GENETIC TARGETS TO ACT ON NITROGEN FIXATION IN ORDER TO IMPROVE PLANT TRAITS

Abstract

A genetically modified bacterium is described with a modification in one or more selected genes from: NAC, ptsH, iaaA, gltA, pga, sdiA, fimA1, fimA2, fimA3, fimA4, wzxE, bolA, iscR, fhuF, sodA, sodB, sodC, FNR, arcA, arcB, rpoS, sbnA, treA, treB, phoP, phoQ, yjjPB, ychM, dauA, actP, yusV1, yieL1, yieL2, yieL3, yieL4, pgaB, rafA, melA, uidA, manA, abfA, abnA, lacZ, and yusV2. Methods of using the genetically modified bacterium to provide fixed nitrogen to plants and compositions containing the bacterium are also provided.

Description

GENE TARGETS TO ACT ON NITROGEN FIXATION IN ORDER TO IMPROVE PLANTS TRAITS RnR7Ln / L7nZ / E / Yli CROSS REFERENCE TO RELATED REQUESTS This application claims priority from US Provisional Application No. s62 / 838,158, filed April 24, 2019, which is incorporated herein in its entirety by reference. TECHNICAL FIELD The present disclosure relates to genetically modified bacterial strains and their compositions. Such bacterial strains, and their compositions, are useful for providing fixed nitrogen to plants. BACKGROUND OF THE INVENTION Plants are linked to the microbiome through a shared metabolome. A multidimensional relationship between a particular crop trait and the underlying metabolome is characterized by an environment with numerous local maxima. Optimizing a lower local maximum to one that represents a better trait by altering the influence of the microbiome on the metabolome may be desirable for a variety of reasons, such as culture optimization. Economically, environmentally and socially sustainable approaches to agriculture and food production are necessary to meet the needs of a growing world population. The Food and Agriculture Organization of the United Nations projects that by 2050, total food production must increase by 70 percent to meet the needs of a growing population, a challenge that is compounded by numerous factors, including 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 global climate drier, warmer and more extreme. One area of ​​interest is the improvement of nitrogen fixation. Nitrogen gas (N2) is an important component of Earth's atmosphere. Furthermore, elemental nitrogen (N) is an important component of many chemical compounds that make up living organisms. However, many organisms cannot use N2 directly to synthesize chemicals used in physiological processes, such as growth and reproduction. To use N2, N2 must be combined with hydrogen. The combination of hydrogen with N2 is called nitrogen fixation. Nitrogen fixation, whether done chemically or biologically, requires the investment of large amounts of energy. In biological systems, an enzyme known as nitrogenase catalyzes the reaction, resulting in nitrogen fixation. 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. Despite significant progress 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 is still unclear. Meanwhile, the challenge of providing sufficient supplemental sources of nitrogen, such as in fertilizers, will continue to increase with the growing need to increase food production. SUMMARY OF THE INVENTION The present disclosure provides a genetically modified bacterium with a modification in a gene selected from: NAC, ptsH, iaaA, gltA, pga, sdiA, fimA1, fimA2, fimA3, fimA4, wzxE, bolA, iscR, fhuF, sodA, sodB, sodC , FNR, arcA, arcB, rpoS, sbnA, treA, treB, phoP, phoQ, yjjPB, ychM, dauA, actP, yusV1, yieL1, yieL2, yieL3, yieL4, pgab, rafA, melA, uidA, manA, abfA, abnA , lacZ, and yusV2. In some embodiments, the genetically modified bacterium has a modification in a gene selected from: NAC, gltA, pga, ptsH, fimA1, fimA2, fimA3, fimA4, iscR, tonB, yusV1, yusV2, yusV3, yusV4, sbnA, fhuF, sodA , sodB and sodC. In some embodiments, the genetically modified bacterium has a modification in a gene selected from: NAC, gltA, pga, ptsH, fimA1, fimA2, fimA3, fimA4, sodA, sodB, and sodC. In some embodiments, the genetically modified bacterium has a modification in a gene selected from: iscR, tonB, yusV1, yusV2, yusV3, yusV4, sbnA, and fhuF. In some embodiments, the genetically modified bacterium is a genetically modified diazotrophic bacterium. In some embodiments, the genetically modified bacterium is intergeneric. In some embodiments, the genetically modified microorganism is not intergeneric. In some embodiments, the genetically modified bacterium is capable of fixing atmospheric nitrogen in the presence of exogenous nitrogen. In some embodiments, the genetically modified bacterium includes a modification in a nitrogen-fixing genetic network. In some embodiments, the modification in a nitrogen fixation genetic network includes a modification in NifA, NifL, NifH, or any combination thereof. In some embodiments, the modification in NifA results in increased expression of NifA. In some embodiments, the modification in NifL causes a decrease in NifL expression. In some embodiments, modification in NifH results in increased expression of NifH. In some embodiments, modification in a nitrogen-fixing genetic network results in increased expression of clustered Nif genes. In some embodiments, the genetically modified bacterium includes a modification in a nitrogen assimilating genetic network. In RnRZLn / LZnZ / E / Yli some modalities, the modification in a genetic network of nitrogen assimilation includes a modification in GlnE. In some embodiments, the modification in GlnE causes a decrease in GlnE activity. In some embodiments, modification in a nitrogen assimilating genetic network results in decreased amtB activity. The present disclosure provides a method for increasing the amount of nitrogen derived from the atmosphere in a plant, wherein the method includes a step of contacting the plant with a plurality of genetically modified bacteria described herein. In some embodiments, the contacting step involves applying the plurality of genetically modified bacteria to a seed of the plant. In some embodiments, the contacting step involves applying the plurality of genetically modified bacteria to a seedling of the plant. In some embodiments, the contacting step involves applying the plurality of genetically modified bacteria to the plant in a liquid formulation. In some embodiments, the contacting step involves applying the plurality of genetically modified bacteria to the plant after planting but before harvesting the plant. In some embodiments, the contacting step involves applying the plurality of genetically modified bacteria to the plant as a top dressing. In some embodiments, the contacting step involves applying the plurality of genetically modified bacteria to the plant between one month and eight months after germination. In some embodiments, the contacting step involves applying the plurality of genetically modified bacteria to the plant between two months and eight months after germination. In some embodiments, the contacting step involves applying the plurality of genetically modified bacteria to the plant one to three months after germination. In some embodiments, the contacting step involves applying the plurality of genetically modified bacteria to the plant between three months and six months after germination. In some embodiments, the plant is a cereal plant. In some embodiments, the plant is a corn plant. In some embodiments, the plant is a rice plant. In some embodiments, the plant is a wheat plant. In some embodiments, the plant is a soybean plant. The present disclosure provides a composition that includes a seed and a seed coat; wherein the seed coat includes a plurality of genetically modified bacteria as described herein. In some embodiments, the seed is a cereal seed. In some embodiments, the seed is selected from the group consisting of: a corn seed, a wheat seed, a rice seed, a soybean seed, a rye seed, and a sorghum seed. The present disclosure provides a composition that includes a plant and a plurality of genetically modified bacteria described herein. In some RnRZLn / LZnZ / E / Yli patterns, the plant is a seedling. In some embodiments, the plant is a cereal plant. In some embodiments, the plant is selected from corn, rice, wheat, soybeans, rye, and sorghum. INCORPORATION BY REFERENCE All publications, patents, and patent applications cited in this specification are incorporated herein by reference to the same extent as if each individual publication, patent, or patent application had been specifically and individually indicated to be incorporated herein. present by reference. In addition, the disclosure of international publication n.eWO 2019 / 084342 is incorporated herein in its entirety by reference. BRIEF DESCRIPTION OF THE DRAWINGS The novel features of the invention are set forth in detail in the appended claims. The features and advantages of the present invention may be better understood by reference to the following detailed description setting forth illustrative embodiments, in which the principles of the invention are used, and by reference to the accompanying drawings in which: Figures 1A-1B depict the enrichment and isolation of nitrogen-fixing bacteria. (1A) An Nfb agar plate was used to isolate single colonies of nitrogen-fixing bacteria. (1B) Semi-solid Nfb agar strained into a Balch tube. The arrow points to a film of enriched nitrogen-fixing bacteria. Figure 2 depicts a representative nifH POR screen. Positive bands at -350 bp were observed for two colonies in this screen. Lower bands represent primer dimers. Figure 3 depicts an example of a POR screen of CRISPR-Cas selected mutagenesis colonies. CI006 colonies were tested with primers specific for the nifL locus. The wild-type POR product is expected at -2.2 kb, while the mutant is expected at -1.1 kb. Seven out of ten colonies unambiguously examined show the desired deletion. Figures 4A-4B depict in vitro phenotypes of various strains. Acetylene reduction assay (ARA) activities of strain CU 37 mutants grown in nitrogen fixation medium supplemented with 0 mM (Figure 4A) or 5 mM ammonium phosphate (Figure 4B). All strains are compared to 137-2084 (parent strain). Figures 5A-5B provide the total ammonium excretion (Figure 5B) and the ammonium excretion profile over time (Figure 5A) for the strains of Figures 4A-4B. All strains are compared to 137-2084 (parent strain). RHRZ Líl / LZ / IZ / E / Yl Figures 6A-6B depict in vitro phenotypes of various strains. ARA assay activities of strain 01137 mutants grown in nitrogen fixation medium supplemented with 0 mM (Figure 6A) or 5 mM (Figure 6B) ammonium phosphate. All strains are compared to 137-2084 (parent strain). Figures 7A-7B provide the total ammonium excretion (Figure 7B) and the ammonium excretion profile over time (Figure 7A) for the strains of Figures 6A-6B. All strains are compared to 137-2084 (parent strain). Figures 8A-8B depict in vitro phenotypes of various strains. ARA assay activities of siderophore gene mutants of strain 01137 grown in nitrogen fixation medium supplemented with 0 mM (Figure 8A) or 5 mM (Figure 8B) ammonium phosphate. All strains are compared to 137 (original strain). Figures 9A-9B provide the total ammonium excretion (Figure 9B) and the ammonium excretion profile over time (Figure 9A) for the strains of Figures 8A-8B. All strains are compared to 137 (original strain). Figures 10A-10B depict in vitro phenotypes of various strains. ARA assay activities of siderophore gene mutants of strain CI137 grown in nitrogen fixation medium supplemented with 0 mM (Figure 10A) or 5 mM (Figure 10B) ammonium phosphate. All strains are compared to 137-2084 (parent strain). Figures 11A-11B provide the total ammonium excretion (Figure 11B) and the ammonium excretion profile over time (Figure 11A) for the strains of Figures 10A10B. All strains are compared to 137-2084 (parent strain). Figures 12A-12B depict in vitro phenotypes of various strains. ARA assay activities of oxygen-tolerant gene mutants of strain 01137 grown in nitrogen-fixation medium supplemented with 0 mM (Figure 12A) or 5 mM (Figure 12B) ammonium phosphate. All strains are compared to 137 (original strain). Figures 13A-13B provide the total ammonium excretion (Figure 13B) and the ammonium excretion profile over time (Figure 13A) for the strains of Figures 12A12B. All strains are compared to 137 (original strain). Figures 14A-14B depict in vitro phenotypes of various strains. ARA assay activities of oxygen-tolerant gene mutants of strain 01137 grown in nitrogen-fixation medium supplemented with 0 mM (Figure 14A) or 5 mM (Figure 14B) ammonium phosphate. All strains are compared to 137-2084 (parent strain). Figures 15A-15B provide the total ammonium excretion (Figure 15B) and the ammonium excretion profile over time (Figure 15A) for the strains of Figures 14A14B. All strains are compared to 137-2084 (parent strain). rhrz lo / lzoz / e / yi Figures 16A-16B depict in vitro phenotypes of various strains. ARA assay activities of siderophore gene mutants of strain 011021 grown in nitrogen fixation medium supplemented with 0 mM (Figure 16A) or 5 mM (Figure 16B) ammonium phosphate. All strains are compared to 1021 (parent strain). Figures 17A-17B provide the total ammonium excretion (Figure 17B) and the ammonium excretion profile over time (Figure 17A) for the strains of Figures 16A16B. All strains are compared to 1021 (parent strain). Figures 18A-18B depict in vitro phenotypes of various strains. ARA assay activities of siderophore gene mutants of strain 011021 grown in nitrogen fixation medium supplemented with 0 mM (Figure 18A) or 5 mM (Figure 18B) ammonium phosphate. All strains are compared to 1021-1615 (parent strain). Figures 19A-19B provide the total ammonium excretion (Figure 19B) and the ammonium excretion profile over time (Figure 19A) for the strains of Figures 18A18B. All strains are compared to 1021-1615 (parent strain). Figures 20A-20B depict in vitro phenotypes of various strains. ARA assay activities of oxygen-tolerant gene mutants of strain 011021 grown in nitrogen-fixation medium supplemented with 0 mM (Figure 20A) or 5 mM (Figure 20B) ammonium phosphate. All strains are compared to 1021 (parent strain). Test carried out in 1% oxygen. Figures 21A-21B provide the total ammonium excretion (Figure 21B) and the ammonium excretion profile over time (Figure 21A) for the strains of Figures 20A20B. All strains are compared to 1021 (parent strain). Test carried out in 1% oxygen. Figures 22A-22B depict in vitro phenotypes of various strains. ARA assay activities of oxygen-tolerant gene mutants of strain 011021 grown in nitrogen-fixation medium supplemented with 0 mM (Figure 22A) or 5 mM (Figure 22B) ammonium phosphate. All strains are compared to 1021-1615 (parent strain). Test carried out in 1% oxygen. Figures 23A-23B provide the total ammonium excretion (Figure 23B) and the ammonium excretion profile over time (Figure 23A) for the strains of Figures 22A22B. All strains are compared to 1021 -1615 (parent strain). Test carried out in 1% oxygen. Figures 24A-24B depict in vitro phenotypes of various strains. ARA assay activities of NAO gene mutants of strain CI137 grown in nitrogen fixation medium supplemented with 0 mM (Figure 24A) or 5 mM (Figure 24B) ammonium phosphate. RnRZLn / LZnZ / E / Yli Figures 25A-25B provide the total ammonium excretion (Figure 25B) and the ammonium excretion profile over time (Figure 25A) for the strains of Figures 24A24B. Figures 26A-26B depict in vitro phenotypes of various strains. ARA assay activities of NAC gene mutants of strain CI1021 grown in nitrogen fixation medium supplemented with 0 mM (Figure 26A) or 5 mM (Figure 26B) ammonium phosphate. Upregulation of the GlnA operon increased ~2-3 fold nitrogen fixation in AnifL::Prm2 strains. Upregulation of the GlnA operon increased -200-fold binding in strain wt 1021. Figures 27A-27B provide the total ammonium excretion (Figure 27B) and the ammonium excretion profile over time (Figure 27A) for the strains of Figures 26A26B. Upregulation of the GlnA operon increased -90-fold nitrogen excretion in wt and 3-fold in repressed background activity. DETAILED DESCRIPTION OF THE INVENTION The terms "polynucleotide", "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 carry out any 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, introns, messenger RNA (mRNA), transfer RNA (tRNA), ribosomal RNA (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, probes of nucleic acid 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 may be interrupted by non-nucleotide components. A polynucleotide can be further modified after polymerization, such as by conjugation with a label 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 be produced by Watson Crick base pairing, Hoogstein junction, or in any other manner specific to RnRZLn / LZnZ / E / Yli sequence according to base complementarity. The complex can comprise two strands forming a duplex structure, three or more strands forming a multi-strand 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 enzymatic cleavage of a polynucleotide by endonuclease. A second sequence that is complementary to a first sequence is called a "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. "Complementarity" refers to the ability of a nucleic acid to form hydrogen bonds with another nucleic acid sequence by traditional Watson-Crick or other non-traditional types. A percent complementarity indicates the percentage of residues in a nucleic acid molecule that can form hydrogen bonds (eg, Watson-Crick 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% in 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, EMBOSS Needle Aligner). available at www.ebi.ac.uk / Tools / psa / emboss_needle / nucleotide.html on the internet, 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 on the internet, optionally with default settings). Optimal alignment can be evaluated using the appropriate parameters of a chosen algorithm, including default parameters. rhrz lo / lzoz / e / yi 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 does not substantially 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 hybridizes 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 hybridization and the strategy of nucleic acid probe assay” , Elsevier, N.Y. In general, "sequence identity" refers to an exact correspondence between nucleotides or amino acids of two polynucleotide or polypeptide sequences, respectively. Commonly, techniques for determining sequence identity include determining the nucleotide sequence of a polynucleotide and / or determining the amino acid sequence encoded by it, and comparing these sequences to a second nucleotide or amino acid sequence. It is possible to compare two or more sequences (polynucleotides or amino acids) by determining their 'percent identity'. The percentage identity of two sequences, whether nucleic acid or amino acid sequences, can be calculated as the number of exact matches between two aligned sequences divided by the length of the shorter sequences and multiplied by 100. In some cases, the percentage The identity of a query sequence and a reference sequence, whether nucleic acid or amino acid sequences, can be calculated as the number of exact matches between two aligned sequences divided by the length of the reference sequence and multiplied by 100. The percentage Identity can also be determined, for example, by comparing the sequence information with advanced BLAST software, including version 2.2.9, available from the National Institutes of Health. The BLAST program is based on the alignment method of Karlin and Altschul, Proc. nati. Acad. Sci. USA 87:2264-2268 (1990) and as mentioned in Altschul, et al., J. Mol. BioL 215:403-410 (1990); Karlin and Altschul, Proc. nati. Acad. Sci. USA 90:5873-5877 (1993); and Altschul et al., Nucleic Acids Res. 25:3389-3402 (1997). In summary, the BLAST program defines identity as the number of identical aligned symbols (usually nucleotides or amino acids), divided by the total number of symbols in the shorter of the two sequences. The program can be used to determine the percent full-length identity of the proteins being compared. Default parameters are provided to optimize searches with short query strings in, for example, the blastp program. The program also allows the use of a SEG filter for rhrz lo / lzoz / e / yi to mask segments of the query sequences as determined by the SEG program of Wootton and Federhen, Computers and Chemistry 17:149-163 (1993). Ranges of desired degrees of sequence identity are from about 80% to 100% and integer values ​​in between. Commonly, percent identity between a disclosed sequence and a claimed sequence are at least 80%, at least 85%, at least 90%, at least 95%, at least 98%, or at least 99%. 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, an amino acid polymer having disulfide bond formation, glycosylation, lipidation, acetylation, phosphorylation, or any other manipulation, such as conjugation with a label 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 the plant is grown. In the case of food crops, such as cereals or vegetables, "plant productivity" can refer to the yield of cereals or fruits harvested from a particular crop. As used herein, improved plant productivity refers to RnRZLn / Lznz / B / Yi in general to improvements in the yield of grains, fruits, flowers or other parts of plants harvested for various purposes, improvements in the growth of parts of plants, including stems, leaves and roots, promotion of plant growth, maintenance of high chlorophyll content in leaves, increase in number of fruits or seeds, increase in unit weight of fruits or seeds, reduction of NO2 emission due to reduced use of nitrogen fertilizers, and similar growth enhancements and plant development. 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 (for example, acquisition of nitrogen, phosphorus, potassium, iron, micronutrients); 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. In some embodiments, the native or endogenous control sequences of genes of the present disclosure are replaced with one or more intragenic 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 colony-forming units (cfu), 104cfu, 105cfu, 106cfu, 107cfu, 108cfu, 109cfu, 1010cfu, 1011cfu, or 1012cfu 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 103cfu, about 104cfu, about 105cfu, about 106cfu, about 107cfu, about 108cfu, about 109cfu, about 1010cfu, about 1011cfu, or about 1012cfu 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 103a 109, 103a 107,103a 105, 105a 109, 105a 107, 106a RnRZLn / Lznz / Em 1010,106 to 107cfu 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 to about 109, about 103 to about 107, about 103 to about 105, about 105 to about 109, about 105 to about 107, about 106 to about 1010 , about 106 to about 107 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 from about 103cfu to about 1020cfu. For example, about 103cfu to about 1015cfu, about 103cfu to about 1010cfu, about 103cfu to about 105cfu, about 1015cfu to about 1020cfu, about 1010cfu to about 1020cfu, or about 105cfu to about 1020cfu. 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, and / 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, "introduced genetic material" means genetic material that is added to and remains a component of the recipient's genome. 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, nif / \, nilB, nifC,.......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 embodiments, the Nif group may comprise NifB, NifH, NifD, NifK, NifE, NifN, NifX, hesA, and RHR7 ίΠ / ί7Π7 / Ε / ΥΙ NifV. In some embodiments, 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%, 32%, 33%, 34%, 35%, %, 37%, 38%, 39%, 40%, 41%, 42%, 43%, 44%, 45%, 46%, 47%, 48%, 49%, 50%, %, 52%, 53%, 54%, 55%, 56%, 57%, 58%, 59%, 60%, 61%, 62%, 63%, 64%, 65%, %, 67%, 68 %, 69%, 70%, 71%, 72%, 73%, 74%, 75%, 76%, 77%, 78%, 79%, 80%, %, 82%, 83%, 84%, 85 %, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, %, 97%, 98%, 99% by weight of nitrogen. In some embodiments, the fertilizer of the present disclosure comprises at least about 5%, about 6%, about 7%, about 8%, about 9%, about 10%, about 11%, about 12%, about 13%, about 14%, about 15%, about 16%, about 17%, about 18%, about 19%, about 20%, about 21%, about 22%, about 23%, about 24%, about 25%, about 26% , about 27%, about 28%, about 29%, about 30%, about 31%, about 32%, about 33%, about 34%, about 35%, about 36%, about 37%, about 38%, about 39%, about 40%, about 41%, about 42%, about 43%, about 44%, about 45%, about 46%, about 47%, about 48%, about 49%, about 50%, about 51% , about 52%, about 53%, about 54%, about 55%, about 56%, about 57%, about 58%, about 59%, about 60%, about 61%, about 62%, about 63%, about 64%, about 65%, about 66%, about 67%, about 68%, about 69%, about 70%, about 71%, about 72%, about 73%, about 74%, about 75%, about 76% , about 77%, about 78%, about 79%, about 80%, about 81%, about 82%, about 83%, about 84%, about 85%, about 86%, about 87%, about 88%, about RnRZLn / Lznz / B / Yi%, about 90%, about 91%, about 92%, about 93%, about 94%, about 95%, about 96%, about 97%, about 98%, or about 99% in nitrogen weight. In some embodiments, the fertilizer of the present disclosure comprises about 5% to about 50%, about 5% to about 75%, about 10% to about 50%, about 10% to about 75%, about 15% to about 50% , about 15% to about 75%, about 20% to about 50%, about 20% to about 75%, about 25% to about 50%, about 25% to about 75%, about 30% to about 50%, about 30% to about 75%, about 35% to about 50%, about 35% to about 75%, about 40% to about 50%, about 40% to about 75%, about 45% to about 50%, about 45% to about 75%, or about 50% to about 75% by weight of nitrogen. In some embodiments, increased nitrogen fixation and / or increased plant nitrogen production of 1% or more is determined relative to control plants, which have not been exposed to the present bacteria. description. All increases or decreases in the activity of the bacteria (for example, any of the activities of the bacteria as described herein, including the nitrogen-fixing activity of the bacteria, the nitrogen-assimilating activity of the bacteria, the plant colonizing activity of the bacteria, ammonium excretion activity of the bacteria and iron uptake activity of the bacteria) are determined relative to control bacteria. All increases or decreases in plant productivity or a property (eg, increases or decreases in plant growth, yield, NO 2 emission, and nitrogen uptake) are determined 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 scoring markers, allowing easy detection and quantification; high level of production of a transcription factor that is part of a regulatory transcription system; production of Rn«7Ln / L7n7 / E / Yli compounds that require ubiquitous activity in the organism; and production of compounds that are required during all stages of development. Illustrative non-limiting constitutive promoters include the 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 both the scientific and patent literature. As used herein, the term "operably linked" refers to the association of nucleic acid sequences in 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 general, the term "genetic modification" or "modification in a gene" refers to any change introduced in a polynucleotide sequence with respect to a polynucleotide Reference RHRZ Ln / LZRZ / E / Yli, such as a reference genome or a part thereof, or a reference gene or a part thereof. A genetic modification may be referred to as a 'mutation' and a sequence or organism comprising a genetic modification may be referred to as a 'genetic variant' or 'mutant'. Genetic modifications can have various effects, such as increasing or decreasing some biological activity, including gene expression, metabolism, and cell signaling. Genetic modifications can be specifically introduced at a target site or introduced randomly. Provided herein is a genetically modified bacterium with a modification in a gene selected from: NAO, ptsH, iaaA, gltA, pga, sdiA, fimA1, fimA2, fimA3, fimA4, wzxE, bolA, iscR, fhuF, sodA, sodB, sodC, FNR, arcA, arcB, rpoS, sbnA, treA, treB, phoP, phoQ, yjjPB, ychM, dauA, actP, yusV1, yieL1, yieL2, yieL3, yieL4, pgab, rafA, melA, uidA, manA, abfA, abnA, lacZ, and yusV2. In some embodiments, the genetically modified bacterium has a modification in a gene selected from: NAO, gltA, pga, ptsH, fimA1, fimA2, fimA3, fimA4, iscR, tonB, yusV1, yusV2, yusV3, yusV4, sbnA, fhuF, sodA , sodB and sodC. In some embodiments, the genetically modified bacterium has a modification in a gene selected from: NAO, gltA, pga, ptsH, fimA1, fimA2, fimA3, fimA4, sodA, sodB and sodC. In some embodiments, the genetically modified bacterium has a modification in a gene selected from: iscR, tonB, yusV1, yusV2, yusV3, yusV4, sbnA, and fhuF. The bacteria described herein can be used in a method of improving nitrogen uptake by plants. Said method may include the step of contacting a plant with a plurality of bacteria. Compositions containing a plurality of bacteria in the form of a seed coat for a seed or in combination with a plant are also provided. Bacteria with modifications in the identified genes may exhibit one or more of the following: increased nitrogen fixation, increased ammonium excretion, increased colonization, increased iron transport, increased oxygen tolerance, and / or or increased tolerance to desiccation relative to bacteria lacking modifications in the identified genes. Regulation of nitrogen fixation One trait that can be improved by using the genetically modified bacteria described herein is nitrogen fixation. 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. The application of chemical fertilizers and residual nitrogen concentrations in field soils signal the microbe to shut down the biochemical pathway for nitrogen fixation. Changes in transcriptional and posttranslational levels of RHR7 ίΠ / ί7Π7 / Ε / ΥΙ nitrogen fixation regulatory network are necessary for the development of a microbe capable of fixing and transferring nitrogen to maize in the presence of fertilizers. Thus, in some embodiments, the genetically modified bacterium contains a modification of one or more genes of the nitrogen fixation regulatory network. 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. Not all organisms can carry out nitrogen fixation. By contrast, nitrogen fixation is limited to diazotrophs (bacteria and archaea that fix atmospheric nitrogen gas) that contain the genetic machinery to carry out nitrogen fixation. Thus, in some embodiments, the genetically modified bacterium is a diazotroph. Due to the energy-intensive nature of biological nitrogen fixation, diazotrophs have evolved a sophisticated and tight regulation of the nif gene cluster, which encodes the machinery responsible for carrying out nitrogen fixation, in response to ambient oxygen and to available nitrogen. To increase nitrogen fixation, it is desirable to increase the expression of the clustered Nif genes. Shamseldin (2013. Global J. Biotechnol. Biochem. 8(4):84-94) provides detailed descriptions of nif genes and their products, and is incorporated herein by reference. Thus, in some embodiments, modification in the nitrogen fixation regulatory network of the genetically modified bacterium results in increased expression of one or more clustered Nif genes. In proteobacteria, regulation of nitrogen fixation centers on the σ54-dependent enhancer-binding protein NifA, the positive transcriptional regulator of the nif cluster whose activation would result in increased expression of the clustered Nif genes. Thus, in some embodiments, the modification in the nitrogen fixation network of the genetically modified bacterium includes a modification in NifA, which, in some embodiments, results in increased expression of NifA. The intracellular levels of active NifA are controlled by two key factors: the transcription of the nifLA operon and the inhibition of NifA activity through the interaction between proteins with NifL, whose activation would produce a decrease in the expression of the Nif clustered genes. Thus, in some embodiments, the modification in the nitrogen fixation network of the genetically modified bacterium includes a modification in NifL, which, in some embodiments, results in decreased NifL expression. In addition to regulating the transcription of the nif 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 (NifH) protein under nitrogen excess conditions, which RHR7 I 0 / 1 7R7 / E / YI1 disrupts its interaction with the MoFe protein complex (NifDK) and abrogates nitrogenase activity. To avoid nitrogenase disruption, it is desirable to increase the NifH available to interact with the MoFe protein complex. Thus, in some embodiments, the modification in the nitrogen fixation network of the genetically modified bacterium includes a modification in NifH, which, in some embodiments, results in increased expression of NifH. Nitrogen fixation may also respond to intracellular or extracellular concentrations of ammonia, urea, or nitrates. It is desirable to avoid nitrogen assimilation to avoid its feedback implications in the nitrogen fixation network. Thus, in some embodiments, the genetically modified bacterium contains a modification in a nitrogen assimilating genetic network. The uptake of ammonia from the environment can be reduced by decreasing the expression level of the amtB protein. Without intracellular ammonia, the endophyte cannot detect the high ammonia content, which prevents the down-regulation of nitrogen fixation genes. Thus, in some embodiments, the modification in the nitrogen uptake genetic network includes a modification in amtB, which, in some embodiments, results in decreased amtB expression. Any ammonia that manages to enter the intracellular compartment is converted to glutamine. Intracellular glutamine concentration is the main currency of nitrogen detection. Decreased intracellular glutamine concentration prevents cells from detecting high concentrations 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 lowering 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 regulated posttranslationally by GS adenylyl transferase (GlnE), a glnE-encoded bifunctional enzyme that catalyzes the adenylation 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. To disrupt ammonia uptake and allow fixed nitrogen to be exported from the cell, it is desirable to decrease this GlnE activity. Thus, in some embodiments, the modification of the genetically modified bacterium into a network Genetic nitrogen uptake RnRZLn / LZnZ / E / Yli includes a modification in GlnE, which, in some modalities, results in decreased GlnE activity. The phosphoenolpyruvate-dependent sugar phosphotransferase (PTS) system is an important carbohydrate transport system in bacteria. The PTS catalyzes the phosphorylation of sugar substrates as they translocalize across the cell membrane. The phosphoryl group of phosphoenolpyruvate (PEP) is transferred to the phosphocarrier protein HPr by enzyme I, and then phospho-HPr transfers it to the PTS EIIA domain. The HPr phosphocarrier protein is encoded by the ptsH gene. In some embodiments, the modification of the genetically modified bacterium is a modification in the ptsH gene, such as a replacement of the promoter that regulates the expression of ptsH. In some embodiments, the genetically modified bacterium's modification in the ptsH gene results in increased sugar transport. In some embodiments, the modification results in an upregulation of the HPr phosphocarrier protein. L-asparaginase (LA), encoded by iaaA, catalyzes the degradation of the amino acid asparagine to ammonia and aspartate. In some embodiments, the modification of the genetically modified bacterium is a modification in the iaaA gene. In some embodiments, the genetically modified bacterium's modification in the iaaA gene results in decreased ammonia assimilation and / or increased ammonia excretion. In some embodiments, the modification results in an upregulation of L-asparaginase. Citrate synthase (E.C. 2.3.3.1), encoded by the gltA gene, is involved in the first stage of the citric acid cycle. It catalyzes the condensation reaction of the two-carbon acetate residue of acetyl coenzyme A and a four-carbon oxaloacetate molecule to form the six-carbon citrate. In some embodiments, the modification of the genetically modified bacterium is a modification in the gltA gene, such as a deletion of the gltA gene. In some embodiments, modification of the genetically modified bacterium in the gltA gene results in increased excretion of ammonia. Methods to impart novel microbial phenotypes can be carried out 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 the interactions between proteins. These changes can be achieved in multiple ways. Reduction of the expression level (or complete abolition) can be achieved by exchanging the ribosome binding site Natural RnRZLn / LZnZ / E / Yli (RBS) or the promoter with another with lower 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 (ORF) will likely produce a premature stop codon along the ORF, thereby creating a non-functional truncated product. Insertion of in-frame stop codons will similarly create a non-functional truncated product. A degradation marker can also be added at the N- or C-termini to reduce the effective concentration of a particular gene. Conversely, a higher level of expression of the genes described herein can be achieved by using 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 level 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 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). Increased nitrogen fixation activity Nitrogenases are enzymes responsible for catalyzing nitrogen fixation. There are three types of nitrogenase found in various nitrogen-fixing bacteria: molybdenum (Mo) nitrogenase, vanadium (V) nitrogenase, and iron-only (Fe) nitrogenase. Nitrogenases are two-component systems consisting of component I (also known as dinitrogenase) and component II (also known as dinitrogenase reductase). Component I is a MoFe protein in molybdenum nitrogenase, a VFe protein in vanadium nitrogenase, and an Fe protein in iron-only nitrogenase. Component II is an Fe protein containing an iron-sulfur (Fe-S) cluster. Varying the supply of cofactors can increase nitrogen fixation. Cofactor supply may be affected by iron absorption. the system of RHRZ Ln / LZRZ / E / Yli tonB transport may influence iron absorption. In some cases, iron absorption can be influenced by upregulating the tonB transporter system genes. Some examples of tonB transport system genes include, but are not limited to, tonB and exbAB. In some cases, siderophores that increase iron uptake in microbes and plants can influence iron uptake. In some cases, iron absorption can be influenced by upregulating siderophore biosynthesis genes. Some examples of siderophore biosynthesis genes include, but are not limited to, yhfA, yusV, sbnA, fiu, yfiZ, and fur. Other genetic modifications that can regulate iron availability include iscR and fhuF. Increased nitrogen fixation can also be achieved by increasing the expression of the clustered nif genes. Increased expression of clustered nif genes can be achieved in multiple different ways. In some embodiments, transcription of nif clusters can be increased by inserting strong promoters upstream of a nifHDK or nifDK operon. In some embodiments, increasing the expression of clustered nif genes is achieved by increasing the copy number of the genes in the genome. These additional copies of the genes can be brought under the control of the native promoter or a strong constitutive promoter. Another way to increase nitrogen fixation is to increase the number of nitrogenase enzymes per cell by increasing the transcription of nif pools. The transcription of nif pools can be increased by increasing the transcription of nifA. In some cases, the transcription of nifA clusters can be influenced by increasing the number of copies of a nifA gene in the genome. The transcription of nif pools can also be increased by increasing the translation of NifA. In some cases, NifA translation can be increased by increasing the strength of the ribosome binding site on the nifA gene. Transcription of nif pools can also be increased by expressing the pool under the control of a mutant form of NifA. Mutant forms of NifA can be obtained by subjecting the gene to mutagenesis and identifying a mutant that has increased translational efficiency or a mutant that expresses a corresponding protein with increased activity. Increased nitrogen fixation can also be achieved by altering the oxygen sensitivity of the cell. Reducing oxygen sensing can influence oxygen sensitivity. In some cases, reducing oxygen sensing can be done by altering the genes that detect oxygen. Some examples of oxygen sensing genes include, but are not limited to, nifT / fixU, fixJ, and fixL. Other genes that can be modified to alter oxygen sensitivity include sodA, sodB, sodC, FNR, arcA, and arcB. RnRZLn / LZnZ / E / Yli In some cases, oxygen sensitivity can be influenced by keeping the cytosolic oxygen content low by promoting respiration mediated by cytochrome bd. In some cases, oxygen sensitivity can be influenced by upregulating the genes encoding cytochrome bd oxidase and / or by inactivating alternative cytochrome systems. Examples of genes encoding cytochrome bd genes include, but are not limited to, cydABX, cydAB, and cydX. In some cases, nitrogenase can be protected from oxidation by altering the oxidation-reduction balance in the cell. The redox equilibrium can be altered by the removal of ROS. One strategy to achieve ROS knockdown is to upregulate the relevant genes. Some examples of ROS knockout genes include, but are not limited to, grxABCD, trxA, trxC, and tpx. In some cases, removal of free oxygen can influence oxygen sensitivity. In some cases, removal of free oxygen can be achieved by upregulating bacterial hemoglobin genes. An example of a hemoglobin gene includes, but is not limited to, gIbN. In some cases, removal of free oxygen can be achieved by upregulating the fixNOPQ genes encoding a high affinity heme-copper cbb3-type oxidase. In some cases, nifA modification may be beneficial in increasing nitrogenase expression. In some cases, it may be beneficial to modify nifA to increase the number of copies of the nifA gene in a cell. The copy number of the nifA gene can be increased by inserting multiple copies of a nifA gene in front of constitutive expression promoters. In some cases, linking a copy of the nifA gene to one or more housekeeping operons can increase the total number of nifA genes in a cell. In some cases, strains that can be used in this process of increasing nitrogenase expression may include, but are not limited to, the strains Rahnella aquatilis and Klebsiella variicola. In some cases, modification of a nitrogenase operon may be beneficial in increasing nitrogenase expression. In some cases, it may be beneficial to upregulate nitrogenase operons to increase transcription of nitrogenase. In some cases, promoters from the bacterium that are active when the bacterium is colonizing the rhizosphere can be inserted in front of the nitrogenase operons to upregulate them. In some cases, nifL can be deleted in the nitrogenase operons to upregulate the nitrogenase operons. In some cases, nifA can be deleted in the nitrogenase operons to upregulate the nitrogenase operons. In some cases, nifA and nifL can be deleted in the nitrogenase operons to upregulate the nitrogenase operons. In some cases, multiple promoters can be placed directly in front of the nifHDK genes to bypass the control of nifA transcription. In some cases, the RnRZLn / LZnZ / E / Yli strains that can be used in this process of increasing nitrogenase expression can include, among others, the strains Rahnella aquatilis and Klebsiella variicola. In some cases, glnE modification may be beneficial in increasing ammonium excretion. In some cases, a conserved aspartate amino acid-aspartate (DXD) motif in the AR domain of glnE can be changed. An amino acid represented as "X" indicates that the amino acid can be any amino acid, including naturally occurring amino acids (eg, a-amino acids), modified amino acids, and non-natural amino acids. It can also include D and L amino acids. In some cases, changing a conserved DXD residue in the AR domain of glnE can be used to eliminate glnE deadenylation activity. In some cases, a D residue can be replaced in a DXD motif in the AR region of glnE. In some cases, substitution of a D residue in a DXD motif in the AR region of glnE can leave the GlnB binding site intact to allow regulation of adenylation activity while decreasing or preventing AR activity. In some cases, strains that can be used in this process of increasing ammonium excretion may include, but are not limited to, the strains Rahnella aquatilis, Kosakonia sacchari, and Klebsiella variicola. Increased nitrogen fixation through assimilation The amount of nitrogen provided to a microbe-associated plant can be increased by decreasing nitrogen uptake into the microbe. Thus, in some embodiments, the genetically modified bacterium includes a modification in a nitrogen uptake network which, in some embodiments, results in decreased nitrogen uptake by the bacterium. Here, the rate of ammonia excretion can influence assimilation. By targeting ammonia assimilation, nitrogen availability can be increased. In some cases, ammonia assimilation can be influenced by slowing the rate of ammonia reuptake after excretion. To decrease the rate of ammonia reuptake after excretion, any relevant gene can be inactivated. An example of an ammonia reuptake gene includes, but is not limited to, amtB. Thus, in some embodiments, the genetically modified bacterium includes a modification in a nitrogen assimilating genetic network which modification results in decreased expression of amtB. The nitrogen assimilation control (NAO) protein is a LysR-like transcriptional regulator (LTTR) that is produced under nitrogen-limited growth conditions. NAO can activate the transcription of σ70-dependent genes whose products provide the cell with ammonia or glutamate. The NAO can also repress genes whose products use ammonia and its own transcription. NAO is encoded by the oxyR gene in K. variicola. In some modes, RnRZLn / Lznz / B / Yi the modification of the genetically modified bacterium is a modification in the oxyR gene, such as a modification such as a replacement of the promoter that regulates the expression of oxyR or a deletion of all or a part of the oxyR gene. In some embodiments, the genetically modified bacterium's modification of the oxyR gene results in increased excretion of ammonia. In some cases, the rate of absorption by the plant can influence assimilation. By targeting the genes and nitrogen uptake pathways of plants, nitrogen availability can be increased. In some cases, ammonia uptake by a plant can be altered by inoculation with nitrogen-fixing plant growth-promoting microbes. Screening can be carried out to identify microbes that induce ammonia uptake in plants. Increased nitrogen fixation through colonization Increasing the colonization ability of microbes can increase the amount of fixed nitrogen that is provided to a plant. Altering the carrying capacity (the abundance of microbes on the root surface) and / or the biological fitness of the microbes can influence colonization. In some cases, the carrying capacity and fitness of microbes can be influenced by altering the transport of organic acids. The transport of organic acids can be improved by upregulating the relevant genes. An example of an organic acid transporter gene includes, but is not limited to, dctA. Other examples of organic acid transport genes include yjjPB, ychM, dauA, and actP. For example, the ability to colonize can be affected by the expression of agglutinins. Increased expression of agglutinins may help microbes adhere to plant roots. Examples of agglutinin genes may include, but are not limited to, fhaB and fhaC. Colonization ability can be affected by increased endophytic entry. For example, endophytic entry can be affected by plant cell wall degrading enzymes (CDWE). Increased expression and / or secretion of CDWE can increase colonization and endophytic entry of microbes. Some examples of CDWE include, but are not limited to, polygalacturonases and cellulases. An example of a polygalacturonase gene is pehA. In some cases, the export of polygalacturonases and cellulases can be increased by providing an export signal with the enzymes. Other examples of CDWE include, but are not limited to, xylanases, xyloglucanases, alpha-galactosidases, beta-mannanases, alpha-arabinosidases, beta-galactosidases, and beta-glucuronidases. Illustrative xylanases include yieL1, yieL2, yieL3, yieL4, and pgab. Illustrative alpha-galactosidases include rafA and melA. Illustrative beta-glucuronidases include uidA. the mananasas Illustrative RnRZLn / Lznz / B / Yi include manA. Illustrative alphaarabinosidases include abfA and abnA. Illustrative beta-galactosidases include lacZ. Variation in carrying capacity can cause a greater amount of nitrogen to be provided to an associated plant. The carrying capacity can be affected by the formation of biofilms. In some cases, the loading capacity may be affected by small RNA rsmZ. The small RNA rsmZ is a negative regulator of biofilm formation. In some cases, biofilm formation can be promoted by knocking out or downregulating rsmZ, leading to increased translation of rsmA (a positive regulator of secondary metabolism) and biofilm formation. In some cases, biofilm formation can be influenced by improving the ability of the strains to adhere to the root surface. In some cases, biofilm formation can be promoted by upregulating large adhesion proteins. An example of a large adhesion protein includes, but is not limited to, lapA. In some cases, load capacity may be affected by quorum sensing. In some cases, quorum sensing can be improved by increasing the copy number of AHL biosynthesis genes. In some cases, root mass can influence rhizosphere colonization. For example, root mass can be affected by microbial IAA biosynthesis. Increased IAA biosynthesis by the microbe can stimulate the formation of root biomass. In some cases, IAA biosynthesis can be influenced by upregulation (over a range of concentrations) of IAA biosynthesis genes. An example of an IAA biosynthesis gene includes, but is not limited to, ipdC. In some cases, ethylene signaling can induce systemic resistance in the plant and affect the colonization ability of the microbe. Ethylene is a plant signaling molecule that elicits a wide range of responses depending on plant tissue and ethylene concentration. The prevailing model for the root response to ethylene is that plants that are exposed to stress respond rapidly by producing a small spike of ethylene that initiates a protective response from the plant, for example, the transcription of genes encoding defensive proteins. If stress persists or is severe, a much larger second ethylene spike occurs, often several days later. This second peak of ethylene induces processes such as senescence, chlorosis, and abscission that can lead to significant inhibition of plant growth and survival. In some cases, plant growth-promoting bacteria can stimulate root growth by producing the auxin IAA, which stimulates a small ethylene response in the roots. At the same time, the bacteria can prevent the second large ethylene spike by producing RHRZ Ln / L7R7 / E / Yli an enzyme (ACC deaminase) that slows down ethylene production in the plant, thus maintaining an ethylene concentration that leads to root growth stimulation. Bacterial IAA can influence the induction of systemic resistance in the plant. In some cases, IAA biosynthesis can be stimulated by upregulation (over a range of concentrations) of IAA biosynthesis genes. An example of a biosynthesis gene includes, but is not limited to, ipdC. In some cases, colonization can be affected by ACC deaminase. ACC deaminase can reduce ethylene production in the root by diverting ACC to a secondary product. In some cases, ACC deaminase can be influenced by upregulation of ACC deaminase genes. Some examples of ACC deaminase genes include, but are not limited to, dcyD. In some cases, the carrying capacity and / or fitness of microbes may influence colonization. For example, the carrying capacity and / or fitness of microbes can be affected by overproduction of trehalose. Overproduction of trehalose can increase tolerance to drought. In some cases, trehalose overproduction can be influenced by upregulation (over a range of concentrations) of trehalose biosynthesis genes. Some examples of trehalose biosynthesis genes include, but are not limited to, otsA, otsB, treZ, and treY. In some cases, upregulation of otsB can also increase nitrogen fixation activity. In some cases, bearing capacity may be affected by root binding. The secretion of exopolysaccharides can influence the attachment to the roots. In some cases, exopolysaccharide secretion can be influenced by upregulating exopolysaccharide-producing proteins. Some examples of exopolysaccharide production proteins include, but are not limited to, yjbE and pssM. In some cases, exopolysaccharide secretion can be influenced by upregulating cellulose biosynthesis. Some examples of cellulose biosynthesis genes include, but are not limited to, acs gene clusters and bes genes. In some cases, the carrying capacity and / or fitness of microbes may be affected by fungal inhibition. Chitinases, which can disrupt fungal cell walls and can lead to biological control of rhizosphere fungi, can influence fungal inhibition. In some cases, fungal inhibition can be influenced by upregulation of chitinase genes. Some examples of chitinase genes include, but are not limited to, chitinase class 1 and chiA. In some cases, efficient iron uptake can help microbes survive in the rhizosphere, where they compete with other microbes in the soil and the plant for food. RHRZ Ln / LZRZ / E / Yli iron absorption. In some cases, high-affinity chelation (siderophores) and transport systems can help with rhizosphere competition by 1) ensuring microbes get enough iron and 2) reducing the iron pool for competing species. Increasing the microbe's ability to do this could increase its competitive fitness in the rhizosphere. In some cases, iron absorption can be influenced by upregulating siderophore genes. Some examples of siderophore genes include, but are not limited to, yhfA, yusV, sbnA, fiu, yfiZ, and fur. Examples of yusV genes include, but are not limited to, yusV1 and yusV2. In some cases, the tonB transport system may influence iron absorption. In some cases, iron absorption can be influenced by upregulating the tonB transporter system genes. Some examples of tonB transport system genes include, but are not limited to, tonB and exbAB. In some cases, the carrying capacity and / or biological fitness of microbes may be affected by the redox balance and / or the removal of ROS. Bacterial glutathione (GSH) biosynthesis can influence the redox balance and / or the clearance of ROS. In some cases, bacterial glutathione (GSH) biosynthesis can be influenced through upregulation of bacterial glutathione biosynthesis genes. Examples of bacterial glutathione biosynthesis genes include, but are not limited to, gshA, gshAB, and gshB. In some cases, the removal of ROS can influence the oxidation-reduction equilibrium. In some cases, ROS clearance can be influenced through upregulation of catalases. Some examples of catalase genes include, but are not limited to, katEG and Mn catalase. In some cases, phosphorus signaling can influence biofilm formation. In some cases, phosphorus signaling can be influenced through altering the expression of phosphorus signaling genes. Some examples of phosphor signaling genes include, but are not limited to, phoR and phoB. In some cases, bearing capacity may be affected by root binding. Surfactin biosynthesis can influence root binding. In some cases, surfactin biosynthesis can be influenced by upregulating surfactin biosynthesis to enhance biofilm formation. An example of surfactin biosynthesis genes includes, but is not limited to, srfAA. In some cases, carrying capacity, competition with other microbes, and / or culture protection from other microbes may influence colonization and / or fitness of microbes. In some cases, quorum sensing and / or quorum neutralization may influence competition with other microbes and / or crop protection from RnRZLn / Lznz / B / Yi other microbes. Quorum neutralization can influence colonization by inhibiting quorum sensing of potential pathogenic / competitive bacteria. In some cases, quorum quenching can be influenced by inserting and / or upregulating genes encoding quorum quenching enzymes. Some examples of quorum quenching genes include, but are not limited to, ahID, Y2-aiiA, aiiA, ytnP, and attM. In some cases, modification of enzymes involved in quorum neutralization, such as Y2-aiiA and / or ytnP, may be beneficial for colonization. In some cases, upregulation of Y2aiiA and / or ytnP can result in hydrolysis of extracellular acyl-homoserine lactone (AHL). aiiA is an N-acyl homoserine lactonase which is an enzyme that degrades homoserine lactone. AHL degradation can stop or slow down the quorum signaling ability of competing gram-negative bacteria. In some cases, strains that can be used in this colonization enhancement process may include, but are not limited to, Rahnella aquatilis, Kosakonia sacchari, and Klebsiella variicola. In some cases, the carrying capacity and / or fitness of microbes may be affected by rhizobitoxin biosynthesis. Rizobitoxin biosynthesis can decrease root ethylene production by inhibiting ACO synthase. In some cases, rhizobitoxin biosynthesis can be influenced by upregulating rhizobitoxin biosynthesis genes. In some cases, bearing capacity may be affected by root binding. The secretion of exopolysaccharides can influence the attachment to the roots. In some cases, exopolysaccharide secretion can be influenced by generating hypermucoid mutants by deletion of mucA. In some cases, phenazine biosynthesis can influence root binding. In some cases, phenazine biosynthesis can be influenced by upregulating phenazine biosynthesis genes to enhance biofilm formation. In some cases, cyclic lipopeptide (CLP) biosynthesis can influence root binding. In some cases, cyclic lipopeptide (CLP) biosynthesis can be influenced by upregulating CLP biosynthesis to enhance biofilm formation. In some cases, the carrying capacity and / or competition may be affected by the synthesis of antibiotics. The synthesis of antibiotics can increase the production of antibiotics to kill competing microbes. In some cases, increased antibiotic production can be achieved by prospecting genomes for pathways of antibiotic biosynthesis and upregulation. In some cases, colonization may be affected by desiccation tolerance. In some cases, rpoE modification can be beneficial for colonization. In RnRZLn / Lznz / B / Yi In some cases, upregulation of rpoE can result in increased expression of genes and stress tolerance pathways. In some cases, rpoE can be upregulated using a unique switchable promoter. In some cases, rpoE can be upregulated using an arabinose promoter. rpoE is a sigma factor similar to phyR. When expressed, rpoE can cause upregulation of multiple stress tolerance genes. Since stress tolerance enzymes cannot be useful during a colonization cycle, a switchable promoter can be used. In some cases, the promoter may be active during biomass growth and / or during seed coating. In some cases, a switchable promoter can be used where the sugar or chemical can be fortified during the log phase of biomass growth, but can also cause the promoter to not activate during one or more other applications of the microbe. In some cases, rpoE can be upregulated at the same time as the downregulation of rseA. In some cases, strains that can be used in this colonization enhancement process may include, but are not limited to, Rahnella aquatilis, Kosakonia sacchari, and Klebsiella variicola strains. In some cases, colonization may be affected by desiccation tolerance. In some cases, modification of rseA may be beneficial for colonization. In some cases, rseA can be down-regulated using a single switchable promoter. In some cases, rseA can be down-regulated using an arabinose promoter. rseA is a sigma antifactor expressed in conjunction with rpoE. In some cases, the enzymes remain bound to each other, which can decrease or disable rpoE's ability to act as a transcription factor. However, during stress conditions, resAse can be cleaved and rpoE can be free to up / down-regulate stress tolerance genes. By disrupting cotranscription with rpoE, rpoE and resA concentrations can be titrated independently, which may be beneficial for optimizing colonization of genetically modified strains. Other gene modifications that may improve desiccation tolerance include modifications in rpoS, treA, treB, phoP, phoQ, and rpoN. In some cases, strains that can be used in this colonization enhancement process may include, but are not limited to, Rahnella aquatilis, Kosakonia sacchari, and Klebsiella variicola strains. Other gene modifications that can improve colonization include modifications in pga, SdiA, fimA1, fimA2, fimA3, fimA4, wzxE, and bolA. Generation of bacterial populations Isolation of bacteria Microbes useful in the methods and compositions described herein RHRZ Ln / LZnZ / E / Yli can be obtained by extracting microbes from surfaces or natural plant tissues. 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. Furthermore, 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, amount of moisture, mineral concentrations, 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. 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. Wild microbe determinations can be obtained for each plant. Determinations of wild microbes in the field can also be obtained by medium throughput methods. The determinations can be carried out successively over time. A model plant system may be used including, but not limited to, Setaria. Microbes in a plant system can be screened by transcriptional profiling of a microbe in a plant system. Examples of screening through transcriptional profiling are the use of quantitative polymerase chain reaction (qPCR) methods, RHRZ Ln / LZRZ / E / Yli molecular rods for transcript detection, next generation sequencing, and labeling of microbes with fluorescent markers. Impact factors can be determined 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 determining 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 18O. Therefore, NanoSIMS can be used for the chemical activity of nitrogen 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 a targeting primer 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 rhizobacteria, 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 the identification of such rhizobacteria include, but are not limited to, genomics, metagenomics, targeted isolation, gene sequencing, transcriptome sequencing, and modeling. Genomic analysis can be used to identify nitrogen-fixing rhizobacteria and Confirm the presence of RnRZLn / LZnZ / E / Yli mutations with next-generation sequencing methods, as described herein, and microbe version control. Metagenomics can be used to identify and isolate nitrogen-fixing rhizobacteria 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 the genotypes that lead to nitrogen-fixing 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 to genetically modify it to have 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 rhizobacteria may be nitrogen fixation. The directed evolution method can be iterative and adaptive depending on the selection process after each iteration. Rhizobacteria with high nitrogen fixation capacity can be generated. The evolution of these rhizobacteria can be carried out by introducing a genetic modification. Genetic modification 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 by using 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 nitrogen fixation properties, improved cereal colonization, increased oxygen sensitivity, increased nitrogen fixation, and increased excretion of ammonia. 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 by 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 liquid handler. Mutants with gene duplications and higher copy numbers express a higher genotype of the desired trait. Selection of plant growth promoting microbes according to nitrogen fixation Microbial colonies can be screened using various RnRZLn / LZnZ / E / Yli assays to assess nitrogen fixation. One way to determine nitrogen fixation is by a single fermentative assay, which determines nitrogen excretion. An alternative method is the acetylene reduction test (ARA) with online sampling over time. ARA can be carried out in high-throughput plates of microtube arrays. ARA can be carried out with live plants and plant tissues. The formulation of the medium and the oxygen concentration of the medium can vary in ARA assays. 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 microfermentors are used to assess oxygen sensitivity, nutritional requirements, nitrogen fixation, and nitrogen excretion. Bacteria can also be cultured in conjunction with competitive or beneficial microbes to elucidate cryptic pathways. Flow cytometry can be used to detect bacteria that produce high concentrations of nitrogen using 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. microbial breeding Microbe 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 clusters, 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 breeding and improve the frequency of selection for breeding in microbiome-encoded traits of agronomic relevance. Bacteria production to improve plant traits (eg nitrogen fixation) can be achieved by signal passage. Production of these bacteria can be accomplished by selecting for plants, which have a particular breeding trait that is influenced by microbial flora, as well as identifying bacteria and / or compositions that are Rn«7Ln / L7n7 / E / Yli capable of imparting one or more enhanced traits to one or more plants. 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 modification into one or more of the bacteria to produce one or more variant bacteria; (c) exposing a plurality of plants to the variant bacteria; (d) isolating bacteria from the tissue or soil of one of the plurality of plants, wherein the plant from which the bacteria is isolated has an improved trait relative to other plants in the plurality of 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 plurality of plants may be more than two plants, such as from about 10 to about 20 plants, or about 20 or more, about 50 or more, about 100 or more, about 300 or more, about 500 or more, or about 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 modifications 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. 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 can be obtained using techniques including: high-throughput screening for chemical components of plant origin, sequencing techniques including high-throughput sequencing of genetic material, differential expression techniques (including DDRT-PCR and DD-PCR), nucleic acid microarray techniques, RNA sequencing (Shotgun whole transcriptome sequencing), and qRT-PCR (real-time quantitative POR). 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 detection of nucleic acid microarrays 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. The RnRZLn / LZnZ / E / Yli 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. The genetic modification 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, nifU, nifS, nifV, nifW, nifZ, nifM, nifF, nifB and nifQ. The genetic modification may be a modification 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 NAD+-dinitrogen reductase aDP-D-ribosyltransferase. The genetic modification can be a mutation 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 scavenging activity of GlnE; or decreased uridylyl scavenging activity of GlnD. The introduction of a genetic modification may comprise the insertion and / or deletion of one or more nucleotides at a target site, such as 1,2,3,4, 5,10, 25, 50,100, 250, 500 or more nucleotides. The genetic modification introduced into one or more bacteria by the methods described herein may be a knock-out mutation (eg, deletion of a promoter, insertion or deletion to produce a premature stop codon, deletion of a complete 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 modification 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 modification may be a predetermined genetic modification that is specifically introduced at a target site. The genetic modification may be a random mutation within the target site. The genetic modification may be an insertion or deletion of one or more nucleotides. In some cases, multiple different genetic modifications (eg, 2, 3, 4, 5, 10 or more) are introduced into one or more of the isolates prior to exposing the bacteria to plants to assess trait improvement. The plurality of modifications Genetic RHRZ LO / LZ / IZ / E / Yl can be any of the above types, the same type or different types, and in any combination. In some cases, a plurality of different genetic modifications are introduced serially, by introducing a first genetic modification after a first stage of isolation, a second genetic modification after a second stage of isolation, and so on, to accumulate a plurality of genetic modifications. genetic modifications in bacteria that impart progressively improved traits in associated plants. A variety of molecular tools and methods are available to introduce genetic modifications. For example, genetic modification 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 for introducing genetic modifications 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, carbon dioxide ethylene, dimethylnitrosamine, 7,12-dimethylbenz(a)anthracene, chlorambucil, hexamethylphosphoramide, bisulfan, and the like. Radiation mutation-inducing agents include ultraviolet radiation, y-radiation, X-rays, and fast neutron bombardment. Genetic modifications 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 for generating genetic modifications. Genetic modifications can be introduced into a nucleic acid during amplification in an in vitro cell-free system, for example, by using a polymerase chain reaction (PCR) technique such as error-prone POR. Genetic modifications 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 modifications 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. 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 that RHRZ Ln / LZRZ / E / Yli encode DNA repair enzymes include, but are not limited to, Mut H, Mut S, Mut L, and Mut U, and the homologues of these in other species (for example, MSH 1 6, PMS 1 2, MLH 1, GTBP, ERCC-1, and the like). Examples of descriptions of various methods for introducing genetic modifications are provided, for example, in Stemple (2004) Nature 5:1-7; Chiang et al. (1993) POR Methods Appl 2(3): 210-217; Stemmer (1994) Proc. nati. Acad. Sci. USA 91:10747-10751; and U.S. Patent Nos. 6,033,861 and 6,773,900. Genetic modifications introduced into microbes can be classified as transgenic, cisgenic, intragenomic, intrageneric, intergeneric, synthetic, evolved, rearranged, or SNP. Genetic modification 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, plant cell wall degrading enzymes or pathways, splicing genes to the root, exopolysaccharide secretion, glutamate synthase pathway, iron absorption pathways, siderophore pathway, chitinase pathway, ACO deaminase, glutathione biosynthesis, phosphorus signaling genes, quorum neutralization pathway, cytochrome pathways, hemoglobin pathway, bacterial hemoglobin-like pathway, small RNA rsmZ, rhizobitoxin biosynthesis, lapA adhesion protein, AHL quorum sensing pathway, phenazine biosynthesis, cyclic lipopeptide biosynthesis, and antibiotic production. CRISPR / Cas9 systems (clustered regularly interspaced j / CRISPR-associated short palindromic repeats (Cas)) can be used to introduce the desired mutations. CRISPR / Cas9 provides bacteria and archaea with adaptive immunity against viruses and plasmids through the use of CRISPR RNA (crRNA) to guide the silencing of invading nucleic acids 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 tracRNA (also called guide RNA).In some cases, the two molecules are covalently linked to form a single molecule (also called simple guide RNA (“gsRNA”)). 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), activating the RnRZLn / LZnZ / E / Yli 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 the target DNA to create a double-strand break, which can lead to genome disruption (i.e., editing: deletion, insertion (when a donor polynucleotide is present). ), replacement, etc.), thereby altering gene expression. Some Cas9 variants (such variants include the term Cas9-like) have been altered in such a way 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 cases, show drastically reduced to zero DNA cleavage activity). Examples of further descriptions of CRISPR systems for introducing genetic modifications can be found, for example, in US Patent No. 8,795,965. 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 original non-hydroxymethylated DNA ; 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 template DNA by the restriction enzyme Dpnl which cleaves only the methylated DNA, whereby the mutagenized unmethylated strands are recovered; or 4) circularization of the mutated PCR products in a further ligation reaction to increase the efficiency of transformation of the mutated DNA. Additional description of example methods can be found in, for example, US Patents 7,132,265, 6,713,285, 6,673,610, 6,391,548, 5,789,166, 5,780,270, 5,354,670, 5,071,743 and US Publication No. 2010 / 02 67147. Oligonucleotide-directed mutagenesis, also called site-directed mutagenesis, typically uses a synthetic DNA primer. This synthetic primer contains the desired mutation and is complementary to the template DNA 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), multiple 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 gene thus copied contains the site RnRZLn / Lznz / B / Yi mutated, and can subsequently 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 modifications 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 (where 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 deletions, additions, clusters of codons, and clusters of particular nucleotide cassettes. Fragment shuffling mutagenesis, also called DNA shuffling, is a way of rapidly propagating beneficial mutations. In one example of a shuffling process, DNase is used to fragment a set of parent genes into pieces, eg, about 50 to 100 bp in length. This is followed by a polymerase chain reaction (PCR) without primers; DNA fragments with sufficient overlapping homologous sequence will hybridize to each other and then be 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 RnRZLn / LZnZ / E / Yli 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. Additional examples of transposition techniques are provided in US Publication No. 2005 / 0266541 . Homologous recombination mutagenesis involves recombination between an exogenous DNA fragment and the target polynucleotide sequence. After a double-strand break occurs, 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 template polynucleotide 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 template polynucleotide is complementary to a part of a polynucleotide that comprises the target sequence. When optimally aligned, a template polynucleotide can 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, 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 further description of the use of such nucleases, see, e.g. e.g., US Patent No. 28,795,965 and US Publication No. 2014 / 0301990. 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 modifications. Mutagens include, but are not limited to, RnRZLn / Lznz / B / Yi Ethyl Methanesulfonate, Methylmethane Sultanate, N-Ethyl-N-Nitrosurea, Triethylmelamine, N-MethylN-Nitrosourea, Procarbazine, Chlorambucil, Cyclotasphamide, 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), dihydrochloride 2-methox¡-6-chloro-9[3-(eth¡l·2-chloro-eth¡l)am¡noprop¡lam¡no]acr¡d¡na and formaldehyde. The introduction of a genetic modification 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 modification. Traditionally, selection for successful genetic variants involved selection for or against some functionality imparted or abolished by the genetic modification, 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, so that it is only necessary to introduce a desired genetic modification (eg, without also requiring a selectable marker). In this case, selection pressure may comprise excision of genomes lacking the introduced genetic modification at a target site, so that selection is effectively directed against the reference sequence into which the genetic modification is sought. 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 modification are more likely to undergo a cleavage 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. RHRZ Ln / LZRZ / E / Yli efficient symbiotes. 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 modification, 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 genetically engineered 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 interruptions. Transcriptional activator-like elector nucleases (TALENs) are artificial DNA endonucleases generated by fusing a TAL effector DNA-binding domain (transcriptional activator-like) to a DNA cleavage domain. TALENs can be easily engineered to bind to virtually any DNA sequence, and when introduced into a cell, TALENs can be used to edit target DNA in the cell (for example, the cell's genome) by inducing double chain interrupts. 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, the GIYYIG family, His-Cyst sequence family and HNH family Examples of homing endonucleases include l-Scel, l-Ceul, Pl-Pspl, Pl-Sce, Ι-ScelV, l-Csml, l-Panl , l-Scell, l-Ppol, IScelll, l-Crel, I-Tevl, I-Tevll and I-Tevlll. 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, fruit size, RHRZ Ln / L7R7 / E / Yli grain, 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 expression of proteomes. 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. In some embodiments, a feature to be introduced or improved is nitrogen fixation, as described herein. In some embodiments, the trait to be introduced or improved is ammonium excretion, colonization, iron transport, oxygen tolerance, desiccation tolerance, or a combination of these. In some embodiments, one or more of ammonium excretion, colonization, iron transport, oxygen tolerance, and desiccation tolerance are increased relative to bacteria lacking modifications in the identified genes. In some cases, a plant produced by the methods described herein exhibits a difference in trait that is at least about 5% greater, eg, 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 greater than a reference agricultural plant grown in the same conditions in the soil that lacks the introduced or improved trait. For example, a plant produced by the methods described herein exhibits an increase in the amount of nitrogen fixation that is at least about 5% greater, eg, at least about 5%, at least about 8%, at least about 10%, at least approximately 15%, at least approximately 20%, at least approximately 25%, at least approximately 30%, at least approximately 40%, at least approximately 50%, at least approximately 60%, at least approximately 75% , at least approximately 80%, at least approximately 80%, at least approximately 90%, or at least approximately 100%, at least approximately RnRZLn / Lznz / B / Yi 200%, at least about 300%, at least about 400% or higher than a reference agricultural plant grown under the same conditions in the soil. In further examples, a plant produced by the methods described herein exhibits a difference in trait that is at least about 5% greater, eg, 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 greater than a reference agricultural plant grown under conditions similar on the ground. In some embodiments, by an assay as described herein, the amount of nitrogen fixation and / or the increase in one or more of ammonium excretion, colonization, iron transport, oxygen tolerance, and desiccation tolerance is determined. compared to a reference agricultural plant grown under similar soil conditions that occur in the plants described herein. For example, the amount of nitrogen fixation can be determined by an acetylene reduction (AR) test. 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 1% or more (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, 1,000-fold, or more) compared to bacteria isolated from the first plant prior to the introduction of any genetic modification. In some cases, bacteria produce 5% or more of a plant's nitrogen. The desired amount of nitrogen fixation can be achieved after repeating the steps of introducing a genetic modification, exposing a plurality of RHRZ Ln / LZRZ / E / Yli plants and isolating bacteria from plants with a trait enhanced one or more times (eg, 1, 2, 3, 4, 5,10,15, 25 or more times). In some cases, enhanced amounts 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. Microbe 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 clusters, 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 breeding and improve the frequency of selection for breeding in microbiome-encoded traits of agronomic relevance. Fixation of nitrogen The genetically modified bacterium described herein can be used in a method for increasing nitrogen fixation in a plant, which method includes a step of contacting the plant with a plurality of the bacteria. In some embodiments, the bacteria produce 1% or more nitrogen in the plant (eg, 2%, 5%, 10% or more), which, in some embodiments, represents a nitrogen-fixing capacity of at least 2 times 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 genetically modified bacterium can include any genetic modification described herein, including the examples provided above, in any amount and in any combination. The genetic modification can be introduced into a gene selected from the group consisting of: nifA, nifL, ntrB, ntrC, glutamine synthetase, glnA, glnB, gInK, draT, amtB, glutaminase, glnD, glnE, nifj, nifH, nifD, nifK, nifY, nifE, nifN, nifU, nifS, nifV, nifW, nifZ, nifM, nifF, nifB, and nifQ. The genetic modification can be a mutation 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 scavenging activity of GlnE; or decreased uridylyl scavenging activity of GlnD. The genetic modification introduced into one or more bacteria by the methods described herein may be an inactivating mutation or may abrogate a regulatory sequence. RnRZLn / Lznz / B / Yi of a target gene, or may comprise insertion of a heterologous regulatory sequence, eg, 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 modification can be produced by chemical mutagenesis. The plant 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 carried out. 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) symptoms of nitrogen deficiency 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 inputs of O2 and NfV pass through a NOR gate, the output of which goes through an AND gate in addition to ATP. In some embodiments, the methods described herein disrupt the influence of NHh on this circuit, at multiple points in the regulatory cascade, so that microbes can produce nitrogen even in fertilized fields. However, the methods described herein also envision altering the impact of ATP or O2 on the circuit, or replacing the circuit with other regulatory cascades in the cell, or altering genetic circuits other than nitrogen fixation. Gene clusters can be re-engineered to generate functional products under the control of a heterologous regulatory system. By removing the 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 being reengineered, the synthetic gene clusters can be controlled by genetic circuitry or other inducible regulatory systems, thereby controlling the expression of products such as RnRZLn / LZnZ / E / Yli is 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 removed 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 a synthetic expression cassette. 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 the present disclosure can 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 RnRZLn / Lznz / B / Yi can 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 herein can be used with archaea, such as, for example, Methanothermobacterthermoautotrophicus. In some instances, bacteria that may be useful include, but are not limited to, Agrobacterium radiobacter, Bacillus acidocaldarius, Bacillus acidoterrestris, Bacillus agri, Bacillus aizawai, Bacillus albolactis, Bacillus alcalophilus, Bacillus alvei, Bacillus aminoglucosidicus, Bacillus aminovorans, Bacillus a mylolyticus ( also known as Paenibacillus amylolyticus) Bacillus amyloliquefaciens, Bacillus aneurinolyticus, Bacillus atrophaeus, Bacillus azotoformans, Bacillus badius, Bacillus cereus (synonyms: Bacillus eodorhythmos, Bacillus medusa), Bacillus chitioosporus, Bacillus circulaos, Bacillus s coagulants, Bacillus eodoparasiticus Bacillus fastidiosus, Bacillus firmus, Bacillus kurstaki, Bacillus lacticola, Bacillus lactimorbus, Bacillus lactis, Bacillus laterosporus (also known as Brevibacillus laterosporus), Bacillus lautus, Bacillus leotimorbus, Bacillus leotus, Bacillus licheoiformis, Bacillus maroccaous, Bacillus megaterium, Bacillus metieos , Bacillus mycoides, Bacillus oatto, Bacillus oematocida, Bacillus oigrificaus, Bacillus oigrum, Bacillus paototheoticus, Bacillus popillae, Bacillus psychrosaccharolyticus, Bacillus pumilus, Bacillus siameosis, Bacillus smithii, Bacillus sphaericus, Bacillus subtilis, Bacillus thuriogieosis, Bacillus uoif lagellatus, Bradyrhizobium japooicum, Brevibacillus brevis Brevibacillus laterosporus (formerly Bacillus laterosporus) , Chromobacterium subtsugae, Delftia acidovoraos, Lactobacillus acidophilus, Lysobacter aotibioticus, Lysobacter eozymogeoes, Paeoibacillus alvei, Paeoibacillus polymyxa, Paeoibacillus popilliae (formerly Bacillus popilliae), Paotoea agglomeraos, Pasteuria peoetraos ( formerly Bacillus peoetraos), Pasteuria usgae, Pectobacterium carotovorum (formerly Erwioia carotovora ), Pseudomoas aerugioosa, Pseudomoas aureofacieos, Pseudomoas cepacia (formerly known as Burkholderia cepacia), Pseudomoas chlororaphis, Pseudomoas fluoresceous, Pseudomoas proradix, Pseudomoas putida, Pseudomoas syriogae, Serratia eotomophila, Serratia marcesce os, Streptomyces colombieosis, Streptomyces galbus, Streptomyces goshikieosis, Streptomyces griseoviridis Bacillus sp. AQ175 (ATOO accession n.2 55608), Bacillus sp. AQ 177 (ATCC Accession No. 2 55609), Bacillus sp. AQ178 (ATCC accession n.2 53522) and strain Streptomyces sp. Access N.2 NRRL B-30145. In some cases, the bacteria may be Azotobacter chroococcum, ROR7 I η / l 7O7 / E / Yl· Methanosarcina barkeri, Klesiella pneumoniae, Azotobacter vinelandii, Rhodobacter spharoides, Rhodobacter capsulatus, Rhodobcter 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 tetani, 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 (eg, Anagaena sp. PCC7120), Nostoc (eg, Nostoc punctiforme), or Synechocystis (eg, Synechocystis sp. PCC6803). 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, (zehr.pmc.ucsc.edu / nifH_Database_Public / on the internet, April 4, 2014), or the database from Buckley lab NifH (css.cornell.edu / faculty / buckley / nifh.htm online and 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): bau001.). 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, (zehr.pmc.ucsc.edu / nifH_Database_Public / online 4 Apr 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 in 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): bau001.). 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. The RnRZLn / LZnZ / E / Yli non-limiting examples of plant tissues include a seed, seedling, leaf, cutting, plant, bulb, or tuber. 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. The bacteria can also be obtained from a reservoir, such as collections of environmental strains, rather than being initially isolated from a first plant. Microbes can be genotyped and phenotyped by sequencing the genomes of isolated microbes; generating profiles of the composition of the in planta communities, characterizing the transcriptomic functionality of communities or isolated microbes; or by screening 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, 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 the genetic modifications, 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 grass 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). The bacterial endophyte carried RnRZLn / LZnZ / E / Yli by seeds can be associated or derived from the seed surface; 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. By way of example, bacteria may include Proteobacteria (such as Pseudomonas, Enterobacter, Stenotrophomonas, Burkholderia, Rhizobium, Herbaspirillum, Pantoea, Serratia, Rahnella, Azospirillum, Azorhizobium, Azotobacter, Duganella, Delftia, Bradyrhizobium, Sinorhizobium, and Halomonas), Firmicutes ( such as Bacillus, Paenibacillus, Lactobacillus, Mycoplasma, and Acetabacterium), and Actinobacteria (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 consortium of bacteria may facilitate or enhance the ability of other bacteria to fix nitrogen. The nitrogen-fixing bacteria and the bacteria that enhance the nitrogen-fixing ability of other bacteria 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, Bradyrhizobium japonicum, Klebsiella pneumoniae and Sinorhizobium 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 bacteria of the genus Clostridium include, but are not limited to, Clostridium acetobutylicum, Clostridium pasteurianum, Clostridium beijehnckii, Clostridium perfringens, and Clostridium tetani. In some cases, the bacteria may be of the genus Paenibacillus, for example, Paenibacillus azotofixans, Paenibacillus borealis, Paenibacillus durus, Paenibacillus macerans, Paenibacillus polymyxa, RHRZ ίΠ / ί^ΠΖ / Ε / ΥΙ Paenibacillus alvei, Paenibacillus amylolyticus, Paenibacillus campinasensis, Paenibacillus chibensis, Paenibacillus glucanolyticus, Paenibacillus illinoisensis, Paenibacillus larvae subsp. Larvae, Paenibacillus larvae subsp. pulvifaciens, 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 disclosure may be a member of one or more of the following taxa: Achromobacter, Acidithiobacillus, Acidovorax, Acidovoraz, Acinetobacter, Actinoplanes, Adlercreutzia, Aerococcus, Aeromonas. Afipia, Agromyces, Ancylobacter, Arthrobacter, Atopostipes, Azospirillum, Bacillus, Bdellovibrio, Beijerinckia, Bosea, Bradyrhizobium, Brevibacillus, Brevundimonas, Burkholderia, Candidatus Haloredivivus, Caulobacter, Cellulomonas, Cellvibrío, Chryseobacterium, Citroba cter, Clostridium, Coraliomargarita, Corynebacterium, Cupriavidus, Curtobactehum , Curvibacter, Deinococcus, Delftia, Desemzia, Devosia, Dokdonella, Dyella, Enhydrobacter, Enterobacter, Enterococcus, Erwinia, Escherichia, Escehchia / Shigella, Exiguobacterium, Ferroglobus, Filimonas, Finegoídla, Flavisolibacter, Flavobacterium, Frigoríbactehum, Gluconace tobacter, Hafnia, Halobaculum, Halomonas , Halosimplex, Herbaspirillum, Hymenobacter, Klebsiella, Kocuría, Kosakonia, Lactobacillus, Leclercia, Lentzea, Luteibacter, Luteimonas, Massilia, Mesorhizobium, Methylobacterium, Microbacterium, Micrococcus, Microvirga, Mycobacterium, Neisseria, Nocardia, Oceanibaculum, Ochrobactrum, Okibacterium, Oligotropha, Oryzihumus , Oxalophagus, Paenibacillus, Panteoa, Pantoea, Pelomonas, Perlucidibaca, Plantibacter, Polynucleobacter, Propionibacterium, Propioniciclava, Pseudoclavibacter, Pseudomonas, Pseudonocardia, Pseudoxanthomonas, Psychrobacter, Ralstonia, Rheinheimera, Rhizobium, Rhodococcus , Rhodopseudomonas, Roseateles, Ruminococcus, Sebaldella, Sediminibacillus, Sediminibacterium , Serratia, Shigella, Shinella, Sinorhizobium, Sinosporangium, Sphingobacterium, Sphingomonas, Sphingopyxis, Sphingosinicella, Staphylococcus, Stenotrophomonas, Strenotrophomonas, Streptococcus, Streptomyces, Stygiolobus, Sulfurisphaera, Tatumella, Tepidimonas, Thermomonas, Thio bacillus, Variovorax, WPS-2 generates incertae sedis , Xanthomonas and Zimmermanella. Bacteria can be obtained from any general terrestrial environment, including soils, plants, fungi, animals (including invertebrates), and other biota, including sediments, water, and lake and river biota; 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 water RnRZLn / LZnZ / E / Yli thaw; the atmosphere (for example, filtered air dust, clouds, and raindrops); urban, industrial, and other man-made environments (for example, accumulated organic and mineral matter in concrete, gutters, roof surfaces, and road surfaces). The plants from which the bacteria 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 conditions of 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 the least 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 fiber content , oil content and the like, or desirable colours, taste or smell. 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 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 media, which may or may not be selective (for example, 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, samples of the root of the plant or of the RHR7 Ln / L7R7 / E / Yli foliage cannot be surface sterilized, but only gently washed, so surface-dwelling epiphytic microorganisms are included in the isolation process, or epiphytic microbes 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 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 plant's phosphere. If not, 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 plant bacteria. Biologically pure cultures of Rahnella aquatilis and Enterobacter sacchari were deposited on July 14, 2015, at the American Type Culture Collection (ATCC; an international depository authority), Manassas, VA, USA, and assigned deposit designation numbers of ATTC patent PTA-122293 and PTA-122294, respectively. These deposits were made in accordance with the provisions of the Budapest Treaty on the International Recognition of the Deposit of Microorganisms for the Purposes of Patent Procedure and the Regulations (Budapest Treaty). 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. 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 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, a surface of a seed may be coated with one or more compositions. In some examples, a seed surface may be coated with one or more compositions as a layer on top of it. In some examples, a composition that coats a seed RnRZLn / LZnZ / E / Yli may be in liquid form, dry product form, foam form, powder and water slurry form, or a flowable 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, Burkholdeha, Chryseobacterium, Curtobacterium, Enterobacter, Escherichia, Methylobacterium, Paenibacillus, Pantoea, Pseudomonas, Palstonia, Saccharibacillus, 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, Sphingomonadaceae, Xanthomonadaceae, Cladosporiaceae, Gnomoniaceae, Incertae sedis, Lasiosphaeriaceae, Netriaceae, 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, Rhizobiaceae, Sphingomonadaceae, Xanthomonadaceae, Cladosporiaceae, Gnomoniaceae, Incertae sedis, Lasiosphaeriaceae, Netriaceae, 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. 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 RnRZLn / Lznz / B / Yi roots by inserting them into the grooves 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 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 amount 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 an adhesive, 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. RnRZLn / Lznz / B / Yi (for example, one or more of a fertilizer, such as a non-naturally occurring fertilizer, a binding agent, such as a non-naturally occurring binding agent, and a pesticide, such as a pesticide of non-natural origin). A non-naturally occurring adhesion agent can be, for example, a polymer, copolymer or synthetic wax. For example, any of the seeds, seedlings or coated plants described herein may contain such 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, a non-naturally occurring adhesion agent 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, which may be nonionic or ionic surfactants, or a combination of these, may be included in the composition. Water-in-oil emulsions can also be used to formulate a composition that includes the isolated bacteria (see, for example, US Pat. No. 27,485,451). Suitable formulations that can be prepared include wettable powders, granules, gels, agar strips or granules, thickeners and the like, microencapsulated particles and the like, liquids such as slurries, slurries, water-in-oil emulsions, etc. The formulation can include grain or legume products, for example, ground grains or legumes, broth or flour derived from grains or legumes, starch, sugar or oil. In some embodiments, the agricultural carrier may be a plant growth medium or soil. Other agricultural carriers that can be used include water, fertilizers, vegetable 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 suspensions. Mixtures of any of the ingredients mentioned above are also contemplated as carriers, such as, but not limited to, pesta (kaolin flour and clay), agar or flour granules in loam, sand or clay, etc. Formulations may include food sources for bacteria, such as barley, RHRZ Ln / LZRZ / E / Yli rice or other biological materials such as seeds, plant parts, sugarcane bagasse, husks or stalks from grain processing, ground plant material or wood from construction site waste, sawdust or small fibers from recycling paper, cloth or wood. For example, a fertilizer can be used to help promote growth or 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, NaCI, yeast extract, NH4H2PO4, (NHDzSCX glycerol, valine, L-leucine, lactic acid, propionic acid, succinic acid, malic acid, citric acid , KH tartrate, xylose, lyxose, and lecithin.In one embodiment, the formulation may include an adhesive or adherent (referred to as a sticking agent) to help bind other active agents to a substance (for example, the surface of a seed).Such agents are useful for combining bacteria with carriers that may contain other compounds (for example, 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, Gum Arabic, 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 block copolymers of polyoxyethylene and polyoxybutylene. 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, Ouncury wax, and bran wax. rice, a polysaccharide (eg, starch, dextins, 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, calcium lignosulfonates, acrylic copolymers, RHRZ Ln / LZRZ / E / Yli polyvinylacrylates, 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 fillers. The formulation may also contain a surfactant. Non-limiting examples of surfactants include nitrogen-surfactant mixtures such as Prefer 28 (Cenex), SurfN(US), Inhance (Brandt), P-28 (Wilfarm) and Patrol (Helena); esterified seed oils include Sun-lt 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. Such an 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 actually 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 or sorbitol). The amount of desiccant introduced into the formulation can range from about 5% to about 50% w / v, for example, from about 10% to about 40%, from about 15% to about 35%, or from 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 examples, the agents may include protectants that provide protection against seed-borne pathogens. In some examples, protectants can provide some level of control over soil-borne pathogens. In some examples, the protectors may be RnRZLn / LZnZ / E / Yli effective predominantly on the surface of a seed. In some examples, a fungicide may include a compound or agent, either chemical or biological, that can inhibit the growth of a fungus or kill it. 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 over soil-borne pathogens. Non-limiting examples of protectant fungicides include captan, maneb, thiram, or fludioxonil. In some examples, a fungicide can 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: 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 pathogenic fungal species sensitivity 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, 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, RnRZLn / Lznz / B / Yi dimethipine, 2,6-dimethylpuridine, ethephon, flumetralin, flurprimidol, flutiacet, forchlorfenuron, gibberellic acid, inabenfide, indole-3-acetic acid, maleic hydrazide, mefluidide, mepiquat (mepiquat chloride), acid naphthalene acetic, 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, it should not be detrimental to the growth or health of the plant). 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 a safety risk, or the compound is sufficiently labile that the plant-derived plant product contains negligible amounts). 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.; arbuscular and vesicular mycorrhizal fungi, Burkholderia spp.; Pasteuria spp., Brevibacillus spp.; Pseudomonas spp.; and Rhizobacteria. Particularly preferred nematode antagonist biocontrol agents include ARF18, Arthrobotrys oligospora, Arthrobotrys dactyloides, Chaetomium globosum, Cylindrocarpon heteronema, Exophilia jeanselmei, Exophilia pisciphila, Fusarium aspergilus, Fusarium solani, Gliocladium catenulatum, Gliocladium roseum, Gliocladium vixen s, Hirsutella rhossiliensis, Hirsutella minnesotensis arbuscular and vesicular mycorrhizal fungi, Burkholderia cepacia, Pasteu ria penetraos, Pasteuria thornei, Pasteuria nishizawae, Pasteuria ramosa, Pastrueia usage, Brevibacillus laterosporus strain G4, Pseudomonas 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-formaldehyde, IBDU, polymer coated urea, RHRZ Ln / L7R7 / E / Yli calcium nitrate, ureaform, and methyleneurea, phosphorous fertilizers such as diammonium phosphate, monoammonium phosphate, ammonium polyphosphate, concentrated superphosphate, and triple superphosphate, and potassium fertilizers such as potassium chloride, Potassium Sulfate, Magnesium Potassium Sulfate, Potassium Nitrate. Such compositions can exist as free salts or ions within the seed coating composition. Alternatively, the nutrients / fertilizers can be complexed or chelated to provide sustained release over time. Some examples of rodenticides may include those selected from the group consisting of 2-isovalerilindan-1,3-dione, 4-(quinoxalin-2-lamino)benzenesulfonamide, alphachlorohydrin, aluminum phosphide, antu, oxide arsenic, barium carbonate, bistiosemi, brodifacoum, bromadiolone, bromethalin, calcium cyanide, chloralose, chlorophacinone, cholecalciferol, coumachlor, coumafuryl, coumatetralyl, crimidine, difenacoum, difethialone, diphacinone, ergocalciferol, flocoumafen, fluoroacetamide, flupropadine, hydrochloride flupropadin , hydrogen cyanide, iodomethane, lindane, magnesium phosphide, methyl bromide, norbormide, fosacetim, phosphine, phosphorus, pindone, potassium arsenite, pyrinuron, scilliroside, sodium arsenite, sodium cyanide, sodium fluoroacetate, strychnine, sulfate stem, warfarin and zinc phosphide. In liquid form, eg solutions or suspensions, bacterial populations can be mixed or suspended in water or aqueous solutions. Suitable liquid diluents or carriers include water, aqueous solutions, petroleum distillates, or other liquid carriers. Solid compositions can be prepared by dispersing 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. In addition, organic fine powders such as wheat flour, wheat bran and rice bran can be used. Liquid carriers include vegetable oils such as soybean oil and cottonseed oil, glycerol, ethylene glycol, polyethylene glycol, propylene glycol, polypropylene glycol, etc. Application of bacterial populations on cultures RHRZ LO / LZ / IZ / E / Yl The composition of bacteria or bacterial population described herein can be applied in furrows, on talc or as a seed treatment. In some embodiments, the bacteria composition or bacterial population described herein may be applied indirectly to a plant. In some embodiments, the composition of bacteria or bacterial population described herein can be applied as a top-dressing. Applying the bacteria or bacterial population indirectly and / or as a top dressing may include applying the bacteria or bacterial population to a shallow groove or band along the side of a plant or in a circle around a plant. The bacterial composition or population can be applied to a seed packet in bulk, in small bulk, in a bag or in talc. The composition of the bacteria or bacterial population described herein can be applied after planting a plant seed but before harvesting. For example, the bacterial composition or population can be applied between one and eight months after germination, including between two and eight months, one and three months, and three and six months after germination. The planter can plant the treated seed and grow the crop in conventional ways, in double rows, or in no-till ways. Seed can be distributed using a control hopper or an individual hopper. Seeds can also be distributed through the use of pressurized air or by hand. Seed placement can be accomplished through the use of variable rate technologies. Furthermore, the application of the bacteria or bacterial population described herein can be effected through the use of variable dose technologies. In some examples, the bacteria can be applied to corn, soybean, canola, sorghum, potato, rice, vegetable, cereal, pseudocereal, and oilseed seeds. Examples of cereals may include barley, fonio, oats, Distichlis palmen, rye, pearl millet, sorghum, spelt, teff, triticale, and wheat. Examples of pseudocereals may include mayan nuts, buckwheat, cattail, chia, flax, amaranth grain, hanza, quinoa, and sesame. In some examples, the seeds may be genetically modified organisms (GMO), non-GMO, organic, or conventional. Additionally, additives such as microfertilizers, plant growth regulators (PGRs), herbicides, insecticides, and fungicides can be used to treat crops. Examples of additives include crop protectants such as insecticides, nematicides, fungicides, potentiating agents such as dyes, polymers, pelleting agents, pregerminators, and disinfectants, and other agents such as inoculants, PGRs, softeners, and micronutrients. PGRs can be natural or synthetic plant hormones that affect root growth, flowering, or stem growth. PGRs can include auxins, RnRZLn / LZnZ / E / Yli gibberellins, cytokinins, ethylene and abscisic acid (ABA). The composition can be applied in a furrow in combination with liquid fertilizer. In some examples, liquid fertilizer can be kept in tanks. NPK fertilizers contain macronutrients of sodium, phosphorus and potassium. The composition can improve plant traits, such as promoting plant growth, maintaining a high chlorophyll content in the leaves, increasing the number of fruits or seeds, and increasing the unit weight of fruits or seeds. 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, tolerance to lower nitrogen stress, nitrogen use efficiency, resistance to nematode stress, resistance to a fungal pathogen, resistance to a pathogen bacterial, resistance to a viral pathogen, level of a metabolite, modulation in the level of a metabolite, expression of proteomes. Desirable traits, including height, overall biomass, root and / or shoot biomass, seed germination, seedling survival, photosynthetic efficiency, transpiration rate, seed / fruit quantity or mass, grain or fruit yield of the 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 introduced and / or improved characteristics) grown under identical conditions. In some examples, 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 yield or fruit of the plant, chlorophyll content of the leaf, 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 similar conditions. An agronomic trait of a host plant may include, but is not limited to, the following: altered oil content, altered protein content, altered seed carbohydrate composition, altered seed oil composition and altered seed protein composition, tolerance chemistry, cold tolerance, delayed senescence, disease resistance, drought tolerance, ear weight, growth enhancement, health enhancement, heat tolerance, herbicide tolerance, herbivore resistance, RHRZ Ln / LZRZ / E / Yli improved nitrogen fixation, improved nitrogen utilisation, improved root architecture, improved water use efficiency, increased biomass, increased root length, increased seed weight , shoot length increase, yield increase, yield increase under water scarcity conditions, grain mass, grain moisture content, metal tolerance, number of ears, number of grains per ear, number of pods, nutrition enhancement, resistance to pathogens, resistance to pests, improvement of photosynthetic capacity, tolerance to salinity, preservation of green color, improvement of vigor, increase in dry weight of mature seeds, increase in fresh weight of seeds ripe seeds, increased number of ripe seeds per plant, increased chlorophyll content, increased number of pods per plant, increased pod length per plant, decreased number of withered leaves per plant, decreased number of very wilted leaves per plant and increased number of non-wilted leaves per plant, a modulation detectable at the level of a metabolite, a modulation detectable at the level of a transcript, and a modulation detectable at the proteome, compared to one plant of isoline grown from seed without said seed treatment formulation. In some cases, plants are inoculated with bacteria or bacterial populations isolated from the same plant species as the plant element of the inoculated plant. For example, a bacterium or bacterial population normally found in one variety of Zea mays (corn) is associated with a plant element of a plant of another variety of Zea mays which in its natural state lacks such bacteria and bacterial populations. In one embodiment, the bacteria and bacterial populations are derived from a plant of a plant species related to the plant element of the inoculated plant. For example, the bacteria and bacterial populations normally found in Zea diploperennis litis et al., (diploperenial teosinte) apply to Zea mays (maize), or vice versa. In some cases, plants are inoculated with bacteria and bacterial populations that are heterologous to the plant element of the inoculated plant. In one embodiment, the bacteria and bacterial populations are derived from a plant of another species. For example, bacteria and bacterial populations normally found in dicots are applied to a monocot plant (eg, by inoculating corn with a bacterium and bacterial populations derived from soybeans), or vice versa. In other cases, the bacteria and bacterial populations being inoculated into a plant are derived from a species related to the plant being inoculated. In one embodiment, the bacteria and bacterial populations are derived from a related taxon, eg, from a related species. The plant of another species may be an agricultural plant. In another embodiment, bacteria and bacterial populations are part of a composition Designed RnRZLn / Lznz / B / Yi inoculated into any element of the host plant. In some examples, the bacterium or bacterial population is exogenous, where the bacterium and bacterial population are isolated from a different plant than the inoculated plant. For example, in one embodiment, the bacterium or bacterial population may be isolated from a different plant of the same species as the inoculated plant. In some cases, the bacteria or bacterial population can be isolated from a species related to the inoculated plant. In some examples, the bacteria and bacterial populations described herein are capable of moving from one type of tissue to another. For example, the detection and isolation of bacteria and bacterial populations of the present invention in mature plant tissues after coating the exterior of a seed demonstrates their ability to move from the exterior of the seed to the vegetative tissues of a plant. mature. Thus, in one embodiment, the bacterial population and the bacterial populations are capable of moving from the exterior of the seed to the vegetative tissues of a plant. In one embodiment, the bacteria and bacterial populations that coat the seed of a plant are capable of localizing to a different tissue of the plant after germination of the seed in a vegetative state. For example, bacteria and bacterial populations may be able to locate in any of the plant tissues, including: root, adventitious root, seminal root, root hair, shoot, leaf, flower , the bud, the panicle, the meristem, the pollen, the pistil, the ovaries, the stamen, the fruit, the stolon, the rhizome, the nodule, the tuber, the trichome, the guard cells, the hydathode, the petal, the sepal, the glume, the rachis, the vascular cambium, the phloem and the xylem. In one embodiment, the bacteria and bacterial populations are capable of localizing to the root and / or root hair of the plant. In another embodiment, the bacteria and bacterial populations are capable of localizing in the photosynthetic tissues, eg, the leaves and shoots of the plant. In other cases, bacteria and bacterial populations are located in the vascular tissues of the plant, for example, in the xylem and phloem. In yet another embodiment, the bacteria and bacterial populations are able to locate in the reproductive tissues (flower, pollen, pistil, ovaries, stamen, fruit) of the plant. In another embodiment, bacteria and bacterial populations are capable of localizing in the root, shoots, leaves, and reproductive tissues of the plant. In yet another embodiment, bacteria and bacterial populations colonize a fruit or seed tissue of the plant. In yet another embodiment, bacteria and bacterial populations can colonize the plant such that they are present on the plant surface (ie, their presence is detectably present on the exterior of the plant or the episphere of the plant). . In yet other embodiments, the bacteria and bacterial populations are capable of localizing in all or substantially all of the plant tissues. In some embodiments, bacteria and RnRZLn / Lznz / B / Yi bacterial populations are not located in the root of a plant. In other cases, the bacteria and bacterial populations are not located in the photosynthetic tissues of the plant. The effectiveness of the compositions can also be assessed by measuring the relative maturity of the crop or the crop thermal unit (CHU). For example, the bacterial population can be applied to corn and the growth of the corn can be evaluated according to the relative maturity of the corn kernel or the time when the corn kernel reaches its maximum weight. The crop thermal unit (CHU) can also be used to predict maize crop maturation. The CHU determines the amount of heat buildup by measuring the maximum daily temperatures in crop growth. In some examples, the bacteria can be located in any of the plant tissues, including: root, adventitious root, seminal root, root hair, shoot, leaf, flower, bud, panicle, the meristem, the pollen, the pistil, the ovaries, the stamen, the fruit, the stolon, the rhizome, the nodule, the tubercle, the trichome, the guard cells, the hydathode, the petal, the sepal, the glume, the rachis, vascular cambium, phloem and xylem. In another embodiment, the bacteria or bacterial population are capable of localizing in the photosynthetic tissues, eg, the leaves and shoots of the plant. In other cases, bacteria and bacterial populations are located in the vascular tissues of the plant, for example, in the xylem and phloem. In another modality, the bacteria or the bacterial population are able to locate themselves in the reproductive tissues (flower, pollen, pistil, ovaries, stamen or fruit) of the plant. In another embodiment, bacteria and bacterial populations are capable of localizing in the root, shoots, leaves, and reproductive tissues of the plant. In another embodiment, the bacterium or bacterial population colonizes a fruit or seed tissue of the plant. In yet another embodiment, bacteria or the bacterial population can colonize the plant so as to be present on the surface of the plant. In another embodiment, the bacteria or bacterial population are capable of localizing in substantially all, or all, of the plant tissues. In some embodiments, the bacteria or bacterial population are not located in the root of a plant. In other cases, the bacteria and bacterial populations are not located in the photosynthetic tissues of the plant. The effectiveness of bacterial compositions applied to crops can be evaluated by determining various growth characteristics of the crop, including, but not limited to, planting speed, planting vigour, root strength, drought tolerance , the height of the plant, the drying and weight of the sample. Vegetable species The methods and bacteria described herein are suitable for any of a variety of plants, such as plants of the genera Hordeum, Oryza, Zea RHR7 ίΠ / ί7Π7 / Ε / ΥΙ and Triticeae. Other non-limiting examples of suitable plants include mosses, lichens, and algae. In some cases, plants have economic, social and / or environmental value, such as food crops, fiber crops, oilseed crops, plants for the forestry or pulp and paper industry, feedstock for the production of biofuels and / or or ornamental plants. In some examples, plants may be used to produce economically valuable products such as a grain, flour, starch, syrup, meal, oil, film, packaging, nutraceutical, paste, feed, animal feed, fish, a bulk product for industrial chemicals, a cereal product, a processed human food product, a sugar, an alcohol and / or a protein. Non-limiting examples of crop plants include corn, rice, wheat, barley, sorghum, millet, oats, rye triticale, buckwheat, sweet corn, sugar cane, onions, tomatoes, strawberries, and asparagus. In some examples, the plants that can be obtained or improved by using the methods and compositions described herein may include plants that are important or interesting for agriculture, horticulture, biomass for the production of biofuel molecules, and others. chemicals and / or forestry. Some examples of these plants may include pineapple, banana, coconut, lilies, peas, alfalfa, tomatillo, cantaloupe, chickpea, endive, clover, kale, lentils, soybeans, tobacco, potato, sweet potato, radish, cabbage, rapeseed, apple trees, grapes , cotton, sunflower, arabidopsis thaliana, canola, citrus (including orange, mandarin, kumquat, lemon, lime, tangerine, tangelo, grapefruit, and grapefruit), bell pepper, bean, lettuce, Panicum virgatum (cortadero), Sorghum bicolor (sorghum , sudan), Miscanthus giganteus (miscanthus), Saccharum sp. (energycane), Populus balsamifera (poplar), Zea mays (corn), Glycine max (soybean), Brassica napus (canola), Triticum aestivum (wheat), Gossypium hirsutum (cotton), Oryza sativa (rice), Helianthus annuus (sunflower) ), Medicago sativa (alfalfa), Beta vulgaris (sugar beet), Pennisetum glaucum (pearl millet), Panicum spp. Sorghum spp., Miscanthus spp., Saccharum spp., Erianthus spp., Populus spp., Secale cereale (rye), Salix spp. (willow), Eucalyptus spp. (eucalyptus), Triticosecale spp. (triticum- 25 wheat X rye), Bamboo, Carthamus tinctorius (safflower), Jatropha curcas (Jatropha), Ricinus communis (castor bean), Elaeis guineensis (oil palm), Phoenix dactylifera (date palm), Archontophoenix cunninghamiana (Australian areca) , Syagrus romanzoffiana (pindo palm), Linum usitatissimum (flax), Brassica júncea, Manihot esculenta (cassava), Lycopersicon esculentum (tomato), Lactuca saliva (lettuce), Musa paradisiaca (banana), Solanum tuberosum (potato), Brassica oleracea ( broccoli, cauliflower, brussels sprouts), Camellia sinensis (tea), Fragaria ananassa (strawberry), Theobroma cacao (cocoa), Coffea arabica (coffee), Vitis vinifera (grape), Ananas comosus (pineapple), Capsicum annum (sweet pepper and spicy), Allium cepa (onion), Cucumis melo (melon), Cucumis sativus (cucumber), Cucurbita maxima (pumpkin), Cucurbita RnRZLn / LZnZ / E / Yli moschata (pumpkin), Spinacea oleracea (spinach), Citrullus lanatus (watermelon), Abelmoschus esculentus (okra), Solanum melongena (aubergine), Papaver somniferum (royal poppy), Papaver oriental, Taxus baccata, Taxus brevifolia, Artemisia annua, Cannabis saliva, Camptotheca acuminate, Catharanthus roseus, Vinca rosea, Cinchona officinalis, Coichicum autumnale, Veratrum californica, Digitalis lanata, Digitalis purpurea, Dioscorea 5 spp., Andrographis paniculata, Atropa belladonna, Datura stomonium, Barbary s pp., Cephalotaxus spp., Ephedra sinica, Ephedra spp., Erythroxylum coca, Galanthus wornorii, Scopolia spp., Lycopodium serratum (Huperzia serrata), Lycopodium spp., Rauwolfia serpentina, Rauwolfia spp., Sanguinaria canadensis, Hyoscyamus spp., Calendula officinali s, Chrysanthemum parthenium, Coleus forskohlii, Tanacetum parthenium, Parthenium argentatum (guayule), Hevea spp. (rubber), Mentha spicata (mint), Mentha piperita (mint), Bixa orellana, Alstroemeria spp., Rosa spp. (pink), Dianthus caryophyllus (carnation), Petunia spp. (petunia), Poinsettia pulcherrima (poinsettia), Nicotiana tabacum (tobacco), Lupinus albus (lupine), Uniola paniculata (oats), Hordeum vulgare (barley), and Lolium spp. (rye). In some examples, a monocot plant may be used. Monocotyledonous plants belong to the orders Alismatales, Arales, Arecales, Bromeliales, Commelinales, Cyclanthales, Cyperales, Eriocaulales, Hydrocharitales, Juncales, Lilliales, Najadales, Orchidales, Pandanales, Poales, Restionales, Triuridales, Typhales, and Zingiberales. Plants belonging to the class of Gymnospermae are Cycadales, Ginkgoales, Gnetales and Piñales. In some examples, the monocot plant may be selected from the group consisting of corn, rice, wheat, barley, and sugarcane. In some examples, a dicotyledonous plant may be used, including those belonging to the orders Aristochiales, Asterales, Batales, Campanulales, Capparales, Caryophyllales, Casuarinales, Celastrales, Cornales, Diapensales, Dilleniales, Dipsacales, Ebenales, Encales, Eucomiales, Euphorbiales, Fabales, Phagales, Gentianales, Geraniales, Haloragales, Hamamelidales, Middles, Juglandales, Lamiales, Laurales, Lecythidales, Leitneriales, Magníolales, Málvales, Myricales, Myrtales, Nymphaeales, Papeverales, Piperales, Plantaginales, Plumb aginales, Podostemales, Polemoniales, Polygalales, Polygonales, Primulales , Proteales, Rafflesiales, Ranunculales, Rhamnales, Rosales, Rubiales, Salicales, Santales, Sapindales, Sarraceniaceae, Scrophulañales, Theales, Trochodendrales, Umbellales, Urticales, and Violates. In some examples, the dicot plant may be selected from the group consisting of cotton, soybean, pepper, and tomato. In some cases, the plant to be improved does not easily adapt to the experimental conditions. For example, a crop plant may take too long to grow large enough to practically evaluate a serially improved trait in multiples. RnRZLn / LZnZ / E / Yli iterations. Accordingly, a first plant from which the bacteria are initially isolated and / or the multiple plants to which genetically engineered bacteria are applied may be a model plant, such as a plant most amenable to evaluation under the desired conditions. Non-limiting examples of model plants include Setaria, Brachypodium, and Arabidopsis. The ability of bacteria isolated according to one method of the disclosure using a model plant can then be applied to a plant of another type (eg, a crop plant) to confirm transfer of the improved trait. Traits that can be improved by the methods described herein include any observable characteristics of the plant, including, for example, growth rate, height, weight, color, taste, odor, and changes in the production of one or more compounds. by the plant (including, for example, metabolites, proteins, drugs, carbohydrates, oils, and any other compounds). Selection of plants based on genotypic information (for example, including the expression pattern of plant genes in response to bacteria, or identification of the presence of genetic markers, such as those associated with increased fixation of plant genes, is also contemplated). nitrogen). Plants can also be selected based on the absence, suppression or inhibition of a certain characteristic or trait (such as an undesirable characteristic or trait) as opposed to the presence of a certain characteristic or trait (such as a desirable characteristic or trait). . EXAMPLES The examples provided herein describe methods of bacterial isolation, bacterial and plant analysis, and improvement of plant traits. Examples are for illustrative purposes only and should not be construed as limiting in any way. Example 1: isolation of microbes from plant tissue The tilled layer was obtained from various agricultural areas in central California. Twenty soils with various textural characteristics were collected, including heavy clay, peaty clay loam, silty clay, and sandy loam. Field corn, sweet corn, traditional corn and tomato seeds were sown in each soil, as shown in Table 1. RnRZLn / Lznz / B / Yi Crop Type Field Corn Sweet Corn Traditional Corn Tomato Varieties Mo17 Ferry-Morse 'Golden Cross Bantam Τ-5Γ Victory Seeds 'Moseby Prolific' Ferry-Morse Roma VF B73 Ferry-Morse 'Silver Queen Hybrid' Victory Seeds 'Reid's Yellow Dent 'Stover Rome DKC 66-40 Ferry-Morse 'Sugar Dots' Victory Seeds 'Hickory King' Totally Tomatoes 'Micro Tom Hybrid' DKC 67-07 Heinz 1015 DKC 70-01 Heinz 2401 Heinz 3402 Heinz 5508 Heinz 5608 Heinz 8504 table 1: type of crop and varieties planted in soil with diverse characteristics RnRZLn / LZnZ / E / Yli The plants were uprooted after 2-4 weeks of growth and excess soil on the root surface was removed with deionized water. After removing the soil, the plants were surface sterilized with bleach and rinsed vigorously in sterile water. A 1 cm clean root section was cut from the plant and placed in a phosphate buffered saline solution containing 3 mm steel beads. A suspension was generated by vigorously shaking the solution with a Qiagen TissueLyser II. The root suspension and saline solution was diluted and inoculated into various types of growth media to isolate rhizospheric, endophytic, epiphytic, and other plant-associated microbes. R2A and Nfb agar media were used to obtain single colonies, and agar slants with semi-solid Nfb medium were used to obtain populations of nitrogen-fixing bacteria. After 2-4 weeks of incubation on agar slants with semisolid Nfb medium, microbial populations were collected and streaked to obtain single colonies on R2A agar, as shown in Figures 1A-1B. Individual colonies were resuspended in a mixture of R2A and glycerol, subjected to POR, and frozen at -80 °C for further analysis. Approximately 1000 individual colonies were obtained and were referred to as "isolated microbes". The isolates were then subjected to a colony PCR screen for the presence of the nifH gene in order to identify diazotrophs. The Ueda 19F / 388R primer set described above, which has been shown to detect more than 90% of diazotrophs in screens, was used to probe for the presence of the nifen group in each isolate (Ueda et al. 1995; J. Bacteriol. 177: 1414-1417). Single colonies of purified isolates were picked, resuspended in PBS, and used as a template for colony PCR, as shown in Figure 2. Colonies of isolates that gave positive PCR bands were replated, and PCR of colonies and the reseeding process were repeated twice to avoid the identification of false positives of diazotrophs. The purified isolates were then referred to as 'candidate microbes'. Example 2: characterization of isolated microbes Sequencing, analysis and phylogenetic characterization 16S rDNA sequencing with the 515f-806r primer set was used to generate preliminary phylogenetic identities for isolates and candidate microbes (see, eg, Vernon et al.; BMC Microbiol. 2002 Dec 23;2:39.). Microbes comprise various genera including: Enterobacter, Burkholderia, Klebsiella, Bradyrhizobium, Rahnella, Xanthomonas, Raoultella, Pantoea, Pseudomonas, Brevundimonas, Agrobacterium, and Paenibacillus, as shown in Table 2. RHRZ Ln / LZRZ / E / Yli Genus Genus Isolates Genus Isolates Achromobacter 7 Paenibaciilus 1 Agrobacterium 117 Paenisporosarcina 3 Agromyces 1 Pantoea 14 Alicyclobacillus 1 Pedobacter 16 Asticcacaulis 6 Pimeiobacter 2 Bacillus 131 Pseudomonas 212 Bradyrhizobium 2 Rhizobi ​​um 4 Brevibacillus 2 Bhodoferax 1 Burkholderia 2 Sphingobacterium 13 Caulobacter 17 Sphingobium 23 Chryseobacterium 42 Sphingomonas 3 Let's eat 1 Sphingopyxis 1 Dyadobacter 2 Stenotrophomonas 59 Flavobacterium 46 Streptococcus 3 Halomonas 3 Variovorax 37 Leptothrix 3 Xylanimicrobium 1 Lysobacter 2 unidentified 75 Neisseria 13 Table 2: Diversity of microbes isolated from tomato plants determined by deep 16S rDNA sequencing. Subsequently, the genomes of 39 candidate microbes were sequenced using the lllumina Miseq platform. Genomic DNA from pure cultures was extracted using the QIAmp DNA Mini Kit (QIAGEN) and total DNA libraries were prepared for sequencing via an external vendor (SeqMatic, Hayward). Then, genome assembly was carried out via the A5 pipeline (Tritt et al. 2012; PLoS One 7(9):e42304). Genes were identified and annotated, and those related to the regulation and expression of nitrogen fixation were designated as targets for mutagenesis. Two microbial-based strains, named CU37 and CU 021, have been identified and are being used for further testing on the effect of various genetic mutations on nitrogen uptake. 01137 represents K. variicola WT and CU 021 represents Kosakonia pseudosacchari WT. Example 3: mutagenesis of candidate microbes Lambda-Red mutagenesis with Cas9 selection Candidate microbial mutants were generated by lambda-red mutagenesis with CRISPR-Cas selection. Knockout cassettes contained an endogenous promoter identified through transcriptional profiling and -250 bp regions of homology flanking the deletion target. Candidate microbes were transformed with plasmids encoding the Lambda-red recombination system (exo, beta, gam genes) under the control of an arabinose-inducible promoter and Cas9 under the control of an IPTG-inducible promoter. The Red and Cas9 recombination systems were induced in the resulting transformants and the strains were prepared for electroporation. Knockout cassettes and a plasmid-encoded selection gRNA were subsequently transformed into the competent cells. In an illustrative reaction for deletion of nifL and replacement of the promoter regulating transcription of the nif operon in candidate strain CI006, after plating Petri dishes with antibiotics selective for both the Cas9 plasmid and the gRNA plasmid, 7 of all 10 colonies examined showed the intended knockout mutation, as shown in Figure 3. This approach was similarly applied to modify the base strains 01137 and CU 021 to create the mutant strains identified in Table 3. Example 4: In vitro phenotyping of candidate molecules The impact of exogenous nitrogen on biosynthesis and nitrogenase activity in various mutants was evaluated. The acetylene reduction assay (ARA) (Temme et al. 2012;109(18):7085-7090) was used to determine nitrogenase activity under pure culture conditions. Strains were grown in airtight test tubes and the reduction of acetylene to ethylene was quantified with an Agilent 6890 Gas Chromatograph. ARA activities of homologous candidate and candidate mutant microbes grown in nitrogen fixation media supplemented with ammonium phosphate 0 or 5 mM are shown in Figures 4A-4B and Figures 6A-6B. As shown in Figures 4A-4B, strains containing a gltA gene deletion demonstrated increased ARA activity relative to a control strain. As shown in Figures 6A-6B, replacement of the promoter that regulates ptsH expression resulted in decreased ARA activity relative to a control strain. The strains of Figures 4A-4B and 6A-6B were also subjected to a test of RnRZLn / Lznz / B / Yi ammonium excretion (AMM), in which ammonia excretion was measured over time under nitrogen fixation conditions by culturing cells in a medium free of nitrogen, pelleting the cells and measuring the free ammonium in the cell-free broth; higher degrees of ammonium excretion indicated greater nitrogen fixation and excretion. As shown in Figures 5A-5B, gltA deletion resulted in increased rate (Figure 5B) and total ammonium excretion (Figure 5A) relative to a control. As shown in Figure 7B, changing the ptsH promoter resulted in an increased rate of ammonium excretion relative to a control strain. Example 5: biofilm formation Biofilm formation can influence the amount of nitrogen provided to an associated plant. An increase in biofilm formation on the root of a plant can increase the amount of nitrogen provided to the plant. Some genes may regulate the formation of biofilms. For example, smZ may be a negative regulator of biofilm regulation. Mutating smZ such that smZ has reduced or abolished its function can increase biofilm formation in bacteria. Mutagenesis to mutate smZ in strains with increased nitrogen excretion and binding activity can be performed to create a library of smZ mutant bacteria. Some proteins can promote the formation of biofilms. For example, large adhesion proteins including lapA can promote biofilm formation. One or more promoters regulating lapA expression can be upregulated such that more lapA is produced, as detected by Western blotting. Additional genes that can be modified to alter biofilm formation include pga, sdiA, fimA1-A4, wzxE, and bolA. The modified strains can be grown in lysogeny buffer (LB) and inoculated into the soil with a seedling. The seedling, soil, and bacterial strain can be in a pot, in a field, indoors, or outdoors. The seedling can be planted in spring, summer, fall or winter. Air can be approximately 0%, 10%, 20%, 30%, 40%, 50%, 60%, 70%, 80%, 90%, or 100% humidity. It can be raining, foggy, cloudy or sunny. The temperature can be about 4°C, 10°C, 15°C, 20°C, 25°C, 30°C, 35°C, 40°C or 45°C. The seedling can be planted at dawn, in the morning, at noon, in the afternoon, at dusk or at night. The seedling can be allowed to grow for approximately 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 20, or 30 days. After the time has elapsed, the plant can be dug up and the amount of biofilm on the roots measured. Example 6: sensitivity to oxygen The oxygen sensitivity of nitrogenase enzymes may affect the fixation of RnRZLn / LZnZ / E / Yli nitrogen, nitrogen excretion, or both. Decreasing the oxygen sensitivity of a nitrogenase enzyme can increase nitrogen fixation activity, increase nitrogen excretion activity, or both. To test this hypothesis, the sodA, sodB and sodC genes were overexpressed by replacing the promoter that regulates gene expression. The overexpressing strains were subjected to an oxygen sensitivity assay in which MMA and ARA assays can be performed under conditions with varying oxygen concentrations. The results are shown in Figures 12A-12B, 13A-13B, 14A-14B, 15A-15B, 20A-20B, 21A-21B, 22A-22B and 23A-23B. To further analyze the impact of oxygen tolerance on nitrogen fixation activity and nitrogen excretion activity, strains with modifications to the FNR, arcA, and arcB genes will be created and subjected to ARA and AMM assays under different conditions. of oxygen. Example 7: Increasing iron transport can increase nitrogen fixation Iron uptake pathway can refer to the metabolic pathway in bacteria that allows iron uptake into the cell. Iron can act as a cofactor to promote nitrogen fixation. Increased iron uptake by cells may increase nitrogen fixation, nitrogen excretion, or both. To test this hypothesis, genetic modifications were created in fhuF and iscR, positive and negative regulators of iron uptake, respectively. Specifically, strains containing iscR deletions or an fhuF promoter substitution were created and tested for ARA and AMM activity. The results are shown in Figures 8A-8B, 9A-9B, 10A-10B, 11A-11B, 16A-16B, 17A-17B, 18A-18B and 19A-19B. Deletion of iscR produced increased ARA activity (see Figures 8A-8B, 10A-10B, 16A-16B and 18A-18B). A library of variants can also be constructed such that the promoter activity of one or more genes in the iron absorption pathway is increased. Western blotting can be used to determine which strains have increased expression of one or more iron uptake genes, and these strains may be variants of interest. To test for increased iron uptake activity, each mutant or variant of interest, as well as the wild-type parent strain for each strain, can be inoculated and grown in three wells of a 96-well plate in LB medium. Once the cells reach OD=0.8, one of the wells from each mutant can be harvested, so that the cells are pelleted, excess LB is washed away, and the cells are resuspended, lysed, and prepared for spectroscopy in a 96-well plate. The iron content can be measured by spectroscopy to establish the reference iron content in the RnRZLn / Lznz / B / Yi samples. The remaining samples can be spiked with iron as FeSO4 in LB or LB alone so that the amount added is 10% or less of the total volume in each well. 0.1 mM acetic acid (final concentration) may be included to aid in iron solubility. The final iron concentration in each assay well may be one of 10 pM, 100 pM, 1 nM, 10 nM, 100 nM, 1 μΜ, 10 μΜ, or 100 μΜ and more than one concentration may be tested. The test can be carried out for one or more of 1 second, 10 seconds, 30 seconds, 1 minute, 2 minutes, 3 minutes, 4 minutes, 5 minutes, 10 minutes, 20 minutes, 30 minutes, and 60 minutes. First, for each concentration, the amount of iron transported to each cell can be plotted as a function of time to determine the optimal duration of the assay. The optimal duration may be a time interval in which steady state has not been reached and the reaction rate is still linear. Then, for the optimal duration, the amount of iron transported to each cell can be plotted as a function of concentration, and a Michaelis-Menten analysis can be performed. Mutant or variant strains of interest that show a significant (p < 0.05) increase in iron transport over the unmutated and unmodified parental strain, as determined by Km comparison, can be selected for further testing. Each strain selected for further testing can then be subjected to an AMM assay and an ARA assay as described herein to determine nitrogen excretion and fixation, respectively. One or more of these mutations or variants can increase the AMM, ARA, or both of one or more of these bacterial strains. Example 8: Increasing Siderophore Biosynthesis Genes Can Increase Nitrogen Fixation YHF siderophores, or iron chelating molecules, can influence iron uptake by bacteria. Increased production of yhf siderophores may increase iron uptake by bacteria. Modifications in siderophore genes, including yhfA, yusV, sbnA, yfiZ, fiu, and fur, can increase the production of yhf siderophores, which in turn can increase iron uptake by cells. These modifications can lead to increased nitrogen fixation or excretion. To assess whether increased siderophore gene expression alters nitrogen fixation or excretion, sbnA, yusV1, and yusV2 were overexpressed, replacing the promoter that regulates gene expression. The modified strains were then subjected to ARA and AMM assays. The results are shown in Figures 16A-16B, 17A-17B, 18A-18B and 19A-19B. Genetic modifications to these genes can be made in bacterial cells of RnRZLn / Lznz / B / Yi so that the modifications produce an increase in siderophore production. To identify such modifications, mutagenesis can be carried out in and around the active sites of the genes encoding yhfA, yusV, sbnA, yfiZ, fiu or fur. A library of mutants can be built for each gene. These libraries can then be screened for further siderophore production. These libraries can be created from wild-type cells or from cells that have already been modified to show increased nitrogen fixation, increased nitrogen excretion, or both. To test for increased siderophore production, each mutant can be grown to OD=0.8 and then spiked with an excess, but non-toxic, amount of siderophore precursors and incubated for 30 minutes or 60 minutes. The amount of siderophores produced after the allotted time period can be normalized, and strains showing increased siderophore production can be tested for increased iron transport. To test for increased iron uptake activity, each mutant or variant of interest, as well as the wild-type parent strain for each strain, can be inoculated and grown in three wells of a 96-well plate in LB medium. Once the cells reach OD=0.8, one of the wells from each mutant can be harvested, so that the cells are pelleted, excess LB is washed away, and the cells are resuspended, lysed, and prepared for spectroscopy in a 96-well plate. Iron content can be measured using spectroscopy to establish the reference iron content in samples. The remaining samples can be spiked with iron as FeSO4 in LB or LB alone so that the amount added is 10% or less of the total volume in each well. 0.1 mM acetic acid (final concentration) may be included to aid in iron solubility. The final iron concentration in each assay well may be one of 10 pM, 100 pM, 1 nM, 10 nM, 100 nM, 1 μΜ, 10 μΜ, or 100 μΜ and more than one concentration may be assayed. The test can be carried out for one or more of 1 second, 10 seconds, 30 seconds, 1 minute, 2 minutes, 3 minutes, 4 minutes, 5 minutes, 10 minutes, 20 minutes, 30 minutes, and 60 minutes. First, for each concentration, the amount of iron transported to each cell can be plotted as a function of time to determine the optimal duration of the assay. The optimal duration may be a time interval in which steady state has not been reached and the reaction rate is still linear. Then, for the optimal duration, the amount of iron transported to each cell can be plotted as a function of concentration, and a Michaelis-Menten analysis can be performed. Mutant or variant strains of interest that show a significant (p < 0.05) increase in iron transport over the original unmutated and unmodified strain, as determined by Km comparison, can be selected. RnRZLn / LZnZ / E / Yli for further assays. Each strain selected for further testing can then be subjected to an AMM assay and an ARA assay as described herein to determine nitrogen excretion and fixation, respectively. One or more of these mutations or variants can increase the AMM, ARA, or both of one or more of these bacterial strains. Example 9: increased tolerance to desiccation Improving desiccation tolerance can increase the colonization of a strain used in a seed coating or other dry application to a plant or field. A genetically modified microbe will be created that comprises an arabinose promoter operably linked to an rpoE gene. Strains containing similar modifications to the rpoS, treA, treB, phoP, phoQ and rpoN genes will also be generated. The GM microbes and the original non-GM control will be grown in arabinose-supplemented medium for 48 hours before being desiccated. After drying, a part of each of the modified and unmodified strains will be revived in a medium that does not contain arabinose, and the number of microbes in the medium will be analyzed after 24 hours. Media containing the genetically modified strain contain more microbes than media containing the original strain without genetic modification. The dried microbes will be applied to maize seeds and planted in the soil, without arabinose, in a greenhouse under conditions suitable for maize seed germination. After 4 weeks, the seedlings will be harvested and the number of colony-forming units of the GM and non-GM microbes on the roots of the plants will be assessed. Plants exposed to the genetically modified microbes will associate with more microbes than plants exposed to the original strain without genetic modification. Example 10: NAC gene mutants To assess the impact of mutations in the NAC gene on nitrogen fixation and excretion, overexpression and knockout mutants of the NAC gene were generated by deleting the gene or replacing the promoter that regulates gene expression. Mutant strains were subjected to AMM and ARA assays. The results are shown in Figures 24A-24B and 25A-25B. The results for the NAC mutants in the CI1021 background are provided in Figures 26A-26B and 27A-27B. RnRZLn / LZnZ / E / Yli Table 3: strains described herein Strain ID Lineage Mutagenic DNA Description Chromosomal Genotype Cured Status CI1021 CI1021 Kosakonia pseudosacchari Original Wild Type WT N / A 1021- 1615 Disruption of the nifL gene with a fragment of the 5' region of the Ipp gene (Prm1) inserted into 5' from nifa. Deletion of 1647 bp after the start codon of the glnE gene containing the adenylyl removal domain of glutamate-ammonia-ligase adenylyltransferase (AglnEARKO2). AnifL::nifA::Prm1, AglnE-AR_KO2 1021- 1617 1021 Disruption of the nifL gene with a 197 bp fragment of the region downstream of the hypothetical gene in CU 021 with strong constitutive expression (Prm2) inserted 5' from nifA. An¡fL::Prm2 1021- 3545 A fragment of the upstream region of the Ipp gene (Prm1) inserted 5' of fhuF. fhuF::Prm1 1021-3553 Deletion of entire iscR CDS AiscR 1021-3555 A fragment of the upstream region of the Ipp gene (Prm1) inserted downstream of sbnA. sbnA::Prm1 1021- 3559 A fragment of the 5' downstream region of the Ipp gene (Prm1) inserted 5' of yusV1. yusV1 ::Prm1 RnRZLn / Lznz / B / Yi Strain ID Lineage Mutagenic DNA Description Chromosomal Genotype Cured Status 1021- 3563 A fragment of the 5' downstream region of the Ipp gene (Prm1) inserted 5' from yusV2. yusV2::Prm1 1021-3547 Disruption of the nifL gene with a fragment of the 5' downstream region of the Ipp gene (Prm1) inserted 5' of nifA. Deletion of 1647 bp after the start codon of the glnE gene containing the adenylyl removal domain of glutamate-ammonia-ligase adenylyltransferase (AglnEARKO2). Prm1 inserted 5' from fhuF. AnifL::nifA::Prm1, AglnE-AR_KO2, fhuF::Prm1 1021- 3591 Disruption of the nifL gene with a fragment of the 5' downstream region of the Ipp gene (Prm1) inserted 5' of nifA. Deletion of 1647 bp after the start codon of the glnE gene containing the adenylyl removal domain of glutamate-ammonia-ligase adenylyltransferase (AglnEAR KO2). iscR CDS deletion. AnifL::nifA::Prm1, AglnE-AR_KO2, AiscR 1021-3557 Disruption of the nifL gene with a fragment of the downstream region of the Ipp gene (Prm1) inserted 5' of nifA. 1647 bp deletion after AnifL::nifA::Prm1, AglnE-AR_KO2, sbnA::Prm1 Strain ID Lineage Description of mutagenic DNA Chromosomal genotype Curing status of the start codon of the glnE gene containing the adenylyl removal domain of glutamate ammonia adenylyltransferase ligase (AglnEARKO2). Prm1 inserted 5' from sbnA. 1021-3561 Disruption of the nifL gene with a fragment of the 5' region of the Ipp gene (Prm1) inserted 5' of nifA. Deletion of 1647 bp after the start codon of the glnE gene containing the adenylyl removal domain of glutamate-ammonia-ligase adenylyltransferase (AglnEAR KO2). Prm1 inserted 5' from yusV1. AnifL::nifA::Prm1, AglnE-AR_KO2, yusV1 ::Prm1 1021- 3565 Disruption of the nifL gene with a fragment of the 5' downstream region of the Ipp gene (Prm1) inserted 5' of nifA. Deletion of 1647 bp after the start codon of the glnE gene containing the adenylyl removal domain of glutamate-ammonia-ligase adenylyltransferase (AglnEAR KO2). Prm1 inserted 5' from yusV2. AnifL::nifA::Prm1, AglnE-AR_KO2, yusV2::Prm1 1021- A fragment of the region in sodA::Prm1 Strain ID Lineage Description of mutagenic DNA Chromosomal genotype State of cure 3515 5' direction of Ipp gene (Prm1) inserted 5' of sodA. 1021-3517 Disruption of the nifL gene with a fragment of the 5' region of the Ipp gene (Prm1) inserted 5' of nifA. Deletion of 1647 bp after the start codon of the glnE gene containing the adenylyl removal domain of glutamate-ammonia-ligase adenylyltransferase (AglnEARKO2). Prm1 inserted 5' from sodA. AnifL::nifA::Prm1, AglnE-AR_KO2, sodA::Prm1 1021- 3519 A fragment of the 5' region of the Ipp gene (Prm1) inserted 5' of sodB. sodB::Prm1 1021- 3521 Disruption of the nifL gene with a fragment of the 5' downstream region of the Ipp gene (Prm1) inserted 5' of nifA. Deletion of 1647 bp after the start codon of the glnE gene containing the adenylyl removal domain of glutamate-ammonia-ligase adenylyltransferase (AglnEAR KO2). Prm1 inserted 5' from sodB. AnifL::nifA::Prm1, AglnE-AR_KO2, sodB::Prm1 1021- 3523 A fragment of the upstream region of the Ipp gene (Prm1) inserted 5' of sodC. sodC::Prm1 Strain ID Lineage Mutagenic DNA description Chromosomal genotype Cured status 1021-3525 Disruption of the nifL gene with a fragment of the 5' downstream region of the Ipp gene (Prm1) inserted 5' of nifA. Deletion of 1647 bp after the start codon of the glnE gene containing the adenylyl removal domain of glutamate-ammonia-ligase adenylyltransferase (AglnEARKO2). Prm1 inserted 5' from sodC. AnifL::nifA::Prm1, AglnE-AR_KO2, sodC::Prm1 1021- 3383 1021 Deletion of the NAC gene (cynR) of 918 bp from start to stop codon ANAC 1021- 3396 Deletion of the NAC gene (oxyR) 918 bp from start to stop AnifL::Prm2 ANAC CI137 CI137 K. variicola original wild type WT N / A 137- 1036 Disruption of the nifL gene with a fragment of the 5' region of the infC gene (PrminfC) inserted downstream 5' from nifa. AnifL:: PrminfC 137- 2084 UC 37 mutant Disruption of the nifL gene with a fragment of the region 5' to the inserted cspE gene (Prm1.2) 5' of nifA. Deletion of 1647 bp after the start codon of the glnE gene containing the cured AnifL::Prm1.2 AglnE-AR_KO2 RnR7Ln / L7nZ / E / Yli Strain ID Lineage Mutagenic DNA Description Chromosomal genotype Cured status adenylyl-removing domain of glutamatoammonia-ligase adenylyltransferase (AglnEARKO2). 137-2448 Disruption of the nifL gene with a fragment of the region 5' to the inserted cspE gene (Prm1.2) upstream of nif A. AnifL::Prm1.2 137-2512 Disruption of the nifL gene with a fragment of the region 5' to the inserted cspE gene (Prm1.2) upstream of nifA. Deletion of 1647 bp after the start codon of the glnE gene containing the adenylyl removal domain of glutamatoammonia ligase adenylyltransferase (AglnEAR KO2). gltA2 deletion CDS AnifL::Prm1.2 AglnE-AR_KO2, AgltA2 137-2534 Disruption of the nifL gene with a fragment of the region downstream of the inserted cspE gene (Prm1.2) downstream of nifA. Deletion of 1647 bp after the start codon of the glnE gene containing the glutamate adenylyl deletion domain- AnifL::Prm1.2 AglnE-AR_KO2, Prm1,2::ptsH RHRZ LO / LZ / IZ / E / Yl Strain ID Lineage Description of mutagenic DNA Chromosomal genotype Cured status ammonia-adenylyltransferase ligase (AglnEARKO2). Prm1.2 inserted upstream of ptsH 137-2837 Deletion of all but 83 bp of 5' end of nifL AnifL_with_RBS 137-3004 137 Fragment of the upstream region of the cspE gene (Prm1.2) inserted upstream of ptsH start codon of the NAC gene (oxyR). Prm1.2_NAC 137- 3006 137-1036 Fragment of the 5' region of the cspE gene (Prm1.2) inserted 5' of the start codon of the NAC gene (oxyR). AnifL::PinfC Prm1.2_NAC 137- 3008 137-2084 Fragment of the 5' region of the cspE gene (Prm1.2) inserted 5' of the start codon of the NAC gene (oxyR). glnE_KO2 AnifL- Prm1.2 Prm1.2_NAC 137- 3012 137-2448 Fragment of the 5' region of the cspE gene (Prm1.2) inserted 5' of the start codon of the NAC gene (oxyR). nifL-Prml .2 Prm1.2_NAC 137- 3014 137-2837 Fragment of the 5' region of the cspE gene (Prm1.2) inserted 5' of the start codon of the NAC gene (oxyR). AnifL_with-3'-RBS Prm1.2_NAC RHR7 ίΠ / ί7Π7 / Ε / ΥΙ Strain ID Lineage Mutagenic DNA Description Chromosomal Genotype Cured Status 137-3161 A fragment of the 5' region of the cspE gene (Prm1.2) inserted 5' of fhuF. Prm1,2::fhuF 137-3214 Deletion of iscR CDS AiscR 137-3193 Disruption of the nifL gene with a fragment of the region 5' to the inserted cspE gene (Prm1.2) 5' of nifA. Deletion of 1647 bp after the start codon of the glnE gene containing the adenylyl removal domain of glutamatoammonia ligase adenylyltransferase (AglnEAR KO2). Prm1.2 inserted into a 5' region of fhuF AnifL::Prm1.2 AglnE-AR_KO2, Prm1.2::fhuF 137- 3195 Disruption of the nifL gene with a fragment of the 5' region of the cspE gene (Prm1 .2) inserted 5' from nifA. Deletion of 1647 bp after the start codon of the glnE gene containing the adenylyl removal domain of glutamatoammonia ligase adenylyltransferase (AglnEAR KO2). iscR CDS deletion AnifL::Prm1.2 AglnE-AR_KO2, AiscR ROR7 Ln / Lznz / Ε / ΥΙΛΙ Strain ID Lineage Mutagenic DNA Description Chromosomal Genotype Cured Status 137-3120 A fragment of the 5' region of the cspE gene (Prm1.2) inserted 5' of sodA. Prm1,2::sodA 137-3122 A fragment of the 5' region of the cspE gene (Prm1.2) inserted 5' of sodB. Prm1,2::sodB 137-3124 A fragment of the 5' region of the cspE gene (Prm1.2) inserted 5' of sodC. Prm1,2::sodC 137-3183 Disruption of the nifL gene with a fragment of the upstream region of the cspE gene (Prm1.2) inserted 5' of nifA. Deletion of 1647 bp after the start codon of the glnE gene containing the adenylyl removal domain of glutamatoammonia ligase adenylyltransferase (AglnEARKO2). Prm1.2 inserted into a 5' region of sodA AnifL::Prm1.2 AglnE-AR_KO2, Prm1,2::sodA 137- 3187 Disruption of the nifL gene with a fragment of the 5' region of the cspE gene (Prm1 .2) inserted 5' from nifA. Deletion of 1647 bp after the start codon of the glnE gene containing the AnifL::Prm1.2 AglnE-AR_KO2, Prm1,2::sodC RnRZLn / Lznz / B / Yi Strain ID Lineage Mutagenic DNA Description Chromosomal genotype Cured status adenylyl-removing domain of glutamatoammonia-ligase adenylyltransferase (AglnEARKO2). Prm1.2 inserted into a 5' region of sodC 137-3322 918 bp NAO (oxyR) gene deletion from start to stop A NAC 137-3324 918 bp NAC (oxyR) gene deletion from start to stop AnifL: :PinfC A NAC 137- 3326 Deletion of the NAC gene (oxyR) of 918 bp from start to finish glnE_KO2 AnifL- Prm1.2 ANAC RHRZ Ln / LZÍtZ / E / Yli The use of the terms "a", "an" and "the" and similar referents in the context of the invention (especially in the context of the following claims) shall be construed as encompassing the singular and the plural, unless otherwise stated herein or clearly contradicted by the context. The terms "comprising", "having", "including" and "containing" are to be construed as having a broad meaning (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 example terms (eg, "as") provided herein is merely intended to further illuminate the invention and does not present a limitation on the scope of the invention unless otherwise noted. claim otherwise. No language in the specification is to be construed as indicating any item not claimed to be essential to the practice of the invention. While preferred embodiments of the present invention have been shown and described herein, it will be apparent to those skilled in the art that such embodiments are provided by way of example only. It will be apparent to those skilled in the art that multiple variations, changes, and substitutions can be made without departing from the invention. It will be understood that various alternatives to the embodiments of the invention described herein may be employed in the practice of the invention. It is intended that the following claims define the scope of the invention and that methods and structures within the scope of these claims and their equivalents are encompassed by them. RnRZLn / LZnZ / E / Yli

Claims

Having described the present invention as above, the following claims are considered novel and therefore claimed as property:

1. A genetically modified bacterium comprising a modification in a gene selected from the group consisting of: NAC, gltA, pga, ptsH, fimA1, fimA2, fimA3, fimA4, iscR, tonB, yusV1, yusV2, yusV3, yusV4, sbnA, fhuF, sodA, sodB, sodC, iaaA, sdiA, wzxE, bolA, FNR, arcA, arcB, rpoS, treA, treB, phoP, phoQ, yjjPB, ychM, dauA, actP, yieL1, yieL2, yieL3, yieL4, pgab, rafA, melA, uidA, manA, abfA, abnA and lacZ.

2. The genetically modified bacterium of claim 1, wherein said genetically modified bacterium comprises a modification in a gene selected from the group consisting of: NAC, gltA, pga, ptsH, fimA1, fimA2, fimA3, fimA4, iscR, tonB, yusV1, yusV2, yusV3, yusV4, sbnA, fhuF, sodA, sodB and sodC.

3. The genetically modified bacterium of claim 1, wherein said genetically modified bacterium comprises a modification in a gene selected from the group consisting of: NAC, gltA, pga, ptsH, fimA1, fimA2, fimA3, fimA4, sodA, sodB and sodC.

4. The genetically modified bacterium of claim 1, wherein said genetically modified bacterium comprises a modification in a gene selected from the group consisting of: iscR, tonB, yusV1, yusV2, yusV3, yusV4, sbnA and fhuF.

5. The genetically modified bacterium of any of claim 14, wherein said genetically modified bacterium is a genetically modified diazotrophic bacterium.

6. The genetically modified bacterium of any of claims 1-5, wherein said genetically modified bacterium is intergeneric.

7. The genetically modified bacterium of any of claims 1-6, wherein said genetically modified bacterium is not intergeneric.

8. The genetically modified bacterium of any of claims 1-7, wherein said genetically modified bacterium is capable of fixing atmospheric nitrogen in the presence of exogenous nitrogen.

9. The genetically modified bacterium of any of claims 1-8, wherein said genetically modified bacterium further comprises a modification in a nitrogen-fixing genetic network.

10. The genetically modified bacterium of claim 9, wherein said modification in a nitrogen fixation genetic network comprises a modification in NifA, RnRZLn / Lznz / B / Yi NifL, NifH or any combination thereof.

11. The genetically modified bacterium of claim 10, wherein said modification in NifA results in an increase in the expression of NifA.

12. The genetically modified bacterium of claim 10, wherein said modification in NifL results in a decrease in NifL expression.

13. The genetically modified bacterium of claim 10, wherein said modification in NifH results in an increase in NifH expression.

14. The genetically modified bacterium of claim 9, wherein said modification in a nitrogen fixation genetic network comprises a modification that produces an increase in the expression of Nif clustered genes.

15. The genetically modified bacterium of any of claims 1-14, wherein said genetically modified bacterium further comprises a modification in a nitrogen assimilation genetic network.

16. The genetically modified bacterium of claim 15, wherein said modification in a nitrogen assimilation genetic network comprises a modification in GlnE.

17. The genetically modified bacterium of claim 16, wherein said modification in GlnE results in a decrease in GlnE activity.

18. The genetically modified bacterium of claim 15, wherein said modification in a nitrogen assimilation genetic network results in a decrease in amtB activity.

19. A method for increasing the amount of nitrogen derived from the atmosphere in a plant, the method comprising contacting said plant with a plurality of said genetically modified bacteria according to any of claims 1-18.

20. The method of claim 19, wherein contacting said plant with a plurality of said genetically modified bacteria comprises applying said plurality of genetically modified bacteria to a seed of said plant.

21. The method of claim 19, wherein contacting said plant with a plurality of said genetically modified bacteria comprises applying said plurality of genetically modified bacteria to a seedling of said plant.

22. The method of claim 19, wherein contacting said plant with a plurality of said genetically modified bacteria comprises applying said plurality of genetically modified bacteria to said plant in a liquid formulation.

23. The method of claim 19, wherein contacting said plant with a plurality of said genetically modified bacteria comprises applying said RnRZLn / LZnZ / E / Yli plurality of genetically modified bacteria to said plant after sowing but before harvesting of said plant.

24. The method of claim 19, wherein contacting said plant with a plurality of said genetically modified bacteria comprises applying said plurality of genetically modified bacteria to said plant as a side-dressing topdressing.

25. The method of claim 19, wherein contacting said plant with a plurality of said genetically modified bacteria comprises applying said plurality of genetically modified bacteria to said plant between approximately one month and approximately eight months after germination.

26. The method of claim 25, wherein applying said plurality of genetically modified bacteria to said plant between approximately one month and approximately eight months after germination comprises applying said plurality of genetically modified bacteria to said plant between two months and eight months after germination.

27. The method of claim 25, wherein applying said plurality of genetically modified bacteria to said plant between approximately one month and approximately eight months after germination comprises applying said plurality of genetically modified bacteria to said plant between approximately one month and approximately three months after germination.

28. The method of claim 25, wherein applying said plurality of genetically modified bacteria to said plant between approximately one month and approximately eight months after germination comprises applying said plurality of genetically modified bacteria to said plant between approximately three months and approximately six months after germination.

29. The method of any of claims 19-28, wherein said plant is a cereal plant.

30. The method of any of claims 19-28, wherein said plant is a corn plant.

31. The method of any of claims 19-28, wherein said plant is a rice plant.

32. The method of any of claims 19-28, wherein said plant is a wheat plant.

33. The method of any of claims 19-28, wherein said plant is a soybean plant.

34. A composition comprising a seed and a seed coating, in RnRZLn / LZnZ / E / Yli 94 wherein the seed coating comprises a plurality of said genetically modified bacteria according to any of claims 1-18.

35. The composition of claim 34, wherein said seed is a cereal seed.

36. The composition of claim 35, wherein said seed is selected from the group consisting of: a corn seed, a wheat seed, a rice seed, a soybean seed, a rye seed, and a sorghum seed.

37. A composition comprising a plant and a plurality of said genetically modified bacteria according to any of claims 1-18.

38. The composition of claim 37, wherein said plant is a seedling.

39. The composition of claim 37, wherein said plant is a cereal plant.

40. The composition of claim 37, wherein said plant is selected from the group consisting of: maize, rice, wheat, soybeans, rye, and sorghum. RnRZLn / LZnZ / E / Yli