PLANT COLONIZATION TRIALS USING NATURAL MICROBIAL BARCODES

Abstract

This description relates to methods for using nucleic acid barcodes and corresponding amplification sites in cells where the barcodes occur naturally. These barcodes and amplification sites are reconfigured onto a single nucleic acid cassette, facilitating its use in labeling particular cell species, strains, or variants, each with a different barcode. These barcodes can then be used to track the colonization capabilities of the barcoded cells. This description also provides assays that use natural barcodes to measure the relative microbial colonization capacity of a plant root system.

Description

PLANT COLCNIZATION ASSAYS BY USING NATURAL MICROBIAL BARCODES CROSS REFERENCE TO RELATED REQUESTS This application claims priority to U.S. Provisional Application Serial No. 62 / 906,419, filed September 26, 2019, and U.S. Provisional Application Serial No. 62 / 789,332, filed January 7, 2019, each of which is fully incorporated herein by reference for all purposes. STATEMENT REGARDING SEQUENCE LISTING The contents of the text file submitted electronically herewith are incorporated herein in their entirety by reference: a machine-readable copy of the sequence listing, file name: PIVO 012 02WO SeqList ST25.txt, date of Creation: Jan 4, 2020, file size ~594 kilobytes. Background of the Invention The Food and Agriculture Organization of the United Nations projects that, by 2050, total food production must increase by 70% to meet the needs of a growing population, a challenge that is compounded by numerous factors, including the dwindling freshwater resources, increased competition for arable land, rising energy prices, rising input costs, and the likely need for crops to adapt to the pressures of a more global climate. drier, hotter and more extreme. Current agricultural practices are ill-equipped to meet this growing demand for food production, while balancing the environmental impacts that result from increased agricultural intensity. One of the main agricultural inputs needed to meet the world demand for food is nitrogenous fertilizer. However, the current industry standard used to produce nitrogenous fertilizers is an artificial nitrogen fixation method called the Haber-Bosch process, which converts atmospheric nitrogen (N2) to ammonia (NH3) through a reaction with hydrogen (H2) using of a metal catalyst at high temperatures and pressures. PRRn / n / Lznz / q / Yii - 2 This process consumes many resources and is harmful to the environment. In contrast to the Haber-Bosch synthetic process, certain biological systems have evolved to fix atmospheric nitrogen. These systems use an enzyme called nitrogenase that catalyzes the reaction between N2 and H2, resulting in nitrogen fixation. For example, rhizobia are diazotrophic bacteria that fix nitrogen after establishing themselves within the root nodules of legumes. An important goal of nitrogen fixation research is the extension of this phenotype to non-legume plants, particularly important agronomic grasses such as wheat, rice, and maize. However, despite the significant progress made in understanding the development of nitrogen-fixing symbiosis between rhizobia and legumes, the path to use that knowledge to induce nitrogen-fixing nodules in non-legume crops remains unclear. Consequently, the vast majority of modern row farming uses nitrogenous fertilizers that are produced through the Haber-Bosch process, which is resource-intensive and environmentally damaging. For example, the USDA indicates that the average US corn farmer typically applies between 130 and 200 pounds of nitrogen per acre (146 to 224 kg / ha). This nitrogen is not only produced in a resource-intensive synthetic process, but is applied with heavy machinery that traverses / impacts field soil, burns oil, and requires hours of human labor. Furthermore, the nitrogenous fertilizer produced by the HaberBosch industrial process is not well utilized by the target crop. Rain, runoff, heat, volatilization, and the soil microbiome degrade the applied chemical fertilizer. This equates not only to wasted money, but also increases pollution instead of harvested yield. To this end, the United Nations has calculated that nearly 80% of fertilizer is lost before a crop can use it. Consequently, the production and supply of modern agricultural fertilizers is not only harmful to the environment, but extremely inefficient. To meet the world's growing food supply needs, while balancing resource utilization and providing minimal impact on environmental systems, a better approach to nitrogen fixation and supply to plants is urgently needed. floors. PRRn / n / Lznz / q / Yii -3Summary of the Invention In some aspects, the disclosure relates to a method of barcoding a host cell, the method comprising: (a) obtaining a donor cell; (b) selecting and isolating a first nucleotide sequence in the donor cell genome, selecting and isolating a second nucleotide sequence in the donor cell genome, and selecting and isolating a third nucleotide sequence in the cell genome donor; (c) creating a native barcode polynucleotide cassette comprising the first, second and third 5' to 3' oriented nucleotide sequences as: (i) the first nucleotide sequence, wherein the first nucleotide sequence is a forward primer binding site, (ii) the second nucleotide sequence, where the second nucleotide sequence is a barcode, and (iii) the third nucleotide sequence, where the third nucleotide sequence is a site reverse primer binding; and (d) inserting the native barcode polynucleotide cassette into the genome of a host cell of the same species as the donor cell in (a); wherein the nucleotide sequences of (i), (ii) and (iii) are native to the host cell. In some aspects, the donor cell and the host cell are selected from a bacterial cell, a fungal cell, a plant cell, an animal cell, a protozoan cell, and an insect cell. In some aspects, each of the donor cell and the host cell is a bacterial cell. In some aspects, the nucleotide sequence of at least one of (i), (ii) and (iii) is isolated from ribosomal DNA or internal transcribed spacer (ITS) DNA. In some aspects, the nucleotide sequences of at least one of (i), (ii) and (iii) are isolated from 16S rDNA or 18S rDNA. In some aspects, at least one of the primer binding sites is selected from 8F, 27F, CCF, 357E, 515F, 533F, 16S.1100.F16, 804F, 1237F, 338R, 519R, CDR, 806R, 907R, 1100R , 1391R, 1392R, 1492R(1), and 1492R(s) In some aspects, the first nucleotide sequence in the donor cell genome and the third nucleotide sequence in the donor cell genome are in the same orientation relative to each other. In some aspects, at least one of (i), (ii) and (iii) are not found naturally immediately adjacent to each other in the host cell genome. In some aspects, the barcode consists of less than 100 nucleotides. In some aspects, one or more of the primer binding sites consist of fewer than 30 nucleotides. In PRRn / n / Lznz / q / Yi -4 In some respects, the nucleotide sequence of the primer binding site and the barcode, together, consist of fewer than 160 nucleotides. In some aspects, the barcode comprises a constant barcode region and a variable barcode region. In some aspects, insertion of the cassette into the host cell genome introduces one or more stop codons in any orientation into the host cell. In some aspects, the cassette is inserted into the host cell genome between two coding regions separated by a termination region. In some aspects, the cassette is inserted between the termination region and one of the two coding regions. In some aspects, the host cell in (d) is of the same strain as the donor cell in (a). In some aspects, the native barcode polynucleotide cassette is inserted into the genome of two or more host cells at loci that are remote from an origin of replication in the host cell's genome. In some aspects, the established distance from the origin of replication is similar or identical in each of the two or more host cells. The origin of replication may be in the host cell genome or in a self-replicating extrachromosomal genetic entity (eg, episome or plasmid). In some aspects, the bacterial host cell is transgenic. In some aspects, the bacterial host cell is a non-intergeneric remodeled bacterium. In some aspects, the non-intergeneric remodeled bacterial host cell is, or is derived from, a bacterium selected from Table 1. In some aspects, the non-intergeneric remodeled bacterium comprises at least one introduced genetic variation in at least one gene, or non-intergeneric polynucleotide. coding, of the genetic regulatory network of nitrogen assimilation or fixation, so that the modified bacterium is capable of fixing atmospheric nitrogen in the presence of exogenous nitrogen. In some aspects, the bacterial host cell is capable of fixing atmospheric nitrogen in the presence of exogenous nitrogen. In some aspects, the bacterial host cell comprises at least one introduced genetic variation in at least one gene, or noncoding polynucleotide, of the nitrogen fixation or assimilation genetic regulatory network. In some aspects, the bacterial host cell comprises an introduced control sequence operatively linked to at least one gene of the gene assimilation or fixation genetic regulatory network. PRRn / n / Lznz / q / Yii -5nitrogen. In some aspects, the bacterial host cell comprises a heterologous promoter operably linked to at least one nitrogen fixation or assimilation genetic regulatory network gene. In some aspects, the bacterial host cell comprises at least one introduced genetic variation in a member selected from the group consisting of: nifA, nifL, ntrB, ntrC, polynucleotide encoding glutamine synthetase, glnA, glnB, glnK, drat, amtB, polynucleotide encoding glutaminase, glnD, glnE, nifJ, nifH, nifD, nifK, nifY, nifE, nifN, nifU, nifS, nifV, nifW, nifZ, nifM, nifE, nifB, nifQ, a gene associated with the biosynthesis of a nitrogenase enzyme , and combinations of these. In some aspects, the bacterial host cell comprises at least one introduced genetic variation in at least one gene, or noncoding polynucleotide, of the nitrogen-fixing or assimilation genetic regulatory network that results in one or more of: increased expression or activity of NifA or glutaminase; decreased expression or activity of NifL, NtrB, glutamine synthetase, GlnB, GlnK, DraT, AmtB; decreased adenylyl scavenging activity of GlnE; and decreased uridylyl scavenging activity of GlnD. In some aspects, the bacterial host cell comprises a mutated nifL gene comprising a heterologous promoter in said nifL gene. In some aspects, the bacterial host cell comprises a mutated glnE gene that produces a truncated GlnE protein lacking an adenylyl removal (AR) domain. In some aspects, the bacterial host cell comprises a mutated amtB gene that results in lack of expression of said amtB gene. In some aspects, the bacterial host cell comprises at least one of: a mutated nifL gene comprising a heterologous promoter in said nifL gene; a mutated glnE gene that produces a truncated GlnE protein lacking an adenylyl removal (AR) domain; a mutated amtB gene that results in lack of expression of said amtB gene; and combinations of these. In some aspects, the bacterial host cell comprises a mutated nifL gene comprising a heterologous promoter in said nifL gene and a mutated glnE gene that produces a truncated GlnE protein lacking an adenylyl removal (AR) domain. In some aspects, the bacterial host cell comprises a mutated nifL gene comprising a heterologous promoter in said nifL gene, a mutated glnE gene that produces a truncated GlnE protein lacking an adenylyl removal (AR) domain, and an amtB gene. mutated that produces the lack of expression of said gene PRRn / n / Lznz / q / Yii -6amtB. In some aspects, the bacterial host cell is selected from Rahnella aquatilis, Klebsiella variicola, Achromobacter spiritinus, Achromobacter marplatensis, Microbacterium murale, Kluyvera intermedia, Kosakonia pseudosacchari, Enterobacter sp., Azospirillum lipoferum, and Kosakonia sacchari. In some aspects, the bacterial host cell is endophytic, epiphytic, or rhizospheric. In some aspects, the bacterial host cell is selected from: a bacterium deposited as ATCC PTA-126575, a bacterium deposited as ATCC PTA-126576, a bacterium deposited as ATCC PTA-126577, a bacterium deposited as ATCC PTA-126578, a bacterium deposited as ATCC PTA-126579, a bacterium deposited as ATCC PTA126580, a bacterium deposited as ATCC PTA-126581, a bacterium deposited as ATCC PTA-126582, a bacterium deposited as ATCC PTA-126583, a bacterium deposited as ATCC PTA-126584, a bacterium deposited as ATCC PTA-126585, a bacterium deposited as ATCC PTA-126586, a bacterium deposited as ATCC PTA126587, a bacterium deposited as ATCC PTA-126588, a bacterium deposited as NCMA 201701001, a bacterium deposited as NCMA 201701002, a bacterium deposited as NCMA 201701003, a bacterium deposited as NCMA 201708004, a bacterium deposited as NCMA 201708003, a bacterium deposited as NCMA 201708002, a bacterium deposited as NCMA 201708001, a bacterium deposited as NCMA 201712001, and a bacterium deposited as gives as NCMA 201712002. In some aspects, the bacterial host cell comprises a nucleic acid sequence that shares at least about 95% sequence identity with a nucleic acid sequence selected from SEQ ID NO: 177-260 and 296303. In some aspects, the bacterial host cell comprises a nucleic acid sequence that shares at least about 99% sequence identity with a nucleic acid sequence selected from SEQ ID NO: 177-260 and 296303. In some aspects, the bacterial host cell comprises a nucleic acid sequence selected from SEQ ID NO: 177-260 and 296-303. In some aspects, the description refers to a composition comprising: (a) one or more modified cells comprising, in their genome: (i) a first nucleotide sequence, a second nucleotide sequence and a third nucleotide sequence of naturally occurring, and (ii) a naturally occurring barcode polynucleotide cassette comprising the first, second, and third 5' to 3' oriented nucleotide sequences as: (1) the first nucleotide sequence, wherein the first nucleotide sequence nucleotide sequence is a forward primer binding site, (2) the second nucleotide sequence, where the second nucleotide sequence is a barcode, and (3) the third nucleotide sequence, where the third nucleotide sequence is a reverse primer binding site; wherein the first, second and third nucleotide sequences of (ii) have a different proximity to each other compared to the naturally occurring sequences of (i). In some aspects, the barcode is unique for each different species of the one or more modified cells. In some aspects, the barcode is unique for each different strain of the one or more modified cells. In some aspects, the one or more modified cells comprise a homogeneous population of cells. In some aspects, the one or more modified cells comprise a heterogeneous population of cells. In some aspects, the heterogeneous population of cells comprises two or more different species. In some aspects, the heterogeneous population of cells comprises two or more different strains. In some aspects, the heterogeneous population of cells comprises two or more strains of each species. In some aspects, the one or more modified cells are selected from a bacterial cell, a fungal cell, a plant cell, an animal cell, a protozoan cell, and an insect cell. In some aspects, the one or more modified cells are a bacterial cell. In some aspects, the nucleotide sequence of at least one of (1), (2) or (3) is isolated from ribosomal DNA or internal transcribed spacer (ITS) DNA. In some aspects, the nucleotide sequence of at least one of (1), (2) or (3) is 16S rDNA or 18S rDNA. In some aspects, at least one of the primer binding sites is selected from 8F, 27F, CCF, 357F, 515F, 533F, 16S.1100.F16, 804F, 1237F, 338R, 519R, CDR, 806R, 907R, 1100R , 1391R, 1392R, 1492R(1), and l492R(s) In some aspects, the first and third naturally occurring nucleotide sequences in the genome of the modified cells are in the same orientation relative to each other. In some aspects, at least one of the first, second, or third naturally occurring nucleotide sequences are not found immediately adjacent to one another in the genome of the modified cell. In some aspects, the barcode consists of less than 100 nucleotides. In some aspects, one or more of the primer binding sites consist of fewer than 30 nucleotides. In some aspects, the nucleotide sequence of the barcode and primer binding sites together consist of less than 160 nucleotides. PRRn / n / Lznz / q / Yi -8 In some aspects, the barcode comprises a constant barcode region and a variable barcode region. In some aspects, the constant barcode region of the barcode is the same in each of the one or more modified cells. In some aspects, the variable barcode region of the barcode is different in each of the one or more modified cells, and only cells of the same strain, species, or other categorical distinction share the same variable region. In some aspects, the cassette possesses one or more stop codons in any orientation in the one or more modified cells. In some aspects, the cassette is present in the genome of the one or more modified cells between two coding regions separated by a termination region. In some aspects, the cassette is present between the termination region and one of the two coding regions. In some aspects, the cassette is present in the genome of each of the one or more modified cells at a set distance from an origin of replication. In some aspects, the established distance from the origin of replication is similar or identical in each of the two or more cells. In some aspects, the one or more modified bacteria are transgenic. In some aspects, the one or more modified bacteria are non-intergeneric remodeled bacteria. In some aspects, the one or more modified bacteria comprise a population of transgenic bacteria. In some aspects, the one or more modified bacteria comprise a population of non-intergeneric remodeled bacteria. In some aspects, non-intergeneric remodeled bacteria comprise, or are derived from, a bacterium selected from Table 1. In some aspects, non-intergeneric engineered bacteria comprise at least one introduced genetic variation in at least one gene, or noncoding polynucleotide, of the genetic regulatory network for nitrogen assimilation or nitrogen fixation, such that the engineered bacterium is capable of fixing nitrogen. atmospheric nitrogen in the presence of exogenous nitrogen. In some aspects, the bacterial cell is capable of fixing atmospheric nitrogen in the presence of exogenous nitrogen. In some aspects, the bacterial host cell comprises at least one introduced genetic variation in at least one gene, or noncoding polynucleotide, of the nitrogen fixation or assimilation genetic regulatory network. In some aspects, the bacterial cell comprises an introduced control sequence operatively linked to at least one gene of the genetic regulatory network of PRRn / n / Lznz / q / Yii -9assimilation or fixation of nitrogen. In some aspects, the bacterial cell comprises a heterologous promoter operably linked to at least one nitrogen fixation or assimilation genetic regulatory network gene. In some aspects, the bacterial cell comprises at least one introduced genetic variation in a member selected from the group consisting of: nifA, nifL, ntrB, ntrC, polynucleotide encoding glutamine synthetase, glnA, glnB, glnK, drat, amtB, polynucleotide encoding encodes glutaminase, glnD, glnE, nifJ, nifH, nifD, nifK, nifY, nifE, nifN, nifU, nifS, nifV, nifW, nifZ, nifM, nifE, nifB, nifQ, a gene associated with the biosynthesis of a nitrogenase enzyme, and combinations of these. In some aspects, the bacterial cell comprises at least one introduced genetic variation in at least one gene, or noncoding polynucleotide, of the genetic regulatory network for nitrogen uptake or fixation that results in one or more of: increased expression or activity of NifA or glutaminase; decreased expression or activity of NifL, NtrB, glutamine synthetase, GlnB, GlnK, DraT, AmtB; decreased adenylyl scavenging activity of GlnE; and decreased uridylyl scavenging activity of GlnD. In some aspects, the bacterial cell comprises a mutated nifL gene comprising a heterologous promoter in said nifL gene. In some aspects, the bacterial cell comprises a mutated glnE gene that produces a truncated GlnE protein lacking an adenylyl removal (AR) domain. In some aspects, the bacterial cell comprises a mutated amtB gene resulting in lack of expression of said amtB gene. In some aspects, the bacterial cell comprises at least one of: a mutated nifL gene comprising a heterologous promoter in said nifL gene; a mutated glnE gene that produces a truncated GlnE protein lacking an adenylyl removal (AR) domain; a mutated amtB gene that results in lack of expression of said amtB gene; and combinations of these. In some aspects, the bacterial cell comprises a mutated nifL gene comprising a heterologous promoter in said nifL gene and a mutated glnE gene that produces a truncated GlnE protein lacking an adenylyl removal (AR) domain. In some aspects, the bacterial cell contains a mutated nifL gene comprising a heterologous promoter in said nifL gene, a mutated glnE gene that produces a truncated GlnE protein lacking an adenylyl removal (AR) domain, and a mutated amtB gene. which produces the lack of expression of said amtB gene. In some aspects, the bacterial cell is selected from Paraburkholderia rRRn / n / Lznz / q / Yi - 10 tropics, Paraburkholderia xenovorans, Herbaspirillum seropedicae, Herbaspirullum frisingense, Pseudomonas protegens, Pseudomonas syringae, Pseudomonas benzenivorans, Metakosakonia massiliensis, Metakosakonia intestinalii, Rahnella aquatilis, Klebsiella variicola, Achromobacter spiri tinus, Achromobacter marplatensis, Microbacterium murale, Kluyvera intermedia, Kosakonia pseudosacchari, Enterobacter sp. , Azospirillum lipoferum, and Kosakonia sacchari. In some aspects, the bacterial cell is endophytic, epiphytic, or rhizospheric. In some aspects, the bacterial cell is selected from: a bacterium deposited as ATCC PTA-126575, a bacterium deposited as ATCC PTA-126576, a bacterium deposited as ATCC PTA-126577, a bacterium deposited as ATCC PTA-126578, a bacterium deposited as as ATCC PTA-126579, a bacterium deposited as ATCC PTA-126580, a bacterium deposited as ATCC PTA-126581, a bacterium deposited as ATCC PTA-126582, a bacterium deposited as ATCC PTA-126583, a bacterium deposited as ATCC PTA126584, a bacterium deposited as ATCC PTA-126585, a bacterium deposited as ATCC PTA-126586, a bacterium deposited as ATCC PTA-126587, a bacterium deposited as ATCC PTA-126588, a bacterium deposited as NCMA 201701001, a bacterium deposited as NCMA 201701002, a bacterium deposited as NCMA 201701003, a bacterium deposited as NCMA 201708004, a bacterium deposited as NCMA 201708003, a bacterium deposited as NCMA 201708002, a bacterium deposited as NCMA 201708001, a bacterium deposited as NCMA 201712001, and a bacterium deposited as NCMA 201712002. In some aspects, the bacterial cell comprises a nucleic acid sequence that shares at least about 95% sequence identity with a nucleic acid sequence selected from SEQ ID NO: 177-260 and 296-303. In some aspects, the bacterial cell comprises a nucleic acid sequence that shares at least about 99% sequence identity with a nucleic acid sequence selected from SEQ ID NO: 177-260 and 296-303. In some aspects, the bacterial cell comprises a nucleic acid sequence selected from SEQ ID NO: 177-260 and 296-303. In some aspects, the disclosure relates to a method of detecting cells in a sample, the method comprising: (a) inserting a native barcode polynucleotide cassette into the genomes of two or more cells, wherein the cassette comprises Natural nucleotide sequences from each of the one or more cells, oriented from 5' to 3' as: (i) a forward primer binding site, (ii) a unique barcode for each cell, species or strain, and (iii) PRRn / n / Lznz / q / Yi - 11 a reverse primer binding site; (b) applying the two or more cells to a proliferative medium; (c) collecting a sample of the proliferative medium comprising the two or more cells; and (d) determining the abundance of the two or more cells in the sample by analyzing the abundance of the barcodes. In some aspects, step (c) further comprises lysing the two or more cells. In some respects, abundance is relative abundance. In some respects, abundance is absolute abundance. In some aspects, abundance is determined by PCR. In some aspects, the PCR is selected from multiplex PCR, dPCR, ddPCR, or qPCR. In some aspects, abundance is determined by generating and using a standard curve. The standard curve can be generated by spiking or spiking into a sample or samples at a known concentration or a range of known concentrations. The sample(s) can be added to nucleic acid isolated from samples processed during any of the methods (eg, the coco-seq assay), as described herein. The sample added may be one or more of the control barcodes, as provided herein. In some aspects, the proliferative medium is selected from a liquid medium, a solid medium, or a semi-solid medium. In some aspects, the proliferative medium is the soil. In some aspects, the soil comprises one or more plants or parts of plants. In some aspects, the one or more plants or plant parts are selected from non-leguminous plants. In some aspects, the one or more non-leguminous plants are maize. In some aspects, the period of time between steps (c) and (d) is a sufficient amount of time for at least one doubling of the two or more cells. In some aspects, the forward primer binding site and / or the reverse primer binding site is the same in each of the two or more cells. In some aspects, the GC content of the forward primer binding site and / or the reverse primer binding site is at least 40%. In some aspects, the two or more cells comprise a homogeneous population of cells. In some aspects, the two or more cells comprise a heterogeneous population of cells. In some aspects, the heterogeneous population of cells comprises two or more different species. In some aspects, the heterogeneous population of cells comprises two or more different strains. In some aspects, the heterogeneous population of cells comprises two or more strains of each species. PRRn / n / Lznz / q / Yii - 12 In some aspects, the two or more cells are selected from bacterial cells, fungal cells, plant cells, animal cells, protozoan cells, and insect cells. In some aspects, the two or more cells are bacterial cells. In some aspects, the nucleotide sequence of at least one of (i), (ii) or (iii) is isolated from ribosomal DNA or internal transcribed spacer (ITS) DNA. In some aspects, the nucleotide sequence of at least one of (i), (ii) or (iii) is 16S rDNA or 18S rDNA. In some aspects, at least one of the primer binding sites is selected from 8F, 27F, CCF, 357F, 515F, 533F, 16S.1100.F16, 804F, 1237F, 338R, 519R, CDR, 806R, 907R, 1100R , 1391R, 1392R, 1492R(1), and 1492R(s) In some aspects, the barcode consists of less than 100 nucleotides. In some aspects, one or more of the primer binding sites consist of fewer than 30 nucleotides. In some aspects, the nucleotide sequence of the barcode and primer binding sites together consist of less than 160 nucleotides. In some aspects, the two or more bacteria are transgenic. In some aspects, the two or more bacteria are non-intergeneric remodeled bacteria. In some aspects, the two or more bacteria comprise a population of transgenic bacteria. In some aspects, the two or more bacteria comprise a population of non-intergeneric remodeled bacteria. In some aspects, the non-intergeneric remodeled bacteria comprise, or are derived from, a bacterium selected from Table 1. In some aspects, the two or more bacteria are capable of fixing atmospheric nitrogen in the presence of exogenous nitrogen. In some aspects, the barcode comprises a constant barcode region and a variable barcode region. In some aspects, the constant barcode region of the barcode inserted into each of the two or more cells is the same in each of the two or more cells. In some aspects, the variable barcode region of the barcode inserted into each of the two or more cells is different, and only cells of the same strain, species, or other categorical distinction share the same variable region. In some aspects, insertion of the cassette into the genome of the two or more cells introduces one or more stop codons in any orientation into the two or more cells. In some aspects, the cassette is present in the genome of two or more PRRn / n / Lznz / q / Yii - 13 cells between two coding regions separated by a termination region. In some aspects, the cassette is present between the termination region and one of the two coding regions. In some aspects, the cassette is present in the genome of each of two or more cells at a set distance from an origin of replication. In some aspects, the established distance from the origin of replication is similar or identical in each of the two or more cells. By ensuring the insertion of the native barcode polynucleotide cassettes at a semi-constant distance from the replication origins in each cell or strain, any bias introduced into sequencing coverage due to distance from the replication origin can be minimized. In some aspects, the disclosure relates to a method of barcoding a population of host cells, the method comprising: (a) obtaining a donor cell; (b) selecting and isolating a first nucleotide sequence in the donor cell genome, selecting and isolating a second nucleotide sequence in the donor cell genome, and selecting and isolating a third nucleotide sequence in the cell genome donor; (c) creating a native barcode polynucleotide cassette comprising the first, second and third 5' to 3' oriented nucleotide sequences as: (i) the first nucleotide sequence, wherein the first nucleotide sequence is a forward primer binding site, (ii) the second nucleotide sequence, where the second nucleotide sequence is a barcode, and (iii) the third nucleotide sequence, where the third nucleotide sequence is a site reverse primer binding; and (d) inserting the native barcode polynucleotide cassette into the genome of a host cell of the same species as the donor cell in (a); and (e) repeating (d) one or more times with a different host cell of the same genus each time; wherein the nucleotide sequences of (i), (ii) and (ii) are native to the host cell, thereby barcoding a population of host cells. In some aspects, the host cell population shares a common species. In some aspects, each of the different host cells of (e) is a different strain. In some aspects, each of the different host cells of (e) is a different species. In some aspects, the barcode comprises a constant barcode region and a variable barcode region. In some respects, the rRRn / n / Lznz / q / Yi - 14 constant barcode region of the barcode inserted into each host cell of the host cell population is the same in each of the host cells. In some aspects, the variable barcode region of the barcode inserted into each cell of the host cell population is different, and only host cells of the same strain, species, or other categorical distinction share the same variable region. In some aspects, insertion of the cassette into the host cell genome introduces one or more stop codons in any orientation into the host cell. In some aspects, the insertion of the cassette into the genome of each cell in the population is between two coding regions separated by a termination region. In some aspects, the cassette insert is between the termination region and one of the two coding regions. In some aspects, the insertion of the cassette into the genome of each cell in the population is a set distance from an origin of replication in each cell. The stated distance can be any distance from the origin of replication, as long as the one or more barcodes are consistently incorporated at the same or similar distance from the origin of replication in every cell of the population in which they are incorporated. includes a barcode. In some aspects, the description refers to a composition comprising: (a) a population of modified cells, in their genome: (i) a first nucleotide sequence, a second nucleotide sequence and a third nucleotide sequence of natural origin , and (ii) a native barcode polynucleotide cassette comprising the first, second, and third 5' to 3' oriented nucleotide sequences as: (1) the first nucleotide sequence, wherein the first nucleotide sequence is a forward primer binding site, (2) the second nucleotide sequence, where the second nucleotide sequence is a barcode, and (3) the third nucleotide sequence, where the third nucleotide sequence is a barcode. reverse primer binding site; wherein the first, second and third nucleotide sequences of (ii) have a different proximity to each other compared to the naturally occurring sequences of (i). In some aspects, the population of modified cells share a common species. In some aspects, the population of modified cells comprises more than one species. In some aspects, the population of modified cells comprises more than one strain of each species. In some aspects, the barcode comprises a code region of PRRn / n / Lznz / q / Yii - 15 constant bars and one variable barcode region. In some aspects, the constant barcode region is the same in each of the modified cells. In some aspects, the variable barcode region is not conserved in the population of modified cells, and only modified cells of the same strain, species, or other categorical distinction share the same variable region. In some aspects, insertion of the cassette into the genome of the modified cell population introduces one or more stop codons in any orientation into the modified cells. In some aspects, the cassette is present in the host cell genome between two coding regions separated by a termination region. In some aspects, the cassette is present between the termination region and one of the two coding regions. In some aspects, the cassette is present in the host cell genome at a set distance from an origin of replication. In some aspects, the established distance from the origin of replication is similar or identical in each modified cell in the population of modified cells. Brief Description of the Figures of the Invention FIGURE 1A illustrates an overview of the guided microbial remodeling process, according to modalities. FIGURE IB illustrates a magnified view of microbiome composition measurement, as shown in FIGURE 1A. FIGURE 1C illustrates a problematic “traditional bioprospecting” approach, which has several disadvantages compared to the described guided microbial remodeling (GMR) platform. FIGURE ID illustrates a problematic “field-first bioprospecting approach” system, which has several drawbacks compared to the described guided microbial remodeling (GMR) platform. FIGURE 1E illustrates the time period in the corn growth cycle when the plant needs the most nitrogen. FIGURE 1F illustrates an overview of a field development process for a remodeled microbe. FIGURE 1G illustrates an overview of a guided microbial remodeling platform modality. FIGURE 1H illustrates an overview of a retrofit deck. PRRn / n / Lznz / q / Yii - 16 computationally guided microbial. FIGURE II describes the use of carpal data combined with modeling in aspects of the guided microbial remodeling platform. FIGURE 1J illustrates 5 properties that the remodeled microbes of the present disclosure may possess. FIGURE 1K illustrates a schematic of a splicing approach for one microbe, PBC6.1. FIGURE 1L illustrates nifA expression uncoupled from endogenous nitrogen regulation in remodeled microbes. FIGURE 1M shows improved assimilation and excretion of fixed nitrogen by remodeled microbes. FIGURE IN illustrates the yield improvement in maize that can be attributed to remodeled microbes. FIGURE 1O illustrates the inefficiency of current nitrogen supply systems, resulting in underfertilized carpals, overfertilized fields, and environmentally damaging nitrogen runoff. FIGURE 2A illustrates a current plant colonization assay used in the GMR process, which is based on absolute colonization. The described assays and processes are not limited to cells that have been produced as a result of the GMR process. FIGURE 2B depicts the hypothetical plant counts required to assess the colonization ability of 19 strains using different approaches. FIGURE 3A-FIGURE 3D illustrate a workflow of the relative colonization assays described from Example 2 that are enabled by using natural microbial barcodes. These relative colonization assays drastically reduce the number of plants needed for a colonization assay. FIGURE 3A illustrates the selection of naturally occurring conserved regions in a bacterial genome for use as universal primers. FIGURE 3B illustrates the selection of natural sequences from bacterial strains to serve as barcode sequences. FIGURE 3C illustrates the cassette containing the primer binding sites and the barcode. FIGURE 3D illustrates the general in planta workflow for the assessment of competitive bacterial colonization. FIGURE 4 illustrates the optimization of primer binding site pairs in PRRn / n / Lznz / q / Yi - 17 a PCR of pooled templates of genomic DNA from a variety of wild-type bacterial strains. Ideally, templates from wild-type strains will not produce any product, as seen in lane 4. FIGURE 5 illustrates barcode drift due to bidirectional replication in a microbial (ie, E. coli) chromosome. FIGURE 6A illustrates possible insertion sites for naturally occurring barcode polynucleotide sequences in a microbe's genome, while FIGURE 6B shows the location of a naturally occurring barcode polynucleotide sequence in a microbe's genome relative to with the two coding sequences and the termination sequence located between them. FIGURE 7 illustrates the lower colonization phenotype of strain 137-1036 versus the parental strain 137, as reflected in the copy number of the strains' genomes by qPCR. Each strain represents a single treatment of 12 plants. FIGURE 8 illustrates the differential colonization of 137 wild-type barcode-containing strains (i.e., barcodes 1, 2, and 7) as reflected by differences in the relative abundances of the different barcode-labeled strains growing in plants inoculated with an inoculum containing each of the wild-type barcodes (ie, barcodes 1, 2, and 7) in a ratio of 100:10:1, respectively. FIGURE 9 illustrates the undercolonization phenotype of strain 137-1036 versus the parental strain 137 as reflected by differences in the relative abundance of different barcode-labeled strains growing on plants inoculated with a set of the different barcode labeled strains. barcode labeled strains. FIGURE 10 illustrates the read counts determined for known copy numbers of control DNA and test DNA using the amplification and sequencing method described in Examples 2 and 3 and throughout this disclosure. Control DNA and test DNA possess the same universal primer binding sites flanking barcode sequences that are unique to control DNA or test DNA. The unique barcode sequence present in the control DNA was based on sea otter genome sequences, whereas the unique barcode sequence present in the test DNA was chosen based on sequences from the parent strain. 137, as described in Example 2. Control DNA was added at different copy numbers spanning several orders of magnitude (i.e., 106, 103, and 100 in run 1 or 107, 104, and 101 in run 1). test 2), while test DNA added rRRn / n / Lznz / q / Yi - 18 at a known level, 105 copies for both tests 1 and 2. FIGURE 11 illustrates the total abundance (cells per gram fresh weight (gfw)) for strains 137, 137-1036, 137-3933, 137-3944, and 137-2285 as determined using the amplification and sequencing method. described in Example 4 and throughout this description. Each of the strains contains natural polynucleotide barcode sequences that contain the same universal primer binding sites flanking barcode sequences that are unique to each of the strains, as described in Example 4. As can be seen, the Coco-seq assay described in Example 4 revealed that each of the barcode strains possesses a weaker colonization ability than the parent strain 137, with strain 137-2285 having the strongest colonization ability. weak. Detailed Description of Invention While various embodiments of the disclosure have been shown and described herein, it will be apparent to those skilled in the art that those embodiments are provided by way of example only. It will be apparent to those skilled in the art that various variations, changes, and substitutions can be made without departing from the description. It will be understood that various alternatives to the embodiments of the description set forth herein may be employed. Increasing the use of fertilizers brings with it environmental concerns and is also likely not to be possible for many economically challenged regions of the world. In addition, many industry players in the microbial carpus are focused on creating intergeneric microbes. However, there is a heavy regulatory burden on genetically modified microbes that are characterized / classified as intergeneric. These intergeneric microbes face not only a greater regulatory burden, making widespread adoption and implementation difficult, but also face great scrutiny from public perception. Currently, there are no genetically modified microbes on the market that are not intergeneric and that are capable of increasing nitrogen fixation in non-leguminous crops. This scarcity of such microbes is a missing element to help usher in a 21st century agricultural system that is truly environmentally friendly and more sustainable. One problem that arises in the development of such an organism is the ability to identify candidates that are not only capable of nitrogen fixation, but also PRRn / n / Lznz / q / Yi - 19 can also colonize the roots of non-leguminous crops. When selecting candidates, organisms that are highly efficient at nitrogen fixation but less efficient at colonization may be difficult to detect in mixed samples. The present description solves the problems mentioned above and provides a method to increase the ability to detect such organisms. The methods described and the non-intergeneric microbes identified by them will serve to help 21st century farmers become less dependent on using increasing amounts of exogenous nitrogen fertilizers. Definitions The use of the terms "a", "an" and "the" and similar referents in the context of the description (especially in the context of the following claims) shall be interpreted as encompassing the singular and the plural, unless otherwise stated herein or clearly contradicted by the context. The terms "containing", "having", "including" and "containing" should be interpreted as broadly defined (i.e., meaning "including, but not limited to"), unless otherwise indicated. else. References to ranges of values ​​herein are intended to serve simply as a shortcut for individually referring to each individual value that is included in the range, unless otherwise noted herein, and each individual value is incorporated into the specification as if individually mentioned herein. For example, if the range 10-15 is described, then 11, 12, 13, and 14 are also described. All of the methods described herein can be performed in any suitable order, unless otherwise noted in the section. present or the context clearly contradicts it. The use of any and all examples, or illustrative language (for example, "such as") herein, is intended to further illustrate the description and not present a limitation on the scope of the description unless otherwise claimed. contrary. No expression in the specification should be construed as indicating that any unclaimed item is essential to the practice of the description. The terms “polynucleotide”, “nucleotide”, “nucleotide sequence”, “nucleic acid”, and “oligonucleotide” are used interchangeably. These refer to a polymeric form of nucleotides of any length, whether deoxyribonucleotides or ribonucleotides, or analogues thereof. Polynucleotides can have any three-dimensional structure and can develop any PRRn / n / Lznz / q / Yii -20 function, known or unknown. The following are non-limiting examples of polynucleotides: coding or non-coding regions of a gene or gene fragment, loci defined from splicing analysis, exons, entrons, messenger RNA (mRNA), transfer RNA (tRNA), RNA ribosomal (rRNA), small interfering RNA (siRNA), short hairpin RNA (shRNA), microRNA (miRNA), ribozymes, cDNA, recombinant polynucleotides, branched polynucleotides, plasmids, vectors, isolated DNA of any sequence, isolated RNA of any sequence , nucleic acid probes and primers. A polynucleotide can comprise one or more modified nucleotides, such as methylated nucleotides and nucleotide analogs. If present, modifications to the nucleotide structure can be imparted before or after polymer assembly. The nucleotide sequence can be interrupted by non-nucleotide components. A polynucleotide can be further modified after polymerization, for example, by conjugation with a tagging component. "Hybridization" refers to a reaction where one or more polynucleotides react to form a complex that is stabilized by hydrogen bonding between the bases of nucleotide residues. Hydrogen bonding can occur by Watson Crick base pairing, Hoogstein junction, or in any other sequence-specific manner according to base complementarity. The complex can comprise two strands that form a duplex structure, three or more strands that form a multi-stranded complex, a single self-hybridizing strand, or any combination of these. A hybridization reaction may be one step in a larger process, such as the initiation of PCR or the cleavage of a polynucleotide by an endonuclease. A second sequence that is complementary to a first sequence is called the "complement" of the first sequence. The term "hybridizable" as applied to a polynucleotide refers to the ability of the polynucleotide to form a complex that is stabilized by hydrogen bonding between the bases of nucleotide residues in a hybridization reaction. As used herein, "biofilm" or "mature biofilm" refers to associated and / or accumulated and / or aggregated microbial cells, their products (e.g., exopolymeric substances), and inorganic particles adhered to a living or inert surface. . "Complementarity" refers to the ability of a nucleic acid to form one or more hydrogen bonds with another nucleic acid sequence by PRRn / n / Lznz / q / Yii - 21 Watson-Crick traditional or other non-traditional types. A percent complementarity indicates the percentage of residues in a nucleic acid molecule that can form hydrogen bonds (eg, WatsonCrick base pairing) with a second nucleic acid sequence (eg, 5, 6, 7, 8, 9 , 10 out of 10, with 50%, 60%, 70%, 80%, 90%, and 100% complementarity, respectively). "Perfectly complementary" means that all contiguous residues in one nucleic acid sequence will hydrogen bond with the same number of contiguous residues in a second nucleic acid sequence. "Substantially complementary," as used herein, refers to a degree of complementarity of at least 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, 97%, 98%, 99%, or 100% over a region of 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 30 , 35, 40, 45, 50, or more nucleotides, or refers to two nucleic acids that hybridize under stringent conditions. Sequence identity, for example for the purpose of assessing percent complementarity, can be determined with any suitable alignment algorithm, including, but not limited to, the Needleman-Wunsch algorithm (see, for example, the EMBOSS Needle Aligner). available at www.ebi.ac.uk / Tools / psa / emboss needle / nucleotide.html, optionally with default settings), the BLAST algorithm (see, for example, the BLAST alignment tool available at blast.ncbi.nlm. nih.gov / Blast.cgi, optionally with default settings), or the Smith-Waterman algorithm (see, for example, the EMBOSS Water aligner, available at www.ebi.ac.uk / Tools / psa / emboss_water / nucleotide. html, optionally with default settings). Optimal alignment can be evaluated by using the appropriate parameters of a chosen algorithm, including default parameters. In general, "stringent conditions" for hybridization refer to conditions in which a nucleic acid having complementarity to a target sequence hybridizes predominantly to a target sequence and substantially does not hybridize to non-target sequences. Stringent conditions are generally sequence dependent and vary depending on a number of factors. In general, the longer the sequence, the higher the temperature at which the sequence specifically anneals to its target sequence. Non-limiting examples of stringent conditions are described in detail in Tijssen (1993), Laboratory Techniques In Biochemistry And Molecular Biology-Hybridization With Nucleic Acid Probes Part I, Second Chapter “OverView of principles of PRRn / n / Lznz / q / Yii - 22 hybridization and the strategy of nucleic acid probe assay”, Elsevier, N.Y. As used herein, "expression" refers to the process by which a polynucleotide is transcribed from a DNA template (such as into an mRNA or other RNA transcript) and / or the process by which a Transcribed mRNA is subsequently translated into peptides, polypeptides, or proteins. The encoded transcripts and polypeptides may be collectively referred to as a "gene product." If the polynucleotide is derived from genomic DNA, expression may include splicing of the mRNA in a eukaryotic cell. The terms "polypeptide", "peptide" and "protein" are used interchangeably herein to refer to amino acid polymers of any length. The polymer can be linear or branched, can comprise modified amino acids, and can be interrupted by something other than amino acids. The terms also encompass an amino acid polymer that has been modified, for example, by disulfide bond formation, glycosylation, lipidation, acetylation, phosphorylation, or any other manipulation, such as conjugation with a tagging component. As used herein, the term "amino acid" includes natural and / or unnatural or synthetic amino acids, including glycine and the D or L optical isomers, and amino acid analogs and peptidomimetics. As used herein, the term "about" is used synonymously with the term "approximately." Illustratively, the use of the term "about" with respect to a quantity indicates that the values ​​are slightly outside the quoted values, for example, plus or minus 0.1% to 10%. The term "biologically pure culture" or "substantially pure culture" refers to a culture of bacterial species described herein that does not contain other bacterial species in amounts sufficient to interfere with replication of the culture or to be detected by normal bacteriological techniques. "Plant productivity" generally refers to any aspect of a plant's growth or development that is a reason why the plant is grown. In the case of food crops, such as cereals or vegetables, "plant productivity" may refer to the yield of cereals or fruits harvested from a particular crop. As used herein, improved plant productivity generally refers to improvements in the yield of grain, fruit, flowers, or other parts of harvested plants. PRRn / n / Lznz / q / YL -23 for various purposes, improvements in the growth of plant parts, including stems, leaves and roots, promotion of plant growth, maintenance of high chlorophyll content in leaves, increase in the number of fruits or seeds, increase of the unit weight of fruits or seeds, reduction of the emission of N02 due to the reduced use of nitrogenous fertilizers and similar improvements of the growth and development of the plants. Microbes in and around food crops can influence the characteristics of those crops. Plant traits that can be influenced by microbes include: yield (eg, grain production, biomass generation, fruit development, flower set); nutrition (eg nitrogen, phosphorus, potassium, iron, micronutrient acquisition); abiotic stress management (eg drought tolerance, salt tolerance, heat tolerance); and biotic stress management (eg, pests, weeds, insects, fungi, and bacteria). Strategies to alter crop traits include: increasing concentrations of key metabolites; change the temporal dynamics of the influence of microbes on key metabolites; link the production / degradation of microbial metabolites with new environmental signals; reduce negative metabolites; and improve the balance of underlying metabolites or proteins. As used herein, a "control sequence" refers to an operator, promoter, silencer, or terminator. As used herein, "in planta" can refer to in the plant, on the plant, or closely associated with the plant, depending on the context of use (eg, endophytic, epiphytic, or rhizospheric associations). The plant may comprise plant parts, tissue, leaves, roots, root hairs, rhizomes, stems, seeds, ovules, pollen, flowers, fruits, etc. In some embodiments, the natural or endogenous control sequences of genes of the present disclosure are replaced with one or more intrageneric control sequences. As used herein, "introduced" refers to introduction through modern biotechnology, and not a naturally occurring introduction. In some embodiments, the bacteria of the present disclosure have been modified so that they are not naturally occurring bacteria. In some embodiments, the bacteria of the present disclosure are present in the plant in an amount of at least 103 cfu, 104 cfu, 105 cfu, 106 PRRn / n / Lznz / q / Yii - 24 cfu, 107 cfu, 108 cfu, 109 cfu, 1010 cfu, 1011 cfu, or 1012 cfu per gram of fresh or dry weight of the plant. In some embodiments, the bacteria of the present disclosure are present in the plant in an amount of at least about 103 cfu, about 104 cfu, about 105 cfu, about 106 cfu, about 107 cfu, about 108 cfu , about 109 cfu, about 1010 cfu, about 1011 cfu, or about 1012 cfu per gram of fresh or dry weight of the plant. In some embodiments, the bacteria of the present disclosure are present in the plant in an amount of at least 103 to 109, 103 to 107, 103 to 105, 105 to 109, 105 to 107, 106 to 1010, 106 to 107 cfu per gram of fresh or dry weight of the plant. Fertilizers and exogenous nitrogen of the present disclosure may comprise the following nitrogen-containing molecules: ammonium, nitrate, nitrite, ammonia, glutamine, etc. Nitrogen sources herein may include anhydrous ammonia, ammonium sulfate, urea, diammonium phosphate, urea form, monoammonium phosphate, ammonium nitrate, nitrogenous solutions, calcium nitrate, potassium nitrate, sodium nitrate, etc As used herein, "exogenous nitrogen" refers to readily available non-atmospheric nitrogen in the soil, field, or growing medium that is present under non-nitrogen-limiting conditions, including ammonia, ammonium, nitrate, nitrite, urea , uric acid, ammonium acids, etc. As used herein, "non-limiting nitrogen conditions" refers to non-atmospheric nitrogen available in the soil, field, or environment at concentrations greater than about 4 mM nitrogen, as described by Kant et al. (2010. J. Exp. Biol. 62(4):1499-1509), which is incorporated herein by reference. As used herein, an "intergeneric microorganism" is a microorganism formed by the deliberate combination of genetic material originally isolated from organisms of different taxonomic genera. An “intergeneric mutant” and “intergeneric microorganism” may be used interchangeably. An illustrative "intergeneric microorganism" includes a microorganism that contains a mobile genetic element, which was first identified in a microorganism of a different genus than the recipient microorganism. Further explanations can be found, among others, in 40 CFR § 725.3. In some aspects, the microbes described herein are "non-intergeneric", meaning that the microbes are not intergeneric. PRRn / n / Lznz / q / Yi -25As used herein, an “intrageneric microorganism” is a microorganism formed by the deliberate combination of genetic material originally isolated from organisms of the same taxonomic genus. An "intrageneric mutant" and "intrageneric microorganism" may be used interchangeably. As used herein, "introduced genetic material" means genetic material that is added to and remains a component of the recipient's genome. As used herein, in the context of non-intergeneric microorganisms, the term "remodeled" is used synonymously with the term "genetically modified." Consequently, a “non-intergeneric remodeled microorganism” has a synonymous meaning with “non-intergeneric genetically modified microorganism” and will be used interchangeably. In addition, the description may refer to a "genetically modified strain" or a "genetically modified derivative" or a "genetically modified non-intergeneric microbe", these terms are used synonymously with "remodeled strain" or "remodeled derivative" or "microbe". remodeled non-intergeneric”. In some embodiments, the nitrogen assimilation and fixation genetic regulatory network comprises polynucleotides encoding genes and non-coding sequences that direct, modulate and / or regulate microbial nitrogen assimilation and / or fixation, and may comprise polynucleotide sequences from the nif group. (for example, nifk, nifB, nífC,......nifZ), polynucleotides encoding nitrogen-regulating protein C, polynucleotides encoding nitrogen-regulating protein B, polynucleotide sequences from the gln group (for example, glnk and glnD), draT, and permeases / ammonia transporters. In some cases, the Nif group may comprise NifB, NifH, NifD, NifK, NifE, NifN, NifX, hesa, and NifV. In some cases, the Nif group may comprise a subset of NifB, NifH, NifD, NifK, NifE, NifN, NifX, hesa, and NifV. In some embodiments, the fertilizer of the present description comprises at least 5%, 6%, 7%, 8%, 9%, 10%, 11%, 12%, 13%, 14%, 15%, 16%, 17 %, 18%, 19%, 20%, 21%, 22%, 23%, 24%, 25%, 26%, 27%, 28%, 29%, 30%, 31%, %, 33%, 34 %, 35%, 36%, 37%, 38%, 39%, 40%, 41%, 42%, 43%, 44%, 45%, %, 47%, 48%, 49%, 50%, 51 %, 52%, 53%, 54%, 55%, 56%, 57%, 58%, 59%, %, 61%, 62%, 63%, 64%, 65%, 66%, 67%, 68 %, 69%, 70%, 71%, 72%, 73%, %, 75%, 76%, 77%, 78%, 79%, 80%, 81%, 82%, 83%, 84%, 85 %, 86%, 87%, %, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% Nitrogen PRRn / n / Lznz / q / Yii by weight. -26 In some embodiments, the fertilizer of the present description comprises at least about 5%, about 6%, about 7%, about 8%, about 9%, about 10%, about 11%, about about 12%, about 13%, about 14%, about 15%, about 16%, about 17%, about 18%, about 19%, about 20%, about 21%, about about 22%, about 23%, about 24%, about 25%, about 26%, about 27%, about 28%, about 29%, about 30%, about 31%, about about 32%, about 33%, about 34%, about 35%, about 36%, about 37%, about 38%, about 39%, about 40%, about 41%, about about 42%, about 43%, about 44%, about 45%, about 46%, about 47%, about 48%, about 49%, about 50%, about 51%, about about 52%, about 53%, about 54%, about 55%, about 56%, about 57%, about 58%, about 59%, about 60%, about 61%, about about 62%, about 63%, about 64%, about 65%, about 66%, about 67%, about 68%, about 69%, about 70%, about 71%, about about 72%, about 73%, about 74%, about 75%, about 76%, about 77%, about 78%, about 79%, about 80%, about 81%, about about 82%, about 83%, about 84%, about 85%, about 86%, about 87%, about 88%, about 89%, about 90%, about 91%, about about 92%, about 93%, about 94%, about 95%, about 96%, about 97%, about 98%, or about 99% nitrogen by weight. In some embodiments, the fertilizer of the present description comprises about 5% to 50%, about 5% to 75%, about 10% to 50%, about 10% to 75%, about 15% to 50% , about 15% to 75%, about 20% to 50%, about 20% to 75%, about 25% to 50%, about 25% to 75%, about 30% to 50%, about 30% to 75%, about 35% to 50%, about 35% to 75%, about 40% to 50%, about 40% to 75%, about 45% to 50%, about 45 % to 75%, or about 50% to 75% nitrogen by weight. In some embodiments, the increase in nitrogen fixation and / or the production of 1% or more of the nitrogen in the plant is measured relative to control plants, which have not been exposed to the bacteria of the present disclosure. All increases or decreases in bacteria are measured relative to PRRn / n / Lznz / q / Yi - 27 control bacteria. All increases or decreases in plants are measured relative to control plants. As used herein, a "constitutive promoter" is a promoter that is active under most conditions and / or during most stages of development. There are several advantages of using constitutive promoters in expression vectors used in biotechnology, such as: high level production of proteins used to select transgenic cells or organisms; high level of expression of reporter proteins or punctual markers, allowing easy detection and quantification; high level of production of a transcription factor that is part of a regulatory transcription system; production of compounds that require ubiquitous activity in the body; and production of compounds that are required during all stages of development. Illustrative non-limiting constitutive promoters include, CaMV 35S promoter, opine promoters, ubiquitin promoter, alcohol dehydrogenase promoter, etc. As used herein, a "non-constitutive promoter" is a promoter that is active under certain conditions, in certain cell types, and / or during certain stages of development. For example, tissue-specific, tissue-preferred, cell-type-specific, cell-type-preferred, inducible promoters, and promoters under developmental control are non-constitutive promoters. Examples of promoters under developmental control include promoters that initiate transcription preferentially in certain tissues. As used herein, the "inducible" or "repressible" promoter is a promoter that is under the control of chemical or environmental factors. Examples of environmental conditions that can affect transcription by inducible promoters include anaerobic conditions, certain chemicals, the presence of light, acidic or basic conditions, etc. As used herein, a "tissue-specific" promoter is a promoter that initiates transcription only in certain tissues. Unlike constitutive gene expression, tissue-specific expression is the result of various levels of interplay of gene regulation. As such, it is sometimes preferred in the art to use promoters from homologous or closely related species to achieve efficient and reliable expression of transgenes in particular tissues. This is one of the main reasons for the large number of tissue-specific promoters isolated from particular tissues found in rRRn / n / Lznz / q / Yi. -28both in the scientific and patent literature. As used herein, the term "operably linked" refers to the association of nucleic acid sequences into a single nucleic acid fragment such that the function of one is regulated by the other. For example, a promoter is operably linked to a coding sequence when it is capable of regulating expression of that coding sequence (ie, the coding sequence is under the transcriptional control of the promoter). Coding sequences can be operatively linked to regulatory sequences in a sense or antisense orientation. In another example, the complementary RNA regions of the disclosure may be operably linked, directly or indirectly, 5' to the target mRNA, or 3' to the target mRNA, or within the target mRNA, or a first complementary region is found at 5' and its 3' complement of the target mRNA. In some aspects, "applying multiple non-intergeneric bacteria to the plant" includes any means by which the plant (including plant parts such as a seed, root, stem, tissue, etc.) comes into contact (i.e. that is, it is exposed) with such bacteria at any stage of the plant's life cycle. Accordingly, "applying multiple non-intergeneric bacteria to the plant" includes any of the following means of exposing the plant (including plant parts such as a seed, root, stem, tissue, etc.) to such bacteria: spraying on the plant, drip onto the plant, apply as a seed cover, apply to a field that will later be seeded, apply to a field already seeded, apply to a field with adult plants, etc. As used herein "MRTN" is an acronym for maximum nitrogen yield and is used as an experimental treatment in the Examples. The MRTN was developed by Towa State University and information can be found at: cnrc.agron.iastate.edu / . The MRTN is the nitrogen rate at which the net economic return from nitrogen application is maximized. The approach to calculating the MRTN is a regional approach to developing corn nitrogen rate guidelines in individual states. Nitrogen rate test data were evaluated for Illinois, Iowa, Michigan, Minnesota, Ohio, and Wisconsin, where an adequate number of research trials were available for corn plantings after soybeans. of the corn. The tests were carried out with nitrogen applied in spring, as a lateral fertilizer, PRRn / n / Lznz / q / Yii -29 or in a crevice prior to side planting / fertilizing, and sites were not irrigated except as listed for Wisconsin irrigated sands. MRTN was developed by Iowa State University due to apparent differences in methods for determining suggested nitrogen rates required for corn production, misperceptions related to nitrogen rate guidelines, and application rate concerns. By calculating the MRTN, practitioners can determine the following: (1) the nitrogen rate at which the net economic return from nitrogen application is maximized, (2) the optimal economic nitrogen rate, which is the point where the last nitrogen increment returns a yield increase large enough to pay for the additional nitrogen, (3) the value of corn kernel increase attributed to nitrogen application, and peak yield, which is the yield where more nitrogen application does not result in increased corn yield. Therefore, the MRTN calculations provide practitioners with the means to maximize corn yields in different regions while maximizing the financial gains from nitrogen applications. The term mmol is an abbreviation for millimole, which is one thousandth (10-3) of a mole, abbreviated herein as mole. As used herein, the terms "microorganism" or "microbe" are to be construed broadly. These terms, which are used interchangeably, include, but are not limited to, the two prokaryotic domains, Bacteria and Archaea. The term can also encompass eukaryotic fungi and protists. The term “microbial consortia” or “microbial consortium” refers to a subset of a microbial community of individual microbial species, or strains of a species, that can be described as carrying out a common function, or can be described as participating in , or that lead to, or correlate with, a recognizable parameter, such as a phenotypic trait of interest. The term "microbial community" means a group of microbes comprising two or more species or strains. Unlike microbial consortia, a microbial community does not have to carry out a common function, or does not have to participate in, lead to, or correlate with a recognizable parameter, such as a phenotypic trait of interest. As used herein, "isolate", "isolated", "isolated microbe" and similar terms are intended to mean that one or more microorganisms PRRn / n / Lznz / q / Yi -30 have separated from at least one of the materials with which it is associated in a particular environment, (eg, soil, water, plant tissue, etc.). Therefore, an "isolated microbe" does not exist in its natural environment; rather, it is through the various techniques described herein that the microbe has been removed from its natural environment and placed in an unnatural state of existence. Thus, the isolate or microbe isolate may exist as, for example, a biologically pure culture or as spores (or other forms of the strain). In some aspects, the isolated microbe may be associated with an acceptable carrier, which may be an agriculturally acceptable carrier. In certain aspects of the description, the isolated microbes exist as "biologically pure isolated cultures." One skilled in the art will appreciate that an isolated and biologically pure culture of a particular microbe indicates that said culture is substantially free of other living organisms and contains only the individual microbe in question. The culture may contain varying concentrations of said microbe. This description notes that isolated and biologically pure microbes often "necessarily differ from less pure or impure materials." See, for example, In re Bergstrom, 427 F.2d 1394, (CCPA 1970) (describing purified prostaglandins), see also, In re Bergy, 596 F.2d 952 (CCPA 1979) (describing purified microbes), see also, ParkeDavis & Co. v. H.K. Mulford & Co., 189 F. 95 (S.D.N.Y. 1911) (Learned Hand describing purified adrenaline), asserted in part, revised in part, 196 F. 496 (2d Cir. 1912), each of which is incorporated into hereby by reference. Furthermore, in some aspects, the disclosure provides certain quantitative measures of concentration, or purity limitations, that must be found within a biologically pure, isolated microbial culture. The presence of these purity values, in certain embodiments, is an additional attribute that distinguishes the microbes described herein from microbes that exist in a natural state. See, for example, Merck & Co. v. Clin Mathieson Chemical Corp., 253 F.2d 156 (4th Cir. 1958) (discussing purity limitations for microbially produced vitamin B12), which is incorporated herein by reference. As used herein, "individual isolates" shall be understood as a composition or culture, comprising a predominance of a single genus, species, or strain of microorganism, after separation from one or more other microorganisms. PRRn / n / Lznz / q / Yi -31 The microbes of the present disclosure may include spores and / or vegetative cells. In some embodiments, the microbes of the present disclosure include microbes in a viable but non-culturable (VBNC) state. As used herein, "spore" or "spores" refer to structures produced by bacteria and fungi that are adapted to survive and disperse. Spores are generally characterized as inactive structures; however, the spores can be differentiated through the germination process. Germination is the differentiation of spores into vegetative cells that are capable of metabolic activity, growth, and reproduction. Germination of a single spore results in a single fungal or bacterial vegetative cell. Fungal spores are units of asexual reproduction and, in some cases, are necessary structures in fungal life cycles. Bacterial spores are structures for survival conditions that are not normally conducive to the survival or growth of vegetative cells. As used herein, "microbial composition" refers to a composition comprising one or more microbes of the present disclosure. In some embodiments, a microbial composition is administered to plants (including various plant parts) and / or to agricultural fields. As used herein, “carrier”, “acceptable carrier” or “agriculturally acceptable carrier” refers to a diluent, adjuvant, excipient or vehicle with which the microbe can be administered, which does not adversely affect the microbe. Regulation of nitrogen fixation In some cases, the nitrogen fixation pathway can act as a target for genetic modification and optimization. One trait that can be targeted for regulation by the methods described herein is nitrogen fixation. Nitrogen fertilizer is the biggest operating expense on a farm and the biggest driver of higher yields in row crops like corn and wheat. Microbial products that can provide renewable forms of nitrogen in non-leguminous crops are described herein. While some endophytes have the genetics necessary to fix nitrogen in pure crops, the fundamental technical challenge is that wild-type endophytes of cereals and grasses fail to fix nitrogen in fertilized fields. Chemical fertilizer application and residual nitrogen levels in field soils signal the microbe to shut down the biochemical pathway for nitrogen fixation. PRRn / n / Lznz / q / Yii -32 Changes in the transcriptional and posttranslational levels of the components of the nitrogen fixation regulatory network may be beneficial for the development of a microbe capable of fixing and transferring nitrogen to maize in the presence of fertilizers. To that end, we describe herein the Host-Microbe Evolution (HoME) technology to precisely develop regulatory networks and elicit novel phenotypes. Exclusive and proprietary libraries of nitrogen-fixing endophytes isolated from maize are also described herein, along with extensive omics data surrounding the interaction of microbes and the host plant under different environmental conditions such as stress and nitrogen excess. In some embodiments, this technology enables precision evolution of the endophyte genetic regulatory network to produce microbes that actively fix nitrogen even in the presence of fertilizers in the field. Also described herein are evaluations of the technical potential of evolving microbes that colonize maize root tissues and produce nitrogen for fertilized plants and evaluations of endophyte compatibility with standard formulation practices and diverse soils to determine the feasibility of integrating microbes into modern nitrogen management strategies. In order to use elemental nitrogen (N) for chemical synthesis, life forms combine nitrogen gas (N2) available in the atmosphere with hydrogen in a process known as nitrogen fixation. Due to the energy-intensive nature of biological nitrogen fixation, diazotrophs (bacteria and archaea that fix atmospheric nitrogen gas) have evolved a sophisticated and tight regulation of the nif gene cluster in response to ambient oxygen and available nitrogen. The nif genes encode enzymes involved in nitrogen fixation (such as the nitrogenase complex) and proteins that regulate nitrogen fixation. Shamseldin (2013. Global J. Biotechnol. Biochem. 8(4):8494) provides detailed descriptions of nif genes and their products, and is incorporated herein by reference. Methods of producing a plant with an improved trait are described herein comprising isolating bacteria from a first plant, introducing genetic variation into a gene from the isolated bacterium to increase nitrogen fixation, exposing a second plant to the variant bacterium, isolating bacteria from the second plant having an improved trait over the first plant, and repeating the steps with the bacteria isolated from the second plant. In Proteobacteria, the regulation of nitrogen fixation centers on the PRRn / n / Lznz / q / Yii -33 o54-dependent enhancer-binding protein NifA, the positive transcriptional regulator of the nif group. Intracellular levels of active NifA are controlled by two key factors: transcription of the nifLA operon and inhibition of NifA activity via protein-protein interaction with NifL. Both processes respond to intracellular glutamine levels through the PII protein signaling cascade. This cascade is mediated by GlnD, which directly senses glutamine and catalyzes the uridylation or deuridylation of two PII regulatory proteins, GlnB and GlnK, in response to the absence or presence, respectively, of bound glutamine. Under nitrogen excess conditions, unmodified GlnB signals inactivation of the nifLA promoter. However, under nitrogen-limiting conditions, GlnB is post-translationally modified, which inhibits its activity and leads to transcription of the nifLA operon. In this way, nifLA transcription is tightly controlled in response to environmental nitrogen through the PII protein signaling cascade. At the post-translational level of NifA regulation, GlnK inhibits the NifL / NifA interaction in a manner that depends on the total level of free GlnK within the cell. NifA is transcribed from the nifLA operon, whose promoter is activated by phosphorylated NtrC, another o54-dependent regulator. The phosphorylation state of NtrC is mediated by the histidine kinase NtrB, which interacts with desuridylated GlnB but not with uridylated GlnB. Under nitrogen excess conditions, a high intracellular level of glutamine leads to desuridylation of GlnB, which then interacts with NtrB to turn off its phosphorylation activity and activate its phosphatase activity, resulting in dephosphorylation of NtrC and promoter inactivation. nifLA. However, under nitrogen-limited conditions, a low level of intracellular glutamine causes uridylation of GlnB, which inhibits its interaction with NtrB and allows phosphorylation of NtrC and transcription of the nifLA operon. In this way, nifLA expression is tightly controlled in response to environmental nitrogen through the PII protein signaling cascade. nifA, ntrB, ntrC and glnB are all genes that can be mutated in the methods described herein. These processes may also respond to intracellular or extracellular levels of ammonia, urea, or nitrates. NifA activity is also post-translationally regulated in response to environmental nitrogen, most typically through NifL-mediated inhibition of NifA activity. In general, the interaction of NifL and NifA is influenced PRRn / n / Lznz / q / Yi -34 by the PII protein signaling cascade through GlnK, although the nature of the interactions between GlnK and NifL / NifA varies significantly between diazotrophs. In Klebsiella pneumoniae, both forms of GlnK inhibit the NifL / NifA interaction, and the interaction between GlnK and NifL / NifA is determined by the total level of free GlnK within the cell. Under conditions of excess nitrogen, desuridylated GlnK interacts with the ammonium transporter AmtB, which serves to block ammonium uptake by AmtB and to sequester GlnK in the membrane, allowing NifL inhibition of NifA. On the other hand, in Azotobacter vinelandíí, interaction with desuridylated GlnK is required for NifL / NifA interaction and inhibition of NifA, while uridylation of GlnK inhibits its interaction with NifL. In diazotrophs lacking the nífL gene, there is evidence that NifA activity is directly inhibited through interaction with desuridylated forms of GlnK and GlnB under conditions of excess nitrogen. In some bacteria, the Nif group may be regulated by glnR, and furthermore, in some cases, this may involve downregulation. Regardless of the mechanism, post-translational inhibition of NifA is an important regulator of the nif group in most known diazotrophs. In addition, nífL, amtB, glnK and glnR are genes that can be killed in the methods described herein. In addition to regulating the transcription of the níf gene cluster, many diazotrophs have evolved a mechanism for direct post-translational modification and inhibition of the nitrogenase enzyme itself, known as nitrogenase disruption. This is mediated by ADP-ribosylation of the Fe protein (NifH) under conditions of excess nitrogen, which disrupts its interaction with the MoFe protein complex (NifDK) and abolishes nitrogenase activity. DraT catalyzes ADP ribosylation of the Fe protein and nitrogenase disruption, whereas DraG catalyzes ADP ribose removal and nitrogenase reactivation. As with nifLA transcription and NifA inhibition, nitrogenase disruption is also regulated through the PII protein signaling cascade. Under nitrogen excess conditions, desuridylated GlnB interacts with and activates DraT, while desuridylated GlnK interacts with DraG and AmtB to form a complex that sequesters DraG in the membrane. Under nitrogen-limited conditions, the uridylated forms of GlnB and GlnK do not interact with DraT and DraG, respectively, resulting in inactivation of DraT and diffusion of DraG into the Fe protein, where it removes ADP-ribose and activates nitrogenase. Methods PRRn / n / Lznz / q / Yii -35 described herein also contemplate the introduction of genetic variation in the nífH, nífD, nífK and draT genes. Although some endophytes have the ability to fix nitrogen in vitro, genetics are often silenced in the field by high levels of exogenous chemical fertilizers. Exogenous nitrogen detection can be decoupled from nitrogenase enzyme expression to facilitate nitrogen fixation in the field. Enhancement of the overall nitrogenase activity over time serves to increase the production of nitrogen for utilization by the crop. Specific targets for genetic variation to facilitate nitrogen fixation in the field using the methods described herein include one or more genes selected from the group consisting of nífA, nifL, ntrB, ntrC, glnA, glnB, glnK , draT, amtB, glnD, glnE, nifJ, nifH, nifD, nifK, nifY, nifE, nifN, nifU, nifS, nifV, nifW, nifZ, nifM, nifF, nifB, and nifQ. An additional target for genetic variation to facilitate nitrogen fixation in the field using the methods described herein is the NifA protein. The NifA protein is typically the activator of nitrogen fixation gene expression. Increased NifA production (either constitutively or during a high ammonia condition) bypasses the natural pathway of ammonia sensing. In addition, the reduction in the production of NifL proteins, a known inhibitor of NifA, also results in an increase in the level of freely active NifA. Furthermore, increasing the level of transcription of the nifAL operon (either constitutively or during a high ammonia condition) also results in a higher total level of NifA proteins. The high level of expression of nifAL is achieved by altering the promoter itself or by reducing the expression of NtrB (part of the signaling cascade of ntrB and ntrC that would originally cause the interruption of the nifAL operon during high nitrogen conditions). The high level of NifA achieved by these or other methods described herein increases the nitrogen fixation activity of endophytes. Another target for genetic variation to facilitate nitrogen fixation in the field using the methods described herein is the PII GlnD / GlnB / GlnK signaling cascade. The intracellular glutamine level is detected via the PII GlnD / GlnB / GlnK signaling cascade. Active site mutations in GlnD that abolish the uridylyl scavenging activity of GlnD disrupt the nitrogen sensing cascade. In addition, the reduction of the GlnB concentration causes a short circuit in the detection cascade of PRRn / n / Lznz / q / YL -36 glutamine. These mutations "trick" cells into sensing a limited nitrogen state, thereby increasing the level of nitrogen fixation activity. These processes may also respond to intracellular or extracellular levels of ammonia, urea, or nitrates. The amtB protein is also a target for genetic variation to facilitate carpal nitrogen fixation using the methods described herein. Ammonia uptake from the environment can be reduced by decreasing the expression level of the amtB protein. Without intracellular ammonia, the endophyte cannot detect the high level of ammonia, which prevents the down-regulation of nitrogen-fixing genes. Any ammonia that manages to enter the intracellular compartment is converted to glutamine. The intracellular glutamine level is the main currency of nitrogen detection. The decreased level of intracellular glutamine prevents cells from detecting high levels of ammonia in the environment. This effect can be achieved by increasing the expression level of glutaminase, an enzyme that converts glutamine to glutamate. In addition, intracellular glutamine can also be reduced by decreasing glutamine synthase (an enzyme that converts ammonia to glutamine). In diazotrophs, fixed ammonia is rapidly assimilated into glutamine and glutamate for use in cellular processes. Disruptions in ammonia uptake may allow diversion of fixed nitrogen for export from the cell as ammonia. Fixed ammonia is predominantly assimilated into glutamine by glutamine synthetase (GS), encoded by glnA, and subsequently into glutamine by glutamine oxoglutatarate aminotransferase (GOGAT). In some examples, glnS encodes a glutamine synthetase. GS is post-translationally regulated by GS adenylyl transferase (GlnE), a glnE-encoded bifunctional enzyme that catalyzes the adenylylation and deadenylation of GS through the activity of its adenylyl transferase (AT) and adenylyl scavenging (AR) domains. , respectively. Under nitrogen-limiting conditions, glnA is expressed and the AR domain of GlnE desadinylyls GS, allowing it to be active. Under nitrogen excess conditions, glnA expression is disrupted and the AT domain of GlnE is allosterically activated by glutamine, causing adenylation and inactivation of GS. In addition, the draT gene can also be a target for genetic variation to facilitate nitrogen fixation in the field using the methods described herein. Once the cell produces the enzymes fixing PRRn / n / Lznz / q / Yii -37 nitrogen, nitrogenase disruption represents another level at which the cell down-regulates fixation activity under high-nitrogen conditions. This disruption could be removed by lowering the expression level of DraT. Methods to impart novel microbial phenotypes can be performed at the transcriptional, translational, and post-translational levels. The transcriptional level includes changes to the promoter (such as changing sigma factor affinity or binding sites for transcription factors, including deletion of all or part of the promoter) or changes to sigma terminators and attenuators. the transcript. The translational level includes changes in ribosome binding sites and changes in mRNA degradation signals. The post-translational level includes mutating the active site of an enzyme and changing protein-protein interactions. These changes can be achieved in multiple ways. Reduction of the expression level (or complete knockdown) can be achieved by exchanging the natural ribosome binding site (RBS) or promoter with one with less resistance / efficiency. ATG start sites can be interchanged with a GTG, TTG or CTG start codon, resulting in reduced translational activity of the coding region. Complete knockdown of expression can be accomplished by inactivating (deleting) the coding region of a gene. The shift of the open reading frame (ORE) will likely result in a premature stop codon along the ORE, thereby creating a non-functional truncated product. Insertion of in-frame stop codons will similarly create a non-functional truncated product. Addition of a degradation tag at the N- or C-termini can also be done to reduce the effective concentration of a particular gene. Rather, the expression level of the genes described herein can be achieved through the use of a stronger promoter. To ensure high promoter activity during a high nitrogen condition (or any other condition), a genome-wide transcription profile could be obtained under a high nitrogen condition and active promoters with a high nitrogen level can be chosen. desired transcription from that data set to replace the weak promoter. Weak start codons can be exchanged with an ATG start codon for better translation initiation efficiency. Weak ribosome binding sites (RBSs) can also be exchanged with a different RBS rRRn / n / Lznz / q / Yi -38 with higher translation initiation efficiency. In addition, site-specific mutagenesis can also be performed to alter the activity of an enzyme. The increased level of nitrogen fixation that occurs in a plant can lead to a reduction in the amount of chemical fertilizer needed for crop production and reduce greenhouse gas emissions (for example, nitrous oxide). Generation of bacterial populations bacteria isolation The microbes useful in the methods and compositions described herein can be obtained by extracting microbes from natural plant tissues or surfaces. The microbes can be obtained by crushing seeds to isolate the microbes. The microbes can be obtained by planting seeds in various soil samples and recovering the microbes from the tissues. In addition, microbes can be obtained by inoculating plants with exogenous microbes and determining which microbes appear in plant tissues. Non-limiting examples of plant tissues may include a seed, seedling, leaf, cutting, plant, bulb, or tuber. One method of obtaining microbes can be by isolating bacteria from soils. The bacteria can be collected from various types of soil. In some examples, the soil may be characterized by traits such as high or low fertility, moisture levels, mineral levels, and various cultivation practices. For example, the soil may be part of a crop rotation in which different crops are planted on the same soil in successive planting seasons. Sequential growing of different crops on the same soil can prevent disproportionate depletion of certain minerals. The bacteria can be isolated from plants growing in selected soils. Seedlings can be harvested at 2-6 weeks of growth. For example, at least 400 isolates can be collected in one harvest round. Soil and plant types reveal the plant phenotype and conditions, allowing for subsequent enrichment of certain phenotypes. Microbes can be isolated from plant tissues to assess microbial traits. Parameters for processing tissue samples can be varied to isolate different types of associative microbes, such as rhizospheric bacteria, epiphytes, or endophytes. Isolates can be grown in nitrogen-free media to enrich for nitrogen-fixing bacteria. óRRn / n / Lznz / q / Yi -39 Alternatively, microbes can be obtained from global strain banks. In planta analyzes are carried out to evaluate microbial traits. In some embodiments, plant tissue can be processed for detection by high throughput processing for DNA and RNA. In addition, non-invasive measures can be used to assess plant characteristics, such as colonization. Measurements in wild microbes can be obtained for each plant. Measurements of wild microbes in the field can also be obtained by mean throughput methods. Measurements can be made successively over time. A model plant system may be used including, but not limited to, Setaria. Microbes in a plant system can be screened for by transcriptional profiling of a microbe in a plant system. Examples of detection through transcriptional profiling are the use of quantitative polymerase chain reaction (qPCR) methods, molecular barcoding for transcript detection, next-generation sequencing, and labeling of microbes with fluorescent markers. Impact factors can be measured to assess colonization in the greenhouse, including but not limited to microbiome, abiotic factors, soil conditions, oxygen, moisture, temperature, inoculum conditions, and root location. Nitrogen fixation can be assessed in bacteria by measuring 15N gas / fertilizer (dilution) with IRMS or NanoSIMS, as described herein NanoSIMS is high resolution secondary ion mass spectrometry. The NanoSIMS technique is a way to investigate the chemical activity of biological samples. The catalysis of the reduction-oxidation reactions that drive the metabolism of microorganisms can be investigated at the cellular, subcellular, molecular, and elemental levels. NanoSIMS can provide a high spatial resolution of more than 0.1 pm. NanoSIMS can detect using isotope tracers such as 13C, 15N and 180. Therefore, NanoSIMS can be used for nitrogen chemical activity in the cell. Automated greenhouses can be used for plant analyses. Plant metrics in response to microbial challenge include, but are not limited to, biomass, chloroplast analysis, CCD camera, volumetric tomography measurements. One way to enrich a population of microbes is by genotype. For example, a polymerase chain reaction (PCR) assay with one primer PRRn / n / Lznz / q / Yii -40 directed or a specific primer. Primers designed for the nifH gene can be used to identify diazotrophs because diazotrophs express the nifH gene in the process of nitrogen fixation. A microbial population can also be enriched by culture-independent single cell approaches and chemotaxis-guided isolation approaches. Alternatively, targeted isolation of microbes can be accomplished by culturing the microbes in selection media. Premeditated approaches to enriching microbial populations for desired traits that can be guided by bioinformatics data are described herein. Enrichment of Nitrogen-Fixing Microbes Using Bioinformatics Bioinformatics tools can be used to identify and isolate plant growth promoting rhizobacteria (PGPR), which are selected based on their ability to perform nitrogen fixation. Microbes with high nitrogen-fixing capacity can promote favorable traits in plants. Bioinformatics modes of analysis for PGPR identification include, but are not limited to, genomics, metagenomics, targeted isolation, gene sequencing, transcriptome sequencing, and modeling. Genomic analysis can be used to identify PGPR and confirm the presence of mutations with next-generation sequencing methods, as described herein, and microbial version control. Metagenomics can be used to identify and isolate PGPR by using a prediction algorithm for colonization. The metadata can also be used to identify the presence of a genetically modified strain in environmental and greenhouse samples. Transcriptome sequencing can be used to predict genotypes leading to PGPR phenotypes. Additionally, transcriptomic data is used to identify promoters to alter gene expression. Transcriptomic data can be analyzed in conjunction with whole genome sequence (WGS) to generate models of metabolism and gene regulatory networks. domestication of microbes Microbes isolated from nature can undergo a domestication process where the microbes are converted into a form that can be identified and traced genetically. One way to tame a microbe is PRRn / n / Lznz / q / Yii -41 genetically modify it so that it has resistance to antibiotics. The process of genetic modification for antibiotic resistance can begin by determining the antibiotic susceptibility of the wild-type microbial strain. If the bacteria are sensitive to the antibiotic, then the antibiotic may be a good candidate for genetic modification for antibiotic resistance. Subsequently, an antibiotic resistant gene or a counterselectable suicide vector can be incorporated into the genome of a microbe using recombinant methods. A counterselectable suicide vector may consist of a deletion of the gene of interest, a selectable marker, and the sacB counterselectable marker. Counterselection can be used to exchange wild-type microbial DNA sequences with antibiotic-resistant genes. A medium throughput method can be used to test multiple microbes simultaneously, allowing for domestication in parallel. Alternative methods of domestication include the use of homing nucleases to prevent deletion of suicide vector sequences or to obtain intermediate vector sequences. DNA vectors can be introduced into bacteria by various methods including electroporation and chemical transformations. A standard vector library can be used for transformations. An example of a gene editing method is CRISPR preceded by Cas9 testing to ensure Cas9 activity in microbes. Non-transgenic genetic modification of microbes A microbial population with favorable traits can be obtained by directed evolution. Direct evolution is an approach where the process of natural selection is mimicked to obtain proteins or nucleic acids with a user-defined goal. An example of direct evolution is when random mutations are introduced into a microbial population, microbes with the most favorable traits are selected, and growth of the selected microbes is continued. The most favorable traits in growth promoting rhizobacteria (PGPR) may be nitrogen fixation. The directed evolution method can be iterative and adaptive based on the selection process after each iteration. Plant growth promoting rhizobacteria (PGPR) with high nitrogen fixation capacity can be generated. The evolution of PGPRs can be accomplished by introducing genetic variation. The genetic variation is PRRn / n / Lznz / q / Yii -42 can be introduced by polymerase chain reaction mutagenesis, oligonucleotide-directed mutagenesis, saturation mutagenesis, rearrangement mutagenesis, homologous recombination, CRISPR / Cas9 systems, chemical mutagenesis, and combinations thereof. These approaches can introduce random mutations into the microbial population. For example, mutants can be generated using synthetic DNA or RNA by oligonucleotide-directed mutagenesis. Mutants can be generated through the use of tools contained in plasmids, which are then cured. Genes of interest can be identified using libraries of other species with improved traits including, but not limited to, improved PGPR properties, improved cereal colonization, increased oxygen sensitivity, increased nitrogen fixation, and increased ammonia excretion. Intrageneric genes can be designed based on these libraries using software such as Geneious or Platypus design software. Mutations can be designed with the help of machine learning. Mutations can be designed with the help of a metabolic model. Automated mutation design can be performed using a la Platypus and will guide RNAs for Cas-directed mutagenesis. Intrageneric genes can be transferred to the host microbe. In addition, the indicator systems can also be transferred to the microbe. Reporter systems characterize promoters, determine transformation success, select for mutants, and act as negative screening tools. Microbes carrying the mutation can be cultured by serial passage. A microbial colony contains a single variant of the microbe. Microbial colonies are examined with the aid of an automatic colony picker and a liquid handler. Mutants with gene duplications and higher copy numbers express a higher genotype of the desired trait. Selection of plant growth promoting microbes based on nitrogen fixation Microbial colonies can be screened using various assays to assess nitrogen fixation. One way to measure nitrogen fixation is by a single fermentative assay, which measures nitrogen excretion. An alternative method is the acetylene reduction test (ARA) with online sampling over time. ARA can be performed in high throughput plates from microtube arrays. ARA can be done with live plants and plant tissues. The formulation of the medium and the oxygen concentration of the PRRn / n / Lznz / q / Yii -43 average may vary in ARA trials. Another method of detecting microbial variants is through the use of biosensors. The use of Raman microspectroscopy and NanoSIMS can be used to investigate the activity of microbes. In some cases, bacteria can also be grown and expanded by using bioreactor fermentation methods. Bioreactors are designed to improve the robustness of bacterial growth and to decrease the sensitivity of bacteria to oxygen. Medium to high TP plate-based microfermentors are used to assess oxygen sensitivity, nutritional requirements, nitrogen fixation, and nitrogen excretion. Bacteria can also be co-cultured with competitive or beneficial microbes to elucidate cryptic pathways. Flow cytometry can be used to detect bacteria that produce high levels of nitrogen through the use of chemical, colorimetric, or fluorescent indicators. The bacteria can be grown in the presence or absence of a nitrogen source. For example, bacteria can be grown with glutamine, ammonia, urea, or nitrates. Guided Microbial Remodeling — Overview Guided microbial remodeling is a method to systematically identify and improve the role of species within the crop microbiome. In some aspects, and according to a particular clustering / categorization methodology, the method comprises three steps: 1) selection of candidate species by mapping plant-microbe interactions and predicting regulatory networks linked to a particular phenotype, 2) pragmatic and predictable enhancement of microbial phenotypes through intraspecies crossing of regulatory networks and gene clusters in a microbe's genome, and 3) detection and selection of new microbial genotypes that produce the desired crop phenotypes. To systematically assess strain improvement, a model is created that links microbial community colonization dynamics with gene activity by key species. The model is used to predict genetic targets for non-intergeneric genetic remodeling (ie, genetically modifying the genetic architecture of the microbe in a non-transgenic manner). See, FIGURE 1A for a graphical representation of one embodiment of the process. As illustrated in FIGURE 1A-1O, rational breeding of the crop microbiome can be used to increase soil biodiversity, adjust the impact of keystone species, and / or alter the timing and expression of important metabolic pathways. PRRn / n / Lznz / q / Yi -44 To this end, the inventors have developed a platform to identify and improve the role of strains within the crop microbiome. In some aspects, the inventors refer to this process as microbial breeding. The process of "Guided Microbial Remodeling" mentioned above will be further developed in the Examples, eg in Example 1, under the title: "Guided Microbial Remodeling - a platform for rational breeding of microbial species for agriculture". serial pass Production of bacteria to improve plant traits (eg nitrogen fixation) can be achieved by serial passage. Production of these bacteria can be accomplished by selecting for plants, which have a particular improved trait that is influenced by microbial flora, as well as identifying bacteria and / or compositions that are capable of imparting one or more improved traits to one or more floors. A method of producing a bacterium to improve a plant trait includes the steps of: (a) isolating bacteria from tissue or soil of a first plant; (b) introducing a genetic variation into one or more of the bacteria to produce one or more variant bacteria; (c) exposing multiple plants to the variant bacteria; (d) isolating bacteria from tissue or soil of one of the multiple plants, wherein the plant from which the bacteria is isolated has an improved trait relative to other plants of the multiple plants; and (e) repeating steps (b) to (d) with bacteria isolated from the plant with an improved trait (step (d)). Stages (b) through (d) can be repeated any number of times (for example, once, twice, three times, four times, five times, ten times, or more) until the improved trait in a plant reaches the level wanted. Furthermore, the multiple plants may be more than two plants, such as 10 to 20 plants, or 20 or more, 50 or more, 100 or more, 300 or more, 500 or more, or 1000 or more plants. In addition to obtaining a plant with an improved trait, a bacterial population is obtained comprising bacteria comprising one or more introduced genetic variations in one or more genes (eg genes regulating nitrogen fixation). By repeating the steps described above, a population of bacteria can be obtained that includes the most suitable members of the population that correlate with a plant trait of interest. The rRRn / n / Lznz / q / Yi bacteria from this population can be identified and their beneficial properties determined, such as by genetic and / or phenotypic analysis. A genetic analysis of the bacteria isolated in step (a) can be performed. Phenotypic and / or genotypic information -45 can be obtained through the use of techniques including: high-throughput detection of chemical components of plant origin, sequencing techniques including high-throughput sequencing of genetic material, differential visualization techniques (including DDRT-PCR and DD- PCR), nucleic acid microarray techniques, RNA sequencing (whole transcriptome sequencing) and qRT-PCR (quantitative real-time PCR). The information obtained can be used to obtain community profiling information on the identity and activity of the bacteria present, such as phylogenetic analysis or microarray-based detection of nucleic acids encoding components of rRNA operons or other taxonomically informative loci. . Examples of taxonomically informative loci include 16S rRNA gene, 23S rRNA gene, 5S rRNA gene, 5.8S rRNA gene, 12S rRNA gene, 18S rRNA gene, 28S rRNA gene, gyrB gene, rpoB gene, fusA gene, recA gene, coxl, nifD gene. US20140155283 describes examples of taxonomic profiling processes to determine the taxa present in a population. Bacterial identification may comprise the characterization activity of one or more genes or one or more signaling pathways, such as genes associated with the nitrogen fixation pathway. Synergistic interactions (where two components, by virtue of their combination, increase a desired effect by more than an additive amount) between different bacterial species may also be present in bacterial populations. Genetic variation — locations and sources of genomic alteration The genetic variation may be a gene selected from the group consisting of: nifA, nifL, ntrB, ntrC, glnA, glnB, glnK, draT, amtB, glnD, glnE, nifJ, nifH, nifD, nifK, nifY, nifE, nifN, nifü, nifS, nifV, nifW, nifZ, nifM, nifF, nifB, and nifQ. The genetic variation may be a variation in a gene encoding a protein with functionality selected from the group consisting of: glutamine synthetase, glutaminase, glutamine synthetase adenylyltransferase, transcriptional activator, antitranscriptional activator, pyruvate flavodoxin oxidoreductase, flavodoxin, or NADH-dinitrogen reductase aDP-Dribosyltransferase. The genetic variation may be a mutation that results in one or more of: increased expression or activity of NifA or glutaminase; decreased expression or activity of NifL, NtrB, glutamine synthetase, GlnB, GlnK, DraT, AmtB; decreased adenylyl scavenging activity of GlnE; or decreased uridylyl scavenging activity of GlnD. The introduction of a genetic variation may involve the insertion and / or deletion of one or PRRn / n / Lznz / q / Yi -46 more nucleotides at a target site, such as 1, 2, 3, 4, 5, 10, 25, 50, 100, 250, 500 or more nucleotides. The genetic variation introduced into one or more bacteria by the methods described herein may be a knockout mutation (eg, deletion of a promoter, insertion or deletion to produce a premature stop codon, deletion of an entire gene), or it may be deletion or abrogation of the activity of a protein domain (for example, point mutation affecting an active site, or deletion of a part of a gene encoding the relevant part of the protein product), or it may alter or abolish a regulatory sequence of a target gene. One or more regulatory sequences may also be inserted, including heterologous regulatory sequences and regulatory sequences found within a genome of a bacterial species or genus corresponding to the bacteria into which the genetic variation is introduced. Furthermore, regulatory sequences can be selected based on the expression level of a gene in bacterial culture or within plant tissue. The genetic variation may be a predetermined genetic variation that is specifically introduced into a target site. The genetic variation may be a random mutation within the target site. The genetic variation can be an insertion or deletion of one or more nucleotides. In some cases, multiple different genetic variations (eg, 2, 3, 4, 5, 10 or more) are introduced into one or more of the bacteria isolates prior to exposing the bacteria to plants to assess trait improvement. The multiple genetic variations can be any of the above types, the same type or different types, and in any combination. In some cases, multiple different genetic variations are introduced serially, by introducing a first genetic variation after a first stage of isolation, a second genetic variation after a second stage of isolation, and so on, to accumulate multiple genetic variations in the cells. bacteria that impart progressively improved traits in associated plants. Genetic Variation — Methods for Introducing Genomic Alteration In general, the term "genetic variation" refers to any change introduced in a polynucleotide sequence with respect to a reference polynucleotide, such as a reference genome or part thereof, or a reference gene or part thereof. . A genetic variation may be referred to as a 'mutation' and a sequence or organism comprising a genetic variation may be referred to as a 'genetic variant' or 'mutant'. Genetic variations can have various PRRn / n / Lznz / q / Yi -47 effects, such as increasing or decreasing some biological activity, including gene expression, metabolism, and cell signaling. Genetic variations can be introduced specifically at a target site or introduced randomly. A variety of molecular tools and methods are available to introduce genetic variations. For example, genetic variation can be introduced by polymerase chain reaction mutagenesis, oligonucleotide-directed mutagenesis, saturation mutagenesis, rearrangement mutagenesis, homologous recombination, recombination-mediated genetic modification, lambda red-mediated recombination, systems CRISPR / Cas9, chemical mutagenesis, and combinations thereof. Chemical methods of introducing genetic variation include exposure of DNA to a chemical mutagen, for example, ethyl methanesulfonate (EMS), methyl methanesulfonate (MMS), N-nitrosourea (EN U), N-methyl-N-nitro- N'-nitrosoguanidine, 4-nitroquinoline N-oxide, diethylsulfate, benzopyrene, cyclophosphamide, bleomycin, triethylmelamine, acrylamide monomer, nitrogen mustard, vincristine, diepoxyalkanes (e.g., diepoxybutane), ICR-170, formaldehyde, procarbazine hydrochloride, ethylene oxide, dimethylnitrosamine, 7,12-dimethylbenz(a)anthracene, chlorambucil, hexamethylphosphoramide, bisulfan, and the like. Radiation mutation-inducing agents include ultraviolet radiation, y-irradiation, X-rays, and fast neutron bombardment. Genetic variation can also be introduced into a nucleic acid, for example, through the use of trimethylpsoralen with ultraviolet light. Random or targeted insertion of a mobile DNA element, eg, a transposable element, is another suitable method of generating genetic variation. Genetic variations can be introduced into a nucleic acid during amplification in an in vitro cell-free system, for example, by use of a polymerase chain reaction (PCR) technique such as error-prone PCR. Genetic variations can be introduced into a nucleic acid in vitro through the use of DNA shuffling techniques (eg, exon shuffling, domain swapping, and the like). Genetic variations may also be introduced into a nucleic acid as a result of a deficiency in a DNA repair enzyme in a cell, for example, the presence in a cell of a mutant gene encoding a mutant DNA repair enzyme is expected to generate a high frequency of mutations (ie, about 1 mutation / 100 genes-1 mutation / 10,000 genes) in the cell's genome. Examples of genes encoding DNA repair enzymes include, but are not limited to, Mut H, Mut S, rRRn / n / Lznz / q / Yi -48 Mut L, and Mut U, and the homologues of these in other species (eg, MSH 1 6, PMS 1 2, MLH 1, GTBP, ERCC-1, and the like). Examples of descriptions of various methods for introducing genetic variations are provided, for example, in Stemple (2004) Nature 5:1-7; Chiang et al. (1993) PCR Methods Appl 2(3): 210-217; Stemmer (1994) Proc. nati. Acad. Sci. USA 91:10747-10751; and US Patent Nos. 6,033,861 and 6,773,900. Genetic variations introduced into microbes can be classified as transgenic, cisgenic, intragenomic, intrageneric, intergeneric, synthetic, evolved, rearranged, or SNP. Genetic variation can be introduced into various metabolic pathways within microbes to cause improvements in the traits described herein. Representative pathways include sulfur uptake pathways, glycogen biosynthesis, glutamine regulation pathway, molybdenum absorption pathway, nitrogen fixation pathway, ammonia assimilation, ammonia excretion or secretion, nitrogen absorption, glutamine biosynthesis, annamox, phosphate solubilization, organic acid transport, organic acid production, agglutinin production, reactive oxygen radical scavenging genes, indoleacetic acid biosynthesis, trehalose biosynthesis, enzymes or pathways that degrade plant cell walls, genes root-binding pathway, exopolysaccharide secretion, glutamate synthase pathway, iron uptake pathways, siderophore pathway, chitinase pathway, ACC deaminase, glutathione biosynthesis, phosphorus signaling genes, quorum inactivation pathway, cytochrome, hemoglobin pathway, bacterial hemoglobin-like pathway, rsmZ small RNA, rhizobitoxin biosynthesis, lapA adhesion protein, AHL quorum sensing pathway, phenazine biosynthesis, cyclic lipopeptide biosynthesis, and antibiotic production. CRISPR / Cas9 (clustered regularly spaced short palindromic repeats) / CRISPR-associated (Cas) systems can be used to introduce the desired mutations. CRISPR / Cas9 provides bacteria and archaea with adaptive immunity against viruses and plasmids by using AFIN CRISPR (crRNA) to guide the silencing of invading nucleic acids. The Cas9 protein (or functional equivalent and / or variant thereof, i.e., Cas9-like protein) naturally contains DNA endonuclease activity that depends on the association of the protein with two naturally occurring or synthetic RNA molecules called crRNA and tracrRNA (also called guide RNA). In some cases, the two molecules are covalently linked to form a single molecule (also called simple guide RNA). PRRn / n / Lznz / q / Yii -49 («gRNAs») ) . Thus, the Cas9 or Cas9-like protein associates with a DNA-targeting RNA (which term encompasses both the two-molecule guide RNA configuration and the single-molecule guide RNA configuration), thus activating the Cas9 or Cas9-like protein. Cas9 or Cas9-like protein and guides the protein to a target nucleic acid sequence. If the Cas9 or Cas9-like protein retains its natural enzymatic function, it will cleave target DNA to create a double-strand break, which can lead to genome disruption (i.e., editing, deletion, insertion (when a polynucleotide is present) donor), replacement, etc.), thereby altering gene expression. Some Cas9 variants (such variants include the term Cas9-like) have been altered such that they exhibit reduced DNA cleavage activity (in some cases, they cleave a single strand rather than both strands of the target DNA, while in others other cases, show drastically reduced to zero DNA cleavage activity). Examples of further descriptions of CRISPR systems for introducing genetic variation can be found, for example, in US8795965. As a cyclic amplification technique, polymerase chain reaction (PCR) mutagenesis uses mutagenic primers to introduce the desired mutations. PCR is performed by cycles of denaturation, hybridization, and extension. After PCR amplification, selection of mutated DNA and removal of original plasmid DNA can be accomplished by: 1) replacement of dCTP with hydroxymethylated dCTP during PCR, followed by restriction enzyme digestion to remove only non-original DNA. hydroxymethylated; 2) simultaneous mutagenesis of both a gene with resistance to antibiotics and the gene studied by changing the plasmid to a different resistance to antibiotics, the new resistance to antibiotics facilitates the selection of the desired mutation later; 3) after introducing a desired mutation, digestion of the original methylated DNA template by the restriction enzyme Dpnl which cleaves only the methylated DNA, whereby the mutagenized unmethylated strands are recovered; or 4) circularization of the motled PCR products in a further ligation reaction to increase the efficiency of transformation of the mutated DNA. Further description of illustrative methods can be found, for example, in US7132265, US6713285, US6673610, US6391548, US5789166, US5780270, US5354670, US5071743, and US20100267147. Oligonucleotide-directed mutagenesis, also called site-directed mutagenesis, typically uses a synthetic DNA primer. This primer rRRn / n / Lznz / q / Yi Synthetic -50 contains the desired mutation and is complementary to the DNA template around the site of the mutation so that it can hybridize to the DNA in the gene of interest. The mutation can be a single base change (a point mutation), multi-base changes, deletion, or insertion, or a combination of these. The single-stranded primer is then extended using a DNA polymerase, which copies the rest of the gene. The thus copied gene contains the mutated site, and can then be introduced into a host cell as a vector and cloned. Finally, the mutants can be selected by DNA sequencing to verify that they contain the desired mutation. Genetic variations can be introduced through the use of error-prone PCR. In this technique, the gene of interest is amplified using a DNA polymerase under conditions of deficient sequence replication fidelity. The result is that the amplification products contain at least one sequence error. When a gene is amplified, and the one or more products resulting from the reaction contain one or more sequence alterations compared to the template molecule, the resulting products are mutagenized compared to the template. Another means of introducing random mutations is to expose cells to a chemical mutagen, such as nitrosoguanidine or ethyl methanesulfonate (Nestmann, Mutat Res 1975 Jun;28(3):323-30), and then the vector containing the gene is isolated from the host. Saturation mutagenesis is another form of random mutagenesis, in which an attempt is made to generate all or nearly all possible mutations at a specific site or narrow region of a gene. In a general sense, saturation mutagenesis comprises the mutagenization of a complete set of mutagenic cassettes (where each cassette is, for example, 1 to 500 bases in length) into a defined polynucleotide sequence to be mutagenized ( wherein the sequence to be mutagenized is, for example, 15 to 100,000 bases in length). Therefore, a group of mutations (eg, ranging from 1 to 100 mutations) is introduced into each cassette to be mutagenized. A pool of mutations to be introduced into a cassette may be different from or the same as a second pool of mutations to be introduced into a second cassette during application of a round of saturation mutagenesis. Such clusters are exemplified by particular codon clusters, deletions, additions, and particular nucleotide cassette clusters. Rearrangement mutagenesis, also called rRRn / n / Lznz / q / Yi -51 DNA shuffling, is a way to quickly spread beneficial mutations. In one example of a shuffling process, DNase is used to fragment a set of parent genes into pieces, eg, about 50-100 bp in length. This is followed by a primerless polymerase chain reaction (PCR), DNA fragments with sufficient overlapping homologous sequence are annealed to each other and then extended by DNA polymerase. Several rounds of this PCR extension are allowed to occur, after some of the DNA molecules reach the size of the original genes. These genes can then be amplified with another PCR, this time with the addition of primers that are designed to complement the ends of the strands. The primers may have additional sequences added to their 5' ends, such as sequences for restriction enzyme recognition sites necessary for ligation into a cloning vector. Further examples of shuffling techniques are provided in US20050266541. Homologous recombination mutagenesis involves recombination between an exogenous DNA fragment and the target polynucleotide sequence. After a double-strand break occurs, the sections of DNA around the 5' ends of the break are cut out in a process called resection. In the next-strand invasion step, a protruding 3' end of the broken DNA molecule then "invades" a similar or identical unbroken DNA molecule. The method can be used to delete a gene, remove exons, add a gene, and introduce point mutations. Homologous recombination mutagenesis can be permanent or conditional. Typically, a recombination template is also provided. A recombination template can be a component of another vector, contained in a separate vector, or provided as a separate polynucleotide. In some embodiments, a recombination template is designed to serve as a template in homologous recombination, such as within or near a target sequence cut or cleaved by a site-specific nuclease. A polynucleotide template can be of any suitable length, such as about or more than about 10, 15, 20, 25, 50, 75, 100, 150, 200, 500, 1000 or more nucleotides in length. In some embodiments, the polynucleotide template is complementary to a part of a polynucleotide that comprises the target sequence. When optimally aligned, a polynucleotide template may overlap one or more nucleotides of a target sequence (for example, about or more than about 1, 5, 10, 15, 20, 25, 30, 35, 40 , 45, 50, 60, PRRn / n / Lznz / q / Yii 70, 80, 90, 100 or more nucleotides). In some embodiments, when a template sequence and a polynucleotide comprising a target sequence are optimally aligned, the closest nucleotide of the template polynucleotide is within about 1, 5, 10, 15, 20, 25, 50 , 75, 100, 200, 300, 400, 500, 1000, 5000, 10,000, or more nucleotides of the target sequence. Non-limiting examples of site-directed nucleases useful in homologous recombination methods include zinc finger nucleases, CRISPR nucleases, TALE nucleases, and meganucleases. For a more detailed description of the use of said nucleases, see, for example, US8795965 and US20140301990. Mutagens that primarily create point mutations and deletions, insertions, transversions, and / or short transitions, including chemical mutagens or radiation, can be used to create genetic variations. Mutagens include, but are not limited to, ethyl methanesulfonate, methylmethane sulfonate, N-ethyl-N-nitrosurea, triethylmelamine, N-methyl-N-nitrosourea, procarbazine, chlorambucil, cyclophosphamide, diethyl sulfate, acrylamide monomer, melphalan , nitrogen mustard, vincristine, dimethylnitrosamine, N-methyl-N'-nitronitrosoguanidine, nitrosoguanidine, 2-aminopurine, 7,12-dimethyl-benz(a)anthracene, ethylene oxide, hexamethylphosphoramide, bisulfan, diepoxyalkanes (diepoxyoctane, diepoxybutane, and the like), 2-methoxy-6-chloro-9[3-(etl-2-chloroetl)aminoproplamino]acridine dihydrochloride and formaldehyde. The introduction of a genetic variation may be an incomplete process, such that some bacteria in a treated population of bacteria carry a desired mutation while others do not. In some cases, it is desirable to apply selection pressure to enrich for bacteria carrying a desired genetic variation. Traditionally, selection for successful genetic variants involved selection for or against some functionality imparted or abolished by the genetic variation, such as the insertion of an antibiotic resistance gene or the abrogation of metabolic activity. capable of converting a non-lethal compound into a lethal metabolite. It is also possible to apply selection pressure based on a polynucleotide sequence itself, such that only a desired genetic variation need be introduced (eg without also requiring a selectable marker). In this case, selection pressure may include excision of genomes lacking the introduced genetic variation at a target site, so that selection is effectively directed against the reference sequence in which the variation is sought. PRRn / n / Lznz / q / Yi -53 genetics. Typically, cleavage occurs within 100 nucleotides of the target site (eg, within 75, 50, 25, 10 or fewer nucleotides from the target site, including cleavage at or within the target site). Cleavage may be directed by a site-specific nuclease selected from the group consisting of a zinc finger nuclease, a CRISPR nuclease, a TALE nuclease (TALEN) or a meganuclease. Such a process is similar to processes for enhancing homologous recombination at a target site, except that no template for homologous recombination is provided. As a result, bacteria that lack the desired genetic variation are more likely to undergo a split that, if not repaired, results in cell death. Bacteria that survive selection can then be isolated for use in plant challenge to assess for granting an improved trait. A CRISPR nuclease can be used as a site-specific nuclease to direct cleavage to a target site. Improved selection of mutated microbes can be obtained by using Cas9 to kill non-mutated cells. Plants are then inoculated with the mutated microbes to reconfirm symbiosis and create evolutionary pressure to select for efficient symbionts. The microbes can then be re-isolated from plant tissues. CRISPR nuclease systems employed for selection against non-variants may employ similar elements to those described above with respect to the introduction of genetic variation, except that no template for homologous recombination is provided. Cleavage directed at the target site thereby enhances the death of affected cells. Other options for specifically inducing cleavage at a target site are available, such as zinc finger nucleases, TALE (TALEN) nuclease systems, and meganuclease. Zinc finger nucleases (ZFNs) are artificial DNA endonucleases generated by fusing a zinc finger DNA binding domain to a DNA cleavage domain. ZFNs can be designed to target desired DNA sequences and this makes it possible for zinc finger nucleases to cleave unique target sequences. When introduced into a cell, ZFNs can be used to edit target DNA in the cell (eg, the cell's genome) by inducing double-strand breaks. Transcription activator-like effector nucleases (TALENs) are artificial DNA endonucleases generated by fusing a TAL effector DNA-binding domain (transcription activator-like) to a PRRn / n / Lznz / q / Yi -54DNA excision. TALENs can be easily engineered to join virtually any DNA sequence, and when introduced into a cell, TALENs can be used to edit target DNA in the cell (eg, the cell's genome) by inducing double-strand breaks. Meganucleases (targeting endonucleases) are endodeoxyribonucleases characterized by a large recognition site (double-stranded DNA sequences from 12 to 40 base pairs. Meganucleases can be used to replace, delete, or modify sequences in a highly targeted manner. By modifying their recognition sequence by genetically modifying proteins, the target sequence can be changed.Meganucleases can be used to modify all types of genomes, whether bacterial, plant, or animal, and are commonly grouped into four families: the LAGLIDADG family (SEQ ID NO: 1), the GIY-YIG family, the His-Cyst box family and the HNH family Examples of homing endonucleases include I-Scel, I-Ceul, PI-PspI, ΡΙ-Sce, I-SceIV , I-Csml, I-PanI, I-SceII, I-Ppol, I-SceIII, I-Creí, I-TevI, I-TevII and I-TevIII. Genetic variation — identification methods The microbes of the present disclosure can be identified by one or more genetic modifications or alterations that have been introduced into said microbe. One method by which said genetic modification or alteration may be identified is by reference to a SEQ ID NO containing a portion of the microbe's genomic sequence sufficient to identify the genetic modification or alteration. In addition, in the case of microbes that have not had a genetic modification or alteration (eg, a wild type, WT) introduced into their genomes, the disclosure may use 16S nucleic acid sequences to identify such microbes. A 16S nucleic acid sequence is an example of a "molecular marker" or "genetic marker", which refers to a reporter that is used in methods to visualize differences in nucleic acid sequence characteristics. Examples of other such reporters are restriction fragment length polymorphism (RFLP) markers, amplified fragment length polymorphism (AFLP) markers, single nucleotide polymorphisms (SNPs), insertion mutations, microsatellite markers (SSRs). ), sequence-characterized amplified regions (SCARs), cleaved amplified polymorphic sequence (CAPS) markers, or isoenzyme markers or combinations of the markers described herein that define a rRRn / n / Lznz / q / Yi location -55specific genetics and chromosomes. Markers also include polynucleotide sequences encoding 16S or 18S rRNA, and internal transcribed spacer sequences (ITS), which are sequences found between small subunit and large subunit rRNA genes that have proven especially useful in elucidating relationships. or distinctions when compared to each other. In addition, the description uses unique sequences found in genes of interest (eg, nif H,D,K,L,A, glnE, amtB, etc.) to identify the microbes described herein. The backbone of the 16S major rRNA subunit comprises a particular combination of conserved, variable, and hypervariable regions that evolve at different rates and allow resolution of very old lineages such as domains, and more modern lineages such as genera. The secondary structure of the 16S subunit includes approximately 50 helices that produce base pairing of approximately 67% of the residues. These highly conserved secondary structural features are of great functional importance and can be used to ensure positional homology in multiple sequence alignments and phylogenetic analyses. During the last decades, the 16S rRNA gene has become the most sequenced taxonomic marker and is the cornerstone of the current systematic classification of bacteria and archaea (Yarza et al. 2014. Nature Rev. Micro. 12:635-45 ). Thus, in certain aspects, the description provides a sequence, sharing at least about 70%, 71%, 72%, 73%, 74%, 75%, 76%, 77%, 78%, 79%, 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96% , 97%, 98%, 99%, or 100% sequence identity to any sequence in Tables 23, 24, 25, and 26. Thus, in certain aspects, the disclosure provides a microbe comprising a sequence, sharing at least about 70%, 71%, 72%, 73%, 74%, 75%, 76%, 77%, 78% , 79%, 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95 %, 96%, 97%, 98%, 99%, or 100% sequence identity to SEQ ID NO: 62-303. These sequences and their associated descriptions can be found in Tables 25 and 26. In some aspects, the disclosure provides a microbe comprising a 16S nucleic acid sequence, sharing at least about 70%, 71%, 72%, 73%, 74%, 75%, 76%, 77%, 78% , 79%, 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95 %, 96%, 97%, 98%, 99%, rRRn / n / Lznz / q / Yi -56ο 100% sequence identity with SEQ ID NO: 85, 96, 111, 121, 122, 123, 124, 136, 149, 157, 167, 261, 262, 269, 277-283. These sequences and their associated descriptions can be found in Table 26. In some aspects, the description provides a microbe comprising a nucleic acid sequence, sharing at least about 70%, 71%, 72%, 73%, 74%, 75%, 76%, 77%, 78%, 79%, 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95% , 96%, 97%, 98%, 99%, or 100% sequence identity to SEQ ID NO: 86-95, 97-110, 112-120, 125-135, 137-148, 150-156, 158-166, 168-176, 263-268, 270-274, 275, 276, 284-295. These sequences and their associated descriptions can be found in Table 26. In some aspects, the description provides a microbe comprising a nucleic acid sequence, sharing at least about 70%, 71%, 72%, 73%, 74%, 75%, 76%, 77%, 78%, 79%, 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95% , 96%, 97%, 98%, 99%, or 100% sequence identity to SEQ ID NO: 177-260, 296-303. These sequences and their associated descriptions can be found in Table 26. In some aspects, the disclosure provides a microbe comprising, or primer comprising, or probe comprising, or non-natural binding sequence comprising, a nucleic acid sequence, sharing at least about 70%, 71%, 72 %, 73%, 74%, 75%, 76%, 77%, 78%, 79%, 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% sequence identity to SEQ ID NO: 304-424. These sequences are described in Table 27. In some aspects, the disclosure provides a microbe comprising a non-natural splicing sequence, sharing at least about 70%, 71%, 72%, 73%, 74%, 75%, 76%, 77%, 78% , 79%, 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95 %, 96%, 97%, 98%, 99%, or 100% sequence identity to SEQ ID NO: 372-405. These sequences are described in Table 27. In some aspects, the description provides a microbe comprising an amino acid sequence, sharing at least about 70%, 71%, 72%, 73%, 74%, 75%, 76%, 77%, 78%, 79 %, 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% sequence identity to SEQ ID NO: 77, 78, 81, 82, or 83. These sequences and their associated descriptions can be found in Table 25. PRRn / n / Lznz / q / Yi -57Genetic variation — detection methods: primers, probes and assays This disclosure describes primers, probes, and assays that are useful for detecting the microbes described herein. In some aspects, the disclosure provides methods for detecting parental WT strains. In other aspects, the disclosure provides methods for detecting non-intergeneric genetically modified microbes derived from WT strains. In some aspects, the present disclosure provides methods for identifying non-intergeneric genetic alterations in a microbe. In some aspects, the genomic modification methods of the present disclosure lead to the creation of unnatural nucleotide "splice" sequences in the derived non-intergeneric microbes. These non-naturally occurring nucleotide linkages can be used as a type of diagnostic indicating the presence of a particular genetic alteration in a microbe described herein. The present techniques are capable of detecting these non-naturally occurring nucleotide junctions using specialized quantitative PCR methods, including proprietary primers and probes. In some aspects, the probes of the disclosure bind to non-naturally occurring nucleotide binding sequences. In some aspects, traditional PCR is used. In other aspects, real-time PCR is used. In some aspects, quantitative PCR (qPCR) is used. Therefore, the description can cover the use of two common methods for the detection of real-time PCR products: (1) non-specific fluorescent dyes that intercalate with any double-stranded DNA, and (2) specific DNA probes. of sequence consisting of oligonucleotides that are labeled with a fluorescent indicator that allows detection only after hybridization of the probe with its complementary sequence. In some aspects, non-naturally occurring nucleotide binding will only be amplified by the indicated primers and, accordingly, can be detected by a non-specific dye or by using a specific hybridization probe. In other aspects, the primers of the disclosure are chosen such that the primers flank both sides of a junction sequence, so that if an amplification reaction occurs, then said junction sequence is present. Aspects of the disclosure involve non-naturally occurring nucleotide binding sequence molecules per se, along with other nucleotide molecules. PRRn / n / Lznz / q / YL -58 that are capable of binding to such non-naturally occurring nucleotide binding sequences under mild to stringent hybridization conditions. In some aspects, nucleotide molecules that are capable of binding to such non-naturally occurring nucleotide binding sequences under mild to stringent hybridization conditions are referred to as "nucleotide probes." In some aspects, genomic DNA can be extracted from samples and used to quantify the presence of microbes of the description using qPCR. The primers used in the qPCR reaction can be primers designed by Primer Blast (www.ncbi.nlm.nih.gov / tools / primer-blast / ) to amplify unique regions of the wild-type genome or unique regions of the non-intergeneric mutant strains. genetically modified The qPCR reaction can be carried out using the SYBR GreenER qPCR SuperMix Universal Kit (Thermo Fisher P / N 11762100), which uses only forward and reverse amplification primers; alternatively, the Kapa Probe Force kit (Kapa Biosystems P / N KK4301) can be used with amplification primers and a TaqMan probe containing a FAM dye label at the 5' end, an internal ZEN quencher, and a minor groove binding agent and fluorescent quencher at the 3' end (Integrated DNA Technologies). Certain unnatural primers, probes, and junction sequences are listed in Table 27. The efficiency of the qPCR reaction can be measured by using a standard curve generated from a known amount of gDNA from the target genome. Data can be normalized to genome copies per g fresh weight by using tissue weight and extraction volume. Quantitative polymerase chain reaction (qPCR) is a method for quantifying, in real time, the amplification of one or more nucleic acid sequences. The real-time quantification of the PCR assay allows the determination of the amount of nucleic acids that are generated by the PCR amplification steps by comparing the enhancer nucleic acids of interest and a suitable control nucleic acid sequence, which can act as a calibration standard. TaqMan probes are often used in qPCR assays that require higher specificity to quantify target nucleic acid sequences. TaqMan probes comprise an oligonucleotide probe with a fluorophore attached to the 5' end and a quencher attached to the 3' end of the probe. When the TaqMan probes remain as they are with the 5' and 3' ends of the probe in close contact with each other, the quencher inhibits transmission of fluorescent signals. PRRn / n / Lznz / q / Yi -59 from the fluorophore. TaqMan probes are designed to anneal within a region of nucleic acid amplified by a specific set of primers. As the Taq polymerase extends the primer and synthesizes the fledgling strand, the 5' to 3' exonuclease activity of the Taq polymerase degrades the probe that hybridized to the template. This degradation of the probe releases the fluorophore, thereby breaking proximity to the quencher and allowing fluorescence of the fluorophore. The fluorescence detected in the qPCR assay is directly proportional to the fluorophore released and the amount of template DNA present in the reaction. The qPCR features allow the practitioner to eliminate the laborious post-amplification step of gel electrophoresis preparation, which is typically required for observation of amplified products from traditional PCR assays. The benefits of qPCR over conventional PCR are considerable and include increased speed, ease of use, reproducibility, and quantitative capability. Trait Enhancement Methods of the present disclosure may be employed to introduce or enhance one or more of a variety of desirable traits. Examples of traits that can be introduced or improved include: root biomass, root length, height, shoot length, number of leaves, water use efficiency, total biomass, yield, fruit size, kernel size , rate of photosynthesis, drought tolerance, heat tolerance, salt tolerance, resistance to nematode stress, resistance to a fungal pathogen, resistance to a bacterial pathogen, resistance to a viral pathogen, level of a metabolite, and proteome expression. Desirable traits, including height, total biomass, root and / or shoot biomass, seed germination, seedling survival, photosynthetic efficiency, transpiration rate, seed / fruit quantity or mass, grain or fruit yield plant, leaf chlorophyll content, rate of photosynthesis, root length, or any combination of these, can be used to measure growth and compared to the growth rate of reference agricultural plants (for example, plants without the improved traits) grown under identical conditions. A preferred trait to introduce or improve is nitrogen fixation, as described herein. In some cases, a plant produced by the methods described herein exhibits a difference in trait that is at least PRRn / n / Lznz / q / Yii -60 5% greater, for example, at least about 5%, at least about 8%, at least about 10%, at least about 15%, at least about 20%, at least about 25% , at least about 30%, at least about 40%, at least about 50%, at least about 60%, at least about 75%, at least about 80%, at least about 80%, at least about 90% or at least about 100%, at least about 200%, at least about 300%, at least about 400% or higher than a reference agricultural plant grown under the same soil conditions . In further examples, a plant produced by the methods described herein exhibits a trait difference that is at least 5% greater, eg, at least about 5%, at least about 8%, at least about 10 %, at least around 15%, at least around 20%, at least around 25%, at least around 30%, at least around 40%, at least around 50%, at least around 60% , at least around 75%, at least around 80%, at least around 80%, at least around 90% or at least around 100%, at least around 200%, at least around 300%, at least about 400% or higher than a reference agricultural plant grown under similar soil conditions. The trait to be improved can be evaluated under conditions that include the application of one or more biotic or abiotic stressors. Examples of stressors include abiotic stress (such as heat stress, salt stress, drought stress, cold stress, and low nutrient stress) and biotic stress (such as nematode stress, insect herbivory stress, fungal pathogen stress, bacterial pathogen stress, and viral pathogen stress). The trait improved by the methods and compositions of the present disclosure may be nitrogen fixation, even in a plant that was previously not capable of nitrogen fixation. In some cases, bacteria isolated according to a method described herein produce more lios (for example, 2%, 3%, 4%, 5%, 6%, 7%, 8%, 9%, 10%, 15%, 20%, or more) of a plant's nitrogen, which can represent an increase in nitrogen-fixing capacity of at least 2-fold (e.g., 3-fold, 4-fold, 5-fold, 6-fold, 7-fold , 8-fold, 9-fold, 10-fold, 20-fold, 50-fold, 100-fold, 1000-fold, or more) compared to bacteria isolated from the first plant before the introduction of any genetic variation. In some cases, bacteria produce 5% or more of a plant's nitrogen. The desired level of nitrogen fixation can be PRRn / n / Lznz / q / Yi -61 achieved after repeating the steps of introducing a genetic variation, exposing multiple plants, and isolating bacteria from plants with an improved trait one or more times (for example, 1, 2, 3, 4, 5, 10, 15, 25 or more times) . In some cases, enhanced levels of nitrogen fixation are achieved in the presence of fertilizer supplemented with glutamine, ammonia, or another chemical source of nitrogen. Methods for evaluating the degree of nitrogen fixation are known, examples of which are described herein. Microbial breeding is a method to systematically identify and improve the role of species within the crop microbiome. The method comprises three steps: 1) selection of candidate species by mapping plant-microbe interactions and predicting regulatory networks linked to a particular phenotype, 2) pragmatic and predictable enhancement of microbial phenotypes through intraspecies crossing of regulatory networks, and gene pools, and 3) detection and selection of new microbial genotypes that produce the desired crop phenotypes. To systematically assess strain improvement, a model is created that links microbial community colonization dynamics with gene activity by key species. The model is used to predict genetic targets for reproduction and improve the frequency of selection for improvements in microbiome-encoded traits of agronomic relevance. Measurement of supplied nitrogen in a field context relevant to agriculture In the field, the amount of nitrogen supplied can be determined by the colonization function multiplied by activity. Nitrogen supplied = J Colonization x activity time and space PRRn / n / Lznz / q / Yi The above equation requires (1) the average colonization per unit of plant tissue, and (2) the activity, either as the amount of nitrogen fixed or the amount of ammonia excreted by each microbial cell. To convert to pounds of nitrogen per acre, growth physiology of corn is tracked over time, for example, plant size and associated root system through stages of maturity. The pounds of nitrogen supplied to a crop per acre-season can be calculated using the following equation: -62 Nitrogen supplied = / Plant tissue(t) x Colonization(t) x Activity(t) dt PRRn / n / Lznz / q / Yi Plant tissue (t) is the fresh weight of maize plant tissue during growing time (t). Values ​​to reasonably perform the calculation are described in detail in the publication entitled Roots, Growth and Nutrient Uptake (Mengel. Dept. of Agronomy Pub.# AGRY-95-08 (Rev. May-95. p. 1-8.) . Colonization (t) is the number of microbes of interest found within plant tissue, per gram of fresh weight of plant tissue, at a particular time, t, during the growing season. In the case of a single available time point, the single time point is normalized as the maximum colonization speed during the season, and the colonization speed of the remaining time points is adjusted accordingly. Activity (t) is the rate at which N is fixed by the microbes of interest per unit of time, at any particular time, t, during the growing season. In the embodiments described herein, this rate of activity is approximated by in vitro acetylene reduction assay (ARA) in ARA medium in the presence of 5 mM glutamine or ARA medium ammonium excretion assay in the presence of ammonium ions. 5mm. The amount of supplied nitrogen is calculated by numerically integrating the above function. In cases where the values ​​of the variables described above are discretely measured at set time points, the values ​​between those time points are approximated by performing linear interpolation. Fixation of nitrogen Described herein are methods of increasing nitrogen fixation in a plant, comprising exposing the plant to bacteria comprising one or more introduced genetic variations in one or more genes that regulate nitrogen fixation, wherein the bacteria produce 1% or more of the nitrogen in the plant (eg, 2%, 5%, 10%, or more), which may represent at least 2-fold nitrogen-fixing capacity compared to the plant in the absence of bacteria. Bacteria can produce nitrogen in the presence of fertilizer supplemented with glutamine, urea, nitrates, or ammonia. The genetic variations can be any genetic variation described herein, including the examples provided above, in any amount and in any combination. Genetic variation can be introduced into a selected gene from the -63 group consisting of: nifA, nifL, ntrB, ntrC, glutamine synthetase, glnA, glnB, glnK, draT, amtB, glutaminase, glnD, glnE, nifJ, nifH, nifD, nifK, nifY, nifE, nifN, nifU, nifS, nifV, nifW, nifZ, nifM, nifE, nifB, and nifQ. The genetic variation may be a mutation that results in one or more of: increased expression or activity of nifA or glutaminase; decreased expression or activity of nifL, ntrB, glutamine synthetase, glnB, glnK, draT, amtB; decreased adenylyl scavenging activity of GlnE; or decreased uridylyl scavenging activity of GlnD. The genetic variation introduced into one or more bacteria by the methods described herein may be an inactivating mutation or may abolish a regulatory sequence of a target gene, or may comprise the insertion of a heterologous regulatory sequence, for example, the insertion of a regulatory sequence found within the genome of the same bacterial species or genus. The regulatory sequence can be chosen based on the expression level of a gene in a bacterial culture or within plant tissue. Genetic variation can be produced by chemical mutagenesis. Plants grown in step (c) can be exposed to biotic or abiotic stressors. The amount of nitrogen fixation that occurs in the plants described herein can be measured in a number of ways, for example, by an acetylene reduction (AR) assay. An in vitro or in vivo acetylene reduction assay can be performed. Evidence that a particular bacterium provides fixed nitrogen to a plant may include: 1) total N in the plant increases significantly after inoculation, preferably with a concomitant increase in plant N concentration; 2) nitrogen deficiency symptoms are alleviated under N-limited conditions after inoculation (which should include an increase in dry matter); 3) N2 fixation is documented through the use of a 15N approach (which can be isotope dilution experiments, 15N2 reduction assays, or 15N natural abundance assays); 4) the fixed N is incorporated into a plant protein or metabolite; and 5) not all of these effects are observed in uninoculated plants or in plants inoculated with a mutant of the inoculum strain. The wild-type nitrogen fixation regulatory cascade can be represented as a digital logic circuit where the 02 and NH4+ inputs pass through a NOR gate, the output of which goes into an AND gate in addition to ATP. In some embodiments, the methods described herein interrupt the influence of NH4+ on this circuit, at multiple points in the regulatory cascade, so that PRRn / n / Lznz / q / Yi -64microbes can produce nitrogen even in fertilized fields. However, the methods described herein also envision altering the impact of ATP or 02 on the circuit, or replacing the circuit with other regulatory cascades in the cell, or altering genetic circuits other than nitrogen fixation. Gene pools can be re-engineered to generate functional products under the control of a heterologous regulatory system. By removing natural regulatory elements outside and within the coding sequences of gene clusters and replacing them with alternative regulatory systems, the functional products of complex gene operons can be controlled, and other gene clusters can be controlled and / or moved accordingly. heterologous cells, including cells from different species other than the species from which the wild-type genes were derived. After reengineering, the synthetic gene pools can be controlled by genetic circuitry or other inducible regulatory systems, thereby controlling the expression of the products as desired. Expression cassettes can be designed to act as logic gates, pulse generators, oscillators, switches, or memory devices. The control expression cassette can be linked to a promoter such that the expression cassette functions as an environmental sensor, such as an oxygen, temperature, touch, osmotic stress, membrane stress, or redox sensor. As an example, the nifL, nifA, nifT and nifX genes can be deleted from the nif gene pool. Synthetic genes can be designed by randomizing the codon of the DNA encoding each amino acid sequence. Codon selection is performed, specifying that the codon usage be as divergent as possible from the codon usage in the wild type gene. Proposed sequences are scanned for unwanted features, such as restriction enzyme recognition sites, transposon recognition sites, repetitive sequences, sigma 54 and sigma 70 promoters, cryptic ribosome binding sites, and rho-independent terminators. Synthetic ribosome binding sites are chosen to match the resistance of each corresponding natural ribosome binding site, for example, by constructing a fluorescent reporter plasmid in which the 150 bp surrounding the start codon of a gene (-60 to +90) to fuse with a fluorescent gene. This chimera can be expressed under the control of the Ptac promoter and fluorescence measured by flow cytometry. To generate synthetic ribosome binding sites, a library of reporter plasmids is generated using 150 bp (-60 to +90) of an expression cassette. PRRn / n / Lznz / q / Yii -65synthetic. Briefly, a synthetic expression cassette may consist of a random DNA spacer, a redundant sequence encoding an RBS library, and the coding sequence for each synthetic gene. Multiple clones are screened to identify the synthetic ribosome binding site that best matches the natural ribosome binding site. Synthetic operons consisting of the same genes as the natural operons are constructed and evaluated for functional complementation. A further illustrative description of synthetic operons is provided in US20140329326. bacterial species Microbes useful in the methods and compositions described herein can be obtained from any source. In some cases, the microbes may be bacteria, archaea, protozoa, or fungi. The microbes of this disclosure may be nitrogen-fixing microbes, for example, nitrogen-fixing bacteria, nitrogen-fixing archaea, nitrogen-fixing fungi, nitrogen-fixing yeast, or nitrogen-fixing protozoa. Microbes useful in the methods and compositions described herein may be spore-forming microbes, eg, spore-forming bacteria. In some cases, the bacteria useful in the methods and compositions described herein may be gram-positive bacteria or gram-negative bacteria. In some cases, the bacteria may be an endospore-forming bacterium of the phylum Firmicute. In some cases, the bacteria can be a diazotroph. In some cases, the bacteria may not be a diazotroph. The methods and compositions of the present disclosure can be used with archaea, such as, for example, Methanothermobacter thermoautotrophicus. In some instances, bacteria that may be useful include, but are not limited to, Agrobacterium radiobacter, Bacillus acidocaldarius, Bacillus acidoterrestris, Bacillus agrá, Bacillus aízawaí, Bacillus albolactis, Bacillus alcalophilus, Bacillus alvei, Bacillus aminoglucosidicus, Bacillus aminovorans, Bacillus amylolyticus ( also known as Paenibacillus amylolyticus) Bacillus amyloliquefaciens, Bacillus aneurinolyticus, Bacillus atrophaeus, Bacillus azotoformans, Bacillus badius, Bacillus cereus (synonyms: Bacillus endorhythmos, Bacillus medusa), Bacillus chitinosporus, Bacillus circulans, Bacillus s coagulans, Bacillus endoparasiticus Bacillus fastidiosa, Bacillus firmus, Bacillus kurstaki, Bacillus lacticola, Bacillus lactimorbus, Bacillus lactis, Bacillus laterosporus (also known as Brevibacillus laterosporus), Bacillus lautus, Bacillus PRRn / n / Lznz / q / Yi -66 lentimorbus, Bacillus lentus, Bacillus licheniformis, Bacillus maroccanus, Bacillus megaterium, Bacillus metiens, Bacillus mycoides, Bacillus natto, Bacillus nematocida, Bacillus nigrificans, Bacillus nigrum, Bacillus pantothenticus, Bacillus popillae, Bacillus psych rosaccharolyticus, Bacillus pumilus, Bacillus siamensis, Bacillus smithii , Bacillus sphaericus, Bacillus subtilis, Bacillus thuringiensis, Bacillus uniflagellatus, Bradyrhizobium japonicum, Brevibacillus brevís Brevibacillus laterosporus (formerly Bacillus laterosporus), Chromobacterium subtsugae, Delftia acidovorans, Herbaspirillum seropedicae, Her baspirillum. frisingense, Lactobacillus acidophilus, Lysobacter antibioticus, Lysobacter enzymogenes, Metakosakonia massiliensis, Metakosakonia intestinei, Paenibacillus alvei, Paenibacillus polymyxa, Paenibacillus popílliae (formerly Bacillus popílliae), Pantoea agglomerans, Pasteuria penetrans (formerly Bacillus penetrans), Pasteuria usgae, Pectobacterium carotovorum (formerly Erwinia carotovora), Pseudomonas aeruginosa, Pseudomonas aureofaciens, Pseudomonas benzenivorans, Pseudomonas cepacia (formerly known as Burkholderia cepacia), Pseudomonas chlororaphis, Pseudomonas fluorescens, Pseudomonas proradix, Pseudomonas protegens, Pseudomonas putida, Pseudomonas syringae , Serratia entomophila, Serratia marcescens, Streptomyces colombiensis, Streptomyces galbus, Streptomyces goshikiensis, Streptomyces griseovirídis, Streptomyces lavendulae, Streptomyces prasinus, Streptomyces saraceticus, Streptomyces venezuelae, Xanthomonas campestris, Xenorhabdus luminescens, Xenorhabdus nematophila, Rhodococcus globerulus AQ719 (NRRL Accession No. B-21663), Bacillus sp. AQ175 (ATCC Accession No. 55608), Bacillus sp. AQ 177 (ATCC Accession No. 55609), Bacillus sp. AQ178 (ATCC Accession No. 53522), and the strain Streptomyces sp. Registry No. NRRL B-30145. In some cases, the bacterium may be Azotobacter chroococcum, Methanosarcina barkeri, Klesiella pneumoniae, Azotobacter vinelandíi, Azospirillum brasílense, Phodobacter spharoides, Phodobacter capsulatus, Phodobcter palustris, Rhodosporillum rubrum, Rhizobium leguminosarum, or Rhizobium etli. In some cases, the bacterium may be a Clostridium species, eg Clostridium pasteurianum, Clostridium beijerinckii, Clostridium perfringens, Clostridium tetan!, Clostridium acetobutylicum. In some cases, the bacteria used with the methods and compositions of the present disclosure may be cyanobacteria. Examples of cyanobacterial genera include Anabaena (for example, Anagaena sp. PCC7120), Nostoc (for example, Nostoc punctiforme), or Synechocystis (for example, Synechocystis sp. rRRn / n / Lznz / q / Yi -67PCC6803). In some cases, the bacteria used with the methods and compositions of the present disclosure may belong to the phylum Chlorobi, eg, Chlorobium tepidum. In some cases, the microbes used with the methods and compositions of the present disclosure may comprise a gene homologous to a known NifH gene. Known NifH gene sequences can be found, for example, in the Zehr lab NifH database, (wwwzehr.pmc.ucsc.edu / nifH Database Public / , April 4, 2014), or the database from Buckley lab NifH (www.css.cornell.edu / faculty / buckley / nifh.htm, and Gaby, John Christian, and Daniel H. Buckley. “A comprehensive aligned nifH gene database: a multipurpose tool for studies of nitroqen-fixing bacteria". Database 2014 ¢2014): bauOOl.). In some cases, the microbes used with the methods and compositions of the present disclosure may comprise a sequence encoding a polypeptide with at least 60%, 70%, 80%, 85%, 90%, 95%, 96%, 96% %, 98%, 99%, or greater than 99% sequence identity to a sequence from the Zehr lab NifH database, (wwwzehr.pmc.ucsc.edu / nifH Database Public / , April 4, 2014). In some cases, the microbes used with the methods and compositions of the present disclosure may comprise a sequence encoding a polypeptide with at least 60%, 70%, 80%, 85%, 90%, 95%, 96%, 96% %, 98%, 99%, or greater than 99% sequence identity to a sequence from the Buckley lab NifH database, (Gaby, John Christian, and Daniel H. Buckley. “A comprehensive aligned nifH gene database: a multipurpose tool for studies of nitrogen~fixing bacteria». Database 2014 (2014): bauOOl.). Microbes useful in the methods and compositions described herein can be obtained by extracting microbes from natural plant surfaces or tissues; seed grinding to isolate microbes; seed planting in various soil samples and recovery of microbes from tissues; or inoculation of plants with exogenous microbes and determination of which microbes appear in plant tissues. Non-limiting examples of plant tissues include a seed, seedling, leaf, cutting, plant, bulb, tuber, root, or rhizome. In some cases, the bacteria are isolated from a seed. Parameters for processing samples can be varied to isolate different types of associative microbes, such as rhizospheric, epiphytic, or endophytic. Bacteria can also be obtained from a repository, such as environmental strain collections, rather than PRRn / n / Lznz / q / Yi -68of initially isolating itself from a first floor. Microbes can be genotyped and phenotyped by sequencing the genomes of isolated microbes; generate profiles of the composition of in planta communities; characterize the transcriptomic functionality of communities or isolated microbes; or screen for microbial characteristics through the use of selective or phenotypic media (eg, nitrogen fixation or phosphate solubilization phenotypes). Selected candidate strains or populations can be obtained from sequence data; phenotype data; plant data (eg, genome, phenotype, and / or performance data); soil data (eg, pH, N / P / K content, and / or bulk soil biotic communities); or any combination of these. The bacteria, and the bacteria production methods described herein, can be applied to bacteria capable of self-propagation efficiently on the leaf surface, root surface, or within plant tissues without inducing a harmful reaction. plant defense responses, or to bacteria that are resistant to plant defense responses. The bacteria described herein can be isolated by culturing a plant tissue extract, or washing the leaf surface in a medium without added nitrogen. However, the bacteria may not be culturable, ie they are not known to be culturable, or are difficult to culture using standard methods known in the art. The bacteria described herein can be an endophyte or an epiphyte or a bacterium that inhabits the rhizosphere of the plant (rhizospheric bacterium). Bacteria obtained after repeating the steps of introducing genetic variation, exposing multiple plants, and isolating bacteria from plants with an improved trait one or more times (for example, 1, 2, 3, 4, 5, 10, 15, 25 or more times) can be endophytic, epiphytic or rhizospheric. Endophytes are organisms that enter the interior of plants without causing disease symptoms or causing the formation of symbiotic structures and are of agronomic interest because they can enhance plant growth and improve plant nutrition (for example, by fixing of nitrogen). The bacteria may be a seed-borne endophyte. Seed-borne endophytes include bacteria associated with or derived from the seed of a herb or plant, such as a seed-borne bacterial endophyte found in mature, dry, undamaged seeds (for example, without cracks, visible fungal infection, or germinated prematurely). Seed-borne bacterial endophyte may be surface-associated or derived rRRn / n / Lznz / q / Yi -69 from the seed; alternatively, or additionally, it may be associated with or derived from the interior compartment of the seed (eg, from a surface sterilized seed). In some cases, a seed-borne bacterial endophyte is capable of replicating within plant tissue, eg, the interior of the seed. Furthermore, in some cases, the seed-borne bacterial endophyte is capable of surviving desiccation. Bacteria isolated according to the methods of the disclosure, or used in the methods or compositions of the disclosure, may comprise multiple different bacterial taxa in combination. As an example, bacteria can include proteobacteria (such as pseudomonas, enterobacter, stenotrophomonas, burkholdería, paraburkholdería, rhizobium, herbaspirillum, pantoa, serratia, rahnella, azospirillum, azorhizobium, whip, dugen Orhízobíum, Metakosakonia and Halomonas ), Firmicutes (such as Bacillus, Paenibacillus, Lactobacillus, Mycoplasma, and Acetabacterium), and Actinobacterium (such as Streptomyces, Rhodacoccus, Microbacterium, and Curtobacterium). The bacteria used in the methods and compositions of this disclosure may include consortia of nitrogen-fixing bacteria of two or more species. In some cases, one or more bacterial species of the consortium of bacteria may be capable of fixing nitrogen. In some cases, one or more species of the bacterial consortium may facilitate or enhance the ability of other bacteria to fix nitrogen. Nitrogen-fixing bacteria and bacteria that enhance the ability of other bacteria to fix nitrogen may be the same or different. In some examples, one bacterial strain can fix nitrogen when combined with a different bacterial strain, or in a given consortium of bacteria, but may be unable to fix nitrogen in monoculture. Examples of bacterial genera that may be found in a consortium of nitrogen-fixing bacteria include, but are not limited to, Herbaspirillum, Azospirillum, Enterobacter, and Bacillus. Bacteria that can be produced by the methods described herein include Azotobacter sp. , Bradyrhizobium sp. , Klebsiella sp. , and Sinorhizobium sp. In some cases, the bacteria may be selected from the group consisting of: Azotobacter vinelandii, Azospirillum brasilense, Bradyrhízobium japonicum, Klebsiella pneumoniae, and Sinorhízobium meliloti. In some cases, the bacteria may be of the genus Enterobacter or Rahnella. In some cases, the bacteria may be of the genus Frankia or Clostridium. Examples of rRRn / n / Lznz / q / Yi bacteria -70 of the genus Clostridium include, but are not limited to, Clostridium acetobutylicum, Clostridium pasteurianum, Clostridium beijerinckii, Clostridium perfringens, and Clostridium tetan!. In some cases, the bacteria may be of the genus Paenibacillus, for example, Paenibacillus azotofixans, Paenibacillus borealis, Paenibacillus durus, Paenibacillus macerans, Paenibacillus polymyxa, Paenibacillus alvei, Paenibacillus amylolyticus, Paenibacillus campinasensis, Paenibacillus ibacillus chibensis, Paenibacillus glucanolyticus, Paenibacillus illinoisensis, Paenibacillus larvae supesp. larvae, Paenibacillus larvae supesp. pulvífaciens, Paenibacillus lautus, Paenibacillus macerans, Paenibacillus macquariensis, Paenibacillus macquariensis, Paenibacillus pabuli, Paenibacillus peoriae, or Paenibacillus polymyxa. In some examples, the bacteria isolated according to the methods of the description may be a member of one or more of the following taxa: Achromobacter, Acidíthíobacillus, Acidovorax, Acidóvoraz, Acinetobacter, Actínoplanes, Adlercreutzía, Aerococcus, Aeromonas, Afípía, Agromyces, Ancylobacter, Arthrobacter, Atopostipes, Azospirillum, Bacillus, Bdellovibrio, Beijerinckia, Bosea, Bradyrhízobium, Brevíbacillus, Brevundimonas, Burkholdería, Candidatus Haloredivivus, Caulobacter, Cellulomonas, Cellvibrio, Chryseobacterium, Citrobacter, Clostridium, Cor alíomargarita, Corynebacterium, Cupriavidus, Curtobacterium, Curvíbacter, Deínococcus , Delftía, Desemzía, Devosía, Dokdonella, Dyella, Enhydrobacter, Enterobacter, Enterococcus, Erwínía, Escheríchía, Escheríchía / Shígella, Exíguobacterium, Ferroglobus, Fílimonas, Finegoldía, Flavísolibacter, Flavobacterium, Frigoríbacterium, Gluconacetobacter, Haf nia, Halobaculum, Halomonas, Halosimplex, Herbaspirillum , Hymenobacter, Klebsíella, Kocuria, Kosakonia, LactobaciHus, Leclercia, Lentzea, Luteíbacter, Luteimonas, Massílía, Mesorhízobium, Methylobacterium, Microbacterium, Micrococcus, Mícrovírga, Mycobacterium, Neíssería, Nocardía, Oceaníbaculum, Ochrobactrum, Okíba cterium, Oligotropha, Oryzihumus, Oxalophagus, Paenibacillus , Panteoa, Pantoea, Pelomonas, Perlucidibaca, Plantibacter, Polynucleobacter, Propionibacterium, Propioniciclava, Pseudoclavibacter, Pseudomonas, Pseudonocardia, Pseudoxanthomonas, Psychrobacter, Rahnella, Ralstonia, Rheinheimera, Rhizobium, Rhodococcus, Rhodopseudomonas, R Oscatels, Ruminococcus, Sebaldella, Sediminibacillus, Sediminibacterium, Serratia , Shigella, Shinella, Sinorhizobium, Sinosporangium, Sphingobacterium, Sphingomonas, Sphingopyxis, Sphingosinicella, Staphylococcus, Stenotrophomonas, Strenotrophomonas, Streptococcus, Streptomyces, Stygiolobus, Sulfurisphaera, PRRn / n / Lznz / q / Yi - 71 Tatumella, Tepidimonas, Thermomonas, Thiobacillus, Variovorax, WPS-2 generates íncertae sedis, Xanthomonas, and Zimmermannella. In some cases, a bacterial species selected from at least one of the following genera is used: Enterobacter, Klebsiella, Kosakonia, and Rahnella. In some cases, a combination of bacterial species from the following genera is used: Enterobacter, Klebsiella, Kosakonia, and Rahnella. In some cases, the species used may be one or more of: Enterobacter sacchari, Klebsiella variicola, Kosakonia sacchari, and Rahnella aquatilis. In some cases, a gram-positive microbe may have an iron-molybdenum nitrogenase system comprising: nifH, nifD, nifK, nifB, nifE, nifN, nifX, hesA, nifV, nifW, nifU, nifS, nifII, and nifI2. In some cases, a gram-positive microbe may have a vanadium nitrogenase system comprising: vnfDG, vnfK, vnfE, vnfN, vupC, vupB, vupA, vnfV, vnfRl, vnfH, vnfR2, vnfA (transcription regulator). In some cases, a gram-positive microbe may have an iron-only nitrogenase system comprising: anfK, anfG, anfD, anfH, anfA (regulator of transcription). In some cases, a gram-positive microbe may have a nitrogenase system comprising glnB and glnK (nitrogen signaling proteins). Some examples of enzymes involved in nitrogen metabolism in gram-positive microbes include glnA (glutamine synthetase), gdh (glutamate dehydrogenase), bdh (3-hydroxybutyrate dehydrogenase), glutaminase, gltAB / gltB / gltS (glutamate synthase), asnA / asnB ( aspartate-ammonia ligase / asparagine synthetase), and ansA / ansZ (asparaginase). Some examples of proteins involved in nitrogen transport in gram-positive microbes include amtB (ammonium transporter), glnK (regulator of ammonium transport), glnPHQ / glnQHMP (ATP-dependent glutamine / glutamate transporters), glnT / alsT / yrbD / yflA (glutamine-like proton transporters), and gltP / gltT / yhcl / nqt (glutamate-like proton transporters). Examples of Gram-positive microbes that may be of particular interest include Paenibacillus polymixa, Paenibacillus riograndensis, Paenibacillus sp. , Frankia sp., Heliobacterium sp., Heliobacterium chlorum, Heliobacillus sp., Heliophilum sp. , Heliorestis sp. , Clostridium acetobutylicum, Clostridium sp. , Mycobacterium flaum, Mycobacterium sp. , Arthrobacter sp. , Agromyces sp. , Corynebacterium autitrophicum, Corynebacterium sp., Micromonspora sp. , Propionibacteria sp., Streptomyces sp. , and Microbacterium sp. PRRn / n / Lznz / q / Yii - 72 Some examples of genetic alterations that can occur in gram-positive microbes include: deletion of glnR to remove downregulation of BNF in the presence of environmental nitrogen, insertion of different promoters directly upstream of the nif cluster to remove regulation by GlnR in response to nitrogen environmental, mutation of glnA to reduce the rate of ammonium uptake via the GS-GOGAT pathway, deletion of amtB to reduce ammonium uptake from media, mutation of glnA to be constitutively in the feedback-inhibited state (FBI-GS ), to reduce ammonium assimilation via the GS-GOGAT pathway. In some cases, glnR is the main regulator of metabolism and N fixation in Paenibacillus species. In some cases, the genome of a Paenibacillus species may not contain a gene to produce glnR. In some cases, the genome of a Paenibacillus species may not contain a gene to produce glnE or glnD. In some cases, it is possible that the genome of a Paenibacillus species contains a gene to produce glnB or glnK. For example, Paenibacillus sp. WLY78 does not contain a gene for glnB, or its homologs found in the archaeon Methanococcus maripaludis, nifll and nif12. In some cases, the genomes of Paenibacillus species may be variable. For example, Paenibacillus polymixa E681 lacks glnK and gdh, has several nitrogen compound transporters, but only amtB appears to be controlled by GlnR. In another example, Paenibacillus sp. TDR2 has glnK, gdh, and most of the other core genes of nitrogen metabolism, has far fewer nitrogen compound transporters, but has glnPHQ controlled by GlnR. Paenibacillus riograndensis SBR5 contains a standard glnRA operon, an fdx gene, a major nif operon, a minor nif operon, and an anf operon (encoding iron-only nitrogenase). Putative glnR / tnrA sites were found before each of these operons. GlnR can regulate all of the above operons except the anf operon. GlnR can bind to each of these regulatory sequences as a dimer. Paenibacillus N-fixing strains can be divided into two subgroups: Subgroup I, which contains only a minimal set of nif genes, and Subgroup II, which contains a minimal set, plus one uncharacterized gene between nifX and hesA, and a often other clusters that duplicate some of the nif genes, such as nifH, nifHDK, nifBEN, or clusters encoding the vanadium nitrogenase (vni) or iron-only nitrogenase (anf) genes. rRRn / n / Lznz / q / Yi -73 In some cases, the genome of a Paenibacillus species may not contain a gene to produce glnB or glnK. In some cases, the genome of a Paenibacillus species may contain a minimal nif pool with 9 genes transcribed from a sigma-70 promoter. In some cases, a group of Paenibacillus nif may be downregulated by nitrogen or oxygen. In some cases, the genome of a Paenibacillus species may not contain a gene to produce sigma-54. For example, Paenibacillus sp. WLY78 does not contain a gene for sigma-54. In some cases, a group of nif may be regulated by glnR and / or TnrA. In some cases, the activity of a nif pool can be altered by altering the activity of glnR and / or TnrA. In Bacilli, glutamine synthetase (GS) is feedback-inhibited by high concentrations of intracellular glutamine, causing a confirmation change (termed FBI-GS). The Nif clusters contain distinct binding sites for the GlnR and TnrA regulators in various Bacilli species. GlnR binds and represses gene expression in the presence of excess intracellular glutamine and AMP. A role of GlnR may be to prevent the influx and intracellular production of glutamine and ammonium under conditions of high nitrogen availability. TnrA can bind to and / or activate (or repress) gene expression in the presence of limiting intracellular glutamine, and / or in the presence of FBI-GS. In some cases, the activity of a group of Bacilli nif can be altered by altering the activity of GlnR. Feedback-inhibited glutamine synthetase (FBI-GS) can bind to GlnR and stabilize GlnR binding to recognition sequences. Several bacterial species have a GlnR / TnrA binding site before the nif cluster. Disruption of the binding of FBI-GS and GlnR can alter the activity of the nif pathway. sources of microbes Bacteria (or any microbe according to the description) can be obtained from any general terrestrial environment, including its soils, plants, fungi, animals (including invertebrates), and other biota, including sediments, water, and the biota of Lakes and rivers; of the marine environment, its biota and sediments (eg seawater, marine mud, marine plants, marine invertebrates (eg sponges), marine vertebrates (eg fish)); the terrestrial and marine geosphere (regolith and k, eg crushed subterranean k, sand and clays); the cryosphere and its meltwater; the atmosphere (for example, filtered air dust, clouds, and raindrops); urban, industrial and other man-made environments (e.g. organic and mineral matter PRRn / n / Lznz / q / Yii - 74 accumulated in concrete, gutters, roof surfaces and road surfaces). The plants from which the bacteria (or any microbe according to the description) are obtained may be a plant that has one or more desirable traits, for example, a plant that grows naturally in a particular environment or under certain growing conditions. interest. By way of example, a given plant may grow naturally in sandy soil or sand of high salinity, or under extreme temperatures, or with little water, or may be resistant to certain pests or diseases present in the environment, and may be desirable for a commercial crop to grow under such conditions, particularly if they are, for example, the only conditions available in a particular geographic location. By way of further example, bacteria can be collected from commercial crops grown in such environments, or more specifically, from individual crop plants that best display a trait of interest among a crop grown in any specific environment: for example, the growing plants faster among crops grown in salinity-limited soils, or less damaged plants in crops exposed to severe insect damage or disease outbreaks, or plants that have the desired amounts of certain metabolites and other compounds, including the content of fiber, oil content, and the like, or desirable colors, flavor, or odor. Bacteria can be collected from a plant of interest or from any material found in the environment of interest, including fungal and other animal and plant biota, soil, water, sediment, and other environmental elements, as mentioned above. . Bacteria (or any microbe according to the description) can be isolated from plant tissue. This isolation can be produced from any suitable plant tissue, including, for example, roots, stems and leaves, and plant reproductive tissues. By way of example, conventional methods for plant isolation typically include sterile excision of plant material of interest (eg, root or stem length, leaves), surface sterilization with a suitable solution (eg, 2% sodium hypochlorite), after which the plant material is placed in a nutrient medium for microbial growth. Alternatively, surface sterilized plant material can be ground in a sterile liquid (usually water) and the liquid suspension, including small pieces of ground plant material, can be spread on the surface of a suitable solid agar medium, or medium, rRRn / n / Lznz / q / Yi -75which may or may not be selective (for example, it only contains phytic acid as a phosphorus source). This approach is especially useful for bacteria that form isolated colonies and can be collected individually for separate nutrient medium plates and purified into a single species by known methods. Alternatively, plant root or foliage samples cannot be surface sterilized but only gently washed, thus surface-dwelling epiphytic microorganisms are included in the isolation process, or microbes Epiphytes can be isolated separately by imprinting and peeling pieces of plant roots, stems, or leaves onto the surface of an agar medium and then isolating individual colonies, as indicated above. This approach is especially useful for bacteria, for example. Alternatively, the roots can be processed without washing small amounts of soil adhering to the roots, thereby including microbes that colonize the rhizosphere of the plant. Otherwise, soil adhering to the roots can be removed, diluted, and spread on agar of a suitable selective and nonselective medium for isolating individual colonies of rhizospheric bacteria. BUDAPEST TREATY ON THE INTERNATIONAL RECOGNITION OF THE DEPOSIT OF MICRO-ORGANISMS FOR PURPOSES OF PATENT PROCEEDINGS The microbial deposits of the present description were made in accordance with the provisions of the Budapest Treaty on the International Recognition of the Deposit of Microorganisms for Purposes of Patent Procedures (Budapest Treaty). Applicants represent that, pursuant to 37 CFR § 1.808(a)(2), "all restrictions imposed by the depositor on the availability to the public of the deposited material will be irrevocably removed upon grant of the patent." This statement is subject to paragraph (b) of this section (ie, 37 CFR § 1.808(b)). Enterobacter sacchari has now been reclassified as Kosakonia sacchari, the name of the organism may be used interchangeably throughout the manuscript. Many microbes of the present disclosure are obtained from two wild-type strains. Strain CI006 is a bacterial species previously classified in the genus Enterobacter (see reclassification mentioned above in Kosakonia). The CI019 strain is a bacterial species classified in the genus Rahnella. Repository information for wild-type (WT) Kosakonia CI006 and Rahnella WT CI019 is found in Table 1 below. rRRn / n / Lznz / q / Yi -76Some microorganisms described in this application were deposited on January 6, 2017 or August 11, 2017 at the Bigelow National Center for Marine Algae and Microbiota (NCMA), located at 60 Bigelow Drive, East Boothbay, Maine 04544, EE As mentioned above, all deposits were made in accordance with the terms of the Budapest Treaty on the International Recognition of the Deposit of Microorganisms for Purposes of Patent Procedure. The Bigelow National Center for Marine Algae and Microbiota registry numbers and deposit dates for the above-mentioned Budapest Treaty deposits are provided in Table 1. Biologically pure cultures of Kosakonia saccharí (WT), Rahnella aquatílís (WT), and a variant / remodeled strain of Kosakonia saccharí were deposited on January 6, 2017 at the Bigelow National Center for Marine Algae and Microbiota (NCMA), located at 60 Bigelow Drive, East Boothbay, Maine 04544, USA, and were assigned NCMA Patent Deposit Designation Numbers 201701001, 201701003, and 201701002, respectively. The applicable deposit information is found below in Table 1. Biologically pure cultures of variant / remodeled strains of Kosakonia sacchari were deposited on August 11, 2017 at the Bigelow National Center for Marine Algae and Microbiota (NCMA), located at 60 Bigelow Drive, East Boothbay, Maine 04544, USA. , and were assigned the NCMA patent deposit designation numbers 201708004, 201708003, and 201708002, respectively. The applicable deposit information is found below in Table 1. The biologically pure culture of Klebsiella variicola (WT) was deposited on August 11, 2017 at the Bigelow National Center for Marine Algae and Microbiota (NCMA), located at 60 Bigelow Drive, East Boothbay, Maine 04544, USA, and assigned NCMA Patent Deposit Designation Number 201708001. Biologically pure cultures of two variant / remodeled strains of Klebsiella variicola were deposited on December 20, 2017 at the Bigelow National Center for Marine Algae and Microbiota (NCMA) , located at 60 Bigelow Drive, East Boothbay, Maine 04544, USA, and assigned NCMA Patent Deposit Designation Numbers 201712001 and 201712002, respectively. The applicable deposit information is found below in Table 1. Biologically pure cultures of two variants / remodeled strains of Kosakonia saccharí were deposited on December 23, 2019, at the American Type Culture Collection (ATCC), located at 10801 University Boulevard, Manassas, Virginia. PRRn / n / Lznz / q / Yii - 77 20110-2209, USA, and assigned ATCC Patent Deposit Numbers PTA-126575 and PTA-126576. Biologically pure cultures of four variants / remodeled strains of Klebsiella variicola were deposited on December 23, 2019, at the American Type Culture Collection (ATCC), located at 10801 University Boulevard, Manassas, Virginia 20110-2209, USA, and They were assigned ATCC Patent Deposit Numbers PTA-126577, PTA-126578, PTA-126579 and PTA-126580. A biologically pure culture of a strain of Paenibacillus polymyxa (WT) was deposited on December 23, 2019 at the American Type Culture Collection (ATCC), located at 10801 University Boulevard, Manassas, Virginia 20110-2209, USA, and it was assigned the ATCC Patent Deposit Number PTA-126581. A biologically pure culture of a Paraburkholderia tropica (WT) strain was deposited on December 23, 2019 at the American Type Culture Collection (ATCC), located at 10801 University Boulevard, Manassas, Virginia 20110-2209, USA, and it was assigned the ATCC Patent Deposit Number PTA-126582. A biologically pure culture of a strain of Herbaspirilluiv. aquaticum (WT) was deposited on December 23, 2019, at the American Type Culture Collection (ATCC), located at 10801 University Boulevard, Manassas, Virginia 20110-2209, USA, and assigned the patent deposit number ATCC PTA-126583. Biologically pure cultures of four variants / remodeled strains of Metakosakonia intestini were deposited on December 23, 2019, at the American Type Culture Collection (ATCC), located at 10801 University Boulevard, Manassas, Virginia 20110-2209, USA, and They were assigned ATCC Patent Deposit Numbers PTA-126584, PTA-126586, PTA-126587 and PTA-126588. A biologically pure culture of a Metakosakonia intestine (WT) strain was deposited on December 23, 2019 at the American Type Culture Collection (ATCC), located at 10801 University Boulevard, Manassas, Virginia 20110-2209, USA, and it was assigned the ATCC Patent Deposit Number PTA-126585. The applicable deposit information is found below in Table 1. PRRn / n / Lznz / q / Yii Table 1: Microorganisms deposited under the Budapest Treaty To deposit! o Pivot strain name (some strains have multiple names) Taxonomy Record Number Date of Deposit NCMA CI006, PBC6.1, 6 Kosakonia sa.ccha.ri (WT) 201701001 Jan 06, 2017 NCMA CI019, 19 Rahnella aquatilis (WT) 201701003 Jan 06, 2017 NCMA CM029, 6-412 Kosakonia sacchari 201701002 Jan 06, 2017 NCMA 6-403 CM037 Kosakonia sacchari 201708004 Aug 11, 2017 NCMA 6- 404, CM38, PBC6.38 Kosakonia sacchari 201708003 Aug 11, 2017 NCMA CM094, 6-881, PBC6.94 Kosakonia sacchari 201708002 Aug 11, 2017 NCMA CI137, 137, PB137 Klebsiella variicola (WT) 201708001 Aug 11, 2017 NCMA 137- 1034 Klebsiella variicola 201712001 December 20 2017 NCMA 137-1036 Klebsiella variicola 201712002 Dec 20, 2017 ATCC 6-2425 Kosakonia sacchari PTA-126575 Dec 23, 2019 ATCC 6-2634 Kosakonia sacchari PTA-126576 Dec 23, 20 19 ATCC 137-1968 Klebsiella variicola PTA- 126577 December 23, 2019 PRRn / n / Lznz / q / Yi To deposit! o Pivot strain name (some strains have multiple names) Taxonomy Record number Date of deposit ATCC 137-2219 Klebsiella variicola PTA-126578 December 23, 2019 ATCC 137-2237 Klebsiella variicola PTA-126579 December 23, 2019 ATCC 137-2285 Klebsiella variicola PTA-126580 December 23, 2019 ATCC 41 Paenibacillus polymyxa (WT) PTA-126581 December 23, 2019 ATCC 8 Paraburkholdería tropica (WT) PTA-126582 December 23, 2019 ATCC 3069 Herba spi rillum aquaticum (WT) PTA-126583 December 23, 2019 ATCC 910-3655 Metakosakonia intes ti ni PTA-126584 December 23, 2019 ATCC 910 Metakosakonia intestini (WT) PTA-126585 December 23, 2019 ATCC 910-396 3 Metakosakonia intestini PTA -126586 December 23, 2019 ATCC 910-3961 Metakosakonia intestine PTA-126587 December 23, 2019 ATCC 910-3994 Metakosakonia intestine PTA-126588 December 23, 2019 PRRn / n / Lznz / q / Yi Isolated and biologically pure microorganisms The present disclosure, in certain embodiments, provides isolated and biologically pure microorganisms that have applications, among others, in agriculture. The microorganisms described can be used in their -80 states in isolation and biologically pure, as well as can be formulated into compositions (see the following section for illustrative composition descriptions). In addition, the description provides microbial compositions containing at least two members of the described isolated and biologically pure microorganisms, as well as methods of using said microbial compositions. In addition, the disclosure provides methods for modulating nitrogen fixation in plants using the described isolated and biologically pure microbes. In some aspects, the isolated and biologically pure microorganisms of the disclosure are those of Table 1. In other aspects, the isolated and biologically pure microorganisms of the disclosure are derived from a microorganism of Table 1. For example, in the Herein a strain, child, mutant or derivative of a microorganism of Table 1 is provided. The description contemplates all possible combinations of microbes listed in Table 1, where such combinations sometimes form a microbial consortium. The microbes in Table 1, either singly or in any combination, can be combined with any plant, active molecule (synthetic, organic, etc.), adjuvant, carrier, supplement, or biologic, mentioned in the description. In some aspects, the disclosure provides microbial compositions comprising species grouped in Tables 2-8. In some aspects, these compositions comprising various microbial species are referred to as consortia or microbial consortia. With respect to Tables 2-8, the letters A to I represent a non-exhaustive selection of microorganisms of the present description, defined as: A = Microbe with accession number 201701001 identified in Table 1; B = Microbe with accession number 201701003 identified in Table 1; C = Microbe with accession number 201701002 identified in Table 1; D = Microbe with registration number 201708004 identified in Table 1; E = Microbe with registration number 201708003 identified in Table 1; F = Microbe with registration number 201708002 identified in Table 1; G = Microbe with registration number 201708001 identified in Table 1; H = Microbe with registration number 201712001 identified in Table 1; and I = Microbe with registration number 201712002 identified in Table 1. rRRn / n / Lznz / q / Yi Table 2: Compositions of eight and nine strains A,B,C,D,E,F ,G,H A,B,C,D,E,F ,G,I A,B,C,D,E,F ,H,I A,B,C,D, E,G, Η, I A,B,C,D,F,G A,B,C,E,F,G A,B,D,E,F,G A,C,D,E,F,G , H, I B,C,D,E,F,G A,B,C,D,E,F,G,H,I Table 3: Compositions of seven strains A,B,C,D,E,F ,G A,B,C,D,E,F ,H A,B,C,D,E,F ,1 A,B,C,D,E,G ,H A ,B,C,D,E,G , I A,B,C,D,E,H , I A,B,C,D,F,G ,H A,B,C,D,F,G , I A, B ,C,D,F,H ,1 A,B,C,D,G,H , I A,B,C,E,F,G ,H A,B,C,E,F,G , I A,B, C,E,F,H , I A,B,C,E,G,H , I A,B,C,F,G,H , I A,B,D,E,F,G , H A,B,D, E,F,G , I A,B,D,E,F,H , I A,B,D,E,G,H , I A,B,D,F,G,H , I A,B,E,F, G,H ,1 A,C,D,E,F,G ,H A,C,D,E,F,G , I A,C,D,E,F,H , I A,C,D,E,G ,H , I A,C,D,F,G,H , I A,C,E,F,G,H ,1 A,D,E,F,G,H , I B,C,D,E,F, G ,H B,C,D,E,F,G , I B,C,D,E, F,H , I B,C,D,E,G,H , I B,C,D,F,G,H , I B,C,E,F,G,H , I B,D,E,F,G,H , I C,D,E,F,G,H , I Table 4: Compositions of six strains A,B,C,D,E , F A,B,C,D,E A,B,C,D,E ,H A,B,C,D,E , I A, B,C,D, F ,G A, B,C,D,F A,B,C,D,F , I A,B,C,D,G A,B,C,D,G A,B,C,D,H A,B,C,E,F A, B,C,E,F A,B,C,E,F A,B,C,E,G ,H , I , I zG / H , I zH A,B,C,E,G A,B,C,E ,H A,B,C, F,G A,B,C,F,G A,B,C,F,H A,B,C,G,H A,B,D,E,F , I , I ,H , I , I , I zG A,B,D,E,F A,B,D,E,F A,B,D,E,G A,B,D,E,G A,B,D,E,H A,B,D ,F,G A,B,D,F,G ,H , I , I , I , I D,E,F,G,H C,E,F,G,H A,B,D,F,H A,B,D ,G,H Α,Β,Ε, F,G A,B,E,F,G A,B,E,F,H , I , I , I , I , I , I A,B,E,G,H A, B,F,G,H A,C,D,E,F A,C,D,E,F A,C,D,E,F A,C,D,E,G A,C,D,E,G , I , I ,G , I , I A,C,D,E,H A,C,D,F,G A,C,D, F,G A, C,D,F,H A,C,D,G,H A,C, E,F,G A,C,E,F,G , I , I , I , I , I A,C,E,F,H A,C,E,G,H A,C, F,G,H A,D, E,F,G A,D,E,F,G A,D,E,F,H A,D,E,G,H , I -82 - , I , I , I ,1 , I A,D,F,G,H A,E,F,G,H B,C,D,E,F B,C,D,E,F B,C, D,E,F B,C,D,E,G B,C,D,E,G , I , I ,G ,H , I ,H , I B,C,D,E,H B,C,D,F, G B,C,D,F,G B,C,D,F,H B,C,D,G,H B,C,E,F,G B,C,E,F,G , I , H , I , I , I ,H , I ω Ω w B,C,E,G,H B,C, F,G,H B,D,E,F,G B,D,E, F,G B,D,E,F,H B, D,E,G,H , I , I , I , I ,1 , I B,D,F,G,H B,E,F,G,H C,D,E,F,G C,D,E,F, G C,D,E,F,H C,D,E,G,H C,D,F,G,H , I , I ,H , I , I ,1 , I Table 5: Compositions of five strains A,B,C,D, E A,B,C,D, F A,B,C,D, G A,B,C,D, H A,B,C,D, I A, B,C,E, F A, B,C,E, G A,B,C,E, H A,B,C,F, H A,B,C,F, G A,B,C,F, I A,B,C,G, H A,B, C,G, I Α,Β,Ο,Η, I A,B,D,E, F A,B,D,E, G A,B,D,E, I A,B,D,F, G A,B,D ,F, H A,B,D,F, I A,B,D,G, H A,B,D,G, I A, B,D,H, I A,B,E,F, G Α,Β,Ε, Ε, I A,B,E,G, H A,B,E,G, I Α,Β,Ε,Η, I A,B,F,G, H A,B,F,G, I Α,Β,Ε, Η, I A, B,G,H, I A,C,D,E, G A,C,D,E, H A,C,D,E, I A,C,D, F, G A,C,D,F, H A,C,D, F, I A, C, D,G, H A,C,D,G, I A,C,E,F, G A,C,E,F, H A,C,E,F, I A, C,E,G, H A,C,E,G, I A,C,E,H, I A, C, F,G, H A,C,F,G, I A,C,G,H, I A, D, E,F, G A,D,E, F, H l-l > ü A, D, E,G, H A, D, E,G, I A, D, E,H, I A, D, F,G, H A, D,F,H, I A, D,G,H, I A,E, F,G, H A,E,F,G, I A,E,F,H, I A,E,G, H, I A, F, G,H, I B,C,D,E, F B,C,D,E, H B,C,D,E, I B,C,D,F, G B,C,D,F, H B,C,D, F, I B,C,D,G, H B,C,D,G, I B,C,D,H, I B,C,E,F, H h ro o Γ3 o W o l-l tü O M o h ro Ω H W B, C, F,G, H B,C,F,G, I B,C, F,H, I B,D,E,F, G B,D,E,F, H B,D,E,F, I B,D, E,G,H B,D,E,G, I B,D,E,H, I B,D, F,G, H B,D, F,G, I B,D,G,H, I B,E, F, G, H B,E, F,G, I B,E,F,H, I B,E,G,H, I B,F,G,H, I C,D,E,F, G C,D,E,F, h C,D,E,G, H C,D,E,G, I C,D,E,H, I -8 C,D,F,G, H 3 - C,D, F,G, I C,D, F, H, I C,D,G,H, I C,E, F,G, H C,E,F,H, I C,E,G,H, I C,F,G,H, I D,E,F, G, H D,E,F,G, I D,E, F,H, I D,E,G,H, I D, F,G,H, I Α,Β,Ο,Ε, I Α,Β,Ο, Ε, H A,B,E,F, H A,C,D,E, F A,C,D,H, I A, 0, F, H, I A, D, F,G, I B,C,D,E, G β,ο,ε,ε, G B,C,G,H, I B,D, F,H, I C,D,E,F, I C,E, F,G, I E,F,G,H, I Table 6: Compositions of four strains A,B,C,D Α,Β,Ο,Ε Α,Β,Ο,Ε A,B,C,G A,B,C,H Α,Β,Ο, I Α,Β,Ο,Ε Α, Β,Ο,Ε D,G,H,I A,B,D,G A,B,D,H A, B,D,I A,B,E,F A, B,E,G A, Β,Ε,Η Α, Β,Ε, I A, B, F,G E, F,G,H A,B, F,H A, D, F,H A,D, F, I A,D,G,H A,D,G,I A,D, H, I A,E, F,G A,E, F,H E, F,G,I A, B,F,I A, B,G,H A, B,G,I Α,Β,Η,Ι A,C, D,E A,C,D, F A,C,D,G A,C,D,H E, Ε,Η,Ι A,C,D,I A, C,E,F A,C,E,G A,Ο,Ε ,Η A,Ο,Ε,Ι A, 0, F,G A,C, F,H Α,Ο,Ε,Ι E,G,H,I A,C,G,H A, C,G,I Α, Ο,Η,Ι A,D,E,F A, D,E,G Α,Ο,Ε,Η A,D,E,I A, D, F,G F,G,H,I A, E, F, I A ,E,G,H A,E,G,I A,Ε,Η,Ι A, F,G,H A, F,G, I A, F, Η, I A,G, Η, I D,E, F,H B, C,D,E B,C, D,F B,C,D,G Β,Ο,ϋ,Η B,C,D, I B,C,E, F ω Ω ra O B,C,E,H D,E, F,I Β,Ο,Ε,Ι B,C, F,G or m Ω T Η B,C,G,H B,C,G, I Β,Ο,Η,Ι ü T D,E,G,H B, D,E,G B,D,E,H Β,Ο,Ε,Ι B,D,F,G B, D, F,H B,D, F, I B,D,G,H B,D,G,I D, E,G,I B,D,H,I Β, E, F,G Β,Ε, F,H Β, E, F, I B,E,G,H B,E,G, I Β,Ε,Η, Ι B, F,G,H Ο,Ε,Η,Ι B, F,G, I B, Ε,Η,Ι B,G,H,I C,D,E,F C,D,E,G C,D, E,H C,D,E,I C,D, F,G D, F,G,H C,D, F,H C,D, F,I C,D,G,H C,D,G,I C,D,H, I C,E,F,G C,E,F,H C,E,F,I D,F,G,I C,E,G,H C,E,G,I Ο,Ε,Η,Ι C,F,G, H C,F,G,I 0, F,H, I C,G,H,I D,E, F,G D,F,H,I Table 7: Compositions of three strains Α,Β,Ο A, B,D Α,Β,Ε Α,Β, F A,B,G Α,Β,Η A, Β, I A,C,D Α,Ο,Ε G,H,I E, F , H A,C, F A,C,G A, Ο,Η Α,Ο, I A, D,E A,D, F A, D, G A,D,H A,D, I Ε,Η,Ι E, F,G A, E, F A,E,G Α,Ε,Η Α,Ε, I A, F,G A, F, H A, F, I A,G,H A,G, I F,G, I D,H, I Α,Η, I B ,C,D ω Ω Μ Β,Ο, F B,C,G Β,Ο,Η Β,Ο, I B,D,E B,D, F F,G,H D,G, I B,D,G B,D, H B ,D, I Β,Ε, F B,E,G Β,Ε,Η Β,Ε, I B,F,G B, F, H Ε,Η,Ι E, F, I B, F, I B,G, H B, G, I Β,Η, I C,D,E C,D, F C,D, G C,D,H C,D, I E,G,I D,G, H C,E, F C,E,G Ο,Ε,Η Ο ,Ε, I C, F,G 0, F, H 0, F, I C,G,H C,G, I E,G,H D, F, I Ο,Η, I D,E, F D,E,G Ο,Ε ,Η D,E,I D,F,G D,F,H -84Table 8: Compositions of two strains A, B A, C A, D A, E A, F A, G A, H A, I B,C B, D B,E B, F Q B,H B,I C,D C,E C, F C,G C,H C, I D,E D, F D,G D,H D, I E, F E,G E,H E, I F,G F,H F, I G,H G, I Η, I PRRn / n / Lznz / q / Yii In some embodiments, the microbial compositions can be selected from any group of members of Tables 2-8. In some embodiments, any microbe of the present disclosure can be modified or optimized to excrete ammonium constitutively or non-constitutively. In some embodiments, the modification of any microbe of the present disclosure is a transgenic modification. In some embodiments, the microbes are already a transgenic organism and the strains are modified such that they no longer contain a transgenic element. In some embodiments, the modification of any microbe of the present disclosure is a non-transgenic modification. In some embodiments, any two or more PGPRs are combined into a microbial consortium. In some embodiments, any two or more microbes of the present disclosure are combined into a microbial consortium. In some embodiments, the microbial consortia are applied to any one or more plants of the present disclosure and / or to the surrounding soil or growth medium. In some embodiments, any PGPR is applied to any one or more plants of the present disclosure and / or to the surrounding soil or growing medium. In some embodiments, the microbes of the present disclosure are modified or optimized to improve or increase the ability to colonize plants. In some embodiments, the improved or increased ability to colonize plants is an improved or increased ability to colonize the root surface. agricultural compositions Compositions comprising bacteria or bacterial populations produced according to the methods described herein and / or having the characteristics described herein may be in the form of a liquid, a foam or a dry product. Compositions comprising bacteria or bacterial populations produced according to the methods described herein and / or having the characteristics described herein may also be used to improve plant traits. In some examples, a composition comprising bacterial populations may be in the form of a dry powder, a suspension of powder and water, or a flowable seed treatment. The compositions that -85comprise bacterial populations may be coated on the surface of a seed and may be in liquid form. The composition can be made in bioreactors such as continuously stirred tank reactors, batch reactors and on the farm. In some examples, the compositions can be stored in a container, such as a jar or small bulk tanks. In some examples, the compositions may be stored within an object selected from the group consisting of a bottle, vial, blister, packet, container, bag, box, pail, envelope, carton, container, silo, shipping container, truck bed. and / or case. The compositions can also be used to improve plant traits. In some examples, a seed may be coated with one or more compositions. In some examples, a seedling may be coated with one or more compositions. In some examples, the surface of a seed may be coated with one or more compositions. In some examples, the surface of a seed may be coated with one or more compositions as a layer thereon. In some examples, a seed coating composition may be in liquid form, in dry product form, in foam form, in the form of a slurry of powder and water, or in a fluid seed treatment. In some examples, one or more compositions may be applied to a seed and / or seedling by spraying, dipping, coating, potting and / or dusting the seed and / or seedling with the one or more compositions. In some examples, a seed and / or seedling of the plant may be coated with multiple bacteria or bacterial populations. In some examples, at least two, at least three, at least four, at least five, at least six, at least seven, at least eight, at least nine, at least ten, or more than ten bacteria from a bacterial combination may be selected. from one of the following genera: Acidovorax, Agrobacterium, Bacillus, Burkholdería, Chryseobacterium, Curtobacterium, Enterobacter, Escheríchía, Methylobacterium, Paenibacillus, Pantoea, Pseudomonas, Ralstonia, Saccharíbacillus, Sphingomonas, and Stenotrophomonas. In some examples, at least two, at least three, at least four, at least five, at least six, at least seven, at least eight, at least nine, at least ten, or more than ten bacteria and bacterial populations of a combination endophyte are selected from one of the following families: Bacillaceae, Burkholderiaceae, Comamonadaceae, Enterobacteriaceae, Flavobacteriaceae, Methylobacteriaceae, Microbacteriaceae, Paenibacillileae, Pseudomonnaceae, Rhizobiaceae, PRRn / n / Lznz / q / Yi -86Sphingomonadaceae, Xanthomonadaceae, Ciadosporiaceae, Gnomoniaceae, Incertae sedis, Lasíosphaeriaceae, Netríaceae, and Pleosporaceae. In some examples, at least two, at least three, at least four, at least five, at least six, at least seven, at least eight, at least nine, at least ten, or more than ten bacteria and bacterial populations of a combination endophyte are selected from one of the following families: Bacillaceae, Burkholderiaceae, Comamonadaceae, Enterobacteriaceae, Flavobacteriaceae, Methylobacteriaceae, Microbacteriaceae, Paenibacillileae, Pseudomonnaceae, Phízobíaceae, Sphíngomonadaceae, Xanthomonadaceae, Ciadosporiaceae, Gnomoniacea e, Incertae sedis, Lasíosphaeriaceae, Netríaceae, Pleosporaceae. Examples of compositions may include seed coats for commercially important agricultural crops, for example, sorghum, canola, tomato, strawberry, barley, rice, corn, and wheat. Examples of compositions may also include corn, soybean, canola, sorghum, potato, rice, vegetable, cereal and oilseed seed coatings. The seeds provided herein may be genetically modified organisms (GMO), non-GMO, organic, or conventional. In some examples, the compositions can be sprayed on the aerial parts of the plant or applied to the roots by inserting them into the furrows in which the seeds of the plant are planted, watering the soil, or dipping the roots in a suspension of the composition. In some examples, the compositions can be dehydrated in a suitable manner that maintains cell viability and the ability to artificially inoculate and colonize host plants. The bacterial species may be present in the compositions at a concentration of between 108 to 1010 CFU / ml. In some examples, the compositions may be supplemented with trace metal ions, such as molybdenum ions, iron ions, manganese ions, or combinations of these ions. The concentration of the ions in exemplary compositions, as described herein, can be between about 0.1 mM and about 50 mM. Some exemplary compositions may also be formulated with a carrier, such as beta-glucan, carboxymethylcellulose (CMC), bacterial extracellular polymeric substance (EPS), sugar, animal milk, or other suitable carriers. In some examples, peat or planting materials may be used as a carrier, or biopolymers may be used as a carrier in which a composition is entrapped in the biopolymer. Compositions comprising the bacterial populations described herein can improve plant traits, such as promoting plant growth, maintaining a high PRRn / n / Lznz / q / Yii -87chlorophyll content in the leaves, increase the number of fruits or seeds, and increase the unit weight of fruits or seeds. Compositions comprising the bacterial populations described herein can be coated on the surface of a seed. As such, compositions comprising a seed coated with one or more bacteria described herein are also contemplated. The seed coat can be formed by mixing the bacterial population with a chemically inert, porous granular carrier. Alternatively, the compositions can be inserted directly into the furrows in which the seed is planted or sprayed on the leaves of the plant or applied by dipping the roots in a suspension of the composition. An effective amount of the composition can be used to populate the subsoil region adjacent to the roots of the plant with viable bacterial growth, or populate the leaves of the plant with viable bacterial growth. In general, an effective amount is an amount sufficient to produce plants with improved traits (eg, a desired level of nitrogen fixation). The bacterial compositions described herein can be formulated using an agriculturally acceptable carrier. The formulation useful for these modalities may include at least one member selected from the group consisting of a tackifier, a microbial stabilizer, a fungicide, an antibacterial agent, a preservative, a stabilizer, a surfactant, an anticomplexing agent, a herbicide, a nematicide, an insecticide, a plant growth regulator, a fertilizer, a rodenticide, a desiccant, a bactericide, a nutrient, or any combination of these. In some examples, the compositions may be storage stable. For example, any of the compositions described herein can include an agriculturally acceptable carrier (for example, one or more of a fertilizer, such as a non-naturally occurring fertilizer, a binder, such as a binder non-naturally occurring, and a pesticide, such as a non-naturally occurring pesticide). A non-naturally occurring adhesion agent can be, for example, a polymer, copolymer or synthetic wax. For example, any of the coated plants, seedlings or seeds described herein may contain an agriculturally acceptable carrier in the seed coat. In any of the compositions or methods described herein, an agriculturally acceptable carrier may be or may include a non-naturally occurring compound (eg, a non-naturally occurring fertilizer, non-naturally occurring bonding agent, etc.). rRRn / n / Lznz / q / Yi -88natural, such as a polymer, copolymer or synthetic wax, or a pesticide of non-natural origin). Non-limiting examples of agriculturally acceptable carriers are described below. Additional examples of agriculturally acceptable carriers are known in the art. In some cases, the bacteria are mixed with an agriculturally acceptable carrier. The carrier can be a solid carrier or a liquid carrier, and can be found in various forms including microspheres, powders, emulsions, and the like. The carrier can be one or more of a number of carriers that impart a variety of properties, such as stability, wettability, or dispersibility. Wetting agents, such as natural or synthetic surfactants, may be nonionic or ionic surfactants or the composition may include a combination of these. Water-in-oil emulsions can also be used to formulate a composition that includes the isolated bacteria (see, for example, US Patent No. 7,485,451). Suitable formulations that can be prepared include wettable powders, granules, gels, agar strips or pellets, thickeners and the like, microencapsulated particles, and the like, liquids such as aqueous fluids, aqueous suspensions, water-in-oil emulsions, etc. The formulation may include grain or legume products, eg, ground grain or beans, broth or flour derived from grains or beans, starch, sugar or oil. In some embodiments, the agricultural carrier may be soil or a growing medium for plants. Other agricultural carriers that can be used include water, fertilizers, vegetable-based oils, humectants, or combinations of these. Alternatively, the agricultural carrier can be a solid, such as diatomaceous earth, loam, silica, alginate, clay, bentonite, vermiculite, pods, other animal and plant products, or combinations, including pellets, sludge, or slurries. Mixtures of any of the above ingredients are also considered carriers, such as, but not limited to, paste (kaolin flour and clay), agar or flour based loam sediments, sand or clay, etc. Formulations may include food sources for bacteria, such as barley, rice, or other biological materials such as seed, plant parts, sugarcane bagasse, hulls or stalks from grain processing, plant material in soil, or wood. from waste from a construction site, sawdust or small fibers from recycling paper, cloth or wood. For example, a fertilizer can be used to help promote growth or rRRn / n / Lznz / q / Yi -89 provide nutrients to a seed, seedling, or plant. Non-limiting examples of fertilizers include nitrogen, phosphorous, potassium, calcium, sulfur, magnesium, boron, chloride, manganese, iron, zinc, copper, molybdenum, and selenium (or a salt thereof). Additional examples of fertilizers include one or more amino acids, salts, carbohydrates, vitamins, glucose, NaCl, yeast extract, NH4H2PO4, (NH4)2SO4, glycerol, valine, L-leucine, lactic acid, propionic acid, succinic acid, malic, citric acid, KH tartrate, xylose, lyxose and lecithin. In one embodiment, the formulation may include a tackifier or cling agent (referred to as a sticking agent) to help bind other active agents to a substance (eg, the surface of a seed). Such agents are useful for combining bacteria with carriers that may contain other compounds (eg, non-biological control agents), to produce a coating composition. Such compositions help create coatings around the plant or seed to maintain contact between the microbe and other agents with the plant or plant part. In one embodiment, the adhesives are selected from the group consisting of: alginate, gums, starches, lecithins, formononetin, polyvinyl alcohol, alkaline formononetinate, hesperetin, polyvinyl acetate, cephalins, acacia, xanthan gum, mineral oil, polyethylene glycol (PEG) , polyvinylpyrrolidone (PVP), Arabinogalactan, methylcellulose, PEG 400, chitosan, polyacrylamide, polyacrylate, polyacrylonitrile, glycerol, triethylene glycol, vinyl acetate, Gellan gum, polystyrene, polyvinyl, carboxymethylcellulose, Ghatti gum, and polyoxyethylene-polyoxybutylene block copolymers . In some embodiments, the adhesives may be, for example, a wax such as carnauba wax, beeswax, china wax, shellac wax, spermaceti wax, candelilla wax, castor wax, Ouricury wax, and bran wax. rice, a polysaccharide (eg, starch, dextrins, maltodextrins, alginates and chitosans), a fat, an oil, a protein (eg, gelatin and zeins), arable gum and shellac. Adhesive agents can be non-naturally occurring compounds, for example, polymers, copolymers, and waxes. For example, non-limiting examples of polymers that can be used as bonding agents include: polyvinyl acetates, polyvinyl acetate copolymers, ethylene vinyl acetate (EVA) copolymers, polyvinyl alcohols, polyvinyl alcohol copolymers, celluloses (for example , ethylcelluloses, methylcelluloses, hydroxymethylcelluloses, hydroxypropylcelluloses and carboxymethylcelluloses), polyvinylpyrrolidones, vinyl chloride, vinylidene chloride copolymers, PRRn / n / Lznz / q / Yii -90 calcium lignosulfonates, aculic copolymers, polyvinyl acrylates, polyethylene oxide, acylamide polymers and copolymers, polyhydroxyethyl acrylate, methylacrylamide monomers and polychloroprene monomers. In some examples, one or more of the adhesion agents, antifungal agents, growth regulating agents, and pesticides (eg, insecticides) are non-naturally occurring compounds (eg, in any combination). Additional examples of agriculturally acceptable carriers include dispersants (eg, polyvinylpyrrolidone / vinyl acetate PVPIVA S-630), surfactants, binders, and bulking agents. The formulation may also contain a surfactant. Non-limiting examples of surfactants include nitrogen-surfactant mixtures such as Prefer 28 (Cenex), Surf-N(US), Inhance (Brandt), P-28 (Wilfarm) and Patrol (Helena); esterified seed oils include Sun-It II (AmCy), MSO (UAP), Scoil (Agsco), Hasten (Wilfarm), and Mes-100 (Drexel); and organosilicone surfactants include Silwet L77 (UAP), Silikin (Terra), Dyne-Amic (Helena), Kinetic (Helena), Sylgard 309 (Wilbur-Ellis), and Century (Precision). In one embodiment, the surfactant is present at a concentration of between 0.01% v / v to 10% v / v. In another embodiment, the surfactant is present at a concentration of between 0.1% v / v to 1% v / v. In certain cases, the formulation includes a microbial stabilizer. Said agent may include a desiccant, which may include any compound or mixture of compounds that can be classified as a desiccant regardless of whether the compound or compounds are used in concentrations such that they do in fact have a drying effect on a liquid inoculant. Such desiccants are ideally compatible with the bacterial population used and should enhance the ability of the microbial population to survive application to the seeds and survive desiccation. Examples of suitable desiccants include one or more of trehalose, sucrose, glycerol, and methylene glycol. Other suitable desiccants include, but are not limited to, non-reducing sugars and sugar alcohols (eg, mannitol and sorbitol). The amount of desiccant introduced into the formulation can vary from about 5% to about 50% w / v, for example, from about 10% to about 40%, from about 15% to about 35% or between about 20% to about 30%. In some cases, it is advantageous if the formulation contains agents such as a fungicide, an antibacterial agent, a herbicide, a nematicide, an insecticide, a plant growth regulator, a rodenticide, a bactericide or a nutrient. In some rRRn / n / Lznz / q / Yi -91 examples, agents may include protectants that provide protection against seed-borne pathogens. In some examples, protectants can provide some level of control of soil-borne pathogens. In some examples, protectants may be effective predominantly on the surface of a seed. In some examples, a fungicide can include a compound or agent, either chemical or biological, that can inhibit the growth of a fungus or kill a fungus. In some examples, a fungicide can include compounds that can be fungistatic or fungicidal. In some examples, the fungicide may be a protectant or agents that are effective predominantly on the seed surface, provide protection against seed-surface-borne pathogens, and provide some level of control of soil-borne pathogens. Non-limiting examples of protective fungicides include captan, maneb, thiram, or fludioxonil. In some examples, the fungicide may be a systemic fungicide, which can be taken up by the emerging seedling and inhibit or kill the fungus within the host plant tissues. Systemic fungicides used for seed treatment include, but are not limited to, the following: azoxystrobin, carboxin, mefenoxam, metalaxyl, thiabendazole, trifloxystrobin, and various triazole fungicides including difenoconazole, ipconazole, tebuconazole, and triticonazole. Mefenoxam and metalaxyl are primarily used to target the water mold fungi Pythium and Phytophthora. Some fungicides are preferred over others, depending on the plant species, either due to subtle differences in sensitivity of pathogenic fungal species or due to differences in fungicide distribution or plant sensitivity. In some examples, the fungicide may be a biological control agent, such as a bacterium or fungus. Such organisms may be parasitic on pathogenic fungi or secrete toxins or other substances that can kill or otherwise prevent fungal growth. Any type of fungicide, particularly those commonly used on plants, can be used as a control agent in a seed composition. In some examples, the seed coating composition comprises a control agent that has antibacterial properties. In one embodiment, the control agent with antibacterial properties is selected from compounds described elsewhere herein. In another embodiment, the compound is streptomycin, rRRn / n / Lznz / q / Yi -92 oxytetracycline, oxolinic acid or gentamicin. Other examples of antibacterial compounds that can be used as part of a seed dressing composition include those based on dichlorophen and hemi formal benzyl alcohol (Proxel® from ICI or Acticide® RS from Thor Chemie and Kathon® MK 25 from Rohm & Haas ) and isothiazolinone derivatives such as alkylisothiazolinones and benzisothiazolinones (Acticide® MBS from Thor Chemie). In some examples, a growth regulator is selected from the group consisting of: abscisic acid, amidochlor, anzimidol, 6-benzylaminopurine, brassinolide, butralin, chlormequat (chlormequat chloride), choline chloride, cyclanilide, daminozide, dicegulaca, dimethipine, 2,6-dimethylpuridine, ethephon, flumetraline, flurprimidol, flutiacet, forchlorfenuron, gibberellic acid, inabenfide, indole-3-acetic acid, maleic hydrazide, mefluidide, mepiquat (mepiquat chloride), naphthaleneacetic acid, Ν-6-benzyladenine, paclobutrazol , prohexadione phosphorotrithioate, 2,3,5-tri-iodobenzoic acid, trinexapac-ethyl and uniconazole. Additional non-limiting examples of growth regulators include brassinosteroids, cytokinins (for example, kinetin and zeatin), auxins (for example, indolilacetic acid and indolilacetyl aspartate), flavonoids and isoflavonoids (for example, formononetin and diosmetin), phytotoxins (for example, glyceolin) and phytoalexin-inducing oligosaccharides (eg pectin, chitin, chitosan, polygalacuronic acid and oligogalacturonic acid) and gibberellins. Such agents are ideally compatible with the agricultural seed or seedling to which the formulation is applied (eg, should not be detrimental to plant growth or health). In addition, the agent is ideally one that does not cause safety concerns for human, animal, or industrial use (for example, it does not present safety concerns or the compound is sufficiently labile that the basic plant-derived plant product contains amounts minimums of the compound). Some examples of preferred nematode antagonist biocontrol agents include ARF18; 30 Arthrobotrys spp.; Chaetomium spp.; Cylindrocarpon spp.; Exophilia spp.; Fusarium spp.; Gliocladium spp.; Hirsutella spp.; Lecanicillium spp.; Monacrosporium spp.; Myrothecium spp.; Neocosmospora spp.; Paecilomyces spp.; Pochonia spp.; Stagonospora spp.; vesicular-arbuscular mycorrhizal fungi, Burkholderia spp.; Pasteuria spp., Brevibacillus spp.; Pseudomonas spp.; and Rhizobacteria. Particularly preferred nematode antagonist biocontrol agents include ARF18, Arthrobotrys oligospora, Arthrobotrys dactyloides, rRRn / n / Lznz / q / Yi -93 Chaetomium globosum, Cylindrocarpon heteronema, Exophilia jeanselmei, Exophilia pisciphila, Fusarium aspergilus, Fusarium solani, Gliocladium catenulatum, Gliocladium roseum, Gliocladium vixens, Hirsutella rhossiliensis, Hirsutella minnesotensis, Lecanicillium lecanii, Monacrosporium drechsleri, Monacrosporium gephyropagum, Myrotehcium verrucaria, Neocosmospora vasinfecta, Paecilomyces lilacinus, Pochonia chlamydosporia, Stagonospora heteroderae, Stagonospora phaseoli, vesicular-arbuscular mycorrhizal fungi, Burkholderia cepacia, Pasteuria penetrans, Pasteuria thornei, Pasteuria nishizawae, Pasteuria ramosa, Pastrueia usage, Brevibacillus laterosporus strain G4, Pseudomonas s fluorescens and Rhizobacteria. Examples of nutrients may be selected from the group consisting of a nitrogen fertilizer including, but not limited to, urea, ammonium nitrate, ammonium sulfate, unpressurized nitrogen solutions, aqueous ammonia, anhydrous ammonia, ammonium thiosulfate, sulfur-coated urea, urea formaldehydes, IBDU, polymer-coated urea, calcium nitrate, Ureaform, and Methyleneurea, phosphorus fertilizers such as diammonium phosphate, monoammonium phosphate, ammonium polyphosphate, concentrated superphosphate, and triple superphosphate, and potassium fertilizers such as potassium chloride, potassium sulfate, potassium-magnesium sulfate, potassium nitrate. Such compositions can exist as free salts or ions within the seed coating composition. Alternatively, nutrients / fertilizers can be complexed or chelated to provide a sustained release over time. Some examples of rodenticides may include those selected from the group consisting of 2-isovalerilindan-1,3-dione, 4-(guinoxalin-2ylamino)benzenesulfonamide, alpha-chlorohydrin, aluminum phosphide, antu, arsenic oxide, carbonate barium, bisthiosemi, brodifacoum, bromadiolone, bromethalin, calcium cyanide, chloralose, chlorophacinone, cholecalciferol, coumachlor, coumafuril, coumatetralyl, crimidine, difenacoum, difethialone, diphacinone, ergocalciferol, flocoumafen, fluoroacetamide, flupropadin, flupropadine hydrochloride, hydrogen cyanide , iodomethane, lindane, magnesium phosphide, methyl bromide, norbormide, fosacetim, phosphine, phosphorus, pindone, potassium arsenite, pyrinuron, scilliroside, sodium arsenite, sodium cyanide, sodium fluoroacetate, strychnine, stem sulfate, warfarin, and zinc phosphide. In liquid form, eg solutions or suspensions, bacterial populations can be mixed or suspended in water or aqueous solutions. The PRRn / n / Lznz / q / Yi Suitable liquid diluents or carriers include water, aqueous solutions, petroleum distillates, or other liquid carriers. Solid compositions can be prepared by dispersing the bacterial populations in and on a suitably divided solid carrier, such as peat, wheat, bran, vermiculite, clay, talc, bentonite, diatomaceous earth, Fuller's earth, pasteurized soil, and the like. When such formulations are used as wettable powders, biologically compatible dispersing agents such as nonionic, anionic, amphoteric or cationic dispersing and emulsifying agents may be employed. Solid carriers used in the formulation include, for example, mineral carriers such as kaolin clay, pyrophyllite, bentonite, montmorillonite, diatomaceous earth, acid white soil, vermiculite and perlite, and inorganic salts such as ammonium sulfate, ammonium phosphate. , ammonium nitrate, urea, ammonium chloride and calcium carbonate. Fine organic powders such as wheat flour, wheat bran, and rice bran may also be used. Liquid carriers include vegetable oils such as soybean oil and cottonseed oil, glycerol, ethylene glycol, polyethylene glycol, propylene glycol, polypropylene glycol, etc. pests The agricultural compositions of the disclosure, which can comprise any microbe described herein, are sometimes combined with one or more pesticides. Pesticides that are combined with the microbes of the description can target any of the pests listed below. "Pest" includes, but is not limited to: insects, fungi, bacteria, nematodes, mites, ticks, and the like. Insect pests include insects selected from the orders Coleoptera, Diptera, Hymenoptera, Lepidoptera, Mallophaga, Homoptera, Hemiptera, Orthroptera, Thysanoptera, Dermaptera, Isoptera, Anoplura, Siphonaptera, Trichoptera, etc., particularly, Lepidoptera and Coleoptera. Those skilled in the art will recognize that not all compounds are equally effective against all pests. Compounds that can be combined with the microbes of the description may show activity against insect pests, which may include economically important agronomic, forestry, greenhouse, nursery, ornamental, food and fiber, public health pests and animal, for domestic and commercial structures, for rRRn / n / Lznz / q / Yi products -95domestic and stored. As mentioned above, the agricultural compositions of the disclosure (which may comprise any microbes disclosed herein) are, in some embodiments, combined with one or more pesticides. These pesticides can be active against any of the following pests: Larvae of the order Lepidoptera include, but are not limited to, fall armyworms, cutworms, false loopers, and heliothinaes in the family Noctuidae and Spodoptera frugiperda J E Smith (fall armyworm); S. exigua Hubner (beet armyworm); S. litura Fabricius (black doughnut, black worm); Mamestra set yourself up Walker (bertha's armyworm); M. brassicae Linnaeus (cabbage noctua); Agrotis ipsilon Hufnagel (cutworm); A. orthogonia Morrison (bean cutworm); A. fabricius subterranean (granular worm); Alabama argillacea Hubner (cotton leaf looper); Trichoplusia ni Hubner (false cabbage looper); Pseudoplusia includens Walker (soybean false looper); Anticarsia gemmatalis Hubner (soybean velvet worm); Hypena scabra Fabricius (green clover worm); Heliothís virescens Fabricius (tobacco budworm); Pseudaletia unipuncta Haworth (corn armyworm); Athetis mindara Barnes and Mcdunnough (rough-skinned cutworm); Euxoa messoria Harris (dark cutworm); Earías insulana Boisduval (cotton bollworm); E. vittella Fabricius (spotted bollworm); Helicoverpa armigera Hubner (cotton bollworm); H. zea Boddie (corn earworm or cotton bollworm); Melanchra picta Harris (zebra caterpillar); Aegira (Xylomyges) curialis Grote (citrus cutworm); borers, bagworms, web worms, cone worms, and grapevine fleshworms of the family Pyralidae Ostrínia nubilalís Hubner (European screwworm); Amyelois transitella Walker (navel orange worm); Anagasta kuehniella Zeller (grey flour moth); Cadra cautella Walker (almond moth); Chilo suppressalis Walker (rice borer); C. partellus, (sorghum borer); Corcyra cephalonica Stainton (rice moth); Crambus caliginosellus Clemens (corn rootworm); C. teterrellus Zincken (turf caterpillar); Cnaphalocrocis medinalis Guenee (rice steamroller); Desmia funeralis Hubner (owner of the grape); Diaphania hyalinata Linnaeus (melon borer); D. nitidalis Stoll (cucumber borer); Diatraea grandiosella Dyar (southwestern corn borer), D. saccharalis Fabricius (sugarcane borer); Eoreuma loftini Dyar PRRn / n / Lznz / q / Yii -96(Mexican rice borer); Ephestia elutella Hubner (tobacco (cocoa) moth); Galleria mellonella Linnaeus (greater hive moth); Herpetogramma lícarsísalís Walker (tropical grass worm); Bomoeosoma electellum Hulst (sunflower moth); Elasmopalpus lignosellus Zeller (jumping worm borer); Achroia grísella Fabricius (small hive moth); Loxostege sticticalis Linnaeus (beet web worm); Orthaga thyrísalis Walker (tea tree moth); Maruca testulalis Geyer (pod borer); Plodia interpunctella Hubner (Indian wheat moth); Scírpophaga incertulas Walker (rice stem borer); Udea rubigalis Guenee (celery larvae); and flattener worms, butterfly larvae, seed worms, and fruit worms in the family Tortricidae Acleris gloverana Walsingham (western blackhead worm); A. variana Fernald (eastern blackhead worm); Archips argyrospila Walker (fruit tree leaf moth); A. resana Linnaeus (fruit tree cacoecia); and other species of Archips, Adoxophyes orana Fischer von Rosslerstamm {summer fruit tortrix); Cochylis hospes Walsingham (banded sunflower moth); Cydia latiferreana Walsingham (hazelnut worm moth); C. pomonella Linnaeus (codling moth); Platynota flavedana Clemens (black-shaded platynota moth); P. stultana Walsingham (curler); Lobesia botrana Denis & Schiffermuller (European vine moth); Spilonota ocellana Denis & Schiffermuller (Bud tortrix); Endopiza viteana Clemens (vine tortiz) ; Eupoecilia ambiguella Hubner (vine moth); Bonagota salubricola Meyrick (Brazilian apple steamroller); Grapholita molesta Busck (peach bud worm); Suleima helianthana Riley (sunflower bud moth); Argyrotaenia spp.; Choritoneura spp. Other selected agricultural pests in the order Lepidoptera include, but are not limited to, Alsophila pometaria Harris (fall canker worm); Anarsia lineatella Zeller (small peach leafminer); Anisota senatoria J. E. Smith (orange-striped oakworm); Antheraea pernyi Guerin-Meneville (oak tassar silk moth); Bombyx mori Linnaeus (silkworm); Bucculatrix thurberiella Busck (cotton leaf borer); Colias eurytheme Boisduval (alfalfa yellow butterfly); Datana integerrima Grote & Robinson (walnut caterpillar moth); Dendrolimus sibiricus Tschetwerikov (white-lined silk moth), Ennomos subsignaria Hubner (elm worm moth); Erannis tiliaria Harris (basswood looper); Euproctis chrysorrhoea Linnaeus (brown-tailed butterfly); Harrisina americana Guerin-Meneville (vine fleshworm) ; rRRn / n / Lznz / q / Yi -97Hemileuca oliviae Cockrell (Range caterpillar); Hyphantria cunea Drury (bag worm); Keiferia lycopersicella Walsingham (tomato pinworm); Lambdina fiscellaria fiscellaria Hulst (eastern dreary thorn); L. fiscellaria lugubrosa Hulst (western dreary thorn); Leucoma salícis Linnaeus (satin moth); Lymantria dispar Linnaeus (hairy holm oak lizard); Manduca quinquemaculata Haworth (five-spotted hawk, tomato hornworm); M. sexta Haworth (tomato hornworm, tobacco hornworm); Cperophtera brumata Linnaeus (winter moth); Paleacrita vernata Peck (spring canker worm); Papilio cresphontes Cramer (citrus dogworm); Phryganidia californica Packard (California oak worm); Phyllocnistis citrella Stainton (citrus leaf miner); Phyllonorycter blancardella Fabricius (Spotted Ientiform leafminer); Pieris brassicae Linnaeus (great cabbage white butterfly); P. rapae Linnaeus (small cabbage white butterfly); P. napi Linnaeus (green-veined white butterfly); Platyptilia carduidactyla Riley (Artichoke Feather Moth); Plutella xylostella Linnaeus (diamondback moth); Pectinophora gossypiella Saunders (pink cotton bollworm); Pontia protodice Boisduval and Leconte (cruciferous worm); Sabulodes aegrotata Guenee (omnivorous looper); Schízura concinna J. E. Smith (red-humped caterpillar); Sitotroga cerealella Olivier (cereal moth); Thaumetopoea pityocampa Schiffermuller (pine processionary moth); Lineóla bisselliella Hummel (clothes moth); Luta absoluta Meyrick (tomato leafminer); Yponomeuta padella Linnaeus (plum spider); Heliothís subflexa Guenee; Malacosoma spp. and Orgyia spp.; Ostrinia nubílalis (European corn borer); germinating corn seed worms; Agrotis ipsilon (cut worm). Larvae and adults of the order Coleoptera include weevils of the families Anthribidae, Bruchidae, and Curculionidae (including, but not limited to: Anthonomus grandís Boheman (cotton weevil); Lissorhoptrus oryzophilus Kuschel (rice water weevil); Sitophilus granarius Linnaeus (water weevil). of grains); S. oryzae Linnaeus (rice weevil); Hypera punctata Fabricius (clover weevil); Cylindrocopturus adspersus LeConte (sunflower stem weevil); Smicronyx fulvus LeConte (red sunflower seed weevil); S. sordidus LeConte (gray sunflower seed weevil); Sphenophorus maidis Chittenden (corn ladybug)); beetles, cucumber beetles, rootworms, leaf beetles, potato beetles, and leafminers in the family Chrysomelidae (including, but not limited to: Leptinotarsa ​​decemlineata PRRn / n / Lznz / q / Yii -98Say (potato leaf beetle); Diabrotica virgifera virgifera LeConte (western corn rootworm); D. barbera Smith and Lawrence (northern corn rootworm); D. undecimpunctata howardí Barber (southern corn rootworm); Chaetocnema pulicaria Melsheimer (corn flea beetle); Phyllotreta cruciferae Goeze (cruciferous flea beetle); Phyllotreta striolata (jumping beetle); Colaspis brunnea Fabricius (grape colaspis); Oulema melanopus Linnaeus (cereal leaf beetle); Zygogramma exclamationis Fabricius (sunflower beetle)); beetles of the family Coccinellidae (including, but not limited to: Epilachna varivestis Mulsant (Mexican bean beetle)); cockroaches and other beetles in the family Scarabaeidae (including, but not limited to: Popillia japonica Newman (Japanese beetle); Cyclocephala borealis Arrow (northern masked cockroach, white worm); C. immaculata Olivier (southern masked cockroach, white worm) ); Rhizotrogus majalis Razoumowsky (European cockroach); Phyllophaga crinita Burmeister (white worm); Ligyrus gibbosus De Geer (carrot beetle)); carpet beetles of the family Dermestidae; wireworms of the families Elateridae, Eleodes spp., Melanotus spp.; Conoderus spp.; Limonius spp.; Agriotes spp.; Ctenicera spp.; Aeolus spp.; bark beetles of the family Scolytidae and beetles of the family Tenebrionidae; Cerotoma trifurcate (bean leaf beetle); and wire worm. Adults and immatures of the order Diptera include Agromyza parvicornis Loew leafminers (corn spot miner); midges (including, but not limited to: Contarinia sorghicola Coquillett (sorghum panicle midge); Mayetiola destructor Say (wheat midge); Sitodiplosis mosellana Gehin (orange wheat midge); Neolasioptera murtfeldtiana Felt, (seed midge sunflower)); fruit flies (Tephritidae), Oscinella frit Linnaeus (fruit flies); Maggots (including, but not limited to: Delia platura Meigen (maize seed worm); D. coarctata Fallen (wheat grain fly) and other Delia spp., Meromyza americana Fitch (wheat stem worm ); Musca domestica Linnaeus (house fly); Fannia canicular!s Linnaeus, F. femoralis Stein (lesser house fly); Stomoxys calcitrans Linnaeus (stable flies)); face flies, horn flies, blowflies, Chrysomya spp.; Phormia spp. and other muscoid pests, horseflies Tabanus spp.; Gastrophilus spp.; Oestrus spp.; Owls Hypoderma spp.; deer flies Chrysops spp.; Melophagus ovinus Linnaeus (keds) and other Brachycera, Aedes spp. mosquitoes; rRRn / n / Lznz / q / Yi -99 Anopheles spp.; Culex spp.; black flies Prosimulium spp.; Simulium spp.; stink bugs, sand flies, sciarides, and other Nematocera. Adults and nymphs of the orders Hemiptera and Homoptera such as, but not limited to, Adelgidae hemiptera, Miridae knuckles, Cicadidae cicadas, leafhoppers, Empoasca spp.; of the Cicadellidae family, planthoppers of the Cixiidae, Flatidae, Fulgoroidea, Issidae and Delphacidae families, treehoppers of the Membracidae family, psyllids of the Psyllidae family, whiteflies of the Aleyrodidae family, aphids of the Aphididae family, phylloxera of the Phylloxeridae family, Mealbugs of the Pseudococcidae family, Scales of the Asterolecanidae, Coccidae, Dactylopiidae, Diaspididae, Eriococcidae Ortheziidae, Phoenicococcidae and Margarodidae families, Lace bugs of the Tingidae family, Brown marbled bug of the Pentatomidae family, True bugs, Blíssus spp. ; and other seed bugs of the family Lygaeidae, cercopoids of the family Cercopidae, sap-sucking insects of the family Coreidae, and red and spotted bugs of the family Pyrrhocoridae. Agriculturally important members of the order Homoptera also include, but are not limited to: Acyrthisiphon pisum Harris (pea aphid); Aphis craccívora Koch (peanut aphid); A. fabae Scopoli (black legume aphid); A. gossypíí Glover (cotton aphid, melon aphid); A. maidiradicis Forbes (corn root aphid); A. pomi De Geer (green citrus aphid); A. spíraecola Patch (citrus aphid); Aulacorthum solaní Kaltenbach (potato aphid); Chaetosíphon fragaefolií Cockerell (strawberry aphid); Díuraphís noxia Kurdjumov / Mordvilko (Russian wheat aphid) ; Dysaphís plantagínea Paaserini (red apple aphid); Eriosoma lanigerum Hausmann (woolly apple aphid); Brevícoryne brassicae Linnaeus (cruciferous mealy aphid); Hyalopterus pruní Geoffroy (mealy plum aphid); Lípaphís erysími Kaltenbach (turnip aphid); Metopolophium dirrhodum Walker (cereal aphid); Macrosiphum euphorbiae Thomas (potato aphid); Myzus persicae Sulzer (green aphid, green peach aphid); Nasonovia ribisnigri Mosley (lettuce aphid); Pemphigus spp. (root aphids and gall-forming aphids); Phopalosiphum maidis Fitch (corn leaf aphid); R. padi Linnaeus (green oat aphid); Schizaphis graminum Rondan! (wheat leaf aphid); Sipha flava Forbes (yellow sugarcane aphid); Sitobion avenae Fabricius (head aphid); Therioaphis maculata Buckton aphid PRRn / n / Lznz / q / Yii - 100 spotted alfalfa); Toxoptera aurantii Boyer de Fonscolombe (black citrus aphid) and T. citrícida Kirkaldy (brown citrus aphid); Melanaphis sacchari (sugarcane aphid); Adelges spp. (adelgids); Phylloxera devastatrix Pergande (caraña phyloxera); Bemisia tabaci Gennadius (tobacco whitefly, sweet potato whitefly); B. argentífolii Bellows & Perring (silverleaf whitefly); Dialearodes citri Ashmead (citrus whitefly); Trialearodes abutiloneus (banded-wing whitefly) and T. vaporariorum Westwood (greenhouse whitefly); Empoasca fabae Harris (potato leafhopper); Laodelphax stríatellus Fallen (little brown leafhopper); Macrolestes quadrílineatus Forbes (Aster leafhopper); Nephotettix cinticeps Uhler (green leafhopper); N. nígropictus Stal (rice leafhopper); Nilaparvata lugens Stal (brown leafhopper); Ashmead maidis peregrinas (corn grasshopper); Sogatella farelfera Horvath (white-backed leafhopper); Sogatodes orízícola Muir (false rice sharpie); Typhlocyba pomaria McAtee (white apple leafhopper); Erythroneoura spp. (grape hopper); Magicicada septendecím Linnaeus (pharaoh's cicada); Icerya purchasi Maskell (cottony citrus scale); Quadraspidíotus perniciosa Comstock (Saint Joseph scale); Planococcus citri Risso (citrus mealybug); Pseudococcus spp. (other mealy lice complexes); Cacopsylla pyricola Foerster (pear tree psyllid); Trioza diospyri Ashmead (Persimmon psyllid). Species in the order Hemiptera include, but are not limited to: Acrosternum hilare Say (green stink bug); Anasa tristis De Geer (squash bug); Blíssus leucopterus leucopterus Say (grain bug); Corythuca gossypii Fabricius (cotton lace bug); Cyrtopeltis modesta Distant (tomato bug); Dysdercus suturellus Herrich-Schaffer (cotton-spotting bugs); Euschistus servas Say (brown stink bug); E. variolarius Palisot de Beauvais (spotted stink bug); Graptostethas spp. (seed bug complex); Leptoglossas corenlas Say (pine seed bug); Lygas lineolaris Palisot de Beauvais (ligus bug); L. Hesperas Knight (western leaf bug); L. pratensis Linnaeus (common meadow bug); L. ragalipennis Poppius (European leaf bug); Lygocoris pabalinas Linnaeus (apple bug); Nezara viridala Linnaeus (green stink bug); Oebalus pugnax Fabricius (rice stink bug); Fascist Dallas Oncopeltas (Milkweed Bug); Pseadatomoscelis seriabas Reuter (jumping cotton flea). Hemiptera such as Calocoris norvegicas Gmelin (strawberry bug); Orthops rRRn / n / Lznz / q / Yi - 101 canpestris Linnaeus; Plesiocoris rugicollis Fallen (apple bug); Cyrtopeltis modesta Distant (tomato bug); Cyrtopeltis notatus Distant (small tobacco bug); Spanagonícus albofascíatus Reuter (black hop flea of ​​cotton); Díaphnocorís chloríónís Say (honey plant bug); Labopídícola thereí Knight (onion plant bug); Pseudatomoscelis seriatus Reuter (cotton fleahopper); Adelphocoris rapidus Say (jumping cotton flea); Poecilocapsus lineatus Fabricius (four-lined plant flea); Nysíus ericae Schilling (false bug); Nysius raphanus Howard (false bed bug); Nezara virídula Linnaeus (southern green stink bug); Eurygaster spp.; Coreidae spp.; Pyrrhocoridae spp.; Tinidae spp.; Blostomatidae spp.; Reduviidae spp. and Cimícidae spp. Adults and larvae of the order Acari (mites) such as Acería tosíchella Keifer (wheat curl mite); Petrobia latens Muller (brown wheat spider); spider mites and red mites in the family Tetranychidae, Panonychus ulmí Koch (European red mite); Tetranychus urticae Koch (two-spotted spider mite); (T. mcdaníelí McGregor (McDaniel mite); T. cínnabarínus Boisduval (common spider mite); T. turkestani Ugarov & Nikolski (strawberry mite); flat mites in the family Tenuipalpidae, Brevípalpus lewísí McGregor (citrus flat mite) ; bud and rust mites in the family Eríophyidae and other leaf-feeding mites and mites important to human and animal health, i.e. dust mites in the family Epidermoptidae, follicle mites in the family Demodicidae, grain mites in the family Glycyphagidae, ticks in the order Ixodidae Ixodes scapularis Say (deer ticks), I. holocyclus Neumann (Australian paralysis tick), Dermacentor variabilis Say (American dog tick); Amblyomma americanum Linnaeus (lone star tick) and ticks that cause itching and lesions in the families Psoroptidae, Pyemotidae, and Sarcoptidae. Insect pests of the order Thysanura, such as Lepisma saccharina Linnaeus (silverfish); Thermobia domestica Packard (Tahona thermobia). Additional arthropod pests include: spiders in the order Araneae such as Loxosceles reclusa Gertsch and Mulaik (brown hermit spider) and Latrodectus mactans Fabricius (black widow) and centipedes in the order Scutigeromorpha such as Scutigera coleoptrata Linnaeus (house centipede). The superfamily of stink bugs and related insects including, but not limited to, species belonging to the family Pentatomidae PRRn / n / Lznz / q / Yii - 102 (Nezara viridula, Halyomorpha halys, Piezodorus guildini, Euschistus servas, Acrosternum hilare, Euschistus heros, Euschistus tristigmus, Acrosternum hilare, Dichelops furcatus, Dichelops melacanthus, and Bagrada hilaris (Bagrada bug)), the family Plataspidae (Megacopta cribraria- shot of the bean) and family Cydnidae (Scaptocoris castanea-root stink bug) and species of Lepidoptera including, but not limited to: diamondback moth, eg, Helicoverpa zea Boddie; soybean looper, eg, Pseudoplusia includens Walker, and soybean velvetworm, eg, Anticarsia gemmatalis Hubner. Nematodes include parasitic nematodes such as root-knot, cyst and lesion nematodes, which include Heterodera spp., Meloidogyne spp. and Globodera spp.; particularly members of the cyst nematode group, including, but not limited to, Heterodera glycinas (soybean cyst nematode); Heterodera schachtii (beetroot cyst nematode); Heterodera avenae (cereal cyst nematode) ; and Globodera rostochiensis and Globodera pailida (potato cyst nematodes). Lesion nematodes include Pratylenchus spp. Pesticide compositions comprising a pesticide and a microbe of the description As mentioned above, the agricultural compositions of the disclosure, which may comprise any microbe described herein, are sometimes combined with one or more pesticides. Pesticides can include herbicides, insecticides, fungicides, nematicides, etc. In some embodiments, the pesticide / microbial combinations may be applied in the form of compositions and may be applied to the crop area or plant to be treated, simultaneously or in succession, with other compounds. These compounds can be fertilizers, herbicides, cryoprotectants, surfactants, detergents, pesticidal soaps, inactive oils, polymers, and / or biodegradable or time-release carrier formulations that allow long-term dosing to a target area after a single application of the formulation. . They can also be selective herbicides, chemical insecticides, virucides, microbicides, amebicides, pesticides, fungicides, bactericides, nematicides, molluscicides, or mixtures of several of these preparations, if desired, together with other carriers, surfactants, or application-promoting adjuvants acceptable for agriculture habitually employed. in the art of formulation. Suitable carriers (i.e., agriculturally acceptable carriers) and adjuvants can PRRn / n / Lznz / q / Yi - 103 be solid or liquid and correspond to substances commonly used in formulation technology, eg natural or regenerated mineral substances, solvents, dispersants, wetting agents, tackifiers, adhesives, binders or fertilizers. Also, the formulations can be prepared as edible "baits" or in the form of pest "traps" to allow feeding on, or ingestion of, the pesticide formulation by a target pest. Illustrative gummy compositions, which may be combined with the microbes of the description, include: Fruit / vegetable herbicides: Atrazine, Bromacil, Diuron, Glyphosate, Linuron, Metribuzin, Simazine, Trifluralin, Fluazifop, Glufosinate, Halo sulfuren Gowan, Paraquat, Propizamide, Setoxydim, Butafenacil, Halosulfuron, Indaziflam; Fruit / vegetable insecticides: Aldicarb, Bacillus thuringiensis, Carbaryl, Carbofuran, Chlorpyrifos, Cypermethrin, Deltamethrin, Diazinon, Malathion, Abamectin, Cyfluthrin / betacyfluthrin, Esfenvalerate, Lambda-cyhalothrin, Acequinocil, Bifenazate, Methoxyfenozide, Chromafenozide, Thiaclo prid, Dinotefuran, FluaCripirim , Tolfenpyrad, Clothianidin, Spirodiclofen, Gamma-cyhalothrin, Spiromesifen, Spinosad, Rinaxipir, Ciazipir, Spinoteram, Triflumuron, Spirotetramat, Flubendiamide, Thiodicarb, Metaflumizone, Sulfoxaflor, Ciflumethofen, Cyanopyrafen, Clothianidin, Thiamethoxam, Spinotoram, Thiodicarb, F lonicamid, Methiocarb, Emamectin Benzoate, Forthiazate, Fenamiphos, Cadusaphos, Pyriproxyfen, Fenbutatin oxide, Hexthiazox, Methomyl, 4-[[(6-Chlorpyridin-3-yl)methyl](2,2difluoroethyl)amino]furan-2(5H)-one; Fruit and vegetable fungicides: Carbendazim, Chlorothalonil, EBDC, sulfur, Thiophanate-methyl, Cymoxanil, Fluazinam, Fosetil, Iprodione, Kresoxim-methyl, Metalaxil / mefenoxam, Trifloxystrobin, Etaboxam, Iprovalicarb, Trifloxystrobin, Fenhexamid, oxpoconazole fumarate, Ciazofami d, Fenamidone, Zoxamide, Picoxystrobin, Pyraclostrobin, Ciflufenamid, Boscalid; Cereal herbicides:: Isoproturon, Bromoxynil, loxinil, Fenoxy, Chlorsulfuron, Clodinafop, Diclofop, Diflufenican, Fenoxaprop, Florasulam, Fluoroxypyr, Metsulfuron, Triasulfuron, Flucarbazone, Iodosulfuron, Propoxycarbazone, Picolin-afen, Mesosulfuron, Beflubutamid, Pinoxaden, Amidosulfuren, Tifensulfuron Methyl, Tribenuron, Flupyrsulfuron, Sulfosulfuron, Pirasulfotol, Piroxsulam, Flufenacet, Tralkoxydim, Pyroxasulfon; Cereal fungicides: Carbendazim, Chlorothalonil, Azoxystrobin, Ciproconazole, Ciprodinil, Fenpropimorph, Epoxiconazole, Kresoxim-methyl, Quinoxyfen, Tebuconazole, Trifloxystrobin, PRRn / n / Lznz / q / Yi - 104 Simeconazole, Picoxystrobin, Pyraclostrobin, Dimoxystrobin, Prothioconazole, Fluoxastrobin; Cereal insecticides: Dimethoate, Lambda-cyhalothrin, Deltamethrin, alpha-Cypermethrin, β-cyfluthrin, Clothianidin, Thiamethoxam, Thiacloprid, Acetamiprid, Dinetofuran, Chlorfirifos, Methamidophos, Oxidemeton methyl, Pirimicarb, Methiocarb; Corn herbicides: Atrazine, Alachlor, Bromoxynil, Acetochlor, Dicamba, Clopyralid, S-Dimethenamid, Glufosinate, Glyphosate, Isoxaflutole, S-Metolachlor, Mesotrione, Nicosulfuron, Primisulfuron, Rimsulfuron, Sulcotrione, Foramsulfuron, Topramezone, Tembotrione, Saflufenacil , Tiencarbazone, Flufenacet, Pyroxasulfon; Corn insecticides: carbofuran, chlorpirifos, fipronyl, lambda-cihalotrina, teflutrine, terbufos, tiametoxam, clotianidine, Spiromesifen, flubenndiamide, triflumuron, rynaxypyr, deltametrina, tiodicarb, β-ciflutrine, cippermetrine Triflumoron, Teflutrina, Tebupirim-Fos, Etiprole, Cyazypyr, Thiacloprid, Acetamiprid, Dinetofuran, Avermectin, Methiocarb, Spirodiclofen, Spiro-tetramat; Maize Fungicides: Fenitropan, Tiram, Prothioconazole, Tebuconazole, Trifloxystrobin; Rice Herbicides: Butachlor, Propanil, Azimsulfuron, Bensulfuron, Cihalo-fop, Daimuron, Fentrazamide, Imazosulfuron, Mefenacet, Oxaziclomefone, Pyrazosulfuron, Piributicarb, Quinclorac, Tiobencarb, Indanofan, Flufenacet, Fentrazamide, Halosulfuron, Oxaziclomefone, Ben zobicyclon, Piriftalid, Penoxsulam, Bispiribac, Oxadiargil, Ethoxysulfuron, Pre-tilachlor, Mesotrione, Tefuryltrione, Oxadiazone, Fenoxaprop, Pirimisulfan; Rice insecticides: Diazinon, Fenitrothion, Fenobucarb, Monocrotophos, Benfuracarb, Buprofezin, Dinotefuran, Fipronil, Isoprocarb, Thiacloprid, Chromafenozide, Thiacloprid, Dinotefuran, Clothianidin, Etiprol, Flubendiamide, Rynaxypyr, Deltamethrin, Acetamiprid, Thiamethoxam, C Yazypyr, Spinosad, Spinotoram, emamectin benzoate, Cypermethrin, Chlorpyrifos, Cartap, Methamidofos, Etofen-prox, Triazofos, 4-[[(6-Chlorpyridin-3-yl)methyl](2,2difluoroethyl)amino]furan-2(5H)-on, Carbofuran , Benfuracarb; Rice fungicides: Thiophanate-methyl, Carpropamid, Edifenfos, Ferimzona, Iprobenfos, Isoprothiolan, Pencicuron, Probenazol, Pyroquilon, Triciclazole, Trifloxystrobin, Diclocimet, Fenoxanil, Simeconazole, Tiadinil; Rice herbicides: Diuron, Fluometuron, MSMA, Oxifluorfen, Prometrin, Trifluralin, Carfentrazone, Clethodim, Fluazifop-butyl, Glyphosate, Norflurazon, Pendimetalin, Pyrithiobac-sodium, Trifloxysulfuron, Tepraloxydim, Glufosinate, Flumioxazin, Tidiazuron; Rice Insecticides: Acetate, Aldicarb, Chlorpyrifos, Cypermethrin, Deltamethrin, Malathion, Monocrotophos, Abamectin, Acetamiprid, Benzoate PRRn / n / Lznz / q / Yi - 105 emamectin, Lambda-Cyhalothrin, Spinosad, Thiodicarb, Gamma-Cyhalothrin, Spiromesifen, Pyridalyl, Flonicamid, Flubendiamide, Triflumuron, Rynaxypyr, BetaCyfluthrin, Spirotetramat, Clothianidin, Thiamethoxam, Thiacloprid, Dinetofuran, Flubendiamide, Cyazypyr, Spinosad, Spinotoram, gamma Cyhalothrin , 4-[[(6- Chlorpyridin-3-yl)methyl] (2, 2-difluoroethyl)amino]furan-2(5H)-on, Thiodicarb, Avermectin, Flonicamid, Pyridalyl, Spiromesifen, Sulfoxaflor, Profenofos, Triazofos, Endosulfan; Rice fungicides: Etridiazole, Metalaxil, Quintozene; Soy herbicides: Alachlor, Bentazone, Trifluralin, Chlorimuron-Ethyl, Chloransulam-Methyl, Fenoxaprop, Eomesafen, Elu-azifop, Glyphosate, Imazamox, Imazaquin, Imazethapyr, (S-)Metolachlor, Metribuzin, Pendimethalin, Tepraloxydim, Glufosinate; Soybean insecticides: Lambda-cyhalothrin, Methomyl, Parathion, Thiocarb, Clothianidin, Thiamethoxam, Thiacloprid, Acetamiprid, Dinetofuran, Flubendiamide, Rynaxypyr, Cyazypyr, Spinosad, Spinotoram, Emamectin benzoate, Fipronil, Etiprol, Deltamethrin, β-Cyfluthrin, gamma and lambda Cyhalothrin, 4-[[(6- Chlorpyridin-3-yl)methyl](2,2-difluoroethyl)amino]furan-2(5H)-on, Spirotetramat, Spinodiclofen, Triflumuron, Flonicamid, Thiodicarb, beta-Cyfluthrin; Soybean fungicides: Azoxystrobin, Cyproconazole, Epoxiconazole, Flutriafol, Pyraclostrobin, Tebuconazole, Trifloxystrobin, Prothioconazole, Tetraconazole; Sugar beet herbicides: Chloridazon, Desmedipham, Etofumesate, Fenmedipham, Trialate, Clopyralid, Fluazifop, Lenacil, Metamitron, Quinmerac, Cicloxydim, Triflusulfuron, Tepral-oxidim, Quizalofop; Sugar beet insecticides: Clothianidin, Thiamethoxam, Thiacloprid, Acetamiprid, Dinetofuran, Deltamethrin, βCyfluthrin, gamma / lambda Cyhalothrin, 4-[[(6-Chlorpyridin-3-yl)methyl](2,2difluoro-ethyl)amino]furan- 2(5H)-on, Tefluthrin, Rynaxypyr, Cyaxypyr, Fipronil, Garbofuran; Canola herbicides: Clopyralid, Diclofop, Fluazifop, Glufosinate, Glyphosate, Metazachlor, Trifluralin Etametsulfuron, Quinmerac, Quizalofop, Clethodim, Tepraloxydim; Canola fungicides: Azoxystrobin, Carbendazim, Fludioxonil, Iprodione, Procloraz, Vinclozolin; Canola insecticides: Carbofuran organophosphates, Pyrethroids, Thiacloprid, Deltamethrin, Clothianidin, Thiamethoxam, Acetamiprid, Dinetofuran, β-Cyfluthrin, gamma and lambda Cyhalothrin, tau-Fluvalerate, Etiprole, Spinosad, Spinotoram, Flubendiamide, Rynaxypyr, Cyazypyr, 4 -[ [(6-chloropyridin-3-yl)methyl](2,2-difluoroethyl)amino]furan-2(5H)-on. Insecticidal compositions comprising an insecticide and a microbe of the description PRRn / n / Lznz / q / Yi - 106 As mentioned above, the agricultural compositions of the disclosure, which may comprise any microbe described herein, are sometimes combined with one or more insecticides. Illustrative insecticides that can be combined with microbes of the description can be found in Table 9. Illustrative pesticides that can be combined with microbes of the description can be found in Table 10. In some embodiments, the insecticidal compositions may be included in the compositions set forth herein, and may be applied to a plant or plants or a portion thereof, simultaneously or in succession, with other compounds. Insecticides include ammonium carbonate, aqueous potassium silicate, boric acid, copper sulfate, elemental sulfur, calcium polysulfide, sucrose octanoate esters, 4-[[(6-chlorpyridin-3-yl)methyl](2,2difluoroethyl )amino]furan-2(5H)-on, abamectin, rotenone, fenazaquin, fenpyroximate, pyridaben, pyrimedifen, tebufenpyrad, tolfenpyrad, acephate, emamectin benzoate, lepimectin, milbemectin, hydroprene, kinoprene, methoprene, phenoxycarb, pyriproxyfen, methyl bromide and other alkyl halides, fulfuryl fluoride, chloropicrin, borax, disodium octaborate, sodium borate, sodium metaborate, tartar emetic, dazomet, metam, pyrifluquinazone, flofentezine, diflovidazin, hexythiazox, biphenazate, thiamethoxam, imidacloprid, fenpyroximate, azadirachtin, permethrin, Esfenvalerate, Acetamiprid, Azadirachtin, Pyrethrin, Imidacloprid, Beta-Cyfluthrin, Sulfotep, Tebupyrimfos, Temephos, Terbufos, Tetrachlorvinphos, Thiometon, Triazophos, Alanicarb, Aldicarb, Bendiocarb, Benfluracarb, Butocarboxim, Butoxycarboxim, Carbaryl, Carbofuran, Carbosulfan , etiofencarb, fenobucarb, formetanate, furathiocarb, isoprocarb, methiocarb, methomyl, metolcarb, oxamyl, primicarb, propoxur, thiodicarb, thiophanox, triazamate, trimetacarb, XMC, xylylcarb, acephate, azamethiphos, azinphos-ethyl, azinphos-methyl, cadusafos, chlorethoxyfox, trichlorfon , vamidothion, chlordane, endosulfan, ethiprole, fipronil, acrinathrin, allethrin, bifenthrin, bioallethrin, bioalleherin X-cyclopentenyl, bioresmethrin, cyclorotrin, cyfluthrin, cyhalothrin, cypermethrin, cyphenothrin [(IR)-transisomers], deltamethrin, empentrin [(EZ)-(IR )- isomers], esfenvalerate, etofenprox, fenpropatrin, fenvalerate, flucitrinate, flumethrin, halfenprox, kadathrin, phenothrin [(IR)-trans-isomer] prallethrin, pyrethrins (pyrethro), resmethrin, silafluofen, tefluthrin, tetramethrin, tetramethrin [(IR )-isomers], tralomethrin, transylutrin, alpha-cypermethrin, beta-cyfluthrin, beta-cypermethrin, d-cis-trans allethrin, d-trans allethrin, gamma-cyhalothrin, lamda-cyhalothrin, taurRRn / n / Lznz / q / Yi - 107 fluvalinate, theta-cypermethrin, zeta-cypermethrin, methoxychlor, nicotine, sulfoxaflor, acetamiprid, clothianidin, dinotefuran, imidacloprid, nitenpyram, thiacloprid, thiamethoxam, tebupirimfos, beta-cyfluthrin, clothianidin, flonicamid, hydramethylnon, amitraz, flu bendyamide, blorantraniliprole, lambda cyhalothrin, spinosad, gamma cyhalothrin, Beauveria bassiana, capsicum oleoresin extract, garlic oil, cabaryl, chlorpyrifos, sulfoxaflor, lambda cyhalothrin, Chlorfenvinphos, Chlormephos, Chlorpyrifos, Chlorpyrifos-methyl, Coumafos, Cyanofos, Demeton-S-methyl, Diazinon, Dichlorvos / DDVP, Dicrotophos, Dimethoate, Dimethylvinphos, Disulfoton, EPN, Ethion, Ethoprofos, Famfur, Fenamifos, Fenitrothion, Fention, Fostiazate, Heptenofos, Imiciafos, Isofenfos, Isopropyl 0-(methoxyaminothio-phosphoryl) salicylate, Isoxation, Malathion, Mecarba m, Methamidophos, Methidation, Mevinfos, Monocrotophos, Naled, Omethoate, Oxidemeton-methyl, Parathion, Parathion-methyl, Fentoate, Phorate, Fosalon, Fosmet, Fosfamidon, Foxim, Pirimifos-methyl, Profenofos, Propetamfos, Prothiofos, Pyraclofos, Pyridafenthion, Quinalphosfluacrypyrim, tebufenozide, chlorantraniliprole, Bacillus thuringiensis subsp. Kurstaki, terbufos, mineral oil, fenpropatrin, metaldehyde, deltamethrin, diazinon, dimethoate, diflubenzuron, pyriproxyfen, rosemary oil, peppermint oil, geraniol, azadirachtin, piperonyl butoxide, cyantraniliprole, alpha-cypermethrin, tefluthrin, pymetrozine, malathion, Bacillus thuringiensis supesp. israelensis, dicofol, bromopropylate, benzoximate, azadirachtin, flonicamid, soybean oil, Chromobacterium subtsugae strain PRAA4-1, zeta cypermethrin, phosmet, methoxyfenocide, paraffin oil, spirotetramat, methomyl, Metarhizium anisopliae strain F52, ethoprop, tetradifon, propargite, fenbutatin oxide , azocyclotin, cyhexatin, diafenthiuron, Bacillus sphaericus, etoxazole, flupyradifurone, azadirachtin, Beauvería bassiana, cyflumethophen, azadirachtin, quinomethionate, acephate, Isaria fumosorosea Apopka strain 97, sodium tetraborohydrate decahydrate, emamectin benzoate, cryolite, spine toram, Chenopodium ambrosioides extract , novaluron, dinotefuran, carbaryl, acequinocyl, flupyradifurone, iron phosphate, kaolin, buprofezin, cyromazine, chromafenozide, halofenozide, methoxyfenozide, tebufenozide, bistrifluron, chlorfluazuron, diflubenzuron, flucycloxuron, flufenoxuron, hexaflumuron, lufenuron, noca luron, noviflumuron, teflubenzuron, triflumuron , bensultap, cartap hydrochloride, thiocyclam, thiosultap-sodium, DNOC, chlorfenapyr, sulfuramid, phorate, tolfenpyrad, sulfoxaflor, neem oil, Bacillus thuringiensis supesp. tenebrionis strain SA-10, cyromazine, Burkholderia spp. Heat Killed, Cyantraniliprole, Cienopyrafen, Cyflumethophene, Sodium Cyanide, Potassium Cyanide, Potassium Cyanide PRRn / n / Lznz / q / Yi - 108 calcium, aluminum phosphide, calcium phosphide, phosphine, zinc phosphide, spriodiclofen, spiromesifen, spirotetramat, metaflumizone, flubendiamide, piflubumide, oxamyl, Bacillus thuringiensis supesp. aizawai, etoxazole and esfenvalerate. Table 9. Illustrative insecticides associated with various modes of action, which may be combined with microbes of the description PRRn / n / Lznz / q / Yi Mode of action Class of compound Examples of insecticides Physiological functions affected Acetylcholinesterase (AChE) inhibitors Carbamates Alanicarb, Aldicarb, Bendiocarb, Benfuracarb, Butocarboxim, Butoxycarboxim, Carbaryl, Carbofuran, Carbosulfan, Ethiofencarb, Fenobucarb, Formethane, Furathiocarb, Isoprocarb, Methiocarb, Methomyl, Metolcarb, Oxamil, Pirimicarb, Propoxur, Thiodicarb, Tiofanox, Triazamate, Trimetacarb, XMC, Xilylcarb Nerve and muscle inhibitors of acetylcholinesterase (AChE) organophosphates Acetate, Azamethifos, Azinphos-ethyl, Azinphos-methylp, Cadusafos, Chlorethoxyphos, Chlorfen vinphos, nerve and muscle - 109 - Mode of action Class of compound Examples of insecticides Physiological functions affected Chlormephos, Chlorpyrifos, Chlorpyrifos-methyl, Coumafos, Cyanofos, Demeton-S-methyl, Diazinon, Dichlorvos / DDVP, Dicrotophos, Dimethoate, Dimethylvinfos, Disulfoton, EPN, Ethion, Ethoprofos , Famfur, Fenamifos, Fenitrothion, Fention, Fostiazate, Heptenofos, Imiciafos, Isofenfos, Isopropyl 0(methoxyaminothiophosphoryl) salicylate, Isoxation, Malathion, Mecarbam, Methamidofos, Metidation, Mevinfos, Monocrotophos, Naled, Omethoate, Oxidemetonmethyl, Parathion, Parathion -methyl, Phentoate, Forate, Phosalon, Fosmet, Fosfamidon, Foxim, Pirimifos-methyl, Profenofos, -110 - Mode of Action Class of Compound Examples of Insecticides Physiological Functions Affected Propetamphos, Prothiophos, Pyraclofos, Pyridafention, Quinalfos, Sulfotep, Tebupirimfos, Temefos, Terbufos, Tetrachlorvinphos, Thiometon, Triazophos, Trichlorfon, Vamidothion Organochlorine cyclodiene GABA-gated chloride channel blockers Chlordane, Endosulfan Nerve and muscle GABA-regulated chloride channel blockers phenylpyrazoles (Fiproles) Etiprole, Eipronil Nerve and muscle sodium channel modulators pyrethroids, pyrethrins Acrinathrin, Allethrin, Bifenthrin, Bioallethrin, Bioallethrin Scyclopentenyl, Bioresmethrin, Cycloprothrin, Cyfluthrin, Cyhalothrin , Cypermethrin, Cyphenothrin [(1R)trans- isomers], Deltamethrin, Empentrin [(EZ)(IR)- isomers], Nerve and muscle PRRn / n / iζηζ / η / γ - 111 - Mode of Action Class of Compound Examples of Insecticides Physiological Functions Affected Esfenvalerate, Ethofenprox, Fenpropatrin, Fenvalerate, Flucitrinate, Flumethrin, Halfenprox, Kadathrin, Phenothrin [(IR)-trans-isomer], Prallethrin, Pyrethrins (pyrethrum), Resmethrin, Silafluofen , Tefluthrin, Tetramethrin, Tetramethrin [(1R)isomers], Tralomethrin, Transfluthrin, alphaCyhalothrin, betaCyfluthrin, betaCypermethrin, d-cistrans Allethrin, dtrans Allethrin, gamma-Cyhalothrin, lambda-Cyhalothrin, tau-Fluvalinate, theta-Cypermethrin, zeta- Cypermethrin sodium channel modulators DDT, methoxychlor DDT, methoxychlor Nerve and muscle modulators neonicotinoids Acetamiprid, Nerve and PRRn / n / iζηζ / ζι / γ - 112 - Mode of Action Class of Compound Examples of Insecticides Physiological Functions Affected Competitive Nicotinic Acetylcholine Receptor (nAChR) Clothianidin, Dinotefuran, Imidacloprid, Nitenpyram, Thiacloprid, Thiamethoxam Muscle Competitive Modulators of the Nicotinic Acetylcholine Receptor (nAChR) Nicotine Nicotine Nerve and Muscle Modulators Competitive Nicotinic Acetylcholine Receptor (nAChR) Modulators Sulfoximines Sulfoxaflor Nerve and Muscle Competitive Nicotinic Acetylcholine Receptor (nAChR) Modulators Butenolides Flupyradifurone Nerve and Muscle Allosteric Modulators of the Nicotinic Acetylcholine Receptor (nAChR) Spinosyns Spinotoram, Spinosad Nerve and Muscle Allosteric Modulators s of the channel glutamate (GluCl)-regulated chloride inhibitors avermectins, milbemycins Abamectin, emamectin benzoate, Lepimectin, MiIbeme ct ina Nerve and muscle mimics Hydroprene analogues, Growth PRRn / n / Lznz / q / Yi -113 - Mode of Action Class of Compound Examples of Insecticides Physiological Functions Affected Juvenile Hormone Juvenile Hormone Kinoprene, Methoprene Juvenile Hormone Mimics Fenoxicarb Fenoxicarb Growth Juvenile Hormone Mimics Pyriproxyfen Pyriproxyfen Growth Non-Specific Inhibitors (Multi-Site) Various Alkyl Halides Methyl Bromide and Others alkyl halides Unknown or non-specific non-specific inhibitors (multi-sites) various Chloropicrin Chloropicrin Unknown or non-specific non-specific inhibitors (multi-sites) various fluoride Cryolite, sulfuryl fluoride Unknown or non-specific non-specific inhibitors (multi-sites) various borates Borax, boric acid, disodium octaborate, sodium borate, sodium metaborate Unknown or nonspecific nonspecific inhibitors (multiple sites) various tartar emetic tartar emetic Unknown or nonspecific nonspecific inhibitors (multisite) various methyl isothiocyanate generators Dazomet, Metam Unknown or non-specific chordotonal organ modulators Pyridine derivatives azornetine Pymetrozine, pyrifluquinazone Nerve and muscle - 114 - Mode of Action Class of Compound Examples of Insecticides Physiological Functions Affected Mite Growth Inhibitors Clofentezine, Diflovidazin, Hexythiazox Clofentezine, Diflovidazin, Hexythiazox Growth Mite Growth Inhibitors Etoxazole Etoxazole Growth Microbial Switches of Midgut Membranes of Insects Bacillus thuringiensis and the insecticidal proteins produced by Bt var. aizawai, Bt var. israelensis, Bt var. kurstakl, Bt var. tenebrionensis Midgut microbial switches of midgut membranes of insects Bacillus sphaericus Bacillus sphaericus Midgut inhibitors of mitochondrial ATP synthase Diafentiuron Diafentiuron Respiration inhibitors of mitochondrial ATP synthase Organotin acarcides Azocyclotine, Cyhexatin, Fenbutatin Oxide Respiration inhibitors of mitochondrial ATP synthase Propargite Propargite Respiration inhibitors of mitochondrial ATP synthase Tetradifon Tetradifon Respiration Oxidative phosphorylation uncouplers via disruption Chlorfenapyr, DNOC, Sulfuramid Chlorfenapyr, DNOC, Sulfuramid Respiration PRRn / n / L7Π7 / Σ1 / Υ -115 - Mode of Action Class of Compound Examples of Insecticides Physiological Functions Affected by Proton Gradient Nicotinic Acetylcholine Receptor (nAChR) Channel Blockers Nereistoxin Analogues Bensultap, Cartap Hydrochloride, Thiociclam, Thiosultap-sodium Nerve and Muscle Chitin Biosynthesis Inhibitors , type 0 benzoylureas Bistrifluron, Chlorfluazuron, Diflubenzuron, Flucycloxuron, Flufenoxuron, Hexaflumuron, Lufenuron, Novaluron, Noviflumuron, Teflubenzuron, Triflumuron Growth inhibitors of chitin biosynthesis, type 1 Buprofezin Buprofezin Growth molt arrester, Dipteran Cyromazine Cyromazine Growth agonists of the receiver of ecdysone diacylhydrazines Chromafenozide, Halofenozide, Methoxyfenozide, Tebufenozide Growth octopamine receptor agonists Amitraz Amitraz Nerve and muscle complex electron transport inhibitors Hidramethylnon Hidramethylnon Respiration PRRn / n / Lznz / q / Yi -116 - Mode of Action Class of Compound Examples of Insecticides Physiological Functions Affected Mitochondrial III Inhibitors of Electron Transport of the Mitochondrial Complex III Acequinocil Acequinocil Respiration Inhibitors of Electron Transport of the Mitochondrial Complex III Fluacripyrim Fluacripirim Respiration Inhibitors of Electron Transport of the Mitochondrial Complex III Bifenazate Biphenazate Respiration Inhibitors of Mitochrondrial III mitochondrial complex electron transport I acaricides and insecticides Meti Fenazaquin, Fenpyroximate, Pyridaben, Pyrimidifen, Tebufenpyrad, Tolfenpyrad Respiration inhibitors of mitochondrial complex electron transport I Rotenone Rotenone Respiration voltage-gated sodium channel blockers oxadiazines Indoxacarb Nerve and muscle semicarbazone blockers Metaflumizone nerve and PRRn / n / Lznz / q / Yi - 117 - Mode of action Class of compound Examples of insecticides Physiological functions affected voltage-gated sodium channel muscle acetyl CoA carboxylase inhibitors tetronic and tetramic acid derivatives Spirodiclofen, Spiromesifen, Spirotetramat Growth inhibitors of electron transport of the mitochondrial complex IV phosphides Aluminum phosphide, calcium phosphine, phosphine, zinc phosphide Breathing inhibitors of electron transport of the mitochondrial complex IV cyanides Calcium cyanide, potassium cyanide, sodium cyanide Breathing inhibitors of the electron transport of the mitochondrial complex II derivatives of beta-ketonitrile Cyenopyraphen, Cyflumethophene Breathing inhibitors of the mitochrondrial complex electron transport II carboxanilides Piflubumide Respiration kidney receptor modulators dina diamides Chlorantraniliprole, Cyantraniliprole, Flubendiamide Nerve and muscle Cordotonal organ modulators target site Flonicamide Flonicamide Nerve and muscle PRRn / n / Lznz / q / Yi -118 - Mode of Action Class of Compound Examples of Insecticides Physiological Functions Affected Undefined Compounds of Unknown or Uncertain Mode of Action Azadirachtin Azadirachtin Unknown Compounds of Unknown or Uncertain Mode of Action Benzoximate Benzoximate Unknown Compounds of Unknown or Uncertain Mode of Action Bromopropylate Bromopropylate Unknown Compounds of Uncertain Mode of Action compounds of unknown or uncertain mode of action Quinomethionate Quinomethionate Unknown compounds of unknown or uncertain mode of action Dicofol Dicofol Unknown compounds of unknown or uncertain mode of action calcium polysulfide calcium polysulfide Unknown compounds of unknown or uncertain mode of action Pyridalyl Pyridalyl Unknown compounds of mode of action unknown or sulfur sulfur Unknown PRRn / n / L7Π7 / Σ1 / Υ -119 - Mode of action Class of compound Examples of insecticides Physiological functions affected uncertain óRRn / n / Lznz / q / Yi Table 10. Illustrative list of pesticides, which can be combined with microbes of the description. Category Insecticidal compounds Arsenical insecticides: calcium arsenate acetoarsenite copper copper arsenate lead arsenate potassium arsenite sodium arsenite botanical insecticides allicin anabasin azadirachtin carvacrol d-limonene matrin nicotine nornicotine oximatrin pyrethrins cinerin I cinerin II jasmolin I jasmolin II pyrethrin I pyrethrin II quassia rhodojaponin-III rotenone - 120 - Category Compounds riania sabadilla sanguinarine triptolide bendiocarb carbaryl carbamate insecticides benzofuranyl methylcarbamate insecticides benfuracarb carbofuran carbosulfan decarbofuran furathiocarb Dimethylcarbamate insecticides dimetan dimethylan hyquincarb isolan pirimicarb pyramat pyrolan al oxime carbamate insecticides anicarb aldicarb aldoxicarb butocarboxim butoxycarboxim methomyl nitrilacarb oxamyl tazimcarb thio carboxime thiodicarb thiophanox insecticides phenyl methylcarbamate allyxycarb aminocarb bufencarb butacarb - 121 - Category Compounds carbonolate cloetocarb CPMC dicresyl dimethacarb dioxacarb EMPC ethiofencarb fenethacarb fenobucarb isoprocarb methiocarb metolcarb mexacarbate promacil pr orne carb propoxur trimetacarb XMC xylylcarb inseati hearsay diamide broflanilide olorantrani1ipro1 ciantraniliprole cyclanilipro le cyhalodiamide flubendiamide tetraniliprol insecti dinitrophenol dinex dinoprop dinosam DNOC insecti fluoride barium hexafluorosilicate cryolite flursulamide - 122 - Category Compounds sodium fluoride sodium hexafluorosilicate sulflur amide formamidine insecticides amitraz chlordimeform formetanate formparanato medimeform seiri amitraz fumigation insecticides acrylonitrile carbon disulfide carbon tetrachloride carbonyl sulfide chloroform chloropicrin cyanogen para-dichlorobenzene 1,2-dichloropropane dithioether ethyl formate dibromide ethylene ethylene dichloride ethylene oxide hydrogen cyanide methyl bromide methyl iodide methyl chloroform methylene chloride naphthalene phosphine sodium tetrathiocarbonate sulfuryl fluoride tetrachloroethane inorganic insecticides borax PRRn / n / iζηζ / ζι / γ - 123 - Category Compounds boric acid calcium polysulfide copper oleate diatomaceous earth mercurous chloride potassium thiocyanate silica gel sodium thiocyanate insect growth regulators chitin synthesis inhibitors buprofezin cyromazine benzoylphenylurea synthesis inhibitors chitin bistrifluron chlorbenzuron chlorfluazuron dichlorbenzuron diflubenzuron flucicloxuron flufenoxuron hexaflumuron lufenuron novaluron novi flumuron penfluron teflubenzuron triflumuron juvenile hormone mimics dayoutong epophenonan phenoxycarb hydroprene kinoprene methoprene pyriproxyfen triprene juvenile hormones juvenile hormone I PRRn / n / Lznz / q / Yi - 124 - Category Compounds juvenile hormone II juvenile hormone III molting hormone agonists chromafenozide furan tebufenozide halofenozide methoxyfenozide tebufenozide yishijing molting hormones o-ecdysone ecdysterone molting inhibitors diofenolan precocene precocene I precocene II precocene III insect growth regulators unclassified dicyclanil macrocyclic lactone insecticides avermectin insecticides abamectin doramectin emamectin eprinomectin ivermectin selamectin milbemycin insecticides lepimectin miIbemectin milbemycin oxime moxidectin spinosyn insecticides spinetoram spinosad neonicotinoid insecticides neonicotinoid nitroguanidine insecticides clothianidinz dinotefuran imidaeloprid imidaclothiz PRRn / n / Lznz / q / Yi - 125 - Category Compounds Thiamethoxam insecticides nitromethylene neonicotinoids nitenpyram nithiazine pyridylmethylamine neonicotinoid insecticides acetamiprid imidacloprid nitenpyram paichongding thiacloprid nereistoxin analogue insecticides bensultap cartap polythialan thiocyclam thiosultap organochlorine insecticides bromine-DDT camphechlor DDT pp '-DDT ethyl-DDD HCH gamma-HCH lindane methoxychlor pentachlorophenol TDE insecticides cyclodiene aldrin bromocyclen chlorbicyclon chlordane chlordecone dieldrin dilor endosulfan alpha-endosulfan endrin PRRn / n / Lznz / q / Yi - 126 - Category Compounds HEOD heptachlor HHDN isobenzan isodrin kelevan mirex organophosphate insecticides organophosphate insecticides bromfenvinphos calvinphos chlorfenvinphos crotoxyphos dichlorvos dicrotophos dime t il vi nf o s phospirate heptenophos methocrotophos mevinfos monocrotophos naled naphthalophos phosphami don propafos TEPP tetrachlorvinphos organothiophosphate insecticides dioxabenzophos fosmethylan phenthoate aliphatic organothiophosphate insecticides acethion acetophos amiton cadusafos chlorethoxyphos - 127 - Category Compounds chlormephos demephion demephion-0 demephion-S demeton demeton-0 demeton-S demeton-methyl demeton-O-methyl demeton-S-methyl demeton-S-methylsulfone disulfoton ethion ethoprophos IPSP isothioate malathion methacryphos methylacetophos oxidemeton-methyl oxideprofos oxydisulfoton phorate sulf otep terbufos thiometon insectioids aliphatic organothiophosphate amide amidithion cyanthoate dimethoate ethoate-methyl formotion mecarbam omethoate protoate PRRn / n / iζηζ / η / γ - 128 - Category Compounds sophamide vamidothion oxime organothiophosphate insecticides chlorphoxim phoxim phox im-methyl z ame heterocyclic organothiophosphate insecticides thipho s rolophonate coumaphos coumitoate dioxation endothion menazon morphothion phosalone pyraclofos pyrazothion pyridafenthion quinothion benzo organothiophosphate insecticides pyran dithycrophos ticrophos organothiophosphate insecticides benzotriazine azinphos- ethyl azinphos-methyl isoindole organothiophosphate insecticides dialifos phosmet isoxazole organothiophosphate insecticides isoxathion zolaprofos pyrazolepyrimidine organothiophosphate insecticides chlorprazophos pyrazophos pyridine organothiophosphate insecticides chlorpyrifos chlorpyrifos-methyl pyrimidine butathio organothiophosphate insecticides phos diazinon etrimphos lyrimphos - 129 - Category Compounds pirimioxyphos pirimiphos-ethyl pirimiphos-methyl primidophos pyrimitate tebupirimfos quinoxaline organothiophosphate insecticides quinalphos quinalphos-methyl thiadiazole organothiophosphate insecticides atidation litidation metidation protidation triazole organothiophosphate insecticides isazophos triazophos organothiophosphate insecticides phenyl azotoate bromophos bromophos-ethyl carbophenothion chlorthiophos cyanophos dicapton cythioate diclofenthion etaphos famphur fenchlorphos fenitrothion fensulfothion fenthion fenthion-ethyl heterophos jodfenphos mesulfenfos parathion ivia / ι / υ / υυυο - 130 - Category Compounds parathion-methyl phenkapton phosnichlor profenofos prothiofos sulprofos temephos trichlormetaphos-3 trifenofos xiaoconglyulin phosphonate insecticides trichlorfon butonate phosphonothioate insecticides mecarphon phenyl ethylphosphonothioate insecticides fonofos trichloronat phenyl phenylphosphono insecticides cyanofenphos thioate EPN leptophos phosphoramidate insecticides crufornate fenamiphos fosthietan mephospholan phospholan phospholan-ethyl pyrimetaphos phosphoramidothioate insecticides phosphoric chloramine acetate isocarbophos isofenphos isofenphos-methyl metamidophos phosglycin propetamphos phosphorodiamide insecticides dimefox ΜΛ / t / ZUZ I ΙΌ fUWÓ - 131 - Category Compounds mazidox mipafox schradan oxadiazine insecticides indoxacarb oxadiazolone insecticides methoxadiazone phthalimide insecticides dialifos phosmet tetramethrin physical insecticides maltodextrin insecticides desiccants boric acid diatomaceous earth silica gel pyrazole insecticides chlorantraniliprole cyantraniliprole cyclanilipro l dimethylan isolan tebufenpyrad tetraniliprol tolfenpyrad phenylpyrazole insecticides acetoprol ethiprole fipronil fluiprole pyraclophos pyrafluprole pyriprole pyrolan vaniliprole pyrethroid insecticides pietroid ester insecticides acrinathrin allethrin bioallethrin esdépalletrinae rRRn / n / Lznz / q / Yi - 132 - Category Compounds barthrin bifenthrin kappa-bifenthrin bioethanemethrin brofenvalerate brofluthrinate bromethrin butethrin chlorempentrin cycloprothrin cyfluthrin beta-cyfluthrin cyhalothrin gamma-cyhalothrin lambda-cyhalothrin cypermethrin alpha-cypermethrin beta-cypermethrin theta-cypermethrin zeta-cypermethrin cyphenothrin deltamethrin dimefluthrin dimethrin empen trina d-fanshiluquebingjuzhi chloroprallethrin fenfluthrin phenpyritrin fenpropatrin fenvalerate esfenvalerate flucytrinaate - 133 - Category Compounds fluvalinate tau-fluvalinate furamethrin furethrin heptafluthrin imiprothrin j apotrins kadethrin methotrin methofluthrin epsilon-methofluthrin momfluorothrin epsilon-momfluorothrin pentmethrin permethrin biopermethrin transpermethrin phenothrin prallethrin profluthrin propartrin pyresmethrin renofluthrin meperfluthrin resmethrin bioresmethrin cisme trina tefluthrin kappa-tefluthrin terallethrin tetramethrin tetramethylfluthrin tralocitrin tralomethrin - 134 - Category Trans compounds fluthrin valerate pyrethroid ether insecticides etofenprox flufenprox halfenprox protrifenbute silafluofen pyrethroid oxime insecticides sulfoxime thiofluoximate pyrimidinamine insecticides flufenerim pyrimidifen pyrrole insecticides chlorfenapyr quaternary ammonium insecticides sanguinarine inse sulfoximine sulfoxaflor insecticides spirotetramat tetramic acid insecticides spiromesifen tetronic acid insecticides thiazol clothianidin imidaclothi z thiamethoxam thiapronil thiazolidine insecticides tazimcarb thiacloprid thiourea insecticides diafentiuron urea insecticides flucofuron sulcofuron zwitterionic insecticides dichloromethiaz triflumezopyrim unclassified insecticides afidopyropen afoxolaner allosamidine closantel na crotamiton copper phthenate EXD - 135 - Category Compounds fenazaflor fenoxacrim fióme toquin flonicamid fluhexafon flupyradifurone fluralaner fluxamethamide hydrameylnon isoprothiolane j iahuanqchongzong malonoben metaflumizone nifluridide plifenate pyridaben pyridalyl pyrifluquinazon rafoxanide thuringiensin triaratene triazamate acarioids botanical carvacrol sanguinarine bridged diphenyl acaricides azobenzene benzoximate benzyl benzoate bromopropylate chlorbenside chlorphenetol chlorfenson chlorphensulfide chlorobenzilate - 136 - Category Compounds chloropropionate cyumetofen DDT dicofol diphenyl sulfone dophenapin fenson fentrifanil fluorbenside genit hexachlorophene penproxide proclonol tetradifon tetrasul carbamate benomyl carbanolate carbaryl carbofuran methiocarb metolcarb promacil propoxur acariai das de carbamate oxime aldicarb buto carboxim o xamil thiocarboxime tiofanox pats carbazate biphenazate dinitrophenol miticides binapacryl dinex dinobuton dinocap dinocap-4 ivia / ι / υ / υυυο - 137 - Category Compounds dinocap-6 dinocton dinopenton dinosulfon dinoterbon DNOC formamidine acarioids amitraz chlordimeform chloromebuform formetanate formparanate medimeform semi amitraz macrocyclic lactone acaricides tetranactin avermectin acaricides abamectin doramectin eprinomectin ivermectin selamectin mil acaricides bemycin milbemectin milbemycin oxime moxidectin mite growth regulators clofentezine cyromazine diflovidazine dofenapin fluazuron flubenzimine flucycloxuron flufenoxuron hexythiazox organochlorine acaricides bromocylen camphechlor DDT - 138 - Category Compounds dienochlor endosulfan lindane organophosphorus acaricides organophosphate acaricides chlorfenvinphos crotoxyphos dichlorvos heptenophos mevinphos monocrotophos naled TEPP tetrachlorvinphos organothiophosphate acaricides amidition amiton azinphos-ethyl azinphos-methyl azotoate benoxafos bromophos bromine phos-ethyl carbophenothion chlorpyrifos chlorthiophos coumaphos cyanthoate demeton demeton-0 demeton-S demeton -methyl demeton-O-methyl demeton-S-methyl demeton-S-methylsulfon dialifos - 139 - Category Compounds diazinon dimethoate dioxation disulfoton endothion ethion ethoate-methyl formotion malathion mecarbam metacryphos omethoate oxideprofos oxydisulfoton parathion phenkapton phorate phosalone phosmet phostin phoxim pirimiphos-methyl protidation protoate pyrimitate quinalphos quinthiofos sophamide sulfotep thiometon triazophos trifenofos varrídothion acarioids of trichlorfon phosphonate ΜΛ / t / ZUZ I ΙΌ ÍOWÓ - 140 - Category Phosphoramidothioate Acarioid Compounds Isocarbophos Metamidophos Propetamphos Phosphorodiamide Acaricides Dimefox Mipafox Schradan Organotin Acaricides Azocyclotin Cyhexatin Phenbutatin Oxide Fostin Phenylsulfamide Acaricides Dichlofluanid Phthalimide Acaricides Dialifos Fosmet Pyrazole Acaricides Cienopirafen fenpyroximate piflubumide tebufenpyrad phenylpyrazole acaricides acetoprol fipronil vaniliprole pyrethroid acaricides ester acaricides pietroid acrinathrin bifenthrin brofluthrinate cyhalothrin cypermethrin alpha-cypermethrin fenpropatrin fenvalerate flucythrinate flumethrin fluvalinate tau-fluvalinate perme trin iviA / ι ιό / υυυο - 141 - Category Pietroide ether acarioid compounds halfenprox pyrimidineinine miticides pyrimidifen pyrrole miticides chlorfenapyr quaternary ammonium miticides sanguinarine quinoxaline miticides quinomethionate thioquinox strobilurin miticides strobilurin miticides methoxyacrylate bifujunzhi fluacripyrim flu phenoxystrobin pyriminostrobin sulfite ester acaricides ar amite proparqite tetronic acid acaricides spirodiclofen acaricides tetrazine clofentezine diflovidazine thiazolidine acaricides flubenz imine hexythiazox thiocarbamate acaricides fenotiocarb thiourea acaricides chloromethiuron diafenthiuron unclassified acaricides acequinocyl afoxolaner amido flumet arsenic oxide clenpirin closantel crotamiton cycloprate cymiazole disulfiram etoxazole fenazaflor fenazaquin - 142 - Category Compounds fluenetil fluralaner mesulfen MNAF nifluridide nikkomycins pyridaben sulfiram sulframid sulfur thuringiensin triaratene chemosterilisants afolate bisazir busulfan diflubenzuron dimatif hemel henpa metepa methiotepa methyl afolate morzid penfluron tepa thiohempa thiotepa tretamine uredepa repellents insect acrep butopyronoxyl camphor - 143 - Category Compounds d-Camphor carboxide dibutyl phthalate diethyltoluamide dimethyl carbate dimethyl phthalate dibutyl succinate ethohexadiol hexamide icaridine methoquinbutyl methylneodecanamide 2-(octylthio)ethanol oxamate quwenzhi quyingding rebemide zengxiaoan nematioides avermectin nematicides abamec tub botanical nematicides carvacrol nematicides carbamate benomyl carbofuran carbosulfan cloetocarb exime carbamate nematicides alanicarb aldicarb aldoxycarb oxamyl thyrpate fumigant nematicides carbon disulfide cyanogen 1,2-dichloropropane 1,3-dichloropropene MA / t / ZUZI ΙΌ ιΌΌΌύ - 144 - Category Compounds dithioether methyl bromide methyl iodide sodium tetrathiocarbonate organophosphorus nematicides organophosphate nematicides diami data fenamiphos fostietan phosphamidon organothiophosphate nematicides cadusafos chlorpyrifos diclofenthion dimethoate ethoprophos fensulfothion phostiazate heterophos isamidofos isazofos phosphocarb phorate terbufos thionazin triazophos phosphonothioate nematicides imiciafos mecarphon unclassified nematicides acetoprol benclothiaz chloropicrin dazomet DBCP DCIP fluazaindolizine fluensulfone - 145 - Category Compounds furfural metam methyl isothiocyanate thioxazafen xylenols PRRn / n / Lznz / q / Yii Insecticides also include synergists or activators which are not considered to be toxic or insecticidal in themselves, but are materials used with insecticides to synergize or enhance the activity of the insecticides. Synergists or activators include piperonyl butoxide. biorational pesticides Insecticides can be biorational or can also be known as biopesticides or biological pesticides. Biorational refers to any naturally occurring substance (or man-made substances resembling naturally occurring substances) that has a detrimental or lethal effect on specific pests, for example, insects, weeds, plant diseases (including nematodes), and They are vertebrate pests, have a unique mode of action, are non-toxic to humans, plants and domestic animals, and have few or no adverse effects on wildlife and the environment. Biorational insecticides (or biopesticides or biological pesticides) can be grouped into: (1) biochemical (hormones, enzymes, pheromones, and natural agents, such as insect and plant growth regulators), (2) microbial (viruses, bacteria, fungi, protozoa, and nematodes), or (3) plant-incorporated protectants (PIPs) - primarily transgenic plants, eg, Bt maize. Biopesticides or biological pesticides can generally include agents made from live microorganisms or a natural product and sold for the control of plant pests. Biopesticides can be: microorganisms, biochemicals and semiochemicals. Biopesticides can also include peptides, proteins, and nucleic acids such as double-stranded DNA, single-stranded DNA, double-stranded RNA, single-stranded RNA, and hairpin DNA or RNA. Bacteria, fungi, oomycetes, viruses and protozoa are used for the biological control of insect pests. The most widely used microbial biopesticide is the insect pathogenic bacterium Bacillus thuringiensis (Bt), which produces a protein crystal (Bt δ-endotoxin) during the formation of bacterial spores that - 146 is capable of causing lysis of intestinal cells when consumed by susceptible insects. Bt microbial biopesticides consist of bacterial spores and δ-endotoxin crystals mass-produced in fermentation tanks and formulated as a sprayable product. Bt does not harm vertebrates and is safe for people, beneficial organisms, and the environment. Therefore, Bt sprays are a growing pest management tactic in fruit and vegetable crops where their high level of selectivity and safety are considered desirable, and where resistance to synthetic chemical insecticides is a problem. Bt sprays have also been used on staple crops such as corn, soybeans, and cotton, but with the advent of plant genetic modification, farmers are growing more and more varieties of GM Bt crops. Other microbial insecticides include products based on entomopathogenic baculoviruses. Baculoviruses that are pathogenic to arthropods belong to the family of viruses and possess large circular, covalently closed, double-stranded DNA genomes that are packaged in nucleocapsids. More than 700 baculoviruses have been identified from insects of the orders Lepidoptera, Hymenoptera, and Diptera. Baculoviruses are usually highly specific to their host insects and are therefore safe for the environment, humans, other plants, and beneficial organisms. More than 50 baculovirus products have been used to control different insect pests throughout the world. In the US and Europe, Cydia pomonella granulovirus (CpGV) is used as an inundative biopesticide against the codling moth on apples. Washington state, as the largest apple grower in the US, uses CpGV on 13% of the apple crop. In Brazil, the soybean velvetworm Anticarsia geminatalis nucleopolyhedrovirus was used on up to 4 million ha (approximately 35%) of the soybean crop in the mid-1990s. Viruses such as Gemstar® (Certis USA) exist to control the larvae of Heliothis and Helicoverpa species. At least 170 different biopesticide products based on entomopathogenic fungi have been developed for use against at least five orders of insects and mites on greenhouse crops, field fruits and vegetables, as well as staple crops. Most of the products are based on the ascomycetes Beauveria bassiana or Metarhizium anisopliae. M. anisopliae has also been developed for the control of locust and grasshopper pests in Africa and Australia and is recommended by the PRRn / n / Lznz / q / Yi - 147 Food and Agriculture Organization of the United Nations (FAO) for locust management. Several microbial pesticides registered in the United States are listed in Table 16 of Kabaluk et al. 2010 (Kabaluk, J.T. et al. (Ed.). 2010. The Use and Regulation of Microbial Pesticides in Representative Jurisdictions Worldwide. IOBC Global. 99pp.) and registered microbial pesticides in selected countries are listed in Annex 4 of Hoeschle-Zeledon et al. 2013 (Hoeschle-Zeledon, I., P. Neuenschwander and L. Kumar. (2013). Regulatory Challenges for biological control. SP-IPM Secretariat, International Institute of Tropical Agriculture (UTA), Ibadan, Nigeria. 43 pp.), each of which is incorporated herein in its entirety. Plants produce a wide variety of secondary metabolites that discourage herbivores from feeding on them. Some of these can be used as biopesticides. They include, for example, pyrethrins, which are fast-acting insecticidal compounds produced by Chrysanthemum cinerariaefolium. They have low mammalian toxicity, but degrade rapidly after application. This short persistence prompted the development of synthetic pyrethrins (pyrethroids). The most commonly used botanical compound is neem oil, a chemical insecticide extracted from the seeds of Azadirachta indica. Two highly active pesticides based on secondary metabolites synthesized by soil actinomycetes are available, but have been evaluated by regulatory authorities as if they were synthetic chemical pesticides. Spinosad is a mixture of two macrolide compounds from Saccharopolyspora spinosa. It has very low mammalian toxicity and residues degrade rapidly in the field. It was widely used by farmers and growers after its introduction in 1997, but resistance has already developed in some major pests such as western flower thrips. Abamectin is a macrocyclic lactone compound produced by Streptomyces avermítilis. It is active against a variety of pest species, but resistance has also developed, for example, in tetranychid mites. Peptides and proteins from various organisms have been found to possess pesticidal properties. Perhaps the most prominent are spider venom peptides (King, G.F. and Hardy, M.C. (2013) Spider-venom peptides: structure, pharmacology, and potential for control of insect pests. Annu. Rev. Entomol. 58: 475-496 ). A unique arrangement of disulfide bonds in spider venom peptides makes them extremely resistant to proteases. As a result, these rRRn / n / Lznz / q / Yi - 148 peptides are very stable in the insect intestine and in the hemolymph and many of them are orally active. The peptides target a wide range of receptors and ion channels in the insect nervous system. Other examples of insecticidal peptides include: Sea anemone venom as a source of insecticidal peptides acting on voltage-gated Na+ channels. Toxicon. 49 (4): 550-560); the peptide PAlb (pea albumin 1, subunit b) from legume seeds with lethal activity against several insect pests, such as mosquitoes, some aphids and cereal weevils (Eyraud, V. et al. (2013) Expression and Biological Activity of the Cystine Knot Bioinsecticide PAlb (Pea Albumin 1 Subunit b), PLoS ONE 8(12): e81619); and a 10 kDa internal peptide generated by enzymatic hydrolysis of urease from Canavalia ensiformas (green bean) in susceptible insects (Martinelli, A.H.S., et al. (2014) Structurefunction studies on jaburetox, a recombinant insecticidal peptide derived from jack bean (Canavalia ensiformis) urease Biochimica et Biophysica Acta 1840: 935-944). Examples of commercially available peptide insecticides include Spear™-T for the treatment of thrips on greenhouse vegetables and ornamentals, Spear™-P for controlling the Colorado potato beetle, and Spear™-C for protecting crops from pests. from Lepidoptera (Vestaron Corporation, Kalamazoo, MI). A novel insecticidal protein from Bacillus bombysepticus, called parasporal crystalline toxin (PC), shows oral pathogenic activity and lethality towards silkworms and CrylAc-resistant strains of Helicoverpa armigera (Lin, P. et al. (2015) PC, a novel oral insecticidal toxin from Bacillus bombysepticus involved in host lethality via APN and BtR-175. Sci. Rep. 5: 11101). A semiochemical is a chemical signal produced by an organism that causes a change in behavior in an individual of the same or a different species. The most widely used semiochemicals for crop protection are insect sex pheromones, some of which can now be synthesized and are used to monitor or control pests through mass trapping, catch-and-kill systems, and mating disturbance. Worldwide, mating disturbance is used on more than 660,000 ha and has been particularly useful in orchard crops. As used herein, "transgenic insecticidal trait" refers to a trait exhibited by a plant that has been genetically modified to express PRRn / n / Lznz / q / Yii - 149 a nucleic acid or polypeptide that is detrimental to one or more pests. In one embodiment, the plants of the present disclosure are resistant to attachment to and / or infestation by any one or more of the pests of the present disclosure. In one embodiment, the trait comprises expression of Bacillus thuringiensis vegetative insecticidal proteins (VIPs), inhibitors of plant lectins and proteinases, terpenoids, Streptomyces spp. cholesterol oxidases, insect chitinases and fungal chitinolytic enzymes, bacterial insecticidal proteins, and genes. resistance to early recognition. In another embodiment, the trait comprises expression of a Bacillus thuringiensis protein that is toxic to a pest. In one embodiment, the Bt protein is a Cry protein (crystal protein). Bt-containing crops include Bt-containing maize, Bt-containing cotton, and Bt-containing soybean. Bt toxins may be of the Cry family (see, for example, Crickmore et al., 1998, Microbiol. Mol. Biol. Rev. 62 : 807-812), which are particularly effective against Lepidoptera, Coleoptera and Diptera. Bt Cry and Cyt toxins belong to a class of bacterial toxins known as pore-forming toxins (PFTs) that are secreted as water-soluble proteins and undergo conformational changes to insert into or translocate through their host's cell membranes. There are two main groups of PFTs: (i) β-helical toxins, in which the helix regions form the transmembrane pore, and (ii) β-barrel toxins, which insert into the membrane forming a β-barrel compound. by β-sheet hairpins of each monomer. See Parker MW, Feil SC, "Pore-forming protein toxins: from structure to function," Prog. Biophys. Mol. Biol. May 2005; 88(1):91-142. The first class of PFTs includes toxins such as the colicins, exotoxin A, diphtheria toxin, and also the tri-domain Cry toxins. On the other hand, aerolysin, α-hemolysin, anthrax protective antigen, cholesterol-dependent toxins such as perfringolysin O and Cyt toxins belong to β-barrel toxins. Id. In general, PFT-producing bacteria secrete their toxins and these toxins interact with specific receptors located on the host cell surface. In most cases, PFTs are activated by host proteases after receptor binding which induces the formation of an oligomeric structure that is competent for insertion. Finally, membrane insertion is triggered, in most cases, by a decrease in pH that induces a molten globule state of the protein. id The development of transgenic crops producing Bt Cry proteins has rRRn / n / Lznz / q / Yi - 150 allowed the replacement of chemical insecticides with ecological alternatives. In transgenic plants, the Cry toxin is produced continuously, protecting the toxin from degradation and making it accessible to chewing and boring insects. Production of Cry protein in plants has been improved by engineering Cry genes with plant-biased codon usage, by deletion of putative splicing signal sequences, and deletion of the carboxy-terminal region of the protoxin. . See, Schuler TH, et al., "Insect-resistant transgenic plants," Trends Biotechnol. 1998;16:168-175. The use of insect resistant crops has considerably decreased the use of chemical pesticides in the areas where these GM crops are grown. See, Qaim M, Zilberman D, “Yield effects of genetically modified crops in developing countries”, Science. 2003 Feb 7; 299(5608):900-2. Known Cry proteins include: δ-endotoxins including, but not limited to: Cryl classes, Cry2, Cry3, Cry4, Cry5, Cry6, Cry7, Cry8, Cry9, CrylO, Cryll, Cryl2, Cryl3, Cryl4, Cryl5, Cryl6 , Cryl7, Cryl8, Cryl9, Cry20, Cry21, Cry22, Cry23, Cry24, Cry25, Cry26, Cry27, Cry28, Cry29, Cry30, Cry31, Cry32, Cry33, Cry34, Cry35, Cry36, Cry37, Cry38, Cry39, Cry40, Cry41, Cry42, Cry43, Cry44, Cry45, Cry 46, Cry47, Cry49, Cry 51, Cry52, Cry 53, Cry 54, Cry55, Cry56, Cry57, Cry58, Cry59, Cry60, Cry61, Cry62, Cry63, Cry64, Cry65, Cry66, Cry67, Cry68, Cry69, Cry70 and Cry71 from δ-endotoxin genes and the B. thuringiensis cytolytic genes cytl and cyt2. Members of these classes of B. thuringiensis insecticidal proteins include, but are not limited to: CrylAal (accession no. AAA22353); CrylAa2 (accession no. accession no. AAA22552); CrylAa3 (accession no. BAA00257); CrylAa4 (accession no. CAA31886); CrylAa5 (accession no. BAA04468); CrylAa6 (accession no. AAA86265); CrylAa7 (accession no. AAD46139); CrylAa8 (accession no. 126149); CrylAa9 (accession no. ΒΑΆ77213); CrylAalO (accession no. AAD55382); CrylAall (Accession # CAA70856) ; CrylAal2 (Accession # AAP80146) ; CrylAal3 (accession no. AAM44305); CrylAal4 (Accession # AAP40639) ; CrylAal5 (Accession # AAY66993) ; CrylAal6 (accession no. HQ439776); CrylAal7 (accession no. HQ439788); CrylAalS (accession no. HQ439790); CrylAal9 (accession no. HQ685121); CrylAa20 (accession no. JF340156); CrylAa21 (Accession No. JN651496); CrylAa22 (accession no. KC158223); CrylAbl (accession no. AAA22330); CrylAb2 (accession no. AAA22613); CrylAb3 (accession no. AÍA22561); CrylAb4 (accession no. ΒΑΆ00071); CrylAb5 (accession no. CAA28405); CrylAb6 (Accession # ΑΑΆ22420) ; PRRn / n / Lznz / q / Yii - 151 CrylAb7 (accession no. CAA31620); CrylAb8 (accession no. AAA22551); CrylAb9 (accession no. CAA38701); CrylAblO (accession no. A29125); CrylAbll (Accession # 112419); CrylAbl2 (accession no. AAC64003); CrylAbl3 (accession no. AAN76494); CrylAbl4 (accession no. AAG16877); CrylAbl5 (accession no. AA013302); CrylAbl6 (accession no. AAK55546); CrylAbl7 (accession no. AAT46415); CrylAbl8 (accession no. AAQ88259); CrylAbl9 (accession no. AAW31761); CrylAb20 (accession no. ABB72460); CrylAb21 (Accession No. ABS18384); CrylAb22 (accession no. ABW87320); CrylAb23 (accession no. HQ439777); CrylAb24 (accession no. HQ439778); CrylAb25 (accession no. HQ685122); CrylAb26 (accession no. HQ847729); CrylAb27 (Accession No. JN135249); CrylAb28 (accession no. JN135250); CrylAb29 (Accession No. JN135251); CrylAb30 (accession no. JN135252); CrylAb31 (accession no. JN135253); CrylAb32 (accession no. JN135254); CrylAb33 (accession no. AAS93798); CrylAb34 (accession no. KC156668); similar to CrylAb (accession no. AAK14336); CrylAb-like (accession no. AAK14337); CrylAb-like (accession no. AAK14338); similar to CrylAb (accession no. ABG88858); CrylAcl (accession no. AAA22331); CrylAc2 (accession no. AAA22338); CrylAc3 (accession no. CAA38098); CrylAc4 (accession no. AAA73077); CrylAc5 (accession no. AAA22339); CrylAc6 (Accession # ΑΆΑ86266) ; CrylAcl (Accession # AAB46989) ; CrylAc8 (Accession # AAC44841) ; CrylAc9 (accession no. AAB49768); CrylAClO (accession no. CAA05505); CrylAcll (accession # CAA10270) ; CrylAcl2 (accession no. 112418); CrylAcl3 (accession no. AAD38701); CrylAcl4 (accession no. AAQ06607); CrylAcl5 (accession no. AAN07788); CrylAcl6 (accession no. AAU87037); CrylAcll (accession no. AAX18704); CrylAcl8 (accession no. AAY88347); CrylAcl9 (accession no. ABD37053); CrylAc20 (accession no. ABB89046); CrylAc21 (accession no. ΑΆΥ66992); CrylAc22 (accession no. ABZ01836); CrylAc23 (accession no. CAQ30431); CrylAc24 (accession no. ABL01535); CrylAc25 (accession no. FJ513324); CrylAc26 (accession no. FJ617446); CrylAc27 (accession no. FJ617447); CrylAc28 (accession no. ACM90319); CrylAc29 (accession no. DQ438941); CrylAc30 (accession no. GQ227507); CrylAc31 (accession no. GU446674); CrylAc32 (accession no. HM061081); CrylAc33 (accession no. GQ866913); CrylAc34 (accession no. HQ230364); CrylAc35 (accession no. JF340157); CrylAc36 (accession no. JN387137); CrylAc37 (accession no. JQ317685); CrylAdl (accession no. AAA22340); CrylAd2 (accession no. CAA01880); CrylAel (accession no. ΆΑΑ22410); CrylAfl (accession no. AAB82749); CrylAgl (accession no. AAD46137); CrylAhl (accession no. AAQ14326); CrylAh2 (accession no. ABB76664); CrylAh3 (accession no. HQ439779); CrylAúl (registry no. rRRn / n / Lznz / q / Yi - 152 ΑΑ039719 ); CrylAi2 (accession no. HQ439780); similar to CrylA (accession no. AAK14339); CrylBal (accession no. CAA29898); CrylBa2 (accession no. CAA65003); CrylBa3 (accession no. AAK63251); CrylBa4 (accession no. AAK51084); CrylBa5 (accession no. AB020894); CrylBa6 (accession no. ABL60921); CrylBa7 (accession no. HQ439781); CrylBbl (accession no. ΑΑΆ22344); CrylBb2 (accession no. HQ439782); CrylBcl (accession no. CAA86568); CrylBdl (accession no. AAD10292); CrylBd2 (accession no. AAM93496); CrylBel (accession no. AAC32850); CrylBe2 (accession no. AAQ52387); CrylBe3 (accession no. ACV96720); CrylBe4 (accession no. HM070026); CrylBfl (accession no. CAC50778); CrylBf2 (accession no. AAQ52380); CrylBgl (accession no. AA039720); CrylBhl (accession no. HQ589331); CrylBil (registration no. KC156700); CrylCal (accession no. CAA30396); CrylCa2 (accession no. CAA31951); CrylCa3 (Accession # ΑΆΑ22343) ; CrylCa4 (accession no. CAA01886); CrylCa5 (accession no. CAA65457); CrylCa6 [1] (accession no. AAF37224); CrylCa7 (accession no. AAG50438); CrylCa8 (accession no. AAM00264); CrylCa9 (accession no. AAL79362); CrylCalO (accession no. AAN16462); CrylCall(registry# AAX53094); CrylCal2 (accession no. HM070027); CrylCal3 (accession no. HQ412621); CrylCal4 (accession no. JN651493); CrylCbl (accession no. M97880); CrylCb2 (accession no. AAG35409); CrylCb3 (accession no. ACD50894); similar to CrylCb (accession no. AAX63901); CrylDal (accession no. CAA38099); CrylDa2 (accession no. 176415); CrylDa3 (accession no. HQ439784); Cryl Dbl (registration no. CAA80234); Cryl Db2 (Accession # AAK48937); Cryl Del (accession no. ABK35074); CrylEal (registration no. CAA37933); CrylEa2 (accession no. CAA39609); CrylEa3 (accession no. ΑΑΆ22345); CrylEa4 (accession no. AAD04732); CrylEa5 (accession no. A15535); CrylEa6 (accession no. AAL50330); CrylEa7 (accession no. AAW72936); CrylEa8 (accession no. ABX11258); CrylEa9 (accession no. HQ439785); CrylEalO (registration no. ADR00398); CrylEall (Accession # JQ652456); CrylEbl (accession no. ΑΆΑ22346); CrylFal (Accession # ΑΆΑ22348); CrylFa2 (accession no. AAA22347); CrylFa3 (accession no. HM070028); CrylFa4 (accession no. HM439638); Cryl Fbl (registration no. CAA80235); CrylFb2 (accession no. BAA25298); CrylFb3 (accession no. AAF21767); CrylFb4 (accession no. AAC10641); CrylFb5 (Accession # AA013295) ; CrylFb6 (accession no. ACD50892); CrylFb7 (accession no. ACD50893); CrylGal (accession no. CAA80233); CrylGa2 (accession no. CAA70506); CrylGbl (accession no. AAD10291); CrylGb2 (accession no. ΑΆ013756); CrylGcl (accession no. AAQ52381); CrylHal (accession no. CAA80236); CrylHbl (accession no. ΑΑΆ79694); CrylHb2 (accession no. rRRn / n / Lznz / q / Yi - 153 HQ439786); similar to CrylH (accession no. AAF01213); Cryllal (Accession # CAA44633) ; Crylla2 (accession no. AAA22354); Crylla3 (accession no. AAC36999); Crylla4 (accession no. ΑΆΒ00958); Crylla5 (accession no. CAA70124); Crylla6 (accession no. AAC26910); Cryllal (Accession No. AAM73516); Crylla8 (Accession # AAK66742) ; Crylla9 (accession no. AAQ08616); CrylIalO (accession no. ΑΆΡ86782) ; Cryllall (Accession # CAC85964); Cryllal2 (Accession # AAV53390) ; Cryllal3 (accession no. ABF83202); Cryllal4 (accession no. ACG63871); Cryllal5 (accession no. FJ617445); Cryllal6 (accession no. FJ617448); Cryllal7 (accession no. GU989199); Cryllal8 (accession no. ADK23801); Cryllal9 (accession no. HQ439787); CrylIa20 (accession no. JQ228426); Crylla21 (Accession # JQ228424); Crylla22 (Accession # 1Q228427); Crylla23 (Accession # JQ228428); Crylla24 (Accession # JQ228429); Crylla25 (accession no. JQ228430); Crylla26 (Accession # JQ228431); Crylla27 (accession no. JQ228432); Crylla28 (accession no. JQ228433); Crylla29 (Accession # JQ228434); CrylIa30 (accession no. JQ317686); Crylla31 (accession no. 1X944038); Crylla32 (accession no. 1X944039); Crylla33 (accession # 0X944040); Cryllbl (accession no. AAA82114); Cryllb2 (accession no. ABW88019); Cryllb3 (accession no. ACD75515); Cryllb4 (accession no. HM051227); Cryllb5 (accession no. HM070028); Cryllb6 (accession no. ADK38579); Cryllb7 (Accession No. JN571740); Cryllb8 (Accession No. JN675714); Cryllb9 (accession no. 1N675715); CrylIblO (accession no. 1Ν675716); Cryllbll (Accession # JQ228423); Cryllcl (accession no. AAC62933); Cryllc2 (Accession # AAE71691); Crylldl (Accession # AAD44366); Crylld2 (Accession # JQ228422); Cryllel (accession no. AAG43526); Crylle2 (accession no. HM439636); Crylle3 (accession no. KC156647); Crylle4 (accession no. KC156681); Cryllfl (accession no. AAQ52382); Cryllgl (Accession No. KC156701); Cryll-like (Accession # AAC31094); similar to Cryll (accession no. ABG88859); CrylJal (accession no. AAA22341); CrylJa2 (accession no. HM070030); CrylJa3 (accession no. JQ228425); Cryllbl (registry no. ΑΆΑ98959); CrylJcl (accession no. AAC31092); Cryllc2 (accession no. AAQ52372); Crylldl (Accession # CAC50779); CrylKal (Accession # AAB00376); CrylKa2 (accession no. HQ439783); CrylLal (Accession # AAS60191); CrylLa2 (accession no. HM070031); CrylMal (accession no. FJ884067); CrylMa2 (Accession # KC156659) ; CrylNal (accession no. KC156648); CrylNbl (accession no. KC156678); Cryl-like (Accession # AAC31091); Cry2Aal (accession no. AAA22335); Cry2Aa2 (accession no. AAA83516); Cry2Aa3 (Accession # D86064); Cry2Aa4 (accession no. AAC04867); Cry2Aa5 (# of rRRn / n / Lznz / q / Yi - 154 registration CAA10671); Cry2Aa6 (accession no. CAA10672); Cry2Aa7 (accession no. CAA10670); Cry2Aa8 (accession no. AA013734); Cry2Aa9 (accession no. AA013750); Cry2Aal O (accession no. AAQ04263); Cry2Aal 1 (accession n...

Claims

1. A method for barcoding a host cell, the method comprising: (a) obtaining a donor cell; (b) selecting and isolating a first nucleotide sequence in the genome of the donor cell, selecting and isolating a second nucleotide sequence in the genome of the donor cell, and selecting and isolating a third nucleotide sequence in the genome of the donor cell; (c) creating a natural barcode polynucleotide cassette comprising the first, second, and third nucleotide sequences oriented 5' to 3' as: (i) the first nucleotide sequence, wherein the first nucleotide sequence is a forward primer binding site, (ii) the second nucleotide sequence, wherein the second nucleotide sequence is a barcode, and (iii) the third nucleotide sequence, wherein the third nucleotide sequence is a reverse primer binding site;and (d) inserting the natural barcode polynucleotide cassette into the genome of a host cell of the same species as the donor cell in (a); wherein the nucleotide sequences of (i), (ii) and (iii) are natural to the host cell.; 2. The method of claim 1, wherein the donor cell and the host cell are selected from a bacterial cell, a fungal cell, a plant cell, an animal cell, a protozoan cell, and an insect cell.

3. The method of claim 2, wherein each of the donor cell and the host cell is a bacterial cell.

4. The method of any of the preceding claims, wherein the nucleotide sequence of at least one of (i), (ii) and (iii) is isolated from ribosomal DNA or internal transcribed spacer (ITS) DNA.

5. The method of claim 1, wherein the nucleotide sequences of at least one of (i), (ii) and (iii) are isolated from 16S rDNA or 18S rDNA.

6. The method of claim 1, wherein at least one of the primer binding sites is selected from 8F, 27F, CCF, 357F, 515F, 533F, 16S.1100.F16, 804F, 1237F, 338R, 519R, CDR, 806R, 907R, 1100R, 1391R, 1392R, 1492R(1), and 1492R(s).

7. The method of claim 1, wherein the first PRRn / n / Lznz / q / Yi -385 nucleotide sequence in the donor cell genome and the third nucleotide sequence in the donor cell genome are in the same orientation to each other.

8. The method of claim 1, wherein at least one of (i), (ii) and (iii) are not naturally found immediately adjacent to each other in the host cell genome.

9. The method of claim 1, wherein the barcode consists of less than 100 nucleotides.

10. The method of claim 1, wherein one or more of the primer binding sites consist of less than 30 nucleotides.

11. The method of claim 1, wherein the nucleotide sequences of the primer binding site and the barcode collectively consist of less than 160 nucleotides.

12. The method of claim 1, wherein the barcode comprises a constant barcode region and a variable barcode region.

13. The method of claim 1, wherein the insertion of the cassette into the host cell genome introduces one or more stop codons in any orientation into the host cell.

14. The method of claim 1, wherein the cassette is inserted into the host cell genome between two coding regions separated by a termination region.

15. The method of claim 14, wherein the cassette is inserted between the termination region and one of the two encoding regions.

16. The method of claim 1, wherein the host cell in (d) is of the same strain as the donor cell in (a).

17. The method of claim 3, wherein the bacterial host cell is transgenic.

18. The method of claim 3, wherein the bacterial host cell is a non-intergeneric remodeled bacterium.

19. The method of claim 18, wherein the non-intergeneric remodeled bacterial host cell is, or derived from, a bacterium selected from Table 1.

20. The method of claim 19, wherein the non-intergeneric remodeled bacterium comprises at least one genetic variation introduced in at least one gene, or non-coding polynucleotide, of the genetic regulatory network for nitrogen assimilation or fixation, such that the modified bacterium is capable of fixing atmospheric nitrogen in the presence of exogenous nitrogen.

21. The method of claim 3 or 18, wherein the bacterial host cell is capable of fixing atmospheric nitrogen in the presence of exogenous nitrogen.

22. The method of claim 3 or 18, wherein the bacterial host cell comprises at least one genetic variation introduced in at least one gene, or non-coding polynucleotide, of the genetic regulatory network for nitrogen assimilation or fixation.

23. The method of claim 3 or 18, wherein the bacterial host cell comprises an introduced control sequence operatively linked to at least one gene of the genetic regulatory network for nitrogen assimilation or fixation.

24. The method of claim 3 or 18, wherein the bacterial host cell comprises a heterologous promoter operatively linked to at least one gene of the genetic regulatory network for nitrogen assimilation or fixation.

25. The testing method 3 or 18, in which the bacterial cell contains at least one genetic variation introduced into a selected member of the group consisting of: nifA, nifL, ntrB, ntrC, polynucleotide encoding glutamine synthesis, glnA, glnE, glnK, drat, amtB, polynucleotide encoding glutaminase, glnD, glnE, nífJ, nífH, nifD, nifK, nifY, nifE, nifN, nifU, nifS, nifV, nifW, nifZ, nifM, nifE, nifB, nifQ, un gen associated with the biosynthesis of a nitrogen enzyme, and combinations of these.

26. The method of claim 3 or 18, wherein the bacterial host cell comprises at least one genetic variation introduced in at least one gene, or non-coding polynucleotide, of the nitrogen assimilation or fixation genetic regulatory network that produces one or more of: increased expression or activity of NifA or glutaminase; decreased expression or activity of NifL, NtrB, glutamine synthetase, GlnB, GlnK, DraT, AmtB; decreased adenylyl removal activity of GlnE; and decreased uridylyl removal activity of GlnD.

27. The method of claim 3 or 18, wherein the bacterial host cell comprises a mutated nifL gene comprising a heterologous promoter in said nifL gene.

28. The method of claim 3 or 18, wherein the bacterial host cell comprises a mutated glnE gene producing a truncated GlnE protein that lacks an adenylyl (AR) deletion domain.

29. The method of claim 3 or 18, wherein the bacterial host cell comprises a mutated amtB gene resulting in the lack of expression of said amtB gene.

30. The method of claim 3 or 18, wherein the bacterial host cell comprises at least one of: a mutated nifL gene comprising a heterologous promoter in said nifL gene; a mutated glnE gene producing a truncated GlnE protein lacking an adenylyl (AR) deletion domain; a mutated amtB gene resulting in the lack of expression of said amtB gene; and combinations thereof.

31. The method of claim 3 or 18, wherein the bacterial host cell comprises a mutated nifL gene comprising a heterologous promoter in said nifL gene and a mutated glnE gene producing a truncated GlnE protein lacking an adenylyl deletion (AR) domain.

32. The method of claim 3 or 18, wherein the bacterial host cell comprises a mutated nifL gene comprising a heterologous promoter in said nifL gene, a mutated glnE gene producing a truncated GlnE protein lacking an adenylyl deletion (AR) domain, and a mutated amtB gene resulting in the lack of expression of said amtB gene.

33. The method of claim 3 or 18, wherein the bacterial host cell is selected from Paraburkholderia tropica, Paraburkholderia xenovorans, Herbaspirillum seropedicae, Herbaspirullum frisingense, Pseudomonas protegens, Pseudomonas syringae, Pseudomonas benzenivorans,; Metacosaconia massiliensis, Metacosaconia intestinii, Pahnella aquatilis, Klebsiella varicola, Achromobacter spiritinus, Achromobacter marplatensis, Microbacterium mural, Kluyvera intermedia, Cossaconia pseudosacchari, Enterobacter sp. , Azospirillum lipoferum, and Kosakonia sacchari.

34. The method of claim 3 or 18, wherein the bacterial host cell is endophyte, epiphyte or rhizospheric.

35. The method of claim 3 or 18, wherein the bacterial host cell is selected from: a bacterium deposited as ATCC PTA-126575, a bacterium deposited as ATCC PTA-126576, a bacterium deposited as ATCC PTA-126577, a bacterium deposited as ATCC PTA-126578, a bacterium deposited as ATCC PTA-126579, a bacterium deposited as ATCC PTA-126580, a bacterium deposited as ATCC PTA-126581, a bacterium deposited as ATCC PTA-126582, a bacterium deposited as ATCC PTA-126583, a bacterium deposited as ATCC PTA-126584, a bacterium deposited as ATCC PTA-126585, a bacterium deposited as ATCC PTA-126586, a bacterium deposited as ATCC; PTA-126587, a bacterium deposited as ATCC; PTA-126588, a bacterium deposited as NCMA 201701001, a bacterium deposited as NCMA 201701002, a bacterium deposited as NCMA 201701003, a bacterium deposited as NCMA 201708004, a bacterium deposited as NCMA 201708003,a bacterium deposited as NCMA 201708002, a bacterium deposited as NCMA 201708001, a bacterium deposited as NCMA 201712001, and a bacterium deposited as NCMA 201712002.

36. The method of claim 3 or 18, wherein the bacterial host cell comprises a nucleic acid sequence that shares at least about 95% sequence identity with a nucleic acid sequence selected from SEQ ID NO: 177-260 and 296-303.

37. The method of claim 3 or 18, wherein the bacterial host cell comprises a nucleic acid sequence that shares at least about 99% sequence identity with a nucleic acid sequence selected from SEQ ID NO: 177-260 and 296-303.

38. The method of claim 3 or 18, wherein the bacterial host cell comprises a nucleic acid sequence selected from SEQ ID NO: 177-260 and 296-303.

39. A composition comprising: (a) one or more modified cells comprising, in their genome: (i) a first naturally occurring nucleotide sequence, a second nucleotide sequence, and a third nucleotide sequence, and (ii) a naturally occurring barcoded polynucleotide cassette comprising the first, second, and third nucleotide sequences oriented 5' to 3' as: (1) the first nucleotide sequence, wherein the first nucleotide sequence is a forward primer binding site, (2) the second nucleotide sequence, wherein the second nucleotide sequence is a barcode, and (3) the third nucleotide sequence, wherein the third nucleotide sequence is a reverse primer binding site; wherein the first, second, and third nucleotide sequences of (ii) have different proximity to each other compared to the naturally occurring sequences of (i). PRRn / n / Lznz / q / Yi -389 - 40. The composition of claim 39, wherein the barcode is unique for different species of the one or more modified cells.

41. The composition of claim 39, wherein the barcode is unique for different strains of the one or more modified cells.

42. The composition of claim 39, wherein the one or more modified cells comprise a homogeneous cell population.

43. The composition of claim 39, wherein the one or more modified cells comprise a heterogeneous cell population.

44. The composition of claim 43, wherein the heterogeneous cell population comprises two or more different species.

45. The composition of claim 43, wherein the heterogeneous cell population comprises two or more different strains.

46. ​​The composition of claim 44, wherein the heterogeneous cell population comprises two or more strains of each species.

47. The composition of claim 39, wherein the one or more modified cells are selected from a bacterial cell, a fungal cell, a plant cell, an animal cell, a protozoan cell, and an insect cell.

48. The composition of claim 39, wherein the one or more modified cells are a bacterial cell.

49. The composition of claim 39, wherein the nucleotide sequence of at least one of (1), (2) or (3) is isolated from ribosomal DNA or internal transcribed spacer (ITS) DNA.

50. The composition of claim 39, wherein the nucleotide sequence of at least one of (1), (2) or (3) is 16S rDNA or 18S rDNA.

51. The composition of claim 39, wherein at least one of the primer binding sites is selected from 8F, 27F, CCF, 357F, 515F, 533F, 16S.1100.F16, 804F, 1237F, 338R, 519R, CDR, 806R, 907R, 1100R, 1391R, 1392R, 1492R(1), and 1492R(s).

52. The composition of claim 39, wherein the first and third naturally occurring nucleotide sequences in the genome of the modified cells are in the same orientation relative to each other.

53. The composition of claim 39, wherein at least one of the first, second, or third naturally occurring nucleotide sequences is not immediately adjacent to each other in the genome of the modified cell.

54. The composition of claim 39, wherein the barcode consists of fewer than 100 nucleotides. PRRn / n / Lznz / q / Yi -390 - 55. The composition of claim 39, wherein one or more of the primer binding sites consist of less than 30 nucleotides.

56. The composition of claim 39, wherein the nucleotide sequences of the primer binding sites and the barcode collectively consist of less than 160 nucleotides.

57. The composition of claim 39, wherein the barcode comprises a constant barcode region and a variable barcode region.

58. The composition of claim 57, wherein the constant barcode region of the barcode is the same in each of the one or more modified cells.

59. The composition of claim 57 or 58, wherein the variable barcode region of the barcode is different in each of the one or more modified cells, and only cells of the same strain, species or other categorical distinction share the same variable region.

60. The composition of claim 39, wherein the cassette has one or more stop codons in any orientation in the one or more modified cells.

61. The composition of claim 39, wherein the cassette is present in the genome of one or more modified cells between two coding regions separated by a termination region.

62. The composition of claim 61, wherein the cassette is present between the termination region and one of the two encoding regions.

63. The composition of claim 39, wherein the cassette is present in the genome of each of the one or more modified cells at a specified distance from an origin of replication.

64. The composition of claim 63, wherein the distance established from the origin of replication is similar or identical in each of the two or more cells.

65. The composition of claim 48, wherein the one or more modified bacteria are transgenic bacteria.

66. The composition of claim 48, wherein the one or more modified bacteria are non-intergeneric remodeled bacteria.

67. The composition of claim 48, wherein the one or more modified bacteria comprise a population of transgenic bacteria.

68. The composition of claim 48 or 66, wherein the one or more modified PRRn / n / Lznz / q / Yi -391 bacteria comprise a population of non-intergeneric remodeled bacteria.

69. The composition of claim 66, wherein the non-intergeneric remodeled bacteria comprise, or are derived from, a bacterium selected from Table 1.

70. The composition of claim 69, wherein the non-intergeneric remodeled bacteria comprise at least one genetic variation introduced in at least one gene, or non-coding polynucleotide, of the genetic regulatory network for nitrogen assimilation or fixation, such that the modified bacteria are capable of fixing atmospheric nitrogen in the presence of exogenous nitrogen.

71. The composition of claim 48, wherein the bacterial cell is capable of fixing atmospheric nitrogen in the presence of exogenous nitrogen.

72. The composition of claim 48, wherein the bacterial cell comprises at least one genetic variation introduced in at least one gene, or non-coding polynucleotide, of the genetic regulatory network for nitrogen assimilation or fixation.

73. The composition of claim 48 or 66, wherein the bacterial cell comprises an introduced control sequence operatively linked to at least one gene of the nitrogen assimilation or fixation genetic regulatory network.

74. The composition of claim 48 or 66, wherein the bacterial cell comprises a heterologous promoter operatively linked to at least one gene of the nitrogen assimilation or fixation genetic regulatory network.

75. The composition of claim 48 or 66, wherein the bacterial cell comprises at least one genetic variation introduced into a selected member of the group consisting of: nif A, nifL, ntrB, ntrC, polynucleotide encoding glutamine synthetase, glnA, glnB, glnK, drat, amtB, polynucleotide encoding glutaminase, glnD, glnE, nifJ, nifH, nifD, nifK, nifY, nifE, nifN, nifU, nifS, nifV, nifW, nifZ, nifM, nifF, nifB, nifQ, a gene associated with the biosynthesis of a nitrogenase enzyme, and combinations thereof.

76. The composition of claim 48 or 66, wherein the bacterial cell comprises at least one genetic variation introduced in at least one gene, or non-coding polynucleotide, of the nitrogen assimilation or fixation genetic regulatory network that produces one or more of: increased expression or activity of NifA or glutaminase; decreased expression or activity of NifL, NtrB, glutamine synthetase, GlnB, GlnK, DraT, AmtB; decreased activity of PRRn / n / Lznz / q / Yi -392 adenyl removal of GlnE; and decreased uridylyl removal activity of GlnD.

77. The composition of claim 48 or 66, wherein the bacterial cell comprises a mutated nifL gene comprising a heterologous promoter in said nifL gene.

78. The composition of claim 48 or 66, wherein the bacterial cell comprises a mutated glnE gene producing a truncated GlnE protein lacking an adenylyl deletion (AR) domain.

79. The composition of claim 48 or 66, wherein the bacterial cell comprises a mutated amtB gene resulting in the lack of expression of said amtB gene.

80. The composition of claim 48 or 66, wherein the bacterial cell comprises at least one of: a mutated nifL gene comprising a heterologous promoter in said nifL gene; a mutated glnE gene producing a truncated GlnE protein lacking an adenylyl (AR) deletion domain; a mutated amtB gene resulting in the lack of expression of said amtB gene; and combinations thereof.

81. The composition of claim 48 or 66, wherein the bacterial cell comprises a mutated nifL gene comprising a heterologous promoter in said nifL gene and a mutated glnE gene producing a truncated GlnE protein lacking an adenylyl deletion (AR) domain.

82. The composition of claim 48 or 66, wherein the bacterial cell comprises a mutated nifL gene comprising a heterologous promoter in said nifL gene, a mutated glnE gene producing a truncated GlnE protein lacking an adenylyl (AR) deletion domain, and a mutated amtB gene resulting in the lack of expression of said amtB gene.

83. The composition of claim 48 or 66, wherein the bacterial cell is selected from Rahnella aquatilis, Klebsíella variícola, Achromobacter spiritinus, Achromobacter marplatensis, Microbacterium múrale, Kluyvera intermedia, Kosakonia pseudosacchari, Enterobacter sp., Azospirillum lípoferum, and Kosakonia sacchari.

84. The composition of claim 48 or 66, wherein the bacterial cell is endophytic, epiphytic or rhizospheric.

85. The composition of claim 48 or 66, wherein the bacterial cell is selected from: a bacterium deposited as ATCC PTA-126575, a bacterium deposited as ATCC PTA-126576, a bacterium deposited as ATCC PTA-126577, a bacterium deposited as ATCC PTA-126578, a bacterium deposited as ATCC PTA-126579, a bacterium deposited as ATCC PTA-126580, a bacterium deposited as ATCC PTA-126581, a bacterium deposited as ATCC PTA-126582, a bacterium PRRn / n / Lznz / q / Yi-393 deposited as ATCC PTA-126583, a bacterium deposited as ATCC PTA-126584, a bacterium deposited as ATCC PTA-126585, a bacterium deposited as ATCC PTA-126586, a bacterium deposited as ATCC PTA-126587, a bacterium deposited as ATCC PTA-126588, a bacterium deposited as NCMA 201701001, a bacterium deposited as NCMA 201701002, a bacterium deposited as NCMA 201701003, a bacterium deposited as NCMA 201708004, a bacterium deposited as NCMA 201708003,a bacterium deposited as NCMA 201708002, a bacterium deposited as NCMA 201708001, a bacterium deposited as NCMA 201712001, and a bacterium deposited as NCMA 201712002.

86. The composition of claim 48 or 66, wherein the bacterial cell comprises a nucleic acid sequence that shares at least about 95% sequence identity with a nucleic acid sequence selected from SEQ ID NO: 177-260 and 296-303.

87. The composition of claim 48 or 66, wherein the bacterial cell comprises a nucleic acid sequence that shares at least about 99% sequence identity with a nucleic acid sequence selected from SEQ ID NO: 177-260 and 296-303.

88. The composition of claim 48 or 66, wherein the bacterial cell comprises a nucleic acid sequence selected from SEQ ID NO: 177-260 and 296-303.

89. A method for detecting cells in a sample, the method comprising: (a) inserting a natural barcode polynucleotide cassette into the genomes of two or more cells, wherein the cassette comprises natural nucleotide sequences from each of the two or more cells, oriented 5' to 3' as: (i) a forward primer binding site, (ii) a unique barcode for each cell, species, or strain, and (iii) a reverse primer binding site; (b) applying the two or more cells to a proliferative medium; (c) collecting a sample of the proliferative medium comprising the two or more cells; and (d) determining the abundance of the two or more cells in the sample by analyzing the abundance of the barcodes.

90. The method of claim 89, wherein step (c) further comprises lysing the two or more cells.

91. The method of claim 89 or 90, wherein the abundance is relative abundance PRRn / n / Lznz / q / Yi -394.

92. The method of claim 89 or 90, wherein abundance is absolute abundance.

93. The method of claim 89, wherein the abundance is determined by PCR.

94. The method of claim 93, wherein the PCR is selected from multiplex PCR, dPCR, ddPCR and qPCR.

95. The method of claim 89, wherein the proliferative medium is selected from a liquid medium, a solid medium, and a semi-solid medium.

96. The method of claim 89, wherein the proliferative medium is the soil.

97. The method of claim 96, wherein the soil comprises one or more plants or parts of plants.

98. The method of claim 97, wherein the one or more plants or parts of plants are selected from non-leguminous plants.

99. The method of claim 98, wherein the one or more non-leguminous plants are maize.

100. The method of claim 89, wherein the time period between steps (c) and (d) is a sufficient amount of time for at least one duplication of the two or more cells.

101. The method of claim 89, wherein the forward primer binding site and / or the reverse primer binding site is the same in each of the two or more cells.

102. The method of claim 89, wherein the GC content of the direct primer binding site and / or the reverse primer binding site is at least 40%.

103. The method of claim 89, wherein the two or more cells comprise a homogeneous cell population.

104. The method of claim 89, wherein the two or more cells comprise a heterogeneous population of cells.

105. The method of claim 104, wherein the heterogeneous cell population comprises two or more different species.

106. The method of claim 104, wherein the heterogeneous cell population comprises two or more different strains.

107. The method of claim 105, wherein the heterogeneous population of PRRn / n / Lznz / q / Yi -395 cells comprises two or more strains of each species.

108. The method of claim 89, wherein the two or more cells are selected from bacterial cells, fungal cells, plant cells, animal cells, protozoan cells, and insect cells.

109. The method of claim 108, wherein the two or more cells are bacterial cells.

110. The method of claim 89, wherein the nucleotide sequence of at least one of (i), (ii) or (iii) is isolated from ribosomal DNA or internal transcribed spacer (ITS) DNA.

111. The method of claim 89, wherein the nucleotide sequence of at least one of (i), (ii) or (iii) is 16S rDNA or 18S rDNA.

112. The method of claim 89, wherein at least one of the primer binding sites is selected from 8F, 27F, CCF, 357F, 515E, 533E, 16S.1100.F16, 804F, 1237F, 338R, 519R, CDR, 806R, 907R, 1100R, 1391R, 1392R, 1492R(1), and 1492R(s).

113. The method of claim 89, wherein the barcode consists of less than 100 nucleotides.

114. The method of claim 89, wherein one or more of the primer binding sites consist of less than 30 nucleotides.

115. The method of claim 89, wherein the nucleotide sequences of the primer binding sites and the barcode collectively consist of less than 160 nucleotides.

116. The method of claim 109, wherein the two or more bacteria are transgenic.

117. The method of claim 109, wherein the two or more bacteria are non-intergeneric remodeled bacteria.

118. The method of claim 109, wherein the two or more bacteria comprise a population of transgenic bacteria.

119. The method of claim 109, wherein the two or more bacteria comprise a population of non-intergeneric remodeled bacteria.

120. The method of claim 117, wherein the non-intergeneric remodeled bacteria comprise, or are derived from, a bacterium selected from Table 1.

121. The method of claim 109 or 117, wherein the two or more bacteria are capable of fixing atmospheric nitrogen in the presence of exogenous nitrogen.

122. The method of claim 89, wherein the barcode comprises a constant barcode region and a variable barcode region. PRRn / n / Lznz / q / Yi -396 - 123. The method of claim 122, wherein the constant barcode region of the barcode inserted in each of the two or more cells is the same in each of the two or more cells.

124. The method of claim 122 or 123, wherein the variable barcode region of the barcode inserted in each of the two or more cells is different, and only cells of the same strain, species, or other categorical distinction share the same variable region.

125. The method of claim 89, wherein the insertion of the cassette into the genome of the two or more cells introduces one or more stop codons in any orientation in the two or more cells.

126. The method of claim 89, wherein the cassette is present in the genome of the two or more cells between two coding regions separated by a termination region.

127. The method of claim 126, wherein the cassette is present between the termination region and one of the two encoding regions.

128. The method of claim 89, wherein the cassette is present in the genome of each of the two or more cells at a specified distance from an origin of replication.

129. The method of claim 128, wherein the distance established from the origin of replication is similar or identical in each of the two or more cells.

130. A method for barcoding a host cell population, the method comprising: (a) obtaining a donor cell; (b) selecting and isolating a first nucleotide sequence in the donor cell genome, selecting and isolating a second nucleotide sequence in the donor cell genome, and selecting and isolating a third nucleotide sequence in the donor cell genome; (c) creating a natural barcode polynucleotide cassette comprising the first, second, and third nucleotide sequences oriented 5' to 3' as: (i) the first nucleotide sequence, wherein the first nucleotide sequence is a forward primer binding site, (ii) the second nucleotide sequence, wherein the second nucleotide sequence is a barcode, and PRRn / n / Lznz / q / Yi-397- (iii) the third nucleotide sequence, wherein the third nucleotide sequence is a reverse primer binding site;(d) inserting the natural barcode polynucleotide cassette into the genome of a host cell of the same genus as the donor cell in (a); and (e) repeating (d) one or more times with a different host cell of the same genus each time; wherein the nucleotide sequences of (i), (ii), and (iii) are natural to the host cell, thus barcoding a population of host cells.

131. The method of claim 130, wherein the host cell population shares a common species.

132. The method of claim 130, wherein each of the host cells different from (e) is of a different strain.

133. The method of claim 130, wherein each of the host cells different from (e) is of a different species.

134. The method of claim 130, wherein the barcode comprises a constant barcode region and a variable barcode region.

135. The method of claim 134, wherein the constant barcode region of the barcode inserted into each host cell of the host cell population is the same in each of the host cells.

136. The method of claim 134 or 135, wherein the variable barcode region of the barcode inserted into each host cell of the host cell population is different, and only host cells of the same strain, species, or other categorical distinction share the same variable region.

137. The method of claim 130, wherein the insertion of the cassette into the host cell genome introduces one or more stop codons in any orientation into the host cell.

138. The method of claim 130, wherein the cassette is present in the host cell genome between two coding regions separated by a termination region.

139. The method of claim 138, wherein the cassette is present between the termination region and one of the two encoding regions.

140. The method of claim 130, wherein the cassette is present in the host cell genome at a specified distance from an origin of replication.

141. The method of claim 140, wherein the distance established from the origin of replication is similar or identical in each host cell of the host cell population.

142. A composition comprising: (a) a modified cell population comprising, in its genome: (i) a first naturally occurring nucleotide sequence, a second nucleotide sequence, and a third nucleotide sequence, and (ii) a naturally occurring barcode polynucleotide cassette comprising the first, second, and third nucleotide sequences oriented 5' to 3' as: (1) the first nucleotide sequence, wherein the first nucleotide sequence is a forward primer binding site, (2) the second nucleotide sequence, wherein the second nucleotide sequence is a barcode, and (3) the third nucleotide sequence, wherein the third nucleotide sequence is a reverse primer binding site; wherein the first, second, and third nucleotide sequences of (ii) have different proximity to each other compared to the naturally occurring sequences of (i).

143. The composition of claim 142, wherein the modified cell population shares a common species.

144. The composition of claim 142, wherein the modified cell population comprises more than one species.

145. The composition of claim 144, wherein the modified cell population comprises more than one strain of each species.

146. The composition of claim 142, wherein the barcode comprises a constant barcode region and a variable barcode region.

147. The composition of claim 146, wherein the constant barcode region is the same in each of the modified cells.

148. The composition of claim 146 or 147, wherein the variable barcode region is not retained in the modified cell population, and only modified cells of the same strain, species or other categorical distinction share the same variable region.

149. The composition of claim 142, wherein, as a result of the presence of the cassette, the modified cell population comprises one or more stop codons in any orientation in the modified cells.

150. The composition of claim 142, wherein the cassette is present in the host cell genome between two coding regions separated by a termination region.

151. The composition of claim 150, wherein the cassette is present between the termination region and one of the two encoding regions.

152. The composition of claim 142, wherein the cassette is present in the host cell genome at a specified distance from an origin 10 of replication.

153. The composition of claim 152, wherein the distance established from the origin of replication is similar or identical in each modified cell of the modified cell population.