469.t1

6.143278
2.028742
−3.66691
−2.13542
−3.40304
0.025067


1951
g9667.t1
3775
g4881.t1
K18757: LARP1
1.474494
5.026138
3.073674
−2.13624
3.40253
0.025072


1952
g12694.t1
3776
g8901.t1

0
4.059599
3.514485
−2.13747
3.401759
0.025087


1953
g3429.t1
3777
g4716.t1
K10755: RFC2_4
6.366861
3.029398
−4.00095
−2.13997
−3.4002
0.02512


1954
g4582.t1
3778
g4118.t1

1.381451
5.626283
4.430383
−2.14063
3.399781
0.025126


1955
g3157.t1
3779
g4989.t1

3.100887
8.957858
6.174002
−2.15214
3.392585
0.025381


1956
g82.t1
3780
g2764.t1
K17422: MRPL41
0
6.458967
4.487087
−2.15351
3.391728
0.025396


1957
g624.t1
3781
g11304.t1

0.779024
4.503237
2.584446
−2.15576
3.390322
0.025427


1958
g1143.t1
3782
g253.t1

0
4.407125
4.086029
−2.16257
3.38606
0.025587


1959
g6371.t1
3783
g780.t1
K08287: E2.7.12.1
2.726445
7.392615
5.376711
−2.17655
3.377322
0.025905


1960
g1751.t1
3784
g9723.t1

2.795334
5.572355
3.187095
−2.17894
3.375831
0.025959


1961
g4236.t1
3785
g1745.t1

4.004311
6.248441
2.562026
−2.18036
3.374942
0.025987


1962
g8695.t1
3786
g11550.t1

4.911201
1.458168
−3.1977
−2.18135
−3.37432
0.026004


859
g490.t1
2536
g5492.t1
K01230: MAN1
3.341994
5.830489
2.819683
−2.18329
3.37311
0.026046


1963
g5421.t1
3787
g5085.t1

8.070442
0.46074
−5.99862
−2.18759
−3.37042
0.026135


1964
g2502.t1
3788
g3530.t1
K13288: orn, REX2,
0
4.539539
4.217905
−2.18823
3.370025
0.026138






REXO2


1965
g2567.t1
3789
g5735.t1

4.150469
7.075168
2.267847
−2.19188
3.367744
0.026205


1966
g4811.t1
3790
g9600.t1

3.984392
2.169587
−2.35064
−2.19298
−3.36706
0.026224


1967
g6775.t1
3791
g4391.t1
K18748: SSD1
7.196236
1.868572
−5.15477
−2.20272
−3.36098
0.026429


1969
g10391.t1
3793
g10558.t1

0
5.449561
5.122671
−2.21155
3.35546
0.026586


1968
g1041.t1
3792
g8112.t1
K11227: PBS2
0
5.802497
5.568864
−2.2107
3.355987
0.026586


1971
g11559.t1
3795
g4170.t1

5.952815
2.501869
−3.41726
−2.21296
−3.35458
0.026603


1970
g13704.t1
3794
g11109.t1

1.780391
5.388679
3.682525
−2.21285
3.354646
0.026603


1972
g3779.t1
3796
g2656.t1

0
2.29459
3.055708
−2.21449
3.353624
0.026623


1973
g2737.t1
3797
g9165.t1

8.111867
3.708757
−3.11076
−2.21608
−3.35263
0.026657


1974
g6644.t1
3798
g10196.t1

0.529024
4.052835
2.69518
−2.21902
3.350793
0.026706


1975
g9251.t1
3799
g10432.t1

6.615159
0.815708
−4.57198
−2.2196
−3.35043
0.02671


1977
g5146.t1
3801
g3831.t1

1.613274
5.642097
3.424626
−2.22255
3.348593
0.026759


1976
g7543.t1
3800
g7264.t1

1.778839
6.311218
3.7799
−2.22228
3.348757
0.026759


1978
g7853.t1
3802
g10510.t1
K15306: RANBP1
0
1.987939
2.649547
−2.22545
3.34678
0.026819


1979
g7747.t1
3803
g7097.t1
K14791: PWP1
1.814601
4.202941
2.631876
−2.22599
3.346441
0.026823


1980
g3283.t1
3804
g8262.t1
K11400: ARP4
0
2.989351
3.88489
−2.22752
3.345492
0.026855


1981
g3579.t1
3805
g3304.t1
K00472: E1.14.11.2
3.489594
9.820105
6.138885
−2.22818
3.345078
0.026862


1982
g4997.t1
3806
g8967.t1

1.989279
5.409008
3.503902
−2.2339
3.341506
0.026993


1983
g466.t1
3807
g8012.t1

4.101739
6.505153
2.812413
−2.23476
3.34097
0.027006


1984
g3042.t1
3808
g1617.t1
K01638: E2.3.3.9, aceB,
4.286461
1.427891
−2.69449
−2.23709
−3.33952
0.027061






glcB


1985
g2105.t1
3809
g2480.t1
K12189: VPS25, EAP20
5.392127
1.688441
−3.98468
−2.24246
−3.33617
0.027171


1986
g10030.t1
3810
g3456.t1
K03952: NDUFA8
4.085114
0.317024
−3.2909
−2.24726
−3.33317
0.027263


1987
g10020.t1
3811
g10918.t1
K01238: E3.2.1.—
0
2.377597
3.865002
−2.24806
3.332671
0.027274


1988
g6440.t1
3812
g9393.t1

1.856577
5.779447
3.68737
−2.25497
3.328362
0.027454


1989
g10867.t1
3813
g124.t1

0
4.39728
4.400864
−2.25581
3.32784
0.027467


1990
g3799.t1
3814
g863.t1

5.870835
2.857198
−2.27046
−2.25914
−3.32576
0.027534


1991
g10346.t1
3815
g44.t1
K18328: DBR1
0
2.241769
3.604053
−2.25968
3.325424
0.027534


1992
g9896.t1
3816
g3480.t1

0
5.417973
5.231502
−2.25972
3.325396
0.027534


1993
g7695.t1
3817
g11508.t1
K01640: E4.1.3.4,
0.184849
4.606471
4.094707
−2.26451
3.322414
0.02764






HMGCL, hmgL


1994
g851.t1
3818
g9450.t1

7.233882
2.603782
−3.98752
−2.26621
−3.32135
0.027678


1995
g13873.t1
3819
g4607.t1
K14845: RAH, DOM3Z
1.75337
5.060998
3.620071
−2.27209
3.317686
0.027818


1996
g5244.t1
3820
g2347.t1
K02877: RP-L15e,
4.414688
11.84847
5.818625
−2.27366
3.316708
0.027853






RPL15


1997
g13106.t1
3821
g9753.t1
K01892: HARS, hisS
0
2.209128
2.453035
−2.27519
3.315751
0.027886


1998
g11726.t1
3822
g5854.t1

5.938268
0.538037
−5.1103
−2.27837
−3.31377
0.02796


1999
g2723.t1
3823
g9178.t1

4.416635
0.748978
−3.32728
−2.28414
−3.31017
0.028107


2000
g5988.t1
3824
g11687.t1

6.638403
4.410083
−2.22473
−2.28525
−3.30948
0.028129


2001
g6939.t1
3825
g6449.t1
K01560: E3.8.1.2
1.458794
5.793547
4.011947
−2.29299
3.304659
0.028315


2003
g13415.t1
3827
g8381.t1
K00618: E2.3.1.1
5.219776
7.979734
3.470781
−2.29519
3.303285
0.028357


2002
g37.t1
3826
g2834.t1
K02926: RP-L4, MRPL4,
1.828605
4.71647
4.723031
−2.29519
3.303285
0.028357






rpID


2004
g3662.t1
3828
g651.t1

0.872427
6.371311
4.041603
−2.29616
3.302681
0.028362


2005
g9235.t1
3829
g3428.t1

0
3.972927
4.57957
−2.29616
3.302679
0.028362


2006
g7674.t1
3830
g7572.t1

5.466518
2.783883
−4.32184
−2.29711
−3.30209
0.028368


2007
g4036.t1
3831
g3210.t1

4.501248
0.83444
−3.4584
−2.29717
−3.30205
0.028368


2008
g5276.t1
3832
g2295.t1

4.938586
0.923903
−3.91412
−2.30002
−3.30028
0.028406


2009
g11802.t1
3833
g12042.t1

3.076257
6.471818
3.398775
−2.30107
3.299622
0.028426


2010
g9414.t1
3834
g3612.t1

6.623875
3.522539
−4.17633
−2.30173
−3.29921
0.028434


656
g16181.t1
2457
g12075.t1
K08257: E3.2.1.101
5.57367
2.794291
−3.13674
−2.30477
−3.29731
0.028477


2012
g10897.t1
3836
g5902.t1

0
2.586402
2.018878
−2.30447
3.297501
0.028477


2011
g7210.t1
3835
g5874.t1
K09780: K09780
1.114388
3.993513
3.261747
−2.30435
3.297579
0.028477


2013
g4453.t1
3837
g6809.t1

5.118903
0.695521
−6.34745
−2.31256
−3.29247
0.028643


2014
g606.t1
3838
g3853.t1
K16261: YAT
3.858126
5.880152
2.075602
−2.32021
3.287698
0.028843


2015
g4470.t1
3839
g6833.t1

1.147637
5.898161
3.859584
−2.3248
3.284838
0.028961


2016
g6738.t1
3840
g7868.t1

5.417721
3.126867
−3.45553
−2.32976
−3.28175
0.029069


2017
g9769.t1
3841
g939.t1
K15326: TSEN54
2.152088
5.841014
4.075185
−2.33059
3.281231
0.029079


2018
g8609.t1
3842
g3035.t1
K11684: BDF1
5.659852
2.072019
−3.03129
−2.33159
−3.28061
0.029098


2019
g7209.t1
3843
g5873.t1

1.535387
3.753918
2.595474
−2.33355
3.279388
0.029145


2020
g9079.t1
3844
g7839.t1

3.237265
5.083271
2.50233
−2.33749
3.276937
0.029238


2021
g488.t1
3845
g5490.t1

5.069028
0.661124
−3.94585
−2.33858
−3.27626
0.02924


2022
g11121.t1
3846
g740.t1

1.095174
5.476241
3.763338
−2.33866
3.276212
0.02924


2023
g7270.t1
3847
g11833.t1
K01649: leuA
0.794723
4.590596
3.756172
−2.34295
3.27354
0.029292


2024
g8493.t1
3848
g3365.t1

3.869494
6.395043
2.369665
−2.35653
3.265084
0.029712


2025
g9798.t1
3849
g10841.t1
K04564: SOD2
6.169922
3.581629
−3.17615
−2.35997
−3.26294
0.029809


2026
g4827.t1
3850
g711.t1

3.138123
5.609277
2.266361
−2.36209
3.261622
0.029865


2027
g7690.t1
3851
g7594.t1
K09705: K09705
6.512504
2.963367
−3.48703
−2.3645
−3.26012
0.029917


2028
g6785.t1
3852
g4403.t1
K06111: EXOC4, SEC8L1
7.141887
3.434524
−3.10329
−2.36545
−3.25954
0.029935


2029
g11719.t1
3853
g2321.t1

4.122011
2.09891
−3.55772
−2.36866
−3.25754
0.030026


2030
g4828.t1
3854
g712.t1

5.692735
2.652303
−3.51649
−2.37281
−3.25496
0.030122


2031
g942.t1
3855
g9313.t1
K09241: GAL4
1.854413
3.96608
2.304511
−2.37691
3.252404
0.030229


2032
g11848.t1
3856
g8790.t1

2.601552
0.409353
−2.22171
−2.37796
−3.25175
0.030251


2033
g21824.t1
3857
g7394.t1

0
5.23534
3.655249
−2.38527
3.247202
0.030464


2034
g2821.t1
3858
g11279.t1

5.756117
3.458502
−2.0711
−2.3872
−3.24601
0.030515


2035
g6696.t1
3859
g11145.t1
K09704: K09704
7.789281
2.074215
−5.24082
−2.38775
−3.24566
0.03052


2036
g4155.t1
3860
g1823.t1
K18551: SDT1
5.022148
1.693257
−2.97251
−2.38832
−3.2453
0.030526


2037
g9766.t1
3861
g942.t1

3.212965
8.164358
4.327837
−2.39337
3.242162
0.030679


2039
g13908.t1
3863
g8736.t1

3.218518
0.78025
−2.44992
−2.39434
−3.24156
0.030685


2038
g9809.t1
3862
g10829.t1

3.118004
5.544287
2.518375
−2.39418
3.24166
0.030685


2040
g6787.t1
3864
g4405.t1

1.161527
5.099231
3.21425
−2.39714
3.239817
0.030752


2041
g9405.t1
3865
g3622.t1

3.567627
5.477382
2.497615
−2.40468
3.23513
0.030977


2042
g2509.t1
3866
g3539.t1
K11874: UBP16
1.872531
5.493777
3.650258
−2.4068
3.233811
0.031035


2043
g5355.t1
3867
g9.t1

2.290026
0.356189
−2.03022
−2.40761
−3.23331
0.031049


2044
g4497.t1
3868
g10803.t1

4.996184
7.333602
3.047979
−2.4116
3.230832
0.031143


2045
g8224.t1
3869
g10058.t1

3.041354
5.822561
3.713464
−2.41714
3.227386
0.031264


2046
g4940.t1
3870
g4580.t1

2.195152
8.603997
5.13217
−2.41716
3.227371
0.031264


2047
g3634.t1
3871
g611.t1
K08331: ATG13
3.988422
0.822981
−3.37249
−2.42114
−3.2249
0.031385


2048
g228.t1
3872
g11036.t1
K14833: NOC2
5.004033
8.298645
2.944132
−2.43094
3.218805
0.031692


2049
g48.t1
3873
g2823.t1
K01433: purU
2.612144
5.741983
3.012018
−2.43232
3.217947
0.031713


2050
g281.t1
3874
g11374.t1

9.37879
4.604117
−4.12735
−2.43274
−3.21769
0.031713


2051
g12734.t1
3875
g5711.t1
K11662: ACTR6, ARP6
0
2.30116
2.840219
−2.43365
3.217125
0.031718


2052
g10764.t1
3876
g12011.t1
K01581: E4.1.1.17,
5.248823
0.219074
−4.66848
−2.4346
−3.21653
0.031737






ODC1, speC, speF


2053
g3828.t1
3877
g2599.t1
K00505: TYR
0.869044
5.111409
3.294953
−2.43787
3.214499
0.031836


2054
g1137.t1
3878
g246.t1

5.271354
1.818388
−3.65818
−2.43939
−3.21355
0.031875


2055
g4066.t1
3879
g3252.t1

3.515498
1.112324
−2.46994
−2.44069
−3.21275
0.031906


2056
g10836.t1
3880
g9834.t1

0.621439
3.119334
2.691703
−2.44409
3.210636
0.03201


2057
g5068.t1
3881
g8335.t1
K14685: SLC40A1, FPN1
0
7.218235
6.29332
−2.44716
3.208723
0.032062


2058
g9620.t1
3882
g7242.t1
K01648: ACLY
0
3.90929
3.533252
−2.45537
3.203626
0.032253


2059
g5229.t1
3883
g2363.t1

5.943001
0.548669
−5.4291
−2.46004
−3.20072
0.032375


2060
g8605.t1
3884
g3038.t1

4.532655
1.818868
−2.9624
−2.46055
−3.20041
0.032379


2061
g10730.t1
3885
g2912.t1
K01469: OPLAH, OXP1,
0
2.379516
2.107655
−2.46555
3.1973
0.032541






oplAH


2062
g4774.t1
3886
g3677.t1
K15631: ABA3
9.027659
4.836111
−4.01499
−2.46683
−3.1965
0.032572


2063
g4508.t1
3887
g10813.t1

0.165642
5.824528
5.711017
−2.46786
3.195865
0.032595


2064
g2571.t1
3888
g5739.t1

0.293052
8.085137
4.840508
−2.46935
3.194939
0.03262


2065
g5434.t1
3889
g3137.t1

5.143051
1.033474
−3.99467
−2.47101
−3.19391
0.032665


2066
g1199.t1
3890
g353.t1
K02895: RP-L24,
6.44631
2.830134
−5.33548
−2.4716
−3.19354
0.032672






MRPL24, rplX


2067
g7868.t1
3891
g10526.t1
K02915: RP-L34e,
5.849423
1.765368
−4.55948
−2.47674
−3.19035
0.032826






RPL34


2068
g1161.t1
3892
g269.t1

5.46016
3.009009
−2.38008
−2.48667
−3.18418
0.033056


2070
g4445.t1
3894
g6797.t1

4.844189
2.596249
−3.82423
−2.48854
−3.18302
0.033082


2069
g10124.t1
3893
g92.t1

4.215995
9.33502
4.637226
−2.48825
3.1832
0.033082


2071
g3873.t1
3895
g4021.t1

2.22259
5.09223
2.889394
−2.49175
3.181028
0.033179


2072
g2508.t1
3896
g3536.t1

0
6.070724
4.543999
−2.49201
3.18087
0.033179


2073
g8450.t1
3897
g2681.t1

0
2.871722
2.959236
−2.4972
3.177646
0.033351


2074
g7865.t1
3898
g10523.t1

7.879406
5.602482
−4.36688
−2.51011
−3.16963
0.033735


2075
g6937.t1
3899
g6455.t1
K13108: SNIP1
0.333353
7.112752
4.778096
−2.51256
3.168111
0.033811


2076
g4596.t1
3900
g6012.t1
K12855: PRPF6, PRP6
1.297068
7.636161
5.013494
−2.51413
3.167137
0.033854


2077
g16131.t1
3901
g11950.t1
K00616: E2.2.1.2, talA,
4.139806
0.380959
−2.80605
−2.51525
−3.16644
0.033861






talB


2078
g465.t1
3902
g8013.t1
K14325: RNPS1
0.1118
6.347517
6.203301
−2.51547
3.166303
0.033861


2079
g1164.t1
3903
g270.t1

0.318216
3.991449
5.225959
−2.51682
3.165462
0.033883


2080
g2408.t1
3904
g9480.t1
K18550: ISN1
5.538089
8.86782
4.347478
−2.51899
3.164117
0.033935


2082
g16130.t1
3906
g7073.t1

4.225688
6.146706
2.4124
−2.52079
3.163002
0.033945


937
g8077.t1
2540
g7846.t1

6.655406
8.379386
2.917067
−2.52044
3.163218
0.033945


2081
g5524.t1
3905
g1651.t1

1.597727
5.655543
3.534574
−2.5205
3.163177
0.033945


2083
g13129.t1
3907
g7779.t1

3.365795
1.169273
−2.39087
−2.52343
−3.16136
0.034028


2084
g10991.t1
3908
g5657.t1
K12627: LSM8
0
2.170848
3.541712
−2.52601
3.159761
0.034109


2085
g1929.t1
3909
g6163.t1
K01930: FPGS
2.613598
6.785311
3.342673
−2.52742
3.158884
0.034147


523
g10740.t1
2319
g11987.t1

0
2.813231
2.132602
−2.52798
3.15854
0.034153


2086
g11974.t1
3910
g12283.t1
K01537: E3.6.3.8
4.46077
8.720128
4.497107
−2.52922
3.15777
0.034185


2087
g2386.t1
3911
g9282.t1

2.552078
5.80107
2.857308
−2.52973
3.157452
0.03419


2088
g11089.t1
3912
g1541.t1

2.958185
5.916026
3.473746
−2.53269
3.155612
0.034271


549
g6123.t1
2346
g7324.t1

9.721609
0
−6.70978
−2.53776
−3.15247
0.034417


2089
g2879.t1
3913
g9507.t1

1.588916
5.963453
4.232111
−2.53843
3.152052
0.034428


2090
g13476.t1
3914
g8719.t1

4.855623
0.713258
−4.14789
−2.54165
−3.15005
0.034492


2091
g10480.t1
3915
g1680.t1

5.35355
2.766663
−3.30455
−2.54237
−3.1496
0.034504


2092
g8013.t1
3916
g3404.t1

5.049113
0.484288
−4.63964
−2.54362
−3.14883
0.034537


2093
g4367.t1
3917
g3791.t1
K03448: FEN2, LIZ1
5.072018
0.779082
−3.52579
−2.54647
−3.14707
0.034587


2094
g6987.t1
3918
g10858.t1

0.511756
5.093495
4.425198
−2.54912
3.145416
0.034644


2095
g10431.t1
3919
g8407.t1
K14861: URB1
9.412961
2.402632
−4.79559
−2.55
−3.14487
0.034663


2096
g8248.t1
3920
g10031.t1
K17424: MRPL43
1.653332
7.208956
3.793246
−2.55139
3.144009
0.034701


2097
g9278.t1
3921
g112.t1

5.376359
0.900471
−5.07129
−2.5543
−3.14221
0.034795


561
g1198.t1
2358
g352.t1
K04513: RHOA
2.185924
5.599431
3.115826
−2.56335
3.136592
0.03508


2098
g7656.t1
3922
g7539.t1

9.484291
3.272208
−4.44358
−2.56665
−3.13455
0.035163


2099
g9071.t1
3923
g8570.t1

0
4.308308
2.935063
−2.5715
3.131534
0.035295


2100
g2276.t1
3924
g10693.t1
K12761: SNF1
5.01028
6.964651
2.286462
−2.57593
3.128788
0.035431


2101
g14507.t1
3925
g11494.t1
K01187: malZ
7.827356
5.131373
−2.97808
−2.5835
−3.12409
0.03565


2102
g4366.t1
3926
g2127.t1

3.108334
0.378977
−3.23784
−2.58635
−3.12232
0.035746


2103
g5569.t1
3927
g7488.t1

2.55743
5.105776
2.804623
−2.58922
3.120544
0.035842


2104
g12588.t1
3928
g2936.t1

5.341725
1.287142
−4.50731
−2.59295
−3.11823
0.035935


2106
g192.t1
3930
g5819.t1

0
4.078839
3.742625
−2.5932
3.118072
0.035935


2105
g935.t1
3929
g9324.t1

1.589025
6.970304
5.205593
−2.59295
3.118226
0.035935


2107
g7460.t1
3931
g6874.t1
K18176: COA3
0.679443
8.132716
6.326235
−2.59401
3.117572
0.035941


2108
g2807.t1
3932
g3734.t1
K01053: E3.1.1.17, gnl,
6.975277
3.879255
−3.8776
−2.59679
−3.11585
0.036035






RGN


2109
g4435.t1
3933
g6774.t1

3.295348
5.340307
2.156098
−2.59927
3.114308
0.036117


2110
g9401.t1
3934
g3633.t1
K12668: OST2, DAD1
5.100436
7.099716
3.045005
−2.60147
3.112946
0.036176


2111
g1263.t1
3935
g448.t1
K17421: MRPL40
0
5.570752
4.940149
−2.60151
3.112921
0.036176


2112
g3490.t1
3936
g2182.t1
K03350: APC3, CDC27
5.226216
7.504737
2.341709
−2.60332
3.111795
0.036225


2113
g10916.t1
3937
g267.t1

3.408478
5.633464
3.418244
−2.60479
3.110889
0.036225


2114
g921.t1
3938
g9342.t1
K18045: SIW14, OCA3
0
3.596272
3.808042
−2.60499
3.11076
0.036225


2116
g7478.t1
3940
g6858.t1

4.55802
0.837774
−3.42667
−2.61758
−3.10295
0.036604


2115
g1744.t1
3939
g9730.t1
K16261: YAT
2.444031
4.709166
2.258978
−2.61755
3.102974
0.036604


2117
g10207.t1
3941
g11173.t1
K17866: DPH2
6.980775
0.764559
−4.05418
−2.62021
−3.10133
0.036689


2118
g11843.t1
3942
g8773.t1
K00993: EPT1
3.000341
0.893639
−2.21354
−2.62048
−3.10116
0.036689


2119
g3656.t1
3943
g636.t1

8.879204
5.164409
−2.89019
−2.62535
−3.09814
0.03685


2120
g4331.t1
3944
g1983.t1

4.236756
1.896176
−3.14722
−2.62618
−3.09762
0.036854


2121
g10256.t1
3945
g7194.t1

4.209344
0.708524
−3.33023
−2.62967
−3.09546
0.036938


2122
g9189.t1
3946
g6521.t1
K05663: ABC.ATM
0.18774
5.583284
5.054504
−2.63044
3.09498
0.036954


2123
g9587.t1
3947
g6638.t1
K02976: RP-S26e,
0
3.89404
2.743634
−2.63219
3.093898
0.037009






RPS26


2124
g3483.t1
3948
g2152.t1
K00472: E1.14.11.2
0
4.019165
3.218586
−2.63269
3.093584
0.037015


2125
g4515.t1
3949
g10820.t1

10.17358
3.683757
−4.93347
−2.6337
−3.09296
0.03704


2126
g5855.t1
3950
g1148.t1
K12874: AQR
0
3.592743
3.462488
−2.63616
3.091433
0.037124


2127
g11080.t1
3951
g1560.t1
K13303: SGK2
3.663667
5.639852
2.488524
−2.63746
3.090627
0.03716


2128
g17161.t1
3952
g9655.t1

3.946776
6.251222
2.716762
−2.63779
3.090423
0.03716


2129
g913.t1
3953
g9352.t1

3.761447
1.842695
−2.6974
−2.64185
−3.08791
0.037284


2131
g4992.t1
3955
g8962.t1

5.568434
1.070393
−4.64888
−2.64356
−3.08685
0.037304


2130
g5921.t1
3954
g11009.t1

0.726064
3.654951
2.376852
−2.64348
3.086896
0.037304


2132
g10214.t1
3956
g11973.t1

4.391352
5.888419
2.232265
−2.64574
3.085498
0.037377


2134
g1192.t1
3958
g2652.t1

7.331953
0
−4.76693
−2.64809
−3.08404
0.037428


2133
g5409.t1
3957
g8611.t1

0.487121
6.397764
4.771873
−2.64784
3.084192
0.037428


2135
g6619.t1
3959
g11272.t1
K11159: K11159
10.02313
7.677217
−2.84367
−2.64911
−3.08341
0.037454


2136
g5978.t1
3960
g11675.t1
K01187: malZ
4.632559
1.508608
−2.55697
−2.65074
−3.0824
0.037506


2137
g9539.t1
3961
g6568.t1
K05906: PCYOX1, FCLY
0
3.166553
5.702237
−2.6513
3.082052
0.037513


2138
g13602.t1
3962
g10129.t1
K09579: PIN4
3.22586
7.700999
4.342095
−2.65456
3.080031
0.037601


2139
g10588.t1
3963
g7031.t1

0
5.84847
4.399222
−2.65698
3.078527
0.03767


2140
g8167.t1
3964
g7975.t1

4.268879
6.362638
3.264487
−2.66061
3.076281
0.037775


2141
g6658.t1
3965
g10210.t1

1.079636
5.470349
3.827162
−2.66129
3.07586
0.037784


2142
g1881.t1
3966
g4234.t1
K01725: cynS
4.230103
2.82032
−2.77283
−2.66619
−3.07282
0.037943


2143
g11727.t1
3967
g5855.t1

3.728683
0.656698
−2.85634
−2.66698
−3.07233
0.03796


2144
g3432.t1
3968
g4712.t1
K00505: TYR
0
3.109455
4.733726
−2.67446
3.067691
0.038224


2145
g20186.t1
3969
g6363.t1

5.012816
7.163425
2.999714
−2.68527
3.060993
0.038598


2146
g447.t1
3970
g8029.t1
K13431: SRPR
4.802134
1.949645
−2.92415
−2.69849
−3.0528
0.039107


2147
g4444.t1
3971
g6795.t1

4.899102
2.093375
−3.84401
−2.69952
−3.05216
0.039136


2148
g18374.t1
3972
g7684.t1
K12856: PRPF8, PRP8
4.95726
1.392127
−3.87785
−2.70169
−3.05082
0.039186


2149
g8150.t1
3973
g7956.t1
K02959: RP-S16,
5.17122
2.06327
−3.42667
−2.70179
−3.05076
0.039186






MRPS16, rpsP


2150
g1210.t1
3974
g364.t1

5.549737
1.972661
−3.45578
−2.70577
−3.04829
0.039324


2151
g8164.t1
3975
g7965.t1

0.264932
6.326912
4.484822
−2.71181
3.044544
0.039565


2153
g8665.t1
3977
g2654.t1

4.448871
0
−4.40278
−2.71535
−3.04235
0.039644


2154
g6421.t1
3978
g5368.t1

3.418022
7.778884
4.446548
−2.71542
3.04231
0.039644


2152
g7000.t1
3976
g6384.t1
K15109: SLC25A20_29,
0
5.827294
5.75825
−2.71486
3.042655
0.039644






CACT, CACL, CRC1


2155
g3832.t1
3979
g2595.t1

1.491655
5.211867
3.871807
−2.71908
3.040044
0.039755


2156
g10272.t1
3980
g2373.t1

6.233817
2.342297
−5.51583
−2.72027
−3.03931
0.039778


2158
g4169.t1
3982
g1810.t1

2.732171
7.333986
3.584184
−2.72283
3.037719
0.039793


2157
g10739.t1
3981
g11986.t1

0
3.441589
3.584342
−2.72269
3.037804
0.039793


2159
g5894.t1
3983
g10982.t1
K03030: PSMD14,
5.235811
0
−4.2666
−2.72651
−3.03544
0.039906






RPN11, POH1


2160
g3017.t1
3984
g8289.t1

4.253797
2.232303
−2.01665
−2.72969
−3.03347
0.040028


2161
g2235.t1
3985
g10642.t1

0
8.944426
6.651699
−2.73008
3.033226
0.040029


2162
g444.t1
3986
g8037.t1

5.926244
1.755078
−4.43879
−2.73748
−3.02864
0.040289


2163
g8162.t1
3987
g7962.t1

2.242593
6.181948
2.975066
−2.7414
3.026215
0.04044


2164
g3781.t1
3988
g2653.t1

0
5.388341
4.391813
−2.74166
3.026051
0.04044


2165
g446.t1
3989
g8030.t1

1.248806
3.196143
2.232547
−2.74479
3.024112
0.040546


2166
g8813.t1
3990
g11548.t1

4.479092
1.564747
−2.31147
−2.75228
−3.01947
0.040844


2168
g484.t1
3992
g5480.t1
K01083: E3.1.3.8
6.104152
1.195312
−3.75188
−2.76953
−3.00879
0.041524


2167
g6382.t1
3991
g762.t1
K11578: ZW10
4.043617
7.246112
3.318946
−2.76929
3.008933
0.041524


2169
g13874.t1
3993
g4606.t1

2.192003
4.933315
3.081033
−2.77099
3.007879
0.04156


2170
g9768.t1
3994
g940.t1

1.599958
5.142409
3.111563
−2.77117
3.00777
0.04156


2171
g7100.t1
3995
g5567.t1

3.101236
4.623123
2.647789
−2.77245
3.006974
0.041602


2172
g7685.t1
3996
g7577.t1

4.579641
1.059627
−4.79509
−2.77348
−3.00633
0.041632


2174
g6166.t1
3998
g9581.t1
K10844: ERCC2, XPD
3.612569
6.046916
2.409001
−2.77444
3.005738
0.041644


2173
g20840.t1
3997
g5601.t1
K09958: K09958
0
3.295785
3.355548
−2.77424
3.005865
0.041644


2175
g4928.t1
3999
g4568.t1
K10752: RBBP4, HAT2,
0.721987
4.891137
3.366959
−2.7761
3.004716
0.041686






CAF1, MIS16


2177
g4731.t1
4001
g2023.t1

3.62063
8.542099
3.637606
−2.78256
3.000712
0.041947


2176
g13702.t1
4000
g7799.t1

1.507271
5.575516
5.445863
−2.78244
3.000783
0.041947


2178
g6999.t1
4002
g6385.t1

0
5.909998
6.710453
−2.78479
2.999326
0.041984


2179
g1200.t1
4003
g354.t1
K03189: ureG
3.906083
6.287127
3.500283
−2.78517
2.999091
0.041985


2180
g894.t1
4004
g9381.t1

1.98344
3.689145
2.509227
−2.78645
2.9983
0.042011


2181
g4606.t1
4005
g11246.t1

6.888917
0.934867
−4.17521
−2.7892
−2.9966
0.04212


2182
g5836.t1
4006
g1169.t1
K01078: E3.1.3.2
4.897435
0.540874
−3.08894
−2.78981
−2.99622
0.042132


2183
g6795.t1
4007
g4420.t1
K00620: argJ
1.412783
6.285553
3.554814
−2.7905
2.995789
0.042148


2184
g13700.t1
4008
g7801.t1
K06666: TUP1
4.676696
9.110953
5.842219
−2.79358
2.993881
0.042237


2185
g4127.t1
4009
g1853.t1

6.883091
3.151116
−3.23591
−2.79424
−2.99347
0.042238


2186
g3498.t1
4010
g2189.t1
K00888: PI4K
4.387206
8.035595
3.806841
−2.79735
2.991549
0.042365


2187
g922.t1
4011
g9339.t1

0.335414
5.594
3.51525
−2.80783
2.985057
0.042832


2188
g2095.t1
4012
g2498.t1

2.312071
5.547566
3.491828
−2.8095
2.984022
0.042893


2189
g3886.t1
4013
g4006.t1

0.369905
5.31491
3.411646
−2.81293
2.981892
0.04302


2191
g2907.t1
4015
g4478.t1
K01361: E3.4.21.96
2.736066
5.91864
3.746675
−2.81508
2.980564
0.043087


2190
g4132.t1
4014
g1848.t1

3.459488
8.742363
3.852241
−2.8149
2.980673
0.043087


2192
g102.t1
4016
g2922.t1
K15628: PXA
4.533487
1.423633
−3.06092
−2.81692
−2.97942
0.043124


2193
g22195.t1
4017
g11335.t1

5.038549
3.116899
−3.18678
−2.82113
−2.97682
0.043256


2194
g6067.t1
4018
g11760.t1

2.556856
5.057211
2.182582
−2.82589
2.973866
0.043414


2195
g7479.t1
4019
g6857.t1

6.476209
0.753273
−5.14745
−2.82832
−2.97236
0.043492


2196
g6849.t1
4020
g1428.t1
K14312: NUP155
5.863337
2.74764
−3.23983
−2.8286
−2.97218
0.043492


2197
g6740.t1
4021
g4353.t1

3.814661
6.39705
3.411605
−2.83035
2.971099
0.043559


2198
g1017.t1
4022
g8086.t1

1.006221
4.462038
2.793294
−2.83106
2.970664
0.043575


2199
g20453.t1
4023
g7824.t1

0
2.0793
2.784209
−2.83156
2.970353
0.043583


2200
g1014.t1
4024
g8083.t1
K13577: SLC25A10, DIC
2.388955
4.532509
2.338145
−2.83672
2.967153
0.04381


2201
g3487.t1
4025
g2179.t1

0
3.411165
3.277123
−2.83823
2.966219
0.04385


2202
g3156.t1
4026
g4990.t1

3.806958
6.990748
5.291192
−2.84227
2.963714
0.043975


2203
g21845.t1
4027
g8491.t1

0
2.721806
3.270562
−2.84342
2.963002
0.044014


2204
g2266.t1
4028
g10682.t1

4.867023
3.323245
−2.83067
−2.84548
−2.96173
0.044069


2205
g11688.t1
4029
g10852.t1

3.032144
0.893416
−2.19305
−2.85456
−2.9561
0.044448


2206
g6381.t1
4030
g763.t1

5.116653
0.131962
−3.22317
−2.85525
−2.95567
0.044464


2208
g10499.t1
4032
g1661.t1

4.339082
6.042177
2.559442
−2.85649
2.954904
0.044491


2207
g17551.t1
4031
g8157.t1
K00558: DNMT1, dcm
2.888377
6.949835
3.089797
−2.85616
2.955108
0.044491


2209
g5340.t1
4033
g9534.t1

0.545456
7.258622
4.798642
−2.85837
2.953743
0.044548


2210
g5285.t1
4034
g2285.t1

2.96395
7.10547
3.24264
−2.85885
2.953444
0.044555


2211
g7357.t1
4035
g10412.t1

5.528929
0.619143
−3.97539
−2.86359
−2.95051
0.044734


2213
g726.t1
4037
g10236.t1

0.483715
2.68877
2.384127
−2.86588
2.949088
0.044811


2212
g3514.t1
4036
g2206.t1
K11397: EAF1, VID21
1.206815
6.642767
4.853325
−2.86574
2.949177
0.044811


2214
g7257.t1
4038
g10783.t1

1.642966
6.188124
2.989166
−2.87117
2.945813
0.045035


2215
g10215.t1
4039
g11972.t1

2.58645
7.403204
4.385523
−2.87151
2.945602
0.045035


2216
g12395.t1
4040
g9538.t1

5.861009
2.002652
−3.8787
−2.87539
−2.9432
0.045174


2217
g341.t1
4041
g8842.t1

5.788696
9.05636
2.247676
−2.87854
2.941243
0.045312


2218
g2488.t1
4042
g3515.t1
K06669: SMC3, CSPG6
1.945941
7.641363
3.740235
−2.88255
2.938761
0.045473


2219
g713.t1
4043
g9934.t1

5.331222
0.664695
−4.38202
−2.88525
−2.93708
0.045565


2220
g3763.t1
4044
g2673.t1

5.825851
3.254634
−2.56829
−2.88539
−2.937
0.045565


2221
g7424.t1
4045
g7209.t1

5.373092
9.386519
3.006451
−2.88618
2.93651
0.04557


2222
g5043.t1
4046
g10906.t1
K01426: E3.5.1.4, amiE
2.242898
6.456313
3.847076
−2.89168
2.933101
0.045808


2223
g7402.t1
4047
g7184.t1

5.091428
2.484421
−2.06938
−2.89544
−2.93077
0.045911


2224
g6538.t1
4048
g10076.t1
K12830: SF3B3,
0
3.092763
3.060265
−2.90278
2.926225
0.046243






SAP130, RSE1


2225
g10909.t1
4049
g5917.t1

2.072461
4.929452
2.681301
−2.90454
2.92513
0.046314


2226
g10722.t1
4050
g4266.t1
K12827: SF3A3, SAP61,
3.415338
6.31204
3.035059
−2.90712
2.923532
0.046427






PRP9


2227
g4840.t1
4051
g4450.t1

3.23602
0.449458
−3.90188
−2.91106
−2.92109
0.046537


2228
g1066.t1
4052
g8139.t1
K01922: PPCS, coaB
1.857534
4.106673
3.234378
−2.91469
2.918841
0.046689


2229
g6576.t1
4053
g10109.t1

3.964575
0
−4.86543
−2.91615
−2.91794
0.046745


2230
g107.t1
4054
g2928.t1
K03539: RPP1, RPP30
3.197967
0.803547
−2.46999
−2.92305
−2.91366
0.047038


2231
g3425.t1
4055
g4720.t1
K02605: ORC3
6.578091
4.722727
−2.20212
−2.92326
−2.91353
0.047038


2232
g1018.t1
4056
g8087.t1
K04565: SOD1
2.947764
8.680712
5.056988
−2.92384
2.913169
0.04705


2234
g5391.t1
4058
g2427.t1

3.793826
0.942173
−4.97661
−2.92597
−2.91185
0.047091


2233
g7764.t1
4057
g879.t1

3.456716
1.497029
−2.42385
−2.92569
−2.91203
0.047091


506
g8644.t1
2302
g2276.t1
K01166: E3.1.27.1
0
10.03085
6.401697
−2.92547
2.91216
0.047091


2236
g1094.t1
4060
g4037.t1
K02358: tuf, TUFM
7.685682
5.149397
−2.8793
−2.93139
−2.90849
0.047263


2235
g712.t1
4059
g9943.t1

2.563775
7.171783
3.80414
−2.93127
2.908563
0.047263


2237
g2419.t1
4061
g11542.t1

0.666287
3.962309
2.387936
−2.93259
2.907749
0.047307


2238
g2608.t1
4062
g9643.t1
K00135: gabD
1.638785
4.294982
3.144001
−2.93448
2.906575
0.047387


2239
g8147.t1
4063
g7952.t1
K11246: SHO1
6.066325
2.713104
−3.95602
−2.93607
−2.90559
0.047433


2240
g5705.t1
4064
g10360.t1

0.642825
4.418076
3.166773
−2.93679
2.905146
0.047433


2241
g1222.t1
4065
g374.t1

2.642618
5.883278
3.175464
−2.93706
2.90498
0.047433


2242
g8664.t1
4066
g3812.t1

7.432168
1.550855
−4.57283
−2.93851
−2.90408
0.04749


2243
g4764.t1
4067
g1994.t1

6.940047
1.130412
−4.17201
−2.93963
−2.90338
0.047531


2244
g6851.t1
4068
g1427.t1

2.284011
3.932777
2.957195
−2.94037
2.902925
0.047551


2245
g10946.t1
4069
g5078.t1
K11236: CDC24
4.982918
0.83865
−3.5024
−2.94195
−2.90195
0.047598


2246
g1752.t1
4070
g9722.t1

2.831268
5.535026
2.675068
−2.94838
2.897963
0.047896


2247
g566.t1
4071
g3892.t1
K14708: SLC26A11
0.609198
5.65481
3.423398
−2.95146
2.896054
0.048021


2248
g3553.t1
4072
g3337.t1

5.206188
1.970138
−6.17884
−2.95714
−2.89253
0.048268


2249
g383.t1
4073
g7452.t1
K03978: engB
3.305487
5.192025
2.780869
−2.95719
2.892499
0.048268


2250
g7722.t1
4074
g3091.t1
K03014: RPB6, POLR2F
0
4.540834
4.042193
−2.96294
2.888936
0.048493


2251
g5453.t1
4075
g3167.t1

4.7696
0.934559
−3.55662
−2.96747
−2.88612
0.048686


2252
g9542.t1
4076
g6565.t1
K01381: E3.4.23.25
0
3.886173
3.681133
−2.969
2.885177
0.048749


2254
g1347.t1
4078
g3449.t1
K01273: E3.4.13.19,
4.946987
0.532441
−3.43411
−2.972
−2.88332
0.048837






DPEP1


2253
g4317.t1
4077
g1977.t1

2.161002
7.174394
3.592405
−2.97197
2.883339
0.048837


2255
g5426.t1
4079
g3123.t1
K09539: DNAJC19
7.936931
3.022359
−5.07555
−2.97281
−2.88282
0.048862


2256
g22408.t1
4080
g9317.t1
K05351: E1.1.1.9
0
5.279355
4.074546
−2.97436
2.881852
0.048927


2257
g6391.t1
4081
g5410.t1
K00480: E1.14.13.1
10.39213
2.102041
−5.87521
−2.97645
−2.88056
0.048977


2258
g4848.t1
4082
g4461.t1

5.837897
1.338468
−3.27267
−2.97698
−2.88023
0.048977


2259
g5255.t1
4083
g2333.t1

5.719887
4.103219
−2.31021
−2.97885
−2.87907
0.049041


2261
g10716.t1
4085
g11754.t1

4.124991
1.869399
−2.24701
−2.98266
−2.87671
0.049173


2260
g5384.t1
4084
g9571.t1
K13099: CD2BP2,
0
5.725959
3.979521
−2.98264
2.876724
0.049173






PPP1R59


2262
g2819.t1
4086
g9111.t1
K16066: ydfG
5.823181
2.29085
−5.24434
−2.98895
−2.87281
0.049421


2265
g10820.t1
4089
g5705.t1

1.446801
4.641792
2.923813
−2.99351
2.869978
0.049577


2263
g10158.t1
4087
g8462.t1

0
2.396169
3.866683
−2.9926
2.870543
0.049577


2264
g844.t1
4088
g9461.t1

0
4.027461
4.070888
−2.99313
2.870218
0.049577


2267
g2834.t1
4091
g9028.t1

4.114412
0.517908
−3.11219
−2.99494
−2.8691
0.0496


2266
g10485.t1
4090
g1675.t1

0
4.900393
4.371976
−2.99484
2.869153
0.0496


2268
g11904.t1
4092
g11956.t1
K00681: ggt
3.288998
0.166182
−3.64625
−2.99768
−2.86739
0.049713


2269
g21731.t1
4093
g6097.t1

2.691539
0.619933
−4.08621
−3.00053
−2.86563
0.049849


2270
g1202.t1
4094
g356.t1
K14768: UTP7, WDR46
1.026847
3.791611
2.583054
−3.00301
2.864088
0.049957


2271
g9859.t1
4095
g11476.t1

0
4.020067
4.04691
−3.00328
2.863921
0.049957










This table describes orthologous genes of Acremonium zea sp. with beneficial and neutral effects on soybean growth, these genes show significant changes in expression between the two genotypes when grown in culture with soybean homogenate. “Median Exp. SYM00577” represents the median expression value in log 2 tpm across biological replicates of the beneficial Acremonium grown in media inoculated with soybean seedling homogenate extracted with 50 mM PBS. “Median Exp. SYM00300” represents the median expression value in log 2 tpm across biological replicates of the neutral Acremonium grown in media inoculated with soybean seedling homogenate extracted with 50 mM PBS. “Log FC” represents the estimate of the log 2-fold-change of the contrast. “B-statistic” represents the log-odds that the gene is differentially expressed. “t-statistic” represents the moderated t-statistic. “Adj. p-value” represents the false discovery rate (Benjamini & Hochberg, 1995) adjusted p-values.














TABLE 603







SEQ ID
sym577
SEQ ID
sym300

Median Exp.


SYM00577
gene
SYM00300
gene
Description
SYM00577





687
g13072.t1
2494
g9142.t1

0


700
g10575.t1
2526
g10634.t1

0


674
g5345.t1
2555
g9530.t1
K03510: POLI
5.845894518


688
g68.t1
2495
g909.t1
K00106: XDH
7.003820996


701
g12045.t1
2524
g804.t1
K12393: AP1M
6.653853259


702
g1230.t1
2527
g388.t1

0


703
g2767.t1
2559
g9144.t1
K02139: ATPeFF, ATP17
0


704
g7900.t1
2560
g8630.t1

6.140021427


686
g857.t1
2491
g9451.t1
K01950: E6.3.5.1,
3.802514601






NADSYN1, QNS1, nadE


675
g5348.t1
2554
g1.t1

0


705
g10859.t1
2552
g120.t1
K17842: carT, CAO-2
0


706
g8300.t1
2561
g5097.t1
K15136: SRB5, MED18
7.025134642


707
g2262.t1
2562
g10678.t1
K11205: GCLM
0


708
g8448.t1
2563
g2683.t1
K00966: GMPP
0


709
g10027.t1
2564
g3454.t1

0


517
g13099.t1
2313
g8761.t1

0


710
g1584.t1
2517
g2859.t1

7.332050712


690
g7926.t1
2497
g8597.t1

6.853860482


711
g9140.t1
2565
g6474.t1
K02434: gatB, PET112
7.89701243


558
g9065.t1
2355
g8585.t1
K03234: EEF2
0


712
g3334.t1
2566
g4792.t1

0


713
g3376.t1
2567
g10478.t1

0


714
g9.t1
2568
g3899.t1

0


692
g5169.t1
2506
g3798.t1

4.865818268


685
g6380.t1
2492
g764.t1
K05857: PLCD
5.073855922


696
g3920.t1
2508
g3972.t1

5.062011561


715
g10569.t1
2569
g8038.t1

0


716
g4884.t1
2570
g5157.t1

3.493672904


717
g12587.t1
2571
g2937.t1

5.143110791


718
g9196.t1
2572
g6530.t1
K01937: pyrG, CTPS
2.877811039


719
g5920.t1
2573
g11008.t1
K02894: RP-L23e, RPL23
2.351855506


720
g5591.t1
2547
g7515.t1

5.584485038


721
g7216.t1
2574
g5885.t1

4.657263756


722
g4371.t1
2575
g2128.t1

5.510282495


698
g657.t1
2503
g9863.t1

4.4628192


723
g5419.t1
2576
g5084.t1

8.315874976


724
g5712.t1
2577
g1012.t1

5.583909958


725
g5938.t1
2578
g8896.t1

0


726
g2504.t1
2579
g3532.t1

0


727
g7969.t1
2580
g10252.t1
K03639: MOCS1, moaA
4.758242645


728
g1770.t1
2581
g1188.t1

6.058400928


729
g815.t1
2582
g8179.t1

7.400064361


730
g3624.t1
2583
g600.t1
K14297: NUP98, ADAR2
5.106519345


731
g3218.t1
2584
g6107.t1

4.600691335


732
g6563.t1
2585
g10099.t1

7.052996504


733
g5058.t1
2586
g8328.t1

6.170884433


734
g2063.t1
2587
g2535.t1
K01426: E3.5.1.4, amiE
6.62697264


735
g7620.t1
2588
g9046.t1

1.469790922


737
g8108.t1
2590
g7917.t1

5.22299962


736
g13149.t1
2589
g4276.t1

0


738
g15293.t1
2591
g6106.t1

2.346160706


739
g10986.t1
2592
g5652.t1
K02141: ATPeFH, ATP14
0


740
g2758.t1
2593
g9152.t1
K10627: RAD18
0


741
g4882.t1
2594
g4502.t1

6.687936705


742
g1999.t1
2595
g6250.t1

0


743
g3555.t1
2596
g3333.t1
K01624: FBA, fbaA
4.536933474


744
g4741.t1
2597
g2013.t1
K03237: EIF2S1
6.043892772


745
g5254.t1
2598
g2334.t1
K02137: ATPeF0O,
5.144250658






ATP5O, ATP5


746
g5568.t1
2529
g7485.t1

2.950253937


747
g19199.t1
2599
g12080.t1
K01102: PDP
4.719048671


748
g4710.t1
2600
g6681.t1
K03457: TC.NCS1
5.545619928


749
g1003.t1
2601
g8072.t1
K03626: EGD2, NACA
9.544725129


750
g12699.t1
2602
g8909.t1

0


751
g3631.t1
2603
g607.t1

5.634764008


752
g10888.t1
2604
g176.t1
K00463: INDO
0


697
g852.t1
2502
g9454.t1
K11824: AP2A
5.513795279


753
g10211.t1
2605
g11976.t1

6.236601553


754
g158.t1
2606
g5219.t1

0


755
g6128.t1
2607
g7318.t1
K13953: adhP
0.559800663


691
g5563.t1
2493
g7478.t1

4.371792513


756
g5223.t1
2608
g3707.t1
K03515: REV1
7.079279048


680
g1340.t1
2553
g523.t1

5.657989905


757
g6031.t1
2609
g11529.t1
K01885: EARS, gltX
8.997952533


758
g5074.t1
2610
g2984.t1

0


759
g6741.t1
2611
g4354.t1

2.11282087


760
g829.t1
2612
g8197.t1
K13577: SLC25A10,
0






DIC


761
g7264.t1
2613
g11828.t1

5.499599524


762
g2074.t1
2614
g2522.t1

4.591860791


763
g9395.t1
2615
g3638.t1
K06116: GPP1
2.323291749


764
g9849.t1
2616
g9778.t1

9.223686565


765
g11803.t1
2617
g12043.t1

2.387616958


766
g11916.t1
2618
g661.t1

7.715759124


767
g1153.t1
2619
g5028.t1

4.692839925


768
g5373.t1
2620
g9561.t1

5.888238765


769
g7390.t1
2621
g7172.t1

7.350351967


770
g10732.t1
2622
g4256.t1

0


771
g10093.t1
2623
g9511.t1

4.296964996


772
g10839.t1
2624
g9837.t1

6.8729034


773
g10191.t1
2625
g11148.t1

6.023102414


774
g3013.t1
2626
g8294.t1

5.470261921


775
g7841.t1
2627
g10495.t1

4.614472875


776
g21528.t1
2512
g10587.t1
K01885: EARS, gltX
3.911232108


777
g9138.t1
2628
g6473.t1

4.198675014


778
g4873.t1
2629
g4492.t1

5.713341579


779
g7446.t1
2630
g6892.t1

7.48417852


780
g8021.t1
2631
g8248.t1

4.309793696


781
g100.t1
2632
g2920.t1

0


782
g1180.t1
2633
g337.t1

6.10473465


783
g14694.t1
2634
g6409.t1

9.825681474


784
g6706.t1
2521
g4310.t1

7.446014886


785
g14790.t1
2635
g5147.t1

1.686007548


786
g8676.t1
2636
g10948.t1

3.991647742


787
g4402.t1
2637
g2161.t1

0


788
g1963.t1
2638
g6215.t1

6.923009485


789
g132.t1
2639
g5829.t1

0


790
g11512.t1
2640
g4219.t1

6.309781587


791
g10280.t1
2641
g10638.t1

0


792
g796.t1
2642
g8160.t1

0.721237136


793
g15000.t1
2643
g3110.t1
K09658: DPM2
5.469156461


794
g7638.t1
2644
g7605.t1

0


795
g11518.t1
2645
g4213.t1

5.935642711


796
g85.t1
2646
g2767.t1

5.850559685


797
g489.t1
2647
g5491.t1
K05857: PLCD
5.789925493


798
g8243.t1
2648
g10036.t1

4.646855045


800
g4842.t1
2650
g4453.t1
K13120: FAM32A
5.230120767


799
g10374.t1
2649
g10541.t1
K15505: RAD5
0


801
g10174.t1
2651
g8450.t1
K11557: SPC24
1.118361424


803
g3427.t1
2653
g4718.t1
K12854: SNRNP200,
7.533706795






BRR2


802
g1849.t1
2652
g1896.t1
K00938: E2.7.4.2, mvaK2
8.103944385


804
g19694.t1
2654
g7947.t1
K02142: ATPeFJ, ATP18
4.724478914


805
g6500.t1
2655
g2087.t1
K11548: NUF2, CDCA1
4.167333488


808
g11718.t1
2657
g2320.t1

6.955332876


807
g2706.t1
2513
g8366.t1
K11649: SMARCC
5.407509356


806
g3663.t1
2656
g656.t1
K00632: E2.3.1.16, fadA
6.107648999


809
g4795.t1
2658
g3691.t1

2.814605061


810
g9159.t1
2659
g6490.t1

12.37001214


812
g7897.t1
2661
g8633.t1
K12191: CHMP2A
6.149239272


811
g4381.t1
2660
g2138.t1
K14846: RPF1
4.661983349


813
g15305.t1
2662
g10450.t1
K01915: glnA, GLUL
1.326818728


814
g12732.t1
2663
g5706.t1

0


815
g9791.t1
2664
g893.t1

4.682251788


816
g14760.t1
2665
g9241.t1

2.816496891


817
g5187.t1
2666
g3776.t1
K01277: E3.4.14.4, DPP3
5.729836476


818
g7634.t1
2667
g7610.t1
K10773: NTH
6.081778745


819
g13477.t1
2668
g8720.t1
K10295: FBXO9
5.178686522


820
g12592.t1
2669
g2931.t1

6.934534554


821
g10987.t1
2670
g5653.t1

0


822
g12590.t1
2671
g2934.t1

6.223414116


823
g10222.t1
2672
g11207.t1

4.643453596


825
g3983.t1
2674
g7058.t1
K01613: psd, PISD
5.451665752


824
g11510.t1
2673
g4221.t1

4.286646074


826
g9393.t1
2675
g3641.t1

8.751164208


827
g9881.t1
2676
g11623.t1

0


828
g13221.t1
2677
g672.t1

0


829
g3561.t1
2678
g3326.t1

4.733400818


830
g8670.t1
2679
g10955.t1

4.749528223


831
g708.t1
2680
g9946.t1

0.954625619


832
g11009.t1
2681
g5663.t1
K11121: SIR2
0


833
g7419.t1
2682
g7204.t1
K13754: SLC24A6, NCKX6
6.27610662


835
g3224.t1
2684
g6091.t1

3.344134063


834
g12947.t1
2683
g9800.t1

0


836
g6094.t1
2685
g7354.t1

6.09853587


837
g7427.t1
2686
g7212.t1
K01549: TIM11, ATP21
5.301910749


838
g6135.t1
2687
g7308.t1
K03844: ALG11
4.695297001


839
g5057.t1
2688
g8325.t1
K00326: E1.6.2.2
5.161405198


840
g3875.t1
2689
g4019.t1

1.368553327


841
g21658.t1
2690
g4834.t1

6.709472946


842
g7438.t1
2691
g7223.t1

4.971359373


843
g7605.t1
2692
g7631.t1
K06942: K06942
4.937065903


844
g6721.t1
2693
g4326.t1

1.642040135


845
g7857.t1
2694
g10514.t1

0


846
g3614.t1
2695
g588.t1
K12604: CNOT1, NOT1
6.72026689


847
g11968.t1
2696
g7463.t1

0


848
g6429.t1
2697
g5353.t1

5.059361503


849
g20508.t1
2698
g3950.t1

0


850
g7165.t1
2699
g555.t1

3.895318144


851
g4535.t1
2700
g4065.t1

8.36766264


852
g20378.t1
2701
g3507.t1

0


853
g8160.t1
2702
g11151.t1

7.072684453


854
g6555.t1
2703
g10091.t1
K00286: E1.5.1.2, proC
5.981191238


855
g5572.t1
2704
g7489.t1

6.099888984


856
g2329.t1
2543
g9194.t1

7.114801788


857
g1250.t1
2705
g434.t1

5.533904052


858
g11133.t1
2706
g753.t1
K06972: K06972
4.000597283


859
g490.t1
2536
g5492.t1
K01230: MAN1
4.455711732


860
g7575.t1
2707
g7666.t1
K11272: MRC1
7.443866007


861
g6402.t1
2708
g5392.t1

0


519
g31.t1
2315
g2840.t1
K02437: gcvH, GCSH
7.667805418


862
g11374.t1
2709
g5061.t1
K16803: CKAP5,
0






XMAP215


863
g6116.t1
2710
g7333.t1
K02258: COX11
0


864
g7600.t1
2711
g7636.t1
K17768: TOM70
5.478745927


865
g7609.t1
2712
g7627.t1

6.110778129


866
g670.t1
2713
g9895.t1

5.389860972


867
g3288.t1
2714
g8848.t1

0


868
g1739.t1
2715
g9739.t1
K01918: panC
1.723333708


869
g2853.t1
2716
g9055.t1

3.661150117


870
g11104.t1
2717
g718.t1

5.331556226


871
g2178.t1
2718
g11917.t1

4.412098474


872
g4449.t1
2719
g6805.t1

7.334855344


873
g5221.t1
2720
g3709.t1
K01240: URH1
4.395333747


874
g2815.t1
2721
g9114.t1
K01193: E3.2.1.26, sacA
6.290191463


875
g2269.t1
2722
g10685.t1

2.551428828


876
g2163.t1
2723
g11902.t1

5.298538589


877
g3515.t1
2724
g2207.t1

3.347586286


878
g6074.t1
2725
g3347.t1

6.324042809


879
g11929.t1
2726
g2071.t1

6.098181798


880
g6915.t1
2727
g1291.t1
K00505: TYR
6.540932521


881
g1756.t1
2728
g1207.t1
K15201: GTP3C3, TFC4
6.731005978


882
g6770.t1
2729
g4386.t1

5.731686881


883
g10376.t1
2730
g10544.t1
K02990: RP-S6, MRPS6,
0






rpsF


884
g9812.t1
2731
g10826.t1
K01899: LSC1
5.913334166


885
g9618.t1
2732
g7244.t1

0


886
g2442.t1
2733
g6711.t1
K10998: CSM3, SWI3
6.56163386


887
g17691.t1
2734
g559.t1

5.586773168


889
g10183.t1
2736
g11138.t1
K17878: NNT1
4.422235435


888
g7714.t1
2735
g3081.t1
K01070: frmB, ESD, fghA
4.789610997


890
g2359.t1
2737
g9253.t1

8.893941672


891
g4991.t1
2738
g8961.t1
K15901: CGI121, TPRKB
5.458778357


892
g106.t1
2739
g2927.t1

4.560793659


893
g7472.t1
2740
g6864.t1
K10839: RAD23, HR23
6.506527453


894
g4849.t1
2741
g4462.t1

6.018049911


895
g4668.t1
2742
g10566.t1
K01312: PRSS
9.271875621


896
g9585.t1
2743
g6636.t1
K06675: SMC4
0


897
g2963.t1
2744
g5934.t1

4.375328682


898
g7232.t1
2745
g10757.t1
K09313: CUTL
8.116353121


899
g19769.t1
2746
g11692.t1

4.972241584


900
g7022.t1
2747
g6357.t1

0


901
g9259.t1
2748
g10437.t1

6.69953931


902
g12328.t1
2749
g7434.t1
K01710: E4.2.1.46, rfbB,
3.685729613






rffG


903
g2849.t1
2750
g9051.t1

7.214498977


904
g17779.t1
2751
g662.t1

4.282054458


905
g8550.t1
2752
g5428.t1
K08838: STK24_25_MST4
5.000505255


906
g10940.t1
2753
g1025.t1
K00100: E1.1.1.—
4.956194307


907
g11117.t1
2754
g735.t1

5.648961974


562
g1904.t1
2359
g5010.t1
K16261: YAT
2.226821689


908
g3804.t1
2755
g8748.t1

5.793251762


909
g3244.t1
2756
g8218.t1
K02838: frr, MRRF, RRF
0


910
g11369.t1
2757
g10756.t1

5.176727673


611
g7102.t1
2410
g5569.t1

4.138124976


911
g677.t1
2758
g9875.t1
K07140: K07140
5.281680888


679
g4287.t1
2759
g1939.t1
K00275: pdxH, PNPO
4.95193285


912
g7511.t1
2760
g10316.t1
K08286: E2.7.11.—
6.009945831


913
g1830.t1
2761
g1716.t1

7.072977042


914
g6552.t1
2762
g10088.t1
K14572: MDN1, REA1
4.349948417


915
g74.t1
2763
g917.t1
K00480: E1.14.13.1
5.955742918


916
g5429.t1
2764
g3125.t1

4.987582363


917
g8498.t1
2765
g3370.t1

5.820660636


918
g7844.t1
2766
g10497.t1

5.848243945


919
g5407.t1
2767
g8613.t1

0


921
g4889.t1
2769
g4523.t1
K14209: SLC36A, PAT
5.82364098


920
g2118.t1
2768
g2464.t1
K01560: E3.8.1.2
3.940755827


922
g4577.t1
2770
g4105.t1

2.560658097


923
g6091.t1
2771
g7357.t1
K12193: VPS24, CHMP3
2.859023838


924
g4043.t1
2772
g3220.t1

5.096464748


925
g10590.t1
2773
g7033.t1
K01190: lacZ
0


926
g11987.t1
2774
g2441.t1
K15172: SUPT5H, SPT5
6.055881291


927
g7118.t1
2775
g5583.t1
K06670: SCC1, MCD1,
7.656991383






RAD21


928
g9841.t1
2776
g9760.t1

8.545788709


929
g10869.t1
2777
g134.t1

0


930
g8799.t1
2778
g9975.t1

4.851135285


931
g3513.t1
2779
g2205.t1
K12041: SLC9A6_7,
4.628300692






NHE6_7


932
g4464.t1
2780
g6823.t1
K00111: glpA, gtpD
4.913318358


933
g912.t1
2781
g9350.t1

6.681560463


934
g6047.t1
2482
g264.t1

5.833182512


935
g8273.t1
2782
g9995.t1

5.609052156


936
g8132.t1
2783
g7944.t1
K14526: POP7, RPP2
5.431104442


937
g8077.t1
2540
g7846.t1

6.924579829


938
g10164.t1
2784
g6116.t1

6.523454108


940
g8187.t1
2785
g7995.t1
K03325: TC.ACR3
8.04995065


939
g4598.t1
2528
g6014.t1

3.985835911


941
g10685.t1
2786
g8531.t1

4.755054229


942
g4368.t1
2787
g3790.t1

5.47962036


944
g5574.t1
2789
g7491.t1
K11370: AHC1
7.953609684


943
g10154.t1
2788
g8466.t1
K03661: ATPeV0B, ATP6F
2.459230154


945
g6618.t1
2790
g11273.t1
K14333: DHBD
8.223627165


946
g4717.t1
2791
g2039.t1

6.556761484


947
g3409.t1
2792
g6220.t1

6.131735085


948
g11995.t1
2793
g2451.t1

4.464464914


949
g2327.t1
2794
g9192.t1

4.697725891


950
g4993.t1
2795
g8964.t1

5.277688941


951
g9979.t1
2796
g9685.t1
K15148: MED7
0


952
g6193.t1
2797
g11718.t1

6.836216759


953
g4069.t1
2798
g3263.t1

4.437917777


954
g10250.t1
2799
g3606.t1

12.0823581


955
g5983.t1
2800
g11682.t1

5.452835216


957
g11115.t1
2802
g733.t1

6.202864972


956
g3228.t1
2801
g6074.t1

4.204057944


958
g9407.t1
2803
g3620.t1

4.931825845


959
g1828.t1
2804
g1714.t1
K13535: CLD1
4.463119082


960
g3944.t1
2805
g3947.t1

5.535649157


961
g7851.t1
2806
g10505.t1

5.044625434


962
g18788.t1
2807
g387.t1

6.532520126


963
g9384.t1
2808
g3650.t1
K02210: MCM7, CDC47
6.91078027


964
g1127.t1
2809
g226.t1
K13210: FUBP
7.124489061


965
g96.t1
2810
g2917.t1

0


966
g6648.t1
2811
g10192.t1
K12868: SYF2
0


967
g1350.t1
2812
g7381.t1

0


968
g13893.t1
2813
g6198.t1
K07034: K07034
6.848687422


969
g4507.t1
2814
g10812.t1

3.840346233


970
g3241.t1
2815
g8215.t1

0


971
g11754.t1
2816
g9856.t1
K01779: E5.1.1.13
5.221579117


972
g1351.t1
2817
g6327.t1

0


973
g2037.t1
2818
g2568.t1
K12659: ARG56
0


974
g1683.t1
2819
g4660.t1
K10625: UBR1
3.398274676


975
g12749.t1
2820
g12137.t1

0


976
g9482.t1
2821
g5768.t1

6.71765746


977
g11380.t1
2822
g5068.t1

0


978
g6127.t1
2823
g7319.t1
K07213: ATOX1, ATX1,
11.50816411






copZ


979
g270.t1
2824
g7700.t1

6.248619031


980
g6423.t1
2825
g5361.t1

3.403273853


981
g10729.t1
2826
g2908.t1
K03448: FEN2, LIZ1
0


982
g3774.t1
2827
g6851.t1

0


983
g8680.t1
2828
g10944.t1
K13621: BTA1
0


985
g11533.t1
2830
g4194.t1
K00928: lysC
8.670529213


984
g2060.t1
2829
g2537.t1

4.647437267


987
g6588.t1
2832
g10117.t1

5.93851127


986
g9187.t1
2831
g6519.t1

0.369867578


988
g2854.t1
2833
g4992.t1

3.667696129


989
g173.t1
2834
g5800.t1
K07119: K07119
9.370340141


545
g10561.t1
2342
g1546.t1

0


990
g5941.t1
2835
g2881.t1

0


991
g2978.t1
2836
g8309.t1

0


992
g1958.t1
2837
g6209.t1

9.099456694


993
g12003.t1
2838
g10167.t1

4.021343839


994
g18673.t1
2839
g8118.t1

1.798228538


996
g11700.t1
2841
g6614.t1
K03860: PIGQ, GPI1
4.969629765


997
g5957.t1
2842
g6229.t1
K01056: PTH1, pth,
0






spoVC


995
g21700.t1
2840
g5543.t1

3.167921414


998
g8304.t1
2843
g5092.t1
K10253: K10253
4.621044993


1000
g697.t1
2845
g9928.t1
K03941: NDUFS8
5.799554424


999
g10287.t1
2844
g36.t1
K15444: TRM9
0


1001
g2303.t1
2846
g10723.t1
K07441: ALG14
5.074009843


1002
g6384.t1
2847
g759.t1

6.12726441


1003
g7586.t1
2848
g7651.t1

5.043611275


1004
g8534.t1
2849
g6285.t1

0


1005
g5408.t1
2850
g8612.t1
K00276: AOC3, AOC2,
0






tynA


1006
g8194.t1
2851
g8514.t1

6.303747883


1007
g13118.t1
2852
g7773.t1

0


1008
g9153.t1
2853
g6485.t1
K18716: NUP42, RIP1
6.170706947


1009
g6545.t1
2854
g10082.t1
K03885: ndh
0


1010
g7749.t1
2855
g7099.t1
K01512: acyP
1.405819898


1011
g19631.t1
2856
g6634.t1

2.571565788


1012
g522.t1
2857
g889.t1

10.81615793


1013
g3484.t1
2858
g2151.t1

0


1014
g12598.t1
2859
g12.t1

5.489807798


1016
g2711.t1
2861
g8361.t1
K07195: EXOC7, EXO70
4.061048103


1015
g579.t1
2860
g3880.t1
K14826: FPR3_4
4.281193383


1017
g5304.t1
2862
g2266.t1

1.064282379


1018
g15818.t1
2863
g5620.t1

5.095758915


1019
g11541.t1
2864
g4185.t1
K15710: SHPRH
9.337717858


1020
g5073.t1
2865
g8342.t1
K08008: NOX, GP91
0


1022
g6955.t1
2867
g6434.t1
K14860: TMA16
5.89989351


1021
g6610.t1
2866
g10146.t1

9.37786699


1023
g11689.t1
2868
g10851.t1
K10405: KIFC1
3.582191481


1024
g4428.t1
2869
g6761.t1

7.515504705


1025
g3928.t1
2870
g3964.t1

7.606070252


1028
g4373.t1
2873
g2130.t1
K13501: TRP1
5.255678294


1027
g10552.t1
2872
g6698.t1

0


1026
g4264.t1
2871
g1718.t1

0


1029
g7551.t1
2874
g7255.t1
K14640: SLC20A, PIT
2.536552173


1030
g73.t1
2875
g914.t1

4.346084349


1031
g10225.t1
2876
g11203.t1

9.413047495


1032
g5522.t1
2877
g1649.t1
K11699: RDR, RDRP
5.864561275


1033
g7042.t1
2878
g6333.t1

4.730082423


1034
g4256.t1
2879
g1726.t1
K11254: H4
5.392555643


1036
g1108.t1
2881
g4055.t1
K11131: DKC1, NOLA4,
4.027072029






CBF5


1035
g8681.t1
2880
g10943.t1
K00237: SDHD, SDH4
0


1037
g11120.t1
2520
g739.t1
K11309: RTT109, KAT11
5.304552729


1038
g10725.t1
2882
g4263.t1
K01495: GCH1, folE
7.095909192


1039
g9660.t1
2883
g4874.t1

0.457027413


1040
g8820.t1
2884
g3030.t1

5.372767428


1041
g4065.t1
2885
g3253.t1
K03362: FBXW1_11,
3.768457818






BTRC, beta-TRCP


1042
g5448.t1
2886
g3163.t1

5.226224828


1043
g7588.t1
2887
g7649.t1

6.811316171


1044
g3582.t1
2888
g5074.t1
K00293: LYS9
3.263233452


1045
g6422.t1
2889
g5364.t1

2.147147382


483
g10693.t1
2485
g8538.t1

5.662368091


1046
g6032.t1
2890
g11214.t1

8.820793561


1047
g6561.t1
2891
g10097.t1

5.654687421


1048
g2191.t1
2892
g11582.t1
K03352: APCS
4.67408688


1049
g8669.t1
2893
g10956.t1

4.818547725


1050
g5585.t1
2894
g7506.t1
K14300: NUP133
5.450216932


1051
g6577.t1
2895
g2327.t1

8.791267353


1052
g4912.t1
2896
g4547.t1

0


1053
g5600.t1
2897
g7522.t1
K17787: AIMS
0


1054
g59.t1
2898
g2750.t1
K09529: DNAJC9
0


1055
g2459.t1
2899
g6731.t1

2.631378842


1056
g3841.t1
2900
g2574.t1

5.178143897


1058
g10928.t1
2902
g11230.t1
K09291: TPR
2.438636081


1057
g4517.t1
2901
g10822.t1

0


1059
g5642.t1
2903
g9240.t1

10.22312916


1060
g5649.t1
2904
g1103.t1

4.544636216


1061
g11163.t1
2905
g4845.t1
K00838: ARO8
0.832183706


1062
g5464.t1
2906
g8437.t1
K01487: E3.5.4.3, guaD
4.270772945


1063
g6448.t1
2907
g5337.t1

0.704996832


1064
g546.t1
2908
g5611.t1

5.264731099


1065
g970.t1
2909
g8041.t1

5.740601251


1066
g196.t1
2910
g5304.t1

4.777372465


1067
g1283.t1
2911
g473.t1

0


1068
g12044.t1
2912
g803.t1

5.498118982


1069
g9074.t1
2913
g8565.t1

0


1070
g10056.t1
2914
g2782.t1
K05351: E1.1.1.9
7.25059785


1071
g12237.t1
2915
g11133.t1
K17878: NNT1
4.149357354


1072
g4465.t1
2916
g6824.t1

5.086524971


1073
g1040.t1
2917
g8111.t1

0


1074
g8432.t1
2918
g2491.t1

0


1075
g9956.t1
2919
g11404.t1

0


1077
g4593.t1
2921
g6010.t1

6.800127858


1076
g449.t1
2920
g8027.t1

2.548177204


1078
g15695.t1
2922
g10590.t1

0


1079
g7238.t1
2923
g10763.t1

6.636516842


1080
g2270.t1
2924
g10687.t1
K01551: arsA, ASNA1
1.338776738


1081
g7667.t1
2925
g7562.t1
K01469: OPLAH, OXP1,
4.982517875






OplAH


1082
g5077.t1
2926
g4465.t1
K01193: E3.2.1.26, sacA
0


1083
g6226.t1
2927
g7123.t1
K12609: CAF120
5.821481969


1084
g5075.t1
2928
g2985.t1

0


1085
g13910.t1
2929
g8741.t1

3.759982388


1086
g8085.t1
2930
g7863.t1

7.812628972


1087
g10423.t1
2931
g8402.t1
K14327: UPF2, RENT2
5.380749971


1088
g11332.t1
2932
g11641.t1

4.160151798


1089
g7007.t1
2933
g6374.t1
K12600: SKI3, TTC37
0


1090
g2160.t1
2934
g11899.t1

2.646205187


1091
g3470.t1
2935
g2763.t1
K00140: mmsA, iolA,
6.130826774






ALDH6A1


1092
g10929.t1
2936
g11231.t1
K14805: DDX24, MAK5
4.672508797


1093
g5608.t1
2937
g7532.t1

0.756308574


1094
g7845.t1
2938
g10498.t1
K03434: PIGL
8.181737455


1095
g15860.t1
2939
g6739.t1
K09831: ERG5
5.065082896


1096
g584.t1
2940
g3874.t1
K01520: dut, DUT
4.447661542


1097
g5992.t1
2941
g11691.t1
K06276: PDPK1
4.323838023


1098
g9408.t1
2942
g3619.t1

6.248005823


1099
g12324.t1
2943
g7430.t1
K03936: NDUFS3
4.250138533


1100
g8165.t1
2944
g7972.t1

0.505090398


1101
g6804.t1
2945
g4428.t1
K15128: MED6
3.937924735


1102
g4151.t1
2946
g1828.t1
K03327: TC.MATE,
5.671937128






SLC47A, norM, mdtK,






dinF


1103
g7170.t1
2947
g560.t1

5.705181185


1104
g8819.t1
2948
g3028.t1
K09252: E3.1.1.73
6.425640233


1105
g10490.t1
2949
g1671.t1

0.267350656


1106
g10438.t1
2950
g8414.t1
K11090: LA, SSB
4.175176818


1107
g7152.t1
2951
g11953.t1

4.892910278


1108
g7945.t1
2952
g9700.t1
K15272: SLC35A1_2_3
3.910911941


1110
g5482.t1
2954
g9825.t1
K03544: clpX, CLPX
5.959845259


1109
g9746.t1
2953
g1027.t1

0


1111
g7512.t1
2955
g10315.t1
K10268: FBXL2_20
5.036102597


1112
g9423.t1
2956
g10310.t1
K17678: MRH4
5.698279892


1113
g4358.t1
2957
g427.t1
K15394: ACE1
8.430767836


1114
g2440.t1
2958
g6709.t1

8.194390826


1115
g7412.t1
2959
g7196.t1
K17786: MOS2
4.719997185


1116
g7292.t1
2960
g11859.t1
K17267: COPG
5.289893047


479
g10141.t1
2484
g8477.t1

5.541093332


1117
g5887.t1
2961
g10973.t1

7.17403047


1119
g1144.t1
2963
g256.t1

4.804829552


1118
g6530.t1
2962
g10068.t1
K12345: SRD5A3
6.05975643


1120
g1388.t1
2964
g3922.t1
K11108: RCL1
0


660
g8547.t1
2461
g10270.t1
K02865: RP-L10Ae,
4.653519091






RPL10A


1121
g1443.t1
2965
g6990.t1

6.353729544


557
g5845.t1
2354
g1158.t1
K02985: RP-S3e, RPS3
6.78958802


1122
g1775.t1
2966
g1180.t1

2.44192219


1123
g5301.t1
2967
g2268.t1

4.832199777


1124
g5630.t1
2968
g1133.t1
K10808: RRM2
3.538433491


1125
g10024.t1
2969
g8702.t1

0


1126
g2219.t1
2970
g2626.t1

5.454955353


1127
g3982.t1
2971
g7057.t1
K07824: E1.14.13.12
4.476939292


1129
g8840.t1
2973
g1272.t1

3.816201878


1128
g9861.t1
2972
g11455.t1
K06101: ASH1L
0


1130
g4800.t1
2974
g676.t1

5.81071258


1131
g11654.t1
2975
g8005.t1

2.909017487


1132
g1136.t1
2976
g245.t1

10.59339274


1133
g7223.t1
2977
g5892.t1

5.576672157


1134
g3646.t1
2978
g623.t1

6.238451943


1135
g11372.t1
2979
g5059.t1

0


1138
g6590.t1
2982
g10119.t1

4.776549031


1136
g1968.t1
2980
g6227.t1

5.415945903


1137
g991.t1
2981
g8058.t1

4.169458418


1139
g14.t1
2983
g11312.t1

5.71723547


1140
g8611.t1
2984
g3033.t1

3.208304365


1141
g6942.t1
2985
g6445.t1
K00988: APA1_2
0.122356187


1142
g4972.t1
2986
g8937.t1
K13953: adhP
1.662757196


1143
g11708.t1
2987
g6617.t1

6.393154936


1144
g6627.t1
2988
g10177.t1

4.492307379


1145
g3793.t1
2989
g2622.t1
K00632: E2.3.1.16,
2.683933449






fadA


1146
g5362.t1
2990
g9549.t1

5.333486397


1147
g14458.t1
2991
g213.t1
K03417: prpB
5.793822468


1148
g3972.t1
2992
g7050.t1
K09274: K09274
4.82960772


1149
g9183.t1
2993
g6515.t1

1.762573342


1150
g3346.t1
2994
g4782.t1

0


1151
g15347.t1
2995
g9963.t1

5.425175011


1152
g610.t1
2996
g3850.t1

0


1153
g5842.t1
2997
g1161.t1

4.563717732


1154
g13891.t1
2998
g7379.t1

0


1155
g13895.t1
2999
g3474.t1
K07407: E3.2.1.22B,
6.607561086






galA, rafA


1156
g5991.t1
3000
g11690.t1
K11650: SMARCD
6.177996747


1157
g6045.t1
3001
g11733.t1

2.901234647


1158
g5636.t1
3002
g1113.t1
K08818: CDC2L
7.197842208


1159
g7137.t1
2541
g530.t1
K09702: K09702
5.111190124


1160
g2933.t1
3003
g5977.t1

6.559889482


1161
g505.t1
3004
g5519.t1

3.863129552


1162
g7769.t1
3005
g7721.t1

5.577160458


1163
g7156.t1
3006
g544.t1

6.758034692


1165
g930.t1
3008
g9329.t1

5.15713035


1164
g13110.t1
3007
g9758.t1

0


1166
g586.t1
3009
g3871.t1

3.781116872


577
g1391.t1
2375
g3917.t1

3.770913064


1168
g10165.t1
3011
g7723.t1
K01455: E3.5.1.49
5.879458438


1167
g2887.t1
3010
g10878.t1
K00102: E1.1.2.4, dld
4.602956869


689
g849.t1
2496
g9453.t1
K06997: K06997
3.120625144


1169
g7214.t1
3012
g5878.t1

4.495077603


1170
g18895.t1
3013
g5859.t1
K10845: TTDA, GTF2H5,
5.98025722






TFB5


1171
g8250.t1
3014
g10029.t1

4.39864019


1172
g2364.t1
3015
g9259.t1

9.213191896


1173
g560.t1
3016
g7760.t1
K07819: B3GALT1
0


1174
g5544.t1
3017
g11318.t1
K01874: MARS, metG
5.478905924


1175
g2772.t1
3018
g9139.t1
K14840: NOP53,
0






GLTSCR2


1176
g5248.t1
3019
g2343.t1

8.877204443


532
g27.t1
2329
g1583.t1

6.169854164


1177
g10546.t1
3020
g6691.t1
K12196: VPS4
0


1178
g12603.t1
3021
g1139.t1
K13201: TIA1, TIAL1
3.823455116


1179
g2082.t1
3022
g2515.t1

4.08648863


1180
g4868.t1
3023
g4487.t1
K18106: GAAA
5.341364148


666
g9261.t1
2467
g10439.t1
K01336: E3.4.21.48
4.328483282


1181
g4732.t1
3024
g2022.t1

3.266778123


1183
g8014.t1
3026
g3407.t1
K05994: E3.4.11.10
5.396879706


1182
g2889.t1
3025
g10880.t1

5.096458376


1184
g6241.t1
3027
g7141.t1

2.980899445


1185
g10185.t1
3028
g11141.t1
K12842: SR140
4.806643797


1186
g3181.t1
3029
g4963.t1

5.389590661


1187
g1146.t1
3030
g259.t1

0


1188
g3478.t1
3031
g4668.t1
K15118: SLC25A38
7.188127807


1189
g10812.t1
3032
g11469.t1

4.970990313


1190
g5729.t1
3033
g5268.t1

4.667119257


1191
g5773.t1
3034
g5183.t1
K18468: VPS35
2.974567603


1192
g8342.t1
3035
g5156.t1

7.147347587


1193
g2809.t1
3036
g9099.t1

8.970300194


1194
g3231.t1
3037
g6067.t1

5.450346027


1195
g15441.t1
3038
g27.t1
K02135: ATPeF1E,
0






ATP5E, ATP15


1196
g4098.t1
3039
g3297.t1

6.95311286


1197
g4149.t1
3040
g1830.t1

5.595722786


1198
g10768.t1
3041
g811.t1
K13281: uvsE, UVE1
6.312249915


1199
g6034.t1
3042
g11722.t1

3.569534287


1200
g7215.t1
3043
g5884.t1
K08141: MAL
4.164169033


1201
g8488.t1
3044
g3354.t1

3.054782379


1202
g8852.t1
3045
g1260.t1

0.276187354


1203
g17481.t1
3046
g6577.t1
K03457: TC.NCS1
4.118885089


1204
g6412.t1
3047
g5378.t1

0


1205
g5249.t1
3048
g2342.t1

4.593408785


1206
g4308.t1
3049
g1957.t1
K01934: E6.3.3.2
4.385816144


1207
g9497.t1
3050
g5756.t1
K12816: CDC40, PRP17
2.377976634


480
g3149.t1
2377
g4998.t1
K01213: E3.2.1.67
0


1208
g16357.t1
3051
g3292.t1

2.274644449


1209
g7653.t1
3052
g7536.t1
K02218: CSNK1, CK1
5.559496827


1210
g2461.t1
3053
g6733.t1
K17498: SPN1, IWS1
4.599947501


1211
g2212.t1
3054
g11601.t1
K15116: SLC25A33_36,
4.637281551






RIM2


1212
g10883.t1
3055
g172.t1

0


1213
g7108.t1
3056
g5573.t1

4.49020983


1214
g4692.t1
3057
g10596.t1
K00559: E2.1.1.41,
5.217966775






SMT1, ERG6


1215
g7001.t1
3058
g6383.t1

0


1217
g11520.t1
3060
g4211.t1
K01273: E3.4.13.19,
5.534704503






DPEP1


1216
g470.t1
3059
g8009.t1
K03235: EF3, TEF3
2.63960049


1218
g2297.t1
3061
g10716.t1

6.357052968


1219
g7855.t1
3062
g10512.t1

5.263495212


1221
g1216.t1
3064
g370.t1

7.767118225


1220
g15283.t1
3063
g10473.t1

0.148112638


1222
g5238.t1
3065
g2356.t1

8.469488529


1223
g16230.t1
3066
g10013.t1

6.19115729


1226
g14146.t1
3069
g3433.t1

5.134598916


1225
g882.t1
3068
g9407.t1
K12468: PAD1
5.834927879


1224
g10984.t1
3067
g5650.t1

0


1227
g6996.t1
3070
g6388.t1
K01104: E3.1.3.48
0


1228
g4042.t1
3071
g3218.t1
K10426: DCTN4
3.476006591


1229
g10440.t1
3072
g8416.t1

4.661283453


1230
g3798.t1
3073
g9469.t1

6.108299926


1233
g5250.t1
3076
g2341.t1

4.192956387


1231
g17491.t1
3074
g10533.t1

2.340628751


1232
g5149.t1
3075
g3828.t1
K11369: RTG2
2.742167769


1234
g10738.t1
3077
g11985.t1
K10798: PARP
0


1235
g188.t1
3078
g5816.t1
K18342: OTUD6
4.706797138


678
g2539.t1
2558
g3572.t1

8.765149435


1236
g9576.t1
3079
g6624.t1
K05355: hexPS, COQ1
0


1237
g7963.t1
3080
g10258.t1

6.877809835


1238
g2081.t1
3081
g2516.t1

3.748359597


1239
g4635.t1
3082
g2418.t1

4.337082348


1240
g1191.t1
3083
g351.t1
K14997: SLC38A11
0.860169772


1241
g3500.t1
3084
g2191.t1

1.215931569


1242
g1860.t1
3085
g1884.t1

5.590523487


1243
g7767.t1
3086
g891.t1

4.764291974


1244
g2268.t1
3087
g10684.t1

5.863717773


1245
g4613.t1
3088
g7741.t1
K00463: INDO
1.444624706


683
g9852.t1
3089
g9791.t1

7.876491011


1246
g4349.t1
3090
g2121.t1

1.532279358


1247
g8581.t1
3091
g6606.t1
K00558: DNMT1, dcm
4.21948707


1249
g9842.t1
3093
g9770.t1
K18576: XEG
6.122795741


1248
g2125.t1
3092
g2952.t1
K01480: E3.5.3.11, speB
4.351289056


1250
g10362.t1
3094
g5453.t1

4.153669397


1257
g12070.t1
3101
g7821.t1
K15356: VRG4, GONST1
4.864054909


1256
g4657.t1
3100
g2389.t1

5.666968159


1252
g6958.t1
3096
g6431.t1
K11968: ARIH1
3.357418226


1253
g19310.t1
3097
g9485.t1

5.087660505


1255
g10767.t1
3099
g12013.t1
K16833: PPP1R2, IPP2
3.101333549


1251
g11977.t1
3095
g12286.t1

5.145090044


1254
g8978.t1
3098
g11390.t1

0


1258
g21710.t1
3102
g9500.t1

1.238938387


1259
g7491.t1
3103
g10328.t1

3.324272702


1260
g7956.t1
3104
g10264.t1

6.737632146


1261
g7964.t1
3105
g10257.t1

6.468663015


1262
g7455.t1
3106
g6879.t1

7.133634176


1264
g7919.t1
3108
g8603.t1

7.707220525


1263
g6189.t1
3107
g9611.t1

3.290429112


1265
g16176.t1
2509
g5232.t1

3.961883001


1266
g8674.t1
3109
g10950.t1

4.335667589


1267
g9656.t1
3110
g4870.t1
K12844: PRPF31
1.499922726


1268
g7488.t1
3111
g10325.t1
K11240: MSG5
4.501108392


1269
g7672.t1
3112
g7571.t1

3.989155638


1270
g55.t1
3113
g2746.t1
K14567: UTP14
5.127910319


1272
g9412.t1
3115
g3614.t1

7.062307238


1271
g1753.t1
3114
g9720.t1

4.044374876


1273
g10977.t1
3116
g5641.t1
K10735: GINS4, SLD5
4.051828119


1274
g17737.t1
3117
g6552.t1
K01893: NARS, asnS
6.388427463


1275
g10487.t1
3118
g1673.t1
K17774: MDM10
2.164706382


1276
g6558.t1
3119
g10094.t1
K00643: E2.3.1.37,
6.31176497






ALAS


1277
g2287.t1
3120
g9659.t1

4.38553855


1278
g842.t1
3121
g9463.t1

0


1279
g2517.t1
3122
g3549.t1

5.937036867


1280
g3451.t1
3123
g4694.t1
K18803: HPM1
7.686438949


1281
g6141.t1
3124
g7301.t1

4.843357772


1282
g12211.t1
3125
g8489.t1

4.086552127


1283
g9200.t1
3126
g6534.t1

6.260040742


1284
g5321.t1
3127
g2239.t1

7.891730863


1285
g3577.t1
3128
g3306.t1

7.444698622


1286
g16033.t1
3129
g8312.t1
K14961: RBBP5, SWD1,
6.814335139






CPS50


1287
g370.t1
3130
g8886.t1
K05351: E1.1.1.9
2.495983173


1288
g11747.t1
3131
g5055.t1

5.579800871


1289
g307.t1
3132
g9470.t1
K00450: E1.13.11.4
0


1290
g4252.t1
3133
g1730.t1
K14554: UTP21, WDR36
5.046177386


1291
g13249.t1
3134
g7068.t1
K00101: E1.1.2.3, lldD
0


1292
g97.t1
3135
g2918.t1
K17550: PPP1R7, SDS22
6.872034629


1293
g11152.t1
3136
g4836.t1
K01736: aroC
4.537533205


1294
g277.t1
3137
g11370.t1

0


1296
g1874.t1
3139
g4227.t1

3.147814191


1295
g10285.t1
3138
g38.t1

0


1297
g7205.t1
3140
g5869.t1
K04712: DEGS
3.678254356


1298
g3975.t1
3141
g7052.t1
K03127: TAF13
5.226674743


1299
g6129.t1
3142
g7317.t1
K18584: ACTR3, ARP3
0.131743499


1300
g1071.t1
3143
g8144.t1
K15163: SRB8, MED12
9.338879184


1301
g9776.t1
3144
g933.t1
K18696: GDE1
4.318349985


1302
g9449.t1
3145
g10284.t1
K08286: E2.7.11.—
0.930122123


1303
g8139.t1
3146
g11353.t1

5.695078874


1304
g3952.t1
3147
g3939.t1

3.467152816


1306
g4583.t1
3149
g3309.t1

1.533947618


1305
g20261.t1
3148
g5213.t1
K15918: GLYK
0


1307
g7529.t1
3150
g7276.t1

6.576826873


1308
g6754.t1
3151
g4367.t1
K02209: MCM5, CDC46
2.459200585


1311
g491.t1
3154
g5498.t1

6.698116368


1309
g7837.t1
3152
g8557.t1

6.106640364


1310
g987.t1
3153
g8056.t1

0


1313
g17939.t1
3156
g10899.t1

6.818707989


1312
g2164.t1
3155
g11903.t1

5.515137675


1314
g3906.t1
3157
g3985.t1
K03190: ureD, ureH
2.671010414


1315
g1097.t1
3158
g4041.t1

0.505695041


1317
g3623.t1
3160
g595.t1
K16466: CETN3
4.801115612


1316
g8411.t1
3159
g4430.t1

0


1318
g20530.t1
3161
g9496.t1

0


1319
g1348.t1
3162
g3450.t1
K10438: E1.14.13.63,
3.588175282






phacB


1320
g3797.t1
3163
g2615.t1

6.056986997


1321
g7399.t1
3164
g7182.t1

5.018202134


1322
g5488.t1
3165
g9822.t1

3.362985644


1323
g9157.t1
3166
g6488.t1
K02324: POLE1
1.973709427


1324
g14847.t1
3167
g1437.t1
K00641: metX
6.994074013


1325
g6957.t1
3168
g6432.t1
K10746: EXO1
6.131134701


1326
g3447.t1
3169
g4698.t1

4.987346272


1327
g9400.t1
3170
g3632.t1

4.819542549


1328
g10198.t1
3171
g11163.t1

5.978274196


1331
g7497.t1
3174
g10332.t1

5.769438155


1330
g7426.t1
3173
g7211.t1
K07151: STT3
6.089321429


1329
g8972.t1
3172
g11360.t1
K00949: thiN, TPK1,
0






THI80


1332
g11012.t1
3175
g5666.t1

0


1335
g2680.t1
3178
g4137.t1
K03305: TC.POT
4.251138075


1334
g12334.t1
3177
g7439.t1

4.832463772


1333
g4070.t1
3176
g3266.t1
K08502: VAM7
5.539846457


1336
g6026.t1
3179
g11719.t1

6.095844652


1337
g3846.t1
3180
g3215.t1

5.151000423


1338
g5774.t1
3181
g5182.t1

4.645161281


1339
g3929.t1
3182
g3963.t1
K08866: TTK, MPS1
6.449588576


1340
g2818.t1
3183
g9112.t1

5.23098229


1341
g4639.t1
3184
g3141.t1

4.295463374


1342
g7766.t1
3185
g886.t1
K00276: AOC3, AOC2,
3.696502907






tynA


1343
g5178.t1
3186
g3785.t1
K10732: GINS1, PSF1
3.205102409


1344
g6934.t1
3187
g8796.t1

5.750734244


1345
g1969.t1
3188
g6228.t1

3.400168294


1346
g172.t1
3189
g12085.t1
K01531: E3.6.3.2,
6.497766777






mgtA, mgtB


1347
g11564.t1
3190
g4163.t1
K00274: MAO, aofH
2.200547724


1348
g6920.t1
3191
g6466.t1
K05607: AUH
3.935782227


1349
g155.t1
3192
g5222.t1
K00129: E1.2.1.5
0


1351
g4054.t1
3194
g3233.t1
K00222: TM7SF2,
4.246709844






ERG24


1350
g259.t1
3193
g11071.t1

2.005826005


1352
g2113.t1
3195
g6610.t1

5.320518398


1353
g18993.t1
3196
g1481.t1

6.460112374


1354
g9213.t1
3197
g9107.t1
K01535: E3.6.3.6
0.221964669


1355
g8608.t1
3198
g3036.t1

6.171130211


1359
g559.t1
3202
g3897.t1

6.201870178


1357
g1111.t1
3200
g4058.t1
K17792: TIM54
5.442528526


1358
g2917.t1
3201
g5991.t1

5.742797006


1356
g13698.t1
3199
g7803.t1
K15015: SLC32A,
3.095824509






VGAT


1360
g3970.t1
3203
g9872.t1
K14455: GOT2
6.495895484


1361
g6219.t1
3204
g7117.t1
K15030: EIF3M
9.064552828


1362
g9425.t1
3205
g10308.t1
K08850: AURKX
4.730673883


1363
g7501.t1
3206
g10336.t1
K18160: NDUFAF2
5.345072335


1364
g859.t1
3207
g9445.t1

6.22964011


1365
g1915.t1
3208
g6151.t1

7.270928698


1366
g12217.t1
3209
g1989.t1
K00826: E2.6.1.42,
3.918920739






ilvE


1367
g4170.t1
3210
g1809.t1

0.622664993


1368
g9398.t1
2532
g3634.t1

4.794435739


1369
g11911.t1
3211
g11961.t1

4.426580032


1370
g1975.t1
3212
g6235.t1
K03676: grxC, GLRX,
5.422460166






GLRX2


1371
g8163.t1
3213
g7963.t1
K16261: YAT
4.292364721


1372
g7701.t1
3214
g5632.t1
K16261: YAT
3.918348151


1373
g9062.t1
3215
g8589.t1

0


1374
g21743.t1
3216
g11779.t1
K01969: E6.4.1.4B
3.581364482


1375
g5576.t1
3217
g7494.t1

8.893181528


1376
g3089.t1
3218
g11792.t1
K00914: PIK3C3,
6.7596142






VPS34


1377
g5685.t1
3219
g1056.t1
K13524: ABAT
0


1378
g4641.t1
3220
g2414.t1
K03685: rnc, DROSHA,
0.412316469






RNT1


1379
g2363.t1
3221
g9258.t1

6.486658248


1380
g21382.t1
3222
g5714.t1
K07734: paiB
6.462845057


1381
g6400.t1
3223
g5394.t1

0


1382
g10337.t1
3224
g56.t1

4.374119128


1383
g5528.t1
3225
g1657.t1
K02896: RP-L24e, RPL24
5.059362323


1384
g11343.t1
3226
g11653.t1
K10981: POL4
6.259801244


1385
g5150.t1
3227
g3827.t1

2.931671142


1386
g6763.t1
3228
g4378.t1
K02321: POLA2
8.302494784


1387
g5671.t1
3229
g1071.t1
K11853: USP34
0


1388
g11809.t1
3230
g12052.t1
K11364: SGF29
3.463947854


1389
g11797.t1
3231
g11951.t1

3.516751262


1390
g10681.t1
3232
g8527.t1

5.58963777


1391
g4325.t1
3233
g11437.t1

13.11970013


1392
g9381.t1
3234
g3653.t1

5.511774101


1393
g7852.t1
3235
g10509.t1

6.882721316


616
g5090.t1
2415
g2954.t1
K08486: STX1B_2_3
0


1394
g3829.t1
3236
g2598.t1

0.266144622


1395
g11535.t1
3237
g4192.t1
K17279: REEP5_6
0.360331706


1396
g6481.t1
3238
g5293.t1
K01886: QARS, glnS
5.748896345


1397
g3005.t1
3239
g8297.t1

4.660135675


1398
g4078.t1
3240
g3277.t1

3.936715366


1399
g2855.t1
3241
g9059.t1
K00627: DLAT, aceF,
5.436104451






pdhC


1400
g3918.t1
3242
g3974.t1
K00297: metF, MTHFR
5.369411331


1401
g7179.t1
3243
g566.t1
K09523: DNAJC3
0.627178139


1402
g12408.t1
3244
g8249.t1

6.349198309


1403
g9652.t1
3245
g6915.t1

4.964995182


1404
g7523.t1
3246
g7288.t1
K13704: ABHD12
1.294755574


1405
g14653.t1
3247
g2855.t1

5.738900905


1406
g4096.t1
3248
g3295.t1
K17362: ACOT13
4.848799761


1407
g18248.t1
3249
g2041.t1

4.35781588


1408
g1237.t1
3250
g7426.t1

5.683015328


1410
g3632.t1
3252
g608.t1

3.639980584


1409
g5562.t1
3251
g7477.t1

4.810359052


1411
g5477.t1
3253
g8419.t1
K01876: DARS, aspS
5.822436425


1412
g9515.t1
3254
g6599.t1
K10729: SLD2
5.470455054


1413
g10318.t1
3255
g72.t1

3.677226697


1414
g24.t1
3256
g12134.t1

2.224553826


1415
g8240.t1
3257
g10040.t1
K17784: MINOS1, MOS1
4.505441621


1416
g7496.t1
3258
g10330.t1

4.295198041


1418
g5019.t1
3260
g8992.t1
K00763: pncB, NAPRT1
5.789644312


1417
g9422.t1
3259
g10311.t1
K17678: MRH4
4.99116655


1419
g6947.t1
3261
g6439.t1

4.318049534


1420
g1449.t1
3262
g6978.t1

7.510804913


1421
g11952.t1
3263
g5425.t1
K11886: ECM29
3.293996124


1422
g4463.t1
3264
g6821.t1
K03441: GLP-F
5.769121905


1423
g4565.t1
3265
g4096.t1

0.919084112


1424
g5152.t1
3266
g3825.t1

3.965633731


1425
g5796.t1
3267
g4861.t1

4.412444745


1426
g2106.t1
3268
g2479.t1
K17877: NIT-6
4.442382018


1427
g2132.t1
3269
g9887.t1

6.595948877


1428
g2743.t1
3270
g8874.t1

10.26584456


1429
g3255.t1
3271
g8226.t1

0


1430
g2515.t1
3272
g3546.t1
K03935: NDUFS2
2.995934045


1431
g11846.t1
3273
g8779.t1

5.108325438


1432
g4309.t1
3274
g1956.t1
K15436: TRPO3, MTR10
3.512784384


1433
g342.t1
3275
g8843.t1
K14617: LMBRD1
5.048487126


1434
g10330.t1
3276
g65.t1
K10592: HUWE1, MULE,
0






ARF-BP1


1435
g12736.t1
3277
g5713.t1

0


1436
g3120.t1
3278
g11825.t1

0


1437
g6122.t1
3279
g7325.t1

3.73309277


1438
g7506.t1
3280
g1313.t1
K02510: hpaI, hpcH
5.681359113


1439
g4219.t1
3281
g1764.t1

5.026702428


1440
g5995.t1
3282
g11694.t1
K08501: STX8
5.459232545


1441
g10838.t1
3283
g9836.t1

4.87039805


626
g2308.t1
2425
g10725.t1

5.237036425


1442
g6039.t1
3284
g11727.t1
K14809: DDX55, SPB4
5.042634955


1443
g4021.t1
3285
g3194.t1

4.255555246


1444
g7825.t1
3286
g8668.t1

7.009481452


1445
g7886.t1
3287
g8663.t1

5.301291022


1446
g13691.t1
3288
g9725.t1

2.720405954


1447
g3039.t1
3289
g8267.t1
K14779: DDX52, ROK1
4.859751136


1448
g5768.t1
3290
g5189.t1
K02948: RP-S11,
3.223518382






MRPS11, rpsK


1449
g8149.t1
3291
g7955.t1

7.075631425


1450
g13905.t1
3292
g4807.t1

5.937192138


1451
g9050.t1
3293
g5712.t1

0


1452
g11913.t1
3294
g658.t1
K14264: BNA3
3.176589195


1453
g11806.t1
3295
g12049.t1
K17260: ACTR2, ARP2
3.412479141

















SEQ ID
Median Exp.



Adj. p-



SYM00577
SYM00300
Log FC
B-statistic
t-statistic
value







687
8.254570732
8.205162
7.709718
15.19085
5.97E−06



700
5.044729998
5.210069
5.708895
10.76568
2.93E−05



674
0.825824927
−4.70074
5.191774
−9.95863
4.34E−05



688
1.8413995
−4.97725
5.089442
−9.80948
4.75E−05



701
0.902872062
−5.9827
4.978805
−9.65176
5.17E−05



702
5.088279289
4.707624
4.928839
9.581698
5.38E−05



703
2.891582245
2.883676
4.49609
9.003087
8.38E−05



704
2.188447902
−4.35168
4.123845
−8.54179
0.000127



686
8.452816333
4.967614
4.058607
8.464065
0.000136



675
4.361478247
4.207187
3.745443
8.102858
0.000183



705
4.099415046
4.001025
3.630507
7.974961
0.000207



706
2.609740762
−4.37343
3.601634
−7.94321
0.000212



707
6.497290601
5.707041
3.4962
7.828495
0.000234



708
11.29461044
9.891677
3.448641
7.777378
0.000245



709
2.522819857
2.630813
3.252018
7.570029
0.00029



517
7.516860158
7.229
2.98496
7.298142
0.000373



710
1.763743187
−5.35718
2.961709
−7.27498
0.00038



690
1.736488111
−4.94929
2.879288
−7.19348
0.000407



711
1.054868326
−8.62274
2.615828
−6.93929
0.000517



558
1.996511676
2.075046
2.565361
6.891657
0.000539



712
2.790411134
2.620375
2.511141
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1330
2.57287541
−2.74784
−2.64279
−3.08733
0.03808



1329
4.277976912
2.876826
−2.64269
3.087385
0.03808



1332
5.38381861
3.856589
−2.6484
3.083847
0.038255



1335
0.905078368
−3.52825
−2.65137
−3.08201
0.038301



1334
1.425823624
−3.26532
−2.65114
−3.08215
0.038301



1333
2.546984577
−2.7732
−2.65099
−3.08224
0.038301



1336
0.68430684
−4.28462
−2.66367
−3.07438
0.038767



1337
1.006964699
−3.90954
−2.66555
−3.07322
0.03883



1338
0
−3.4513
−2.66704
−3.07229
0.038877



1339
3.278968193
−3.36947
−2.66843
−3.07143
0.03892



1340
2.042748595
−4.97039
−2.67161
−3.06946
0.038992



1341
0
−3.88825
−2.67162
−3.06945
0.038992



1342
1.950100615
−2.2513
−2.67226
−3.06906
0.039003



1343
0.465489204
−2.9998
−2.67294
−3.06864
0.039016



1344
3.373972395
−2.72485
−2.67465
−3.06758
0.039072



1345
1.126194748
−2.65712
−2.67603
−3.06672
0.039115



1346
1.752973654
−3.4052
−2.67672
−3.0663
0.039129



1347
5.983180821
3.284934
−2.67943
3.064613
0.039212



1348
1.559896558
−2.81933
−2.68386
−3.06187
0.039338



1349
2.038635734
2.662139
−2.68959
3.058314
0.039519



1351
0.753125695
−3.82499
−2.6984
−3.05285
0.039787



1350
6.702898665
4.844188
−2.69807
3.053061
0.039787



1352
1.691648425
−3.58956
−2.70003
−3.05185
0.039841



1353
2.188072612
−3.62105
−2.70385
−3.04948
0.039958



1354
4.444533441
4.861882
−2.70441
3.049135
0.039966



1355
2.686136331
−2.9841
−2.70848
−3.04661
0.040111



1359
1.933937599
−3.99892
−2.71429
−3.04301
0.040268



1357
1.477478055
−3.04273
−2.71355
−3.04347
0.040268



1358
3.575636867
−2.07424
−2.71393
−3.04323
0.040268



1356
6.420340227
3.453954
−2.71294
3.043849
0.040268



1360
1.144303422
−3.38447
−2.71544
−3.0423
0.040287



1361
7.245420142
−3.3623
−2.71784
−3.04081
0.040375



1362
0.868742846
−4.27344
−2.72342
−3.03735
0.040551



1363
0.733430789
−4.13019
−2.72367
−3.03719
0.040551



1364
1.992693147
−3.27148
−2.72413
−3.03692
0.040555



1365
4.976410906
−2.43324
−2.73052
−3.03295
0.040756



1366
1.387924318
−2.78762
−2.73448
−3.0305
0.040915



1367
6.671635624
3.839574
−2.74399
3.024609
0.041257



1368
1.682112273
−3.12889
−2.74644
−3.02309
0.041334



1369
0.838075179
−3.7127
−2.75198
−3.01966
0.04155



1370
3.194829169
−2.95272
−2.75339
−3.01878
0.041581



1371
2.128178192
−2.1584
−2.75419
−3.01829
0.041601



1372
2.429142725
−2.02558
−2.76273
−3.013
0.041938



1373
4.231781639
4.010053
−2.76633
3.010768
0.042068



1374
0.847557335
−4.15212
−2.76857
−3.00938
0.042138



1375
1.120853281
−5.86159
−2.77127
−3.00771
0.042212



1376
1.576374675
−4.25202
−2.77342
−3.00637
0.042277



1377
2.065375591
2.44012
−2.78145
3.001401
0.042547



1378
4.991257678
3.332549
−2.78404
2.999796
0.042649



1379
1.454471294
−6.28212
−2.79029
−2.99592
0.042862



1380
2.264599961
−3.14521
−2.79042
−2.99584
0.042862



1381
4.971894272
4.307014
−2.7932
2.994118
0.042975



1382
0.945262194
−2.67548
−2.79768
−2.99134
0.043133



1383
2.912712707
−2.81694
−2.80156
−2.98894
0.043281



1384
1.648126626
−4.35678
−2.80503
−2.98679
0.043411



1385
5.392109666
3.102784
−2.81072
2.983263
0.043629



1386
5.13409511
−2.44481
−2.81189
−2.98254
0.043667



1387
4.496504481
3.601192
−2.81539
2.98037
0.043799



1388
6.116692885
2.833623
−2.81691
2.979429
0.043837



1389
1.679255644
−2.65677
−2.82277
−2.9758
0.044083



1390
3.099515857
−2.57245
−2.82433
−2.97483
0.04413



1391
2.933682888
−7.21408
−2.82725
−2.97302
0.044229



1392
1.012685905
−3.81034
−2.82909
−2.97188
0.044293



1393
5.021376437
−3.07319
−2.8293
−2.97175
0.044293



616
3.867535804
3.836476
−2.8345
2.968529
0.044458



1394
4.669261532
3.50036
−2.8361
2.967538
0.044518



1395
9.163288499
7.510402
−2.83657
2.967251
0.044524



1396
1.179880874
−5.49899
−2.83881
−2.96586
0.044606



1397
0.923693205
−4.96111
−2.83903
−2.96573
0.044606



1398
2.213435275
−2.83788
−2.83933
−2.96554
0.044606



1399
0.350451845
−3.90005
−2.84415
−2.96255
0.044805



1400
6.805636855
2.484666
−2.84783
2.960272
0.044957



1401
4.16165657
3.409315
−2.84799
2.960173
0.044957



1402
4.267606287
−4.36478
−2.85278
−2.9572
0.045157



1403
3.229940066
−3.59518
−2.85436
−2.95623
0.045182



1404
5.275553403
5.591409
−2.85471
2.95601
0.045182



1405
1.835542251
−3.20682
−2.86057
−2.95238
0.045453



1406
1.091069648
−3.86237
−2.86465
−2.94985
0.045602



1407
7.901252086
3.784351
−2.86851
2.947457
0.045759



1408
2.488598283
−2.99706
−2.87184
−2.94539
0.045853



1410
1.944176831
−2.64596
−2.87251
−2.94498
0.045853



1409
9.131036427
4.168862
−2.87246
2.945014
0.045853



1411
3.686550344
−3.1569
−2.87291
−2.94473
0.045855



1412
2.40515865
−2.98726
−2.87443
−2.94379
0.045909



1413
5.754668913
3.289688
−2.88275
2.938638
0.046244



1414
7.898332502
4.242374
−2.8828
2.938606
0.046244



1415
2.059214773
−3.2426
−2.88456
−2.93751
0.046298



1416
0.62681007
−4.62511
−2.88616
−2.93652
0.046343



1418
0
−4.02631
−2.88687
−2.93608
0.046344



1417
2.76827123
−2.74095
−2.8868
−2.93613
0.046344



1419
0.859611004
−3.26378
−2.89495
−2.93107
0.046698



1420
5.552335444
−3.23923
−2.89616
−2.93033
0.046742



1421
0.612527291
−2.70149
−2.90035
−2.92773
0.046902



1422
0.957880078
−3.49533
−2.90325
−2.92593
0.047032



1423
5.08912066
3.486226
−2.90372
2.925643
0.047038



1424
9.790435178
4.134104
−2.9047
2.925032
0.047071



1425
6.978987815
2.714293
−2.9071
2.923548
0.047159



1426
1.795290638
−2.90776
−2.90858
−2.92263
0.047216



1427
2.130028726
−3.56948
−2.91683
−2.91752
0.047586



1428
3.775688511
−5.63147
−2.91883
−2.91628
0.047669



1429
4.623799698
4.753278
−2.91912
2.916098
0.047669



1430
5.779005536
2.983913
−2.91952
2.915847
0.047672



1431
0.456052036
−4.50763
−2.91997
−2.91557
0.047677



1432
0.746291622
−3.75578
−2.92157
−2.91458
0.047742



1433
6.613903693
2.614424
−2.92704
2.91119
0.047918



1434
6.217591133
4.494671
−2.92903
2.909954
0.048004



1435
2.67764343
3.587796
−2.93123
2.908589
0.048101



1436
2.782475712
2.382813
−2.93213
2.908034
0.048112



1437
0
−3.82204
−2.93383
−2.90698
0.048183



1438
2.954196465
−4.30541
−2.93555
−2.90591
0.048255



1439
3.19824011
−2.28706
−2.93664
−2.90523
0.048294



1440
0.507403584
−3.61957
−2.94175
−2.90207
0.048544



1441
2.795973757
−2.14792
−2.94515
−2.89996
0.048705



626
3.494277968
−2.61152
−2.94809
−2.89814
0.048825



1442
2.144742508
−3.54449
−2.95453
−2.89415
0.049112



1443
1.771901086
−3.07477
−2.95556
−2.89351
0.049148



1444
4.830504535
−2.37807
−2.95614
−2.89315
0.049161



1445
3.603605432
−2.98612
−2.95905
−2.89135
0.049265



1446
4.969707656
2.361023
−2.95911
2.891306
0.049265



1447
2.56647477
−2.80026
−2.95956
−2.89103
0.049269



1448
6.638489334
3.700189
−2.95986
2.890843
0.049269



1449
1.400206991
−4.60509
−2.96226
−2.88936
0.049369



1450
4.105355745
−2.28795
−2.96241
−2.88926
0.049369



1451
1.428557276
2.850041
−2.96403
2.888256
0.049437



1452
0.818863118
−2.7115
−2.96755
−2.88608
0.049608



1453
8.573811497
4.004772
−2.96831
2.885605
0.049628











This table describes orthologous genes of Acremonium zea sp. with beneficial and neutral effects on soybean growth, these genes show significant changes in expression between the two genotypes when grown in culture without soybean homogenate. “Median Exp. SYM00577” represents the median expression value in log 2 tpm across biological replicates of the beneficial Acremonium grown in media inoculated with 50 mM PBS buffer. “Median Exp. SYM00300” represents the median expression value in log 2 tpm across biological replicates of the neutral Acremonium grown in media inoculated with 50 mM PBS buffer. “Log FC” represents the estimate of the log 2-fold-change of the contrast. “B-statistic” represents the log-odds that the gene is differentially expressed. “t-statistic” represents the moderated t-statistic. “Adj. p-value” represents the false discovery rate (Benjamini & Hochberg, 1995) adjusted p-values.















TABLE 604












Median Exp.
Median Exp.


SEQ ID
sym577
SEQ ID
sym300

SYM00577
SYM00577


SYM00577
gene
SYM00300
gene
Description
Plant
Mock





685
g6380.t1
2492
g764.t1
K05857: PLCD
3.20141475
5.073855922


686
g857.t1
2491
g9451.t1
K01950:
3.886920369
3.802514601






E6.3.5.1,






NADSYN1,






QNS1, nadE


687
g13072.t1
2494
g9142.t1

0
0


675
g5348.t1
2554
g1.t1

5.703283097
0


674
g5345.t1
2555
g9530.t1
K03510: POLI
0
5.845894518


688
g68.t1
2495
g909.t1
K00106: XDH
6.788107371
7.003820996


689
g849.t1
2496
g9453.t1
K06997: K06997
2.698992601
3.120625144


690
g7926.t1
2497
g8597.t1

6.166677332
6.853860482


680
g1340.t1
2553
g523.t1

0
5.657989905


691
g5563.t1
2493
g7478.t1

4.68326473
4.371792513


692
g5169.t1
2506
g3798.t1

4.28203011
4.865818268


677
g13489.t1
2556
g8733.t1

4.049293359
0


694
g3058.t1
2499
g1604.t1

0
0


693
g2076.t1
2498
g2520.t1

3.957231552
3.655783096


695
g3790.t1
2501
g2628.t1
K12486: SMAP
0
0


676
g7741.t1
2557
g7091.t1

7.176505771
2.550284622


697
g852.t1
2502
g9454.t1
K11824: AP2A
4.880882459
5.513795279


696
g3920.t1
2508
g3972.t1

4.127763996
5.062011561


678
g2539.t1
2558
g3572.t1

2.326788417
8.765149435


699
g2257.t1
2504
g10668.t1

0
0


698
g657.t1
2503
g9863.t1

4.688200862
4.4628192



















Median Exp.
Median Exp.







SEQ ID
SYM00300
SYM00300

B-
t-
Adj. p-



SYM00577
Plant
Mock
Log FC
statistic
statistic
value







685
9.359327016
0.295559632
10.14621
4.342538
10.54136
0.005738



686
0.533450094
8.452816333
−8.12443
3.977388
−9.78835
0.005838



687
2.137400252
8.254570732
−6.46147
3.201272
−8.45884
0.009315



675
4.093445794
4.361478247
−5.78572
2.800585
−7.87932
0.009315



674
0.472127747
0.825824927
5.241458
2.780518
7.851832
0.009315



688
7.792433369
1.8413995
5.850131
2.994894
8.152802
0.009315



689
7.963289978
0.692301308
7.186104
2.979489
8.13062
0.009315



690
8.618339677
1.736488111
7.728272
2.846411
7.942614
0.009315



680
5.308190284
2.558100341
8.898276
3.336937
8.669616
0.009315



691
9.926472681
0
8.941653
2.765035
7.830714
0.009315



692
6.198143572
0.928859379
6.202992
2.4341
7.397597
0.014126



677
1.530959943
1.496465963
−3.96529
2.150927
−7.05207
0.018531



694
5.62596164
1.924786245
3.932304
2.090546
6.981083
0.018531



693
13.01166964
2.835668263
10.44786
2.127351
7.024242
0.018531



695
6.121031288
1.019511648
5.080878
1.93808
6.80576
0.021595



676
3.981693891
3.632045248
−4.74363
1.718895
−6.56295
0.02595



697
7.286171288
2.276512626
5.32327
1.68203
6.523118
0.02595



696
6.356788736
0.848055404
5.962067
1.696466
6.538681
0.02595



678
6.873536849
6.260432332
7.696947
1.344744
6.171118
0.039348



699
3.910887164
10.12999017
−6.28123
1.22348
−6.04968
0.042032



698
5.925534706
1.558896118
4.563314
1.235076
6.061179
0.042032











This table describes orthologous genes of Acremonium zea sp. with beneficial and neutral effects on soybean growth, these genes show significant genotype specific changes in expression when grown in culture with and without plant homogenate. “Median Exp. SYM00577 Plant” represents the median expression value in log 2 tpm across biological replicates of the beneficial Acremonium grown in media inoculated with soybean seedling homogenate extracted with 50 mM PBS. “Median Exp. SYM00577 Mock” represents the median expression value in log 2 tpm across biological replicates of the beneficial Acremonium grown in media inoculated with 50 mM PBS buffer. “Median Exp. SYM00300 Plant” seedling homogenate extracted with 50 mM PBS. “Median Exp. SYM00300” represents the median expression value in log 2 tpm across biological replicates of the neutral Acremonium grown in media inoculated with soybean seedling homogenate extracted with 50 mM PBS. “Median Exp. SYM00300 Mock” represents the median expression value in log 2 tpm across biological replicates of the neutral Acremonium grown in media inoculated with 50 mM PBS buffer. “Log FC” represents the estimate of the log 2-fold-change of the contrast. “B-statistic” represents the log-odds that the gene is differentially expressed. “t-statistic” represents the moderated t-statistic. “Adj. p-value” represents the false discovery rate (Benjamini & Hochberg, 1995) adjusted p-values.

















TABLE 605





SEQ

sym577
Median Exp.
Median Exp.

B-
t-
Adj. p-


ID
Description
gene
Plant
Mock
Log FC
statistic
statistic
value























674
K03510: POLI
g5345.t1
0
5.845894518
−5.48202
5.274576
−11.6138
0.002239


675

g5348.t1
5.703283097
0
5.589081
4.886533
10.76433
0.002344


677

g13489.t1
4.049293359
0
3.940048
4.438055
9.909633
0.002595


676

g7741.t1
7.176505771
2.550284622
5.088009
4.463602
9.955217
0.002595


678

g2539.t1
2.326788417
8.765149435
−7.03125
3.150667
−7.97247
0.014249


680

g1340.t1
0
5.657989905
−5.64042
2.991613
−7.77178
0.014249


679
K00275: pdxH,
g4287.t1
0.807562533
4.95193285
−4.19518
3.005051
−7.78848
0.014249



PNPO


681
K00574: E2.1.1.79,
g4581.t1
0.51190239
5.56764375
−4.84984
2.75309
−7.48306
0.017529



cfa


682
K06874: K06874
g9772.t1
1.832873801
5.323512963
−3.59486
2.657715
−7.37145
0.017819


683

g9852.t1
0.939929541
7.876491011
−5.93834
2.189836
−6.85242
0.030523


684

g2536.t1
9.671862421
2.653812149
6.993491
1.944631
6.59743
0.03853










This table describes genes of a Acremonium zea sp. with beneficial effects on soybean growth, these genes show significant changes in expression when grown in culture with and without plant homogenate. “Median Exp. Plant” represents the median expression value in log 2 tpm across biological replicates grown in media inoculated with soybean seedling homogenate extracted with 50 mM PBS. “Median Exp. Mock” represents the median expression value in log 2_tpm across biological replicates grown in media inoculated with 50 mM PBS buffer. “Log FC” represents the estimate of the log 2-fold-change of the contrast. “B-statistic” represents the log-odds that the gene is differentially expressed. “t-statistic” represents the moderated t-statistic. “Adj. p-value” represents the false discovery rate (Benjamini & Hochberg, 1995) adjusted p-values.


Example 7: Functional Characterization of Endophytes (Secreted Proteomics Experiments)

This Example describes the ability of synthetic compositions comprising plant seeds and a single endophyte strain or a plurality of endophyte strains described herein, to confer beneficial traits to a host plant. Among other things, this Example provides exemplary characterization of modulations in a beneficial endophyte's secretome, as compared to the secretome of a neutral microbe of the same genus.


Mass spectrometry was used to explore differences in secreted proteins between beneficial endophytes and neutral microbes. Four genera were selected for the secreted proteomic analysis (two fungal and two bacterial): Acremonium, Phoma, Stenotrophomonas, and Agrobacterium. For each genus, a beneficial endophyte and neutral microbe were selected: SYM00577 (SEQ ID NO: 344) and SYM00300 (SEQ ID NO: 449); SYM15774 (SEQ ID NO: 447) and SYM01331 (SEQ ID NO: 450); SYM00906 (SEQ ID NO: 439) and SYM00865 (SEQ ID NO: 451); and SYM01004 (SEQ ID NO: 441) and SYM00091 (SEQ ID NO: 427).


Microbes were cultivated in three biological replicates for each strain. Briefly, each bacterium was initially streaked on Reasoner's 2A (R2A) agar, distinct CFUs selected and cultured in 10 mL R2A broth for 4 days. Fungal strains were streaked on potato dextrose (PD) agar and individual plugs containing spores and mycelial tissues were used to initiate growth in 10 mL PD broth for 6 days. All strains were grown with agitation at room temperature. Microbial culture filtrate was harvested by centrifuging at 4500 RPM for 20 minutes in 15 mL Falcon tubes to allow culture separation and removal of the supernatant. Five mL of culture supernatant were used for secreted proteomics analysis. All steps were performed in sterile conditions. Culture filtrates were kept in dry ice after harvest at all times to preserve protein stability. Media only samples consisting of PDB and R2A were tested independently to ensure the absence of intact proteins that could potentially interfere with the secreted microbial peptides.


Prior to mass spectrometry, samples were concentrated on a Pall 3 kD MWCO MicroSep Spin Column (VWR Cat #89132-006) and quantified at 1:10 dilution by Qubit fluorometry (Life Technologies). 12 μg of each sample was separated ˜1.5 cm on a 10% Bis-Tris Novex mini-gel (Invitrogen) using the MES buffer system. The gel was stained with coomassie and each lane was excised into ten equally sized segments.


Gel pieces were processed using a robot (ProGest, DigiLab) with the following protocol:

    • Washed with 25 mM ammonium bicarbonate followed by acetonitrile.
    • Reduced with 10 mM dithiothreitol at 60° C. followed by alkylation with 50 mM iodoacetamide at RT.
    • Digested with trypsin (Promega) at 37° C. for 4 h.
    • Quenched with formic acid and the supernatant was analyzed directly without further processing.


Mass Spectrometry


The digests were analyzed by nano LC/MS/MS with a Waters NanoAcquity HPLC system interfaced to a ThermoFisher Q Exactive. Peptides were loaded on a trapping column and eluted over a 75 μm analytical column at 350 nL/min; both columns were packed with Proteo Jupiter resin (Phenomenex). A 30 min gradient was employed (5 h total). The mass spectrometer was operated in data-dependent mode, with MS and MS/MS performed in the Orbitrap at 70,000 FWHM and 17,500 FWHM resolution, respectively. The fifteen most abundant ions were selected for MS/MS.


Data were searched using a local copy of Mascot with the following parameters: Fixed modification: Carbamidomethyl (C); Variable modifications: Oxidation (M), Acetyl (Protein N-term), Pyro-Glu (N-term Q), Deamidation (NQ); Mass values: Monoisotopic; Peptide Mass Tolerance: 10 ppm; Fragment Mass Tolerance: 0.02 Da; Max Missed Cleavages: 2.


Mascot DAT files were parsed into the Scaffold software for validation, filtering and to create a non-redundant list per sample. Data were filtered 1% protein and peptide level false discovery rate (FDR) and requiring at least two unique peptides per protein.


Differential Secreted Protein Expression and Functional Enrichment Analysis


Data Acquisition and Processing


Protein sequence data, KEGG annotations and corresponding protein mass spectrometry spectral count data were provided to a vendor. Data were provided for beneficial (A) and non-beneficial (B) species pairs from two fungal and two bacterial genera. All data were converted into file formats and a local database suitable for subsequent processing, analysis and parallelization.


Protein Ortholog Identification


Pairs/groups of orthologous proteins were identified using a modified version of the OrthoMCL pipeline. Orthologs were identified as reciprocal best BLASTP hits, and then clusters of orthologous proteins were defined using the modified OrthoMCL pipeline. This process was done independently for the within genera and the between genera analyses. BLASTP was run in parallel on the Georgia Tech PACE HPC environment.


Protein Functional Annotation


KEGG annotations for individual proteins were provided to the vendor based on the whole genome sequence annotations. The program BLAST2GO was used to annotate proteins with gene ontology (GO) terms based on sequence similarity to previously annotated proteins.


Protein Expression Quantification and Normalization


Individual protein expression levels were taken as the number of observed spectra (i.e. the spectra count) corresponding to each protein. Protein spectra counts were retrieved across three replicates for each species. Missing counts for any given ortholog or replicate were assigned values of 0. Individual protein expression levels (spectra counts) were then normalized by the total number of observed spectra for each replicate. This process was done independently for the three replicates corresponding to each member of the A-B pair of every species. Fold-change (FC) values for orthologous pairs/groups were computed as log2 A/B spectra counts for the purpose of functional enrichment analysis


Protein Differential Expression Analysis


Differential protein expression analysis was done for a) pairs of orthologous proteins from the within genera analysis and b) groups of orthologous proteins from the between genera analysis. Differential expression was quantified by comparing the within group normalized spectra count variation to the between group normalized spectra count variation using the Students ttest. A Benjamini-Hochberg False Discover Rate threshold of 0.2 was used to identify differentially abundant orthologous proteins.


Pathway and Functional Enrichment Analysis


Enrichment analysis was done in parallel using both KEGG and GO annotations with the hypergeometric test and via Gene Set Enrichment Analysis (GSEA). For the hypergeometric test, for any given functional annotation category (i.e. KEGG pathway or GO term), the number of proteins up-regulated in the beneficial member of the orthologous pair (species A) was compared to the total number of proteins up-regulated in the complete set of orthologs. For GSEA analysis, orthologous protein pairs/groups were ranked by FC values and the distribution of FC values was evaluated for a shift using the clusterprofiler R package.


SYM00577 Secreted Proteomic Analysis









TABLE 700







25 most abundant proteins secreted by SYM00577; “Median Abundance”


represents the median value across three biological replicates in units of


spectra per hundred spectra











SEQ
Protein
Median




ID
ID
Abundance
GO Terms
KEGG Terms














477
1AXg13463.t1
1.171575
GO: 0008152: metabolic
none





process; GO: 0016798:





hydrolase activity, acting on





glycosyl bonds


478
1AXg10805.t1
1.042072
GO: 0004348:
none





glucosylceramidase activity;





GO: 0005576: extracellular





region; GO: 0005975:





carbohydrate metabolic





process; GO: 0006665:





sphingolipid metabolic





process; GO: 0030248:





cellulose binding


479
1AXg10141.t1
0.63105
GO: 0005975: carbohydrate
none





metabolic process;





GO: 0016787: hydrolase





activity


480
1AXg3149.t1
0.581995
GO: 0005975: carbohydrate
KEGG Orthology: K01213: E3.2.1.67: galacturan





metabolic process;
1,4-alpha-galacturonidase [EC: 3.2.1.67]; KEGG





GO: 0016798: hydrolase
PATHWAY: ko00040: Pentose and glucuronate





activity, acting on glycosyl
interconversions:; KEGG PATHWAY: ko00500:





bonds
Starch and sucrose metabolism:


481
1AXg5293.t1
0.516427
GO: 0003723: RNA binding;
KEGG Orthology: K01166: E3.1.27.1:





GO: 0033897: ribonuclease
ribonuclease T2 [EC: 3.1.27.1]





T2 activity; GO: 0090502:





RNA phosphodiester bond





hydrolysis, endonucleolytic


482
1AXg10578.t1
0.498434
GO: 0004190: aspartic-type
none





endopeptidase activity;





GO: 0006508: proteolysis


483
1AXg10693.t1
0.404474
GO: 0000328: fungal-type
none





vacuole lumen;





GO: 0016020: membrane;





GO: 0032366: intracellular





sterol transport


484
1AXg11973.t1
0.336207
GO: 0005886: plasma
none





membrane; GO: 0005975:





carbohydrate metabolic





process; GO: 0016021:





integral component of





membrane; GO: 0016740:





transferase activity;





GO: 0016787: hydrolase





activity; GO: 0031225:





anchored component of





membrane


485
1AXg1240.t1
0.322054
GO: 0003993: acid
KEGG Orthology: K01078: E3.1.3.2: acid





phosphatase activity;
phosphatase [EC: 3.1.3.2]; KEGG PATHWAY:





GO: 0016311:
ko00627: Aminobenzoate degradation:; KEGG





dephosphorylation;
PATHWAY: ko00740: Riboflavin metabolism:;





GO: 0046872: metal ion
KEGG PATHWAY: ko05152: Tuberculosis:





binding
Tuberculosis, or TB, is an infectious disease






caused by Mycobacterium tuberculosis. One






third of the world's population is thought to be






infected with TB. About 90% of those infected






result in latent infections, and about 10% of






latent infections develop active diseases when






their immune system is impaired due to the






age, other diseases such as AIDS or exposure to






immunosuppressive drugs. TB is transmitted






through the air and primarily attacks the lungs,






then it can spread by the circulatory system to






other parts of body. Once TB bacilli have






entered the host by the respiratory route and






infected macrophages in the lungs, they






interfere with phagosomal maturation, antigen






presentation, apoptosis and host immune






system to establish persistent or latent






infection.


486
1AXg4516.t1
0.315618
GO: 0005975: carbohydrate
none





metabolic process;





GO: 0016740: transferase





activity; GO: 0031224:





intrinsic component of





membrane


487
1AXg5358.t1
0.294999
GO: 0005976:
KEGG Orthology: K01178: E3.2.1.3:





polysaccharide metabolic
glucoamylase [EC: 3.2.1.3]; KEGG PATHWAY:





process; GO: 0016798:
ko00500: Starch and sucrose metabolism:





hydrolase activity, acting on





glycosyl bonds;





GO: 0030246: carbohydrate





binding


488
1AXg9478.t1
0.283328
GO: 0044464: cell part
none


489
1AXg3273.t1
0.275195
GO: 0008233: peptidase
KEGG Orthology: K01312: PRSS: trypsin





activity
[EC: 3.4.21.4]; KEGG PATHWAY: ko04080:






Neuroactive ligand-receptor interaction:; KEGG






PATHWAY: ko04972: Pancreatic secretion: The






pancreas performs both exocrine and






endocrine functions. The exocrine pancreas






consists of two parts, the acinar and duct cells.






The primary functions of pancreatic acinar cells






are to synthesize and secrete digestive






enzymes. Stimulation of the cell by






secretagogues such as acetylcholine (ACh) and






cholecystokinin (CCK) causes the generation of






an intracellular Ca2+ signal. This signal, in turn,






triggers the fusion of the zymogen granules






with the apical plasma membrane, leading to






the polarised secretion of the enzymes. The






major task of pancreatic duct cells is the






secretion of fluid and bicarbonate ions (HCO3−),






which neutralize the acidity of gastric contents






that enter the duodenum. An increase in






intracellular cAMP by secretin is one of the






major signals of pancreatic HCO3− secretion.






Activation of the CFTR Cl− channel and the






CFTR-dependent Cl−/HCO3− exchange activities






is responsible for cAMP-induced HCO3−






secretion.; KEGG PATHWAY: ko04974: Protein






digestion and absorption: Protein is a dietary






component essential for nutritional






homeostasis in humans. Normally, ingested






protein undergoes a complex series of






degradative processes following the action of






gastric, pancreatic and small intestinal






enzymes. The result of this proteolytic activity is






a mixture of amino acids and small peptides.






Amino acids (AAs) are transported into the






enterocyte (intestinal epithelial cell) by a






variety of AA transporters that are specific for






cationic (basic) AA, neutral AA, and anionic






(acidic) AA. Small peptides are absorbed into






enterocytes by the PEPT1 transporter. Inside






enterocytes peptides are hydrolyzed, and the






resulting amino acids are released together






with those absorbed by AA transporters into






blood via multiple, basolateral, AA transporters.






Hydrolysis-resistant peptides, however, are






transported out of the cells by a basolateral






peptide transporter that has not been






identified molecularly.; KEGG PATHWAY:






ko05164: Influenza A: Influenza is a contagious






respiratory disease caused by influenza virus






infection. Influenza A virus is responsible for






both annual seasonal epidemics and periodic






worldwide pandemics. Novel strains that cause






pandemics arise from avian influenza virus by






genetic reassortment among influenza viruses






and two surface glycoproteins HA and NA form






the basis of serologically distinct virus types.






The innate immune system recognizes invaded






virus through multiple mechanisms. Viral non-






structural NS1 protein is a multifunctional






virulence factor that interfere IFN-mediated






antiviral response. It inhibits IFN production by






blocking activation of transcription factors such






as NF-kappa B, IRF3 and AP1. NS1 further






inhibits the activation of IFN-induced antiviral






genes. PB1-F2 protein is another virulence






factor that induce apoptosis of infected cells,






which results in life-threatening bronchiolitis.


490
1AXg8115.t1
0.234864
GO: 0008152: metabolic
none





process; GO: 0016787:





hydrolase activity


491
1AXg12530.t1
0.232187
GO: 0000103: sulfate
KEGG Orthology: K03671: trxA: thioredoxin 1





assimilation; GO: 0005634:





nucleus; GO: 0005829:





cytosol; GO: 0006457:





protein folding;





GO: 0015035: protein





disulfide oxidoreductase





activity; GO: 0016671:





oxidoreductase activity,





acting on a sulfur group of





donors, disulfide as





acceptor; GO: 0034599:





cellular response to





oxidative stress;





GO: 0044281: small





molecule metabolic





process; GO: 0045454: cell





redox homeostasis;





GO: 0055114: oxidation-





reduction process;





GO: 0071704: organic





substance metabolic





process; GO: 1900429:





negative regulation of





filamentous growth of a





population of unicellular





organisms


492
1AXg9266.t1
0.218366
GO: 0016491:
none





oxidoreductase activity


493
1AXg12742.t1
0.214329
GO: 0004553: hydrolase
none





activity, hydrolyzing O-





glycosyl compounds;





GO: 0071704: organic





substance metabolic





process


494
1AXg6959.t1
0.213513
GO: 0004190: aspartic-type
none





endopeptidase activity;





GO: 0006508: proteolysis


495
1AXg936.t1
0.208768
GO: 0008152: metabolic
none





process; GO: 0019239:





deaminase activity


496
1AXg13882.t1
0.208427
GO: 0008152: metabolic
KEGG Orthology: K01078: E3.1.3.2: acid





process; GO: 0016788:
phosphatase [EC: 3.1.3.2]; KEGG PATHWAY:





hydrolase activity, acting on
ko00627: Aminobenzoate degradation:; KEGG





ester bonds
PATHWAY: ko00740: Riboflavin metabolism:;






KEGG PATHWAY: ko05152: Tuberculosis:






Tuberculosis, or TB, is an infectious disease






caused by Mycobacterium tuberculosis. One






third of the world's population is thought to be






infected with TB. About 90% of those infected






result in latent infections, and about 10% of






latent infections develop active diseases when






their immune system is impaired due to the






age, other diseases such as AIDS or exposure to






immunosuppressive drugs. TB is transmitted






through the air and primarily attacks the lungs,






then it can spread by the circulatory system to






other parts of body. Once TB bacilli have






entered the host by the respiratory route and






infected macrophages in the lungs, they






interfere with phagosomal maturation, antigen






presentation, apoptosis and host immune






system to establish persistent or latent






infection.


497
1AXg9750.t1
0.191554
GO: 0005576: extracellular
none





region; GO: 0030248:





cellulose binding;





GO: 0045493: xylan





catabolic process;





GO: 0046373: L-arabinose





metabolic process;





GO: 0046556: alpha-L-





arabinofuranosidase activity


498
1AXg6573.t1
0.188047
GO: 0004568: chitinase
none





activity; GO: 0005975:





carbohydrate metabolic





process; GO: 0006032: chitin





catabolic process


499
1AXg92.t1
0.186476
GO: 0016998: cell wall
none





macromolecule catabolic





process; GO: 0052861:





glucan endo-1,3-beta-





glucanase activity, C-3





substituted reducing group;





GO: 0052862: glucan endo-





1,4-beta-glucanase activity,





C-3 substituted reducing





group


500
1AXg9192.t1
0.167015
GO: 0005975: carbohydrate
none





metabolic process


501
1AXg11043.t1
0.1663
GO: 0003824: catalytic
none





activity; GO: 0044238:





primary metabolic process;





GO: 0071704: organic





substance metabolic





process









SYM00577 Versus SYM00300









TABLE 701





Differential secreted protein abundance between SYM00577 and SYM00300.




















SEQ ID

SEQ ID





Beneficial
A.protein
Neutral
B.protein
KEGG
GO





502
1AXg1022.t1
2297
1BXg8091.t1
Biosynthesis of
carbohydrate metabolic






amino acids,
process, cytosol, nucleus,






Carbon
pentose-phosphate shunt,






metabolism,
non-oxidative branch,






E2.2.1.2, talA,
sedoheptulose-7-






talB, Pentose
phosphate:D-






phosphate
glyceraldehyde-3-






pathway
phosphate







glyceronetransferase







activity


487
1AXg5358.t1
2298
1BXg9546.t1
E3.2.1.3, Starch
carbohydrate binding,






and sucrose
hydrolase activity, acting on






metabolism
glycosyl bonds,







polysaccharide metabolic







process


503
1AXg8841.t1
2299
1BXg1271.t1
Cysteine and
adenosylhomocysteinase






methionine
activity, cytosol, one-carbon






metabolism,
metabolic process,






E3.3.1.1, ahcY
phosphatidylcholine







biosynthetic process, S-







adenosylhomocysteine







catabolic process,







triglyceride metabolic







process


504
1AXg20808.t1
2300
1BXg8757.t1
None
carbohydrate metabolic







process, hydrolase activity,







acting on glycosyl bonds,







hydrolase activity,







hydrolyzing O-glycosyl







compounds, metabolic







process


505
1AXg10583.t1
2301
1BXg10631.t1
None
cell wall macromolecule







catabolic process, lysozyme







activity, peptidoglycan







catabolic process


506
1AXg8644.t1
2302
1BXg2276.t1
E3.1.27.1
cytoplasmic part,







ribonuclease T2 activity,







RNA binding, RNA







phosphodiester bond







hydrolysis, endonucleolytic,







single-organism cellular







process


507
1AXg360.t1
2303
1BXg8875.t1
None
None


508
1AXg9960.t1
2304
1BXg11250.t1
Purine
None






metabolism,






ylbA, UGHY


509
1AXg10066.t1
2305
1BXg2721.t1
None
nuclease activity


510
1AXg9954.t1
2306
1BXg11402.t1
None
hydrolase activity,







metabolic process


511
1AXg11078.t1
2307
1BXg1562.t1
None
None


512
1AXg7160.t1
2308
1BXg550.t1
Aminobenzoate
None






degradation,






Folate






biosynthesis,






phoD, Two-






component






system


513
1AXg7978.t1
2309
1BXg10240.t1
None
hydrolase activity


514
1AXg8599.t1
2310
1BXg3056.t1
None
None


515
1AXg11864.t1
2311
1BXg8819.t1
None
glucose metabolic process,







L-xylulose reductase







(NADP+) activity, mannitol







2-dehydrogenase (NADP+)







activity, mitochondrion,







oxidation-reduction







process, protein







homotetramerization,







xylulose metabolic process


516
1AXg13464.t1
2312
1BXg8758.t1
None
hydrolase activity,







metabolic process


517
1AXg13099.t1
2313
1BXg8761.t1
None
carbohydrate metabolic







process, hydrolase activity,







hydrolyzing O-glycosyl







compounds, intracellular







part


518
1AXg10728.t1
2314
1BXg4259.t1
None
hydrolase activity,







metabolic process


519
1AXg31.t1
2315
1BXg2840.t1
gcvH, GCSH,
glycine cleavage complex,






Glycine, serine
glycine decarboxylation via






and threonine
glycine cleavage system,






metabolism,
mitochondrion, one-carbon






Glyoxylate and
metabolic process,






dicarboxylate
oxidation-reduction






metabolism
process, protein lipoylation


520
1AXg4476.t1
2316
1BXg5721.t1
None
endonuclease activity,







exonuclease activity,







nuclease activity, nucleic







acid phosphodiester bond







hydrolysis


521
1AXg11059.t1
2317
1BXg2900.t1
Fatty acid
endoplasmic reticulum,






elongation, Fatty
palmitoyl-(protein)






acid metabolism,
hydrolase activity, protein






Lysosome, PPT
depalmitoylation, vacuolar







acidification, vacuole


522
1AXg10328.t1
2318
1BXg8689.t1
None
None


523
1AXg10740.t1
2319
1BXg11987.t1
None
cell part


524
1AXg18392.t1
2320
1BXg11664.t1
Adrenergic
ascospore-type prospore-






signaling in
specific spindle pole body






cardiomyocytes,
remodeling, ATP hydrolysis






Alcoholism,
coupled proton transport,






Alzheimer's
barrier septum, calcium ion






disease,
binding, calcium-dependent






Amphetamine
protein binding, cell






addiction,
budding, cell division site,






Calcium signaling
cellular bud neck, cellular






pathway, CALM,
bud tip, central plaque of






cAMP signaling
spindle pole body, cytosol,






pathway, cGMP-
hydrogen ion






PKG signaling
transmembrane transporter






pathway,
activity, incipient cellular






Circadian
bud site, integral






entrainment,
component of membrane,






Dopaminergic
karyogamy involved in






synapse,
conjugation with cellular






Estrogen
fusion, lysosomal






signaling
microautophagy,






pathway, Gastric
maintenance of protein






acid secretion,
location in spindle pole






Glioma, GnRH
body, mating projection tip,






signaling
mitotic spindle assembly,






pathway,
mitotic spindle pole body,






Inflammatory
mycelium development,






mediator
new growing cell tip, NLS-






regulation of TRP
bearing protein import into






channels, Insulin
nucleus, nucleus, old






signaling
growing cell tip,






pathway, Long-
phosphatidylinositol






term
biosynthetic process,






potentiation,
proton-transporting V-type






Melanogenesis,
ATPase, V0 domain,






Neurotrophin
receptor-mediated






signaling
endocytosis, regulation of






pathway,
cell cycle, spitzenkorper,






Olfactory
spore germination,






transduction,
transcription factor import






Oocyte meiosis,
into nucleus, vacuole






Oxytocin
fusion, non-autophagic






signaling






pathway,






Pertussis,






Phosphatidylinositol






signaling






system,






Phototransduction,






Phototransduction -






fly, Plant-






pathogen






interaction, Rap1






signaling






pathway, Ras






signaling






pathway,






Salivary






secretion,






Tuberculosis,






Vascular smooth






muscle






contraction


525
1AXg3446.t1
2321
1BXg4699.t1
None
None


526
1AXg3959.t1
2322
1BXg3931.t1
Amino sugar and
hydrolase activity,






nucleotide sugar
hydrolyzing O-glycosyl






metabolism,
compounds, organic






E3.2.1.14
substance metabolic







process


494
1AXg6959.t1
2323
1BXg7026.t1
None
aspartic-type







endopeptidase activity,







proteolysis


527
1AXg4985.t1
2324
1BXg8953.t1
None
FMN binding, oxidation-







reduction process,







oxidoreductase activity


528
1AXg4291.t1
2325
1BXg1944.t1
E3.2.1.101
hydrolase activity


529
1AXg6728.t1
2326
1BXg4339.t1
ndk, NME,
ATP binding, CDP






Purine
phosphorylation, cellular






metabolism,
response to DNA damage






Pyrimidine
stimulus, CTP biosynthetic






metabolism
process, cytosol, GTP







biosynthetic process,







identical protein binding,







integral component of







membrane, mitochondrial







intermembrane space,







nucleoside diphosphate







kinase activity, nucleus, UTP







biosynthetic process


530
1AXg10268.t1
2327
1BXg2378.t1
None
hydrolase activity, acting on







glycosyl bonds, metabolic







process


531
1AXg3277.t1
2328
1BXg3155.t1
None
hydrolase activity,







membrane


532
1AXg27.t1
2329
1BXg1583.t1
None
acid phosphatase activity,







dephosphorylation


533
1AXg1627.t1
2330
1BXg7860.t1
None
cell redox homeostasis,







Golgi trans cisterna, integral







component of plasma







membrane, oligopeptide







transport, oligopeptide







transporter activity,







peroxisome, positive







regulation of monopolar







cell growth, regulation of







phospholipid translocation,







regulation of vacuole







organization,







transmembrane transport,







vacuole fusion, non-







autophagic


534
1AXg5235.t1
2331
1BXg2358.t1
Antigen
ATP binding, integral






processing and
component of membrane






presentation,






Endocytosis,






Epstein-Barr






virus infection,






Estrogen






signaling






pathway,






HSPA1_8,






Influenza A,






Legionellosis,






MAPK signaling






pathway,






Measles, Protein






processing in






endoplasmic






reticulum,






Spliceosome,






Toxoplasmosis


535
1AXg7693.t1
2332
1BXg9970.t1
None
carbohydrate binding,







carbohydrate catabolic







process, hydrolase activity,







hydrolyzing O-glycosyl







compounds


536
1AXg7827.t1
2333
1BXg8670.t1
Ribosome, RP-
ribosome, structural






S16e, RPS16
constituent of ribosome,







translation


537
1AXg9662.t1
2334
1BXg4876.t1
None
integral component of







membrane, transmembrane







transport, transmembrane







transporter activity


538
1AXg5289.t1
2335
1BXg2280.t1
Alanine,
calmodulin binding, cellular






aspartate and
response to oxidative






glutamate
stress, cytoplasm,






metabolism,
glutamate catabolic






beta-Alanine
process, glutamate






metabolism,
decarboxylase activity,






Butanoate
pyridoxal phosphate






metabolism,
binding






E4.1.1.15, gadB,






gadA, GAD,






GABAergic






synapse, Taurine






and hypotaurine






metabolism,






Type I diabetes






mellitus


539
1AXg10486.t1
2336
1BXg1674.t1
SLC39A1_2_3,
integral component of






ZIP1_2_3
membrane, low-affinity zinc







II ion transport, low-affinity







zinc ion transmembrane







transporter activity, plasma







membrane, zinc II ion







transmembrane transport,







zinc ion transmembrane







transporter activity


540
1AXg12100.t1
2337
1BXg7176.t1
Cell cycle,
monooxygenase activity,






Epstein-Barr
oxidation-reduction






virus infection,
process, protein domain






Hippo signaling
specific binding






pathway, Hippo






signaling






pathway - fly,






Neurotrophin






signaling






pathway, Oocytemeiosis,






PI3K-Akt






signaling






pathway, Viral






carcinogenesis,






YWHAE


541
1AXg5383.t1
2338
1BXg9570.t1
Alzheimer's
glucose metabolic process,






disease,
glyceraldehyde-3-






Biosynthesis of
phosphate dehydrogenase






amino acids,
(NAD+) (phosphorylating)






Carbon fixation
activity, glycolytic process,






in
NAD binding, NADP binding,






photosynthetic
oxidation-reduction process






organisms,






Carbon






metabolism,






GAPDH, gapA,






Glycolysis/






Gluconeogenesis,






HIF-1 signaling






pathway


542
1AXg10197.t1
2339
1BXg11161.t1
E3.1.4.46, glpQ,
glycerophosphodiester






ugpQ,
phosphodiesterase activity,






Glycerophospholipid
lipid metabolic process






metabolism


543
1AXg4433.t1
2340
1BXg6768.t1
E3.2.1.6
hydrolase activity,







hydrolyzing O-glycosyl







compounds, metabolic







process


544
1AXg3932.t1
2341
1BXg3960.t1
FoxO signaling
cytosol, identical protein






pathway, PRMT1
binding, mRNA export from







nucleus, negative regulation







of DNA-templated







transcription, termination,







nucleus, peptidyl-arginine







methylation, to







asymmetrical-dimethyl







arginine, positive regulation







of transcription elongation







from RNA polymerase II







promoter, protein-arginine







omega-N asymmetric







methyltransferase activity,







protein-arginine omega-N







monomethyltransferase







activity


545
1AXg10561.t1
2342
1BXg1546.t1
None
oxidoreductase activity


546
1AXg3216.t1
2343
1BXg6110.t1
None
lipid metabolic process,







organic substance







metabolic process,







phosphoric diester







hydrolase activity, primary







metabolic process


547
1AXg7277.t1
2344
1BXg11845.t1
EEF1A,
cytoplasm, GTP binding,






Legionellosis,
GTPase activity, translation






RNA transport
elongation factor activity,







translational elongation


548
1AXg10803.t1
2345
1BXg2053.t1
None
carbohydrate metabolic







process, cellulose binding,







extracellular region,







hydrolase activity,







hydrolyzing O-glycosyl







compounds


549
1AXg6123.t1
2346
1BXg7324.t1
None
None


550
1AXg4834.t1
2347
1BXg4445.t1
None
carbohydrate metabolic







process, hydrolase activity,







hydrolyzing O-glycosyl







compounds, integral







component of membrane


551
1AXg13304.t1
2348
1BXg9661.t1
None
carbohydrate metabolic







process, hydrolase activity,







hydrolyzing O-glycosyl







compounds


552
1AXg3171.t1
2349
1BXg2692.t1
E3.2.1.4, Starch
hydrolase activity,






and sucrose
hydrolyzing O-glycosyl






metabolism
compounds, polysaccharide







catabolic process


553
1AXg7126.t1
2350
1BXg5592.t1
Amino sugar and
ATP binding, canonical






nucleotide sugar
glycolysis, carbohydrate






metabolism,
phosphorylation, cellular






Butirosin and
glucose homeostasis,






neomycin
cytosol, fructokinase






biosynthesis,
activity, fructose 6-






Carbohydrate
phosphate metabolic






digestion and
process, fructose import,






absorption,
fructose metabolic process,






Carbon
glucokinase activity, glucose






metabolism,
6-phosphate metabolic






Central carbon
process, glucose binding,






metabolism in
glucose import,






cancer, Fructose
mannokinase activity,






and mannose
mannose metabolic






metabolism,
process, mitochondrion,






Galactose
nucleus, regulation of






metabolism,
transcription by glucose,






Glycolysis/
replicative cell aging






Gluconeogenesis,






HIF-1 signaling






pathway, HK,






Insulin signaling






pathway, Starch






and sucrose






metabolism,






Streptomycin






biosynthesis,






Type II diabetes






mellitus


554
1AXg1749.t1
2351
1BXg9726.t1
None
None


555
1AXg10973.t1
2352
1BXg5639.t1
K16330,
cytoplasm, endonucleolytic






Pyrimidine
cleavage in 5′-ETS of






metabolism
tricistronic rRNA transcript







(SSU-rRNA, 5.8S rRNA, LSU-







rRNA), endonucleolytic







cleavage in ITS1 to separate







SSU-rRNA from 5.8S rRNA







and LSU-rRNA from







tricistronic rRNA transcript







(SSU-rRNA, 5.8S rRNA, LSU-







rRNA), endonucleolytic







cleavage to generate







mature 5′-end of SSU-rRNA







from (SSU-rRNA, 5.8S rRNA,







LSU-rRNA), hydrolase







activity, acting on glycosyl







bonds, kinase activity,







phosphorylation,







pseudouridine synthesis,







Pwp2p-containing







subcomplex of 90S







preribosome, small-subunit







processome


556
1AXg2695.t1
2353
1BXg6589.t1
None
None


557
1AXg5845.t1
2354
1BXg1158.t1
Ribosome, RP-
cytoplasmic translation,






S3e, RPS3
cytosolic small ribosomal







subunit, DNA catabolic







process, endonucleolytic,







DNA-(apurinic or







apyrimidinic site) lyase







activity, preribosome, small







subunit precursor,







ribosomal small subunit







export from nucleus, RNA







binding, rRNA export from







nucleus, structural







constituent of ribosome


558
1AXg9065.t1
2355
1BXg8585.t1
AMPK signaling
GTP binding, GTPase






pathway, EEF2,
activity, integral component






Oxytocin
of membrane, translation






signaling
elongation factor activity,






pathway
translational elongation


559
1AXg10539.t1
2356
1BXg6684.t1
None
None


560
1AXg4683.t1
2357
1BXg10580.t1
E3.2.1.8, xynA
D-xylose metabolic process,







endo-1,4-beta-xylanase







activity, xylan catabolic







process


561
1AXg1198.t1
2358
1BXg352.t1
Adherens
1,3-beta-D-glucan synthase






junction, Axon
complex, actin cytoskeleton






guidance,
reorganization, budding cell






Bacterial
bud growth, cellular bud






invasion of
neck, cellular bud tip, Golgi






epithelial cells,
apparatus, GTP binding,






cAMP signaling
GTPase activity, incipient






pathway, cGMP-
cellular bud site, mating






PKG signaling
projection tip, peroxisome,






pathway,
positive regulation of






Chemokine
endocytosis, positive






signaling
regulation of protein kinase






pathway,
C signaling, protein






Colorectal
transport, regulation of cell






cancer,
size, regulation of cell wall






Endocytosis,
(1->3)-beta-D-glucan






Focal adhesion,
biosynthetic process,






Leukocyte
regulation of exocyst






transendothelial
localization, regulation of






migration, MAPK
fungal-type cell wall






signaling
organization, regulation of






pathway - yeast,
vacuole fusion, non-






MicroRNAs in
autophagic, small GTPase






cancer,
mediated signal






Neurotrophin
transduction






signaling






pathway,






Oxytocin






signaling






pathway,






Pancreatic






secretion,






Pathogenic







Escherichia coli







infection,






Pathways in






cancer,






Pertussis,






Platelet






activation,






Proteoglycans in






cancer, Rap1






signaling






pathway, Ras






signaling






pathway,






Regulation of






actin






cytoskeleton,






RHOA,






Sphingolipid






signaling






pathway, T cell






receptor






signaling






pathway, TGF-






beta signaling






pathway, Tight






junction,






Tuberculosis,






Vascular smooth






muscle






contraction, Viral


562
1AXg1904.t1
2359
1BXg5010.t1
YAT
amino acid transmembrane







transport, amino acid







transmembrane transporter







activity, integral component







of membrane


563
1AXg3176.t1
2360
1BXg4958.t1
HXT, Meiosis -
integral component of






yeast
membrane, substrate-







specific transmembrane







transporter activity,







transmembrane transport


564
1AXg10060.t1
2361
1BXg2790.t1
E3.2.1.8, xynA
endo-1,4-beta-xylanase







activity, xylan catabolic







process


565
1AXg5709.t1
2362
1BXg9980.t1
2-Oxocarboxylic
3-isopropylmalate






acid metabolism,
dehydrogenase activity, ATP






Biosynthesis of
binding, ATP hydrolysis






amino acids, C5-
coupled proton transport,






Branched dibasic
ATP metabolic process,






acid metabolism,
cytosol, glyoxylate cycle,






leuB, Valine,
leucine biosynthetic






leucine and
process, magnesium ion






isoleucine
binding, NAD binding,






biosynthesis
oxidation-reduction







process, proton-







transporting ATPase







activity, rotational







mechanism, proton-







transporting V-type ATPase,







V1 domain


566
1AXg8275.t1
2363
1BXg5365.t1
None
None


567
1AXg1909.t1
2364
1BXg6126.t1
None
peptidase activity


568
1AXg4752.t1
2365
1BXg2001.t1
AMPK signaling
ascospore-type prospore






pathway,
assembly, autophagy,






Pancreatic
cytosol, exocytosis, Golgi to






secretion,
plasma membrane






RAB8A, MEL
transport, GTP binding,







GTPase activity, incipient







cellular bud site,







intracellular protein







transport, membrane,







membrane addition at site







of cytokinesis, metabolic







process, nucleocytoplasmic







transport, nucleus, small







GTPase mediated signal







transduction, transport







vesicle, vesicle fusion


569
1AXg3765.t1
2366
1BXg2666.t1
None
catalytic activity, integral







component of membrane,







metabolic process


570
1AXg2891.t1
2367
1BXg10882.t1
None
carboxypeptidase activity,







metallocarboxypeptidase







activity, proteolysis, zinc ion







binding


478
1AXg10805.t1
2368
1BXg9667.t1
None
carbohydrate metabolic







process, cellulose binding,







extracellular region,







glucosylceramidase activity,







sphingolipid metabolic







process


571
1AXg5891.t1
2369
1BXg10979.t1
E5.2.1.8
apoptotic process, cytosol,







mitochondrion, nucleus,







peptidyl-prolyl cis-trans







isomerase activity, protein







folding, protein peptidyl-







prolyl isomerization


572
1AXg10065.t1
2370
1BXg2722.t1
None
None


573
1AXg19725.t1
2371
1BXg7679.t1
Ribosome, RP-
ribosome






L7e, RPL7


574
1AXg20723.t1
2372
1BXg2050.t1
None
integral component of







membrane, transmembrane







transport, transmembrane







transporter activity


575
1AXg21175.t1
2373
1BXg6238.t1
Ribosome, RP-
large ribosomal subunit,






L13Ae, RPL13A
structural constituent of







ribosome, translation


576
1AXg2292.t1
2374
1BXg10710.t1
ARN
integral component of







membrane, transmembrane







transport


577
1AXg1391.t1
2375
1BXg3917.t1
None
cytosol, nucleus,







proteolysis, serine-type







peptidase activity


578
1AXg8174.t1
2376
1BXg7986.t1
None
catalytic activity, cell, cell







redox homeostasis, glycerol







ether metabolic process,







integral component of







membrane, membrane,







oxidation-reduction







process, protein disulfide







oxidoreductase activity,







single-organism cellular







process, single-organism







metabolic process,







translation


480
1AXg3149.t1
2377
1BXg4998.t1
E3.2.1.67,
carbohydrate metabolic






Pentose and
process, cell wall






glucuronate
organization, extracellular






interconversions,
region, hydrolase activity,






Starch and
acting on glycosyl bonds,






sucrose
polygalacturonase activity






metabolism


579
1AXg4184.t1
2378
1BXg1792.t1
None
integral component of







membrane


580
1AXg5751.t1
2379
1BXg7894.t1
Carbohydrate
alpha-amylase activity,






digestion and
carbohydrate metabolic






absorption,
process, cation binding,






E3.2.1.1, amyA,
oxidation-reduction






malS, Starch and
process, oxidoreductase






sucrose
activity, starch binding






metabolism


581
1AXg10745.t1
2380
1BXg11993.t1
None
None


582
1AXg8977.t1
2381
1BXg11388.t1
TC.POT
integral component of







membrane, oligopeptide







transport, transporter







activity


583
1AXg2503.t1
2382
1BXg3531.t1
Amino sugar and
carbohydrate metabolic






nucleotide sugar
process, intramolecular






metabolism,
transferase activity,






Galactose
phosphotransferases,






metabolism,
magnesium ion binding,






Glycolysis/
nucleus






Gluconeogenesis,






Pentose






phosphate






pathway, pgm,






Purine






metabolism,






Starch and






sucrose






metabolism,






Streptomycin






biosynthesis


584
1AXg3358.t1
2383
1BXg4769.t1
None
None


585
1AXg8317.t1
2384
1BXg5117.t1
None
None


586
1AXg4278.t1
2385
1BXg1931.t1
AFG1, LACE1,
ATP binding, cellular






zapE
response to oxidative







stress, misfolded or







incompletely synthesized







protein catabolic process,







mitochondrial inner







membrane, protein import







into peroxisome matrix


587
1AXg11050.t1
2386
1BXg2887.t1
None
proteolysis, serine-type







carboxypeptidase activity


588
1AXg8247.t1
2387
1BXg10032.t1
Biosynthesis of
canonical glycolysis,






amino acids,
gluconeogenesis,






Carbon fixation
mitochondrion, nucleus,






in
pentose-phosphate shunt,






photosynthetic
triose-phosphate isomerase






organisms,
activity






Carbon






metabolism,






Fructose and






mannose






metabolism,






Glycolysis/






Gluconeogenesis,






Inositol






phosphate






metabolism, TPI,






tpiA


589
1AXg5531.t1
2388
1BXg11344.t1
E3.2.1.6
carbohydrate metabolic







process, hydrolase activity,







hydrolyzing O-glycosyl







compounds


590
1AXg9521.t1
2389
1BXg6591.t1
None
cellular aromatic compound







metabolic process, ferric







iron binding, integral







component of membrane,







oxidation-reduction







process, oxidoreductase







activity, acting on single







donors with incorporation







of molecular oxygen,







incorporation of two atoms







of oxygen


591
1AXg11377.t1
2390
1BXg307.t1
XEG
carbohydrate etabolicm







process, hydrolase activity,







acting on glycosyl bonds,







hydrolase activity,







hydrolyzing O-glycosyl







compounds


592
1AXg7658.t1
2391
1BXg7553.t1
Cysteine and
cellular response to,






methionine
oxidative stress, cytoplasm,






metabolism,
methionine-R-sulfoxide






E1.8.4.14
reductase activity,







oxidation-reduction process


593
1AXg1255.t1
2392
1BXg439.t1
None
None


594
1AXg11060.t1
2393
1BXg1582.t1
None
integral component of







membrane, transmembrane







transport


595
1AXg6907.t1
2394
1BXg8642.t1
None
None


596
1AXg1976.t1
2395
1BXg6237.t1
None
intracellular







ribonucleoprotein complex


597
1AXg10216.t1
2396
1BXg11971.t1
None
cell redox homeostasis,







cellular response to







oxidative stress, glutathione







peroxidase activity,







mitochondrion, oxidation-







reduction process, response







to cadmium ion,







thioredoxin peroxidase







activity


598
1AXg8251.t1
2397
1BXg10028.t1
None
hydrolase activity, acting on







carbon-nitrogen (but not







peptide) bonds, metabolic







process


599
1AXg6457.t1
2398
1BXg5328.t1
None
integral component of







membrane, membrane,







transmembrane transport


600
1AXg11201.t1
2399
1BXg8976.t1
None
None


601
1AXg21445.t1
2400
1BXg11743.t1
Ribosome, RP-
cytosolic small ribosomal






SAe, RPSA
subunit, ribosomal small







subunit assembly, structural







constituent of ribosome,







translation


602
1AXg12610.t1
2401
1BXg3489.t1
None
acid phosphatase activity,







dephosphorylation, integral







component of membrane


603
1AXg81.t1
2402
1BXg10975.t1
None
None


604
1AXg3188.t1
2403
1BXg9954.t1
None
None


605
1AXg7341.t1
2404
1BXg10389.t1
None
None


606
1AXg8340.t1
2405
1BXg5140.t1
Oxidative
aerobic respiration, cellular






phosphorylation,
metabolic process,






ppa
cytoplasm, inorganic







diphosphatase activity,







magnesium ion binding,







mitochondrion, phosphate-







containing compound







metabolic process


607
1AXg6585.t1
2406
1BXg10114.t1
FTR, efeU
high-affinity iron ion







transmembrane transport,







high-affinity iron permease







complex, integral







component of membrane,







iron ion transmembrane







transporter activity,







metabolic process,







transferase activity


608
1AXg1785.t1
2407
1BXg1175.t1
Amino sugar and
beta-N-






nucleotide sugar
acetylhexosaminidase






metabolism,
activity, carbohydrate






Glycosaminoglycan
metabolic process






degradation,






Glycosphingolipid






biosynthesis-






ganglio series,






Glycosphingolipid






biosynthesis-






globo series,






HEXA_B,






Lysosome, Other






glycan






degradation


609
1AXg2827.t1
2408
1BXg9091.t1
map
aminopeptidase activity,







fumagillin biosynthetic







process, metal ion binding,







metalloexopeptidase







activity, proteolysis


610
1AXg3285.t1
2409
1BXg8264.t1
None
cell part


611
1AXg7102.t1
2410
1BXg5569.t1
None
None


612
1AXg9751.t1
2411
1BXg1036.t1
E3.6.3.6,
ATP binding, ATP






Oxidative
biosynthetic process,






phosphorylation
hydrogen ion







transmembrane transport,







hydrogen-exporting ATPase







activity, phosphorylative







mechanism, integral







component of membrane,







metal ion binding


613
1AXg3114.t1
2412
1BXg11816.t1
None
hydrolase activity, positive







regulation of translation,







positive regulation of







translational elongation,







positive regulation of







translational termination,







ribosome binding, RNA







binding, translation







elongation factor activity,







translational elongation,







translational frameshifting


614
1AXg2047.t1
2413
1BXg2549.t1
None
carbohydrate metabolic







process, cell wall, cell wall







organization, hydrolase







activity, hydrolyzing O-







glycosyl compounds,







transferase activity


615
1AXg524.t1
2414
1BXg8254.t1
None
integral component of







membrane, transmembrane







transport


616
1AXg5090.t1
2415
1BXg2954.t1
SNARE
integral component of






interactions in
membrane, vesicle-






vesicular
mediated transport






transport,






STX1B_2_3,






Synaptic vesicle






cycle


617
1AXg6524.t1
2416
1BXg2065.t1
Alzheimer's
2 iron, 2 sulfur cluster






disease, Cardiac
binding, aerobic respiration,






muscle
hydrogen ion






contraction,
transmembrane transport,






Huntington's
metal ion binding,






disease, Non-
mitochondrial electron






alcoholic fatty
transport, ubiquinol to






liver disease
cytochrome c,






(NAFLD),
mitochondrial respiratory






Oxidative
chain complex III, ubiquinol-






phosphorylation,
cytochrome-c reductase






Parkinson's
activity






disease, Two-






component






system,






UQCRFS1, RIP1,






petA


618
1AXg9485.t1
2417
1BXg5765.t1
None
ATP binding, ATPase







activity, endoplasmic







reticulum, integral







component of membrane,







metabolic process


619
1AXg3460.t1
2418
1BXg4685.t1
Biosynthesis of
ATP






amino acids,
phosphoribosyltransferase






hisG, Histidine
activity, cytosol, histidine






metabolism
biosynthetic process,







magnesium ion binding


620
1AXg3259.t1
2419
1BXg8229.t1
PMPCB, MAS1
metal ion binding,







metalloendopeptidase







activity, mitochondrial







processing peptidase







complex, protein processing







involved in protein







targeting to mitochondrion


621
1AXg7607.t1
2420
1BXg7629.t1
None
integral component of







membrane


622
1AXg3160.t1
2421
1BXg1334.t1
PHO84
inorganic phosphate







transmembrane transporter







activity, integral component







of membrane, phosphate







ion transport,







transmembrane transport


623
1AXg459.t1
2422
1BXg8019.t1
E3.2.1.101
catalytic activity, membrane


624
1AXg11134.t1
2423
1BXg6417.t1
None
cytoplasmic part,







endomembrane system,







integral component of







membrane, intracellular







membrane-bounded







organelle, transmembrane







transport


625
1AXg14833.t1
2424
1BXg6900.t1
Calcium signaling
ADP transport, ATP:ADP






pathway, cGMP-
antiporter activity, DNA






PKG signaling
repair, integral component






pathway, HTLV-I
of membrane, kinetochore






infection,
assembly, mitochondrial






Huntington's
ATP transmembrane






disease,
transport, mitochondrial






Parkinson's
inner membrane






disease,






SLC25A4S, ANT


626
1AXg2308.t1
2425
1BXg10725.t1
None
NAD(P)+ transhydrogenase







activity, single-organism







process


627
1AXg7369.t1
2426
1BXg10420.t1
SLC25A23S
3′-phospho-5′-adenylyl







sulfate transmembrane







transport, 3′-







phosphoadenosine 5′-







phosphosulfate







transmembrane transporter







activity, 5′-adenylyl sulfate







transmembrane transport,







5′-adenylyl sulfate







transmembrane transporter







activity, integral component







of membrane, intracellular







ribonucleoprotein complex,







mitochondrion, ribosome,







structural constituent of







ribosome, translation


628
1AXg1858.t1
2427
1BXg1886.t1
None
intracellular part


629
1AXg8166.t1
2428
1BXg7974.t1
None
membrane


630
1AXg2960.t1
2429
1BXg5945.t1
None
None


631
1AXg4213.t1
2430
1BXg1766.t1
None
membrane


632
1AXg4083.t1
2431
1BXg3283.t1
None
integral component of







membrane, plasma







membrane, transport


633
1AXg3175.t1
2432
1BXg2690.t1
E3.2.1.—
carbohydrate metabolic







process, cellulose binding,







extracellular region,







hydrolase activity,







hydrolyzing O-glycosyl







compounds


634
1AXg11576.t1
2433
1BXg11481.t1
None
flavin adenine dinucleotide







binding, oxidation-







reduction process,







oxidoreductase activity,







acting on CH—OH group of







donors


635
1AXg511.t1
2434
1BXg3351.t1
None
oxidoreductase activity


636
1AXg8734.t1
2435
1BXg11562.t1
None
chitin binding, chitin







catabolic process, chitinase







activity, extracellular







region, pathogenesis,







polysaccharide catabolic







process


637
1AXg6748.t1
2436
1BXg4362.t1
E3.2.1.58, Starch
endoplasmic reticulum,






and sucrose
fungal-type cell wall beta-






metabolism
glucan biosynthetic process,







glucan endo-1,6-beta-







glucosidase activity, integral







component of membrane,







regulation of cell shape


638
1AXg10079.t1
2437
1BXg2701.t1
HSPA5, BIP,
‘de novo’ posttranslational






Prion diseases,
protein folding, ATP






Protein export,
binding, ATPase activity, ER-






Protein
associated ubiquitin-






processing in
dependent protein






endoplasmic
catabolic process, Golgi






reticulum,
apparatus, karyogamy






Thyroid
involved in conjugation with






hormone
cellular fusion, luminal






synthesis
surveillance complex,







nuclear membrane,







posttranslational protein







targeting to membrane,







translocation, response to







unfolded protein, SRP-







dependent cotranslational







protein targeting to







membrane, translocation,







unfolded protein binding


639
1AXg10129.t1
2438
1BXg8487.t1
None
None


482
1AXg10578.t1
2439
1BXg12089.t1
None
aspartic-type







endopeptidase activity,







proteolysis


640
1AXg12554.t1
2440
1BXg3576.t1
Ribosome, RP-
cytoplasmic translation,






S13e, RPS13
cytosolic small ribosomal







subunit, maturation of SSU-







rRNA from tricistronic rRNA







transcript (SSU-rRNA, 5.8S







rRNA, LSU-rRNA), mycelium







development, small







ribosomal subunit rRNA







binding, structural







constituent of ribosome


641
1AXg15417.t1
2441
1BXg6538.t1
Protein
acid-amino acid ligase






processing in
activity, APC-Cdc20 complex






endoplasmic
activity, ATP binding,






reticulum,
cytosol, nuclear SCF






UBE2D_E, UBC4,
ubiquitin ligase complex,






UBC5, Ubiquitin
positive regulation of






mediated
mitotic






proteolysis
metaphase/anaphase







transition, protein







processing, protein







ubiquitination involved in







ubiquitin-dependent







protein catabolic process,







SCF-dependent







proteasomal ubiquitin-







dependent protein







catabolic process, ubiquitin







conjugating enzyme activity


642
1AXg4473.t1
2442
1BXg9969.t1
SLC39A1_2_3,
cellular response to zinc ion






ZIP1_2_3
starvation, endoplasmic







reticulum, high-affinity zinc







II ion transport, high-affinity







zinc uptake transmembrane







transporter activity, integral







component of plasma







membrane, regulation of







transcription from RNA







polymerase II promoter in







response to iron ion







starvation


643
1AXg13171.t1
2443
1BXg1289.t1
E3.2.1.28, treA,
alpha,alpha-trehalase






treF, Starch and
activity, trehalose metabolic






sucrose
process






metabolism


644
1AXg4544.t1
2444
1BXg4073.t1
Ribosome, RP-
ribosome, rRNA binding,






L9e, RPL9
structural constituent of







ribosome, translation


645
1AXg13885.t1
2445
1BXg12241.t1
Ether lipid
hydrolase activity, acting on






metabolism,
ester bonds, metabolic






Glycerophospholipid
process






metabolism,






Inositol






phosphate






metabolism,






plcC, Thyroid






hormone






signaling






pathway


646
1AXg8079.t1
2446
1BXg7852.t1
None
hydrolase activity,







metabolic process


647
1AXg1002.t1
2447
1BXg8071.t1
Alzheimer's
ATP synthesis coupled






disease,
proton transport,






ATPeFOD,
mitochondrial proton-






ATP5H, ATP7,
transporting ATP synthase,






Huntington's
stator stalk, protein






disease,
complex assembly, proton-






Oxidative
transporting ATP synthase






phosphorylation,
activity, rotational






Parkinson's
mechanism, proton-






disease
transporting ATPase







activity, rotational







mechanism


648
1AXg14938.t1
2448
1BXg3779.t1
ARF1,
Golgi apparatus, GTP






Endocytosis,
binding, hydrolase activity,






Legionellosis,
intracellular protein






Vibrio cholerae
transport, metabolic






infection
process, small GTPase







mediated signal







transduction


649
1AXg2148.t1
2449
1BXg11881.t1
Adherens
ascospore formation, cell






junction,
division, conidium






Amyotrophic
formation, developmental






lateral sclerosis
pigmentation,






(ALS), Axon
endomembrane system,






guidance, B cell
fungal-type vacuole






receptor
membrane, GTP binding,






signaling
GTPase activity, intracellular






pathway,
protein transport,






Bacterial
metabolic process,






invasion of
nucleocytoplasmic






epithelial cells,
transport, pathogenesis,






cAMP signaling
plasma membrane, small






pathway,
GTPase mediated signal






Chemokine
transduction






signaling






pathway,






Choline






metabolism in






cancer,






Colorectal






cancer, Epithelial






cell signaling in







Helicobacter








pylori infection,







Fc epsilon RI






signaling






pathway, Fc






gamma R-






mediated






phagocytosis,






Focal adhesion,






Leukocyte






transendothelial






migration, MAPK






signaling






pathway,






Natural killer cell






mediated






cytotoxicity,






Neurotrophin






signaling






pathway, Non-






alcoholic fatty






liver disease






(NAFLD),






Osteoclast






differentiation,






Pancreatic






cancer,






Pancreatic






secretion,






Pathways in






cancer,






Phagosome,






PI3K-Akt






signaling






pathway,






Proteoglycans in






cancer, RAC1,






Rap1 signaling






pathway, Ras






signaling


650
1AXg7481.t1
2450
1BXg6855.t1
None
integral component of







membrane, membrane,







transmembrane transport


651
1AXg9624.t1
2451
1BXg7238.t1
None
anchored component of







membrane, carbohydrate







metabolic process, fungal-







type cell wall, hydrolase







activity, plasma membrane,







transferase activity


652
1AXg7771.t1
2452
1BXg7838.t1
None
proteolysis, serine-type







endopeptidase activity


653
1AXg1042.t1
2453
1BXg8113.t1
None
membrane


654
1AXg10247.t1
2454
1BXg3602.t1
None
None


493
1AXg12742.t1
2455
1BXg2905.t1
None
hydrolase activity,







hydrolyzing O-glycosyl







compounds, mycelium







development, organic







substance metabolic







process


655
1AXg15299.t1
2456
1BXg10457.t1
K07975
cellular bud, cytosol,







establishment or







maintenance of actin







cytoskeleton polarity,







establishment or







maintenance of cell polarity







regulating cell shape, GTP







binding, GTPase activity,







membrane, metabolic







process, microtubule







cytoskeleton organization,







nucleus, positive regulation







of exocytosis, positive







regulation of formin-







nucleated actin cable







assembly, protein







transport, regulation of cell







separation after cytokinesis,







small GTPase mediated







signal transduction


656
1AXg16181.t1
2457
1BXg12075.t1
E3.2.1.101
carbohydrate catabolic







process, hydrolase activity,







mannan endo-1,6-alpha-







mannosidase activity


657
1AXg4820.t1
2458
1BXg705.t1
None
None


658
1AXg4879.t1
2459
1BXg4499.t1
Amoebiasis,
cytosol, fungal-type vacuole






Endocytosis,
membrane, GTP binding,






Phagosome,
GTPase activity, intracellular






RAB7A,
protein transport,







Salmonella

mitochondrial outer






infection,
membrane,






Tuberculosis
nucleocytoplasmic







transport, piecemeal







microautophagy of nucleus,







plasma membrane, positive







regulation of vacuole







fusion, non-autophagic,







protein localization to







vacuole, regulation of







endocytosis, retrograde







transport, endosome to







Golgi, small GTPase







mediated signal







transduction, vacuolar







acidification, vacuole







inheritance, vesicle fusion







with vacuole


659
1AXg5864.t1
2460
1BXg10898.t1
APRT, apt,
adenine






Purine
phosphoribosyltransferase






metabolism
activity, adenine salvage,







AMP salvage, cytosol


660
1AXg8547.t1
2461
1BXg10270.t1
Ribosome, RPL10Ae,
large ribosomal subunit,






RPL10A
RNA binding, structural







constituent of ribosome,







translation


661
1AXg2128.t1
2462
1BXg11919.t1
None
carboxypeptidase activity,







membrane


662
1AXg7452.t1
2463
1BXg6885.t1
cdd, CDA, Drug
cytidine deaminase activity,






metabolism -
cytidine deamination,






other enzymes,
cytoplasm, zinc ion binding






Pyrimidine






metabolism


663
1AXg4563.t1
2464
1BXg4094.t1
ribH, RIB4,
6,7-dimethyl-8-






Riboflavin
ribityllumazine synthase






metabolism
activity, mitochondrial







intermembrane space,







riboflavin binding, riboflavin







biosynthetic process,







riboflavin synthase







complex, transferase







activity


664
1AXg10907.t1
2465
1BXg5915.t1
None
cytosol, GU repeat RNA







binding, intracellular part,







microsatellite binding,







nucleus, RNA binding,







sequence-specific DNA







binding, single-stranded







telomeric DNA binding


665
1AXg4299.t1
2466
1BXg1953.t1
Acute myeloid
GTP binding, GTPase






leukemia,
activity, intracellular,






Alcoholism,
intracellular protein






Aldosterone-
transport, metabolic






regulated
process, nucleocytoplasmic






sodium
transport, plasma






reabsorption,
membrane, small GTPase






Axon guidance, B
mediated signal






cell receptor
transduction






signaling






pathway,






Bladder cancer,






Central carbon






metabolism in






cancer,






Chemokine






signaling






pathway,






Choline






metabolism in






cancer,






Cholinergic






synapse, Chronic






myeloid






leukemia,






Colorectal






cancer, Dorso-






ventral axis






formation,






Endometrial






cancer, ErbB






signaling






pathway,






Estrogen






signaling






pathway, Fc






epsilon RI






signaling






pathway, FoxO






signaling






pathway, Gap






junction, Glioma,






GnRH signaling






pathway,






Hepatitis B,






Hepatitis C,






HTLV-I infection,






Insulin signaling






pathway, KRAS,






KRAS2, Long-






term depression,






Long-term






potentiation,






MAPK signaling






pathway, MAPK






signaling






pathway - fly,






Melanogenesis,






Melanoma,






MicroRNAs in






cancer, Natural






killer cell






mediated


666
1AXg9261.t1.
2467
1BXg10439.t1
E3.4.21.48
dibasic protein processing,







serine-type endopeptidase







activity


667
1AXg9193.t1
2468
1BXg8760.t1
None
chitosanase activity,







extracellular region,







polysaccharide catabolic







process


668
1AXg4669.t1
2469
1BXg10567.t1
None
hydrolase activity, acting on







carbon-nitrogen (but not







peptide) bonds, integral







component of membrane,







metabolic process


669
1AXg19989.t1
2470
1BXg9824.t1
glgB, Starch and
1,4-alpha-glucan branching






sucrose
enzyme activity, ATP






metabolism
binding, ATP hydrolysis







coupled proton transport,







ATP synthesis coupled







proton transport, cation







binding, cytoplasm,







glycogen biosynthetic







process, hydrolase activity,







hydrolyzing O-glycosyl







compounds, proton-







transporting ATP synthase







activity, rotational







mechanism, proton-







transporting ATP synthase







complex, catalytic core F(1)


670
1AXg2882.t1
2471
1BXg10869.t1
Glycerophospholipid
lysophospholipase activity,






metabolism,
phospholipid catabolic






PLB
process


671
1AXg5521.t1
2472
1BXg1647.t1
Ribosome, RPS4e,
ribosome, rRNA binding,






RPS4
structural constituent of







ribosome, translation


672
1AXg2908.t1
2473
1BXg6003.t1
AXL2
None


673
1AXg6960.t1
2474
1BXg9737.t1
None
aspartic-type







endopeptidase activity,







proteolysis

















SEQ ID


Fold-





Beneficial
A.mean
B.mean
change
absFC
FDR q-value







502
0
0.37
−8.5
8.5
0.03



487
0.3
0
8.2
8.2
0.02



503
0
0.24
−7.9
7.9
0.01



504
0
0.24
−7.9
7.9
0.02



505
0.16
0
7.4
7.4
0.05



506
0
0.13
−7.1
7.1
0.02



507
0
0.12
−6.9
6.9
0.01



508
0
0.12
−6.9
6.9
0.02



509
0
0.12
−6.9
6.9
0.03



510
0
0.12
−6.9
6.9
0.04



511
0
0.1
−6.7
6.7
0.02



512
0
0.1
−6.7
6.7
0.02



513
0
0.09
−6.6
6.6
0.02



514
0.1
0
6.6
6.6
0.02



515
0
0.1
−6.6
6.6
0.02



516
0
0.09
−6.6
6.6
0.02



517
0
0.09
−6.5
6.5
0.02



518
0.09
0
6.5
6.5
0.05



519
0
0.08
−6.4
6.4
0.02



520
0
0.09
−6.4
6.4
0.02



521
0.08
0
6.3
6.3
0.02



522
0
0.06
−6
6
0.01



523
0
0.24
−6
6
0.02



524
0
0.06
−6
6
0.03



525
0
0.06
−6
6
0.03



526
0
0.06
−6
6
0.04



494
0.23
0
5.9
5.9
0.02



527
0
0.06
−5.9
5.9
0.04



528
0.05
0
5.8
5.8
0.02



529
0
0.06
−5.8
5.8
0.02



530
0.05
0
5.8
5.8
0.02



531
0.06
0
5.8
5.8
0.03



532
0
0.05
−5.8
5.8
0.04



533
0
0.05
−5.7
5.7
0.02



534
0
0.05
−5.7
5.7
0.02



535
0
0.05
−5.7
5.7
0.03



536
0
0.05
−5.6
5.6
0.02



537
0
0.05
−5.6
5.6
0.02



538
0
0.05
−5.6
5.6
0.02



539
0
0.05
−5.6
5.6
0.03



540
0
0.05
−5.6
5.6
0.03



541
0
0.05
−5.5
5.5
0.02



542
0
0.04
−5.4
5.4
0.01



543
0
0.04
−5.4
5.4
0.04



544
0
0.04
−5.4
5.4
0.04



545
0
0.04
−5.3
5.3
0.02



546
0
0.04
−5.3
5.3
0.05



547
0
0.04
−5.2
5.2
0.02



548
0
0.04
−5.2
5.2
0.02



549
0
0.04
−5.2
5.2
0.02



550
0.03
0
5.1
5.1
0.02



551
0.01
0.19
−5
5
0.01



552
0
0.03
−5
5
0.02



553
0
0.03
−5
5
0.04



554
0
0.03
−4.9
4.9
0.02



555
0
0.03
−4.9
4.9
0.02



556
0
0.03
−4.9
4.9
0.03



557
0
0.03
−4.9
4.9
0.04



558
0
0.03
−4.9
4.9
0.04



559
0
0.03
−4.8
4.8
0.02



560
0
0.03
−4.8
4.8
0.02



561
0
0.03
−4.8
4.8
0.04



562
0
0.03
−4.7
4.7
0.02



563
0
0.02
−4.6
4.6
0.02



564
0
0.02
−4.5
4.5
0.02



565
0
0.02
−4.5
4.5
0.02



566
0.02
0
4.5
4.5
0.02



567
0.02
0
4.5
4.5
0.03



568
0
0.02
−4.5
4.5
0.03



569
0
0.02
−4.4
4.4
0.02



570
0
0.02
−4.4
4.4
0.03



478
0.98
0.05
4.4
4.4
0.04



571
0
0.02
−4.4
4.4
0.05



572
0.36
0.02
4.3
4.3
0.02



573
0
0.02
−4.3
4.3
0.02



574
0
0.02
−4.3
4.3
0.02



575
0
0.02
−4.3
4.3
0.04



576
0
0.02
−4.2
4.2
0.01



577
0
0.02
−4.2
4.2
0.05



578
0
0.02
−4.1
4.1
0.03



480
0.55
0.03
4
4
0.02



579
0.02
0
4
4
0.03



580
0.02
0
4
4
0.03



581
0.02
0
4
4
0.03



582
0
0.02
−4
4
0.04



583
0
0.02
−4
4
0.05



584
0
0.07
−3.9
3.9
0



585
0
0.07
−3.9
3.9
0



586
0
0.01
−3.9
3.9
0.02



587
0.06
0
3.9
3.9
0.03



588
0.01
0.09
−3.9
3.9
0.04



589
0
0.01
−3.8
3.8
0.02



590
0
0.01
−3.8
3.8
0.02



591
0
0.01
−3.8
3.8
0.03



592
0
0.01
−3.8
3.8
0.04



593
0.14
0.01
3.8
3.8
0.04



594
0
0.01
−3.7
3.7
0.02



595
0.01
0
3.7
3.7
0.02



596
0.01
0
3.7
3.7
0.02



597
0
0.01
−3.7
3.7
0.02



598
0
0.01
−3.7
3.7
0.03



599
0
0.01
−3.7
3.7
0.03



600
0.2
0.01
3.7
3.7
0.05



601
0
0.01
−3.6
3.6
0.03



602
0.05
0
3.6
3.6
0.04



603
0
0.01
−3.6
3.6
0.04



604
0.01
0
3.5
3.5
0.02



605
0
0.01
−3.5
3.5
0.03



606
0
0.01
−3.5
3.5
0.04



607
0
0.01
−3.5
3.5
0.04



608
0.02
0.17
−3.4
3.4
0.01



609
0.01
0
3.4
3.4
0.02



610
0
0.01
−3.4
3.4
0.02



611
0
0.01
−3.4
3.4
0.02



612
0
0.01
−3.4
3.4
0.02



613
0
0.01
−3.4
3.4
0.03



614
0.05
0.46
−3.3
3.3
0.02



615
0
0.01
−3.3
3.3
0.02



616
0
0.01
−3.3
3.3
0.02



617
0
0.01
−3.3
3.3
0.03



618
0.01
0
3.3
3.3
0.04



619
0
0.05
−3.2
3.2
0.01



620
0
0.01
−3.2
3.2
0.02



621
0
0.01
−3.2
3.2
0.02



622
0.01
0.1
−3.1
3.1
0



623
0.03
0
3.1
3.1
0.01



624
0
0.01
−3.1
3.1
0.02



625
0
0.01
−3.1
3.1
0.02



626
0
0.01
−3.1
3.1
0.02



627
0
0.01
−3.1
3.1
0.04



628
0
0.01
−3.1
3.1
0.05



629
0
0.01
−3.1
3.1
0.05



630
0.13
0.02
3
3
0.01



631
0
0.01
−3
3
0.02



632
0
0.01
−3
3
0.02



633
0.01
0
3
3
0.03



634
0
0.01
−3
3
0.04



635
0.1
0.01
2.9
2.9
0.01



636
0
0.01
−2.9
2.9
0.02



637
0
0.01
−2.9
2.9
0.05



638
0
0.01
−2.8
2.8
0.02



639
0
0.01
−2.8
2.8
0.05



482
0.53
0.08
2.7
2.7
0.02



640
0.01
0
2.7
2.7
0.02



641
0.01
0
2.7
2.7
0.02



642
0.01
0.06
−2.6
2.6
0.01



643
0.03
0
2.6
2.6
0.02



644
0.01
0
2.6
2.6
0.02



645
0.06
0.36
−2.5
2.5
0



646
0.01
0.05
−2.5
2.5
0.02



647
0
0
2.4
2.4
0.02



648
0
0
2.4
2.4
0.02



649
0
0
2.4
2.4
0.02



650
0
0
−2.4
2.4
0.02



651
0.01
0.06
−2.4
2.4
0.03



652
0.11
0.02
2.4
2.4
0.03



653
0.02
0.1
−2.3
2.3
0.01



654
0
0.02
−2.3
2.3
0.02



493
0.21
1.08
−2.3
2.3
0.02



655
0
0
2.3
2.3
0.02



656
0
0
−2.3
2.3
0.02



657
0.19
0.95
−2.3
2.3
0.02



658
0
0
2.3
2.3
0.02



659
0
0
2.3
2.3
0.02



660
0
0
2.3
2.3
0.02



661
0.02
0
2.2
2.2
0.01



662
0.09
0.02
2.2
2.2
0.03



663
0.02
0.08
−2.2
2.2
0.04



664
0
0
2.1
2.1
0.02



665
0
0
2.1
2.1
0.02



666
0.01
0.03
−2.1
2.1
0.02



667
0.17
0.04
2.1
2.1
0.02



668
0
0
−2.1
2.1
0.03



669
0
0
−2.1
2.1
0.05



670
0.06
0.01
2
2
0



671
0
0
2
2
0.02



672
0.02
0
2
2
0.02



673
0.1
0.03
2
2
0.05











This table describes the differential protein expression between pairs of orthologous proteins from a genus, where one member of the pair has a beneficial effect on plant growth and the other has a neutral effect. “A.mean” represents the average normalized spectral counts between biological replicates of the beneficial member of the pair. “B.mean” represents the average normalized spectral counts between biological replicates of the neutral member of the pair. “Fold change” represents the fold change difference between the two organisms. “FDR q-value” represents the false discovery rate corrected q-value.


A total of 892 proteins were detected across all Acremonium samples with two or more unique peptides at the false discovery rates indicated above.


SYM15774 Secreted Proteomic Analysis









TABLE 702







25 most abundant proteins secreted by SYM15774; “Median Abundance”


represents the median value across three biological replicates in units of


spectra per hundred spectra











SEQ

Median




ID
Protein ID
Abundance
GO Terms
KEGG Terms














4510
3AXg6236.t1
1.09684
GO: 0005576: extracellular region
none


4511
3AXg9048.t1
1.031017
GO: 0000287: magnesium ion
none





binding; GO: 0006400: tRNA





modification; GO: 0008193: tRNA





guanylyltransferase activity;





GO: 0016787: hydrolase activity


4512
3AXg678.t1
0.62687
GO: 0016787: hydrolase activity
none


4513
3AXg934.t1
0.558301
GO: 0003735: structural constituent
KEGG Orthology: K02927: RP-L40e,





of ribosome; GO: 0005840: ribosome;
RPL40: large subunit ribosomal





GO: 0006412: translation
protein L40e; KEGG PATHWAY:






ko03010: Ribosome:


4514
3AXg7460.t1
0.527389
GO: 0005886: plasma membrane;
none





GO: 0005975: carbohydrate





metabolic process; GO: 0016021:





integral component of membrane;





GO: 0016740: transferase activity;





GO: 0016787: hydrolase activity;





GO: 0031225: anchored component





of membrane


4515
3AXg10862.t1
0.523646
GO: 0004650: polygalacturonase
KEGG Orthology: K01213:





activity; GO: 0005576: extracellular
E3.2.1.67: galacturan 1,4-alpha-





region; GO: 0005975: carbohydrate
galacturonidase [EC: 3.2.1.67];





metabolic process; GO: 0071555: cell
KEGG PATHWAY: ko00040: Pentose





wall organization
and glucuronate interconversions:;






KEGG PATHWAY: ko00500: Starch






and sucrose metabolism:


4516
3AXg8590.t1
0.400556
GO: 0008061: chitin binding
KEGG Orthology: K00799: GST, gst:






glutathione S-transferase






[EC: 2.5.1.18]; KEGG PATHWAY:






ko00480: Glutathione metabolism:;






KEGG PATHWAY: ko00980:






Metabolism of xenobiotics by






cytochrome P450:; KEGG






PATHWAY: ko00982: Drug






metabolism - cytochrome P450:;






KEGG PATHWAY: ko05204:






Chemical carcinogenesis: It has






been estimated that exposure to






environmental chemical






carcinogens may contribute






significantly to the causation of a






sizable fraction, perhaps a majority,






of human cancers. Human






carcinogens act through a variety of






genotoxic and non-genotoxic






mechanisms. Genotoxic






carcinogens can attack biological






macromolecules such as DNA and






RNA either directly or indirectly






through metabolism, resulting in






the formation of adducts with






these macromolecules. If DNA






adducts escape cellular repair






mechanisms and persist, they may






lead to miscoding, resulting in






permanent mutations. Non-






genotoxic carcinogens act by the






mechanisms such as induction of






inflammation, immunosuppression,






formation of reactive oxygen






species, activation of receptors, and






epigenetic silencing. Together,






these genotoxic and non-genotoxic






mechanisms can alter signal-






transduction pathways that finally






result in hypermutability, genomic






instability, loss of proliferation






control, and resistance to apoptosis -






some of the characteristic






features of cancer cells.


4517
3AXg5014.t1
0.375314
GO: 0004553: hydrolase activity,
none





hydrolyzing O-glycosyl compounds;





GO: 0005975: carbohydrate





metabolic process


4518
3AXg2998.t1
0.374684
GO: 0016614: oxidoreductase
none





activity, acting on CH—OH group of





donors; GO: 0018130: heterocycle





biosynthetic process; GO: 0044550:





secondary metabolite biosynthetic





process; GO: 0050660: flavin adenine





dinucleotide binding; GO: 0055114:





oxidation-reduction process;





GO: 1901362: organic cyclic





compound biosynthetic process


4519
3AXg4073.t1
0.311962
GO: 0005975: carbohydrate
none





metabolic process; GO: 0016787:





hydrolase activity


4520
3AXg3348.t1
0.291735
GO: 0006629: lipid metabolic
none





process; GO: 0008081: phosphoric





diester hydrolase activity


4521
3AXg1507.t1
0.287808
GO: 0005886: plasma membrane;
none





GO: 0005975: carbohydrate





metabolic process; GO: 0016021:





integral component of membrane;





GO: 0016740: transferase activity;





GO: 0031225: anchored component





of membrane


4522
3AXg2571.t1
0.275402
GO: 0008152: metabolic process;
none





GO: 0016787: hydrolase activity


4523
3AXg9962.t1
0.272744
GO: 0016020: membrane
none


4524
3AXg965.t1
0.254561
GO: 0003723: RNA binding;
none





GO: 0004521: endoribonuclease





activity; GO: 0016020: membrane;





GO: 0090502: RNA phosphodiester





bond hydrolysis, endonucleolytic


4525
3AXg5987.t1
0.252385
GO: 0004252: serine-type
KEGG Orthology: K01279: TPP1,





endopeptidase activity; GO: 0005576:
CLN2: tripeptidyl-peptidase I





extracellular region; GO: 0006508:
[EC: 3.4.14.9]; KEGG PATHWAY:





proteolysis; GO: 0008240: tripeptidyl-
ko04142: Lysosome: Lysosomes are





peptidase activity
membrane-delimited organelles in






animal cells serving as the cell's






main digestive compartment to






which all sorts of macromolecules






are delivered for degradation. They






contain more than 40 hydrolases in






an acidic environment (pH of about






5). After synthesis in the ER,






lysosomal enzymes are decorated






with mannose-6-phosphate






residues, which are recognized by






mannose-6-phosphate receptors in






the trans-Golgi network. They are






packaged into clathrin-coated






vesicles and are transported to late






endosomes. Substances for






digestion are acquired by the






lysosomes via a series of processes






including endocytosis,






phagocytosis, and autophagy.


4526
3AXg8810.t1
0.232932
GO: 0004252: serine-type
KEGG Orthology: K01279: TPP1,





endopeptidase activity; GO: 0006508:
CLN2: tripeptidyl-peptidase I





proteolysis
[EC: 3.4.14.9]; KEGG PATHWAY:






ko04142: Lysosome: Lysosomes are






membrane-delimited organelles in






animal cells serving as the cell's






main digestive compartment to






which all sorts of macromolecules






are delivered for degradation. They






contain more than 40 hydrolases in






an acidic environment (pH of about






5). After synthesis in the ER,






lysosomal enzymes are decorated






with mannose-6-phosphate






residues, which are recognized by






mannose-6-phosphate receptors in






the trans-Golgi network. They are






packaged into clathrin-coated






vesicles and are transported to late






endosomes. Substances for






digestion are acquired by the






lysosomes via a series of processes






including endocytosis,






phagocytosis, and autophagy.


4527
3AXg1658.t1
0.226403
GO: 0016614: oxidoreductase
none





activity, acting on CH—OH group of





donors; GO: 0050660: flavin adenine





dinucleotide binding; GO: 0055114:





oxidation-reduction process


4528
3AXg2961.t1
0.220484
GO: 0016491: oxidoreductase
KEGG Orthology: K00505: TYR:





activity; GO: 0046872: metal ion
tyrosinase [EC: 1.14.18.1]; KEGG





binding; GO: 0055114: oxidation-
PATHWAY: ko00350: Tyrosine





reduction process
metabolism:; KEGG PATHWAY:






ko00740: Riboflavin metabolism:;






KEGG PATHWAY: ko00950:






Isoquinoline alkaloid biosynthesis:






Isoquinoline alkaloids are tyrosine-






derived plant alkaloids with an






isoquinoline skeleton. Among them






benzylisoquinoline alkaloids form






an important group with potent






pharmacological activity, including






analgesic compounds of morphine






and codeine, and anti-infective






agents of berberine, palmatine, and






magnoflorine. Biosynthesis of






isoquinoline alkaloids proceeds via






decarboxylation of tyrosine or






DOPA to yield dopamine, which






together with 4-






hydroxyphenylacetaldehyde, an






aldehyde derived from tyrosine, is






converted to reticuline, an






important precursor of various






benzylisoquinoline alkaloids.; KEGG






PATHWAY: ko00965: Betalain






biosynthesis: Betalains are water-






soluble nitrogen-containing






pigments that are present in plants






belonging to the order






Caryophyllales (such as cactus and






amaranth families) and in higher






fungi. They contain betalamic acid






as the chromophore and are






classified into two types:






betacyanins and betaxanthins.






Betacyanins contain a cyclo-DOPA






residue and exhibit red/violet






coloration, while betaxanthins






contain different amino acids or






amino side chains and exhibit a






yellow/orange coloration. The






condensation of betalamic acid






with amino acids (including cyclo-






DOPA or amines) in plants is a






spontaneous reaction, not an






enzyme-catalyzed reaction.; KEGG






PATHWAY: ko04916:






Melanogenesis: Cutaneous melanin






pigment plays a critical role in






camouflage, mimicry, social






communication, and protection






against harmful effects of solar






radiation. Melanogenesis is under






complex regulatory control by






multiple agents. The most






important positive regulator of






melanogenesis is the MC1 receptor






with its ligands melanocortic






peptides. MC1R activates the cyclic






AMP (cAMP) response-element






binding protein (CREB). Increased






expression of MITF and its






activation by phosphorylation (P)






stimulate the transcription of






tyrosinase (TYR), tyrosinase-related






protein 1 (TYRP1), and dopachrome






tautomerase (DCT), which produce






melanin. Melanin synthesis takes






place within specialized






intracellular organelles named






melanosomes. Melanin-containing






melanosomes then move from the






perinuclear region to the dendrite






tips and are transferred to






keratinocytes by a still not well-






characterized mechanism.


4529
3AXg1976.t1
0.215291
GO: 0004190: aspartic-type
none





endopeptidase activity; GO: 0006508:





proteolysis


4530
3AXg11128.t1
0.213705
GO: 0005619: ascospore wall;
none





GO: 0005783: endoplasmic





reticulum; GO: 0030476: ascospore





wall assembly


4531
3AXg4486.t1
0.20608
GO: 0008152: metabolic process;
none





GO: 0016491: oxidoreductase





activity; GO: 0016787: hydrolase





activity; GO: 0046872: metal ion





binding


4532
3AXg6046.t1
0.205931
GO: 0005975: carbohydrate
none





metabolic process; GO: 0008810:





cellulase activity


4533
3AXg3384.t1
0.192121
GO: 0003824: catalytic activity
none


4534
3AXg2856.t1
0.187827
GO: 0006508: proteolysis;
none





GO: 0008236: serine-type peptidase





activity









SYM15774 Versus SYM01331









TABLE 703







Differential secreted protein abundance between SYM15774 and SYM01331.
















SEQ ID

SEQ ID





Fold-
FDR q-


Beneficial
A. protein
Neutral
B. protein
KEGG
GO
A. mean
B. mean
change
value



















4535
3AXg4278.t1
4337
3BXg6074.t1
E3.1.1.73
carboxylic ester
0.136
0
7.1
1.20E−02







hydrolase activity


4536
3AXg230.t1
4338
3BXg7469.t1
Axon guidance, CFL, Fc
actin cortical patch,
0.041
0
5.4
1.20E−02






gamma R-mediated
actin filament






phagocytosis, Pertussis,
binding, actin






Regulation of actin
filament






cytoskeleton
depolymerization,







actin filament







severing, ATP







binding, cell division







site, cell tip,







endocytosis, Golgi to







plasma membrane







protein transport,







integral component







of membrane,







protein refolding


4537
3AXg6225.t1
4339
3BXg6585.t1
Arginine and proline
oxidation-reduction
0.028
0
4.9
1.20E−02






metabolism, beta-
process,






Alanine metabolism,
oxidoreductase






MPAO, PAO1
activity


4538
3AXg8418.t1
4340
3BXg7838.t1
None
flavin adenine
0.015
0
4
1.20E−02







dinucleotide binding,







oxidation-reduction







process,







oxidoreductase







activity, acting on







CH—OH group of







donors,







phosphatidylinositol







binding


4539
3AXg6767.t1
4341
3BXg3303.t1
None
cell wall, cell wall
0.045
0.003
3.4
1.20E−02







modification,







hydrolase activity,







acting on ester







bonds, metabolic







process,







pectinesterase







activity


4519
3AXg4073.t1
4342
3BXg8531.t1
None
carbohydrate
0.297
0.054
2.4
1.20E−02







metabolic process,







hydrolase activity


4540
3AXg10237.t1
4343
3BXg1101.t1
XEG
cellulase activity,
0.127
0.03
2
1.20E−02







polysaccharide







catabolic process


4541
3AXg6263.t1
4344
3BXg11238.t1
None
None
0.204
0.049
2
1.20E−02


4542
3AXg5745.t1
4345
3BXg6273.t1
None
fungal-type cell wall,
0.054
0.246
−2.2
1.20E−02







fungal-type vacuole,







metallopeptidase







activity, proteolysis


4543
3AXg10791.t1
4346
3BXg9786.t1
bglX, Cyanoamino acid
beta-glucosidase
0.003
0.094
−4.4
1.20E−02






metabolism,
activity,






Phenylpropanoid
carbohydrate






biosynthesis, Starch
metabolic process






and sucrose






metabolism


4544
3AXg7602.t1
4347
3BXg11695.t1
None
aspartic-type
0
0.06
−5.9
1.20E−02







endopeptidase







activity, proteolysis


4545
3AXg8955.t1
4348
3BXg2490.t1
None
None
0
0.132
−7.1
1.20E−02


4546
3AXg1865.t1
4349
3BXg9015.t1
None
carbohydrate
0
0.145
−7.2
1.20E−02







metabolic process,







hydrolase activity,







hydrolyzing O-







glycosyl compounds


4547
3AXg10977.t1
4350
3BXg7338.t1
None
None
0.062
0.009
2.6
1.30E−02


4548
3AXg8244.t1
4351
3BXg2216.t1
E3.4.11.10
aminopeptidase
0
0.003
−2
1.30E−02







activity, extracellular







region, metal ion







binding, nuclear







pore,







nucleocytoplasmic







transport,







proteolysis,







structural







constituent of







nuclear pore


4549
3AXg2047.t1
4352
3BXg7322.t1
E3.1.1.73
hydrolase activity,
0
0.007
−3
1.30E−02







metabolic process


4550
3AXg2487.t1
4353
3BXg4014.t1
CTSA, Lysosome,
proteolysis, serine-
0
0.018
−4.2
1.30E−02






Renin-
type






angiotensin system
carboxypeptidase







activity


4551
3AXg3683.t1
4354
3BXg679.t1
None
metallocarboxypeptidase
0
0.054
−5.8
1.30E−02







activity,







proteolysis, zinc ion







binding


4552
3AXg5735.t1
4355
3BXg6263.t1
E3.4.21.48
dibasic protein
0
0.07
−6.2
1.30E−02







processing, serine-







type endopeptidase







activity


4553
3AXg8371.t1
4356
3BXg11001.t1
E4.2.2.10
extracellular region,
0
0.171
−7.4
1.30E−02







pectin lyase activity,







polysaccharide







catabolic process


4554
3AXg8798.t1
4357
3BXg4519.t1
None
integral component
0.041
0
5.4
1.40E−02







of membrane,







membrane, negative







regulation of G2/M







transition of mitotic







cell cycle


4555
3AXg3404.t1
4358
3BXg4400.t1
None
choline
0.169
0.004
5
1.40E−02







dehydrogenase







activity, flavin







adenine dinucleotide







binding, oxidation-







reduction process


4556
3AXg3735.t1
4359
3BXg4453.t1
None
membrane
0.023
0
4.6
1.40E−02


4557
3AXg9146.t1
4360
3BXg2444.t1
None
integral component
0.017
0
4.2
1.40E−02







of membrane


4558
3AXg10088.t1
4361
3BXg1846.t1
None
endonuclease
0.075
0.009
3
1.40E−02







activity, exonuclease







activity, integral







component of







membrane, nucleic







acid phosphodiester







bond hydrolysis


4559
3AXg10485.t1
4362
3BXg821.t1
Amino sugar and
beta-N-
0.027
0.156
−2.5
1.40E−02






nucleotide sugar
acetylglucosaminidase






metabolism,
activity,






Glycosaminoglycan
carbohydrate






degradation,
metabolic process,






Glycosphingolipid
extracellular region,






biosynthesis - ganglio
N-acetylglucosamine






series,
catabolic process






Glycosphingolipid






biosynthesis - globo






series, HEXA_B,






Lysosome, Other






glycan degradation


4560
3AXg8514.t1
4363
3BXg7997.t1
None
choline
0.074
0.551
−2.9
1.40E−02







dehydrogenase







activity, flavin







adenine dinucleotide







binding, oxidation-







reduction process


4561
3AXg8930.t1
4364
3BXg5868.t1
None
integral component
0
0.008
−3.2
1.40E−02







of membrane


4562
3AXg6329.t1
4365
3BXg3212.t1
E1.1.99.1, betA, CHDH,
alcohol metabolic
0.039
0.388
−3.3
1.40E−02






Glycine, serine and
process, choline






threonine metabolism
dehydrogenase







activity, DNA binding,







flavin adenine







dinucleotide binding,







metal ion binding,







oxidation-reduction







process, regulation







of transcription,







DNA-templated


4563
3AXg9850.t1
4366
3BXg11232.t1
None
catalytic activity,
0
0.023
−4.6
1.40E−02







chromatin silencing







by small RNA,







cytosol, endoplasmic







reticulum unfolded







protein response,







nucleus


4564
3AXg1923.t1
4367
3BXg9196.t1
None
hydrolase activity,
0
0.033
−5.1
1.40E−02







metabolic process


4565
3AXg6350.t1
4368
3BXg12502.t1
None
proteolysis, serine-
0.015
0.67
−5.4
1.40E−02







type peptidase







activity


4566
3AXg9423.t1
4369
3BXg390.t1
Betalain biosynthesis,
ion binding,
0
0.048
−5.6
1.40E−02






Isoquinoline alkaloid
metabolic process,






biosynthesis,
metal ion binding,






Melanogenesis,
oxidation-reduction






Riboflavin metabolism,
process,






TYR, Tyrosine
oxidoreductase






metabolism
activity


4567
3AXg5033.t1
4370
3BXg7845.t1
None
cellular process,
0
0.098
−6.6
1.40E−02







membrane,







metabolic process,







single-organism







process


4568
3AXg4645.t1
4371
3BXg8440.t1
None
None
0
0.121
−6.9
1.40E−02


4527
3AXg1658.t1
4372
3BXg6710.t1
None
flavin adenine
0.219
0
7.8
1.50E−02







dinucleotide binding,







oxidation-reduction







process,







oxidoreductase







activity, acting on







CH—OH group of







donors


4569
3AXg8951.t1
4373
3BXg5043.t1
None
hydrolase activity,
0.169
0
7.4
1.50E−02







acting on ester







bonds, nucleic acid







metabolic process


4570
3AXg3962.t1
4374
3BXg2058.t1
None
flavin adenine
0.098
0
6.6
1.50E−02







dinucleotide binding,







oxidation-reduction







process,







oxidoreductase







activity, acting on







CH—OH group of







donors


4571
3AXg9121.t1
4375
3BXg2385.t1
E3.1.1.11, Pentose and
aspartyl esterase
0.098
0
6.6
1.50E−02






glucuronate
activity, cell wall, cell






interconversions,
wall modification,






Starch and sucrose
extracellular region,






metabolism
pectin catabolic







process,







pectinesterase







activity


4572
3AXg6312.t1
4376
3BXg3233.t1
None
flavin adenine
0.059
0
5.9
1.50E−02







dinucleotide binding,







oxidation-reduction







process,







oxidoreductase







activity, acting on







CH—OH group of







donors


4573
3AXg4810.t1
4377
3BXg1560.t1
E3.2.1.4, Starch and
carbohydrate
0.049
0
5.7
1.50E−02






sucrose metabolism
metabolic process,







hydrolase activity,







hydrolyzing O-







glycosyl compounds


4574
3AXg1577.t1
4378
3BXg3030.t1
None
hydrolase activity,
0.026
0
4.8
1.50E−02







metabolic process


4575
3AXg5120.t1
4379
3BXg10267.t1
EEF1B
cytosol, eukaryotic
0.015
0
4
1.50E−02







translation







elongation factor 1







complex, guanyl-







nucleotide exchange







factor activity,







maintenance of







translational fidelity,







negative regulation







of actin filament







bundle assembly,







positive regulation of







GTPase activity,







regulation of







translational







termination,







translation







elongation factor







activity, translational







elongation


4576
3AXg2881.t1
4380
3BXg6431.t1
msrA
cellular response to
0.005
0
2.7
1.50E−02







hydrogen peroxide,







cytosol, integral







component of







membrane, L-







methionine







biosynthetic process







from methionine







sulphoxide, L-







methionine-(S)-S-







oxide reductase







activity, nucleus,







oxidation-reduction







process, peptide-







methionine (S)-S-







oxide reductase







activity, protein







repair


4577
3AXg2995.t1
4381
3BXg8638.t1
Influenza A,
proteolysis, serine-
0.071
0.01
2.7
1.50E−02






Neuroactive ligand-
type endopeptidase






receptor interaction,
activity






Pancreatic secretion,






Protein digestion and






absorption, PRSS


4578
3AXg6701.t1
4382
3BXg7716.t1
Epstein-Barr virus
cytosol, GTP binding,
0.005
0
2.7
1.50E−02






infection, HTLV-I
GTPase activity,






infection, RAN,
intracellular'protein






Ribosome biogenesis in
transport,






eukaryotes, RNA
membrane,






transport
metabolic process,







negative regulation







of G2/M transition of







mitotic cell cycle,







nuclear pore,







nucleocytoplasmic







transport, small







GTPase mediated







signal transduction,







structural







constituent of







nuclear pore


4579
3AXg10558.t1
4383
3BXg10095.t1
None
None
0.005
0
2.6
1.50E−02


4580
3AXg9106.t1
4384
3BXg2351.t1
None
cytoplasm
0.004
0
2.3
1.50E−02


4581
3AXg573.t1
4385
3BXg5286.t1
None
aspartic-type
0.044
0.009
2.2
1.50E−02







endopeptidase







activity, membrane,







proteolysis


4525
3AXg5987.t1
4386
3BXg5319.t1
Lysosome, TPP1, CLN2
extracellular region,
0.261
0.057
2.2
1.50E−02







proteolysis, serine-







type endopeptidase







activity, tripeptidyl-







peptidase activity


4582
3AXg10624.t1
4387
3BXg1050.t1
None
choline
0.172
0.038
2.1
1.50E−02







dehydrogenase







activity, flavin







adenine dinucleotide







binding, integral







component of







membrane,







oxidation-reduction







process,







transmembrane







transport,







transporter activity


4520
3AXg3348.t1
4388
3BXg5195.t1
None
lipid metabolic
0.286
0.065
2.1
1.50E−02







process, phosphoric







diester hydrolase







activity


4583
3AXg1574.t1
4389
3BXg791.t1
None
ATP binding,
0.003
0
2
1.50E−02







calmodulin binding,







calmodulin-







dependent protein







kinase activity,







cytosol, glucose







catabolic process,







manganese ion







binding, negative







regulation of







calcineurin-NFAT







signaling cascade,







negative regulation







of G2/M transition of







mitotic cell cycle,







negative regulation







of transcription by







transcription factor







localization, negative







regulation of







transcription from







RNA polymerase II







promoter, nucleus,







phosphoglycerate







mutase activity,







protein







phosphorylation,







regulation of nuclear







division


4584
3AXg3704.t1
4390
3BXg4116.t1
None
None
0.04
0.176
−2.1
1.50E−02


4585
3AXg7050.t1
4391
3BXg10636.t1
E3.2.1.101
catalytic activity,
0.014
0.064
−2.1
1.50E−02







hydrolase activity


4586
3AXg11147.t1
4392
3BXg3457.t1
None
defense response to
0.01
0.065
−2.6
1.50E−02







bacterium, defense







response to fungus,







spore wall


4587
3AXg809.t1
4393
3BXg9916.t1
None
acetyltransferase
0
0.016
−4.1
1.50E−02







activity, metabolic







process, transferase







activity


4588
3AXg1606.t1
4394
3BXg8171.t1
Betalain biosynthesis,
metabolic process,
0
0.038
−5.3
1.50E−02






Isoquinoline alkaloid
N-acetyltransferase






biosynthesis,
activity, oxidation-






Melanogenesis,
reduction process,






Riboflavin metabolism,
oxidoreductase






TYR, Tyrosine
activity, transferase






metabolism
activity, transferring







acyl groups


4589
3AXg5600.t1
4395
3BXg3227.t1
None
None
0
0.086
−6.4
1.50E−02


4590
3AXg676.t1
4396
3BXg6951.t1
None
None
0
0.319
−8.3
1.50E−02


4591
3AXg8215.t1
4397
3BXg2453.t1
None
None
0.002
0.054
−4.3
1.70E−02


4592
3AXg4581.t1
4398
3BXg7071.t1
None
hydrolase activity,
0.076
0
6.3
1.80E−02







metabolic process


4593
3AXg3000.t1
4399
3BXg8643.t1
None
flavin adenine
0
0.042
−5.4
1.80E−02







dinucleotide binding,







oxidation-reduction







process,







oxidoreductase







activity,







oxidoreductase







activity, acting on







CH—OH group of







donors


4594
3AXg3931.t1
4400
3BXg1983.t1
None
choline
0.081
0
6.4
1.90E−02







dehydrogenase







activity, flavin







adenine dinucleotide







binding, oxidation-







reduction process


4595
3AXg3946.t1
4401
3BXg1965.t1
None
copper ion binding,
0.025
0
4.7
1.90E−02







oxidation-reduction







process,







oxidoreductase







activity


4596
3AXg1894.t1
4402
3BXg9149.t1
None
carbohydrate
0.016
0
4
2.00E−02







metabolic process,







catalytic activity


4597
3AXg3686.t1
4403
3BXg689.t1
None
copper ion binding,
0.022
0.166
−2.9
2.00E−02







oxidation-reduction







process,







oxidoreductase







activity


4598
3AXg9632.t1
4404
3BXg8688.t1
None
beta-N-
0
0.026
−4.8
2.00E−02







acetylhexosaminidase







activity,







carbohydrate







metabolic process,







integral component







of membrane


4599
3AXg7875.t1
4405
3BXg925.t1
E3.1.3.25, IMPA, suhB,
DNA binding, integral
0
0.031
−5
2.00E−02






Inositol phosphate
component of






metabolism,
membrane,






Phosphatidylinositol
phosphatidylinositol






signaling system,
phosphorylation






Streptomycin






biosynthesis


4600
3AXg6708.t1
4406
3BXg7541.t1
None
membrane
0
0.036
−5.2
2.00E−02


4601
3AXg7523.t1
4407
3BXg2252.t1
None
hydrolase activity,
0.029
0.007
2
2.10E−02







metabolic process


4602
3AXg9481.t1
4408
3BXg11985.t1
Amino sugar and
carbohydrate
0.059
0.345
−2.5
2.10E−02






nucleotide sugar
metabolic process,






metabolism, E3.2.1.14
chitin catabolic







process, chitinase







activity, hydrolase







activity, hydrolyzing







O-glycosyl







compounds, organic







substance metabolic







process, transferase







activity, transferring







glycosyl groups


4603
3AXg11091.t1
4409
3BXg13016.t1
None
hydrolase activity,
0
0.007
−3
2.10E−02







hydrolyzing O-







glycosyl compounds,







metabolic process


4604
3AXg505.t1
4410
3BXg6843.t1
Amino sugar and
ATP binding,
0
0.011
−3.6
2.10E−02






nucleotide sugar
carbohydrate






metabolism, Butirosin
phosphorylation,






and neomycin
cellular glucose






biosynthesis,
homeostasis, cytosol,






Carbohydrate digestion
fructokinase activity,






and absorption, Carbon
fructose 6-phosphate






metabolism, Central
metabolic process,






carbon metabolism in
glucokinase activity,






cancer, Fructose and
glucose 6-phosphate






mannose metabolism,
metabolic process,






Galactose metabolism,
glucose binding,






Glycolysis/
glycolytic






Gluconeogenesis, HIF-1
fermentation,






signaling pathway, HK,
glycolytic process,






Insulin signaling
integral component






pathway, Starch and
of membrane,






sucrose metabolism,
mannokinase






Streptomycin
activity, mannose






biosynthesis, Type II
metabolic process,






diabetes mellitus
nuclear pore,







nucleocytoplasmic







transport, structural







constituent of







nuclear pore


4605
3AXg671.t1
4411
3BXg6947.t1
None
FMN binding,
0
0.015
−4
2.10E−02







membrane,







oxidation-reduction







process,







oxidoreductase







activity


4606
3AXg907.t1
4412
3BXg10711.t1
None
None
0
0.048
−5.6
2.10E−02


4607
3AXg10465.t1
4413
3BXg14385.t1
E3.2.1.58, Starch and
carbohydrate
0
0.235
−7.9
2.10E−02






sucrose metabolism
metabolic process,







hydrolase activity,







hydrolyzing O-







glycosyl compounds,







integral component







of membrane,







transmembrane







transport


4608
3AXg1008.t1
4414
3BXg9515.t1
None
choline
0.068
0
6.1
2.20E−02







dehydrogenase







activity, flavin







adenine dinucleotide







binding, oxidation-







reduction process


4609
3AXg2591.t1
4415
3BXg1833.t1
Betalain biosynthesis,
metal ion binding,
0.126
0.023
2.4
2.20E−02






Isoquinoline alkaloid
oxidation-reduction






biosynthesis,
process,






Melanogenesis,
oxidoreductase






Riboflavin metabolism,
activity






TYR, Tyrosine






metabolism


4610
3AXg4824.t1
4416
3BXg1527.t1
None
None
0.04
0
5.4
2.30E−02


4518
3AXg2998.t1
4417
3BXg8641.t1
None
flavin adenine
0.37
0.038
3.3
2.30E−02







dinucleotide binding,







heterocycle







biosynthetic process,







organic cyclic







compound







biosynthetic process,







oxidation-reduction







process,







oxidoreductase







activity, acting on







CH—OH group of







donors, secondary







metabolite







biosynthetic process


4611
3AXg8768.t1
4418
3BXg429.t1
None
hydrolase activity,
0.011
0.145
−3.6
2.30E−02







metabolic process


4612
3AXg11131.t1
4419
3BXg7381.t1
None
None
0
0.021
−4.5
2.30E−02


4613
3AXg3576.t1
4420
3BXg5515.t1
None
None
0
0.063
−6
2.30E−02


4614
3AXg10565.t1
4421
3BXg10107.t1
None
metallocarboxypeptidase
0.016
0
4.1
2.50E−02







activity,







proteolysis, zinc ion







binding


4615
3AXg4536.t1
4422
3BXg3121.t1
Galactose metabolism,
carbohydrate
0.047
0.003
3.8
2.50E−02






malZ, Starch and
binding,






sucrose metabolism
carbohydrate







metabolic process,







cellular process,







glucosidase activity,







hydrolase activity,







hydrolyzing O-







glycosyl compounds,







integral component







of membrane


4616
3AXg4165.t1
4423
3BXg6890.t1
bglX, Cyanoamino acid
hydrolase activity,
0
0.01
−3.4
2.50E−02






metabolism,
hydrolyzing O-






Phenylpropanoid
glycosyl compounds,






biosynthesis, Starch
integral component






and sucrose
of membrane,






metabolism
polysaccharide







catabolic process


4617
3AXg8420.t1
4424
3BXg7817.t1
yteR, yesR
hydrolase activity,
0.007
0.147
−4.3
2.50E−02







metabolic process


4618
3AXg6634.t1
4425
3BXg5671.t1
None
acid phosphatase
0.004
0.022
−2.1
2.60E−02







activity,







dephosphorylation


4619
3AXg5462.t1
4426
3BXg503.t1
None
carbohydrate
0
0.03
−5
2.60E−02







metabolic process,







hydrolase activity


4620
3AXg9660.t1
4427
3BXg10410.t1
None
copper ion binding,
0
0.032
−5
2.60E−02







oxidation-reduction







process,







oxidoreductase







activity


4621
3AXg736.t1
4428
3BXg7066.t1
None
biosynthetic process,
0
0.062
−6
2.60E−02







carbohydrate







metabolic process,







cellulose binding,







extracellular region,







hydrolase activity,







hydrolyzing O-







glycosyl compounds,







positive regulation of







GTPase activity,







pyridoxal phosphate







binding, regulation of







Rho protein signal







transduction, Rho







guanyl-nucleotide







exchange factor







activity


4622
3AXg3304.t1
4429
3BXg5239.t1
None
None
0.07
0
6.1
2.70E−02


4511
3AXg9048.t1
4430
3BXg11565.t1
None
hydrolase activity,
0.974
0.079
3.6
2.70E−02







magnesium ion







binding, tRNA







guanylyltransferase







activity, tRNA







modification


4623
3AXg2688.t1
4431
3BXg10864.t1
AMPK signaling
6-phosphofructo-2-
0.01
0
3.5
2.70E−02






pathway, Fructose and
kinase activity, ATP






mannose metabolism,
binding,






HIF-1 signaling
carbohydrate






pathway, PFKFB
phosphorylation,







cytosol,







dephosphorylation,







fructose 2,6-







bisphosphate







metabolic process,







fructose metabolic







process, fructose-







2,6-bisphosphate 2-







phosphatase activity


4624
3AXg9670.t1
4432
3BXg5175.t1
CTSA, Lysosome,
fungal-type vacuole,
0.005
0.046
−3
2.70E−02






Renin-
nuclear pore,






angiotensin system
nucleocytoplasmic







transport,







phytochelatin







biosynthetic process,







proteolysis, serine-







type







carboxypeptidase







activity, structural







constituent of







nuclear pore


4625
3AXg2904.t1
4433
3BXg6481.t1
E3.2.1.58, Starch and
carbohydrate
0
0.021
−4.5
2.70E−02






sucrose metabolism
metabolic process,







hydrolase activity,







hydrolyzing O-







glycosyl compounds,







membrane part


4626
3AXg10815.t1
4434
3BXg9780.t1
None
heme binding,
0.125
0
7
2.90E−02







oxidation-reduction







process, peroxidase







activity, response to







oxidative stress


4627
3AXg2002.t1
4435
3BXg2128.t1
CNBP
nucleic acid binding,
0.026
0
4.8
3.10E−02







zinc ion binding


4628
3AXg3713.t1
4436
3BXg4131.t1
None
hydrolase activity,
0.026
0
4.7
3.10E−02







metabolic process


4629
3AXg3872.t1
4437
3BXg4226.t1
COPB1, SEC26
COPI vesicle coat,
0.022
0
4.5
3.10E−02







cytosol, ER to Golgi







transport vesicle, ER







to Golgi vesicle-







mediated transport,







intracellular protein







transport, kinase







activity,







phosphorylation,







structural molecule







activity


4630
3AXg6318.t1
4438
3BXg3226.t1
None
hydrolase activity,
0.012
0
3.7
3.10E−02







hydrolase activity,







acting on glycosyl







bonds, organic







substance metabolic







process,







oxidoreductase







activity, primary







metabolic process,







single-organism







metabolic process


4631
3AXg10010.t1
4439
3BXg11186.t1
None
dephosphorylation,
0
0.088
−6.5
3.10E−02







phosphatase activity


4632
3AXg1263.t1
4440
3BXg1724.t1
None
chitin binding,
0.03
0
4.9
3.20E−02







copper ion binding,







oxidation-reduction







process,







oxidoreductase







activity


4633
3AXg8122.t1
4441
3BXg9830.t1
None
None
0.024
0
4.6
3.20E−02


4515
3AXg10862.t1
4442
3BXg9632.t1
E3.2.1.67, Pentose and
carbohydrate
0.552
0.095
2.5
3.20E−02






glucuronate
metabolic process,






interconversions,
cell wall






Starch and sucrose
organization,






metabolism
extracellular region,







polygalacturonase







activity


4634
3AXg5813.t1
4443
3BXg1361.t1
Ascorbate and aldarate
hydrolase activity,
0
0.12
−6.9
3.40E−02






metabolism,
metabolic process






Caprolactam






degradation, Carbon






metabolism,






Degradation of






aromatic compounds,






E3.1.1.17, gnl, RGN,






Pentose phosphate






pathway


4635
3AXg2285.t1
4444
3BXg5413.t1
None
heme binding,
0.045
0
5.5
3.60E−02







integral component







of membrane,







oxidation-reduction







process, peroxidase







activity, response to







oxidative stress


4636
3AXg3048.t1
4445
3BXg8570.t1
None
copper ion binding,
0
0.01
−3.5
3.60E−02







endoplasmic







reticulum, ferrous







iron import into cell,







metal ion binding,







oxidation-reduction







process,







oxidoreductase







activity


4637
3AXg3573.t1
4446
3BXg5567.t1
None
None
0
0.019
−4.4
3.60E−02


4638
3AXg457.t1
4447
3BXg2952.t1
gcvH, GCSH, Glycine,
glycine cleavage
0.039
0
5.3
3.90E−02






serine and threonine
complex, glycine






metabolism, Glyoxylate
decarboxylation via






and dicarboxylate
glycine cleavage






metabolism
system,







mitochondrion, one-







carbon metabolic







process, oxidation-







reduction process,







protein lipoylation


4639
3AXg2903.t1
4448
3BXg6482.t1
None
None
0
0.017
−4.1
3.90E−02


4640
3AXg10837.t1
4449
3BXg9608.t1
None
cellular process,
0
0.043
−5.5
3.90E−02







membrane part,







pectin catabolic







process, pectin lyase







activity


4641
3AXg10151.t1
4450
3BXg10552.t1
None
1,3-beta-
0.058
0
5.9
4.10E−02







glucanosyltransferase







activity, anchored







component of







membrane,







ascospore wall







assembly,







carbohydrate







metabolic process,







endoplasmic







reticulum, hydrolase







activity, integral







component of







membrane, plasma







membrane


4642
3AXg9889.t1
4451
3BXg7932.t1
None
extracellular region,
0.009
0
3.4
4.10E−02







mannan catabolic







process, mannan







endo-1,4-beta-







mannosidase activity


4643
3AXg6766.t1
4452
3BXg3304.t1
None
integral component
0.061
0
6
4.20E−02







of membrane,







transmembrane







transport


4644
3AXg9025.t1
4453
3BXg3854.t1
None
carbon-nitrogen
0.015
0
4
4.20E−02







ligase activity, with







glutamine asamido-







N-donor, metabolic







process, transferase







activity


4645
3AXg9960.t1
4454
3BXg7994.t1
ABC.MR
ATP binding, ATPase
0
0.041
−5.4
4.20E−02







activity, coupled to







transmembrane







movement of







substances, integral







component of







membrane,







isomerase activity,







metabolic process,







mitochondrion,







transmembrane







transport


4646
3AXg8755.t1
4455
3BXg86.t1
None
acid phosphatase
0.011
0
3.6
4.30E−02







activity,







dephosphorylation,







heme binding,







integral component







of membrane, iron







ion binding,







membrane,







oxidation-reduction







process,







oxidoreductase







activity, acting on







paired donors, with







incorporation or







reduction of







molecular oxygen


4647
3AXg1998.t1
4456
3BXg2125.t1
None
aminopeptidase
0
0.019
−4.3
4.30E−02







activity, integral







component of







membrane,







metallopeptidase







activity, proteolysis,







zinc ion binding


4648
3AXg4651.t1
4457
3BXg12484.t1
Nicotinate and
hydrolase activity,
0.031
0
5
4.40E−02






nicotinamide
integral component






metabolism, Purine
of membrane,






metabolism, Pyrimidine
metabolic process,






metabolism, surE
substrate-specific







transmembrane







transporter activity,







transmembrane







transport


4649
3AXg1281.t1
4458
3BXg5746.t1
Antigen processing and
ATP binding
0.027
0
4.8
4.50E−02






presentation,






Endocytosis, Epstein-






Barr virus infection,






Estrogen signaling






pathway, HSPA1_8,






Influenza A,






Legionellosis, MAPK






signaling pathway,






Measles, Protein






processing in






endoplasmic reticulum,






Spliceosome,






Toxoplasmosis


4650
3AXg2954.t1
4459
3BXg10202.t1
None
cutiriase activity,
0.02
0
4.4
4.50E−02







extracellular region,







metabolic process


4651
3AXg8116.t1
4460
3BXg9765.t1
E3.2.1.8, xynA
endo-1,4-beta-
0
0.047
−5.6
4.50E−02







xylanase activity,







polysaccharide







catabolic process


4652
3AXg9229.t1
4461
3BXg511.t1
None
cell cycle, cell
0.02
0
4.4
4.60E−02







division, cyclin-







dependent protein







serine/threonine







kinase regulator







activity, integral







component of







membrane,







regulation of protein







kinase activity


4653
3AXg5237.t1
4462
3BXg5596.t1
Aminobenzoate
metabolic process,
0.067
0
6.1
4.70E−02






degradation, Folate
oxidation-reduction






biosynthesis, phoD,
process






Two-component






system


4654
3AXg9949.t1
4463
3BXg5805.t1
None
None
0.061
0
6
5.00E−02


4655
3AXg11247.t1
4464
3BXg648.t1
None
integral component
0.009
0
3.3
5.00E−02







of membrane


4656
3AXg9208.t1
4465
3BXg534.t1
None
integral component
0.011
0.168
−3.8
5.00E−02







of membrane,







membrane


4657
3AXg7858.t1
4466
3BXg1035.t1
None
flavin adenine
0
0.076
−6.3
5.00E−02







dinucleotide binding,







membrane,







oxidation-reduction







process,







oxidoreductase







activity, acting on







CH—OH group of







donors










This table describes the differential protein expression between pairs of orthologous proteins from a genus, where one member of the pair has a beneficial effect on plant growth and the other has a neutral effect. “A.mean” represents the average normalized spectral counts between biological replicates of the beneficial member of the pair. “B.mean” represents the average normalized spectral counts between biological replicates of the neutral member of the pair. “Fold change” represents the fold change difference between the two organisms. “FDR q-value” represents the false discovery rate corrected q-value.


A total of 697 proteins were detected across all Phoma samples with two or more unique peptides at the false discovery rates indicated above.


SYM01004 Secreted Proteomic Analysis









TABLE 704







25 most abundant proteins secreted by SYM01004; “Median Abundance”


represents the median value across three biological replicates in units of


spectra per hundred spectra











SEQ
Protein
Median




ID
ID
Abundance
GO Terms
KEGG Terms














4742
5AYg748.t1
0.999348
GO: 0005198: structural
KEGG Orthology: K02406: fliC: flagellin; KEGG





molecule activity;
PATHWAY: ko02020: Two-component system:





GO: 0005576: extracellular
Two-component signal transduction systems





region; GO: 0009420:
enable bacteria to sense, respond, and adapt to





bacterial-type flagellum
changes in their environment or in their





filament; GO: 0071973:
intracellular state. Each two-component system





bacterial-type flagellum-
consists of a sensor protein-histidine kinase (HK)





dependent cell motility
and a response regulator (RR). In the






prototypical two-component pathway, the






sensor HK phosphorylates its own conserved His






residue in response to a signal(s) in the






environment. Subsequently, the phosphoryl






group of HK is transferred onto a specific Asp






residue on the RR. The activated RR can then






effect changes in cellular physiology, often by






regulating gene expression. Two-component






pathways thus often enable cells to sense and






respond to stimuli by inducing changes in






transcription.; KEGG PATHWAY: ko02040:






Flagellar assembly:; KEGG PATHWAY: ko04626:






Plant-pathogen interaction: Plants lack animal-






like adaptive immunity mechanisms, and






therefore have evolved a specific system with






multiple layers against invading pathogens. The






primary response includes the perception of






pathogens by cell-surface pattern-recognition






receptors (PRRs) and is referred to as PAMP-






triggered immunity (PTI). Activation of FLS2 and






EFR triggers MAPK signaling pathway that






activates defense genes for antimictobial






compounds. The increase in the cytosolic Ca2+






concentration is also a regulator for production






of reactive oxygen species and localized






programmed cell death/hypersensitive






response. The secondary response is called






effector-triggered immunity (ETI). Pathogens






can acquire the ability to suppress PTI by






directly injecting effector proteins into the plant






cell through secretion systems. In addition,






pathogens can manipulate plant hormone






signaling pathways to evade host immune






responses using coronatine toxin. Some plants






possess specific intracellular surveillance






proteins (R proteins) to monitor the presence of






pathogen virulence proteins. This ETI occurs






with localized programmed cell death to arrest






pathogen growth, resulting in cultivar-specific






disease resistance.; KEGG PATHWAY: ko05132:







Salmonella infection: Salmonella infection







usually presents as a self-limiting gastroenteritis






or the more severe typhoid fever and






bacteremia. The common disease-causing







Salmonella species in human is a single species,








Salmonella enterica, which has numerous







serovars.; KEGG PATHWAY: ko05134:






Legionellosis: Legionellosis is a potentially fatal






infectious disease caused by the bacterium







Legionella pneumophila and other legionella







species. Two distinct clinical and






epidemiological syndromes are associated with







Legionella species: Legionnaires' disease is the







more severe form of the infection, which may






involve pneumonia, and Pontiac fever is a






milder respiratory illness.


4743
5AYg747.t1
0.973878
GO: 0005198: structural
KEGG Orthology: K02406: fliC: flagellin; KEGG





molecule activity;
PATHWAY: ko02020: Two-component system:





GO: 0005576: extracellular
Two-component signal transduction systems





region; GO: 0009420:
enable bacteria to sense, respond, and adapt to





bacterial-type flagellum
changes in their environment or in their





filament; GO: 0071973:
intracellular state. Each two-component system





bacterial-type flagellum-
consists of a sensor protein-histidine kinase (HK)





dependent cell motility
and a response regulator (RR). In the






prototypical two-component pathway, the






sensor HK phosphorylates its own conserved His






residue in response to a signal(s) in the






environment. Subsequently, the phosphoryl






group of HK is transferred onto a specific Asp






residue on the RR. The activated RR can then






effect changes in cellular physiology, often by






regulating gene expression. Two-component






pathways thus often enable cells to sense and






respond to stimuli by inducing changes in






transcription.; KEGG PATHWAY: ko02040:






Flagellar assembly:; KEGG PATHWAY: ko04626:






Plant-pathogen interaction: Plants lack animal-






like adaptive immunity mechanisms, and






therefore have evolved a specific system with






multiple layers against invading pathogens. The






primary response includes the perception of






pathogens by cell-surface pattern-recognition






receptors (PRRs) and is referred to as PAMP-






triggered immunity (PTI). Activation of FLS2 and






EFR triggers MAPK signaling pathway that






activates defense genes for antimictobial






compounds. The increase in the cytosolic Ca2+






concentration is also a regulator for production






of reactive oxygen species and localized






programmed cell death/hypersensitive






response. The secondary response is called






effector-triggered immunity (ETI). Pathogens






can acquire the ability to suppress PTI by






directly injecting effector proteins into the plant






cell through secretion systems. In addition,






pathogens can manipulate plant hormone






signaling pathways to evade host immune






responses using coronatine toxin. Some plants






possess specific intracellular surveillance






proteins (R proteins) to monitor the presence of






pathogen virulence proteins. This ETI occurs






with localized programmed cell death to arrest






pathogen growth, resulting in cultivar-specific






disease resistance.; KEGG PATHWAY: ko05132:







Salmonella infection: Salmonella infection







usually presents as a self-limiting gastroenteritis






or the more severe typhoid fever and






bacteremia. The common disease-causing







Salmonella species in human is a single species,








Salmonella enterica, which has numerous







serovars.; KEGG PATHWAY: ko05134:






Legionellosis: Legionellosis is a potentially fatal






infectious disease caused by the bacterium







Legionella pneumophila and other legionella







species. Two distinct clinical and






epidemiological syndromes are associated with







Legionella species: Legionnaires' disease is the







more severe form of the infection, which may






involve pneumonia, and Pontiac fever is a






milder respiratory illness.


4744
5AYg746.t1
0.393566
GO: 0005198: structural
KEGG Orthology: K02406: fliC: flagellin; KEGG





molecule activity;
PATHWAY: ko02020: Two-component system:





GO: 0005576: extracellular
Two-component signal transduction systems





region; GO: 0009420:
enable bacteria to sense, respond, and adapt to





bacterial-type flagellum
changes in their environment or in their





filament; GO: 0071973:
intracellular state. Each two-component system





bacterial-type flagellum-
consists of a sensor protein-histidine kinase (HK)





dependent cell motility
and a response regulator (RR). In the






prototypical two-component pathway, the






sensor HK phosphorylates its own conserved His






residue in response to a signal(s) in the






environment. Subsequently, the phosphoryl






group of HK is transferred onto a specific Asp






residue on the RR. The activated RR can then






effect changes in cellular physiology, often by






regulating gene expression. Two-component






pathways thus often enable cells to sense and






respond to stimuli by inducing changes in






transcription.; KEGG PATHWAY: ko02040:






Flagellar assembly:; KEGG PATHWAY: ko04626:






Plant-pathogen interaction: Plants lack animal-






like adaptive immunity mechanisms, and






therefore have evolved a specific system with






multiple layers against invading pathogens. The






primary response includes the perception of






pathogens by cell-surface pattern-recognition






receptors (PRRs) and is referred to as PAMP-






triggered immunity (PTI). Activation of FLS2 and






EFR triggers MAPK signaling pathway that






activates defense genes for antimictobial






compounds. The increase in the cytosolic Ca2+






concentration is also a regulator for production






of reactive oxygen species and localized






programmed cell death/hypersensitive






response. The secondary response is called






effector-triggered immunity (ETI). Pathogens






can acquire the ability to suppress PTI by






directly injecting effector proteins into the plant






cell through secretion systems. In addition,






pathogens can manipulate plant hormone






signaling pathways to evade host immune






responses using coronatine toxin. Some plants






possess specific intracellular surveillance






proteins (R proteins) to monitor the presence of






pathogen virulence proteins. This ETI occurs






with localized programmed cell death to arrest






pathogen growth, resulting in cultivar-specific






disease resistance.; KEGG PATHWAY: ko05132:







Salmonella infection: Salmonella infection







usually presents as a self-limiting gastroenteritis






or the more severe typhoid fever and






bacteremia. The common disease-causing







Salmonella species in human is a single species,








Salmonella enterica, which has numerous







serovars.; KEGG PATHWAY: ko05134:






Legionellosis: Legionellosis is a potentially fatal






infectious disease caused by the bacterium







Legionella pneumophila and other legionella







species. Two distinct clinical and






epidemiological syndromes are associated with







Legionella species: Legionnaires' disease is the







more severe form of the infection, which may






involve pneumonia, and Pontiac fever is a






milder respiratory illness.


4745
5AYg329.t1
0.208236
GO: 0004519: endonuclease
KEGG Orthology: K00940: ndk, NME:





activity; GO: 0004550:
nucleoside-diphosphate kinase [EC: 2.7.4.6];





nucleoside diphosphate
KEGG PATHWAY: ko00230: Purine metabolism:;





kinase activity;
KEGG PATHWAY: ko00240: Pyrimidine





GO: 0005524: ATP binding;
metabolism:





GO: 0005737: cytoplasm;





GO: 0006165: nucleoside





diphosphate





phosphorylation;





GO: 0006183: GTP





biosynthetic process;





GO: 0006228: UTP





biosynthetic process;





GO: 0006241: CTP





biosynthetic process;





GO: 0046872: metal ion





binding; GO: 0090305:





nucleic acid phosphodiester





bond hydrolysis


4746
5AYg1483.t1
0.204231
GO: 0015288: porin activity;
none





GO: 0016020: membrane;





GO: 0055085:





transmembrane transport


4747
5AYg1901.t1
0.201732
GO: 0004970: ionotropic
KEGG Orthology: K02030: ABC.PA.S: polar





glutamate receptor activity;
amino acid transport system substrate-binding





GO: 0006810: transport;
protein





GO: 0016020: membrane;





GO: 0030288: outer





membrane-bounded





periplasmic space;





GO: 0035235: ionotropic





glutamate receptor





signaling pathway


4748
5AYg2621.t1
0.184662
GO: 0003735: structural
KEGG Orthology: K02884: RP-L19, MRPL19, rplS:





constituent of ribosome;
large subunit ribosomal protein L19; KEGG





GO: 0005840: ribosome;
PATHWAY: ko03010: Ribosome:





GO: 0006412: translation


4749
5AYg1882.t1
0.177
GO: 0003735: structural
KEGG Orthology: K02879: RP-L17, MRPL17,





constituent of ribosome;
rplQ: large subunit ribosomal protein L17; KEGG





GO: 0005840: ribosome;
PATHWAY: ko03010: Ribosome:





GO: 0006412: translation


4750
5AYg89.t1
0.175201
GO: 0000049: tRNA binding;
KEGG Orthology: K02992: RP-S7, MRPS7, rpsG:





GO: 0003735: structural
small subunit ribosomal protein S7; KEGG





constituent of ribosome;
PATHWAY: ko03010: Ribosome:





GO: 0006412: translation;





GO: 0015935: small





ribosomal subunit;





GO: 0019843: rRNA binding


4751
5AYg1281.t1
0.167696
GO: 0006935: chemotaxis;
KEGG Orthology: K10546: ABC.GGU.S, chvE:





GO: 0042597: periplasmic
putative multiple sugar transport system





space
substrate-binding protein; KEGG PATHWAY:






ko02010: ABC transporters: The ATP-binding






cassette (ABC) transporters form one of the






largest known protein families, and are






widespread in bacteria, archaea, and






eukaryotes. They couple ATP hydrolysis to






active transport of a wide variety of substrates






such as ions, sugars, lipids, sterols, peptides,






proteins, and drugs. The structure of a






prokaryotic ABC transporter usually consists of






three components; typically two integral






membrane proteins each having six






transmembrane segments, two peripheral






proteins that bind and hydrolyze ATP, and a






periplasmic (or lipoprotein) substrate-binding






protein. Many of the genes for the three






components form operons as in fact observed in






many bacterial and archaeal genomes. On the






other hand, in a typical eukaryotic ABC






transporter, the membrane spanning protein






and the ATP-binding protein are fused, formirig






a multi-domain protein with the membrane-






spanning domain (MSD) and the nucleotide-






binding domain (NBD).


4752
5AYg777.t1
0.156177
GO: 0000413: protein
KEGG Orthology: K03768: PPIB, ppiB: peptidyl-





peptidyl-prolyl
prolyl cis-trans isomerase B (cyclophilin B)





isomerization; GO: 0003755:
[EC: 5.2.1.8]





peptidyl-prolyl cis-trans





isomerase activity;





GO: 0006457: protein





folding


4753
5AYg1692.t1
0.155178
GO: 0003677: DNA binding;
KEGG Orthology: K03704: cspA: cold shock





GO: 0005737: cytoplasm;
protein (beta-ribbon, CspA family)





GO: 0006355: regulation of





transcription, DNA-





templated


4754
5AYg1247.t1
0.152662
GO: 0006865: amino acid
KEGG Orthology: K01999: livK: branched-chain





transport
amino acid transport system substrate-binding






protein; KEGG PATHWAY: ko02010: ABC






transporters: The ATP-binding cassette (ABC)






transporters form one of the largest known






protein families, and are widespread in bacteria,






archaea, and eukaryotes. They couple ATP






hydrolysis to active transport of a wide variety






of substrates such as ions, sugars, lipids, sterols,






peptides, proteins, and drugs. The structure of a






prokaryotic ABC transporter usually consists of






three components; typically two integral






membrane proteins each having six






transmembrane segments, two peripheral






proteins that bind and hydrolyze ATP, and a






periplasmic (or lipoprotein) substrate-binding






protein. Many of the genes for the three






components form operons as in fact observed in






many bacterial and archaeal genomes. On the






other hand, in a typical eukaryotic ABC






transporter, the membrane spanning protein






and the ATP-binding protein are fused, forming






a multi-domain protein with the membrane-






spanning domain (MSD) and the nucleotide-






binding domain (NBD).


4755
5AYg2256.t1
0.149078
GO: 0016021: integral
KEGG Orthology: K16079: omp31: outer





component of membrane
membrane immunogenic protein


4756
5AYg208.t1
0.14751
GO: 0003735: structural
KEGG Orthology: K02986: RP-54, rpsD: small





constituent of ribosome;
subunit ribosomal protein S4; KEGG PATHWAY:





GO: 0006412: translation;
ko03010: Ribosome:





GO: 0015935: small





ribosomal subunit;





GO: 0019843: rRNA binding


4757
5AYg1876.t1
0.146416
GO: 0000049: tRNA binding;
KEGG Orthology: K02931: RP-L5, MRPL5, rplE:





GO: 0003735: structural
large subunit ribosomal protein L5; KEGG





constituent of ribosome;
PATHWAY: ko03010: Ribosome:





GO: 0005840: ribosome;





GO: 0006412: translation;





GO: 0019843: rRNA binding


4758
5AYg998.t1
0.145775
GO: 0004801:
KEGG Orthology: K00616: E2.2.1.2, talA, talB:





sedoheptulose-7-
transaldolase [EC: 2.2.1.2]; KEGG PATHWAY:





phosphate: D-
ko00030: Pentose phosphate pathway: The





glyceraldehyde-3-
pentose phosphate pathway is a process of





phosphate
glucose turnover that produces NADPH as





glyceronetransferase
reducing equivalents and pentoses as essential





activity; GO: 0005737:
parts of nucleotides. There are two different





cytoplasm; GO: 0005975:
phases in the pathway. One is irreversible





carbohydrate metabolic
oxidative phase in which glucose-6P is





process; GO: 0006098:
converted to ribulose-5P by oxidative





pentose-phosphate shunt
decarboxylation, and NADPH is generated






[MD: M00006]. The other is reversible non-






oxidative phase in which phosphorylated sugars






are interconverted to generate xylulose-5P,






ribulose-5P, and ribose-5P [MD: M00007].






Phosphoribosyl pyrophosphate (PRPP) formed






from ribose-5P [MD: M00005] is an activated






compound used in the biosynthesis of histidine






and purine/pyrimidine nucleotides. This






pathway map also shows the Entner-Doudoroff






pathway where 6-P-gluconate is dehydrated






and then cleaved into pyruvate and






glyceraldehyde-3P [MD: M00008].; KEGG






PATHWAY: ko01200: Carbon metabolism:






Carbon metabolism is the most basic aspect of






life. This map presents an overall view of central






carbon metabolism, where the number of






carbons is shown for each compound denoted






by a circle, excluding a cofactor (CoA, CoM, THF,






or THMPT) that is replaced by an asterisk. The






map contains carbon utilization pathways of






glycolysis (map00010), pentose phosphate






pathway (map00030), and citrate cycle






(map00020), and six known carbon fixation






pathways (map00710 and map00720) as well as






some pathways of methane metabolism






(map00680). The six carbon fixation pathways






are: (1) reductive pentose phosphate cycle






(Calvin cycle) in plants and cyanobacteria that






perform oxygenic photosynthesis, (2) reductive






citrate cycle in photosynthetic green sulfur






bacteria and some chemolithoautotrophs, (3) 3-






hydroxypropionate bi-cycle in photosynthetic






green nonsulfur bacteria, two variants of 4-






hydroxybutyrate pathways in Crenarchaeota






called (4) hydroxypropionate-hydroxybutyrate






cycle and (5) dicarboxylate-hydroxybutyrate






cycle, and (6) reductive acetyl-CoA pathway in






methanogenic bacteria.; KEGG PATHWAY:






ko01230: Biosynthesis of amino acids: This map






presents a modular architecture of the






biosynthesis pathways of twenty amino acids,






which may be viewed as consisting of the core






part and its extensions. The core part is the






KEGG module for conversion of three-carbon






compounds from glyceraldehyde-3P to pyruvate






[MD: M00002], together with the pathways






around serine and glycine. This KEGG module is






the most conserved one in the KEGG MODULE






database and is found in almost all the






completely sequenced genomes. The extensions






are the pathways containing the reaction






modules RM001, RM033, RM032, and RM002






for biosynthesis of branched-chain amino acids






(left) and basic amino acids (bottom), and the






pathways for biosynthesis of histidine and






aromatic amino acids (top right). It is interesting






to note that the so-called essential amino acids






that cannot be synthesized in human and other






organisms generally appear in these extensions.






Furthermore, the bottom extension of basic






amino acids appears to be most divergent






containing multiple pathways for lysine






biosynthesis and multiple gene sets for arginine






biosynthesis.


4759
5AYg1162.t1
0.144833
GO: 0006006: glucose
KEGG Orthology: K00134: GAPDH, gapA:





metabolic process;
glyceraldehyde 3-phosphate dehydrogenase





GO: 0016620:
[EC: 1.2.1.12]; KEGG PATHWAY: ko00010:





oxidoreductase activity,
Glycolysis/Gluconeogenesis: Glycolysis is the





acting on the aldehyde or
process of converting glucose into pyruvate and





oxo group of donors, NAD
generating small amounts of ATP (energy) and





or NADP as acceptor;
NADH (reducing power). It is a central pathway





GO: 0050661: NADP
that produces important precursor metabolites:





binding; GO: 0051287: NAD
six-carbon compounds of glucose-6P and





binding; GO: 0055114:
fructose-6P and three-carbon compounds of





oxidation-reduction process
glycerone-P, glyceraldehyde-3P, glycerate-3P,






phosphoenolpyruvate, and pyruvate






[MD: M00001]. Acetyl-CoA, another important






precursor metabolite, is produced by oxidative






decarboxylation of pyruvate [MD: M00307].






When the enzyme genes of this pathway are.






examined in completely sequenced genomes,






the reaction steps of three-carbon compounds






from glycerone-P to pyruvate form a conserved






core module [MD: M00002], which is found in






almost all organisms and which sometimes






contains operon structures in bacterial






genomes. Gluconeogenesis is a synthesis






pathway of glucose from noncarbohydrate






precursors. It is essentially a reversal of






glycolysis with minor variations of alternative






paths [MD: M00003].; KEGG PATHWAY:






ko00710: Carbon fixation in photosynthetic






organisms:; KEGG PATHWAY: ko01200: Carbon






metabolism: Carbon metabolism is the most






basic aspect of life. This map presents an overall






view of central carbon metabolism, where the






number of carbons is shown for each compound






denoted by a circle, excluding a cofactor (CoA,






CoM, THF, or THMPT) that is replaced by an






asterisk. The map contains carbon utilization






pathways of glycolysis (map00010), pentose






phosphate pathway (map00030), and citrate






cycle (map00020), and six known carbon






fixation pathways (map00710 and map00720)






as well as some pathways of methane






metabolism (map00680). The six carbon fixation






pathways are: (1) reductive pentose phosphate






cycle (Calvin cycle) in plants and cyanobacteria






that perform oxygenic photosynthesis, (2)






reductive citrate cycle in photosynthetic green






sulfur bacteria and some chemolithoautotrophs,






(3) 3-hydroxypropionate bi-cycle in






photosynthetic green nonsulfur bacteria, two






variants of 4-hydroxybutyrate pathways in






Crenarchaeota called (4) hydroxypropionate-






hydroxybutyrate cycle and (5) dicarboxylate-






hydroxybutyrate cycle, and (6) reductive acetyl-






CoA pathway in methanogenic bacteria.; KEGG






PATHWAY: ko01230: Biosynthesis of amino






acids: This map presents a modular architecture






of the biosynthesis pathways of twenty amino






acids, which may be viewed as consisting of the






core part and its extensions. The core part is the






KEGG module for conversion of three-carbon






compounds from glyceraldehyde-3P to pyruvate






[MD: M00002], together with the pathways






around serine and glycine. This KEGG module is






the most conserved one in the KEGG MODULE






database and is found in almost all the






completely sequenced genomes. The extensions






are the pathways containing the reaction






modules RM001, RM033, RM032, and RM002






for biosynthesis of branched-chain amino acids






(left) and basic amino acids (bottom), and the






pathways for biosynthesis of histidine and






aromatic amino acids (top right). It is interesting






to note that the so-called essential amino acids






that cannot be synthesized in human and other






organisms generally appear in these extensions.






Furthermore, the bottom extension of basic






amino acids appears to be most divergent






containing multiple pathways for lysine






biosynthesis and multiple gene sets for arginine






biosynthesis.; KEGG PATHWAY: ko04066: HIF-1






signaling pathway: Hypoxia-inducible factor 1






(HIF-1) is a transcription factor that functions as






a master regulator of oxygen homeostasis. It






consists of two subunits: an inducibly-expressed






HIF-1alpha subunit and a constitutively-






expressed HIF-1beta subunit. Under normoxia,






HIF-1 alpha undergoes hydroxylation at specific






prolyl residues which leads to an immediate






ubiquitination and subsequent proteasomal






degradation of the subunit. In contrast, under






hypoxia, HIF-1 alpha subunit becomes stable






and interacts with coactivators such as






p300/CBP to modulate its transcriptional






activity. Eventually, HIF-1 acts as a master






regulator of numerous hypoxia-inducible genes






under hypoxic conditions. The target genes of






HIF-1 encode proteins that increase O2 delivery






and mediate adaptive responses to O2






deprivation. Despite its name, HIF-1 is induced






not only in response to reduced oxygen






availability but also by other stimulants, such as






nitric oxide, or various growth factors.; KEGG






PATHWAY: ko05010: Alzheimer's disease:






Alzheimer's disease (AD) is a chronic disorder






that slowly destroys neurons and causes serious






cognitive disability. AD is associated with senile






plaques and neurofibrillary tangles (NFTs).






Amyloid-beta (Abeta), a major component of






senile plaques, has various pathological effects






on cell and organelle function. The extracellular






Abeta oligomers may activate caspases through






activation of cell surface death receptors.






Alternatively, intracellular Abeta may contribute






to pathology by facilitating tau hyper-






phosphorylation, disrupting mitochondria






function, and triggering calcium dysfunction. To






date genetic studies have revealed four genes






that may be linked to autosomal dominant or






familial early onset AD (FAD). These four genes






include: amyloid precursor protein (APP),






presenilin 1 (PS1), presenilin 2 (PS2) and






apolipoprotein E (ApoE). All mutations






associated with APP and PS proteins can lead to






an increase in the production of Abeta peptides,






specfically the more amyloidogenic form,






Abeta42. FAD-linked PS1 mutation






downregulates the unfolded protein response






and leads to vulnerability to ER stress.


4760
5AYg287.t1
0.138824
GO: 0003677: DNA binding;
KEGG Orthology: K03530: hupB: DNA-binding





GO: 0030261: chromosome
protein HU-beta





condensation


4761
5AYg677.t1
0.137328
GO: 0005524: ATP binding;
KEGG Orthology: K04077: groEL, HSPD1:





GO: 0005737: cytoplasm;
chaperonin GroEL; KEGG PATHWAY: ko03018:





GO:0016491:
RNA degradation: The correct processing,





oxidoreductase activity;
quality control and turnover of cellular RNA





GO: 0042026: protein
molecules are critical to many aspects in the





refolding; GO: 0051082:
expression of genetic information. In





unfolded protein binding;
eukaryotes, two major pathways of mRNA





GO: 0055114: oxidation-
decay exist and both pathways are initiated by





reduction process
poly(A) shortening of the mRNA. In the 5′ to 3′






pathway, this is followed by decapping which






then permits the 5′ to 3′ exonucleolytic






degradation of transcripts. In the 3′ to 5′






pathway, the exosome, a large multisubunit






complex, plays a key role. The exosome exists in






archaeal cells, too. In bacteria,






endoribonuclease E, a key enzyme involved in






RNA decay and processing, organizes a protein






complex called degradosome. RNase E or R






interacts with the phosphate-dependent






exoribonuclease polynucleotide phosphorylase,






DEAD-box helicases, and additional factors in






the RNA-degrading complex.; KEGG PATHWAY:






ko04940: Type I diabetes mellitus: Type I






diabetes mellitus is a disease that results from.






autoimmune destruction of the insulin-






producing beta-cells. Certain beta-cell proteins






act as autoantigens after being processed by






antigen-presenting cell (APC), such as






macrophages and dendritic cells, and presented






in a complex with MHC-II molecules on the






surface of the APC. Then immunogenic signals






from APC activate CD4+ T cells, predominantly






of the Th1 subset. Antigen-activated Th1 cells






produce IL-2 and IFNgamma. They activate






macrophages and cytotoxic CD8+ T cells, and






these effector cells may kill islet beta-cells by






one or both of two types of mechanisms: (1)






direct interactions of antigen-specific cytotoxic






T cells with a beta-cell autoantigen-MHC-I






complex on the beta-cell, and (2) non-specific






inflammatory mediators, such as free






radicals/oxidants and cytokines (IL-1, TNFalpha,






TNFbeta, IFNgamma).; KEGG PATHWAY:






ko05134: Legionellosis: Legionellosis is a






potentially fatal infectious disease caused by






the bacterium Legionella pneumophila and






other legionella species. Two distinct clinical






and epidemiological syndromes are associated






with Legionella species: Legionnaires' disease is






the more severe form of the infection, which






may involve pneumonia, and Pontiac fever is a






milder respiratory illness.; KEGG PATHWAY:






ko05152: Tuberculosis: Tuberculosis, or TB, is an






infectious disease caused by Mycobacterium







tuberculosis. One third of the world's







population is thought to be infected with TB.






About 90% of those infected result in latent






infections, and about 10% of latent infections






develop active diseases when their immune






system is impaired due to the age, other






diseases such as AIDS or exposure to






immunosuppressive drugs. TB is transmitted






thrciugh the air and primarily attacks the lungs,






then it can spread by the circulatory system to






other parts of body. Once TB bacilli have






entered the host by the respiratory route and






infected macrophages in the lungs, they






interfere with phagosomal maturation, antigen






presentation, apoptosis and host immune






system to establish persistent or latent






infection.


4762
5AYg2260.t1
0.135
GO: 0043190: ATP-binding
KEGG Orthology: K12368: dppA: dipeptide





cassette (ABC) transporter
transport system substrate-binding protein;





complex; GO: 0055085:
KEGG PATHWAY: ko02010: ABC transporters:





transmembrane transport
The ATP-binding cassette (ABC) transporters






form one of the largest known protein families,






and are widespread in bacteria, archaea, and






eukaryotes. They couple ATP hydrolysis to






active transport of a wide variety of substrates






such as ions, sugars, lipids, sterols, peptides,






proteins, and drugs. The structure of a






prokaryotic ABC transporter usually consists of






three components; typically two integral






membrane proteins each having six






transmembrane segments, two peripheral






proteins that bind and hydrolyze ATP, and a






periplasmic (or lipoprotein) substrate-binding






protein. Many of the genes for the three






components form operons as in fact observed in






many bacterial and archaeal genomes. On the






other hand, in a typical eukaryotic ABC






transporter, the membrane spanning protein






and the ATP-binding protein are fused, forming






a multi-domain protein with the membrane-






spanning domain (MSD) and the nucleotide-






binding domain (NBD).; KEGG PATHWAY:






ko02030: Bacterial chemotaxis: Chemotaxis is






the process by which cells sense chemical






gradients in their environment and then move






towards more favorable conditions. In






chemotaxis, events at the receptors control






autophosphorylation of the CheA histidine






kinase, and the phosphohistidine is the






substrate for the response regulator CheY,






which catalyzes the transfer of the phosphoryl






group to a conserved aspartate. The resulting






CheY-P can interact with the switch mechanism






in the motor. This interaction causes a change in






behavior, such as in direction or speed of






rotation of flagella.


4763
5AYg980.t1
0.133866
GO: 0016021: integral
KEGG Orthology: K16079: omp31: outer





component of membrane
membrane immunogenic protein


4764
5AYg2744.t1
0.131774
GO: 0000413: protein
KEGG Orthology: K03769: ppiC: peptidyl-prolyl





peptidyl-prolyl
cis-trans isomerase C [EC:5.2.1.8]





isomerization; GO: 0003755:





peptidyl-prolyl cis-trans





isomerase activity


4765
5AYg2575.t1
0.130147
GO: 0003735: structural
KEGG Orthology: K02899: RP-L27, MRPL27,





constituent of ribosome;
rpmA: large subunit ribosomal protein L27;





GO: 0005840: ribosome;
KEGG PATHWAY: ko03010: Ribosome:





GO: 0006412: translation;





GO: 0019843: rRNA binding


4766
5AYg676.t1
0.128736
GO: 0005524: ATP binding;
KEGG Orthology: K04078: groES, HSPE1:





GO: 0005737: cytoplasm;
chaperonin GroES





GO: 0006457: protein





folding









SYM01004 Versus SYM00091









TABLE 705







Differential secreted protein abundance between SYM01004 and SYM00091.
















SEQ ID

SEQ ID





Fold-
FDR


Beneficial
A.protein
Neutral
B.protein
KEGG
GO
A.mean
B.mean
change
q-value



















4734
5AYg1329.t1
4671
5BYg3790.t1
ade, Purine
adenine catabolic process,
0.057
0
5.9
3.90E−02






metabolism
adenine deaminase activity


4735
5AYg1185.t1
4672
5BYg649.t1
Biosynthesis of amino
L-serine biosynthetic
0
0.009
−3.3
4.90E−02






acids, Carbon
process, NAD binding,






metabolism, Glycine,
oxidation-reduction process,






serine and threonine
phosphoglycerate






metabolism, Methane
dehydrogenase activity






metabolism, serA,






PHGDH


4736
5AYg1107.t1
4673
5BYg1291.t1
ABC transporters,
ATP binding, ATP-binding
0.008
0
3.2
4.40E−02






ABC.MS.S, msmX,
cassette (ABC) transporter






msmK, malK, sugC,
complex, ATPase activity,






ggtA, msiK
carbohydrate transport,







hydrolase activity, acting on







acid anhydrides, catalyzing







transmembrane movement







of substances, metabolic







process, transmembrane







transport, transporter







activity


4737
5AYg12621.t1
4674
5BYg1034.t1
None
integral component of
0
0.007
−3.1
4.00E−02







membrane, transport,







transporter activity


4738
5AYg1075.t1
4675
5BYg577.t1
E2.4.1.1, glgP, PYG,
carbohydrate metabolic
0
0.007
−2.9
3.00E−02






Insulin signaling
process, glycogen






pathway, Starch and
phosphorylase activity,






sucrose metabolism
pyridoxal phosphate binding


4739
5AYg1184.t1
4676
5BYg648.t1
Biosynthesis of amino
cytoplasm, L-serine
0.036
0.005
2.7
4.90E−02






acids, Carbon
biosynthetic process, O-






metabolism, Glycine,
phospho-L-serine:2-






serine and threonine
oxoglutarate






metabolism, Methane
aminotransferase activity






metabolism, serC,






PSAT1, Vitamin B6






metabolism


4740
5AYg126.t1
4677
5BYg3243.t1
Carbon metabolism,
glycine decarboxylation via
0.032
0.006
2.2
3.90E−02






GLDC, gcvP, Glycine,
glycine cleavage system,






serine and threonine
glycine dehydrogenase






metabolism
(decarboxylating) activity,







lyase activity, oxidation-







reduction process


4741
5AYg124.t1
14678
5BYg3241.t1
K09796
None
0.019
0.004
2.1
3.90E−02










This table describes the differential protein expression between pairs of orthologous proteins from a genus, where one member of the pair has a beneficial effect on plant growth and the other has a neutral effect. “A.mean” represents the average normalized spectral counts between biological replicates of the beneficial member of the pair. “B.mean” represents the average normalized spectral counts between biological replicates of the neutral member of the pair. “Fold change” represents the fold change difference between the two organisms. “FDR q-value” represents the false discovery rate corrected q-value.


A total of 1390 proteins were detected across all Agrobacterium samples with two or more unique peptides at the false discovery rates indicated above.


KEGG Pathway Enrichment of Beneficial Fungi Versus Neutral Fungi









TABLE 706







KEGG Pathway enrichment of beneficial fungi versus neutral fungi























FDR






SEQ ID

SEQ ID

q-


Category
KEGG ID
Name
Description
Beneficial
A.Protein.ID
Neutral
B.Protein.ID
value


















KEGG PATHWAY
ko00500
Starch and
none
643; 2293;
1AXg13171.t1,
4104;
1BXg10106.t1,
2.92E−10




sucrose

2292; 874;
1AXg2246.t1,
4126;
1BXg10460.t1,




metabolism

480; 2288;
1AXg2742.t1,
4125;
1BXg10656.t1,






487; 2285;
1AXg2815.t1,
2443;
1BXg1289.t1,






580; 2279;
1AXg3149.t1,
4097;
1BXg135.t1,






4543;
1AXg4053.t1,
4122;
1BXg1561.t1,






4515;
1AXg5358.t1,
2349;
1BXg2692.t1,






4669;
1AXg5538.t1,
4118;
1BXg3232.t1,






4668;
1AXg5751.t1,
2382;
1BXg3531.t1,






4666;
1AXg8814.t1,
2436;
1BXg4362.t1,






4615;
3AXg10791.t1,
2377;
1BXg4998.t1,






4573;
3AXg10862.t1,
2350;
1BXg5592.t1,






4661;
3AXg1436.t1,
2721;
1BXg9114.t1,






4659;
3AXg192.t1,
2470;
1BXg9824.t1,






4571
3AXg2790.t1,
4508;
3BXg11320.t1,







3AXg4536.t1,
4413;
3BXg14385.t1,







3AXg4810.t1,
4507;
3BXg1864.t1,







3AXg6314.t1,
4505;
3BXg2317.t1,







3AXg7872.t1,
4422;
3BXg3121.t1,







3AXg9121.t1
4500;
3BXg3387.t1,








4433;
3BXg6481.t1,








4410;
3BXg6843.t1,








4423;
3BXg6890.t1,








4491;
3BXg7356.t1,








4487;
3BXg928.t1,








4442;
3BXg9632.t1,








4346;
3BXg9786.t1,








4484
3BXg9960.t1


KEGG Orthology
K08257
E3.2.1.101
mannan endo-
2277; 528;
1AXg10033.t1,
2457;
1BXg12075.t1,
2.62E−05





1,6-alpha-
623; 2278;
1AXg4291.t1,
4121;
1BXg1595.t1,





mannosidase
4663;
1AXg459.t1,
4112;
1BXg6031.t1,





[EC: 3.2.1.101]
4585
1AXg9931.t1,
2422;
1BXg8019.t1,







3AXg512.t1,
4391;
3BXg10636.t1,







3AXg7050.t1
4499;
3BXg3817.t1,








4492
3BXg7176.t1


KEGG
K18576
XEG
xyloglucan-
2273;
1AXg6048.t1,
2390;
1BXg307.t1,
4.04E−05


Orthology


specific endo-
1249;
1AXg9842.t1,
4109;
1BXg8240.t1,





beta-1,4-
4540
3AXg10237.t1
3093;
1BXg9770.t1,





glucanase


4509;
3BXg10794.t1,





[EC: 3.2.1.151]


4343
3BXg1101.t1


KEGG
ko00040
Pentose and
none
480; 4515;
1AXg3149.t1,
4099;
1BXg12260.t1,
0.000335


PATHWAY

glucuronate

4666;
3AXg10862.t1,
2377;
1BXg4998.t1,




interconversions

4571
3AXg2790.t1,
4106;
1BXg941.t1,







3AXg9121.t1
4442
3BXg9632.t1


KEGG Orthology
K00505
TYR
tyrosinase
2275;
1AXg11951.t1,
4096;
1BXg5424.t1,
0.002931





[EC: 1.14.18.1]
4609;
3AXg2591.t1,
4113;
1BXg5696.t1,






4528;
3AXg2961.t1,
4415;
3BXg1833.t1,






4660
3AXg6319.t1
4501;
3BXg3225.t1,








4369;
3BXg390.t1,








4498;
3BXg3977.t1,








4495;
3BXg6039.t1,








4394;
3BXg8171.t1,








4488
3BXg8955.t1


KEGG PATHWAY
ko00052
Galactose
none
874; 2291;
1AXg2815.t1,
4097;
1BXg135.t1,
0.003136




metabolism

4669;
1AXg325.t1,
2382;
1BXg3531.t1,






4615;
3AXg1436.t1,
2350;
1BXg5592.t1,






4661
3AXg4536.t1,
2721;
1BXg9114.t1,







3AXg6314.t1
4508;
3BXg11320.t1,








4422;
3BXg3121.t1,








4496;
3BXg5975.t1,








4494;
3BXg6701.t1,








4410;
3BXg6843.t1,








4491;
3BXg7356.t1,








4484
3BXg9960.t1


KEGG PATHWAY
ko00965
Betalain
Betalains are
2275;
1AXg11951.t1,
4096;
1BXg5424.t1,
0.003618




biosynthesis
water-soluble
4609;
3AXg2591.t1,
4113;
1BXg5696.t1,





nitrogen-
4528;
3AXg2961.t1,
4415;
3BXg1833.t1,





containing
4660
3AXg6319.t1
4501;
3BXg3225.t1,





pigments that are


4369;
3BXg390.t1,





present in plants


4498;
3BXg3977.t1,





belonging to the


4495;
3BXg6039.t1,





order


4394;
3BXg8171.t1,





Caryophyllales


4488
3BXg8955.t1





(such as cactus





and amaranth





families) and in





higher fungi. They





contain betalamic





acid as the





chromophore and





are classified into





two types:





betacyanins and





betaxanthins.





Betacyanins





contain a cyclo-





DOPA residue and





exhibit red/violet





coloration, while





betaxanthins





contain different





amino acids or





amino side chains





and exhibit a





yellow/orange





coloration. The





condensation of





betalamic acid





with amino acids





(including cyclo-





DOPA or amines)





in plants is a





spontaneous





reaction, not an





enzyme-catalyzed





reaction.


KEGG PATHWAY
ko04916
Melanogenesis
Cutaneous
2275; 665;
1AXg11951.t1,
2320;
1BXg11664.t1,
0.005636





melanin pigment
4609;
1AXg4299.t1,
4096;
1BXg5424.t1,





plays a critical
4528;
3AXg2591.t1,
4113;
1BXg5696.t1,





role in
4660
3AXg2961.t1,
4415;
3BXg1833.t1,





camouflage,

3AXg6319.t1
4501;
3BXg3225.t1,





mimicry, social


4369;
3BXg390.t1,





communication,


4498;
3BXg3977.t1,





and protection


4495;
3BXg6039.t1,





against harmful


4394;
3BXg8171.t1,





effects of solar


4488
3BXg8955.t1





radiation.





Melanogenesis is





under complex





regulatory control





by multiple





agents. The most





important





positive regulator





of melanogenesis





is the MC1





receptor with its





ligands





melanocortic





peptides. MC1R





activates the





cyclic AMP





(cAMP) response-





element binding





protein (CREB).





Increased





expression of





MITF and its





activation by





phosphorylation





(P) stimulate the





transcription of





tyrosinase (TYR),





tyrosinase-related





protein 1 (TYRP1),





and dopachrome





tautomerase





(DCT), which





produce melanin.





Melanin synthesis





takes place within





specialized





intracellular





organelles named





melanosomes.





Melanin-





containing





melanosomes





then move from





the perinuclear





region to the





dendrite tips and





are transferred to





keratinocytes by a





still not well-





characterized





mechanism.


KEGG PATHWAY
ko04142
Lysosome
Lysosomes are
521; 2295;
1AXg11059.t1,
4102;
1BXg10249.t1,
0.009426





membrane-
608; 2290;
1AXg12307.t1,
4124;
1BXg11338.t1,





delimited
2289;
1AXg1785.t1,
2407;
1BXg1175.t1,





organelles in
2286;
1AXg3652.t1,
4116;
1BXg4075.t1,





animal cells
2282;
1AXg3653.t1,
4111;
1BXg7402.t1,





serving as the
4559;
1AXg5534.t1,
4107;
1BXg9090.t1,





cell's main
4670;
1AXg7972.t1,
4506;
3BXg2203.t1,





digestive
4665;
3AXg10485.t1,
4353;
3BXg4014.t1,





compartment to
4525;
3AXg10865.t1,
4497;
3BXg4508.t1,





which all sorts of
4526;
3AXg3114.t1,
4432;
3BXg5175.t1,





macromolecules
4624
3AXg5987.t1,
4386;
3BXg5319.t1,





are delivered for

3AXg8810.t1,
4362;
3BXg821.t1,





degradation. They

3AXg9670.t1
4485
3BXg9634.t1





contain more





than 40





hydrolases in an





acidic





environment (pH





of about 5). After





synthesis in the





ER, lysosomal





enzymes are





decorated with





mannose-6-





phosphate





residues, which





are recognized by





mannose-6-





phosphate





receptors in the





trans-Golgi





network. They are





packaged into





clathrin-coated





vesicles and are





transported to





late endosomes.





Substances for





digestion are





acquired by the





lysosomes via a





series of





processes





including





endocytosis,





phagocytosis, and





autophagy.


KEGG PATHWAY
ko00950
Isoquinoline
Isoquinoline
2275;
1AXg11951.t1,
4098;
1BXg12278.t1,
0.011241




alkaloid
alkaloids are
1342;
1AXg7766.t1,
4119;
1BXg2903.t1,




biosynthesis
tyrosine-derived
4609;
3AXg2591.t1,
4096;
1BXg5424.t1,





plant alkaloids
4528;
3AXg2961.t1,
4113;
1BXg5696.t1,





with an
4660
3AXg6319.t1
4108;
1BXg8510.t1,





isoquinoline


3185;
1BXg886.t1,





skeleton. Among


4415;
3BXg1833.t1,





them


4501;
3BXg3225.t1,





benzylisoquinoline


4369;
3BXg390.t1,





alkaloids form


4498;
3BXg3977.t1,





an important


4495;
3BXg6039.t1,





group with potent


4493;
3BXg6827.t1,





pharmacological


4394;
3BXg8171.t1,





activity, including


4488
3BXg8955.t1





analgesic





compounds of





morphine and





codeine, and anti-





infective agents





of berberine,





palmatine, and





magnoflorine.





Biosynthesis of





isoquinoline





alkaloids





proceeds via





decarboxylation





of tyrosine or





DOPA to yield





dopamine, which





together with 4-





hydroxyphenylacetaldehyde,





an





aldehyde derived





from tyrosine, is





converted to





reticuline, an





important





precursor of





various





benzylisoquinoline





alkaloids.


KEGG
ko00630
Glyoxylate
none
2272;
1AXg6636.t1,
4103;
1BXg10186.t1,
0.011241


PATHWAY

and

4638;
3AXg457.t1,
2315;
1BXg2840.t1,




dicarboxylate

4658
3AXg9876.t1
4110;
1BXg7797.t1,




metabolism



4490
3BXg7921.t1


KEGG PATHWAY
ko00740
Riboflavin
none
2275; 485;
1AXg11951.t1,
4100;
1BXg11698.t1,
0.011241




metabolism

496; 663;
1AXg1240.t1,
4123;
1BXg11921.t1,






2283;
1AXg13882.t1,
4117;
1BXg3956.t1,






2280;
1AXg4563.t1,
2464;
1BXg4094.t1,






4609;
1AXg5998.t1,
4096;
1BXg5424.t1,






4528;
1AXg8556.t1,
4114;
1BXg5433.t1,






4660
3AXg2591.t1,
2477;
1BXg5689.t1,







3AXg2961.t1,
4113;
1BXg5696.t1,







3AXg6319.t1
4415;
3BXg1833.t1,








4503;
3BXg246.t1,








4501;
3BXg3225.t1,








4369;
3BXg390.t1,








4498;
3BXg3977.t1,








4469;
3BXg443.t1,








4495;
3BXg6039.t1,








4489;
3BXg8118.t1,








4394;
3BXg8171.t1,








4488
3BXg8955.t1


KEGG PATHWAY
ko00520
Amino sugar
none
2276;
1AXg10429.t1,
4101;
1BXg11696.t1,
0.041684




and

2296; 608;
1AXg11997.t1,
2407;
1BXg1175.t1,




nucleotide

2294;
1AXg1785.t1,
4122;
1BXg1561.t1,




sugar

2287;
1AXg2013.t1,
2483;
1BXg2454.t1,




metabolism

2284;
1AXg5017.t1,
4120;
1BXg2483.t1,






2281;
1AXg5996.t1,
2382;
1BXg3531.t1,






2279;
1AXg8113.t1,
2322;
1BXg3931.t1,






4559;
1AXg8814.t1,
4115;
1BXg4950.t1,






4667;
3AXg10485.t1,
2350;
1BXg5592.t1,






4664;
3AXg2394.t1,
4105;
1BXg9514.t1,






4662;
3AXg407.t1,
4408;
3BXg11985.t1,






4602
3AXg618.t1,
4505;
3BXg2317.t1,







3AXg9481.t1
4502;
3BXg251.t1,








4410;
3BXg6843.t1,








4362;
3BXg821.t1,








4486
3BXg9283.t1


KEGG PATHWAY
ko00350
Tyrosine
none
2275;
1AXg11951.t1,
4098;
1BXg12278.t1,
0.045141




metabolism

1342;
1AXg7766.t1,
4119;
1BXg2903.t1,






4609;
3AXg2591.t1,
4096;
1BXg5424.t1,






4528;
3AXg2961.t1,
4113;
1BXg5696.t1,






4660
3AXg6319.t1
4108;
1BXg8510.t1,








3185;
1BXg886.t1,








4415;
3BXg1833.t1,








4501;
3BXg3225.t1,








4369;
3BXg390.t1,








4498;
3BXg3977.t1,








4495;
3BXg6039.t1,








4493;
3BXg6827.t1,








4394;
3BXg8171.t1,








4488
3BXg8955.t1


KEGG
ko00240
Pyrimidine
none
2274;
1AXg2750.t1,
2968;
1BXg1133.t1,
0.064093


PATHWAY

metabolism

1124; 662;
1AXg5630.t1,
2326;
1BXg4339.t1,






4648
1AXg7452.t1,
2352;
1BXg5639.t1,







3AXg4651.t1
2463;
1BXg6885.t1,








4504
3BXg2357.t1









Gene Ontology Enrichment of Beneficial Fungi Versus Neutral Fungi









TABLE 707







GO enrichment of beneficial fungi versus neutral fungi















SEQ ID

SEQ ID

FDR q-


GO Term
Description
Beneficial
A.Protein.ID
Neutral
B.Protein.ID
value
















GO: 0005576
extracellular
478; 4917;
1AXg10805.t1,
4926;
1BXg1054.t1,
1.82E−14



region
4918; 874;
1AXg1317.t1,
2435;
1BXg11562.t1,




633; 2291;
1AXg21242.t1,
4101;
1BXg11696.t1,




2287; 2285;
1AXg2815.t1,
4099;
1BXg12260.t1,




2284; 4947;
1AXg3175.t1,
4859;
1BXg1692.t1,




2281; 667;
1AXg325.t1,
4927;
1BXg177.t1,




497; 4948;
1AXg5017.t1,
4858;
1BXg2047.t1,




4877; 4919;
1AXg5538.t1,
2345;
1BXg2053.t1,




4878; 4559;
1AXg5996.t1,
4928;
1BXg4311.t1,




4879; 4920;
1AXg8019.t1,
4929;
1BXg4617.t1,




4515; 4880;
1AXg8113.t1,
4115;
1BXg4950.t1,




4921; 4666;
1AXg9193.t1,
2377;
1BXg4998.t1,




4650; 4922;
1AXg9750.t1,
4895;
1BXg6497.t1,




4923; 4881;
1AXg9874.t1,
4930;
1BXg6576.t1,




4525; 4510;
3AXg10204.t1,
4896;
1BXg7924.t1,




4661; 4882;
3AXg10215.t1,
4109;
1BXg8240.t1,




4924; 4925;
3AXg10410.t1,
2468;
1BXg8760.t1,




4571; 4883;
3AXg10485.t1,
2721;
1BXg9114.t1,




4658; 4642
3AXg10796.t1,
4932;
3BXg10428.t1,





3AXg10814.t1,
4897;
3BXg10792.t1,





3AXg10862.t1,
4356;
3BXg11001.t1,





3AXg2666.t1,
4898;
3BXg11l47.t1,





3AXg2755.t1,
4933;
3BXg11837.t1,





3AXg2790.t1,
4468;
3BXg12052.t1,





3AXg2954.t1,
4934;
3BXg14356.t1,





3AXg5176.t1,
4351;
3BXg2216.t1,





3AXg5370.t1,
4935;
3BXg2769.t1,





3AXg5893.t1,
4899;
3BXg3018.t1,





3AXg5987.t1,
4900;
3BXg3920.t1,





3AXg6236.t1,
4386;
3BXg5319.t1,





3AXg6314.t1,
4936;
3BXg5448.t1,





3AXg7257.t1,
4901;
3BXg6241.t1,





3AXg7674.t1,
4428;
3BXg7066.t1,





3AXg8315.t1,
4902;
3BXg7579.t1,





3AXg9121.t1,
4490;
3BXg7921.t1,





3AXg9736.t1,
4362;
3BXg821.t1,





3AXg9876.t1,
4937;
3BXg9358.t1,





3AXg9889.t1
4442;
3BXg9632.t1,






4938
3BXg9781.t1


GO: 0008812
choline
4608; 4582
3AXg1008.t1,
4387;
3BXg1050.t1,
3.00E−06



dehydrogenase
4555; 4594
3AXg10624.t1,
4365;
3BXg3212.t1,



activity
4562; 4829
3AXg3404.t1,
4358;
3BXg4400.t1,




4560
3AXg3931.t1,
4811;
3BXg5049.t1,





3AXg6329.t1,
4363
3BXg7997.t1





3AXg8145.t1,





3AXg8514.t1


GO: 0005618
cell wall
4939; 614;
1AXg12959.t1,
2413;
1BXg2549.t1,
1.22E−05




934; 4571;
1AXg2047.t1,
4475;
3BXg11145.t1,




4940
1AXg6047.t1,
4341
3BXg3303.t1





3AXg9121.t1,





3AXg9980.t1


GO: 0016614
oxidoreductase
4803; 4876;
1AXg11202.t1,
2433;
1BXg11481.t1,
2.62E−05



activity,
4865; 4864;
1AXg1148.t1,
4857;
1BXg3389.t1,



acting on
4863; 4840;
1AXg7074.t1,
4844;
1BXg8979.t1,



CH—OH
4527; 4518;
1AXg7314.t1,
4843;
1BXg9251.t1,



group of
4570; 4884;
1AXg8008.t1,
4824;
3BXg10091.t1,



donors
4885; 4886;
3AXg10359.t1,
4466;
3BXg1035.t1,




4572; 4887;
3AXg1658.t1,
4823;
3BXg10533.t1,




4888; 4538
3AXg2998.t1,
4479;
3BXg13120.t1,





3AXg3962.t1,
4906;
3BXg3860.t1,





3AXg5234.t1,
4907;
3BXg5594.t1,





3AXg5286.t1,
4908;
3BXg7349.t1,





3AXg6307.t1,
4909;
3BXg7537.t1,





3AXg6312.t1,
4910;
3BXg8146.t1,





3AXg7030.t1,
4417;
3BXg8641.t1,





3AXg7536.t1,
4399;
3BXg8643.t1,





3AXg8418.t1
4911
3BXg9353.t1


GO: 0000272
polysaccharide
2293; 2284;
1AXg2246.t1,
4125;
1BXg10656.t1,
3.30E−05



catabolic
2273; 667;
1AXg5996.t1,
2435;
1BXg11562.t1,



process
1249; 4540;
1AXg6048.t1,
4101;
1BXg11696.t1,




4668; 4941;
1AXg9193.t1,
2349;
1BXg2692.t1,




4923
1AXg9842.t1,
4928;
1BXg4311.t1,





3AXg10237.t1,
2468;
1BXg8760.t1,





3AXg192.t1,
3093;
1BXg9770.t1,





3AXg2760.t1,
4509;
3BXg10794.t1,





3AXg5370.t1
4356;
3BXg11001.t1,






4343;
3BXg1101.t1,






4500;
3BXg3387.t1,






4942;
3BXg6628.t1,






4423;
3BXg6890.t1,






4460
3BXg9765.t1


GO: 0045490
pectin
4948; 4666;
1AXg9874.t1,
4099;
1BXg12260.t1,
3.30E−05



catabolic
4943; 4571
3AXg2790.t1,
4937;
3BXg9358.t1,



process

3AXg5277.t1,
4449
3BXg9608.t1





3AXg9121.t1


GO: 0004252
serine-type
4804; 652;
1AXg11086.t1,
2467;
1BXg10439.t1,
3.92E−05



endopeptidase
4947; 666;
1AXg7771.t1,
4850;
1BXg782.t1,



activity
4670; 4921;
1AXg8019.t1,
2452;
1BXg7838.t1,




4577; 4834;
1AXg9261.t1,
4814;
3BXg1720.t1,




4922; 4525;
3AXg10865.t1,
4497;
3BXg4508.t1,




4526
3AXg2755.t1,
4386;
3BXg5319.t1,





3AXg2995.t1,
4936;
3BXg5448.t1,





3AXg3480.t1,
4355;
3BXg6263.t1,





3AXg5176.t1,
4944;
3BXg6633.t1,





3AXg5987.t1,
4381;
3BXg8638.t1,





3AXg8810.t1
4485;
3BXg9634.t1,






4945
3BXg9880.t1


GO: 0006979
response to
2272; 4626;
1AXg6636.t1,
4103;
1BXg10186.t1,
1.11E−04



oxidative
4635
3AXg10815.t1,
4860;
1BXg11947.t1,



stress

3AXg2285.t1
4946
3BXg8947.t1


GO: 0030248
cellulose
478; 4917;
1AXg10805.t1,
4926;
1BXg1054.t1,
1.51E−04



binding
4918; 633;
1AXg1317.t1,
4927;
1BXg177.t1,




2291; 2287;
1AXg21242.t1,
2345;
1BXg2053.t1,




2285; 2281;
1AXg3175.t1,
4929;
1BXg4617.t1,




497; 4920;
1AXg325.t1,
4115;
1BXg4950.t1,




4924; 4925
1AXg5017.t1,
4930;
1BXg6576.t1,





1AXg5538.t1,
4933;
3BXg11837.t1,





1AXg8113.t1,
4934;
3BXg14356.t1,





1AXg9750.t1,
4935;
3BXg2769.t1,





3AXg10814.t1,
4428;
3BXg7066.t1,





3AXg7674.t1,
4938;
3BXg9781.t1





3AXg8315.t1


GO: 0016788
hydrolase
4805; 4873;
1AXg10964.t1,
2489;
1BXg11282.t1,
3.35E−04



activity,
496; 645;
1AXg1296.t1,
4862;
1BXg11329.t1,



acting on
4836; 4539;
1AXg13882.t1,
2445;
1BXg12241.t1,



ester bonds
4569
1AXg13885.t1,
2477;
1BXg5689.t1,





3AXg1785.t1,
4852;
1BXg6844.t1,





3AXg6767.t1,
4847;
1BXg8700.t1,





3AXg8951.t1
4818;
3BXg12041.t1,






4467;
3BXg3959.t1,






4469;
3BXg443.t1,






4905
3BXg5704.t1


GO: 0004190
aspartic-
482; 494;
1AXg10578.t1,
2439;
1BXg12089.t1,
3.46E−04



type
673; 2252;
1AXg6959.t1,
4853;
1BXg5763.t1,



endopeptidase
4919; 4529;
1AXg6960.t1,
4076;
1BXg6565.t1,



activity
4833; 4581;
1AXg9542.t1,
2323;
1BXg7026.t1,




4894
3AXg10215.t1,
2474;
1BXg9737.t1,





3AXg1976.t1,
4842;
1BXg9738.t1,





3AXg3738.t1,
4932;
3BXg10428.t1,





3AXg573.t1,
4347;
3BXg11695.t1,





3AXg9318.t1
4472;
3BXg4394.t1,






4385;
3BXg5286.t1,






4483;
3BXg8935.t1,






4904
3BXg9882.t1


GO: 0004650
polygalacturonase
4515; 4666;
3AXg10862.t1,
2377;
1BXg4998.t1,
3.46E−04



activity
4943
3AXg2790.t1,
4937;
3BXg9358.t1,





3AXg5277.t1
4442
3BXg9632.t1


GO: 0004185
serine-type
587; 2282;
1AXg11050.t1,
4102;
1BXg10249.t1,
0.000484



carboxypeptidase
4838; 4837;
1AXg7972.t1,
2386;
1BXg2887.t1,



activity
4827; 4826;
3AXg10866.t1,
4825;
3BXg10049.t1,




4624
3AXg1190.t1,
4812;
3BXg3887.t1,





3AXg891.t1,
4353;
3BXg4014.t1,





3AXg9023.t1,
4432;
3BXg5175.t1,





3AXg9670.t1
4810;
3BXg5715.t1,






4807
3BXg9635.t1


GO: 0016798
hydrolase
530; 2296;
1AXg10268.t1,
4800;
1BXg10455.t1,
0.000484



activity,
4875; 477;
1AXg11997.t1,
3811;
1BXg10918.t1,



acting on
4872; 2292;
1AXg12212.t1,
2483;
1BXg2454.t1,



glycosyl
480; 2290;
1AXg13463.t1,
4949;
1BXg4330.t1,



bonds
2289; 487;
1AXg15301.t1,
2352;
1BXg5639.t1,




4891; 4667;
1AXg2742.t1,
4849;
1BXg817.t1,




4892; 4893
1AXg3149.t1,
2300;
1BXg8757.t1,





1AXg3652.t1,
4813;
3BXg2207.t1,





1AXg3653.t1,
4480
3BXg8858.t1





1AXg5358.t1,





1AXg7786.t1,





3AXg2394.t1,





3AXg7003.t1,





3AXg8007.t1


GO: 0005507
copper ion
4802; 1342;
1AXg12235.t1,
2539;
1BXg10115.t1,
0.000489



binding
4632; 4597;
1AXg7766.t1,
4098;
1BXg12278.t1,




4595; 4831
3AXg1263.t1,
4856;
1BXg3746.t1,





3AXg3686.t1,
3185;
1BXg886.t1,





3AXg3946.t1,
4427;
3BXg10410.t1,





3AXg5094.t1
4817;
3BXg12053.t1,






4403
3BXg689.t1


GO: 0008810
cellulase
4918; 1249;
1AXg21242.t1,
4927;
1BXg177.t1,
0.000644



activity
4540; 4839;
1AXg9842.t1,
4929;
1BXg4617.t1,




4941; 4532
3AXg10237.t1,
4930;
1BXg6576.t1,





3AXg10372.t1,
4109;
1BXg8240.t1,





3AXg2760.t1,
3093;
1BXg9770.t1,





3AXg6046.t1
4509;
3BXg10794.t1,






4343;
3BXg1101.t1,






4934;
3BXg14356.t1,






4942;
3BXg6628.t1,






4903
3BXg9093.t1


GO: 0071555
cell wall
4939; 614;
1AXg12959.t1,
4099;
1BXg12260.t1,
0.001751



organization
934; 4515;
1AXg2047.t1,
2413;
1BXg2549.t1,




4666; 4659;
1AXg6047.t1,
2482;
1BXg264.t1,




4940
3AXg10862.t1,
2377;
1BXg4998.t1,





3AXg2790.t1,
4475;
3BXg11145.t1,





3AXg7872.t1,
4487;
3BXg928.t1,





3AXg9980.t1
4937;
3BXg9358.t1,






4442
3BXg9632.t1


GO: 0008081
phosphoric
4520; 4950;
3AXg3348.t1,
2343;
1BXg6110.t1,
0.003097



diester
4951
3AXg429.t1,
4952;
3BXg10729.t1,



hydrolase

3AXg8372.t1
4953;
3BXg10989.t1,



activity


4954;
3BXg1818.t1,






4388
3BXg5195.t1


GO: 0004601
peroxidase
4626; 4635
3AXg10815.t1,
2539;
1BXg10115.t1,
0.003136



activity

3AXg2285.t1
4808;
3BXg8361.t1,






4946
3BXg8947.t1


GO: 0044238
primary
501; 4835;
1AXg11043.t1,
4798
3BXg2943.t1
0.008701



metabolic
4630; 4830;
3AXg3154.t1,



process
4828
3AXg6318.t1,





3AXg8054.t1,





3AXg8258.t1


GO: 0006629
lipid
4520; 4950;
3AXg3348.t1,
2339;
1BXg11161.t1,
0.022235



metabolic
4832; 4951
3AXg429.t1,
2343;
1BXg6110.t1,



process

3AXg4906.t1,
4822;
3BXg10687.t1,





3AXg8372.t1
4952;
3BXg10729.t1,






4953;
3BXg10989.t1,






4954;
3BXg1818.t1,






4388
3BXg5195.t1


GO: 0030246
carbohydrate
4801; 487;
1AXg4233.t1,
4097;
1BXg135.t1,
0.022419



binding
4615
1AXg5358.t1,
4949;
1BXg4330.t1,





3AXg4536.t1
4854;
1BXg5733.t1,






2332;
1BXg9970.t1,






4815;
3BXg144.t1,






4422;
3BXg3121.t1,






4489;
3BXg8118.t1,






4484
3BXg9960.t1


GO: 0008233
peptidase
567; 489;
1AXg1909.t1,
4124;
1BXg11338.t1,
0.026107



activity
1013; 2286
1AXg3273.t1,
4861;
1BXg11861.t1,





1AXg3484.t1,
2858;
1BXg2151.t1,





1AXg5534.t1
4846;
1BXg8705.t1,






4809
3BXg7109.t1


GO: 0016311
dephosphorylation
485; 602;
1AXg1240.t1,
2329;
1BXg1583.t1,
0.028109




4870; 4869;
1AXg12610.t1,
2401;
1BXg3489.t1,




4868; 4867;
1AXg2072.t1,
4855;
1BXg4136.t1,




4866; 4841;
1AXg2679.t1,
4114;
1BXg5433.t1,




4889; 4623;
1AXg3651.t1,
2478;
1BXg6623.t1,




4618; 4646;
1AXg5280.t1,
4821;
3BXg10709.t1,




4890
1AXg7026.t1,
4439;
3BXg11186.t1,





3AXg10295.t1,
4816;
3BXg12884.t1,





3AXg2325.t1,
4912;
3BXg23.t1,





3AXg2688.t1,
4503;
3BXg246.t1,





3AXg6634.t1,
4913;
3BXg383.t1,





3AXg8755.t1,
4914;
3BXg4227.t1,





3AXg9415.t1
4915;
3BXg5208.t1,






4425
3BXg5671.t1


GO: 0005886
plasma
484; 4874;
1AXg11973.t1,
2336;
1BXg1674.t1,
0.120452



membrane
4871; 649;
1AXg12543.t1,
2431;
1BXg3283.t1,




665; 658;
1AXg20005.t1,
2451;
1BXg7238.t1,




651; 4641;
1AXg2148.t1,
4851;
1BXg7733.t1,




4521; 4955;
1AXg4299.t1,
4848;
1BXg8189.t1,




4956; 4514;
1AXg4879.t1,
4845;
1BXg8837.t1,




4957
1AXg9624.t1,
4820;
3BXg11471.t1,





3AXg10151.t1,
4819;
3BXg11779.t1,





3AXg1507.t1,
4916;
3BXg11859.t1,





3AXg1833.t1,
4473
3BXg8700.t1





3AXg3620.t1,





3AXg7460.t1,





3AXg7667.t1


GO: 0008168
methyltransferase
4799; 4663;
3AXg3246.t1,
4797;
3BXg5144.t1,
0.14079



activity
4662
3AXg512.t1,
4492
3BXg7176.t1





3AXg618.t1









These data suggest that numerous biological processes are different in beneficial endophytes, for example as compared to neutral endophytes. Some of these processes include cell wall degradation, starch and sucrose metabolism, and protection from oxidative stress.


One mechanism of entry of endophytes into intact plant tissue is by enzymatic processes involving degradation of cell walls. Beneficial endophytes used in this example show increased levels of secreted proteins that may be involved in such degradation, for example those that fall within the following gene ontology annotations: GO:0005618 (cell wall), GO:0000272 (polysaccharide catabolic process), GO:0045490 (pectin catabolic process), GO:0030248 (cellulose binding), GO:0004650 (polygalacturonase activity), GO:0008810 (cellulase activity), GO:0071555 (cell wall organization), GO:0004185 (serine-type carboxypeptidase activity), GO:0016798 (hydrolase activity, acting on glycosyl bonds), and GO:0030246 (carbohydrate binding). Certain of the proteins that fall within these gene ontology annotations may also be involved in starch and sucrose metabolism.


Beneficial endophytes of the invention secreted proteins that may provide a benefit to the plant, such as proteins involved in protection against oxidative stress (GO:0016614 (oxidoreductase activity, acting on CH—OH group of donors); GO:0006979 (response to oxidative stress); GO:0005507 (copper ion binding), and GO:0004601 (peroxidase activity)).


Example 8: Greenhouse Characterization

Setup and Watering Conditions


A sandy loam growth substrate is mixed in the greenhouse and consisting of 60% loam and 40% mortar sand (Northeast Nursery, Peabody, Mass.). Prior to mixing, loam is sifted through a ⅜″ square steel mesh screen to remove larger particles and debris. Half of the appropriate fertilizers and soil treatments to be applied during the season is added to the soil mixture prior to sowing. The remaining components are provided dissolved in irrigation water at the onset of the reproductive stages of development. Substrate surface area per pot is calculated based on pot diameter in order to approximate the “acreage” of individual pots. An equivalent volume of fertilized soil is then gently added to each pot in order to minimize compaction of the soil. The substrate is saturated with water 3-4 hours before sowing.


Commercially available seeds (e.g., seeds described herein) are coated with microbial treatments using the formulation used for field trials and described herein. Treatments included microbial coatings and two controls (non-treated and formulation). Three seeds are sown evenly spaced at the points of a triangle. Soil is then overlaid atop the seeds and an additional 200 mL water was added to moisten the overlaying substrate.


Midseason Measurements and Harvest


Emergence percentage is observed. Further, at various times through the growing season, plants are assessed for onset of and recovery from stress symptoms, for example but not limited to: leaf senescence, anthesis-silking interval, leaf chlorophyll content, grain weight, and total yield.


To compare treated plants to controls, a fully Bayesian robust t-test is performed. Briefly, R (R Core Team, 2015) was used with the BEST package (Kruschke and Meredith, 2015) and JAGS (Plummer, 2003) to perform a Markov Chain Monte Carlo estimation of the posterior distribution the likely differences between the two experimental groups. A 95% highest density interval (HDI) is overlayed onto this distribution to aid in the interpretation of whether the two biological groups truly differ.


Tissue Collection and Processing for Transcriptomics, Hormone, and Metabolomics Analysis


In order to assess the effects of endophyte treatment on plant growth at the transcriptomic, phytohormone, and metabolomic levels, plants are harvested. Three pots from each treatment are selected. Once separated, the tissues (roots, stems, leaves, other plant elements as appropriate) from the three pots of each treatment are pooled. For collection, first all loosely attached substrate is removed from the roots by gently tapping and shaking the roots. Any adherent substrate is removed by submerging the roots in water and manually dislodging attached soil and debris. The roots are then blotted dry before being cut from the aerial tissue, followed by separating petioles and leaves from the stem. As tissues are removed from the plant they are immediately bagged and frozen in liquid nitrogen. All harvested tissues are kept in liquid nitrogen or stored at −80° C. until further processing.


To prepare for analyses, the tissues are ground with liquid nitrogen using a pre-chilled mortar and pestle. Approximately 100-200 micrograms of each ground sample pool is transferred to a chilled 1.5 mL microtube for RNA extraction and subsequent transcriptome, phytohormone and metabolite analysis. For proteomic analysis, 3 g of each ground sample pool is used. The remaining ground tissue is then transferred to a chilled 50 mL conical tube and stored in liquid nitrogen or at −80° C. until shipment for further analyses.


Example 9: Assessment of Plant Colonization

The protocols described in this section allow confirmation of successful colonization of plants by endophytes, for example by direct recovery of viable colonies from various tissues of the inoculated plant.


Recovery of Viable Colonies from Seeds


Seeds are surface-sterilized by exposing them to chlorine gas overnight, using the methods described elsewhere. Sterile seeds are then inoculated with submerged in 0.5 OD overnight cultures (Tryptic Soy Broth, TSB) of bacteria and allowed to briefly air dry. The seeds are then placed in tubes filled partially with a sterile sand-vermiculite mixture [(1:1 wt:wt)] and covered with 1 inch of the mixture, watered with sterile water, sealed and incubated in a greenhouse for 7 days. After incubation, various tissues of the plants are harvested and used as donors to isolate bacteria by placing tissue section in a homogenizer (TSB 20%) and mechanical mixing. The slurry is then serially diluted in 10-fold steps to 10-3 and dilutions 1 through 10-3 are plated on TSA 20% plates (1.3% agar). Plates are incubated overnight and pictures are taken of the resulting plates as well as colony counts for CFU. Bacteria are identified visually by colony morphotype and molecular methods described herein. Representative colony morphotypes are also used in colony PCR and sequencing for isolate identification via ribosomal gene sequence analysis as described herein. These trials are repeated twice per experiment, with 5 biological samples per treatment.


Culture-Independent Methods to Confirm Colonization of the Plant or Seeds by Bacteria or Fungi.


One way to detect the presence of endophytes on or within plants or seeds is to use quantitative PCR (qPCR). Internal colonization by the endophyte can be demonstrated by using surface-sterilized plant tissue (including seed) to extract total DNA, and isolate-specific fluorescent MGB probes and amplification primers are used in a qPCR reaction. An increase in the product targeted by the reporter probe at each PCR cycle therefore causes a proportional increase in fluorescence due to the breakdown of the probe and release of the reporter. Fluorescence is measured by a quantitative PCR instrument and compared to a standard curve to estimate the number of fungal or bacterial cells within the plant.


Experimental Description

The design of both species-specific amplification primers, and isolate-specific fluorescent probes are well known in the art. Plant tissues (seeds, stems, leaves, flowers, etc.) are pre-rinsed and surface sterilized using the methods described herein.


Total DNA is extracted using methods known in the art, for example using commercially available Plant-DNA extraction kits, or the following method.


1. Tissue is placed in a cold-resistant container and 10-50 mL of liquid nitrogen is applied. Tissues are then macerated to a powder.


2. Genomic DNA is extracted from each tissue preparation, following a chloroform:isoamyl alcohol 24:1 protocol (Sambrook et al., 1989).


Quantitative PCR is performed essentially as described by Gao et al. (2010) with primers and probe(s) specific to the desired isolate using a quantitative PCR instrument, and a standard curve is constructed by using serial dilutions of cloned PCR products corresponding to the specie-specific PCR amplicon produced by the amplification primers. Data are analyzed using instructions from the quantitative PCR instrument's manufacturer software.


As an alternative to qPCR, Terminal Restriction Fragment Length Polymorphism, (TRFLP) can be performed, essentially as described in Johnston-Monje and Raizada (2011). Group specific, fluorescently labelled primers are used to amplify a subset of the microbial population, especially bacteria, especially fungi, especially archaea, especially viruses. This fluorescently labelled PCR product is cut by a restriction enzyme chosen for heterogeneous distribution in the PCR product population. The enzyme cut mixture of fluorescently labelled and unlabeled DNA fragments is then submitted for sequence analysis on a Sanger sequence platform such as the Applied Biosystems 3730 DNA Analyzer.


Immunological Methods to Detect Microbes in Seeds and Vegetative Tissues


A polyclonal antibody is raised against specific bacteria X or fungus Y strains via standard methods. A polyclonal antibody is also raised against specific GUS and GFP proteins via standard methods. Enzyme-linked immunosorbent assay (ELISA) and immunogold labeling is also conducted via standard methods, briefly outlined below.


Immunofluorescence microscopy procedures involve the use of semi-thin sections of plant element or adult plant tissues transferred to glass objective slides and incubated with blocking buffer (20 mM Tris (hydroxymethyl)-aminomethane hydrochloride (TBS) plus 2% bovine serum albumin, pH 7.4) for 30 min at room temperature. Sections are first coated for 30 min with a solution of primary antibodies and then with a solution of secondary antibodies (goat anti-rabbit antibodies) coupled with fluorescein isothiocyanate (FITC) for 30 min at room temperature. Samples are then kept in the dark to eliminate breakdown of the light-sensitive FITC. After two 5-min washings with sterile potassium phosphate buffer (PB) (pH 7.0) and one with double-distilled water, sections are sealed with mounting buffer (100 mL 0.1 M sodium phosphate buffer (pH 7.6) plus 50 mL double-distilled glycerine) and observed under a light microscope equipped with ultraviolet light and a FITC Texas-red filter.


Ultrathin (50- to 70-nm) sections for TEM microscopy are collected on pioloform-coated nickel grids and are labeled with 15-nm gold-labeled goat anti-rabbit antibody. After being washed, the slides are incubated for 1 h in a 1:50 dilution of 5-nm gold-labeled goat anti-rabbit antibody in IGL buffer. The gold labeling is then visualized for light microscopy using a BioCell silver enhancement kit. Toluidine blue (0.01%) is used to lightly counterstain the gold-labeled sections. In parallel with the sections used for immunogold silver enhancement, serial sections are collected on uncoated slides and stained with 1% toluidine blue. The sections for light microscopy are viewed under an optical microscope, and the ultrathin sections are viewed by TEM.


Example 10: Assessment of Improved Plant Characteristics: Differentially Regulated Hormones

Methods


For hormone analysis, 100±10 mg tissue is measured into microtubes (chilled with liquid nitrogen), and sent on dry ice to a vendor. Plant hormone analysis is performed per Christiansen et al. (2014) with slight modification. Briefly, hormones are extracted from 100±10 mg of frozen tissue and tissue weights are recorded for quantification. A mixture containing 10 microliters of 2.5 microMolar internal standards and 500 microliters of extraction buffer [1-propanol/H2O/concentrated HCl (2:1:0.002, vol/vol/vol) is added to each sample and vortexed until thawed. Samples are agitated for 30 min at 4° C., then 500 microliters of dichloromethane (CH2Cl2) is added. Samples are agitated again for 30 min at 4° C., and then centrifuged at 13,000×g for 5 min. in darkness. The lower organic layer is removed into a glass vial and the solvent is evaporated by drying samples for 30-40 min under a N2 stream. Samples are re-solubilized in 150 microliters of MeOH, shaken for 1 min and centrifuged at 14,000×g for 2 min. A supernatant of 90 microliters is transferred into the autosampler vial and hormones are analyzed by ultraperformance liquid chromatography, coupled to mass spectrometry (UPLC-MS/MS). Ascentis Express C-18 Column (3 cm×2.1 mm, 2.7 cm) is connected to an API 3200 using electrospray ionization-tandem mass spectrometry (MS/MS) with scheduled multiple reaction monitoring (SMRM). The injection volume is 5 microliters and has a 300 microliters/min mobile phase consisting of Solution A (0.05% acetic acid in water) and Solution B (0.05% acetic acid in acetonitrile) with a gradient consisting of (time-% B): 0.3-1%, 2-45%, 5-100%, 8-100%, 9-1%, 11-stop. Quantitation is carried out with Analyst software (AB Sciex), using the internal standards as a reference for extraction recovery. Leaf, root, and/or other tissue is saved in −62° C. and saved for subsequent gene expression analysis.


Mass spectra of plant hormones are obtained. Fold changes between control and treated samples are calculated by dividing the mass spectrum value from the treated sample by the value from the control sample.


Modulation of hormones related to growth as well as related to resistance to abiotic and biotic stresses are found in plants treated with endophytes as compared to isoline plants lacking such treatment.


Example 11: Assessment of Improved Plant Characteristics and Differentially Regulated Metabolites

Methods


For metabolite analysis, 150±10 mg of each sample is transferred into 1.5 mL microtubes (chilled in liquid nitrogen) and sent on dry ice to the Proteomics and Metabolomics Facility at Colorado State University. Metabolomics data acquisition is performed per the following methods provided by Dr. Corey Broeckling at CSU. To prepare the samples for analysis, phytohormones are extracted from ground plant material using a biphasic protocol. One mL of a methyl tert-butyl ether (MTBE): methanol:water mixture (6:3:1) is added to each sample then shaken for 1 hour. Next, 250 microliters cold water and a mix of internal standards are added to each sample to promote phase separation. Samples are shaken again for 5 minutes. Samples are then centrifuged at 2,095×g at 4° C. for 15 minutes. The organic top phase is removed for hormone analysis, dried under an inert nitrogen environment, then re-suspended in 400 microliters of 50% acetonitrile. Extracts are then directly analyzed by LC-MS.


For GC-MS, the polar (lower phase) extract is dried using a speedvac, resuspended in 50 microliters of pyridine containing 50 mg/mL of methoxyamine hydrochloride, incubated at 60° C. for 45 min, sonicated for 10 min, and incubated for an additional 45 min at 60° C. Next, 25 microliters of N-methyl-N-trimethylsilyltrifluoroacetamide with 1% trimethylchlorosilane (MSTFA+1% TMCS, Thermo Scientific) is added and samples re incubated at 60° C. for 30 min, centrifuged at 3000×g for 5 min, cooled to room temperature, and 80 microliters of the supernatant is transferred to a 150 microliters glass insert in a GC-MS autosampler vial. Metabolites are detected using a Trace GC Ultra coupled to a Thermo ISQ mass spectrometer (Thermo Scientific). Samples are injected in a 1:10 split ratio twice in discrete randomized blocks. Separation occurs using a 30 m TG-5MS column (Thermo Scientific, 0.25 mm i.d., 0.25 micrometer film thickness) with a 1.2 mL/min helium gas flow rate, and the program consists of 80° C. for 30 sec, a ramp of 15° C. per min to 330° C., and an 8 min hold. Masses between 50-650 m/z re scanned at 5 scans/sec after electron impact ionization. The ionization source is cleaned and retuned and the injection liner replaced between injection replicates. Analysis for plant hormones is performed by UPLC-MS/MS as follows.


Metabolites are detected and mass spectra annotated by comparing to libraries of known spectra including an in-house database at CSU (LC-MS only), the National Institute of Standards and Technology databases, Massbank MS database, and the Golm Metabolite Database. Initial annotation is automated, followed by manual validation of annotations. Following annotation, compounds are identified. After removal of technical artifacts (e.g. siloxane), and ambiguous or vague annotations (e.g. carbohydrate or saccharide), identified compounds remain for analysis. These compounds are assessed for fold change over control plants. Metabolites are grouped by pathways (e.g. carbohydrate metabolism or alkaloid biosynthesis) and the KEGG database and literature are manually referenced to identify pertinent shifts in metabolic patterns in plants treated with microbes. Any compound without an appreciable shift compared to that observed in control plants is removed from further analysis.


Modulation of metabolites related to growth as well as related to resistance to abiotic and biotic stresses are found in plants treated with endophytes as compared to isoline plants lacking such treatment.


Example 12: Efficacy Testing of Endophytes in Crop Production

Method


Whole plants or plant elements, such as seeds, roots, or leaves, from any of the crops useful in the invention are treated with endophytes as described in Examples 3, 4, or 8. They are then sown in a variety in different growing regions for efficacy testing. Trials consist of ten replicate plots for each treatment and control respectively arranged in a spatially balanced randomized complete block design (Van Es et al. 2007). In addition to measuring total yield, metrics such as seedling emergence, normalized difference vegetation index (NDVI) and time to flowering are assessed. Endophytes are applied alone as a seed treatment, as well as in combination with other endophytes.


Results


Crop plants that have been treated with the endophyte(s) of the present invention demonstrate improvements in one or more agronomically-important characteristic, for example but not limited to: disease resistance, drought tolerance, heat tolerance, cold tolerance, salinity tolerance, metal tolerance, herbicide tolerance, chemical tolerance, improved water use efficiency, improved nitrogen utilization, improved nitrogen fixation, pest resistance, herbivore resistance, pathogen resistance, increased yield, increased yield under water-limited conditions, health enhancement, vigor improvement, growth improvement, photosynthetic capability improvement, nutrition enhancement, altered protein content, altered oil content, increased biomass, increased shoot length, increased root length, improved root architecture, improved plant standability, increased plant element weight, altered plant element carbohydrate composition, altered plant element oil composition, number of pods, delayed senescence, stay-green, and altered plant element protein composition.


Example 13: Generating/Isolating Endophytes Compatible with Agrochemicals

The application of pesticides against fungal pathogens of agriculturally-relevant plants is a common practice in agriculture to ensure higher yields. One method of pesticide delivery is to cover the seeds with a coating with pesticides. Although pesticides are meant to deter the growth and propagation of pathogenic microorganisms, they may also affect endophyte populations residing inside of the seed. For this purpose, conferring compatibility mechanisms to endophytic fungi providing beneficial properties which are sensitive to these compounds is desirable for the maintenance of endophytes in the seeds.


Compatibility with pesticides can be intrinsic (naturally pesticide compatible fungi, for example) or acquired (due to mutations in the genetic material of the microorganism, or to the introduction of exogenous DNA by natural DNA transfer).


Fungicides used as protectants are effective only on the seed surface, providing protection against seed surface-borne pathogens and providing some level of control of soil-borne pathogens. These products generally have a relatively short residual. Protectant fungicides such as captan, maneb, thiram, or fludioxonil help control many types of soil-borne pathogens, except root rotting organisms. Systemic fungicides are absorbed into the emerging seedling and inhibit or kill susceptible fungi inside host plant tissues. Systemic fungicides used for seed treatment include the following: azoxystrobin, carboxin, mefenoxam, metalaxyl, thiabendazole, trifloxystrobin, and various triazole fungicides, including difenoconazole, ipconazole, tebuconazole, and triticonazole. Mefenoxam and metalaxyl are primarily used to target the oomycetes such as species of Pythium and Phytophthora.


Strobilurin analogues, such as azoxystrobin, inhibit mitochondrial respiration by blocking electron transfer at the cytochrome bcl complex. Phenylamides, including metalaxyl, interfere with RNA synthesis in target fungi. Oxathiin systemic fungicides like carboxin inhibits the incorporation of phenylalanine into protein and of uracil into RNA. Azole fungicides BAS 480F, flusilazole, and tebuconazole are inhibitors of sterol 14α-demethylase, and block sterol biosynthesis.


I. Determination of Intrinsic Resilience Against Agrochemicals of Bacteria Cultured from Seeds


To test the intrinsic resilience pesticides of bacteria isolated as described herein, minimum inhibitory concentration (MIC) assays are performed on all isolated bacteria of interest, as described in Wiegand, Irith, Kai Hilpert, and Robert E W Hancock. Nature protocols 3.2 (2008): 163-175, which is incorporated herein by reference in its entirety. Briefly, known concentrations of bacterial cells or spores are used to inoculate plates containing solid media with different concentrations of the pesticide, or to inoculate liquid media containing different concentrations of the pesticide (in a 96-well plate). The pesticides are used at the concentration recommended by the manufacturer for seed coating, and two-fold dilutions down to 0.000125 (12 two-fold dilutions). Growth is assessed after incubation for a defined period of time (16-20 h) and compared to cultures grown in the same manner without any pesticides as control. The MIC value is determined as described in Wiegand, Irith, Kai Hilpert, and Robert E W Hancock. Nature protocols 3.2 (2008): 163-175.


II. Determination of Intrinsic Resilience Against Agrochemicals of Fungi Cultured from Seeds


To test the intrinsic resilience against pesticides of the fungi isolated as described in this application, minimum inhibitory concentration (MIC) assays are performed on all isolated fungi of interest, as described in Mohiddin, F. A., and M. R. Khan. African Journal of Agricultural Research 8.43 (2013): 5331-5334 (incorporated herein by reference in its entirety), with the following changes: Briefly, double strength potato dextrose agar is prepared containing different concentrations of each pesticide. The pesticides are applied at the concentration recommended by the manufacturer, and also in two fold dilutions to 0.000125× (12 two-fold dilutions). Thereafter, the plates are seeded centrally with a 3 mm disc of 4 days old culture of each fungus that had been centrifuged and rinsed twice in sterile phosphate buffer. PDA plates without a fungicide but inoculated with the fungi serve as a control. The inoculated plates are incubated at 25±2° C. for 5 days. The radial growth of the colony in each treatment is measured and the percent inhibition of growth is calculated as described by Mohiddin, F. A., and M. R. Khan. African Journal of Agricultural Research 8.43 (2013): 5331-5334 (incorporated herein by reference in its entirety). Fungal isolates are classified as resilience against the particular pesticide if their maximum tolerance concentration (MTC) is 2× or above the concentration of pesticides recommended to be used in seed coatings.


III. Generating Fungal Species with Compatibility with Commercial Pesticides Coated onto Seeds


When a fungal strain of interest that provides a beneficial property to its plant host is found to be sensitive to a commercially-relevant pesticide, pesticide-compatible variants of the strains need to be generated for use in this application. Generation of compatibility to multiple pesticides or cocktails of pesticides is accomplished by sequentially selecting compatible variants to each individual pesticide and then confirming compatibility with a combination of the pesticides. After each round of selection, fungi are tested for their ability to form symbiotic relationships with the plants and to confirm that they provide a beneficial property on the plant as did the parental strain, with or without application of the pesticide product as described herein.


Generation and isolation of pesticide-compatible strains derived from endophytic strains isolated from seeds and shown to provide beneficiary traits to plants is performed as described by Shapiro-Ilan, David I., et al. Journal of invertebrate pathology 81.2 (2002): 86-93 (incorporated herein by reference in its entirety), with some changes. Briefly, spores of the isolated fungi are collected and solutions containing between ˜1×103 spores are used to inoculate potato dextrose agar (PDA) plates containing 2, 5, and 10 times the MTC of the particular strain. Plates are incubated for 1-5 days and a single colony from the highest concentration of pesticide which allows growth is inoculated onto a fresh plate with the same pesticide concentration 7 consecutive times. After compatibility has been established, the strain is inoculated onto PDA plates 3 consecutive times and then inoculated onto a PDA plate containing the pesticide to confirm that the compatibility trait is permanent.


Alternatively, if this method fails to provide a compatible strain, a spore suspension is treated with ethyl methanesulfonate to generate random mutants, similarly as described by Leonard, Cory A., Stacy D. Brown, and J. Russell Hayman. International journal of microbiology 2013 (2013), Article ID 901697 (incorporated herein by reference in its entirety) and spores from this culture are used in the experiment detailed above.


To develop fungal endophytes compatible with multiple pesticides or cocktails of pesticides, spores of a strain compatible with one or more pesticides are used to select for variants to a new pesticide as described above. Strains developed this way are tested for retention of the pesticide-compatibility traits by inoculating these strains onto PDA plates containing each single pesticide or combinations of pesticides.


IV. Generating Bacterial Species with Compatibility to Commercial Pesticides Coated onto Seeds


When a bacterial strain of interest is found to be sensitive to a commercially-relevant pesticide, generation of pesticide-compatible variants of the strains can be generated for use in this application. Generation of compatible with multiple pesticides or cocktails of pesticides is accomplished by first sequentially selecting variants compatible with incrementally higher concentrations of each individual pesticide (as described by Thomas, Louise, et al. Journal of Hospital Infection 46.4 (2000): 297-303, which is incorporated herein by reference in its entirety). To develop bacterial endophytes compatible with multiple pesticides or cocktails of pesticides, bacterial cells of a strain compatible with one or more pesticides is used to select for variants to a new pesticide as described above. Strains developed this way are tested for retention of the pesticide-compatible traits by inoculating these strains onto PDA plates containing each single pesticide or combinations of pesticides.


After each round of selection, bacteria are tested for their ability to live within plants and for their ability to provide the same beneficial property to the plant as did the parental strain, with or without application of the pesticide product to the plants as described herein.


V. Generation of Pesticide-Compatible Bacteria by Insertion of a Resistance Plasmid


Many bacterial plasmids that confer compatible pesticides have been described in the literature (Don, R. H., and J. M. Pemberton. Journal of Bacteriology 145.2 (1981): 681-686; and Fisher, P. R., J. Appleton, and J. M. Pemberton. Journal of bacteriology 135.3 (1978): 798-804, each of which is incorporated herein by reference in its entirety)


For cases in which obtaining naturally occurring compatible bacteria is not feasible, use of these plasmids is a possible way to develop endophytic strains compatible with multiple pesticides.


For example, a Pseudomonas fluorescens strain that provides anti-nematode properties to plants but is sensitive to the pesticides 2,4-dichlorophenoxyacetic acid and 4-chloro-2-methylphenoxyacetic can be transformed with the plasmid pJP2 (isolated from Alcaligenes eutrophus) which provides transmissible compatible with these compounds, as described by Don and Pemberton, 1981. Briefly, plasmids are transferred by conjugation to Pseudomonas, using the method described in Haas, Dieter, and Bruce W. Holloway. Molecular and General Genetics 144.3 (1976): 243-251 (incorporated herein by reference in its entirety).


After the generation of bacteria carrying pesticide-compatibility conferring plasmids, these endophytes are tested for their ability to live inside plant tissues and for their ability to provide the same beneficial property to the plant as it did for the parental strain, with or without application of the pesticide product to the plants as described herein.


VI. Growth and Scale-Up of Bacteria for Inoculation on Solid Media


The bacterial isolates are grown by loop-inoculation of a single colony into R2A broth (supplemented with appropriate antibiotics) in 100 mL flasks. The bacterial culture is incubated at 30±2° C. for 2 days at 180 rpm in a shaking incubator (or under varying temperatures and shaking speeds as appropriate). This liquid suspension is then used to inoculate heat sterilized vermiculite powder that is premixed with sterile R2A broth (without antibiotics), resulting in a soil like mixture of particles and liquid. This microbial powder is then incubated for an additional couple of days at 30±2° C. with daily handshaking to aerate the moist powder and allow bacterial growth. Microbially inoculated vermiculite powder is now ready for spreading on to soil or onto plant parts. Alternatively, the R2A broth is used to inoculate Petri dishes containing R2A or another appropriate nutrient agar where lawns of bacteria are grown under standard conditions and the solid colonies scraped off, resuspended in liquid and applied to plants as desired.


VII. Growth & Scale-Up of Fungi for Inoculation on Solid Media


Once a fungal isolate has been characterized, conditions are optimized for growth in the lab and scaled-up to provide sufficient material for assays. For example, the medium used to isolate the fungus is supplemented with nutrients, vitamins, co-factors, plant-extracts, and other supplements that can decrease the time required to grow the fungal isolate or increase the yield of mycelia and/or spores the fungal isolate produces. These supplements can be found in the literature or through screening of different known media additives that promote the growth of all fungi or of the particular fungal taxa.


To scale up the growth of fungal isolates, isolates are grown from a frozen stock on several Petri dishes containing media that promotes the growth of the particular fungal isolate and the plates are incubated under optimal environmental conditions (temperature, atmosphere, light). After mycelia and spore development, the fungal culture is scraped and resuspended in 0.05M Phosphate buffer (pH 7.2, 10 mL/plate). Disposable polystyrene Bioassay dishes (500 cm2, Thermo Scientific Nunc UX-01929-00) are prepared with 225 mL of autoclaved media with any required supplements added to the media, and allowed to solidify. Plates are stored at room temperature for 2-5 days prior to inoculation to confirm sterility. 5 mL of the fungal suspension is spread over the surface of the agar in the Bioassay plate in a biosafety cabinet, plates are allowed to dry for 1 h, and they are then incubated for 2-5 days, or until mycelia and/or spores have developed.


A liquid fungal suspension is then created via the following. Fungal growth on the surface of the agar in the Bioassay plates are then scraped and resuspended in 0.05M Phosphate buffer (pH 7.2). OD600 readings are taken using a spectrometer and correlated to previously established OD600/CFU counts to estimate fungal population densities, and the volume adjusted with additional sodium phosphate buffer to result in 100 mL aliquots of fungi at a density of approximately 106-1011 spores/mL. This suspension may or may not be filtered to remove mycelia and can be used to create a liquid microbial formulation as described herein to apply the fungal isolate onto a plant, plant part, or seed.


VIII. Growth & Scale-Up of Bacteria for Inoculation in Liquid Media


Bacterial strains are grown by loop-inoculation of one single colony into R2A broth (amended with the appropriate antibiotics) in 100 mL flasks. The bacterial culture is incubated at 28±2° C. for 1 day at 180 rpm in a shaking incubator (or under varying temperatures and shaking speeds as appropriate). The bacteria are pelleted by centrifugation and resuspended in sterile 0.1 M sodium phosphate. OD600 readings are taken using a spectrometer and correlated to previously established OD600/CFU counts to estimate bacterial population densities, and the volume adjusted with additional sodium phosphate buffer to result in 100 mL aliquots of bacteria at a density of 1×108 cells/mL. To help break surface tension, aid bacterial entry into plants and provide microbes for some energy for growth, 10 μL of Silwet L-77 surfactant and 1 g of sucrose is added to each 100 mL aliquot (resulting in 0.01% v/v and 1% v/v concentrations, respectively) in a similar way as in the protocol for Agrobacterium-mediated genetic transformation of Arabidopsis thaliana seed [Clough, S., Bent, A. (1999) The Plant Journal 16(6): 735-743].


IX. Growth & Scale-Up of Fungi for Inoculation in Liquid Media


Once a fungal isolate has been characterized, conditions are optimized for growth in the lab and scaled-up to provide enough material for assays. For example, the medium used to isolate the fungi is supplemented with nutrients, vitamins, co-factors, plant-extracts, and/or other supplements that can decrease the time required to grow the fungal isolate and/or increase the yield of mycelia and/or spores the fungal isolate produces. These supplements can be found in the literature or through screening of different known media additives that promote the growth of all fungi or of the particular fungal taxa.


To scale up the growth of fungal isolates, isolates are grown from a frozen stock on Petri dishes containing media that promotes the growth of the particular fungal isolate and the plates are incubated under optimal environmental conditions (temperature, atmosphere, light). After mycelia and spore development, the fungal culture is scraped and resuspended in 0.05M Phosphate buffer (pH 7.2, 10 mL/plate). 1 liter of liquid media selected to grow the fungal culture is prepared in 2 L glass flasks and autoclaved and any required supplements added to the media. These are stored at room temperature for 2-5 days prior to inoculation to confirm sterility. 1 mL of the fungal suspension is added aseptically to the media flask, which is then incubated for 2-5 days, or until growth in the liquid media has reached saturation. Spore counts are determined using hemacytometer and correlated to previously established OD600/CFU counts to estimate fungal population densities, and the volume adjusted with additional sodium phosphate buffer to result in 100 mL aliquots of fungi at a density of approximately 106-1011 spores/mL. This suspension may or may not be filtered to remove mycelia and can be used to create a liquid microbial formulation as described herein to apply the fungal isolate onto a plant, plant part, or seed.


X. Creation of Liquid Microbial Formulations or Preparations for the Application of Microbes to Plants


Bacterial or fungal cells are cultured in liquid nutrient broth medium to between 102-1012 CFU/mL. The cells are separated from the medium and suspended in another liquid medium if desired. The microbial formulation may contain one or more bacterial or fungal strains. The resulting formulation contains living cells, lyophilized cells, or spores of the bacterial or fungal strains. The formulation may also contain water, nutrients, polymers and binding agents, surfactants or polysaccharides such as gums, carboxymethylcellulose and polyalcohol derivatives. Suitable carriers and adjuvants can be solid or liquid and include natural or regenerated mineral substances, solvents, dispersants, wetting agents, tackifiers, thickeners, binders or fertilizers. Compositions can take the form of aqueous solutions, oil-in-water emulsions, or water-in-oil emulsions. Small amounts of insoluble material can optionally be present, for example in suspension in the medium, but it is generally preferred to minimize the presence of such insoluble material.


XI. Inoculation of Plants by Coating Microbes Directly onto Seed


Seed is treated by coating it with a liquid microbial formulation (prepared as described herein) comprising microbial cells and other formulation components, directly onto the seed surface at the rate of 102-108 microbial CFU per seed. Seeds are soaked in liquid microbial formulation for 1, 2, 3, 5, 10, 12, 18 or 24 hours or 2, 3, or 5 days. After soaking in microbial formulation, seeds are planted in growing containers or in an outdoor field. Seeds may also be coated with liquid microbial formulation by using an auger or a commercial batch treater. One or more microbial formulations or other seed treatments are applied concurrently or in sequence. Treatment is applied to the seeds using a variety of conventional treatment techniques and machines, such as fluidized bed techniques, augers, the roller mill method, rotostatic seed treaters, and drum coaters. Other methods, such as spouted beds may also be useful. The seeds are pre-sized before coating. Optionally the microbial formulation is combined with an amount of insecticide, herbicide, fungicide, bactericide, or plant growth regulator, or plant micro- or macro-nutrient prior to or during the coating process. After coating, the seeds are typically dried and then transferred to a sizing machine for grading before planting. Following inoculation, colonization of the plants or seeds produced therefrom is confirmed via any of the various methods described herein. Growth promotion or stress resilience benefits to the plant are tested via any of the plant growth testing methods described herein.


XII. Inoculation of Plants with a Combination of Two or More Microbes


Seeds can be coated with bacterial or fungal endophytes. This method describes the coating of seeds with two or more bacterial or fungal strains. The concept presented here involves simultaneous seed coating of two microbes (e.g., both a gram negative endophytic bacterium Burkholderia phytofirmans and a gram positive endophytic bacterium Bacillus mojavensis). Optionally, both microbes are genetically transformed by stable chromosomal integration as follows. Bacillus mojavensis are transformed with a construct with a constitutive promoter driving expression of a synthetic operon of GFPuv and spectinomycin resistance genes, while Burkholderia phytofirmans are transformed with a construct with a constitutive promoter driving expression of the lac operon with an appended spectinomycin resistance gene. Seeds are coated with a prepared liquid formulation of the two microbes the various methods described herein. Various concentrations of each endophyte in the formulation is applied, from 102 CFU/seed to about 108 CFU/seed. Following inoculation, colonization of the plants or seeds produced therefrom may be confirmed via any of the various methods described herein. Growth promotion or stress resilience benefits to the plant are tested via any of the plant growth testing methods described herein.


XIII. Culturing to Confirm Colonization of Plant by Bacteria


The presence in the seeds or plants of GFPuv or gusA-labeled endophytes can be detected by colony counts from mashed seed material and germinated seedling tissue using R2A plates amended with 5-Bromo-4-chloro-3-indolyl β-D-glucuronide (X-glcA, 50 μg/mL), IPTG (50 μg/mL) and the antibiotic spectinomycin (100 μg/mL). Alternatively, bacterial or fungal endophytes not having received transgenes can also be detected by isolating microbes from plant, plant tissue or seed homogenates (optionally surface-sterilized) on antibiotic free media and identified visually by colony morphotype and molecular methods described herein. Representative colony morphotypes are also used in colony PCR and sequencing for isolate identification via ribosomal gene sequence analysis as described herein. These trials are repeated twice per experiment, with 5 biological samples per treatment.


XIV. Culture-Independent Methods to Confirm Colonization of the Plant or Seeds by Bacteria or Fungi


One way to detect the presence of endophytes on or within plants or seeds is to use quantitative PCR (qPCR). Internal colonization by the endophyte can be demonstrated by using surface-sterilized plant tissue (including seed) to extract total DNA, and isolate-specific fluorescent MGB probes and amplification primers are used in a qPCR reaction. An increase in the product targeted by the reporter probe at each PCR cycle therefore causes a proportional increase in fluorescence due to the breakdown of the probe and release of the reporter. Fluorescence is measured by a quantitative PCR instrument and compared to a standard curve to estimate the number of fungal or bacterial cells within the plant.


XV. Experimental Description


The design of both species-specific amplification primers, and isolate-specific fluorescent probes are well known in the art. Plant tissues (seeds, stems, leaves, flowers, etc.) are pre-rinsed and surface sterilized using the methods described herein.


Total DNA is extracted using methods known in the art, for example using commercially available Plant-DNA extraction kits, or the following method.

    • 1. Tissue is placed in a cold-resistant container and 10-50 mL of liquid nitrogen is applied. Tissues are then macerated to a powder.
    • 2. Genomic DNA is extracted from each tissue preparation, following a chloroform:isoamyl alcohol 24:1 protocol (Sambrook, Joseph, Edward F. Fritsch, and Thomas Maniatis. Molecular cloning. Vol. 2. New York: Cold spring harbor laboratory press, 1989.).


Quantitative PCR is performed essentially as described by Gao, Zhan, et al. Journal of clinical microbiology 48.10 (2010): 3575-3581 with primers and probe(s) specific to the desired isolate using a quantitative PCR instrument, and a standard curve is constructed by using serial dilutions of cloned PCR products corresponding to the specie-specific PCR amplicon produced by the amplification primers. Data are analyzed using instructions from the quantitative PCR instrument's manufacturer software.


As an alternative to qPCR, Terminal Restriction Fragment Length Polymorphism, (TRFLP) can be performed, essentially as described in Johnston-Monje D, Raizada M N (2011) PLoS ONE 6(6): e20396. Group specific, fluorescently labelled primers are used to amplify a subset of the microbial population, especially bacteria, especially fungi, especially archaea, especially viruses. This fluorescently labelled PCR product is cut by a restriction enzyme chosen for heterogeneous distribution in the PCR product population. The enzyme cut mixture of fluorescently labelled and unlabeled. DNA fragments is then submitted for sequence analysis on a Sanger sequence platform such as the Applied Biosystems 3730 DNA Analyzer.


XVI. Immunological Methods to Detect Microbes in Seeds and Vegetative Tissues


A polyclonal antibody is raised against specific bacteria X or fungus Y strains via standard methods. A polyclonal antibody is also raised against specific GUS and GFP proteins via standard methods. Enzyme-linked immunosorbent assay (ELISA) and immunogold labeling is also conducted via standard methods, briefly outlined below.


Immunofluorescence microscopy procedures involve the use of semi-thin sections of seed or seedling or adult plant tissues transferred to glass objective slides and incubated with blocking buffer (20 mM Tris (hydroxymethyl)-aminomethane hydrochloride (TBS) plus 2% bovine serum albumin, pH 7.4) for 30 min at room temperature. Sections are first coated for 30 min with a solution of primary antibodies and then with a solution of secondary antibodies (goat anti-rabbit antibodies) coupled with fluorescein isothiocyanate (FITC) for 30 min at room temperature. Samples are then kept in the dark to eliminate breakdown of the light-sensitive FITC. After two 5-min washings with sterile potassium phosphate buffer (PB) (pH 7.0) and one with double-distilled water, sections are sealed with mounting buffer (100 mL 0.1 M sodium phosphate buffer (pH 7.6) plus 50 mL double-distilled glycerine) and observed under a light microscope equipped with ultraviolet light and a FITC Texas-red filter.


Ultra-thin (50- to 70-nm) sections for TEM microscopy are collected on pioloform-coated nickel grids and are labeled with 15-nm gold-labeled goat anti-rabbit antibody. After being washed, the slides are incubated for 1 h in a 1:50 dilution of 5-nm gold-labeled goat anti-rabbit antibody in IGL buffer. The gold labeling is then visualized for light microscopy using a BioCell silver enhancement kit. Toluidine blue (0.01%) is used to lightly counterstain the gold-labeled sections. In parallel with the sections used for immunogold silver enhancement, serial sections are collected on uncoated slides and stained with 1% toluidine blue. The sections for light microscopy are viewed under an optical microscope, and the ultrathin sections are viewed by TEM.


XVII. Characterization of Uniformity of Endophytes in a Population of Seeds


To test for the homogeneity of endophytes either on the surface or colonizing the interior tissues in a population of seeds, seeds are tested for the presence of the microbes by culture-dependent and/or -independent methods. Seeds are obtained, surface sterilized and pulverized, and the seed homogenate is divided and used to inoculate culture media or to extract DNA and perform quantitative PCR. The homogeneity of colonization in a population of seeds is assessed through detection of specific microbial strains via these methods and comparison of the culture-dependent and culture-independent results across the population of seeds. Homogeneity of colonization for a strain of interest is rated based on the total number of seeds in a population that contain a detectable level of the strain, on the uniformity across the population of the number of cells or CFU of the strain present in the seed, or based on the absence or presence of other microbial strains in the seed.


XVIII. Experimental Description


Surface sterilized seeds are obtained as described herein. For culture-dependent methods of microbial-presence confirmation, bacterial and fungi are obtained from seeds essentially as described herein with the following modification. Seed homogenate is used to inoculate media containing selective and/or differential additives that will allow to identification of a particular microbe.


For qPCR, total DNA of each seed is extracted using methods known in the art, as described herein.


XIX. Characterization of Homogeneity of Colonization in Population of Plants


To test for the homogeneity of microorganisms (including endophytes) colonizing the interior in a population of plants, tissues from each plant are tested for the presence of the microbes by culture-dependent and/or -independent methods. Tissues are obtained, surface sterilized and pulverized, and the tissue material is divided and used to inoculate culture media or to extract DNA and perform quantitative PCR. The homogeneity of colonization in a population of plants is assessed through detection of specific microbial strains via these methods and comparison of the culture-dependent and culture-independent results across the population of plants or their tissues. Homogeneity of colonization for a strain of interest is rated based on the total number of plants in a population that contain a detectable level of the strain, on the uniformity across the population of the number of cells or CFU of the strain present in the plant tissue, or based on the absence or presence of other microbial strains in the plant.


XX. Experimental Description


Surface sterilized plant tissues are obtained as described herein. For culture-dependent methods of microbial-presence confirmation, bacterial and fungi are obtained from plant tissues essentially as described herein with the following modification. Plant tissue homogenate is used to inoculate media containing selective and/or differential additives that will allow identification of a particular microbe.


For qPCR, total DNA of each plant tissue is extracted using methods known in the art, as described herein.


Other embodiments will be apparent to those skilled in the art from consideration of the specification and practice of the embodiments. Consider the specification and examples as exemplary only, with a true scope and spirit being indicated by the following claims.

Claims
  • 1. A synthetic combination comprising a purified microbial population in association with a plurality of seeds or seedlings of an agricultural plant, wherein the purified microbial population comprises a first endophyte, wherein the first endophyte comprises a 16S rRNA or ITS rRNA nucleic acid sequence at least 97% identical to a nucleic acid sequence selected from the group consisting of SEQ ID NOs:1-395 and 397-455, and wherein the first endophyte is heterologously disposed to the seeds or seedlings in an amount effective to provide a benefit to the seeds or seedlings or the plants derived from the seeds or seedlings.
  • 2. The synthetic combination of claim 1, wherein the synthetic combination is present within a packaging material selected from a bag, box, bin, envelope, carton, and container.
  • 3. The synthetic combination of claim 1, wherein the purified microbial population further comprises a second endophyte, wherein the second endophyte comprises a 16S rRNA or ITS rRNA nucleic acid sequence that is less than 95% identical to that of the first endophyte.
  • 4. The synthetic combination of claim 1, wherein the purified microbial population further comprises a second endophyte, and wherein the first and second endophytes are independently capable of at least one of production of an auxin, nitrogen fixation, production of an antimicrobial, production of a siderophore, mineral phosphate solubilization, production of a cellulase, production of a chitinase, production of a xylanase, or production of acetoin, or a combination of two or more thereof.
  • 5. The synthetic combination of claim 1, wherein the purified microbial population further comprises a second endophyte, wherein the first and second endophytes are independently capable of metabolizing at least one substrate selected from the group consisting of: a-D-glucose, arabinose, arbutin, b-methyl-D-galactoside, b-methyl-D-glucoside, D-alanine, D-arabitol, D-aspartic acid, D-cellobiose, dextrin, D-fructose, D-galactose, D-gluconic acid, D-glucosamine, dihydroxyacetone, DL-malic acid, D-mannitol, D-mannose, D-melezitose, D-melibiose, D-raffinose, D-ribose, D-serine, D-threonine, D-trehalose, D-xylose, g-amino-N-butyric acid, g-cyclodextrin, gelatin, gentiobiose, glycogen, glycyl-L-aspartic acid, glycyl-L-glutamic acid, glycyl-L-proline, glyoxylic acid, i-erythritol, inosine, L-alanine, L-alanyl-glycine, L-arabinose, L-asparagine, L-aspartic acid, L-galactonic acid-g-lactone, L-glutamic acid, L-glutamine, L-histidine, L-proline, L-rhamnose, L-serine, L-threonine, maltitol, maltose, maltotriose, mannose, N-acetyl-D-glucosamine, oxalic acid, palatinose, pectin, proline, salicin, stachyose, sucrose, trehalose, turanose, tyramine, uridine, and xylose, or a combination of two or more thereof.
  • 6. The synthetic combination of claim 1, wherein the benefit is selected from the group consisting of: increased root biomass, increased root length, increased height, increased shoot length, increased leaf number, increased water use efficiency, increased tolerance to low nitrogen stress, increased nitrogen use efficiency, increased overall biomass, increased grain yield, increased photosynthesis rate, increased tolerance to drought, increased heat tolerance, increased salt tolerance, increased resistance to nematode stress, increased resistance to a fungal pathogen, increased resistance to a bacterial pathogen, increased resistance to a viral pathogen, a detectable modulation in the level of a metabolite, a detectable modulation in the transcriptome, and a detectable modulation in the proteome, relative to reference seeds or agricultural plants derived from reference seeds.
  • 7. The synthetic combination of claim 1, wherein the combination comprises seedlings and the first endophyte is contacted with the seedlings as a spray applied to one or more leaves and/or one or more roots of the seedlings.
  • 8. The synthetic combination of claim 1, wherein the first endophyte is present in an amount of at least 10 CFU or spores, at least 100 CFU or spores, at least 300 CFU or spores, at least 1,000 CFU or spores, at least 3,000 CFU or spores, at least 10,000 CFU or spores, at least 30,000 CFU or spores, at least 100,000 CFU or spores, at least 300,000 CFU or spores, or at least 1,000,000 CFU spores per seed.
  • 9. The synthetic combination of claim 1, further comprising one or more of the following selected from the group consisting of: a stabilizer, a preservative, a carrier, a surfactant, an anticomplex agent, a fungicide, a nematicide, a bactericide, a insecticide, a herbicide, and any combination thereof.
  • 10. The synthetic combination of claim 1, wherein the first endophyte is present in the synthetic combination in an amount effective to provide a benefit to the seeds or seedlings or the plants obtained from the seeds or seedlings under water limited conditions.
  • 11. The synthetic combination of claim 1, wherein the combination comprises seeds and wherein the benefit is a detectable increase in germination rate of the seeds.
  • 12. The synthetic combination of claim 1, wherein the combination comprises seedlings and the first endophyte expresses one or more genes encoding a protein whose amino acid sequence is at least 95%, at least 96%, at least 97%, at least 98%, at least 99%, or 100% identical to an amino acid sequence selected from the group consisting of SEQ ID NOs: 479, 483, 519, 532, 549, 557, 561, 562, 577, 578, 611, 626, 640, 656, 660, 666, 674, 676, 677, 678, 679, 680, 682, 683, 684, 685, 686, 688, 689, 690, 691, 692, 693, 696, 697, 698, 701, 704, 706, 710, 711, 716, 717, 718, 719, 720, 721, 722, 723, 724, 727, 728, 729, 730, 731, 732, 733, 734, 735, 737, 738, 741, 743, 744, 745, 746, 747, 748, 749, 751, 753, 756, 757, 759, 761, 762, 763, 764, 765, 766, 767, 768, 769, 771, 772, 773, 774, 775, 776, 777, 778, 779, 780, 782, 783, 784, 785, 786, 788, 790, 793, 795, 796, 797, 798, 800, 801, 802, 803, 804, 805, 806, 807, 808, 809, 810, 811, 812, 813, 815, 816, 817, 818, 819, 820, 822, 823, 824, 825, 826, 829, 830, 833, 835, 836, 837, 838, 839, 840, 841, 842, 843, 844, 846, 848, 850, 851, 853, 854, 855, 856, 857, 858, 859, 860, 864, 865, 866, 868, 869, 870, 871, 872, 873, 874, 875, 876, 877, 878, 879, 880, 881, 882, 884, 886, 887, 888, 889, 890, 891, 892, 893, 894, 895, 897, 898, 899, 901, 902, 903, 904, 905, 906, 907, 908, 910, 911, 912, 913, 914, 915, 916, 917, 918, 920, 921, 922, 923, 924, 926, 927, 928, 930, 931, 932, 933, 934, 935, 936, 937, 938, 939, 940, 941, 942, 943, 944, 945, 946, 947, 948, 949, 950, 952, 953, 954, 955, 956, 957, 958, 959, 960, 961, 962, 963, 964, 968, 969, 971, 974, 976, 978, 979, 980, 984, 985, 987, 988, 989, 992, 993, 994, 995, 996, 998, 1000, 1001, 1002, 1003, 1006, 1008, 1010, 1011, 1012, 1014, 1015, 1016, 1017, 1018, 1019, 1021, 1022, 1023, 1024, 1025, 1028, 1029, 1030, 1031, 1032, 1033, 1034, 1036, 1037, 1038, 1040, 1041, 1042, 1043, 1044, 1045, 1046, 1047, 1048, 1049, 1050, 1051, 1055, 1056, 1058, 1059, 1060, 1062, 1064, 1065, 1066, 1068, 1070, 1071, 1072, 1076, 1077, 1079, 1080, 1081, 1083, 1085, 1086, 1087, 1088, 1090, 1091, 1092, 1094, 1095, 1096, 1097, 1098, 1099, 1101, 1102, 1103, 1104, 1106, 1107, 1108, 1110, 1111, 1112, 1113, 1114, 1115, 1116, 1117, 1118, 1119, 1121, 1122, 1123, 1124, 1126, 1127, 1129, 1130, 1131, 1132, 1133, 1134, 1136, 1137, 1138, 1139, 1140, 1142, 1143, 1144, 1145, 1146, 1147, 1148, 1149, 1151, 1153, 1155, 1156, 1157, 1158, 1159, 1160, 1161, 1162, 1163, 1165, 1166, 1167, 1168, 1169, 1170, 1171, 1172, 1174, 1176, 1178, 1179, 1180, 1181, 1182, 1183, 1184, 1185, 1186, 1188, 1189, 1190, 1191, 1192, 1193, 1194, 1196, 1197, 1198, 1199, 1200, 1201, 1203, 1205, 1206, 1207, 1208, 1209, 1210, 1211, 1213, 1214, 1216, 1217, 1218, 1219, 1221, 1222, 1223, 1225, 1226, 1228, 1229, 1230, 1231, 1232, 1233, 1235, 1237, 1238, 1239, 1241, 1242, 1243, 1244, 1245, 1246, 1247, 1248, 1249, 1250, 1251, 1252, 1253, 1255, 1256, 1257, 1258, 1259, 1260, 1261, 1262, 1263, 1264, 1265, 1266, 1267, 1268, 1269, 1270, 1271, 1272, 1273, 1274, 1275, 1276, 1277, 1279, 1280, 1281, 1282, 1283, 1284, 1285, 1286, 1287, 1288, 1290, 1292, 1293, 1296, 1297, 1298, 1300, 1301, 1303, 1304, 1306, 1307, 1308, 1309, 1311, 1312, 1313, 1314, 1317, 1319, 1320, 1321, 1322, 1323, 1324, 1325, 1326, 1327, 1328, 1330, 1331, 1333, 1334, 1335, 1336, 1337, 1338, 1339, 1340, 1341, 1342, 1343, 1344, 1345, 1346, 1347, 1348, 1350, 1351, 1352, 1353, 1355, 1356, 1357, 1358, 1359, 1360, 1361, 1362, 1363, 1364, 1365, 1366, 1368, 1369, 1370, 1371, 1372, 1374, 1375, 1376, 1379, 1380, 1382, 1383, 1384, 1385, 1386, 1388, 1389, 1390, 1391, 1392, 1393, 1396, 1397, 1398, 1399, 1400, 1402, 1403, 1404, 1405, 1406, 1407, 1408, 1409, 1410, 1411, 1412, 1413, 1414, 1415, 1416, 1417, 1418, 1419, 1420, 1421, 1422, 1424, 1425, 1426, 1427, 1428, 1430, 1431, 1432, 1433, 1437, 1438, 1439, 1440, 1441, 1442, 1443, 1444, 1445, 1446, 1447, 1448, 1449, 1450, 1452, 1453, 1456, 1459, 1466, 1467, 1469, 1471, 1478, 1479, 1482, 1483, 1484, 1485, 1487, 1488, 1489, 1490, 1495, 1497, 1498, 1499, 1500, 1501, 1504, 1505, 1506, 1508, 1511, 1513, 1514, 1516, 1520, 1526, 1529, 1534, 1535, 1537, 1538, 1540, 1545, 1547, 1548, 1549, 1550, 1551, 1552, 1553, 1554, 1556, 1559, 1561, 1562, 1565, 1566, 1568, 1569, 1570, 1571, 1573, 1574, 1575, 1576, 1577, 1578, 1579, 1580, 1581, 1582, 1583, 1585, 1588, 1589, 1591, 1592, 1593, 1594, 1595, 1596, 1597, 1598, 1601, 1603, 1604, 1605, 1607, 1608, 1609, 1611, 1612, 1613, 1614, 1615, 1616, 1617, 1618, 1619, 1620, 1622, 1624, 1625, 1626, 1627, 1628, 1629, 1630, 1632, 1633, 1636, 1637, 1638, 1639, 1640, 1641, 1642, 1643, 1644, 1646, 1647, 1648, 1650, 1651, 1652, 1654, 1657, 1659, 1660, 1661, 1664, 1665, 1666, 1667, 1668, 1671, 1673, 1675, 1676, 1678, 1679, 1681, 1684, 1685, 1686, 1689, 1690, 1692, 1693, 1694, 1695, 1696, 1697, 1698, 1701, 1705, 1706, 1707, 1709, 1711, 1712, 1713, 1714, 1716, 1717, 1718, 1720, 1721, 1723, 1724, 1725, 1726, 1728, 1729, 1731, 1732, 1734, 1735, 1736, 1737, 1738, 1739, 1740, 1741, 1743, 1744, 1745, 1746, 1747, 1750, 1751, 1753, 1754, 1755, 1760, 1761, 1762, 1763, 1764, 1765, 1767, 1770, 1771, 1772, 1775, 1776, 1777, 1778, 1779, 1780, 1781, 1782, 1786, 1787, 1788, 1789, 1791, 1792, 1793, 1794, 1795, 1797, 1798, 1799, 1800, 1801, 1803, 1804, 1805, 1806, 1809, 1810, 1811, 1814, 1815, 1818, 1819, 1820, 1821, 1822, 1823, 1824, 1825, 1826, 1828, 1830, 1831, 1833, 1835, 1836, 1837, 1838, 1839, 1840, 1841, 1842, 1843, 1846, 1851, 1852, 1854, 1857, 1858, 1860, 1861, 1862, 1863, 1864, 1866, 1868, 1869, 1870, 1872, 1873, 1874, 1875, 1876, 1878, 1879, 1880, 1881, 1883, 1884, 1885, 1887, 1888, 1892, 1893, 1894, 1896, 1898, 1899, 1900, 1901, 1902, 1903, 1904, 1905, 1906, 1907, 1910, 1911, 1913, 1915, 1916, 1917, 1918, 1920, 1921, 1924, 1925, 1926, 1927, 1928, 1930, 1932, 1933, 1934, 1935, 1938, 1939, 1940, 1942, 1943, 1945, 1946, 1948, 1949, 1950, 1951, 1953, 1954, 1955, 1959, 1960, 1961, 1962, 1963, 1965, 1966, 1967, 1970, 1971, 1973, 1975, 1976, 1977, 1979, 1981, 1982, 1983, 1984, 1985, 1986, 1988, 1990, 1994, 1995, 1996, 1998, 1999, 2000, 2001, 2002, 2003, 2006, 2007, 2008, 2009, 2010, 2011, 2013, 2014, 2015, 2016, 2017, 2018, 2019, 2020, 2021, 2022, 2024, 2025, 2026, 2027, 2028, 2029, 2030, 2031, 2032, 2034, 2035, 2036, 2037, 2038, 2039, 2040, 2041, 2042, 2043, 2044, 2045, 2046, 2047, 2048, 2049, 2050, 2052, 2054, 2055, 2059, 2060, 2062, 2065, 2066, 2067, 2068, 2069, 2070, 2071, 2074, 2076, 2077, 2080, 2081, 2082, 2083, 2085, 2086, 2087, 2088, 2089, 2090, 2091, 2092, 2093, 2095, 2096, 2097, 2098, 2100, 2101, 2102, 2103, 2104, 2105, 2108, 2109, 2110, 2112, 2113, 2115, 2116, 2117, 2118, 2119, 2120, 2121, 2125, 2127, 2128, 2129, 2131, 2132, 2134, 2135, 2136, 2138, 2140, 2141, 2142, 2143, 2145, 2146, 2147, 2148, 2149, 2150, 2153, 2154, 2155, 2156, 2158, 2159, 2160, 2162, 2163, 2165, 2166, 2167, 2168, 2169, 2170, 2171, 2172, 2174, 2176, 2177, 2179, 2180, 2181, 2182, 2183, 2184, 2185, 2186, 2188, 2190, 2191, 2192, 2193, 2194, 2195, 2196, 2197, 2198, 2200, 2202, 2204, 2205, 2206, 2207, 2208, 2210, 2211, 2212, 2214, 2215, 2216, 2217, 2218, 2219, 2220, 2221, 2222, 2223, 2225, 2226, 2227, 2228, 2229, 2230, 2231, 2232, 2233, 2234, 2235, 2236, 2238, 2239, 2241, 2242, 2243, 2244, 2245, 2246, 2248, 2249, 2251, 2253, 2254, 2255, 2257, 2258, 2259, 2261, 2262, 2265, 2267, 2268, 2269, and 2270; wherein protein expression is modulated in response to the first endophyte contacting the seedlings.
  • 13. A method for preparing a seed comprising an endophyte population, said method comprising heterologously disposing to an exterior surface a seed formulation comprising an endophyte population comprising an endophyte comprising a 16S rRNA or ITS rRNA nucleic acid sequence at least 97% identical to a nucleicacid sequence selected from the group consisting of SEQ ID NOs: 1-395 and 397-455 in an amount effective to provide a benefit to the seed or plant derived from the seed.
  • 14. The method of claim 13, wherein the endophyte is capable of a function or activity selected from the group consisting of auxin production, nitrogen fixation, production of an antimicrobial compound, mineral phosphate solubilization, siderophore production, cellulase production, chitinase production, xylanase production, and acetoin production.
  • 15. The method of claim 13, wherein the benefit is selected from the group consisting of: increased root biomass, increased root length, increased height, increased shoot length, increased leaf number, increased water use efficiency, increased tolerance to low nitrogen stress, increased nitrogen use efficiency, increased overall biomass, increased grain yield, increased photosynthesis rate, increased tolerance to drought, increased heat tolerance, increased salt tolerance, increased resistance to nematode stress, increased resistance to a fungal pathogen, increased resistance to a bacterial pathogen, increased resistance to a viral pathogen, a detectable modulation in the level of a metabolite, a detectable modulation in the transcriptome, and a detectable modulation in the proteome, relative to reference seeds or agricultural plants derived from reference seeds.
  • 16. The method of claim 13, wherein the formulation comprises at least one member selected from the group consisting of an agriculturally compatible carrier, a tackifier, a microbial stabilizer, a fungicide, an antibacterial agent, an herbicide, a nematicide, an insecticide, a plant growth regulator, a rodenticide, and a nutrient.
  • 17. The method of claim 13, wherein the seed is contacted with at least 10 CFU or spores, at least 100 CFU or spores, at least 300 CFU or spores, at least 1,000 CFU or spores, at least 3,000 CFU or spores, at least 10,000 CFU or spores, at least 30,000 CFU or spores, at least 100,000 CFU or spores, at least 300,000 CFU or spores, at least 1,000,000 CFU or spores, or more, of the endophyte.
  • 18. The method of claim 13, wherein the formulation comprises at least two endophyte populations comprising a nucleic acid sequence that is at least 97% identical, at least 98% identical, at least 99% identical, at least 99.5% identical, or 100% identical, to a nucleic acid sequence selected from the group consisting of SEQ ID NOs: 1-395 and 397-455, wherein the at least two endophyte populations are present in the formulation in an amount effective to colonize the mature agricultural plant.
  • 19. The method of claim 13, wherein the plant is a monocot.
  • 20. The method of claim 19, wherein the monocot is selected from the group consisting of corn, wheat, barley and rice.
  • 21. The method of claim 13, wherein the plant is a dicot.
  • 22. The method of claim 21, wherein the dicot is selected from the group consisting of a soybean, peanut, canola, cotton, Brassica Napus, cabbage, lettuce, melon, strawberry, turnip, watermelon, tomato and pepper.
  • 23. The method of claim 13, wherein the endophyte is present in the formulation in an amount effective to increase the biomass and/or yield of the fruit or seed produced by the plant by at least 1%, at least 2%, at least 3%, at least 5%, at least 10%, at least 15%, at least 20%, at least 30%, at least 40%, at least 50%, at least 60%, at least 70%, at least 80%, at least 90%, at least 100%, or more, when compared with the fruit or seed of a reference agricultural plant.
  • 24. The method of claim 13, wherein the endophyte is present in the formulation in an amount effective to detectably increase the rate of germination of the seed.
  • 25. The method of claim 13, wherein the benefit to the seeds or seedlings or the plants derived from the seeds is conferred under water limited conditions.
  • 26. The method of claim 13, wherein the plant derived from the seed is a soybean plant in water limited conditions and the plant expresses one or more genes whose nucleic acid sequence is at least 95%, at least 96%, at least 97%, at least 98%, at least 99%, or 100% identical to a nucleic acid sequence selected from the group consisting of SEQ ID NOs: 4131, 4140, 4142, 4150, 4153, 4162, 4167, 4181, 4183, 4184, 4195, 4199, 4201, 4206, 4213, 4222, 4223, 4250, 4253, and 4269, wherein the one or more plant genes are modulated in response to the first endophyte contacting the plant as compared to a reference microorganism contacting the plant.
  • 27. A method for modulating a plant trait comprising heterologously disposing to vegetation or an area adjacent the vegetation, a formulation comprising an endophyte population comprising an endophyte comprising a 16S rRNA or ITS rRNA nucleicacid sequence at least 97% identical to a nucleicacid sequence selected from the group consisting of SEQ ID NOs: 1-395 and 397-455, wherein the formulation is capable of providing a benefit to the vegetation, or to a crop produced from the vegetation.
  • 28. The method of claim 27, wherein the plant is a soybean plant in water limited conditions and the plant expresses one or more genes whose nucleic acid sequence is at least 95%, at least 96%, at least 97%, at least 98%, at least 99%, or 100% identical to a nucleic acid sequence selected from the group consisting of SEQ ID NOs: 4131, 4140, 4142, 4150, 4153, 4162, 4167, 4181, 4183, 4184, 4195, 4199, 4201, 4206, 4213, 4222, 4223, 4250, 4253, and 4269, wherein the one or more plant genes are modulated in response to the endophyte contacting the plant as compared to a reference microorganism contacting the plant.
Priority Claims (1)
Number Date Country Kind
PCT/US2015/03818 Jun 2015 WO international
CROSS-REFERENCE TO RELATED APPLICATIONS

This application is the National Stage of International Application No. PCT/US2015/068206, filed Dec. 30, 2015, which claims the benefit of and priority to International Application No. PCT/US2015/038187, filed Jun. 26, 2015, U.S. Provisional Application No. 62/156,021, filed May 1, 2015, U.S. Provisional Application No. 62/156,028, filed May 1, 2015, U.S. Provisional Application No. 62/098,296, filed Dec. 30, 2014, U.S. Provisional Application No. 62/098,298, filed Dec. 30, 2014, U.S. Provisional Application No. 62/098,299, filed Dec. 30, 2014, U.S. Provisional Application No. 62/098,302, filed Dec. 30, 2014, and U.S. Provisional Application No. 62/098,304, filed Dec. 30, 2014, each of which is incorporated by reference it its entirety.

PCT Information
Filing Document Filing Date Country Kind
PCT/US2015/068206 12/30/2015 WO 00
Publishing Document Publishing Date Country Kind
WO2016/109758 7/7/2016 WO A
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Related Publications (1)
Number Date Country
20180020677 A1 Jan 2018 US
Provisional Applications (7)
Number Date Country
62098296 Dec 2014 US
62098298 Dec 2014 US
62098299 Dec 2014 US
62098302 Dec 2014 US
62098304 Dec 2014 US
62156021 May 2015 US
62156028 May 2015 US