Endophytes, associated compositions, and methods of use

Patent metadata

Field	Value
Publication number	US-2025353797-A1
Application number	US-202519030008-A
Country	US
Kind code	A1
Filing date	Jan 17, 2025
Priority date	Jun 26, 2014
Publication date	Nov 20, 2025
Grant date	—

Abstract

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

First claim

1 . (canceled)

2 . (canceled)

3 . 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.

4 . The method of claim 3 , wherein:
a) the first endophyte is a bacterial endophyte; b) the second endophyte is a bacterial endophyte; c) the first endophyte is a bacterial endophyte and the second endophyte is a bacterial endophyte; d) the second endophyte is a fungal endophyte; e) the first endophyte is a bacterial endophyte and the second endophyte is a fungal endophyte; f) the first endophyte is a fungal endophyte; g) the first endophyte is a fungal endophyte and the second endophyte is a fungal endophyte; h) the first endophyte is capable of metabolizing at least two 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; i) the second 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; j) at least one of the endophytes is capable of localizing in a plant element of a plant grown from said seed, said 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; k) the formulation comprises the purified microbial population at a concentration of at least about 10{circumflex over ( )}2 CFU/ml or spores/ml in a liquid formulation or about 10{circumflex over ( )}2 CFU/gm or spores/ml in a non-liquid formulation; l) 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; m) the formulation further comprises one or more of the following: fungicide, nematicide, bactericide, insecticide, and herbicide; n) the plant element is a transgenic seed; o) the plurality of plant elements are placed into a substrate that promotes plant growth; p) at least one of the endophytes comprises a nucleic acid sequence that is at least 97% identical to any nucleic acid provided in Tables 1A, 2A, 3A, 4A, 5-14, or 16-23; q) the seed or plant is contacted with 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; r) the formulation comprises at least two endophytes provided in any of Tables 2B, 3B, 4B, and 15; s) the plant is a monocot, optionally wherein the monocot is selected from the group consisting of corn, wheat, barley and rice; t) the plant is a dicot, optionally wherein the dicot is selected from the group consisting of a soybean, canola, cotton, tomato, and pepper; u) the endophyte is present in the formulation in an amount effective to be detectable within a target tissue of the plant elements selected from a fruit, seed, leaf, root, or portion thereof; v) the population is detected in an amount of 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; w) 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; x) the endophyte is present in the formulation in an amount effective to detectably increase the biomass of the plant, or a part or a tissue type thereof; y) the biomass of the plant, or a part or tissue type 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; z) the plant element is a seed and the endophyte is present in the formulation in an amount effective to detectably increase the rate of germination of the seed; and/or aa) the plant element is a seed and 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.

5 .- 8 . (canceled)

9 . The method of claim 4 , wherein:
a) the bacterial endophyte is of a genus selected from the group consisting of: Acidovorax, Agrobacterium, Bacillus, Burkholderia, Chryseobacterium, Curtobacterium, Enterobacter, Escherichia, Methylobacterium, Paenibacillus, Pantoea, Pseudomonas, Ralstonia, Saccharibacillus, Sphingomonas , and Stenotrophomonas; b) the bacterial endophyte has a 16S rRNA sequence t

Assignees

• Indigo Ag Inc

Inventors

• Von Maltzahn Geoffrey
• Flavell Richard Bailey
• Toledo Gerardo V
• Leff Jonathan W
• Samayoa Phillip
• Marquez Luis Miguel
• Johnston David Morris
• Djonovic Slavica
• Millet Yves Alain
• Sadowski Craig
• Lyford Jeffrey
• Ambrose Karen V
• Zhang Xuecheng

Classifications

• A01H17/00

  Symbiotic or parasitic combinations including one or more new plants, e.g. mycorrhiza (lichens A01H15/00) · CPC title

• A01N63/20

  Bacteria; Substances produced thereby or obtained therefrom · CPC title

• A01N63/30

  Microbial fungi; Substances produced thereby or obtained therefrom · CPC title

• C05F11/08 Primary

  Organic fertilisers containing added bacterial cultures, mycelia or the like · CPC title