Systems for production of products to promote nitrogen use efficiency in plants

Abstract

The present disclosure provides methods and systems for production of biostimulants that promote nitrogen use efficiency in plants. Embodiments described include methods of making a biostimulant compo

Description

[0001] SYSTEMS FOR PRODUCTION OF PRODUCTS TO PROMOTE NITROGEN USE

[0002] EFFICIENCY IN PLANTS

[0003] CROSS-REFERENCE TO RELATED APPLICATIONS

[0004] [1] This application claims benefit of U.S. Patent Application No. 18 / 541,671, filed December 15, 2023, U.S. Patent Application No. 18 / 541,917, filed December 15, 2023, U.S. Provisional Application No. 63 / 509,263, filed June 20, 2023, U.S. Provisional Application No. 63 / 510,615, filed June 27, 2023, and U.S. Provisional Application No. 63 / 610,535, filed on December 15, 2023, each of which is entirely incorporated herein by reference.

[0005] BACKGROUND

[0006] [2] The disclosure is generally related to biostimulant compositions and methods of using such biostimulant compositions to promote plant growth.

[0007] [3] Promoting efficient production of food crops and other crops is an important goal for environmental and economic reasons. Plant growth promoting products sourced from organic materials can help to enhance crop growth, improve the efficacy of agricultural products, such as fertilizers, and reduce the environmental impacts of synthetic fertilizers and climate change. There exists a need for plant growth promoting biostimulant compositions that use abundant and available organic feedstocks.

[0008] SUMMARY

[0009] [4] In an aspect, the present disclosure provides a method of making a biostimulant composition, the method comprising: (a) providing a bioreactor system comprising two or more containers arranged in a series, each of the two or more containers comprising a volume of a working fluid, wherein a first container comprises an established population of a first nitrogen use efficiency-promoting microbial strain; (b) operating the bioreactor system for a duration of time by: (i) transferring into the first container an aqueous feedstock comprising a microbial consortium; (ii) transferring a portion of the working fluid out of each of the two or more containers into either a subsequent container of the bioreactor system or a product outflow stream; (iii) maintaining a concentration of the first nitrogen use efficiency-promoting microbial strain throughout the duration of time in at least the first container at at least 80% of a concentration of the first nitrogen use efficiency -promoting microbial strain at the beginning of the duration of time; and (iv) collecting at least a portion of the product outflow stream as the biostimulant composition; wherein the duration of time is at least 5 days; and wherein the first nitrogen use efficiency-promoting microbial strain is not present in the aqueous feedstock or any other input into the bioreactor system during the duration of time at a concentration that is higher than 1% of the concentration of the first nitrogen use efficiency-promoting microbial strain in the first container.

[0010] [5] In some embodiments, the first nitrogen use efficiency-promoting microbial strain is one that performs nitrogen fixation, promotes nitrogen fixation in the tissues of plants, recruits nitrogen fixers to the root zones or other tissues of plants, or increases organic nitrogen content and / or mineralization of organic nitrogen in soil. In some embodiments, the first nitrogen use efficiency-promoting microbial strain is positive for a nifH gene. In some embodiments, the first nitrogen use efficiency-promoting microbial strain is one that promotes plant growth in a nitrogen-poor growth medium. In some embodiments, the nitrogen-poor growth medium comprises nitrate at less than 10 ppm.

[0011] [6] In some embodiments, the first nitrogen use efficiency-promoting microbial strain is of the genus Kosakonia, Klebsiella, Rahnella, Kluyvera, Enterobacter, Achromobacter, Microbacterium, Gluconobacter, Methylobacterium, Pseudomonas, Pantoea, Azospirillum, Azocarus, Herbaspirillum, Burkholderia, Cyanobacteria, Bacillus, and Paenibacillus . In some embodiments, the first nitrogen use efficiency-promoting microbial strain is of the species Kosakonia sacchari, Klebsiella variicola, Rahnella aquatilis, Kluyvera intermedia, Kosakonia pseusosacchari, Enterobacter spp., Achromobacter marplatensis, Azopirillum lipoferum, Microbacterium murale, Gluconobacter diazotrophicus, Methylobacterium symbioticum, Paenibacillus borealis, Bacillus megaterium (Priestia megaterium), or Paenibacillus sonchi.

[0012] [7] In some embodiments, the first nitrogen use efficiency-promoting microbial strain is the strain deposited under ATCC Accession No. PTA-127654 (MS3907), the strain deposited under ATCC Accession No. PTA-127653 (MS3900), the strain deposited under ATCC Accession No. PTA-127655 (MS4921), or the strain deposited under ATCC Accession No. PTA-127652 (MS2748).

[0013] [8] In some embodiments, the first nitrogen use efficiency-promoting microbial strain is not present in the aqueous feedstock or any other input into the bioreactor system during the duration of time at a concentration of greater than 100 CFU / ml. In some embodiments, the first nitrogen use efficiency-promoting microbial strain is not present in the aqueous feedstock or any other input into the bioreactor system during the duration of time. In some embodiments, the maintaining of step (b)(iii) comprises maintaining the concentration of the first nitrogen use efficiency-promoting microbial strain at at least IxlO3CFU / ml. [9] In some embodiments, the first container further comprises an established population of a second nitrogen use efficiency-promoting microbial strain and wherein the operating of step (b) further comprises (v) maintaining a concentration of the second nitrogen use efficiencypromoting microbial strain at at least 80% of a concentration of the second nitrogen use efficiency-promoting microbial strain at the beginning of the duration of time; wherein the second nitrogen use efficiency -promoting microbial strain is not present in the aqueous feedstock or any other input into the bioreactor system during the duration of time at a concentration that is higher than 1% of the concentration of the second nitrogen use efficiencypromoting microbial strain in the first container.

[0014]

[0010] In some embodiments, the first container further comprises an established population of a third nitrogen use efficiency -promoting microbial strain and wherein the operating of step (b) further comprises (v) maintaining a concentration of the third nitrogen use efficiency-promoting microbial strain at at least 80% of a concentration of the third nitrogen use efficiency-promoting microbial strain at the beginning of the duration of time; wherein the third nitrogen use efficiency-promoting microbial strain is not present in the aqueous feedstock or any other input into the bioreactor system during the duration of time at a concentration that is higher than 1% of the concentration of the third nitrogen use efficiency-promoting microbial strain in the first container. In some embodiments, before step (b), the first container further comprises an established population of other nitrogen use efficiency-promoting microbes that are not the first nitrogen use efficiency-promoting microbial strain, the second nitrogen use efficiencypromoting microbial strain, or the third nitrogen use efficiency-promoting microbial strain, and wherein step (b)(iii) further comprises maintaining a concentration of the other nitrogen use efficiency-promoting microbes in at least the first container throughout the duration of time at at least IxlO4CFU / ml or at at least 80% of a concentration of the other nitrogen use efficiencypromoting microbes at the beginning of the duration of time, wherein the other nitrogen use efficiency-promoting microbes are not added to the bioreactor system during the duration of time at a concentration that is higher than 1% of the concentration of the other nitrogen use efficiency-promoting microbes in the first container.

[0015]

[0011] In some embodiments, the other nitrogen use efficiency -promoting microbes are not present in the aqueous feedstock or any other input into the bioreactor system at a concentration of greater than 105CFU / ml. In some embodiments, the population of the other nitrogen use efficiency-promoting microbes in the first container is at least IxlO4CFU / ml at the beginning of the duration of time. In some embodiments, the other nitrogen use efficiency -promoting microbes comprise microbes that perform nitrogen fixation, promote nitrogen fixation in the tissues of plants, recruit nitrogen fixers to the root zones or other tissues of plants, or increases organic nitrogen content and / or mineralization of organic nitrogen in soil. In some embodiments, the other nitrogen use efficiency -promoting microbes are positive for a nifH gene.

[0016]

[0012] In some embodiments, the method further comprises, before step (a), adding an inoculum of the first nitrogen use efficiency-promoting microbial strain to the bioreactor system, wherein the inoculum of the first nitrogen use efficiency-promoting microbial strain produces an initial population of the first nitrogen use efficiency-promoting microbial strain of at least 0.5xl04CFU / ml in at least one container. In some embodiments, before adding the inoculum of the first nitrogen use efficiency-promoting microbial strain, the concentration of the first nitrogen use efficiency-promoting microbial strain is less than IxlO2CFU / ml.

[0017]

[0013] In some embodiments, the aqueous feedstock further comprises an organic material at least partially digestible by microbes present in at least one of the containers.

[0018]

[0014] In some embodiments, before the transferring of step (b)(i), the organic material had been partially digested by microbes endogenous to the organic material. In some embodiments, the method further comprises digesting the organic material in two or more serially connected containers before the transferring of step (b)(i).

[0019]

[0015] In some embodiments, the organic material comprises manure and / or material produced by microbial digestion of manure. In some embodiments, the aqueous feedstock further comprises an inorganic material. In some embodiments, the inorganic material comprises rock phosphate particles. In some embodiments, prior to the transferring of step (b)(i), the rock phosphate particles had been partially digested by microbes present in the aqueous feedstock. In some embodiments, the method further comprises partially digesting the rock phosphate particles in two or more serially connected containers before the transferring of step (b)(i).

[0020]

[0016] In some embodiments, the microbial consortium comprises at least IxlO5CFU / ml. In some embodiments, the microbial consortium comprises microbes derived from manure and from rock phosphate particles. In some embodiments, the operating of step (b) further comprises producing microbial metabolites that directly or indirectly promote nitrogen use efficiency in plants. In some embodiments, the transferring of step (b)(i), the transferring of step (b)(ii), and the collecting of step (b)(iv) are performed continuously throughout the duration of time. In some embodiments, the transferring of step (b)(i), the transferring of step (b)(ii), and the collecting of step (b)(iv) are performed periodically throughout the duration of time.

[0021]

[0017] In some embodiments, the method further comprises adding one or more carbon sources to at least one container of the bioreactor system. In some embodiments, the one or more carbon sources are included in the aqueous feedstock. In some embodiments, the method further comprises maintaining a malate concentration in at least one container of the bioreactor system at a concentration of at least 0.2% w / v in relation to the volume of working fluid in the at least one container. In some embodiments, the method further comprises adding one or more nitrogen sources to at least one container of the bioreactor system.

[0022]

[0018] In some embodiments, the one or more nitrogen sources comprise one or more of ammonium sulfate, ammonium chloride, ammonium nitrate, sodium nitrate, yeast extract, yeast, or any combination thereof. In some embodiments, the method further comprises adding one or more of soy flour, lentil flour, chickpea flour, green pea flour, yellow pea flour, white bean flour, corn flour, cereal flour, corn gluten, soy flour protein, or soy protein hydrolysate, or any combination thereof to at least one container of the bioreactor system. In some embodiments, the soy flour is added, and wherein the soy flour is included in the aqueous feedstock. In some embodiments, the method further comprises maintaining a soy flour concentration in at least one container of the bioreactor system at a concentration of at least 0.2% w / v in relation to the volume of the working fluid in the at least one container.

[0023]

[0019] In some embodiments, the bioreactor system comprises a clarifier container comprising a clarifier working fluid. In some embodiments, the method further comprises separating a supernatant portion of the clarifier working fluid from a floc portion of the clarifier working fluid within the clarifier container. In some embodiments, the separating comprises gravity separation. In some embodiments, the method further comprises folding the floc portion of the clarifier working fluid. In some embodiments, the folding further comprises releasing a population of the first nitrogen use efficiency-promoting microbial strain into the supernatant portion without introducing floc solids into the supernatant portion. In some embodiments, the folding is performed by folding wipers in a bottom portion of the clarifier container.

[0024]

[0020] In some embodiments, the operating further comprises transferring the floc portion from the clarifier container to an earlier container in the bioreactor system. In some embodiments, the product outflow stream comprises the supernatant portion of the clarifier working fluid.

[0025]

[0021] In some embodiments, the method further comprises producing at least IxlO2CFU / ml of the first nitrogen use efficiency -promoting microbial strain in the product outflow stream. In some embodiments, the bioreactor system comprises the first container comprising a volume of a first working fluid, a second container comprising a volume of a second working fluid, and a third container comprising a volume of a third working fluid. In some embodiments, the first container comprises an outlet port fluidly connected to an inlet port of the second container and the second container comprises an outlet port fluidly connected to an input port of the third container. In some embodiments, the third container comprises an outlet port fluidly connected to a clarifier container. In some embodiments, the method further comprises maintaining the volume of each of the first working fluid, the second working fluid, and the third working fluid constant throughout the duration of time.

[0026]

[0022] In some embodiments, step (b) comprises operating the bioreactor system in a hydraulically balanced manner. In some embodiments, the transferring of step (b)(i), the transferring of step (b)(ii), and the collecting of step (b)(iv) are driven by gravity. In some embodiments, the operating comprises maintaining a flow rate that results in a hydraulic retention time of at least 5 days. In some embodiments, the operating comprises maintaining the product outflow stream at a flow rate of at least 100 gallons per day. In some embodiments, the volume of working fluid in each of the two or more containers is at least 100 gallons.

[0027]

[0023] In some embodiments, at least one of the two or more containers is a fluidized bed reactor. In some embodiments, at least one of the two or more containers is a packed bed reactor.

[0028]

[0024] In some embodiments, the method further comprises maintaining at least one of the two or more containers under aerobic conditions. In some embodiments, the method further comprises maintaining at least one of the two or more containers under microaerobic conditions. In some embodiments, the bioreactor system is operated continuously for at least 90 days.

[0029]

[0025] In some embodiments, one or more species of one or more of the following genera are among five most abundant species in the microbial consortium: Haliscomenobacler. I.ew inella. Caldilinea, Terrimonas. and Acidobacterium. In some embodiments, one or more of the following species are among five most abundant species in the microbial consortium: Lewinella cohaerens. Thauera phenylacelica. Thauera mechernichensis. Solitalea canadensis, and Nitrospira moscoviensis .

[0030]

[0026] In some embodiments, the microbial consortium comprises microbes endogenous to the organic material. In some embodiments, at least a portion of the aqueous feedstock is produced by the method described herein. In some embodiments, at least one of the first working fluid, the second working fluid, or the third working fluid comprises a pH buffering system. In some embodiments, the method further comprises maintaining the pH of at least one of the first working fluid, the second working fluid, or the third working fluid between 6 and 8 throughout the duration of time.

[0031]

[0027] In some embodiments, the aqueous feedstock does not include the first nitrogen use efficiency-promoting microbial strain at a concentration higher than 10 CFU / ml. In some embodiments, the first nitrogen use efficiency-promoting microbial strain is not added to the bioreactor system during the duration of time at a concentration that is higher than 10 CFU / ml.

[0028] In some embodiments, the bioreactor system comprises at least one container placed in the series before the first container. In some embodiments, the volume of working fluid of one of the two or more containers comprises the microbial consortium, wherein each microbial consortium is distinct from all of the microbial consortia in other working fluids. In some embodiments, the method further comprises producing a population of sporulated bacteria in the product outflow stream. In some embodiments, the method further comprises producing a population of the first nitrogen use efficiency-promoting microbial strain in the product outflow stream that is sporulated. In some embodiments, the population of the first nitrogen use efficiency-promoting microbial strain that is sporulated comprises at least IxlO2CFU / ml. In some embodiments, the method further comprises adding an additional population of the first nitrogen use efficiency-promoting microbial strain, the second nitrogen use efficiencypromoting microbial strain, or the third nitrogen use efficiency-promoting microbial strain to the biostimulant product.

[0032]

[0029] A bioreactor system comprising: (a) a stream of an aqueous feedstock in fluid communication with a first container comprising a volume of a first working fluid, wherein the aqueous feedstock comprises a microbial consortium, wherein the first working fluid comprises a population of a first nitrogen use efficiency-promoting strain, wherein a concentration of the first nitrogen use efficiency-promoting microbial strain in the first working fluid is at least 100 times higher than a concentration of the first nitrogen use efficiency-promoting microbial strain in the aqueous feedstock stream or in any other input into the bioreactor system; (b) one or more additional containers arranged in a series that includes the first container, wherein each of the one or more additional containers comprises a volume of a working fluid and is in fluid communication with at least one other container in the series, and wherein at least one of the one or more additional containers comprises a product outflow stream port; and (c) a product outflow stream in fluid communication with the product outflow stream port.

[0033]

[0030] In some embodiments, the first nitrogen use efficiency-promoting microbial strain is one that performs nitrogen fixation, promotes nitrogen fixation in the tissues of plants, recruits nitrogen fixers to the root zones or other tissues of plants, or increases organic nitrogen content and / or mineralization of organic nitrogen in soil. In some embodiments, the first nitrogen use efficiency-promoting microbial strain is positive for a nifH gene. In some embodiments, the first nitrogen use efficiency-promoting microbial strain is one that promotes plant growth in a nitrogen-poor growth medium. In some embodiments, the nitrogen-poor growth medium comprises nitrate at less than 10 ppm.

[0031] In some embodiments, the first nitrogen use efficiency-promoting microbial strain is of the genus Kosakonia, Klebsiella, Rahnella, Kluyvera, Enterobacter, Achromobacter, Microbacterium, Gluconobacter, Methylobacterium, Pseudomonas, Pantoea, Azospirillum, Azocarus, Herbaspirillum, Burkholderia, Cyanobacteria, Bacillus, or Paenibacillus . In some embodiments, the first nitrogen use efficiency-promoting microbial strain is of the species Kosakonia sacchari, Klebsiella variicola, Rahnella aquatilis, Kluyvera intermedia, Kosakonia pseusosacchari, Enterobacter spp., Achromobacter marplatensis, Azopirillum lipoferum, Microbacterium murale, Gluconobacter diazotrophicus, Methylobacterium symbioticum, Paenibacillus borealis, Bacillus megaterium (Priestia megaterium), or Paenibacillus sonchi.

[0034]

[0032] In some embodiments, the first nitrogen use efficiency-promoting microbial strain is the strain deposited under ATCC Accession No. PTA-127654 (MS3907), the strain deposited under ATCC Accession No. PTA-127653 (MS3900), the strain deposited under ATCC Accession No. PTA-127655 (MS4921), or the strain deposited under ATCC Accession No. PTA-127652 (MS2748).

[0035]

[0033] In some embodiments, the bioreactor system is a continuous flow bioreactor system and the stream of the aqueous feedstock is a continuous stream. In some embodiments, each of the volume of the working fluid is constant. In some embodiments, each of the first container and the one or more additional containers comprises a concentration of the first nitrogen use efficiency-promoting microbial strain that remains at least IxlO4CFU / ml during operation of the bioreactor system. In some embodiments, the aqueous feedstock and any other input into the bioreactor system does not comprise the population of the first nitrogen use efficiencypromoting microbial strain or does not comprise a concentration of the first nitrogen use efficiency-promoting microbial strain at level higher than 100 CFU / ml. In some embodiments, the microbial consortium comprises at least IxlO5CFU / ml of microbes.

[0036]

[0034] In some embodiments, the aqueous feedstock further comprises an organic material digestible by microbes present in the containers. In some embodiments, the organic material comprises manure or material derived from manure. In some embodiments, the aqueous feedstock further comprises rock phosphate particles. In some embodiments, the microbial consortium comprises microbes derived from manure and rock phosphate particles.

[0037]

[0035] In some embodiments, the container comprising the product outflow stream port is a clarifier container configured to separate a portion of a working fluid in the clarifier container into a supernatant portion and a floc portion. In some embodiments, the clarifier container comprises one or more floc folding flights configured to agitate settled floc in the clarifier container without resuspending solids in the floc portion into the supernatant portion. In some embodiments, the system further comprises a floc return stream that flows from the clarifier to an earlier container in the series. In some embodiments, the product outflow stream comprises the supernatant portion. In some embodiments, the product outflow stream comprises at least IxlO4CFU / ml of the first nitrogen use efficiency-promoting microbial strain. In some embodiments, the product outflow stream comprises at least IxlO2CFU / ml of a sporulated form of the first nitrogen use efficiency-promoting microbial strain. In some embodiments, the product outflow stream comprises a total dry weight of 0.2 to 2.5 mg / ml. In some embodiments, the product outflow stream has a chemical oxygen demand between 80 to 500 mg / L. In some embodiments, the product outflow stream has an electrical conductivity between 1.3 and 3.0 mS / cm.

[0038]

[0036] In another aspect, the present disclosure provides a method comprising: (a) transferring water and rock phosphate into a first container comprising a volume of a first working fluid, wherein products of digestion of manure by microbes derived from the manure are not transferred into the first container; (b) transferring a portion of the first working fluid into a second container comprising a second working fluid; (c) transferring into the second container: (i) a liquid comprising (A) a first microbial consortium comprising microbes derived from a first organic material, and (B) digestion products produced by anaerobic digestion of the first organic material by the microbes; (ii) a second organic material; and (iii) yeast.

[0039]

[0037] In some embodiments, the method further comprises transferring a portion of the second working fluid into a third container comprising a third working fluid, and transferring a portion of the third working fluid into a fourth container comprising a fourth working fluid. In some embodiments, the method further comprises separating a portion of the fourth working fluid into a floc portion and a supernatant portion. In some embodiments, the method further comprises transferring the floc portion to the first container. In some embodiments, the method further comprises maintaining the first container, the second container, the third container, and / or the fourth container under aerobic conditions. In some embodiments, the first container, the second container, the third container, and / or the fourth container are fluidized bed reactors, wherein the rock phosphate is continuously circulated within the first container, the second container, the third container, and / or the fourth container. In some embodiments, a total volume of material added to the first container over a given time period is equal to a total volume of the first working fluid transferred to the second container over a same time period. In some embodiments, a total volume of material transferred into the second container, the third container, and the fourth container over a given time period is equal to a total volume transferred out of the second container, the third container, and the fourth container over a same time period. In some embodiments, the method further comprises maintaining a volume of the first working fluid, a volume of the second working fluid, and a volume of the third working fluid constant.

[0040]

[0038] In some embodiments, the first organic material is manure. In some embodiments, the second organic material is manure. In some embodiments, the yeast is Saccharomyces cerevisiae. In some embodiments, the method further comprises producing a product stream from a second microbial consortium, a third microbial consortium, or a fourth microbial consortium, wherein the product stream comprises bacteria from one or more of the following species: Lewinella cohaerens, Thauera phenylacetica, Thauera mechernichensis. Solitalea canadensis. In some embodiments, bacteria from one or more of the following species are among the five most abundant microbes in the second microbial consortium: Lewinella cohaerens, Thauera phenylacetica, Thauera mechernichensis, Solitalea canadensis, and Nitrospira moscoviensis. In some embodiments, the five most abundant microbes in the second microbial consortium do not include bacteria from any of the following genera: Haliscomenobacter, Caldilinea, Terrimonas, and Acidobacterium. In some embodiments, the second microbial consortium is comprised in a fifth working fluid. In some embodiments, low- rank coal is not transferred into the first container.

[0041]

[0039] In an aspect, the present disclosure provides a biostimulant composition made by the method described herein or the system described herein.

[0042]

[0040] In an aspect, the present disclosure provides a method of promoting plant growth comprising contacting a plant, seed, or plant growth medium with the biostimulant composition described herein.

[0043]

[0041] In an aspect, the present disclosure provides a method of increasing nitrogen use efficiency of a plant, the method comprising contacting a plant, seed, or plant growth medium with the biostimulant composition described herein.

[0044]

[0042] In an aspect, the present disclosure provides a method of increasing phosphate solubilization in a plant growth medium, the method comprising contacting a plant, seed, or the plant growth medium with the biostimulant composition described herein.

[0045]

[0043] In an aspect, the present disclosure provides a composition comprising: (a) a Bacillus megaterium strain having one or more of the following: (i) a 16S rRNA gene sequence at least 95% identical to SEQ ID NO: 1; (ii) a gyrB gene sequence at least 95% identical to SEQ ID NO: 4; and (iii) an rpoB gene sequence at least 95% identical to SEQ ID NO: 7; and (b) a carrier.

[0046]

[0044] In some embodiments, the Bacillus megaterium strain is the MS3900 strain deposited under ATCC Accession No. PTA-127653, or an isolated clone thereof. In some embodiments, the composition further comprises products of digestion of an organic substrate by the Bacillus megaterium strain. In some embodiments, the carrier comprises a fertilizer. In some embodiments, the carrier is a solid coated by the Bacillus megaterium strain. In some embodiments, the carrier is a liquid. In some embodiments, the composition further comprises an adjuvant selected from a wetting agent, spreading agent, dispersing agent, sticking agent, dust control agent, and adhesive. In some embodiments, the concentration of the Bacillus megaterium strain in the composition ranges from IxlO3to IxlO11CFU / ml.

[0047]

[0045] In an aspect, the present disclosure provides a composition comprising: (a) a Paenibacillus borealis strain having one or more of the following: (i) a 16S rRNA gene sequence at least 95% identical to SEQ ID NO: 2; (ii) a gyrB gene sequence at least 95% identical to SEQ ID NO: 5; (iii) an rpoB gene sequence at least 95% identical to SEQ ID NO: 8; and (iv) a nifH gene sequence at least 95% identical to SEQ ID NO: 13; and (b) a carrier.

[0048]

[0046] In some embodiments, the Paenibacillus borealis strain is the MS3907 strain deposited under ATCC Accession No. PTA-127654, or an isolated clone thereof. In some embodiments, the composition further comprises products of digestion of an organic substrate by the Paenibacillus borealis strain. In some embodiments, the carrier comprises a fertilizer. In some embodiments, the carrier is a solid coated by the Paenibacillus borealis strain. In some embodiments, the carrier is a liquid. In some embodiments, the composition further comprises an adjuvant selected from a wetting agent, spreading agent, dispersing agent, sticking agent, dust control agent, and adhesive. In some embodiments, the concentration of the Paenibacillus borealis strain in the composition ranges from IxlO3to IxlO11CFU / ml.

[0049]

[0047] In an aspect, the present disclosure provides a composition comprising: (a) a Paenibacillus sonchi strain having one or more of the following: (i) a 16S rRNA gene sequence at least 95% identical to SEQ ID NO: 3; (ii) a gyrB gene sequence at least 95% identical to SEQ ID NO: 6; (iii) an rpoB gene sequence at least 95% identical to SEQ ID NO: 9; and (iv) a nifH gene sequence at least 95% identical to SEQ ID NO: 14; and (b) a carrier.

[0050]

[0048] In some embodiments, the Paenibacillus sonchi strain is the MS4921 strain deposited under ATCC Accession No. PTA-127655, or an isolated clone thereof. In some embodiments, the composition further comprises products of digestion of an organic substrate by the Paenibacillus sonchi strain. In some embodiments, the carrier comprises a fertilizer. In some embodiments, the carrier is a solid coated by the Paenibacillus sonchi strain. In some embodiments, the carrier is a liquid. In some embodiments, the composition further comprises an adjuvant selected from a wetting agent, spreading agent, dispersing agent, sticking agent, dust control agent, and adhesive. In some embodiments, the concentration of the Paenibacillus sonchi strain in the composition ranges from IxlO3to IxlO11CFU / ml.

[0049] In an aspect, the present disclosure provides a composition comprising: (a) Bacillus megaterium strain having one or more of the following: (i) a 16S rRNA gene sequence at least 95% identical to SEQ ID NO: 10; (ii) a gyrB gene sequence at least 95% identical to SEQ ID NO: 11; and (iii) an rpoB gene sequence at least 95% identical to SEQ ID NO: 12; and (b) a carrier.

[0051]

[0050] In some embodiments, the Bacillus megaterium strain is the MS2748 strain deposited under ATCC Accession No. PTA-127652, or an isolated clone thereof. In some embodiments, the composition further comprises products of digestion of an organic substrate by the Bacillus megaterium strain. In some embodiments, the carrier comprises a fertilizer. In some embodiments, the carrier is a solid coated by the Bacillus megaterium strain. In some embodiments, the carrier is a liquid. In some embodiments, the composition further comprises an adjuvant selected from a wetting agent, spreading agent, dispersing agent, sticking agent, dust control agent, and adhesive. In some embodiments, the concentration of the Bacillus megaterium strain in the composition ranges from IxlO3to IxlO11CFU / ml. In some embodiments, the composition further comprises at least one or more of the following: (c) a Bacillus megaterium strain having one or more of the following: (i) a 16S rRNA gene sequence at least 95% identical to SEQ ID NO: 1; (ii) a gyrB gene sequence at least 95% identical to SEQ ID NO: 4; and (iii) an rpoB gene sequence at least 95% identical to SEQ ID NO: 7; (d) a Paenibacillus borealis strain having one or more of the following: (i) a 16S rRNA gene sequence at least 95% identical to SEQ ID NO: 2; (ii) a gyrB gene sequence at least 95% identical to SEQ ID NO: 5; (iii) an rpoB gene sequence at least 95% identical to SEQ ID NO: 8; and (iv) a nifH gene sequence at least 95% identical to SEQ ID NO: 13; and (d) a Paenibacillus sonchi strain having one or more of the following: (i) a 16S rRNA gene sequence at least 95% identical to SEQ ID NO: 3; (ii) a gyrB gene sequence at least 95% identical to SEQ ID NO: 6; (iii) an rpoB gene sequence at least 95% identical to SEQ ID NO: 9; and (iv) a nifH gene sequence at least 95% identical to SEQ ID NO: 14.

[0052]

[0051] In an aspect, the present disclosure provides an isolated strain of the species Bacillus megaterium having one or more of the following: (a) a 16S rRNA gene sequence at least 95% identical to SEQ ID NO: 1; (b) a gyrB gene sequence at least 95% identical to SEQ ID NO: 4; and (c) an rpoB gene sequence at least 95% identical to SEQ ID NO: 7.

[0053]

[0052] In some embodiments, the Bacillus megaterium strain is the MS3900 strain deposited under ATCC Accession No. PTA-127653, or an isolated clone thereof.

[0054]

[0053] In an aspect, the present disclosure provides an isolated strain of the species Paenibacillus borealis having one or more of the following: (a) a 16S rRNA gene sequence at least 95% identical to SEQ ID NO: 2; (b) a gyrB gene sequence at least 95% identical to SEQ ID NO: 5; (c) an rpoB gene sequence at least 95% identical to SEQ ID NO: 8; and (d) a nifH gene sequence at least 95% identical to SEQ ID NO: 13.

[0055]

[0054] In some embodiments, the Paenibacillus borealis strain is the MS3907 strain deposited under ATCC Accession No. PTA-127654, or an isolated clone thereof.

[0056]

[0055] In an aspect, the present disclosure provides an isolated strain of the species Paenibacillus sonchi having one or more of the following: (a) a 16S rRNA gene sequence at least 95% identical to SEQ ID NO: 3; (b) a gyrB gene sequence at least 95% identical to SEQ ID NO: 6; (c) an rpoB gene sequence at least 95% identical to SEQ ID NO: 9; and (d) a nifH gene sequence at least 95% identical to SEQ ID NO: 14.

[0057]

[0056] In some embodiments, the Paenibacillus sonchi strain is the MS4921 strain deposited under ATCC Accession No. PTA-127655, or an isolated clone thereof.

[0058]

[0057] In an aspect, the present disclosure provides an isolated strain of the species Bacillus megaterium having one or more of the following: (a) a 16S rRNA gene sequence at least 95% identical to SEQ ID NO: 10; (b) a gyrB gene sequence at least 95% identical to SEQ ID NO: 11; and (c) an rpoB gene sequence at least 95% identical to SEQ ID NO: 12.

[0059]

[0058] In some embodiments, the Bacillus megaterium strain is the MS2748 strain deposited under ATCC Accession No. PTA-127652, or an isolated clone thereof.

[0060]

[0059] In an aspect, the present disclosure provides a method for promoting growth of a plant growing in a medium, the method comprising contacting the plant or the medium with the composition described herein or the isolated strain described herein.

[0061]

[0060] In some embodiments, the contacting increases a plant nitrogen content by at least 5%. In some embodiments, the contacting increases a nitrogen fixation activity and / or nitrogen use efficiency in plant tissues by at least 5%. In some embodiments, the contacting increases a population of nitrogen fixing bacteria in the root and root rhizospheres of the plant by at least 5%. In some embodiments, the contacting causes recruitment of nitrogen fixing bacteria present in the medium to the root zone of the plant. In some embodiments, the contacting causes an increase plant growth by at least 10 percent as compared to a control. In some embodiments, the medium comprises soil, a hydroponic medium, turface, or isolite.

[0062]

[0061] In an aspect, the present disclosure provides a method of enhancing nitrogen fixing activity or plant tissue colonization capability of a bacterium, the method comprising incubating the bacterium in the presence of strain MS3900.

[0063]

[0062] In some embodiments, the bacterium is strain MS3907.

[0063] In an aspect, the present disclosure provides a composition comprising: (a) a microbial consortium comprising one or more bacterial strains selected from MS3900 (ATCC Accession No. PTA-127653), MS3907 (ATCC Accession No. PTA-127654), MS4921 (ATCC Accession No. PTA-127655), and MS2748 (ATCC Accession No. PTA-127652); and (b) metabolites produced by digestion of an organic substrate by microbes within the microbial consortium.

[0064]

[0064] In some embodiments, the microbial consortium further comprises an enriched nitrogen- fixing microbial community. In some embodiments, the organic substrate is derived from cow manure, rock phosphate, or ground plant matter, or any combination thereof. In some embodiments, the microbial consortium comprises microbes derived from cow manure, rock phosphate, or ground plant matter. In some embodiments, the ground plant matter is soy flour, lentil flour, chickpea flour, green pea flour, yellow pea flour, white bean flour, corn flour, cereal flour, corn gluten, soy flour protein, soy protein hydrolysate, or any combination thereof. In some embodiments, the microbial consortium comprises from 5xl07to 1.5xl08CFU / ml of bacteria. In some embodiments, the microbial consortium comprises from 5xl05to 1.5xl07CFU / ml of nitrogen fixing bacteria. In some embodiments, the microbial consortium comprises from 5xl04to 5xl05CFU / ml of spore forming bacteria. In some embodiments, the microbial consortium comprises from IxlO3to IxlO4CFU / ml of MS3900 spores, MS4921 spores, or any combination thereof. In some embodiments, the microbial consortium comprises from IxlO2to IxlO4CFU / ml of MS3907 spores. In some embodiments, the pH of the composition is from 7 to 9. In some embodiments, the COD of the composition is from 120 to 500 mg / L. In some embodiments, the conductivity of the composition is from 0.5 to 2.0 mS / cm. In some embodiments, the composition has a total dry weight of 0.2 to 2.5 mg / ml.

[0065]

[0065] In an aspect, the present disclosure provides a method of making a biostimulant composition, the method comprising: (a) providing a bioreactor system comprising two or more containers arranged in a series, each of the two or more containers comprising a volume of a working fluid, wherein at least one of the containers comprises a population of a first microbial strain derived from an inoculum of the first microbial strain that has been added to the bioreactor system and a population of other microbes; (b) operating the bioreactor system for a duration of time by: (i) transferring into a first container an aqueous feedstock comprising a microbial consortium; (ii) transferring a portion of the working fluid out of each of the two or more containers into either a subsequent container of the bioreactor system or a product outflow stream; (iii) collecting at least a portion of the product outflow stream as the biostimulant composition; and (iv) maintaining the population of the first microbial strain throughout the duration of time in at least the first container at a level that is at least 80% of the population of the first microbial strain at the beginning of the duration of time; wherein the duration of time is at least 5 days; and wherein the first microbial strain is not present in the aqueous feedstock or any other input into the bioreactor system during the duration of time at a concentration that is higher than 1% of the concentration of the population of the first microbial strain in the first container.

[0066]

[0066] In some embodiments, the first microbial strain has a plant growth promoting property. In some embodiments, the method further comprises providing conditions in the bioreactor system that promote establishment of an enriched population of the first microbial strain relative to a population of the first microbial strain in the aqueous feedstock or any other input into the bioreactor system. In some embodiments, the method further comprises applying a selective pressure in the bioreactor system that favors growth of the first microbial strain relative to the other microbes. In some embodiments, the aqueous feedstock further comprises an organic material digestible by the first microbial strain and by at least some of the other microbes. In some embodiments, the method further comprises producing metabolites that have the plant growth promoting property by digestion of the organic material.

[0067]

[0067] In some embodiments, the first working fluid comprises malate at a concentration of at least 0.2% w / v. In some embodiments, the first working fluid comprises soy flour at a concentration of at least 0.2% w / v. In some embodiments, the first working fluid comprises microaerobic conditions. In some embodiments, the working fluid in at least one of the one or more additional containers comprises microaerobic conditions. In some embodiments, the system has a hydraulic retention time of at least 5 days. In some embodiments, the first working fluid further comprises an established population of a second nitrogen use efficiency -promoting microbial strain, wherein a concentration of the second nitrogen use efficiency -promoting microbial strain in the first working fluid is at least 100 times higher than a concentration of the second nitrogen use efficiency -promoting microbial strain in the aqueous feedstock stream and in any other input into the bioreactor system.

[0068]

[0068] In some embodiments, the second nitrogen use efficiency -promoting microbial strain is of the species Kosakonia sacchari, Klebsiella variicola, Rahnella aquatilis, Kluyvera intermedia, Kosakonia pseusosacchari, Enterobacter spp., Achromobacter marplatensis, Azopirillum lipoferum, Microbacterium murale, Gluconobacter diazotrophicus, Methylobacterium symbioticum, Paenibacillus borealis, Bacillus megaterium (Priestia megaterium), or Paenibacillus sonchi. In some embodiments, the first working fluid further comprises an established population of a third nitrogen use efficiency -promoting microbial strain, wherein a concentration of the third nitrogen use efficiency-promoting microbial strain in the first working fluid is at least 100 times higher than a concentration of the third nitrogen use efficiency-promoting microbial strain in the aqueous feedstock stream and in any other input into the bioreactor system. In some embodiments, the third nitrogen use efficiency-promoting microbial strain is of the species Kosakonia sacchari, Klebsiella variicola, Rahnella aquatilis, Kluyvera intermedia, Kosakonia pseusosacchari, Enterobacter spp., Achromobacter marplatensis, Azopirillum lipoferum, Microbacterium murale, Gluconobacter diazotrophicus, Methylobacterium symbioticum, Paenibacillus borealis, Bacillus megaterium (Priestia megaterium), o Paenibacillus sonchi. In some embodiments, the first working fluid comprises a total population of microbes positive for a nifH gene of at least IxlO5CFU / ml.

[0069]

[0069] In an aspect, the present disclosure provides a method comprising: (a) transferring an aqueous feedstock and an inoculum of an isolated microbe that is capable of promoting nitrogen use efficiency in plants into a first container comprising a volume of a first working fluid, wherein the aqueous feedstock comprises: (i) a first microbial consortium; and (ii) digestion products produced by digestion of an organic substrate by microbes in the first microbial consortium; and (b) incubating the inoculum under conditions that promote growth of the microbe.

[0070]

[0070] In some embodiments, promoting nitrogen use efficiency comprises performing nitrogen fixation, promoting nitrogen fixation in the tissues of plants, recruiting nitrogen fixers to the root zones and other tissues of plants, or increasing organic nitrogen content and / or mineralization of organic nitrogen in soils to enable uptake. In some embodiments, the conditions promote growth of one or more microbes in the first microbial consortium that are capable of promoting nitrogen fixation, nitrogen use efficiency, or recruitment of nitrogen fixing microbes to the roots of plants, or of generating metabolites capable of promoting plant growth, nitrogen fixation, nitrogen use efficiency, or recruitment of nitrogen fixing microbes to the roots of plants. In some embodiments, during the incubating the microbe or one or more microbes in the first microbial consortium generate metabolites capable of promoting nitrogen use efficiency. In some embodiments, the incubating sustains or increases a population of one or more microbes in the microbial consortium capable of promoting plant growth. In some embodiments, the incubating causes the population of the microbe to be at least sustained. In some embodiments, the incubating causes the population of the microbe to increase.

[0071]

[0071] In some embodiments, the incubating causes an enrichment of the population of microbes capable of promoting nitrogen use efficiency. In some embodiments, the conditions sustain the growth of one or more microbes that are capable of promoting nitrogen fixation, nitrogen use efficiency, or recruitment of nitrogen fixing microbes to the roots of plants, or of generating metabolites capable of promoting nitrogen fixation, nitrogen use efficiency, or recruitment of nitrogen fixing microbes to the roots of plants.

[0072]

[0072] In some embodiments, the organic substrate comprises a manure or a lignocellulosic material. In some embodiments, the aqueous feedstock further comprises an inorganic substrate. In some embodiments, the first microbial consortium further comprises microbes derived from the inorganic substrate. In some embodiments, the inorganic substrate comprises rock phosphate.

[0073]

[0073] In some embodiments, the microbe is a bacterium selected from the following: Kosakonia, Klebsiella, Rahnella, Kluyvera, Enterobacter, Achromobacter, Microbacterium, Gluconobacter, Methylobacterium, Pseudomonas, Pantoea, Azospirillum, Azocarus, Herbaspirillum, Burkholderia, Cyanobacteria, Bacillus, and Paenibacillus . In some embodiments, the microbe is of the species Kosakonia sacchari, Klebsiella variicola, Rahnella aquatilis, Kluyvera intermedia, Kosakonia pseusosacchari, Enterobacter spp., Achromobacter marplatensis, Azopirillum lipoferum, Microbacterium murale, Gluconobacter diazotrophicus, Methylobacterium symbioticum, Paenibacillus borealis, Bacillus megaterium (Priestia megaterium), and Paenibacillus sonchi. In some embodiments, the microbe is the strain deposited under ATCC Accession No. PTA-127654 (MS3907), the strain deposited under ATCC Accession No. PTA-127653 (MS3900), the strain deposited under ATCC Accession No. PTA-127655 (MS4921), or the strain deposited under ATCC Accession No. PTA-127652 (MS2748).

[0074]

[0074] In some embodiments, the aqueous feedstock further comprises one or more carbon sources capable of being metabolized by the microbe or by microbes in the first microbial consortium. In some embodiments, the one or more carbon sources comprise one or more simple sugars. In some embodiments, the one or more simple sugars comprise glucose, malate, lactose, sucrose, or pyruvate, or any combination thereof. In some embodiments, the aqueous feedstock further comprises a nitrogen source. In some embodiments, the nitrogen source comprises one or more of ammonium sulfate, ammonium chloride, ammonium nitrate, sodium nitrate, yeast extract, or yeast, or any combination thereof. In some embodiments, the aqueous feedstock further comprises soy flour, corn flour, cereal flour, corn gluten, soy flour protein, or soy protein hydrolysate, or any combination thereof.

[0075]

[0075] In some embodiments, the aqueous feedstock and the inoculum are transferred separately. In some embodiments, the aqueous feedstock and the inoculum of the isolated microbe are combined together before being transferred into the first container. In some embodiments, the first working fluid comprises (a) a second microbial consortium derived from the aqueous feedstock, and / or (b) digestion products produced by digestion of substances present in the aqueous feedstock by the first microbial consortium and / or the microbe. In some embodiments, the method further comprises transferring a portion of the first working fluid into a second container comprising a second working fluid and incubating the second working fluid in the second container. In some embodiments, the second working fluid comprises (a) a third microbial consortium derived from the first working fluid, and (b) digestion products produced by digestion of substances present in the first working fluid by the third microbial consortium and the microbe.

[0076]

[0076] In some embodiments, the total amount of fluid transferred into the first container over a time period is equal to the amount of the first working fluid transferred into the second container over the same time period. In some embodiments, the volume of the first working fluid in the first container is maintained constant. In some embodiments, transferring the aqueous feedstock into the first container comprises continuously flowing the aqueous feedstock into the first container at a first flow rate, transferring the portion of the first working fluid into the second container comprises continuously flowing the portion of the first working fluid into the second container at a second flow rate. In some embodiments, the first flow rate and the second flow rate are equal.

[0077]

[0077] In some embodiments, the method further comprises transferring a portion of the second working fluid to a third container comprising a third working fluid and incubating the third working fluid in the third container. In some embodiments, the method further comprises transferring a portion of the third working fluid into a fourth container comprising a fourth working fluid and incubating the fourth working fluid in the fourth container. In some embodiments, the first working fluid, the second working fluid, the third working fluid, and the fourth working fluid are maintained at constant volumes. In some embodiments, the microbe is present in the second working fluid, the third working fluid, and / or the fourth working fluid. In some embodiments, the first working fluid and any subsequent working fluids are maintained under microaerobic conditions.

[0078]

[0078] In some embodiments, one or more of the five most abundant microbial species in the first microbial consortium are from the following genera: Haliscomenobacter , I. ew ine Ila. Caldilinea, Terrimonas. and Acidobacterium. In some embodiments, one or more of five most abundant microbial species in the first microbial consortium comprise Lewinella cohaerens. Thauera phenylacelica. Thauera mechernichensis. Solitalea canadensis, or Nitrospira moscoviensis .

[0079] In some embodiments, the method further comprises transferring into the first container one or more additional isolated microbes that are capable of promoting nitrogen use efficiency in plants. In some embodiments, the one or more additional isolated microbes comprise one or more of MS3900, MS3907, MS4921, and MS2748, or any combination thereof. In some embodiments, two or more of MS3900, MS3907, MS4921, and MS2748 are transferred into the first container. In some embodiments, the method further comprises transferring the microbe and / or one or more additional isolated microbes capable of promoting nitrogen use efficiency in plants to the second working fluid, the third working fluid, or the fourth working fluid, or any subsequent working fluid if more than four containers are fluidly connected in the method. In some embodiments, the one or more additional isolated microbes comprise one or more of MS3900, MS3907, MS4921, and MS2748, or any combination thereof.

[0079]

[0080] In some embodiments, the method further comprises filtering the first working fluid, the second working fluid, the third working fluid, the fourth working fluid, or any subsequent working fluid if more than four containers are fluidly connected in the method. In some embodiments, the filtering removes bacteria from the respective working fluid. In some embodiments, the filtering removes at least 99% or at least 99.9% of all bacteria from the respective working fluid. In some embodiments, the filtering produces a sterile fluid. In some embodiments, the pH is monitored and adjusted during the incubation. In some embodiments, the first working fluid is transferred directly to a clarifier in which floc from the first working fluid is separated from the first working fluid. In some embodiments, a portion of the first working fluid is not continuously transferred out of the first container. In some embodiments, the incubation in the first container is operated in a batch mode. In some embodiments, the dissolved oxygen content in the first working fluid during the incubation in the first container is maintained between 0.1 and 0.8 mg / L. In some embodiments, the pH of the first working fluid is between 3.5 and 8 during the incubation in the first container.

[0080]

[0081] In an aspect, the present disclosure provides a method of making a biostimulant composition, the method comprising: (a) providing a bioreactor system comprising two or more containers arranged in a series, each of the two or more containers comprising a volume of a working fluid, wherein at least one of the containers comprises a population of a first microbial strain derived from an inoculum of the first microbial strain that has been added to the bioreactor system and a population of other microbes; (b) operating the bioreactor system for a duration of time by: (i) transferring into a first container an aqueous feedstock comprising a microbial consortium; (ii) transferring a portion of the working fluid out of each of the two or more containers into either a subsequent container of the bioreactor system or a product outflow stream; (iii) collecting at least a portion of the product outflow stream as the biostimulant composition; and (iv) maintaining the population of the first microbial strain throughout the duration of time in at least the first container at a level that is at least 80% of the population of the first microbial strain at the beginning of the duration of time; wherein the duration of time is at least 5 days; and wherein the first microbial strain is not present in the aqueous feedstock or any other input into the bioreactor system during the duration of time at a concentration that is higher than 1% of the concentration of the population of the first microbial strain in the first container.

[0081]

[0082] In some embodiments, the first microbial strain has a plant growth promoting property.

[0082]

[0083] In some embodiments, the method further comprises providing conditions in the bioreactor system that promote establishment of an enriched population of the first microbial strain relative to a population of the first microbial strain in the aqueous feedstock or any other input into the bioreactor system. In some embodiments, the method further comprises applying a selective pressure in the bioreactor system that favors growth of the first microbial strain relative to the other microbes. In some embodiments, the aqueous feedstock further comprises an organic material digestible by the first microbial strain and by at least some of the other microbes. In some embodiments, the method further comprises producing metabolites that have the plant growth promoting property by digestion of the organic material.

[0083]

[0084] In some embodiments, the first working fluid comprises malate at a concentration of at least 0.2% w / v. In some embodiments, the first working fluid comprises soy flour at a concentration of at least 0.2% w / v. In some embodiments, the first working fluid comprises microaerobic conditions. In some embodiments, the working fluid in at least one of the one or more additional containers comprises microaerobic conditions. In some embodiments, the system has a hydraulic retention time of at least 5 days.

[0084]

[0085] In some embodiments, the first working fluid further comprises an established population of a second nitrogen use efficiency -promoting microbial strain, wherein a concentration of the second nitrogen use efficiency -promoting microbial strain in the first working fluid is at least 100 times higher than a concentration of the second nitrogen use efficiency -promoting microbial strain in the aqueous feedstock stream and in any other input into the bioreactor system. In some embodiments, the second nitrogen use efficiency-promoting microbial strain is of the species Kosakonia sacchari, Klebsiella variicola, Rahnella aquatilis, Kluyvera intermedia, Kosakonia pseusosacchari, Enterobacter spp., Achromobacter marplatensis, Azopirillum lipoferum, Microbacterium murale, Gluconobacter diazotrophicus, Methylobacterium symbioticum, Paenibacillus borealis, Bacillus megaterium Priestia megaterium), or Paenibacillus sonchi.

[0085]

[0086] In some embodiments, the first working fluid further comprises an established population of a third nitrogen use efficiency-promoting microbial strain, wherein a concentration of the third nitrogen use efficiency -promoting microbial strain in the first working fluid is at least 100 times higher than a concentration of the third nitrogen use efficiency -promoting microbial strain in the aqueous feedstock stream and in any other input into the bioreactor system. In some embodiments, the third nitrogen use efficiency-promoting microbial strain is of the species Kosakonia sacchari, Klebsiella variicola, Rahnella aquatilis, Kluyvera intermedia, Kosakonia pseusosacchari, Enter obacter spp., Achromobacter marplatensis, Azopirillum lipoferum, Microbacterium murale, Gluconobacter diazotrophicus, Methylobacterium symbioticum, Paenibacillus borealis, Bacillus megaterium (Priestia megaterium), or Paenibacillus sonchi. In some embodiments, the first working fluid comprises a total population of microbes positive for a nifH gene of at least IxlO5CFU / ml.

[0086]

[0087] In an aspect, the present disclosure provides a method of promoting plant growth, comprising: (a) contacting a plant and / or medium in which the plant is growing with a composition comprising one or more compounds, wherein the one or more compounds is selected from acinospesigenin-C, 3-cyclohexyl-6-[4-[3-(trifluoromethyl)phenyl]-l-piperazinyl]- lH-pyrimidine-2, 4-dione, Arg-Thr-Ala-Arg, (2R)-2-[[4-(2,6-dipyrrolidin-l-ylpyrimidin-4- yl)piperazin-l-yl]methyl]-2,5,7,8-tetramethyl-3,4-dihydrochromen-6-ol;dihydrochloride, Gly- Leu-Arg-Val-Phe, westiellamide, thrombin receptor activator for peptide 5 (TRAP-5), tungstic acid, fercomin, threoninyl-isoleucine, BW-A868C, Lys-Ala-Leu-Glu, N- Benzyloxycarbonylglycine, Glu-Asp-Asn, Glu-Asp-Asn, Ile-Glu-His-Lys, Chaps, didemethylcital opram, Lys-Tyr-Thr-Ser-Ser, 3-amino-4,6-dimethyl-N-(l- phenylethyl)thieno[2,3-b]pyridine-2-carboxamide, Asn-Ala-Leu-Ala-His, Met-Asp-Arg, His- Arg-Lys-Glu, Asn-Cys-Phe, 7-Hydroxylauric acid, Phe-Tyr-Lys-Arg, k-Strophanthoside, disopyramide, estra-4,9-diene-3, 17-dione, HoPhe-Asp-OH, tert-butyl 5-methyl-6-oxo-5,6- dihydro-4h-imidazo[l,5-a]thieno[2,3-f][l,4]diazepine-3-carboxylate, 2,6-naphthalenediol, zonisamide, Ser-Gln-Leu-Lys, Pro-Ala-Phe, Ala-Thr-Ile-Lys, mycophenolic acid, PC(15:0 / 18:3(6Z,9Z,12Z)), 6-[(2Z)-2-benzylideneheptoxy]-3,4,5-trihydroxyoxane-2-carboxylic acid, 7"-Deoxybonaspectin D 4"-methyl ether, Reciniferatoxin, Acetic acid trans-2-hepten-l-YL ester, Acetoxy-6-gingerol, Dubini dine, N-l -Naphthylbenzamide, one or more derivatives thereof, or combination thereof.

[0088] In some embodiments, the plant growth property is nitrogen use efficiency. In some embodiments, the concentration of the one or more compound in the composition is at least about 1 nanomolar (nM). In some embodiments, the concentration of the one or more compounds in the composition is at least about 0.00001% of a dry weight of the composition. In some embodiments, the contacting comprises contacting the plant with the composition. In some embodiments, the contracting comprises contacting a plant seed with the composition. In some embodiments, the contacting comprises contacting a leaf of the plant with the composition. In some embodiments, the medium comprises soil, a hydroponic medium, turface, or isolite. In some embodiments, the contacting comprises increasing a plant nitrogen content by at least 5%. In some embodiments, the contacting comprises increasing a nitrogen fixation activity in plant tissues by at least 5%. In some embodiments, the contacting comprises increasing a population of nitrogen fixation bacteria in the root and root rhizospheres of the plant by at least 5%. In some embodiments, the contacting causes recruitment of nitrogen fixing bacteria present in the medium to a root zone of the plant. In some embodiments, the contacting causes an increase in plant growth by at least 10 percent as compared to the plant and / or the medium not contacted with the one or more compounds.

[0087]

[0089] In an aspect, the present disclosure provides a composition for promoting plant growth, comprising: (i) at least one microbial strain selected from a Bacillus megaterium strain, a Paenibacillus borealis strain, or a Paenibacillus sonchi strain; and (ii) one or more compounds selected from acinospesigenin-C, 3-cyclohexyl-6-[4-[3-(trifluoromethyl)phenyl]-l-piperazinyl]- lH-pyrimidine-2, 4-dione, Arg-Thr-Ala-Arg, (2R)-2-[[4-(2,6-dipyrrolidin-l-ylpyrimidin-4- yl)piperazin-l-yl]methyl]-2,5,7,8-tetramethyl-3,4-dihydrochromen-6-ol;dihydrochloride, Gly- Leu-Arg-Val-Phe, westiellamide, thrombin receptor activator for peptide 5 (TRAP-5), tungstic acid, fercomin, threoninyl-isoleucine, BW-A868C, Lys-Ala-Leu-Glu, N- Benzyloxycarbonylglycine, Glu-Asp-Asn, Glu-Asp-Asn, Ile-Glu-His-Lys, Chaps, didemethylcital opram, Lys-Tyr-Thr-Ser-Ser, 3-amino-4,6-dimethyl-N-(l- phenylethyl)thieno[2,3-b]pyridine-2-carboxamide, Asn-Ala-Leu-Ala-His, Met-Asp-Arg, His- Arg-Lys-Glu, Asn-Cys-Phe, 7-Hydroxylauric acid, Phe-Tyr-Lys-Arg, k-Strophanthoside, disopyramide, estra-4,9-diene-3, 17-dione, HoPhe-Asp-OH, tert-butyl 5-methyl-6-oxo-5,6- dihydro-4h-imidazo[l,5-a]thieno[2,3-f][l,4]diazepine-3-carboxylate, 2,6-naphthalenediol, zonisamide, Ser-Gln-Leu-Lys, Pro-Ala-Phe, Ala-Thr-Ile-Lys, mycophenolic acid, PC(15:0 / 18:3(6Z,9Z,12Z)), 6-[(2Z)-2-benzylideneheptoxy]-3,4,5-trihydroxyoxane-2-carboxylic acid, 7"-Deoxybonaspectin D 4"-methyl ether, Reciniferatoxin, Acetic acid trans-2-hepten-l-YL ester, Acetoxy-6-gingerol, Dubini dine, N-l -Naphthylbenzamide, oxalacetic acid, l-Oleoyl-2- palmitoyl-sn-glycero-3-phosphocholine, Undeca-2-ene-8,10-diynoic acid isobutylamide, ent- Corey PG-Lactone Diol, one or more derivatives thereof, or combination thereof.

[0088]

[0090] In some embodiments, the Paenibacillus sonchi strain comprises one or more of the following: (i) a 16S rRNA gene sequence at least 95% identical to SEQ ID NO: 3; (ii) a gyrB gene sequence at least 95% identical to SEQ ID NO: 6; (iii) an rpoB gene sequence at least 95% identical to SEQ ID NO: 9; and (iv) a nifH gene sequence at least 95% identical to SEQ ID NO: 14. In some embodiments, the Paenibacillus borealis strain comprises one or more of the following: (i) a 16S rRNA gene sequence at least 95% identical to SEQ ID NO: 2; (ii) a gyrB gene sequence at least 95% identical to SEQ ID NO: 5; (iii) an rpoB gene sequence at least 95% identical to SEQ ID NO: 8; and (iv) a nifH gene sequence at least 95% identical to SEQ ID NO: 13. In some embodiments, the Bacillus megaterium strain comprises one or more of the following: (i) a 16S rRNA gene sequence at least 95% identical to SEQ ID NO: 1; (ii) a gyrB gene sequence at least 95% identical to SEQ ID NO: 4; and (iii) an rpoB gene sequence at least 95% identical to SEQ ID NO: 7.

[0089]

[0091] In some embodiments, oxalacetic acid, l-Oleoyl-2-palmitoyl-sn-glycero-3- phosphocholine, Undeca-2-ene-8,10-diynoic acid isobutylamide, and ent-Corey PG-Lactone Diol, oxalacetic acid is the most abundant and ent-Corey PG-Lactone Diol is the least abundant. In some embodiments, l-Oleoyl-2-palmitoyl-sn-glycero-3 -phosphocholine is present at a concentration of l%-2% of the concentration of oxalacetic acid. In some embodiments, Undeca- 2-ene-8,10-diynoic acid isobutylamide is present at a concentration of l%-2% of the concentration of oxalacetic acid. In some embodiments, ent-Corey PG-Lactone Diol is present at a concentration of 0.5%-l .5% of the concentration of oxalacetic acid.

[0090]

[0092] In some embodiments, the composition further comprises a carrier. In some embodiments, the carrier is formulated for application to a plant and / or medium in which the plant is growing.

[0091]

[0093] In an aspect, the present disclosure provides a composition for promoting plant growth , comprising: (i) two or more compounds selected from acinospesigenin-C, 3-cyclohexyl-6-[4-[3- (trifluoromethyl)phenyl]-l-piperazinyl]-lH-pyrimidine-2, 4-dione, Arg-Thr-Ala-Arg, (2R)-2-[[4- (2,6-dipyrrolidin-l-ylpyrimidin-4-yl)piperazin-l-yl]methyl]-2,5,7,8-tetramethyl-3,4- dihydrochromen-6-ol;dihydrochloride, Gly-Leu-Arg-Val-Phe, westiellamide, thrombin receptor activator for peptide 5 (TRAP-5), tungstic acid, fercomin, threoninyl-isoleucine, BW-A868C, Lys-Ala-Leu-Glu, N-Benzyloxycarbonylglycine, Glu-Asp-Asn, Glu-Asp-Asn, Ile-Glu-His-Lys, Chaps, didemethylcitalopram, Lys-Tyr-Thr-Ser-Ser, 3-amino-4,6-dimethyl-N-(l- phenylethyl)thieno[2,3-b]pyridine-2-carboxamide, Asn-Ala-Leu-Ala-His, Met-Asp-Arg, His- Arg-Lys-Glu, Asn-Cys-Phe, 7-Hydroxylauric acid, Phe-Tyr-Lys-Arg, k-Strophanthoside, disopyramide, estra-4,9-diene-3, 17-dione, HoPhe-Asp-OH, tert-butyl 5-methyl-6-oxo-5,6- dihydro-4h-imidazo[l,5-a]thieno[2,3-f][l,4]diazepine-3-carboxylate, 2,6-naphthalenediol, zonisamide, Ser-Gln-Leu-Lys, Pro-Ala-Phe, Ala-Thr-Ile-Lys, mycophenolic acid, PC(15:0 / 18:3(6Z,9Z,12Z)), 6-[(2Z)-2-benzylideneheptoxy]-3,4,5-trihydroxyoxane-2-carboxylic acid, 7"-Deoxybonaspectin D 4"-methyl ether, Reciniferatoxin, Acetic acid trans-2-hepten-l-YL ester, Acetoxy-6-gingerol, Dubini dine, N-l -Naphthylbenzamide, oxalacetic acid, l-Oleoyl-2- palmitoyl-sn-glycero-3-phosphocholine, Undeca-2-ene-8,10-diynoic acid isobutylamide, ent- Corey PG-Lactone Diol, one or more derivatives thereof, or a combination thereof; and (ii) a carrier.

[0092]

[0094] In some embodiments, the carrier is formulated for application to a plant and / or medium in which the plant is growing. In some embodiments, the carrier comprises a fertilizer. In some embodiments, the fertilizer is a solid. In some embodiments, the carrier is a liquid. In some embodiments, the composition is configured to promote and / or is capable of promoting nitrogen use efficiency when applied to a plant or plant growth medium.

[0093]

[0095] In some embodiments, oxalacetic acid, l-Oleoyl-2-palmitoyl-sn-glycero-3- phosphocholine, Undeca-2-ene-8,10-diynoic acid isobutylamide, and ent-Corey PG-Lactone Diol, oxalacetic acid is the most abundant and ent-Corey PG-Lactone Diol is the least abundant. In some embodiments, l-Oleoyl-2-palmitoyl-sn-glycero-3 -phosphocholine is present at a concentration of l%-2% of the concentration of oxalacetic acid. In some embodiments, Undeca- 2-ene-8,10-diynoic acid isobutylamide is present at a concentration of l%-2% of the concentration of oxalacetic acid. In some embodiments, ent-Corey PG-Lactone Diol is present at a concentration of 0.5%-l .5% of the concentration of oxalacetic acid. In some embodiments, the concentration of the one or more compounds in the composition is at least about 1 nM. In some embodiments, the concentration of the one or more compounds in the composition is at least about 0.00001% of a total dry weight of the composition. In some embodiments, the composition further comprises an adjuvant selected from a wetting agent, spreading agent, dispersing agent, sticking agent, dust control agent, and adhesive.

[0094]

[0096] In some embodiments, the composition is configured to increase and / or is capable of increasing a plant nitrogen content by at least 5%. In some embodiments, composition is configured to increase and / or is capable of increasing a nitrogen fixation activity in plant tissues by at least 5%. In some embodiments, composition is configured to increase and / or is capable of increasing a population of nitrogen fixing bacteria in a root and root rhizospheres of the plant by at least 5%. In some embodiments, the composition is configured to cause and / or is capable of causing recruitment of nitrogen fixing bacteria present in a medium of the plant to a root zone of the plant. In some embodiments, the composition is configured to cause and / or is capable of causing an increase in plant growth by at least 10 percent as compared to a control.

[0095]

[0097] In an aspect, the present disclosure provides a method of promoting plant growth, comprising: (a) contacting a plant and / or medium in which the plant is growing with a composition comprising one or more compounds, wherein the one or more compounds is selected from 4-(2-Pyridylazo)-N,N-dimethylaniline, LPC(18:2 / 0:0), LPE(18:2 / 0:0), 7-[3- (Dimethylamino)propoxy]-6-Methoxy-2-(4-Methyl-l,4-Diazepan-l-Yl)-N-(l-Methylpiperidin- 4-Yl)quinazolin-4-Amine, 7-chloro-2-(3,4-dimethoxyphenyl)-3,5,8-trihydroxy-6-methoxy-4H- chromen-4-one, l-(2,4,5-Trimethoxyphenyl)-l,2-propanedione, 3-(4-hydroxy-2,3,5- trimethoxyphenyl)prop-2-enal, LPE(18: 1 / 0:0), 9-((2-Phosphonylmethoxy)ethyl)guanine, PC(P- 16:0 / 20:5(5Z,8Z,l 1Z,14Z,17Z)), Diellagilactone, 13-Methylmyristic acid, D-Limonene, one or more derivatives thereof, 3-Phosphoadenylylselenate, l,3-bis(4-Bromophenyl)-5-phenyl-2,4- imidazolidinedione, F-Amidine, LPC(0:0 / 18:3), Undecanedioic acid, Muzanzagenin, or combination thereof.

[0096]

[0098] In some embodiments, the contacting increases nitrogen use efficiency by the plant. In some embodiments, the concentration of the one or more compound in the composition is at least about 1 nM. In some embodiments, the concentration of the one or more compounds in the composition is at least about 0.00001% of a total dry weight of the composition. In some embodiments, the contacting comprises contacting the plant with the composition. In some embodiments, the contracting comprises contacting a plant seed with the composition. In some embodiments, the contacting comprises contacting a leaf of the plant with the composition. In some embodiments, the medium comprises soil, a hydroponic medium, turface, or isolite. In some embodiments, the contacting increases a plant nitrogen content by at least 5%. In some embodiments, the contacting increases a nitrogen fixation activity in plant tissues by at least 5%. In some embodiments, the contacting increases a population of nitrogen fixation bacteria in the root and root rhizospheres of the plant by at least 5%. In some embodiments, the contacting causes recruitment of nitrogen fixing bacteria present in the medium to a root zone of the plant.

[0097]

[0099] In some embodiments, the contacting causes an increase in plant growth by at least 10 percent as compared to the plant and / or the medium not contacted with the one or more compounds.

[0098]

[0100] In an aspect, the present disclosure provides a composition for promoting plant growth, comprising: (i) at least one microbial strain selected from a Bacillus megaterium strain, a Paenibacillus borealis strain, or a Paenibacillus sonchi strain; and (ii) one or more compounds selected from 4-(2-Pyridylazo)-N,N-dimethylaniline, LPC(18:2 / 0:0), LPE(18:2 / 0:0), 7-[3- (Dimethylamino)propoxy]-6-Methoxy-2-(4-Methyl-l,4-Diazepan-l-Yl)-N-(l-Methylpiperidin- 4-Yl)quinazolin-4-Amine, 7-chloro-2-(3,4-dimethoxyphenyl)-3,5,8-trihydroxy-6-methoxy-4H- chromen-4-one, l-(2,4,5-Trimethoxyphenyl)-l,2-propanedione, 3-(4-hydroxy-2,3,5- trimethoxyphenyl)prop-2-enal, LPE(18: 1 / 0:0), 9-((2-Phosphonylmethoxy)ethyl)guanine, PC(P- 16:0 / 20:5(5Z,8Z,l 1Z,14Z,17Z)), Diellagilactone, 13-Methylmyristic acid, D-Limonene, 3- Phosphoadenylylselenate, l,3-bis(4-Bromophenyl)-5-phenyl-2,4-imidazolidinedione, F- Amidine, LPC(0:0 / 18:3), Undecanedioic acid, Muzanzagenin, oxalacetic acid, l-Oleoyl-2- palmitoyl-sn-glycero-3-phosphocholine, Undeca-2-ene-8,10-diynoic acid isobutylamide, ent- Corey PG-Lactone Diol, one or more derivatives thereof, or combination thereof.

[0099]

[0101] In some embodiments, the Paenibacillus sonchi strain comprises one or more of the following: (i) a 16S rRNA gene sequence at least 95% identical to SEQ ID NO: 3; (ii) a gyrB gene sequence at least 95% identical to SEQ ID NO: 6; (iii) an rpoB gene sequence at least 95% identical to SEQ ID NO: 9; and (iv) a nifH gene sequence at least 95% identical to SEQ ID NO: 14. In some embodiments, the Paenibacillus borealis strain comprises one or more of the following: (i) a 16S rRNA gene sequence at least 95% identical to SEQ ID NO: 2; (ii) a gyrB gene sequence at least 95% identical to SEQ ID NO: 5; (iii) an rpoB gene sequence at least 95% identical to SEQ ID NO: 8; and (iv) a nifH gene sequence at least 95% identical to SEQ ID NO: 13. In some embodiments, the Bacillus megaterium strain comprises one or more of the following: (i) a 16S rRNA gene sequence at least 95% identical to SEQ ID NO: 1; (ii) a gyrB gene sequence at least 95% identical to SEQ ID NO: 4; and (iii) an rpoB gene sequence at least 95% identical to SEQ ID NO: 7.

[0100]

[0102] In some embodiments, of oxalacetic acid, l-Oleoyl-2-palmitoyl-sn-glycero-3- phosphocholine, Undeca-2-ene-8,10-diynoic acid isobutylamide, and ent-Corey PG-Lactone Diol, oxalacetic acid is the most abundant and ent-Corey PG-Lactone Diol is the least abundant. In some embodiments, l-Oleoyl-2-palmitoyl-sn-glycero-3 -phosphocholine is present at a concentration of l%-2% of the concentration of oxalacetic acid. In some embodiments, Undeca- 2-ene-8,10-diynoic acid isobutylamide is present at a concentration of l%-2% of the concentration of oxalacetic acid. In some embodiments, ent-Corey PG-Lactone Diol is present at a concentration of 0.5%-l .5% of the concentration of oxalacetic acid.

[0101]

[0103] In some embodiments, the composition further comprises a carrier. In some embodiments, the carrier is formulated for application to a plant and / or medium in which the plant is growing.

[0104] In an aspect, the present disclosure provides a composition for promoting plant growth, comprising: (i) two or more compounds selected from 4-(2-Pyridylazo)-N,N-dimethylaniline, LPC(18:2 / 0:0), LPE(18:2 / 0:0), 7-[3-(Dimethylamino)propoxy]-6-Methoxy-2-(4-Methyl-l,4- Diazepan-1-Yl)-N-(1-Methylpiperi din-4- Yl)quinazolin-4- Amine, 7-chloro-2-(3,4- dimethoxyphenyl)-3,5,8-trihydroxy-6-methoxy-4H-chromen-4-one, 1 -(2,4,5- Trimethoxyphenyl)-l,2-propanedione, 3-(4-hydroxy-2,3,5-trimethoxyphenyl)prop-2-enal, LPE(18:l / 0:0), 9-((2-Phosphonylmethoxy)ethyl)guanine, PC(P-16:0 / 20:5(5Z,8Z,l 1Z,14Z,17Z)), Diellagilactone, 13-Methylmyristic acid, D-Limonene, 3-Phosphoadenylylselenate, l,3-bis(4- Bromophenyl)-5-phenyl-2,4-imidazolidinedione, F-Amidine, LPC(0:0 / 18:3), Undecanedioic acid, Muzanzagenin, one or more derivatives thereof, or combination thereof; and (ii) a carrier.

[0102]

[0105] In some embodiments, the carrier is formulated for application to a plant and / or medium in which the plant is growing. In some embodiments, the carrier comprises a fertilizer. In some embodiments, the fertilizer is a solid. In some embodiments, the carrier is a liquid. In some embodiments, the composition is configured to increase and / or is capable of increasing nitrogen use efficiency when applied to a plant.

[0103]

[0106] In some embodiments, of oxalacetic acid, l-Oleoyl-2-palmitoyl-sn-glycero-3- phosphocholine, Undeca-2-ene-8,10-diynoic acid isobutylamide, and ent-Corey PG-Lactone Diol, oxalacetic acid is the most abundant and ent-Corey PG-Lactone Diol is the least abundant. In some embodiments, l-Oleoyl-2-palmitoyl-sn-glycero-3 -phosphocholine is present at a concentration of l%-2% of the concentration of oxalacetic acid. In some embodiments, Undeca- 2-ene-8,10-diynoic acid isobutylamide is present at a concentration of l%-2% of the concentration of oxalacetic acid. In some embodiments, ent-Corey PG-Lactone Diol is present at a concentration of 0.5%-l .5% of the concentration of oxalacetic acid. In some embodiments, the concentration of the one or more compounds in the composition is at least about 1 nM. In some embodiments, the concentration of the one or more compounds in the composition is at least about 0.00001%. In some embodiments, the composition further comprises an adjuvant selected from a wetting agent, spreading agent, dispersing agent, sticking agent, dust control agent, and adhesive.

[0104]

[0107] In some embodiments, composition is configured to increase and / or is capable of increasing a plant nitrogen content by at least 5%. In some embodiments, composition is configured to increase and / or is capable of increasing a nitrogen fixation activity in plant tissues by at least 5%. In some embodiments, composition is configured to increase and / or is capable of increasing a population of nitrogen fixing bacteria in a root and root rhizospheres of the plant by at least 5%. In some embodiments, the composition is configured to cause and / or is capable of causing recruitment of nitrogen fixing bacteria present in a medium of the plant to a root zone of the plant. In some embodiments, the composition is configured to cause and / or is capable of causing an increase in plant growth by at least 10 percent as compared to a control.

[0105]

[0108] In an aspect, the present disclosure provides a method of promoting plant growth, comprising: (a) contacting a plant and / or medium in which the plant is growing with a composition comprising one or more compounds, wherein the one or more compounds is selected from zearalanone, dodecanal dimethyl acetal, l-[5-Ethyl-2-hydroxy-4-[[6-methyl-6- (lH-tetrazol-5-YL)heptyl]oxy]phenyl]ethanone, N-[5-(lH-indol-3-ylmethyl)-l,3,4-thiadiazol-2- yl]-4-methoxybenzamide, trandolaprilat, lythidathion, chrysanthetriol, a derivative thereof, or a combination thereof.

[0106]

[0109] In some embodiments, the contacting increases phosphate solubilization in the plant growth medium. In some embodiments, the concentration of the one or more compound in the composition is at least about 1 nM. In some embodiments, the concentration of the one or more compounds in the composition is at least about 0.00001% of a total dry weight of the composition. In some embodiments, the contacting comprises contacting the plant with the composition. In some embodiments, the contracting comprises contacting a plant seed with the composition. In some embodiments, the contacting comprises contacting a leaf of the plant with the composition. In some embodiments, the medium comprises soil, a hydroponic medium, turface, or isolite.

[0107] [HO] In an aspect, the present disclosure provides a composition for promoting plant growth, comprising: (a) at least one microbial strain selected from one or more of Lewinella coharens. Thauera phenylacetica, Thauera mechernichensis. Solitalea canadensis, and Nitrospira moscoviensis,' and (b) one or more compounds selected from zearalanone, dodecanal dimethyl acetal, l-[5-Ethyl-2-hydroxy-4-[[6-methyl-6-(lH-tetrazol-5-YL)heptyl]oxy]phenyl]ethanone, N- [5-(lH-indol-3-ylmethyl)-l,3,4-thiadiazol-2-yl]-4-methoxybenzamide, trandolaprilat, lythidathion, chrysanthetriol, oxalacetic acid, l-Oleoyl-2-palmitoyl-sn-glycero-3- phosphocholine, Undeca-2-ene-8,10-diynoic acid isobutylamide, ent-Corey PG-Lactone Diol or a derivative thereof, or a combination thereof.

[0108] [Hl] In some embodiments, the concentration of the one or more compound in the composition is at least about 1 nM. In some embodiments, the concentration of the one or more compounds in the composition is at least about 0.00001% of a total dry weight of the composition.

[0109]

[0112] In some embodiments, of oxalacetic acid, l-Oleoyl-2-palmitoyl-sn-glycero-3- phosphocholine, Undeca-2-ene-8,10-diynoic acid isobutylamide, and ent-Corey PG-Lactone Diol, oxalacetic acid is the most abundant and ent-Corey PG-Lactone Diol is the least abundant. In some embodiments, l-Oleoyl-2-palmitoyl-sn-glycero-3 -phosphocholine is present at a concentration of l%-2% of the concentration of oxalacetic acid. In some embodiments, Undeca-

[0110] 2-ene-8,10-diynoic acid isobutylamide is present at a concentration of l%-2% of the concentration of oxalacetic acid. In some embodiments, ent-Corey PG-Lactone Diol is present at a concentration of 0.5%-l .5% of the concentration of oxalacetic acid.

[0111]

[0113] In some embodiments, the composition further comprises a carrier. In some embodiments, the carrier is formulated for application to a plant and / or medium in which the plant is growing.

[0112]

[0114] In an aspect, the present disclosure provides a composition for promoting plant growth, comprising: (a) two or more of zearalanone, dodecanal dimethyl acetal, l-[5-Ethyl-2-hydroxy-4- [[6-methyl-6-(lH-tetrazol-5-YL)heptyl]oxy]phenyl]ethanone, N-[5-(lH-indol-3-ylmethyl)- l,3,4-thiadiazol-2-yl]-4-methoxybenzamide, trandolaprilat, lythidathion, chrysanthetriol, oxalacetic acid, l-Oleoyl-2-palmitoyl-sn-glycero-3 -phosphocholine, Undeca-2-ene-8,10-diynoic acid isobutyl ami de, ent-Corey PG-Lactone Diol, a derivative thereof, or a combination thereof; and (b) a carrier.

[0113]

[0115] In some embodiments, the carrier is formulated for application to a plant and / or medium in which the plant is growing. In some embodiments, the carrier comprises a fertilizer. In some embodiments, the fertilizer is a solid. In some embodiments, the carrier is a liquid. In some embodiments, the composition is configured to and / or is capable of promoting phosphate solubilization when applied to a plant or a plant growth medium.

[0114]

[0116] In some embodiments, of oxalacetic acid, l-Oleoyl-2-palmitoyl-sn-glycero-3- phosphocholine, Undeca-2-ene-8,10-diynoic acid isobutylamide, and ent-Corey PG-Lactone Diol, oxalacetic acid is the most abundant and l-Oleoyl-2-palmitoyl-sn-glycero-3- phosphocholine is the least abundant. In some embodiments, l-Oleoyl-2-palmitoyl-sn-glycero-

[0115] 3 -phosphocholine is present at a concentration of l%-2% of the concentration of oxalacetic acid. In some embodiments, Undeca-2-ene-8,10-diynoic acid isobutylamide is present at a concentration of 8%-12% of the concentration oxalacetic acid. In some embodiments, ent-Corey PG-Lactone Diol is present at a concentration of 8%-12%of the concentration oxalacetic acid. In some embodiments, the concentration of the one or more compounds in the composition is at least about 1 nM. In some embodiments, the concentration of the one or more compounds in the composition is at least about 0.00001% of the total dry weight of the composition. In some embodiments, the composition further comprises an adjuvant selected from a wetting agent, spreading agent, dispersing agent, sticking agent, dust control agent, and adhesive. In some embodiments, the composition is configured to increase and / or is capable of increasing phosphate solubilization in a plant growth medium.

[0116] INCORPORATION BY REFERENCE

[0117]

[0117] All publications, patents, and patent applications mentioned in this specification are herein incorporated by reference to the same extent as if each individual publication, patent, or patent application was specifically and individually indicated to be incorporated by reference.

[0118] BRIEF DESCRIPTION OF THE DRAWINGS

[0119]

[0118] The novel features of the disclosure are set forth with particularity in the appended claims. A better understanding of the features and advantages of the present disclosure will be obtained by reference to the following detailed description that sets forth illustrative embodiments, in which the principles of the disclosure are utilized, and the accompanying drawings (also “figure” and “FIG.” herein), of which:

[0120]

[0119] FIGs. 1A-1B are a series of graphs showing corn nitrogen content and yield between control and a combination of MS3900 and MS3907 isolates. FIG. 1A depicts the percentage of nitrogen content in V9 growth stage corn plants. FIG. IB depicts corn yield (in bushels / A).

[0121]

[0120] FIGs. 2A-2B are a series of graphs showing nitrogen content and yield in corn plants between control, a first prototype consortia with isolates (MS3900 and MS3907), a second prototype consortia with isolates (MS3900 and MS3907), and isolates only (MS3900 and MS3907). All conditions were tested in 80% growers standard practice GSP and 100% GSP (where 80% GSP is 80% of the full 100% nitrogen in GSP). FIG. 2A depicts results of nitrogen content in V9 growth stage corn plants. FIG. 2B depicts results from corn yield.

[0122]

[0121] FIGs. 3A-3B are a series of graphs showing the recruitment of beneficial nitrogen- fixing microbes in corn plants between control, a first prototype consortia with isolates (MS3900 and MS3907), a second prototype consortia with isolates (MS3900 and MS3907), and isolates only (MS3900 and MS3907). All conditions were tested in 80% GSP and 100% GSP. FIG. 3A depicts the copy number of rhizosphere nifH gene across conditions. FIG. 3B depicts the acetylene reduction activity across conditions.

[0123]

[0122] FIGs. 4A-4B are a series of graphs showing the levels of nifH gene abundance of NTS systems. FIG. 4A shows the base product from NTS-4 (NTS 1.4) had greater nifH enrichment compared to that from the base inoculum. FIG. 4B shows that the base product of NTS-4 (NTS 1.4) had higher nifH content compared to that from the base product of other NTS systems after last process changes.

[0123] FIGs. 5A-5C are a series of graphs showing plant growth promotion (PGP) qualities of the NTS-4 (NTS 1.4) system and controls. FIG. 5A shows NTS-4 (NTS 1.4) has improved corn biomass compared to that from the untreated control condition (UTC). FIG. 5B shows NTS-4 (NTS 1.4) has improved nitrogen content compared to that from UTC. FIG. 5C shows NTS-4 (NTS 1.4) has an increased number of associated nitrogen fixers in com roots (measured as nifH copy numbers) compared to that from UTC.

[0124]

[0124] FIG. 6 shows an exemplary schematic of a NTS system with packed bed reactors.

[0125]

[0125] FIG. 7 shows an exemplary schematic of a NTS system with fluidized bed reactors.

[0126]

[0126] FIGs. 8A-8C are a series of graphs showing measures of nitrogen use efficiency across a control condition, NTS-4 with MS3900 and MS4921 isolates, NTS-4 with MS4921, and a HighN condition with an additional 10 lbs N / A. FIG. 8A shows root / basal stem nitrogen-fixing capacity. FIG. 8B shows dry shoot weight. FIG. 8C shows shoot nitrogen content.

[0127]

[0127] FIGs. 9A-9C are a series of graphs showing measures of nitrogen use efficiency across control, isolates MS3900 and MS3907 applied at 1 qt. / A, nitrogen-fixing isolates applied at 2 qt. / A, and a High N condition with an additional 5 lbs N / A. Isolates were applied in-furrow to corn. FIG. 9A shows soil organic matter. FIG. 9B shows soil organic nitrogen. FIG. 9C shows estimated nitrogen release.

[0128]

[0128] FIGs. 10A-10C show improved nitrogen fixing capacity of microbes to plants grown in a greenhouse test across testing conditions. FIG. 10A shows an airtight jar with root, stem, and soil with 10% acetylene. Gas was analyzed for ethylene content. FIG. 10B shows a concept of acetylene reduction by a nitrogenase enzyme. FIG. 10C shows the result of acetylene reduction of corn roots / basal stem across UTC, NTS-4 (NTS 1.4) with MS3900 and MS4921, NTS-4 (NTS 1.4) with MS4921, and a control condition with added 10 lbs N.

[0129]

[0129] FIGs. 11A-11B are a series of graph showing leaf chlorophyll contents across treatment conditions. FIG. HA shows results from V5 growth stage in com. FIG. 11B shows results from V8 growth stage in corn.

[0130]

[0130] FIG. 12 is a graph depicting the photosynthetic quantum yield across treatment conditions tested in corn at V9 growth stage. NTS treatments at both applications rates and isolates showed increased photosystem light capture efficiency.

[0131]

[0131] FIG. 13 is a graph depicting photosynthetic electron transport rate across treatment conditions in corn at V9 growth stage.

[0132]

[0132] FIG. 14 is a graph depicting the number of corn tillers per com plant across treatment conditions, measured at V5 growth stage.

[0133] FIG. 15 is a graph depicting corn plant height across treatment conditions, measured at V7 growth stage.

[0133]

[0134] FIG. 16 is a graph depicting the stem diameter across treatment conditions.

[0134]

[0135] FIG. 17 is a graph depicting the stomatai conductance (the rate of CO2 and H2O gas exchange) across treatment conditions in corn, at V9 growth stage.

[0135]

[0136] FIG. 18 is a graph depicting the transpiration rate (efficiency of water movement into and through the plant) across treatment conditions, measured at V9 growth stage in corn.

[0136]

[0137] FIG. 19 is a graph depicting the corn dry biomass, measured as dry shoot weight, across treatment conditions.

[0137]

[0138] FIG. 20 is a graph depicting results of acetylene reduction in com root / basal stem, measured across treatment conditions.

[0138]

[0139] FIGs. 21A-21B show increased plant nitrogen content in plants treated with MS3907. FIG. 21A shows results in com plants. FIG. 21B shows results in sorghum plants.

[0139]

[0140] FIGs. 22A-22B show the plant growth promotion traits following treatment with MS3900, MS3907, or both isolates. FIG. 22A shows that adding MS3900 with MS3907 synergistically improves plant growth under low nitrogen (20mg N “NC-20”). FIG. 22B shows that adding MS3900 with MS3907 led to similar green leaf area (as measured in pixels) as treatment with MS3907 alone.

[0140]

[0141] FIG. 23 shows results from the sorghum grass study testing shake flasks using isolates with different aeration. All treatments showed significantly more leaf area than that of untreated control (UTC). ANOVA student’s t-test (p<0.05) Levels not connected by same letter are significantly different.

[0141]

[0142] FIG. 24 shows average pixel shoot area when shake flasks performance is grouped by aeration conditions.

[0142]

[0143] FIG. 25 shows average performance of shake flasks when different ratios of PST WB are used. Shake flask treatments were grouped based on the ratio of PST WB used under both aerobic and anaerobic conditions.

[0143]

[0144] FIG. 26 shows results from an Arabidopsis plant growth promotion rockwool test for NTS 1.1,1.2, 1.3 and 1.4 lines with three reactors. All treatments showed numerically greater average leaf area measurement from the UTC with all having significant plant growth promotion (p=0.0008).

[0144]

[0145] FIG. 27 shows results across NTS 1.0 systems with either three or four reactors in the system. There was a general increase of performance in the output solutions when the retention time of the system was extended by about 42.86%.

[0146] FIGs. 28A-28B show the results of com leaf area measurements between NTS treatment solutions with or without added isolate. NTS-4 systems with MS3900 or MS4921 showed increased corn leaf area compared to that from UTC.

[0145]

[0147] FIG. 29 shows that the isolates only (MS3900 and MS3907) treatment demonstrated higher nitrogen fixer recruitment compared to that from control plants.

[0146]

[0148] FIG. 30 shows there were significantly different N-fixing community compositions in the root zone between treatment conditions. 3300-3303 show N-fixing communities with 80%- GSP-N and 3304-3307 show N-fixing communities with 100%-GSP-N. 3000 is the N-fixing community of UTC at 80%-GSP, 3301 is the N-fixing community of PTl+Iso (Isolates) at 80% GSP-N, 3302 is the N-fixing community of PT2+Iso at 80% GSP-N, 3303 is the N-fixing community of Isolate alone at 80% GSP-N, 3304 is the N-fixing community of UTC at 100%- GSP-N, 3305 is the N-fixing community of PTl+Iso at 100%-GSP-N, 3306 is the N-fixing community of PT2+Iso at 100%-GSP-N, and 3307 is the N-fixing community of Isolate alone at 100%-GSP-N.

[0147]

[0149] FIG. 31 shows that the isolates only (MS3900 and MS3907) treatment demonstrated highest corn yield compared to other treatment conditions.

[0148]

[0150] FIG. 32 shows that plants treated with isolates only (MS3900 and MS3907) demonstrated more N-fixing activity in com roots / basal stem.

[0149]

[0151] FIG. 33 shows isolates only (MS3900 and MS3907) and prototype consortia solution NTS-PT2 (e.g., NTS batch product) with added isolates demonstrated high plant nitrogen content.

[0150]

[0152] FIGs. 34A-34B shows the results of a titration assay with isolates MS3900 and MS3907. Plants treated with the isolates at low rates (8 pl / plant and 16 pl / plant) showed high dry shoot weights (FIG. 34A) and dry root weights (FIG. 34B).

[0151]

[0153] FIGs. 35A-35B show the results of isolate treatment on nitrogen in bulk soil. FIG. 35A shows rates of 16 pl / plant and 32 pl / plant resulted in higher percent nitrogen compared to that of other treatments. FIG. 35B shows all rates with isolates MS3900 and MS3907 resulted in higher ppm nitrogen in bulk soil.

[0152]

[0154] FIGs. 36A-36B show the results of isolate treatments on dry weights. FIG. 36A shows that MS4921 alone resulted in highest shoot dry weight. FIG. 36B shows that MS4921 alone and a combination of all three isolates (MS4921, MS3900, and MS3907) led to highest root dry weights.

[0153]

[0155] FIG. 37 shows strong acetylene reduction assay in single isolate culture in nitrogen-free nutrient media, with or without nitrogen headspace flushing (N2). UTC designates untreated control, i.e. the N-free media was not inoculated; A or B = replicate A or replicate B; N2 designates the headspace was flushed with nitrogen gas before injecting acetylene to remove all oxygen.

[0154]

[0156] FIG. 38 shows addition of carbon and nutrients (Hoagland + C) boosts acetylene reduction of MS4921 in sterile system corn roots.

[0155]

[0157] FIG. 39 shows treatment with NTS-1.4 solution with MS4921 led to highest root acetylene reduction, as measured as %UTC.

[0156]

[0158] FIGs. 40A-40B show results of nitrogen fixing capacity of MS4921 or MS3907 as seed drench or seed soak on corn seedlings. FIG. 40A shows seed drench of MS4921 at 107cfu / ml led to the greatest nitrogen fixing capacity. FIG. 40B shows com treatment results in the greatest N-fixing capacity. Among the MS3907 treatments, seed soak with MS3907 at 106cfu / ml or MS3907 at 105cfu / ml led to the greatest N-fixing capacity. The star above a bar indicates the bar denotes the average of the 3 previous bars.

[0157]

[0159] FIG. 41 is a table summarizing plant colonizing properties of MS3900 and MS3907.

[0158]

[0160] FIG. 42 shows that NTS base product enriches nifH content from starting inoculum.

[0159]

[0161] FIG. 43 shows results of NTS 1.0 systems tested for nifH enrichment. NTS-2 (e.g., NTS 1.2) showed the greatest nifH enrichment from starting inoculum.

[0160]

[0162] FIG. 44 shows results of NTS 1.0 systems tested for nitrogen fixation capacity in an acetylene reduction assay. NTS-2 (e.g., NTS 1.2) showed the highest level of ethylene released.

[0161]

[0163] FIGs. 45A-45B show the N-fixing bacteria of NTS 1.0 systems in root extracts. FIG. 45A shows that there was evidence of nitrogen recruitment of N-fixing bacteria into the roots with NTS-1.4 base product treatment. FIG. 45B shows that NTS-1.4 treatment resulted in improved rhizosphere nifH content over that of UTC plants.

[0162]

[0164] FIGs. 46A-46B show the effects of NTS 1.0 system base products on the ratio of nifH gene to 16S rRNA gene content in root extracts (FIG. 46A) and rhizosphere (FIG. 46B).

[0163]

[0165] FIG. 47 shows the capacity of NTS 1.0 systems in an acetylene reduction assay, used as a proxy to nitrogenase activity. NTS-1.4 showed the highest levels of ethylene production.

[0164]

[0166] FIG. 48 shows the capacity of NTS 1.0 systems in an acetylene reduction assay of corn roots, with an additional control of High N (e.g., high nitrogen).

[0165]

[0167] FIG. 49 shows the level of target isolate MS3907 in base products of the NTS 1.0 systems. Isolate concentration was measured after four months of inoculation in reactor 1.

[0166]

[0168] FIGs. 50A-50B show the results of MS3907 sporulation and retention in the base products of NTS 1.0 systems. FIG. 50A shows that the addition of malate had a positive impact on sporulation. FIG. 50B shows that fluidized bed reactors, in NTS-1.2 and NTS-1.4 systems, had a positive impact of MS3907 retention.

[0167]

[0169] FIG. 51 shows the average leaf area in Arabidopsis across NTS 1.0 systems at 0.05% or 0.2% application rate. NTS-1 at a 0.05% application rate showed the greatest plant growth promotion capacity compared to that of UTC and other NTS treatment conditions.

[0168]

[0170] FIG. 52 shows the effects of NTS solutions on nitrogen levels in soil. NTS-1.2 product showed the highest percentage nitrogen in bulk soil compared to that of other NTS solutions.

[0169]

[0171] FIG. 53 shows that NTS-1.2 solution had the greatest estimated nitrogen release (ENR) in bulk soil compared to that of UTC and other NTS solutions. ENR is an estimate of the amount of nitrogen (Ibs / acre) that will be released over the season.

[0170]

[0172] FIG. 54 shows that plants treated with NTS-1.2 solution exhibited increased organic nitrogen in bulk soil compared to that of UTC and other NTS treatments.

[0171]

[0173] FIGs. 55A-55B show the abundance of total bacteria in root extracts of plants treated with NTS 1.0 system solutions. FIG. 55A shows recruitment of total bacteria into roots of plants treated with NTS- 1.1 and NTS-1.4 solutions. FIG. 55B shows NTS-1.4 had the greatest total bacteria in the rhizosphere compared to that of UTC and other NTS treatments.

[0172]

[0174] FIGs. 56A-56B show plant growth promotion of plants treated with NTS 1.0 solutions. FIG. 56A shows that NTS-1 treated plants had the highest dry shoot weights compared to those of UTC plants and other NTS treatments. FIG. 56B shows NTS-1.1, NTS-1.3, and NTS-1.4 treated plants had significantly higher dry roots weights than those of UTC plants.

[0173]

[0175] FIG. 57 shows the NTS-1.2 and 1.4 treated plants increased plant height greater than the UTC.

[0174]

[0176] FIG. 58 shows all NTS treated plants had significantly greater stem diameter than that of UTC plants.

[0175]

[0177] FIG. 59 shows NTS-1.2 and NTS-1.3 treated plants had significantly greater leaf chlorophyll content than that of UTC plants.

[0176]

[0178] FIG. 60 shows the effects of NTS solutions on corn shoot dry weights. NTS-1.3 and NTS-1.4 treated plants had significantly higher dry shoot weights than that of UTC.

[0177]

[0179] FIG. 61 shows the effects of NTS solutions on corn shoot dry weights in a separate study. NTS-4 treated plants had significantly higher dry shoot weights than that of UTC.

[0178]

[0180] FIG. 62 is an exemplary schematic of a NTS 2.0 system with floc flights present in the clarifier.

[0179]

[0181] FIG. 63 is an exemplary schematic emphasizing the floc flights present in the clarifier of the NTS 2.0 system.

[0182] FIG. 64 shows testing for DNA markers of MS3907 and MS3900 in NTS 1.0 treated plant roots. MS3907 was identified by MS3907-specific DNA markers in the microbial populations colonizing the plant roots of NTS-1.2 and NTS-1.4 treated seedlings.

[0180]

[0183] FIG. 65 shows ARA activity of com stems tissue. Application of MS3900 and MS4921 together resulted in greater N-fixing capacity compared to that of UTC.

[0181]

[0184] FIG. 66 is an exemplary schematic labelling the parts of a NTS digestion system.

[0182]

[0185] FIGs. 67A-67B are exemplary schematics of the NTS batch systems. FIG. 67A shows the prototype 1 (e.g., PT1) system. FIG. 67B shows the prototype 2 (e.g., PT2) system.

[0183]

[0186] FIG. 68 shows the effects of products from the NTS batch systems (e.g., PT1 and PT2) on ethylene production. PT1 product shows the greatest ethylene peak compared to that from UTC and PT2.

[0184]

[0187] FIGs. 69A-69B show two graphs with results from a plant growth promotion test of the PT1 and PT2. Products of the NTs batch system were applied at 2 qt / acre or 4 qt / acre. On both Day 10 (FIG. 69 A) and Day 14 (FIG. 69B), PT2 showed the greatest leaf area compared to that from PT1.

[0185]

[0188] FIG. 70 shows application of MS3900 and MS3907 resulted in greater root and shoot biomass compared to that from UTC.

[0186]

[0189] FIG. 71 shows application of MS2748 resulted in greater root and shoot biomass compared to that from UTC.

[0187]

[0190] FIG. 72 is an exemplary schematic depicting the PWST system. Water is the hydraulic source.

[0188]

[0191] FIG. 73 is a table showing the microbial characterization of water-based phosphate solubilizing technology (PwST) whole broth (WB) across four months. Zinc solubilization (Z- sol) and phosphate solubilization (P-sol) were measured in mediums containing different sources of insoluble phosphate (National Botanical Research Institute’s phosphate growth medium (NBRIP), hydroxyapatite (HA) medium, and phytate medium).

[0189]

[0192] FIG. 74 is a table depicting the top five bacterial species for PwST WB. WB is a blend of the supernatant and floc at a specific ratio to use for various applications.

[0190]

[0193] FIG. 75 is a graph showing the plant growth production of Arabidopsis (measured in average leaf area, cm2) for UTC and PwST samples from across four months.

[0191]

[0194] FIG. 76 is a graph showing average ethylene produced (in area / hr) for PwST samples across four months. Average ethylene produced was compared to UTC.

[0192]

[0195] FIG. 77 is a table depicting the characteristics of functional enzymes of interest in (PwST) WB samples.

[0196] FIG. 78 is a table depicting the average abundance of PQQ, nitrogenase, gluconate 2- dehydrogenase, cellulase, and pectin lyase from PwST WB.

[0193]

[0197] FIG. 79 is a graph showing dry shoot biomass (g) between com treated with monoammonium phosphate (MAP) fertilizer coated with water (UTC) or with PwST supernatant (SPN).

[0194]

[0198] FIG. 80 is a graph showing dry shoot biomass (g) between corn treated with an infurrow application of water (UTC) or PWST supernatant at planting.

[0195]

[0199] FIG. 81 is a graph showing nutrient uptake (measured as %UTC) across six shoot macronutrients in com treated with MAP fertilizer coated with PWST SPN (shown from left to right: nitrogen (N), sulfur (S), phosphorus (P), potassium (K), magnesium (Mg), and calcium(Ca)). An asterisk indicates statistically significantly different from UTC at p = 0.1.

[0196]

[0200] FIG. 82 is a graph showing nutrient uptake in com treated with in-furrow application of PWST SPN (measured as % UTC) across six corn shoot macronutrients (shown from left to right: nitrogen (N), sulfur (S), phosphorus (P), potassium (K), magnesium (Mg), and calcium (Ca)). An asterisk indicates statistically significantly different using ANOVA from UTC at p = 0.1.

[0197]

[0201] FIG. 83 is a graph showing micronutrient uptake in com treated with an in-furrow application of PwST SPN (measured as % UTC) across five shoot micronutrients (shown from left to right: boron (B), zinc (Zn), manganese (Mg), iron (Fe), and copper (Cu)). An asterisk indicates statistically significantly different from UTC at p = 0.1.

[0198]

[0202] FIGs. 84A-84D are a series of graphs showing the release (in mg / L) of micronutrients such as magnesium (FIG. 84A), iron (FIG. 84B), and zinc (FIG. 84C) from MAP fertilizer coated with PWST cSPN. FIG. 84D is a table depicting the measures of each micronutrient, as a percentage of UTC, on Day 6 post-coating.

[0199]

[0203] FIGs. 85A-85B show a series of graphs showing phosphate solubilization (in mg / L) between untreated control (UTC) and PWST cSPN. FIG. 85A shows the average phosphate solubilization in water measured for nutrients after six days. FIG. 85B shows the phosphate solubilization in water between the two conditions for each timepoint.

[0200]

[0204] FIG. 86 shows the plant growth promotion of intact NTS solutions and metabolites. Intact NTS 1.0 system solutions and their metabolites showed increased average leaf area compared to that from UTC plants.

[0201]

[0205] FIG. 87 shows the nitrogen fixation gene (niftf) enriched in systems without the addition of nitrogen-fixing isolates.

[0202]

[0206] FIG. 88 shows nitrogen-fixer capacity (measured as enrichment of riifH) across reactors of the serialized NTS 2.3 system.

[0207] FIGs. 89A-89B show Arabidopsis plant growth using only inorganic N as the nitrogen source in NTS 1.4 and NTS 1.5 systems. FIG. 89A shows average leaf area under full N (30 mM N). FIG. 89B shows average leaf area under reduced N (1 mM N).

[0203]

[0208] FIGs. 90A-90B show Arabidopsis plant growth using only inorganic N as the nitrogen source in NTS 2.2 and NTS 2.3 systems. FIG. 90A shows average leaf area under full N (30 mM N). FIG. 90B shows average leaf area under reduced N (1 mM N).

[0204]

[0209] FIGs. 91A-91B show Arabidopsis plant growth using inorganic N and organic N as the nitrogen source in NTS 2.2 and NTS 2.3 systems. FIG. 91A shows shoot surface area with inorganic nitrogen under full N (30 mM N) and reduced N conditions (lOmM, 1 mM N and 0.1 mM N) FIG. 91B shows shoot surface area with inorganic nitrogen under full N (30 mM N) and reduced organic N conditions (1 mM N).

[0205]

[0210] FIG. 92 shows Arabidopsis plant growth in NTS 2.2 and NTS 2.3 systems with intact solution or metabolites. All NTS 2.0 system treatments showed greater average leaf area than untreated control.

[0206]

[0211] FIGs. 93A-93B show Arabidopsis plant growth in NTS 1.4 and NTS 1.5 systems with intact solution or metabolites. FIG. 93 A shows the results from intact solution treatments. FIG. 93B shows the results from metabolite treatments. All NTS system treatments showed greater average leaf area than untreated control, with NTS 1.4 BP intact and metabolite showing the greatest plant growth promotion.

[0207]

[0212] FIG. 94 shows corn leaf chlorophyll contents 10 days after foliar treatment application.

[0208]

[0213] FIG. 95 shows corn plant height before and after foliar treatment. Black bars indicate plant height pre-treatment and gray bars indicate plant height ten days post-foliar treatment.

[0209]

[0214] FIG. 96 shows corn stem diameter measured prior to harvest. Both NTS 1.4 treatment conditions showed greater stem diameter compared to that of untreated control plants.

[0210]

[0215] FIG. 97 shows corn leaf area measured before and after foliar treatment. Black bars indicate leaf area pre-treatment and gray bars indicate leaf area ten days post-foliar treatment.

[0211]

[0216] FIG. 98 shows sorghum leaf chlorophyll contents at vegetative growth stage V6 following in-furrow or foliar treatment application of NTS 1.4 with MS3900 or MS3900 and MS4921 (gray bars indicate foliar treatment application).

[0212]

[0217] FIG. 99 shows sorghum plant height 10 days following in-furrow or foliar treatment application of NTS 1.4 with MS3900 or MS3900 and MS4921 (gray bars indicate foliar treatment application).

[0213]

[0218] FIGs. 100A-100D show results of plant physiological trait tests following in-furrow or foliar treatment application of NTS 1.4 with MS3900 or MS3900 and MS4921 (gray bars indicate foliar treatment application). FIG. 100A shows results of stomatai conductance. FIG. 100B shows results of transpiration rate. FIG. 100C shows results of photosynthesis quantum yield FIG. 100D shows results photosynthesis electron transport rate.

[0214]

[0219] FIG. 101 shows sorghum grain yield following in-furrow or foliar treatment application of NTS 1.4 with MS3900 or MS3900 and MS4921 (gray bars indicate foliar treatment application).

[0215]

[0220] FIG. 102 shows leaf chlorophyll content before and after soybean foliar treatment application across NTS 2.0 systems.

[0216]

[0221] FIG. 103 shows acetylene reduction activity in soybean following treatment with NTS 2.0 systems alone or spiked with isolate.

[0217]

[0222] FIGs. 104A-104C show results of plant physiological trait tests following soybean foliar treatment application of NTS 2.0 solutions with MS4921 or MS3900 and MS4921. FIG. 104A shows results of transpiration rate. FIG. 104B shows results of quantum yield. FIG. 104C shows results of photosynthetic electron transport rate.

[0218]

[0223] FIG. 105 shows results of normalized difference vegetation index (ND VI) measurements following soybean foliar treatment application of NTS 2.0 solutions with MS4921 or MS3900 and MS4921.

[0219]

[0224] FIG. 106 shows the number of soybean pods per four plants across conditions with foliar treatment application of NTS 2.0 solutions with MS4921 or MS3900 and MS4921.

[0220]

[0225] FIG. 107 shows soybean grain yield (in grams) across conditions following foliar treatment application of NTS 2.0 solutions with MS4921 or MS3900 and MS4921.

[0221]

[0226] FIG. 108 shows average corn leaf chlorophyll contents measured prior to harvest following in-furrow treatment application of NTS 1.4 solutions with MS3900 or MS3900 and MS4921.

[0222]

[0227] FIG. 109 shows average corn plant height (in centimeters) measured prior to harvest following in-furrow treatment application of NTS 1.4 solutions with MS3900 or MS3900 and MS4921.

[0223]

[0228] FIG. 110 shows stem diameter (in millimeters) measured prior to harvest following infurrow treatment application of NTS 1.4 solutions with MS3900 or MS3900 and MS4921.

[0224]

[0229] FIG. Ill shows corn leaf area measured 28 days after in-furrow treatment application of NTS 1.4 solutions with MS3900 or MS3900 and MS4921.

[0225]

[0230] FIG. 112 shows corn root ethylene output from acetylene reduction assay (ARA) increased by broadcast treatment application (NTS 1.4 with MS3900 and MS4921 at 36 uL / pot).

[0231] FIG. 113 shows non-metric dimensional scaling (NMDS) display of whole bacterial community compositions for rhizosphere communities of plants treated with NTS 1.4 with isolates solutions and controls. Each symbol represents one DNA extraction (e.g., one rhizosphere soil community).

[0226]

[0232] FIGs. 114A-114B show rhizosphere soil quantifications. FIG. 114A shows rhizosphere soil bacterial diversity (* indicates significantly different from untreated control, p < 0.1). FIG.

[0227] 114B shows rhizosphere soil N-fixer abundance (* indicates significantly different from untreated control, p < 0.05).

[0228]

[0233] FIG. 115 shows corn leaf chlorophyll contents at vegetative growth (V8) stage for untreated controls or following in-furrow treatment application of NTS 1.4 solutions with MS3900 or MS3900 and MS4921.

[0229]

[0234] FIG. 116 shows corn plant height at vegetative growth stage (V7) for untreated controls or following in-furrow treatment application of NTS 1.4 solutions with MS3900 or MS3900 and MS4921.

[0230]

[0235] FIG. 117 shows corn stem diameter at V7 growth stage for untreated controls or following in-furrow treatment application of NTS 1.4 solutions with MS3900 or MS3900 and MS4921.

[0231]

[0236] FIG. 118 shows that corn root crown ethylene output from an acetylene reduction assay (ARA) increased by in-furrow treatment application compared to that of untreated control plant.

[0232]

[0237] FIGs. 119A-119D show measures of plant physiological parameters in untreated control plants or plants that received in-furrow treatment application of NTS 1.4 solutions with MS3900 or MS3900 and MS4921. FIG. 119A shows results of corn stomatai conductance. FIG. 119B shows results of com transpiration rate. FIG. 119C shows results of com quantum yield. FIG.

[0233] 119D shows results of corn photosynthetic electron transport rate.

[0234]

[0238] FIGs. 120A-120D show results of grain yields and physical com ear measures. FIG. 120A shows in-furrow treatment application of NTS 1.4 solutions with MS3900 or MS3900 and MS4921 increased corn ear length. FIG. 120B shows in-furrow treatment application of NTS 1.4 solutions with MS3900 or MS3900 and MS4921. FIG. 120C shows in-furrow treatment application of NTS 1.4 solutions with MS3900 or MS3900 and MS4921. FIG. 120D shows infurrow treatment application of NTS 1.4 solutions with MS3900 or MS3900 and MS4921.

[0235]

[0239] FIG. 121 shows the rhizosphere soil N-fixer abundance significantly increased by NTS1.4 spiked with MS3900 and MS4921 at application rate of 36 pL / pot (* indicates significantly different from untreated control 80% GSP, p < 0.1).

[0240] FIG. 122 shows top collar height after treatment of NTS 1.4 spiked with MS4921 and MS3900.

[0236]

[0241] FIG. 123 shows stem diameter after treatment of NTS 1.4 spiked with MS4921 and MS3900 or treatment with NTS 1.4 spiked with MS3907 and MS3900.

[0237]

[0242] FIG. 124 shows corn leaf chlorophyll levels after treatment with NTS 1.4 spiked with MS3907 and MS3900.

[0238]

[0243] FIG. 125 shows corn shoot dry weight (e.g., shoot biomass) following treatment with NTS-1.4 spiked with MS4921+MS3900.

[0239]

[0244] FIG. 126 shows corn root dry weight (e.g., root biomass) following treatment with NTS- 1.4 spiked with MS4921+MS3900 or NTS-1.4 spiked with MS3907+MS3900.

[0240]

[0245] FIG. 127 shows corn leaf chlorophyll contents 17 days after in-furrow treatment application in corn plants receiving NTS-2.2 or NTS-2.3.

[0241]

[0246] FIGs. 128A-128B show corn plant height and stem diameter measured 17 days after infurrow treatment application. Both treatment groups receiving products from NTS 2.0 systems showed increased plant height (FIG. 128A) and stem diameter (FIG. 128B) compared to that measured in untreated control plants.

[0242]

[0247] FIG. 129 shows corn leaf area 18 days after planting and in-furrow treatment application with NTS 2.0 solutions.

[0243]

[0248] FIG. 130 shows corn root ethylene output from acetylene reduction assay (ARA) in plants treated with NTS-2.2, untreated control and plants treated with NTS-2.3.

[0244]

[0249] FIG. 131 shows corn shoot nitrogen uptake following in-furrow treatment application with NTS-2.2 and NTS2.3 compared to that from untreated control plants.

[0245]

[0250] FIGs. 132A-132B shows com biomass between treatment conditions. FIG. 132A shows NTS2.2 and NTS2.3 significantly increased dry shoot biomass by in-furrow treatment application. FIG. 132B shows NTS2.2 and NTS2.3 significantly increased dry root biomass by in-furrow treatment application.

[0246]

[0251] FIG. 133 shows the com total dry weight from in-furrow and foliar treatments with target isolates. MS4921 was applied alone or in combination with MS3900 as an in-furrow treatment, and MS4921 was also applied alone as a foliar treatment.

[0247]

[0252] FIG. 134 shows foliar treatment of com with isolate MS4921 resulted in roots and / or root crowns with greater acetylene reduction activity than that quantified from untreated control (UTC) or the in-furrow treatments with MS4921 or MS4921+MS3900.

[0248]

[0253] FIG. 135 shows corn leaf chlorophyll content across treatment conditions 7 days after broadcast application with urea ammonium nitrate (UAN) fertilizer. UAN with NTS spiked with MS3900 and MS4921 at 18 pL / pot showed greater chlorophyll content compared to that of UAN alone.

[0249]

[0254] FIG. 136 shows corn plant height 7 days across treatment conditions after broadcast application with urea ammonium nitrate (UAN32) fertilizer. UAN with NTS spiked with MS3900 and MS4921 at 18 pL / pot showed greater plant height compared to that of UAN alone.

[0250]

[0255] FIG. 137 shows corn stem diameter 7 days across treatment conditions after broadcast application with urea ammonium nitrate (UAN32) fertilizer. UAN with NTS spiked with MS3900 and MS4921 at 36 pL / pot showed greater stem diameter compared to that of UAN alone at 18 pL / pot.

[0251]

[0256] FIG. 138 shows corn leaf area before (12 days after planting, dap) and after broadcast application of treatment (20 days after planting). All UAN with NTS treatment conditions showed greater leaf area at 20 dap compared to that of UAN alone. Black bars indicate 12 dap and gray bars indicate 20 dap.

[0252]

[0257] FIG. 139 shows acetylene reduction activity (ARA), as measured by ethylene output, in corn roots / root crown after broadcast application of treatments. UAN with NTS spiked with MS3900 at 36 pL / pot showed the greatest ARA activity across treatment conditions.

[0253]

[0258] FIG. 140 shows stomatai conductance (the rate of CO2 and H2O gas exchange) results in wheat after planting and treatment application, measured in moles of H2O / meter2 / second (mol H2O / m2 / s). Applying pre-plant broadcast at 1 qt / A improved gas exchange even more than 2 qt / A. All the treatments significantly increase leaf stomatai conductance at the heading stage, and UAN32+NTS-2.3+MS3900+MS4921 at 2 qt / A significantly increased stomatai conductance. In-furrow, pre-plant broadcast, and UAN32 additive treatment application significantly increased the wheat stomatai conductance.

[0254]

[0259] FIG. 141 shows transpiration rate (efficiency of water movement into and through the plant) results in wheat, measured in millimoles H2O / m2 / s (mmol H2O / m2 / s). All the treatments significantly increased leaf transpiration rate at heading stage, and UAN32+NTS- 2.3+MS3900+MS4921 at 2 qt / A significantly increased transpiration rate. In-furrow, pre-plant broadcast, and UAN32 additive treatment application significantly increased the wheat transpiration rate.

[0255]

[0260] FIG. 142 shows quantum yield (% of light energy used in photosynthesis) results in wheat, measured in the percent of light used in photosynthesis. NTS treatments using both rates and with two spiked isolates significantly increased photosystem light capture efficiency and NTS-2.3 spiked with two isolates had significantly greater quantum yield at heading stage (infurrow at 1 qt. / A rate), and UAN32+NTS-2.3+MS3900+MS4921 at 2 qt / A significantly increased quantum yield (pre-plant broadcast). In-furrow, pre-plant broadcast, and UAN32 additive treatment application significantly increased the wheat quantum yields.

[0256]

[0261] FIG. 143 shows electron transport rate (photosynthetic capacity to assimilate carbon) results in wheat, measured in pmoles electrons / meters2 / second (pmol electrons / m2 / s). As with quantum yield, NTS treatments using both rates and with two spiked isolates significantly increased photosystem energy transfer to ATP production and all the treatments increased leaf electron transport rate at heading stage. In-furrow, pre-plant broadcast, and UAN32 additive treatment application significantly increased the wheat. In-furrow, pre-plant broadcast, and UAN32 additive treatment application significantly increased the wheat electron transport rate.

[0257]

[0262] FIG. 144 shows normalized difference vegetation index (ND VI) results in wheat. Treatment with UAN32 additive significantly increased the normalized difference vegetation index of wheat leaves. ND VI measurements can range from -1 to 1, with higher values indicating greater plant health.

[0258]

[0263] FIG. 145 shows chlorophyll index results in wheat. In-furrow, pre-plant broadcast, and UAN32 additive treatment application significantly increased the wheat leaf chlorophyll index of wheat leaves.

[0259]

[0264] FIG. 146 shows normalized difference red edge (NDRE) results in wheat. In-furrow, pre-plant broadcast, and UAN32 additive treatment application significantly increased the wheat leaf normalized difference red edge (NDRE).

[0260]

[0265] FIG. 147 shows winter wheat root acetylene reduction activity results. Pre-plant broadcast treatment application increased the root acetylene reduction activity of winter wheat.

[0261]

[0266] FIG. 148 shows winter wheat dry shoot biomass results with standard error bars. Treatment with UAN32 additive treatment applications increased the wheat dry shoot biomass.

[0262]

[0267] FIGs. 149A-149C shows winter wheat shoot macronutrient results. Treatment with UAN32 additive treatment applications significantly increased the wheat shoot nitrogen uptake (FIG. 149A). Treatment with UAN32 additive treatment applications increased the wheat shoot phosphorous uptake (FIG. 149B). Treatment with UAN32 additive treatment applications significantly increased the wheat shoot potassium uptake (FIG. 149C).

[0263]

[0268] FIGs. 150A-150E shows winter wheat shoot micronutrient results. Treatment with UAN32 additive treatment applications significantly increased the wheat shoot boron uptake (FIG. 150A). Treatment with UAN32 additive treatment applications increased the wheat shoot zinc uptake (FIG. 150B). Treatment with UAN32 additive treatment applications increased the wheat shoot manganese uptake (FIG. 150C). Treatment with UAN32 additive treatment applications increased the wheat shoot iron uptake (FIG. 150D). Treatment with UAN32 additive treatment applications increased the wheat shoot copper uptake (FIG. 150E).

[0264]

[0269] FIG. 151 shows bulk soil nutrient results with standard error bars. Treatment with UAN32 additive treatment applications increased the bulk soil organic nitrogen.

[0265]

[0270] FIG. 152 shows that in-furrow, pre-plant broadcast, and UAN32 additive treatment application significantly increased the wheat grain yields.

[0266]

[0271] FIG. 153 shows non-metric dimensional scaling (NMDS) display of whole bacterial community composition for root extract bacterial communities of winter wheat treated with different application methods of NTS 2.3 with isolates and controls. Each symbol represents one DNA extraction (e.g., one rhizosphere soil community). Connected lines indicate treatment groups. Treatment groups are distinguished by operational taxonomic unit (OTU).

[0267]

[0272] FIG. 154 shows non-metric dimensional scaling (NMDS) display of whole N-fixing bacterial community composition for root extract communities of winter wheat treated with different application methods of NTS 2.3 with isolates and controls. Each symbol represents one DNA extraction (e.g., one rhizosphere soil community). Connected lines indicate treatment groups. Treatment groups are distinguished by operational taxonomic unit (OTU).

[0268]

[0273] FIG. 155 shows root extract total bacteria abundance results, by quantitative PCR of the 16S rRNA gene, with standard deviation bars.

[0269]

[0274] FIG. 156 shows root extract N-fixer abundance, by quantitative PCR of the nifH gene, with standard deviation bars.

[0270]

[0275] FIGs. 157A-157C show the base peak chromatograms for UHPLC-Triple-TOF-MS / MS including T3 positive (FIG. 157A), T3 negative (FIG. 157B), and HILIC negative (FIG. 157C).

[0271]

[0276] FIG. 158 shows an orthogonal partial least squares discriminant analysis (OPLSDA) score diagram of NTS 1.4 and NTS 1.5 to show the differences in metabolites between and within groups. The X-axis represents the predicted principal component, and the difference between groups can be seen in the horizontal direction. The Y-axis represents the orthogonal principal component, and the vertical direction shows the difference within the group. Percentage indicates the degree to which the component explains the data set. Each dot in the figure represents a sample, samples in the same Group are represented by the same oval, and Group indicates sample groups.

[0272]

[0277] FIG. 159 shows an orthogonal partial least squares discriminant analysis (OPLSDA) score diagram of NTS 1.4 and NTS 1.5 to show the differences in top ranked metabolites between and within groups. The X-axis represents the predicted principal component, and the difference between groups can be seen in the horizontal direction. The Y-axis represents the orthogonal principal component, and the vertical direction shows the difference within the group. Percentage indicates the degree to which the component explains the data set. Each dot in the figure represents a sample, samples in the same Group are represented by the same oval, and Group indicates sample groups.

[0273]

[0278] FIG. 160 shows dynamic distribution of metabolite content difference. In the figure, the X-axis represents the rank number of metabolites based on FC value. The Y-axis represents the log2FC value. Each point represents a metabolite. Labeled points at the bottom left represent the top 10 down-regulated metabolites and the labeled points at the top right represent the top 10 up regulated metabolites.

[0274]

[0279] FIG. 161 shows a principle component analysis of sample population PwST system outputs compared to a sample NTS system outputs. PCI represents the first principal component and PC2 represents the second principal component. Percentage represents the interpretation rate of the principal component to the data set. Each shape in the figure represents a sample. FS = filter sterilized, IN = intact material (not filter sterilized).

[0275]

[0280] FIG. 162 shows leaf area results of Arabidopsis plants treated with select chemical compounds.

[0276]

[0281] FIG. 163 shows leaf area results of Arabidopsis plants treated with select chemical compounds.

[0277]

[0282] FIG. 164 shows leaf area results of Arabidopsis plants treated with select chemical compounds.

[0278] DETAILED DESCRIPTION

[0279]

[0283] While various embodiments of the invention have been shown and described herein, it will be obvious to those skilled in the art that such embodiments are provided by way of example only. Numerous variations, changes, and / or substitutions may occur to those skilled in the art without departing from the invention. It should be understood that various alternatives to the embodiments of the invention described herein may be employed.

[0280]

[0284] Described herein are systems and methods that employ microbial digestion of various feedstocks. A system of the present disclosure may comprise a continuous system capable of serialized isolate production (e.g., sIP system). The isolate production of the sIP system can occur within a mixed consortium of microbes. The target isolates of a sIP digestion system may become enriched in the microbial environment and may demonstrate improved efficacy and functionality. The main targeted functionality may be nitrogen use efficiency and / or nitrogen fixation from soil or fertilizer and improved nutrient uptake in plants. A target isolate may possess commercially valuable properties and can be introduced into a continuous (e.g., serialized) reactor system comprised of a complex microbial consortia that has been modified for functionality (e.g., for nitrogen use efficiency). Without wishing to be bound by theory, a target isolate may provide a performance benefit to a microbial community of the digestions systems described herein, providing a chemical and / or functional synergistic relationship as it grows in the system.

[0281]

[0285] The products of digestion methods and systems described herein can include microbes and metabolites produced by microbial digestion of feedstock substrates. In some embodiments, the products of digestion methods and systems described herein can comprise biostimulant compositions that have plant growth promoting properties when applied to plants or to a medium in which plants are growing (e.g., soil). In some embodiments, methods and systems described herein are arranged to selectively promote growth of microbes that have a desired plant growth promoting property themselves or that produce metabolites that have the desired plant growth promoting property, such that the biostimulant product has the desired plant growth promoting property. Applications of the products of the digestion systems described herein may be on dry-fertilizers, applied in conjunction with the application of fertilizers, in formulations with additional components including liquid fertilizers or micronutrient coating formulations, in foliar applications, or any combinations thereof. Applications of the products of the digestion systems described herein may be to a part of a plant, such as a shoot, a stem, a leaf, a lateral bud, a terminal bud, a flower, a leaf axil, a root (e.g., a primary root, a lateral root, a root hair, a root cap), or any combination thereof. These and other features of embodiments disclosed herein are described in more detail below.

[0282] I. Certain Definitions

[0283]

[0286] In the following description, certain specific details are set forth in order to provide a thorough understanding of various embodiments. However, one skilled in the art will understand that the embodiments provided may be practiced without these details. Unless the context requires otherwise, throughout the specification and claims which follow, the word “comprise” and variations thereof, such as, “comprises” and “comprising” are to be construed in an open, inclusive sense, that is, as “including, but not limited to.” As used in this specification and the appended claims, the singular forms “a,” “an,” and “the” include plural referents unless the content clearly dictates otherwise. It should also be noted that the term “or” is generally employed in its sense including “and / or” unless the content clearly dictates otherwise. Further, headings provided herein are for convenience only and do not interpret the scope or meaning of the claimed embodiments.

[0284]

[0287] The term “about” or “approximately” means within an acceptable error range for the particular value as determined by one of ordinary skill in the art, which will depend in part on how the value is measured or determined, e.g., the limitations of the measurement system. For example, “about” can mean within 1 or more than 1 standard deviation, per the practice in the given value. Where particular values are described in the application and claims, unless otherwise stated the term “about” should be assumed to mean an acceptable error range for the particular value.

[0285]

[0288] The term “culturing”, as used herein, may refer to the propagation of organisms on or in media of various kinds. Non-limiting examples of suitable media include tryptic soy agar (TSA), zinc agar, nutrient medium, lysogeny broth (LB medium), and / or plate count agar.

[0286]

[0289] The term “digestion system” can refer to one or more reactors (e.g., containers) by which a volume of fluid can pass through. The terms “digestion system” and “bioreactor system” can be used interchangeably.

[0287]

[0290] As used herein, the term “enriched culture” of an isolated microbial strain can refer to a microbial culture wherein the total microbial population of the culture contains a percentage of a target isolated strain. An enriched culture may comprise an increased amount of a target isolated strain and / or a target population of microbes compared to a total microbial population of a culture. An enriched culture may comprise a growing population of a target isolated strain and a population of microbes enriched for a particular functionality (e.g., nitrogen use efficiency) over a time period. An enriched culture may comprise a percentage of a target isolated strain and a population of microbes enriched for a particular functionality (e.g., nitrogen use efficiency). In some embodiments, an enriched culture may comprise a percentage of a target isolated strain, a population of microbes enriched for a particular functionality, and metabolites enriched for a particular functionality (e.g., nitrogen use efficiency). The enriched culture may comprise a percentage of a total bacteria population in a container of digestion system described herein. The enriched culture may comprise a percentage of a total bacteria population in an output product (e.g., biostimulant) described herein. In some embodiments, an enriched culture can refer to a microbial culture wherein the total microbial population of the culture contains at least about 0.001%, at least about 0.01%, at least about 0.05%, at least about 0.1%, at least about 0.5%, at least about 1%, at least about 1.5%, at least about 2%, at least about 2.5%, at least about 5%, at least about 10%, at least about 15%, at least about 20%, at least about 25%, at least about 50%, or at least about 75% of a target isolated strain, a population of microbes enriched for a particular functionality, metabolites enriched for a particular functionality, or any combination thereof. In some embodiments, an enriched culture can refer to a microbial culture wherein the total microbial population of the culture contains at most about 75%, at most about 50%, at most about 25%, at most about 20%, at most about 15%, at most about 10%, at most about 5%, at most about 2.5%, at most about 2%, at most about 1.5%, at most about 1%, or at most about 0.5% of a target isolated strain, a population of microbes enriched for a particular functionality, metabolites enriched for a particular functionality, or any combination thereof. In some embodiments, an enriched culture can refer to a microbial culture wherein the total microbial population of the culture contains from about 0.5% to about 75% of a target isolated strain, a population of microbes enriched for a particular functionality, metabolites enriched for a particular functionality, or any combination thereof. In some embodiments, an enriched culture can refer to a microbial culture wherein the total microbial population of the culture contains from about 0.5% to about 1%, about 0.5% to about 2%, about 0.5% to about 3%, about 0.5% to about 5%, about 0.5% to about 10%, about 0.5% to about 15%, about 0.5% to about 20%, about 0.5% to about 25%, about 0.5% to about 50%, about 0.5% to about 60%, about 0.5% to about 75%, about 1% to about 2%, about 1% to about 3%, about 1% to about 5%, about 1% to about 10%, about 1% to about 15%, about 1% to about 20%, about 1% to about 25%, about 1% to about 50%, about 1% to about 60%, about 1% to about 75%, about 2% to about 3%, about 2% to about 5%, about 2% to about 10%, about 2% to about 15%, about 2% to about 20%, about 2% to about 25%, about 2% to about 50%, about 2% to about 60%, about 2% to about 75%, about 3% to about 5%, about 3% to about 10%, about 3% to about 15%, about 3% to about 20%, about 3% to about 25%, about 3% to about 50%, about 3% to about 60%, about 3% to about 75%, about 5% to about 10%, about 5% to about 15%, about 5% to about 20%, about 5% to about 25%, about 5% to about 50%, about 5% to about 60%, about 5% to about 75%, about 10% to about 15%, about 10% to about 20%, about 10% to about 25%, about 10% to about 50%, about 10% to about 60%, about 10% to about 75%, about 15% to about 20%, about 15% to about 25%, about 15% to about 50%, about 15% to about 60%, about 15% to about 75%, about 20% to about 25%, about 20% to about 50%, about 20% to about 60%, about 20% to about 75%, about 25% to about 50%, about 25% to about 60%, about 25% to about 75%, about 50% to about 60%, about 50% to about 75%, or about 60% to about 75% of a target isolated strain, a population of microbes enriched for a particular functionality, metabolites enriched for a particular functionality, or any combination thereof.

[0288]

[0291] The term “composition” as used herein can refer to a combination of an active agent (e.g., a microbial strain described herein) and at least one other compound, carrier, or composition, which can be inert (for example, a detectable agent or liquid carrier) or active, such as, but not limited to, a fertilizer, nutrient, or pesticide. A microbial composition refers to a composition comprising at least one microbial species. A composition may comprise microbial metabolites generated in a microbial consortium of a digestion system described herein.

[0289]

[0292] An “effective amount”, as used herein, can refer to an amount sufficient to effect beneficial and / or desired results. An effective amount can be administered in one or more administrations. An “effective microorganism” may refer to a subject strain exhibiting a degree of promotion of plant health, growth and / or yield, at a statistically significant level, compared to that of an untreated control. In some instances, the expression “an effective amount” can be used herein in reference to that quantity of microbial treatment which can be used to obtain a beneficial or desired result relative to that occurring in an untreated control under suitable conditions of treatment as described herein. For example, the expression “an agriculturally effective amount” can be used herein in reference to that quantity of microbial treatment which can be used to obtain an agriculturally beneficial or desired result relative to that occurring in an untreated control under suitable conditions of treatment as described herein. The effective amount of an agricultural formulation or composition that may be applied for the improvement of plant health, growth and / or yield, can be readily determined.

[0290]

[0293] A “carrier” as used herein can refer to a substance or a composition that support the survival of the microbes. Such carriers may be either organic or non-organic.

[0291]

[0294] “Percentage of sequence identity”, as used herein, can be determined by comparing two optimally locally aligned sequences over a comparison window defined by the length of the local alignment between the two sequences. The amino acid sequence in the comparison window may comprise additions or deletions (e. g., gaps or overhangs) as compared to the reference sequence (which does not comprise additions or deletions) for optimal alignment of the two sequences.

[0292]

[0295] Local alignment between two sequences may include segments of each sequence that are deemed to be sufficiently similar according to a criterion that depends on the algorithm used to perform the alignment (e. g. BLAST). The percentage of sequence identity is calculated by determining the number of positions at which the identical nucleic acid base or amino acid residue occurs in both sequences to yield the number of matched positions, dividing the number of matched positions by the total number of positions in the window of comparison and multiplying the result by 100. Optimal alignment of sequences for comparison may be conducted by the local homology algorithm of Smith and Waterman (Add. APL. Math. 2:482, 1981), by the global homology alignment algorithm of Needleman and Wunsch (J Mol. Biol. 48:443, 1970), by the search for similarity method of Pearson and Lipman (Proc. Natl. Acad. Sci. USA 85:2444, 1988), by heuristic implementations of these algorithms (NCBI BLAST, WU-BLAST, BLAT, SIM, BLASTZ), or by inspection. Given that two sequences have been identified for comparison, GAP and BESTFIT may be employed to determine their optimal alignment. Typically, the default values of 5.00 for gap weight and 0.30 for gap weight length are used. The term “substantial sequence identity” between polynucleotide or polypeptide sequences refers to polynucleotide or polypeptide comprising a sequence that has at least about 50% sequence identity, at least about 60% sequence identity, at least about 70% sequence identity, at least about 80% sequence identity, at least about 85% sequence identity, at least about 90% sequence identity, at least about 95% sequence identity, at least about 96% sequence identity, at least about 97% sequence identity, at least about 98% sequence identity, or at least about 99% sequence identity compared to a reference sequence using the programs. In addition, pairwise sequence homology or sequence similarity, as used, refers to the percentage of residues that are similar between two sequences aligned. Families of amino acid residues having similar side chains have been well defined in the art. These families include amino acids with basic side chains (e.g., lysine, arginine, histidine), acidic side chains (e.g., aspartic acid, glutamic acid), uncharged polar side chains (e.g., glycine, asparagine, glutamine, serine, threonine, tyrosine, cysteine), nonpolar side chains (e.g., alanine, valine, leucine, isoleucine, proline, phenylalanine, methionine, tryptophan), beta-branched side chains (e.g., threonine, valine, isoleucine) and aromatic side chains (e.g., tyrosine, phenylalanine, tryptophan, histidine). Query nucleic acid and amino acid sequences can be searched against subject nucleic acid or amino acid sequences residing in public or proprietary databases. Such searches can be done using the National Center for Biotechnology Information Basic Local Alignment Search Tool (NCBI BLAST v 2.18) program. The NCBI BLAST program is available on the internet from the National Center for Biotechnology Information (blast.ncbi.nlm.nih.gov / Blast.cgi). Typically the following parameters for NCBI BLAST can be used: Filter options set to “default”, the Comparison Matrix set to “BLOSUM62”, the Gap Costs set to “Existence: 11, Extension: 1”, the Word Size set to 3, the Expect (E threshold) set to le-3, and the minimum length of the local alignment set to 50% of the query sequence length. Sequence identity and similarity may also be determined using GenomeQuest™ software (Gene-IT, Worcester Mass. USA).

[0293]

[0296] The term “plant growth promotion” (c.g, “PGP”) can refer to processes that can promote plant health, growth, yield, or any combinations thereof. In some embodiments, PGP can encompass a wide range of improved plant properties, including but not limited to, improved nitrogen fixation, improved phosphate uptake, improved zinc uptake, improved root development, increased leaf area, increased plant yield, increased uptake of macronutrients, increased uptake of micronutrients, increased seed germination, enhancing seed germination, enhancing early plant development, improving root growth, improving shoot growth, improving plant height, increasing nutrient uptake, improving tolerance to abiotic stress, mitigating transplant shock, improving plant reproduction, improving soil microbial activity, increased photosynthesis, increased abundance of functional enzymes, increased dry biomass, or an increase in accumulated biomass of the plant. In some embodiments, the microbial strains, isolates, cultures, compositions or synthetic consortia as described herein improve stress tolerance (e.g., tolerance to drought, flood, salinity, heat, pest), improve nutrient uptake, plant health and vigor, improve root development, increase leaf area, increase plant yield, increased uptake of macronutrients, increased uptake of micronutrients, increase seed germination, increased abundance of functional enzymes, increased dry biomass, or an increase in accumulated biomass of the plant. In some embodiments, the microbial strains, isolates, cultures, or compositions as described herein increase the size or mass of a plant or parts thereof, as compared to a control plant, or a plant that has not been treated with a substance, or parts thereof or as compared to a predetermined standard. In some embodiments, the microbial strains, isolates, cultures, compositions or synthetic consortia as described herein improve the health, vigor and yield of a plant, as compared to a control plant or a plant that has not been treated with a substance, but also can survive and multiply in microhabitats associated with the root surface.

[0294]

[0297] As used herein, the term “yield” can refer to the amount of harvestable plant material or plant-derived product, and is normally defined as the measurable produce of economic value of a crop.

[0295]

[0298] For crop plants, “yield” can also mean the amount of harvested material per acre or unit of production. Yield may be defined in terms of quantity or quality. The harvested material may vary from crop to crop, for example, it may be seeds, above ground biomass, roots, fruits, cotton fibers, any other part of the plant, or any plant-derived product which is of economic value.

[0296]

[0299] In some embodiments, the microbial strains, isolates, cultures and compositions according to the embodiments of this application lead to plant growth promotion or plant growth improvement that is an at least 5% increase, at least 10% increase, at least 25% increase, at least 50% increase, at least 75% increase, or at least a 100% increase in the property being measured. In some embodiments, the microbial strains, isolates, cultures and compositions according to the embodiments of this application lead to plant growth promotion or plant growth improvement that is an at least 1%, 2%, 3%, 4%, 5%, 10%, 15%, 20%, 25%, 30%, 35%, 40%, 45%, 50%, 60%, 70%, 80%, 90%, 95%, 96%, 97%, 98%, 99%, or 100% increase in the property being measured. In some embodiments, the microbial strains, isolates, cultures and compositions of this application may produce an above stated percentage increase in nitrogen fixation, an above stated increase in nitrogen content, an above stated increase in nitrogen acquisition, an above stated increase in nitrogen uptake, an above stated increase in total root weight, or in leaf area or in plant product yield (e.g., an above stated percentage increase in plant product weight).

[0297]

[0300] A “control plant”, as used herein, can provide a reference point for measuring changes in phenotype of the subject plant, and may be any suitable plant cell, seed, plant component, plant tissue, plant organ or whole plant. A control plant may comprise, but is not limited to, (a) a plant which is genetically identical to the subject plant but which is not exposed to the same treatment (c.g, inoculant treatment) as the subject plant or (b) the subject plant itself, under conditions in which it has not been exposed to a particular treatment such as, for example, an inoculant or combination of inoculants and / or other chemicals. A control plant can also refer to a plant that has received no treatment. A control plant can also refer to a plant that has received a standard fertilizer. A control plant can also refer to a plant that has received water only. A treated plant may comprise a plant that has had an inoculum of a microbe or a biostimulant composition as described herein applied to any part of the plant (e.g., seed, stem, root, shoot, leaf, or combination thereof). A treated plant may comprise a plant that has had an inoculum of a microbe or a biostimulant composition as described herein applied using an in-furrow application. A treated plant may comprise a plant that has had an inoculum of a microbe or a biostimulant composition as described herein applied using a side-dress application. A treated plant may comprise a plant that has had an inoculum of a microbe or a biostimulant composition as described herein applied to the soil. An untreated plant may comprise a plant that that has not had an inoculum of a microbe or a biostimulant composition as described herein applied directly or indirectly.

[0298]

[0301] “ Inoculant” as used herein can refer to any culture or preparation that comprises at least one microorganism. In some embodiments, an inoculant (sometimes as microbial inoculant, or soil inoculant) is an agricultural addition that uses beneficial microbes (including, but not limited to endophytes) to promote plant health, growth, yield, or any combinations thereof. Many of the microbes suitable for use in an inoculant form symbiotic relationships with the target crops where both parties benefit (mutualism). For example, an isolated microbial strain as described herein may benefit from carbon sources from the roots of a plant and the plant may benefit from metabolites generated by metabolism of the microbe. Without wishing to be bound by theory, a plant may be colonized by the isolate and the colonization of the roots may block plant pathogens from accessing the roots. An inoculant (e.g., inoculum of a microbe) can be added at one time point during a digestion system process.

[0299]

[0302] The term “serialized isolate production”, (e.g., sIP), can refer to specialized manipulated continuous serialized reactors that may enable the growth and enrichment of the microbes, isolates, target isolates, and / or microorganisms as described herein.

[0300]

[0303] The term “floc” can refer to a mass formed by the aggregation of a number of fine suspended particles. For example, a floc can comprise organic materials recovered from a feedstock, waste, wastewater, and / or sludge material of a fluid used in a digestion system. A floc can comprise biosolids and / or particles from digestion products of organic materials. Floc can comprise an aggregated mass of microorganisms (e.g., bacteria).

[0301]

[0304] The term “whole broth” (e.g., WB) can refer to a blend of supernatant and floc at a ratio for use in the technologies as described herein. A whole broth may comprise microbial populations (e.g., nitrogen use efficiency -promoting microbes), enzymes, fungi, biosolids, or any combination thereof. For example, bacterial genera of a whole broth may comprise Haliscomenobacter, Lewinella, Caldilinea, Terrimonas, Acidobacterium, Lewinella cohaerens, Thauera phenylacetica, Thauera mechernichensis, Solitalea canadensis, Nitrospira moscoviensis, or any combination thereof. A whole broth may have plant growth promotion properties. For example, a whole broth may have nitrogen-fixation capacity.

[0302]

[0305] The terms “microbial consortium” or “microbial population” can refer to a group of microorganisms in an environment. Consortiums may be endosymbiotic or ectosymbiotic. Microorganisms in a microbial consortium can include, but are not limited to, bacteria, fungi, yeasts, lichens, algae, protozoa, archaea, molds, or any combinations thereof.

[0303]

[0306] The term “supernatant” (e.g., “base product”) can refer to the final product of the digestion system. The supernatant can be measured for amount of a microbial isolate, number of members within a microbial consortium, or types and amount of microbial metabolites with plant growth promotion capacity.

[0304]

[0307] The term “load rate” can refer to a rate at which a source material is introduced into a digestion system. In some embodiments, load rate may refer to “organic load rate” or “hydraulic load rate”. Organic load rate comprises a rate at which organic feedstock is introduced into the system. Hydraulic load rate comprises a rate at which a hydraulic source is introduced into the system.

[0305]

[0308] The term “internal recycle rate” can refer to a rate at which a working fluid is recycled within a phase space.

[0309] The term “hydraulic feed rate” can refer to a rate at which working fluid is transferred between phase spaces.

[0306]

[0310] The term “hydraulic dwell time” can refer to an amount of time that a working fluid is present in a phase space.

[0307]

[0311] The term “working fluid” can refer to a fluid substance supporting and transporting biology and nutrients through a system of contains. For example, a working fluid may comprise a organic materials, microorganisms (e.g., microbes and / or metabolites), biosolids, macronutrients, micronutrients, organic nutrients, inorganic nutrients, or any combination thereof. A working fluid can comprise a solution that flows throughout a digestion system and may provide an enriched environment for microbes of the digestion system.

[0308]

[0312] Whenever the term “at least,” “greater than,” or “greater than or equal to” precedes the first numerical value in a series of two or more numerical values, the term “at least,” “greater than” or “greater than or equal to” can apply to each of the numerical values in that series of numerical values. For example, greater than or equal to 1, 2, or 3 is equivalent to greater than or equal to 1, greater than or equal to 2, or greater than or equal to 3.

[0309]

[0313] Whenever the term “no more than,” “less than,” or “less than or equal to” precedes the first numerical value in a series of two or more numerical values, the term “no more than,” “less than,” or “less than or equal to” can apply to each of the numerical values in that series of numerical values. For example, less than or equal to 3, 2, or 1 is equivalent to less than or equal to 3, less than or equal to 2, or less than or equal to 1.

[0310] II. Multi-pronged Approach to Nitrogen Use Efficiency

[0311]

[0314] Embodiments of systems and methods described herein produce biostimulant products that may have a multi-modal way of promoting efficient use of nitrogen by plants. Biostimulant products produced by embodiments described herein may be used to promote plant growth by applying the products to plants and / or plant growth media (e.g., soil). One mode of action of products produced in some embodiments is nitrogen-fixing activity of nitrogen fixing bacteria included in the products. Another mode of action may be the recruitment of plant associated nitrogen fixers already present in the soil to the roots of plants, thereby increasing nitrogen fixing activity in the root zone and potentially in other plant tissues if the recruited N-fixing microbes become endophytic and can move systemically throughout the plant. Such recruitment may be accomplished by bacterial metabolites present in the biostimulant product and / or by bacterial isolates. Another mode of action may be increases in soil organic nitrogen and mineralization and uptake of organic nitrogen stimulated by microbes and / or microbial metabolites present in the products produced in embodiments described herein.

[0312]

[0315] Biostimulant products described herein may provide plants with N fixation by microbes directly via microbial endophytes and symbionts present in the products, and indirectly via mineralization or decomposition of organically bound N in soil produced by soil N-fixers. Plants may be provided with N through decomposition of organically bound N in the soil.

[0313] Embodiments of biostimulant products may also provide plants with the ability to access additional N in soil organic matter. Embodiments of biostimulant products may provide a combination of these strategies to provide better access to biological / organic sources of nitrogen and improve nitrogen use efficiency (NUE).

[0314]

[0316] The following microbe genera can promote nitrogen use efficiency in plants: Kosakonia, Klebsiella, Rahnella, Kluyvera, Enterobacter, Achromobacter, Microbacterium, Gluconobacter, Methylobacterium, Pseudomonas, Pantoea, Azospirillum, Azocarus, Herbaspirillum, Burkholderia, Cyanobacteria, Bacillus, and Paenibacillus. The following microbe species can promote nitrogen use efficiency in plants: Kosakonia sacchari, Klebsiella variicola, Rahnella aquatilis, Kluyvera intermedia, Kosakonia pseusosacchari, Enterobacter spp., Achromobacter marplatensis, Azopirillum lipoferum, Microbacterium murale, Gluconobacter diazotrophicus, Methylobacterium symbioticum, Paenibacillus borealis, Bacillus megaterium (Priestia megaterium), and Paenibacillus sonchi. Embodiments of products described herein may include one or more of these microbes. Microbes of these genera may comprise endophytic N fixers (diazotrophs) of monocots.

[0315]

[0317] The inoculum of the microbe, nitrogen use efficiency-promoting microbes of the microbial consortium, nitrogen use efficiency-promoting metabolites, or any combination thereof may be nitrogen use efficiency-promoting microbes in the working fluid of the system and / or in the output product (e.g., base product) of the digestion system. These nitrogen use efficiency-promoting microbes may have a nifH gene. A nifH gene can comprise a gene having at least about 70%, at least about 75%, at least about 80%, at least about 85%, at least about 90%, at least about 91%, at least about 92%, at least about 93%, at least about 94%, at least about 95%, at least about 96%, at least about 97%, at least about 98%, at least about 99%, at least about 99.5%, at least about 99.9%, or 100% sequence identity to a nucleotide sequence as set forth in SEQ ID NOs: 13-14. A nifH gene can comprise a gene that encodes a nitrogenase reductase polypeptide. In some embodiments, the nitrogenase reductase polypeptide has an amino acid sequence that has at least about 70%, at least about 75%, at least about 80%, at least about 85%, at least about 90%, at least about 91%, at least about 92%, at least about 93%, at least about 94%, at least about 95%, at least about 96%, at least about 97%, at least about 98%, at least about 99%, at least about 99.5%, at least about 99.9%, or 100% sequence identity to an amino acid sequence encoded by SEQ ID NO: 13 or 14.

[0316]

[0318] Plant associated N-fixers that may be beneficial in biostimulant products described herein may include those that can associate with plant roots and other tissues and become endophytic, demonstrate nitrogen fixation activity when associated with roots and other plant tissues, and show consistent increases in plant nitrogen use efficiency, or any combination thereof. Biostimulant products may include the following capabilities with respect to nitrogen fixer recruitment: increase the number of associated and / or endophytic N-fixers with plant roots through N-fixer recruitment, nitrogen fixation activity in treated plants, show consistent increases in nitrogen use efficiency, or any combination thereof. Microbial metabolites in biostimulant products may provide for an increased ability of plants to access organically bound nitrogen generated by soil N-fixers and other organic matter, increase soil microbial respiration and biomass, and increase recruitment of beneficial microbes.

[0317]

[0319] In some embodiments, a serialized set of reaction chambers that may be used in a method of producing a biostimulant product are described herein. In some embodiments, conditions within reactor chambers may be established to selectively promote the production of one or more microbes that have a specific desired plant growth promoting effect (e.g., nitrogen use efficiency).

[0318]

[0320] In an aspect, the present disclosure provides a method, comprising (a)transferring an aqueous organic feedstock and an inoculum of a microbe or several microbes that are capable of promoting nitrogen use efficiency in plants into a first container comprising a volume of a first working fluid, wherein the aqueous organic feedstock comprises: (i) a first microbial consortium; and (ii) digestion products produced by digestion of an organic material by microbes in the first microbial consortium; and (b) incubating the inoculum under conditions that promote growth of the nitrogen fixing microbes supplied by the microbial consortia and as well as the specifically introduced microbes, thereby increasing the population of nitrogen fixing microbes and enabling a sustained presence of the specifically introduced microbes.

[0319]

[0321] In some embodiments, the bioreactor system (e.g., the digestion system) comprises an established population of one or more nitrogen use efficiency -promoting microbial strains in one or more containers of the system. An “established population” of a particular microbial strain is a population that remains within an operating bioreactor system without replenishing the microbial strain from outside the bioreactor system. In some embodiments, an established population is one that has not been diminished by more than 1, 3, 5, 10, 15, 20, or 25% during continuous operation of the bioreactor system for at least 5, 10, 15, 20, 25, 30, 60, or 90 days without adding a population of the microbial strain to the bioreactor system at a concentration higher than 1, 10, 50, or 100 CFU / ml. In some embodiments, an established population of a microbial strain has been established by making one or more inoculations of the microbial strain into one or more containers of the bioreactor system. In some embodiments, an established population is a population that is derived from a population that was inoculated into the system at least 10, 30, 60, or 90 days previous.

[0320]

[0322] In some embodiments, a bioreactor system comprises at least one microbial strain. In some embodiments, a bioreactor system comprises at least one nitrogen use efficiencypromoting microbial strain. In some embodiments, a bioreactor system comprises an established population of a first nitrogen use efficiency-promoting microbial strain and an established population of a second nitrogen use efficiency -promoting microbial strain. In some embodiments, the bioreactor system further comprises an established population of a third nitrogen use efficiency-promoting microbial strain. The established populations of the respective microbial strains may be established in individual or combined inoculations into the bioreactor system. An individual inoculation may comprise one inoculum of a microbial strain (e.g., microbe). A combined inoculation may comprise an inoculum comprising at least two microbial strains. The combined inoculation may comprise the same isolated microbial strains. The combined inoculation may comprise an isolated microbial strain and non-isolated microbial strain. The combined inoculation may comprise two or more isolated microbial strains.

[0321]

[0323] In some embodiments, a concentration of the second nitrogen use efficiency -promoting microbial strain in the first working fluid is at least 100 times higher than a concentration of the second nitrogen use efficiency -promoting microbial strain in the aqueous feedstock stream and in any other input into the bioreactor system. For example, a concentration of the second nitrogen use efficiency-promoting microbial strain in the first working fluid may be at least about 2 times higher, at least about 5 times higher, at least about 10 times higher, at least about 25 times higher, at least about 50 times higher, at least about 100 times higher, at least about 150 times higher, at least about 200 times higher, at least about 250 times higher, at least about 500 times higher, or greater than about 500 times higher than a concentration of the second nitrogen use efficiency-promoting microbial strain in the aqueous feedstock stream or in any other input into the bioreactor system. A concentration of the second nitrogen use efficiency-promoting microbial strain in the first working fluid may be at most about 500 times higher, at most about 250 times higher, at most about 200 times higher, at most about 150 times higher, at most about 100 times higher, at most about 50 times higher, at most about 25 times higher, at most about 10 times higher, at most about 5 times higher, at most about 2 times higher, or less than about 2 times higher than a concentration of the second nitrogen use efficiency-promoting microbial strain in the aqueous feedstock stream or in any other input into the bioreactor system.

[0322]

[0324] In some embodiments, nitrogen use efficiency promotion may comprise increasing nitrogen fixation, promoting nitrogen fixation in the root and other tissues of plants, recruiting nitrogen fixers to the roots of plants, promoting soil organic nitrogen content and mineralization and uptake of organic nitrogen from soil, or any combination thereof. In some embodiments, the microbe is capable of nitrogen fixation, promoting nitrogen fixation in the root and other tissues of plants, recruiting nitrogen fixers to the roots of plants, promoting soil organic nitrogen content and mineralization and uptake of organic nitrogen from soil, or any combination thereof. In some embodiments, the conditions promote growth of one or more microbes in the first microbial consortium that are capable of promoting plant growth, nitrogen fixation, nitrogen use efficiency, or recruitment of nitrogen fixers to the roots of plants, or of generating metabolites capable of promoting plant growth, nitrogen fixation, nitrogen use efficiency, enhancing organic nitrogen in the soil and mineralization and plant uptake of organic nitrogen, or recruitment of nitrogen fixing microbes to the roots of plants. In some embodiments, during the incubating the microbe or one or more microbes in the first microbial consortium, metabolites are produced capable of promoting plant growth and nitrogen use efficiency. In some embodiments, the incubating increases a population of one or more microbes in the microbial consortium capable of promoting plant growth. In some embodiments, the aqueous organic feedstock further comprises an inorganic substrate. In some embodiments, the first microbial consortium further comprises microbes derived from the inorganic substrate. In some embodiments, the inorganic substrate comprises rock phosphate. In some embodiments, the microbe or microbes are of the species Paenibacillus borealis, Bacillus megaterium, or Paenibacillus sonchi. In some embodiments, the microbe is the Paenibacillus borealis strain deposited under ATCC Accession No. PTA-127654 (MS3907), the Bacillus megaterium (or Priestia megaterium) strain deposited under ATCC Accession No. PTA-127653 (MS3900), the Paenibacillus sonchi strain deposited under ATCC Accession No. PTA-127655 (MS4921), or the Bacillus megaterium strain deposited under ATCC Accession No. PTA-127652 (MS2748). In some embodiments, the first working fluid comprises (a) a second microbial consortium derived from the aqueous organic feedstock, and / or (b) digestion products produced by digestion of substances present in the organic feedstock by the first microbial consortium and the microbe(s). In some embodiments, the method further comprises transferring a portion of the first working fluid into a second container. The second container can comprise a second working fluid. The method may further comprise incubating the second working fluid in the second container. In some embodiments, the method further comprises transferring a portion of the first working fluid into a second container comprising a second working fluid and incubating the second working fluid in the second container. The second working fluid may comprise a third microbial consortium and the third microbial consortium may be derived from the first working fluid. The second working fluid may comprise digestion products produced by digestion of substances present in the first working fluid by the third microbial consortium, the microbial strain, or any combination thereof. In some embodiments, the second working fluid comprises (a) a third microbial consortium derived from the first working fluid, and (b) digestion products produced by digestion of substances present in the first working fluid by the third microbial consortium and the microbe. In some embodiments, the amount of the aqueous organic feedstock transferred into the first container over a time period is equal to the amount of the first working fluid transferred into the second container over the same time period. In some embodiments, the amount of the aqueous organic feedstock transferred into the first container over a time period is not equal to the amount of the first working fluid transferred into the second container over the same time period. In some embodiments, the volume of the first working fluid in the first container is maintained constant. In some embodiments, the volume of the first working fluid in the first container is not maintained constant. In some embodiments, transferring the aqueous organic feedstock into the first container comprises continuously flowing the aqueous organic feedstock into the first container at a first flow rate, transferring the portion of the first working fluid into the second container comprises continuously flowing the portion of the first working fluid into the second container at a second flow rate, and the first flow rate and the second flow rate are equal. In some embodiments, the method further comprises transferring a portion of the second working fluid to a third container comprising a third working fluid and incubating the third working fluid in the third container. In some embodiments, the method further comprises transferring a portion of the third working fluid into a fourth container comprising a fourth working fluid and incubating the fourth working fluid in the fourth container. In some embodiments, the first working fluid, the second working fluid, the third working fluid, and the fourth working fluid are maintained at constant volumes. In some embodiments, a plant growth promoting product made by the method described herein may promote nitrogen use efficiency in a plant. In some embodiments, a method of promoting nitrogen use efficiency of a plant comprises contacting the plant and / or a medium in which the plant is growing with the product. III. Microbial Digestion Methods and Systems

[0323] A. System Overview

[0324]

[0325] Certain embodiments disclosed herein include methods and systems in which microbes comprised in microbial consortia digest substances provided in a feedstock. The digestion systems may be comprised of a series of separate, fluidly connected containers, also referred to herein as “reactors.” In each reactor, a different microbial consortium may be established and maintained throughout continuous operation of the digestion system. The unique microbial consortia present in each reactor may provide for different physiological activities in the different reactors. Thus, different steps in digestion of a feedstock may be performed in different reactors, which may result in (1) a more complete digestion — i.e., more complete breakdown of macromolecules in the feedstock — than other types of digestion systems, and / or (2) production of a variety of microbial digestion products having plant growth promoting properties (e.g., ability to recruit nitrogen fixers to plant tissues or otherwise promote nitrogen use efficiency).

[0325]

[0326] In some embodiments, a reactor or a series of reactors functions to contribute to the growth of one or more microbes having desired plant growth promoting properties and / or to the production of digestion products having plant growth promoting properties. The system can comprise 2, 3, 4, 5, 6, or more reactors. In some embodiments, the operation of a digestion system may lead to growth of one or more microbes having a desired plant growth promoting effect. The one or more microbes may be one or more isolated microbes added separately as an inoculum to the digestion system. The one or more microbes may also be input into the system as part of a feed material that includes a mixture of microbes. The one or more microbes may be endogenous to an organic material such as, for example, a manure, a plant, a lignocellulosic material, or an algae. The one or more microbes may also be endogenous to other types of feed materials, such as rock phosphate or coal. In some embodiments, endogenous microbes are those microbes naturally present in feedstock material (e.g., a manure, a plant, a lignocellulosic material, or an algae). These microbes may naturally reside in a closed system and / or are present in the ecosystem of the feedstock material.

[0326]

[0327] Inputs into digestion systems may include one or more of water, a microbial inoculum, nutrients (e.g., carbon, nitrogen, phosphorous, or any combination thereof), and a digestion substrate. Fluid within reactors of a digestion system may be referred to herein as a “working fluid.” In continuous operation, each reactor may have a constant volume of working fluid therein, with the rate of fluid flowing into each reactor matching the rate of fluid flowing out of each reactor. As each reactor may include a different microbial consortium and have different conditions from other reactors, the working fluid within each reactor may be considered to be distinct from working fluids within the other reactors. The total volume of working fluid within a digestion system may be referred to herein as the “total working volume” of the digestion system.

[0327]

[0328] Digestion substrates included in an input stream into a digestion system may include, for example, organic materials that can be digested by microbes in the digestion system. Such organic materials may include, for example, manure, lignocellulosic material, wastewater biosolids, food waste, energy crops, yeast, agricultural waste, algae, or any combination thereof . The manure may be cow manure, chicken manure, horse manure, sheep manure, alpaca manure, rabbit manure, pig manure, guano or any combination thereof. In some embodiments, the manure is a mixture of one, two, three, or more manures. Digestion substrates input into digestion systems may have been subject to a partial digestion before being input into the system. Thus, the input into the system may include products of digestion of an original digestion substrate by microbes endogenous to the original digestion substrate, as well as digestible materials still present in the input. In some embodiments, digestion substrates included in an input stream may include an inorganic substrate. The inorganic substrate may include, for example, sand, vermiculite, perlite, pumice, or any combination thereof. In some embodiments, the inorganic substrates comprises a mineral. In some embodiments, the inorganic substrate comprises rock phosphate.

[0328]

[0329] In some embodiments, a microbial inoculum comprises a single isolated microbe. In some embodiments, the microbial inoculum may comprise between 1 and 5 isolated microbes. In some embodiments, the inoculum may comprise at least about 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, or more isolated microbes. In some embodiments, the inoculum may comprise greater than 5 isolated microbes. In some embodiments, the inoculum may comprise at most about 10, 9, 8, 7, 6, 5, 4, 3, 2, 1, or less isolated microbes. In some embodiments, in addition to one or more isolated microbes, a microbial inoculum input into a digestion system may include a complex mixture of microbes, which may include at least about 5, 10, 20, 25, 50, 100, 200, 225, 250, 275, 300, 350, 400, or more species of microbes. In some embodiments, in addition to one or more isolated microbes, a microbial inoculum input into a digestion system may include a complex mixture of microbes, which may include at most about 400, 350, 300, 275, 250, 225, 200, 100, 50, 25, 20, 10, 5, or less species of microbes.

[0329]

[0330] An inoculum of a microbe as described herein may have at least one plant growth promotion property (e.g., a property of plant growth). A plant growth promotion property may comprise shoot biomass, root biomass, nutrient uptake, crop yield, leaf area, chlorophyll content, increased photosynthesis, heat tolerance, cold tolerance, drought tolerance, or salt tolerance, or total biomass. A digestion system may be configured to enhance production of the inoculum of the microbe. A microbe may be a bacterial species, a fungal species, or an algal species. An inoculum of a microbe may be an individual inoculation of a microbial strain.

[0330]

[0331] In some embodiments, the inoculum of a microbe may comprise at least two isolated microbes. In some embodiments, the inoculum of a microbe may comprise at least one isolated microbe and at least one non-isolated microbe. An inoculum of a microbe may be transferred to a first container (e.g., reactor) of a digestion system one time, two times, three times, four times, five times, or more. An inoculum of a microbe may be transferred to a second container, a third container, a fourth container, a fifth container, a sixth container, or any container of a system described herein.

[0331]

[0332] An inoculum of a microbe may have a concentration of at least about 1.0 x 102cfu / ml, 1.0 x 103cfu / ml, 1.0 x 104cfu / ml, 1.0 x 105cfu / ml, 1.0 x 106cfu / ml, 1.0 x 107cfu / ml, 1.0 x 108cfu / ml, 1.0 x 109cfu / ml, 1.0 x 1010cfu / ml, 1.0 x 1011cfu / ml, or 1.0 x 1012cfu / ml prior to transferring to a first container of a digestion system. An inoculum of a microbe may have a concentration of at most about 1.0 x 1012cfu / ml, 1.0 x 1011cfu / ml, 1.0 x 1010cfu / ml, 1.0 x 109cfu / ml, 1.0 x 108cfu / ml, 1.0 x 107cfu / ml, 1.0 x 106cfu / ml, 1.0 x 105cfu / ml, 1.0 x 104cfu / ml, 1.0 x 103cfu / ml, 1.0 x 102cfu / ml, or less than about 1.0 x 102cfu / ml prior to transferring to a first container of a digestion system.

[0332]

[0333] An inoculum of a microbe may have a concentration of at least about 1.0 x 102cfu / ml, 1.0 x 103cfu / ml, 1.0 x 104cfu / ml, 1.0 x 105cfu / ml, 1.0 x 106cfu / ml, 1.0 x 107cfu / ml, 1.0 x 108cfu / ml, 1.0 x 109cfu / ml, 1.0 x 1010cfu / ml, 1.0 x 1011cfu / ml, or 1.0 x 1012cfu / ml after incubation in a digestion system described herein. An inoculum of a microbe may have a concentration of at most about 1.0 x 1012cfu / ml, 1.0 x 1011cfu / ml, 1.0 x 1010cfu / ml, 1.0 x 109cfu / ml, 1.0 x 108cfu / ml, 1.0 x 107cfu / ml, 1.0 x 106cfu / ml, 1.0 x 105cfu / ml, 1.0 x 104cfu / ml, 1.0 x 103cfu / ml, 1.0 x 102cfu / ml, or less than about 1.0 x 102cfu / ml after incubation in a digestion system described herein.

[0333]

[0334] In some embodiments, the aqueous organic feedstock and microbial inoculum can be transferred to the first reactor separately. In some embodiments, the aqueous organic feedstock can be transferred to the first reactor before the microbial inoculum. In some embodiments, the microbial inoculum can be transferred to the first reactor before the aqueous organic feedstock. In some embodiments, the aqueous organic feedstock and microbial inoculum can be transferred to the first reactor together at the same time.

[0334]

[0335] In some embodiments, the aqueous feedstock may not contain the target isolate strain (e.g., an inoculum of the microbe). For example, the aqueous feedstock may not contain the target isolate strain prior to transfer to a first container. The concentration of the target isolate microbial strain (e.g., nitrogen use-efficiency promoting strain) may be 0 cfu / ml. In some embodiments, the aqueous feedstock may contain the target isolate strain prior to transfer to a first container. In some embodiments, a total composition of the aqueous feedstock may contain at most about 5%, at most about 4%, at most about 3%, at most about 2%, at most about 1%, at most about 0.5%, at most about 0.1%, at most about 0.05%, at most about, 0.04%, at most about 0.03%, at most about 0.02%, at most about 0.01%, at most about 0.008%, at most about 0.005%, at most about 0.004%, at most about 0.003%, at most about 0.002%, at most about 0.001%, at most about 0.0001%, or less than about 0.0001% of the target isolate strain. In some embodiments, the aqueous feedstock may not include the microbial strain (e.g., the nitrogen use efficiency -promoting microbial strain) at a concentration higher than about 1 CFU / ml, 2 CFU / ml, 3 CFU / ml, 4 CFU / ml, 5 CFU / ml, 6 CFU / ml, 7 CFU / ml, 8 CFU / ml, 9 CFU / ml, 10 CFU / ml, 11 CFU / ml, 12 CFU / ml, 13 CFU / ml, 14 CFU / ml, 15 CFU / ml, 20 CFU / ml, 25 CFU / ml, 30 CFU / ml, 40 CFU / ml, or 50 CFU / ml.

[0335]

[0336] In some embodiments, the digestion system comprises a clarifier chamber or clarifier tank (CLF). The terms “clarifier chamber”, “clarifier tank”, and “clarifier container” can be used interchangeably. The clarifier can contain working fluid (e.g., clarifier working fluid). The clarifier may comprise a single in-flow port and a single out-flow port. The clarifier may comprise a single in-flow port and multiple out-flow ports. In some embodiments, the clarifier comprises one or more floc-folding wipers which can rotate and release microbes that have been immobilized in the floc without introducing solids in the supernatant. The floc-folding wipers may move a working fluid in the clarifier to re-suspend microbes within the working fluid. In some embodiments, the microbes and / or an amount of target isolate strain may be re-suspended in the solution in the clarifier and transferred to the supernatant (e.g., base product). In some embodiments, the clarifier further comprises a flow line to return floc to the first reactor. The flow line may comprise a conduit from the clarifier to a container or combination of containers of the digestion system (e.g., a first container, a second container, a third container, a fourth container, a fifth container, a sixth container, or any combination thereof). The clarifier may return flow to any container (e.g., a first container, a second container, a third container, a fourth container, a fifth container, a sixth container, or any combination thereof) of a digestion system to provide a recirculation of working fluid. The working fluid recirculated from the clarifier may comprise a different microbial community (e.g., different amounts of microbes) than a working fluid of another container in the digestion system (e.g., a first working fluid, a second working fluid, a third working fluid, a fourth working fluid, a fifth working fluid, and / or a sixth working fluid). Without wishing to be bound by theory, the recirculation of flow from the clarifier to a container of the digestion system may help enrich a microbial community of a microbial consortium of a digestion system by providing working fluid from the clarifier to a different point (e.g., container) of the system. The recirculated working fluid may comprise one or more organic materials, one or more microbes of a microbial consortium, a target isolate, one or more metabolites, or any combination thereof.

[0336]

[0337] In the clarifier, a floc portion of a working fluid (e.g., a clarifier working fluid) may separate from a supernatant portion of a working fluid. The floc-folding wipers of the clarifier may help in separating the working fluid of the clarifier. In some embodiments, the separating may comprise gravity separation. The floc may settle on the bottom of the clarifier and the supernatant may be collected. The folding of the floc-folding wipers may comprise releasing a population of a microbial strain. The population of a microbial strain may release into the supernatant portion (e.g., the supernatant portion of the clarifier working fluid). While the folding can release the population of the microbial strain into a supernatant portion of the clarifier working fluid, the folding may not introduce solid from the floc portion (e.g., floc solids) into the supernatant portion of the clarifier working fluid.

[0337]

[0338] Biostimulant compositions produced by digestion processes as described herein may be used as-is or may be further processed before being used. For example, the outflow from the digestion system, referred to herein as “base product,” may be concentrated, sterilized, filtered, pasteurized, or dehydrated before being used, or any combination of these. In some embodiments, the base product may be concentrated by at least about 2x, at least about 3x, at least about 4x, at least about 5x, at least about 6x, at least about 7x, at least about 8x, at least about 9x, at least about lOx, or greater than about lOx. In some embodiments, the base product may be concentrated by at most about lOx, at most about 9x, at most about 8x, at most about 7x, at most about 6x, at most about 5x, at most about 4x, at most about 3x, at most about 2x, or less than 2x. In some embodiments, the base product may be filter sterilized to remove any bacteria or other microbes in the composition.

[0338]

[0339] In an aspect, provided herein is a method comprising transferring an aqueous organic feedstock into a first container. An inoculum of a microbe may be transferred into a first container. An aqueous organic feedstock may be transferred into a first container. An aqueous organic feedstock and an inoculum of a microbe may be transferred into a first container. The first container may comprise a volume of a first working fluid. The aqueous organic feedstock may comprise a microbial consortium. The aqueous organic feedstock may comprise one or more digestion products produced by digestion of one or more organic materials. The aqueous organic feedstock may comprise a microbial consortium and digestion products produced by digestion of an organic material. In some cases, the feedstock may comprise at least about 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, or greater than about 10 digestion products. In some cases, the feedstock may comprise at most about 10, 9, 8, 7, 6, 5, 4, 3, 2, or less than 2 digestion products. The organic material may be digested by one or more microbes in the microbial consortium. The organic material may be digested by a population of microbes of the inoculum of a microbe. The digestion products described herein may comprise one or more sugars (e.g., monosaccharides, disaccharides, oligosaccharides, polysaccharides, or any combination thereof). The digestion products described herein may comprise sugars (e.g., xylose, mannose, glucose, or any combination thereof), one or more metabolites generated by microbes of the working fluid, one or more fatty acids, one or more dead microorganisms, one or more fragments of dead microorganisms, one or more microorganism fermentation products, one or more enzymes, one or more biological plant growth modulators, one or more organic acids, one or more chelators, or any combination thereof. The method may further comprise incubating the inoculum of a microbe under conditions that selectively promotes growth of the microbes and increases the population of the microbes. The method may further comprise incubating the inoculum of a microbe under one or more conditions described herein that selectively promotes growth of at least a portion of microbes in the microbial consortium. The terms “microbial digestion” and “digestion” can be used interchangeably.

[0339]

[0340] In some embodiments, the digestion is anaerobic digestion. In some embodiments, the digestion is aerobic digestion. In some embodiments, the digestion is microaerobic digestion. In some embodiments, the digestion is aerobic digestion, microaerobic digestion, anaerobic digestion, or some combination thereof. Without wishing to be bound by theory, it is believed that during the digestion process, microbes digest the biomolecules and other nutrients present in the manure, yeast, kelp, and / or produce digestion products that include compounds that promote plant growth and soil health. In some embodiments of a digestion process, the organic feedstock may be mixed with water to make an organic feedstock for an anaerobic digestion system. The anaerobic digestion system may include a mixing tank in which the organic feedstock is mixed to make a fluid feed mixture or working fluid. In some embodiments, the fluid feed mixture may include manure, water, and Saccharomyces cerevisiae yeast. In some embodiments, anaerobic digestion comprises a process by which bacteria break down organic biomaterials in the absence of oxygen. The biostimulant may also contain microbes that contribute to the plant-beneficial properties of the biostimulant product. The microbes in the biostimulant product may be derived from the microbial population present in the organic feedstock.

[0341] As an example system of the present disclosure, a series of reactors functions to contribute to the growth of an inoculum of a microbe (e.g., isolate) having desired plant growth promoting properties. A series of reactors (e.g., serialized assembly of reactors) may also function to contribute to the production of microbial metabolites having desired plant growth promoting properties. The digestion system described herein can enrich an inoculum of a target microbe, a population of microbes within a microbial consortium with plant-growth promotion properties (e.g., nitrogen use efficiency), a population of metabolites with plant-growth promotion properties (e.g., nitrogen use efficiency), or any combination thereof. This system provides added benefits to other digestion systems in that it can target a functional community of microbes and / or metabolites with specific functionality and enrich and / or maintain the community in the digestion system. The system can comprise two, three, four, five, or more reactors chambers (e.g., containers or chambers). Without wishing to be bound by theory, the serialized reactors enable the growth and enrichment of proprietary specialist target microbes with optimal plant growth promoting properties. The system may direct a flow of working fluid comprising an inoculum, carbon source, and / or nutrient source from an input organic feedstock to produce a base product (BP). A hydraulic source can flow into a reactor via in-flow port to comprise a first working fluid in a reactor tank. A hydraulic source may input into a first reactor or any reactor of the system. In some embodiments, a hydraulic source may input (e.g., flow) into a tank or container prior to a first reactor. In some embodiments, the container may comprise a “complete mixed reactor” (CMR). Other inputs into a system described herein may flow into any reactor of the system, including but not limited to a first reactor, a second reactor, a third reactor, or any other reactor following a first reactor.

[0340]

[0342] An inoculum of a microbe may incubate in a reactor (e.g., container) of a digestion system described herein. In some embodiments, the inoculum of a microbe may be incubated under conditions that selectively enrich and / or retain the inoculum of the microbe in the digestion system. In some cases, the inoculum of the microbe may survive in the digestion system in a vegetative or sporulated state (e.g., a dormant state in the system). Without wishing to be bound by theory, the conditions of reactors of a digestions system (e.g., a hydraulic retention time of the system (e.g., flow rate), floc recirculation, pH level of the system, aerobic conditions, or any combination thereof) may shift the complex microbial consortia of the digestion system to enrich at least a portion of microbes within a microbial consortium with plant growth promotion properties (e.g., nitrogen use efficiency). The conditions of one or more reactors of a digestions system (e.g., a hydraulic retention time of the system (e.g., flow rate), floc recirculation, pH level of the system, aerobic conditions, or any combination thereof) may shift the complex microbial consortia of the digestion system to enrich a population of a microbial strain (e.g., provide an established population of a microbial strain). Incubation of the inoculum of the microbe and / or the portion of microbes within a microbial consortium with plant growth promotion properties may further generate metabolites with plant growth promotion properties (e.g., nitrogen use efficiency).

[0341]

[0343] The inoculum of the microbe may comprise a nitrogen use efficiency -promoting microbial strain that can be maintained as a population of the microbial strain in a bioreactor system described herein. Maintenance (e.g., survival) of an inoculum of a microbe may comprise a population of the microbe configured to maintain its initial amount in the environment caused by conditions in a reactor of the digestion system. Maintenance (e.g., survival) of an inoculum of a microbe may comprise an instance where an amount of the inoculum of the microbe is alive at the end of a retention period of the digestion system (e.g., in a reactor or clarifier chamber). For example, following initial inoculation, a population of a nitrogen use efficiency-promoting microbial strain may survive incubation in conditions (e.g., nutrients, flow rate, pH, aerobic parameters, or any combination thereof) of a digestion system described herein. In some embodiments, at least a portion of microbes of the microbial consortium may enrich (e.g., grow or increase in number). These microbes of the portion of microbes in the microbial consortium may have nitrogen use efficiency capacities. A proportion of the nitrogen use efficiency -promoting microbial strain and nitrogen use efficiency-promoting microbes of the microbial consortium relative to a total population count of bacteria may be maintained in a first container of a digestion system. A proportion of the nitrogen use efficiencypromoting microbial strain and nitrogen use efficiency-promoting microbes of the microbial consortium relative to a total population count of bacteria may be maintained in a second, third, fourth, fifth, sixth, seventh, or eighth container of a digestion system. A proportion of the nitrogen use efficiency-promoting microbial strain and nitrogen use efficiency-promoting microbes of the microbial consortium relative to a total population count of bacteria may be maintained in any combination of containers of a bioreactor system described herein. A maintained population of a nitrogen use efficiency -promoting microbial strain may change its amount in a working fluid of a digestion system less than about 0.001%, less than about 0.01%, less than about 0.1%, less than about 0.5%, less than about 1%, less than about 5%, or less than about 10% over a duration of time. The duration of time may comprise at least about 1 hour, 2 hours, 3 hours, 4 hours, 5 hours, 6 hours, 12 hours, 18 hours, 24 hours, 2 days, 3 days, 4 days, 5 days, 6 days, 7 days, 8 days, 9 days, 10 days, 11 days, 12 days, 13 days, 14 days, 3 weeks, 4 weeks, 5 weeks, 6 weeks, 7 weeks, 8 weeks, 3 months, 4 months, 5 months, 6 months, 9 months, or greater than 12 months. The duration of time may comprise at most about 10 years, 5 years, 4 years, 3 years, 24 months, 18 months, 12 months, 9 months, 6 months, 5 months, 4 months, 3 months, 8 weeks, 7 weeks, 6 weeks, 6 weeks, 5 weeks, 4 weeks, 3 weeks, 14 days, 13 days, 12 days, 11 days, 10 days, 9 days, 8 days, 7 days, 6 days, 5 days, 4 days, 3 days, 2 days, 24 hours, 18 hours, 12 hours, 6 hours, 5 hours, 4 hours, 3 hours, 2 hours, 1 hour, or less than about 1 hour.

[0342]

[0344] In some cases, parameters comprising nutrients added to the system, a hydraulic retention time of the system (e.g., flow rate), floc recirculation, pH level of the system, aerobic conditions, or any combination thereof may promote the growth of microbes or at least a portion of microbes in the microbial consortium. These microbes may be nitrogen use efficiencypromoting microbes. An amount of microbes or at least a portion of microbes in the microbial consortium may grow by at least about 0.0001%, 0.001%, 0.01%, 0.1%, 1%, 2%, 3%, 4%, 5%, 10%, 15%, 20%, or 30% as they incubate in conditions of the reactors of the digestion system (e.g., nutrients added to the system, a hydraulic retention time of the system (e.g., flow rate), floc recirculation, pH level of the system, aerobic conditions, or any combination thereof). An amount of microbes or at least a portion of microbes in the microbial consortium may grow by at most about 30%, 20%, 15%, 10%, 5%, 4%, 3%, 2%, 1%, 0.1%, 0.01%, 0.001%, 0.0001% as they incubate in conditions of the reactors of the digestion system (e.g., nutrients added to the system, a hydraulic retention time of the system (e.g., flow rate), floc recirculation, pH level of the system, aerobic conditions, or any combination thereof). In some cases, at least a portion of nitrogen use efficiency-promoting microbes in the microbial consortium may enrich and / or grow in the system without addition of the inoculum of the microbe.

[0343]

[0345] Without wishing to be bound by theory, parameters comprising nutrients added to the system, a hydraulic retention time of the system (e.g., flow rate), floc recirculation, pH level of the system, aerobic conditions, or any combination thereof, may inhibit growth of a microbe and / or a population of microbes. Without wishing to be bound by theory, parameters comprising nutrients added to the system, a hydraulic retention time of the system (e.g., flow rate), floc recirculation, pH level of the system, aerobic conditions, or any combination thereof, may inhibit growth of a microbe and / or a population of microbes and enhance growth of a target microbe and / or target population of microbes (e.g., nitrogen use efficiency-promoting microbes). Without wishing to be bound by theory, the parameters of the bioreactor system may cause a selective shift in a microbial population to favor microbes with a targeted functionality (e.g., nitrogen use efficiency). Nutrients (e.g., macronutrients, micronutrients, inorganic nutrients, or any combination thereof) can be present in the digestion system to provide an environment for bacterial growth. The nitrogen-use efficiency promoting microbes can comprise the inoculum of the microbe (e.g., a population of a nitrogen-use efficiency promoting microbial strain), nitrogen-use efficiency promoting microbes of a microbial consortium, nitrogen-use efficiency promoting metabolites produced by the inoculum of the microbe and / or the nitrogenuse efficiency promoting microbes of the microbial consortium, or any combination thereof.

[0344]

[0346] An inoculum of a microbe described herein may contact (e.g., be applied to) a plant. In some embodiments, the contacting of an inoculum of a microbe to a plant may enhance at least one plant growth promotion property of the plant. In some embodiments, one, two, three, four, or more inoculums of a microbe may be transferred to a digestion system. An inoculum of a microbe and another inoculum of a microbe may be the same. An inoculum of a microbe and another inoculum of a microbe may be different. In some embodiments, the inoculum of the microbe and the aqueous organic feedstock are transferred to a container of the digestion system at the same time. In some embodiments, the inoculum of the microbe and the aqueous organic feedstock are not transferred to a container of the digestion system at the same time. In some embodiments, the inoculum of the microbe is transferred to a container of the digestion system prior to the aqueous organic feedstock. In some embodiments, the inoculum of the microbe is transferred to a container of the digestion system after the aqueous organic feedstock.

[0345]

[0347] As a working fluid flows through a digestion system, an absolute number of nitrogen use efficiency -promoting microbes may increase. In some embodiments, an absolute number of nitrogen use efficiency-promoting microbes can be higher in a second container compared an absolute number of nitrogen use efficiency -promoting microbes in a first container. In some embodiments, an absolute number of nitrogen use efficiency -promoting microbes can be higher in a third container compared an absolute number of nitrogen use efficiency-promoting microbes in a first container. In some embodiments, an absolute number of nitrogen use efficiencypromoting microbes can be higher in a fourth container compared an absolute number of nitrogen use efficiency-promoting microbes in a first container. In some embodiments, an absolute number of nitrogen use efficiency -promoting microbes can be higher in a fifth container compared an absolute number of nitrogen use efficiency -promoting microbes in a first container. In some embodiments, an absolute number of nitrogen use efficiency-promoting microbes can be higher in a sixth container compared an absolute number of nitrogen use efficiency-promoting microbes in a first container. In some embodiments, an absolute number of nitrogen use efficiency-promoting microbes can be higher in a seventh container compared an absolute number of nitrogen use efficiency -promoting microbes in a first container. In some embodiments, an absolute number of nitrogen use efficiency -promoting microbes can be higher in an eighth container compared an absolute number of nitrogen use efficiency-promoting microbes in a first container. In some embodiments, an absolute number of nitrogen use efficiency-promoting microbes can be higher in a ninth container compared an absolute number of nitrogen use efficiency -promoting microbes in a first container. In some embodiments, an absolute number of nitrogen use efficiency -promoting microbes can be higher in a tenth container compared an absolute number of nitrogen use efficiency -promoting microbes in a first container.

[0346]

[0348] As working fluid flows through a digestion system, a proportion of nitrogen use efficiency -promoting microbes relative to a total population of bacteria may increase. In some embodiments, a proportion of nitrogen use efficiency -promoting microbes relative to a total population of bacteria can be higher in a second container compared a proportion of nitrogen use efficiency -promoting microbes relative to a total population of bacteria in a first container. In some embodiments, a proportion of nitrogen use efficiency-promoting microbes relative to a total population of bacteria can be higher in a third container compared a proportion of nitrogen use efficiency -promoting microbes relative to a total population of bacteria in a first container. In some embodiments a proportion of nitrogen use efficiency -promoting microbes relative to a total population of bacteria can be higher in a fourth container compared a proportion of nitrogen use efficiency-promoting microbes relative to a total population of bacteria in a first container. In some embodiments, a proportion of nitrogen use efficiency -promoting microbes relative to a total population of bacteria can be higher in a fifth container compared a proportion of nitrogen use efficiency -promoting microbes relative to a total population of bacteria in a first container. In some embodiments, a proportion of nitrogen use efficiency -promoting microbes relative to a total population of bacteria can be higher in a sixth container compared a proportion of nitrogen use efficiency -promoting microbes relative to a total population of bacteria in a first container. In some embodiments, a proportion of nitrogen use efficiency -promoting microbes relative to a total population of bacteria can be higher in a seventh container compared a proportion of nitrogen use efficiency -promoting microbes relative to a total population of bacteria in a first container. In some embodiments, a proportion of nitrogen use efficiencypromoting microbes relative to a total population of bacteria can be higher in an eighth container compared a proportion of nitrogen use efficiency-promoting microbes relative to a total population of bacteria in a first container. In some embodiments, a proportion of nitrogen use efficiency -promoting microbes relative to a total population of bacteria can be higher in a ninth container compared a proportion of nitrogen use efficiency-promoting microbes relative to a total population of bacteria in a first container. In some embodiments, a proportion of nitrogen use efficiency -promoting microbes relative to a total population of bacteria can be higher in a tenth container compared a proportion of nitrogen use efficiency-promoting microbes relative to a total population of bacteria in a first container.

[0347]

[0349] In some embodiments, an amount (e.g., a concentration and / or number) of a population of a microbial strain (e.g., an established population of a microbial strain) may differ one container to another container of the bioreactor system by at least about 0.01%, 0.05%, 0.1%, 0.5%, 1%, 2%, 3%, 4%, 5%, 10%, 15%, 20%, or greater than about 20%. In some embodiments, an amount (e.g., a concentration and / or number) of a population of a microbial strain (e.g., an established population of a microbial strain) may differ one container to another container of the bioreactor system by at most about 20%, 15%, 10%, 5%, 4%, 3%, 2%, 1%, 0.5%, 0.1%, 0.05%, 0.01%, or less than about 0.1%.

[0348]

[0350] An inoculum of a microbe may generate one or more metabolites in a digestion system as described herein. Microbes of the microbial consortium and / or the inoculum of the microbe may be metabolized by catalytic enzymes to produce metabolites. One or more metabolites may be generated by microbial metabolism. Metabolites may be generated by enzymes catalyzing biochemical reactions of the organic substrates of the aqueous organic feedstock in a working fluid of a digestion system as described herein. The metabolites generated by the inoculum of the microbe may have a plant growth promotion property. The metabolites generated by the inoculum of the microbe may have two or more plant growth promotion properties. The plant growth promotion properties may comprise shoot biomass, root biomass, nutrient uptake, crop yield, photosynthesis, deaminase activity, acid production, leaf area, chlorophyll content, heat tolerance, cold tolerance, drought tolerance, or salt tolerance, or total biomass. Metabolites may be used in biostimulant compositions and / or may be applied to plants.

[0349]

[0351] In some embodiments, the aqueous organic feedstock comprises one or more metabolites. In some embodiments, the aqueous organic feedstock comprises one or more metabolites produced by microbes endogenous to the organic feedstock. Primary metabolites can include carbohydrates, proteins, fats, vitamins, and nucleic acid components. Metabolites can further comprise alkaloids, amino acids, biogenic amines, carboxylic acids, cresols, terpenoids, phenols (e.g., flavonoids, coumarins, tannins, lignans, stilbenes, or chromones), polyketides, eicosanoids, hormones or derivatives thereof, indoles or derivatives thereof, nucleobases, citric acid, ceramides, diglycerides, triglycerides, amides, alkanes, alcohols, stearates, sterols, organic acids or fatty acids. In some embodiments, metabolites comprise sugars and / or fatty acids. Sugars can comprise fructose, hexose, galactose, glucose, lactose, maltose, sucrose, xylose, or any combination thereof. Fatty acids can comprise stearic acid, lauric acid, myristic acid, palmitic acid, octadecenoic acid, octadecadienoic acid, oleic acid, arachidic acid, behenic acid, erucic acid, adrenic acid, tricosanoic acid, lignoceric acid, nervonic acid, nonadecanoic acid, arachidic acid, myristolic acid, hydroxylated myristic acid, or any combination thereof.

[0350]

[0352] One or more metabolites generated by the inoculum of the microbe or by at least a portion of microbes of the microbial consortium may be present in a supernatant (e.g., base product) of a digestion system. In some embodiments, the metabolites may be present by weight in a volume of solution (e.g., in mg in 100 ml). In some embodiments, a weight of metabolites per 100 ml of a base product solution can be at least about 10 mg, at least about 20 mg, at least about 30 mg, at least about 40 mg, at least about 50 mg, at least about 60 mg, at least about 70 mg, at least about 80 mg, at least about 90 mg, at least about 100 mg, at least about 120 mg, at least about 140 mg, at least about 160 mg, at least about 180 mg, at least about 200 mg, at least about 220 mg, at least about 240 mg, at least about 260 mg, at least about 280 mg, at least about 300 mg, at least about 400 mg, at least about 500 mg, or greater than about 500 mg. In some embodiments, a weight of metabolites per 100 ml of a base product solution can be at most about 500 mg, at most about 400 mg, at most about 300 mg, at most about 280 mg, at most about 260 mg, at most about 240 mg, at most about 220 mg, at most about 200 mg, at most about 180 mg, at most about 160 mg, at most about 140 mg, at most about 120 mg, at most about 100 mg, at most about 90 mg, at most about 80 mg, at most about 70 mg, at most about 60 mg, at most about 50 mg, at most about 40 mg, at most about 30 mg, at most about 20 mg, at most about 10 mg, or less than about 10 mg. In some embodiments, a weight of metabolites per 100 ml of a base product solution can be from about 10 mg to about 500 mg. In some embodiments, a weight of metabolites per 100 ml of a base product solution can be from about 10 mg to about 20 mg, about 10 mg to about 30 mg, about 10 mg to about 40 mg, about 10 mg to about 50 mg, about 10 mg to about 75 mg, about 10 mg to about 100 mg, about 10 mg to about 125 mg, about 10 mg to about 150 mg, about 10 mg to about 175 mg, about 10 mg to about 250 mg, about 10 mg to about 500 mg, about 20 mg to about 30 mg, about 20 mg to about 40 mg, about 20 mg to about 50 mg, about 20 mg to about 75 mg, about 20 mg to about 100 mg, about 20 mg to about 125 mg, about 20 mg to about 150 mg, about 20 mg to about 175 mg, about 20 mg to about 250 mg, about 20 mg to about 500 mg, about 30 mg to about 40 mg, about 30 mg to about 50 mg, about 30 mg to about 75 mg, about 30 mg to about 100 mg, about 30 mg to about 125 mg, about 30 mg to about 150 mg, about 30 mg to about 175 mg, about 30 mg to about 250 mg, about 30 mg to about 500 mg, about 40 mg to about 50 mg, about 40 mg to about 75 mg, about 40 mg to about 100 mg, about 40 mg to about 125 mg, about 40 mg to about 150 mg, about 40 mg to about 175 mg, about 40 mg to about 250 mg, about 40 mg to about 500 mg, about 50 mg to about 75 mg, about 50 mg to about 100 mg, about 50 mg to about 125 mg, about 50 mg to about 150 mg, about 50 mg to about 175 mg, about 50 mg to about 250 mg, about 50 mg to about 500 mg, about 75 mg to about 100 mg, about 75 mg to about 125 mg, about 75 mg to about 150 mg, about 75 mg to about 175 mg, about 75 mg to about 250 mg, about 75 mg to about 500 mg, about 100 mg to about 125 mg, about 100 mg to about 150 mg, about 100 mg to about 175 mg, about 100 mg to about 250 mg, about 100 mg to about 500 mg, about 125 mg to about 150 mg, about 125 mg to about 175 mg, about 125 mg to about 250 mg, about 125 mg to about 500 mg, about 150 mg to about 175 mg, about 150 mg to about 250 mg, about 150 mg to about 500 mg, about 175 mg to about 250 mg, about 175 mg to about 500 mg, or about 250 mg to about 500 mg.

[0351]

[0353] The term “organic feedstock” described herein can refer to raw biomaterials such as carbon compounds, proteins, and / or carbohydrates. In some embodiments, the organic feedstock may comprise organic substrates comprising cottonseed, algae, neem, orange seed, linseed, jojoba, kusum, rubber seed, alfalfa, sugarcane, Opuntia, coffee, Deccan hemp, or any combination thereof. In some embodiments, the feedstock can comprise an inorganic feedstock. In some embodiments, the organic feedstock may include, but is not limited to, manure, kelp, lignocellulose, wastewater biosolids, food waste, energy crops, glucose solution, ammonium sulfate, oils, fats, grease. In some embodiments, the feedstock is added at the beginning of the system (e.g., into a first reactor and / or a CMR). In some embodiments, the feedstock is added in a middle reactor of the system (e.g., not in the first or last reactor of the system). In some embodiments, the feedstock is added once to the system. In some embodiments, the feedstock is added two, three, four, or more times to the system. In some embodiments, the organic feedstock is a composition of one raw biomaterial. In some embodiments, the organic feedstock is a blend of two, three, four, five, six, seven, eight, nine, ten, or more biomaterials.

[0352]

[0354] Organic feedstock comprising carbon and nitrogen sources can flow into a reactor tank. Organic feedstock comprising carbon and nitrogen sources can flow into a reactor tank via a conduit (e.g., a pipe). In some embodiments, a reactor tank circulates working fluid within itself to recycle working fluid, wherein reactor tanks can comprise out-flow pipes to circulate and recycle working fluid within each tank. Ports and piping between tanks can assist in transferring working fluid to adjacent reactor tanks. A working fluid in a final clarifier of a system may transfer from the reactor tank to a clarifier may produce a supernatant (e.g, base product). Working fluid flows through the serialized reactor system which can aid in selective growth of the added isolate and other microbes present that have the same property as the added isolate. Base product from the clarifier can be accessed and further analyzed for microbial composition. In a digestion system described herein, a working fluid may flow from a mixing chamber through at least one reaction and to a clarifier chamber.

[0353]

[0355] An organic feedstock can comprise one or more digestion products from digestion of organic substrates present in the organic feedstock. Organic substrates may improve stability of the fluid feed mixture. Organic substrates can comprise coconut coir, peat moss, hemp, wood fiber, or any combination thereof. In some embodiments, organic substrates comprise raw biomaterials present in the aqueous organic feedstock. A digestion system may comprise a plurality of microbes and / or microorganisms derived from digestion of organic substrates in an aqueous organic feedstock.

[0354]

[0356] An organic feedstock described herein may comprise one or more organic and / or biological materials. In some embodiments, the organic feedstock further comprises Saccharomyces cerevisiae yeast, Saccharomyces arboricola yeast, Saccharomyces mikatae yeast, Saccharomyces jurei yeast, Saccharomyces eubayanus yeast, Saccharomyces kudriavzevii yeast, Saccharomyces uvarum yeast, or any combination thereof. In some embodiments, the organic feedstock further comprises a lignocellulosic material. In some embodiments, the organic feedstock may be an aqueous mixture of at least one feedstock material and water. In some embodiments, the organic feedstock may be an aqueous mixture of cow manure, S. cerevisiae yeast, water, or any combination thereof. An organic feedstock can be an aqueous organic feedstock (e.g., an organic feedstock comprising water).

[0355]

[0357] Parameters of the digestion system, such as flow rate and the solids content of the organic feedstock, may be varied to achieve desired properties in the outflow biostimulant base product. In some embodiments, the hydraulic source is water. In some embodiments, the hydraulic source is a base product of another system. In some embodiments, the hydraulic source is a combination of water and a base product of another system. Water from the hydraulic source can be added to the organic feedstock of the digestion system to make an aqueous organic feedstock.

[0356]

[0358] In some embodiments, the aqueous organic feedstock may further comprise a inorganic substrate. In some embodiments, the aqueous organic feedstock may include more than one inorganic substrate. The inorganic substrate may improve stability of the fluid feed mixture. In some embodiments, the inorganic substrate comprises sand, vermiculite, perlite, diatomaceous earth, pumice, or any combination thereof. In some embodiments, the inorganic substrates comprises a mineral. In some embodiments, the inorganic substrate comprises rock phosphate.

[0357]

[0359] In some embodiments, loading inputs into a reactor can comprise one or more carbon sources, one or more nitrogen sources, one or more flours, one or more isolates, or any combination thereof. In some embodiments, the flour is soy flour. In some embodiments, the loading inputs comprise recycled floc from the system. In some embodiments, the loading inputs comprise a whole broth (WB). The inoculum of a microbe as described herein may metabolize the carbon source. Metabolism of carbon by the inoculum of the microbe may comprise transfer of carbon-based moieties of the carbon source to substrates in the working fluid.

[0358]

[0360] The inoculum of a microbe as described herein may metabolize the nitrogen source. Metabolism of nitrogen by the inoculum of the microbe may comprise transfer of nitrogen-based moieties of the nitrogen source to substrates in the working fluid. In some embodiments, the carbon source may be transferred to a first container of the digestion system. In some embodiments, the carbon source may be transferred to a second, third, fourth, fifth, or sixth container of the digestion system. In some embodiments, the nitrogen source may be transferred to a first container of the digestion system. In some embodiments, the nitrogen source may be transferred to a second, third, fourth, fifth, or sixth container of the digestion system.

[0359]

[0361] In some embodiments, the organic feedstock is mixed within a reactor. In some embodiments, the organic feedstock is mixed outside of a reactor. In some embodiments, the organic feedstock is mixed between one, two, three, or more reactors. In some embodiments, the organic feedstock is a homogenous mixture.

[0360]

[0362] In some embodiments, the organic feedstock further comprises a microbial consortium. The terms “microbe”, “microbial strain” and “microorganism” may refer to microscopic organisms, including, but not limited to bacteria, fungi, lichens, algae, protozoa, archaea, and / or molds. The terms “microbe” and microorganism” may be used interchangeably herein. The organic feedstock can comprise a microbial consortium with at least about 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 20, 30, 40, 50, 60, 70, 80, 90, 100, 200, 300, 400, 500, 600, 700, 800, 900, 1,000, 2,000, 3,000, 4,000, 5,000, 10,000, or more microorganisms. The organic feedstock can comprise a microbial consortium with at most about 10,000, 5,000, 4,000, 3,000, 2,000, 1,000, 900, 800, 700, 600, 500, 400, 300, 200, 100, 90, 80, 70, 60, 50, 40, 30, 20, 10, 9, 8, 7, 6, 5, 4, 3, 2, 1, or less microorganisms. The organic feedstock can comprise a microbial consortium with at least about 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 20, 30, 40, 50, 60, 70, 80, 90, 100, 200, 300, 400, 500, 600, 700, 800, 900, 1,000, 2,000, 3,000, 4,000, 5,000, 10,000, or more groups of microorganisms. The organic feedstock can comprise a microbial consortium with at most about 10,000, 5,000, 4,000, 3,000, 2,000, 1,000, 900, 800, 700, 600, 500, 400, 300, 200, 100, 90, 80, 70, 60, 50, 40, 30, 20, 10, 9, 8, 7, 6, 5, 4, 3, 2, 1, or less groups of microorganisms. The organic feedstock can comprise a microbial consortium with 1 group of microorganisms. The microbial consortium can comprise different microorganisms. The microbial consortium can comprise the same microorganism. The microbes in the consortia may be derived from the microbes originally present within the organic feedstock. The microbes may digest the manure, yeast, other organic raw materials, or any combination thereof to produce digestion products.

[0361]

[0363] In some embodiments, microbes can be added to the start of the system (e.g., into the first reactor). In some embodiments, microbes can be added to the middle of the system (e.g., into a reactor that is not the first reactor or the final reactor of the system) or microbes can be added to the end of the system (e.g., into the final reactor). Microbes can be added concurrently with the organic feedstock. Microbes can be added separately from the organic feedstock. In some embodiments, microbes may be added to the system with the organic feedstock in the same reactor. In some embodiments, microbes may be added to the system with the organic feedstock in different reactors. In some embodiments, microbes may be added to the system prior to the organic feedstock. In some embodiments, microbes may be added to the system after the organic feedstock. In some embodiments, a period of time between addition of microbes to the system and addition of organic feedstock to the system can be at least about 1 minute, at least about 5 minutes, at least about 10 minutes, at least about 15 minutes, at least about 20 minutes, at least about 30 minutes, at least about 40 minutes, at least about 50 minutes, or at least about 1 hours. In some embodiments, a period of time between addition of microbes to the system and addition of organic feedstock to the system can be at most about 2 hours, at most about 1 hours, at most about 45 minutes, at most about 30 minutes, at most about 15 minutes, at most about 10 minutes, at most about 5 minutes, at most about 1 minute, or at most about 30 seconds.

[0362]

[0364] A microbe may have nutrient solubilization properties and / or plant growth promotion properties. For example, a microbe may increase plant growth, increase shoot and / or root biomass, increase crop yield, increase soil enzymatic activity, increase photosynthetic efficiency, lower heavy metal uptake, decrease soil pH, or any combination thereof. A microbe may enhance plant growth on land with high salinity, on land with heavy metal contamination, or on land with drought conditions. A microbe (e.g., isolate) described herein may have nitrogen use efficiency properties.

[0363]

[0365] In some embodiments, the digestion system may comprise a retention time. A retention time may comprise a time an inoculum of a microbe spends in a digestion system or a time an inoculum of a microbe spends following transfer into a first container and until collection from the digestion system. A longer retention time may be advantageous for growth or enrichment of an inoculum of a microbe of the digestion system. A shorter retention time may be advantageous for growth or enrichment of an inoculum of a microbe of the digestion system. A retention time of a digestion system may comprise at least about 1 day, 2 days, 3 days, 4 days, 5 days, 6 days, 1 week, 2 weeks, 3 weeks, 4 weeks, 1 month, 2 months, 3 months, 6 months, 9 months, or greater than about 9 months. A retention time of a digestion system may comprise at most about 9 months, 6 months, 3 months, 2 months, 1 month, 4 weeks, 3 weeks, 2 weeks, 1 week, 6 days, 5 days, 4 days, 3 days, 2 days, 1 day, or less than about 1 day. The terms “retention time” and “hydraulic retention time” may be used interchangeably.

[0364]

[0366] In the first reactor, the working fluid may be agitated at a rate that allows heavier or undigested solids to settle to the bottom. An outlet at the top of the first reactors may allow the fluid to flow into the second reactor. An outlet at the bottom of the first reactor may transfer the settled solids back into a reactor tank. Each of the reactors in the series of reactors may have submerged scaffolding that provide a surface for biofilm growth. The scaffolding can be referred to as “fixed media substrates”. The flow of fluid from reactor to reactor may comprise a plug flow model, in which particles of an input fluid have the same velocity and direction of motion. In some embodiments, the flow of fluid in the digestion system is driven by gravity. In some embodiments, the bioreactor system may be operated in a hydraulically balanced manner. A hydraulically balanced manner can comprise working fluid transferring from one container of the system to another container to a further container at an equal rate. In some embodiments, the transferring and / or collecting of the methods described herein may be driven by gravity. The outlet port of a container may be higher than an inlet port of another container so that the working fluid transfers via gravity between containers of the bioreactor system. In some embodiments, the opening of an outlet port of a first container is at the same level as the top of the working fluid or slightly below the level of the working fluid (i.e., the bottom of the opening of the outlet port may be 1, 2, 3, or 4 cm below the level of the working fluid) so that the rate of flow of liquid into the first container can be equaled by the rate of flow of liquid out of the first container. The first container may be fluidly connected to a second container, e.g., by a pipe or other conduit connected to the outlet port of the first container. The pipe or other conduit may connect to an inlet port of a second container. The inlet port of the second container may be below the level of the outlet port of the first container such that the working fluid from the first container may flow by gravity alone into the second container. The second container may have an outlet port with an opening that is at the same level or is at least partially below the level of the working fluid in the second container (i.e., the bottom of the opening of the outlet port may be 1, 2, 3, or 4 cm below the level of the working fluid) so that the rate of flow of liquid into the first container can be equaled by the rate of flow of liquid out of the first container solely due to the effect of gravity. Additional containers (e.g., a third, fourth, fifth, sixth, seventh, or more containers) can have inlet and outlet ports arranged in the same way, with each subsequent container having inlet and outlet ports arranged such that flow between containers can be continuous and driven solely by gravity, i.e., the inlet and outlet ports of each subsequent container in a series of containers is at a level lower than the outlet port of the previous container. In some embodiments, all the inlet and outlet ports of containers in the system are open at all times to allow continuous flow driven solely by gravity (i.e., without any pumps needed to drive flow from any container to a subsequent container in the system). In some embodiments, the flow of fluid in the digestion system is driven by a pump. The outflow from the top of the last reactor, may be used to create a product. Products of the methods and systems as described herein can be biostimulants. Biostimulants can promote plant growth or improve soil quality.

[0365] B. Reactors

[0366]

[0367] A digestion process to produce the biostimulant may be performed in a digestion system that includes a series of tanks, containers, or vessels (e.g., reactors) through which the feedstock continuously flows. A reactor can be a fluidly connected container, system, vessel, or tank in which microbial consortia including the microbes, isolates, and / or microorganisms as described herein can be grown. A reactor can be separate or continuous. A reactor may be a physical containment system arranged in a discrete order to favor growth of particular microbes. Types of reactors can include, but are not limited to, fluidized-bed reactors (FBRs) or packed-bed reactors (PBRs).

[0367]

[0368] In an aspect, the present disclosure provides a bioreactor system. The bioreactor system can comprise a stream of an aqueous feedstock. The stream may be in fluid communication with a container (e.g., a first container). The container can comprise a volume of working fluid. For example, the stream may be in fluid communication with a first container of the bioreactor system comprising a volume of a first working fluid. The aqueous feedstock can comprise a microbial consortium, wherein the microbial consortium can comprise a microbial consortium described herein. The working fluid (e.g., the first working fluid) may comprise a microbial strain. The microbial strain can be a population of a microbial strain (e.g., a nitrogen useefficiency strain) and may comprise a plant growth promoting property (e.g., a desired plant growth promoting property). A first container of the bioreactor system may comprise a mixer. The mixer can be configured to aerate the working fluid (e.g., the first working fluid) in a container.

[0368]

[0369] In some embodiments, a concentration of the microbial strain (e.g., the nitrogen useefficiency strain) may be higher in the working fluid than in the aqueous feedstock. In some embodiments, a concentration of the microbial strain may be higher in the working fluid than in any other input to the bioreactor. For example, a concentration of the microbial strain (e.g., the nitrogen use-efficiency strain) in the first working fluid may be at least about 2 times higher, at least about 5 times higher, at least about 10 times higher, at least about 25 times higher, at least about 50 times higher, at least about 100 times higher, at least about 150 times higher, at least about 200 times higher, at least about 250 times higher, at least about 500 times higher, or greater than about 500 times higher than a concentration of the microbial strain in the aqueous feedstock stream or in any other input into the bioreactor system. A concentration of the microbial strain in the first working fluid may be at most about 500 times higher, at most about 250 times higher, at most about 200 times higher, at most about 150 times higher, at most about 100 times higher, at most about 50 times higher, at most about 25 times higher, at most about 10 times higher, at most about 5 times higher, at most about 2 times higher, or less than about 2 times higher than a concentration of the microbial strain (e.g., the nitrogen use-efficiency strain) in the aqueous feedstock stream or in any other input into the bioreactor system.

[0369]

[0370] The bioreactor system described herein may comprise one or more additional containers (e.g., one or more containers in addition to a first container). The container can be arranged in a series. In some embodiments, the series of containers can comprise a first container, a second container, a third container, a fourth container, a fifth container, a sixth container, and any additional contained s). One or more additional containers in the bioreactor system may comprise a volume of working fluid. In some embodiments, each container of the one or more additional containers comprises a volume of working fluid. The one or more additional containers may be in fluid communication with a container of the series in the bioreactor system. In some embodiments, at least one of the containers of the bioreactor system can comprise a product outflow stream port. In some embodiments, each container of the series of containers may comprise a product outflow stream port. A product outflow stream (e.g., stream of the volume of working fluid of a container) can be in fluid communication with the product outflow stream port.

[0370]

[0371] As an example, the present disclosure provides a bioreactor system comprising: (a) a stream of an aqueous feedstock in fluid communication with a first container comprising a volume of a first working fluid, wherein the aqueous feedstock comprises a microbial consortium, wherein the first working fluid comprises an established population of a first nitrogen use efficiency-promoting microbial strain, wherein a concentration of the first nitrogen use efficiency -promoting microbial strain in the first working fluid is at least 100 times higher than a concentration of the first nitrogen use efficiency -promoting microbial strain in the aqueous feedstock stream and in any other input into the bioreactor system; (b) one or more additional containers arranged in a series that includes the first container, wherein each of the one or more additional containers comprises a volume of a working fluid and is in fluid communication with at least one other container in the series, and wherein at least one of the one or more additional containers comprises a product outflow stream port; and (c) a product outflow stream in fluid communication with the product outflow stream port.

[0371]

[0372] In some embodiments, the product outflow stream may comprise a biostimulant composition. The biostimulant composition can comprise an amount of the microbial strain (e.g., a nitrogen use efficiency-promoting microbial strain), wherein the amount (e.g., concentration and / or bacterial number) of the microbial strain can be an amount described herein. The biostimulant composition can comprise a plant growth promoting property (e.g., a desired plant growth promoting property). In some embodiments, the microbial strain can be configured to promote a plant growth promoting property (e.g., an ability to performing nitrogen fixation, promoting nitrogen fixation in the tissues of plants, recruiting nitrogen fixers to the root zones or other tissues of plants, increasing organic nitrogen content and / or mineralization of organic nitrogen in soil, or any combination thereof).

[0372]

[0373] The bioreactor system can be a continuous flow system. A continuous flow system can comprise a system wherein the flow of fluid is not interrupted. The stream of aqueous feedstock can be a continuous stream. In some embodiments, the bioreactor system can comprise a periodic flow, wherein there can be interruptions to the flow stream. In some embodiments, as a continuous flow bioreactor system, the volume of working fluid may be constant.

[0373]

[0374] In some embodiments, the bioreactor system can comprise the clarifier container as described herein. The clarifier container can be configured to separate a portion of a working fluid in the clarifier container into a supernatant portion and a floc portion. In some embodiments, the product outflow stream of the system can comprise the supernatant portion.

[0374]

[0375] In some embodiments, the product outflow stream comprises at least about 100 CFU / ml, at least about IxlO3CFU / ml, at least about IxlO4CFU / ml, at least about IxlO5CFU / ml, at least about IxlO6CFU / ml, at least about IxlO7CFU / ml, at least about IxlO8CFU / ml, at least about IxlO9CFU / ml, at least about IxlO10CFU / ml, or greater than about IxlO10CFU / ml of the microbial strain (e.g., the nitrogen use efficiency-promoting microbial strain). In some embodiments, the product outflow stream comprises at most about IxlO10CFU / ml, at most about IxlO9CFU / ml, at most about IxlO8CFU / ml, at most about IxlO7CFU / ml, at most about IxlO6CFU / ml, at most about IxlO5CFU / ml, at most about IxlO4CFU / ml, at most about IxlO3CFU / ml, at most about 100 CFU / ml, or less than about 100 CFU / ml of the microbial strain (e.g., the nitrogen use efficiency-promoting microbial strain).

[0376] In some embodiments, the product outflow stream comprises at least about 100 CFU / ml, at least about IxlO3CFU / ml, at least about IxlO4CFU / ml, at least about IxlO5CFU / ml, at least about IxlO6CFU / ml, at least about IxlO7CFU / ml, at least about IxlO8CFU / ml, at least about IxlO9CFU / ml, at least about IxlO10CFU / ml, or greater than about IxlO10CFU / ml of a sporulated form of the microbial strain (e.g., the nitrogen use efficiency -promoting microbial strain). In some embodiments, the product outflow stream comprises at most about IxlO10CFU / ml, at most about IxlO9CFU / ml, at most about IxlO8CFU / ml, at most about IxlO7CFU / ml, at most about IxlO6CFU / ml, at most about IxlO5CFU / ml, at most about IxlO4CFU / ml, at most about IxlO3CFU / ml, at most about 100 CFU / ml, or less than about 100 CFU / ml of a sporulated form of the microbial strain (e.g., the nitrogen use efficiency -promoting microbial strain).

[0375]

[0377] In some embodiments, the product outflow stream may comprise a total dry weight. The total dry weight of the product outflow stream may be at least about 0.05 mg / ml, at least about 0.1 mg / ml, at least about 0.2 mg / ml, at least about 0.3 mg / ml, at least about 0.4 mg / ml, at least about 0.5 mg / ml, at least about 1.0 mg / ml, at least about 1.5 mg / ml, at least about 2.0 mg / ml, at least about 2.5 mg / ml, at least about 3.0 mg / ml, at least about 3.5 mg / ml, at least about 4.0 mg / ml, at least about 5.0 mg / ml, or greater than about 5.0 mg / ml. The total dry weight of the product outflow stream may be at most about 5.0 mg / ml, at most about 4.0 mg / ml, at most about 3.5 mg / ml, at most about 3.0 mg / ml, at most about 2.5 mg / ml, at most about 2.0 mg / ml, at most about 1.5 mg / ml, at most about 1.0 mg / ml, at most about 0.5 mg / ml, at most about 0.4 mg / ml, at most about 0.3 mg / ml, at most about 0.2 mg / ml, at most about 0.1 mg / ml, at most about 0.05 mg / ml, or less than about 0.05 mg / ml. The total dry weight of the product outflow stream may be between about 0.05 mg / ml to about 4 mg / ml. The total dry weight of the product outflow stream may be between about 0.05 mg / ml to about 0.1 mg / ml, about 0.05 mg / ml to about 0.2 mg / ml, about 0.05 mg / ml to about 0.3 mg / ml, about 0.05 mg / ml to about 0.4 mg / ml, about 0.05 mg / ml to about 0.5 mg / ml, about 0.05 mg / ml to about 1 mg / ml, about 0.05 mg / ml to about 1.5 mg / ml, about 0.05 mg / ml to about 2 mg / ml, about 0.05 mg / ml to about 2.5 mg / ml, about 0.05 mg / ml to about 3 mg / ml, about 0.05 mg / ml to about 4 mg / ml, about 0.1 mg / ml to about 0.2 mg / ml, about 0.1 mg / ml to about 0.3 mg / ml, about 0.1 mg / ml to about 0.4 mg / ml, about 0.1 mg / ml to about 0.5 mg / ml, about 0.1 mg / ml to about 1 mg / ml, about 0.1 mg / ml to about 1.5 mg / ml, about 0.1 mg / ml to about 2 mg / ml, about 0.1 mg / ml to about 2.5 mg / ml, about 0.1 mg / ml to about 3 mg / ml, about 0.1 mg / ml to about 4 mg / ml, about 0.2 mg / ml to about 0.3 mg / ml, about 0.2 mg / ml to about 0.4 mg / ml, about 0.2 mg / ml to about 0.5 mg / ml, about 0.2 mg / ml to about 1 mg / ml, about 0.2 mg / ml to about 1.5 mg / ml, about 0.2 mg / ml to about 2 mg / ml, about 0.2 mg / ml to about 2.5 mg / ml, about 0.2 mg / ml to about 3 mg / ml, about 0.2 mg / ml to about 4 mg / ml, about 0.3 mg / ml to about 0.4 mg / ml, about 0.3 mg / ml to about 0.5 mg / ml, about 0.3 mg / ml to about 1 mg / ml, about 0.3 mg / ml to about 1.5 mg / ml, about 0.3 mg / ml to about 2 mg / ml, about 0.3 mg / ml to about 2.5 mg / ml, about 0.3 mg / ml to about 3 mg / ml, about 0.3 mg / ml to about 4 mg / ml, about 0.4 mg / ml to about 0.5 mg / ml, about 0.4 mg / ml to about 1 mg / ml, about 0.4 mg / ml to about 1.5 mg / ml, about 0.4 mg / ml to about 2 mg / ml, about 0.4 mg / ml to about 2.5 mg / ml, about 0.4 mg / ml to about 3 mg / ml, about 0.4 mg / ml to about 4 mg / ml, about 0.5 mg / ml to about 1 mg / ml, about 0.5 mg / ml to about 1.5 mg / ml, about 0.5 mg / ml to about 2 mg / ml, about 0.5 mg / ml to about 2.5 mg / ml, about 0.5 mg / ml to about 3 mg / ml, about 0.5 mg / ml to about 4 mg / ml, about 1 mg / ml to about 1.5 mg / ml, about 1 mg / ml to about 2 mg / ml, about 1 mg / ml to about 2.5 mg / ml, about 1 mg / ml to about 3 mg / ml, about 1 mg / ml to about 4 mg / ml, about 1.5 mg / ml to about 2 mg / ml, about 1.5 mg / ml to about 2.5 mg / ml, about 1.5 mg / ml to about 3 mg / ml, about 1.5 mg / ml to about 4 mg / ml, about 2 mg / ml to about 2.5 mg / ml, about 2 mg / ml to about 3 mg / ml, about 2 mg / ml to about 4 mg / ml, about 2.5 mg / ml to about 3 mg / ml, about 2.5 mg / ml to about 4 mg / ml, or about 3 mg / ml to about 4 mg / ml.

[0376]

[0378] In some embodiments, the product outflow stream may comprise a chemical oxygen demand. The chemical oxygen demand of the product outflow stream may be at least about 10 mg / L, at least about 20 mg / L, at least about 30 mg / L, at least about 40 mg / L, at least about 50 mg / L, at least about 60 mg / L, at least about 70 mg / L, at least about 80 mg / L, at least about 90 mg / L, at least about 100 mg / L, at least about 250 mg / L, at least about 500 mg / L, at least about 750 mg / L, at least about 1000 mg / L, or greater than about 1000 mg / L. The chemical oxygen demand of the product outflow stream may be at most about 1000 mg / L, at most about 750 mg / L, at most about 500 mg / L, at most about 250 mg / L, at most about 100 mg / L, at most about 90 mg / L, at most about 80 mg / L, at most about 70 mg / L, at most about 60 mg / L, at most about 50 mg / L, at most about 40 mg / L, at most about 30 mg / L, at most about 20 mg / L, at most about 10 mg / L, or less than about 10 mg / L. The chemical oxygen demand of the product outflow stream may be between about 10 mg / L to about 1,000 mg / L. The chemical oxygen demand of the product outflow stream may be between about 10 mg / L to about 20 mg / L, about 10 mg / L to about 30 mg / L, about 10 mg / L to about 40 mg / L, about 10 mg / L to about 50 mg / L, about 10 mg / L to about 80 mg / L, about 10 mg / L to about 100 mg / L, about 10 mg / L to about 150 mg / L, about 10 mg / L to about 200 mg / L, about 10 mg / L to about 500 mg / L, about 10 mg / L to about 750 mg / L, about 10 mg / L to about 1,000 mg / L, about 20 mg / L to about 30 mg / L, about 20 mg / L to about 40 mg / L, about 20 mg / L to about 50 mg / L, about 20 mg / L to about 80 mg / L, about 20 mg / L to about 100 mg / L, about 20 mg / L to about 150 mg / L, about 20 mg / L to about 200 mg / L, about 20 mg / L to about 500 mg / L, about 20 mg / L to about 750 mg / L, about 20 mg / L to about 1,000 mg / L, about 30 mg / L to about 40 mg / L, about 30 mg / L to about 50 mg / L, about 30 mg / L to about 80 mg / L, about 30 mg / L to about 100 mg / L, about 30 mg / L to about 150 mg / L, about 30 mg / L to about 200 mg / L, about 30 mg / L to about 500 mg / L, about 30 mg / L to about 750 mg / L, about 30 mg / L to about 1,000 mg / L, about 40 mg / L to about 50 mg / L, about 40 mg / L to about 80 mg / L, about 40 mg / L to about 100 mg / L, about 40 mg / L to about 150 mg / L, about 40 mg / L to about 200 mg / L, about 40 mg / L to about 500 mg / L, about 40 mg / L to about 750 mg / L, about 40 mg / L to about 1,000 mg / L, about 50 mg / L to about 80 mg / L, about 50 mg / L to about 100 mg / L, about 50 mg / L to about 150 mg / L, about 50 mg / L to about 200 mg / L, about 50 mg / L to about 500 mg / L, about 50 mg / L to about 750 mg / L, about 50 mg / L to about 1,000 mg / L, about 80 mg / L to about 100 mg / L, about 80 mg / L to about 150 mg / L, about 80 mg / L to about 200 mg / L, about 80 mg / L to about 500 mg / L, about 80 mg / L to about 750 mg / L, about 80 mg / L to about 1,000 mg / L, about 100 mg / L to about 150 mg / L, about 100 mg / L to about 200 mg / L, about 100 mg / L to about 500 mg / L, about 100 mg / L to about 750 mg / L, about 100 mg / L to about 1,000 mg / L, about 150 mg / L to about 200 mg / L, about 150 mg / L to about 500 mg / L, about 150 mg / L to about 750 mg / L, about 150 mg / L to about 1,000 mg / L, about 200 mg / L to about 500 mg / L, about 200 mg / L to about 750 mg / L, about 200 mg / L to about 1,000 mg / L, about 500 mg / L to about 750 mg / L, about 500 mg / L to about 1,000 mg / L, or about 750 mg / L to about 1,000 mg / L.

[0377]

[0379] In some embodiments, the product outflow stream may comprise an electrical conductivity. The electrical conductivity of the product outflow stream may be at least about 0.01 mS / cm, at least about 0.05 mS / cm, at least about 0.1 mS / cm, at least about 0.5 mS / cm, at least about 1.0 mS / cm, at least about 1.5 mS / cm, at least about 2.0 mS / cm, at least about 2.5 mS / cm, at least about 3.0 mS / cm, at least about 4.0 mS / cm, at least about 5.0 mS / cm, at least about 10.0 mS / cm, or greater than about 10.0 mS / cm. The electrical conductivity of the product outflow stream may be at most about 10.0 mS / cm, at most about 5.0 mS / cm, at most about 4.0 mS / cm, at most about 3.0 mS / cm, at most about 2.5 mS / cm, at most about 2.0 mS / cm, at most about 1.5 mS / cm, at most about 1.0 mS / cm, at most about 0.5 mS / cm, at most about 0.1 mS / cm, at most about 0.05 mS / cm, at most about 0.01 mS / cm, or less than about 0.01 mS / cm. The electrical conductivity of the product outflow stream may be between about 0.01 mS / cm to about 10 mS / cm. The electrical conductivity of the product outflow stream may be between about 0.01 mS / cm to about 0.05 mS / cm, about 0.01 mS / cm to about 0.1 mS / cm, about 0.01 mS / cm to about 0.5 mS / cm, about 0.01 mS / cm to about 1 mS / cm, about 0.01 mS / cm to about 1.5 mS / cm, about 0.01 mS / cm to about 2 mS / cm, about 0.01 mS / cm to about 2.5 mS / cm, about 0.01 mS / cm to about 3 mS / cm, about 0.01 mS / cm to about 4 mS / cm, about 0.01 mS / cm to about 5 mS / cm, about 0.01 mS / cm to about 10 mS / cm, about 0.05 mS / cm to about 0.1 mS / cm, about 0.05 mS / cm to about 0.5 mS / cm, about 0.05 mS / cm to about 1 mS / cm, about 0.05 mS / cm to about 1.5 mS / cm, about 0.05 mS / cm to about 2 mS / cm, about 0.05 mS / cm to about 2.5 mS / cm, about 0.05 mS / cm to about 3 mS / cm, about 0.05 mS / cm to about 4 mS / cm, about 0.05 mS / cm to about 5 mS / cm, about 0.05 mS / cm to about 10 mS / cm, about 0.1 mS / cm to about 0.5 mS / cm, about 0.1 mS / cm to about 1 mS / cm, about 0.1 mS / cm to about 1.5 mS / cm, about 0.1 mS / cm to about 2 mS / cm, about 0.1 mS / cm to about 2.5 mS / cm, about 0.1 mS / cm to about 3 mS / cm, about 0.1 mS / cm to about 4 mS / cm, about 0.1 mS / cm to about 5 mS / cm, about 0.1 mS / cm to about 10 mS / cm, about 0.5 mS / cm to about 1 mS / cm, about 0.5 mS / cm to about 1.5 mS / cm, about 0.5 mS / cm to about 2 mS / cm, about 0.5 mS / cm to about 2.5 mS / cm, about 0.5 mS / cm to about 3 mS / cm, about 0.5 mS / cm to about 4 mS / cm, about 0.5 mS / cm to about 5 mS / cm, about 0.5 mS / cm to about 10 mS / cm, about 1 mS / cm to about 1.5 mS / cm, about 1 mS / cm to about 2 mS / cm, about 1 mS / cm to about 2.5 mS / cm, about 1 mS / cm to about 3 mS / cm, about 1 mS / cm to about 4 mS / cm, about 1 mS / cm to about 5 mS / cm, about 1 mS / cm to about 10 mS / cm, about

[0378] 1.5 mS / cm to about 2 mS / cm, about 1.5 mS / cm to about 2.5 mS / cm, about 1.5 mS / cm to about 3 mS / cm, about 1.5 mS / cm to about 4 mS / cm, about 1.5 mS / cm to about 5 mS / cm, about 1.5 mS / cm to about 10 mS / cm, about 2 mS / cm to about 2.5 mS / cm, about 2 mS / cm to about 3 mS / cm, about 2 mS / cm to about 4 mS / cm, about 2 mS / cm to about 5 mS / cm, about 2 mS / cm to about 10 mS / cm, about 2.5 mS / cm to about 3 mS / cm, about 2.5 mS / cm to about 4 mS / cm, about

[0379] 2.5 mS / cm to about 5 mS / cm, about 2.5 mS / cm to about 10 mS / cm, about 3 mS / cm to about 4 mS / cm, about 3 mS / cm to about 5 mS / cm, about 3 mS / cm to about 10 mS / cm, about 4 mS / cm to about 5 mS / cm, about 4 mS / cm to about 10 mS / cm, or about 5 mS / cm to about 10 mS / cm.

[0380]

[0380] In some embodiments, reactors may be arranged so that fluid can flow from an outflow port of a reactor into an adjacent reactor or tank. Fluid from near the top of the working fluid in a reactor may flow into the next reactor continuously. Fluid from the middle of a reactor may flow into the next reactor continuously. Fluid from the bottom of a reactor may flow into the next reactor continuously. Fluid may also be reintroduced from any outflow source into the same reactor. In some embodiments, an outflow port is between 0.1 and 35 inches below the top of the working fluid within a reactor. In some embodiments, an outflow port is at least about 1 inch, at least about 2 inches, at least about 5 inches, at least about 10 inches, at least about 20 inches, at least about 50 inches, at least about 100 inches, at least about 250 inches, at least about 500 inches, at least about 750 inches, at least about 1,000 inches, at least about 2,500 inches, at least about 5,000 inches, at least about 7,500 inches, or at least about 10,000 inches below the top of the working fluid within a reactor. In some embodiments, an outflow port is at most about 10,000 inches, at most about 7,500 inches, at most about 5,000 inches, at most about 2,500 inches, at most about 1,000 inches, at most about 750 inches, at most about 500 inches, at most about 250 inches, at most about 100 inches, at most about 50 inches, at most about 20 inches, at most about 10 inches, at most about 5 inches, at most about 2 inches, or at most about 1 inch below the top of the working fluid within a reactor. In some embodiments, the rate of outflowing product from a digestion system may match the rate of inflowing feedstock, providing for a hydraulically balanced flow throughout the system. A reactor within the system may have a unique, stable microbial consortium with distinct physiological characteristics and digestion capabilities as compared to consortia in other tanks in the system. A reactor within the system may have the same microbial consortium with similar physiological characteristics and digestion capabilities as another reactor within the system. Each reactor within the system may have the same volume capacity. Each reactor within the system may have a different volume capacity. The digestion system may comprise at least two reactors. The digestion system may comprise at least about 2, 3, 4, 5, 6, 7, 8, 9, 10, or more reactors. The digestion system may comprise at most about 10, 9, 8, 7, 6, 5, 4, 3, 2, or less reactors. Reactors of a digestion system may be arranged as a serialized assembly of reactors. A serialized assembly of reactors may have conduits (e.g., ports or outputs) connecting each reactor to an adjacent reactor and / or container. A serialized assembly of reactors may have a continuous flow of working fluid through each reactor to the adjacent reactor.

[0381]

[0381] In some embodiments, a reactor may have a single in-flow port and a single out-flow port. In some embodiments, a reactor may have multiple in-flow ports and out-flow ports. In some embodiments, a reactor may have a single in-flow port and multiple out-flow ports. In some embodiments, a reactor may have multiple in-flow ports and a single out-flow port. A reactor may have another in-flow port to provide a carbon source and / or consortium inoculum. An in-flow port may be present at any location of a reactor of the digestion system. An in-flow port may be present at the top of the reactor or at the bottom of the reactor. An out-flow port may be present at the top of the reactor or at the bottom of the reactor. In some embodiments, the out-flow ports or in-flow ports described herein comprise pipes, pumps, ventilations, or other conduits for transferring fluid from one vessel to another.

[0382]

[0382] A reactor may have a single fluid connection. A reactor may have multiple fluid connections (e.g., at least 2, 3, 4, 5, 6, 7, 8, 9, 10, or more fluid connections). The fluid connections may be present at the top of the working fluid in each reactor or near the top of the working fluid in each reactor. In some embodiments, the reactor may have flow from the bottom of the container back to the top to prevent build-up of sludge in the bottom of the reactor. In some embodiments, a reactor may have stirrers in the bottom of the container. In some embodiments, a reactor may have wipers in the bottom of the container. The wipers may stir the feedstock and prevent clogging within the reactor. The wipers may fold floc and ease floc return.

[0383]

[0383] In some embodiments, the reactors may comprise one or more packed bed reactors. In some embodiments, each of the packed bed reactors has an open cell design to allow free movement of working fluid. A fixed media (e.g., scaffolding) may be secured to the inside of each packed bed reactor. The fixed media comprises materials that increase the contact surface area for the communities of microbes with working fluid. Without wishing to be bound by theory, the increased surface area provided by the scaffolding can provide increased contact for biofilm (e.g., microbes of a microbial consortium, an established microbial strain, or any combination thereof) to grow. The fixed media also provides a stable platform for anchoring biofilm. The packed bed reactors may be packed with scaffolding to increase surface area within the reactor. The scaffolding within the reactor may increase biofilm. The packed bed reactor may improve contact between the biofilm and substrates within the reactor. The fixed media can be of several types, including durable plastic, polyvinyl chloride (PVC), metal, metal alloy, glass, glass compounds, fiberglass, or any suitably robust inert material. The design and configuration of the fixed media can assume various geometric patterns that allow working fluid to freely move through each packed bed reactor and prevents fouling. Free flow supports controlled hydraulic shearing which in time promotes even distribution of working fluid. In this embodiment, the fixed media is dispersed throughout a cross sectional area of each packed bed reactor.

[0384]

[0384] The scaffolding may comprise one or more tubes, one or more rings, or other one or more packing materials. In some embodiments, the packed bed reactors provided herein may comprise a bundle of tubes or columns. In some embodiments, the scaffolding may comprise hexagonal, grid-like, perforated tubing, or any combination thereof. Without wishing to be bound by theory, hexagonal, grid-like, and / or perforated scaffolding can increase the surface area and the flow through the columns within the container. In some embodiments, the tubes or columns of the scaffolding can comprise a diameter between 0.25 and 50 inches. In some embodiments, the scaffolding can comprise a diameter of at least about 0.5 inches, at least about 0.6 inches, at least about 0.7 inches, at least about 0.8 inches, at least about 0.9 inches, at least about 1 inch, at least about 2 inches, at least about 3 inches, at least about 4 inches, at least about 5 inches, at least about 10 inches, at least about 15 inches, at least about 20 inches, at least about 25 inches, at least about 30 inches, at least about 40 inches, at least about 50 inches, at least about 60 inches, or at least about 75 inches. In some embodiments, the scaffolding can comprise a diameter of at most about 75 inches, at least about 60 inches, at most about 50 inches, at most about 40 inches, at most about 30 inches, at most about 25 inches, at most about 20 inches, at most about 15 inches, at most about 10 inches, at most about 5 inches, at most about 4 inches, at most about 3 inches, at most about 2 inches, at most about 1 inches, at most about 0.9 inches, at most about 0.8 inches, at most about 0.7 inches, at most about 0.6 inches, or at most about 0.5 inches. Without wishing to be bound by theory, a system with packed bed reactors may improve production of bacterial isolates or other microbes. In some embodiments, reactors without scaffolding (i.e., reactors that are not packed bed reactors) improve production of bacterial isolates or other microbes or improves digestion of digestible substrates.

[0385]

[0385] In some embodiments, the reactors may comprise one or more fluidized bed reactors. In fluidized bed reactors, solid particles may be circulated within working fluid of the reactors, which may provide a surface for microbial colonization. Such particles may include, for example, particles of an inorganic substrate such as rock phosphate particles. In some embodiments, the fluidized bed reactors may be the same volume. In some embodiments, the fluidized bed reactors may be different volumes. In some embodiments, the fluidized bed reactors increase uniformity of particle mixing within the digestion system. The solid material of the fluidized bed reactor can have intrinsic fluid-like properties and allow for a more complete mixing. Reduction or elimination of radial and axial concentration gradients can provide for better fluid-solid contact and can achieve better uniformity of particle mixing. In some embodiments, the fluidized bed reactors increase the uniformity of temperature gradients within the digestion system. Without wishing to be bound by theory, the open container of the fluidized bed reactor can provide for a reduction in isolated hot or cold spots in the container, allowing for a uniform temperature distribution of the fluid.

[0386]

[0386] The flow rate of the digestion system may be chosen to allow for sufficient dwell time within each of the reactor for a stable and unique microbial consortium to form within each of the reactors. In some embodiments, working fluid in each reactor is continuously recycled at a rate ratio in a range of approximately 25: 1 to 35: 1, 25 to 35 gallons per minute of the recycle rate to one gallon per minute of the hydraulic feed rate. In some embodiments, working fluid in each reactor is continuously recycled at a rate ratio of at least about 10: 1, at least about 12: 1, at least about 14: 1, at least about 16: 1, at least about 18: 1, at least about 20: 1, at least about 22: 1, at least about 24: 1, at least about 26: 1, at least about 28: 1, at least about 30: 1, at least about 32: 1, at least about 34: 1, at least about 36: 1, at least about 38: 1, at least about 40: 1, at least about 45: 1, or at least about 50: 1. In some embodiments, working fluid in each reactor is continuously recycled at a rate ratio of at most about 50: 1 at most about 45: 1, at most about 40: 1, at most about 38: 1, at most about 36: 1, at most about 34: 1, at most about 32: 1, at most about 30: 1, at most about 28: 1, at most about 26: 1, at most about 24: 1, at most about 22: 1, at most about 20: 1, at most about 18: 1, at most about 16: 1, at most about 14: 1, at most about 12: 1, or at most about 10: 1. Working fluid may be recycled by one or more pumps to prevent solids settling and to provide sufficient velocity and hydraulic shear to prevent excessive buildup and sloughing of biofilm. A digestion system provided herein may comprise a first flow rate, second flow rate, third flow rate, fourth flow rate, fifth flow rate, sixth flow rate, or seventh flow rate.

[0387]

[0387] Reactors can be maintained at specific temperatures which may aid in digestion and growth of microbial consortia within the system. In some embodiments, a temperature of a reactor is at least about 15°C, at least about 20°C, at least about 21 °C, at least about 22°C, at least about 23°C, at least about 24°C, at least about 25°C, at least about 26°C, at least about 27°C, at least about 28°C, at least about 29°C, at least about 30°C, at least about 35°C, at least about 40°C, at least about 45°C, or at least about 50°C. In some embodiments, a temperature of a reactor is at most about 50°C, at most about 45°C, at most about 40°C, at most about 35°C, at most about 30°C, at most about 29°C, at most about 28°C, at most about 27°C, at most about 26°C, at most about 25 °C, at most about 24°C, at most about 23 °C, at most about 22°C, at most about 21 °C, at most about 20°C, or at most about 15°C. In some embodiments, the temperature is at most about 45°C. In some embodiments, the temperature is maintained in a mesophilic range (e.g., less than 45°C). In some embodiments, the temperature may not be thermophilic (e.g., greater than 45°C). In some embodiments, thermophilic conditions are avoided in one or more containers of a bioreactor system described herein.

[0388]

[0388] In some embodiments, a temperature of a reactor is about 15°C to about 45°C. In some embodiments, a temperature of a reactor is about 15°C to about 20°C, about 15°C to about 22°C, about 15°C to about 24°C, about 15°C to about 26°C, about 15°C to about 28°C, about 15°C to about 30°C, about 15°C to about 32°C, about 15°C to about 34°C, about 15°C to about 36°C, about 15°C to about 40°C, about 15°C to about 45°C, about 20°C to about 22°C, about 20°C to about 24°C, about 20°C to about 26°C, about 20°C to about 28°C, about 20°C to about 30°C, about 20°C to about 32°C, about 20°C to about 34°C, about 20°C to about 36°C, about 20°C to about 40°C, about 20°C to about 45°C, about 22°C to about 24°C, about 22°C to about 26°C, about 22°C to about 28°C, about 22°C to about 30°C, about 22°C to about 32°C, about 22°C to about 34°C, about 22°C to about 36°C, about 22°C to about 40°C, about 22°C to about 45°C, about 24°C to about 26°C, about 24°C to about 28°C, about 24°C to about 30°C, about 24°C to about 32°C, about 24°C to about 34°C, about 24°C to about 36°C, about 24°C to about 40°C, about 24°C to about 45°C, about 26°C to about 28°C, about 26°C to about 30°C, about 26°C to about 32°C, about 26°C to about 34°C, about 26°C to about 36°C, about 26°C to about 40°C, about 26°C to about 45°C, about 28°C to about 30°C, about 28°C to about 32°C, about 28°C to about 34°C, about 28°C to about 36°C, about 28°C to about 40°C, about 28°C to about 45°C, about 30°C to about 32°C, about 30°C to about 34°C, about 30°C to about 36°C, about 30°C to about 40°C, about 30°C to about 45°C, about 32°C to about 34°C, about 32°C to about 36°C, about 32°C to about 40°C, about 32°C to about 45°C, about 34°C to about 36°C, about 34°C to about 40°C, about 34°C to about 45°C, about 36°C to about 40°C, about 36°C to about 45°C, or about 40°C to about 45°C.

[0389]

[0389] Reactors may be maintained under aerobic, microaerobic, or anaerobic conditions. The series of reactors in a digestion system may have different aerobic conditions. The series of reactors in a digestion system may have the same aerobic conditions. In some embodiments, a reactor may have the same aerobic condition as an adjacent reactor. In some embodiments, a reactor may have a different aerobic condition than an adjacent reactor. In some embodiments, a digestion system may have aerobic, microaerobic, anaerobic conditions, or any combination thereof.

[0390]

[0390] In some embodiments, aerobic conditions comprise conditions with a dissolved oxygen measurement of greater than 2 mg / L. In some embodiments, aerobic conditions comprise conditions with a dissolved oxygen measurement of at least about 2 mg / L , at least about 3 mg / L , at least about 4 mg / L, at least about 5 mg / L, at least about 6 mg / L, at least about 7 mg / L, at least about 8 mg / L, at least about 9 mg / L, at least about 10 mg / L, at least about 12 mg / L, at least about 14 mg / L, at least about 15 mg / L, or greater than about 15 mg / L. In some embodiments, aerobic conditions comprise conditions with a dissolved oxygen measurement from about 2 mg / L to about 15 mg / L. In some embodiments, aerobic conditions comprise conditions with a dissolved oxygen measurement from about 2 mg / L to about 3 mg / L, about 2 mg / L to about 4 mg / L, about 2 mg / L to about 5 mg / L, about 2 mg / L to about 6 mg / L, about 2 mg / L to about 7 mg / L, about 2 mg / L to about 8 mg / L, about 2 mg / L to about 9 mg / L, about 2 mg / L to about 10 mg / L, about 2 mg / L to about 12 mg / L, about 2 mg / L to about 14 mg / L, about 2 mg / L to about 15 mg / L, about 3 mg / L to about 4 mg / L, about 3 mg / L to about 5 mg / L, about 3 mg / L to about 6 mg / L, about 3 mg / L to about 7 mg / L, about 3 mg / L to about 8 mg / L, about 3 mg / L to about 9 mg / L, about 3 mg / L to about 10 mg / L, about 3 mg / L to about 12 mg / L, about 3 mg / L to about 14 mg / L, about 3 mg / L to about 15 mg / L, about 4 mg / L to about 5 mg / L, about 4 mg / L to about 6 mg / L, about 4 mg / L to about 7 mg / L, about 4 mg / L to about 8 mg / L, about 4 mg / L to about 9 mg / L, about 4 mg / L to about 10 mg / L, about 4 mg / L to about 12 mg / L, about 4 mg / L to about 14 mg / L, about 4 mg / L to about 15 mg / L, about 5 mg / L to about 6 mg / L, about 5 mg / L to about 7 mg / L, about 5 mg / L to about 8 mg / L, about 5 mg / L to about 9 mg / L, about 5 mg / L to about 10 mg / L, about 5 mg / L to about 12 mg / L, about 5 mg / L to about 14 mg / L, about 5 mg / L to about 15 mg / L, about 6 mg / L to about 7 mg / L, about 6 mg / L to about 8 mg / L, about 6 mg / L to about 9 mg / L, about 6 mg / L to about 10 mg / L, about 6 mg / L to about 12 mg / L, about 6 mg / L to about 14 mg / L, about 6 mg / L to about 15 mg / L, about 7 mg / L to about 8 mg / L, about 7 mg / L to about 9 mg / L, about 7 mg / L to about 10 mg / L, about 7 mg / L to about 12 mg / L, about 7 mg / L to about 14 mg / L, about 7 mg / L to about 15 mg / L, about 8 mg / L to about 9 mg / L, about 8 mg / L to about 10 mg / L, about 8 mg / L to about 12 mg / L, about 8 mg / L to about 14 mg / L, about 8 mg / L to about 15 mg / L, about 9 mg / L to about 10 mg / L, about 9 mg / L to about 12 mg / L, about 9 mg / L to about 14 mg / L, about 9 mg / L to about 15 mg / L, about 10 mg / L to about 12 mg / L, about 10 mg / L to about 14 mg / L, about 10 mg / L to about 15 mg / L, about 12 mg / L to about 14 mg / L, about 12 mg / L to about 15 mg / L, or about 14 mg / L to about 15 mg / L. In some embodiments, aerobic conditions comprise conditions with a dissolved oxygen measurement of between 2 mg / L and 10 mg / L. In some embodiments, microaerobic conditions comprise conditions with a dissolved oxygen measurement of less than 2 mg / L. In some embodiments, microaerobic conditions comprise conditions with a dissolved oxygen measurement of at most about 1.99 mg / L, at most about 1.8 mg / L, at most about 1.6 mg / L, at most about 1.5 mg / L, at most about 1.4 mg / L, at most about 1.3 mg / L, at most about 1.2 mg / L, at most about 1.1 mg / L, at most about 1 mg / L, at most about 0.9 mg / L, at most about 0.8 mg / L, at most about 0.7 mg / L, at most about 0.6 mg / L, at most about 0.5 mg / L, at most about 0.4 mg / L, at most about 0.3 mg / L, at most about 0.2 mg / L, at most about 0.1 mg / L, or less than about 0.1 mg / L but not 0 mg / L. In some embodiments, microaerobic conditions comprise conditions with a dissolved oxygen measurement from about 0.1 mg / L to about 1.99 mg / L. In some embodiments, microaerobic conditions comprise conditions with a dissolved oxygen measurement from about 0.1 mg / L to about 0.2 mg / L, about 0.1 mg / L to about 0.3 mg / L, about 0.1 mg / L to about 0.4 mg / L, about 0.1 mg / L to about 0.5 mg / L, about 0.1 mg / L to about 0.8 mg / L, about 0.1 mg / L to about 1 mg / L, about 0.1 mg / L to about 1.2 mg / L, about 0.1 mg / L to about 1.4 mg / L, about 0.1 mg / L to about 1.6 mg / L, about 0.1 mg / L to about 1.8 mg / L, about 0.1 mg / L to about 1.99 mg / L, about 0.2 mg / L to about 0.3 mg / L, about 0.2 mg / L to about 0.4 mg / L, about 0.2 mg / L to about 0.5 mg / L, about 0.2 mg / L to about 0.8 mg / L, about 0.2 mg / L to about 1 mg / L, about 0.2 mg / L to about 1.2 mg / L, about 0.2 mg / L to about 1.4 mg / L, about 0.2 mg / L to about 1.6 mg / L, about 0.2 mg / L to about 1.8 mg / L, about 0.2 mg / L to about 1.99 mg / L, about 0.3 mg / L to about 0.4 mg / L, about 0.3 mg / L to about 0.5 mg / L, about 0.3 mg / L to about 0.8 mg / L, about 0.3 mg / L to about 1 mg / L, about 0.3 mg / L to about 1.2 mg / L, about 0.3 mg / L to about 1.4 mg / L, about 0.3 mg / L to about 1.6 mg / L, about 0.3 mg / L to about 1.8 mg / L, about 0.3 mg / L to about 1.99 mg / L, about 0.4 mg / L to about 0.5 mg / L, about 0.4 mg / L to about 0.8 mg / L, about 0.4 mg / L to about 1 mg / L, about 0.4 mg / L to about 1.2 mg / L, about 0.4 mg / L to about 1.4 mg / L, about 0.4 mg / L to about 1.6 mg / L, about 0.4 mg / L to about 1.8 mg / L, about 0.4 mg / L to about 1.99 mg / L, about 0.5 mg / L to about 0.8 mg / L, about 0.5 mg / L to about 1 mg / L, about 0.5 mg / L to about 1.2 mg / L, about 0.5 mg / L to about 1.4 mg / L, about 0.5 mg / L to about 1.6 mg / L, about 0.5 mg / L to about 1.8 mg / L, about 0.5 mg / L to about 1.99 mg / L, about 0.8 mg / L to about 1 mg / L, about 0.8 mg / L to about 1.2 mg / L, about 0.8 mg / L to about 1.4 mg / L, about 0.8 mg / L to about 1.6 mg / L, about 0.8 mg / L to about 1.8 mg / L, about 0.8 mg / L to about 1.99 mg / L, about 1 mg / L to about 1.2 mg / L, about 1 mg / L to about 1.4 mg / L, about 1 mg / L to about 1.6 mg / L, about 1 mg / L to about 1.8 mg / L, about 1 mg / L to about 1.99 mg / L, about 1.2 mg / L to about 1.4 mg / L, about 1.2 mg / L to about 1.6 mg / L, about 1.2 mg / L to about 1.8 mg / L, about 1.2 mg / L to about 1.99 mg / L, about 1.4 mg / L to about 1.6 mg / L, about 1.4 mg / L to about 1.8 mg / L, about 1.4 mg / L to about 1.99 mg / L, about 1.6 mg / L to about 1.8 mg / L, about 1.6 mg / L to about 1.99 mg / L, or about 1.8 mg / L to about 1.99 mg / L. In some embodiments, anaerobic conditions comprise conditions with a dissolved oxygen measurement of 0 mg / L.

[0391]

[0391] Reactors of a digestion system described herein may comprise a working volume used to hold a volume of working fluid. A working volume of a reactor of a digestion system described herein may be at least about 5 gallons, at least about 10 gallons, at least about 20 gallons, at least about 50 gallons, at least about 75 gallons, at least about 100 gallons, at least about 250 gallons, at least about 500 gallons, at least about 750 gallons, at least about 1,000 gallons, at least about 2,000 gallons, at least about 3,000 gallons, at least about 4,000 gallons, at least about 5,000 gallons, at least about 7,500 gallons, at least about 10,000 gallons, at least about 15,000 gallons, at least about 20,000 gallons, at least about 50,000 gallons, or more than about 50,000 gallons. A working volume of a reactor of a digestion system described herein may be at most about 50,000 gallons, at most about 20,000 gallons, at most about 15,000 gallons, at most about 10,000 gallons, at most about 7,500 gallons, at most about 5,000 gallons, at most about 4,000 gallons, at most about 3,000 gallons, at most about 2,000 gallons, at most about 1,000 gallons, at most about 750 gallons, at most about 500 gallons, at most about 250 gallons, at most about 100 gallons, at most about 75 gallons, at most about 50 gallons, at most about 20 gallons, at most about 10 gallons, at most about 5 gallons, or less than about 5 gallons.

[0392] Reactors may be maintained at different pH levels within a digestion system. Reactors may be maintained at the same pH levels within a digestion system. The pH of a reactor in a digestion system may be at least about 4.0, at least about 4.5, at least about 5.0, at least about

[0392] 5.5, at least about 6.0, at least about 6.5, at least about 7.0, at least about 7.5, at least about 8.0, at least about 8.5, at least about 9.0, at least about 9.5, or at least about 10.0. In some embodiments, the pH of a reactor in a digestion system may be at most about 10.0, at most about

[0393] 9.5, at most about 9.0, at most about 8.5, at most about 8.0, at most about 7.5, at most about 7.0, at most about 6.5, at most about 6.0, at most about 5.5, at most about 5.0, at most about 4.5, or at most about 4.0.

[0394]

[0393] In some embodiments, the pH of a reactor in a digestion system may be about 3 to about 9. In some embodiments, the pH of a reactor in a digestion system may be about 3 to about 3.5, about 3 to about 4, about 3 to about 4.5, about 3 to about 5, about 3 to about 5.5, about 3 to about 6, about 3 to about 6.5, about 3 to about 7, about 3 to about 7.5, about 3 to about 8, about

[0395] 3 to about 9, about 3.5 to about 4, about 3.5 to about 4.5, about 3.5 to about 5, about 3.5 to about

[0396] 5.5, about 3.5 to about 6, about 3.5 to about 6.5, about 3.5 to about 7, about 3.5 to about 7.5, about 3.5 to about 8, about 3.5 to about 9, about 4 to about 4.5, about 4 to about 5, about 4 to about 5.5, about 4 to about 6, about 4 to about 6.5, about 4 to about 7, about 4 to about 7.5, about 4 to about 8, about 4 to about 9, about 4.5 to about 5, about 4.5 to about 5.5, about 4.5 to about 6, about 4.5 to about 6.5, about 4.5 to about 7, about 4.5 to about 7.5, about 4.5 to about 8, about 4.5 to about 9, about 5 to about 5.5, about 5 to about 6, about 5 to about 6.5, about 5 to about 7, about 5 to about 7.5, about 5 to about 8, about 5 to about 9, about 5.5 to about 6, about 5.5 to about 6.5, about 5.5 to about 7, about 5.5 to about 7.5, about 5.5 to about 8, about 5.5 to about 9, about 6 to about 6.5, about 6 to about 7, about 6 to about 7.5, about 6 to about 8, about 6 to about 9, about 6.5 to about 7, about 6.5 to about 7.5, about 6.5 to about 8, about 6.5 to about 9, about 7 to about 7.5, about 7 to about 8, about 7 to about 9, about 7.5 to about 8, about 7.5 to about 9, or about 8 to about 9.

[0397]

[0394] In some embodiments, the reactors may comprise distribution components (e.g., a distribution ring) that is subsurface of the discharge volume. The distribution component can reduce the amount of surface disruption, and / or keep the environment in the reactor anaerobic. The environment of the reactor may be anaerobic, microaerobic, or aerobic. Without wishing to be bound by theory, the microaerobic conditions of the reactors of the digestion system may enrich nitrogen-fixing microbes and / or microbes with nitrogen use efficiency capability in the microbial consortium of the system. C. Working Fluids and Microbial Consortia

[0398]

[0395] A working fluid may comprise a fluidic substance that moves through a digestion system as described herein. A working fluid can comprise solid components, liquid components, gaseous components, or any combination thereof. A working fluid can comprise microbial consortia, one or more isolated microbes or inoculum of a microbial strain (e.g., target isolates), additional organic and / or materials, or any combination thereof. The mixture of microbial consortia, isolated microbes (e.g., target isolates), additional organic and / or materials within a working fluid may allow for the expansion of microbes or act as a culture for an inoculum of a microbe to grow. A working fluid may comprise a pH, viscosity, temperature, surface tension, adhesion, volume, or any combination thereof that enhances the growth and / or functioning of microbes or microorganisms. In some embodiments, a volume of working fluid within each reactor is continuously being replenished and drawn from. In some embodiments, a volume of working fluid within each reactor can be replenished and drawn from in batches (e.g., discontinuously). In some embodiments, a working fluid in a first reactor may comprise a first working fluid. In some embodiments, a working fluid in a second reactor may comprise a second working fluid. In some embodiments, a working fluid in a third reactor may comprise a third working fluid. In some embodiments, a working fluid in a fourth reactor may comprise a fourth working fluid. In some embodiments, a working fluid in a fifth reactor may comprise a fifth working fluid. In some embodiments, at least a portion of the second working fluid may be transferred to the third reactor. In some embodiments, at least a portion of the third working fluid may be transferred to the fourth reactor. In some embodiments, at least a portion of the fourth working fluid may be transferred to the fifth reactor. In some embodiments, a working fluid may be mixed in a reactor (e.g., chamber or container) prior to a first reactor. In some embodiments, the working fluid in each reactor may be distinct from the working fluid in other reactors in the digestion system. Distinct working fluids may comprise different microbial populations. The different microbial populations may include different microbes, (e.g., bacteria, fungi, algae, or any combination thereof). Distinct working fluids may comprise different concentrations of a target isolate. Distinct working fluids may comprise different concentrations of a carbon source and / or a nitrogen source. Distinct working fluids may comprise different microbial populations, different concentrations of a target isolate, different concentrations of a carbon source, different combinations of a nitrogen source, or any combination thereof. The working fluid in a reactor of a digestion system may be similar to a working fluid of a different reactor of the digestion system. The working fluid in each reactor may comprise different microbial populations. The different microbial populations may include different bacteria, fungi, algae, or any combination thereof.

[0399]

[0396] The working fluid within a container of the bioreactor system may comprise one or more enzymes. The working fluid within one or more reactors (e.g., within each reactor) may comprise the same enzymes, which may be produced by microbes within the working fluid. The working fluid within one or more reactors (e.g., within each reactor) may comprise different enzymes, which may be produced by microbes within the working fluid. An enzyme within a working fluid may comprise a dehydrogenase, a hydrogenase, an oxidase, a catalase, a peroxidase, a phenol o-hydroxylase, a dextransucrase, an aminotransferase, a rhodanese, a carboxylesterase, a lipase, a phosphatase, a nuclease, a phytase, an aryl sulphatase, an amylase, a cellulase, an inulase, a xylanase, a dextranase, a levanase, a poly-galacturonase, a glucosidase, a galactosidase, an invertase, a peptidase, an asparaginase, a glutaminase, an amidase, a urease, an aspartate decarboxylase, a glutamate decarboxylase an aromatic amino acid decarboxylase, or any combination thereof. An enzyme within a working fluid may comprise nitrogenase, 1- aminocyclopropane-1 -carboxylate deaminase (e.g., ACC-deaminase), quinoprotein glucose dehydrogenase (e.g., PQQ or quinone), gluconate 2-dehydrogenase, cellulase, endo-l,3(4)-P- glucanase, pectin lyase, or any combination thereof. The working fluid within each reactor may comprise different concentrations of enzymes. The working fluid within each reactor may comprise a different average abundance of an enzyme. An enzyme may be present at an average abundance of less than 0.001%. An enzyme may be present at an average abundance of greater than 1%. In some embodiments, an enzyme may be present at an average abundance of at least about 0.0001%, 0.001%, 0.01%, 0.02%, 0.03%, 0.04%, 0.05%, 0.06%, 0.07%, 0.08%, 0.09%, 0.1%, 0.2%, 0.3%, 0.4%, 0.5%, 0.6%, 0.7%, 0.8%, 0.9%, 1%, 2%, 3%, 4%, 5%, or greater than about 5%. In some embodiments, an enzyme may be present at an average abundance of at most about 5% 4%, 3%, 2%, 1%, 0.9%, 0.8%, 0.7%, 0.6%, 0.5%, 0.4%, 0.3%, 0.2%, 0.1%, 0.09%, 0.08%, 0.07%, 0.06%, 0.05%, 0.04%, 0.03%, 0.02%, 0.01%, 0.001%, 0.0001%, or less than about 0.0001%. The working fluid within each reactor may comprise enzymes with different enzymatic activity. Enzymatic activity may include, but is not limited to, nitrogen fixation, ammonia production, phosphate solubilization, nitrogen use efficiency, cell wall lysing, or any combination thereof.

[0400]

[0397] A working fluid may comprise different digestion products from working fluid within other reactors of the system. In some embodiments, a working fluid may comprise digestion products from an aqueous organic feedstock and microbial consortium at least partially derived from a previous working fluid.

[0398] The pH of a working fluid within each reactor may be different from working fluid in other reactors. The pH of a working fluid within each reactor may be the same. The pH of a working fluid may be less than 6. The pH of a working fluid may be greater than 6. The pH of a working fluid may be in a range from 2 to 11. The pH of a working fluid may be at least about 2, 2.5, 3, 3.5, 4, 4.5, 5, 5.5, 6, 6.5, 7, 7.5, 8, 8.5, 9, 9.5, 10, 10.5, 11, or greater than 11. The pH of a working fluid may be at most about 11,10.5, 10, 9.5, 9, 8.5, 8, 7.5, 7, 6.5, 6, 5.5, 5, 4.5, 4, 3.5, 3, 2.5, 2, or less than 2.

[0401]

[0399] The microbial consortia of the present invention may be stable. In a stable microbial consortium, the identity and relative abundance of bacteria may not appreciably change over time, such as over the space of at least about 1 day, 2 days, 3 days, 4 days, 5 days, 6 days, 7 days, 1 week, 2 weeks, 3 weeks, 4 weeks, 5 weeks, or greater than about 5 weeks. In a stable microbial consortium, the identity and relative abundance of bacteria may not appreciably change over time, such as over the space of at most about 5 weeks 4 weeks, 3 weeks, 2 weeks, 1 week, 7 days, 6 days, 5 days, 4 days, 3 days, 2 days, 1 day, or less than 1 day.

[0402]

[0400] In some embodiments, the microbial consortia may be characterized by population analysis. The population analysis may comprise a community analysis, determination of the core community, and computation of a microbial-community distance matrix. In some embodiments, the microbial consortia may be characterized in batches. Characterization of the microbial consortia may be measured in at least about 1, 2, 3, 4, 5, 6, 7, 8 or more batches.

[0403] Characterization of the microbial consortia may be measured in at most about 7, 6, 5, 4, 3, 2, 1, or less batches. From the population analysis, the most abundant species of the microbial consortia may be determined. The most abundant species of the microbial consortia may be referred to as a “top microbial species”. In some embodiments, the most abundant species of a microbial consortia comprise at least the top 2 species, 3 species, 4 species, 5 species, 10 species, 15 species, or 20 species. In some embodiments, different reactors may have microbial consortia with different species being the most abundant.

[0404]

[0401] In some embodiments, a first microbial consortium may be established in a mixing chamber, in which various inputs may be mixed into a homogenous aqueous mixture to be input into a digestion reactor. In some embodiments, a digestion system described herein may comprise one or more mixing chambers in which a microbial consortium may be established. The first microbial consortium may be derived from microbes originally present in one or more digestion substrates and / or from other inputs into the mixing chamber. A first microbial consortium may be derived from inputs to a reactor in a digestion system described herein. In some embodiments, a second microbial consortium is established in a first reactor. The second microbial consortium may be derived from microbes within the mixing chamber. In some embodiments, a third microbial consortium is established in a second reactor. The third microbial consortium may be derived from the first working fluid present in the first reactor and transferred to the second reactor. In some embodiments, a fourth microbial consortium is established in a third reactor. The fourth microbial consortium may be derived from the second working fluid present in the second reactor and transferred to the third reactor. In some embodiments, a fifth microbial consortium is established in a fourth reactor. The fifth microbial consortium may be derived from the fourth working fluid present in the fourth reactor and transferred to the fifth reactor. A microbial consortium can be present in any reactor of a digestion system described herein. A microbial consortium can be derived from the working fluid of a reactor of a digestion system described herein. A first microbial consortium may be derived from inputs to a first reactor and may be present in a base product of a digestion system. A first microbial consortium may be present in a first reactor, a second reactor, a third reactor, or a clarifier. Without wishing to be bound by theory, a first microbial consortium in a working fluid may shift its microbial population and form a second microbial consortium. A second microbial consortium may be present in a first reactor, a second reactor, a third reactor, or a clarifier. Without wishing to be bound by theory, a second microbial consortium in a working fluid may shift its microbial population and form a third microbial consortium. A third microbial consortium may be present in a first reactor, a second reactor, a third reactor, or a clarifier. Without wishing to be bound by theory, a third microbial consortium in a working fluid may shift its microbial population and form a fourth microbial consortium. A fourth microbial consortium may be present in a first reactor, a second reactor, a third reactor, or a clarifier. Without wishing to be bound by theory, a fourth microbial consortium in a working fluid may shift its microbial population and form a fifth microbial consortium. A fifth microbial consortium may be present in a first reactor, a second reactor, a third reactor, or a clarifier. Microbial consortia of the digestion system described herein may develop shifts in microbial communities based on conditions (e.g., nutrients, retention time, flow rate, pH, oxygen content, digestion products) of the reactors of the system and the working fluid.

[0405]

[0402] A portion of a first working fluid may be transferred to a second container of a serialized assembly of containers of a digestion system described herein. The working fluid of the second container may comprise a second working fluid. A portion of a second working fluid may be transferred to a third container of a serialized assembly of containers of a digestion system described herein. The working fluid of the third container may comprise a third working fluid. A portion of a third working fluid may be transferred to a fourth container of a serialized assembly of containers of a digestion system described herein. The working fluid of the fourth container may comprise a fourth working fluid. A portion of a fourth working fluid may be transferred to a fifth container of a serialized assembly of containers of a digestion system described herein. The working fluid of the fifth container may comprise a fifth working fluid. A portion of a fifth working fluid may be transferred to a sixth container of a serialized assembly of containers of a digestion system described herein. The working fluid of the sixth container may comprise a sixth working fluid.

[0406]

[0403] The working fluid of a container in the digestion system may incubate in the container. A flow rate of the digestion system may increase or decrease a volume of working fluid. The working fluid of a first, second, third, fourth, fifth, or sixth container may increase in volume over a time period. The working fluid of a first, second, third, fourth, fifth, or sixth container may decrease in volume over a time period. The working fluid of a first, second, third, fourth, fifth, or sixth container may not increase or decrease in volume over a time period. The volume of working fluid in each of the containers of a digestion system may be the same. The volume of working fluid in each of the containers of a digestion system may be different. The volumes of the first working fluid, second working fluid, third working fluid, fourth working fluid, fifth working fluid, and / or sixth working fluid may be constant (e.g., unchanging over a time period). A constant volume may comprise a volume that may not increase or decrease over 1 minute, 5 minutes, 10 minutes, 30 minutes, 1 hours, 5 hours, 12 hours, 1 day, 2 days, 3 days, 4 days, 5 days, or 1 week.

[0407]

[0404] As working fluid flows from each container of digestion system, the working fluid may comprise a flow rate. A first flow rate may comprise a flow rate of an aqueous feedstock inputted into a first container from a source outside the digestion system. A second flow rate may comprise a flow rate of a working fluid from a first container into a second container. A third flow rate may comprise a flow rate of a working fluid from a second container into a third container. A fourth flow rate may comprise a flow rate of a working fluid from a third container into a fourth container. A fifth flow rate may comprise a flow rate of a working fluid from a fourth container into a fifth container. A flow rate (e.g., first flow rate, second flow rate, third flow rate, fourth flow rate, fifth flow rate) may be at least about 0.5 gallons / min, 1 gallon / min, 5 gallons / min, 10 gallons / min, 15 gallons / min, 20 gallons / min, 25 gallons / min, 30 gallons / min, 40 gallons / min, 50 gallons / min, 100 gallons / min, 200 gallons / min, 300 gallons / min, 400 gallons / min, 500 gallons / min, 1,000 gallons / min, or 10,000 gallons / min. A flow rate (e.g., first flow rate, second flow rate, third flow rate, fourth flow rate, fifth flow rate) may be at most about 10,000 gallons / min 1,000 gallons / min, 500 gallons / min, 400 gallons / min, 300 gallons / min, 200 gallons / min, 100 gallons / min, 50 gallons / min, 40 gallons / min, 30 gallons / min, 25 gallons / min, 20 gallons / min, 15 gallons / min, 10 gallons / min, 5 gallons / min, 1 gallon / min, 0.5 gallons / min, or less than about 0.5 gallons / min.

[0408]

[0405] A microbial consortium can comprise one or more populations of microbes. The population of microbes can be generated from an input to the digestion system. An aqueous organic feedstock inputted into the digestion system may comprise a microbial consortium. Incubation in the digestion system may promote the growth of microbes within a microbial consortium (e.g., a first microbial consortium, a second microbial consortium, a third microbial consortium, a fourth microbial consortium, a fifth microbial consortium, a sixth microbial consortium). The microbes of a microbial consortium or at least a portion of microbes within the microbial consortium may have a desired plant growth promotion property. The plant growth promotion property may comprise shoot biomass, root biomass, nutrient uptake, photosynthetic activity, crop yield, deaminase activity, acid production, leaf area, chlorophyll content, or total biomass.

[0409]

[0406] Reactors of a digestion system may be fluidly connected. A portion of a working fluid in a first container may be transferred to a fluidly connected second container. A portion of a working fluid in a second container may be transferred to a fluidly connected third container. A portion of a working fluid in a third container may be transferred to a fluidly connected fourth container. A portion of a working fluid in a fourth container may be transferred to a fluidly connected fifth container. A portion of a working fluid in a fifth container may be transferred to a fluidly connected sixth container. In some embodiments, a transfer of working fluid between containers of a digestion system described herein may be continuous. A continuous flow of working fluid may comprise a flow of working fluid that does not stop or a flow of working fluid that stops for less than about 5 seconds, less than about 4 seconds, less than about 3 seconds, less than about 2 seconds, less than about 1 second, less than about 0.5 seconds, or less than about 0.1 seconds. A continuous flow of working fluid within a digestion system described herein (e.g., between containers of a digestion system) may have a first flow rate. A continuous flow of working fluid within a digestion system described herein (e.g., between containers of a digestion system) may have a second flow rate. In some embodiments, the first flow rate and the second flow rate are equal. A first flow rate may comprise a flow rate of fluid transferred from a source outside the digestion system into a first container. A second flow rate may comprise a rate of fluid flow from a first container to a second container. In some embodiments, an amount of working fluid and / or aqueous organic feedstock transferred into the first container over a time period is equal to an amount of working fluid and / or aqueous organic feedstock transferred into a second fluidly connected container over the same time period. In some embodiments, the first flow rate and the second flow rate are different.

[0410]

[0407] In some embodiments, a first container of a digestion system comprises a constant volume. In some embodiments, a volume of a first container of a digestion system is different over time. In some embodiments, the flow rate between containers of the digestion system may maintain a constant volume in each container. A first container, a second container, a third container, a fourth container, a fifth container, and / or a sixth container may be maintained at a constant volume. A constant volume may be maintained by a continuous flow of fluid through a digestion system described herein.

[0411]

[0408] In some embodiments, a digestion system may be inoculated with an inoculum of a microbe (e.g., an inoculum of a microbial strain). The inoculum of a microbial strain may be an isolated microbe. An isolated microbe can comprise a microbe grown or enriched outside of a natural environment (e.g., in a culture medium or a streak plate method). In some embodiments, the inoculum of a microbe may comprise a mixture of multiple isolated microbes. The inoculum of a microbe may comprise a mixture of at least about 2, at least about 3, at least about 4, at least about 5, at least about 6, at least about 7, at least about 8, or more isolated microbes. The inoculum of a microbe may comprise a mixture of at most about 8, at most about 7, at most about 6, at most about 5, at most about 4, at most about 3, at most about 2, or less isolated microbes.

[0412]

[0409] In some cases, a digestion system may not be reinoculated with an isolate (e.g., microbial strain) or combination of isolates following a first inoculation. Reinoculation of a digestion system may comprise providing a microbial strain following a previous inoculation.

[0413] Reinoculation of a digestion system may comprise introducing a target isolate (e.g., microbial strain) in a container of the digestion system at a time point during operating of the digestion system. In some cases, a digestion system may be reinoculated with an isolate or combination of isolates at least every 20 days, at least every 50 days, at least every 100 days, at least every 200 days, at least every 300 days, at least every 400 days, at least every 500 days, or more. In some cases, a digestion system may be inoculated with an isolate or combination of isolates on day 1 of a digestion process and reinoculated at least 1, 2, 3, 4, 5, or more times after day 1 of the digestion process. In some cases, a digestion system may be inoculated with an isolate or combination of isolates on day 1 of a digestion process and reinoculated at most 1, 2, 3, 4, 5, or more times after day 1 of the digestion process. In some cases, a digestion system may be reinoculated with a microbial strain described herein after operating the digestion system for a time period. For example, a digestion system may be reinoculated with a microbial strain described herein after operating the digestion system for a duration of time of at least about 1 day, 2 days, 3 days, 4 days, 5 days, 6 days, 7 days, 8 days, 9 days, 10 days, 11 days, 12 days, 13 days, 14 days, 3 weeks, 4 weeks, 5 weeks, 6 weeks, 7 weeks, 8 weeks, 3 months, 4 months, 5 months, 6 months, 9 months, 12 months, 18 months, 24 months, 3 years, 4 years, 5 years, or 10 years. For example, a digestion system may be reinoculated with a microbial strain described herein after operating the digestion system for a duration of time of at most about 10 years, 5 years, 4 years, 3 years, 24 months, 18 months, 12 months, 9 months, 6 months, 5 months, 4 months, 3 months, 8 weeks, 7 weeks, 6 weeks, 5 weeks, 4 weeks, 3 weeks, 14 days, 13 days, 12 days, 11 days, 10 days, 9 days, 8 days, 7 days, 6 days, 5 days, 4 days, 3 days, 2 days, or 1 day.

[0410] In some embodiments, the population of the microbial strain (e.g., concentration of the microbial strain) is maintained (e.g., retained) by at least about 0.00001%, at least about 0.0001%, at least about 0.001%, at least about 0.01%, at least about 0.1%, at least about 0.5%, at least about 1%, at least about 5%, at least 10%, at least about 15%, at least about 20%, at least about 25%, at least about 30%, at least about 35%, at least about 40%, at least about 45%, at least about 50%, at least about 55%, at least about 60%, or at least about 75% from the concentration of the microbial strain added into a container (e.g., a first container) of the digestion system. In some embodiments, the population of the microbial strain (e.g., concentration of the microbial strain) is maintained (e.g., retained) by at most about 75% at most about 60%, at most about 55%, at most about 50%, at most about 45%, at most about 40%, at most about 35%, at most about 30%, at most about 25%, at most about 20%, at most about 15%, at most 10%, at most about 5%, at most about 1%, at most about 0.5%, at most about 0.1%, at most about 0.01%, at most about 0.001%, at most about 0.0001%, at most about 0.00001% from the concentration of the microbial strain added into a container (e.g., a first container) of the digestion system. Biosolids (e.g., floc) may comprise small particles from a working fluid of a digestion system. The biosolids (e.g., floc) may accumulate in a clarifier chamber over time and separate from a supernatant (e.g., base product). In some embodiments, the population of the microbial strain may be retained in the floc (e.g., biosolids) of the digestion system. In some embodiments, a majority (e.g., at least about 95%, 96%, 97%, 98%, 99%, 99.5%, 99.6%, 99.7%, 99.8%, or 99.9%) of the inoculum of the microbe may be retained in the floc (e.g., biosolids) of the digestion system. Floc may be generated at any point during operating of a bioreactor system as described herein. For example, floc may be generated in a reactor of the bioreactor system (e.g., a first container, a second container, a third container, a fourth container, a fifth container, a sixth container, or any container of the system). For example, floc may be generated in a clarifier chamber of a bioreactor system. In some embodiments, floc may comprise at least a portion of nitrogen use efficiency -promoting microbes generated in a digestion system described herein.

[0414]

[0411] In some embodiments, there may be at least about 1 log CFU / ml, at least about 2 logs

[0415] CFU / ml, at least about 3 logs CFU / ml, at least about 4 logs CFU / ml, at least about 5 logs CFU / ml, or greater than about 5 logs CFU / ml increase in a concentration of the population of the microbial strain after inoculation in a container (e.g., first container) of the digestion system described herein. In some embodiments, there may be at most about 5 logs CFU / ml, at most about 4 logs CFU / ml, at most about 3 logs CFU / ml, at most about 2 logs CFU / ml, at most about 1 log CFU / ml, or less than about 1 log CFU / ml increase in a concentration of the population of the microbial strain after inoculation in a container (e.g., first container) of the digestion system described herein. In some embodiments, there may be from about 1 log CFU / ml to about 8 logs CFU / ml increase in a concentration of the population of the microbial strain after inoculation in a container (e.g., first container) of the digestion system described herein. In some embodiments, there may be from about 1 log CFU / ml to about 2 logs CFU / ml, about 1 log CFU / ml to about 3 logs CFU / ml, about 1 log CFU / ml to about 4 logs CFU / ml, about 1 log CFU / ml to about 5 logs CFU / ml, about 1 log CFU / ml to about 6 logs CFU / ml, about 1 log CFU / ml to about 7 logs CFU / ml, about 1 log CFU / ml to about 8 logs CFU / ml, about 2 logs CFU / ml to about 3 logs CFU / ml, about 2 logs CFU / ml to about 4 logs CFU / ml, about 2 logs CFU / ml to about 5 logs

[0416] CFU / ml, about 2 logs CFU / ml to about 6 logs CFU / ml, about 2 logs CFU / ml to about 7 logs

[0417] CFU / ml, about 2 logs CFU / ml to about 8 logs CFU / ml, about 3 logs CFU / ml to about 4 logs

[0418] CFU / ml, about 3 logs CFU / ml to about 5 logs CFU / ml, about 3 logs CFU / ml to about 6 logs

[0419] CFU / ml, about 3 logs CFU / ml to about 7 logs CFU / ml, about 3 logs CFU / ml to about 8 logs

[0420] CFU / ml, about 4 logs CFU / ml to about 5 logs CFU / ml, about 4 logs CFU / ml to about 6 logs

[0421] CFU / ml, about 4 logs CFU / ml to about 7 logs CFU / ml, about 4 logs CFU / ml to about 8 logs

[0422] CFU / ml, about 5 logs CFU / ml to about 6 logs CFU / ml, about 5 logs CFU / ml to about 7 logs

[0423] CFU / ml, about 5 logs CFU / ml to about 8 logs CFU / ml, about 6 logs CFU / ml to about 7 logs

[0424] CFU / ml, about 6 logs CFU / ml to about 8 logs CFU / ml, or about 7 logs CFU / ml to about 8 logs CFU / ml increase in a concentration of the population of the microbial strain after inoculation in a container (e.g., first container) of the digestion system described herein.

[0425]

[0412] In some embodiments, there may be at least about 1 log CFU / ml, at least about 2 logs CFU / ml, at least about 3 logs CFU / ml, at least about 4 logs CFU / ml, at least about 5 logs CFU / ml, or greater than about 5 logs CFU / ml decrease in a concentration of the population of the microbial strain after inoculation in a container (e.g., first container) of the digestion system described herein. In some embodiments, there may be at most about 5 logs CFU / ml, at most about 4 logs CFU / ml, at most about 3 logs CFU / ml, at most about 2 logs CFU / ml, at most about 1 log CFU / ml, or less than about 1 log CFU / ml decrease in a concentration of the population of the microbial strain after inoculation in a container (e.g., first container) of the digestion system described herein. In some embodiments, there may be from about 1 log CFU / ml to about 8 logs CFU / ml decrease in a concentration of the population of the microbial strain after inoculation in a container (e.g., first container) of the digestion system described herein. In some embodiments, there may be from about 1 log CFU / ml to about 2 logs CFU / ml, about 1 log CFU / ml to about 3 logs CFU / ml, about 1 log CFU / ml to about 4 logs CFU / ml, about 1 log CFU / ml to about 5 logs CFU / ml, about 1 log CFU / ml to about 6 logs CFU / ml, about 1 log CFU / ml to about 7 logs CFU / ml, about 1 log CFU / ml to about 8 l...

Claims

CLAIMSWHAT IS CLAIMED IS:

1. A method of making a biostimulant composition, the method comprising:(a) providing a bioreactor system comprising two or more containers arranged in a series, each of the two or more containers comprising a volume of a working fluid, wherein a first container comprises an established population of a first nitrogen use efficiencypromoting microbial strain;(b) operating the bioreactor system for a duration of time by:(i) transferring into the first container an aqueous feedstock comprising a microbial consortium;(ii) transferring a portion of the working fluid out of each of the two or more containers into either a subsequent container of the bioreactor system or a product outflow stream;(iii) maintaining a concentration of the first nitrogen use efficiency-promoting microbial strain throughout the duration of time in at least the first container at at least 80% of a concentration of the first nitrogen use efficiency-promoting microbial strain at the beginning of the duration of time; and(iv) collecting at least a portion of the product outflow stream as the biostimulant composition; wherein the duration of time is at least 5 days; and wherein the first nitrogen use efficiency-promoting microbial strain is not present in the aqueous feedstock or any other input into the bioreactor system during the duration of time at a concentration that is higher than 1% of the concentration of the first nitrogen use efficiency-promoting microbial strain in the first container.

2. The method of claim 1, wherein the first nitrogen use efficiency -promoting microbial strain is one that performs nitrogen fixation, promotes nitrogen fixation in the tissues of plants, recruits nitrogen fixers to the root zones or other tissues of plants, or increases organic nitrogen content and / or mineralization of organic nitrogen in soil.

3. The method of claim 1, wherein the first nitrogen use efficiency -promoting microbial strain is positive for a nifH gene.

4. The method of claim 1, wherein the first nitrogen use efficiency -promoting microbial strain is one that promotes plant growth in a nitrogen-poor growth medium.

5. The method of claim 4, wherein the nitrogen-poor growth medium comprises nitrate at less than 10 ppm.

6. The method of claim 1, wherein the first nitrogen use efficiency -promoting microbial strain is of the genus Kosakonia, Klebsiella, Rahnella, Kluyvera, Enter obacter, Achromobacter, Microbacterium, Gluconobacter, Methylobacterium, Pseudomonas, Pantoea, Azospirillum, Azocar us, Herbaspirillum, Burkholderia, Cyanobacteria, Bacillus, and Paenibacillus .

7. The method of claim 1, wherein the first nitrogen use efficiency -promoting microbial strain is of the species Kosakonia sacchari, Klebsiella variicola, Rahnella aquatilis, Kluyvera intermedia, Kosakonia pseusosacchari, Enterobacter spp., Achromobacter marplatensis, Azopirillum lipoferum, Microbacterium murale, Gluconobacter diazotrophicus, Methylobacterium symbioticum, Paenibacillus borealis, Bacillus megaterium (Priestia megaterium), or Paenibacillus sonchi.

8. The method of claim 1, wherein the first nitrogen use efficiency-promoting microbial strain is the strain deposited under ATCC Accession No. PTA-127654 (MS3907), the strain deposited under ATCC Accession No. PTA-127653 (MS3900), the strain deposited under ATCC Accession No. PTA-127655 (MS4921), or the strain deposited under ATCC Accession No. PTA-127652 (MS2748).

9. The method of any one of claims 1 to 8, wherein the first nitrogen use efficiency -promoting microbial strain is not present in the aqueous feedstock or any other input into the bioreactor system during the duration of time at a concentration of greater than 100 CFU / ml.

10. The method of any one of claims 1 to 9, wherein the first nitrogen use efficiency -promoting microbial strain is not present in the aqueous feedstock or any other input into the bioreactor system during the duration of time.

11. The method of any one of claims 1 to 10, wherein the maintaining of step (b)(iii) comprises maintaining the concentration of the first nitrogen use efficiency-promoting microbial strain at at least IxlO3CFU / ml.

12. The method of any one of claims 1 to 11, wherein the first container further comprises an established population of a second nitrogen use efficiency -promoting microbial strain and wherein the operating of step (b) further comprises (v) maintaining a concentration of thesecond nitrogen use efficiency-promoting microbial strain at at least 80% of a concentration of the second nitrogen use efficiency -promoting microbial strain at the beginning of the duration of time; wherein the second nitrogen use efficiency -promoting microbial strain is not present in the aqueous feedstock or any other input into the bioreactor system during the duration of time at a concentration that is higher than 1% of the concentration of the second nitrogen use efficiency-promoting microbial strain in the first container.

13. The method of claim 12, wherein the first container further comprises an established population of a third nitrogen use efficiency-promoting microbial strain and wherein the operating of step (b) further comprises (v) maintaining a concentration of the third nitrogen use efficiency-promoting microbial strain at at least 80% of a concentration of the third nitrogen use efficiency-promoting microbial strain at the beginning of the duration of time; wherein the third nitrogen use efficiency -promoting microbial strain is not present in the aqueous feedstock or any other input into the bioreactor system during the duration of time at a concentration that is higher than 1% of the concentration of the third nitrogen use efficiency-promoting microbial strain in the first container.

14. The method of any one of claims 1 to 13, wherein, before step (b), the first container further comprises an established population of other nitrogen use efficiency-promoting microbes that are not the first nitrogen use efficiency-promoting microbial strain, the second nitrogen use efficiency-promoting microbial strain, or the third nitrogen use efficiency-promoting microbial strain, and wherein step (b)(iii) further comprises maintaining a concentration of the other nitrogen use efficiency-promoting microbes in at least the first container throughout the duration of time at at least IxlO4CFU / ml or at at least 80% of a concentration of the other nitrogen use efficiency-promoting microbes at the beginning of the duration of time, wherein the other nitrogen use efficiency-promoting microbes are not added to the bioreactor system during the duration of time at a concentration that is higher than 1% of the concentration of the other nitrogen use efficiency-promoting microbes in the first container.

15. The method of claim 14, wherein the other nitrogen use efficiency-promoting microbes are not present in the aqueous feedstock or any other input into the bioreactor system at a concentration of greater than 105CFU / ml.

16. The method of claim 14 or 15, wherein the population of the other nitrogen use efficiencypromoting microbes in the first container is at least IxlO4CFU / ml at the beginning of the duration of time.

17. The method of any one of claims 14 to 16, wherein the other nitrogen use efficiencypromoting microbes comprise microbes that perform nitrogen fixation, promote nitrogen fixation in the tissues of plants, recruit nitrogen fixers to the root zones or other tissues of plants, or increases organic nitrogen content and / or mineralization of organic nitrogen in soil.

18. The method of any one of claims 14 to 16, wherein the other nitrogen use efficiencypromoting microbes are positive for a nifH gene.

19. The method of any one of claims 1 to 18, further comprising, before step (a), adding an inoculum of the first nitrogen use efficiency-promoting microbial strain to the bioreactor system, wherein the inoculum of the first nitrogen use efficiency -promoting microbial strain produces an initial population of the first nitrogen use efficiency -promoting microbial strain of at least 0.5xl04CFU / ml in at least one container.

20. The method of claim 19, wherein, before adding the inoculum of the first nitrogen use efficiency -promoting microbial strain, the concentration of the first nitrogen use efficiencypromoting microbial strain is less than IxlO2CFU / ml.

21. The method of any one of claims 1 to 20, wherein the aqueous feedstock further comprises an organic material at least partially digestible by microbes present in at least one of the containers.

22. The method of claim 21, wherein, before the transferring of step (b)(i), the organic material had been partially digested by microbes endogenous to the organic material.

23. The method of claim 21, further comprising digesting the organic material in two or more serially connected containers before the transferring of step (b)(i).

24. The method of any one of claims 21 to 23, wherein the organic material comprises manure and / or material produced by microbial digestion of manure.

25. The method of any one of claims 1 to 24, wherein the aqueous feedstock further comprises an inorganic material.

26. The method of claim 25, wherein the inorganic material comprises rock phosphate particles.

27. The method of claim 26, wherein, prior to the transferring of step (b)(i), the rock phosphate particles had been partially digested by microbes present in the aqueous feedstock.

28. The method of claim 26, further comprising partially digesting the rock phosphate particles in two or more serially connected containers before the transferring of step (b)(i).

29. The method of any one of claims 1 to 28, wherein the microbial consortium comprises at least IxlO5CFU / ml.

30. The method of claim 26, wherein the microbial consortium comprises microbes derived from manure and from rock phosphate particles.

31. The method of any one of claims 1 to 30, wherein the operating of step (b) further comprises producing microbial metabolites that directly or indirectly promote nitrogen use efficiency in plants.

32. The method of any one of claims 1 to 31, wherein the transferring of step (b)(i), the transferring of step (b)(ii), and the collecting of step (b)(iv) are performed continuously throughout the duration of time.

33. The method of any one of claims 1 to 31, wherein the transferring of step (b)(i), the transferring of step (b)(ii), and the collecting of step (b)(iv) are performed periodically throughout the duration of time.

34. The method of any one of claims 1 to 33, further comprising adding one or more carbon sources to at least one container of the bioreactor system.

35. The method of claim 34, wherein the one or more carbon sources are included in the aqueous feedstock.

36. The method of claim 34 or 35, further comprising maintaining a malate concentration and / or glucose concentration in at least one container of the bioreactor system at a concentration of at least 0.2% w / v in relation to the volume of working fluid in the at least one container.

37. The method of any one of claims 1 to 36, further comprising adding one or more nitrogen sources to at least one container of the bioreactor system.

38. The method of claim 37, wherein the one or more nitrogen sources comprise one or more of ammonium sulfate, ammonium chloride, ammonium nitrate, sodium nitrate, yeast extract, yeast, or any combination thereof.

39. The method of any one of claims 1 to 38, further comprising adding one or more of soy flour, lentil flour, chickpea flour, green pea flour, yellow pea flour, white bean flour, com flour, cereal flour, corn gluten, soy flour protein, or soy protein hydrolysate, or any combination thereof to at least one container of the bioreactor system.

40. The method of claim 39, wherein the soy flour is added, and wherein the soy flour is included in the aqueous feedstock.

41. The method of claim 39 or 40, further comprising maintaining a soy flour concentration in at least one container of the bioreactor system at a concentration of at least 0.2% w / v in relation to the volume of the working fluid in the at least one container.

42. The method of any one of claims 1 to 41, wherein the bioreactor system comprises a clarifier container comprising a clarifier working fluid.

43. The method of claim 42, further comprising separating a supernatant portion of the clarifier working fluid from a floc portion of the clarifier working fluid within the clarifier container.

44. The method of claim 43, wherein the separating comprises gravity separation.

45. The method of any one of claims 42 to 44, further comprising folding the floc portion of the clarifier working fluid.

46. The method of claim 45, wherein the folding further comprises releasing a population of the first nitrogen use efficiency -promoting microbial strain into the supernatant portion without introducing floc solids into the supernatant portion.

47. The method of claim 45 or 46, wherein the folding is performed by folding wipers in a bottom portion of the clarifier container.

48. The method of any one of claims 43 to 47, wherein the operating further comprises transferring the floc portion from the clarifier container to an earlier container in the bioreactor system.

49. The method of any one of claims 43 to 47, wherein the product outflow stream comprises the supernatant portion of the clarifier working fluid.

50. The method of any one of claims 1 to 49, wherein the method further comprises producing at least 1x102CFU / ml of the first nitrogen use efficiency-promoting microbial strain in the product outflow stream.

51. The method of any one of claims 1 to 50, wherein the bioreactor system comprises the first container comprising a volume of a first working fluid, a second container comprising a volume of a second working fluid, and a third container comprising a volume of a third working fluid.

52. The method of claim 51, wherein the first container comprises an outlet port fluidly connected to an inlet port of the second container and the second container comprises an outlet port fluidly connected to an input port of the third container.

53. The method of claim 52, wherein the third container comprises an outlet port fluidly connected to a clarifier container.

54. The method of any one of claims 51 to 53, further comprising maintaining the volume of each of the first working fluid, the second working fluid, and the third working fluid constant throughout the duration of time.

55. The method of any one of claims 1 to 54, wherein step (b) comprises operating the bioreactor system in a hydraulically balanced manner.

56. The method of any one of claims 1 to 55, wherein the transferring of step (b)(i), the transferring of step (b)(ii), and the collecting of step (b)(iv) are driven by gravity.

57. The method of any one of claims 1 to 56, wherein the operating comprises maintaining a flow rate that results in a hydraulic retention time of at least 5 days.

58. The method of any one of claims 1 to 57, wherein the operating comprises maintaining the product outflow stream at a flow rate of at least 100 gallons per day.

59. The method of any one of claims 1 to 58, wherein the volume of working fluid in each of the two or more containers is at least 100 gallons.

60. The method of any one of claims 1 to 59, wherein at least one of the two or more containers is a fluidized bed reactor.

61. The method of any one of claims 1 to 60, wherein at least one of the two or more containers is a packed bed reactor.

62. The method of any one of claims 1 to 61, further comprising maintaining at least one of the two or more containers under aerobic conditions.

63. The method of any one of claims 1 to 62, further comprising maintaining at least one of the two or more containers under microaerobic conditions.

64. The method of any one of claims 1 to 63, wherein the bioreactor system is operated continuously for at least 90 days.

65. The method of any one of claims 1 to 64, wherein one or more species of one or more of the following genera are among five most abundant species in the microbial consortium: Haliscomenobacler. I.ew inella. Caldilinea, Terrimonas. and Acidobacterium.

66. The method of any one of claims 1 to 65, wherein one or more of the following species are among five most abundant species in the microbial consortium: Lewinella cohaerens. Thauera phenylacetica, Thauera mechernichensis. Solitalea canadensis, and Nitrospira moscoviensis .

67. The method of any one of claims 1 to 66, wherein the microbial consortium comprises microbes endogenous to the organic material.

68. The method of any one of claims 1 to 67, wherein at least a portion of the aqueous feedstock is produced by the method of any one of claims 105 to 121.

69. The method of any one of claims 51 to 68, wherein at least one of the first working fluid, the second working fluid, or the third working fluid comprises a pH buffering system.

70. The method of any one of claims 51 to 69, further comprising maintaining the pH of at least one of the first working fluid, the second working fluid, or the third working fluid between 6 and 8 throughout the duration of time.

71. The method of any one of claims 1 to 70, wherein the aqueous feedstock does not include the first nitrogen use efficiency -promoting microbial strain at a concentration higher than 10 CFU / ml.

72. The method of any one of claims 1 to 71, wherein the first nitrogen use efficiencypromoting microbial strain is not added to the bioreactor system during the duration of time at a concentration that is higher than 10 CFU / ml.

73. The method of any one of claims 1 to 72, wherein the bioreactor system comprises at least one container placed in the series before the first container.

74. The method of any one of claims 1 to 73, wherein the volume of working fluid of one of the two or more containers comprises the microbial consortium, wherein each microbial consortium is distinct from all of the microbial consortia in other working fluids.

75. The method of any one of claims 1 to 74, further comprising producing a population of sporulated bacteria in the product outflow stream.

76. The method of any one of claims 1 to 75, further comprising producing a population of the first nitrogen use efficiency-promoting microbial strain in the product outflow stream that is sporulated.

77. The method of claim 76, wherein the population of the first nitrogen use efficiencypromoting microbial strain that is sporulated comprises at least IxlO2CFU / ml.

78. The method of any one of claims 1 to 77, further comprising adding an additional population of the first nitrogen use efficiency-promoting microbial strain, the second nitrogen use efficiency-promoting microbial strain, or the third nitrogen use efficiencypromoting microbial strain to the biostimulant product.

79. A bioreactor system comprising:(a) a stream of an aqueous feedstock in fluid communication with a first container comprising a volume of a first working fluid, wherein the aqueous feedstock comprises a microbial consortium, wherein the first working fluid comprises a population of a first nitrogen use efficiency-promoting strain, wherein a concentration of the first nitrogen use efficiency-promoting microbial strain in the first working fluid is at least 100 times higher than a concentration of the first nitrogen useefficiency -promoting microbial strain in the aqueous feedstock stream or in any other input into the bioreactor system;(b) one or more additional containers arranged in a series that includes the first container, wherein each of the one or more additional containers comprises a volume of a working fluid and is in fluid communication with at least one other container in the series, and wherein at least one of the one or more additional containers comprises a product outflow stream port; and(c) a product outflow stream in fluid communication with the product outflow stream port.

80. The system of claim 79, wherein the first nitrogen use efficiency -promoting microbial strain is one that performs nitrogen fixation, promotes nitrogen fixation in the tissues of plants, recruits nitrogen fixers to the root zones or other tissues of plants, or increases organic nitrogen content and / or mineralization of organic nitrogen in soil.

81. The system of claim 79, wherein the first nitrogen use efficiency -promoting microbial strain is positive for a nifH gene.

82. The system of claim 79, wherein the first nitrogen use efficiency -promoting microbial strain is one that promotes plant growth in a nitrogen-poor growth medium.

83. The system of claim 79, wherein the nitrogen-poor growth medium comprises nitrate at less than 10 ppm.

84. The system of claim 79, wherein the first nitrogen use efficiency-promoting microbial strain is of the genus Kosakonia, Klebsiella, Rahnella, Kluyvera, Enter obacter, Achromobacter, Microbacterium, Gluconobacter, Methylobacterium, Pseudomonas, Pantoea, Azospirillum, Azocarus, Herbaspirillum, Burkholderia, Cyanobacteria, Bacillus, or Paenibacillus .

85. The system of claim 79, wherein the first nitrogen use efficiency-promoting microbial strain is of the species Kosakonia sacchari, Klebsiella variicola, Rahnella aquatilis, Kluyvera intermedia, Kosakonia pseusosacchari, Enter obacter spp., Achromobacter marplatensis, Azopirillum lipoferum, Microbacterium murale, Gluconobacter diazotrophicus, Methylobacterium symbioticum, Paenibacillus borealis, Bacillus megaterium (Priestia megaterium), or Paenibacillus sonchi.

86. The system of claim 79, wherein the first nitrogen use efficiency-promoting microbial strain is the strain deposited under ATCC Accession No. PTA-127654 (MS3907), the strain deposited under ATCC Accession No. PTA-127653 (MS3900), the strain deposited under ATCC Accession No. PTA-127655 (MS4921), or the strain deposited under ATCC Accession No. PTA-127652 (MS2748).

87. The system of claim 79, wherein the bioreactor system is a continuous flow bioreactor system and the stream of the aqueous feedstock is a continuous stream.

88. The system of any one of claims 79 to 87, wherein each of the volume of the working fluid is constant.

89. The system of any one of claims 79 to 88, wherein each of the first container and the one or more additional containers comprises a concentration of the first nitrogen use efficiencypromoting microbial strain that remains at least IxlO4CFU / ml during operation of the bioreactor system.

90. The system of any one of claims 79 to 89, wherein the aqueous feedstock and any other input into the bioreactor system does not comprise the population of the first nitrogen use efficiency-promoting microbial strain or does not comprise a concentration of the first nitrogen use efficiency-promoting microbial strain at level higher than 100 CFU / ml.

91. The system of any one of claims 79 to 90, wherein the microbial consortium comprises at least IxlO5CFU / ml of microbes.

92. The system of any one of claims 79 to 91, wherein the aqueous feedstock further comprises an organic material digestible by microbes present in the containers.

93. The system of claim 92, wherein the organic material comprises manure or material derived from manure.

94. The system of any one of claims 79 to 93, wherein the aqueous feedstock further comprises rock phosphate particles.

95. The system of claim 94, wherein the microbial consortium comprises microbes derived from manure and rock phosphate particles.

96. The system of any one of claims 79 to 95, wherein the container comprising the product outflow stream port is a clarifier container configured to separate a portion of a working fluid in the clarifier container into a supernatant portion and a floc portion.

97. The system of claim 96, wherein the clarifier container comprises one or more floc folding flights configured to agitate settled floc in the clarifier container without resuspending solids in the floc portion into the supernatant portion.

98. The system of claim 96 or 97, further comprising a floc return stream that flows from the clarifier to an earlier container in the series.

99. The system of any one of claims 96 to 98, wherein the product outflow stream comprises the supernatant portion.

100. The system of claim 99, wherein the product outflow stream comprises at least IxlO4CFU / ml of the first nitrogen use efficiency-promoting microbial strain.

101. The system of claim 99 or 100, wherein the product outflow stream comprises at least IxlO2CFU / ml of a sporulated form of the first nitrogen use efficiency-promoting microbial strain.

102. The system of any one of claims 99 to 101, wherein the product outflow stream comprises a total dry weight of 0.2 to 2.5 mg / ml.

103. The system of any one of claims 99 to 102, wherein the product outflow stream has a chemical oxygen demand between 80 to 500 mg / L.

104. The system of any one of claims 99 to 103, wherein the product outflow stream has an electrical conductivity between 1.3 and 3.0 mS / cm.

105. A method comprising:(a) transferring water and rock phosphate into a first container comprising a volume of a first working fluid, wherein products of digestion of manure by microbes derived from the manure are not transferred into the first container;(b) transferring a portion of the first working fluid into a second container comprising a second working fluid;(c) transferring into the second container:(i) a liquid comprising (A) a first microbial consortium comprising microbes derived from a first organic material, and (B) digestion products produced by anaerobic digestion of the first organic material by the microbes;(ii) a second organic material; and(iii) yeast.

106. The method of claim 105, further comprising transferring a portion of the second working fluid into a third container comprising a third working fluid, and transferring a portion of the third working fluid into a fourth container comprising a fourth working fluid.

107. The method of claim 106, further comprising separating a portion of the fourth working fluid into a floc portion and a supernatant portion.

108. The method of claim 107, further comprising transferring the floc portion to the first container.

109. The method of any one of claims 106 to 108, further comprising maintaining the first container, the second container, the third container, and / or the fourth container under aerobic conditions.

110. The method of any one of claims 106 to 108, wherein the first container, the second container, the third container, and / or the fourth container are fluidized bed reactors, wherein the rock phosphate is continuously circulated within the first container, the second container, the third container, and / or the fourth container.

111. The method of any one of claims 105 to 110, wherein a total volume of material added to the first container over a given time period is equal to a total volume of the first working fluid transferred to the second container over a same time period.

112. The method of any one of claims 106 to 111, wherein a total volume of material transferred into the second container, the third container, and the fourth container over a given time period is equal to a total volume transferred out of the second container, the third container, and the fourth container over a same time period.

113. The method of any one of claims 106 to 112, further comprising maintaining a volume of the first working fluid, a volume of the second working fluid, and a volume of the third working fluid constant.

114. The method of any one of claims 105 to 113, wherein the first organic material is manure.

115. The method of any one of claims 105 to 114, wherein the second organic material is manure.

116. The method of any one of claims 105 to 115, wherein the yeast is Saccharomyces cerevisiae.

117. The method of any one of claims 106 to 116, further comprising producing a product stream from a second microbial consortium, a third microbial consortium, or a fourth microbial consortium, wherein the product stream comprises bacteria from one or more of the following species: Lewinella cohaerens, Thauera phenylacetica, Thauera mechernichensis. Solitalea canadensis.

118. The method of claim 117, wherein bacteria from one or more of the following species are among the five most abundant microbes in the second microbial consortium: Lewinella cohaerens, Thauera phenylacetica, Thauera mechernichensis, Solitalea canadensis, and Nitrospira moscoviensis.

119. The method of claim 117 or 118, wherein the five most abundant microbes in the second microbial consortium do not include bacteria from any of the following genera: Haliscomenobacter, Caldilinea, Terrimonas, and Acidobacterium.

120. The method of any one of claims 117 to 119, wherein the second microbial consortium is comprised in a fifth working fluid.

121. The method of any one of claims 105 to 120, wherein low-rank coal is not transferred into the first container.

122. A biostimulant composition made by the method of any one of claims 1 to 78, the system of any one of claims 79 to 104, or the method of any one of claims 105 to 121.

123. A method of promoting plant growth comprising contacting a plant, seed, or plant growth medium with the biostimulant composition of claim 122.

124. A method of increasing nitrogen use efficiency of a plant, the method comprising contacting a plant, seed, or plant growth medium with the biostimulant composition of claim 122.

125. A method of increasing phosphate solubilization in a plant growth medium, the method comprising contacting a plant, seed, or the plant growth medium with the biostimulant composition of claim 122.

126. A composition comprising:(a) a Bacillus megaterium strain having one or more of the following:(i) a 16S rRNA gene sequence at least 95% identical to SEQ ID NO: 1;(ii) a gyrB gene sequence at least 95% identical to SEQ ID NO: 4; and(iii) an rpoB gene sequence at least 95% identical to SEQ ID NO: 7; and(b) a carrier.

127. The composition of claim 126, wherein the Bacillus megaterium strain is the MS3900 strain deposited under ATCC Accession No. PTA-127653, or an isolated clone thereof.

128. The composition of claim 126 or 127, further comprising products of digestion of an organic substrate by the Bacillus megaterium strain.

129. The composition of any one of claims 126 to 128, wherein the carrier comprises a fertilizer.

130. The composition of any one of claims 126 to 129, wherein the carrier is a solid coated by the Bacillus megaterium strain.

131. The composition of any one of claims 126 to 130, wherein the carrier is a liquid.

132. The composition of any one of claims 126 to 131, wherein the composition further comprises an adjuvant selected from a wetting agent, spreading agent, dispersing agent, sticking agent, dust control agent, and adhesive.

133. The composition of any one of claims 126 to 132, wherein the concentration of the Bacillus megaterium strain in the composition ranges from IxlO3to IxlO11CFU / ml.

134. A composition comprising:(a) a Paenibacillus borealis strain having one or more of the following:(i) a 16S rRNA gene sequence at least 95% identical to SEQ ID NO: 2;(ii) a gyrB gene sequence at least 95% identical to SEQ ID NO: 5;(iii) an rpoB gene sequence at least 95% identical to SEQ ID NO: 8; and(iv) a nifH gene sequence at least 95% identical to SEQ ID NO: 13; and(b) a carrier.

135. The composition of claim 134, wherein the Paenibacillus borealis strain is the MS3907 strain deposited under ATCC Accession No. PTA-127654, or an isolated clone thereof.

136. The composition of claim 134 or 135, further comprising products of digestion of an organic substrate by the Paenibacillus borealis strain.

137. The composition of any one of claims 134 to 136, wherein the carrier comprises a fertilizer.

138. The composition of any one of claims 134 to 137, wherein the carrier is a solid coated by the Paenibacillus borealis strain.

139. The composition of any one of claims 134 to 138, wherein the carrier is a liquid.

140. The composition of any one of claims 134 to 139, wherein the composition further comprises an adjuvant selected from a wetting agent, spreading agent, dispersing agent, sticking agent, dust control agent, and adhesive.

141. The composition of any one of claims 134 to 140, wherein the concentration of the Paenibacillus borealis strain in the composition ranges from IxlO3to IxlO11CFU / ml.

142. A composition comprising:(a) a Paenibacillus sonchi strain having one or more of the following:(i) a 16S rRNA gene sequence at least 95% identical to SEQ ID NO: 3;(ii) a gyrB gene sequence at least 95% identical to SEQ ID NO: 6;(iii) an rpoB gene sequence at least 95% identical to SEQ ID NO: 9; and(iv) a nifH gene sequence at least 95% identical to SEQ ID NO: 14; and(b) a carrier.

143. The composition of claim 142, wherein the Paenibacillus sonchi strain is the MS4921 strain deposited under ATCC Accession No. PTA-127655, or an isolated clone thereof.

144. The composition of claim 142 or 143, further comprising products of digestion of an organic substrate by the Paenibacillus sonchi strain.

145. The composition of any one of claims 142 to 144, wherein the carrier comprises a fertilizer.

146. The composition of any one of claims 142 to 145, wherein the carrier is a solid coated by the Paenibacillus sonchi strain.

147. The composition of any one of claims 142 to 145, wherein the carrier is a liquid.

148. The composition of any one of claims 142 to 147, wherein the composition further comprises an adjuvant selected from a wetting agent, spreading agent, dispersing agent, sticking agent, dust control agent, and adhesive.

149. The composition of any one of claims 142 to 148, wherein the concentration of the Paenibacillus sonchi strain in the composition ranges from IxlO3to IxlO11CFU / ml.

150. A composition comprising:(a) a Bacillus megaterium strain having one or more of the following:(i) a 16S rRNA gene sequence at least 95% identical to SEQ ID NO: 10;(ii) a gyrB gene sequence at least 95% identical to SEQ ID NO: 11; and(iii) an rpoB gene sequence at least 95% identical to SEQ ID NO: 12; and(b) a carrier.

151. The composition of claim 150, wherein the Bacillus megaterium strain is the MS2748 strain deposited under ATCC Accession No. PTA-127652, or an isolated clone thereof.

152. The composition of claim 150 or 151, further comprising products of digestion of an organic substrate by the Bacillus megaterium strain.

153. The composition of any one of claims 150 to 152, wherein the carrier comprises a fertilizer.

154. The composition of any one of claims 150 to 153, wherein the carrier is a solid coated by the Bacillus megaterium strain.

155. The composition of any one of claims 150 to 154, wherein the carrier is a liquid.

156. The composition of any one of claims 150 to 155, wherein the composition further comprises an adjuvant selected from a wetting agent, spreading agent, dispersing agent, sticking agent, dust control agent, and adhesive.

157. The composition of any one of claims 150 to 156, wherein the concentration of the Bacillus megaterium strain in the composition ranges from IxlO3to IxlO11CFU / ml.

158. The composition of any one of claims 150 to 157, further comprising at least one or more of the following:(b) a Bacillus megaterium strain having one or more of the following:(i) a 16S rRNA gene sequence at least 95% identical to SEQ ID NO: 1;(ii) a gyrB gene sequence at least 95% identical to SEQ ID NO: 4; and(iii) an rpoB gene sequence at least 95% identical to SEQ ID NO: 7;(c) a Paenibacillus borealis strain having one or more of the following:(i) a 16S rRNA gene sequence at least 95% identical to SEQ ID NO: 2;(ii) a gyrB gene sequence at least 95% identical to SEQ ID NO: 5;(iii) an rpoB gene sequence at least 95% identical to SEQ ID NO: 8; and(iv) a nifH gene sequence at least 95% identical to SEQ ID NO: 13; and(d) a Paenibacillus sonchi strain having one or more of the following:(i) a 16S rRNA gene sequence at least 95% identical to SEQ ID NO: 3;(ii) a gyrB gene sequence at least 95% identical to SEQ ID NO: 6;(iii) an rpoB gene sequence at least 95% identical to SEQ ID NO: 9; and(iv) a nifH gene sequence at least 95% identical to SEQ ID NO: 14.

159. An isolated strain of the species Bacillus megaterium having one or more of the following:(a) a 16S rRNA gene sequence at least 95% identical to SEQ ID NO: 1;(b) a gyrB gene sequence at least 95% identical to SEQ ID NO: 4; and(c) an rpoB gene sequence at least 95% identical to SEQ ID NO: 7.

160. The isolated strain of claim 159, wherein the Bacillus megaterium strain is the MS3900 strain deposited under ATCC Accession No. PTA-127653, or an isolated clone thereof.

161. An isolated strain of the species Paenibacillus borealis having one or more of the following:(a) a 16S rRNA gene sequence at least 95% identical to SEQ ID NO: 2;(b) a gyrB gene sequence at least 95% identical to SEQ ID NO: 5;(c) an rpoB gene sequence at least 95% identical to SEQ ID NO: 8; and(d) a nifH gene sequence at least 95% identical to SEQ ID NO: 13.

162. The isolated strain of claim 161, wherein the Paenibacillus borealis strain is the MS3907 strain deposited under ATCC Accession No. PTA-127654, or an isolated clone thereof.

163. An isolated strain of the species Paenibacillus sonchi having one or more of the following:(a) a 16S rRNA gene sequence at least 95% identical to SEQ ID NO: 3;(b) a gyrB gene sequence at least 95% identical to SEQ ID NO: 6;(c) an rpoB gene sequence at least 95% identical to SEQ ID NO: 9; and(d) a nifH gene sequence at least 95% identical to SEQ ID NO: 14.

164. The isolated strain of claim 163, wherein the Paenibacillus sonchi strain is the MS4921 strain deposited under ATCC Accession No. PTA-127655, or an isolated clone thereof.

165. An isolated strain of the species Bacillus megaterium having one or more of the following:(a) a 16S rRNA gene sequence at least 95% identical to SEQ ID NO: 10;(b) a gyrB gene sequence at least 95% identical to SEQ ID NO: 11; and(c) an rpoB gene sequence at least 95% identical to SEQ ID NO: 12.

166. The isolated strain of claim 165, wherein the Bacillus megaterium strain is the MS2748 strain deposited under ATCC Accession No. PTA-127652, or an isolated clone thereof.

167. A method for promoting growth of a plant growing in a medium, the method comprising contacting the plant or the medium with the composition of any one of claims 126 to 158 or the isolated strain of any one of claims 159 to 166.

168. The method of claim 167, wherein the contacting increases a plant nitrogen content by at least 5%.

169. The method of claim 167 or 168, wherein the contacting increases a nitrogen fixation activity and / or nitrogen use efficiency in plant tissues by at least 5%.

170. The method of any one of claims 167 to 169, wherein the contacting increases a population of nitrogen fixing bacteria in the root and root rhizospheres of the plant by at least 5%.

171. The method of any one of claims 167 to 170, wherein the contacting causes recruitment of nitrogen fixing bacteria present in the medium to the root zone of the plant.

172. The method of any one of claims 167 to 171, wherein the contacting causes an increase plant growth by at least 10 percent as compared to a control.

173. The method of any one of claims 167 to 172, wherein the medium comprises soil, a hydroponic medium, turface, or isolite.

174. A method of enhancing nitrogen fixing activity or plant tissue colonization capability of a bacterium, the method comprising incubating the bacterium in the presence of strain MS3900.

175. The method of claim 174, wherein the bacterium is strain MS3907.

176. A composition comprising:(a) a microbial consortium comprising one or more bacterial strains selected from MS3900 (ATCC Accession No. PTA-127653), MS3907 (ATCC Accession No. PTA- 127654), MS4921 (ATCC Accession No. PTA-127655), and MS2748 (ATCC Accession No. PTA-127652); and(b) metabolites produced by digestion of an organic substrate by microbes within the microbial consortium.

177. The composition of claim 176, wherein the microbial consortium further comprises an enriched nitrogen-fixing microbial community.

178. The composition of claim 176 or 177, wherein the organic substrate is derived from cow manure, rock phosphate, or ground plant matter, or any combination thereof.

179. The composition of any one of claims 176 to 178, wherein the microbial consortium comprises microbes derived from cow manure, rock phosphate, or ground plant matter.

180. The composition of claim 178 or 179, wherein the ground plant matter is soy flour, lentil flour, chickpea flour, green pea flour, yellow pea flour, white bean flour, corn flour, cereal flour, corn gluten, soy flour protein, soy protein hydrolysate, or any combination thereof.

181. The composition of any one of claims 176 to 180, wherein the microbial consortium comprises from 5xl07to 1.5xl08CFU / ml of bacteria.

182. The composition of any one of claims 176 to 181, wherein the microbial consortium comprises from IxlO5to 1.5xl07CFU / ml of nitrogen fixing bacteria.

183. The composition of any one of claims 176 to 181, wherein the microbial consortium comprises from 5xl04to 5xl05CFU / ml of spore forming bacteria.

184. The composition of any one of claims 176 to 183, wherein the microbial consortium comprises from IxlO3to IxlO4CFU / ml of MS3900 spores, MS4921 spores, or any combination thereof.

185. The composition of any one of claims 176 to 184, wherein the microbial consortium comprises from IxlO2to IxlO4CFU / ml of MS3907 spores.

186. The composition of any one of claims 176 to 185, wherein the pH of the composition is from 7 to 9.

187. The composition of any one of claims 176 to 186, wherein the COD of the composition is from 120 to 500 mg / L.

188. The composition of any one of claims 176 to 187, wherein the conductivity of the composition is from 0.5 to 2.0 mS / cm.

189. The composition of any one of claims 176 to 188, wherein the composition has a total dry weight of 0.2 to 2.5 mg / ml.

190. A method of making a biostimulant composition, the method comprising:(a) providing a bioreactor system comprising two or more containers arranged in a series, each of the two or more containers comprising a volume of a working fluid, wherein at least one of the containers comprises a population of a first microbial strain derived from an inoculum of the first microbial strain that has been added to the bioreactor system and a population of other microbes;(b) operating the bioreactor system for a duration of time by:(i) transferring into a first container an aqueous feedstock comprising a microbial consortium;(ii) transferring a portion of the working fluid out of each of the two or more containers into either a subsequent container of the bioreactor system or a product outflow stream;(iii) collecting at least a portion of the product outflow stream as the biostimulant composition; and(iv) maintaining the population of the first microbial strain throughout the duration of time in at least the first container at a level that is at least 80% of the population of the first microbial strain at the beginning of the duration of time; wherein the duration of time is at least 5 days; and wherein the first microbial strain is not present in the aqueous feedstock or any other input into the bioreactor system during the duration of time at a concentration that is higher than 1% of the concentration of the population of the first microbial strain in the first container.

191. The method of claim 190, wherein the first microbial strain has a plant growth promoting property.

192. The method of claim 190 or 191, further comprising providing conditions in the bioreactor system that promote establishment of an enriched population of the first microbial strain relative to a population of the first microbial strain in the aqueous feedstock or any other input into the bioreactor system.

193. The method of claim 190 or 191, further comprising applying a selective pressure in the bioreactor system that favors growth of the first microbial strain relative to the other microbes.

194. The method of any one of claims 191 to 193, wherein the aqueous feedstock further comprises an organic material digestible by the first microbial strain and by at least some of the other microbes.

195. The method of claim 194, further comprising producing metabolites that have the plant growth promoting property by digestion of the organic material.

196. The system of any one of claims 79 to 104, wherein the first working fluid comprises malate at a concentration of at least 0.2% w / v.

197. The system of any one of claims 79-104 and 196, wherein the first working fluid comprises soy flour at a concentration of at least 0.2% w / v.

198. The system of any one of claims 79-104, 196, and 197, wherein the first working fluid comprises microaerobic conditions.

199. The system of claim 198, wherein the working fluid in at least one of the one or more additional containers comprises microaerobic conditions.

200. The system of any one of claims 79-104 and 196-199, wherein the system has a hydraulic retention time of at least 5 days.

201. The system of any one of claims 79-104 and 196-200, wherein the first working fluid further comprises an established population of a second nitrogen use efficiency -promoting microbial strain, wherein a concentration of the second nitrogen use efficiency -promoting microbial strain in the first working fluid is at least 100 times higher than a concentration of the second nitrogen use efficiency-promoting microbial strain in the aqueous feedstock stream and in any other input into the bioreactor system.

202. The system of claim 201, wherein the second nitrogen use efficiency-promoting microbial strain is of the species Kosakonia sacchari, Klebsiella variicola, Rahnella aquatilis, Kluyvera intermedia, Kosakonia pseusosacchari, Enter obacter spp., Achromobacter marplatensis, Azopirillum lipoferum, Microbacterium murale, Gluconobacter diazotrophicus, Methylobacterium symbioticum, Paenibacillus borealis, Bacillus megaterium (Priestia megaterium), or Paenibacillus sonchi.

203. The system of any one of claims 79-104 and 196-202, wherein the first working fluid further comprises an established population of a third nitrogen use efficiency -promoting microbial strain, wherein a concentration of the third nitrogen use efficiency -promoting microbial strain in the first working fluid is at least 100 times higher than a concentration of the third nitrogen use efficiency -promoting microbial strain in the aqueous feedstock stream and in any other input into the bioreactor system.

204. The system of claim 203, wherein the third nitrogen use efficiency-promoting microbial strain is of the species Kosakonia sacchari, Klebsiella variicola, Rahnella aquatilis, Kluyvera intermedia, Kosakonia pseusosacchari, Enterobacter spp., Achromobacter marplatensis, Azopirillum lipoferum, Microbacterium murale, Gluconobacter diazotrophicus, Methylobacterium symbioticum, Paenibacillus borealis, Bacillus megaterium (Priestia megaterium), or Paenibacillus sonchi.

205. The system of any one of claims 79-104 and 196-204, wherein the first working fluid comprises a total population of microbes positive for a nifH gene of at least IxlO5CFU / ml.

206. A method of promoting plant growth, comprising:(a) contacting a plant and / or medium in which the plant is growing with a composition comprising one or more compounds, wherein the one or more compounds is selected from acinospesigenin-C, 3-cyclohexyl-6-[4-[3-(trifluoromethyl)phenyl]-l-piperazinyl]-lH- pyrimidine-2, 4-dione, Arg-Thr-Ala-Arg, (2R)-2-[[4-(2,6-dipyrrolidin-l-ylpyrimidin-4- yl)piperazin-l-yl]methyl]-2,5,7,8-tetramethyl-3,4-dihydrochromen-6-ol;dihydrochloride, Gly-Leu-Arg-Val-Phe, westiellamide, thrombin receptor activator for peptide 5 (TRAP-5), tungstic acid, fercomin, threoninyl-isoleucine, BW-A868C, Lys-Ala-Leu-Glu, N- Benzyloxycarbonylglycine, Glu-Asp-Asn, Glu-Asp-Asn, Ile-Glu-His-Lys, Chaps, didemethylcital opram, Lys-Tyr-Thr-Ser-Ser, 3-amino-4,6-dimethyl-N-(l- phenylethyl)thieno[2,3-b]pyridine-2-carboxamide, Asn- Ala-Leu- Ala-His, Met-Asp-Arg,His-Arg-Lys-Glu, Asn-Cys-Phe, 7-Hydroxylauric acid, Phe-Tyr-Lys-Arg, k- Strophanthoside, disopyramide, estra-4,9-diene-3, 17-dione, HoPhe-Asp-OH, tert-butyl 5- methyl-6-oxo-5,6-dihydro-4h-imidazo[l,5-a]thieno[2,3-f][l,4]diazepine-3-carboxylate, 2,6-naphthalenediol, zonisamide, Ser-Gln-Leu-Lys, Pro-Ala-Phe, Ala-Thr-Ile-Lys, mycophenolic acid, PC(15:0 / 18:3(6Z,9Z,12Z)), 6-[(2Z)-2-benzylideneheptoxy]-3,4,5- trihydroxyoxane-2-carboxylic acid, 7"-Deoxybonaspectin D 4"-methyl ether, Reciniferatoxin, Acetic acid trans-2-hepten-l-YL ester, Acetoxy-6-gingerol, Dubini dine, N-l -Naphthylbenzamide, one or more derivatives thereof, or combination thereof.

207. The method of claim 206, wherein the plant growth property is nitrogen use efficiency.

208. The method of claim 206 or 207, wherein the concentration of the one or more compound in the composition is at least about 1 nanomolar (nM).

209. The method of any one of claims 206-208, wherein the concentration of the one or more compounds in the composition is at least about 0.00001% of a dry weight of the composition.

210. The method of any one of claims 206-209, wherein the contacting comprises contacting the plant with the composition.

211. The method of any one of claims 206-210, wherein the contracting comprises contacting a plant seed with the composition.

212. The method of any one of claims 206-211, wherein the contacting comprises contacting a leaf of the plant with the composition.

213. The method of any one of claims 206-212, wherein the medium comprises soil, a hydroponic medium, turface, or isolite.

214. The method of any one of claims 206-213, wherein the contacting comprises increasing a plant nitrogen content by at least 5%.

215. The method of any one of claims 206-214, wherein the contacting comprises increasing a nitrogen fixation activity in plant tissues by at least 5%.

216. The method of any one of claims 206-215, wherein the contacting comprises increasing a population of nitrogen fixation bacteria in the root and root rhizospheres of the plant by at least 5%.

217. The method of any one of claims 206-216, wherein the contacting causes recruitment of nitrogen fixing bacteria present in the medium to a root zone of the plant.

218. The method of any one of claims 206-217, wherein the contacting causes an increase in plant growth by at least 10 percent as compared to the plant and / or the medium not contacted with the one or more compounds.

219. A composition for promoting plant growth, comprising:(i) at least one microbial strain selected from a Bacillus megaterium strain, a Paenibacillus borealis strain, or a Paenibacillus sonchi strain; and(ii) one or more compounds selected from acinospesigenin-C, 3-cyclohexyl-6-[4-[3- (trifluoromethyl)phenyl]-l-piperazinyl]-lH-pyrimidine-2, 4-dione, Arg-Thr-Ala-Arg, (2R)- 2-[[4-(2,6-dipyrrolidin-l-ylpyrimidin-4-yl)piperazin-l-yl]methyl]-2,5,7,8-tetramethyl-3,4- dihydrochromen-6-ol;dihydrochloride, Gly-Leu-Arg-Val-Phe, westiellamide, thrombin receptor activator for peptide 5 (TRAP-5), tungstic acid, fercomin, threoninyl-isoleucine, BW-A868C, Lys-Ala-Leu-Glu, N-Benzyloxycarbonylglycine, Glu-Asp-Asn, Glu-Asp-Asn, Ile-Glu-His-Lys, Chaps, didemethylcitalopram, Lys-Tyr-Thr-Ser-Ser, 3-amino-4,6- dimethyl-N-(l-phenylethyl)thieno[2,3-b]pyridine-2-carboxamide, Asn-Ala-Leu-Ala-His, Met-Asp-Arg, His-Arg-Lys-Glu, Asn-Cys-Phe, 7-Hydroxylauric acid, Phe-Tyr-Lys-Arg, k- Strophanthoside, disopyramide, estra-4,9-diene-3, 17-dione, HoPhe-Asp-OH, tert-butyl 5- methyl-6-oxo-5,6-dihydro-4h-imidazo[l,5-a]thieno[2,3-f][l,4]diazepine-3-carboxylate, 2,6-naphthalenediol, zonisamide, Ser-Gln-Leu-Lys, Pro-Ala-Phe, Ala-Thr-Ile-Lys, mycophenolic acid, PC(15:0 / 18:3(6Z,9Z,12Z)), 6-[(2Z)-2-benzylideneheptoxy]-3,4,5- trihydroxyoxane-2-carboxylic acid, 7"-Deoxybonaspectin D 4"-methyl ether, Reciniferatoxin, Acetic acid trans-2-hepten-l-YL ester, Acetoxy-6-gingerol, Dubinidine, N- 1 -Naphthylbenzamide, oxalacetic acid, l-Oleoyl-2-palmitoyl-sn-glycero-3-phosphocholine, Undeca-2-ene-8,10-diynoic acid isobutylamide, ent-Corey PG-Lactone Diol, one or more derivatives thereof, or combination thereof.

220. The composition of claim 219, wherein the Paenibacillus sonchi strain comprises one or more of the following:(i) a 16S rRNA gene sequence at least 95% identical to SEQ ID NO: 3;(ii) a gyrB gene sequence at least 95% identical to SEQ ID NO: 6;(iii) an rpoB gene sequence at least 95% identical to SEQ ID NO: 9; and(iv) a nifH gene sequence at least 95% identical to SEQ ID NO: 14.

221. The composition of claim 219 or 220, wherein the Paenibacillus borealis strain comprises one or more of the following:(i) a 16S rRNA gene sequence at least 95% identical to SEQ ID NO: 2;(ii) a gyrB gene sequence at least 95% identical to SEQ ID NO: 5;(iii) an rpoB gene sequence at least 95% identical to SEQ ID NO: 8; and(iv) a nifH gene sequence at least 95% identical to SEQ ID NO: 13.

222. The composition of any one of claims 219-221, wherein the Bacillus megaterium strain comprises one or more of the following:(i) a 16S rRNA gene sequence at least 95% identical to SEQ ID NO: 1;(ii) a gyrB gene sequence at least 95% identical to SEQ ID NO: 4; and(iii) an rpoB gene sequence at least 95% identical to SEQ ID NO: 7.

223. The composition of any one of claims 219-222, wherein of oxalacetic acid, l-Oleoyl-2- palmitoyl-sn-glycero-3-phosphocholine, Undeca-2-ene-8,10-diynoic acid isobutylamide, and ent-Corey PG-Lactone Diol, oxalacetic acid is the most abundant and ent-Corey PG- Lactone Diol is the least abundant.

224. The composition of any one of claims 219-223, wherein l-Oleoyl-2-palmitoyl-sn-glycero- 3 -phosphocholine is present at a concentration of l%-2% of the concentration of oxalacetic acid.

225. The composition of any one of claims 219-224, wherein Undeca-2-ene-8,10-diynoic acid isobutylamide is present at a concentration of l%-2% of the concentration of oxalacetic acid.

226. The composition of any one of claims 219-225, wherein ent-Corey PG-Lactone Diol is present at a concentration of 0.5%-l .5% of the concentration of oxalacetic acid.

227. The composition of any one of claims 219-226, further comprising a carrier.

228. The composition of claim 228, wherein the carrier is formulated for application to a plant and / or medium in which the plant is growing.

229. A composition for promoting plant growth , comprising:(i) two or more compounds selected from acinospesigenin-C, 3-cyclohexyl-6-[4-[3- (trifluoromethyl)phenyl]-l-piperazinyl]-lH-pyrimidine-2, 4-dione, Arg-Thr-Ala-Arg, (2R)- 2-[[4-(2,6-dipyrrolidin-l-ylpyrimidin-4-yl)piperazin-l-yl]methyl]-2,5,7,8-tetramethyl-3,4- dihydrochromen-6-ol;dihydrochloride, Gly-Leu-Arg-Val-Phe, westiellamide, thrombin receptor activator for peptide 5 (TRAP-5), tungstic acid, fercomin, threoninyl-isoleucine, BW-A868C, Lys-Ala-Leu-Glu, N-Benzyloxycarbonylglycine, Glu-Asp-Asn, Glu-Asp-Asn, Ile-Glu-His-Lys, Chaps, didemethylcitalopram, Lys-Tyr-Thr-Ser-Ser, 3-amino-4,6- dimethyl-N-(l-phenylethyl)thieno[2,3-b]pyridine-2-carboxamide, Asn-Ala-Leu-Ala-His, Met-Asp-Arg, His-Arg-Lys-Glu, Asn-Cys-Phe, 7-Hydroxylauric acid, Phe-Tyr-Lys-Arg, k- Strophanthoside, disopyramide, estra-4,9-diene-3, 17-dione, HoPhe-Asp-OH, tert-butyl 5- methyl-6-oxo-5,6-dihydro-4h-imidazo[l,5-a]thieno[2,3-f][l,4]diazepine-3-carboxylate, 2,6-naphthalenediol, zonisamide, Ser-Gln-Leu-Lys, Pro-Ala-Phe, Ala-Thr-Ile-Lys, mycophenolic acid, PC(15:0 / 18:3(6Z,9Z,12Z)), 6-[(2Z)-2-benzylideneheptoxy]-3,4,5- trihydroxyoxane-2-carboxylic acid, 7"-Deoxybonaspectin D 4"-methyl ether, Reciniferatoxin, Acetic acid trans-2-hepten-l-YL ester, Acetoxy-6-gingerol, Dubinidine, N- 1 -Naphthylbenzamide, oxalacetic acid, l-Oleoyl-2-palmitoyl-sn-glycero-3-phosphocholine, Undeca-2-ene-8,10-diynoic acid isobutylamide, ent-Corey PG-Lactone Diol, one or more derivatives thereof, or a combination thereof; and(ii) a carrier.

230. The composition of claim 229, wherein the carrier is formulated for application to a plant and / or medium in which the plant is growing.

231. The composition of claim 229 or 230, wherein the carrier comprises a fertilizer.

232. The composition of claim 231, wherein the fertilizer is a solid.

233. The composition of any one of claims 229-232, wherein the carrier is a liquid.

234. The composition of any one of claims 219-233, wherein the composition is configured to promote and / or is capable of promoting nitrogen use efficiency when applied to a plant or plant growth medium.

235. The composition of any one of claims 229-234, wherein of oxalacetic acid, l-Oleoyl-2- palmitoyl-sn-glycero-3-phosphocholine, Undeca-2-ene-8,10-diynoic acid isobutylamide, and ent-Corey PG-Lactone Diol, oxalacetic acid is the most abundant and ent-Corey PG- Lactone Diol is the least abundant.

236. The composition of claim 235, wherein l-Oleoyl-2-palmitoyl-sn-glycero-3 -phosphocholine is present at a concentration of l%-2% of the concentration of oxalacetic acid.

237. The composition of claim 235, wherein Undeca-2-ene-8,10-diynoic acid isobutylamide is present at a concentration of l%-2% of the concentration of oxalacetic acid.

238. The composition of claim 235, wherein ent-Corey PG-Lactone Diol is present at a concentration of 0.5%-l .5% of the concentration of oxalacetic acid.

239. The composition of any one of claims 219-238, wherein the concentration of the one or more compounds in the composition is at least about 1 nM.

240. The composition of any one of claims 219-239, wherein the concentration of the one or more compounds in the composition is at least about 0.00001% of a total dry weight of the composition.

241. The composition of any one of claims 219-240, wherein the composition further comprises an adjuvant selected from a wetting agent, spreading agent, dispersing agent, sticking agent, dust control agent, and adhesive.

242. The composition of any one of claims 219-241, wherein the composition is configured to increase and / or is capable of increasing a plant nitrogen content by at least 5%.

243. The composition of any one of claims 219-242, wherein composition is configured to increase and / or is capable of increasing a nitrogen fixation activity in plant tissues by at least 5%.

244. The composition of any one of claims 219-243, wherein composition is configured to increase and / or is capable of increasing a population of nitrogen fixing bacteria in a root and root rhizospheres of the plant by at least 5%.

245. The composition of any one of claims 219-244, wherein the composition is configured to cause and / or is capable of causing recruitment of nitrogen fixing bacteria present in a medium of the plant to a root zone of the plant.

246. The composition of any one of claims 219-245, wherein the composition is configured to cause and / or is capable of causing an increase in plant growth by at least 10 percent as compared to a control.

247. A method of promoting plant growth, comprising:(a) contacting a plant and / or medium in which the plant is growing with a composition comprising one or more compounds, wherein the one or more compounds is selected from 4-(2-Pyridylazo)-N,N-dimethylaniline, LPC( 18:2 / 0:0), LPE( 18:2 / 0:0), 7-[3- (Dimethylamino)propoxy]-6-Methoxy-2-(4-Methyl-l,4-Diazepan-l-Yl)-N-(l- Methylpiperidin-4-Yl)quinazolin-4-Amine, 7-chloro-2-(3,4-dimethoxyphenyl)-3,5,8- trihydroxy-6-methoxy-4H-chromen-4-one, l-(2,4,5-Trimethoxyphenyl)-l,2-propanedione, 3-(4-hydroxy-2,3,5-trimethoxyphenyl)prop-2-enal, LPE(18: 1 / 0:0), 9-((2- Phosphonylmethoxy)ethyl)guanine, PC(P- 16:0 / 20:5(5Z,8Z,l lZ,14Z,l 7Z)), Diellagilactone, 13 -Methylmyristic acid, D-Limonene, one or more derivatives thereof, 3- Phosphoadenylylselenate, l,3-bis(4-Bromophenyl)-5-phenyl-2,4-imidazolidinedione, F- Amidine, LPC(0:0 / 18:3), Undecanedioic acid, Muzanzagenin, or combination thereof.

248. The method of claim 247, wherein the contacting increases nitrogen use efficiency by the plant.

249. The method of claim 247 or 248, wherein the concentration of the one or more compound in the composition is at least about 1 nM.

250. The method of any one of claims 248-249, wherein the concentration of the one or more compounds in the composition is at least about 0.00001% of a total dry weight of the composition.

251. The method of any one of claims 248-250, wherein the contacting comprises contacting the plant with the composition.

252. The method of any one of claims 248-251, wherein the contracting comprises contacting a plant seed with the composition.

253. The method of any one of claims 248-252, wherein the contacting comprises contacting a leaf of the plant with the composition.

254. The method of any one of claims 248-253, wherein the medium comprises soil, a hydroponic medium, turface, or isolite.

255. The method of any one of claims 248-254, wherein the contacting increases a plant nitrogen content by at least 5%.

256. The method of any one of claims 248-255, wherein the contacting increases a nitrogen fixation activity in plant tissues by at least 5%.

257. The method of any one of claims 248-256, wherein the contacting increases a population of nitrogen fixation bacteria in the root and root rhizospheres of the plant by at least 5%.

258. The method of any one of claims 248-257, wherein the contacting causes recruitment of nitrogen fixing bacteria present in the medium to a root zone of the plant.

259. The method of any one of claims 248-258, wherein the contacting causes an increase in plant growth by at least 10 percent as compared to the plant and / or the medium not contacted with the one or more compounds.

260. A composition for promoting plant growth, comprising:(i) at least one microbial strain selected from a Bacillus megaterium strain, a Paenibacillus borealis strain, or a Paenibacillus sonchi strain; and(ii) one or more compounds selected from 4-(2-Pyridylazo)-N,N-dimethylaniline, LPC(18:2 / 0:0), LPE(18:2 / 0:0), 7-[3-(Dimethylamino)propoxy]-6-Methoxy-2-(4-Methyl- l,4-Diazepan-l-Yl)-N-(l-Methylpiperidin-4-Yl)quinazolin-4-Amine, 7-chloro-2-(3,4- dimethoxyphenyl)-3,5,8-trihydroxy-6-methoxy-4H-chromen-4-one, 1 -(2,4,5-Trimethoxyphenyl)-l,2-propanedione, 3-(4-hydroxy-2,3,5-trimethoxyphenyl)prop-2-enal, LPE(18:l / 0:0), 9-((2-Phosphonylmethoxy)ethyl)guanine, PC(P-16:0 / 20:5(5Z,8Z,l 1Z,14Z,17Z)), Diellagilactone, 13-Methylmyristic acid, D-Limonene, 3- Phosphoadenylylselenate, l,3-bis(4-Bromophenyl)-5-phenyl-2,4-imidazolidinedione, F-Amidine, LPC(0:0 / 18:3), Undecanedioic acid, Muzanzagenin, oxalacetic acid, l-Oleoyl-2- palmitoyl-sn-glycero-3-phosphocholine, Undeca-2-ene-8,10-diynoic acid isobutylamide, ent-Corey PG-Lactone Diol, one or more derivatives thereof, or combination thereof.

261. The composition of claim 260, wherein the Paenibacillus sonchi strain comprises one or more of the following:(i) a 16S rRNA gene sequence at least 95% identical to SEQ ID NO: 3;(ii) a gyrB gene sequence at least 95% identical to SEQ ID NO: 6;(iii) an rpoB gene sequence at least 95% identical to SEQ ID NO: 9; and(iv) a nifH gene sequence at least 95% identical to SEQ ID NO: 14.

262. The composition of claim 260 or 261, wherein the Paenibacillus borealis strain comprises one or more of the following:(i) a 16S rRNA gene sequence at least 95% identical to SEQ ID NO: 2;(ii) a gyrB gene sequence at least 95% identical to SEQ ID NO: 5;(iii) an rpoB gene sequence at least 95% identical to SEQ ID NO: 8; and(iv) a nifH gene sequence at least 95% identical to SEQ ID NO: 13.

263. The composition of any one of claims 260-262, wherein the Bacillus megaterium strain comprises one or more of the following:(i) a 16S rRNA gene sequence at least 95% identical to SEQ ID NO: 1;(ii) a gyrB gene sequence at least 95% identical to SEQ ID NO: 4; and(iii) an rpoB gene sequence at least 95% identical to SEQ ID NO: 7.

264. The composition of any one of claims 260-263, wherein of oxalacetic acid, l-Oleoyl-2- palmitoyl-sn-glycero-3-phosphocholine, Undeca-2-ene-8,10-diynoic acid isobutylamide, and ent-Corey PG-Lactone Diol, oxalacetic acid is the most abundant and ent-Corey PG- Lactone Diol is the least abundant.

265. The composition of claim 264, wherein l-Oleoyl-2-palmitoyl-sn-glycero-3 -phosphocholine is present at a concentration of l%-2% of the concentration of oxalacetic acid.

266. The composition of claim 264, wherein Undeca-2-ene-8,10-diynoic acid isobutylamide is present at a concentration of l%-2% of the concentration of oxalacetic acid.

267. The composition of claim 264, wherein ent-Corey PG-Lactone Diol is present at a concentration of 0.5%-l .5% of the concentration of oxalacetic acid.

268. The composition of any one of claims 260-267, further comprising a carrier.

269. The composition of claim 268, wherein the carrier is formulated for application to a plant and / or medium in which the plant is growing.

270. A composition for promoting plant growth, comprising:(i) two or more compounds selected from 4-(2-Pyridylazo)-N,N-dimethylaniline, LPC(18:2 / 0:0), LPE(18:2 / 0:0), 7-[3-(Dimethylamino)propoxy]-6-Methoxy-2-(4-Methyl- l,4-Diazepan-l-Yl)-N-(l-Methylpiperidin-4-Yl)quinazolin-4-Amine, 7-chloro-2-(3,4- dimethoxyphenyl)-3,5,8-trihydroxy-6-methoxy-4H-chromen-4-one, 1 -(2,4,5-Trimethoxyphenyl)-l,2-propanedione, 3-(4-hydroxy-2,3,5-trimethoxyphenyl)prop-2-enal, LPE(18:l / 0:0), 9-((2-Phosphonylmethoxy)ethyl)guanine, PC(P-16:0 / 20:5(5Z,8Z,l 1Z,14Z,17Z)), Diellagilactone, 13-Methylmyristic acid, D-Limonene, 3- Phosphoadenylylselenate, l,3-bis(4-Bromophenyl)-5-phenyl-2,4-imidazolidinedione, F- Amidine, LPC(0:0 / 18:3), Undecanedioic acid, Muzanzagenin, one or more derivatives thereof, or combination thereof; and(ii) a carrier.

271. The composition of claim 270, wherein the carrier is formulated for application to a plant and / or medium in which the plant is growing.

272. The composition of claim 270 or 271, wherein the carrier comprises a fertilizer.

273. The composition of claim 272, wherein the fertilizer is a solid.

274. The composition of any one of claims 270-273, wherein the carrier is a liquid.

275. The composition of any one of claims 260-274, wherein the composition is configured to increase and / or is capable of increasing nitrogen use efficiency when applied to a plant.

276. The composition of any one of claims 270-274, wherein of oxalacetic acid, l-Oleoyl-2- palmitoyl-sn-glycero-3-phosphocholine, Undeca-2-ene-8,10-diynoic acid isobutylamide, and ent-Corey PG-Lactone Diol, oxalacetic acid is the most abundant and ent-Corey PG- Lactone Diol is the least abundant.

277. The composition of claim 276, wherein l-Oleoyl-2-palmitoyl-sn-glycero-3 -phosphocholine is present at a concentration of l%-2% of the concentration of oxalacetic acid.

278. The composition of claim 276, wherein Undeca-2-ene-8,10-diynoic acid isobutylamide is present at a concentration of l%-2% of the concentration of oxalacetic acid.

279. The composition of claim 276, wherein ent-Corey PG-Lactone Diol is present at a concentration of 0.5%-l .5% of the concentration of oxalacetic acid.

280. The composition of any one of claims 260-279, wherein the concentration of the one or more compounds in the composition is at least about 1 nM.

281. The composition of any one of claims 260-280, wherein the concentration of the one or more compounds in the composition is at least about 0.00001%.

282. The composition of any one of claims 260-281, wherein the composition further comprises an adjuvant selected from a wetting agent, spreading agent, dispersing agent, sticking agent, dust control agent, and adhesive.

283. The composition of any one of claims 260-282, wherein composition is configured to increase and / or is capable of increasing a plant nitrogen content by at least 5%.

284. The composition of any one of claims 260-283, wherein composition is configured to increase and / or is capable of increasing a nitrogen fixation activity in plant tissues by at least 5%.

285. The composition of any one of claims 260-284, wherein composition is configured to increase and / or is capable of increasing a population of nitrogen fixing bacteria in a root and root rhizospheres of the plant by at least 5%.

286. The composition of any one of claims 260-285, wherein the composition is configured to cause and / or is capable of causing recruitment of nitrogen fixing bacteria present in a medium of the plant to a root zone of the plant.

287. The composition of any one of claims 260-286, wherein the composition is configured to cause and / or is capable of causing an increase in plant growth by at least 10 percent as compared to a control.

288. A method of promoting plant growth, comprising:(a) contacting a plant and / or medium in which the plant is growing with a composition comprising one or more compounds, wherein the one or more compounds is selected from zearalanone, dodecanal dimethyl acetal, l-[5-Ethyl-2-hydroxy-4-[[6-methyl-6-(lH-tetrazol- 5-YL)heptyl]oxy]phenyl]ethanone, N-[5-(lH-indol-3-ylmethyl)-l,3,4-thiadiazol-2-yl]-4- methoxybenzamide, trandolaprilat, lythidathion, chrysanthetriol, a derivative thereof, or a combination thereof.

289. The method of claim 288, wherein the contacting increases phosphate solubilization in the plant growth medium.

290. The method of claim 288 or 289, wherein the concentration of the one or more compound in the composition is at least about 1 nM.

291. The method of any one of claims 288-290, wherein the concentration of the one or more compounds in the composition is at least about 0.00001% of a total dry weight of the composition.

292. The method of any one of claims 288-291, wherein the contacting comprises contacting the plant with the composition.

293. The method of any one of claims 288-292, wherein the contracting comprises contacting a plant seed with the composition.

294. The method of any one of claims 288-293, wherein the contacting comprises contacting a leaf of the plant with the composition.

295. The method of any one of claims 288-294, wherein the medium comprises soil, a hydroponic medium, turface, or isolite.

296. A composition for promoting plant growth, comprising:(a) at least one microbial strain selected from one or more of Lewinella coharens, Thauera phenylacetica, Thauera mechernichensis. Solitalea canadensis, and Nitrospira moscoviensis and(b) one or more compounds selected from zearalanone, dodecanal dimethyl acetal, l-[5- Ethyl-2-hydroxy-4-[[6-methyl-6-(lH-tetrazol-5-YL)heptyl]oxy]phenyl]ethanone, N-[5- (lH-indol-3-ylmethyl)-l,3,4-thiadiazol-2-yl]-4-methoxybenzamide, trandolaprilat, lythidathion, chrysanthetriol, oxalacetic acid, l-Oleoyl-2-palmitoyl-sn-glycero-3- phosphocholine, Undeca-2-ene-8,10-diynoic acid isobutylamide, ent-Corey PG-Lactone Diol or a derivative thereof, or a combination thereof.

297. The composition of claim 296, wherein the concentration of the one or more compound in the composition is at least about 1 nM.

298. The composition of claim 296 or 297, wherein the concentration of the one or more compounds in the composition is at least about 0.00001% of a total dry weight of the composition.

299. The composition of any one of claims 296-298, wherein of oxalacetic acid, l-Oleoyl-2- palmitoyl-sn-glycero-3-phosphocholine, Undeca-2-ene-8,10-diynoic acid isobutylamide, and ent-Corey PG-Lactone Diol, oxalacetic acid is the most abundant and ent-Corey PG- Lactone Diol is the least abundant.

300. The composition of claim 299, wherein l-Oleoyl-2-palmitoyl-sn-glycero-3 -phosphocholine is present at a concentration of l%-2% of the concentration of oxalacetic acid.

301. The composition of claim 299, wherein Undeca-2-ene-8,10-diynoic acid isobutylamide is present at a concentration of l%-2% of the concentration of oxalacetic acid.

302. The composition of claim 299, wherein ent-Corey PG-Lactone Diol is present at a concentration of 0.5%-l .5% of the concentration of oxalacetic acid.

303. The composition of any one of claims 296-302, further comprising a carrier.

304. The composition of claim 303, wherein the carrier is formulated for application to a plant and / or medium in which the plant is growing.

305. A composition for promoting plant growth, comprising:(a) two or more of zearalanone, dodecanal dimethyl acetal, l-[5-Ethyl-2-hydroxy-4-[[6- methyl-6-(lH-tetrazol-5-YL)heptyl]oxy]phenyl]ethanone, N-[5-(lH-indol-3-ylmethyl)- l,3,4-thiadiazol-2-yl]-4-methoxybenzamide, trandolaprilat, lythidathion, chrysanthetriol, oxalacetic acid, l-Oleoyl-2-palmitoyl-sn-glycero-3 -phosphocholine, Undeca-2-ene-8,10- diynoic acid isobutylamide, ent-Corey PG-Lactone Diol, a derivative thereof, or a combination thereof; and(b) a carrier.

306. The composition of claim 305, wherein the carrier is formulated for application to a plant and / or medium in which the plant is growing.

307. The composition of claim 305 or 306, wherein the carrier comprises a fertilizer.

308. The composition of claim 307, wherein the fertilizer is a solid.

309. The composition of any one of claims 305-308, wherein the carrier is a liquid.

310. The composition of any one of claims 296-309, wherein the composition is configured to and / or is capable of promoting phosphate solubilization when applied to a plant or a plant growth medium.

311. The composition of any one of claims 305-309, wherein of oxalacetic acid, l-Oleoyl-2- palmitoyl-sn-glycero-3-phosphocholine, Undeca-2-ene-8,10-diynoic acid isobutylamide, and ent-Corey PG-Lactone Diol, oxalacetic acid is the most abundant and l-Oleoyl-2- palmitoyl-sn-glycero-3-phosphocholine is the least abundant.

312. The composition of claim 311, wherein l-Oleoyl-2-palmitoyl-sn-glycero-3 -phosphocholine is present at a concentration of l%-2% of the concentration of oxalacetic acid.

313. The composition of claim 311, wherein Undeca-2-ene-8,10-diynoic acid isobutylamide is present at a concentration of 8%-12% of the concentration oxalacetic acid.

314. The composition of claim 311, wherein ent-Corey PG-Lactone Diol is present at a concentration of 8%-12%of the concentration oxalacetic acid.

315. The composition of any one of claims 296-314, wherein the concentration of the one or more compounds in the composition is at least about 1 nM.

316. The composition of any one of claims 296-315, wherein the concentration of the one or more compounds in the composition is at least about 0.00001% of the total dry weight of the composition.

317. The composition of any one of claims 296-316, wherein the composition further comprises an adjuvant selected from a wetting agent, spreading agent, dispersing agent, sticking agent, dust control agent, and adhesive.

318. The composition of any one of claims 296-317, wherein the composition is configured to increase and / or is capable of increasing phosphate solubilization in a plant growth medium.

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