Endophytes, associated compositions, and methods of use

A method of improving a plant phenotype during water limited conditions, comprising treating a plurality of plant elements with a formulation comprising a purified microbial population that comprises at least a first endophyte and a second endophyte that are heterologous to the plant elements, wherein the first endophyte is capable of metabolizing at least one of D-alanine, D-aspartic acid, D-serine, D-threonine, glycyl-L-aspartic acid, glycyl-L-glutamic acid, glycyl-L-proline, glyoxylic acid, inosine, L-alanine, L-alanyl-glycine, L-arabinose, L-asparagine, L-aspartic acid, L-glutamic acid, L-glutamine, L-proline, L-serine, L-threonine, tyramine, uridine, proline, arabinose, xylose, mannose, sucrose, maltose, D-glucosamine, trehalose, oxalic acid, and salicin, said phenotype improvement selected from the group consisting of:

• disease resistance, heat tolerance, cold tolerance, salinity tolerance, metal tolerance, herbicide tolerance, chemical tolerance, improved nitrogen utilization, improved resistance to nitrogen stress, improved nitrogen fixation, pest resistance, herbivore resistance, pathogen resistance, increased yield, 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, increased seed weight, altered seed carbohydrate composition, altered seed oil composition, number of pods, delayed senescence, stay-green, and altered seed protein composition, 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 method for (i) preparing a seed comprising an endophyte population or (ii) treating plants, said method comprising:

• a) 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:
• 1-3700;
• or
• b) contacting foliage or the rhizosphere of a plurality of agricultural plant plants with 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:
• 1-3700;
• and growing the contacted plants.

A method for improving an agricultural trait in an agricultural plant, the method comprising:

• a. Providing an agricultural plant;
• b. Contacting said plant with a formulation comprising an endophyte derived from an ancestral plant or 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
• c. Allowing the plant to grow under conditions that allow the endophyte to colonize the plant;
• wherein optionally the method further comprises:
• d. growing the plants under conditions that allow the endophyte to improve a trait in the plant.

A synthetic combination comprising a purified microbial population in association with a treatment formulation, wherein:

• a) the purified microbial population comprises a first endophyte 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;
• or
• b) the purified microbial population comprises a first endophyte wherein the first endophyte is capable of metabolizing at least one of D-alanine, D-aspartic acid, D-serine, D-threonine, glycyl-L-aspartic acid, glycyl-L-glutamic acid, glycyl-L-proline, glyoxylic acid, inosine, L-alanine, L-alanyl-glycine, L-arabinose, L-asparagine, L-aspartic acid, L-glutamic acid, L-glutamine, L-proline, L-serine, L-threonine, tyramine, uridine, proline, arabinose, xylose, mannose, sucrose, maltose, D-glucosamine, trehalose, oxalic acid, and salicin;
• and
• wherein the first 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:
• 1-3700, and wherein the endophyte is present in the synthetic combination in an amount effective to provide a benefit to seeds or seedlings or plants derived from the seeds or seedlings.