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	6.840843	0.000565
	713	2.519717879	2.387448	2.41189	6.748785	0.000619
	714	4.899566565	4.139604	2.330919	6.674579	0.000663
	692	0.928859379	−3.94891	2.315037	−6.66012	0.00067
	685	0.295559632	−4.51752	2.290181	−6.63754	0.000686
	696	0.848055404	−4.26687	2.268441	−6.61786	0.0007
	715	2.348179343	2.481725	2.246454	6.598008	0.000711
	716	7.387448493	4.164462	2.159094	6.519689	0.000767
	717	1.384010569	−3.67942	1.930876	−6.31914	0.000935
	718	6.539766193	3.910187	1.874559	6.270516	0.000984
	719	0	−2.24072	1.759813	−6.17247	0.001088
	720	0.894846762	−4.42228	1.658568	−6.08708	0.001189
	721	1.441622985	−3.3104	1.633153	−6.0658	0.001218
	722	0	−4.44208	1.572778	−6.01551	0.001275
	698	1.558896118	−3.19078	1.546359	−5.99361	0.001305
	723	0.383504801	−6.22029	1.532513	−5.98216	0.001318
	724	0.874379809	−5.05512	1.414511	−5.88532	0.001468
	725	3.178052882	3.1153	1.380226	5.857421	0.001515
	726	2.743866247	2.530417	1.349556	5.832557	0.001563
	727	8.67938655	4.03496	1.313775	5.803657	0.001613
	728	1.675692023	−4.12482	1.299312	−5.79201	0.001627
	729	4.320735935	−3.01739	1.245211	−5.74859	0.001712
	730	1.117898542	−4.15716	1.207594	−5.71856	0.001762
	731	0.295759975	−4.21399	1.185637	−5.70109	0.001799
	732	3.472329984	−3.5087	1.155325	−5.67703	0.001844
	733	0	−5.05686	1.131697	−5.65833	0.001884
	734	2.303932777	−4.90902	1.127765	−5.65523	0.001886
	735	4.894808598	3.487075	1.017153	5.568359	0.002056
	737	2.496100539	−2.7244	0.995641	−5.55158	0.002086
	736	3.748353789	3.251627	0.996266	5.552068	0.002086
	738	0.097742219	−2.19296	0.994155	−5.55042	0.002087
	739	4.494039562	5.038067	0.963629	5.526686	0.002143
	740	4.883694275	4.299834	0.927171	5.498432	0.002209
	741	3.543460499	−3.27253	0.888456	−5.46854	0.00228
	742	3.201001736	3.227374	0.878381	5.460786	0.002292
	743	1.134755003	−3.43033	0.868413	−5.45312	0.002307
	744	1.31228389	−4.40225	0.830737	−5.42421	0.002375
	745	2.18981705	−3.00766	0.818268	−5.41466	0.002395
	746	7.105767696	4.126379	0.80081	5.401317	0.002438
	747	1.219706529	−3.83331	0.756008	−5.36718	0.002518
	748	1.014147489	−4.86358	0.686637	−5.31463	0.002646
	749	5.108026741	−4.51544	0.681969	−5.3111	0.002652
	750	6.189343256	5.968321	0.664673	5.298059	0.00269
	751	1.594206545	−4.0374	0.625713	−5.26876	0.00276
	752	4.02637883	3.250628	0.610465	5.257326	0.002793
	697	2.276512626	−3.03289	0.608594	−5.25592	0.002796
	753	2.916440322	−3.19554	0.597045	−5.24728	0.002823
	754	5.582396377	5.11116	0.592518	5.243887	0.002833
	755	7.127819277	5.646838	0.588484	5.24087	0.002836
	691	0	−4.207	0.547655	−5.2104	0.002938
	756	1.723275185	−5.46022	0.54628	−5.20937	0.00294
	680	2.558100341	−3.77627	0.53802	−5.20322	0.002955
	757	1.491025779	−7.37296	0.51175	−5.18369	0.003013
	758	6.655679639	7.343952	0.499918	5.174915	0.003026
	759	5.448500076	4.101199	0.496168	5.172135	0.003035
	760	6.849405724	6.555104	0.494322	5.170766	0.003039
	761	1.415264641	−4.13804	0.465403	−5.14936	0.003123
	762	7.078833392	3.299493	0.45963	5.145095	0.003137
	763	7.447835109	4.197994	0.459465	5.144973	0.003137
	764	4.691855389	−4.09505	0.428461	−5.1221	0.003216
	765	6.765913108	4.656261	0.394211	5.096913	0.003318
	766	1.189911629	−6.35022	0.3901	−5.09389	0.003321
	767	0.711873688	−4.12247	0.378768	−5.08558	0.003347
	768	0.935705267	−4.23339	0.376965	−5.08426	0.00335
	769	1.129748696	−5.65043	0.372725	−5.08115	0.00336
	770	2.447676888	2.51643	0.360788	5.072408	0.003395
	771	7.412793324	2.89405	0.344563	5.060539	0.003447
	772	0	−6.33439	0.32456	−5.04593	0.003498
	773	1.409452743	−5.2232	0.315504	−5.03933	0.00352
	774	0	−5.44413	0.305958	−5.03237	0.003541
	775	0.757799789	−3.27057	0.251911	−4.9931	0.003718
	776	0.261005346	−4.64558	0.221495	−4.97108	0.003811
	777	0.770128672	−3.1553	0.143776	−4.91509	0.004074
	778	2.816941964	−3.86408	0.10615	−4.88812	0.004228
	779	1.943606982	−5.03828	0.095087	−4.88021	0.004261
	780	6.49982563	2.314873	0.091858	4.8779	0.004272
	781	2.543445727	2.527428	0.077045	4.867319	0.00432
	782	0.378277281	−5.07738	0.074749	−4.86568	0.004327
	783	1.554052399	−6.86013	0.073057	−4.86447	0.004331
	784	3.740313179	−3.30861	0.057195	−4.85316	0.004389
	785	6.647954724	6.114271	0.049884	4.847953	0.004415
	786	0.809756341	−3.46435	0.037282	−4.83898	0.004447
	787	4.419507408	4.457627	0.01987	4.826605	0.004499
	788	1.722062181	−5.09666	0.004896	−4.81597	0.004554
	789	8.147623562	6.459604	−0.00779	4.806976	0.004594
	790	3.849786723	−2.31991	−0.01622	−4.80101	0.004625
	791	6.450195037	4.96722	−0.02376	4.795666	0.00466
	792	8.130353179	6.315026	−0.03164	4.790094	0.004696
	793	0.297925928	−5.04598	−0.03768	−4.78582	0.004716
	794	5.862148582	5.707939	−0.06956	4.763314	0.004863
	795	3.230236428	−2.8374	−0.10943	−4.73525	0.005047
	796	1.199045091	−4.36726	−0.11833	−4.729	0.00509
	797	0.871860339	−7.01828	−0.12739	−4.72264	0.005126
	798	0.330447252	−5.92622	−0.1483	−4.70798	0.005219
	800	1.098104153	−4.19885	−0.16955	−4.6931	0.005312
	799	2.933131491	3.290135	−0.16944	4.69318	0.005312
	801	6.021652199	4.83424	−0.17145	4.691775	0.005318
	803	2.002833589	−5.05292	−0.19244	−4.67711	0.005407
	802	3.578287021	−4.08273	−0.18889	−4.67959	0.005407
	804	0.648456799	−3.72185	−0.21394	−4.66212	0.005504
	805	2.020784202	−2.43559	−0.21784	−4.6594	0.005514
	808	0.580666117	−6.38818	−0.22369	−4.65532	0.005525
	807	2.809100574	−2.35658	−0.22257	−4.65611	0.005525
	806	4.097390482	−2.23548	−0.2214	−4.65692	0.005525
	809	5.263030629	2.68504	−0.23653	4.646388	0.005581
	810	1.906016093	−7.95994	−0.23905	−4.64464	0.005585
	812	3.374272912	−2.55359	−0.24971	−4.63722	0.005633
	811	2.229412642	−2.2735	−0.24919	−4.63759	0.005633
	813	5.191947	3.218252	−0.25601	4.632846	0.005659
	814	5.175711473	5.284348	−0.27649	4.618638	0.005755
	815	0.457571639	−3.67907	−0.28594	−4.61209	0.0058
	816	5.901553526	3.155387	−0.2866	4.611627	0.0058
	817	1.938854906	−4.27181	−0.29258	−4.60749	0.005825
	818	3.751441415	−2.52835	−0.29951	−4.60269	0.005855
	819	0.847940328	−3.32137	−0.32592	−4.58442	0.006017
	820	2.5557465	−4.96282	−0.34887	−4.56858	0.006156
	821	5.505094032	4.420758	−0.36167	4.559767	0.006238
	822	2.080339763	−3.66131	−0.36679	−4.55624	0.006268
	823	0.715469044	−4.2781	−0.38183	−4.54589	0.006357
	825	1.425755818	−3.75003	−0.3861	−4.54296	0.006362
	824	0.732571213	−3.30399	−0.38598	−4.54303	0.006362
	826	1.858084528	−5.0271	−0.39476	−4.537	0.006412
	827	5.108233831	5.231226	−0.39838	4.534514	0.006433
	828	2.220629054	2.40642	−0.40728	4.528399	0.00648
	829	0.999936795	−4.02216	−0.42399	−4.51694	0.006569
	830	0.956968472	−3.3446	−0.42698	−4.51489	0.006581
	831	7.666771535	4.889688	−0.44251	4.504248	0.006673
	832	4.462106061	3.362316	−0.44719	4.501046	0.006692
	833	0.798417819	−5.95745	−0.45635	−4.49478	0.006748
	835	0.745638707	−2.59361	−0.48058	−4.47822	0.006877
	834	2.039008683	2.449259	−0.48038	4.478357	0.006877
	836	1.272304701	−4.60015	−0.49143	−4.47081	0.006946
	837	3.138905614	−2.18675	−0.49273	−4.46993	0.006946
	838	0	−3.96218	−0.49789	−4.46641	0.006961
	839	0.441358118	−4.38384	−0.50196	−4.46364	0.006974
	840	4.07697119	2.537012	−0.50227	4.463427	0.006974
	841	3.744824974	−2.67465	−0.52217	−4.44987	0.007097
	842	0.658532988	−3.53015	−0.52453	−4.44827	0.007102
	843	0	−4.46853	−0.54372	−4.43522	0.007224
	844	5.483246572	3.820601	−0.54429	4.434824	0.007224
	845	4.218558155	3.368666	−0.54552	4.433987	0.007229
	846	0.531333536	−5.80897	−0.5699	−4.41744	0.007352
	847	5.125810617	4.200583	−0.57194	4.416052	0.007359
	848	1.508836141	−4.45308	−0.57862	−4.41153	0.007396
	849	4.196864651	4.108622	−0.58006	4.410547	0.007402
	850	0	−4.14265	−0.58148	−4.40958	0.007408
	851	2.386025864	−6.90475	−0.60002	−4.39703	0.007531
	852	7.391829386	7.341373	−0.61198	4.388939	0.007608
	853	0.280401415	−6.23052	−0.6128	−4.38838	0.007609
	854	0	−5.84296	−0.61807	−4.38482	0.007637
	855	10.89359383	4.483809	−0.62462	4.380391	0.00768
	856	3.574070188	−2.75777	−0.63106	−4.37604	0.007723
	857	3.185653977	−2.63104	−0.63216	−4.3753	0.007727
	858	0	−3.93177	−0.63567	−4.37293	0.007745
	859	0.821736911	−3.64067	−0.66191	−4.35523	0.007924
	860	1.513388401	−5.92967	−0.67062	−4.34936	0.007991
	861	5.288562871	5.164408	−0.67364	4.347332	0.008003
	519	2.153109228	−5.17926	−0.68969	−4.33653	0.008113
	862	2.924286464	3.494282	−0.6901	4.33625	0.008113
	863	4.831002225	5.170113	−0.7042	4.326775	0.008209
	864	0.350736603	−4.55951	−0.71336	−4.32062	0.008262
	865	0.897423937	−5.14471	−0.71421	−4.32005	0.008264
	866	3.02046933	−2.23527	−0.72773	−4.31098	0.008362
	867	4.148359441	4.700775	−0.72891	4.310188	0.008367
	868	7.241823447	4.71758	−0.73179	4.308255	0.008388
	869	0.362821722	−3.21259	−0.73646	−4.30512	0.008418
	870	1.94750928	−2.81205	−0.74858	−4.297	0.008489
	871	0	−3.47396	−0.75224	−4.29455	0.00851
	872	0.627760328	−5.29907	−0.7639	−4.28674	0.008589
	873	0.951987955	−3.0524	−0.76717	−4.28455	0.008614
	874	0.734008502	−6.22448	−0.77307	−4.28061	0.008657
	875	0.296780765	−2.07634	−0.77841	−4.27704	0.008695
	876	2.694353324	−2.70682	−0.79002	−4.26927	0.008782
	877	6.450463175	3.82448	−0.79922	4.263133	0.008844
	878	2.140747407	−6.13606	−0.81393	−4.25332	0.008927
	879	2.173954682	−4.47826	−0.81655	−4.25157	0.00894
	880	1.6914174	−4.77307	−0.81897	−4.24996	0.008951
	881	2.35645327	−4.64979	−0.83531	−4.23907	0.009074
	882	3.30963121	−2.17414	−0.83911	−4.23654	0.009106
	883	2.158000596	2.42587	−0.84519	4.232488	0.00916
	884	2.531678954	−3.1414	−0.84671	−4.23148	0.009169
	885	2.194869885	2.402679	−0.84832	4.230406	0.009172
	886	2.193043465	−3.49995	−0.85623	−4.22514	0.009214
	887	0.314001411	−5.55798	−0.86027	−4.22245	0.009226
	889	0.712887218	−4.88085	−0.86671	−4.21817	0.009265
	888	0.611123391	−3.75978	−0.86634	−4.21842	0.009265
	890	1.141019105	−7.87059	−0.88299	−4.20736	0.009375
	891	1.709043647	−3.91338	−0.8871	−4.20463	0.009395
	892	1.101158731	−3.40776	−0.88917	−4.20326	0.009404
	893	2.213804236	−4.55459	−0.90647	−4.19178	0.00955
	894	1.275657111	−4.20948	−0.91395	−4.18682	0.009596
	895	0.352165126	−7.40328	−0.918	−4.18414	0.009626
	896	2.683347982	2.354425	−0.92977	4.176344	0.00973
	897	0.740211298	−2.9098	−0.93127	−4.17535	0.00974
	898	2.395376228	−4.44254	−0.9342	−4.17341	0.009764
	899	0.686771667	−4.62795	−0.94048	−4.16926	0.009812
	900	4.469180465	6.919872	−0.94401	4.166923	0.009837
	901	2.882217215	−4.44428	−0.94674	−4.16512	0.009859
	902	0	−2.81719	−0.9494	−4.16336	0.009881
	903	3.486426657	−4.11858	−0.95426	−4.16014	0.009921
	904	1.24041635	−3.15204	−0.95549	−4.15933	0.009928
	905	0.925832893	−3.77285	−0.9583	−4.15747	0.009945
	906	1.938081563	−3.28418	−0.95965	−4.15658	0.009953
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	1106	0.564083606	−3.119	−1.94491	−3.52258	0.022022
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	1108	6.892708872	2.844791	−1.94782	3.520755	0.022069
	1110	3.962799023	−2.6218	−1.95044	−3.5191	0.02211
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	1112	0.794188824	−4.53867	−1.95601	−3.5156	0.02221
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	1115	0.149385666	−4.56381	−1.96848	−3.50776	0.022424
	1116	1.985649581	−3.35694	−1.96926	−3.50726	0.022424
	479	2.791373031	−2.40723	−1.9695	−3.50711	0.022424
	1117	0.786931333	−5.65287	−1.97046	−3.50651	0.022436
	1119	0.756889395	−4.9479	−1.97225	−3.50539	0.022447
	1118	0.765101758	−4.56855	−1.97188	−3.50562	0.022447
	1120	3.606104684	4.172772	−1.97523	3.50351	0.022506
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	1121	3.715374057	−2.42559	−1.97777	−3.50191	0.022536
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	1123	1.450036735	−4.59182	−1.9812	−3.49976	0.022576
	1124	8.044277291	4.332171	−1.98319	3.498506	0.022613
	1125	4.379295342	4.698935	−1.98525	3.497209	0.022641
	1126	0.251432019	−3.8457	−1.99306	−3.4923	0.02281
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	1129	6.770081287	3.045058	−1.99951	3.488248	0.022869
	1128	4.633512356	4.527713	−1.99917	3.488465	0.022869
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	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 OD_600/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 OD_600/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.