Methods for improving plant response to pests and pathogens

Abstract

Methods for increasing a plant response to pests and / or pathogens by increasing the plant's production of one or plant defense compounds derived from anthranilate. Also provided are methods for identifying and selecting microbial strains that can be used in plant treatments to increase a plant response to attack by pests and / or pathogens.

Description

Agent Ref.: P14472WO00 1 METHODS FOR IMPROVING PLANT RESPONSE TO PESTS AND PATHOGENS REFERENCE TO PRIORITY APPLICATIONS

[0001] This patent application claims benefit of U.S. provisional patent application serial number 63 / 561,055, filed March 4, 2024; U.S. provisional patent application serial number 63 / 606,485, filed December 5, 2023; and U.S. provisional patent application serial number 63 / 504,299, filed May 25, 2023. SEQUENCE LISTING STATEMENT

[0002] The instant application contains a sequence listing, which has been submitted in XML file format by electronic submission and is hereby incorporated by reference in its entirety. The XML file, created on May 16, 2024, is named P14472WO00.xml and is 251,036 bytes in size. BACKGROUND

[0003] Plants have developed a variety of defense mechanisms to ward off attacks by various organisms including fungi, bacteria, viruses, nematodes and insects. Defense mechanisms include structural barriers, production of chemicals that are toxic to invading organisms, production of chemicals that attract natural enemies of the target pest or pathogen, and a hypersensitive response characterized by rapid cell death at the point of infection. Despite these natural protection mechanisms, crop losses due to damage by plant pathogens and pests occur annually at a significant cost to the global economy. New methods are needed to reduce the impacts of pest and pathogen attacks on plants. SUMMARY

[0004] Methods of improving a plant response to attack by a pathogen or pest by increasing the level of one or more plant defense compounds that are produced in a plant are provided herein. Such methods comprise treating a plant, plant part or seed with a microbial strain that is not pathogenic to said plant, wherein said treatment increases expression in said plant of one or more gene transcripts involved in production of a plant defense compound; and growing the plant in the presence of the pathogen or pest, whereby the level of one or more plant defense compounds in said plant is increased as compared to a control plant, and the response of said plant to said pathogen or pest is improved as compared to a control plant, wherein the control plant is not genetically modified or treated with said microbial strain. In some embodiments, a microbial strain used in methods provided herein expresses one or more genes in a pathway for production of siderophores, and / or one or more genes in a pathway for production of a polyketide. In some embodiments, such microbial strain will enhance an induced systemic resistance (ISR) plant defense response in the treated plant or a plant grown from a treated seed,Agent Ref.: P14472WO00 2 plant part, or grown in treated soil. In some embodiments, a plant defense response provides for production of metabolites that repel or otherwise reduce the impact on the plant of a plant pest or pathogen. In some embodiments, the plant pest is an insect. In some embodiments, proteins in a pathway for production of a polyketide that induces a plant response to a pathogen or pest are present on a plasmid. In some embodiments, proteins in a pathway for production of a polyketide are encoded by genes on SEQ ID NO: 87 or a variant thereof. In some embodiments, proteins in a pathway for production of a polyketide that induces a plant response to a pathogen or pest are encoded by genes on SEQ ID NO: 86 or a variant thereof. In some embodiments, proteins in a pathway for production of a polyketide that induces a plant response to a pathogen or pest are encoded by a polynucleotide having at least 70%, 80%, 85%, 90%, 95%, 98%, 99%, or 100% sequence identity to SEQ ID NOS: 36-50. In some embodiments, proteins in a pathway for production of a polyketide that induces a plant response to a pathogen or pest comprise a polypeptide sequence having at least 70%, 80%, 85%, 90%, 95%, 98%, 99%, or 100% sequence identity to any one of SEQ ID NOS: 21-35. In some embodiments, a protein in a microbe that induces a plant response to a pathogen or pest is a homolog or ortholog of any one of SEQ ID NOS: 21-35. In some embodiments, a gene in a pathway for production of a polyketide is a bfmBAB_2 gene. In some embodiments, the bfmBAB_2 comprises a polynucleotide sequence having at least 70%, 80%, 85%, 90%, 95%, 98%, 99%, or 100% sequence identity to SEQ ID NO:36. In some embodiments a bfmBAB_2 gene encodes a protein having a sequence of SEQ ID NO:21. In some embodiments, the bfmBAB_2 gene has at least 70% identity with SEQ ID NO:36, and / or encodes a protein having at least 80%, 85%, 90%, 95%, 98%, 99%, or 100% sequence identity with SEQ ID NO:21. In some embodiments, the bacterial strain is a Methylobacterium or Methylorubrum strain. In some embodiments, the bacterial strain is NLS0042 (NRRL B-50932). In some embodiments, the bacterial strain is not NLS0042 (NRRL B-50932). In some embodiments, the plant defense compound reduces foraging of insect larvae on plant roots. In some embodiments, insect larvae are repelled from plant roots. In some embodiments, the plant defense compound reduces foraging of insect larvae on plant roots in comparison to the control plant. In some embodiments, the plant is corn, and the insect pest is corn rootworm. In some embodiments, root regrowth following exposure to the pathogen or pest is increased in comparison to the control plant.

[0005] In some embodiments provided herein, methods of improving a plant response to attack by a pathogen or pest increases the level of one or more plant defense compounds derived from anthranilate that are produced in a plant. Such methods comprise the steps of modifying a plant genome to increase expression of one or more gene transcripts involved in production of one orAgent Ref.: P14472WO00 3 more plant defense compounds derived from anthranilate in said plant, and / or treating a plant, plant part or seed with a microbial strain that is not pathogenic to said plant, wherein said treatment increases expression in said plant of one or more gene transcripts involved in production of a plant defense compound derived from anthranilate; and growing the plant in the presence of the pathogen or pest, whereby the level of one or more plant defense compounds in said plant is increased as compared to a control plant, and the response of said plant to said pathogen or pest is improved as compared to a control plant, wherein the control plant is not genetically modified or treated with said microbial strain. In some embodiments, the expression of one or more gene transcripts associated with production of anthranilate and / or conversion of anthranilate to a plant defense compound is increased in comparison to the control plant. In some embodiments, transcription of a gene encoding an anthranilate synthase protein component is increased in comparison to the control plant. In some embodiments, transcription of an anthranilate synthase alpha or beta subunit component gene is increased in comparison to the control plant. In some embodiments, transcription of a gene encoding anthranilate N- benzoyltransferase is increased in comparison to the control plant. In some embodiments, the plant defense compound is an anthranilate ester. In some embodiments, the anthranilate ester is selected from the group consisting of methyl anthranilate, dimethyl anthranilate, ethyl anthranilate, phenylethyl anthranilate and menthyl anthranilate. In some embodiments, the plant defense compound is an anthranilate derived phytoalexin. In some embodiments, a microbial strain that enhances a plant response to a pathogen or pest is a bacterial strain. In some embodiments, the bacterial strain is a Methylobacterium or Methylorubrum strain. In some embodiments, the bacterial strain is NLS0042 (NRRL B-50932). In some embodiments, the bacterial strain is not NLS0042 (NRRL B-50932). In some embodiments, the plant defense compound reduces foraging of insect larvae on plant roots. In some embodiments, the plant defense compound reduces foraging of insect larvae on plant roots in comparison to the control plant. In some embodiments, the plant is corn, and the insect pest is corn rootworm. In some embodiments, root regrowth following exposure to the pathogen or pest is increased in comparison to the control plant. In some embodiments, expression of an anthranilate synthase protein component having the amino acid sequence of SEQ ID NO:2 or SEQ ID NO:4 or protein having the amino acid sequence of SEQ ID NO:2 or SEQ ID NO:4 is increased in comparison to the control plant. In some embodiments, expression of an anthranilate synthase protein or protein component comprising an amino acid sequence having at least 70%, 80%, 85%, 90%, 95%, 98%, 99%, or 100% sequence identity to SEQ ID NO: 9, 10, 12, 14, 15, 17, 18, or 20 is increased in comparison to the control plant. In some embodiments, expression of a geneAgent Ref.: P14472WO00 4 encoding an anthranilate N-benzoyltransferase of SEQ ID NO: 6 or SEQ ID NO:7 is increased in comparison to the control plant. In some embodiments, expression of a gene encoding an anthranilate N-benzoyltransferase having at least 70%, 80%, 85%, 90%, 95%, 98%, or 99% sequence identity SEQ ID NO: 6 or SEQ ID NO:7 is increased in comparison to the control plant. In some embodiments of methods provided herein, the plant defense compound is not an indole derivative.

[0006] In some embodiments of methods provided herein, an insect pest is a thrips, and the treated plant is corn, soybean, cotton, peanut, potato, tomato, or strawberry. In some embodiments, an insect pest is an aphid, and the plant is soybean, cotton, wheat, potato, tomato, strawberry or a pepper plant. In some embodiments, an insect pest is a fall army worm, and the plant is soybean, cotton, wheat, rice or strawberry plant. In some embodiments, an insect pest is a leaf hopper, and the plant is rice, potato, tomato or snap bean plant. In some embodiments, an insect pest is a lepidopteran, and the plant is soybean, tomato, pepper or snap bean. In some embodiments, an insect pest is a nematode, and the plant is a soybean, cotton, potato or tomato plant. In some embodiments, an insect pest is a wireworm, and the plant is a corn, soybean or potato plant. In some embodiments, an insect pest is a lygus bug, and the plant is a cotton, tomato or strawberry plant. In some embodiments, an insect pest is a cut worm, and the plant is a corn or strawberry plant. In some embodiments, an insect pest is a flea beetle, and the plant is a brassica plant. In some embodiments, an insect pest is a gall midge and the plant is a soybean plant. In some embodiments, an insect pest is a stink bug, and the plant is a tomato plant. In some embodiments, an insect pest is a potato beetle, and the plant is a potato plant. In some embodiments, an insect pest is a water weevil, and the plant is a rice plant. In some embodiments, an insect pest is a wheat stem sawfly, a cereal leaf beetle or a wheat mite, and the plant is a wheat plant. In some embodiments, an insect pest is an alfalfa hopper, a corn earworm, or a burrower bug, and the plant is a peanut plant. In some embodiments, an insect pest is a white grub, and the plant is a soybean plant. In some embodiments, an insect pest is a corn root worm, and the plant is a corn plant.

[0007] Methods of reducing or repelling a pathogen or pest by increasing a level of one or more plant defense compounds are provided, wherein such microbial strain protects the roots of a plant from attack by a pathogen or pest. In some embodiments, proteins in a pathway for production of a polyketide that induces a plant response to a pathogen or pest are present on a mobilizable plasmid, optionally wherein the mobilizable plasmid is heterologous to the bacterial strain containing the mobilizable plasmid. In some embodiments, proteins in a pathway for production of a polyketide are encoded by genes on SEQ ID NO: 87 or a variant thereof.Agent Ref.: P14472WO00 5 Variants of SEQ ID NO: 87 include: (i) DNA sequences having at least 80%, 85%, 90%, 95%, 98%, or 99% sequence identity to SEQ ID NO: 87 and / or (ii) DNA sequences encoding proteins encoded by SEQ ID NO: 87. In some embodiments, proteins in a pathway for production of a polyketide that induces a plant response to a pathogen or pest are encoded by genes on SEQ ID NO: 86 or a variant thereof. Variants of SEQ ID NO: 86 include: (i) DNA sequences having at least 80%, 85%, 90%, 95%, 98%, or 99% sequence identity to SEQ ID NO: 86 and / or (ii) DNA sequences encoding proteins encoded by SEQ ID NO: 86. In some embodiments, proteins in a pathway for production of a polyketide that induces a plant response to a pathogen or pest are encoded by a polynucleotide SEQ ID NOS: 36-50. In some embodiments, proteins in a pathway for production of a polyketide that induces a plant response to a pathogen or pest comprise a polypeptide having at least 70%, 80%, 85%, 90%, 95%, 98%, 99%, or 100% sequence identity to of any one of SEQ ID NOS:21-35. In some embodiments, a protein in a microbe that induces a plant response to a pathogen or pest is a homolog or ortholog of any one of SEQ ID NOS:21- 35. In some embodiments, a gene in a pathway for production of a polyketide is a bfmBAB_2 gene. In some embodiments, bfmBAB_2 has the sequence of SEQ ID NO:36. In some embodiments a bfmBAB_2 gene encodes a protein having a sequence of SEQ ID NO:21. In some embodiments, a bfmBAB_2 gene has at least 70% identity with SEQ ID NO:36, and / or encodes a protein having at least 80% identity with SEQ ID NO:21. In some embodiments, the bacterial strain is a Methylobacterium or Methylorubrum strain. In some embodiments, the bacterial strain is NLS0042 (NRRL B-50932). In some embodiments, the bacterial strain is not NLS0042 (NRRL B-50932). In some embodiments, the plant defense compound reduces foraging of insect larvae on plant roots. In some embodiments, insect larvae are repelled from plant roots. In some embodiments, the plant defense compound reduces foraging of insect larvae on plant roots in comparison to the control plant. In some embodiments, the plant is corn, and the insect pest is corn rootworm. In some embodiments, root regrowth following exposure to the pathogen or pest is increased in comparison to the control plant. In some embodiments, the plant defense compound reduces foraging of insect larvae on plant roots. In some embodiments, the plant defense compound reduces foraging of insect larvae on plant roots in comparison to the control plant. In some embodiments, the plant is corn, and the insect pest is corn rootworm. In some embodiments, the microbial strain is a Methylobacterium or Methylorubrum strain. In some embodiments, the microbial strain is NLS0042 (NRRL B-50932) or a derivative thereof. In some embodiments, the microbial strain is not NLS0042 (NRRL B-50932). In some embodiments, the plant defense compound reduces foraging of insect larvae on plant roots. In some embodiments, the plant defense compound reduces foraging of insect larvae on plant rootsAgent Ref.: P14472WO00 6 in comparison to the control plant. In some embodiments, the plant is corn, and the insect pest is corn rootworm.

[0008] Methods of reducing or repelling a pathogen or pest by treating soil, a plant, plant part, or seed with a microbial strain, producing a metabolite derived from such microbial strain, wherein such metabolite increases a defense mechanism of a plant, plant part or seed and the defense mechanism protects the roots of a plant from attack by a pathogen or pest. In some embodiment, a method of reducing feeding or repelling of a pathogen or pest comprises treating soil, a plant, a plant part or a seed with a microbial strain, wherein said microbial strain expresses a metabolite; and growing the plant in the presence of the pathogen or pest, whereby the treated plant, plant part or seed pathogen or pest repels the pathogen or pest more or reduces feeding of the pathogen or pest as compared to a control plant, wherein the control plant is not genetically modified or treated with said microbial strain. Methods of reducing or repelling a pathogen or pest by treating soil, a plant, plant part, or seed with a microbial strain, producing one or more metabolites and / or peptides derived from such microbial strain, wherein said one or more metabolites and / or peptides increases a defense mechanism of a plant, plant part or seed and the defense mechanism protects the roots of a plant from attack by a pathogen or pest, are also provided. In some embodiments, a method of reducing feeding or repelling of a pathogen or pest comprises treating soil, a plant, a plant part or a seed with a microbial strain, wherein said microbial strain expresses a gene, genes or pathway of genes involved in metabolite biosynthesis, wherein the metabolite or metabolites enhance a plant response to a pathogen and / or pest; and growing the plant in the presence of the pathogen or pest, whereby the treated plant, plant part or seed t repels the pathogen or pest or reduces feeding of the pathogen or pest as compared to a control plant, wherein the control plant is not or treated with said microbial strain. In some embodiments, the microbial strain produces a siderophore or a polyketide. In some embodiments, a polyketide produced by the microbial strain is an antimicrobial compound. In some embodiments, proteins in a pathway for production of a polyketide that induces a plant response to a pathogen or pest are present on a mobilizable plasmid. In some embodiments, proteins in a pathway for production of a polyketide are encoded by genes in SEQ ID NO: 87 or a variant thereof. Variants of SEQ ID NO: 87 include: (i) DNA sequences having at least 80%, 85%, 90%, 95%, 98%, or 99% sequence identity to SEQ ID NO: 87 and / or (ii) DNA sequences encoding proteins encoded by SEQ ID NO: 87. In some embodiments, proteins in a pathway for production of a polyketide that induces a plant response to a pathogen or pest are encoded by genes on SEQ ID NO: 86 or a variant thereof. Variants of SEQ ID NO: 86 include: (i) DNA sequences having at least 80%, 85%, 90%, 95%, 98%, or 99% sequenceAgent Ref.: P14472WO00 7 identity to SEQ ID NO: 86 and / or (ii) DNA sequences encoding proteins encoded by SEQ ID NO: 86. In some embodiments, proteins in a pathway for production of a polyketide that induces a plant response to a pathogen or pest are encoded by SEQ ID NOS: 36-50. In some embodiments, proteins in a pathway for production of a polyketide that induces a plant response to a pathogen or pest have a sequence of any one of SEQ ID NOS:21-35. In some embodiments, a protein in a microbe that induces a plant response to a pathogen or pest is a homolog or ortholog of any one of SEQ ID NOS:21-35. In some embodiments, a gene in a pathway for production of a polyketide is a bfmBAB_2 gene. In some embodiments, bfmBAB_2 has the sequence of SEQ ID NO:36. In some embodiments a bfmBAB_2 gene encodes a protein having a sequence of SEQ ID NO:21. In some embodiments, a bfmBAB_2 gene has at least 70%, 80%, 85%, 90%, 95%, 98%, 99%, or 100% sequence identity to SEQ ID NO:36, and / or encodes a protein having at least 80%, 85%, 90%, 95%, 98%, 99%, or 100% identity with SEQ ID NO:21. In some embodiments, the plant is a cereal grain crop, such as corn, rice, wheat, rye, oats, barley and millet, or the plant is a turfgrass, soybean, strawberry or cotton, and the insect pest is an armyworm. In some embodiments, the armyworm is a fall armyworm. In some embodiments, the armyworm is a Spodoptera species, including without limitation S. frugiperda and S. exiqua. In some embodiments, the plant is a solanaceous plant such as tomato, tobacco, eggplant, pepper and potato, and the insect pest is a hornworm. In some embodiments, the hornworm is a Manduca species, including M. quinquemaculata and M. sexta. In some embodiments, the plant is soybean, and the insect pest is soybean looper. In some embodiments, the plant is tobacco or cotton and the pest is a thrips. In some embodiments, the thrips is a western flower thrips. In some embodiments, the microbial strain is a Methylobacterium or Methylorubrum strain. In some embodiments, the microbial strain is NLS0042 (NRRL B-50932) or a derivative thereof. In some embodiments, the microbial strain is not NLS0042 (NRRL B-50932). In some embodiments, the plant defense compound reduces foraging of insect larvae on plant roots. In some embodiments, the plant defense compound reduces foraging of insect larvae on plant roots in comparison to the control plant. In some embodiments, the plant is corn, and the insect pest is corn rootworm.

[0009] Methods to identify a microbial strain that enhances the response of a plant to a pathogen or pest, wherein said microbial strain is not pathogenic to said plant, are provided herein. Such methods comprise the steps of (i) treating a plant, plant part or plant seed with at least a first microbial strain that is not a pathogen of said plant to obtain a treated seed and / or a treated plant; (ii) growing the treated plant, or growing a plant from a treated plant part or treated seed, in the presence of said pathogen or pest; (iii) harvesting one or more tissue samples from said plantAgent Ref.: P14472WO00 8 and from an untreated control plant, wherein said tissue samples are harvested at a growing stage during which said pest or pathogen is attacking said plant tissue; and (iv) assaying said samples to identify increased production of one or more plant defense compounds derived from anthranilate in said treated plants as compared to an control plant, whereby a microbial strain that enhances the response of a plant to said pathogen or pest is identified. In some embodiments, a control plant is an untreated plant. In some embodiments, a control plant is treated with a different microbe. In some embodiments, such methods further comprise the step of selecting samples for analysis from treated plants that exhibit reduced damage from said pathogen or pest as compared to control plants. In some embodiments, samples are assayed to determine the levels of one or more gene transcripts associated with production of anthranilate and / or conversion of anthranilate to a plant defense compound. In some embodiments, the samples are assayed to determine the levels of one or more plant defense compounds derived from anthranilate. In some embodiments, the pathogen or pest is a fungus, bacteria, nematode, insect, or virus. In some embodiments, the treated plant part is selected from the group consisting of a leaf, stem, shoot, flower, fruit, bud, root, tuber, rhizome, runner, bulb, and corm. In some embodiments, the harvested tissue sample is selected from the group consisting of a leaf, stem, shoot, flower, fruit, bud, root, tuber, rhizome, runner, bulb, and corm tissue sample. In some embodiments plant tissue samples are analyzed to determine the level of one or more gene transcripts encoding an anthranilate synthase protein component or the level of the anthranilate synthase protein component (e.g., by an enzymatic or immune- assay). In some embodiments, the anthranilate synthase protein component is an alpha or beta subunit. In some embodiments plant tissue samples are analyzed to determine the level of a gene transcript encoding anthranilate N-benzoyltransferase or the level of anthranilate N-benzoyltransferase (e.g., by an enzymatic or immune- assay). In some embodiments, the plant defense compound is an anthranilate ester. In some embodiments, the anthranilate ester is selected from the group consisting of methyl anthranilate, dimethyl anthranilate, ethyl anthranilate, phenylethyl anthranilate and menthyl anthranilate. In some embodiments, the plant defense compound is an anthranilate derived phytoalexin.

[0010] Further methods that can be used to identify a microbial strain that enhances the response of a plant to a pathogen or pest, wherein said microbial strain is not pathogenic to said plant, comprise screening a sample comprising a microbial strain or strains for the presence of a gene or genes that encode a protein or proteins for production of a compound that enhances the response of a plant to a pathogen or pest. In some embodiments, a microbial strain is identified by the presence of a gene or genes in the siderophore biosynthesis pathway. In someAgent Ref.: P14472WO00 9 embodiments, a microbial strain is identified by the presence of a gene or genes in a polyketide biosynthesis pathway. In some embodiments, the polyketide is an antimicrobial compound. In some embodiments, proteins in a pathway for production of a polyketide that induces a plant response to a pathogen or pest are present on a mobilizable plasmid. In some embodiments, proteins in a pathway for production of a polyketide are encoded by genes on SEQ ID NO: 87 or variants of those genes comprising DNA sequences having at least 70%, 80%, 85%, 90%, 95%, 98%, or 99% sequence identity to the protein encoding sequences of SEQ ID NO: 87. In some embodiments, proteins in a pathway for production of a polyketide that induces a plant response to a pathogen or pest are encoded by genes on SEQ ID NO: 86 or variants of those genes comprising DNA sequences having at least 70%, 80%, 85%, 90%, 95%, 98%, or 99% sequence identity to the protein encoding sequences of SEQ ID NO: 86. In some embodiments, proteins in a pathway for production of a polyketide that induces a plant response to a pathogen or pest are encoded by polynucleotides comprising DNA sequences having at least 70%, 80%, 85%, 90%, 95%, 98%, 99%, or 100% sequence identity to one or more of SEQ ID NOS: 36-50. In some embodiments, proteins in a pathway for production of a polyketide that induces a plant response to a pathogen or pest comprise an amino acid sequence having at least 70%, 80%, 85%, 90%, 95%, 98%, 99%, or 100% sequence identity to of any one of SEQ ID NOS:21-35. In some embodiments, a protein in a microbe that induces a plant response to a pathogen or pest is a homolog or ortholog of any one of SEQ ID NOS:21-35. In some embodiments, a gene in a pathway for production of a polyketide is a bfmBAB_2 gene. In some embodiments, bfmBAB_2 comprises a polynucleotide sequence having at least 70%, 80%, 85%, 90%, 95%, 98%, 99%, or 100% sequence identity to SEQ ID NO:36. In some embodiments a bfmBAB_2 gene encodes a protein having at least 70%, 80%, 85%, 90%, 95%, 98%, 99%, or 100% sequence identity to SEQ ID NO:21. In some embodiments, a bfmBAB_2 gene has at least 70%, 85%, 90%, 95%, 98%, 99%, or 100% sequence identity with SEQ ID NO:36, and / or encodes a protein having at least 80%, 85%, 90%, 95%, 98%, 99%, or 100% sequence identity to SEQ ID NO:21. In some embodiment of any of the above described methods and compositions, the microbial strain is a bacterial strain or fungal strain. In some embodiments, the bacterial strain is a Methylobacterium or Methylorubrum strain. In some embodiments, the plant is selected from the group consisting of corn, wheat, rye, rice, alfalfa, barley, oats, rye, sorghum, millet, soybean, Brassica sp., Cannabis sp., tobacco, potato, peanut, carrot, cotton, coffee, coconut, sugar beet, oat, barley, tomato, squash, cucumber, cucurbits, lettuce, peppers, pea, onion, green bean, snap bean, sunflower, safflower, sweet potato, cassava, coffee, coconut, conifers, turfgrass, leafy greens, microgreens, herbs, fruit plants, such as strawberry, and fruit trees, including, but not limited toAgent Ref.: P14472WO00 10 apple trees, nut trees, and ornamentals. In some embodiments, the plant is a corn plant. In some embodiments, the pest is an insect. In some embodiments, the tissue sample is a root sample. In some embodiments, the pest is corn rootworm.

[0011] Also provided herein are methods and compositions that can be used to treat plants with microbes identified using methods described herein to enhance a plant response to one or more pathogens or pests. In some embodiments, microbial compositions provided herein will comprise a microbial strain that enhances a plant defense response to a pathogen and / or pest, and additional components to enhance long term storage of the microbial strains, facilitate treatment of plants and / or plant parts, and / or to serve as a plant growth regulator. In some embodiments, microbial strains provided herein will be in solid compositions, for example as an essentially dry product having approximately 5% or less water content. In some embodiments, a solid composition is in a powder or granular form. In some embodiments, compositions provided herein will be liquid cultures containing water, oils and / or polymers. In some embodiments, microbes provided herein are provided as a liquid flowable. In some embodiments, microbes are stabilized in suspension-like concentrates where the continuous phase is miscible in water but is not water. For example, the continuous phase in such suspension-like concentrates can be a polymer, such as a polyether. In some embodiments microbial compositions are provided as oil dispersions. In some embodiments, microbes are encapsulated in a protective carrier. In some embodiments, compositions provided herein comprise Methylobacterium strain NLS0042 (NRRL B-50932) or a derivative thereof as a dried powder. In some embodiments, compositions comprising Methylobacterium strain NLS0042 (NRRL B-50932) or a derivative thereof comprise additional components to facilitate long term storage as a dried composition. In some embodiments, long term stability of Methylobacterium strain NLS0042 (NRRL B-50932) or a derivative thereof in the compositions comprising the dried powders and / or on treated seeds is enhanced in comparison to undried compositions or compositions lacking additional components that enhance long term storage of the microbial strains and / or facilitate treatment of plants and / or plant part. In some embodiments compositions comprising Methylobacterium strain NLS0042 (NRRL B-50932) or a derivative thereof comprise one or more oligosaccharides or polysaccharides. In some embodiments compositions comprising Methylobacterium strain NLS0042 (NRRL B-50932) or a derivative thereof comprise one or more polysaccharides selected from dextrins, maltodextrins, disaccharides, starches, chitosan, alginates, and gums, including but not limited to karaya gum, jaguar gum, xanthan gum, glucomannan, tragacanth gum, Konjac gum, polysaccharide gums, mucilage, gum arabics and other natural gums. In some embodiments a dried composition comprising Methylobacterium strain NLS0042 (NRRLAgent Ref.: P14472WO00 11 B-50932) or a derivative thereof with enhanced stability in comparison to other compositions further comprises maltodextrin, trehalose, and / or glucomannan. BRIEF DESCRIPTION OF THE DRAWINGS

[0012] Figure 1. Results of feeding choice assay when choice is between NLS0042-treated and untreated corn roots. The larvae overwhelming chose the untreated roots over the NLS0042- treated roots. The circles indicate the percent of larvae making a given choice in each of the 12 replicates of this experiment.

[0013] Figure 2. Results of feeding choice assay when choice is between two NLS0042-treated corn roots. In this instance, most larvae do not make a choice but instead stay in the middle petri dish where they began. The circles indicate the percent of larvae making a given choice in each of the 12 replicates of this experiment.

[0014] Figure 3. Results of feeding choice assay when choice is between two untreated corn roots. The circles indicate the percent of larvae making a given choice in each of the 12 replicates of this experiment. DETAILED DESCRIPTION Definitions

[0015] The term "and / or" where used herein is to be taken as specific disclosure of each of the two or more specified features or components with or without the other. Thus, the term “and / or" as used in a phrase such as "A and / or B" herein is intended to include "A and B," "A or B," "A" (alone), and "B" (alone). Likewise, the term "and / or" as used in a phrase such as "A, B, and / or C" is intended to encompass each of the following embodiments: A, B, and C; A, B, or C; A or C; A or B; B or C; A and C; A and B; B and C; A (alone); B (alone); and C (alone).

[0016] As used herein, the terms “include,” “includes,” and “including” are to be construed as at least having the features or encompassing the items to which they refer while not excluding any additional unspecified features or unspecified items.

[0017] As used herein, the term “biological” refers to a component of a composition for treatment of plants or plant parts comprised of or derived from a microorganism. Biologicals include biocontrol agents, other beneficial microorganisms, microbial extracts, natural products, plant growth activators or plant defense agents. Non-limiting examples of biocontrol agents include bacteria, fungi, beneficial nematodes, and viruses. In certain compositions, a biological can comprise a mono-culture or co-culture of Methylobacterium, or a combination of Methylobacterium strains or isolates that have been separately cultured.

[0018] As used herein, the term “Methylobacterium” refers to genera and species in the methylobacteriaceae family, including bacterial species in the Methylobacterium genus andAgent Ref.: P14472WO00 12 proposed Methylorubrum genus (Green and Ardley (2018)). Methylobacterium includes pink- pigmented facultative methylotrophic bacteria (PPFM) and also encompasses the non-pink- pigmented Methylobacterium nodulans, as well as colorless mutants of Methylobacterium isolates. For example, and not by way of limitation, “Methylobacterium” refers to bacteria of the species listed below as well as any new Methylobacterium species that have not yet been reported or described that can be characterized as Methylobacterium or Methylorubrum based on phylogenetic analysis: Methylobacterium adhaesivum; Methylobacterium oryzae; Methylobacterium aerolatum; Methylobacterium oxalidis; Methylobacterium aquaticum; Methylobacterium persicinum; Methylobacterium brachiatum; Methylobacterium phyllosphaerae; Methylobacterium brachythecii; Methylobacterium phyllostachyos; Methylobacterium bullatum; Methylobacterium platani; Methylobacterium cerastii; Methylobacterium pseudosasicola; Methylobacterium currus; Methylobacterium radiotolerans; Methylobacterium dankookense; Methylobacterium soli; Methylobacterium frigidaeris; Methylobacterium specialis; Methylobacterium fujisawaense; Methylobacterium tardum; Methylobacterium gnaphalii; Methylobacterium tarhaniae; Methylobacterium goesingense; Methylobacterium thuringiense; Methylobacterium gossipiicola; Methylobacterium trifolii; Methylobacterium gregans; Methylobacterium variabile; Methylobacterium haplocladii; Methylobacterium aminovorans (Methylorubrum aminovorans); Methylobacterium hispanicum; Methylobacterium extorquens (Methylorubrum extorquens); Methylobacterium indicum; Methylobacterium podarium (Methylorubrum podarium); Methylobacterium iners; Methylobacterium populi (Methylorubrum populi); Methylobacterium isbiliense; Methylobacterium pseudosasae (Methylorubrum pseudosasae); Methylobacterium jeotgali; Methylobacterium rhodesianum (Methylorubrum rhodesianum); Methylobacterium komagatae; Methylobacterium rhodinum (Methylorubrum rhodinum); Methylobacterium longum; Methylobacterium salsuginis (Methylorubrum salsuginis); Methylobacterium marchantiae; Methylobacterium suomiense (Methylorubrum suomiense; Methylobacterium mesophilicum; Methylobacterium thiocyanatum (Methylorubrum thiocyanatum); Methylobacterium nodulans; Methylobacterium zatmanii (Methylorubrum zatmanii); or Methylobacterium organophilum.

[0019] As used herein “mineral nutrients” (also sometime referred to simply as “nutrients”) are micronutrients or macronutrients required or useful for plants or plant parts including for example, but not limited to, nitrogen (N), potassium (K), calcium (Ca), magnesium (Mg), phosphorus (P), and sulfur (S), and the micronutrients chlorine (Cl), Iron (Fe), Boron (B), manganese (Mn), zinc (Z), cobalt (Co), copper (Cu), molybdenum (Mo), and nickel (Ni).Agent Ref.: P14472WO00 13

[0020] As used herein, “vitamins” are organic compounds required in small amounts for normal growth and metabolism. Vitamins are important for human and / or animal growth, and some vitamins have been reported to be beneficial to plants. Vitamins include but are not limited to vitamin A (including but not limited to all-trans-retinol and all-trans-retinyl-esters, as well as all- trans-beta-carotene and other provitamin A carotenoids), vitamin B1 (thiamine), vitamin B2 (riboflavin), vitamin B3 (niacin), vitamin B5 (pantothenic acid), vitamin B6 (pyridoxine), vitamin B7 (biotin), vitamin B9 (folic acid or folate), vitamin B12 (cobalamins), vitamin C (ascorbic acid), vitamin D (calciferols), vitamin E (tocopherols and tocotrienols), and vitamin K (quinones).

[0021] As used herein, the term “strain” shall include all isolates of such strain.

[0022] As used herein the phrase “mobilizable plasmid” refers to a plasmid that can be transferred from a donor strain to a recipient strain. A mobilizable plasmid as defined herein contains cis-acting DNA elements (i.e. oriT) required for conjugation and has an origin of replication functional in Methylobacterium. Other elements required for conjugation may also be encoded on a mobilizable plasmid. A conjugative or self-transmissible plasmid contains cis- acting DNA required for conjugation and encodes all of the genes required for DNA transfer to a recipient cell / strain or isolate, and is also considered a mobilizable plasmid for use in methods defined herein. As used herein, “variant” when used in the context of a Methylobacterium isolate, refers to any isolate that has chromosomal genomic DNA with at least 99%, 99.9%, 99.8%, 99.7%, 99.6%, or 99.5% sequence identity to chromosomal genomic DNA of a reference Methylobacterium isolate, such as, for example, a deposited Methylobacterium isolate provided herein. A variant of an isolate can be obtained from various sources including soil, plants or plant material, and water, particularly water associated with plants and / or agriculture. Variants include derivatives obtained from deposited isolates. Methylobacterium isolates or strains can be sequenced (for example as taught by Sanger et al. (1977), Bentley et al. (2008) or Caporaso et al. (2012)) and genome-scale comparison of the sequences conducted (Konstantinidis et al. (2005)) using sequence analysis tools, such as BLAST, as taught by Altschul et al. (1990) or clustalw (www.ebi.ac.uk / Tools / msa / clustalw2 / ). Variants can be identified, for example, by the presence of a 16S sequence of a reference strain, where the variant also demonstrates a plant production enhancement trait of the reference strain.

[0023] As used herein, “derivative” when used in the context of a Methylobacterium isolate, refers to any Methylobacterium that is obtained from a deposited Methylobacterium isolate provided herein. Derivatives of a Methylobacterium isolate include, but are not limited to, derivatives obtained by selection, derivatives selected by mutagenesis and selection, andAgent Ref.: P14472WO00 14 genetically transformed Methylobacterium obtained from a Methylobacterium isolate. A “derivative” can be identified, for example, based on genetic identity to the strain or isolate from which it was obtained and will generally exhibit chromosomal genomic DNA with at least 99%, 99.9%, 99.8%, 99.7%, 99.6%, or 99.5% sequence identity to chromosomal genomic DNA of the strain or isolate from which it was derived.

[0024] As used herein, “sequence identity” or “percent identity” when used to evaluate whether a particular Methylobacterium strain is a variant or derivative of a Methylobacterium strain provided herein refers to a measure of nucleotide-level genomic similarity between the coding regions of two genomes. Sequence identity between the coding regions of bacterial genomes can be calculated, for example, by determining the Average Nucleotide Identity (ANI) score using FastANI (Jain et al. “High throughput ANI analysis of 90K prokaryotic genomes reveals clear species boundaries”, Nat Communications 9, 5114 (2018)) and Han et al. (“ANI tools web: a web tool for fast genome comparison within multiple bacterial strains”; Database, 2016, 1–5).

[0025] As used herein, a “leafy green plant” refers to a vegetable crop with edible leaves and includes, without limitation, spinach, kale, lettuce (including but not limited to romaine, butterhead, iceberg, and loose-leaf lettuces), collard greens, cabbage, beet greens, watercress, swiss chard, arugula, escarole, endive, bok choy, and turnip greens. Leafy green plants as used herein also refers to plants grown for harvest of microgreens and / or herbs, including but not limited to lettuce, cauliflower, broccoli, cabbage, watercress, arugula, garlic, onion, leek, amaranth, swill chard, been, spinach, melon, cucumber, squash, basil, celery, cilantro, radish, radicchio, chicory, dill, rosemary, French tarragon, basil, Pennisetum, carrot, fennel, beans, peas, chickpeas, and lentils. Leafy green plants also refer to mixes of assorted leafy green plants, such as mesclun or other mixed salad greens or mixed microgreens. “Leafy green plants” as used herein also encompasses other brassica or cruciferous field greens not specifically mentioned herein by name.

[0026] As used herein, a “fruit” or “fruit bearing plant” can be a fleshy fruit bearing plant, including but not limited to, melon (including watermelon and cantaloupe), berry (including strawberry, blueberry, blackberry, and raspberry), grape, kiwi, mango, papaya, pineapple, banana, pepper, tomato, squash, and cucumber plants. As used herein, a “fruit” or “fruit bearing plant” can also refer to a tree fruit or fruit bearing tree, including but not limited to apple, peach, pear, lemon, lime, orange (and other citrus fruit), cherry, plum, apricot, nectarine, elderberry, pomegranate, persimmon, papaya, fig, avocado and guava.

[0027] As used herein, an “ornamental” plant refers to a plant grown primarily for display purposes rather than a functional purpose, including but not limited to perennials and woodyAgent Ref.: P14472WO00 15 shrubs, including but not limited to azalea, hydrangea, forsythia, hibiscus, roses and regional native plants; ornamental grasses; potted flowers, cut flowers and bulbs, including but not limited to tulips, hyacinths, daffodils, petunias, and carnations; and potted flowers produced from vegetatively propagated cuttings, including but not limited to poinsettia and chrysanthemum.

[0028] As used herein a “genetic element” refers to an element in a DNA or RNA molecule that comprises a series of adjacent nucleotides at least 20 nucleotides in length and up to 50, 100, 1000, or 10000 or more nucleic acids in length. A genetic element may comprise different groups of adjacent nucleic acids, for example, where the genome of a plant-associated microorganism contains introns and exons. The genetic element may be present on a chromosome or on an extrachromosomal element, such as a plasmid. In eukaryotic plant- associated microorganisms, the genetic element may be present in the nucleus or in the mitochondria. In some embodiments, the genetic element is a functional genetic element (e.g., a gene) that encodes a peptide or protein.

[0029] As used herein, the terms "homologous"' or "homologue" or "ortholog" refer to related genetic elements or proteins encoded by the genetic elements that are determined based on the degree of sequence identity. These terms describe the relationship between a genetic element or encoded protein found in one isolate, species, or strain and the corresponding or equivalent genetic element or protein in another isolate, species, or strain. As used herein, a particular genetic element in a first isolate, species, or strain is considered equivalent to a genetic element present in a second isolate, species, or strain when the proteins encoded by the genetic element in the isolates, species, or strains have at least 50 percent identity. Percent identity can be determined using a number of software programs available in the art including BLASTP, ClustalW, ALLALIGN, DNASTAR, SIM, SEQALN, NEEDLE, SSEARCH, and the like.

[0030] As used herein, the term “metabolite” refers to a substance produced during metabolism of a microbial strain including but not limited to a siderophore, non-ribosomal peptide, polyketide or a combination thereof.

[0031] Where a term is provided in the singular, other embodiments described by the plural of that term are also provided.

[0032] To the extent to which any of the preceding definitions is inconsistent with definitions provided in any patent or non-patent reference incorporated herein by reference, any patent or non-patent reference cited herein, or in any patent or non-patent reference found elsewhere, it is understood that the preceding definition will be used herein.Agent Ref.: P14472WO00 16 Further Description

[0033] Methods and compositions provided herein may be used to improve plant response to attack by pests and / or pathogens by increasing the levels of one or more plant defense compounds in a plant. In some embodiments of methods provided herein, a plant or plant part or seed reduces or repels a pathogen or pest following treatment of soil, a plant, plant part, or seed with a microbial strain that produces a metabolite, wherein such metabolite induces a defense response in a plant and protects the plant from attack by a pathogen or pest. In some embodiments, a plant response is improved by increasing the levels of one or more plant defense compounds derived from anthranilate in a plant. Anthranilate, the conjugate base of anthranilic acid, is synthesized in plants from chorismate by the action of the enzyme anthranilate synthase (EC 4.1.3.27), a heterotetrameric enzyme consisting of two α and 2 β subunits. This reaction is a branching point from the aromatic amino acid pathway to tryptophan biosynthesis, and the binding site of tryptophan involved in feedback inhibition of tryptophan synthesis is present in the alpha subunit. Overexpression of a Trp-insensitive anthranilate synthase (AS) α-subunit has been reported to increase tryptophan levels in transgenic plants, and hypothesized to increase the content of indole related compounds involved in resistance to insects in a biosynthesis pathway branching off of the tryptophan pathway. Anthranilate is also involved in the production of other plant secondary metabolites, including anthranilate esters and anthramides in various plants. Methyl anthranilate (MA) occurs naturally in various plants and has been used as a repellent against birds and insects. MA occurs in maize roots in very small quantities and has been reported to elicit a strong repellent response by neonate rootworm larvae in laboratory bioassays (Bernklau et al. (2016) J. Economic Entomology 109:1683-1690).

[0034] In some embodiments, the anthranilate derived plant defense compounds are not derived from indole. In some embodiments, an anthranilate derived plant defense compound is an anthranilate ester. In some embodiments, an anthranilate ester is selected from the group consisting of methyl anthranilate, dimethyl anthranilate, ethyl anthranilate, phenylethyl anthranilate and menthyl anthranilate. In some embodiments, an anthranilate derived plant defense compound is a phytoalexin. In some embodiments, a phytoalexin is an amide biosynthesized following conversion of anthranilate to N-benzoylanthranilate catalyzed by anthranilate N-benzoyltransferase (EC 2.3.1.44).

[0035] In some embodiments of methods provided herein, a plant genome is modified to provide for an increased levels of a plant defense compound derived from anthranilate. In some embodiments a plant genome is modified to enhance the expression of one or more gene transcripts involved in production of such plant defense compounds. In other embodiments, aAgent Ref.: P14472WO00 17 plant genome is modified to reduce expression of genes that contribute to synthesis of trypthophan to provide for accumulation of anthranilate for use in enzymatic reactions that result in production of anthranilate esters and anthramides. In some embodiments, a plant is genetically modified to express a heterologous transcript for a gene involved in production of a plant defense compound. A heterologous transcript can be derived, for example, from a different plant source, from a microbial source, or may be synthetically produced. Various plant regulatory elements are employed in such methods, including for example, tissue specific promoters to target increased expression in a particular tissue or tissues subject to attack by a plant pathogen or pest. In some embodiments, root, leaf, green tissue, fruit, tuber, seed or vascular tissue specific promoters are employed. Also of use in the present methods are constitutive promoters that provide for expression in a broad range of plants, plant parts and plant tissues. In some embodiments, the expression of a native plant gene transcript is increased.

[0036] In some embodiments, genetic modification is accomplished by gene editing techniques enabling specific modification of endogenous genes in the plant genome, including those involving CRISPR / CAS (e.g., as disclosed in US Patent Application Publications 20150344912, 20160138008, 20180179547, 20200172886, and 20220282244, which are incorporated herein by reference in its entirety), meganucleases, zinc-finger nucleases (ZFNs), and transcription activator-like effector nucleases (TALENs). In certain embodiments, the gene editing reagents can be used to integrate DNA comprising a transcriptional enhancer element (e.g., US Patent Application publication US2016 / 0168584, incorporated herein by reference in its entirety) by either Homology-Directed Repair (HDR) or Non-Homologous End Joining (NHEJ) into the promoter of one or more of the genes of the plant involved in production of a plant defense compound derived from anthranilate to increase their expression. In certain embodiments the promoter or promoter comprising the enhancer insertion is operably linked to an anthranilate synthase protein component, which optionally comprises an amino acid sequence of SEQ ID NO:2, SEQ ID NO:4, or a sequence having at least 90%, 95%, 98%, or 99% sequence identity thereto. In certain embodiments, the promoter or the promoter comprising the enhancer insertion is operably linked to a gene encoding an anthranilate N-benzoyltransferase; which optionally comprises the polypeptide sequence of SEQ ID NO: 6 and / or SEQ ID NO:7 is increased in comparison to the control plant, or a sequence having at least 90%, 95%, 98%, or 99% sequence identity thereto. In certain embodiments, the promoter or the promoter comprising the enhancer insertion is operably linked to a maize gene provided in Table 6 and is optionally located in a maize or other monocot plant.Agent Ref.: P14472WO00 18

[0037] In other embodiments provided herein, levels of anthranilate derived plant defense compounds are increased as the result of treatment of said plant, or a part thereof, including a seed, with a microbial strain or strains that is not pathogenic to said plant, and which treatment results in increased expression in said plant of one or more gene transcripts involved in production of a plant defense compound derived from anthranilate. In some embodiments, a microbial strain is not pathogenic to the treated plant, even though the microbe may be a pathogen to other plants not treated in the methods described herein. In some embodiments, the microbial strain is beneficial to the treated plant.

[0038] In some embodiments of methods provided herein, a plant or plant part or seed reduces or repels a pathogen or pest following treatment of soil, a plant, plant part, or seed with a microbial strain that produces a metabolite, wherein such metabolite increases a defense mechanism of a plant, plant part or seed and the defense mechanism protects the roots of a plant or a plant from attack by a pathogen or pest. In some embodiments, a plant defense mechanism includes increased production of anthranilate and / or anthranilate derived compounds. In some embodiments, production of anthranilate and / or anthranilate derived compounds in roots is enhanced. In some embodiments, the plant defense response protects the plant roots from attack. In some embodiments, a plant response is improved by treatment of a plant, plant part, seed or soil with a microbe that expresses a gene involved in induction of an ISR response, including for example a gene involved in biosynthesis of siderophores and / or polyketides. In some embodiments, proteins in a pathway for production of a polyketide that induces a plant response to a pathogen or pest are present on a mobilizable plasmid. In some embodiments, proteins in a pathway for production of a polyketide are encoded by genes on DNA having a sequence of SEQ ID NO: 87 or variants thereof comprising (i) DNA sequences having at least 80%, 85%, 90%, 95%, 98%, or 99% sequence identity to SEQ ID NO: 87 and / or (ii) DNA sequences encoding proteins encoded by SEQ ID NO: 87. In some embodiments, proteins in a pathway for production of a polyketide that induces a plant response to a pathogen or pest are encoded by genes on DNA having a sequence SEQ ID NO: 86 or variants thereof comprising (i) DNA sequences having at least 80%, 85%, 90%, 95%, 98%, or 99% sequence identity to SEQ ID NO: 86 and / or (ii) DNA sequences encoding proteins encoded by SEQ ID NO: 86. In some embodiments, proteins in a pathway for production of a polyketide that induces a plant response to a pathogen or pest are encoded by a polynucleotide comprising a DNA sequence having at least 70%, 80%, 85%, 90%, 95%, 98%, 99%, or 100% sequence identity to SEQ ID NOS: 36- 50. In some embodiments, proteins in a pathway for production of a polyketide that induces a plant response to a pathogen or pest comprise a polypeptide sequence plant response to aAgent Ref.: P14472WO00 19 pathogen or pest are encoded by a polynucleotide comprising a DNA sequence having at least 70%, 80%, 85%, 90%, 95%, 98%, 99%, or 100% sequence identity to any one of SEQ ID NOS:21-35. In some embodiments, a protein in a microbe that induces a plant response to a pathogen or pest is a homolog or ortholog of any one of SEQ ID NOS:21-35. In some embodiments, a gene in a pathway for production of a polyketide is a bfmBAB_2 gene. In some embodiments, the bfmBAB_2 gene comprises a polynucleotide sequence of SEQ ID NO:36. In some embodiments a bfmBAB_2 gene encodes a protein having a sequence of SEQ ID NO:21. In some embodiments, thebfmBAB_2 gene comprises a polynucleotide having at least 70%, 80%, 85%, 90%, 95%, 98%, 99%, or 100% sequence identity with SEQ ID NO:36, and / or encodes a protein comprising an amino acid sequence having at least 80%, 85%, 90%, 95%, 98%, 99%, or 100% sequence identity with SEQ ID NO:21. In some embodiments, the bacterial strain is a Methylobacterium or Methylorubrum strain. In some embodiments, the bacterial strain is NLS0042 (NRRL B-50932). In some embodiments, the bacterial strain is not NLS0042 (NRRL B-50932). In some embodiments, a method of reducing feeding or repelling of a pathogen or pest comprises treating soil, a plant, a plant part or a seed with a microbial strain, wherein said microbial strain expresses a metabolite; and growing the plant in the presence of the pathogen or pest, whereby the treated plant, plant part or seed pathogen or pest repels the pathogen or pest more or reduces feeding of the pathogen or pest as compared to a control plant, wherein the control plant is not genetically modified or treated with said microbial strain. In some embodiments, the plant defense compound reduces foraging of insect larvae on plant roots. In some embodiments, the plant defense compound reduces foraging of insect larvae on plant roots in comparison to the control.

[0039] In some embodiments, plants are treated with a bacterial strain to increase expression in said plant of one or more gene transcripts involved in production of a plant defense compound derived from anthranilate or reduce or repel or a plant pathogen or pest. In some embodiments, a plant defense compound is derived from anthranilate.

[0040] Microbial strains comprising heterologous DNA which can confer resistance, act as a repellant, tolerance, reduced damage, forage, reduced infection, and / or reduced infestation of a plant to a pest or pathogen as well as methods of making such microbial strains are provided. In some embodiments, DNA is transferred from a microbial strain which can confer resistance, act as a repellant, tolerance, reduced damage, forage, reduced infection, and / or reduced infestation of a plant to a pest or pathogen to a distinct microbial strain lacking that DNA. In certain embodiments, the heterologous DNA which is transferred to the distinct microbial strain encodes a protein having a sequence of any one of SEQ ID NO:21-35, or a protein sequence atAgent Ref.: P14472WO00 20 least 80%, 85%, 90%, 95%, 98%, 99%, or 100 sequence identity to any one of SEQ ID NO:21- 35. In some embodiments, DNA is transferred on a mobilizable plasmid from a microbial strain that induces a plant response to an insect and / or pathogen. In some embodiments, a mobilizable plasmid is transferred from a Methylobacterium or Methylorubrum strain to a second Methylobacterium or Methylorubrum strain. In some embodiments, a mobilizable plasmid comprises SEQ ID NO:87 or a variant thereof comprising (i) DNA sequences having at least 80%, 85%, 90%, 95%, 98%, or 99% sequence identity to SEQ ID NO: 87; and / or (ii) DNA sequences encoding proteins encoded by SEQ ID NO: 87. In other embodiments, a mobilizable plasmid comprises SEQ ID NO:86 or a variant thereof comprising (i) DNA sequences having at least 80%, 85%, 90%, 95%, 98%, or 99% sequence identity to SEQ ID NO: 86; and / or (ii) DNA sequences encoding proteins encoded by SEQ ID NO: 86. In further embodiments, a mobilizable plasmid that is transferred to a microorganism to impart the ability to induce a plant defense response encodes one or more of the proteins comprising an amino acid sequence having at least 70%, 80%, 85%, 90%, 95%, 98%, 99%, or 100% sequence identity to SEQ ID NO:21-35. In some embodiments, genes encoding proteins that enhance plant response to an insect and / or pathogen are heterologous to a microbial host. In some embodiments, genes encoding one or more of SEQ ID NO:21-35 or derivatives, variants, homologs or orthologs thereof are genetically manipulated to prepare recombinant constructs that provide for expression of one or more proteins comprising an amino acid sequence having at least SEQ ID NO:21-35. In some embodiments, such recombinant constructs comprise regulatory sequences to provide for expression of said protein or proteins in a target microbial host. In some embodiments, recombinant DNA constructs for expression of any one or more of a protein comprising an amino acid sequence having at least 70%, 80%, 85%, 90%, 95%, 98%, 99%, or 100% sequence identity to SEQ ID NO:21-35 are stably integrated into the genome of a target microbial host. In some embodiments, constructs for expression of any one or more of a protein comprising an amino acid sequence having at least 70%, 80%, 85%, 90%, 95%, 98%, 99%, or 100% sequence identity to SEQ ID NO:21-35 are introduced and maintained on a plasmid or other extrachromosomal element in a target microbial host. In some embodiments, one or more of the genes encoding a protein comprising an amino acid sequence having at least 70%, 80%, 85%, 90%, 95%, 98%, 99%, or 100% sequence identity to SEQ ID NO:21-35 are present in and expressed from an operon. In other embodiments, one or more of the genes encoding the proteins comprising an amino acid sequence having at least 70%, 80%, 85%, 90%, 95%, 98%, 99%, or 100% sequence identity to SEQ ID NO:21-35 are present in individual recombinant expression constructs. Also provided are recombinant DNA constructs comprising aAgent Ref.: P14472WO00 21 heterologous promoter which is operably linked to one or more of the genes encoding the proteins comprising an amino acid sequence having at least 70%, 80%, 85%, 90%, 95%, 98%, 99%, or 100% sequence identity to SEQ ID NO:21-35, as well as microbial cells comprising the recombinant DNA constructs. In some embodiments, microbial strains that are engineered to express one or more proteins comprising an amino acid sequence having at least 70%, 80%, 85%, 90%, 95%, 98%, 99%, or 100% sequence identity to SEQ ID NO:21-35 are bacterial strains. In certain embodiments, the aforementioned or otherwise provided DNA molecules are introduced into a microbial strain other than Methylobacterium sp. #4 (NLS0042; NRRL B- 50932). In certain embodiments, the aforementioned or otherwise provided DNA molecules are introduced into a microbial strain in Table 1 selected from the group consisting of Methylobacterium sp. #1 to 3, #5 to #53, and #54. In certain embodiments, the aforementioned or otherwise provided DNA molecules are introduced into a Methylorubrum sp. including Methylorubrum sp. #63 of Table 1. In some embodiments, microbial strains that are engineered to express one or more proteins comprising an amino acid sequence having at least 70%, 80%, 85%, 90%, 95%, 98%, 99%, or 100% sequence identity to SEQ ID NO:21-35 are fungal strains.

[0041] Bacterial strains of use in the present methods include, but are not limited to bacterial strains of the genera Actinomycetes, Agrobacterium, Arthrobacter, Alcaligenes, Aureobacterium, Azobacter, Azorhizobium, Azospirillum, Azotobacter, Beijerinckia, Bacillus, Brevibacillus, Burkholderia, Chromobacterium, Clostridium, Clavibacter, Comomonas, Corynebacterium, Curtobacterium, Enterobacter, Flavobacterium, Gluconacetobacter, Gluconobacter, Herbaspirillum, Hydrogenophage, Klebsiella, Luteibacter, Lysinibacillus, Mesorhizobium, Methylobacterium, Methylorubrum, Microbacterium, Ochrobactrum, Paenibacillus, Pantoea, Pasteuria, Phingobacterium, Photorhabdus, Phyllobacterium, Pseudomonas, Rhizobium, Rhodococcus, Bradyrhizobium, Serratia, Sinorhizobium, Sphingomonas, Streptomyces, Stenotrophomonas, Variovorax, Xanthomonas and Xenorhadbus. In some embodiments the bacteria is selected from the group consisting of Bacillus amyloliquefaciens, Bacillus cereus, Bacillus firmus, Bacillus, lichenformis, Bacillus pumilus, Bacillus sphaericus, Bacillus subtilis, Bacillus thuringiensis, Chromobacterium suttsuga, Pasteuria penetrans, Pasteuria usage, and Pseudomonas fluorescens.

[0042] In some embodiments plants are treated with a beneficial fungus, including but not limited to strains of the genera Acremonium, Alternaria, Ampelomyces, Aspergillus, Aureobasidium, Beauveria, Botryosphaeria, Cladosporium, Cochliobolus, Colletotrichum, Coniothyrium, Embellisia, Epicoccum, Fusarium, Gigaspora, Gliocladium, Glomus, Laccaria, Metarhisium, Muscodor, Nigrospora, Paecilonyces, Paraglomus, Penicillium, Phoma,Agent Ref.: P14472WO00 22 Pisolithus, Podospora, Rhizopogon, Scleroderma, Trichoderma, Typhula, Ulocladium, and Verticillium. In particular embodiments, the fungus is Beauveria bassiana, Coniothyrium minitans, Gliocladium vixens, Muscodor albus, Paecilomyces lilacinus, and Trichoderma polysporum.

[0043] In some embodiments, plants are treated with a Methylobacterium or Methylorubrum bacterial strain. In some embodiments, a Methylobacterium or Methylorubrum strain is a deposited strain disclosed in Table 1. TABLE 1 USDA ARS Deposit Identifier NLS #1Strain TaxonomyAgent Ref.: P14472WO00 23 USDA ARS Deposit Identifier NLS # Strain Taxonomy NRRL No1Agent Ref.: P14472WO00 24 USDA ARS Deposit Identifier NLS # Strain Taxonomy NRRL No1cancon er res stance, repe ant, toerance, reduced damage, reduced n ect on, reduced orage, and / or reduced infestation to or by a pest or pathogen disclosed herein are obtained by transferring DNA from a microbial strain which can confer resistance, act as a repellant, tolerance, reduced damage, forage, reduced infection, and / or reduced infestation to a pest or pathogen by increasing production of one or more plant defense compounds derived from anthranilate in a plant to a microbial strain which does not confer such resistance, tolerance, reduced damage, reduced infection, and / or reduced infestation and recovering or selecting a new microbial strain with the pest or pathogen resistance, tolerance, reduced damage, reduced infection, and / or reduced infestation conferred by the transferred DNA. In other embodiments, DNA transferred from a microbial strain which can confer resistance, act as a repellant, tolerance, reduced damage, forage, reduced infection, and / or reduced infestation to a pest or pathogen, encodes a protein having a sequence of any one of SEQ ID NO:21-35, or a protein having a sequence at least 80%, 85%, 90%, 95%, 98%, 99%, or 100% sequence identity to any one of SEQ ID NO:21-35. In some embodiments, DNA is transferred on a mobilizable plasmid from a microbial strain that induces a plant response to an insect and / or pathogen. In some embodiments, a mobilizable plasmid is transferred from a Methylobacterium or Methylorubrum strain to a second Methylobacterium or Methylorubrum strain. In some embodiments, a mobilizable plasmid comprises SEQ ID NO:87 or a variant thereof comprising: (i) DNA sequences having at least 80%, 85%, 90%, 95%, 98%, or 99% sequence identity to SEQ ID NO: 87 and / or (ii) DNA sequences encoding proteins encoded by SEQ ID NO: 87. In other embodiments, a mobilizable plasmid comprises SEQ ID NO:86 or a variant thereof comprising: (i) DNA sequences having at least 80%, 85%, 90%, 95%, 98%, or 99% sequence identity to SEQ ID NO: 86; and / or (ii) DNA sequences encoding proteins encoded by SEQ ID NO: 86. In further embodiments, a mobilizable plasmid that is transferred to a microorganism to impart the ability to induce a plant defense response encodes one or more proteins comprising a polypeptide sequence having at least 70%, 80%, 85%, 90%, 95%, 98%, 99%, or 100% sequence identity to SEQ ID NO:21-35. In some embodiments, a mobilizable plasmid that is transferred to a microorganism to impart the ability to induce a plant defense response comprises one or moreAgent Ref.: P14472WO00 25 sequences having at least 70%, 80%, 85%, 90%, 95%, 98%, 99%, or 100% sequence identity to SEQ ID NO:36-50. In some embodiments, a mobilizable plasmid that is transferred to a microorganism to impart the ability to induce a plant defense response encodes one or more proteins comprising a polypeptide sequence having at least 70%, 80%, 85%, 90%, 95%, 98%, 99%, or 100% sequence identity to SEQ ID NO:51-85. In some embodiments, one or more proteins having a sequence of SEQ ID NO:51-85 or a sequence having at least 70%, 80%, 85%, 90%, 95%, 98%, 99% or 100% sequence identity to SEQ ID NO:51-85 facilitates transfer of a mobilizable plasmid.

[0045] In certain embodiments, the DNA that can confer resistance, tolerance, reduced damage, reduced infection, and / or reduced infestation to or by a pest or pathogen by increasing production by a plant of one or more plant defense compounds derived from anthranilate or one or more plant defense compounds is DNA from NLS0042 or a derivative thereof (e.g., DNA donor strain) and / or the microbial strain which does not confer such resistance, tolerance, reduced damage, reduced infection, and / or reduced infestation (e.g., DNA recipient strain) is a strain other than NLS0042 which is provided in Table 1. Methods for transferring DNA from a donor strain (e.g., NLS0042) to a recipient strain (e.g., another strain in Table 1) include but are not limited to DNA transfer methods disclosed in US patent application publication US20210171961, which is incorporated herein by reference in its entirety.

[0046] In some embodiments of methods provided herein a gene transcript involved in production of one or more plant defense compounds from anthranilate encodes an AS alpha or beta component. In some embodiments, a gene transcript encodes an AS beta component. In some embodiments an AS beta gene transcript is a corn plant transcript. In some embodiments, expression of an AS beta subunit protein having a sequence of SEQ ID NO:2 or a homolog or ortholog, thereof is increased. Homologs and orthologs of SEQ ID NO:2 include Arabidopsis proteins AT1G24909, AT1G25155, AT1G24807, AT1G25083, ASB2, and ASB1; and rice proteins OASB1 (Os04g0463500), and OASB2 (Os03g0718000). In some embodiments, a gene transcript encodes an AS alpha component. In some embodiments an AS alpha gene transcript is a corn plant transcript. In some embodiments, expression of an AS alpha subunit protein having a sequence of SEQ ID NO:4 or a homolog or ortholog, thereof is increased. Homologs and orthologs of SEQ ID NO:4 include Arabidopsis proteins AT3G55870, ASA1, and ASA2; and rice proteins OASA2 (Os03g0264400), and OASA1 (Os03g0826500). Additional plant AS alpha and beta subunit genes can be identified, for example, from plant genome sequences. In some embodiments, a gene encoding an AS alpha or beta protein component is transcribed toAgent Ref.: P14472WO00 26 produce multiple transcripts and translated proteins. Examples of additional corn AS genes for use in the methods described herein are provided in Example 4.

[0047] In other embodiments of methods disclosed herein a gene transcript involved in production of one or more plant defense compounds from anthranilate encodes an anthranilate N-benzoyltransferase protein that catalyzes the production of N-benzoylanthranilate from benzoyl-CoA and anthranilate, a reaction involved in the production of anthramide phytoalexins. The enzyme, EC 2.3.1.144, is sometimes referred to as anthranilate N-hydroxycinammoyl / benzoyltransferase due to its ability to use other thioesters of coenzyme A as donors in the reaction with anthranilate, including cinnamoyl-CoA, 4-coumaroyl-CoA and salicyloyl-CoA. Compounds resulting from reaction with such other donor substrates may also be involved in production of plant defense compounds. In one embodiment of methods described herein, a gene transcript involved in production of one or more plant defense compounds encodes maize anthranilate N-benzoyltransferase protein represented by SEQ ID NO:6 and / or SEQ ID NO:7. Other plant anthranilate N-benzoyltransferase proteins are also of interest in the methods described herein, including DcHCBT2_Z84386 from Dianthus caryophyllus.

[0048] In other embodiments of methods disclosed herein a gene transcript involved in production a protein that enhances the response of a plant to a pathogen or pest, encodes a protein having a sequence at least 80% identical to SEQ ID NO:21. In some embodiments, a gene transcript encodes a protein comprising an amino acid sequence having at least 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 8990, 91, 92, 93, 94, 95, 96, 97, 98, 99% or 100% sequence identity to SEQ ID NO:21.

[0049] The methods disclosed herein are applicable to improving plant response to a variety of plant pests and pathogen, including bacterial and fungal pathogens, viruses, nematodes and insects. Such pathogens may attack one or more parts of a plant, including but not limited to a leaf, stem, shoot, flower, fruit, bud, root, tuber, rhizome, runner, bulb, and corm. An improved plant response to a pathogen or pest will result in decreased damage or other adverse effects of the pathogen or pest. Adverse effects of pathogen or pest attack on a plant include, but are not limited to, any type of plant tissue damage or necrosis, any type of plant yield reduction, any reduction in the value of the crop plant product, and / or production of undesirable metabolites or growth products of the pathogen or pest, including, but not limited to fungal metabolites or fungal growth by-products including, but not limited to, mycotoxins.

[0050] In some embodiments, methods provided herein improve a plant response to a fungal pathogen selected from the group consisting of an Alternaria sp., an Ascochyta sp., an Aspergillus sp., a Bipolaris sp., a Botrytis sp., a Bremia sp., a Cercospora sp., a CochliobolusAgent Ref.: P14472WO00 27 sp., a Colletotrichum sp., a Diplodia sp., an Erysiphe sp., an Exserohilum sp., a Fusarium sp., Gaeumanomyces sp., Macrophomina sp., a Magnaporthe sp., a Nectria sp., a Peronospora sp., a Phakopsora sp., a Phialophora sp., a Phoma sp., a Phymatotrichum sp., a Phytophthora sp., a Plasmopara sp., a Puccinia sp., a Podosphaera sp., a Pyrenophora sp., a Pyricularia sp, a Pythium sp., a Rhizoctonia sp., a Sclerotium sp., a Sclerotinia sp., a Septoria sp., a Stagonospora sp., a Thielaviopsis sp., an Uncinula sp, an Ustilago sp., a Venturia sp., and a Verticillium sp.

[0051] In some embodiments, methods provided herein improve a plant response to a bacterial pathogen selected from the group consisting of a Pseudomonas sp., a Ralstonia sp., an Agrobacterium sp., a Xanthomonas sp., an Erwinia sp., a Xylella sp., a Dickeya sp., a Pectobacterium sp., a Clavibacter sp., and a Candidatus sp.

[0052] In some embodiments where a plant is attacked by an insect, an improved response can result in reduction of damage caused by an insect directly, and / or can reduce damage caused by a plant pathogen transmitted by the insect. Some viruses that affect agriculture crops are topoviruses and gemini viruses. Some common viruses that can severely affect plants include tomato spotted wilt virus, beet curly top virus, tomato yellow leaf curl virus, cucumber mosaic virus, potato virus y, potato virus x, cauliflower mosaic virus, african cassava mosaic virus, plum pox virus, brome mosaic virus, potato virus, tobacco mosaic virus, tomato spotted wilt virus, tomato yellow leaf curl virus, cucumber mosaic virus, cauliflower mosaic virus, african cassava mosaic virus, plum pox virus, and brome mosaic virus.

[0053] Piercing-sucking insects, for example, cause damage such as spotting or stippling of foliage, leaf curling, and stunted or misshapen fruits, in addition to effects caused by vectored pathogens. Piercing-sucking insects include leafhoppers, thrips and aphids, and attack plant vascular tissues, such as are present in roots, stems, leaves and other plant organs.

[0054] In some embodiments of methods and compositions described herein, an improved plant response to insects with chewing mouthparts (chewing insects) is obtained. Damage caused by chewing insects can take many forms. In some cases, foliage or flowers are completely consumed by some insects, or plants or plant parts appear ragged and have chewed edges or centers. In some cases, only upper or lower surfaces are consumed and can be observed as a brown, scorched appearance, or openings between the veins. Chewing damage inside a plant is sometimes referred to as mining or boring. Chewing and biting pests may bite into and chew leaves, stems, buds, flowers, and / or roots of plants. Damage from such pests can include defoliation from extensive feeding; tunneling, for example from burrowing of insects such as leaf miners into plant leaves; girdling from beetles that feed on living wood; and root damage from insect feeding, leading to lodging. Common chewing insect pests include snails, slugs,Agent Ref.: P14472WO00 28 caterpillars, borers, cutworms, hornworms and beetles. Non-limiting examples of crops and target pests for which the methods, microbial strains, and compositions provided herein find use include: Peppers - aphids and lepidopterans; Tomato – stinkbugs, aphids, white fly, beet leafhopper (BCTV vector), tobacco hornworm; Snap bean - potato leaf hopper, Mexican bean beetle, lepidopteran insects; Brassicas - flea beetles; Soybean - Fall armyworm, Soybean looper, nematodes; Cotton - Western flower thrips, Fall armyworm, nematodes, aphids; Rice - Fall armyworm, water weevil; and Corn - corn rootworm, cutworms, beetles, corn leaf and root aphids, white grubs, mites, armyworms and wireworms.

[0055] In some embodiments of methods described herein, an insect pest is a corn rootworm (CRW), a member of the widespread beetle genus, Diabrotica. In some embodiments, methods described herein enhance the response of a corn plant to attack by Western corn rootworm (WCR), leading to decreased lodging and / or increased yield in comparison to control plants.In some embodiments of methods and compositions described herein, improved response of a corn plant to feeding by CRW is obtained by treatment of a corn plant, part or seed with a beneficial microbe. In some embodiments, a corn plant is treated with a beneficial bacterium. In some embodiments, a corn plant is treated with a Methylobacterium or Methylorubrum species. In some embodiments, a corn plant is treated with a deposited Methylobacterium or Methylorubrum species listed in Table 1. In some embodiments, a corn plant is treated with NLS0042 (NRRL B-50932). In some embodiments, a corn plant is treated with a Methylobacterium or Methylorubrum species other than NLS0042 (NRRL B-50932). In some embodiments, improved response of a corn plant to feeding by CRW is obtained by modifying a corn plant genome to increase expression of one or more gene transcripts involved in production of one or more plant defense compounds. In some embodiments, a corn plant genome is modified to increase expression of a native corn gene transcript. In some embodiments, a corn plant genome is modified to increase expression of a heterologous gene transcript, for example from a microbial source or from a plant other than corn. In some embodiments, a plant is modified to increase expression of an anthranilate synthase subunit transcript. In some embodiments, expression of an alpha and / or beta subunit transcript is increased. In some embodiments, expression of an anthranilate N-benzoyltransferase is increased. In some embodiments, expression of an anthranilate synthase beta subunit transcript and an anthranilate N-benzoyltransferase transcript are increased. In some embodiments, expression of one or more gene transcripts encoding a protein having a sequence of SEQ ID NO:2, SEQ ID NO:4, SEQ ID NO:6, or SEQ ID NO:7 is increased.Agent Ref.: P14472WO00 29

[0056] Plants that can be treated and / or genetically modified in the methods provided herein include a wide range of plants including, but not limited to field crops, leafy greens, fruits or fruit trees, ornamentals, turf grasses, and trees grown in commercial production. Without limitation, such plant species include corn, soybean, cruciferous or Brassica sp. vegetables (e.g., B. napus, B. rapa, B. juncea), alfalfa, rice, rye, wheat, barley, oats, sorghum, millet (e.g., pearl millet (Pennisetum glaucum), proso millet (Panicum miliaceum), foxtail millet (Setaria italica), and finger millet (Eleusine coracana)), sunflower, safflower, carrot, pepper, tomato, squash, cucumber, melon and other curcubits, beans, peas, chickpeas, lentils, tobacco, potato, peanuts, cotton, berries, grape, kiwi, mango, papaya, pineapple, banana, species in the genus Cannabis (including, but not limited to, Cannabis sativa and industrial hemp varieties), sweet potato (Ipomoea batatus), cassava, coffee, coconut, ornamentals (including, but not limited to, azalea, hydrangea, hibiscus, roses, tulips, daffodils, petunias, carnation, poinsettia, and chrysanthemum), conifers (including, but not limited to pines such as loblolly pine, slash pine, ponderosa pine, lodge pole pine, and Monterey pine; Douglas-fir; Western hemlock; Sitka spruce; redwood; true firs such as silver fir and balsam fir; and cedars such as Western red cedar and Alaska yellow-cedar), and turfgrass (including, but are not limited to, annual bluegrass, annual ryegrass, Canada bluegrass, fescue, bentgrass, wheatgrass, Kentucky bluegrass, orchard grass, ryegrass, redtop, Bermuda grass, St. Augustine grass, and zoysia grass). Identification and Selection of Microbes that Enhance a Plant Response to Pest or Pathogens

[0057] Also provided herein are methods to identify a microbe that enhances the response of a plant to one or more pathogens or pests, wherein the microbe is not a pathogen of said plant, and wherein the plant response is enhanced by increased production in the plant of one or more plant defense compounds derived from anthranilate. In some embodiments, a method to identify a microbe that enhances a plant response to one or more pathogens or pests comprises the steps of treating a plant, plant part or plant seed with at least a first microbial strain that is not a pathogen of said plant to obtain a treated seed and / or a treated plant; growing the treated plant, or growing a plant from a treated plant part or treated seed, in the presence of said pathogen or pest; harvesting one or more tissue samples from said plant and from an untreated control plant, wherein said tissue samples are harvested at a growing stage during which said pest or pathogen is attacking said plant tissue; and assaying said samples to identify a microbe that provides for increased production of one or more plant defense compounds derived from anthranilate. In some embodiments, such methods comprise the additional step of selecting samples for analysis of levels of said one or more plant defense compounds from treated plants that exhibit reducedAgent Ref.: P14472WO00 30 damage from said pathogen or pest as compared to untreated control plants, or that exhibit reduced damage from said plant pathogen or pest as compared to other plants treated with said microbe.

[0058] In some embodiments a method of selecting a microbial strain that enhances the response of a plant to a pathogen or pest comprises the steps of: (i) assaying one or more tissue samples from a plant treated with at least a first microbial strain that is not a pathogen of said plant or from a plant grown from a plant part or seed treated with the first microbial strain for increased levels of one or more plant defense compounds derived from anthranilate as compared to one or more control tissue samples from an untreated control plant, wherein said tissue samples were harvested from the treated and untreated plant during or after said pest or pathogen attacked said plant tissue; and; (ii) selecting a microbial strain that is not a pathogen of said plant and that provides the increased levels of the one or more plant defense compounds, thereby selecting a microbial strain that enhances the response of a plant to said pathogen or pest.

[0059] In some embodiments, a plant tissue extract or plant part, such as a germinating seedling is treated and assayed in vitro, for example in a culture dish or test tube. In some embodiments a method of selecting a microbial strain that enhances the response of a plant to a pathogen or pest comprises the steps of: (i) assaying one or more plant tissue samples treated with at least a first microbial strain that is not a pathogen of said plant for increased levels of one or more plant defense compounds derived from anthranilate as compared to one or more untreated control plant tissue samples, wherein said tissue samples were exposed to said pest or pathogen during or after treatment with said first microbial strain; and; (ii) selecting a microbial strain that provides the increased levels of the one or more plant defense compounds, thereby selecting a microbial strain that enhances the response of a plant to said pathogen or pest.

[0060] Additional methods can also be employed to identify a microbe that enhances the response of a plant to one or more pathogens or pests, wherein the microbe is not a pathogen of said plant, and wherein the plant response is enhanced by expression of a gene in said microbe. In certain embodiments, such methods can comprise subjecting a sample to a nucleic acid analysis technique and determining that the sample contains nucleic acids expressing one or more proteins involved in production a protein that enhances the response of a plant to a pathogen or pest. In some embodiments, a microbe is identified as having one or more genes that encode proteins involved in biosynthesis of polyketides. In some embodiment, genes encoding one or more polyketide synthesis proteins are encoded by sequences present in SEQ ID NO:86, SEQ ID NO: 87, or variants thereof. Variants of SEQ ID NO: 87 include: (i) DNA sequences having at least 80%, 85%, 90%, 95%, 98%, or 99% sequence identity to SEQ ID NO:Agent Ref.: P14472WO00 31 87 and / or (ii) DNA sequences encoding proteins encoded by SEQ ID NO: 87. Variants of SEQ ID NO: 86 include: (i) DNA sequences having at least 80%, 85%, 90%, 95%, 98%, or 99% sequence identity to SEQ ID NO: 86; and / or (ii) DNA sequences encoding proteins encoded by SEQ ID NO: 86. In some embodiment, genes encoding polyketide synthesis proteins are homologs or orthologs of polyketide synthesis protein expressing sequences present in SEQ ID NO:86 and / or SEQ ID NO: 87. In some embodiments, polyketide biosynthesis protein encoding sequences identified in microorganisms encode a protein having at least 80% identity to a protein having a sequence of SEQ ID NO:21-35. In some embodiments, such polyketide biosynthesis protein encoding sequences have at least 70% identity to a polyketide biosynthesis protein encoding sequence of SEQ ID NO:36-50. In some embodiments, a polyketide biosynthesis protein has the sequence of SEQ ID NO:21 or has about 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 8990, 91, 92, 93, 94, 95, 96, 97, 98, 99% or 100% sequence identity to SEQ ID NO:21. Nucleic acid analysis to identify such sequences include, but are not limited to, techniques based on sequencing, using BLAST to compare sequences, nucleic acid hybridization, polymerase chain reactions (PCR), mass spectroscopy, nanopore based detection, branched DNA analyses, combinations thereof, and the like. In some embodiments, a nucleic acid analysis can be used to detect microbial strains present at a concentration of 103, 104, 105, 106or more per gram of sample. Samples of interest for identification of microbial strains that enhance the response of a plant to a pathogen or pest include soil samples, plants, plant parts, residual plant material, various water sources, including water from rice paddies or crop irrigation.

[0061] Various methods can be employed to treat plants with a microbe to identify or select one or more microbes that enhance a plant response to a target pathogen or pest. Such methods can include, but are not limited to, spraying, coating, partially coating, immersing, and / or imbibing the plant, plant part or seed with one or more microbes or compositions comprising such microbes. Compositions comprising microbes for application to plants can be without limitation aqueous or non-aqueous liquids, dried compositions or emulsions. In certain embodiments, plant seeds or cuttings can be immersed and / or imbibed with compositions comprising a microbial strain. In certain embodiments, seed imbibition and / or immersion can be performed with gentle agitation. Seed treatments can be effected with both continuous and / or batch seed treaters. In certain embodiments, coated seeds can be prepared by slurrying seeds with a coating composition comprising a microbial strain. Alternatively, microbial strains may be applied to soil or other growth medium where plants are grown. Soil treatments or applications can include, but are not limited to, in-furrow applications (e.g., before, during, and / or after seedAgent Ref.: P14472WO00 32 deposition), soil drenches, and distribution of granular or other dried formulations to the soil (e.g., before, during, and / or after seed deposition or plant growth). Treatments for plants grown in hydroponic systems can include seed treatments prior to germination, foliar applications to germinated plants or parts thereof, and applications in a liquid solution used in the hydroponic system.

[0062] The plant, plant part or seed for use in screening methods to identify a microbe that enhances a plant response to a target pathogen or pest can be any plant subject to attack and damage by a target pest or pathogen, or a plant part or seed from such plant. Without limitation, a plant can be an agricultural field crop plant, a leafy green plant, a fruit bearing plant or tree, an ornamental plant, a turf grass, or a tree grown for commercial production, such as a conifer or nut tree. Without limitation, such plant species include corn, soybean, cruciferous or Brassica sp. vegetables (e.g., B. napus, B. rapa, B. juncea), alfalfa, rice, rye, wheat, barley, oats, sorghum, millet (e.g., pearl millet (Pennisetum glaucum), proso millet (Panicum miliaceum), foxtail millet (Setaria italica), and finger millet (Eleusine coracana)), sunflower, safflower, carrot, pepper, tomato, squash, cucumber, melon and other curcubits, beans, peas, chickpeas, lentils, tobacco, potato, peanuts, cotton, berries, grape, kiwi, mango, papaya, pineapple, banana, species in the genus Cannabis (including, but not limited to, Cannabis sativa and industrial hemp varieties), sweet potato (Ipomoea batatus), cassava, coffee, coconut, ornamentals (including, but not limited to, azalea, hydrangea, hibiscus, roses, tulips, daffodils, petunias, carnation, poinsettia, and chrysanthemum), conifers (including, but not limited to pines such as loblolly pine, slash pine, ponderosa pine, lodge pole pine, and Monterey pine; Douglas-fir; Western hemlock; Sitka spruce; redwood; true firs such as silver fir and balsam fir; and cedars such as Western red cedar and Alaska yellow-cedar), and turfgrass (including, but are not limited to, annual bluegrass, annual ryegrass, Canada bluegrass, fescue, bentgrass, wheatgrass, Kentucky bluegrass, orchard grass, ryegrass, redtop, Bermuda grass, St. Augustine grass, and zoysia grass).

[0063] In some embodiments, a microbe that is used to treat a plant, plant part or plant seed in assays to identify microbes that enhance a plant response to a target pathogen or pest is a beneficial microbe that provides additional benefits to the treated plant. In some embodiments the beneficial microbe is a bacterial strain. Bacterial strains that can be used in the assays described herein to identify a microbe that enhances a plant response to a target pathogen or pest include, but are not limited to nonpathogenic bacterial strains of the genus Actinomycetes, Agrobacterium, Arthrobacter, Alcaligenes, Aureobacterium, Azobacter, Azorhizobium, Azospirillum, Azotobacter, Beijerinckia, Bacillus, Brevibacillus, Burkholderia,Agent Ref.: P14472WO00 33 Chromobacterium, Clostridium, Clavibacter, Comomonas, Corynebacterium, Curtobacterium, Enterobacter, Flavobacterium, Gluconacetobacter, Gluconobacter, Herbaspirillum, Hydrogenophage, Klebsiella, Luteibacter, Lysinibacillus, Mesorhizobium, Methylobacterium, Methylorubrum, Microbacterium, Ochrobactrum, Paenibacillus, Pantoea, Pasteuria, Phingobacterium, Photorhabdus, Phyllobacterium, Pseudomonas, Rhizobium, Rhodococcus, Bradyrhizobium, Serratia, Sinorhizobium, Sphingomonas, Streptomyces, Stenotrophomonas, Variovorax, Xanthomonas and Xenorhadbus. In some embodiments the beneficial microbe is a fungal strain. In some embodiments, a fungal strain tested in an assay to identify an enhanced plant response to attack by a pathogen or pest is a nonpathogenic strain of the genus Acremonium, Alternaria, Ampelomyces, Aspergillus, Aureobasidium, Beauveria, Botryosphaeria, Cladosporium, Cochliobolus, Colletotrichum, Coniothyrium, Embellisia, Epicoccum, Fusarium, Gigaspora, Gliocladium, Glomus, Laccaria, Metarhisium, Muscodor, Nigrospora, Paecilonyces, Paraglomus, Penicillium, Phoma, Pisolithus, Podospora, Rhizopogon, Scleroderma, Trichoderma, Typhula, Ulocladium, or Verticillium.

[0064] In some embodiments a microbe that enhances a plant response to a pathogen or pest will enhance an induced systemic resistance (ISR) response in the plant. Some plant beneficial microbes, such plant growth promoting rhizobacterium (PGPR) are capable of eliciting broad- spectrum induced systemic resistance (ISR). Some PGPR strains elicit responses similar to pathogen-induced systemic acquired resistance (SAR). In some embodiments, one or more genes involved in elicitation of an ISR response are jasmonic acid-dependent defense genes. In some embodiments, a gene involved in elicitation of an ISR response is identified in a microbe encodes a siderophore. In some embodiments one or more gene clusters that contribute to production of an ISR in a treated plant are involved in the biosynthesis of metabolites. In some embodiments, a gene cluster that contributes to production of an ISR response is a polyketide synthase gene cluster, a siderophore gene cluster, non-ribosomal peptide synthase, or a combination thereof.

[0065] In some embodiments a method to identify or select a microbial strain that enhances the response of a plant to a pathogen or pest described herein comprises the step of growing the treated plant in the presence of a pathogen or pest of said plant. In other embodiments, a plant or plant part is exposed to a pest or pathogen in vitro, for example in a culture medium. The plant can be exposed to the pest or pathogen in any plant growth medium, including without limitation, soil, liquid, such as hydroponic media, and nutrient culture media such as used for plant tissue culture or micropropagation. Thus, in some embodiments, the treated plant part canAgent Ref.: P14472WO00 34 be a plant part for use in micropropagation, such as stem tips, anthers, petals, pollen and other plant tissues, or may be a germinating seedling or undifferentiated plant tissue, such as callus.

[0066] Target pathogens or pests for use in the assay methods described herein include bacterial and fungal pathogens, and insect pests. Fungal pathogens include strains of Alternaria, Ascochyta, an Aspergillus, Bipolaris, Botrytis, Bremia, Cercospora, Cochliobolus, Colletotrichum, Diplodia, Erysiphe, Exserohilum, Fusarium, Gaeumanomyces, Macrophomina, Magnaporthe, Nectria, Peronospora, Phakopsora, Phialophora, Phoma, Phymatotrichum, Phytophthora, Plasmopara, Puccinia, Podosphaera, Pyrenophora, Pyricularisp, Pythium, Rhizoctonia, Sclerotium, Sclerotinia, Septoria, Stagonospora, Thielaviopsis, Uncinula, Ustilago, Venturia, and Verticillium. Target bacterial pathogens for use in screening methods provided herein include strains of Pseudomonas, Ralstonia, Agrobacterium, Xanthomonas, Erwinia, Xylella, Dickeya, Pectobacterium, Clavibacter, and Candidatus. Target insects for use in the screening methods described can be any insect that causes damage to a plant, including without limitation leafhoppers, thrips, aphids, snails, slugs, caterpillars, borers, miners, cutworms, hornworms and beetles. Most insect pests have four distinct stages of growth, egg, larva, pupa and adult. Sucking and chewing insects have three stages of growth, egg, nymph and adult. In some embodiments of screening methods disclosed herein, an insect pest is applied to the plant to allow screening for an enhanced response of the plant to said pest. Pests can be applied in any growth stage that will result in the pathogen attacking and damaging the plant. In some embodiments, the target pest is naturally present in the plant growth medium, for example when the plant is grown in soil in a field. In some embodiments of screening methods described herein, the target insect is applied at the larval stage to a plant, plant part, or plant culture medium. In some embodiments of screening methods described herein, a target insect pest is a corn rootworm (CRW), a member of the widespread beetle genus, Diabrotica.

[0067] A method to identify a microbial strain that enhances the response of a plant to a pathogen or pest described herein further comprises the step of harvesting one or more tissue samples from the treated plant. In some embodiments, tissue samples are harvested at a growing stage of the plant, plant part or plant tissue at which the target pest or pathogen is attacking the plant, plant part or plant tissue. The tissue to be sampled will be selected based on the target pest, and can include leaf, stem, shoot, flower, fruit, bud, root, tuber, rhizome, runner, bulb, corm, germinating seedlings, and callus tissue.

[0068] A method to identify a microbial strain that enhances the response of a plant to a pathogen or pest described herein further comprises the step of assaying the harvested tissue sample or samples to identify increased production of plant defense compounds derived fromAgent Ref.: P14472WO00 35 anthranilate and / or increased production of transcripts encoding a protein associated with production of anthranilate and / or conversion of anthranilate to a plant defense compound. In some embodiments, samples from treated plants grown in the presence of a target pathogen or pest are assayed to identify increased levels of one or more gene transcripts associated with production of anthranilate and / or conversion of anthranilate to a plant defense compound, as compared to levels of such transcripts in a control sample from an untreated plant or from a plant treated with a microbe that does not enhance the response of said plant to the target pathogen or pest. Assays for gene transcript levels include RNA extraction and quantitative RNAseq analysis, microarray analysis, high-throughput sequencing, and the like. In some embodiments, samples are assayed using a metabolomics approach that captures volatile and nonvolatile metabolites, to identify plants having increased levels of one or more plant defense compounds. In some embodiments, a microbe that enhances the response of a plant to a target pathogen or pest is identified by the presence of increased levels of a gene transcript encoding an anthranilate synthase alpha or beta subunit protein component in samples from treated plants as compared to the levels of such transcripts in intreated plants, or from a plant treated with a microbe that does not enhance a plant response to said pathogen or pest. In some embodiments, increased levels of transcripts encoding a beta subunit component are indicative of a microbe that enhances the response of a plant to the target pathogen or pest. In some embodiments, a microbe that enhances the response of a plant to a target pathogen or pest is identified by the presence of increased levels of a gene transcript encoding an enzyme encoding a protein involved in the synthesis of one or more anthranilate derived plant defense compounds in samples from treated plants as compared to the levels of such transcripts in intreated plants, or from a plant treated with a microbe that does not enhance a plant response to said pathogen or pest. In some embodiments, said plant defense compound is an anthranilate derived phytoalexin. In some embodiments, increased levels of a transcript encoding anthranilate N- benzoyltransferase are indicative of a microbe that improves a plant response to attack by a pathogen or pest. In some embodiments, samples are assayed to determine increased expression of one or more gene transcripts encoding a protein having a sequence of SEQ ID NO:2, SEQ ID NO:4, SEQ ID NO:6, and / or SEQ ID NO:7.

[0069] Target pathogens or pests for use in the assay methods described herein include bacterial and fungal pathogens, and insect pests. Fungal pathogens include strains of Alternaria, Ascochyta, an Aspergillus, Bipolaris, Botrytis, Bremia, Cercospora, Cochliobolus, Colletotrichum, Diplodia, Erysiphe, Exserohilum, Fusarium, Gaeumanomyces, Macrophomina, Magnaporthe, Nectria, Peronospora, Phakopsora, Phialophora, Phoma, Phymatotrichum,Agent Ref.: P14472WO00 36 Phytophthora, Plasmopara, Puccinia, Podosphaera, Pyrenophora, Pyricularisp, Pythium, Rhizoctonia, Sclerotium, Sclerotinia, Septoria, Stagonospora, Thielaviopsis, Uncinula, Ustilago, Venturia, and Verticillium. Target bacterial pathogens for use in screening methods provided herein include strains of Pseudomonas, Ralstonia, Agrobacterium, Xanthomonas, Erwinia, Xylella, Dickeya, Pectobacterium, Clavibacter, and Candidatus. Target insects for use in the screening methods described can be any insect that causes damage to a plant, including without limitation leafhoppers, thrips, aphids, snails, slugs, caterpillars, borers, miners, cutworms, hornworms and beetles. In some embodiments of screening methods described herein, the plant is corn, and a target insect pest is corn rootworm (CRW), a member of the widespread beetle genus, Diabrotica. Compositions for Treating Plants

[0070] In certain embodiments of any of the methods identified herein, compositions for treating plants to improve response of a plant to attack by pests and / or pathogens, will comprise a microbe that enhances a plant response by increasing production of one or more plant defense compounds derived from anthranilate and at least one additional component. In other embodiments, the compositions will comprise a microbe that enhances a plant response by increasing production of one or more plant defense compounds and at least one additional component. In some embodiments an additional component can be an additional active ingredient, for example, a pesticide or a second biological. In certain embodiments, the pesticide can be an insecticide, a fungicide, an herbicide, a nematicide, or other biocide. Non-limiting examples of insecticides and nematicides include carbamates, diamides, macrocyclic lactones, neonicotinoids, organophosphates, phenylpyrazoles, pyrethrins, spinosyns, synthetic pyrethroids, tetronic and tetramic acids. In particular embodiments insecticides and nematicides include abamectin, aldicarb, aldoxycarb, bifenthrin, carbofuran, chlorantraniliporle, chlothianidin, cyfluthrin, cyhalothrin, cypermethrin, deltamethrin, dinotefuran, emamectin, ethiprole, fenamiphos, fipronil, flubendiamide, fosthiazate, imidacloprid, ivermectin, lambda- cyhalothrin, milbemectin, nitenpyram, oxamyl, permethrin, tioxazafen, spinetoram, spinosad, spirodichlofen, spirotetramat, tefluthrin, thiacloprid, thiamethoxam, and thiodicarb. Non- limiting examples of useful fungicides include aromatic hydrocarbons, benzimidazoles, benzthiadiazole, carboxamides, carboxylic acid amides, morpholines, phenylamides, phosphonates, quinone outside inhibitors (e.g. strobilurins), thiazolidines, thiophanates, thiophene carboxamides, and triazoles. Particular examples of fungicides include acibenzolar-S- methyl, azoxystrobin, benalaxyl, bixafen, boscalid, carbendazim, cyproconazole, dimethomorph, epoxiconazole, fluopyram, fluoxastrobin, flutianil, flutolanil, fluxapyroxad, fosetyl-Al,Agent Ref.: P14472WO00 37 ipconazole, isopyrazam, kresoxim-methyl, mefenoxam, metalaxyl, metconazole, myclobutanil, orysastrobin, penflufen, penthiopyrad, picoxystrobin, propiconazole, prothioconazole, pyraclostrobin, sedaxane, silthiofam, tebuconazole, thifluzamide, thiophanate, tolclofos-methyl, trifloxystrobin, and triticonazole. Non-limiting examples of other biocides include isothiazolinones, for example 1,2 Benzothiazolin-3-one (BIT), 5-Chloro-2-methyl-4- isothiazolin-3-one (CIT), 2-Methyl-4-isothiazolin-3-one (MIT), octylisothiazolinone (OIT), dichlorooctylisothiazolinone (DCOIT), and butylbenzisothiazolinone (BBIT); 2-Bromo-2-nitro- propane-1,3-diol (Bronopol), 5-bromo-5-nitro-1,3-dioxane (Bronidox), Tris(hydroxymethyl)nitromethane, 2,2-Dibromo-3-nitrilopropionamide (DBNPA), and alkyl dimethyl benzyl ammonium chlorides. Non-limiting examples of herbicides include ACCase inhibitors, acetanilides, AHAS inhibitors, carotenoid biosynthesis inhibitors, EPSPS inhibitors, glutamine synthetase inhibitors, PPO inhibitors, PS II inhibitors, and synthetic auxins. Particular examples of herbicides include acetochlor, clethodim, dicamba, flumioxazin, fomesafen, glyphosate, glufosinate, mesotrione, quizalofop, saflufenacil, sulcotrione, and 2,4-D.

[0071] In some embodiments, the composition or method disclosed herein may comprise an additional active ingredient selected from the group consisting of clothianidin, ipconazole, imidacloprid, metalaxyl, mefenoxam, tioxazafen, azoxystrobin, thiomethoxam, fluopyram, prothioconazole, pyraclostrobin, and sedaxane.

[0072] In some embodiments, the second biological can be an additional beneficial microorganism, microbial extracts, plant extracts, yeast extracts, vegetal chitosan, natural products, plant growth activators or plant defense agent. Non-limiting examples of the second biological could include bacteria, fungi, beneficial nematodes, and viruses. In certain embodiments, the second biological is a Methylobacterium or Methylorubrum strain, including but not limited to strains listed in Table 1. In some embodiments a plant is treated with a methanotroph bacterium. Strains of methanotrophic bacteria useful in the compositions and methods described herein include bacterial species from a genus selected from the group consisting of Methyloacidimicrobium, Methyloacidiplilum, Methylobacter, Methylocaldum, Methylocapsa, Methylocella, Methylococcus, Methylocystis, Methyloferula, Methylogaea, Methyloglobus, Methylohalobius, Methylomagnum, Methylomarinum, Methylomicrobium, Methylomonas, Methyloparacoccus, Methyloperedens, Methyloprofundus, Methylosarcina, Methylosinus, Methylosoma, Methylosphaera, Methylothermus, and Methylovulum. In some embodiments, a methanotroph is a species of Methylobacter, Methylocystis, Methylomicrobium, Methylomonas, Methylosarcina, or Methylosinus. In some embodiments, a methanotroph is a strain of Methylomicrobium lacus, Methylosarcina fibrata, Methylosinus trichosporium,Agent Ref.: P14472WO00 38 Methylosinus sporium, Methylocystis rosea, Methylocystis parvus or Methylocystis hirsuta. In some embodiments, a Methylomicrobium lacus is deposited strain NRRL B-68261. In some embodiments, a Methylocystis hirsuta is deposited strain NRRL B-68262. In some embodiments, a Methylocystis sp. is a deposited strain selected from NRRL B-68282, NRRL B- 68283, NRRL B-68284, NRRL B-68285, NRRL B-68286, NRRL B-68319, NRRL B-68321, NRRL B-68323 and NRRL B-68347. In some embodiments, a Methylosarcina sp. is deposited strain NRRL B-68281. In some embodiments, a Methylosinus sp. is a deposited strain selected from NRRL B-68320, NRRL B-68322 and NRRL B-68348.

[0073] In certain embodiments, the second biological can be a bacterium of the genus Actinomycetes, Agrobacterium, Arthrobacter, Alcaligenes, Aureobacterium, Azobacter, Azorhizobium, Azospirillum, Azotobacter, Beijerinckia, Bacillus, Brevibacillus, Burkholderia, Chromobacterium, Clostridium, Clavibacter, Comomonas, Corynebacterium, Curtobacterium, Enterobacter, Flavobacterium, Gluconacetobacter, Gluconobacter, Herbaspirillum, Hydrogenophage, Klebsiella, Luteibacter, Lysinibacillus, Mesorhizobium, Microbacterium, Ochrobactrum, Paenibacillus, Pantoea, Pasteuria, Phingobacterium, Photorhabdus, Phyllobacterium, Pseudomonas, Rhizobium, Rhodococcus, Bradyrhizobium, Serratia, Sinorhizobium, Sphingomonas, Streptomyces, Stenotrophomonas, Variovorax, Xanthomonas and Xenorhadbus. In particular embodiments the bacteria is selected from the group consisting of Bacillus amyloliquefaciens, Bacillus cereus, Bacillus firmus, Bacillus, lichenformis, Bacillus pumilus, Bacillus sphaericus, Bacillus subtilis, Bacillus thuringiensis, Chromobacterium suttsuga, Pasteuria penetrans, Pasteuria usage, and Pseudomona fluorescens.

[0074] In certain embodiments the second biological can be a fungus of the genus Acremonium, Alternaria, Ampelomyces, Aspergillus, Aureobasidium, Beauveria, Botryosphaeria, Cladosporium, Cochliobolus, Colletotrichum, Coniothyrium, Embellisia, Epicoccum, Fusarium, Gigaspora, Gliocladium, Glomus, Laccaria, Metarhisium, Muscodor, Nigrospora, Paecilonyces, Paraglomus, Penicillium, Phoma, Pisolithus, Podospora, Rhizopogon, Scleroderma, Trichoderma, Typhula, Ulocladium, and Verticilium. In particular embodiments, the fungus is Beauveria bassiana, Coniothyrium minitans, Gliocladium vixens, Muscodor albus, Paecilomyces lilacinus, or Trichoderma polysporum. In certain embodiments, compositions comprise multiple additional biological ingredients, including consortia comprising combinations of any of the above bacterial or fungal genera or species.

[0075] In further embodiments, the second biological can include, but are not limited to, various Bacillus sp., Pseudomonas sp., Coniothyrium sp., Pantoea sp., Streptomyces sp., and Trichoderma sp. Microbial biopesticides can be a bacterium, fungus, virus, or protozoan.Agent Ref.: P14472WO00 39 Particularly useful biopesticidal microorganisms include various Bacillus subtilis, Bacillus thuringiensis, Bacillus pumilis, Pseudomonas syringae, Trichoderma harzianum, Trichoderma virens, and Streptomyces lydicus strains. Other microorganisms that are added can be genetically engineered or wild-type isolates that are available as pure cultures. In certain embodiments, it is anticipated that the second biological can be provided in the composition in the form of a spore. In further embodiments the second biological can be a biostimulant, including but not limited to seaweed extract or hummates, plant growth activators or plant defense agents including, but not limited to harpin, Reynoutria sachalinensis, jasmonate, lipochito-oligosaccharides, and isoflavones.

[0076] In some embodiments for plant treatment, microbial inoculants as dried powders or particulates into a non-aqueous continuous phase comprising a non-aqueous solvent (e.g., a water-immiscible solvent). In some embodiments, the microbial inoculant is homogeneously dispersed into the non-aqueous continuous phase. Such compositions comprise additional components to enhance mixing of the microbial inoculants with aqueous compositions comprising agricultural chemicals and / or to enhance the stability of microbial inoculants in such aqueous compositions. See, for example US patent publication US20230337681, incorporated herein by reference in its entirety, for non-limiting examples of components useful in such compositions. Various methods can be used to generate dried microbial powders for use in such compositions, including but not limited to spray drying, freeze drying, air drying, fluid bed drying, electrospray drying, or other drying methods. See US patent publication US20220312772, incorporated herein by reference in its entirety, for non-limiting examples of methods to prepare dried microbial compositions.

[0077] In certain embodiments, the composition used to treat a plant, plant part or plant seed will contain a microbial strain that enhances a plant defense response to a pathogen and / or pest, and an agriculturally acceptable excipient or agriculturally adjuvant. Agriculturally acceptable excipients include, but are not limited to, woodflours, clays, activated carbon, diatomaceous earth, fine-grain inorganic solids, calcium carbonate, and the like. Clays and inorganic solids that can be used include, but are not limited to, calcium bentonite, kaolin, china clay, talc, perlite, mica, vermiculite, silicas, quartz powder, montmorillonite, and mixtures thereof. Agriculturally acceptable excipients also include various lubricants such as talc, graphite, polyethylene wax based powders (such as Fluency Agent), protein powders, for example soybean protein powders, or a combination of protein powders and a lipid, for example lecithin or a vegetable oil. In some embodiments compositions comprise additional components to facilitate or enhance long term storage and / or stability as a dried composition. In someAgent Ref.: P14472WO00 40 embodiments, long term stability as a dried powder and / or on treated seeds is enhanced in comparison to other compositions (e.g., compositions lacking components that facilitate long term storage and / or stability, including stability on a treated plant part or seed). Additional components which can facilitate or enhance long term storage and / or stability can include, but are not limited to, one or more oligosaccharides or polysaccharides. In some embodiments polysaccharides are selected from dextrins, maltodextrins, disaccharides, starches, chitosan, alginates, and gums, including but not limited to karaya gum, jaguar gum, xanthan gum, glucomannan, tragacanth gum, Konjac gum, polysaccharide gums, mucilage, gum arabics and other natural gums. In some embodiments combinations of any of the above or other agriculturally acceptable excipients and / or agriculturally acceptable adjuvants are employed. Agriculturally acceptable adjuvants that promote sticking to the seed can be used and include, but are not limited to, polyvinyl acetates, polyvinyl acetate copolymers, hydrolyzed polyvinyl acetates, polyvinylpyrrolidone-vinyl acetate copolymer, polyvinyl alcohols, polyvinyl alcohol copolymers, polyethers, polyvinyl methyl ether, polyvinyl methyl ether-maleic anhydride copolymer, waxes, latex polymers, celluloses including ethylcelluloses and methylcelluloses, hydroxy methylcelluloses, hydroxypropylcellulose, hydroxymethylpropylcelluloses, polyvinyl pyrrolidones, alginates, dextrins, malto-dextrins, polysaccharides, fats, oils, proteins, karaya gum, jaguar gum, tragacanth gum, polysaccharide gums, mucilage, gum arabics, shellacs, vinylidene chloride polymers and copolymers, soybean-based protein polymers and copolymers, lignosulfonates, acrylic copolymers, starches, polyvinylacrylates, zeins, gelatin, carboxymethylcellulose, chitosan, polyethylene oxide, acrylamide polymers and copolymers, polyhydroxyethyl acrylate, methylacrylamide monomers, alginate, ethylcellulose, polychloroprene, and syrups or mixtures thereof. Other useful agriculturally acceptable adjuvants that can promote coating include, but are not limited to, polymers and copolymers of vinyl acetate, polyvinylpyrrolidone-vinyl acetate copolymer, and water-soluble waxes. Further, agriculturally acceptable adjuvants also include various lubricants (which can provide for smooth flow and separation (singulation) of seeds) such as talc, graphite, polyethylene wax based powders (such as Fluency Agent), protein powders, for example soybean protein powders, or a combination of protein powders and a lipid, for example lecithin or a vegetable oil. Various surfactants, dispersants, anticaking-agents, foam-control agents, and dyes disclosed herein and in US Patent No.8,181,388 can be adapted for use with compositions for treatment with a microbial strain that enhances a plant response to a pathogen and / or pest. In some embodiments, dried compositions comprise a Methylobacterium strain and other components selected from theAgent Ref.: P14472WO00 41 group consisting of maltodextrin, trehalose, glucomannan, soybean protein, soybean-based protein polymers and copolymers, talc and graphite.

[0078] Application methods for treating plants with microbes and additional components include spraying, coating, partially coating, immersing, drenching, and / or imbibing the seed, plant, or plant parts with the compositions. In certain embodiments, seed and / or seedlings are exposed to the composition in soil or other plant growth medium in which the plant or a plant arising from the seed are grown. Examples of application methods where the microbial strain is provided in soil include in-furrow applications, soil drenches, and the like. In certain embodiments, an effective amount of a microbial strain or strains that provides for enhanced plant response to a pathogen and / or pest that is provided in a treatment of a seed or plant part is at least about 103, 104, 105, or 106CFU per seed or treated plant part. Additional Embodiments

[0079] Additionally, the following non-limiting embodiments are included in the disclosure.

[0080] Embodiment 1. A method of improving a plant response to a pathogen or pest, wherein said method comprises increasing the level of a plant defense compound produced in a plant by: (i) modifying a plant genome to increase expression of one or more gene transcripts involved in production of one or more plant defense compounds derived from anthranilate in said plant, and / or treating a plant, plant part or seed with a microbial strain that is not pathogenic to said plant, wherein said treatment increases expression in said plant of one or more gene transcripts involved in production of a plant defense compound derived from anthranilate; and (ii) growing said plant in the presence of said pathogen or pest, whereby the level of one or more plant defense compounds in said plant is increased in comparison to a control plant, and the response of said plant to said pathogen or pest is improved as compared to a control plant, wherein the control plant is not modified or treated as in (i).

[0081] 2. The method of embodiment 1 wherein expression of one or more gene transcripts or polypeptides associated with production of anthranilate and / or conversion of anthranilate to a plant defense compound is increased.

[0082] 3. The method of embodiment 2 wherein said gene transcript encodes an anthranilate synthase protein component or said polypeptide is an anthranilate synthase protein component.

[0083] 4. The method of embodiment 3 wherein said anthranilate synthase protein component is an alpha or beta subunit.Agent Ref.: P14472WO00 42

[0084] 5. The method of embodiment 2 wherein said gene transcript encodes anthranilate N- benzoyltransferase or said polypeptide is anthranilate N-benzoyltransferase.

[0085] 6. The method of embodiment 1 wherein said plant defense compound is an anthranilate ester.

[0086] 7. The method of embodiment 6 wherein said anthranilate ester is selected from the group consisting of methyl anthranilate, dimethyl anthranilate, ethyl anthranilate, phenylethyl anthranilate and menthyl anthranilate.

[0087] 8. The method of embodiment 1 wherein said plant defense compound is anthranilate derived phytoalexin.

[0088] 9. The method of any one of embodiments 1 to 8 wherein said microbial strain is a bacterial strain.

[0089] 10. The method of any one of embodiments 1 to 9 wherein said microbial strain comprises one or more genes encoding a protein involved in polyketide biosynthesis.

[0090] 11. The method of embodiment 10 wherein said one or more genes: (i) encodes one or more proteins having a sequence with at least 80%, 85%, 90%, 95%, 97%, 98%, or 99% sequence identity to one or more of SEQ ID NO:21-35; (ii) encodes one or more proteins having at least 80%, 85%, 90%, 95%, 97%, 98%, or 99% sequence identity to SEQ ID NO:21 ; (iii) comprises a sequence of one or more of SEQ ID NO:36-50; and / or (iv) is present on a plasmid comprising SEQ ID NO:86 or a variant thereof having at least 80%, 85%, 90%, 95%, 97%, 98%, or 99% identity to SEQ ID NO:86.

[0091] 12. The method of any one of embodiments 9 - 11 wherein said bacterial strain is a Methylobacterium or Methylorubrum strain.

[0092] 13. The method of any one of embodiments 9 - 12 wherein said bacterial strain is a bacterial strain other than NLS0042 (NRRL B-50932) which comprises heterologous DNA from NLS0042 (NRRL B-50932) which confers on the bacterial strain other than NLS0042 the phenotype of increasing expression in said plant of the one or more gene transcripts involved in production of a plant defense compound, optionally wherein the heterologous DNA encodes one of more proteins with at least 80%, 85%, 90%, 95%, 97%, 98%, or 99% sequence identity to one or more of SEQ ID NO:21-35.

[0093] 14. The method of embodiment 13 wherein the bacterial strain other than NLS0042 is a bacterial strain set forth in Table 1.Agent Ref.: P14472WO00 43

[0094] 15. The method of any one of embodiments 1-14 wherein said plant defense compound reduces foraging of insect larvae on plant roots in comparison to the control plant.

[0095] 16. The method of embodiments 3 or 4 wherein said anthranilate synthase protein component has the amino acid sequence of SEQ ID NO:2 or SEQ ID NO:4.

[0096] 17. The method of embodiment 5 wherein expression of a gene encoding an anthranilate N-benzoyltransferase comprising the polypeptide sequence of SEQ ID NO: 6 or SEQ ID NO:7 is increased in comparison to the control plant.

[0097] 18. The method of any one of embodiments 1-17 wherein said plant defense compound is not an indole derivative.

[0098] 19. The method of any one of embodiments 1-18, wherein the plant is a crop plant set forth in Table 10 and / or wherein the pathogen or pest is set forth in Table 10 and / or 11 or wherein said plant is a corn plant.

[0099] 20. A method to identify a microbial strain that enhances the response of a plant to a pathogen or pest comprising: (i) treating a plant, plant part or plant seed with at least a first microbial strain that is not a pathogen of said plant to obtain a treated seed and / or a treated plant; (ii) growing the treated plant, or growing a plant from a treated plant part or treated seed, in the presence of said pathogen or pest; (iii) harvesting one or more tissue samples from said plant and from an untreated control plant, wherein said tissue samples are harvested at a growing stage during or after which said pest or pathogen is attacking or has attacked said plant and untreated control plant; and (iv) assaying said samples to identify increased production of one or more plant defense compounds derived from anthranilate in said treated plants as compared to an untreated control plant, whereby a microbial strain that enhances the response of a plant to said pathogen or pest is identified.

[0100] 21. A method of selecting a microbial strain that enhances the response of a plant to a pathogen or pest comprising: (i) assaying one or more tissue samples from a plant treated with at least a first microbial strain that is not a pathogen of said plant or from a plant grown from a plant part or seed treated with the first microbial strain for increased levels of one or more plant defense compounds derived from anthranilate as compared to one or more control tissue samples from an untreatedAgent Ref.: P14472WO00 44 control plant, wherein said tissue samples were harvested from the treated and untreated plant during or after said pest or pathogen attacked said plant tissue; and (ii) selecting a microbial strain that is not a pathogen of said plant and that provides the increased levels of the one or more plant defense compounds, thereby selecting a microbial strain that enhances the response of a plant to said pathogen or pest.

[0101] 22. The method of embodiment 20 or 21, further comprising the step of selecting samples for analysis from treated plants that exhibit reduced damage from said pathogen or pest as compared to said untreated control plant.

[0102] 23. The method of embodiment 20 or 21 wherein said samples are assayed to determine the levels of one or more gene transcripts or polypeptides associated with production of anthranilate and / or conversion of anthranilate to a plant defense compound.

[0103] 24. The method of embodiment 20 wherein said samples are assayed to determine the levels of one or more plant defense compounds derived from anthranilate.

[0104] 25. The method of embodiment 20 or 21 wherein said pathogen or pest is a fungus, bacteria, nematode, insect, or virus.

[0105] 26. The method of embodiment 20 wherein said treated plant part is selected from the group consisting of a leaf, stem, shoot, flower, fruit, bud, root, tuber, rhizome, runner, bulb, and corm.

[0106] 27. The method of embodiment 20 wherein said harvested tissue sample is selected from the group consisting of a leaf, stem, shoot, flower, fruit, bud, root, tuber, rhizome, runner, bulb, and corm tissue sample.

[0107] 28. The method of any one of embodiments 20 - 27 wherein the level of one or more gene transcripts encoding an anthranilate synthase protein component in said treated and untreated tissues is determined.

[0108] 29. The method of embodiment 28 wherein said anthranilate synthase protein component is an alpha or beta subunit.

[0109] 30. The method of embodiment 23 wherein the level of a gene transcript encoding anthranilate N-benzoyltransferase in said treated and untreated tissues is determined.

[0110] 31. The method of embodiment 21 or 24 wherein said plant defense compound is an anthranilate ester.Agent Ref.: P14472WO00 45

[0111] 32. The method of embodiment 31 wherein said anthranilate ester is selected from the group consisting of methyl anthranilate, dimethyl anthranilate, ethyl anthranilate, phenylethyl anthranilate and menthyl anthranilate.

[0112] 33. The method of embodiment 21 or 24 wherein said plant defense compound is an anthranilate derived phytoalexin.

[0113] 34. The method of any one of embodiments 20-33 wherein said microbial strain is a bacterial strain or fungal strain.

[0114] 35. The method of embodiment 34, wherein said bacterial strain is a Methylobacterium or Methylorubrum strain.

[0115] 36. The method of any one of embodiments 20-35 wherein said plant is selected from the group consisting of corn, wheat, rye, rice, alfalfa, barley, oats, rye, sorghum, millet, soybean, Brassica sp., Cannabis sp., tobacco, potato, peanut, carrot, cotton, coffee, coconut, sugar beet, oat, barley, tomato, squash, cucumber, cucurbits, lettuce, pepper, pea, onion, green bean, sunflower, safflower, sweet potato, cassava, coffee, coconut, conifers, turfgrass, leafy greens, microgreens, herbs, fruit plants, including fruit trees, and ornamentals.

[0116] 37. The method of embodiment 36 wherein said plant is corn.

[0117] 38. The method of embodiment 36 or 37 wherein said tissue sample is a root sample.

[0118] 39. The method of any one of embodiments 20 to 38 wherein said pest is corn rootworm.

[0119] 40. The method of any one of embodiments 20 to 39, wherein the first microbial strain is obtained by transferring DNA from a second microbial strain which can confer resistance, tolerance, reduced damage, reduced infection, and / or reduced infestation to or by the pest or pathogen by increasing production of one or more plant defense compounds derived from anthranilate in a treated plant to a third microbial strain which does not confer resistance, tolerance, reduced damage, reduced infection, and / or reduced infestation to or by the pest or pathogen in a plant treated with the third microbial strain; optionally wherein the a second microbial strain is NLS0042 and / or optionally wherein the third microbial strain is a microbial strain other than NLS0042 provided in Table 1; optionally wherein the transferred DNA: (i) encodes one or more proteins having a sequence with at least 80%, 85%, 90%, 95%, 97%, 98%, or 99% sequence identity to one or more of SEQ ID NO:21-35; or (ii) is present on a plasmid comprising SEQ ID NO: 86 or a variant thereof having at least 80%, 85%, 90%, 95%, 97%, 98%, or 99% sequence identity to SEQ ID NO: 86; and / or (iii) comprises the sequence of one orAgent Ref.: P14472WO00 46 more of SEQ ID NO:37-50 or a variant thereof with at least 80%, 85%, 90%, 95%, 97%, 98%, or 99% identity to one or more of SEQ ID NO:37-50.

[0120] 41. A method for monitoring pest or pathogen resistance, tolerance, reduced damage, reduced infection, and / or reduced infestation in a plant comprising assaying one or more tissue samples from a plant treated with at least a first microbial strain that can confer said pest or pathogen resistance, tolerance, reduced damage, reduced infection, and / or reduced infestation and that is not a pathogen of said plant or from a plant grown from a plant part or seed treated with the first microbial strain for: (i) increased levels of one or more plant defense compounds derived from anthranilate; and / or (ii) increased expression of one or more gene transcripts or polypeptides associated with production of anthranilate and / or conversion of anthranilate to a plant defense compound; wherein the increased levels and / or increased expression are as compared to one or more control tissue samples from an untreated control plant, wherein said tissue samples were harvested from the treated and untreated control plant during or after said pest or pathogen attacked said plant tissue, and whereby increased levels of the one or more plant defense compounds, gene transcripts, and / or polypeptides in the tissue samples from the treated plant in comparison to the control plant is indicative of increased pest or pathogen resistance, tolerance, damage reduction, infection reduction, and / or infestation reduction in said treated plant.

[0121] 42. The method of embodiment 41, wherein said treated plant does not exhibit increased levels of the one or more plant defense compounds, gene transcripts, and / or polypeptides and wherein the method further comprises retreating with the first microbial strain and / or treating with another biocontrol agent, an insecticide, fungicide, or pesticide.

[0122] 43. A method of selecting a microbial strain that enhances the response of a plant to a pathogen or pest comprising: (i) assaying one or more tissue samples from a plant treated with at least a first microbial strain that is not a pathogen of said plant or from a plant grown from a plant part or seed treated with the first microbial strain for increased levels of one or more plant defense compounds derived from anthranilate as compared to one or more control tissue samples from an untreated control plant, wherein said tissue samples were harvested from the treated and untreated plant during or after said pest or pathogen attacked said plant tissue; and (ii) selecting a microbial strain that is not a pathogen of said plant and that provides the increased levels of the one or more plant defense compounds, thereby selecting a microbial strain that enhances the response of a plant to said pathogen or pest.Agent Ref.: P14472WO00 47

[0123] 44. A method of selecting a microbial strain that enhances the response of a plant to a pathogen or pest comprising: (i) assaying one or more plant tissue samples treated with at least a first microbial strain that is not a pathogen of said plant for increased levels of one or more plant defense compounds derived from anthranilate as compared to one or more untreated control plant tissue samples, wherein said tissue samples were exposed to said pest or pathogen during or after treatment with said first microbial strain; and (ii) selecting a microbial strain that provides the increased levels of the one or more plant defense compounds, thereby selecting a microbial strain that enhances the response of a plant to said pathogen or pest.

[0124] 45. A method of improving a plant response to a pathogen or pest, wherein said method comprises, increasing the level of a plant defense compound produced in a plant by: (i) modifying a plant genome to increase expression of one or more gene transcripts involved in production of one or more plant defense compounds in said plant, and / or treating a plant, plant part or seed with a microbial strain that is not pathogenic to said plant, wherein said treatment increases expression in said plant of one or more gene transcripts involved in production of a plant defense compound; and (ii) growing said plant in the presence of said pathogen or pest, whereby the level of one or more plant defense compounds in said plant is increased in comparison to a control plant, and the response of said plant to said pathogen or pest is improved as compared to a control plant, wherein the control plant is not modified or treated as in (i).

[0125] 46. The method of embodiment 45 wherein the plant defense compound is derived from anthranilate.

[0126] 47. A method of repelling a pathogen or pest, wherein said method comprises, increasing a level of a plant defense compound produced in a plant comprising (i) treating soil, a plant, plant part or seed with a microbial strain that is not pathogenic to a plant, wherein said treatment increases expression in said plant of one or more gene transcripts involved in production of a plant defense compound; and (ii) growing said plant in the presence of said pathogen or pest, whereby the level of one or more plant defense compounds in said plant is increased in comparison to a control plant, and the plant repels said pathogen or pest more than a control plant, wherein the control plant is not modified or treated as in (i).

[0127] 48. The method of embodiment 47, wherein the plant defense compound is derived from anthranilate.Agent Ref.: P14472WO00 48

[0128] 49. The method of embodiment 47, wherein the microbial strain produces a metabolite, wherein such metabolite increases the production of such plant defense compound as compared to the control plant.

[0129] 50. The method of embodiment 49, wherein the metabolite is selected from the group consisting of a siderophore, non-ribosomal peptide, a polyketide, or a combination thereof.

[0130] 51. The method of embodiment 50, wherein said microbial strain comprises one or more gene clusters encoding proteins involved in biosynthesis of said metabolite.

[0131] 52. The method of any one of embodiments 47 to 51, wherein said microbial strain comprises one or more genes encoding: (i) one or more proteins having a sequence with at least 80%, 85%, 90%, 95%, 97%, 98%, or 99% sequence identity to one or more of SEQ ID NO:21- 35; (ii) one or more proteins having at least 80%, 85%, 90%, 95%, 97%, 98%, or 99% sequence identity to SEQ ID NO:21; (iii) comprises a sequence of one or more of SEQ ID NO:36-50; and / or (iv) is present on a plasmid comprising SEQ ID NO:86 or a variant thereof having at least 80%, 85%, 90%, 95%, 97%, 98%, or 99% identity to SEQ ID NO:86; optionally wherein the plant is a crop plant set forth in Table 10 and / or wherein the pathogen or pest is set forth in Table 10 and / or 11.

[0132] 53. A method of selecting a microbial strain that confers pest or pathogen resistance, tolerance, reduced damage, reduced infection, and / or reduced infestation to a plant comprising identifying in said microbial strain: (i) one or more polynucleotides encoding a protein in a polyketide biosynthetic pathway; and / or (ii) one or more proteins in a polyketide biosynthetic pathway.

[0133] 54. The method of embodiment 53, wherein said polynucleotides are identified by detecting at least one polynucleotide: (i) encoding one or more proteins having a sequence with at least 80%, 85%, 90%, 95%, 97%, 98%, or 99% sequence identity to one or more of SEQ ID NO:21-35; (ii) encoding one or more proteins having at least 80% sequence identity to SEQ ID NO:21; (iii) comprising the sequence of one or more of SEQ ID NO: 36-50 or a sequence or sequences having at least 80%, 85%, 90%, 95%, 97%, 98%, or 99% sequence identity to any one of SEQ ID NO: 36-50; and / or (iv) present on a plasmid comprising SEQ ID NO:86 or a sequence having at least 80%, 85%, 90%, 95%, 97%, 98%, or 99% sequence identity to SEQ ID NO: 86.

[0134] 55. The method of embodiment 53 or 54, wherein said polynucleotide is identified with a nucleic acid amplification, hybridization, and / or sequencing technique.Agent Ref.: P14472WO00 49

[0135] 56. The method of embodiment 53 or 54, wherein said proteins are identified by detecting: (i) one or more proteins having a sequence with at least 80%, 85%, 90%, 95%, 97%, 98%, or 99% sequence identity to one or more of SEQ ID NO:21-35; or (ii) one or more proteins having at least 80%, 85%, 90%, 95%, 97%, 98%, or 99% sequence identity to SEQ ID NO:21.

[0136] 57. The method of embodiment 56, wherein said protein is identified by an immunoaffinity and / or mass-spectroscopy technique.

[0137] 58. The method of any one of embodiments 53-57, further comprising the step(s) of isolating and / or culturing the identified microbial stain comprising the polynucleotide and / or protein.

[0138] 59. The method of any one of embodiments 53-58, wherein said microbial strain comprises a gene: (i) encoding one or more proteins having a sequence with at least 80%, 85%, 90%, 95%, 97%, 98%, or 99% sequence identity to one or more of SEQ ID NO:21-35; (ii) encoding one or more proteins having at least 80% sequence identity to SEQ ID NO:21; or (iii) comprising a sequence of one or more of SEQ ID NO:36-50 or a variant thereof having at least 80%, 85%, 90%, 95%, 97%, 98%, or 99% sequence identity to SEQ ID NO:36-50.

[0139] 60. The method of any one of embodiments 53-58, wherein said microbial strain is genetically modified with DNA: (i) encoding one or more proteins having a sequence with at least 80%, 85%, 90%, 95%, 97%, 98%, or 99% sequence identity to one or more of SEQ ID NO:21-35; (ii) encoding one or more proteins having at least 80%, 85%, 90%, 95%, 97%, 98%, or 99% sequence identity to SEQ ID NO:21; (iii) comprising the sequence of one or more of SEQ ID NO: 36-50 or a sequence or sequences having at least 80%, 85%, 90%, 95%, 97%, 98%, or 99% sequence identity to any one of SEQ ID NO: 36-50; and / or (iv) present on a plasmid comprising SEQ ID NO:86 or a sequence having at least 80%, 85%, 90%, 95%, 97%, 98%, or 99% sequence identity to SEQ ID NO: 86.

[0140] 61. A method of improving a plant response to a pathogen or pest, wherein said method comprises: (i) treating a plant, plant part or seed with NLS0042 or a microbial stain comprising DNA: (i) encoding one or more proteins having a sequence with at least 80%, 85%, 90%, 95%, 97%, 98%, or 99% sequence identity to one or more of SEQ ID NO:21-35; (ii) encoding one or more proteins having at least 80%, 85%, 90%, 95%, 97%, 98%, or 99% sequence identity to SEQ ID NO:21; (iii) comprising the sequence of one or more of SEQ ID NO:37-50 or a variant thereof with at least 80%, 85%, 90%, 95%, 97%, 98%, or 99% identity to one or more of SEQ ID NO:37-50; and / or (iv) is present on a plasmid comprising SEQ ID NO:86, 85%, 90%, 95%,Agent Ref.: P14472WO00 50 97%, 98%, or 99% or a variant thereof having at least 80%, 85%, 90%, 95%, 97%, 98%, or 99% identity to SEQ ID NO:86; and (ii) growing said plant or a plant grown from the seed in the presence of said pathogen or pest, whereby the response of said plant to said pathogen or pest is improved as compared to a control plant; and wherein said plant is not a corn plant.

[0141] 62. The method of embodiment 61, wherein said plant is selected from the group consisting of a pepper plant, tomato, snap bean, a Brassica plant, soybean, cotton, and rice.

[0142] 63. The method of embodiment 61 or 62, wherein the level of one or more plant defense compounds in said plant is increased in comparison to a control plant.

[0143] 64. The method of any one of embodiments 61-63, wherein said pathogen or pest is an insect pest selected from the group consisting of aphids, lepidopterans, stinkbugs, white fly, beet leafhopper, tobacco hornworm, potato leaf hopper, Mexican bean beetle, flea beetles, fall armyworm, soybean looper, western flower thrips, and water weevil.

[0144] 65. The method of any one of embodiments 61 to 64, wherein the improved response of the treated plant or plant grown from the treated part or seed comprises improved pest or pathogen resistance, tolerance, reduced damage, reduced infection, and / or reduced infestation to the treated plant or plant grown from the treated part or seed in comparison to an untreated control plant.

[0145] 66. The method of any one of embodiments 61 to 65, wherein the plant is a crop plant set forth in Table 10 and / or wherein the pathogen or pest is set forth in Table 10 and / or 11. EXAMPLES Example 1 Analysis of Upregulated Corn Genes in Field Trials

[0146] Field trials were established such that fields either contained a trap crop to attract corn rootworm (CRW) or were planted several years corn on corn to increase CRW pressure. Plants were treated with Methylobacterium strain NLS0042 or were untreated (UNT) in a full factorial design. The corn varieties in the trials were P1197AM and P1197AMXT and are described in Pioneer 2022 Corn Hybrid-Herbicide Management Guide as follows: ^ AM - Optimum® AcreMax® insect protection system with YGCB, HX1, LL, RR2. Contains a single-bag integrated refuge solution for aboveground insects. In EPA- designated cotton-growing counties, a 20% separate corn borer refuge must be planted with Optimum AcreMax products. ^ AMXT (Optimum® AcreMax® XTreme) - Contains a single-bag integrated refuge solution for above- and below-ground insects. The major component contains theAgent Ref.: P14472WO00 51 Agrisure® RW trait, the Bt trait and the Herculex® XTRA gene. In EPA designated cotton-growing counties, a 20% separate corn borer refuge must be planted with Optimum AcreMax XTreme products. ^ Methylobacterium in the form of a spray dried powder was applied to seeds in furrow at planting at a rate of at least 1 x 106CFU per seed.

[0147] Roots were collected when CRW larval feeding was at its peak. Root samples from each of the 4 treatments (NLS0042 on P1197AM corn, UNT on P1197AM corn, NLS0042 on P1197AMXT corn, and UNT on P1197AMXT corn) were dug from the ground, as much dirt as possible was removed, and the roots were immediately frozen on dry ice. The samples were returned to the lab and the roots ground under liquid nitrogen. RNA was extracted from the roots using Qiagen RNeasy mini kit. The RNA was DNase treated using DNase Max, and quality checked by Bioanalyzer. Quantseq (3’RNAseq) was performed by Lexogen (Greenland, NH). Samples with the desired CRW phenotype as in Table 2 (NLS0042-treated plants with lower Node Injury Scores (NIS) than UTC in the same genetic background and UTC plants with higher root damage scores than NLS0042-treated plants in the same genetic background) were analyzed for differentially expressed (DE) genes using the Bluebee platform and the B73 maize genome as the reference. NIS, also called the Iowa State Root Damage Scores, range from 0-3 with 0 being no damage and 3 being 3 nodes eaten within 2 inches of the stalk (Oleson et al., 2005). There were 3 samples of each condition for each of the four treatments. Table 2. Node Injury Scores (NIS) for field samples analyzed by RNAseq Difference Avefrom UTC Average Difference Tr tm nt C rn G n ti ragel Yi ld fr m UTC lobtained from MaizeGDB. Differentially expressed genes with significant p-values after multiple comparison correction were manually searched for additional annotation information. Table 3. Differentially expressed genes up regulated in NLS0042-treated corn roots. log2 Fold-value v3 Gene Model IDv4 Gene Modelv5 Gene Model IDGeneFull NameAgent Ref.: P14472WO00 52 log2 Foldp-value v3 Gene Model IDv4 Gene Modelv5 Gene Model IDGene Full NamhangeID SyeCmboltormebe associated with anthranilate in maize. Anthranilate N-benzoyltransferase protein 2 and anthranilate synthase homolog1(AS beta subunit) transcripts were each significantly increased in Methylobacterium treated AMXT corn plants as compared to untreated corn plants. Smaller gene expression increases were also observed for transcripts encoding other anthranilate synthase protein components. Example 2 Greenhouse Assay Results

[0150] Corn plants were treated as shown in Table 4 with NLS0042, formulated as a lyophilized powder, applied as a seed treatment prior to sowing and compared to non-treated seeds (UTC). An additional set of non-PPFM treated seeds received jasmonic acid applied as a foliar spray (1 mM concentration, spray to run off) to seedlings prior to infestation with Western corn rootworm, Diabrotica virgifera, larvae which served as a positive control for ISR. Two types of destructive harvesting occurred in a parallel set of pots at 3, 6 and 9 days after larval infestation where 1) roots and soil were moved to a Berlese funnel for extraction of live larvae, which were then enumerated, weighed and measured for length individually and 2) roots were removed and processed for RNA extraction and analysis of gene expression. A parallel set of seedlings were potted into 2-gallon pots, grown to near maturity and evaluated for root damage at VT growth stage using the Iowa State nodal injury scale (NIS). Table 4 Label Seed treatment Foliar drench CRW inoculationAgent Ref.: P14472WO00 53 Table 5. Root damage ratings on the Iowa State nodal injury scale (NIS) of 0 - 3 at VT stage for corn rootworm inoculated “CRW-inoculated” and non-inoculated “UTC” corn plants. UTC CRW inoculated Label Seed treatment Foliar drench Average NIS score Average NIS scoreseed treatment with Methylobacterium NLS0042 or seedling drench with jasmonic acid. Both NLS0042 as a seed treatment and jasmonic acid as a foliar drench showed a trend towards decreased root damage compared to untreated controls as measured via the Iowa State nodal injury score (NIS) with 0 being no larval root feeding pressure and 3 being extremely high root feeding pressure (Table 5). Gene expression results comparing NLS0042 treated samples NLS0042_UTC) and jasmonic acid treated samples (UTC_JA) with untreated controls showed a strong signal at 9 DAI for jasmonic acid – regulated genes; Ribosome Inactivating Protein 2 (rip2), Terpene Synthase (tps23) and Maize Protease Inhibitor (mpi) in both the NLS0042 seed treated and jasmonic acid drenched plants compared to the untreated control plants. Example 3 Method of Selecting a Microbe that Enhances a Corn Plant Response to CRW

[0152] An assay to identify and / or select a plant beneficial microbe that enhances the response of a corn plant to corn rootworm larvae is conducted as follows. Corn seeds are treated with a microbe that is not a corn pathogen, for example a strain of Methylobacterium or Methylorubrum, sown in growing media and grown to seedling stages V2-V4. Plants are removed from the growing media and gently washed to clean growing media from the roots. Root systems are placed into a petri dish lined with moistened cellulose filter paper and infested with early instar corn rootworm larvae. The larvae are allowed to feed on the corn roots and then removed. Roots and / or root exudates and headspace are evaluated in genetic and / or metabolomic assays to determine levels of anthranilate-derived plant defense compounds and / or gene transcripts associated with production of anthranilate-derived plant defense compounds. A microbe that increases production of anthranilate-derived plant defense compounds and / or increases levels of gene transcripts associated with production of anthranilate-derived plant defense compounds as compared to levels in an untreated control plant is selected as a microbe that enhances a corn plant response to corn rootworm.Agent Ref.: P14472WO00 54

[0153] A further step for selection of samples for analysis includes evaluation of larval insect feeding behavior prior to analysis of root samples. After feeding, larvae are removed gently from the roots using a paintbrush and positioned away from the roots. Larval behavior is tracked and the time to arrival at the root surface is recorded. Larval behavior with control roots from untreated plants is compared to their behavior with roots from treated plants The presence of a chemical feeding deterrent, such a methyl anthranilate, in the root exudates will cause larvae to not return to the corn roots, or to take a significantly longer time to return to the roots of treated plants compared to the roots of untreated control plants.

[0154] Choice assays for analysis of larval insect feeding behavior are conducted with treated and control roots as described above with NLS0042 using the following treatments: 1) 10-day old untreated plants with no WCR feeding 2) 10-day old NLS0042-treated plants with no WCR feeding 3) 10-day old untreated plants with 3 days of WCR larval feeding pressure 4) 10-day old NLS0042-treated plants with 3 days of WCR larval feeding pressure.

[0155] When the choice was between an NLS0042-treated root and an untreated root, the larvae overwhelming chose the untreated root (Figure 1). This basic condition was tested in four of the six possible combinations of treatments, and it only mattered slightly if the root had received the WCR larvae feeding pressure before the choice test.

[0156] When the choice was between two NLS0042-treated roots, most larvae do not make a choice, and instead stay in the middle petri dish where they began (Figure 2). This means that these larvae are unable to feed.

[0157] When the choice is between two untreated roots, larvae choose either untreated root with a slight preference for untreated roots that did receive the WCR larvae feeding pressure before the choice test (Figure 3).

[0158] These results indicate that the NLS0042-treated plants are emitting a volatile chemical(s) that is deterring feeding by WCR larvae. These results are consistent with the response of WCR larvae to methyl anthranilate. Example 4. Analysis of Metabolite Production by Methylobacterium The contribution of metabolites produced by Methylobacterium NLS0042 to reducing damage of corn roots by corn rootworm is examined. Two biosynthetic gene clusters involved in metabolite production were identified in the genome of NLS0042. Two genes, one from each of the clusters, were selected for the creation of knock-out mutants: asbA, predicted to be involved in the production of a siderophore, and bfmBAB, predicted to be involved in the biosynthesis of an antimicrobial compound. Allelic exchange vectors for each of the gene targets wereAgent Ref.: P14472WO00 55 assembled and moved into NLS0042 via conjugation and integration at the target site. Counterselection and screening was performed to identify the knock-out mutants. PCR evidence supporting the creation of knock-out mutants for both gene targets was obtained. Sequencing of the region expected to contain the deletion confirm production of the desired knockout mutants. The asbA and bfmBAB mutant strains are tested in a feeding choice assay as described above to determine if the mutations block the ability of Methylobacterium to repel CRW larval feeding. Example 5. Choice Assays and Identification of Volatiles produced by treated corn plants.

[0159] Additional choice assays are conducted as described above using treated and non- treated corn roots. Treatments will include 1) untreated seed, 2) seed treated with NLS0042, 3) seed treated with NLS0042mut1, and 4) seed treated with NLS0042mut2. Ten neonate larvae will be placed in the middle and the location of the larvae will be recorded after 5 hours in the dark. The following sets of treatments will be evaluated with a minimum of 10 replications:

[0160] Treatment 1 versus Treatment 2

[0161] Treatment 1 versus Treatment 3

[0162] Treatment 1 versus Treatment 4

[0163] Treatment 2 versus Treatment 3

[0164] Treatment 2 versus Treatment 4

[0165] Treatment 3 versus Treatment 4

[0166] Choice of larvae between the treatments will be analyzed and volatile compounds responsible for the choice will be identified as follows.

[0167] Untreated non-Bt corn seeds will be rinsed and incubated at 25 °C overnight in distilled water to speed germination. The seeds will be dried, weighed and treated under a biosafety cabinet following the protocol at the rate of 1E6 cfu / seed. Corn seeds will be planted and allowed to germinate and grow for at least ten days without larval feeding to allow the priming activity characteristic of ISR and defense volatile chemical(s) production to occur. After 10 days of growth, a vacuum will be applied to pull the volatiles onto the solid substrate. The substrate will be used to identify known plant volatiles using GC-MS, including methyl anthranilate as a control compound.

[0168] The two treatments in this experiment will be untreated control and original NLS0042 powder, and the comparison will be between the volatiles produced in untreated plants vs. those produced by NLS0042-treated plants after 10 days of growth.Agent Ref.: P14472WO00 56 Example 6. Corn Genes and Sequences and Homologs Table 6 Maize anthranilate synthase genes Gene Name Gene B73 V5 B73 V4 gene B73 V3 O. sativa Arabidopsis symbol Gene Model model gene model Indica Group thaliana homologs Homolog G 07 B 1 G 07 B G 07 B“maizegdb.org / .”Agent Ref.: P14472WO00 57 Example 7. Evaluation of larval insect feeding behavior prior to analysis of root samples.

[0169] Larval feeding choice assays were conducted essentially as described in Example 5. Larval behavior with control roots from untreated plants is compared to their behavior with roots from treated plants, and results are provided in Table 7. The presence of methyl anthranilate, in the root exudates will cause larvae to not return to the corn roots, or to take a significantly longer time to return to the roots of treated plants compared to the roots of untreated control plants. Table 7. Feeding choice assay results using either untreated corn roots or methyl anthranilate at different concentrations Larvae choice Standard Connecting Letters (%) Error at p<0.05s.

[0170] Additional choice assays were conducted as described above using treated and non- treated corn roots. Treatments include 1) untreated seed, 2) seed treated with NLS0042, and 3) seed treated with NLS0042mut2 (bfmBAB mutant). The NLS0042mut2 strain was obtained as described in Example 4. Ten neonate larvae were placed in the middle and the location of the larvae was recorded after incubation in the dark. Results are shown in Table 8 below. The bfmBAB mutant significantly decreased the repellent effect of NLS0042, demonstrating that this gene contributes to induction of the repellent effect of NLS0042in the corn plant. Other genes identified in the polyketide synthase pathway are evaluated in a similar manner to identify similar effects on the induced insect defense response in corn plants.Agent Ref.: P14472WO00 58 Table 8 Feeding choice assay results using combinations of treatments with untreated roots or roots treated with NLS0042 wild type or NLS0042 mut2. Larvae Standard Connecting LettersA method to identify microbes for the presence of sequences is as follows. Whole or partial genome sequences of a microbe or metagenomic sequences from an environmental sample are obtained. For an isolated microbe or combination of cultured microbes, a sequence of interest is identified using BLAST (Basic Local Alignment Search Tool; Altschul et al.1990) or other nucleic acid analysis software. Sequences can be either nucleotide or protein sequences. Sequences can also be searched using annotations for genes, gene clusters, and / or protein domains. Alternatively, standard PCR or qPCR primers that are unique to the sequence of interest can be used to identify microbes of interest. Environmental samples containing multiple characterized or uncharacterized microbes are also screened in this manner and microbes that have positive signals are purified from an aliquot of the original sample. Colony PCR and or aliquot dilution methods are employed to identify a positive microbe. Sequences used in the analysis are provided in Table 9. Table 9. Genes in NLS0042 in polyketide synthetic cluster. Nucleotide Gene Name Description PROTEINAgent Ref.: P14472WO00 59 Nucleotide Gene Name Description PROTEIN SEQ ID SEQ IDvariants thereof; or (ii) sequences encoding one or more proteins having a sequence of SEQ ID NO:21-35 or a homolog or ortholog thereof are identified. Microbes identified in this manner are screened to identify microbes that enhance a plant defense response to a pathogen and / or insect pests. Example 10. Field Trial Analysis of Effects of Methylobacterium strain NLS0042 on Infestation of Specialty Crops.

[0172] Field trials are conducted on peppers to determine the ability of NLS0042 to enhance plant defense against aphids and caterpillars.

[0173] Field trials are conducted on tomato to determine the ability of NLS0042 to enhance plant defense against aphids and stinkbugs.

[0174] Field trials are conducted on snapbean to determine the ability of NLS0042 to enhance plant defense against potato leaf hopper, Mexican bean beetle, and lepidopterans.Agent Ref.: P14472WO00 60

[0175] Field trials are conducted on Brassica species to determine the ability of NLS0042 to enhance plant defense against fleabeetles.

[0176] Plants, plant parts and / or seeds are treated with NLS0042 as a foliar spray, a seed treatment, a drench (e.g., soil drench), an in-furrow treatment, or combinations thereof. Treated plants are grown in the presence of natural and / or artificially supplemented infestations of the target insect pests. Plants are evaluated for yield and insect damage and compared to control plants to identify enhanced plant response to the insect pests resulting from treatment with NLS0042. Example 11. Greenhouse Tomato Trials for NLS0042 Effect on White Fly.

[0177] Tomato plants, parts and / or seeds are treated with NLS0042 as a foliar spray, a seed treatment, a drench, or combinations thereof. Treated plants and untreated control plants are inoculated with white fly. White fly counts are made weekly following inoculation and compared to counts in control plants not treated with NLS0042 to identify enhanced plant response to white fly. Example 12. Tomato Trials for NLS0042 Effect on Leafhoppers.

[0178] Treated and untreated tomato plants are exposed to viruliferous leafhoppers carrying beet curly top virus (BCTV) in a greenhouse. NLS0042 is applied as a foliar spray, a seed treatment, a drench, or combinations thereof. Treated plants are assessed with digital PCR to determine viral loads. Treated and untreated control are transplanted into a field trial to determine effects on plant vigor (hyperspectral imaging), yield, and fruit quality. Insect presence is also determined using sweep netting and / or sticky cards. Example 13. Greenhouse Experiments to Evaluate NLS0042 Effects on Caterpillar Pests of Solanaceous, Soybean, Cotton and Rice Crops.

[0179] Tomato, eggplant, pepper, soybean, cotton and rice plants are treated with NLS0042 as a foliar spray, a seed treatment, a drench, or combinations thereof. Pre-weighed caterpillars of tobacco hornworm are allowed to feed on treated and untreated control tomato plants at various phenological stages for a fixed period of time. Pre-weighed caterpillars of soybean looper and fall armyworm are allowed to feed separately on treated and untreated control soybean plants at various phenological stages for a fixed period of time. Pre-weighed caterpillars of fall armyworm are allowed to feed on treated and untreated control soybean, cotton and rice plants at various phenological stages for a fixed period of time. During the treatment period for all experiments, data on caterpillar growth, mortality, volume, and developmental milestones are collected and analyzed to identify enhanced plant response to the insect pests resulting from treatment with NLS0042.Agent Ref.: P14472WO00 61

[0180] In a second experiment, an artificial diet fortified with 10% leaf material from treated and untreated control plants is prepared. Hornworm, fall armyworm and soybean looper caterpillars are allowed to feed and develop and complete their life cycle on these diets. Data on life history traits is collected to further evaluate the effect of NLS0042 treatment of plants on insect pests.

[0181] A choice assay is conducted between treated and control plants to evaluate the effect of treatment with NLS0042 on herbivore choice, and to evaluate potentail antibiosis effects. Example 14. Greenhouse Experiments to Evaluate NLS0042 Effects on Thrips and Aphid Pests of Cotton.

[0182] A population assay is conducted using a known numbers of western flower thrips or aphids. The thrips or aphids are allowed to feed and develop on NLS0042 treated and untreated control plants. plants and are monitored for population growth over an extended period of time. Electrophysiology experiments are also run using a technique called electrical penetration graph that provides information on how the NLS0042 treated and untreated control plants vary in their antibiosis and antixenotic properties.

[0183] A choice assay is also conducted between treated and control plants to evaluate the effect of treatment with NLS0042 on herbivore choice, and to evaluate potential antibiosis effects. Example 15. Evaluation of Effects of Microbes Comprising Genes Providing for Induction of a Plant Defense Response to Insect and / or Pathogen Pests

[0184] Microbial strains comprising one or more genes for expression of one or more polyketide synthesis proteins having a sequence of any one of SEQ ID NOS: 21-35, or homologs or orthologs thereof, are identified by genome screening and / or selection as described herein. Alternatively, such strains are generated by transfer of genes encoding polyketide synthesis proteins identified herein by plasmid transfer and / or genetic transformation with recombinant constructs. The microbial strains are used to treat target plants in greenhouse, growth chamber and / or field assays, and the plants are evaluated for enhanced plant defense response to a target pest. Treatments include foliar applications, imbibition or drench, and seed treatments. Table 10 below shows plants and pests that are evaluated. Table 10 Evaluation of Plant Defense Response to Insect Pests Insect or DiseaseAgent Ref.: P14472WO00 62 Insect or Disease Crops Nematode Pest scientific vector P t nm P t t rAgent Ref.: P14472WO00 63 Insect or Disease Crops Nematode Pest scientific vector P t nm P t t r , pAgent Ref.: P14472WO00 64 Insect or Disease Crops Nematode Pest scientific vector P t nm P t t rAgent Ref.: P14472WO00 65 Insect or Disease Crops Nematode Pest scientific vector P t nm P t t rs including but not limited to Corn, Soybean, Peanut, and Cotton Pest SPP Common name Vaquita | Vaquinha patriota ou verde eAgent Ref.: P14472WO00 66 Pest SPP Common name Elasmopalpus lignosellus Barrenador menor del maíz

Claims

Agent Ref.: P14472WO00 67 What is claimed is: Claim 1. A method of improving a plant response to a pathogen or pest, wherein said method comprises increasing the level of a plant defense compound produced in a plant by: (i) treating a plant, plant part or seed with a microbial strain that is not pathogenic to said plant, wherein said treatment increases expression in said plant of one or more gene transcripts involved in production of a plant defense compound derived from anthranilate and / or modifying a plant genome to increase expression of one or more gene transcripts involved in production of one or more plant defense compounds derived from anthranilate in said plant; and (ii) growing said plant in the presence of said pathogen or pest, whereby the level of one or more plant defense compounds in said plant is increased in comparison to a control plant, and the response of said plant to said pathogen or pest is improved as compared to a control plant, wherein the control plant is not modified or treated as in (i).

2. The method of claim 1 wherein expression of one or more gene transcripts or polypeptides associated with production of anthranilate and / or conversion of anthranilate to a plant defense compound is increased.

3. The method of claim 2 wherein said gene transcript encodes an anthranilate synthase protein component or said polypeptide is an anthranilate synthase protein component.

4. The method of claim 3 wherein said anthranilate synthase protein component is an alpha or beta subunit.

5. The method of claim 2 wherein said gene transcript encodes anthranilate N- benzoyltransferase or said polypeptide is anthranilate N-benzoyltransferase.

6. The method of claim 1 wherein said plant defense compound is an anthranilate ester.

7. The method of claim 6 wherein said anthranilate ester is selected from the group consisting of methyl anthranilate, dimethyl anthranilate, ethyl anthranilate, phenylethyl anthranilate and menthyl anthranilate.

8. The method of claim 1 wherein said plant defense compound is anthranilate derived phytoalexin.

9. The method of claim 1 wherein said microbial strain is a bacterial strain.

10. The method of claim 1 wherein said microbial strain comprises one or more genes encoding a protein involved in polyketide biosynthesis.Agent Ref.: P14472WO00 68 11. The method of claim 10 wherein said one or more genes: (i) encodes one or more proteins having a sequence with at least 80% sequence identity to one or more of SEQ ID NO:21-35; (ii) encodes one or more proteins having at least 80% sequence identity to SEQ ID NO:21 ; (iii) comprises a sequence of one or more of SEQ ID NO:36-50; and / or (iv) is present on a plasmid comprising SEQ ID NO:86 or a variant thereof having at least 80% identity to SEQ ID NO:

86.

12. The method of claim 11 wherein said bacterial strain is a Methylobacterium or Methylorubrum strain.

13. The method of claim 11 wherein said bacterial strain is a bacterial strain other than NLS0042 (NRRL B-50932) which comprises heterologous DNA from NLS0042 (NRRL B-50932) which confers on the bacterial strain other than NLS0042 the phenotype of increasing expression in said plant of the one or more gene transcripts involved in production of a plant defense compound, optionally wherein the heterologous DNA encodes one of more proteins with at least 80% sequence identity to one or more of SEQ ID NO:21-35.

14. The method of claim 13 wherein the bacterial strain other than NLS0042 is a bacterial strain set forth in Table 1.

15. The method of claim 1 wherein said plant defense compound reduces foraging of insect larvae on plant roots in comparison to the control plant.

16. The method of claim 3 wherein said anthranilate synthase protein component has the amino acid sequence of SEQ ID NO:2 or SEQ ID NO:

4.

17. The method of claim 5 wherein expression of a gene encoding an anthranilate N- benzoyltransferase comprising the polypeptide sequence of SEQ ID NO: 6 or SEQ ID NO:7 is increased in comparison to the control plant.

18. The method of claim 1 wherein said plant defense compound is not an indole derivative.

19. The method of any one of claims 1-18 wherein said plant is a corn plant.

20. A method to identify a microbial strain that enhances the response of a plant to a pathogen or pest comprising: (i) treating a plant, plant part or plant seed with at least a first microbial strain that is not a pathogen of said plant to obtain a treated seed and / or a treated plant; (ii) growing the treated plant, or growing a plant from a treated plant part or treated seed, in the presence of said pathogen or pest;Agent Ref.: P14472WO00 69 (iii) harvesting one or more tissue samples from said plant and from an untreated control plant, wherein said tissue samples are harvested at a growing stage during or after which said pest or pathogen is attacking or has attacked said plant and untreated control plant; and (iv) assaying said samples to identify increased production of one or more plant defense compounds derived from anthranilate in said treated plants as compared to an untreated control plant, whereby a microbial strain that enhances the response of a plant to said pathogen or pest is identified.

21. A method of selecting a microbial strain that enhances the response of a plant to a pathogen or pest comprising: (i) assaying one or more tissue samples from a plant treated with at least a first microbial strain that is not a pathogen of said plant or from a plant grown from a plant part or seed treated with the first microbial strain for increased levels of one or more plant defense compounds derived from anthranilate as compared to one or more control tissue samples from an untreated control plant, wherein said tissue samples were harvested from the treated and untreated plant during or after said pest or pathogen attacked said plant tissue; and (ii) selecting a microbial strain that is not a pathogen of said plant and that provides the increased levels of the one or more plant defense compounds, thereby selecting a microbial strain that enhances the response of a plant to said pathogen or pest.

22. The method of claim 20 or 21, further comprising the step of selecting samples for analysis from treated plants that exhibit reduced damage from said pathogen or pest as compared to said untreated control plant.

23. The method of claim 20 or 21 wherein said samples are assayed to determine the levels of one or more gene transcripts or polypeptides associated with production of anthranilate and / or conversion of anthranilate to a plant defense compound.

24. The method of claim 20 wherein said samples are assayed to determine the levels of one or more plant defense compounds derived from anthranilate.

25. The method of claim 20 or 21 wherein said pathogen or pest is a fungus, bacteria, nematode, insect, or virus.

26. The method of claim 20 wherein said treated plant part is selected from the group consisting of a leaf, stem, shoot, flower, fruit, bud, root, tuber, rhizome, runner, bulb, and corm.Agent Ref.: P14472WO00 70 27. The method of claim 20 wherein said harvested tissue sample is selected from the group consisting of a leaf, stem, shoot, flower, fruit, bud, root, tuber, rhizome, runner, bulb, and corm tissue sample.

28. The method of claim 23 wherein the level of one or more gene transcripts encoding an anthranilate synthase protein component in said treated and untreated tissues is determined.

29. The method of claim 28 wherein said anthranilate synthase protein component is an alpha or beta subunit.

30. The method of claim 23 wherein the level of a gene transcript encoding anthranilate N- benzoyltransferase in said treated and untreated tissues is determined.

31. The method of claim 21 or 24 wherein said plant defense compound is an anthranilate ester.

32. The method of claim 31 wherein said anthranilate ester is selected from the group consisting of methyl anthranilate, dimethyl anthranilate, ethyl anthranilate, phenylethyl anthranilate and menthyl anthranilate.

33. The method of claim 21 or 24 wherein said plant defense compound is an anthranilate derived phytoalexin.

34. The method of claim 20 or 21 wherein said microbial strain is a bacterial strain or fungal strain.

35. The method of claim 34, wherein said bacterial strain is a Methylobacterium or Methylorubrum strain.

36. The method of claim 20 or 21 wherein said plant is selected from the group consisting of corn, wheat, rye, rice, alfalfa, barley, oats, rye, sorghum, millet, soybean, Brassica sp., Cannabis sp., tobacco, potato, peanut, carrot, cotton, coffee, coconut, sugar beet, oat, barley, tomato, squash, cucumber, cucurbits, lettuce, pepper, pea, onion, green bean, sunflower, safflower, sweet potato, cassava, coffee, coconut, conifers, turfgrass, leafy greens, microgreens, herbs, fruit plants, including fruit trees, and ornamentals.

37. The method of claim 36 wherein said plant is corn.

38. The method of claim 37 wherein said tissue sample is a root sample.

39. The method of claim 20 or 21 wherein said pest is corn rootworm.

40. The method of claim 20 or 21, wherein the first microbial strain is obtained by transferring DNA from a second microbial strain which can confer resistance, tolerance, reduced damage,Agent Ref.: P14472WO00 71 reduced infection, and / or reduced infestation to or by the pest or pathogen by increasing production of one or more plant defense compounds derived from anthranilate in a treated plant to a third microbial strain which does not confer resistance, tolerance, reduced damage, reduced infection, and / or reduced infestation to or by the pest or pathogen in a plant treated with the third microbial strain; optionally wherein the a second microbial strain is NLS0042 and / or optionally wherein the third microbial strain is a microbial strain other than NLS0042 provided in Table 1; optionally wherein the transferred DNA: (i) encodes one or more proteins having a sequence with at least 80% sequence identity to one or more of SEQ ID NO:21-35; or (ii) is present on a plasmid comprising SEQ ID NO: 86 or a variant thereof having at least 80% sequence identity to SEQ ID NO: 86; and / or (iii) comprises the sequence of one or more of SEQ ID NO:37-50 or a variant thereof with at least 80% identity to one or more of SEQ ID NO:37-50.

41. A method for monitoring pest or pathogen resistance, tolerance, reduced damage, reduced infection, and / or reduced infestation in a plant comprising assaying one or more tissue samples from a plant treated with at least a first microbial strain that can confer said pest or pathogen resistance, tolerance, reduced damage, reduced infection, and / or reduced infestation and that is not a pathogen of said plant or from a plant grown from a plant part or seed treated with the first microbial strain for: (i) increased levels of one or more plant defense compounds derived from anthranilate; and / or (ii) increased expression of one or more gene transcripts or polypeptides associated with production of anthranilate and / or conversion of anthranilate to a plant defense compound; wherein the increased levels and / or increased expression are as compared to one or more control tissue samples from an untreated control plant, wherein said tissue samples were harvested from the treated and untreated control plant during or after said pest or pathogen attacked said plant tissue, and whereby increased levels of the one or more plant defense compounds, gene transcripts, and / or polypeptides in the tissue samples from the treated plant in comparison to the control plant is indicative of increased pest or pathogen resistance, tolerance, damage reduction, infection reduction, and / or infestation reduction in said treated plant.

42. The method of claim 41, wherein said treated plant does not exhibit increased levels of the one or more plant defense compounds, gene transcripts, and / or polypeptides and wherein the method further comprises retreating with the first microbial strain and / or treating with another biocontrol agent, an insecticide, fungicide, or pesticide.Agent Ref.: P14472WO00 72 43. A method of selecting a microbial strain that enhances the response of a plant to a pathogen or pest comprising: (i) assaying one or more tissue samples from a plant treated with at least a first microbial strain that is not a pathogen of said plant or from a plant grown from a plant part or seed treated with the first microbial strain for increased levels of one or more plant defense compounds derived from anthranilate as compared to one or more control tissue samples from an untreated control plant, wherein said tissue samples were harvested from the treated and untreated plant during or after said pest or pathogen attacked said plant tissue; and (ii) selecting a microbial strain that is not a pathogen of said plant and that provides the increased levels of the one or more plant defense compounds, thereby selecting a microbial strain that enhances the response of a plant to said pathogen or pest.

44. A method of selecting a microbial strain that enhances the response of a plant to a pathogen or pest comprising: (i) assaying one or more plant tissue samples treated with at least a first microbial strain that is not a pathogen of said plant for increased levels of one or more plant defense compounds derived from anthranilate as compared to one or more untreated control plant tissue samples, wherein said tissue samples were exposed to said pest or pathogen during or after treatment with said first microbial strain; and (ii) selecting a microbial strain that provides the increased levels of the one or more plant defense compounds, thereby selecting a microbial strain that enhances the response of a plant to said pathogen or pest.

45. A method of improving a plant response to a pathogen or pest, wherein said method comprises, increasing the level of a plant defense compound produced in a plant by: (i) modifying a plant genome to increase expression of one or more gene transcripts involved in production of one or more plant defense compounds in said plant, and / or treating a plant, plant part or seed with a microbial strain that is not pathogenic to said plant, wherein said treatment increases expression in said plant of one or more gene transcripts involved in production of a plant defense compound; and (ii) growing said plant in the presence of said pathogen or pest, whereby the level of one or more plant defense compounds in said plant is increased in comparison to a control plant, and the response of said plant to said pathogen or pest is improved as compared to a control plant, wherein the control plant is not modified or treated as in (i).

46. The method of claim 45 wherein the plant defense compound is derived from anthranilate.

47. A method of repelling a pathogen or pest, wherein said method comprises, increasing a level of a plant defense compound produced in a plant comprisingAgent Ref.: P14472WO00 73 (i) treating soil, a plant, plant part or seed with a microbial strain that is not pathogenic to a plant, wherein said treatment increases expression in said plant of one or more gene transcripts involved in production of a plant defense compound; and (ii) growing said plant in the presence of said pathogen or pest, whereby the level of one or more plant defense compounds in said plant is increased in comparison to a control plant, and the plant repels said pathogen or pest more than a control plant, wherein the control plant is not modified or treated as in (i).

48. The method of claim 47, wherein the plant defense compound is derived from anthranilate.

49. The method of claim 47, wherein the microbial strain produces a metabolite, wherein such metabolite increases the production of such plant defense compound as compared to the control plant.

50. The method of claim 49, wherein the metabolite is selected from the group consisting of a siderophore, non-ribosomal peptide, a polyketide, or a combination thereof.

51. The method of claim 50, wherein said microbial strain comprises one or more gene clusters encoding proteins involved in biosynthesis of said metabolite.

52. The method of claim 47, wherein said microbial strain comprises one or more genes encoding: (i) one or more proteins having a sequence with at least 80% sequence identity to one or more of SEQ ID NO:21-35; (ii) one or more proteins having at least 80% sequence identity to SEQ ID NO:

21.

53. A method of selecting a microbial strain that confers pest or pathogen resistance, tolerance, reduced damage, reduced infection, and / or reduced infestation to a plant comprising identifying in said microbial strain: (i) one or more polynucleotides encoding a protein in a polyketide biosynthetic pathway; and / or (ii) one or more proteins in a polyketide biosynthetic pathway.

54. The method of claim 53, wherein said polynucleotides are identified by detecting at least one polynucleotide: (i) encoding one or more proteins having a sequence with at least 80% sequence identity to one or more of SEQ ID NO:21-35; (ii) encoding one or more proteins having at least 80% sequence identity to SEQ ID NO:21; (iii) comprising the sequence of one or more of SEQ ID NO: 36-50 or a sequence or sequences having at least 80% sequence identity to any one of SEQ ID NO: 36-50; and / or (iv) present on a plasmid comprising SEQ ID NO:86 or a sequence having at least 80% sequence identity to SEQ ID NO:

86.

55. The method of claim 54, wherein said polynucleotide is identified with a nucleic acid amplification, hybridization, and / or sequencing technique.Agent Ref.: P14472WO00 74 56. The method of claim 53, wherein said proteins are identified by detecting: (i) one or more proteins having a sequence with at least 80% sequence identity to one or more of SEQ ID NO:21-35; or (ii) one or more proteins having at least 80% sequence identity to SEQ ID NO:

21.

57. The method of claim 56, wherein said protein is identified by an immunoaffinity and / or mass-spectroscopy technique.

58. The method of claim 53, further comprising the step(s) of isolating and / or culturing the identified microbial stain comprising the polynucleotide and / or protein.

59. The method of any one of claims 53-58, wherein said microbial strain comprises a gene: (i) encoding one or more proteins having a sequence with at least 80% sequence identity to one or more of SEQ ID NO:21-35; (ii) encoding one or more proteins having at least 80% sequence identity to SEQ ID NO:21; or (iii) comprising a sequence of one or more of SEQ ID NO:36-50or a variant thereof having at least 80% sequence identity to SEQ ID NO:36-50.

60. The method of any one of claims 53-58, wherein said microbial strain is genetically modified with DNA: (i) encoding one or more proteins having a sequence with at least 80% sequence identity to one or more of SEQ ID NO:21-35; (ii) encoding one or more proteins having at least 80% sequence identity to SEQ ID NO:21; (iii) comprising the sequence of one or more of SEQ ID NO: 36-50 or a sequence or sequences having at least 80% sequence identity to any one of SEQ ID NO: 36-50; and / or (iv) present on a plasmid comprising SEQ ID NO:86 or a sequence having at least 80% sequence identity to SEQ ID NO:

86.

61. A method of improving a plant response to a pathogen or pest, wherein said method comprises: (i) treating a plant, plant part or seed with NLS0042 or a microbial stain comprising DNA: (i) encoding one or more proteins having a sequence with at least 80% sequence identity to one or more of SEQ ID NO:21-35; (ii) encoding one or more proteins having at least 80% sequence identity to SEQ ID NO:21; (iii) comprising the sequence of one or more of SEQ ID NO:37-50 or a variant thereof with at least 80% identity to one or more of SEQ ID NO:37-50; and / or (iv) is present on a plasmid comprising SEQ ID NO:86 or a variant thereof having at least 80% identity to SEQ ID NO:86; and (ii) growing said plant or a plant grown from the seed in the presence of said pathogen or pest, whereby the response of said plant to said pathogen or pest is improved as compared to a control plant; and wherein said plant is not a corn plant.Agent Ref.: P14472WO00 75 62. The method of claim 61, wherein said plant is selected from the group consisting of a pepper plant, tomato, snap bean, a Brassica plant, soybean, cotton, and rice.

63. The method of claim 61, wherein the level of one or more plant defense compounds in said plant is increased in comparison to a control plant.

64. The method of claim 61, wherein said pathogen or pest is an insect pest selected from the group consisting of aphids, lepidopterans, stinkbugs, white fly, beet leafhopper, tobacco hornworm, potato leaf hopper, Mexican bean beetle, flea beetles, fall armyworm, soybean looper, western flower thrips, and water weevil.

65. The method of any one of claims 61 to 64, wherein the improved response of the treated plant or plant grown from the treated part or seed comprises improved pest or pathogen resistance, tolerance, reduced damage, reduced infection, and / or reduced infestation to the treated plant or plant grown from the treated part or seed in comparison to an untreated control plant.

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