Methanotroph strains for mitigating methane and methods related thereto

Abstract

Methanotroph strains that enhance early growth of plants, improve propagation / transplant vigor, increase nutrient uptake, improve stand establishment, improve stress tolerance and / or increase a plant's ability to utilize nutrients are provided herein. Uses of compositions comprising such strains and optionally methylotroph strains, for methane mitigation and crop improvement is provided. Also provided are methods to reduce green-house gas emission and convert methane to methanol with methanotroph strains.

Description

METHANOTROPH STRAINS FOR MITIGATINGMETHANE AND METHODS RELATED THERETOREFERENCE TO PRIORITY APPLICATIONS

[0001] This patent application claims benefit of U.S. Patent Application No. 63 / 606,003, filed December 4, 2023; U.S. Patent Application No. 63 / 606,485, filed December 5, 2023; U.S. Patent Application No. 63 / 624,133, filed January 23, 2024; U.S. Patent Application No. 63 / 561,055, filed March 4, 2024; U.S. Patent Application No. 63 / 651,168, filed May 23, 2024; PCT Application No. PCT / US24 / 31017, filed May 24, 2024; U.S. Patent Application No. 63 / 694,457, filed September 13, 2024; U.S. Patent Application No. 63 / 716,491, filed on November 5, 2024; U.S. Patent Application No. 63 / 716,398, filed on November 5, 2024; and PCT Application No. > , having Attorney Docket No. P14472WOOO filed concurrently herewith.SEQUENCE LISTING STATEMENT

[0002] A computer readable form of the Sequence Listing XML containing the file named "NLSYM7010.WO Sequence Listing. xml," which is 395,427 bytes in size (as measured in MICROSOFT WINDOWS® EXPLORER) and was created on November 21, 2024, is provided herein and is herein incorporated by reference. This Sequence Listing consists of SEQ ID NOs: 1-171.BACKGROUND OF THE INVENTION

[0003] Methylotrophic and methanotrophic bacteria are capable of utilizing single-carbon compounds as carbon and energy sources, but they differ in whether they can use methane as a source.

[0004] Obligate methanotrophs, such as Methylomicrobium, Methylosarcina, Methylocystis, Methylomonas, and Melhylosiniis. can use methane and / or methanol but no other sources.

[0005] In contrast, methylotrophs cannot use methane due to the absence of an enzyme required for methane oxidation. Instead, obligate methylotrophs can use methanol and possibly methylamine or formate, and facultative methylotrophs can use methanol and multi-carbon compounds, such as organic acids, higher alcohols, and sugars. Some facultative methylotrophs, such sMethylobacterium and Melhylonibriim. are pink-pigmented and are conventionally referred to as PPFMs.

[0006] Methanotrophs possess the enzyme methane monooxygenase (MMO) which incorporates an atom of oxygen from O2 into methane, forming methanol. There are two forms of the MMO enzyme, a soluble methane monooxygenase (sMMO), and a particulate methane monooxygenase (pMMO). Most known methanotrophs possess pMMO, although sMMO is also present in some methanotrophs.

[0007] Methanotrophs are classified into three groups, Type I, Type II and Type X on the basis of various physiological and morphological differences. Type I and Type X methanotrophs aregammaproteobacteria, while Type II methanotrophs are alphaproteobacterial. Some methanotrophs have been reported to contain two distinct isozymes of particulate methane monooxygenase (pMMO). pMMOl facilitates oxidation of methane in high methane concentration environments. pMM02 also facilitates oxidation of methane in low methane concentration environments, including oxidation of atmospheric methane. pMMO comprises three protein subunits, PmoA, PmoB and PmoC, which are encoded on an operon present in the methanotroph genome.SUMMARY OF THE INVENTION

[0008] The present invention provides methods and compositions that are shown to have the following beneficial characteristics when applied to plants: a) improved growth metrics, including plant size, tiller counts, plant height; b) improved yield, including panicle counts, panicle weights, and shoot biomass; c) improved methane mitigation; and d) improved colonization of beneficial microorganisms.

[0009] Moreover, the present invention provides methods to identify and use methanotrophic compositions useful for improved growth metrics, yield, methane mitigation, and colonization.

[0010] Provided herein are strains of methanotrophic bacteria and compositions comprising one or more methanotroph strains, wherein the strains are capable of using methane (CPU) as a carbon source for growth. Also provided are methods that utilize such strains for mitigating methane production, for example: methane present in enteric fermentation in livestock, manure and septic management; landfill and wastewater management; agricultural residue decomposition mitigation; anaerobic digester systems; and flooded field plant cultivation.

[0011] For example, the present strains and methods are useful in rice cultivation environments and in the cattle and dairy industries. Other examples include use in wastewater reclamation / treatment and natural water sources, (for example, wetlands, lakes, rivers, mangroves, marshes, bogs and streams). In addition, the present invention is useful in geological environments (natural gas, coal, or other extractive processes), and in gases produced as the result of wildfires, wild animals, or insects.

[0012] In some embodiments provided herein, methanotrophs are applied to rice plants resulting in methane mitigation and enhanced plant growth. In some embodiments, an overall reduction in methane per rice plant is observed. In plants with increased yield, methane is mitigated despite the increased yield. In some embodiment, a reduction in methane is measured as an increase in rice biomass yield per unit of methane emitted.Summary of representative embodiments.

[0013] The present invention provides compositions comprising a microbial strain selected from the group consisting of: NLS1546; NLS1557; NLS1558; NLS1561; NLS1563; NLS1564; NLS1572;NLS1578; NLS1581; NLS1591; NLS1601; NLS1618; NLS1631; and NLS1632.

[0014] Also provided are such compositions comprising two or more microbial strains wherein at least one of said microbial strains is selected from the group consisting of: NLS1501; NLS1504; NLS1505; NLS1506; NLS1508; NLS1509; NLS1511; NLS1512; NLS1546; NLS1557; NLS1558; NLS1561; NLS1563; NLS1564; NLS1572; NLS1578; NLS1581; NLS1591; NLS1601; NLS1618; NLS1631; and NLS1632.

[0015] Also provided are such compositions, wherein the two or more microbial strain is a number selected from the group consisting of: 2; 3; 4; 5; 6; 7; and 8.

[0016] Also provided are such compositions, further comprising a microbial strain selected from the group consisting of: NLS1501; NLS1504; NLS1505; NLS1506; NLS1508; NLS1509; NLS1511; NLS1512; NLS1546; NLS1557; NLS1558; NLS1561; NLS1563; NLS1564; NLS1572; NLS1578; NLS1581; NLS1591; NLS1601; NLS1618; NLS1631; and NLS1632.

[0017] The present invention also provides a consortium of microbial strains, wherein the consortium is selected from the group consisting of: a) NLS1501, NLS1504, NLS1508, NLS1561, NLS1563, NLS1578, andNLS1581; b)NLS1504, NLS1508, NLS1561, NLS1578, NLS1581, andNLS1631; and c) NLS1508, NLS1561, and NLS1581.

[0018] Also provided are such compositions, wherein said compositions further comprise a methylotroph.

[0019] Also provided are such compositions, wherein said compositions further comprise a methylotroph described in Table 1 A.

[0020] Also provided are such compositions, wherein the methylotroph is selected from the group consisting of: NLS0017; NLS0020; NLS0042; NLS0089; NLS0109; NLS0610; NLS0662; NLS0648; NLS0807; and NLS0934.

[0021] Also provided are such compositions, wherein said compositions further comprise an additional methanotroph.

[0022] Also provided are such compositions, wherein said compositions further comprise a methanotroph described in Table IB.

[0023] Also provided are such compositions, wherein said methanotroph is selected from the group consisting of: NLS1501, NLS1508; NLS1504; NLS1505; NLS1506; NLS1509; NLS1511; NLS1512;NLS1546; NLS1557; NLS1558; NLS1561; NLS1563; NLS1564; NLS1572; NLS1578; NLS1581; NLS1591; NLS1601; NLS1618; NLS1631; and NLS1632.

[0024] Also provided are such compositions, which further comprise a methylotroph selected from the the group consisting of: NLS0017; NLS0020; NLS0042; NLS0064; NLS0089; NLS0109; NLS0610; NLS0648; NLS662; NLS0807; and NLS0934.

[0025] Also provided are such compositions, wherein said compositions further comprise at least one additional component.

[0026] Also provided are such compositions, wherein the at least one additional component is selected from the group consisting of: active ingredient; additional biological; adjuvant; bacterium; biopesticide; biostimulant; excipients; fungicide; fungus; herbicide; insecticides; lubricant; methanotroph; methylotrophs; nemacide.

[0027] The present invention also provides plants, plant parts, and seeds at least partially coated with a composition herein.

[0028] Also provided are such plants, plant parts, and seeds, selected from the group consisting of: rice; row crop and specialty crop.

[0029] Also provided are such plants, plant parts, and seeds, selected from the group consisting of: alfalfa, barley, brassica sp.; cannabis sp.; carrot, cassava; coconut; coffee; conifers; com; cotton; cucurbits; cucumber; fruit plants (including fruit trees); green bean; herbs; leafy greens; lettuce; microgreens; millet, oat; onion, ornamental, pea; peanut; pepper; potato; rice; rye; safflower; sorghum; soybean; squash; sugar beet; sunflower; sweet potato; tobacco; tomato; turfgrass; and wheat.

[0030] The present invention also provides isolated microorganisms selected from the group consisting of: NLS1546; NLS1557; NLS1558; NLS1561; NLS1563; NLS1564; NLS1572; NLS1578;NLS1581; NLS1591; NLS1601; NLS1618; NLS1631; and NLS1632.

[0031] The present invention also provides methods for mitigating methane in a methane-producing environment comprising: a) introducing a composition herein to a methane-producing environment, and b) growing the composition under conditions sufficient to mitigate methane in the methane- producing environment.

[0032] Also provided are such methods, wherein the methane-producing environment is selected from the group consisting of: pasture; landfill; manure field; septic field; wastewater pond; lake; river; mangrove; marsh; bog; stream; gas mine; coal mine; wildfire area; anaerobic digester system; and flooded field.

[0033] Also provided are such methods, wherein the methane-producing environment is a rice paddy.

[0034] Also provided are such methods, wherein said composition is applied on seed, plant foliage and / or plant part, plant, field soil, and / or field flood water.

[0035] Also provided are such methods, wherein the composition is applied at a time selected from the group consisting of: seedling before transplant; transplant; week 1 after transplant; week 2 after transplant; week 3 after transplant; week 4 after transplant; week 5 after transplant; week 6 after transplant; week 7 after transplant; week 8 after transplant; week 9 after transplant; week 10 after transplant; more than 10 weeks after transplant.

[0036] Also provided are such methods, wherein the composition is applied at a time selected from the group consisting of: 1 time during the growing cycle; 2 times during the growing cycle; 3 times during the growing cycle; 4 times during the growing cycle; 5 times during the growing cycle; 6 times during the growing cycle; and more than 6 times during the growing cycle.

[0037] Also provided are such methods, wherein the composition is applied at transplant and another time during the growing cycle.

[0038] Also provided are such methods, which further comprise improving one or more growth metric and / or yield.

[0039] The present invention also provides methods for mitigating methane in a rice paddy environment, comprising: a) introducing a composition of any one of claims 1 through 13 to a rice paddy environment, and b) growing the composition under conditions sufficient to mitigate methane in the rice paddy environment.

[0040] Also provided are such methods, wherein said composition is applied to plant foliage.

[0041] Also provided are such methods, wherein the composition is applied during transplant and during a week selected from the group consisting of: week 4 after transplant; week 5 after transplant; week 6 after transplant; and week 7 after transplant.

[0042] Also provided are such methods, wherein said composition is applied to plant foliage during transplant and during week 4 after transplant.

[0043] The present invention also provides methods for improving growth metrics in a plant, comprising: a) introducing a composition of any one of claims 1 through 13 to a plant, plant part, or seed; and b) growing the plant, plant part, or seed under conditions sufficient improve growth metrics.

[0044] Also provided are such methods, wherein the growth metrics are selected from the group consisting of: plant size; tiller counts; root length; and plant height.

[0045] Also provided are such methods, wherein the plant, plant part, or seed is rice or corn.

[0046] Also provided are such methods, wherein the composition is selected from the group consisting of: NLS1546; NLS1557; NLS1558; NLS1561; NLS1563; NLS1564; NLS1572; NLS1578; NLS1581;NLS1591; NLS1601; NLS1618; NLS1631; and NLS1632.

[0047] Also provided are such methods, wherein the composition is selected from the group consisting of: a) NLS1501, NLS1504, NLS1508, NLS1561, NLS1563, NLS1578, and NLS1581; b) NLS1504, NLS1508, NLS1561, NLS1578, NLS1581, andNLS1631; and c) NLS1508, NLS1561, andNLS1581.

[0048] The present invention also provides methods for improving yield metrics in a plant, comprising: a) introducing a composition of any one of claims 1 through 12 to a plant, plant part, or seed; and b) growing the plant, plant part, or seed under conditions sufficient improve yield metrics.

[0049] Also provided are such methods, wherein the improved yield metrics are selected from the group consisting of: panicle counts; panicle weights; and shoot biomass.

[0050] Also provided are such methods, wherein the plant, plant part, or seed is rice or corn.

[0051] Also provided are such methods, wherein the composition is selected from the group consisting of: a) NLS1501, NLS1504, NLS1508, NLS1561, NLS1563, NLS1578, and NLS1581; b) NLS1504, NLS1508, NLS1561, NLS1578, NLS1581, andNLS1631; and c) NLS1508, NLS1561, andNLS1581.

[0052] The present invention also provides methods for improving colonization of beneficial microorganisms on a plant, comprising: a) introducing a composition of any one of claims 1 through 13 to a plant, plant part, or seed; and b) growing the plant, plant part, or seed under conditions sufficient colonization.

[0053] Also provided are such methods, wherein the composition is selected from the group consisting of: NLS1546; NLS1557; NLS1558; NLS1561; NLS1563; NLS1564; NLS1572; NLS1578; NLS1581; NLS1591; NLS1601; NLS1618; NLS1631; and NLS1632.

[0054] Also provided are such methods, wherein the composition is selected from the group consisting of: a) NLS1501, NLS1504, NLS1508, NLS1561, NLS1563, NLS1578, and NLS1581; b) NLS1504, NLS1508, NLS1561, NLS1578, NLS1581, andNLS1631; and c) NLS1508, NLS1561, andNLS1581.

[0055] The present invention also provides methods to identify a consortium of methanotrophs useful to mitigate methane in plants, comprising: a) identifying one or more methanotrophs having increased colonization compared to a library of methanotrophs; and b) identifying combinations of one or more methanotrophs that mitigate methane in plants.

[0056] Also provided are such methods, wherein the combinations are selected from the group of methanotrophs in Table IB.

[0057] Also provided are such methods, wherein the combinations are selected from the group consisting of: NLS1546; NLS1557; NLS1558; NLS1561; NLS1563; NLS1564; NLS1572; NLS1578; NLS1581; NLS1591; NLS1601; NLS1618; NLS1631; and NLS1632.DETAILED DESCRIPTION

[0058] Definitions.

[0059] " And / or" where used herein is to be taken as specific disclosure of each of the two or more specified features or components with or without the other. Thus, the term “and / or" as used in a phrase such as "A and / or B" herein is intended to include "A and B," "A or B," "A" (alone), and "B" (alone). Likewise, the term "and / or" as used in a phrase such as "A, B, and / or C" is intended to encompass each of the following embodiments: A, B, and C; A, B, or C; A or C; A or B; B or C; A and C; A and B; B and C; A (alone); B (alone); and C (alone).

[0060] “Biological” refers to a component of a composition for treatment of plants or plant parts comprised of or derived from a microorganism. Biologicals include biocontrol agents, other beneficial microorganisms, microbial extracts, natural products, plant growth activators or plant defense agents. Non-limiting examples of biocontrol agents include bacteria, fungi, beneficial nematodes, and viruses.

[0061] “ Colonization efficiency” as used herein refers to the relative ability of a given microbial strain to colonize a plant host cell or tissue as compared to non-colonizing control samples or other microbial strains. Colonization efficiency can be assessed, for example and without limitation, by determining colonization density, reported for example as colony forming units (CFU) per mg of plant tissue, or by quantification of nucleic acids specific for a strain in a colonization screen, for example using qPCR.

[0062] “Correlation” refers to a statistical measure that indicates the extent to which two or more variables, here plant growth enhancement and identified genetic elements, occur together. A positive correlation indicates that a microbial strain containing a given genetic element is likely to enhance plant growth.

[0063] “ Cultivate” means to grow a plant. A cultivated plant can be one grown and raised on a large agricultural scale or on a smaller scale, including for example a single plant.

[0064] “Derivative” when used in the context of a methanotrophic bacterial isolate, refers to any methanotrophic bacterial that is obtained from a deposited methanotrophic bacterial isolate provided herein. Derivatives of a methanotrophic bacterial isolate include, but are not limited to, derivatives obtained by selection, derivatives selected by mutagenesis and selection, and genetically transformed methanotrophic bacteria obtained from a methanotrophic bacterial isolate. A “derivative” can be identified, for example based on genetic identity to the strain or isolate from which it was obtained andwill generally exhibit chromosomal genomic DNA with at least 99%, 99.9%, 99.8%, 99.7%, 99.6%, or 99.5% sequence identity to chromosomal genomic DNA of the strain or isolate from which it was derived.

[0065] “Fertilizer” can be a single nutrient nitrogen fertilizer, such as urea, ammonia or ammonia solutions (including ammonium nitrate, ammonium sulfate, calcium ammonium nitrate, and urea ammonium nitrate). In certain embodiments, the fertilizer can be a single nutrient phosphate fertilizer, such as a superphosphate or triple superphosphate or mixtures thereof, including double superphosphate. In certain embodiments, the fertilizer can be a single nutrient potassium-based fertilizer, such as muriate of potash. In certain embodiments, the compositions comprise multinutrient fertilizers including binary fertilizers (NP, NK, PK), including, for example monoammonium phosphate, diammonium phosphate, potassium nitrate and potassium chloride. In further embodiments, three-component fertilizers (NPK) providing nitrogen, phosphorus, and potassium are present in the aqueous compositions. In still further embodiments, the fertilizer comprises micronutrients, which may be chelated or non-chelated. In some embodiments, combinations of various fertilizers can be present in the aqueous solution, including combinations of nitrogen, phosphorus and / or micronutrient fertilizers. Nutrient solutions provided in hydroponic plant growth systems are also considered “fertilizers” in methods and compositions described herein.

[0066] “ Genetic element” refers to an element in a DNA or RNA molecule that comprises a series of adjacent nucleotides at least 20 nucleotides in length and up to 50, 100, 1,000, or 10,000 or more, nucleic acids in length. A genetic element may comprise different groups of adjacent nucleic acids, for example, where the genome of a plant-associated microorganism contains introns and exons. The genetic element may be present on a chromosome or on an extrachromosomal element, such as a plasmid. In eukaryotic plant-associated microorganisms, the genetic element may be present in the nucleus or in the mitochondria. In some embodiments, the genetic element is a functional genetic element (e.g., a gene) that encodes a protein.

[0067] “Homologous"' or "homologue" or "ortholog" refer to related genetic elements or proteins encoded by the genetic elements that are determined based on the degree of sequence identity. These terms describe the relationship between a genetic element or encoded protein found in one isolate, species or strain and the corresponding or equivalent genetic element or protein in another isolate, species or strain. As used herein, a particular genetic element in a first isolate, species or strain is considered equivalent to a genetic element present in a second isolate, species or strain when the proteins encoded by the genetic element in the isolates, species or strains have at least 50 percent identity. Percent identity can be determined using a number of software programs available in the artincluding BLASTP, ClustalW, ALLALIGN, DNASTAR, SIM, SEQALN, NEEDLE, SSEARCH and the like.

[0068] “Hydroponic”, “hydroponics”, or “hydroponically” refers to a method of cultivating plants in the absence of soil.

[0069] “Include,” “includes,” and “including” are to be construed as at least having the features or encompassing the items to which they refer while not excluding any additional unspecified features or unspecified items.

[0070] “Methanotrophic bacteria” or “methanotroph” refers to genera and species of bacteria that are capable of using methane as their carbon source for growth and / or a species that contains a pMMO gene. Methanotrophic bacteria include species in the genera Methyloacidimicrobium, Methyloacidiplilum, Methylobacter, Methylocaldum, Methylocapsa, Methylocella, Methylococcus, Methylocystis, Methyloferula, Methylogaea, Methyloglobus, Methylohalobius, Methylomagnum, Methylomarinum, Methylomicrobium, Methylomonas, Methyloparacoccus, Methyloperedens, Methyloprofundus, Methylosarcina, Methylosinus, Methylosoma, Methylosphaera, Methylothermus, and Methylovulum.

[0071] ‘' ethylobacterium" refers to methylotroph genera and species in the methylobacteriaceae family, including bacterial species in k\Q Methylobacterium genus and proposed Methylorubrum genus (Green and Ardley (2018)). Methylobacterium includes pink-pigmented facultative methyl otrophic bacteria (PPFM) and also encompasses the non-pink-pigmented Methylobacterium nodulans. as well as colorless mutants of Methylobacterium isolates. For example, and not by way of limitation, ‘Methylobacterium” refers to bacteria of the species listed below as well as any new Methylobacterium species that have not yet been reported or described that can be characterized as Methylobacterium or Methylorubrum based on phylogenetic analysis: Methylobacterium adhaesivum; Methylobacterium oryzae; Methylobacterium aerolatum; Methylobacterium oxalidis; Methylobacterium aquaticum; Methylobacterium persicinum; Methylobacterium brachiatum; Methylobacterium phyllosphaerae; Methylobacterium brachythecii; Methylobacterium phyllostachyos; Methylobacterium bullatum; Methylobacterium platani; Methylobacterium cerastii; Methylobacterium pseudosasicola;Methylobacterium currus; Methylobacterium radiotolerans; Methylobacterium dankookense; Methylobacterium soli; Methylobacterium frigidaeris; Methylobacterium specialis;Methylobacterium fujisawaense; Methylobacterium tardum; Methylobacterium gnaphalii;Methylobacterium tarhaniae; Methylobacterium goesingense; Methylobacterium thuringiense;Methylobacterium gossipiicola; Methylobacterium trifolii; Methylobacterium gregans;Methylobacterium variabile; Methylobacterium haplocladii; Methylobacterium aminovorans(Methylorubrum aminovorans); Methylobacterium hispanicum; Methylobacterium extorquens (Methylorubrum extorquens); Methylobacterium indicum; Methylobacterium podarium (Methylorubrum podarium); Methylobacterium iners; Methylobacterium populi (Methylorubrum populi) ; Methylobacterium isbiliense; Methylobacterium pseudosasae (Methylorubrum pseudosasae) ; Methylobacterium jeotgali; Methylobacterium rhodesianum (Methylorubrum rhodesianum); Methylobacterium komagatae; Methylobacterium rhodinum (Methylorubrum rhodinum); Methylobacterium longum; Methylobacterium salsuginis (Methylorubrum salsuginis); Methylobacterium marchantiae; Methylobacterium suomiense (Methylorubrum suomiense; Methylobacterium mesophilicum; Methylobacterium thiocyanatum (Methylorubrum thiocyanatum) ; Methylobacterium nodulans; Methylobacterium zatmanii (Methylorubrum zatmanii); Methylobacterium symbiota; o Methylobacterium organophilum.

[0072] “Mineral nutrients” (also sometime referred to simply as “nutrients”) are micronutrients or macronutrients required or useful for plants or plant parts including for example, but not limited to, nitrogen (N), potassium (K), calcium (Ca), magnesium (Mg), phosphorus (P), and sulfur (S), and the micronutrients chlorine (Cl), Iron (Fe), Boron (B), manganese (Mn), zinc (Z), cobalt (Co), copper (Cu), molybdenum (Mo) and nickel (Ni).

[0073] “Mitigating”, “mitigate”, or “mitigation” refers to a reduction of something or a combination of things as compared to a standard.

[0074] “Mitigate methane” refers to either decreasing methane levels by reducing methane emissions, reduction in methane per plant, including, a reduction in methane measured as an increase in plant biomass yield per unit of methane emitted, or by enhancing removal of methane from sources such as agricultural soil, wetlands, landfills, waste facilities, animal feed, water or air. Mitigation of methane may be the result of methane oxidation by the activity of pMMO and / or sMMO enzymes in the methanotrophic bacterial strains provided herein, or may be the result of secondary effects of the provided methanotroph and / or Methylobacterium strains on the microbiome of a treated plant or plant part.

[0075] “Pan-genome” refers to the entire set of genes for the microbial population being screened in a plant colonization efficiency screen. Thus, a pan-genome may represent the entire set of genes for a particular species, or the entire set of genes in multiple different species of the same genus or even the entire set of genes for multiple species classified in more than a single genus, where the strains in the population are from closely related genera.

[0076] “Sequence identity” when used to evaluate whether a particular methanotrophic bacterial strain is a variant or derivative of a methanotrophic bacterial strain provided herein refers to a measureof nucleotide-level genomic similarity between the coding regions of two genomes. Sequence identity between the coding regions of bacterial genomes can be calculated, for example, by determining the Average Nucleotide Identity (ANI) score using FastANI (Jain et al. “High throughput ANI analysis of 90K prokaryotic genomes reveals clear species boundaries”, Nat Communications 9, 5114 (2018)) and Han et al. (“ANI tools web: a web tool for fast genome comparison within multiple bacterial strains”; Database, 2016, 1-5).

[0077] “ Strain” shall include and / all isolates of such strain.

[0078] “Variant” when used in the context of a methanotrophic bacterial isolate, refers to any isolate that has chromosomal genomic DNA with at least 99%, 99.9%, 99.8%, 99.7%, 99.6%, or 99.5% sequence identity to chromosomal genomic DNA of a reference methanotrophic bacterial isolate, such as, for example, a deposited methanotrophic bacterial isolate provided herein. A variant of an isolate can be obtained from various sources including soil, plants or plant material, and water, particularly water associated with plants and / or agriculture. Variants include derivatives obtained from deposited isolates. Methanotrophic bacterial isolates or strains can be sequenced (for example as taught by Sanger et al. (1977), Bentley et al. (2008) or Caporaso et al. (2012)) and genome-scale comparison of the sequences conducted (Konstantinidis etal. (2005)) using sequence analysis tools, such as BLAST, as taught by Altschul et al. (1990) or clustalw (www.ebi.ac.uk / Tools / msa / clustalw2 / ).

[0079] “Vitamins” are organic compounds required in small amounts for normal growth and metabolism. Vitamins are important for human and / or animal growth and some vitamins have been reported to be beneficial to plants. Vitamins include but are not limited to vitamin A (including but not limited to all-trans-retinol, all-trans-retinyl-esters, as well as all-trans-beta-carotene and other provitamin A carotenoids), vitamin Bl (thiamine), vitamin B2 (riboflavin), vitamin B3 (niacin), vitamin B5 (pantothenic acid), vitamin B6 (pyridoxine), vitamin B7 (biotin), vitamin B9 (folic acid or folate), vitamin B12 (cobalamins), vitamin C (ascorbic acid), vitamin D (calciferols), vitamin E (tocopherols and tocotri enols), and vitamin K (quinones).

[0080] Where a term is provided in the singular, other embodiments described by the plural of that term are also provided.

[0081] To the extent to which any of the preceding definitions is inconsistent with definitions provided in any patent or non-patent reference incorporated herein by reference, any patent or non-patent reference cited herein, or in any patent or non-patent reference found elsewhere, it is understood that the preceding definition will be used herein.Description.

[0082] Methane Mitigation. Isolated methanotrophic bacteria (methanotrophs) herein oxidize methane, and can be formulated into compositions that can be used to mitigate methane in environments where methane is emitted or produced, such as in landfills, agricultural lands, wastewater treatment, wetlands, landfills, waste facilities, and dairy farms.

[0083] Fields, plants or harvested plant parts having mitigated methane in comparison to a control field, plant, or plant part are provided, as are methods for obtaining and using such plants and plant parts. In certain embodiments, the methane is mitigated by at least about 0.1%, .5%, 1%, or 2% to about 3%, 4%, 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%, or 30%.

[0084] Growth metrics and Yield. Methanotrophic bacteria herein enhance early growth of plants, improve propagation / transplant vigor, increase nutrient uptake, improve stand establishment, improve stress tolerance, increase yield, and / or increase a plant’s ability to utilize nutrients. In some embodiments, methanotrophs herein provide for nitrogen fixation, and or enhance nitrogen use efficiency of a treated plant. In some embodiments, application of methanotrophs herein increases yield at harvest, for example increased harvested seed yield.

[0085] Strains. Non-limiting examples of strains that can be used in compositions and methods provided herein are disclosed in Table 1 A and Table IB. Other strains useful in certain compositions and methods provided herein include variants of the strains disclosed in Table 1 A and Table IB. Also of use are various combinations of two or more strains or variants of strains disclosed in Table 1A and / or Table IB for compositions and treatment of plants or parts thereof.[intentionally blank continued on next page]Table 1A. MethylotrophsTable 1A.ContinuedTable IB. MethanotrophsDeposit Statement.

[0086] The NRRL numbers referenced herein are the deposit identification numbers for strains deposited with the AGRICULTURAL RESEARCH SERVICE CULTURE COLLECTION (NRRL) of the National Center for Agricultural Utilization Research, Agricultural Research Service, U.S. Department of Agriculture, 1815 North University Street, Peoria, Illinois 61604 U. S. A. under the terms of the Budapest Treaty on the International Recognition of the Deposit of Microorganisms for the Purposes of Patent Procedure. Subject to 37 CFR § 1.808(b), all restrictions imposed by the depositor on the availability to the public of the deposited material will be irrevocably removed upon the granting of any patent from this patent application.Table 1C. Example Consortium StrainsAdditional Components.

[0087] In certain embodiments of the methods provided herein, plants, plant seeds and / or plant parts are treated with both a methanotroph strain and at least one additional component. In some embodiments an additional component can be an additional active ingredient, for example, a pesticide or a second biological. In certain embodiments, the pesticide can be an insecticide, a fungicide, an herbicide, a nematicide or other biocide. The second biological could be a strain that improves yield or controls an insect, pest, fungi, weed, or nematode. In some embodiments, a second biological is an additional methanotroph strain. In some embodiments, a second biological is a Methylobacterium strain. In some embodiments, an additional strain in the methods and compositions provided herein is selected from the Methylotrophs listed in Table 1 A and / or a Methanotroph in Table IB.

[0088] Insecticides and Nemacides. Non-limiting examples of insecticides and nematicides include carbamates, diamides, macrocyclic lactones, neonicotinoids, organophosphates, phenylpyrazoles, pyrethrins, spinosyns, synthetic pyrethroids, tetronic and tetramic acids. In particular embodiments insecticides and nematicides include abamectin, aldicarb, aldoxycarb, bifenthrin, carbofuran,chlorantraniliporle, chlothianidin, cyfluthrin, cyhalothrin, cypermethrin, deltamethrin, dinotefuran, emamectin, ethiprole, fenamiphos, fipronil, flubendiamide, fosthiazate, imidacloprid, ivermectin, lambda-cyhalothrin, milbemectin, nitenpyram, oxamyl, permethrin, tioxazafen, spinetoram, spinosad, spirodi chi ofen, spirotetramat, tefluthrin, thiacl oprid, thiamethoxam, and thiodicarb.

[0089] Fungicides. Non-limiting examples of useful fungicides include aromatic hydrocarbons, benzimidazoles, benzthiadiazole, carboxamides, carboxylic acid amides, morpholines, phenylamides, phosphonates, quinone outside inhibitors (e.g. strobilurins), thiazolidines, thiophanates, thiophene carboxamides, and triazoles. Particular examples of fungicides include acibenzolar-S-methyl, azoxystrobin, benalaxyl, bixafen, boscalid, carbendazim, cyproconazole, dimethomorph, epoxiconazole, fluopyram, fluoxastrobin, flutianil, flutolanil, fluxapyroxad, fosetyl-Al, ipconazole, isopyrazam, kresoxim-methyl, mefenoxam, metalaxyl, metconazole, myclobutanil, orysastrobin, penflufen, penthiopyrad, picoxystrobin, propiconazole, prothioconazole, pyraclostrobin, sedaxane, silthiofam, tebuconazole, thifluzamide, thiophanate, tolclofos-methyl, trifloxystrobin, and triticonazole. Non-limiting examples of other biocides, include isothiazolinones, for example 1,2 Benzothiazolin-3-one (BIT), 5-Chloro-2-methyl-4-isothiazolin-3-one (CIT), 2-Methyl-4-isothiazolin- 3-one (MIT), octylisothiazolinone (OIT), dichlorooctylisothiazolinone (DCOIT), and butylbenzisothiazolinone (BBIT); 2-Bromo-2-nitro-propane- 1,3 -diol (Bronopol), 5-bromo-5-nitro- 1,3-dioxane (Bronidox), Tris(hydroxymethyl)nitromethane, 2,2-Dibromo-3-nitrilopropionamide (DBNPA), and alkyl dimethyl benzyl ammonium chlorides.

[0090] Herbicides. Non-limiting examples of herbicides include ACCase inhibitors, acetanilides, AHAS inhibitors, carotenoid biosynthesis inhibitors, EPSPS inhibitors, glutamine synthetase inhibitors, PPO inhibitors, PS II inhibitors, and synthetic auxins, Particular examples of herbicides include acetochlor, clethodim, dicamba, flumioxazin, fomesafen, glyphosate, glufosinate, mesotrione, quizalofop, saflufenacil, sulcotrione, and 2,4-D.

[0091] Active Ingredient. In some embodiments, the composition or method disclosed herein may comprise a methanotroph strain and an additional active ingredient selected from the group consisting of clothianidin, ipconazole, imidacloprid, metalaxyl, mefenoxam, tioxazafen, azoxystrobin, thiomethoxam, fluopyram, prothioconazole, pyraclostrobin, and sedaxane.

[0092] Additional biological.

[0093] The second biological could be a biological control agent, other beneficial microorganisms, microbial extracts, plant extracts, yeast extracts, vegetal chitosan, natural products, plant growth activators or plant defense agent. Non-limiting examples of the second biological could include bacteria, fungi, beneficial nematodes, and viruses. In certain embodiments, the second biological canbe a Methylotroph and / or a Methanotroph. In certain embodiments, the second biological is a strain listed in Table 1 A and / or Table IB.

[0094] Methylotrophs. In certain embodiments, the second biological can be a Methylobacterium selected from M. gregans, M. radiotolerans, M. extorquens, M. populi, M. salsuginis, M. brachiatum, andM. komagatae.

[0095] Methanotrophs. In certain embodiments, the second biological can be a Methanotroph selected from Methyloacidimicrobium, Methyloacidiplilum, Methylobacter, Methylocaldum, Methylocapsa, Methylocella, Methylococcus, Methylocystis, Methyloferula, Methylogaea, Methyloglobus, Methylohalobius, Methylomagnum, Methylomarinum, Methylomicrobium, Methylomonas, Methyloparacoccus, Me thy loper edens, Methyloprofundus, Methylosarcina, Methylosinus, Methylosoma, Methylosphaera, Methylothermus, and Methylovulum. In some embodiments, a methanotroph provided herein is Methylocystis species selected from AT. hirsuta, M. rosea and AT. parvus. In some embodiments, a methanotroph provided herein is Methylosinus species selected from M. trichosporium and M. sporium. In some embodiments, a methanotroph provided herein is Methylomicrobium lacus o Methylosarcina fibrate strain.

[0096] Bacterium. In certain embodiments, the second biological can be a bacterium of the genus Actinomycetes, Agrobacterium, Arthrobacter, Alcaligenes, Aureobacterium, Azobacter, Azorhizobium, Azospirillum, Azotobacter, Beijerinckia, Bacillus, Brevibacillus, Burkholderia, Chromobacterium, Clostridium, Clavibacter, Comomonas, Corynebacterium, Curtobacterium, Enterobacter, Flavobacterium, Gluconacetobacter, Gluconobacter, Herbaspirillum, Hydrogenophage, Klebsiella, Luteibacter, Lysinibacillus, Mesorhizobium, Methylobacterium, Microbacterium, Ochrobactrum, Paenibacillus, Pantoea, Pasteuria, Phingobacterium, Photorhabdus, Phyllobacterium, Pseudomonas, Rhizobium, Rhodococcus, Bradyrhizobium, Serratia, Sinorhizobium, Sphingomonas, Streptomyces, Stenotrophomonas, Variovorax, Xanthomonas and Xenorhadbus. In particular embodiments the bacteria is selected from the group consisting of Bacillus amyloliquefaciens, Bacillus cereus, Bacillus firmus, Bacillus, lichenformis, Bacillus pumilus, Bacillus sphaericus, Bacillus subtilis, Bacillus thuringiensis, Chromobacterium suttsuga, Pasteuria penetrans, Pasteuria usage, and Pseudomona fluorescens.

[0097] Fungus. In certain embodiments the second biological can be a fungus of the genus Acremonium, Alternaria, Ampelomyces, Aspergillus, Aureobasidium, Beauveria, Botryosphaeria, Cladosporium, Cochliobolus, Colletotrichum, Coniothyrium, Embellisia, Epicoccum, Fusarium, Gigaspora, Gliocladium, Glomus, Laccaria, Metarhisium, Muscodor, Nigrospora, Paecilonyces, Paraglomus, Penicillium, Phoma, Pisolithus, Podospora, Rhizopogon, Scleroderma, Trichoderma,Typhula, Ulocladium, and Verticilium. In particular embodiments, the fungus is Beauveria bassiana, Coniothyrium minitans, Gliocladium vixens, Muscodor albus, Paecilomyces lilacinus, or Trichoderma polysporum.

[0098] Biostimulant. In further embodiments the second biological can be a biostimulant, including but not limited to seaweed extract or hummates, plant growth activators or plant defense agents including, but not limited to harpin, Reynoutria sachalinensis, j asm onate, lipochitooligosaccharides, and isoflavones.

[0099] Biopesticides. In further embodiments, the second biological can include, but are not limited to, various Bacillus sp., Pseudomonas sp., Coniothyrium sp., Pantoea sp., Streptomyces sp., and Trichoderma sp. Microbial biopesticides can be a bacterium, fungus, virus, or protozoan. Particularly useful biopesticidal microorganisms include various Bacillus subtilis, Bacillus thuringiensis, Bacillus pumilis, Pseudomonas syringae, Trichoderma harzianum, Trichoderma virens, and Streptomyces lydicus strains. Other microorganisms that are added can be genetically engineered or wild-type isolates that are available as pure cultures. In certain embodiments, it is anticipated that the second biological can be provided in the composition in the form of a spore.

[0100] Lubricants. In certain embodiments where plant seeds are treated with methanotroph compositions provided herein, the compositions further comprise one or more lubricants to ensure smooth flow and separation (singulation) of seeds in the seeding mechanism, for example a planter box. Lubricants for use in such compositions include talc, graphite, polyethylene wax based powders (such as Fluency Agent), protein powders, for example soybean protein powders, or a combination of protein powders and a lipid, for example lecithin or a vegetable oil. Lubricants can be applied to seeds simultaneously with application of a methanotroph, or may be mixed with a methanotroph prior to application of the compositions to the seeds.

[0101] Excipients. Agriculturally acceptable excipients include, but are not limited to, woodflours, clays, activated carbon, diatomaceous earth, fine-grain inorganic solids, calcium carbonate and the like. Clays and inorganic solids that can be used with the include, but are not limited to, calcium bentonite, kaolin, china clay, talc, perlite, mica, vermiculite, silicas, quartz powder, montmorillonite and mixtures thereof. Agriculturally acceptable excipients also include various lubricants such as talc, graphite, polyethylene wax based powders (such as Fluency Agent), protein powders, for example soybean protein powders, or a combination of protein powders and a lipid, for example lecithin or a vegetable oil.

[0102] Adjuvants. Preferably, the agriculturally acceptable adjuvant comprises kaolin, talc, graphite, mica, vermiculite, soyobean protein powder, or a combination thereof. Agriculturally acceptableadjuvants that promote sticking to the seed that can be used include, but are not limited to, polyvinyl acetates, polyvinyl acetate copolymers, hydrolyzed polyvinyl acetates, polyvinylpyrrolidone-vinyl acetate copolymer, polyvinyl alcohols, polyvinyl alcohol copolymers, polyvinyl methyl ether, polyvinyl methyl ether-maleic anhydride copolymer, waxes, latex polymers, celluloses including ethylcelluloses and methylcelluloses, hydroxy methylcelluloses, hydroxypropylcellulose, hydroxymethylpropylcelluloses, polyvinyl pyrrolidones, alginates, dextrins, malto-dextrins, polysaccharides, fats, oils, proteins, karaya gum, jaguar gum, tragacanth gum, polysaccharide gums, mucilage, gum arabics, shellacs, vinylidene chloride polymers and copolymers, soybean-based protein polymers and copolymers, lignosulfonates, acrylic copolymers, starches, polyvinylacrylates, zeins, gelatin, carboxymethylcellulose, chitosan, polyethylene oxide, acrylamide polymers and copolymers, polyhydroxyethyl acrylate, methylacrylamide monomers, alginate, ethylcellulose, polychloroprene and syrups or mixtures thereof. Other useful agriculturally acceptable adjuvants that can promote coating include, but are not limited to, polymers and copolymers of vinyl acetate, polyvinylpyrrolidone-vinyl acetate copolymer and water-soluble waxes. Further, agriculturally acceptable adjuvants also include various lubricants (which can provide for smooth flow and separation (singulation) of seeds) such as talc, graphite, polyethylene wax based powders (such as Fluency Agent), protein powders, for example soybean protein powders, or a combination of protein powders and a lipid, for example lecithin or a vegetable oil. Various surfactants, dispersants, anticaking-agents, foam-control agents, and dyes disclosed herein and in US Patent No. 8,181,388 can be adapted for use with compositions comprising a suitable methanotroph strain. In certain embodiments, the seed and / or seedling is exposed to the composition by providing the methanotroph strain in soil in which the plant or a plant arising from the seed are grown, or other plant growth media in which the plant or a plant arising from the seed are grown. Examples of methods where the methanotroph strain is provided in the field and soil include in furrow applications, soil drenches, and the like. Preferably, agriculturally acceptable adjuvants that promote sticking to the seed are celluloses dextrins, maltodextrins, polysaccharides, polysaccharide gums, or a combination thereof.

[0103] The agriculturally acceptable adjuvant, excipient, lubricant, and / or other ingredients, can be present in the composition at a concentration of from 0 wt.% to about 95 wt.%, from about 0.1 wt.% to about 95 wt.%, from about 0.5 wt.% to about 95 wt.%, from about 1 wt.% to about 95 wt.%, from about 2 wt.% to about 95 wt.%, from about 3 wt.% to about 95 wt.%, from about 4 wt.% to about 95 wt.%, from about 5 wt.% to about 95 wt.%, from about 0.1 wt.% to about 90 wt.%, from about 0.5 wt.% to about 90 wt.%, from about 1 wt.% to about 90 wt.%, from about 2 wt.% to about 90 wt.%, from about 3 wt.% to about 90 wt.%, from about 4 wt.% to about 90 wt.%, from about 5 wt.% to about 90 wt.%, from about 0.1 wt.% to about 85 wt.%, from about 0.5 wt.% to about 85 wt.%, from about 1wt.% to about 85 wt.%, from about 2 wt.% to about 85 wt.%, from about 3 wt.% to about 85 wt.%, from about 4 wt.% to about 85 wt.%, from about 5 wt.% to about 85 wt.%, from about 0.1 wt.% to about 80 wt.%, from about 0.5 wt.% to about 80 wt.%, from about 1 wt.% to about 80 wt.%, from about 2 wt.% to about 80 wt.%, from about 3 wt.% to about 80 wt.%, from about 4 wt.% to about 80 wt.%, or more preferably, from about 5 wt.% to about 80 wt.%.Treatments.

[0104] The compositions and methods herein are useful for treatment of various methane-containing environments, and can be applied in a variety of locations and timing intervals.

[0105] Environments. The invention is useful for mitigating methane in various environments, for example: in wetlands, landfills, and agricultural applications, including plant production in flooded fields; for reducing methane produced in animal production, such as cattle or dairy industries; for reducing natural methane sources such as exist in wetlands or other natural water sources, (including but not limited to lakes, rivers, mangroves, marshes, bogs and streams); in geological sources; and in gases produced as the result of wildfires, wild animals, or insects. By reducing methane resulting from such practices or present in such sources, the concentration of atmospheric greenhouse gases can be reduced and decrease the potential for methane to have detrimental effects, particularly in contributing to global warming. In some embodiments, methanotroph strains provided herein not only mitigate methane levels associated with agricultural crop production, but also provide additional benefits to a treated plant, such as increases in growth metrics and / or yield.

[0106] Application. Compositions comprising methanotrophs and optionally one or more methylotroph strain may be applied to soil or other growth medium where plants are grown. Methanotroph and optionally methylotroph soil treatments or applications can include, but are not limited to, fields (e.g. flooded or irrigated fields), in-furrow applications (e.g., before, during, and / or after seed deposition), soil drenches, distribution of granular or other dried formulations to the soil (e.g., before, during, and / or after seed deposition or plant growth). Treatments for plants grown in hydroponic systems can include seed treatments prior to germination, foliar applications to germinated plants or parts thereof, and applications in a liquid solution used in the hydroponic system. In certain embodiments, treatment of a plant can include application to the seed, plant, and / or a part of the plant and can thus comprise any methanotroph treatment or application resulting in colonization of the plant by the methanotroph. In some embodiments, application of one or more methanotrophs and optionally one or more methylotrophs to crops that are propagated by cutting can enhance growth and / or rooting of such plants. Field transplants of such treated and rooted cuttings may demonstrate decreased cycling time, and / or improved biomass and / or yield as a result of such treatments.

[0107] Treatments or applications to plants described herein can include, but are not limited to, spraying, coating, partially coating, immersing, drenching, and / or imbibing the field, seed, plant or plant parts with the methanotroph, and optionally one or more methylotroph, strains, or compositions comprising such strains. In certain embodiments, soil, a seed, a leaf, a stem, a root, a tuber, or a shoot can be sprayed, immersed drenched and / or imbibed with a liquid, semi-liquid, emulsion, or slurry of a composition provided herein. In some embodiments, one or more methanotroph strains may be applied together or separately with one or more methylotroph strains. In some embodiments, methanotroph, and optionally methylotroph strains, are applied to multiple plant parts and / or at multiple stages of plant growth. In certain embodiments, methane oxidizing methanotrophs described herein are applied as foliar sprays or seed treatments to row crops. In some embodiments, the crop is corn and a methanotroph is applied as a seed treatment. In some embodiments, the corn crop is grown under nitrogen limited conditions and the ability of the applied methanotroph to enhance nutrient uptake efficiency (NUE) is observed.

[0108] Timing and Conditions. In some embodiments, com seeds are treated in a planter box application. In some embodiments, the crop is rice, and plants are treated with an initial foliar application at a flooded stage. In some embodiments, foliar applications are made when a rice paddy is at full flood stage. In some embodiments, additional foliar applications of methanotroph are made. In some embodiments, a second foliar application of methanotroph is made from 20-40 days following the initial application. In some embodiments, methanotroph is also applied as a foliar spray prior to the booting stage of development (characterized by swelling of the flag leaf sheath caused by an increase in the size of the panicle). In some embodiments, a foliar spray is applied 14 days prior to booting stage. In some embodiments, a methanotroph is applied initially as a foliar spray at full flood stage, followed by a second foliar application approximately 4-6 weeks later, for example around 30 days later. In some embodiments, a third foliar application of a methanotroph is made not later than 14 days prior to booting stage. In some embodiments, a methanotroph applied as a foliar spray to rice.

[0109] Such treatments, applications, seed immersion, or imbibition can be sufficient to provide for mitigation of green-house gas emissions, enhanced early growth and / or increased levels of one or more mineral nutrients and / or vitamins content in harvestable tissue from a treated plant or plant grown from a treated seed in comparison to an untreated plant or plant grown from an untreated seed. Enhanced early growth can lead to further improvements in plant production including an increase in biomass of treated plants, such as increased shoot, root, or whole seedling biomass. Enhanced early growth can result in various additional improvements in plant production, including for example increased yield of harvested plants or harvested plant parts, increased and / or more uniform fruit production, fasterseed set, earlier maturation, increased rate of leaf growth, increased rate of root growth, increased seed yield, and decreased cycle time.

[0110] In certain embodiments, plant seeds or cuttings can be immersed and / or imbibed for at least 1, 2, 3, 4, 5, or 6 hours. Such immersion and / or imbibition can, in certain embodiments, be conducted at temperatures that are not deleterious to the plant seed or the methanotroph. In certain embodiments, the seeds can be treated at about 15 to about 30 degrees Centigrade or at about 20 to about 25 degrees Centigrade. In certain embodiments, seed imbibition and / or immersion can be performed with gentle agitation. Seed treatments can be effected with both continuous and / or batch seed treaters. In certain embodiments, the coated seeds can be prepared by slurrying seeds with a coating composition comprising a methanotroph strain that increases the levels of one or more mineral nutrients and / or vitamins and air-drying the resulting product. Air-drying can be accomplished at any temperature that is not deleterious to the seed or the methanotroph, but will typically not be greater than 30 degrees Centigrade. The proportion of coating that comprises the methanotroph strain includes, but is not limited to, a range of 0.1% to 25% by weight of the seed or other plant part, 0.5 to 5% by weight of the seed or other plant part, and 0.5 to 2.5% by weight of the seed or other plant part. In certain embodiments, a solid substance used in the seed coating or treatment will have a methanotroph strain that increases mineral nutrient and or vitamin content adhered to a solid substance as a result of being grown in biphasic media comprising the methanotroph strain, solid substance, and liquid media.

[0111] Hydroponics. In certain embodiments, treated plants are cultivated in a hydroponic system. In some embodiments, plant seeds are treated and plants are grown from the treated seeds continuously in the same cultivation system. In some embodiments, plant seeds are treated and cultivated in a hydroponic nursery to produce seedlings. The seedlings transferred to a different hydroponic system, for example for commercial production of leafy greens. In some embodiments, a methanotroph strain that enhances early growth or increases the levels of one or more mineral nutrients and / or vitamins persists in the seedlings transferred to a greenhouse production system and continues to provide advantages such as improved micronutrient and / or vitamin content and / or biomass production, through the further growth of the leafy green plant.

[0112] In some embodiments, plant seedlings transferred to a greenhouse production system may be further treated with LGP2009, LGP2022, LGP2023, LGP2021, LGP2033 or variants thereof, or with one or more other Methylobacterium strains that increase the levels of one or more mineral nutrients and / or vitamins prior to, during or after transfer to the production system.Plants.

[0113] Plant compositions and methods to treat plants include, for example, alfalfa; barley; brassica sp.; cannabis sp.; carrot; cassava; coconut; coffee; conifers; corn; cotton; cucurbits; cucumber; fruit plants (including fruit trees); green bean; herbs; leafy greens; lettuce; microgreens; millet; oat; onion; ornamental; pea; peanut; pepper; potato; rice; rye; safflower; sorghum; soybean; squash; sugar beet; sunflower, sweet potato; tobacco; tomato; turfgrass; and wheat.

[0114] For instance, the following plants are commercially improved by the present invention and included in the present compositions and methods:

[0115] Cereal grain crops: amaranth (pseudocereal), arborio rice, barley, basmati rice, black rice, brown rice, buckwheat (pseudocereal), bulgur, com (maize), durum wheat, emmer, farro, fonio, glutinous rice, jasmine rice, millet, oats, pearl millet, quinoa (pseudocereal), red rice, rye, sorghum, spelt, teff, triticale, wheat, white rice, and wild rice.

[0116] Fruiting vegetables: acom squash, avocado, bell pepper, bitter melon, calabash, cantaloupe, caper berries, chayote, cherry tomato, chili pepper, cucumber, eggplant, gourds, ground cherry, honeydew melon, jicama, kabocha, luffa, okra, pattypan squash, pepino melon, pumpkin, roselle (Hibiscus sabdariffa), snap peas, spaghetti squash, squash, string beans, taro fruit, tomatillo, tomato, watermelon, winter melon, and zucchini.

[0117] Legume vegetables: adzuki bean, black bean, black-eyed pea (cowpea), butter bean, cannellini bean, chickpea (garbanzo bean), cranberry bean, edamame (young soybean), fava bean (broad bean), green bean, hyacinth bean, kidney bean, lentil, lima bean, mung bean, navy bean, pigeon pea, pinto bean, runner bean, snap pea, snow pea, sugar snap pea, winged bean, and yardlong bean.

[0118] Pome fruit: apple, loquat, medlar, nashi pear (Asian pear), pear, and quince.

[0119] Seed crops: amaranth, basil, black cumin, buckwheat, canola, caraway, chia, coriander, cumin, flax, hemp, millet, mustard, nigella, poppy, pumpkin, quinoa, safflower, sesame, squash, sunflower, and watermelon.

[0120] Small fruit crops and berries: aronia (chokeberry), barberry, blackberry, blackcurrant, blueberry, boy senberry, buffaloberry, cloudberry, cranberry, currant, elderberry, feijoa (pineapple guava), fig, gooseberry, grape, huckleberry, jostaberry, juneberry (serviceberry), kiwi, lingonberry, loganberry, mulberry, olallieberry, pomegranate, raspberry, redcurrant, salal berry, saskatoon berry, sea buckthorn, serviceberry (Juneberry), strawberry, tayberry, and white currant.

[0121] Lastly, the following plants are also within the scope of the present invention: For instance, plants include: arugula; azalea; B. juncea; B. napus; B. rapa; basil; beans; beet greens; bentgrass; Bermuda grass; bok choy; broccoli; cabbage; Canada bluegrass; carnation; cauliflower; celery;chickpeas; chicory; clover; collard greens; cover-crops; daffodils; dill; Douglas-fir; endive; escarole; fennel; fescue; finger millet; foxtail millet; French tarragon; fruit; garlic; golf grass; hibiscus; hydrangea; iceberg lettuce; kale; Kentucky bluegrass; leek; loblolly pine; lodgepole pine; melon; Monterey pine; nuts; oats; orchard grass; ornamentals; peanuts; pearl millet; peas; Pennisetum; petunias; pines; poinsettia; pome fruit; ponderosa pine; proso millet; radicchio; radish; redtop; redwood; romaine lettuce; rosemary; roses; ryegrass; Sitka spruce; slash pine; spinach; St. Augustine grass; swiss chard; tea; trees; tropical fruit; turnip greens; tulips; watercress; watermelon; wheatgrass; zoysia grass.Further description of embodiments.

[0122] In certain embodiments, a methanotroph or Methylobacteirum strain used to treat a given cultivar or variety of plant seed, plant or plant part can be a strain that was isolated from a different plant species, or a different cultivar or variety of the plant species being treated, and is thus heterologous or non-resident to the treated plant or plant part.

[0123] In certain embodiments, a manufactured combination composition comprising two or more methanotroph strains or a combination of one or more methanotroph strains with one or more Methylobacterium strains can be used to treat a field, seed or plant part in any of the methods provided herein. Such manufactured combination compositions can be made by methods that include harvesting monocultures of each strain and mixing the harvested monocultures to obtain the manufactured combination composition. In certain embodiments, the manufactured combination composition of one or more methanotrophs and optionally one or more Methylobacterium strains can comprise a methanotroph and Methylobacterium strains isolated from different plant species or from different cultivars or varieties of a given plant.

[0124] In certain embodiments, a manufactured combination composition comprising one or more methanotroph strains and a second biological can be used to treat a field, seed or plant part in any of the methods provided herein. Such manufactured combination compositions can be made by methods that include harvesting monocultures of each strain and mixing the harvested monocultures to obtain the manufactured combination composition of methanotrophs. In certain embodiments, the manufactured combination composition of a methanotroph and the second biological can comprise isolates from different plant species or from different cultivars or varieties of a given plant. In certain embodiments, a manufactured combination composition comprising one or more methanotroph strains and a. Methylobacterium can be used to treat a field, seed or plant part in any of the methods provided herein.

[0125] In certain embodiments, an effective amount of the methanotroph or Methylobacterium strain or strains used in treatment of plants, seeds or plant parts is a composition having a titer of at least about IxlO6colony-forming units per milliliter, at least about 5xl06colony-forming units per milliliter, at least about IxlO7colony-forming units per milliliter, at least about 5 x 108colony-forming units per milliliter, at least about I x lO9colony-forming units per milliliter, at least about I x lO10colonyforming units per milliliter, or at least about 3 x IO10colony-forming units per milliliter. In certain embodiments, an effective amount of the strain or strains is a composition with the methanotroph at a titer of about least about IxlO6colony-forming units per milliliter, at least about 5xl06colony-forming units per milliliter, at least about IxlO7colony-forming units per milliliter, or at least about 5 x 108colony-forming units per milliliter to at least about 6 x IO10colony-forming units per milliliter of a liquid or an emulsion. In certain embodiments, an effective amount of the methanotroph strain or strains is a composition with the methanotroph at least about IxlO6colony-forming units per gram, at least about 5xl06colony-forming units per gram, at least about IxlO7colony-forming units per gram, or at least about 5 x 108colony-forming units per gram to at least about 6 x 1010colony-forming units of methanotroph per gram of the composition. In certain embodiments, an effective amount of a composition provided herein can be a composition with a methanotroph titer of at least about IxlO6colony-forming units per gram, at least about 5xl06colony-forming units per gram, at least about IxlO7colony-forming units per gram, or at least about 5xl08colony-forming units per gram to at least about 6xlO10colony-forming units of methanotroph per gram of particles in the composition containing the particles that comprise a solid substance wherein a mono-culture or co-culture of methanotroph strain or strains is adhered thereto. In certain embodiments, an effective amount of a composition provided herein to a plant or plant part can be a composition with a methanotroph titer of at least about IxlO6colony-forming units per mL, at least about 5xl06colony-forming units per mL, at least about IxlO7colony-forming units per mL, or at least about 5 x 108colony-forming units per mL to at least about 6 x IO10colony-forming units of methanotroph per mL in a composition comprising an emulsion wherein a mono-culture or co-culture of a methanotroph strain or strains adhered to a solid substance is provided therein or grown therein. In certain embodiments, an effective amount of a composition provided herein can be a composition with a methanotroph titer of at least about IxlO6colony-forming units per mL, at least about 5xl06colony-forming units per mL, at least about IxlO7colony-forming units per mL, or at least about 5 x 108colony-forming units per mL to at least about 6 x IO10colony -forming units of methanotroph per mL in a composition comprising an emulsion wherein a mono-culture or co-culture of a methanotroph strain or strains is provided therein or grown therein. Where a second biological, such as a Methylobacterium strain is present in the composition, the second biological will be present at similar titers as noted above for methanotrophs.

[0126] In certain embodiments, an effective amount of a methanotroph strain or strains that provides for mitigation of green-house gas emissions is at least about 103, 104, 105, or 106CFU per seed or treated plant part. In certain embodiments, an effective amount of methanotroph provided in a treatment of a seed or plant part is at least about 103, 104, 105, or 106CFU to about 107, 108, 109, or IO10CFU per seed or treated plant part. In certain embodiments, the effective amount of methanotroph provided in a treatment of a seed or plant part is an amount where the CFU per seed or treated plant part will exceed the number of CFU of any resident naturally occurring methanotroph strain by at least 5-, 10-, 100-, or 1000-fold. In certain embodiments, the effective amount of methanotroph provided in a treatment of a seed or plant part is an amount where the CFU per seed or treated plant part will exceed the number of CFU of any resident naturally occurring methanotroph by at least 2-, 3-, 5-, 8-, 10-, 20- , 50-, 100-, or 1000-fold. In certain embodiments where the treated plant is cultivated in a hydroponic system, populations of naturally occurring methanotroph or other soil microbes will be minimal.Additional Embodiments

[0127] Some methanotrophs are present in soil samples that are collected from various sources, particularly rice fields. For example NLS1501 is known to be present at a detectable level in soil samples prior to addition of an isolated NLS 1501 sample. Even though the sample contains a detectable level of a methanotroph, treating the soil or plants grown in the soil with a known titer of the methanotroph shows significant improvement in plant growth and / or mitigation in methane release.

[0128] In certain embodiments, a methanotrophic bacteria is a Type II (Alphaproteobacteria) strain that comprises a pMM02 methane monooxygenase encoded by an operon comprising expression sequences for pMM02 protein components PmoA2, PmoB2 and PmoC2. In some embodiments, the Type II methanotroph is a Methylocystis species. In some embodiments, a methanotroph provided herein is a Methylocystis species selected from M. hirsuta, M. rosea and M. parvus. In some embodiments a methanotroph provided herein is a Methylocystis hirsuta isolate comprising PmoA2, PmoB2 and PmoC2 protein sequences of SEQ ID NOS: 76-78 or SEQ ID NOS: 79-81. In some embodiments, a Methylocystis hirsuta strain comprises a pMM02 monooxygenase having PmoA2, PmoB2 and PmoC2 proteins with sequences at least 97%, 98%, or 99% identical to SEQ ID NOS:76- 78 or SEQ ID NOS: 79-81. In some embodiments Methylocystis isolate is selected from the group consisting of NLS1505, NLS1506, NLS1508, NLS1509, NLS1511, NLS1512, NLS1546, NLS1561, NLS1581, NLS1591, NLS1597, NLS1601, variants thereof, or combinations thereof. In some embodiments, the Type II methanotroph is a Methylosinus species. In some embodiments, a Methylosinus species is NLS1563, NLS1578, or NLS1618.

[0129] Also provided are isolated methanotroph strains NLS1501, NLS1504, NLS1505, NLS1506, NLS1508, NLS1509, NLS1511, NLS1512, NLS1561, NLS1563, NLS1564, NLS1578, NLS1581, NLS1546, NLS1557, NLS1558, NLS1572, NLS1591, NLS1597, NLS1601, and NLS1618. In certain embodiments the methanotrophic bacteria in the composition has the ability to mitigate methane directly by oxidation of methane by pMMO. In some embodiments, Methylocystis hirsuta bacterial strains provided herein comprise sMMO proteins in addition to pMMO proteins. In some embodiments, methanotrophic bacterial strains facilitate oxidation of CH4 into methanol (CH3OH) followed by the incorporation of that carbon into bacterial biomass, or its oxidation to CO2 and H2O.

[0130] In some embodiments, methanotroph strains in the methods and compositions provided herein are Type I (Gammaproteobacter) strains. In some embodiments, Type I methanotrophs are species of Methylomicrobium or Methylosarcina. In some embodiments, a Methylomicrobium isolate comprises a PmoA protein at least 97%, 98%, or 99% identical to SEQ ID NO:83 or SEQ ID NO:84. In some embodiments, a Methylomicrobium isolate comprises a PmoB protein at least 97%, 98%, or 99% identical to SEQ ID NO:85 or SEQ ID NO:86. In some embodiments, Methylomicrobium isolate comprises a PmoC protein at least 97%, 98%, or 99% identical to SEQ ID NO:87 or SEQ ID NO:88. In some embodiments, Methylosarcina isolate comprises a PmoA protein at least 97%, 98%, or 99% identical to SEQ ID NO: 89, SEQ ID NO: 90 or SEQ ID NO:91. In some embodiments, a Methylosarcina isolate comprises a PmoB protein at least 97%, 98%, or 99% identical to SEQ ID NO:92 or SEQ ID NO:93. In some embodiments, a Methylosarcina isolate comprises a PmoC protein at least 97%, 98%, or 99% identical to SEQ ID NO:94, SEQ ID NO:95 or SEQ ID NO:96. In some embodiments the methanotrophs are isolates of Methylomicrobium lacus o Methylosarcina fibrata. In some embodiments, a Methylomicrobium lacus isolate is NLS1501. In some embodiments a Methylosarcina fibrata isolate is NLS1504. In some embodiments, methanotroph bacterial strains provided herein comprise sMMO proteins in addition to pMMO proteins. In some embodiments, a methanotroph strain for use in the compositions and methods provided herein comprises a 16S encoding sequence of any one of SEQ ID NO: 118-120.

[0131] In certain embodiments, the methanotroph in the composition is NLS1501, NLS1504, NLS1505, NLS1506, NLS1508, NLS1509, NLS1511, NLS1512, NLS1561, NLS1563, NLS1564, NLS1578, NLS1581, NLS1546, NLS1557, NLS1558, NLS1572, NLS1591, NLS1597, NLS1601, NLS1618, variants thereof, or a combination thereof. In certain embodiments, the methanotroph in the composition has the ability to use methane as a carbon source for growth.

[0132] Further provided are methods of improving production of plants by treatment with one or more Type II or Type I methanotroph strains provided herein. In certain embodiments, treated plants are grown in a field, an irrigated or flooded field, hvdroponically or in an aeroponic plant cultivationsystem. Such plants can be without limitation, agricultural crop plants, including without limitation corn, soybean, rice, millet, canola, and wheat, fruits and vegetables, leafy green plants, herbs, ornamentals, turf grasses, golf grass, shrubs, and trees. In certain embodiments, the methanotroph in the composition is NLS1501, NLS1504, NLS1505, NLS1506, NLS1508, NLS1509, NLS1511, NLS1512, NLS1561, NLS1563, NLS1564, NLS1578, NLS1581, NLS1546, NLS1557, NLS1558, NLS1572, NLS1591, NLS1597, NLS1601, NLS1618, variants thereof, or a combination thereof.

[0133] In some embodiments, a treated plant is a corn or rice plant and the methanotroph is selected from the group consisting of NLS1501, NLS1504, NLS1505, NLS1506, NLS1508, NLS1509, NLS1511, NLS1512, NLS1561, NLS1563, NLS1564, NLS1578, NLS1581, NLS1546, NLS1557, NLS1558, NLS1572, NLS1591, NLS1597, NLS1601, NLS1618, variants thereof, and combinations thereof. In some embodiments, a treated plant is a corn or rice plant and the methanotroph is NLS 1501 , NLS1504 or NLS1508. In some embodiments, production is improved by enhanced early growth of treated plants or plants grown from treated seeds in comparison to an untreated control plant or in comparison to a control plant grown from an untreated seed. Such enhanced early growth is measured, for example, by an increase in biomass of treated plants, including increased shoot, leaf, root, or whole seedling biomass. Increased early growth can result in various improvements in plant production, including for example increased biomass production or yield of harvested plants, increased and / or more uniform fruit production, faster seed set, earlier maturation, increased rate of leaf growth, increased rate of root growth, increased seed yield, and decreased cycle time in comparison to an untreated control plant or in comparison to a control plant grown from an untreated seed. In certain embodiments, application of methanotroph strains as provided herein provides for a 1%, 2%, 3%, 4%, 5%, 6%, 7%, 8%, 9%, 10%, 12%, 15%, 17%, 20%, 30% or 40% increase in any of the aforementioned traits in comparison to an untreated control plant or in comparison to a control plant grown from an untreated seed. In some embodiments, production is enhanced by increased rooting, for example of plant cuttings, where such increased rooting can result in decreased cycling time and / or increased biomass or yield of the treated plants.

[0134] In some embodiments of methods provided herein, a pasture, wasteland or field is treated. In some embodiments of methods provided herein, treatment is done in a waste facility. In some embodiments of method provided herein, the field is flooded or irrigated. In some embodiments of the method provided herein, a plant seed is treated. In certain other embodiments, a plant seedling or part thereof is treated. In some embodiments, a plant shoot or seedling is treated.

[0135] Various methods for identifying a methanotroph strain that mitigates methane are also provided herein. In one method, a wetland, field, plant, plant part or seed is treated with at least a first methanotroph strain and methane emissions measured and compared to emissions from control strainsand / or other tested strains to identify strains that mitigate methane. In some embodiments, a control strain is a Methylocystis strain that does not contain pMM02, such as NLS1500. In some embodiments, a methanotroph strain useful for methane mitigation comprises genetic elements encoding one or more of the PmoA, PmoB and PmoC proteins provided herein as SEQ ID NOS:76- 96. In some embodiments, a genetic element encoding a PmoA, PmoB and PmoC protein has a nucleotide sequence of SEQ ID NOS:97-117. In some embodiments, a methanotroph strain useful for methane mitigation comprises a 16S sequence of SEQ ID NO: 118-120.

[0136] Compositions described herein may comprise consortia of methanotroph. Consortia of methanotroph can comprise 2, 3, 4, 5, 6, 7, 8, 9, 10, or more strains of methanotrophic bacteria, wherein the strains are capable of using methane as a carbon source for growth.

[0137] In some embodiments of compositions and methods provided herein, a combination of a methanotroph strain and one or more methylotroph bacterial strains are employed to improve plant production and / or mitigate methane. In some embodiments, useful methyl otrophic bacterial strains are from a species selected from the group consisting of Methylobacterium, Methylorubrum, Hyphomicrobiiim. Me thy lophilus, Melhylobacilhis, Methylophaga, Aminobacler, Methylorhabdus, Methylopila, Methylosulfonomonas, Marinosulfonomonas, Paracoccus, Xanthobacter, Ancylobacter (also known as Microcyclus), Thiobacillus, Rhodopseudomonas, Rhodobacter, Acetobacter, Bacillus, Mycobacterium, Arthobacter, and Nocardia. In some embodiments, methylotrophic bacteria in the compositions and methods provided herein are species of Methylobacterium or Methylrubrum. As shown herein, application to plants of compositions comprising methanotrophs and methyltrophs, such as Methylobacterium o Methylrubrum, results in methane mitigation and enhanced growth and yield of treated plants. Without being limited by way of explanation, methylotrophic bacteria may enhance growth and yield of treated plants directly, but may also enhance growth and activity of applied methanotroph strains by consuming compounds (for example, waste products) produced by methanotrophs, thus allowing the methanotrophs to grow and function more efficiently. In some embodiments, a methylotroph that enhances activity of a methanotrophic bacteria is a Methylobacterium strain provided in Table 1A. In some embodiments the Methylobacterium strain is aM radiotolerans, M. extorquens or aM populi strain. In some embodiments, the Methylobacterium strain is selected from the group consisting of LGP2019 (NRRL B-67743), LGP2020 (NRRL-B- 67892), and NLS7725

[0138] In some embodiments, a composition comprising one or more methanotroph and methane oxidizing Methylobacterium strains that mitigate or decrease methane from agriculture lands, also impart a trait improvement to said plant selected from increased biomass production, decreased cycle time, increased rate of leaf growth, decreased time to develop two true leaves, increased rate of rootgrowth, increased nutrients, and increased seed yield. In some embodiments, additional trait improvements are provided by the presence of nif genes for nitrogen fixation in a methanotroph strain. In some embodiments, enhanced nitrogen use efficiency is provided by a Methylobacterium strain. In some embodiments a Methylobacterium strain that enhances nitrogen use efficiency is selected from the group consisting of LGP2001 (NRRL B-50930), LGP2002 (NRRL B-50931), LGP2009 (NRRL B-50938), LGP2015 (NRRL B-67340), LGP2016 (NRRL B-67341), LGP2017 (NRRL B-67741), LGP2018 (NRRL B-67742), LGP2019 (NRRL B-67743), NLS0693 (NRRL B-67926), LGP2167 (NRRL B-67927), LGP2020 (NRRL-B-67892), LGP2021 (NRRL-B-68032), LGP2022 (NRRL-B- 68033), LGP2023 (NRRL-B-68034), LGP2029 (NRRL B-68065), LGP2030 (NRRL B-68066), LGP2031 (NRRL B-68067), LGP2033 (NRRL B-68068), LGP2034 (NRRL B-68069), NLS0665 (NRRL B-68194), NLS0754 (NRRL B-68197), NLS0672 (NRRL B-68196), NLS0729 (NRRL B- 68195), NLS0049 (NRRL-B-68236), NLS0591 (NRRL-B-68215), NLS0439 (NRRL-B-68216), NLS1310 (NRRL-B-68217), NLS1312 (NRRL-B-68218), NLS0612 (NRRL-B-68237), NLS0706 (NRRL-B-68238), NLS0725 (NRRL-B-68239), NLS7725, and variants thereof.

[0139] In some embodiments, methanotrophic bacterial strains and / or methylotroph strains in compositions provided herein contribute to methane mitigation by impacting other microbial populations and / or the activity of other microbes in a plant environment or other environment where methane is present. For example growth and activity of methanotrophs present in an environment is enhanced and / or activity and / or populations of methanogens in the environment are decreased. In some embodiments, treatment with a methanotroph strain provides for an increase in the total methanotroph populations. In some embodiments, a plant is treated and an increase in methanotroph population in the root rhizosphere is obtained. In some embodiments, a treated plant is a rice plant. In some embodiments, a methanotroph that results in increased total methanotroph populations in the root rhizosphere of a plant is a Methylocystis strain. In some embodiments, the plant is a rice plant. In some embodiments, treatment with a methylotroph strain provides for an increase in the ratio of methanotrophs to methylotrophs in the environment and resulting reduction in methane emissions. In some embodiments, a methylotroph strain that provides for an increase in the ratio of methanotrophs to methylotrophs is a Methylobacterium or Methylorubrum strain disclosed in Table 1 A. In some embodiments, a strain that provides for an increase in the ratio of methanotrophs to methylotrophs is a strain deposited as NRRL B-67892.

[0140] Also disclosed is a method for selecting a methanotroph isolate capable of utilizing methane as a food source, wherein the method comprises (a) selecting a methanotroph isolate; (b) isolating the methanotroph isolate; (c) detecting in the genome of the methanotroph isolate, a genetic element, wherein the genetic element comprises a component of a particulate methane monooxygenase; (d)treating a field, water, plant, plant part or seed with the methanotroph isolate, and (e) measuring greenhouse gas emissions. In some embodiments, a treated plant is grown in a low methane environment to identify reduction in methane gas. In further embodiments, additional plant production improvements, including enhanced plant growth and yield, are evaluated in such a method. In some embodiments, enhanced plant growth and yield resulting from treatment with one or more methanotrophs is evaluated for plants growing in a high methane environments. In some embodiments, a low methane environment is one in which methane gas is produced at less than 20 kg / acre. In some embodiments, a high methane environment is one in which methane gas is produced at greater than 100 kg / acre. In this manner, a methanotroph strain or strains is identified and selected, wherein the strain provides for reduction of methane produced during growth of a treated cultivated plant or a plant part in comparison to an untreated control plant or plant part. Such methods may also be used for identification of combinations of one or more methanotroph and methylotroph strains that reduce methane emissions and enhance plant growth and biomass.

[0141] In other embodiments, the ability of a methanotroph strain or a combination of one or more methanotroph and methylotroph strains to enhance nitrogen use efficiency (NUE) and enhance growth of treated plants as a results of increased NUE are identified. In some embodiments, a rice seed is treated. In some embodiments, field, plants, seeds or seedlings are separately treated with two, three, four or more methanotroph strains and growth and nitrogen content are compared for plants or plant parts treated with different strains, and a methanotroph strain or strains demonstrating increased yield or nitrogen content and / or increased growth under nitrogen limited conditions is selected and identified as providing for enhanced nitrogen use efficiency. In other embodiments, methanotroph strains are applied to seeds for planting and plants grown under nitrogen limited conditions are harvested to determine effect of the strain on plant yield.

[0142] Various methods of using methanotrophic bacteria or a combination of a methanotroph strain and Methylobacterium strains to mitigate methane, enhance early growth or rooting, improve propagation / transplant vigor, increase nutrient uptake, improve stand establishment, improve stress tolerance and / or increase a plant’s ability to uptake and / or utilize nutrients, such as nitrogen, potassium, sulfur, cobalt, copper, zinc, phosphorus, boron, iron and manganese in plants, such as leafy green plants, row crops, ornamentals, turf grasses, golf grasses, shrubs, cannabis and other specialty crops are provided herein. In certain embodiments, methanotroph treatment of a row crop, including but not limited to corn, soybean, rice, millet, canola, and wheat, results in enhanced plant growth and yield. In some embodiments, a methanotroph strain is NLS1501, NLS1504 or NLS1508 and a methylotroph strain is LGP2019 (NRRL B-67743), LGP2020 (NRRL-B-67892) orNLS7725. In some embodiment, a methytroph is a species selected from the group consisting of M. radiotolerans, M.populi and M. extorquens. In some embodiments, a methylotroph strain in the methods and compositions provided herein is selected from the group consisting of LGP2002 (NRRL B-50931), LGP2003 (NRRL B-50932), LGP2004 (NRRL B-50933), LGP2009 (NRRL B-50938), LGP2015 (NRRL B-67340), LGP2016 (NRRL B-67341), LGP2017 (NRRL B-67741), LGP2019 (NRRL B- 67743), NLS0693 (NRRL B-67926), LGP2020 (NRRL-B-67892), and NLS7725. In some embodiments, a methanotroph is NLS1508 and a methylotroph is LGP2019 (NRRL B-67743). In some embodiments, a methanotroph is NLS1501 and a methylotroph is NLS7725. In some embodiments, a methanotroph is NLS1501 and a methylotroph is LGP2020 (NRRL-B-67892). In certain embodiments, the treated crop is rice and the methanotroph is selected from the group consisting of NLS1501, NLS1504, NLS1505, NLS1506, NLS1508, NLS1509, NLS1511, NLS1512, NLS1561, NLS1563, NLS1564, NLS1578, NLS1581, NLS1546, NLS1557, NLS1558, NLS1572, NLS1591, NLS1597, NLS1601, NLS1618, variants thereof, or a combination thereof. In certain embodiments, a treatment includes a methanotroph and one or more Methylotroph listed in Table 1A and / or a Methanotroph in Table IB. In certain embodiments, a treatment includes a methanotroph and one or more Methylobacterium, wherein the one or more Methylobacterium mitigates methane and / or enhances rice yield. A Methylobacterium strain that mitigates methane is selected from the group consisting of NLS0707, NLS0737, NLS5278, NLS5334, NLS5480, NLS5549, and variants thereof. A Methylobacterium strain that enhances rice yield is selected from the group consisting of LGP2016, LGP2017, LGP2019, and LGP2020. In certain embodiments, methanotroph treatment of soil, agriculture land, including a field or a flooded and irrigated field, a seed, a leaf, a stem, a root, or a shoot can enhance early growth, propagation / transplant vigor, stand establishment, and / or stress tolerance as well as or alternatively enhance nutrient use efficiency.

[0143] In some embodiments, a methanotroph is NLS1508 and a methylotroph is LGP2019 (NRRL B-67743), in some embodiments, a methanotroph is NLS1508 and a methylotroph is LGP2020 (NRRL-B-67892), in some embodiments, a methanotroph is NLS1508 and a methylotroph is NLS7725. In some embodiments, a methanotroph is NLS 1501 and a methylotroph is LGP2019 (NRRL B-67743), in some embodiments, a methanotroph is NLS 1501 and a methylotroph is LGP2020 (NRRL-B-67892), in some embodiments, a methanotroph is NLS 1501 and a methylotroph is NLS7725. In some embodiments, a methanotroph is NLS 1504 and a methylotroph is LGP2019 (NRRL B-67743), in some embodiments, a methanotroph is NLS 1504 and a methylotroph is LGP2020 (NRRL-B-67892), in some embodiments, a methanotroph is NLS 1504 and a methylotroph is NLS7725. In some embodiments, a methanotroph is NLS1501 and a methylotroph is NLS7725. In some embodiments, a methanotroph is NLS1501 and a methylotroph is LGP2020 (NRRL-B-67892). In some embodiments, a methanotroph is NLS 1508 and a methylotroph is LGP2019 (NRRL B-67743).In some embodiments, a methanotroph is NLS1501 and a methylotroph is NLS7725. In some embodiments, a methanotroph is NLS1501 and a methylotroph is LGP2020 (NRRL-B-67892).

[0144] Variants of a Methylobacterium or methanotroph isolate listed in Table 1 A and / orTable IB include isolates obtained therefrom by genetic transformation, mutagenesis and / or insertion of a heterologous sequence. In some embodiments, such variants are identified by the presence of chromosomal genomic DNA with at least 99%, 99.9%, 99.8%, 99.7%, 99.6%, or 99.5% sequence identity to chromosomal genomic DNA of the strain from which it was derived.

[0145] In certain embodiments of the methods provided herein, the Methylobacterium strain or methanotroph strain or strains used to treat a plant seed and / or a plant part are selected from the group consisting of LGP2000 (NRRL B-50929), LGP2001 (NRRL B-50930), LGP2002 (NRRL B-50931), LGP2003 (NRRL B-50932), LGP2004 (NRRL B-50933), LGP2005 (NRRL B-50934), LGP2006 (NRRL B-50935), LGP2007 (NRRL B-50936), LGP2008 (NRRL B-50937), LGP2009 (NRRL B- 50938), LGP2010 (NRRL B-50939), LGP2011 (NRRL B-50940), LGP2012 (NRRL B-50941), LGP2013 (NRRL B-50942), LGP2014 (NRRL B-67339), LGP2015 (NRRL B-67340), LGP2016 (NRRL B-67341), LGP2017 (NRRL B-67741), LGP2018 (NRRL B-67742), LGP2019 (NRRL B- 67743), NLS0497 (NRRL B-67925), NLS0693 (NRRL B-67926), NLS1179 (NRRL B-67929), LGP2167 (NRRL B-67927), LGP2020 (NRRL B-67892), LGP2021 (NRRL-B-68032), LGP2022 (NRRL-B-68033), LGP2023 (NRRL-B-68034), LGP2028 (NRRL B-68064), LGP2029 (NRRL B- 68065), LGP2030 (NRRL B-68066), LGP2031 (NRRL B-68067), LGP2033 (NRRL B-68068), LGP2034 (NRRL B-68069), NLS0665 (NRRL-B-68194), NLS0729 (NRRL-B-68195), NLS0672 (NRRL-B-68196), NLS0754 (NRRL-B-68197), NLS0049 (NRRL-B-68236), NLS0591 (NRRL-B- 68215), NLS0439 (NRRL-B-68216), NLS1310 (NRRL-B-68217), NLS1312 (NRRL-B-68218), NLS0612 (NRRL-B-68237), NLS0706 (NRRL-B-68238), NLS0725 (NRRL-B-68239), NLS7725, NLS0770 (NRRL-B-68075), NLS0737 (NRRL-B-68074), NLS5278 (NRRL-B-68186), NLS5334 (NRRL-B-68187), NLS5480 (NRRL-B-68188), NLS5549 (NRRL-B-68189), NLS1501, NLS1504, NLS1505, NLS1506, NLS1508, NLS1509, NLS1511, NLS1512, NLS1561, NLS1563, NLS1564, NLS1578, NLS1581, NLS1546, NLS1557, NLS1558, NLS1572, NLS1591, NLS1597, NLS1601 (NRRL B-68347), NLS1618 (NRRL B-68348), variants thereof, or any combination thereof. In certain embodiments, one or more of the Methylobacterium strains used in the methods can comprise total genomic DNA (chromosomal and plasmid DNA) or average nucleotide identity (ANI) with at least 99%, 99.9, 99.8, 99.7, 99.6%, or 99.5% sequence identity or ANI to total genomic DNA of LGP2000 (NRRL B-50929), LGP2001 (NRRL B-50930), LGP2002 (NRRL B-50931), LGP2003 (NRRL B- 50932), LGP2004 (NRRL B-50933), LGP2005 (NRRL B-50934), LGP2006 (NRRL B-50935), LGP2007 (NRRL B-50936), LGP2008 (NRRL B-50937), LGP2009 (NRRL B-50938), LGP2010(NRRL B-50939), LGP2011 (NRRL B-50940), LGP2012 (NRRL B-50941), LGP2013 (NRRL B- 50942), LGP2014 (NRRL B-67339), LGP2015 (NRRL B-67340), LGP2016 (NRRL B-67341), LGP2017 (NRRL B-67741), LGP2018 (NRRL B-67742), LGP2019 (NRRL B-67743), NLS0497 (NRRL B-67925), NLS0693 (NRRL B-67926), NLS1179 (NRRL B-67929), LGP2167 (NRRL B- 67927), LGP2020 (NRRL B-67892), LGP2021 (NRRL-B-68032), LGP2022 (NRRL-B-68033), LGP2023 (NRRL-B-68034), LGP2028 (NRRL B-68064), LGP2029 (NRRL B-68065), LGP2030 (NRRL B-68066), LGP2031 (NRRL B-68067), LGP2033 (NRRL B-68068), LGP2034 (NRRL B- 68069), NLS0665 (NRRL-B-68194), NLS0729 (NRRL-B-68195), NLS0672 (NRRL-B-68196), NLS0754 (NRRL-B-68197), NLS0049 (NRRL-B-68236), NLS0591 (NRRL-B-68215), NLS0439 (NRRL-B-68216), NLS1310 (NRRL-B-68217), NLS1312 (NRRL-B-68218), NLS0612 (NRRL-B- 68237), NLS0706 (NRRL B-68238), NLS0725 (NRRL-B-68239), NLS0770 (NRRL-B-68075), NLS0737 (NRRL-B-68074), NLS5278 (NRRL-B-68186), NLS5334 (NRRL-B-68187), NLS5480 (NRRL-B-68188), or NLS5549 (NRRL-B-68189). In certain embodiments, one or more of the methanotroph strains used in the methods can comprise total genomic DNA (chromosomal and plasmid DNA) or average nucleotide identity (ANI) with at least 99%, 99.9, 99.8, 99.7, 99.6%, or 99.5% sequence identity or ANI to total genomic DNA of NLS1501, NLS1504, NLS1505, NLS1506, NLS1508, NLS1509, NLS1511, NLS1512, NLS1561, NLS1563, NLS1564, NLS1578, NLS1581, NLS1546, NLS1557, NLS1558, NLS1572, NLS1591, NLS1597, NLS1601, or NLS1618. In certain embodiments, the percent ANI can be determined as disclosed by Konstantinidis etal., 2006. In certain embodiments of the methods provided herein, a methanotroph strain or strains used to treat soil, water, a plant, a seed and / or a plant part is NLS1501, NLS1504, NLS1505, NLS1506, NLS1508, NLS1509, NLS1511, NLS1512, NLS1561, NLS1563, NLS1564, NLS1578, NLS1581, NLS1546, NLS1557, NLS1558, NLS1572, NLS1591, NLS1597, NLS1601, or NLS1618.EXAMPLES

[0146] The following examples are given for purely illustrative and non-limiting purposes of the present invention.Example 1.Example 1 A: Early Growth Promotion - Methylotrophs - Greenhouse - Rice

[0147] Methylobacterium isolates were tested for their ability to enhance early growth of rice seedlings. A randomized complete block design was used, with 12 treatments in each run; 10 unique Methylobacterium isolates, a Methylobacterium positive control, LGP2018, that demonstrated consistent root growth promotion of rice seedlings during assay development and increased yield levels in corn field trials (W02020117690). The untreated control sample (UTC) was Methylobacteriumgrowth medium applied in the same amount as used for the Methylobacterium isolates. Each treatment level had an n of 10. All 10 blocks were grown in the same growth chamber, and on the same shelf.

[0148] Inoculation: Each Methylobacterium isolate or the culture medium control was applied as an 80uL streak to the bottom portion of the plate (one isolate per plate) and spread by gently tilting the plate back and forth. A target concentration of 1 x 106CFU per seed was applied. Plates were allowed to dry for at least on hour and placed in a randomized layout in a Percival growth chamber set to 25°C and 16 hour days. Seeds were allowed to grow undisturbed for 8 days.

[0149] Harvest: At 8 days after plating the plates were removed from the growth chambers, and the plants (approximately V2 stage) were measured as follows. Plants that were not impeded from growing normally (by physical surroundings unrelated to presence of Methylobacterium) were removed from plates, and the number of seedlings for that plate recorded. Seedlings were scanned using WinRhizo and the images analyzed to determine root length for each plant.

[0150] The results of this experiment are shown below in Table 2.Table 2. Early Growth Promotion - Methylotrophs - Greenhouse - RiceExample IB. Gene correlation - Methylotrophs - Identification.

[0151] Forty-eight Methylobacterium strains were selected for gene correlation analysis from the 176 strains tested, including 15 non-hits and 33 hits. The strains were selected from those having the highest and lowest normalized root scores, excluding any isolates that had any signs of any type of microbial contamination. The normalized score standardized each isolate's mean root length value to the UTC (a value of 0) and the positive control, LGP2018 (a value of 100).

[0152] Genomes of the selected isolates were assembled and putative genes identified. The genes were assigned a putative function by sequence analysis to databases of known genes and gene signatures. A pan-genome for Methylobacterium was constructed as described by Page et al. (Roary: rapid large- scale prokaryote pan genome analysis, Bioinformatics (2015) 31 :3691-3693) except that genome sequences from greater than 1000 different species of Methylobacterium were assembled and used to construct the pan-genome as opposed to the single Salmonella species described by Page et al.

[0153] The genomes of strains identified as enhancing rice seedling growth, “hits”, and strains identified as “non-hits”, were compared to determine the presence or absence in each strain of each genetic element in the pan-genome. For this analysis, translated genes were clustered across strains using BLASTP with a sequence identity of at least 50% to identify homologous genetic elements across genomes. These results were used to determine which genetic elements are the same or different across strains, leading to a score for each genetic element as present or absent in a given strain. The presence / absence scores were used in a correlation analysis to identify genetic elements that correlate positively with enhancing rice seedling growth as described by Brynildsrud et al. (Rapid scoring of genes in microbial pan-genome-wide association studies with Scoary, Genome Biology (2016) 17:238).

[0154] The steps in the process were as follows. Correlated genetic elements were collapsed so that genes that are typically inherited together, for example genes on the same plasmid, were combined into a single unit. Each genetic element in the pan-genome received a null hypothesis of no association to the trait. A Fisher’s exact test was performed on each genetic element with the assumption that all strains had a random and independently distributed probability for exhibiting each state, i.e. presence or absence of the genetic element. To control spurious associations due to population structure, the pairwise comparisons algorithm was applied using a phylogenetic tree of the Methylobacterium genus, constructed using the same genome sequences described above. Empirical - value was computed using label-switching permutations, i.e. the test statistic was generated over random permutations of the phenotype data. The genetic elements that were significantly positively correlated with enhancing rice seedling root growth were identified based on p value using a threshold for statistical significance ofp less than or equal to 0.05. Sensitivity and specificity cutoffs were also employed based on the number of hits and non-hits a gene was present in.

[0155] Gene elements that were positively correlated Methylobacterium enhancement of growth in rice seedlings are shown in Table 3 A below.Table 3 A. Gene correlation - Methylotrophs - Identification.

[0156] Methylobacterium consensus protein sequences for the above identified genes that positively correlate with enhanced growth or rice seedlings are provided as SEQ ID NO: 17 through SEQ ID NO:23 disclosed in the Sequence Listing. Consensus sequences are generated by aligning the encoded protein sequences from all isolates from a comprehensive database of Methylobacterium genome sequences from public and internal databases. EMBOSS cons was used to generate consensus sequences from the multiple sequence alignment. Where no consensus was found at a position an 'x' character is used. An upper case letter for an amino acid residue indicates that most of the sequences have that amino acid at that position. In the consensus sequences, X can be any amino acid residue or can be absent.

[0157] Representative amino acid sequences for proteins correlated with enhancing growth of rice seedlings from specific Methylobacterium strains are provided below as SEQ ID NOs: 24-30 and SEQ ID NOs: 123-128. The strain from which a representative sequence was obtained is referenced below in Table 3B.Table 3B. Gene correlation - Methylotrophs - Identification.Example 1C. Nitrogen Utilization / Growth Metrics - Methylotrophs - Greenhouse - Rice.

[0158] Methylobacterium isolates were tested for their ability to enhance shoot nitrogen content and / or concentration in rice. A randomized complete block design was used, with 12 treatments in each run; five Methylobacterium isolates and a control at two nitrogen levels. The untreated control sample (UTC) was Methylobacterium growth medium applied in the same amount as used for the Methylobacterium isolates. Each treatment level had an n of 10. All 10 blocks were grown in the same growth chamber and on the same shelf.

[0159] Inoculation: Each Methylobacterium isolate or the culture medium control was applied as an 80uL streak to the bottom portion of the plate (one isolate per plate) and spread by gently tilting the plate back and forth. A target concentration of 1 x 106CFU per seed was applied. Plates were allowed to dry for at least on hour and placed in a randomized layout in a Percival growth chamber set to 25°C and 16 hour days. Seeds were allowed to grow undisturbed for 8 days.

[0160] Harvest: At 8 days after plating the plates were removed from the growth chambers, and the plants were measured as follows. Plants that were not impeded from growing normally (by physical surroundings unrelated to presence of Methylobacterium) were removed from plates, and the number of seedlings for that plate recorded. Seedlings were scanned using WinRhizo and the images analyzed to determine root and shoot area for each plant. Seedlings were rinsed to remove any remaining plate media and the shoots separated from the seedlings and dried in a drying oven for at least 3 days. Dried shoots were combined for each treatment and the mass measured. The plant material was then ground to a powder to be used for nitrogen testing. Nitrogen analysis was conducted on the powdered samples by Atlantic Microlab (Norcross, GA).

[0161] Results of the analyses are shown below. In all tables, pairwise results are presented separately for the High N and Low N treatments. Data was analyzed using Student’s t-test and different letters indicate a significant difference between treatments at p < 0.05.Table 4. Shoot Area - Nitrogen Utilization / Growth Metrics - Methylotrophs - Greenhouse - Rice.4A Low Nitrogen Treatment 4B High Nitrogen TreatmentTable 5. Root Area - Nitrogen Utilization / Growth Metrics - Methylotrophs - Greenhouse - Rice.5A Low Nitrogen Treatment 5B High Nitrogen TreatmentTable 6. Shoot Nitrogen - Nitrogen Utilization / Growth Metrics - Methylotrophs - Greenhouse - Rice.6A Low Nitrogen Treatment 6B High Nitrogen Treatment

[0162] Significant and substantial shoot growth promotion was observed for some isolates at high nitrogen. Shoot growth promotion was not observed for the Methylobacterium treatments at low nitrogen, consistent with some literature reports which indicate that growth promotion effects from plant-beneficial microbes may not be observed when nutrient availability is too low. Root growth promotion was evident at both nitrogen levels and Root / Shoot ratios are higher under low N than under highN. As expected, plants grown on highN media showed substantially greater shoot N concentration than those grown on low N media. Several Methylobacterium isolates demonstrated significantly enhanced shoot nitrogen concentration under high nitrogen growth conditions. Three isolates, LGP2020, LGP2022 , and LGP2033, demonstrated the greatest enhancements of shoot growth, root growth and shoot nitrogen concentration.

[0163] The above experiment was repeated using four of the same Methylobacterium isolates and one additional isolate. Results were similar to those observed in the first assay and are shown in the tables below. LGP2020 (NRRL-B-67892), LGP2022 (NRRL-B-68033), and LGP2033, again demonstrated enhancements of shoot growth, root growth and shoot nitrogen concentration.Table 7. Shoot Area - Nitrogen Utilization / Growth Metrics - Methylotrophs - Greenhouse - Rice.7 A Low Nitrogen Treatment 7B High Nitrogen TreatmentTable 8. Root Area - Nitrogen Utilization / Growth Metrics - Methylotrophs - Greenhouse - Rice.8A Low Nitrogen Treatment 8B High Nitrogen TreatmentTable 9. Shoot Nitrogen - Nitrogen Utilization / Growth Metrics - Methylotrophs - Greenhouse - Rice.9A Low Nitrogen Treatment 9B High Nitrogen Treatment

[0164] Percent difference between Methylobacterium treatments and UTC at high and low N for 3 different variables: projected root area, projected shoot area and foliar nitrogen concentration, are shown for each experiment. Bold italics are used to denote a statistically significant difference from UTC at / ? < 0.05 using Student’s / -test.Table 10. Percent Differences - Nitrogen Utilization / Growth Metrics - Methylotrophs -Greenhouse - Rice.Example ID. Nitrogen Dose / Growth Metrics - Methylotrophs - Greenhouse - Rice

[0165] The high nitrogen dose in the experiments described above is the amount in 0.5X MS media, a general plant growth medium, and provides the optimal amount of nitrogen for plant growth. To evaluate plant response to Methyl obacterium treatment under various reduced nitrogen levels,including a nitrogen level that approximates the amount of nitrogen in a field treated with a 25-30% reduction of optimal nitrogen level, two low nitrogen dose experiments were conducted.

[0166] Nitrogen doses used for evaluation of effect of Methylobacterium treatment on plant growth were: 5200 uM nitrogen (50% of rice optimal nitrogen level), 7280 uM nitrogen (70% of rice optimal nitrogen level) and 10400 uM nitrogen (100% of rice optimal nitrogen level). Results are shown in Tables 11-13 below. Data was analyzed using Student’ s t-test and different letters indicate a significant difference between treatments at p < 0.05.Table 11. Shoot Area - Nitrogen Dose / Growth Metrics - Methylotrophs - Greenhouse - Rice.Table 12. Root Area - Nitrogen Dose / Growth Metrics - Methylotrophs - Greenhouse - Rice.Table 13. Shoot Nitrogen - Nitrogen Dose / Growth Metrics - Methylotrophs - Greenhouse - Rice.

[0167] Nitrogen doses used for evaluation of effect of Methylobacterium treatment on plant growth were: 1560 uM nitrogen (15% of rice optimal nitrogen level), 2600 uM nitrogen (25% of rice optimal nitrogen level) and 5200 uM nitrogen. (50% of rice optimal nitrogen level). Results are shown in Tables 14-16 below.Table 14. Shoot Area - Nitrogen Dose / Growth Metrics - Methylotrophs - Greenhouse - Rice.Table 15. Root Area - Nitrogen Dose / Growth Metrics - Methylotrophs - Greenhouse - Rice.Table 16 Shoot Nitrogen - Nitrogen Dose / Growth Metrics - Methylotrophs - Greenhouse - Rice.

[0168] Results again demonstrate significant and substantial shoot and root growth promotion and increased levels of shoot nitrogen levels resulting from treatment with Methylobacterium isolates. Shoot area correlated closely to nitrogen levels measured in shoots. Although root area measurements were not observed to be in proportion to increased nitrogen uptake as measured in shoots, additional observations noted that numbers of root tips were increased in line with enhanced nitrogen uptake as measured in shoot nitrogen concentration.Example IE. Yield - Methylotrophs - Field - Rice - Arkansas.

[0169] Rice field trials were conducted at three locations, all near Humphrey, AR, for the purpose of evaluating the effects of three Methylobacterium isolates applied as a seed treatment. Treatments included each Methylobacterium isolate and an untreated control applied to rice seeds with and without a base treatment of insecticide only (active ingredient Clothiandin). The trial was conducted using aRandomized Complete Block Design (RCBD) with 4 reps per location. LGP2016 (NRRL B-67341), LGP2019 (NRRL B-67743) and LGP2017 (NRRL B-67741) were applied to rice seeds at a target concentration of 106CFU / seed.

[0170] The Methylobacterium isolates increased yield in rice field trials as compared to the untreated control both with and without insecticide treatment as shown in the Table below.Table 17. Yield - Methylobacterium - Field - Rice - Arkansas.Table 17. Mean yield (Bu / A) Increase over control and percent increase shown (Bold italics indicates a significant difference at p < 0.05 using Fisher ’s LSD test.)

[0171] Also provided herein are methods of improving growth and yield of rice plants by treating rice plants, plant parts or seeds with one or more Methylobacterium isolates. In some embodiments, harvested seed yield and / or nutrient content of rice plants is improved. In some embodiments, rice seeds are treated and such treatment provides for increased rice seed yield. In some embodiments, the Methylobacterium isolate is selected from the group consisting of LGP2016 (NRRL B-67341), LGP2017 (NRRL B-67741), LGP2019 (NRRL B-67743) and variants of these isolates. Rice plants, plant parts or seeds coated with Methylobacterium isolates and / or compositions are also provided herein. In certain embodiments, the Methylobacterium has chromosomal genomic DNA having at least 99%, 99.9%, 99.8%, 99.7%, 99.6%, or 99.5% sequence identity to chromosomal genomic DNA of LGP2016, LGP2017, or LGP2019. In certain embodiments, the Methylobacterium has genomic DNA comprising one or more polynucleotide marker fragments of at least 50, 60, 100, 120, 180, 200, 240, or 300 nucleotides of SEQ ID NOS: 37-39 or SEQ ID NOS: 25-27.Example IF. Nitrogen Utilization / Growth Metrics - Methylotrophs - Rice.

[0172] Additional Methylobacterium strains, including Methylobacterium strains that caused increased root length during early rice growth from Example 1 were tested for Methylobacterium inoculation effect on nitrogen utilization in rice.

[0173] The experiment was conducted replacing the high and low nitrogen conditions with using 7280 uM nitrogen (70% of rice optimal nitrogen level). Data was analyzed using Student’s t-test todetermine significant differences between strains at p < 0.05 to determine strains that have increased nitrogen uptake compared to untreated control samples.

[0174] Results shown in Table 18 below provide percent differences in foliar N concentration in treated rice plants compared to N levels in untreated seedlings. Foliar tissue was harvested, dried, and assayed for nitrogen concentration via elemental combustion analysis.Table 18. Nitrogen Utilization / Growth Metrics - Methylotrophs - Rice.Example 1G. Isolate growth on methane - Methylotrophs with sMMO genes - laboratory

[0175] Methylobacterium strains and positive and negative controls were grown on ammonium mineral salts (AMS) media plates, and serial dilutions conducted to determine the appropriate dilution for a target range of 30-300 colonies per plate. For the initial sample tube, 20ml of 0.9% saline was added and vortexed for 5 minutes individually using a standard test tube adaptor or up to 6 at a time using a horizontal tube adaptor (SI-V506 for vertical holder). 1 : 10 dilution series were created from initial tube (10E0) to 10E-6. The first time a sample was analyzed, all dilutions were plated to identify the target range of 30-300 colonies per plate. A pure Methylobacterium positive control sample was plated so there was 50-100 colonies per plate.

[0176] After completion of the dilution series, the appropriate dilutions were plated onto AMS agar plates in triplicate, and a spreader was used to spread the cells around the plate. A new sterile plastic spreader was used for each dilution or flame a glass spreader between dilutions. When finished with the previous step, the plates were placed upside down in the acrylic vacuum chamber. A vacuum was applied to create partial vacuum in the gas-tight vessel (typically -15 psig). High-purity methane (99.999%) was added to create an internal vessel pressure of 0 psig. This created a methane:air ratio of~l:2.

[0177] After 10 days, the number of colony forming units per sample was counted and recorded. Any plates that had no colonies were returned to the incubator and checked at 14 days and then 21 days if necessary. Growth of strains containing pMMO genes and positive control strains was observed, whereas no growth was observed on negative control plates.Example 8: Sequences of sMMO Genes and Components

[0178] Sequences of genes from representative Methylobacterium strains that encode sMMO protein components are provided in the Tables 19 and 20 below.Table 19. Sequences of sMMO Genes and ComponentsTable 20.Example IE. Yield and Methane Emissions- Methylotrophs - Field - Rice - Argentina

[0179] Mitigation of methane (CH4) emission from the rice crop-soil system was evaluated following the application of NLS0737 and NLS0770 to rice seeds and evaluation of methane levels during the crop season. Two sites near Ita Ibate and Mercedes were used in the testing program. Both locations were in the main rice growing areas in the Corrientes province of Argentina. The plots were installed and cultivated using conventional rice farming operations. Trial layouts are provided below.Table 21. Field Planting - Yield and Methane Emissions- Methylotrophs - Field - Rice - Argentina*33 rows x 17.5 cm**11 rows x 17.5 cmTable 21. Macro plots with replicates. RCBD with 5 true replicates. 2 locations.Table 22. Treatments - Yield and Methane Emissions- Methylotrophs - Field - Rice - Argentina

[0180] Seed treatment and planting process: Rice seeds were treated in rotating drums in small batches. A photographic record of the process and final seed appearance for each treated batch were collected. Seed was treated with base fungicide + insecticide for all treatments ((Acronis (BASF) - thiophanate methyl 36.9% + pyraclostrobin 4.1% or Thiram + Carbendazim + Imacloprid). NLS0737 and NLS0770 were applied at a rate of 62.5 g in 600ml of water / 100 kg of seed for a target of 106CFU per seed. Seed was enumerated for CFU of viable PPFMs and planted within seven days of seed treatment. Both locations were planted using conventional methods on a commonly farmed varietal, IRGA 424 RI seed, at lOOKg / ha.

[0181] Fertilizer was applied pre-plant broadcast using 60 - 100 kg KC1, and 100 kg / ha MAP at planting, in the seed row. Urea was applied pre-irrigation at 100 kg / ha and post irrigation at 50 kg / ha during the spike differentiation stage.

[0182] Untreated check: includes base chemical fungicide / insecticide treatments following farmer standards. Seed included professional seed treatment - all biological treatments were added as over treatments. At Mercedes seed was treated with Thiram + Carbendazim + Imidacloprid. At Ita Ibate the seed was treated with Acronis (BASF) - thiophanate methyl 36.9% + pyraclostrobin 4.1%

[0183] Commercial control: included a biostimulant / biofertilizer treatment on top of the base chemical treatment. Rizoderma (Trichoderma harzianum) was applied per recommended label rate.

[0184] Foliar Spray: Additional treatments were applied as foliar applications using NLS0737 and NLS0770. Conventional backpack spray technologies with a 2 meter boom were used to deliver 125g / acre of the dried powder inoculant (~109CFU per gram) in water at nine gallons / acre and ~20 psig. Applications were made three times throughout the growing season at approximately 15, 35 and 50 days after sowing. Plots were split to allow randomized complete block analysis.

[0185] Pre-plant soil sampling and crop measurements: Soil was analyzed (0-20 centimeteres depth) to determine % organic matter, % total nitrogen, NO3, NFU, pH, complete macro-micro nutrient analysis and cations + EC, and soil texture.

[0186] Crop measurements included early stand count at four and 20-days post first observed emergence in the field. Plant diseases throughout all crop stages were scouted using quantitative incidence and severity scales. Digital images for NDVI and other spectral indices for visual andquantitative assessment of treatment effects were collected using two drone flights at vegetative and reproductive stages with multispectral sensors. Weekly satellite images were analyzed from Planetscope satellite imagery at 3-m resolution for ND VI time series. GPS coordinates at each corner of trial polygons were used to digitize data and analyze statistical comparisons of treatment effects through different spectral indices associated with crop growth and health. Digital elevation models were included in the two field-scale trials to assess elevation effect on crop performance. Grain yield at plot and sub-strip scale were collected by hand. Grain samples containing one kilogram from each block were assessed for grain quality: % whole grain, % broken, % chalky grain. Complete daily weather information and irrigation scheduling and amounts were recorded.

[0187] Methane measurements: Greenhouse gas collections methods were designed and planted in Buenos Aires, Argentina. Gas samples were collected using standard methods recognized by the ICCP following standard GC protocols. Headspace gas samples were analyzed at using dedicated gas chromatography methods on an Agilent Gas Chromatotraphy system. Cylinder head space samples were collected between 9am and 11am. There were 5 samples collected per plot at 15-20-min intervals. A total of 100 samples were collected per time point, from 20 chambers installed per field. Measurements were taken six times during the crop season:1. Early tillering. 5 days after first irrigation, approx. 20 days after emergence - expected peak2. Mid tillering: approx. 35 days after emergence3. Late tillering: 50 days after emergence4. Pre flowering: 65 days after emergence5. Flowering: 80 days after emergence - expected peak6. Advanced grain filling (pre-maturity): 100 days after emergence

[0188] Under paddy rice conditions, peak methane emissions are generally recognized between time points 5 and 6. Response variables include Methane (CH4), Nitrous oxide (N2O) and Carbon Dioxide (CO2), expressed in kg / ha / day. Using the six measurements across the season, a model was fit to estimate total emission in kg / ha during the entire crop cycle.

[0189] Methane Emissions - Methylotrophs - Field - Rice - Argentina

[0190] Peak emission occurred between late tillering and flowering. Total emissions were strongly influenced by temperature fluctuations. Overall lower emission at Ita Ibate vs Mercedes were most likely related to later planting which led to overall lower crop growth, both below and above ground. Average lower temperature & radiation during CH4 measurements combined with significant soil texture differences (Italbate sandier) also contributed to the difference in both methane emissions and reduced yield.

[0191] NLS0737 and NLS0770 showed reductions in CT emissions during peak rice growth at both locations in Argentina. At the Mercedes site, NLS0737 reduced methane emissions 28% (151 kg / ha) and NLS0770 reduced emissions 23% (125 kg / ha). At the Ita Ibate site, NLS0737 reduced methane emissions 7% (19 kg / ha) and NLS0770 reduced emissions 4% (11 kg / ha).Table 23. Methane Emissions- Methylotrophs - Field - Rice - ArgentinaTable 24. Methane Emissions- Methylotrophs - Field - Rice - ArgentinaTable 25. Methane Emissions- Methylotrophs - Field - Rice - Argentina

[0192] Methane measurements showing patterns across dates at the Mercedes locations are provided in Table 26 below. Different letters represent statistically significant differences between treatments at late tillering and flowering stages. The decrease in methane at pre-flowering correlates with the lowest temperature of the season.Table 26. Methane Emissions- Methylotrophs - Field - Rice - Argentina*DAF - days after flooding initiation

[0193] Yield - Methylotrophs - Field - Rice - Argentina

[0194] Rice yield at the Mercedes site was increased over the untreated control 17% by NLS0737 (+27 bu / acre) and 6% by NLS0770 (+9 bu / acre). Due to the delayed planting, the lower solar incidence and the late season rains, the yield from the Ita Ibate site was reduced 44% below the Mercedes site. No differences in yield by treatment were seen in Ita Ibate. At an alpha of 0.15 only the seed treated and sprayed yield from the NLS0737 blocks were considered significantly different from the untreated check. The NLS0737 and the NLS0770 seed treated yields were similar but not different from each other. The NLS0770 seed treated and sprayed blocks were lower, but not significantly different from the untreated check. The biological check blocks were similar to the NLS0737 seed treated and sprayed treatments.Table 27. Yield - Methylotrophs - Field - Rice - Argentina* Seed treatment followed by three folar applications• a Different letters represent statistically significant differences between treatments at a= 0.15Example IF. Yield, Growth Metrics, Methane Emissions - Methanotrophs - Greenhouse - Rice.

[0195] Methanotrophic bacterial strains were evaluated for growth enhancement and methane mitigation in a simulated rice paddy ecosystem in a greenhouse. Methane gas flux from the rice paddy was monitored periodically by the closed-chamber method, and the plants were harvested at maturity to measure yield and biomass. Additional studies evaluated results of application of methanotrophic bacteria in combination with methyl otrophic bacterial strains.

[0196] Rice seeds, Kitaake variety, were planted in 6 cell plug trays, 6 trays per treatment and arranged in a Random Complete Block Design (RCBD) in a greenhouse. Dried / sieved paddy soil was prepared by mixing 1 part paddy soil with 1 part 50 / 50 field soil / sand mixture and wetting before planting. Riceseeds were placed on the soil mixture and covered with a thin layer of sand. Greenhouse conditions were set at 30°C, 14 hour days, and 70% relative humidity with flood tables placed on the floor.

[0197] Plants were grown for approximately two weeks to an average plant height of approximately 10 cm. The four strongest plants from each tray were transplanted to 2 gallon pots containing a simulated flooded rice paddy soil, and a top down foliar spray of the bacterial strain or strains to be tested was applied. Pots containing the simulated flooded rice paddy soil were prepared as follows: a. For “Amended soil”, 50 g of finely milled alfalfa hay was added to a 2 gallon pot without holes.No alfalfa was added for samples containing “Unamended soil.” b . 1 g of 30- 10-30 fertilizer was added. c. 3 kg (approx. 1 gallon) of dry and pulverized paddy soil was added and mixed 1 : 1 with 50 / 50 steam sterilized field soil and sand. d. Steps 2a-2c were respeated for as many pots as necessary. (30 for a typical experiment) e. Soil and hay were gently mixed with gloved hands to incorporate hay evenly through soil. f. The plants were thinned to be transplanted to 1 plant per 6-cell insert by selecting the strongest plant in each cell. g. The four strongest plants were removed from each 6 cell insert and place on the soil surface of the appropriate pot, and arranged in a square with vertices halfway along the radius of the pot. h. The pots were filled to the surface of the root ball with an additional 1kg of 50 / 50 steam sterilized sand / soil mixture. i. dH20 was added until soil is fully hydrated, then continue adding dH20 until the soil was covered by 5 cm of standing water.

[0198] A top-down foliar spray of the appropriate bacterial preparation was applied to each pot (5 reps per treatment), and pots were randomized on a greenhouse flood table in an RCBD.

[0199] Plants were grown to maturity and water added as needed to maintain a 5-7 cm layer of water over the soil. Three weeks after transplant, another foliar application of the bacterial strain or strains to be tested was applied. Fertilizer (1.5 grams of 30-10-10 NPK) was added to each pot at 4 weeks post-transplant.

[0200] Gas headspace sampling was conducted at 3, 4, and 5 weeks after transplant as described below. a. Sampling was done at approximately the same time of day each round (generally at 9 AM) and the sampling sequence was randomized and conducted by block. b. Tables containing the pots were flooded to a depth of 2-3 inches. c. An ambient gas sample (TO) was taken by withdrawing 30 ml of air from the center of the growth chamber.d. A 10 gallon bucket equipped with a gas sampling port and running computer fan was placed over the first pot to be sampled and weighted down. e. The above was repeated for all pots to be measured at time intervals to allow consistent sampling times for each pot. f. Each pot was sampled 20 minutes after placing the gas sampling buckets using a 35 mL plastic syringe positioned into the silicon sampling port. The headspace gas was mixed by gently drawing 10 mL gas into the syringe and evacuating 3x while needle was still in sampling port. g. To obtain the sample, 30 mL gas was drawn into the syringe from the chamber. The syringe was removed from the sampling port and 5 mL of gas was pushed out of syringe before transferring the remaining 25 mL of headspace gas to a labeled silicon sealed 12 mL glass exetainer vial. h. The above was repeated for the remaining pots. The plastic syringe was flushed with ambient air 3x before drawing headspace gas from chamber to clean plastic syringe with any contamination from the previous flux chamber. Each pot was sampled 20 minutes after its lid was originally sealed. i. Sampling was repeated at 40 and 60 minutes after sealing the pots. j . Exetainers® were labeled with unique identifiers and analyzed to determine gas content.

[0201] Plants were harvested when they reached the Hard Dough stage to determine yield and biomass. For each pot, all panicles were removed by cutting at the base. After panicles were removed, all foliar tissue was cut at the soil surface. Collected panicles and foliar tissue was dried (50°C oven for 4-7 days) and weighed to determine biomass.Table 28. Methane Emissions - Methanotrophs - Greenhouse - Rice.

[0202] A significant reduction in methane was observed following treatment of rice plants grown in unamended soil, a low methane environment, with both NLS1501 and NLS1508. NLS1501 treatment resulted in a decrease in methane in amended soil where high levels of methane were generated. Treatment under the same conditions with NLS1508 resulted in an increase in methane.

[0203] A more in-depth analysis of background levels of NLS1501 in root-associated (rhizosphere) soil identified a clear signal, using strain-specific qPCR, of NLS1501 related DNA in 9 of the 30 samples analyzed, with an approximate assay limit of detection of 1 x 102genome equivalents per gram of soil. The average level of the 9 positive samples was 1.54 x 102genomes per gram soil.

[0204] Based on these results, it was concluded that the background of NLS1501 (and closely related strains) in the GH pot assays described above to be at approximately the assay limit of detection of 1 x 102.Table 29. Growth Metrics - Methanotrophs - Greenhouse - Rice.

[0205] Growth promotion of rice following treatment with NLS1508 is observed for rice plants grown in soil amended to contain alfalfa hay.

[0206] Growth promotion analysis following treatment with NLS1504 with and without the addition of Methylobacterium strain NLS7725 was conducted. Rice plants treated as described above with NLS1504 (Methylosarcina fibrata) and NLS1504 + Methylorubrum populi strain NLS7725 were observed to evaluate growth promotion. The grain at observation was approximately half ripe, R8 growth stage, for plants grown in alfalfa amended soil. The plants in unamended soil were at growth stage R9, where seed is ripe and the plants are senescing. Plants that were treated with NLS1504 +Methylorubrum populi and grown in amended soil were approximately 6 inches taller than the UTC plants. The treated plants had significantly more panicles, corresponding with an increase in number of tillers. The growth promotion effect was not observed in the pots with unamended soil. The plants are further analyzed at maturity to identify increases in biomass and yield. It was also observed that the application of NLS1504 and NLS7725 alleviated chlorosis of the plants grown in the amended soil containing high methane. This reduction of chlorosis, a common symptom of nitrogen limitation, resulted in dramatic growth promotion and yield enhancement for the treated plants. Methane samples were collected as described above and analyzed to evaluate reduction in methane levels.Table 30. Growth Metrics - Methanotrophs - Greenhouse - Rice.Table 30. Panicle Dry Weight Measurements - Alfalfa Amended Soil R8 StageTable 31. Growth Metrics - Methanotrophs - Greenhouse - Rice.Table 31. Unamended Soil R9 Stage

[0207] Different letters in the “S” column in the above results indicates significant differences between the treatments.

[0208] Results of methane analysis and yield results at maturity for the above described experiment is shown below.Table 32. Yield, Growth Metrics, Methane Emissions - Methanotrophs - Greenhouse - Rice.Linear mixed model for student’s t-test: Yield, Biomass, Methane ~ Treatment + Block (& random)Rice plants were treated as described above with NLS1501 alone and in combination with Methylobacterium radiotolerans strain LGP2020, deposited as NRRL-B-67892. Plants were grown to maturity and analyzed for their ability to reduce methane and enhance growth and yield. Soil used in this study was amended with 25g alfalfa hay, down from 50g in previous treatments. Microbes were inoculated onto the plants via a foliar spray at transplant and again 3-4 weeks after transplant. All pots were sampled for their rate of methane evolution at 3-, 4- and 5-weeks post-transplant and then grown to approximately R8, or the hard dough stage, at which time shoot biomass and grain biomass were determined. Methane production in these soil conditions was reduced when compared to rates seen in previous studies. No treatment resulted in a significantly lower rate of methane production when compared to an uninoculated control. Significant growth promotion was observed when NLS 1501 was applied alone or in combination with LGP2020.Table 33. Yield, Growth Metrics, Methane Emissions - Methanotrophs - Greenhouse - Rice.

[0209] Additional experiments evaluated growth enhancement and methane mitigation resulting from application of methanotroph bacterial strains to rice. The assay described above was modified to include methane and biomass assessments at later timepoints, up to 9 weeks after transplant. At later timepoints, the size of the rice plants correlated with methane emissions and results demonstrated that plants inoculated with methanotrophs emitted less methane over the entire emission sampling period as compared to untreated control plants.

[0210] At earlier timepoints, 2-5 weeks post-transplant, methanotroph treated rice plants emitted less methane than untreated control plants.

[0211] At later timepoints, 5-9 weeks post-transplant, methanotroph treated rice plants emitted similar levels of methane compared to untreated controls, but the treated plants had approximately 35% more shoot biomass. This demonstrated that methanotroph inoculation increased rice plant yield per unit of methane emitted, with some strains demonstrating an overall reduction in total methane emissions.

[0212] Results of measurements of seedling vigor and yield, and methane emissions for individual methanotroph strains and a consortium of 8 methanotroph strains are provided in the tables below. Strains present in the consortium are NLS1501, NLS1504, NLS1508, NLS1561, NLS1563, NLS1578, NLS1581, and NLS1630, a Methylomonas methanica strain.Table 34. Growth Metrics - Methanotrophs - Greenhouse - Rice.Table 34. Methanotroph Enhancement of Rice Seedling VigorTable 35. Yield - Methanotrophs - Greenhouse - Rice.Table 35 Methanotroph Enhancement of Rice Yield at HarvestTable 36. Methane - Methanotrophs - Greenhouse - Rice.Table 36. Methanotroph Treatment Effect on Methane EmissionsExample 1G. Yield under reduced N - Methanotroph and Methylotroph - Field - Corn.

[0213] Corn seeds treated with Methylobacterium or methanotroph strains were grown in a large-scale field trial at 5 locations under reduced nitrogen conditions to determine effects on foliar nitrogen levels and corn yield. The trial was conducted using a randomized complete block design with 4 reps per location. Methylobacterium strains LGP2019 (NRRL B-67743), LGP2017 (NRRL B-67741), LGP2020 (NRRL B-67892) and NLS0754 (NRRL B-68197), and methanotroph strain NLS1508 (NRRL B-68262) were applied at a rate of approximately 1 X 106CFU per seed. Fertilizer control treatments included standard 100% N, 70% N, 35% N, and 0% N. Fertilizer levels in microbe treatments included 70% N (all 5 strains) and 35% N (Methylobacterium strain LGP2019 and methanotroph strain NLS1508). Foliar tissue from the ear leaf at the R2-R4 developmental stage was sampled for micronutrient concentrations, including nitrogen, phosphorus, and potassium. Corn seed was harvested at maturity and analyzed to identify increases in seed yield. Results are shown in Table 37 below.Table 37. Yield under reduced N - Methanotroph and Methylotroph - Field - Corn.Example 1H. Yield under reduced N - Methanotrophs and Methylotrophs - Field - Rice.

[0214] Rice seeds treated with Methylobacterium or methanotroph strains were grown in a large-scale field trial at two locations under reduced nitrogen conditions to determine effects on foliar nitrogen levels and on rice yield. The trial was conducted using a randomized complete block design with 4 reps per location. Methylobacterium strains LGP2019 (NRRL B-67743), LGP2017 (NRRL B-67741), LGP2020 (NRRL B-67892) and NLS0754 (NRRL B-68197), were applied at a rate of approximately 1 X 106CFU per seed. Methanotroph strain NLS1508 (NRRL B-68262) was applied as a foliar treatment before flooding the rice field at a rate exceeding 1 x 106CFU per plant. Fertilizer control treatments include standard 100% N, 70% N, 35% N, and 0% N. Fertilizer levels in microbe treatments include 70% N (all 5 strains) and 35% N (Methylobacterium strain LGP2019 and methanotroph strain NLS1508). Foliar tissue from the ear leaf at the R2-R4 developmental stage is sampled for micronutrient concentrations, including nitrogen, phosphorus, and potassium. Rice seed is harvested at maturity and analyzed to identify increases in seed yield. Results are shown in Table 38 below.Table 38. Yield under reduced N - Methanotrophs and Methylotrophs - Field - Rice.Example II Yield - Methanotrophs and Methylotrophs - Field - Rice.

[0215] Rice seeds were treated with Methylobacterium strain LGP2019 (NRRL B-67743), methanotroph strain NLS1508 (NRRL B-68262), and a combination of LGP2019 and NLS1508. The trial was conducted using a randomized complete block design with 4 reps per location. Rice seed is harvested at maturity and analyzed to identify increases in seed yield.Table XX. Yield - Methanobacteria and Methylobacteria - Field - Rice.Example 1 J. Sequences - Methylotrophs - Identification methods

[0216] Genomic sequences that can be used to identity and distinguish NLS0737 and NLS0770 from other Methylobacterium strains are identified by an exact k-mer analysis of whole genome sequences of over 5000 public and proprietary Methylobacterium isolates. NLS0737 and NLS0770 are closely related and may be, or originate from, a single Methylobacterium isolate. A 300 nt DNA fragment common to both isolates, but not found in other Methylobacterium strains analyzed is provided as SEQ ID NO:31. Genomic sequences that can be used to identity and distinguish NLS5278, NLS5334, NLS5480, and NLS5549 from other Methylobacterium isolates are identified in the same manner. NLS5278, NLS5334, NLS5480, and NLS5549 are closely related and may be, or originate from, a single Methylobacterium isolate. A 300 nt DNA fragment common to NLS5278, NLS5334, and NLS5480, but not found in other Methylobacterium strains analyzed is provided as SEQ ID NO:32.

[0217] Assays for detection or identification of specific Methylobacterium strains and closely related derivatives are developed using the disclosed unique genomic DNA essentially as described in WO2022076588 Example 3.

[0218] Unique genomic DNA sequences of additional Methylobacterium strains disclosed herein were identified by BLAST analysis of approximately 300bp genomic DNA fragments using a sliding window of from 1-25 nucleotides and compared to whole genome sequences of over 1000 public andproprietary Methylobacterium isolates. Genomic DNA fragments were identified that have weak BLAST alignments, indicative of approximately 60-95% identity over the entire fragment, to corresponding fragments of a Methylobacterium of interest. Unique fragments from the various disclosed strains useful for assay development are provided as SEQ ID NOS: 33-75 as shown in the table below.Table 40. Genome Fragments - Sequences - Methylobacteria - Identification methods.ADDITIONAL EXAMPLESExample 2. Rhizosphere Population - Methanotrophs - Rice.

[0219] The abundance of methanotrophs present in rice root rhizosphere was measured 6 weeks after transplant. Abundance was determined by qPCR of pmoA. Results are presented in the table below with values expressed as mean Ct'1+ / - standard deviation. Most of the methanotroph strains tested led to increased total methanotroph populations in rice root rhizosphere. Strains that showed a significant difference compared to an untreated control (FDR < 0.05, pairwise Wilcox test) are marked with an asterisk.Table 39. Rhizosphere Population - Methanotrophs - Rice.Example 3. Sequences - Methanotrophs - Identification methods

[0220] Sequences that encode pMMO protein components, 16S sequences, primers, and probes can be used to identify methanotroph strains provided herein and variants and derivatives thereof are provided below.Table 41. Amino Acid / Nucleic Acid components - Sequences - Methanotrophs - Identification methodsTable 42A. 16S - Sequences - Methanotrophs - Identification methodsTable 42B. Primers - Sequences - Methanotrophs - Identification methodsTable 42B. - Probes - Sequences - Methanotrophs - Identification methodsExample 4. Methane, Growth Metrics, Yield - Methanotrophs - Greenhouse - Rice.

[0221] This experiment consisted of 3 rounds of 42 pots each: 21 UTC (untreated control) and 21 consortium-inoculated pots. The total replication was 63 pots per treatment spread across 3 reps, encompassing 126 pots total. The individual isolates comprising the consortium were the same strains, but came from different lots than the previous work (528-530PB). Application volumes were adjusted to relative OD to provide consistency with previous experiments. The consortium members were as follows and were applied at the following rates:Table 43. Application rates - Methane, Growth Metrics, Yield - Methanotrophs - Greenhouse - Rice.

[0222] The following microorganisms were applied at the intervals indicated and data was subsequently obtained.NL S 1501 = Me thylomicrobium lacusNLS1504 = Methylosarcina fibrataNLS1508 = Methylocystis hirsutaNL S 1561 = Me thylocystis hirsutaNLS1563 = Methylosinus trichosporiumNLS1578 = Methylosinus trichosporiumNL S 1581 = Me thylosinus sporiumNLS1630 = Methylomonas methanicaExperimental Timing: Week 0 - Seedlings were planted. Week 2 - Paddy pots were established, rice was transplanted into paddy pots and first foliar inoculation was completed as well as first fertilizer application. Weeks 7-13 (weeks 5-11 post-transplant) - Gas was sampled weekly from the rice / paddy pot setup. Weeks 5-6 (weeks 3-4 post-transplant) - a second microbial foliar application was completed and fertilizer was re-applied.Week 6 (week 4 post-transplant) - Plant heights and tillers were measured. Week 8 (week 6 post-transplant) - Root samples for methanotroph colonization enumeration on rhizosphere soils was collected, and used for in vitro experiments. Week 14 (week 12 post-transplant) - Yield and biomass data was collected .

[0223] Treatment list: (1) Untreated control and (2) 8-strain consortium

[0224] Planting: Seeds were placed and watered in starter cells and placed in a greenhouse at 10C. Plants received UV filtered RO water for two weeks. Seedlings were thinned.Transplanting, Fertilizing, and Inoculation: To pots containing finely milled alfalfa, base fertilizer, and soil, urea dissolved in deionized water was added. Seedlings were placed in the pots and watered in. Water was added until pots were flooded to a depth of 5 cm. Seedlings were sprayed with a foliar treatment of inoculant.

[0225] Plant Care: Plants were watered daily and no fertilizer applied. Water level remained at least 5 cm above soil level. At 4 weeks, base fertilizer and urea dissolved in deionized water was added.

[0226] Second Inoculation; At week 4 after transplanting, a second foliar inoculant application was applied.

[0227] Data Collection: Plants were covered with a container that had been modified to allow collection and measurement of gas. Gas sampling occurred at 5, 6, 7, 8, 9, 10 and 11 weeks after transplanting by measuring methane gas in headspace of the containers.

[0228] Heights: At 4 weeks after transplanting, plant heights were measured.

[0229] Tiller Count: At 4 weeks after transplanting, tillers were measured.

[0230] Colonization: At 6 weeks after transplanting, colonization was measured.

[0231] Harvest: At maturity, panicles, grain, and shoots were harvested and measured.Table 44. Strains - Methane, Growth Metrics, Yield - Methanotrophs - Greenhouse - Rice.Table 45. Methane - Methanotrophs - Greenhouse - Rice.

[0232] Table 45. Methane emission rates over time. Methane emissions are represented as kilograms of methane per hectare per day. All experiments were sampled for methane emissions using the closed chamber method weekly from 5-11 weeks post-transplant. P-value represent the student’s t, and are calculated using a linear mixed model with block nested-in experiment as a random effect.Table 46. Methane - Methanotrophs - Greenhouse - Rice.Table 46. Total methane emissions weeks 5-11 post-transplant.Total methane is calculated by obtaining the area under the curve for Figure 3 and represents the approximate cumulative methane emitted over the course of the experiment, then adjusted to a per-hectare rate. P-valuerepresent the student’s t, and are calculated using a linear mixed model with block nested-in experiment as a random effect.

[0233] Methane Reduction Metrics

[0234] The timepoints where methane emissions are reduced by greater than or equal to 10% for consortium-treated plants than UTC plants were at weeks 6 and 7. Table 45. Those timepoints are when plant roots may exudate and other root-derived carbon become more proportionally abundant.Table 47. Growth Metrics - Methanotrophs - Greenhouse - Rice.Table 47. Plant heights and tiller counts of 6-week-old plants. A derived variable (‘Plant Size’) was calculated by multiplying the number of tillers per plant, by the height in millimeters, to produce a more holistic view of relative plant size at 6 weeks-old (4 weeks post-transplantation). Mean plant size, tiller count, and plant height compared to an uninoculated control across 3 independent experiments. P-values represent the student’s t, and are calculated using a linear mixed model with block nested-in experiment as a random effect.

[0235] Growth MetricsTable 48. Yield - Methanotrophs - Greenhouse - Rice.Table 48. Harvest metrics. Plants were harvested for yield and shoot biomass at the R8 growth stage, 11 weeks post-transplant. Whole panicles were harvested and counted, then dried for obtaining yield (i.e., panicle biomass). Then, all remaining aboveground biomass was harvested and dried to measure shoot biomass. P-values represent the student’s t, and are calculated using a linear mixed model with block nested-in experiment as a random effect.

[0236] Rice plants treated with the methanotroph consortium had significantly improved growth metrics. Consortium treatment resulted in +45% plant size, a metric that includes tiller counts (+33.68%) and plant height (+9.07%) at 6 weeks of age (4 weeks after transplantation), as compared to untreated control (UTC). Yield metrics at harvest were also higher for consortium-treated plants. Averaged across experiments, panicle counts were +20.30%, panicle weights were +22.46%, and shoot biomass was +32.48%, as compared to UTC.

[0237] Example 5. Growth on Methane -Methanotrophs - Low Nitrogen

[0238] The mineral salt liquid growth medium (NMS) was prepared as described previously, with the key difference being the exclusion of the nitrogen source, KNO3. Separate experiments with this nitrogen-free medium were performed with different carbon sources, either methane or methanol. Methane cultures were performed in sealed serum bottles containing 20 ml of the mineral salt media and methane gas added via needle and syringe to -10% vol / vol. Methanol cultures were performed in 50 ml bioreactor tubes containing 10 ml of the mineral salt media and 0.05% vol / vol methanol. After inoculation, cultures were incubated at 30°C and monitored over time for turbidity changes. If an isolate grew, a new culture was prepared by transferring a portion of the active culture to a new culture vessel containing fresh sterile media. The process was repeated until growth ceased.

[0239] Growth with methane as the carbon source: The following two NLS methanotrophs showed good growth after the first culture grown in nitrogen-free media: NLS 1563 and NLS 1581. Growth of NLS 1563 in nitrogen-free media with methane as the carbon source has continued through two subsequent transfers and a fourth culture is currently incubating. Growth of NLS 1581 with methane as the carbon source ceased after the first transfer into fresh nitrogen-free media. See Table 49 for full results.Table 49. Methanotrophs grown on methane in N-free mediaNA: not applicable

[0240] Growth with methanol as the carbon source: The following four NLS methanotrophs showed at least some growth after the first culture grown in nitrogen-free media: NLS1504, NLS1563, NLS1581, and NLS1618. The following two methanotrophs continued to show growth on methanol in nitrogen-free after the first transfer: NLS 1581 and NLS 1618. Growth of all methanotrophs had ceased after the second transfer, culture #3, into nitrogen-free media. See Table 50 for full results.Table 50. Methanotrophs grown on methanol in N-free media

[0241] Maintenance of growth under these conditions provides further evidence for an organism’s ability to perform nitrogen fixation, since it is believed that the only source of nitrogen capable of supporting sustainable growth under these conditions is the nitrogen gas (N2) present in the headspace of the culture vessels.Example 6. Colonization - Methanotrophs - individual

[0242] Colonization studies found that prevalence of each methanotroph was higher in most consortium-treated plants compared to UTC.Table 51: Colonization - Methanotrophs - individualTable 51 : Colonization values for consortium-treated and untreated rice plants. Rice plants treated with the 8-member methanotroph consortium had root tissue harvested 6 weeks after transplantation. DNA was extracted from the rhizosphere (soil closely-associated with the roots), and qPCR was done with primers specific to each methanotroph to determine their relative colonization strength. Colonization values are reported as inverse Ct from qPCR (meaning a greater value corresponds to more copy numbers of the qPCR target and by extension higher colonization for a given methanotroph), and averaged across all replicates tested for either the methanotroph consortium-treated or untreated plants.Table 52. Colonization - Methanotrophs - individualTable 52: Correlations between colonization strength and methane emissions. Colonization values (inverse Ct) for each methanotroph were analyzed for any correlation with methane levels, i.e. to see if greater presence of any particular methanotroph(s) resulted in mitigation of methane emissions. For both colonization values and methane emissions, data from both consortium-treated and untreated plants are combined. Samples in which colonization was below the threshold of detection have ‘NA’ values replaced with ‘0’ values. Correlation was assessed using Kendall’s tau; both the value for Kendall’s tau as well as p-values are reported.Example 7. Selection of Consortia - Methanotrophs

[0243] Consortia useful for improving growth metrics, yield, and / or methane mitigation are selected based on the types of experiments as described in Examples IF, 2 - 5, as well as additional data from similar experiments. Methanotrophs having growth metrics, yield, sequence, colonization, and / or methane mitigation are selected for further studies.

[0244] Consortia are selected based on data from Examples IF, 2 - 5, as well as additional data from similar experiments. Strains from Table IB having sequence, colonization, and / or methane mitigation are selected for further studies. 8-member consortium strains were selected based on phylogenetic diversity. Strains were prioritized for inclusion in the reduced 6-member consortium and 3-member consortium based on Rice Yield Enhancement by individual strains in Example IF Table 35, Growth on Nitrogen Free Media in Example 5, and ability to colonize the plant correlated with reduction in methane in Example 6, Table 52.Example 8. Methane, Growth Metrics, Yield - Methanotroph Consortia - Greenhouse - Rice. This experiment consist of UTC (untreated control) and consortium-inoculated pots, with replicates. Each Consortium is applied at an equivalent number of total viable colony forming units for all strains combined, each individual strain being applied at an equivalent number of total viable colony forming units to each other strain. The consortium members are as follows and application are as follows:Inoculation Treatment 1 :Inoculation Treatment 2:Inoculation Treatment 3.Inoculation Treatment 4.Experimental Timing: Week 0 - Seedlings are planted. Week 2 - Paddy pots are established, rice is transplanted into paddy pots and first foliar inoculation is completed as well as first fertilizer application. Weeks 7-13 (weeks 5-11 post-transplant) - Gas is sampled weekly from the rice / paddy pot setup. Weeks 5-6 (weeks 3-4 post-transplant) - a second microbial foliar application is completed and fertilizer is re-applied. Week 6 (week 4 post-transplant) - Plant heights and tillers are measured. Week 8 (week 6 post-transplant) - Root samples for methanotroph colonization enumeration on rhizosphere soils is collected, and used for in vitro experiments. Week 14 (week 12 post-transplant) - Yield and biomass data is collected.

[0245] Planting: Seeds are placed and watered in starter cells and placed in a greenhouse at 10C. Plants receive UV filtered RO water for two weeks. Seedlings are thinned.Transplanting, Fertilizing, and Inoculation: To pots containing finely milled alfalfa, base fertilizer, and soil, urea dissolved in deionized water is added. Seedlings are placed in the pots and watered in. Water is added until pots were flooded to a depth of 5 cm. Seedlings are sprayed with a foliar treatment of inoculant.

[0246] Plant Care: Plants are watered daily and no fertilizer applied. Water level remains at least 5 cm above soil level. At 4 weeks, base fertilizer and urea dissolved in deionized water is added.

[0247] Second Inoculation; At week 4 after transplanting, a second foliar inoculant application is applied.

[0248] Data Collection: Plants are covered with a container that has been modified to allow collection and measurement of gas. Gas sampling occurrs at 5, 6, 7, 8, 9, 10 and 11 weeks after transplanting by measuring methane gas in headspace of the containers.

[0249] Heights: At 4 weeks after transplanting, plant heights are measured.

[0250] Tiller Count: At 4 weeks after transplanting, tillers are measured.

[0251] Colonization: At 6 weeks after transplanting, colonization are measured.

[0252] Harvest: At maturity, panicles, grain, and shoots are harvested and measured.

[0253] Growth metrics, methane mitigation, sequences, and yield are measured.SEQUENCESTarget sequences for methanotroph identification.References

[0254] Green, P.N. and Ardley, J.K. 2018. Review of the genus Methylobacterium and closely related organisms: a proposal that some Methylobacterium species be reclassified into a new genus, Methylorubrum gen. nov. Int J Syst Evol Microbiol. 2018 Sep;68(9):2727-2748. doi: 10.1099 / ijsem.0.002856 .

[0255] Konstantinidis K. T., Ramette A., Tiedje J. M.. ( 2006). The bacterial species definition in the genomic era. Philos Trans R Soc Lond B Biol Sci 361 :, 1929 — 1940.

[0256] Lidstrom, M.E. 2006. Aerobic methylotrophic prokaryotes. In Dworkin, M., S. Falkow, E. Rosenberg, K.-H. Schleifer, and E. Stackebrandt (eds.). “The Prokaryotes. A Handbook on the Biology of Bacteria. Volume 2. Ecophysiology and biochemistry. “ Third edition. Springer, New York. Pages 618-634.

[0257] The breadth and scope of the present disclosure should not be limited by any of the abovedescribed embodiments, but should be defined only in accordance with the following claims and their equivalents.

Claims

CLAIMSWe claim:

1. A composition comprising a microbial strain selected from the group consisting of: NLS1546; NLS1557; NLS1558; NLS1561; NLS1563; NLS1564; NLS1572; NLS1578; NLS1581; NLS1591; NLS1601; NLS1618; NLS1631; and NLS1632.2 A composition comprising two or more microbial strains wherein at least one of said microbial strains is selected from the group consisting of: NLS1501; NLS1504; NLS1505; NLS1506; NLS1508; NLS1509; NLS1511; NLS1512; NLS1546; NLS1557; NLS1558; NLS1561; NLS1563; NLS1564; NLS1572; NLS1578; NLS1581; NLS1591; NLS1601; NLS1618; NLS1631; and NLS1632.3 The composition of claim 2, wherein the two or more microbial strain is a number selected from the group consisting of: 2; 3; 4; 5; 6; 7; and 8.4 The composition of claim 1, further comprising a microbial strain selected from the group consisting of: NLS1501; NLS1504; NLS1505; NLS1506; NLS1508; NLS1509; NLS1511; NLS1512; NLS1546; NLS1557; NLS1558; NLS1561; NLS1563; NLS1564; NLS1572; NLS1578; NLS1581; NLS1591; NLS1601; NLS1618; NLS1631; and NLS1632.5 A composition comprising a consortium of microbial strains, wherein the consortium is selected from the group consisting of: a) NLS1501, NLS1504, NLS1508, NLS1561, NLS1563, NLS1578, and NLS1581; b) NLS1504, NLS1508, NLS1561, NLS1578, NLS1581, and NLS1631; or c) NLS1508, NLS1561, and NLS1581.6 The composition of any one of claims 1 through 5, wherein said composition further comprises a methyl otroph.7 The composition of claim 6, wherein said composition further comprises a methylotroph described in Table 1 A.8 The composition of claim 6, wherein the methylotroph is selected from the group consisting of: NLS0017; NLS0020; NLS0042; NLS0064, NLS0089; NLS0109; NLS0610; NLS0662; NLS0648; NLS0807; and NLS0934.9 The composition of any one of claims 1 through 8, wherein said composition further comprises an additional methanotroph.

10. The composition of any one of claims 1 through 5, wherein said composition further comprises a methanotroph described in Table IB.

11. The composition of claim 10, wherein said methanotroph is selected from the group consisting of: NLS1501, NLS1508; NLS1504; NLS1505; NLS1506; NLS1509; NLS1511; NLS1512; NLS1546; NLS1557; NLS1558; NLS1561; NLS1563; NLS1564; NLS1572; NLS1578; NLS1581; NLS1591; NLS1601; NLS1618; NLS1631; and NLS1632.

12. The composition of claim 11, which further comprises a methylotroph selected from the the group consisting of: NLS0017; NLS0020; NLS0042; NLS0064; NLS0089; NLS0109; NLS0610; NLS0648; NLS662; NLS0807; and NLS0934.

13. The composition of any of claims 1 through 12, wherein said composition further comprises at least one additional component.

14. The composition of claim 13, wherein the at least one additional component is selected from the group consisting of: fungicide; fungus; herbicide; insecticides; lubricant; methanotroph; methylotrophs; nemacide.

15. A plant, plant part, or seed at least partially coated with a composition of any one of claims 1 through 14.

16. The plant, plant part, or seed of claim 15, selected from the group consisting of: rice; row crop and specialty crop.

17. The plant, plant part, or seed of claim 15, selected from the group consisting of: alfalfa; barley; brassica sp.; cannabis sp.; carrot; cassava; coconut; coffee; conifers; com; cotton; cucurbits; cucumber; fruit plants (including fruit trees); green bean; herbs; leafy greens; lettuce; microgreens; millet; oat; onion; ornamental; pea; peanut; pepper; potato; rice; rye; safflower; sorghum; soybean; squash; sugar beet; sunflower; sweet potato; tobacco; tomato; turfgrass; and wheat.

18. An isolated microorganism selected from the group consisting of: NLS1546; NLS1557; NLS1558; NLS1561; NLS1563; NLS1564; NLS1572; NLS1578; NLS1581; NLS1591; NLS1601; NLS1618; NLS1631; and NLS1632.

19. A method for mitigating methane in a methane-producing environment, comprising: a) introducing a composition of any one of claims 1 through 14 to a methane- producing environment, andb) growing the composition under conditions sufficient to mitigate methane in the methane-producing environment.

20. The method of claim 19, wherein the methane-producing environment is selected from the group consisting of: pasture; landfill; manure field; septic field; wastewater pond; lake; river; mangrove; marsh; bog; stream; gas mine; coal mine; wildfire area; anaerobic digester system; and flooded field.

21. The method of claim 20, wherein the methane-producing environment is a rice paddy.

22. The method of any one of claims 19 to 21, wherein said composition is applied on seed, plant foliage and / or plant part, plant, field soil, and / or field flood water.

23. The method of any one of claims 19 to 22, wherein the composition is applied at a time selected from the group consisting of: seedling before transplant; transplant; week 1 after transplant; week 2 after transplant; week 3 after transplant; week 4 after transplant; week 5 after transplant; week 6 after transplant; week 7 after transplant; week 8 after transplant; week 9 after transplant; week 10 after transplant; more than 10 weeks after transplant.

24. The method of any one of claims 19 to 23, wherein the composition is applied at a time selected from the group consisting of: 1 time during the growing cycle; 2 times during the growing cycle; 3 times during the growing cycle; 4 times during the growing cycle; 5 times during the growing cycle; 6 times during the growing cycle; and more than 6 times during the growing cycle.

25. The method of any one of claims 19 to 24, wherein the composition is applied at transplant and another time during the growing cycle.

26. The method of any one of claims 19 through 25, which further comprises improving one or more growth metric and / or yield.

27. A method for mitigating methane in a rice paddy environment, comprising: a) introducing a composition of any one of claims 1 through 14 to a rice paddy environment, and b) growing the composition under conditions sufficient to mitigate methane in the rice paddy environment.

28. The method of claim 27, wherein said composition is applied to plant foliage.

29. The method of claim 27 or 28, wherein the composition is applied during transplant and during a week selected from the group consisting of: week 4 after transplant; week 5 after transplant; week 6 after transplant; and week 7 after transplant.

30. The method of claim 27, wherein said composition is applied to plant foliage during transplant and during week 4 after transplant.

31. A method for improving growth metrics in a plant, comprising: a) introducing a composition of any one of claims 1 through 14 to a plant, plant part, or seed; and b) growing the plant, plant part, or seed under conditions sufficient improve growth metrics.

32. The method of claim 31, wherein the growth metrics are selected from the group consisting of: plant size; tiller counts; root length; and plant height.

33. The method of claim 31 or 32, wherein the plant, plant part, or seed is rice or com.

34. The method of claim 31, wherein the composition is selected from the group consisting of: NLS1546; NLS1557; NLS1558; NLS1561; NLS1563; NLS1564; NLS1572; NLS1578; NLS1581; NLS1591; NLS1601; NLS1618; NLS1631; and NLS1632.

35. The method of claim 31, wherein the composition is selected from the group consisting of: a) NLS1501, NLS1504, NLS1508, NLS1561, NLS1563, NLS1578, and NLS1581; b) NLS1504, NLS1508, NLS1561, NLS1578, NLS1581, and NLS1631; or c) NLS1508, NLS1561, and NLS1581.

36. A method for improving yield metrics in a plant, comprising: a) introducing a composition of any one of claims 1 through 12 to a plant, plant part, or seed; and b) growing the plant, plant part, or seed under conditions sufficient improve yield metrics.

37. The method of claim 36, wherein the improved yield metrics are selected from the group consisting of: panicle counts; panicle weights; and shoot biomass.

38. The method of claim 36, wherein the plant, plant part, or seed is rice or com.

39. The method of claim 36, wherein the composition is selected from the group consisting of:a) NLS1501, NLS1504, NLS1508, NLS1561, NLS1563, NLS1578, and NLS1581; b) NLS1504, NLS1508, NLS1561, NLS1578, NLS1581, and NLS1631; or c) NLS1508, NLS1561, and NLS1581.

40. The method for improving colonization of beneficial microorganisms on a plant, comprising a) introducing a composition of any one of claims 1 through 13 to a plant, plant part, or seed; and b) growing the plant, plant part, or seed under conditions sufficient colonization.

41. The method of claim 40, wherein the composition is selected from the group consisting of: NLS1546; NLS1557; NLS1558; NLS1561; NLS1563; NLS1564; NLS1572; NLS1578; NLS1581; NLS1591; NLS1601; NLS1618; NLS1631; and NLS1632.

42. The method of claim 40, wherein the composition is selected from the group consisting of: a) NLS1501, NLS1504, NLS1508, NLS1561, NLS1563, NLS1578, and NLS1581; b) NLS1504, NLS1508, NLS1561, NLS1578, NLS1581, and NLS1631; or c) NLS1508, NLS1561, and NLS1581.

43. A method to identify a consortium of methanotrophs useful to mitigate methane in plants, comprising: a) identifying one or more methanotrophs having increased colonization compared to a library of methanotrophs; and b) identifying combinations of one or more methanotrophs that mitigate methane in plants.

44. The method of claim 43, wherein the combinations are selected from the group of methanotrophs in Table IB.

45. The method of claim 44, wherein the combinations are selected from the group consisting of: NLS1546; NLS1557; NLS1558; NLS1561; NLS1563; NLS1564; NLS1572; NLS1578; NLS1581; NLS1591; NLS1601; NLS1618; NLS1631; and NLS1632.

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