Systems, methods, and compositions for promoting plant health and disease resistance

Abstract

The present disclosure provides methods and systems for production of compositions that promote biocontrol properties in plants. The biocontrol properties can include treatment against plant disease or resistance to one or more plant pathogens. Embodiments described herein include methods of making a product in a bioreactor system with one or more containers. The bioreactor system can include a microbial biocontrol agent. The method can include operating a multistage bioreactor system by transferring into the system an aqueous feedstock that comprises a microbial consortium, transferring working fluid between containers of the system, and collecting a product. The method can further include enriching microbes of the working fluid with biocontrol properties.

Description

WSGR Docket No. 63472-722.601SYSTEMS, METHODS, AND COMPOSITIONS FOR PROMOTING PLANT HEALTH AND DISEASE RESISTANCECROSS-REFERENCE

[0001] This application claims the benefit of U. S. Provisional Application No. 63 / 737,534, filed on December 20, 2024, which is incorporated herein by reference in its entirety.BACKGROUND

[0002] The disclosure is generally related to compositions and methods of using such compositions to promote plant growth and enhancing resistance to plant pathogens.

[0003] 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 compositions that use abundant and available organic feedstocks.SUMMARY

[0004] In some aspects, provided herein is a method of treating a disease of a plant or promoting resistance to a disease of a plant, the method comprising: (a) contacting a plant and / or a growth medium in which the plant is growing with a composition comprising one or more compounds, wherein the one or more compounds is selected from the group consisting of Oleanolic acid, Myo-inositol, N-Heptadecanol-1, 1-(Trimethylsilyl)cyclopropyl phenyl sulfide, Vitexicarpin, 1,3 -Benzenedicarboxylic acid, 5-(l,l-dimethylethyl)-, 1 -tridecanethiol, Trans-p-Dimethylaminocinnamonitrile, Stigmasteryl trimethylsilyl ether, Pentadecane, Methyl 5-methyl-3-keto-4-hexenoate, l,l-Dichloro-l-sila-2,3-benzo-4,5-thiophenocyclopentadiene, Cis-4-octene, 7-hydroxy cholesterol, 25-Methyl-21-tritriacontene-l,9,l 1-triol, Fosfomycin calcium, 2-chloroethanol, 2-Pyridyl hydroxymethane sulfonic acid, 4-(2,4-Dichlorophenoxy)butanoic acid, 1-deoxynojirimycin, l,2-Diarachidoyl-sn-glycero-3-phosphocholine, 2,3,6-Trichlorobenzoic acid, L-serine, 3-methoxytyramine, 5-(4-Chloro-3-hydroxy-l-butynyl)-2,2'-bithiophene, 27-norcholestanehexol, Dehydroabietamide, 2,4-dihydroxybenzophenone, 5 -Nonadecyl- 1,3-benzenediol, Tiformin, Benzamide, N-(5-chloro-2-pyridinyl)-3-(trifluoromethyl)-, Isoduartin methyl ether, 4-Bromo-l-((2-bromophenyl)sulfonyl)-lH-pyrazole, (3ar,4R,5R,6as)-5-Hydroxy-4-((S, E)-3-hydroxyoct- 1 -en- 1 -yl)hexahydro-2H-cyclopenta[b]furan-2-one, Ampiroxicam, 3 -(2,3 - Dihydroxyphenyl)propanoic acid, 1 -phenylpiperazine, 3-Oxazolidinecarboxylic acid, 2,2-dimethyl-4-(l-oxo-2-hexadecyn-l-yl)-, 1,1 -dimethylethyl ester, (4S)-, Trenbolone acetate, Methyl thieno[3,2-d]thiadiazole-6-carboxylate, N-(2,2,2-trifluoroethyl)morpholine-4-carbothioamide, Butonate, 3,5-dinitrocatechol, 9-aminoacridine, Pyridinoline, Xanthotoxol, Gramine(l+), Lanosol,WSGR Docket No. 63472-722.601PG(22:6(4z,7z,10z, 13z, 16z, 19z) / 20:2(l Iz, 14z)), 2-deoxystreptamine, (4-Chloro-3-nitro-benzoylamino)-acetic acid, Pentedrone, (S)-10,16-Dihydroxyhexadecanoic acid, 2-Amino-3-[4-hydroxy-3-(3-methylbut-2-enyl)phenyl]propanoic acid, (2S,4S)-l-Acetoxy-16-heptadecene-2,4-diol, Flutamide, 2-Aminobenzoic acid, Psilocin, (R)-2-Hydroxysterculic acid, Tg(16:0 / 16:0 / 16: l(9z)), 2-hydroxy-3-({3-[3-methoxy-4-(sulfooxy )phenyl]prop-2 -enoyl }oxy)butanedioic acid, Dimethyl adipate, Ps(22:6(4z,7z,10z,13z,16z,19z) / 20:4(5z,8z,l lz,14z)), Thr-tyr-glu, Pro-phe-lys, Ubiquinone-1, Methoxydihydrosorgoleone, (6S,8Z)-6-Hydroxy-3-oxotetradecenoic acid, (9z)-N-[(2s,3r,4e)-l-(Beta-D-Glucopyranosyloxy)-3-Hydroxyoctadec-4-En-2-Yl]octadec-9-Enamide, D-Glucono-l,5-lactone 6-phosphate, Hexadecanedioic acid, 6k-PGFld4, Brefeldin A, Nifenazone, Anethole, Alpha-Mangostin, Karbutilate, L-Asparaginyl-L-lysine, 4-Hydroxy-3-methoxybenzenemethanol, (1R,2R,3R,4R)-1-[(R)-1,5-Dimethyl-l-hydroxy-4-hexenyl]-4-methylcyclohexane-l,2,3,4-tetrol, 2,3',4,5'-tetramethoxystilbene, N4-(N-acetylaminopropyl)spermidine, Maltose, Ethion, 2,3,5-Triiodobenzoic acid, Isonicotinylglycine, (R*, S*)-4-[l-Ethyl-2-(4-fluorophenyl)butyl]phenol, 2,3 -bisphosphogly cerate, 2',5'-Dichlorobiphenyl-3-ol, Artemisinin, Lys-tyr-gln-glu-ala, Prometon, Shogaol, Rolipram, Bis(2,3-dihydroxypropyl) phosphate, 4-Hydroxy-2-oxoglutaric acid, Mesulfenfos, 3 -Sulfobenzoic acid, Athidathion, Novaluron, 5-Bromo-7-methoxy-l-benzofuran-2-carboxylic acid, 4-(Hydroxymethyl)-2-iodo-6-methoxyphenol, 5-(3',4’,5'-Trihydroxyphenyl)-gamma-valerolactone-4'-O-sulphate, [Trpll] neurotensin (8-13), Dibutyl phthalate, Cavipetin C, Monobutyl phthalate, Lys-gly-his, Disulfoton sulfone, 3 -Formylsalicylic acid, Dxtp, Hco3-, Sodium sulfate, 13-docosenamide, 6-acetoxydihydrotheaspirane, His-ala-gly, N-(5 -methyl- 1,3 -thiazol-2-yl)-2-(phenylsulfanyl)acetamide, 8, 8-Diethoxy-2,6-dimethyl-2 -octanol, 13,14-dihydro-15-keto-tetranor Prostaglandin E2, 1-Deoxyvaleric-acid, 2-Propyl-2-pentenoic acid, 6,8a-Seco-6,8a-deoxy-5-oxoavermectin"lb" aglycone, L-Tyrosyl-L-serine, Ciclopirox, 1 -ethenyl -4-methoxy-benzene, 5-Chloro-6-hydroxy-2-oxohexa-3,5-dienoic acid, Desalkyl verapamil D617, N-(Tetradecanoyl)-sphing-4-enine, 3,4,5-trihydroxy-6-({8-hydroxy-2-oxo-2H-furo[2,3-h]chromen-4-yl}oxy)oxane-2-carboxylic acid, Vitamin E, Phosphoadenosine phosphosulfate, Permethrin, Kenpaullone, Andrographolide, Neopikromycin, 0,0-Diethyl hydrogen thiophosphate, Naringenin chaicone, Tris(2-chloroethyl) phosphate, Trimetazidine, 9.10-epome, 6-(2-Prop-2-ynoxyphenyl)hexanoic acid, Imperialine, 2,2,6,6-Tetramethyl-l,3-dithiane-4-thione, Ethyl 2-cyano-3-(lh-indol-3-yl)prop-2-enoate, 17alpha-Estradiol, [(6S,7S, 10R)-4, 10,11,11-tetramethyl-3-oxo-6-tricyclo[5.3.1.01,5]undec-4-enyl] acetate, Monoisobutyl phthalate, Tris(2-butoxyethyl) phosphate, l-(2-Bromophenyl)-3-(2-hydroxy-4-nitrophenyl)urea, Arg-pro-thr, Met-pro-tyr, 4-Hydroxyphenyl thiocyanate, 2-Amino-3-chloro-5 -nitrobenzotrifluoride, Phosphoric acid, Fenethylline, Pc(20:5(5z,8z,llz,14z,17z) / 18:4(6z,9z,12z,15z)), Thr-arg-gly, Heliocide H4, 2,4-diacetylphloroglucinol, N-[(R)-4-phosphopantothenoyl]-L-cysteine, 5,7-Dichlorokynurenic acid, Octyl-beta-d-glucopyranoside, 9.11 -methane -epoxy Prostaglandin fl alpha, Betulinic acid, 2, 2, 4-Trimethyl- 1,3 -pentanediol diisobutyrate, 4,4'-Diaponeurosporen-4-al, Methyl (E,2R)-2-hydroxytritriacont-7-enoate, 3abeta,4,5,5a,6,7,8,9,9aalpha,9bbeta-Decahydro-8beta,9alpha-dihydroxy-3alpha,5abeta,9-trimethylnaphtho[l,2-b]furan-2(3H)-one, 3-Methoxy-4-methyldotriacontane-9,l 1-diol, GlycolithocholicWSGR Docket No. 63472-722.601acid, Val-gln-ile-asp, 5-hydroxyemedastine, Ethiprole, Propoxur, 7,7-Dimethyl-(5Z,8Z)-eicosadienoic acid, -octene, or any combination thereof.

[0005] In some aspects, provided herein is a method of treating a disease of a plant or promoting resistance to a disease of a plant, the method comprising: (a) contacting a plant and / or a growth medium in which the plant is growing with a composition comprising one or more compounds, wherein the one or more compounds is selected from the group consisting of DG(20:5(5Z,8Z, IIZ, I4Z, I7Z) / 22:6(4Z,7Z, I0Z, I3Z, I6Z, I9Z) / 0:0), Methylparaben, alpha-Neo-Endorphin (1-7), l-(2-Fluorophenyl)-3-(pyridin-4-ylmethyl)urea, (2S,3R)-4-methylidene-2-octyl-5-oxooxolane-3 -carboxylic acid, Epsilon-caprolactam, Pyruvic Acid, Tyrosol, 16,16-dimethyl-6-keto Prostaglandin El, Todralazine, Crufomate, Methyl-D-erythritol Phosphate, LPE(16: 1 / 0:0), JWH 018 4-hydroxyindole metabolite-d9, 3,7-Dihydroxy-12-oxocholanoic acid, Arachidonoyl m-Nitroaniline, Pyrazinecarboxamide, N-(piperidinomethyl)-, LPC(0-16:0 / 2:0), Carvedilol, 9-Oxo-l l-(3-pentyloxiran-2-YL)undec- 10-enoic acid, 3 -Hydroxy-2 -phenylpropyl carbamate, Phe4Cl-His-OH, Zoledronic acid, 3-Hydroxydodecanoic acid, Dichlorprop-P, Acetylthiocholine, Oxasulfuron, L-Arabitol, Octodrine, Sodium l-[2-deoxy-5-O-(hydroxyphosphinato)pentofuranosyl]-5-fluoropyrimidine-2,4(lH,3H)-dione, 15-keto Latanoprost(free acid), Arg-Gly-Tyr-Val-Tyr-Gln-Gly-Leu, Ascorbate 2-sulfate, l-pentadecanoyl-2-(9Z-tetradecenoyl)-glycero-3-phosphocholine, {[l-(6-hydroxy-7-methoxy-2-oxo-2H-chromen-8-yl)-3-methylbut-3-en-2-yl]oxy} sulfonic acid, (S)-5-oxo-2,5-dihydro-2 -furylacetic acid, Daphnetin, Sulfamonomethoxine, 8-[(2-O,4-O-Disulfo-beta-D-glucopyranuronosyl)oxy]-5,7-dihydroxy-2-(4-methoxyphenyl)-4H-l-benzopyran-4-one, 5-Hydroxyisourate, 2-Amino-5-fluoro-3 -iodopyridine, (5Z,8Z,1 lZ,14Z)-N-(3-Furanylmethyl)-5,8,l 1,14-eicosatetraenamide, Niclosamide, Tiopronin, (3E,6Z)-3,6-Nonadien-l-ol, DL-Glyceraldehyde 2-Phosphate, Desaminotyrosine, Benzenebutanoic acid, Ibutilide, 4,4'-Methylenebis(2,6-DI-tert-butylphenol), Lyso-PAF C-16-d4, Swertianin, or any combination thereof.

[0006] 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.

[0007] 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 growth medium comprises soil, a hydroponic medium, turface, or isolite.

[0008] In some embodiments, the promoting resistance to the disease of the plant comprises upregulating one or more biotic defense genes of the plant. In some embodiments, the promoting resistance to the disease of the plant comprises preventing a lesion caused by a plant pathogen or reducing a size of a lesion caused by a plant pathogen. In some embodiments, the plant pathogen is of a genera selected from the group consisting of Mycosphaerella, Colletotrichum, Puccinia, Botrytis, Fusarium, Alternaria, Blumeria, Ustilago, Melampsora, and any combination thereof. In some embodiments, the plant pathogen is of a species selected from the group consisting of Mycosphaerella graminicola, Colletotrichum spp., PucciniaWSGR Docket No. 63472-722.601spp., Botrytis cinerea, Fusarium graminearum, Fusarium oxysporum, Blumeria graminis, Ustilago maydis, Melampsora lini, and any combination thereof.

[0009] In some embodiments, the composition comprises five or more of the compounds. In some embodiments, the composition comprises ten or more of the compounds. In some embodiments, the composition comprises five or more of the compounds. In some embodiments, the composition comprises ten or more of the compounds.

[0010] 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. In some embodiments, the carrier comprises a fertilizer. In some embodiments, the fertilizer is a solid.

[0011] In some aspects, provided herein is a composition for treating a disease of a plant or promoting resistance to a disease of a plant, comprising: (i) at least one microbial strain selected from Paenibacillus ottowii strain or a Bacillus amyloliquefaciens strain; and (ii) one or more compounds selected from the group consisting of DG(20:5(5Z,8Z, I IZ, I4Z, I7Z) / 22:6(4Z,7Z, I0Z, I3Z, I6Z, I9Z) / 0:0), Methylparaben, alpha-Neo-Endorphin (1-7), I-(2-Fluorophenyl)-3-(pyridin-4-ylmethyl)urea, (2S,3R)-4-methylidene-2-octyl-5 -oxooxolane-3 -carboxylic acid, Epsilon-caprolactam, Pyruvic Acid, Tyrosol, I6, I6-dimethyl-6-keto Prostaglandin El, Todralazine, Crufomate, Methyl-D-erythritol Phosphate, LPE(16: 1 / 0:0), JWH 018 4-hydroxyindole metabolite-d9, 3,7-Dihydroxy-12-oxocholanoic acid, Arachidonoyl m-Nitroaniline, Pyrazinecarboxamide, N-(piperidinomethyl)-, LPC(0-16:0 / 2:0), Carvedilol, 9-Oxo-I I-(3-pentyloxiran-2-YL)undec- 10-enoic acid, 3 -Hydroxy-2 -phenylpropyl carbamate, Phe4Cl-His-OH, Zoledronic acid, 3-Hydroxydodecanoic acid, Dichlorprop-P, Acetylthiocholine, Oxasulfuron, L-Arabitol, Octodrine, Sodium l-[2-deoxy-5-O-(hydroxyphosphinato)pentofuranosyl]-5-fluoropyrimidine-2,4(lH,3H)-dione, 15-keto Latanoprost(free acid), Arg-Gly-Tyr-Val-Tyr-Gln-Gly-Leu, Ascorbate 2-sulfate, l-pentadecanoyl-2-(9Z-tetradecenoyl)-glycero-3-phosphocholine, {[I-(6-hydroxy-7-methoxy-2-oxo-2H-chromen-8-yl)-3-methylbut-3-en-2-yl]oxy} sulfonic acid, (S)-5-oxo-2,5-dihydro-2 -furylacetic acid, Daphnetin, Sulfamonomethoxine, 8-[(2-O,4-O-Disulfo-beta-D-glucopyranuronosyl)oxy]-5,7-dihydroxy-2-(4-methoxyphenyl)-4H-I-benzopyran-4-one, 5-Hydroxyisourate, 2-Amino-5-fluoro-3 -iodopyridine, (5Z,8Z,1 lZ,14Z)-N-(3-Furanylmethyl)-5,8,l 1,14-eicosatetraenamide, Niclosamide, Tiopronin, (3E,6Z)-3,6-Nonadien-I-ol, DL-Glyceraldehyde 2-Phosphate, Desaminotyrosine, Benzenebutanoic acid, Ibutilide, 4,4'-Methylenebis(2,6-DI-tert-butylphenol), Lyso-PAF C-16-d4, Swertianin, or any combination thereof.

[0012] In some embodiments, the Paenibacillus ottowii strain comprises one or more of the following: (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: 2; or (c) a rpoB gene sequence at least 95% identical to SEQ ID NO: 3. In some embodiments, the Bacillus amyloliquefaciens strain comprises one or more of the following: (a) a 16S rRNA gene sequence at least 95% identical to SEQ ID NO: 4; (b) a gyrB gene sequence at least 95% identical to SEQ ID NO: 5; or (c) a rpoB gene sequence at least 95% identical to SEQ ID NO: 6. In some embodiments, the Bacillus amyloliquefaciens strain comprises one or more of the following: (a) a 16S rRNA gene sequence at least 95% identical to SEQ ID NO: 7; (b) a gyrB gene sequence at least 95%WSGR Docket No. 63472-722.601identical to SEQ ID NO: 8; or (c) a rpoB gene sequence at least 95% identical to SEQ ID NO: 9. In some embodiments, the Bacillus amyloliquefaciens strain comprises 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; or (c) a rpoB gene sequence at least 95% identical to SEQ ID NO: 12. In some embodiments, the at least one microbial strain is selected from the group consisting of MS2379 (ATCC Accession No. PTA-124703), MS2697 (ATCC Accession No. PTA-124708), MS2681 (ATCC Accession No. PTA-124707), and MS2335 (ATCC Accession No. PTA-124702). In some embodiments, the composition comprises two or more microbial strains.

[0013] In some aspects, provided herein is a composition for treating a disease of a plant or promoting resistance to a disease of a plant, comprising: one or more compounds is selected from the group consisting of Oleanolic acid, Myo-inositol, N-Heptadecanol-1, l-(Trimethylsilyl)cyclopropyl phenyl sulfide, Vitexicarpin, 1,3 -Benzenedicarboxy lie acid, 5 -(1,1 -dimethylethyl)-, 1 -tridecanethiol, Trans-p-Dimethylaminocinnamonitrile, Stigmasteryl trimethylsilyl ether, Pentadecane, Methyl 5-methyl-3-keto-4-hexenoate, l,l-Dichloro-l-sila-2,3-benzo-4,5-thiophenocyclopentadiene, Cis-4-octene, 7-hydroxycholesterol, 25-Methyl-21-tritriacontene-l,9,ll-triol, Fosfomycin calcium, 2-chloroethanol, 2-Pyridyl hydroxymethane sulfonic acid, 4-(2,4-Dichlorophenoxy)butanoic acid, I-deoxynojirimycin, 1,2-Diarachidoyl-sn-glycero-3-phosphocholine, 2,3,6-Trichlorobenzoic acid, L-serine, 3-methoxytyramine, 5-(4-Chloro-3 -hydroxy- 1 -butynyl)-2,2'-bithiophene, 27-norcholestanehexol, Dehydroabietamide, 2,4-dihydroxybenzophenone, 5-Nonadecyl-l,3-benzenediol, Tiformin, Benzamide, N-(5-chloro-2-pyridinyl)-3 -(trifluoromethyl)-, Isoduartin methyl ether, 4-Bromo-l-((2-bromophenyl)sulfonyl)-lH-pyrazole, (3ar,4R,5R,6as)-5-Hydroxy-4-((S, E)-3-hydroxyoct-l-en-l-yl)hexahydro-2H-cyclopenta[b]furan-2-one, Ampiroxicam, 3-(2,3-Dihydroxyphenyl)propanoic acid, 1 -phenylpiperazine, 3-Oxazolidinecarboxylic acid, 2,2-dimethyl-4-( I -oxo-2 -hexadecyn-I-yl)-, 1,1 -dimethylethyl ester, (4S)-, Trenbolone acetate, Methyl thieno[3,2-d]thiadiazole-6-carboxylate, N-(2,2,2-trifluoroethyl)morpholine-4-carbothioamide, Butonate, 3, 5 -dinitrocatechol, 9-aminoacridine, Pyridinoline, Xanthotoxol, Gramine(I+), Lanosol, PG(22:6(4z,7z, I0z, I3z, I6z, I9z) / 20:2(I Iz, 14z)), 2-deoxystreptamine, (4-Chloro-3-nitro-benzoylamino)-acetic acid, Pentedrone, (S)-I0, I6-Dihydroxyhexadecanoic acid, 2-Amino-3-[4-hydroxy-3-(3-methylbut-2-enyl)phenyl]propanoic acid, (2S,4S)-l-Acetoxy-16-heptadecene-2,4-diol, Flutamide, 2-Aminobenzoic acid, Psilocin, (R)-2-Hydroxysterculic acid, Tg(16:0 / 16:0 / 16: l(9z)), 2-hydroxy-3-({3-[3-methoxy-4-(sulfooxy )phenyl]prop-2 -enoyl }oxy)butanedioic acid, Dimethyl adipate, Ps(22:6(4z,7z, I0z, I3z, I6z, I9z) / 20:4(5z,8z, I Iz, I4z)), Thr-tyr-glu, Pro-phe-lys, Ubiquinone-1, Methoxydihydrosorgoleone, (6S,8Z)-6-Hydroxy-3-oxotetradecenoic acid, (9z)-N-[(2s,3r,4e)-l-(Beta-D-Glucopyranosyloxy)-3-Hydroxyoctadec-4-En-2-Yl]octadec-9-Enamide, D-Glucono-l,5-lactone 6-phosphate, Hexadecanedioic acid, 6k-PGFld4, Brefeldin A, Nifenazone, Anethole, Alpha-Mangostin, Karbutilate, L-Asparaginyl-L-lysine, 4-Hydroxy-3-methoxybenzenemethanol, (IR,2R,3R,4R)-I-[(R)-I,5-Dimethyl-I-hydroxy-4-hexenyl]-4-methylcyclohexane-I,2,3,4-tetrol, 2,3',4,5'-tetramethoxystilbene, N4-(N-acetylaminopropyl)spermidine, Maltose, Ethion, 2,3,5-Triiodobenzoic acid, Isonicotinylglycine,WSGR Docket No. 63472-722.601(R*, S*)-4-[l-Ethyl-2-(4-fluorophenyl)butyl]phenol, 2,3 -bisphosphogly cerate, 2',5'-Dichlorobiphenyl-3-ol, Artemisinin, Lys-tyr-gln-glu-ala, Prometon, Shogaol, Rolipram, Bis(2,3-dihydroxypropyl) phosphate, 4-Hydroxy-2-oxoglutaric acid, Mesulfenfos, 3 -Sulfobenzoic acid, Athidathion, Novaluron, 5-Bromo-7-methoxy-l-benzofuran-2-carboxylic acid, 4-(Hydroxymethyl)-2-iodo-6-methoxyphenol, 5-(3',4’,5'-Trihydroxyphenyl)-gamma-valerolactone-4'-O-sulphate, [Trpll] neurotensin (8-13), Dibutyl phthalate, Cavipetin C, Monobutyl phthalate, Lys-gly-his, Disulfoton sulfone, 3 -Formylsalicylic acid, Dxtp, Hco3-, Sodium sulfate, 13-docosenamide, 6-acetoxydihydrotheaspirane, His-ala-gly, N-(5 -methyl- 1,3 -thiazol-2-yl)-2-(phenylsulfanyl)acetamide, 8, 8-Diethoxy-2,6-dimethyl-2 -octanol, 13,14-dihydro-15-keto-tetranor Prostaglandin E2, 1-Deoxyvaleric-acid, 2-Propyl-2-pentenoic acid, 6,8a-Seco-6,8a-deoxy-5-oxoavermectin"lb" aglycone, L-Tyrosyl-L-serine, Ciclopirox, 1 -ethenyl -4-methoxy-benzene, 5-Chloro-6-hydroxy-2-oxohexa-3,5-dienoic acid, Desalkyl verapamil D617, N-(Tetradecanoyl)-sphing-4-enine, 3,4,5-trihydroxy-6-({8-hydroxy-2-oxo-2H-furo[2,3-h]chromen-4-yl}oxy)oxane-2-carboxylic acid, Vitamin E, Phosphoadenosine phosphosulfate, Permethrin, Kenpaullone, Andrographolide, Neopikromycin, 0,0-Diethyl hydrogen thiophosphate, Naringenin chaicone, Tris(2-chloroethyl) phosphate, Trimetazidine, 9.10-epome, 6-(2-Prop-2-ynoxyphenyl)hexanoic acid, Imperialine, 2,2,6,6-Tetramethyl-l,3-dithiane-4-thione, Ethyl 2-cyano-3-(lh-indol-3-yl)prop-2-enoate, 17alpha-Estradiol, [(6S,7S, 10R)-4, 10,11,11-tetramethyl-3-oxo-6-tricyclo[5.3.1.01,5]undec-4-enyl] acetate, Monoisobutyl phthalate, Tris(2-butoxyethyl) phosphate, l-(2-Bromophenyl)-3-(2-hydroxy-4-nitrophenyl)urea, Arg-pro-thr, Met-pro-tyr, 4-Hydroxyphenyl thiocyanate, 2-Amino-3-chloro-5 -nitrobenzotrifluoride, Phosphoric acid, Fenethylline, Pc(20:5(5z,8z,llz,14z,17z) / 18:4(6z,9z,12z,15z)), Thr-arg-gly, Heliocide H4, 2,4-diacetylphloroglucinol, N-[(R)-4-phosphopantothenoyl]-L-cysteine, 5,7-Dichlorokynurenic acid, Octyl-beta-d-glucopyranoside, 9.11 -methane -epoxy Prostaglandin fl alpha, Betulinic acid, 2, 2, 4-Trimethyl- 1,3 -pentanediol diisobutyrate, 4,4'-Diaponeurosporen-4-al, Methyl (E,2R)-2-hydroxytritriacont-7-enoate, 3abeta,4,5,5a,6,7,8,9,9aalpha,9bbeta-Decahydro-8beta,9alpha-dihydroxy-3alpha,5abeta,9-trimethylnaphtho[l,2-b]furan-2(3H)-one, 3-Methoxy-4-methyldotriacontane-9,l 1-diol, Glycolithocholic acid, Val-gln-ile-asp, 5-hydroxyemedastine, Ethiprole, Propoxur, 7,7-Dimethyl-(5Z,8Z)-eicosadienoic acid, -octene, or any combination thereof.

[0014] 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. In some embodiments, the carrier comprises a fertilizer. In some embodiments, the fertilizer is a solid. In some embodiments, the carrier is a liquid.

[0015] In some embodiments, the composition is configured to prevent a lesion caused by a plant pathogen or reduce a size of a lesion caused by a plant pathogen. In some embodiments, the plant pathogen is of a genera selected from the group consisting of Mycosphaerella, Colletotrichum, Puccinia, Botrytis, Fusarium, Alternaria, Blumeria, Ustilago, Melampsora, and any combination thereof. In some embodiments, the plant pathogen is of a species selected from the group consisting of Mycosphaerella graminicola, Colletotrichum spp., Puccinia spp., Botrytis cinerea, Fusarium graminearum, FusariumWSGR Docket No. 63472-722.601oxysporum, Blumeria graminis, Ustilago maydis, Melampsora lini, and any combination thereof. 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.

[0016] In some aspects, provided herein is a method of making a product having an enriched population of a microbial biocontrol agent, the method comprising: (a) providing a bioreactor system comprising two or more containers, wherein the two or more containers comprise a working fluid and the microbial biocontrol agent; and (b) collecting the product from the bioreactor system, wherein, relative to a total bacterial population, the product has a greater proportion of the microbial biocontrol agent relative to a proportion of the microbial biocontrol agent in at least one of the two or more containers.

[0017] In some embodiments, the microbial biocontrol agent is a cellulase -active bacteria. In some embodiments, the product has a greater relative abundance of one or more enzymes associated with biocontrol activity relative to a relative abundance of the one or more enzymes associated with biocontrol activity in at least one of the two or more containers. In some embodiments, the one or more enzymes associated with biocontrol activity comprise a cellulase, a glucanase, a chitinase, a protease, a xylanase, an amylase, or a lipase.

[0018] In some embodiments, the product has a greater proportion of the microbial biocontrol agent relative to a proportion of the microbial biocontrol agent in a first container of the bioreactor system. In some embodiments, the product has a greater proportion of the microbial biocontrol agent relative to a proportion of the microbial biocontrol agent in at least two of the two or more containers.

[0019] In some embodiments, the one or more containers of the bioreactor system comprise an aqueous feedstock comprising a microbial consortium. In some embodiments, the aqueous feedstock comprises an organic substrate. In some embodiments, the organic substrate comprises seaweed, manure, or any combination thereof. In some embodiments, the organic substrate comprises seaweed. In some embodiments, the seaweed comprises kelp. In some embodiments, the kelp is of the genus Ascophyllum. In some embodiments, the kelp is of the species Ascophyllum nodosum. In some embodiments, the bioreactor system comprises chitin. In some embodiments, the bioreactor system comprises yeast. In some embodiments, the bioreactor system comprises a bacterial growth medium. In some embodiments, the bacterial growth medium comprises rice flour, sucrose, soy flour, bran, micronutrients, or any combination thereof.

[0020] In some embodiments, the bioreactor system comprises at least six containers. In some embodiments, the two or more containers comprise fluidized bed reactors. In some embodiments, the bioreactor system comprises a manifold air system, wherein the method further comprises continuously supplying air to the one or more second stage containers using the manifold air system. In some embodiments, the product comprises one or more microbial metabolites.

[0021] In some embodiments, the product is configured to (i) promote resistance of a plant disease or a plant pathogen and / or (ii) treat a plant disease or a plant pathogen. In some embodiments, the plant pathogen is of a genera selected from the group consisting of Mycosphaerella, Colletotrichum, Puccinia,WSGR Docket No. 63472-722.601Botrytis, Fusarium, Alternaria, Blumeria, Ustilago, Melampsora, and any combination thereof. In some embodiments, the plant pathogen is of a species selected from the group consisting of Mycosphaerella graminicola, Colletotrichum spp., Puccinia spp., Botrytis cinerea, Fusarium graminearum, Fusarium oxysporum, Blumeria graminis, Ustilago maydis, Melampsora lini, and any combination thereof.INCORPORATION BY REFERENCE

[0022] 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. To the extent publications and patents or patent applications incorporated by reference contradict the disclosure contained in the specification, the specification is intended to supersede and / or take precedence over any such contradictory material.BRIEF DESCRIPTION OF THE DRAWINGS

[0023] The novel features of the disclosure are set forth with particularity in the appended claims. A better understanding of the features and the 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:

[0024] FIG. 1 shows an exemplary schematic of a bioreactor system described herein. The biocontrol bioreactor system (BCX system) shows multiple stages and a series of containers.

[0025] FIG. 2 shows a schematic of the process of the working fluid in a BCX system described herein.

[0026] FIG. 3 shows results of an in vitro antibiosis against Botrytis observed from BCX-2.1 systems (300) and BCX 2.2 systems (310).

[0027] FIG. 4 shows results of an in vitro antibiosis against Botrytis observed from BCX 2.3 systems (400) and BCX 2.4 systems (410).

[0028] FIG. 5 shows results of the detached leaf antibiosis assay with treatments applied in-furrow at a rate of 2 quart / acre (qt / A). The graph depicts results across test from intact base product and filter-sterilized product (metabolites) of BCX system samples. Filter-sterilized product solution from the BCX 2.4 system reduced Botrytis cinerea lesion size (mm) compared to the negative water control after 5 days at 2 qt. / A rate.

[0029] FIG. 6 shows the chlorophyll content of leaves treated with intact and filter-sterilized product of the BCX systems described herein following the in-furrow long term assay. Chlorophyll content was compared with untreated water control (UTC). Leaves treated with filter-sterilized product solution from the BCX-2.4 system had significantly greater leaf chlorophyll contents compared to those from negative water control after 5 days at 2 qt. / A rate.WSGR Docket No. 63472-722.601

[0030] FIG. 7 shows the temperature of leaves treated with intact and filter-sterilized product of the BCX systems described herein. Temperature was evaluated as the change relative to untreated water control (UTC). Leaves treated with filter-sterilized product solution from the BCX -2.4 system had significantly lowest leaf temperature compared to the negative water control after 5 days at 4 qt. / A rate.

[0031] FIG. 8 shows results of the detached leaf antibiosis assay with treatments applied in-furrow at a rate of 2 quart / acre (qt / A). The graph depicts results across test from intact base product and filter-sterilized product (metabolites) of BCX system samples. Filter-sterilized product solutions from the BCX 2.2 system and BCX 2.4 system reduced Botrytis cinerea lesion size (mm) compared to the negative water control after 5 days at 2 qt. / A rate.

[0032] FIGs. 9A-9B show photographs with visual results of the antibiosis assay of FIG. 8. FIG. 9A shows comparison of a single leaf from UTC condition, a single leaf from BCX 2.1 system intact solution, a single leaf from BCX 2.1 system filter-sterilized solution, a single leaf from BCX 2.2 system intact solution, and a single leaf from BCX 2.2 system filter-sterilized solution. FIG. 9B shows comparison of a single leaf from UTC, a single leaf from BCX 2.3 system intact solution, a single leaf from BCX 2.3 system filter-sterilized solution, a single leaf from BCX 2.4 system intact solution, and a single leaf from BCX 2.4 system filter-sterilized solution.

[0033] FIG. 10 shows the chlorophyll content of leaves treated with intact and filter-sterilized product of the BCX systems described herein. Chlorophyll content was compared with untreated water control (UTC). Leaves treated with intact solutions from BCX-2.4 system had significantly greater leaf chlorophyll contents compared to the negative water control after 5 days at 2 qt. / A rate.

[0034] FIG. 11 shows the temperature of leaves treated with intact and filter-sterilized product of the BCX systems described herein. Temperature was evaluated as the change relative to untreated water control (UTC). Leaves treated with intact product solution from the BCX-2.4 system had significantly lowest leaf temperature compared to the negative water control after 5 days at 2 qt. / A rate.

[0035] FIGs. 12A-12C show isolate retention over time in the base product (BP) and floc, measured as isolate concentration in colony-forming units per ml (cfu / ml). FIG. 12A shows results for MS2379, from BCX 2.2 system. The photograph shows heated counts of the target isolate MS2379, with the black circles indicating presence of the isolate in the dish. FIG. 12B shows results for MS2697, from BCX 2.3 system. The photograph shows heated counts of the target isolate MS2697, with the black circles indicating presence of the isolate in the dish. FIG. 12C shows results for MS2335, from BCX 2.4 system. The photograph shows heated counts of the target isolate MS2335, with the black circles indicating presence of the isolate in the dish.

[0036] FIG. 13 shows a graph depicting the plant growth production of Arabidopsis (measured in average leaf area, cm2) for across UTC and samples from BCX systems. The leaf area of Arabidopsis was measured for intact and filter-sterilized product solutions of the BCX systems described herein.

[0037] FIG. 14 shows results of a detached leaf assay examining effects of different feedstocks on biocontrol efficacy. The assay was an in situ detached soybean leaf assay against Botrytis cinerea. TheWSGR Docket No. 63472-722.601conditions were the following: A, processed manure-based solution with isolate MS2379 added; B, processed manure-based solution with no isolate; C, processed kelp solution with MS2379 added; D, processed kelp solution with no isolate; E, processed manure-based solution with rock phosphate and isolate MS2379 added; and F, processed manure-based solution with rock phosphate and no isolate added.

[0038] FIG. 15 shows results of a detached leaf assay examining effects of different feedstocks on biocontrol efficacy. The assay was an in situ detached soybean leaf assay against Botrytis cinerea. The treatment conditions were the same as those in FIG. 14.

[0039] FIG. 16 shows results of a detached leaf assay examining effects of multiple isolates on biocontrol efficacy. The assay was an in situ detached soybean leaf assay against Botrytis cinerea. The conditions were the following: Al, processed kelp solution with isolates MS2335 and MS2697; A2, processed kelp solution with isolates MS2335 and MS2697; Bl, processed kelp solution with isolates MS2335 and MS2681; B2, processed kelp solution with isolates MS2335 andMS2681; Cl, processed kelp solution with isolates MS2697 and MS2681; and C2, processed kelp solution with isolates MS2697 and MS2681.

[0040] FIGs. 17A-17C show results of the chemical characterization of the shake flask solutions. FIG.17A shows the chromatogram for Sample A, comprising processed kelp solution with isolates MS2335 and MS2697. The chromatogram depicts overlapped ESI-MS / MS chromatograms of sample A inoculated with MS2335 and MS2697 extracted from shake flask solutions in different time periods (Front to end: Al -Day 0, Al - Day 0, Al - Day 3, A2-Day 3, Al -Day 7, A2- Day 7). FIG. 17B shows the chromatogram for Sample B, comprising processed kelp solution with isolates MS2335 and MS2681. The chromatogram depicts overlapped ESI-MS / MS chromatograms of sample B inoculated with MS2335 and MS2681 extracted from shake flask solutions at different time periods (Front to end: Bl -Day 0, B2- Day 0, Bl - Day 3, B2-Day 3, Bl-Day 7, B2- Day 7). FIG. 17C shows the chromatogram for Sample C, comprising processed kelp solution with isolates MS2697 and MS2681. The chromatogram depicts overlapped ESI-MS / MS chromatograms of sample C inoculated with MS2681and MS2697 extracted from shake flask solutions at different time periods (Front to end: Cl-Day 0, C2- Day 0, Cl- Day 3, C2-Day 3, Cl-Day 7, C2- Day 7).

[0041] FIG. 18 shows results of a detached leaf assay examining effects of different isolates when grown in shake flasks containing Ascophyllum kelp feedstocks on biocontrol efficacy. The assay was an in situ detached soybean leaf assay against Botrytis cinerea. The conditions were the following: A, Ascophyllum Kelp with isolate MS2379 added; B, Ascophyllum Kelp with no isolate added; C, Ascophyllum Kelp with isolate MS2379 added and 1% chitin added; D, Ascophyllum Kelp with no isolate added and 1% chitin added; E, processed Ascophyllum Kelp-based solution with isolate MS2379 added; F, processed Ascophyllum Kelp-based solution with no isolate added; G, processed Ascophyllum Kelp-based solution with isolate MS2379 added and 1% chitin added; H, processed Ascophyllum Kelp-based solution with no isolate added and 1% chitin added.

[0042] FIG. 19 shows results of a detached leaf assay examining effects of different isolates when grown in shake flasks containing Ecklonia kelp feedstocks on biocontrol efficacy. The assay was an in situWSGR Docket No. 63472-722.601detached soybean leaf assay against Botrytis cinerea. The conditions were the following: A, Ecklonia Kelp with isolate MS2379 added; B, Ecklonia Kelp with no isolate added; C, Ascophyllum Kelp with isolate MS2379 added and 1% chitin added; D, Ecklonia Kelp with no isolate added and 1% chitin added; E, processed Ecklonia Kelp-based solution with isolate MS2379 added; F, processed Ecklonia Kelp-based solution with no isolate added; G, processed Ecklonia Kelp-based solution with isolate MS2379 added and 1% chitin added; H, processed Ecklonia Kelp-based solution with no isolate added and 1% chitin added.

[0043] FIG.20 shows results of a detached leaf assay to examine biocontrol against a plant pathogen. The assay was an in situ detached soybean leaf assay against Botrytis cinerea. Intact and filter-sterilized product solutions from the BCX systems described herein were applied at 1. Ox and 0. lx application rates. All BCX system treatment conditions showed lower average lesion diameter compared to that from untreated control (UTC). For each condition, the black bar indicates l. Ox application rate and the gray bar indicates O.lx application rate.

[0044] FIG.21 shows results of a detached leaf assay to examine biocontrol against a plant pathogen. The assay was an in situ detached soybean leaf assay against Botrytis cinerea. Intact and filter-sterilized product solutions from the BCX systems described herein were applied at O.lx and 0.0 lx application rates. All BCX system treatment conditions showed lower average lesion diameter compared to that from untreated control (UTC). For each condition, the black bar indicates 0. lx application rate and the gray bar indicates 0.0 lx application rate.

[0045] FIG. 22 shows the chlorophyll content of leaves treated with intact and filter-sterilized product of the BCX systems described herein at different application rates. All BCX system treatment conditions showed higher chlorophyll content (measured in SPAD unit) compared to that from untreated control (UTC). For each condition, the black bar indicates l. Ox application rate and the gray bar indicates O.lx application rate.

[0046] FIG. 23 shows the chlorophyll content of leaves treated with intact and filter-sterilized product of the BCX systems described herein at different application rates. All BCX system treatment conditions showed higher chlorophyll content (measured in SPAD unit) compared to that from untreated control (UTC). For each condition, the black bar indicates O.lx application rate and the gray bar indicates O. Olx application rate.

[0047] FIG. 24 shows the temperature of leaves treated with intact and filter-sterilized product of the BCX systems described herein at different application rates. All BCX system treatment conditions, excluding intact solution of BCX 2.1, showed greater relative change in temperature (measured in°C) relative to the measured temperature from untreated control (UTC). For each condition, the black bar indicates l. Ox application rate and the gray bar indicates O.lx application rate.

[0048] FIG. 25 shows the temperature of leaves treated with intact and filter-sterilized product of the BCX systems described herein at different application rates. All BCX system treatment conditions, excluding intact solution of BCX 2.1, showed greater relative change in temperature (measured in°C)WSGR Docket No. 63472-722.601relative to the measured temperature from untreated control (UTC). For each condition, the black bar indicates O.lx application rate and the gray bar indicates 0.0 lx application rate.

[0049] FIG. 26 shows NMDS ordination of the functional bacteria at the whole community level for the BCX reactor solutions using the PICRUST2 functional community analysis for BCX-2.1 system.

[0050] FIG. 27 shows NMDS ordination of the functional bacteria at the whole community level for the BCX reactor solutions using the PICRUST2 functional community analysis for BCX-2.2 system.

[0051] FIG. 28 shows NMDS ordination of the functional bacteria at the whole community level for the BCX reactor solutions using the PICRUST2 functional community analysis for BCX-2.3 system.

[0052] FIG. 29 shows BCX 2.3 reactor solutions in vitro antibiosis activity testing for two fungal pathogens, Botrytis and Fusarium, at 2pL and lOpL of solution, respectively. Different letters indicate treatments that are significantly different.

[0053] FIG. 30 shows BCX 2.3 reactor solutions in situ detached soybean leaf biocontrol assay against Botrytis cinerea at two rates 0.1X and 0.0 IX, respectively. Different letters indicate treatments that are significantly different.

[0054] FIG. 31 shows NMDS ordination of the functional bacteria at the whole community level for the BCX reactor solutions using the PICRUST2 functional community analysis for BCX-2.4 system.

[0055] FIG. 32 shows BCX 2.4 reactor solutions in vitro antibiosis activity testing for two fungal pathogens, Botrytis and Fusarium, at 2pL and lOpL of solution, respectively. Different letters indicate treatments that are significantly different.

[0056] FIG. 33 shows PCA of intact versions of 4 different batches of BCX lines considering the abundance of annotated chemical compounds. Comparisons were done among all 4 lines.

[0057] FIG. 34 shows PCA of filter-sterilized versions of 4 different batches of BCX lines considering the abundance of annotated chemical compounds. Comparisons were done among all 4 lines.

[0058] FIG. 35 shows LC-MS overlapped ESI-MS / MS chromatograms of BCX 2.1 line for batches 1-4 of the chemical characterization.

[0059] FIG. 36 shows LC-MS overlapped ESI-MS / MS chromatograms of BCX 2.2 line for batches 1-4 of the chemical characterization.

[0060] FIG. 37 shows LC-MS overlapped ESI-MS / MS chromatograms of BCX 2.3 line for batches 1-4 of the chemical characterization.

[0061] FIG. 38 shows LC-MS overlapped ESI-MS / MS chromatograms of BCX 2.4 line for batches 1-4 of the chemical characterization.

[0062] FIG. 39 shows PCA based on untargeted LC-MS analysis of the output of the BCX lines.

[0063] FIGs.40A-40C show PLS-DA based on untargeted LC-MS analysis comparing the outputs of the different BCX lines. FIG. 40A shows BCX 2.2 vs BCX 2.1. FIG. 40B shows BCX 2.3 vs BCX 2.1. FIG.40C shows BCX 2.4 vs BCX 2.1.

[0064] FIG. 41 shows a principal components analysis of upregulated defense genes at 2 qt / a application rate of intact treatments.WSGR Docket No. 63472-722.601

[0065] FIG. 42 shows a principal components analysis of upregulated defense genes at 2 qt / a application rate of filter sterilized treatments.

[0066] FIGs. 43A-43D show principal components analysis (PCA) across treatments. FIG. 43A shows PCA of upregulated defense genes at 2 qt / a application rate for intact treatments. FIG. 43B shows PCA of upregulated defense genes at 2 qt / a application rate for intact treatments (Int_2.3, Int_2.4) and the untreated control (UTC). FIG. 43C shows PCA of upregulated defense genes at 2 qt / a application rate for filter sterilized treatments. FIG.43D shows PCA of upregulated defense genes at 2 qt / a application rate for filter sterilized treatments.

[0067] FIG. 44 shows results of the plate wash DNA detection of target isolates. The isolates MS2379, MS2335, MS2697, and MS2681 were effectively enriched across replicates.

[0068] FIG. 45 shows results of the antibiosis in vitro assay. All treatments demonstrated activity against the tested pathogens, with efficacy varying depending on the pathogen, isolate, and application rate.

[0069] FIG.46 shows results of the in situ Detached Leaf Assay (Direct antibiosis / ISR) for intact product. All treatments showed significant biocontrol activity at both application rates (0.1X and 0.01X), with differences depending on the target isolate.

[0070] FIG.47 shows results of the in situ Detached Leaf Assay (Direct antibiosis / ISR) for filter-sterilized product. All treatments showed significant biocontrol activity at both application rates (0.1X and 0.0 IX), with differences depending on the target isolate.

[0071] FIG. 48 shows results of the ex situ ISR Detached Leaf Assay. Treatments were applied in-furrow at different application rates (Iqt / A and 4qt / A), and a detached leaf assay was conducted to evaluate the ISR response provided by these treatments against Botrytis cinerea compared to the untreated control.

[0072] FIG. 49 shows results of the detached leaf assay. There was a significant reduction in lesion size against the untreated control for most treatments.

[0073] FIG. 50 shows all treatments, intact and filter-sterilized, showed significantly greater chlorophyll content compared to the UTC.

[0074] FIG. 51 shows most BCX BP treatments, both intact and filter-sterilized, leaf temperatures were significantly lower than the control (UTC).

[0075] FIG. 52 shows some significantly different bacterial community compositions in the rhizosphere of BCX-BP treated soybean plants compared to the UTC plants. Top-left plot: Only the UTC and BCX-2.1 filter-sterilized (FS) and intact (I) treated. Top-right plot: only the UTC and BCX-2.2 FS and I treated. Bottom-left plot: only the UTC and BCX-2.3 FS and I treated. Bottom-right plot: only the UTC and BCX-2.4 FS and I treated. Soybean plants were grown in a peat-lite mix for two weeks before harvesting.

[0076] FIG. 53 shows some significantly different fungal community compositions in the rhizosphere of BCX-BP treated soybean plants compared to the UTC plants. Top-left plot: Only the UTC and BCX-2.1 filter-sterilized (FS) and intact (I) treated. Top-right plot: only the UTC and BCX-2.2 FS and I treated. Bottom-left plot: only the UTC and BCX-2.3 FS and I treated. Bottom-right plot: only the UTC and BCX-2.4 FS and I treated. Soybean plants were grown in a peat-lite mix for two weeks before harvesting.WSGR Docket No. 63472-722.601

[0077] FIG. 54 shows results of the detached leaf assay for soybean plants grown in a 9: 1 peat-lite soil potting mix. Leaves from BP treated plants from all BCX systems showed a significant lesion size reduction over the untreated control and a strong ISR response.

[0078] FIG. 55 shows all treatments, intact and filter-sterilized, showed significantly greater chlorophyll content compared to the UTC, for soybean plants grown in a 9: 1 peat-lite soil potting mix.

[0079] FIG. 56 shows most BCX BP treatments, both intact and filter-sterilized, leaf temperatures were significantly lower than the control (UTC), for soybean plants grown in a 9: 1 peat-lite soil potting mix.

[0080] FIG. 57 shows the abundance of total bacteria in the rhizosphere soil of soybean plants treated with water only (UTC) or the BCX base product (BP) intact (I) or filter-sterilized (FS) solutions. Soybean plants were grown in a 9 parts peat-lite 1 part Iowa soil mix for two weeks before harvesting.

[0081] FIG. 58 shows some significantly different bacterial community compositions in the rhizosphere of BCX-BP treated soybean plants compared to the UTC plants. Top-left plot: Only the UTC and BCX-2.1 filter-sterilized (FS) and intact (I) treated. Top-right plot: only the UTC and BCX-2.2 FS and I treated. Bottom-left plot: only the UTC and BCX-2.3 FS and I treated. Bottom-right plot: only the UTC and BCX-2.4 FS and I treated. Soybean plants were grown in a 9 parts peat-lite 1 part Iowa soil mix for two weeks before harvesting.

[0082] FIG. 59 shows some significantly different fungal community compositions in the rhizosphere of BCX-BP treated soybean plants compared to the UTC plants. Top-left plot: Only the UTC and BCX-2.1 filter-sterilized (FS) and intact (I) treated. Top-right plot: only the UTC and BCX-2.2 FS and I treated. Bottom-left plot: only the UTC and BCX-2.3 FS and I treated. Bottom-right plot: only the UTC and BCX-2.4 FS and I treated. Soybean plants were grown in a 9 parts peat-lite 1 part Iowa soil mix for two weeks before harvesting.

[0083] FIG. 60 shows bacterial diversity (Shannon’s diversity index) differences in the rhizosphere communities of BCX base product (BP) intact (I) or filter-sterilized (FS) treated soybean plants compared to the UTC plants. Soybean plants were grown in a 9 parts peat-lite 1 part Iowa soil mix for two weeks before harvesting.

[0084] FIG. 61 shows fungal diversity (Shannon’s diversity index) differences in the rhizosphere communities of BCX base product (BP) intact (I) or filter-sterilized (FS) treated soybean plants compared to the UTC plants. Soybean plants were grown in a 9 parts peat-lite 1 part Iowa soil mix for two weeks before harvesting.

[0085] FIG. 62A shows results of a detached leaf assay examining the effects of non-concentrated or 5-fold concentrated, intact or filter-sterilized, BCX-2.1 base products prepared according to PC2 BCX process on induced systemic resistance (ISR) to Botrytis cincerea, as measured by leaf lesion diameter in treatment and control groups.

[0086] FIG. 62B shows results of a detached leaf assay examining the effects of non-concentrated or 5-fold concentrated, intact or filter-sterilized, BCX-2.2 base products prepared according to the PC2 BCXWSGR Docket No. 63472-722.601on induced systemic resistance (ISR) to Botrytis cincerea, as measured by leaf lesion diameter in treatment and control groups.

[0087] FIG. 63A shows results of a detached leaf assay examining the effects of non-concentrated or 5-fold concentrated, intact or filter-sterilized, BCX-2.3 base products prepared according to the PC2 BCX process on induced systemic resistance (ISR) to Botrytis cincerea, as measured by leaf lesion diameter in treatment and control groups.

[0088] FIG. 63B shows results of a detached leaf assay examining the effects of non-concentrated or 5-fold concentrated, intact or filter-sterilized, BCX-2.4 base products prepared according to the PC2 BCX process on induced systemic resistance (ISR) to Botrytis cincerea, as measured by leaf lesion diameter in treatment and control groups.

[0089] FIG.64A shows results of an in situ detached soybean leaf assay against spread of Botrytis cinerea 4 days after inoculation with non-concentrated or 5x-concentrated, intact or filter-sterilized, BCX-2.1 and BCX-2.2 base products prepared under Process Change 2 (PC2) of a first PC2 batch, which were applied at O.lx or 0.0 lx application rates compared to UTC and negative control groups.

[0090] FIG.64B shows results of an in situ detached soybean leaf assay against spread of Botrytis cinerea 5 days after inoculation with non-concentrated or 5x-concentrated, intact or filter-sterilized, BCX-2.3 base products prepared under Process Change 2 (PC2) of a third PC2 batch, which were applied at O.lx or 0.0 lx application rates and compared to UTC and negative control groups.

[0091] FIG.64C shows results of an in situ detached soybean leaf assay against spread of Botrytis cinerea 5 days after inoculation with non-concentrated or 5x-concentrated, intact or filter-sterilized, BCX-2.4 base products prepared under Process Change 2 (PC2) of a third PC2 batch, which were applied at O.lx or 0.0 lx application rates and compared to UTC and negative control groups.

[0092] FIG.64D shows results of an in situ detached soybean leaf assay against spread of Botrytis cinerea 6 days after inoculation with 5x-concentrated or 5 Ox-concentrated, intact or filter-sterilized, base products form BCX-2.1-4 systems prepared under Process Change 2 (PC2) of the second PC2 batch (Batch 8), which were applied at 0.0 lx or 0.00 lx application rates and compared to UTC and negative control groups.

[0093] FIG.65A shows a Cohen’s d analysis of effect size of BCX base product treatment on overall crop yield of conducted field trials in soybean, cucumber, and com crops.

[0094] FIG. 65B shows a Cohen’s d analysis of effect size of BCX base product treatment on crop yield of conducted field trials in soybean, cucumber, and com crops.

[0095] FIG. 65C shows a Cohen’s d analysis of effect size of BCX base product treatment on overall disease incidence of conducted field trials in soybean, cucumber, and com crops.

[0096] FIG. 65D shows a Cohen’s d analysis of effect size of BCX base product treatment on overall disease severity of conducted field trials in soybean, cucumber, and com crops.

[0097] FIG. 65E shows a Cohen’s d analysis of effect size of BCX base product treatment on overall stand count of conducted field trials in soybean, cucumber, and com crops.WSGR Docket No. 63472-722.601

[0098] FIG. 66 shows differences in the rhizosphere bacterial communities after in-furrow treatment of com fields with intact or filter-sterilized base products of the BCX systems. FIG. 66A shows differences in the rhizosphere bacterial communities after treatment with intact or filter-sterilized base products of the BCX2.1 system compared to UTC. FIG. 66B shows differences in the rhizosphere bacterial communities after treatment with intact or filter-sterilized base products of the BCX2.2 system compared to UTC. FIG.66C shows differences in the rhizosphere bacterial communities after treatment with intact or filter-sterilized base products of the BCX2.3 system compared to UTC. FIG. 66D shows differences in the rhizosphere bacterial communities after treatment with intact or filter-sterilized base products of the BCX2.4 system compared to UTC.

[0099] FIG.67 shows differences in the rhizosphere fungal communities after in-furrow treatment of com fields with intact or filter-sterilized base products of the BCX systems. FIG. 67A shows differences in the rhizosphere fungal communities after treatment with intact or filter-sterilized base products of the BCX2.2 system compared to UTC. FIG. 67B shows differences in the rhizosphere fungal communities after treatment with intact or filter-sterilized base products of the BCX2.2 system compared to UTC. FIG. 67C shows differences in the rhizosphere fungal communities after treatment with intact or filter-sterilized base products of the BCX2.3 system compared to UTC. FIG. 67D shows differences in the rhizosphere fungal communities after treatment with intact or filter-sterilized base products of the BCX2.4 system compared to UTC.

[0100] FIG. 68A depicts a grouped quantification of the average relative abundance of enriched fungal plant growth-promoting species detected in the rhizospheres of soybean, com, and sorghum fields that were treated with intact or filter-sterilized BCX2.1-4 base products. The relative abundance represents a sum of detected plant growth-promoting fungal species with positive percentage changes compared to the UTC and meeting inclusion criteria across all four trials. Error bars represent standard deviation. Horizontal line represents the average relative abundance of the untreated control (UTC).

[0101] FIG. 68B depicts a grouped quantification of the average relative abundance of enriched fungal biocontrol species detected in the rhizospheres of soybean, com, and sorghum fields that were treated with intact or filter-sterilized BCX2.1-4 base products. The relative abundance represents a sum of detected biocontrol fungal species with positive percentage changes compared to the UTC and meeting inclusion criteria across all four trials. Error bars represent standard deviation. Horizontal line represents the average relative abundance of the untreated control (UTC).

[0102] FIG. 68C depicts a grouped quantification of the average relative abundance of enriched mycorrhizal fungal species detected in the rhizospheres of soybean, com, and sorghum fields that were treated with intact or filter-sterilized BCX2.1-4 base products. The relative abundance represents a sum of detected mycorrhizal fungal species with positive percentage changes compared to the UTC and meeting inclusion criteria across all four trials. Error bars represent standard deviation. Horizontal line represents the average relative abundance of the untreated control (UTC).WSGR Docket No. 63472-722.601

[0103] FIG. 69 depicts a grouped quantification of the average relative abundance of suppressed fungal pathogens detected in the rhizospheres of soybean, com, and sorghum fields that were treated with intact or filter-sterilized BCX2.1-4 base products. The relative abundance represents a sum of detected pathogenic fungal species with negative percentage changes compared to the UTC and meeting inclusion criteria across all four trials. Error bars represent standard deviation. Horizontal line represents the average relative abundance of the untreated control (UTC).DETAILED DESCRIPTION

[0104] Described herein are systems and methods that employ microbial digestion of various feedstocks. A system described herein can comprise a continuous system capable of serialized isolate production (e.g., sIP system). A system described herein can comprise a continuous system without serialized isolate production (e.g., non-sIP system). An isolate (e.g., target isolate) described herein can be characterized as a microbe, a bacterium, a microbial strain, or any combination thereof. The isolate production of the sIP system can occur within a mixed consortium of microbes. The isolates (e.g., target isolates) of a sIP digestion system can become enriched in the microbial environment and can demonstrate improved efficacy and functionality. For example, the isolates described herein can comprise one or more biocontrol properties. Application of one or more isolates described herein to a plant can treat a plant disease. Application of one or more isolates described herein to a plant can confer resistance to a plant disease (e.g., protect against future infection by a plant pathogen).

[0105] The main targeted functionality can be biocontrol efficacy in plants. A target isolate can possess commercially valuable properties and can be introduced into a continuous (e.g., serialized) bioreactor system. The bioreactor system can comprise one stage. The bioreactor system can comprise two or more stages (e.g., a multi-stage reactor system). The bioreactor system can comprise a complex microbial consortium that has been modified for functionality (e.g., for biocontrol efficacy). Without wishing to be bound by theory, a target isolate can 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. Addition of a microbial isolate described herein can be advantageous to a system by providing an environment for other microbes and / or metabolites of the working fluids of the system to enrich. The isolate can be a microbial biocontrol agent. The microbial biocontrol agent can have one or more biocontrol properties.

[0106] 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 products (e.g., biocontrol compositions) that have one or more biocontrol properties. The products (e.g., biocontrol compositions) made by the systems described herein can comprise 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 property (e.g., aWSGR Docket No. 63472-722.601biocontrol property and / or plant growth promoting property). In some embodiments, methods and systems described herein are arranged to selectively promote growth of metabolites that have a desired property (e.g., a biocontrol property and / or plant growth promoting property). Applications of the products of the digestion systems described herein can 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 can be to a part of a plant, such as a shoot, a seed, 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. The product (e.g., biocontrol product) described herein may be applied with another composition. For example, the product (e.g., biocontrol product) described herein may be applied with a fungicide, insecticide, or any combination thereof. In some embodiments, the product (e.g., biocontrol product) described herein may be applied with an additional microbial inoculant and / or biostimulant.

[0107] The biocontrol system technologies (BCX technologies) can be a continuous and serialized process. The products generated by the BCX systems described herein can demonstrate the ability of fungal biocontrol by reducing pathogen impact in situ. An in situ plant assay can be a technique that analyzes plant tissue or cells to study gene expression, plant-microbe interactions, or other processes. The products generated by the BCX systems described herein can be intact, as in the products are not fdter-sterilized. The products generated by the BCX systems described herein can be fdter-sterilized to provide metabolites without microbes. The products generated by the BCX systems described herein can confer resilience to plants under biotic stress. In some embodiments, the products generated by the BCX systems described herein can confer resilience to plants under biotic stress at an application rate (e.g., at even field application rates). The products of the BCX systems described herein can have biocontrol efficacy even at low applications rates. For example, the one or more products can have biocontrol efficacy in treating a plant disease (e.g., plant pathogen) and / or conferring resistance to a plant against a plant disease at an application rate of l. Ox (e.g., no dilution when applied to a plant), O.lx (e.g., lOx dilution when applied to a plant), O. Olx (e.g., lOOx dilution when applied to a plant), O. OOlx (e.g., l,000x dilution when applied to a plant), or less than about O. OOlx. The one or more products can have biocontrol efficacy in treating a plant disease (e.g., plant pathogen) and / or conferring resistance to a plant against a plant disease at an application rate of at least about 1 quart per acre (1 qt / acre), at least about 2 qt / acre, at least about 3 qt / acre, at least about 4 qt / acre, at least about 5 qt / acre, at least about 6 qt / acre, at least about 7 qt / acre, at least about 8 qt / acre, at least about 9 qt / acre, at least about 10 qt / acre, at least about 15 qt / acre, at least about 20 qt / acre, or greater than about 20 qt / acre. In some embodiments, the one or more products can have biocontrol efficacy in treating a plant disease (e.g., plant pathogen) and / or conferring resistance to a plant against a plant disease at an application rate of at most about 20 qt / acre, at most about 15 qt / acre, at most about 10 qt / acre, at most about 9 qt / acre, at most about 8 qt / acre, at most about 7 qt / acre, at most about 6 qt / acre, at most about 5WSGR Docket No. 63472-722.601qt / acre, at most about 4 qt / acre, at most about 3 qt / acre, at most about 2 qt / acre, at most about 1 qt / acre, or less than about 1 qt / acre.

[0108] In some embodiments, the one or more products can have biocontrol efficacy in treating a plant disease (e.g., plant pathogen) and / or conferring resistance to a plant against a plant disease at an application rate between about 1 qt / acre to about 20 qt / acre. In some embodiments, the one or more products can have biocontrol efficacy in treating a plant disease (e.g., plant pathogen) and / or conferring resistance to a plant against a plant disease at an application rate between about 1 qt / acre to about 2 qt / acre, about 1 qt / acre to about 3 qt / acre, about 1 qt / acre to about 4 qt / acre, about 1 qt / acre to about 5 qt / acre, about 1 qt / acre to about 6 qt / acre, about 1 qt / acre to about 7 qt / acre, about 1 qt / acre to about 8 qt / acre, about 1 qt / acre to about 9 qt / acre, about 1 qt / acre to about 10 qt / acre, about 1 qt / acre to about 15 qt / acre, about 1 qt / acre to about 20 qt / acre, about 2 qt / acre to about 3 qt / acre, about 2 qt / acre to about 4 qt / acre, about 2 qt / acre to about 5 qt / acre, about 2 qt / acre to about 6 qt / acre, about 2 qt / acre to about 7 qt / acre, about 2 qt / acre to about 8 qt / acre, about 2 qt / acre to about 9 qt / acre, about 2 qt / acre to about 10 qt / acre, about 2 qt / acre to about 15 qt / acre, about 2 qt / acre to about 20 qt / acre, about 3 qt / acre to about 4 qt / acre, about 3 qt / acre to about 5 qt / acre, about 3 qt / acre to about 6 qt / acre, about 3 qt / acre to about 7 qt / acre, about 3 qt / acre to about 8 qt / acre, about 3 qt / acre to about 9 qt / acre, about 3 qt / acre to about 10 qt / acre, about 3 qt / acre to about 15 qt / acre, about 3 qt / acre to about 20 qt / acre, about 4 qt / acre to about 5 qt / acre, about 4 qt / acre to about 6 qt / acre, about 4 qt / acre to about 7 qt / acre, about 4 qt / acre to about 8 qt / acre, about 4 qt / acre to about 9 qt / acre, about 4 qt / acre to about 10 qt / acre, about 4 qt / acre to about 15 qt / acre, about 4 qt / acre to about 20 qt / acre, about 5 qt / acre to about 6 qt / acre, about 5 qt / acre to about 7 qt / acre, about 5 qt / acre to about 8 qt / acre, about 5 qt / acre to about 9 qt / acre, about 5 qt / acre to about 10 qt / acre, about 5 qt / acre to about 15 qt / acre, about 5 qt / acre to about 20 qt / acre, about 6 qt / acre to about 7 qt / acre, about 6 qt / acre to about 8 qt / acre, about 6 qt / acre to about 9 qt / acre, about 6 qt / acre to about 10 qt / acre, about 6 qt / acre to about 15 qt / acre, about 6 qt / acre to about 20 qt / acre, about 7 qt / acre to about 8 qt / acre, about 7 qt / acre to about 9 qt / acre, about 7 qt / acre to about 10 qt / acre, about 7 qt / acre to about 15 qt / acre, about 7 qt / acre to about 20 qt / acre, about 8 qt / acre to about 9 qt / acre, about 8 qt / acre to about 10 qt / acre, about 8 qt / acre to about 15 qt / acre, about 8 qt / acre to about 20 qt / acre, about 9 qt / acre to about 10 qt / acre, about 9 qt / acre to about 15 qt / acre, about 9 qt / acre to about 20 qt / acre, about 10 qt / acre to about 15 qt / acre, about 10 qt / acre to about 20 qt / acre, or about 15 qt / acre to about 20 qt / acre.

[0109] In some embodiments, the product can have biocontrol efficacy in treating a plant disease (e.g., plant pathogen) and / or conferring resistance to a plant against a plant disease at a low application rate (e.g., at most about 2 qt / acre, at most about 1 qt / acre, at most about 0.5 qt / acre, at most about 0.1 qt / acre, or less than about 0.1 qt / acre). The product can have biocontrol efficacy in treating a plant disease (e.g., plant pathogen) and / or conferring resistance to a plant against a plant disease at a low application rate due to an effectiveness of the product in treating the one or more plant pathogens (e.g., the product may have a potent effect on a plant in treating the one or more plant pathogens). The product can have biocontrol efficacy in treating a plant disease (e.g., plant pathogen) and / or conferring resistance to a plant against a plant diseaseWSGR Docket No. 63472-722.601at a low application rate due to an effectiveness of the product in preventing infection by one or more plant pathogens (e.g., the product may have a potent effect on a plant in conferring resistance to one or more plant pathogens).

[0110] Products (e.g., compositions) generated by the BCX systems described herein can have one or more plant growth promotion properties. For example, a plant (e.g., a leaf) applied a product generated by the bioreactor systems described herein can show higher chlorophyll level. The higher chlorophyll level can be indicative of better plant health, absence of plant disease, reduction of plant disease, resistance to plant disease, or any combination thereof. As another example, a plant (e.g., a leaf) applied a product generated by the bioreactor systems described herein can show lower temperature. The lower temperature can be indicative of better plant health, absence of plant disease, reduction of plant disease, resistance to plant disease, or any combination thereof. Without wishing to be bound by theory, the bioreactor systems described herein can generate one or more products comprising elevated biocontrol efficacy for pathogen suppression, reduction of biotic stress, or any combination thereof.

[0111] Definitions

[0112] 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 can 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.

[0113] 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.

[0114] The term “culturing”, as used herein, can 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.

[0115] 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”, “reactor system”, and “bioreactor system” can be used interchangeably. The bioreactor system described herein can be a biocontrol system (BCX system).WSGR Docket No. 63472-722.601

[0116] 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 can 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. In a continuous process using the methods and systems described herein, a microbial strain and / or microbes / metabolites of a microbial consortium may be enriched if they are detected past a process (e.g., system’s) hydraulic retention time. For example, if an isolate (e.g., microbial biocontrol agent) can be detected after a system’s 14 day hydraulic retention time, the isolate may be considered enriched.

[0117] An enriched culture can comprise a growing population of a target isolated strain and a population of microbes enriched for a particular functionality (e.g., biocontrol) over a time period. An enriched culture can comprise a percentage of a target isolated strain and a population of microbes enriched for a particular functionality (e.g., biocontrol). In some embodiments, an enriched culture can 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., biocontrol). The enriched culture can comprise a percentage of a total bacteria population in a container of digestion system described herein. The enriched culture can 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%,WSGR Docket No. 63472-722.601about 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.

[0118] As used herein, the term “enriching” or “enriched” are used interchangeably to refer to a process of increasing an amount of a target compound in a working fluid of a subsequent container relative to a working fluid of a reference container. For example, when four containers are fluidically coupled in-series, a target compound is “enriched” when a third working fluid of a third container contains a higher amount of the target compound compared to a second working fluid of a second container or a first working fluid of a first container. “Enriching” for a target compound is achieved or performed when a concentration of the target compound in a working solution of a subsequent container is present at a higher concentration in a reference working fluid of a reference container, regardless of whether the amount of the target compound is reduced in any one or more intermediate working fluids of intermediate containers compared to the amount of the target compound in the reference working fluid of the reference container. For example, “enriching” is achieved when a target compound is present at a higher concentration in a fourth container compared to a concentration of the target compound in a second working fluid of a second container even when a concentration of the target compound is decreased compared to either the second working fluid of the second container or a fourth working fluid of a fourth container. It shall be understood that “enriching” a target compound also describes an instance when the target compound is detectable in a subsequent working fluid of a subsequent container and was undetectable in a reference working fluid of a reference container. Enriching for a target compound can be performed by any suitable metric, including but not limited to determining a mass, a concentration (e.g., a molar concentration, a percentage weight per volume concentration, a percentage volume per volume concentration, etc.), a weight, or a volume of the target compound. Enriching a target compound can also refer to a process of increasing an amount of a target compound across a plurality of fluidically coupled containers.

[0119] 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,1WSGR Docket No. 63472-722.601nutrient, or pesticide. A microbial composition refers to a composition comprising at least one microbial species. A composition can comprise microbial metabolites generated in a microbial consortium of a digestion system described herein. The terms “composition”, “product”, “biostimulant product”, and “bioproduct” can be used interchangeably herein.

[0120] 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” can 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 can be applied for the improvement of plant health, growth and / or yield, can be readily determined.

[0121] A “carrier” as used herein can refer to a substance or a composition that support the survival of the microbes. Such carriers can be either organic or non-organic.

[0122] “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 can 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.

[0123] Local alignment between two sequences can 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 can 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 can 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 sequenceWSGR Docket No. 63472-722.601that 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 can also be determined using GenomeQuest™ software (Gene-IT, Worcester Mass. USA).

[0124] The term “plant growth promotion” (e.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,WSGR Docket No. 63472-722.601as 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.

[0125] In some embodiments, plant growth promotion can refer to plant vigor and / or plant health. Plant vigor can refer to a stage of a plant determined by an ability to product growth, survive stress (e.g., period of drought and / or heavy rainfall), successfully compete with other plants for soil, sunlight, or moisture, carry out reproductive processes, or any combination thereof.

[0126] The term “biocontrol” can refer to the ability of a product described herein to control one or more pests, one or more weeds, or one or more diseases of a plant. Biocontrol can refer to the ability of a product described herein to confer resistance to one or more plant disease (e.g., one or more plant pathogens). Resistance can be induced systemic resistance (ISR). ISR can refer to a plant defense mechanism that protects a plant from one or more pathogens (e.g., fungi, bacteria, nematodes, or any combination thereof). Resistance can refer to systemic acquired resistance (SAR). SAR can refer to a defense mechanism of a plant that protects a plant (e.g., an entire plant or a portion of a plant) from a range of pathogens, for example those pathogens described herein, following an exposure (e.g., a localized exposure). In some embodiments, SAR may be triggered at a site of infection (e.g., at a site of pathogen infection and / or a site of an insect bite). As an example, biocontrol may refer to resistance to one or more weeds comprising crabgrass, dandelion, chickweed, quackgrass, Canada thistle, bindweed, henbit, broadleaf plantain, white clover, lambsquarters, ragweed, doveweed, yellow nutsedge, dallisgrass, bermudagrass, knotweed, or any combination thereof. Biocontrol may refer to treating one or more weeds comprising crabgrass, dandelion, chickweed, quackgrass, Canada thistle, bindweed, henbit, broadleaf plantain, white clover, lambsquarters, ragweed, doveweed, yellow nutsedge, dallisgrass, bermudagrass, knotweed, or any combination thereof. As another example, biocontrol may refer to resistance to one or more plant pests comprising spider mites, aphids, fungus gnats, thrips, scale, mealybugs, whiteflies, codling moth, leafhoppers, whitefly, cabbageworm, springtails, gastropods, com earworm, beetle (e.g., Japanese beetle and / or Colorado potato beetle), or any combination thereof. Biocontrol may refer to treating one or more plant pests comprising spider mites, aphids, fungus gnats, thrips, scale, mealybugs, whiteflies, codling moth, leafhoppers, whitefly, cabbageworm, springtails, gastropods, com earworm, beetle (e.g., Japanese beetle and / or Colorado potato beetle), or any combination thereof. Biocontrol may refer to resistance to one plant pathogens (e.g., fungal pathogens). The plant pathogen may be of the genus Mycosphaerella, Colletotrichum, Puccinia, Botrytis, Fusarium, Alternaria, Blumeria, Ustilago, Melampsora, or any combination thereof. For example, biocontrol may refer to resistance to one plant pathogens (e.g., fungal pathogens) comprising Mycosphaere Ila graminicola, Colletotrichum spp., Puccinia spp., Botrytis cinerea, Fusarium graminearum, Fusarium oxysporum, Blumeria graminis, Ustilago maydis, Melampsora lini, or any combination thereof.WSGR Docket No. 63472-722.601

[0127] 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.

[0128] For crop plants, “yield” can also mean the amount of harvested material per acre or unit of production. Yield can be defined in terms of quantity or quality. The harvested material can vary from crop to crop, for example, it can 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.

[0129] 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 can produce 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).

[0130] A “control plant”, as used herein, can provide a reference point for measuring changes in phenotype of the subject plant, and can be any suitable plant cell, seed, plant component, plant tissue, plant organ or whole plant. A control plant can 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 (e.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 can comprise a plant that has had an inoculum of a microbe or a biocontrol product as described herein applied to any part of the plant (e.g., seed, stem, root, shoot, leaf, or combination thereof). A treated plant can comprise a plant that has had an inoculum of a microbe or a biocontrol product as described herein applied using an in-furrow application. A treated plant can comprise a plant that has had an inoculum of a microbe or a biocontrol product as described herein applied using a side-dress application. A treated plant can comprise a plant that has had an inoculum of a microbe or a biocontrol product as described herein applied to the soil. An untreated plant can comprise a plant that that has not had an inoculum of a microbe or a biocontrol product as described herein applied directly or indirectly.

[0131] ‘ ‘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). ForWSGR Docket No. 63472-722.601example, an isolated microbial strain as described herein can benefit from carbon sources from the roots of a plant and the plant can benefit from metabolites generated by metabolism of the microbe. Without wishing to be bound by theory, a plant can be colonized by the isolate and the colonization of the roots can 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.

[0132] The term “serialized isolate production”, (e.g., sIP), can refer to specialized manipulated continuous serialized reactors that can enable the growth and enrichment of the microbes, isolates, target isolates, and / or microorganisms as described herein.

[0133] 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).

[0134] The terms “microbial consortium” or “microbial population” can refer to a group of microorganisms in an environment. Consortiums can 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.

[0135] 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.

[0136] 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 can 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.

[0137] The term “internal recycle rate” can refer to a rate at which a working fluid is recycled within a phase space.

[0138] The term “hydraulic feed rate” can refer to a rate at which working fluid is transferred between phase spaces.

[0139] The term “hydraulic dwell time” can refer to an amount of time that a working fluid is present in a phase space.

[0140] 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 can 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 can provide an enriched environment for microbes of the digestion system.WSGR Docket No. 63472-722.601

[0141] 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.

[0142] 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.Multi-Stage Approach to Generating a Biocontrol Product

[0143] Embodiments of systems and methods described herein produce biostimulant products that can have a multi-modal way of promoting biocontrol efficacy by plants. Biostimulant products produced by embodiments described herein can be used to promote plant growth by applying the products to plants and / or plant growth media (e.g., soil).

[0144] The following microbe genera can promote biocontrol efficacy in plants: Agrobacterium, Bacillus, Paenibacillus, Burkholderia, Chromobacterium, Pseudomonas, Ampelomyces, Aspergillus, Beauveria, Chaetomium, Coniothyrium, Gliocladium, Metarhizium, Pseudozyma, Streptomyces, Trichoderma and Verticillium.. The following microbe species can promote biocontrol in plants: Agrobacterium radiobacter, Bacillus subtilis, B. firmus, B. licheniformis, B. pumilus, B. thuringiensis, B. amyloliquefaciens (B. velezsis), Paenibacillus ottowii, Burkholderia spp., Chromobacterium subtsugae, Pseudomonas chlororaphis, P. fluoroscens, P. aureofaciens, Ampelomyces quisqualis, Aspergillus flavus, Beauveria spp., Chaetomium globosum, Coniothyrium minitans, Gliocladium catenulatum, Gliocladium virens, Metarhizium anisopliae, Pseudozyma flocculosa, Streptomyces lydicus, S. griseoviridis, Trichoderma harzianum, T. album and Verticillium lecanii.. Embodiments of products described herein can include one or more of these microbes. Microbes of these genera can comprise endophytic N fixers (diazotrophs) of monocots.

[0145] In some embodiments, a serialized set of reaction chambers that can be used in a method of producing a biostimulant product are described herein. In some embodiments, conditions within reactor chambers can be established to selectively promote the production of one or more microbes that have a specific desired property (e.g., biocontrol property and / or plant growth promoting property).

[0146] In some aspects, provided herein are methods of making a product having one or more biocontrol properties. The method can comprise providing a bioreactor system. The system can comprise one or more containers (e.g., reactors). For example, the system can comprise at least about 1, 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, at least about 9, at least about 10, or greater than about 10 containers. A container of the bioreactor system can comprise aWSGR Docket No. 63472-722.601working fluid. In some embodiments, each container of the bioreactor system can comprise a volume of working fluid. In some embodiments, each container of the bioreactor system can comprise a same volume of working fluid. In some embodiments, each container of the bioreactor system can comprise a different volume of working fluid. In some embodiments, a container of the bioreactor system can comprise a microbial biocontrol agent. In some embodiments, the microbial biocontrol agent can be a microbe, a microbial strain, a metabolite, or any combination thereof. The microbial biocontrol agent can be multiple (e.g., 2, 3, 4, 5, 6, 7, 8, or more) of a microbe, a microbial strain, a metabolite, or any combination thereof. The microbial biocontrol agent can be a bacterium, a fungi, or any combination thereof. A fungal biocontrol agent can comprise a naturally occurring microorganism that can help manage (e.g., treat and / or prevent) plant disease. A fungal biocontrol agent can comprise a naturally occurring microorganism that can help manage (e.g., treat and / or prevent) plant pests. A fungal biocontrol agent can be a fungus of the genera comprising Alternaria, Aspergillus, Candida, Fusarium, Penicillium, Pichia, Talaromyces, Trichoderma, or Verticillium.

[0147] The method can comprise collecting the product from the bioreactor system. The product can be collected following any amount of time (e.g., any amount of time after operating the bioreactor system). The product can be collected when the system is operating. The product can be collected when the system is not operating. For example, the product can be collected after at least about 1 hour, 2 hours, 3 hours, 6 hours, 12 hours, 1 day, 2 days, 3 days, 4 days, 5 days, 6 days, 1 week, 2 weeks, 3 weeks, 1 month, 2 months, 3 months, 4 months, 5 months, 6 months, 1 year, 2 years, or greater than 2 years. As another example, the product can be collected after at most about 1 hour, 2 hours, 3 hours, 6 hours, 12 hours, 1 day, 2 days, 3 days, 4 days, 5 days, 6 days, 1 week, 2 weeks, 3 weeks, 1 month, 2 months, 3 months, 4 months, 5 months, 6 months, 1 year, 2 years, or greater than 2 years.

[0148] The product collected from the bioreactor system can be termed a collected product. The product collected from the bioreactor system can have one or more biocontrol properties. For example, the product can treat a plant disease (e.g., a plant pathogen). The product can provide resistance to a plant against a plant disease (e.g., a plant pathogen). In some embodiments, the product has a concentration of an isolate (e.g., a microbial biocontrol agent). In some embodiments, the product can have a concentration of a microbial biocontrol agent that is less than a concentration of the microbial biocontrol agent in the bioreactor system (e.g., in any container of the bioreactor system). In some embodiments, the product can have a concentration of a microbial biocontrol agent that is greater than a concentration of the microbial biocontrol agent in the bioreactor system (e.g., in any container of the bioreactor system).

[0149] In some embodiments, the microbial biocontrol agent can be present in the collected product at a concentration of at least about 1.0 x IO2colony forming units per milliliter (cfu / ml), at least about 5.0 x IO2cfu / ml, at least about 1.0 x IO3cfu / ml, at least about 5.0 x IO3cfu / ml, at least about 1.0 x I04cfu / ml, at least about 5.0 x I04cfu / ml, at least about 1.0 x IO5cfu / ml, at least about 5.0 x IO5cfu / ml, at least about 1.0 x 106cfu / ml, at least about 1.0 x 107cfu / ml, at least about 1.0 x 108cfu / ml, or greater than about 1.0 x I08cfu / ml. In some embodiments, the microbial biocontrol agent can be present in the collected productWSGR Docket No. 63472-722.601at a concentration of at most about 1.0 x 102colony forming units per milliliter (cfu / ml), at least about 5.0 x 102cfu / ml, at least about 1.0 x 103cfu / ml, at least about 5.0 x 103cfu / ml, at least about 1.0 x 104cfu / ml, at least about 5.0 x 104cfu / ml, at least about 1.0 x 105cfu / ml, at least about 5.0 x 105cfu / ml, at least about 1.0 x 106cfu / ml, at least about 1.0 x 107cfu / ml, at least about 1.0 x 108cfu / ml, or greater than about 1.0 x 108cfu / ml.

[0150] As an example, provided herein are methods of making a product having a biocontrol property, the method comprising: (a) providing a bioreactor system comprising one or more containers, wherein the one or more containers comprise a working fluid and a microbial biocontrol agent; and (b) collecting the product from the bioreactor system, wherein the product has the biocontrol property, and wherein the microbial biocontrol agent is present in the product collected from the bioreactor system at a concentration of at least 1.0 x 104colony forming units per milliliter (cfu / ml).

[0151] In some embodiments, the bioreactor system (e.g., the digestion system) comprises an established population of one or more microbial strains (e.g., microbial biocontrol agents) in one or more containers of the system. An “established population” of a particular microbial strain can be 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 can be 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 can have 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 can be a population that is derived from a population that was inoculated into the system at least 10, 30, 60, or 90 days previous.

[0152] In some embodiments, a bioreactor system comprises at least one microbial strain (e.g., microbial biocontrol agent). In some embodiments, a bioreactor system comprises at least one microbial biocontrol agent. In some embodiments, a bioreactor system comprises an established population of a first microbial biocontrol agent and an established population of a second microbial biocontrol agent. In some embodiments, the bioreactor system further comprises an established population of a third microbial biocontrol agent The established populations of the respective microbial biocontrol agents can be established in individual or combined inoculations into the bioreactor system. An individual inoculation can comprise one inoculum of a microbial strain (e.g., microbial biocontrol agent). A combined inoculation can comprise an inoculum comprising at least two microbial strains (e.g., at least two microbial biocontrol agents). The combined inoculation can comprise the same isolated microbial strains. The combined inoculation can comprise an isolated microbial strain and non-isolated microbial strain. The combined inoculation can comprise two or more isolated microbial strains.

[0153] The microbial biocontrol agent described herein can comprise a microbial strain of the genus Bacillus or Paenibacillus. The microbial biocontrol agent described herein can comprise a microbial strainWSGR Docket No. 63472-722.601of the species Bacillus amyloliquefaciens or Paenibacillus ottowii. In some embodiments, the microbial biocontrol agent described herein can comprise a microbial strain deposited under ATCC Accession No. PTA-124703 (MS 2379), ATCC Accession No. PTA-124708 (MS2697), ATCC Accession No. PTA-124707 (MS2681), or ATCC Accession No. PTA-124702 (MS2335).Microbial Digestions Methods and SystemsSystem Overview

[0154] Certain embodiments disclosed herein include methods and systems in which microbes comprised in microbial consortia digest substances provided in a feedstock. The digestion systems can be comprised of a series of separate, fluidly connected containers, also referred to herein as “reactors.” In each reactor, a different microbial consortium can be established and maintained throughout the continuous operation of the digestion system. The unique microbial consortia present in each reactor can provide for different physiological activities in the different reactors. Without wishing to be bound by theory, different steps in digestion of a feedstock can be performed in different reactors, which can 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 biocontrol efficacy plant growth promoting properties.

[0155] As an example, provided herein is a bioreactor system comprising: (i) 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 microbial biocontrol agent; (ii) a second container arranged in a series with the first container, wherein the second container comprises a volume of a second working fluid, and wherein the second container comprises a product outflow stream port; and (iii) a product outflow stream in fluid communication with the product outflow stream port, wherein the product outflow stream comprises a biocontrol product, wherein the biocontrol product comprises an amount of the microbial biocontrol agent, and wherein the amount of the microbial biocontrol agent promotes a biocontrol property of a plant administered the biocontrol product as compared to an otherwise identical plant not administered the biocontrol product.

[0156] 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 can lead to growth of one or more microbes having a desired property (e.g., a biocontrol property and / or plant growth promoting property). The one or more microbes can be one or more isolated microbes added separately as an inoculum to the digestion system. The one or more microbes can also be input into the system as part of a feed material that includes a mixture of microbes. The one or more microbes can be endogenous to an organic material such as, for example, a manure, a kelp, a plant, a lignocellulosic material, an alga, or any combination thereof. In someWSGR Docket No. 63472-722.601embodiments, endogenous microbes can be those microbes naturally present in feedstock material (e.g., a manure, a plant, a lignocellulosic material, a kelp, an alga, or any combination thereof). These microbes can naturally reside in a closed system and / or are present in the ecosystem of the feedstock material.

[0157] Inputs into digestion systems can comprise water, a microbial inoculum, nutrients (e.g., carbon, nitrogen, phosphorous, or any combination thereof), a digestion substrate, chitin, yeast, or any combination thereof. Fluid within reactors of a digestion system can be referred to herein as a “working fluid.” In continuous operation, each reactor can 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 can include a different microbial consortium and have different conditions from other reactors, the working fluid within each reactor can be considered to be distinct from working fluids within the other reactors. The total volume of working fluid within a digestion system can be referred to herein as the “total working volume” of the digestion system.

[0158] Digestion substrates comprising an input stream into a digestion system can include, for example, organic materials that can be digested by microbes in the digestion system. An input stream to the system can comprise an aqueous feedstock. The aqueous feedstock can comprise digestion substrates. Such organic materials can include, for example, manure, kelp, lignocellulosic material, wastewater biosolids, food waste, energy crops, yeast, agricultural waste, algae, or any combination thereof. The manure can 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 can have been subject to a partial digestion before being input into the system. Thus, the input into the system can 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. The manure can be processed manure. The processed manure can have been digested by a reactor system. An input can also comprise processed manure with rock phosphate. In some embodiments, the aqueous feedstock and / or digestion substrates can comprise seaweed. The seaweed can comprise kelp. The kelp can be of the genus Ascophyllum, Ecklonia, Fucus, Sargassum, Laminaria, Macrocystis, Asparagopsis, Kappaphycus, Gracilaria, or Rhodophyta. The kelp can be of the species Ascophyllum nodosum, Ecklonia maxima, Fucus vesiculosus, Sargassum spp., Laminaria spp., Macrocystis pyrifera, or Rhodophyta spp.

[0159] In some embodiments, digestion substrates comprising an input stream can include an inorganic substrate. The inorganic substrate can 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. The inputs into the bioreactor system can comprise magnesium sulfate, iron sulfate, manganese sulfate, calcium carbonate, dipotassium phosphate, mono potassium phosphate, sodium chloride, or any combination thereof. In some embodiments, an input into the bioreactor system can be a carbon source. The carbon source can be sucrose, simple sugars, glycerol, or any combination thereof. In some embodiments, the carbon source can be sucrose. In someWSGR Docket No. 63472-722.601embodiments, an input into the bioreactor system can be a nitrogen source. The nitrogen source can be a yeast and / or yeast extract. In some embodiments, the nitrogen source can be yeast, yeast extract, ammonium chloride, ammonium nitrate, sodium nitrate, proteose peptone #3, ammonium sulfate, or any combination thereof. An input into the bioreactor system can comprise chitin and / or chitosan. In some embodiments, an input into the bioreactor system can comprise a flour. The flour can comprise soy flour, rice flour, wheat bran, byproducts of soybean processing, byproducts of oil seed bioprocessing, or any combination thereof. In some embodiments, an input to the bioreactor system can be an olive mill waste. Any of the inputs to the bioreactor system can be provided alone or in combination.

[0160] In some embodiments, a microbial inoculum comprises a single isolated microbe. In some embodiments, the microbial inoculum can comprise between 1 and 5 isolated microbes. In some embodiments, the inoculum can comprise at least about 1,2, 3, 4, 5, 6, 7, 8, 9, 10, or more isolated microbes. In some embodiments, the inoculum can comprise greater than 5 isolated microbes. In some embodiments, the inoculum can 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 can include a complex mixture of microbes, which can 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 can include a complex mixture of microbes, which can include at most about 400, 350, 300, 275, 250, 225, 200, 100, 50, 25, 20, 10, 5, or less species of microbes.

[0161] A microbial strain (e.g., microbial biocontrol agent) described herein can have at least one plant growth promotion property (e.g., a property of plant growth). A microbial strain (e.g., microbial biocontrol agent) described herein can have at least one biocontrol property (e.g., treating a plant disease, enhancing resistance to a plant disease, or any combination thereof). A plant growth promotion property can 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 can be configured to enhance production of the microbial biocontrol agent. A microbe can be a bacterial species, a fungal species, or an algal species. An inoculum of a microbe can be an individual inoculation of a microbial strain.

[0162] In some embodiments, the microbial strain (e.g., microbial biocontrol agent) can comprise at least two isolated microbes. In some embodiments, the microbial biocontrol agent can comprise at least one isolated microbe and at least one non-isolated microbe. The microbial biocontrol agent can be provided to a container (e.g., reactor) of a digestion system one time, two times, three times, four times, five times, or more than five times. An inoculum of a microbe can 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.

[0163] A microbial biocontrol agent described herein can have a concentration of at least about 1.0 x IO2cfu / ml, 1.0 x IO3cfu / ml, 1.0 x I04cfu / ml, 1.0 x IO5cfu / ml, 1.0 x IO6cfu / ml, 1.0 x I07cfu / ml, 1.0 x I08cfu / ml, 1.0 x IO9cfu / ml, 1.0 x IO10cfu / ml, 1.0 x I011cfu / ml, or 1.0 x IO12cfu / ml prior to transferring to aWSGR Docket No. 63472-722.601first container of a digestion system. A microbial biocontrol agent can have a concentration of at most about 1.0 x 1012cfu / ml, 1.0 x 1011cfu / ml, 1.0 x IO10cfu / 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.

[0164] A microbial biocontrol agent can 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. A microbial biocontrol agent can 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.

[0165] 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 strain (e.g., microbial biocontrol agent). In some embodiments, the microbial strain (e.g., microbial biocontrol agent) can be transferred to the first reactor before the aqueous organic feedstock. In some embodiments, the aqueous organic feedstock and microbial strain (e.g., microbial biocontrol agent) can be transferred to the first reactor together at the same time.

[0166] In some embodiments, a total composition of the aqueous feedstock can 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 microbial strain (e.g., microbial biocontrol agent). In some embodiments, the aqueous feedstock can not include the microbial strain (e.g., microbial biocontrol agent)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.

[0167] In some embodiments, the digestion system comprises a clarifier chamber or clarifier tank (CLF). The terms “clarifier chamber”, “clarifier tank”, “clarifier”, and “clarifier container” can be used interchangeably. In some embodiments, a bioreactor system described herein can comprise at least about 1, at least about 2, at least about 3, at least about 4, at least about 5, or greater than about 5 clarifiers. A first clarifier can be termed a “primary clarifier”. A second clarifier can be termed a “secondary clarifier”. The clarifier can contain working fluid (e.g., clarifier working fluid). The clarifier can comprise a single in-flow port and a single out-flow port. The clarifier can comprise a single in-flow port and multiple outflow ports. The clarifier can comprise multiple in-flow ports and a single out-flow port. The clarifier can comprise multiple in-flow ports and multiple out-flow ports. For example, a clarifier may contain one or more in-flow ports (e.g., 1, 2, 3, 4, 5, 6, or more in-flow ports) and / or one or more out-flow ports (e.g., 1, 2, 3, 4, 5, 6, or more out-flow ports). In some embodiments, the clarifier comprises one or more floc-foldingWSGR Docket No. 63472-722.601wipers which can rotate and release microbes that have been immobilized in the floc without introducing solids in the supernatant. The floc -folding wipers can 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 can 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 can 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 can 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 can 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 can 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 can 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.

[0168] In the clarifier, a floc portion of a working fluid (e.g., a clarifier working fluid) can separate from a supernatant portion of a working fluid. The floc-folding wipers of the clarifier can help in separating the working fluid of the clarifier. In some embodiments, the separating can comprise gravity separation. The floc can settle on the bottom of the clarifier and the supernatant can be collected. The folding of the flocfolding wipers can comprise releasing a population of a microbial strain. The population of a microbial strain can 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 can not introduce solids from the floc portion (e.g., floc solids) into the supernatant portion of the clarifier working fluid.

[0169] Biocontrol products produced by digestion processes as described herein can be used as-is or can be further processed before being used. For example, the outflow from the digestion system, referred to herein as “product” or “base product,” can be concentrated, sterilized, filtered, pasteurized, or dehydrated before being used, or any combination of these. In some embodiments, the base product can 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 can 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 can be filter sterilized to remove any bacteriaWSGR Docket No. 63472-722.601or other microbes in the composition. The clarifier of the bioreactor system can comprise one or more outlet ports for floc harvest. The clarifier of the bioreactor system can comprise one or more return lines. The return line (e.g., recycling port or recycling line) can bring a portion of floc to a container of the bioreactor system.

[0170] In an aspect, provided herein is a method comprising transferring an aqueous organic feedstock into a container. A microbial strain (e.g., an inoculum of a microbe or microbial biocontrol agent) can be transferred into a first container. An aqueous organic feedstock can be transferred into a first container. An aqueous organic feedstock and an inoculum of a microbe can be transferred into a first container. The first container can comprise a volume of a first working fluid. The aqueous organic feedstock can comprise a microbial consortium. The aqueous organic feedstock can comprise one or more digestion products produced by digestion of one or more organic materials. The aqueous organic feedstock can comprise a microbial consortium and digestion products produced by digestion of an organic material. In some cases, the feedstock can comprise at least about 1, 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, at least about 9, at least about 10, at least about 15, at least about 20, at least about 25, at least about 50, at least about 100, or greater than about 100 digestion products. In some cases, the feedstock can comprise at most about 100, at most about 50, at most about 25, at most about 20, at most about 15, at most about 10, at most about 9, 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 than 2 digestion products. The organic material can be digested by one or more microbes in the microbial consortium. The organic material can be digested by a population of microbes of the inoculum of a microbe. The digestion products described herein can comprise one or more sugars (e.g., monosaccharides, disaccharides, oligosaccharides, polysaccharides, or any combination thereof). The digestion products described herein can 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 can 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 can 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.

[0171] In some embodiments, the digestion is aerobic digestion. In some embodiments, the digestion is anaerobic 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 aWSGR Docket No. 63472-722.601digestion process, the organic feedstock can be mixed with water to make an organic feedstock for an aerobic digestion system. The aerobic digestion system can 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 can include manure, kelp, water, yeast (e.g., Saccharomyces cerevisiae yeast), or any combination thereof. In some embodiments, aerobic digestion comprises a process by which bacteria break down organic biomaterials in the presence of oxygen. The biostimulant can also contain microbes that contribute to the plant-beneficial properties of the biostimulant product. The microbes in the biostimulant product can be derived from the microbial population present in the organic feedstock.

[0172] In some embodiments, the bioreactor system can comprise an air supply system to provide air (e.g., oxygen) to the bioreactor system. The air supply system can be a regulated manifold air system. The air supply system can provide increased air to one or more containers of the bioreactor system. The air supply system can comprise a blower. The blower can blow air into one or more containers. The air supply system can enhance aerobic digestion through supply of oxygen. In some embodiments, the air supply system can air at a rate of liters per minute (L / min). In some embodiments, the air supply system of the bioreactor system described herein supplies air at a rate of at least about, at most about, or about 5 L / min, 6 L / min, 7 L / min, 8 L / min, 9 L / min, 10 L / min, 15 L / min, 20 L / min, 25 L / min, 30 L / min, or any range between two of these values.

[0173] As an example, system of the present disclosure, a series of reactors can function to contribute to the growth of one or more microbes having a desired property (e.g., a biocontrol property and / or plant growth promoting property). A series of reactors (e.g., serialized assembly of reactors) can also function to contribute to the production of microbial metabolites having desired biocontrol properties and / or 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 biocontrol properties and / or plantgrowth promotion properties, a population of metabolites with biocontrol properties and / or plant-growth promotion properties, or any combination thereof. This system can provide 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, six, seven, eight, nine, ten, or more reactor 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 biocontrol properties and / or plant growth promoting properties. The system can 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 can input into a first reactor or any reactor of the system. In some embodiments, a hydraulic source can input (e.g., flow) into a tank or container prior to a first reactor. In some embodiments, the container can comprise a “complete mixed reactor” (CMR). Other inputs into a system described herein can flow intoWSGR Docket No. 63472-722.601any 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.

[0174] In some embodiments, the bioreactor system described herein can comprise a multi-stage bioreactor system. The multi-stage bioreactor system can comprise one or more stages. A first stage can comprise one or more containers. A second stage can comprise one or more containers. The first stage can comprise a complete mixed reactor (CMR). The CMR can receive a hydraulic source. The CMR can comprise a mixer. The mixer can assist with mixing one or more inputs to the CMR. In some embodiments, the CMR receives one or more organic feedstocks. The organic feedstocks can comprise an organic feedstock described herein. For example, the organic feedstock can comprise seaweed (e.g., kelp), manure, or any combination thereof. The CMR can receive any inputs to the digestion system described herein. The CMR can comprise one or more input ports. The input ports can be used for transferring in of feedstock, water, or any other inputs or combination of inputs described herein. The CMR can comprise a port for a return line of the system. The return line can be from another container of the system. For example, the return line can bring floc from a clarifier of the bioreactor system to the CMR. In some embodiments, the first stage can comprise a clarifier (e.g., a primary clarifier). The CMR and clarifier can mix one or more feedstocks (e.g., organic feedstocks). The CMR and clarifier can rehydrate one or more feedstocks (e.g., organic feedstocks) and provide an aqueous feedstock.

[0175] In the CMR a hydraulic source can be introduced. The hydraulic source can be water. The hydraulic source can be continuously introduced at a hydraulic rate to maintain a retention time of the total system. The retention time can be at least about 1 day, at least about 2 days, at least about 3 days, at least about 4 days, at least about 5 days, at least about 6 days, at least about 7 days, at least about 8 days, at least about 9 days, at least about 10 days, at least about 11 days, at least about 12 days, at least about 13 days, at least about 14 days, at least about 15 days, at least about 16 days, at least about 17 days, at least about 18 days, at least about 19 days, at least about 20 days, at least about 25 days, at least about 30 days, at least about 40 days, at least about 50, or greater than about 50 days. The retention time can be at most about 50 days, at most about 40 days, at most about 30 days, at most about 25 days, at most about 20 days, at most about 19 days, at most about 18 days, at most about 17 days, at most about 16 days, at most about 15 days, at most about 14 days, at most about 13 days, at most about 12 days, at most about 11 days, at most about 10 days, at most about 9 days, at most about 8 days, at most about 7 days, at most about 6 days, at most about 5 days, at most about 4 days, at most about 3 days, at most about 2 days, at most about 1 day, or less than 1 day. In some embodiments, the retention time of a system described herein can be from about 1 day to about 50 days. In some embodiments, the retention time of a system described herein can be from about 1 day to about 90 days, about 1 day to about 80 days, about 1 day to about 70 days, about 1 day to about 50 days, about 1 day to about 40 days, about 1 day to about 30 days, about 1 day to about 25 days, about 1 day to about 21 days, about 1 day to about 14 days, about 1 day to about 10 days, about 10 days to about 90 days, about 10 days to about 80 days, about 10 days to about 70 days, about 10 days to about 50 days, about 10 days to about 40 days, about 10 days to about 30 days, about 10 days to about 25 days, or fromWSGR Docket No. 63472-722.601about 10 days to about 21 days. The retention time can be about 14 days. The retention time can be about 21 days. The hydraulic rate of the system can be at least about 1 L / min, at least about 2 L / min, at least about 3 L / min, at least about 4 L / min, at least about 5 L / min, at least about 10 L / min, at least about 15 L / min, at least about 20 L / min, at least about 25 L / min, at least about 30 L / min, at least about 40 L / min, at least about 50 L / min, or greater than about 50 L / min.

[0176] In some embodiments, the hydraulic rate of the system can be at least about 5 mL / min, 10 mL / min, 15 mL / min, 20 mL / min, 25 mL / min, 30 mL / min, 35 mL / min, 40 mL / min, 45 mL / min, 50 mL / min, 55 mL / min, 60 mL / min, 65 mL / min, 70 mL / min, 75 mL / min, 80 mL / min, 85 mL / min, 90 mL / min, 95 mL / min, 100 mL / min, 120 mL / min, 140 mL / min, 160 mL / min, 180 mL / min, 200 mL / min, 250 mL / min, 300 mL / min, 400 mL / min, 500 mL / min, or more. In some embodiments, the hydraulic rate of the system can be no more than about 600 mL / min, 500 mL / min, 400 mL / min, 300 mL / min, 250 mL / min, 200 mL / min, 180 mL / min, 160 mL / min, 140 mL / min, 120 mL / min, 100 mL / min, 95 mL / min, 90 mL / min, 85 mL / min, 80 mL / min, 75 mL / min, 70 mL / min, 65 mL / min, 60 mL / min, 55 mL / min, 50 mL / min, 45 mL / min, 40 mL / min, 35 mL / min, 30 mL / min, 25 mL / min, 20 mL / min, 15 mL / min, 10 mL / min, or less.

[0177] The multi-stage bioreactor system can comprise a second stage. The second stage can comprise one or more containers. The one or more containers can be any containers described herein. In some embodiments, the second stage can comprise at least about 1 reactor, at least about 2 reactors, at least about 3 reactors, at least about 4 reactors, at least about 5 reactors, at least about 6 reactors, at least about 7 reactors, at least about 8 reactors, or greater than about 8 reactors. The one or more containers of the second stage can receive one or more inputs. The inputs can comprise a microbial biocontrol agent described herein. In some embodiments, the microbial biocontrol agent is present in the first stage. In some embodiments, the microbial biocontrol agent is not present in the first stage. In some embodiments, the microbial biocontrol agent is present in the second stage. In some embodiments, the microbial biocontrol agent is not present in the second stage. In some embodiments, an input to the second stage can be a media. The media can assist with production of compounds associated with biocontrol. In some embodiments, the media can be targeted for the genus of the microbial strain (e.g., microbial biocontrol agent). For example, the media can be targeted for Bacillus and / or Paenibacillus microbial biocontrol agents. The second stage can be provided chitin, calcium carbonate, flour (e.g., rice flour and / or soy flour), bran, micronutrients, or any combination thereof. In some embodiments, the second stage can comprise a series of reactors (e.g., fluidized bed reactors). The reactors can be any type of reactor described herein. The second stage can comprise a clarifier. The clarifier can be a primary clarifier. The clarifier can be a secondary clarifier. A container of the second stage can comprise an outlet port. The outlet port can comprise a stream for a base product to flow. In some embodiments, methods described herein can comprise collecting base product from the container (e.g., the second stage container).

[0178] The multi-stage bioreactor system can comprise an output volume of biocontrol product. In some embodiments, the output volume can vary depending on the retention time. In some embodiments, the output volume of base product can be at least about or at most about 10 gallons, 25 gallons, 50 gallons,WSGR Docket No. 63472-722.601100 gallons, 250 gallons, 500 gallons, 750 gallons, 1,000 gallons, 2,000 gallons, 3,000 gallons, 4,000 gallons, 5,000 gallons, 6,000 gallons, 7,000 gallons, 8,000 gallons, 9,000 gallons, 10,000 gallons, 15,000 gallons, 20,000 gallons, 25,000 gallons, 30,000 gallons, 35,000 gallons, 40,000 gallons, 45,000 gallons, 50,000 gallons, or greater than about 50,000 gallons per day based on the span of the retention time of the system. In some embodiments, the output volume of base product can be at most about 50000 gallons per day, 40000 gallons per day, 30000 gallons per day, 20000 gallons per day, 10000 gallons per day, 5000 gallons per day, 1000 gallons per day, 900 gallons per day, 800 gallons per day, 700 gallons per day, 600 gallons per day, 500 gallons per day, 400 gallons per day, 300 gallons per day, 200 gallons per day, 100 gallons per day, 80 gallons per day, 60 gallons per day, 50 gallons per day, 40 gallons per day, 30 gallons per day, 25 gallons per day, 20 gallons per day, 15 gallons per day, 10 gallons per day, 25 gallons per day, 20 gallons per day, 15 gallons per day, 10 gallons per day,. In some embodiments, the output volume of base product can be from about 1,000 gallons to about 40,000 gallons.

[0179] A process of a working fluid proceeding through a bioreactor system (e.g., a multi-stage bioreactor system) can be that as shown in FIG. 2. A hydraulic source (e.g., water) can be added to a container of stage 1 of the system 200. The water can be added continuously. The water can be added via a pathway (e.g., a water pathway). The water can have an adjusted conductivity described herein. In some embodiments, a hydraulic source can also be introduced to the second stage of the process. Introduction of a hydraulic source to a first stage and / or second stage can create a different retention time of a system described herein. A hydraulic rate of a second stage (e.g., a second stage comprising a secondary hydraulic source) can be faster than a hydraulic rate of a first stage (e.g., a first stage comprising a primary hydraulic source). A hydraulic rate of a second stage (e.g., a second stage comprising a secondary hydraulic source) can be slower than a hydraulic rate of a first stage (e.g., a first stage comprising a primary hydraulic source.

[0180] The inputs to stage 1 can be added to a container (e.g., a first stage container) 201. The inputs can comprise seaweed (e.g., kelp), chitin, yeast, or any combination thereof. The kelp can be a genus or species of kelp described herein. In some embodiments, the inputs to stage 1 can be added to the CMR. Inputs can be added via a pathway (e.g., a feedstock pathway). In some embodiments, the inputs to stage 1 can be added separately. In some embodiments, the inputs to stage 1 can be added simultaneously. In some embodiments, the inputs to stage 1 can be added over a duration of time, from any amount of time ranging from 5 seconds to 12 hours. In some embodiments, the inputs to stage 1 can be added over a period of days (e.g., 1 day, 2 days, 3 days, 4 days, 5 days, 6 days, 7 days, or more). A clarifier (e.g., a primary clarifier) can allow for biosolids to settle 202. A flight drive can power floc flights of the clarifier of stage 1. The floc flights can ease solid management in the working fluid of the clarifier. The clarifier can have 1 port, 2 ports, 3 ports, 4 ports, 5 ports, or more than 5 ports. A portion of biosolids from the clarifier (e.g., primary clarifier) can be returned to a container 203. For example, a portion of biosolids from the clarifier can be returned to the CMR. The solid returned to the CMR can be further mixed and / or processed. The floc can be returned via a pathway (e.g., a floc pathway). In some embodiments, the floc can be collected from the floc pathway.WSGR Docket No. 63472-722.601

[0181] A portion of working fluid can be transferred from a container of the first phase to a container of the second stage 204. In some embodiments, the portion of working fluid transferred to the second stage cannot contain any solids of the initial inputs to the first stage. For example, all of the organic material in=putted to the first stage can be mixed and / or processed such that the working fluid transferred to the second stage is a processed aqueous feedstock. The working fluid and / or processed aqueous feedstock can comprise a microbial consortium. The microbial consortium can comprise one or more microbes having biocontrol-promoting properties. The working fluid transferred to the second stage can be a supernatant stage of the material originally inputted into stage 1. Stage 2 can begin upon transferring of the working fluid from stage 1. Stage 2 can begin at any time after initiation of stage 1. For example, stage 2 can begin at a time after initiation of stage 1, ranging from 1 hour to 1 week. As another example, stage 2 can begin following more than 1 week of operating stage 1. The inputs to stage 2 can be provided 205. In some embodiments, the inputs to stage 2 comprise an inoculation of the microbial strain (e.g., microbial biocontrol agent). The inputs to stage 2 can be provided in any container (e.g., second stage container). In some embodiments, the inputs to stage 2 can be provided in a first container (e.g., a container immediately following the clarifier (e.g., primary clarifier) of stage 1. A container of stage 2 can be a fluidized bed reactor. In some embodiments, the inputs to stage 2 are provided in a fluidized bed reactor. The inputs can comprise a carbon source, a nitrogen source, a media, a microbial strain (e.g., microbial biocontrol agent), or any combination thereof. A container of the second stage can comprise 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, or more ports. The port can be an input port and / or an outlet port.

[0182] Air can be supplied to a container of stage 2 (e.g., a stage 2 container) 206. Air can be continuously supplied. Air can be supplied by a regulated manifold air system described herein. The regulated manifold air system can assist in the aerobic digestion of the multi-stage bioreactor system. Air can be supplied in each of the second stage containers. In some embodiments, air can be supplied at the same rate to each second stage container. In some embodiments, air can be supplied at different rates to the second stage containers. In some embodiments, air can be supplied at the same rate to some second stage containers and a different rate to other second stage containers. The air can be blown into the container (e.g., second stage container) from an entry point on the top of the container. The air can be blown into the container (e.g., second stage container) from an entry point on one or more sides of the container. The air can be blown into the container (e.g., second stage container) from an entry point on the bottom of the container. The air can be provided to the containers via an air pathway. The air pathway can comprise one or more valves. The valves can regulate the air flow (e.g., the rate of air flow).

[0183] The working fluid of the containers (e.g., second stage containers) can undergo fermentation 207.The fermentation can be aerobic fermentation. The aerobic fermentation can be beneficial for enrichment of microbes (e.g., biocontrol-promoting microbes) of the microbial consortium. The microbes can be enriched in a working fluid of one container (e.g., second stand container) compared to a working fluid of another container (e.g., second stand container). In some embodiments, the microbes can be enriched in a working fluid of one container (e.g., second stand container) compared to a container of the first stage (e.g.,WSGR Docket No. 63472-722.601the CMR and / or clarifier). For example, a working fluid collected from a first second-stage container, a second second-stage container, a third second-stage container, a fourth second-stage container, or a fifth second-stage container can show enrichment of a level of microbes (e.g., biocontrol-promoting microbes) compared to a level of microbes (e.g., biocontrol-promoting microbes) in a working fluid of the CMR and / or clarifier (e.g., primary clarifier) of the first stage. A container of the second stage can comprise a recycling pathway. Working fluid can be recycled within a container (e.g., second stage container). Recycling of the working fluid can be advantageous for digestion of the microbes (e.g., biocontrolpromoting microbes).

[0184] The second stage can comprise a clarifier (e.g., a secondary clarifier). The secondary clarifier can be a last container in the second stage. In some embodiments, the secondary clarifier cannot be a last container in the second stage. The secondary clarifier can comprise an outlet port for a product of the bioreactor system. The product (e.g., product having one or more biocontrol properties) can be collected from the outlet port. The clarifier (e.g., secondary clarifier) can allow for biosolids to settle 208. In some embodiments, the secondary clarifier can allow for biosolids to settle and floc flights can ease solids management. The clarifier (e.g., secondary clarifier) can be connected to a floc drive to power the floc flights. The secondary clarifier can comprise an outlet port. The outlet port can comprise a floc pathway. The floc pathway can allow a portion of biosolids (e.g., biosolids collected at the bottom of the clarifier) to return to a container of the second stage 209. In some embodiments, the floc pathway can allow a portion of biosolids (e.g., biosolids collected at the bottom of the clarifier) to return to a first container of the second stage. In some embodiments, the floc can be collected from the floc pathway. The output of the bioreactor system (e.g., the multi-stage bioreactor system) can be collected as base product 210. The output can be collected via a base product pathway. The base product can comprise a concentration of any input to the first stage or second stage of the multi-stage bioreactor system. For example, the base product can comprise a concentration of kelp, chitin, yeast, microbial strain (e.g., microbial biocontrol agent), calcium source, nitrogen source, organic material, inorganic material, or any combination thereof that was provided to the system. As another example, the base product may not comprise a concentration of kelp, chitin, yeast, microbial strain (e.g., microbial biocontrol agent), calcium source, nitrogen source, organic material, inorganic material, or any combination thereof that was provided to the system.

[0185] A microbial strain (e.g., a microbial biocontrol agent) can incubate in a reactor (e.g., container) of a digestion system described herein. In some embodiments, the microbial strain (e.g., a microbial biocontrol agent) can be incubated under conditions that selectively enrich and / or retain the microbial strain (e.g., a microbial biocontrol agent) in the digestion system. In some cases, the microbial strain (e.g., a microbial biocontrol agent) can 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) can shift a microbial consortia of the digestion system to enrich at least a portion of microbes within a microbial consortium with biocontrolWSGR Docket No. 63472-722.601properties and / or plant growth promotion properties. 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) can shift a microbial consortia of the digestion system to enrich a population of a microbial strain (e.g., provide an established population of a microbial strain (e.g., microbial biocontrol agent). Incubation of the microbial strain (e.g., a microbial biocontrol agent) and / or the portion of microbes within a microbial consortium with biocontrol properties and / or plant growth promotion properties can further generate metabolites with biocontrol properties and / or plant growth promotion properties.

[0186] The microbial strain (e.g., a microbial biocontrol agent) can comprise a biocontrol-promoting microbial strain that can be maintained as a population of the microbial strain in a bioreactor system described herein. Maintenance (e.g., survival or retention) of a microbial strain (e.g., a microbial biocontrol agent) can 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 or retention) of a microbial strain (e.g., a microbial biocontrol agent) can comprise an instance where an amount of the microbial strain (e.g., a microbial biocontrol agent) is alive at the end of a retention period of the digestion system. For example, the maintenance of the microbial strain (e.g., a microbial biocontrol agent) can comprise presence a portion of the microbial strain (e.g., a microbial biocontrol agent) in a reactor (e.g., second stage reactor), clarifier, base product, or any combination thereof. For example, following initial inoculation, a population of a microbial strain (e.g., a microbial biocontrol agent) can 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 a microbial consortium can enrich (e.g., grow or increase in number). These microbes of the portion of microbes in the microbial consortium can have biocontrol capacities. A proportion of the biocontrolpromoting microbial strain and biocontrol-promoting microbes of the microbial consortium relative to a total population count of bacteria can be maintained in a container of a digestion system. A proportion of the biocontrol-promoting microbial strain and biocontrol-promoting microbes of the microbial consortium relative to a total population count of bacteria can be maintained in a second, third, fourth, fifth, sixth, seventh, eighth, ninth, or tenth container of a digestion system. A proportion of the biocontrol-promoting microbial strain and biocontrol-promoting microbes of the microbial consortium relative to a total population count of bacteria can be maintained in any combination of containers of a bioreactor system described herein. A maintained population of a biocontrol-promoting microbial strain can 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 can 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 can comprise atWSGR Docket No. 63472-722.601most 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.

[0187] 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 can promote the growth of microbes or at least a portion of microbes in the microbial consortium. These microbes can be biocontrol-promoting microbes. An amount of microbes or at least a portion of microbes in the microbial consortium can 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 can 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 biocontrol-promoting microbes in the microbial consortium can enrich and / or grow in the system without addition of the inoculum of the microbe.

[0188] 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, can 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, can 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., biocontrol-promoting microbes). Without wishing to be bound by theory, the parameters of the bioreactor system can cause a selective shift in a microbial population to favor microbes with a targeted functionality (e.g., biocontrol). 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 biocontrol-promoting microbes can comprise the microbial strain (e.g., a microbial biocontrol agent), biocontrol -promoting microbes of a microbial consortium, biocontrol-promoting metabolites produced by the microbial strain (e.g., a microbial biocontrol agent) and / or the biocontrol- promoting microbes of the microbial consortium, or any combination thereof.

[0189] A microbial strain (e.g., a microbial biocontrol agent) described herein can contact (e.g., be applied to) a plant. In some embodiments, the contacting of a microbial strain (e.g., a microbial biocontrol agent) to a plant can enhance at least one biocontrol property and / or plant growth promotion property of the plant. In some embodiments, one, two, three, four, or more microbial biocontrol agents can be transferred to aWSGR Docket No. 63472-722.601digestion system. A first microbial strain (e.g., a microbial biocontrol agent) and another microbial strain (e.g., a microbial biocontrol agent) can be the same. A microbial strain (e.g., a microbial biocontrol agent) and another microbial strain (e.g., a microbial biocontrol agent) can be different. In some embodiments, the microbial strain (e.g., a microbial biocontrol agent) and an aqueous organic feedstock are transferred to a container of the digestion system at the same time. In some embodiments, the microbial strain (e.g., a microbial biocontrol agent) and the aqueous organic feedstock are not transferred to a container of the digestion system at the same time. In some embodiments, the microbial strain (e.g., a microbial biocontrol agent) can be transferred to a container of the digestion system prior to the aqueous organic feedstock. In some embodiments, the microbial strain (e.g., a microbial biocontrol agent) can be transferred to a container of the digestion system after the aqueous organic feedstock.

[0190] As a working fluid flows through a digestion system, an absolute number of biocontrol -promoting microbes can increase. In some embodiments, an absolute number of biocontrol -promoting microbes can be higher in a second container compared an absolute number of biocontrol-promoting microbes in a first container. In some embodiments, an absolute number of biocontrol-promoting microbes can be higher in a third container compared an absolute number of biocontrol-promoting microbes in a first container. In some embodiments, an absolute number of biocontrol-promoting microbes can be higher in a fourth container compared an absolute number of biocontrol-promoting microbes in a first container. In some embodiments, an absolute number of biocontrol-promoting microbes can be higher in a fifth container compared an absolute number of biocontrol-promoting microbes in a first container. In some embodiments, an absolute number of biocontrol-promoting microbes can be higher in a sixth container compared an absolute number of biocontrol-promoting microbes in a first container. In some embodiments, an absolute number of biocontrol-promoting microbes can be higher in a seventh container compared an absolute number of biocontrol -promoting microbes in a first container. In some embodiments, an absolute number of biocontrol -promoting microbes can be higher in an eighth container compared an absolute number of biocontrol-promoting microbes in a first container. In some embodiments, an absolute number of biocontrol-promoting microbes can be higher in a ninth container compared an absolute number of biocontrol-promoting microbes in a first container. In some embodiments, an absolute number of biocontrol-promoting microbes can be higher in a tenth container compared an absolute number of biocontrol-promoting microbes in a first container.

[0191] As working fluid flows through a digestion system, a proportion of biocontrol-promoting microbes relative to a total population of bacteria can increase. In some embodiments, a proportion of biocontrolpromoting microbes relative to a total population of bacteria can be higher in a second container compared a proportion of biocontrol-promoting microbes relative to a total population of bacteria in a first container. In some embodiments, a proportion of biocontrol-promoting microbes relative to a total population of bacteria can be higher in a third container compared a proportion of biocontrol -promoting microbes relative to a total population of bacteria in a first container. In some embodiments a proportion of biocontrolpromoting microbes relative to a total population of bacteria can be higher in a fourth container comparedWSGR Docket No. 63472-722.601a proportion of biocontrol-promoting microbes relative to a total population of bacteria in a first container. In some embodiments, a proportion of biocontrol-promoting microbes relative to a total population of bacteria can be higher in a fifth container compared a proportion of biocontrol-promoting microbes relative to a total population of bacteria in a first container. In some embodiments, a proportion of biocontrolpromoting microbes relative to a total population of bacteria can be higher in a sixth container compared a proportion of biocontrol-promoting microbes relative to a total population of bacteria in a first container. In some embodiments, a proportion of biocontrol-promoting microbes relative to a total population of bacteria can be higher in a seventh container compared a proportion of biocontrol-promoting microbes relative to a total population of bacteria in a first container. In some embodiments, a proportion of biocontrol-promoting microbes relative to a total population of bacteria can be higher in an eighth container compared a proportion of biocontrol-promoting microbes relative to a total population of bacteria in a first container. In some embodiments, a proportion of biocontrol-promoting microbes relative to a total population of bacteria can be higher in a ninth container compared a proportion of biocontrol -promoting microbes relative to a total population of bacteria in a first container. In some embodiments, a proportion of biocontrol-promoting microbes relative to a total population of bacteria can be higher in a tenth container compared a proportion of biocontrol-promoting microbes relative to a total population of bacteria in a first container.

[0192] 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) can 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) can 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%.

[0193] An inoculum of a microbe can generate one or more metabolites in a digestion system as described herein. Microbes of the microbial consortium and / or the inoculum of the microbe can be metabolized by catalytic enzymes to produce metabolites. One or more metabolites can be generated by microbial metabolism. Metabolites can 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 can have a biocontrol property and / or a plant growth promotion property. The metabolites generated by the inoculum of the microbe can have two or more biocontrol properties and / or plant growth promotion properties. The plant growth promotion properties can 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 can be used in biocontrol products and / or can be applied to plants.WSGR Docket No. 63472-722.601

[0194] 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.

[0195] One or more metabolites generated by the microbial strain (e.g., microbial biocontrol agent) or by at least a portion of microbes of the microbial consortium can be present in a supernatant (e.g., base product) of a digestion system. In some embodiments, the metabolites can 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 toWSGR Docket No. 63472-722.601about 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.Organic Feedstock

[0196] 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 can 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 can include, but is not limited to, manure, kelp, lignocellulose, wastewater biosolids, food waste, energy crops, glucose solution, ammonium sulfate, oils, fats, grease, or any combination thereof. 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. The organic feedstock can comprise a feedstock described herein.

[0197] Organic feedstock comprising carbon and / or nitrogen sources can flow into a reactor tank. Organic feedstock comprising carbon and / or 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 port and / or piping between two containers of a system described herein can comprise a transfer line. The transfer line can assist with providing a portion of working fluid from one container to another container of the system. A working fluid in a final clarifier of a system can transfer from the reactor tank to a clarifier can produce a supernatant (e.g., base product). Working fluid flows through the serialized reactor systemWSGR Docket No. 63472-722.601which 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 can flow from a mixing chamber through at least one reactor and to a clarifier.

[0198] An organic feedstock can comprise one or more digestion products from digestion of organic substrates present in the organic feedstock. Organic substrates can 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 can comprise a plurality of microbes and / or microorganisms derived from digestion of organic substrates in an aqueous organic feedstock.

[0199] An organic feedstock described herein can 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 euhayanus 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 can be an aqueous mixture of at least one feedstock material and water. In some embodiments, the organic feedstock can 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). The organic feedstock can comprise seaweed (e.g., kelp). The kelp can be of the genus Ascophyllum, Ecklonia, Fucus, Sargassum, Laminaria, Macrocystis, or Rhodophyta. The kelp can be of the species Ascophyllum nodosum, Ecklonia maxima, Fucus vesiculosus, Sargassum spp., Laminaria spp., Macrocystis pyrifera, or Rhodophyta spp.

[0200] Parameters of the digestion system, such as flow rate and the solids content of the organic feedstock, can 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.

[0201] The bioreactor system can comprise a retention time. The retention time can comprise an amount of time for an input to the bioreactor system to reach an end (e.g., be collected in product). The retention time of the multi-stage bioreactor system described herein can comprise one or more retention times. A retention time of a first stage of the multi-stage bioreactor system can be the same as a retention time of a second stage of the multi-stage bioreactor system. A retention time of a first stage of the multi-stage bioreactor system can be different than a retention time of a second stage of the multi-stage bioreactor system. A retention time of a bioreactor system (e.g., multi-stage bioreactor system) described herein can be at least about, at most about, or about 5 days, 6 days, 7 days, 8 days, 9 days, 10 days, 11 days, 12 days, 13 days, 14 days, 15 days, 20 days, 30 days, 40 days, 50 days, 60 days, 3 months, 6 months, 1 year, 2 years,WSGR Docket No. 63472-722.6015 years, or any range between two of these values. In some embodiments, the method further comprises maintaining a flow rate of the working fluid in the bioreactor system that results in a hydraulic retention time of at least 10 days, at least 14 days, at least 18 days, at least 21 days, at least 24 days, at least 30 days, at least 36 days, at least 40 days, at least 45 days, or at least 48 days. In some embodiments, the method further comprises maintaining a flow rate of working fluid in the bioreactor system that results in a hydraulic retention time of at most 10 days, at most 14 days, at most 18 days, at most 21 days, at most 24 days, at most 30 days, at most 36 days, at most 40 days, at most 45 days, or at most 48 days. In some embodiments, the method further comprises maintaining a flow rate of working fluid in the bioreactor system that results in a hydraulic retention time of from about 10 days to about 90 days, about 10 days to about 80 days, about 10 days to about 70 days, about 10 days to about 60 days, about 10 days to about 50 days, about 10 days to about 40 days, about 10 days to about 50 days, about 10 days to about 40 days, about 15 days to about 80 days, about 15 days to about 60 days, about 15 days to about 40 days, about 15 days to about 30 days, about 10 days to about 50 days, about 10 days to about 30 days, or from about 10 days to about 20 days.

[0202] In some embodiments, the aqueous organic feedstock can further comprise an inorganic substrate. In some embodiments, the aqueous organic feedstock can include more than one inorganic substrate. The inorganic substrate can 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.

[0203] 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 can be a rice flour, a bran (e.g., a wheat bran), a soy flour, or any combination thereof. In some embodiments, the loading inputs comprise recycled floc from the system. The inoculum of a microbe as described herein can metabolize the carbon source. Metabolism of carbon by the inoculum of the microbe can comprise transfer of carbon-based moieties of the carbon source to substrates in the working fluid.

[0204] The inoculum of a microbe as described herein can metabolize the nitrogen source. Metabolism of nitrogen by the inoculum of the microbe can comprise transfer of nitrogen-based moieties of the nitrogen source to substrates in the working fluid. In some embodiments, the carbon source can be transferred to a container of the digestion system. In some embodiments, the carbon source can be transferred to a first container, second container, third container, fourth container, fifth container, sixth container, seventh container, eighth container, ninth container, or tenth container of the digestion system. In some embodiments, the nitrogen source can be transferred to a container of the digestion system. In some embodiments, the nitrogen source can be transferred to a first container, second container, third container, fourth container, fifth container, sixth container, seventh container, eighth container, ninth container, or tenth container of the digestion system.WSGR Docket No. 63472-722.601

[0205] 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.

[0206] In some embodiments, the organic feedstock further comprises a microbial consortium. The terms “microbe”, “microbial strain” and “microorganism” can refer to microscopic organisms, including, but not limited to bacteria, fungi, lichens, algae, protozoa, archaea, and / or molds. The terms “microbe” and microorganism” can 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 can be derived from the microbes originally present within the organic feedstock. The microbes can digest the manure, yeast, other organic raw materials, or any combination thereof to produce digestion products.

[0207] 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 can be added to the system with the organic feedstock in the same reactor. In some embodiments, microbes can be added to the system with the organic feedstock in different reactors. In some embodiments, microbes can be added to the system prior to the organic feedstock. In some embodiments, microbes can 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 aboutWSGR Docket No. 63472-722.60115 minutes, at most about 10 minutes, at most about 5 minutes, at most about 1 minute, or at most about 30 seconds.

[0208] A microbe can have nutrient solubilization properties and / or plant growth promotion properties. For example, a microbe can 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 can 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 can have biocontrol properties.

[0209] In some embodiments, the digestion system can comprise a retention time. A retention time can 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 can be advantageous for growth or enrichment of an inoculum of a microbe of the digestion system. A shorter retention time can be advantageous for growth or enrichment of an inoculum of a microbe of the digestion system. A retention time of a digestion system can 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 can 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” can be used interchangeably.

[0210] In the first reactor, the working fluid can 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 can allow the fluid to flow into the second reactor. An outlet at the bottom of the first reactor can transfer the settled solids back into a reactor tank. Each of the reactors in the series of reactors can 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 can 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 can 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 can be driven by gravity. The outlet port of a container can 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 can be about 0.1 cm, about 0.2 cm, about 0.3 cm, about 0.4 cm, about 0.5 cm, about 1 cm, about 2 cm, about 3 cm, about 4 cm, about 5 cm, or about 10 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 can be fluidly connectedWSGR Docket No. 63472-722.601to 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 can connect to an inlet port of a second container. The inlet port of the second container can be below the level of the outlet port of the first container such that the working fluid from the first container can flow by gravity alone into the second container. The second container can 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 can be about 0.1 cm, about 0.2 cm, about 0.3 cm, about 0.4 cm, about 0.5 cm, about 1 cm, about 2 cm, about 3 cm, about 4 cm, about 5 cm, or about 10 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, can 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.Reactor Containers

[0211] A digestion process to produce the biostimulant can 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 can 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).

[0212] In an aspect, the present disclosure provides a bioreactor system. The bioreactor system can comprise a stream of an aqueous feedstock. The stream can 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 can 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) can comprise a microbial strain. The microbial strain can be a population of a microbial strain (e.g., a microbial biocontrol agent) and can comprise a plant growth promoting property (e.g., aWSGR Docket No. 63472-722.601desired plant growth promoting property). A first container of the bioreactor system can comprise a mixer. The mixer can be configured to aerate the working fluid (e.g., the first working fluid) in a container.

[0213] In some embodiments, a concentration of the microbial strain (e.g., the microbial biocontrol agent) can be higher in the working fluid than in the aqueous feedstock. In some embodiments, a concentration of the microbial strain can 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 microbial biocontrol agent) in the first working fluid can 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 can 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 microbial biocontrol agent) in the aqueous feedstock stream or in any other input into the bioreactor system.

[0214] The bioreactor system described herein can 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 container(s). One or more additional containers in the bioreactor system can 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 can 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 can 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.

[0215] In some embodiments, a product outflow stream can comprise a biocontrol product. The biocontrol product can comprise an amount of the microbial strain (e.g., a microbial biocontrol agent), wherein the amount (e.g., concentration and / or bacterial number) of the microbial strain can be an amount described herein. The biocontrol product can comprise a biocontrol property and / or a plant growth promoting property. In some embodiments, the microbial strain can be configured to promote a biocontrol property and / or a plant growth promoting property.

[0216] 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 beWSGR Docket No. 63472-722.601interruptions to the flow stream. In some embodiments, as a continuous flow bioreactor system, the volume of working fluid can be constant.

[0217] 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.

[0218] In some embodiments, one or more reactors, the product outflow stream, the base product, or any combination thereof comprises at least about 100 CFU / ml, at least about 1 x 103CFU / ml, at least about 1 x 104CFU / ml, at least about 1 x 105CFU / ml, at least about 1 x 106CFU / ml, at least about 1 x 107CFU / ml, at least about 1 x 108CFU / ml, at least about 1 x 109CFU / ml, at least about 1 x 1010CFU / ml, or greater than about 1 x 1010CFU / ml of the microbial strain (e.g., the microbial biocontrol agent). In some embodiments, one or more reactors, the product outflow stream, the base product, or any combination thereof comprises at most about 1 x 1010CFU / ml, at most about 1 x 109CFU / ml, at most about 1 x 108CFU / ml, at most about 1 x 107CFU / ml, at most about 1 x 106CFU / ml, at most about 1 x 105CFU / ml, at most about 1 x 104CFU / ml, at most about 1 x 103CFU / ml, at most about 100 CFU / ml, or less than about 100 CFU / ml of the microbial strain (e.g., the microbial biocontrol agent).

[0219] In some embodiments, one or more reactors, the product outflow stream, the base product, or any combination thereof 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 microbial biocontrol agent). In some embodiments, one or more reactors, the product outflow stream, the base product, or any combination thereof comprises at most about IxlO10CFU / ml, at most about IxlO9CFU / ml, at most about IxlO8CFU / ml, at most about 1 x 107CFU / ml, at most about IxlO6CFU / ml, at most about IxlO5CFU / ml, at most about IxlO4CFU / ml, at most about 1 x 103CFU / 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 microbial biocontrol agent).

[0220] In some embodiments, one or more reactors, the product outflow stream, the base product, or any combination thereof can comprise a total dry weight. The total dry weight of one or more reactors, the product outflow stream, the base product, or any combination thereof can 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 one or more reactors, the product outflow stream, the base product, or any combination thereof can 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 0.05WSGR Docket No. 63472-722.601mg / ml, or less than about 0.05 mg / ml. The total dry weight of one or more reactors, the product outflow stream, the base product, or any combination thereof can be between about 0.05 mg / ml to about 4 mg / ml. The total dry weight of one or more reactors, the product outflow stream, the base product, or any combination thereof can 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.

[0221] In some embodiments, one or more reactors, the product outflow stream, the base product, or any combination thereof can comprise a chemical oxygen demand. The chemical oxygen demand of one or more reactors, the product outflow stream, the base product, or any combination thereof can be at least about 10 mg / L, 20 mg / L, 30 mg / L, 40 mg / L, 50 mg / L, 60 mg / L, 70 mg / L, 80 mg / L, 90 mg / L, 100 mg / L, 150 mg / L, 200 mg / L, 250 mg / L, 300 mg / L, 350 mg / L, 400 mg / L, 450 mg / L, 500 mg / L, 600 mg / L, 700 mg / L, 800 mg / L, 900 mg / L, 1000 mg / L, 2000 mg / L, 3000 mg / L, 4000 mg / L, or at least about 5000 mg / L.. The chemical oxygen demand of one or more reactors, the product outflow stream, the base product, or any combination thereof can be at most about 5000 mg / L, at most about 4000 mg / L, at most about 3000 mg / L, at most about 2000 mg / L, 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, atWSGR Docket No. 63472-722.601most about 20 mg / L, at most about 10 mg / L, or less than about 10 mg / L. The chemical oxygen demand of one or more reactors, the product outflow stream, the base product, or any combination thereof can be between about 10 mg / L to about 1,000 mg / L or between about 10 mg / L to about 5,000 mg / L.

[0222] In some embodiments, one or more reactors, the product outflow stream, the base product, or any combination thereof can comprise an electrical conductivity. The electrical conductivity of one or more reactors, the product outflow stream, the base product, or any combination thereof can 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 one or more reactors, the product outflow stream, the base product, or any combination thereof can 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 one or more reactors, the product outflow stream, the base product, or any combination thereof can be between about 0.01 mS / cm to about 10 mS / cm.

[0223] In some embodiments, reactors can 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 can flow into the next reactor continuously. Fluid from the middle of a reactor can flow into the next reactor continuously. Fluid from the bottom of a reactor can flow into the next reactor continuously. Fluid can 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 can match the rate of inflowing feedstock, providing for a hydraulically balanced flow throughout the system. A reactor within the system can 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 can have the same microbial consortium with similar physiological characteristics and digestion capabilities as another reactor within the system. Each reactor within the system can have the same volume capacity. Each reactorWSGR Docket No. 63472-722.601within the system can have a different volume capacity. The digestion system can comprise at least two reactors. The digestion system can comprise at least about 2, 3, 4, 5, 6, 7, 8, 9, 10, or more reactors. The digestion system can comprise at most about 10, 9, 8, 7, 6, 5, 4, 3, 2, or less reactors. Reactors of a digestion system can be arranged as a serialized assembly of reactors. A serialized assembly of reactors can have conduits (e.g., ports or outputs) connecting each reactor to an adjacent reactor and / or container. A serialized assembly of reactors can have a continuous flow of working fluid through each reactor to the adjacent reactor.

[0224] In some embodiments, a reactor can have a single in-flow port and a single out-flow port. In some embodiments, a reactor can have multiple in-flow ports and out-flow ports. In some embodiments, a reactor can have a single in -flow port and multiple out-flow ports. In some embodiments, a reactor can have multiple in-flow ports and a single out-flow port. A reactor can have another in-flow port to provide a carbon source and / or consortium inoculum. An in-flow port can be present at any location of a reactor of the digestion system. An in-flow port can be present at the top of the reactor or at the bottom of the reactor. An out-flow port can 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.

[0225] A reactor can have a single fluid connection. A reactor can have multiple fluid connections (e.g., at least 2, 3, 4, 5, 6, 7, 8, 9, 10, or more fluid connections). The fluid connections can 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 can have flow from the bottom of the container back to the top to prevent buildup of sludge in the bottom of the reactor. In some embodiments, a reactor can have stirrers in the bottom of the container. In some embodiments, a reactor can have wipers in the bottom of the container. The wipers can stir the feedstock and prevent clogging within the reactor. The wipers can fold floc and ease floc return.

[0226] In some embodiments, the reactors can 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) can 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 can be packed with scaffolding to increase surface area within the reactor. The scaffolding within the reactor can increase biofilm. The packed bed reactor can 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 promotesWSGR Docket No. 63472-722.601even distribution of working fluid. In this embodiment, the fixed media is dispersed throughout a cross-sectional area of each packed bed reactor.

[0227] The scaffolding can 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 can comprise a bundle of tubes or columns. In some embodiments, the scaffolding can 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 can 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.

[0228] In some embodiments, the reactors can comprise one or more fluidized bed reactors. In fluidized bed reactors, solid particles can be circulated within working fluid of the reactors, which can provide a surface for microbial colonization. Such particles can include, for example, particles of an inorganic substrate such as rock phosphate particles. In some embodiments, the fluidized bed reactors can be the same volume. In some embodiments, the fluidized bed reactors can 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.

[0229] The flow rate of the digestion system can 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 someWSGR Docket No. 63472-722.601embodiments, 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 can 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 can comprise a first flow rate, second flow rate, third flow rate, fourth flow rate, fifth flow rate, sixth flow rate, or seventh flow rate.

[0230] Reactors can be maintained at specific temperatures which can 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 can 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.

[0231] 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 from about 15°C to about 20°C, about 15°C to about 25°C, from about 15°C to about 30°C, from about 15°C to about 35, from about 15°C to about 40°C.

[0232] Reactors can be maintained under aerobic, microaerobic, or anaerobic conditions. The series of reactors in a digestion system can have different aerobic conditions. The series of reactors in a digestion system can have the same aerobic conditions. In some embodiments, a reactor can have the same aerobic condition as an adjacent reactor. In some embodiments, a reactor can have a different aerobic condition than an adjacent reactor. In some embodiments, a digestion system can have aerobic, microaerobic, anaerobic conditions, or any combination thereof.WSGR Docket No. 63472-722.601

[0233] 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 0.001 mg / mL, at least about 0.01 mg / mL, at least about 0.1 mg / mL, at least about 1 mg / mL, 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 0.001 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 notWSGR Docket No. 63472-722.6010 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.

[0234] Reactors of a digestion system described herein can comprise a working volume used to hold a volume of working fluid. A working volume of a reactor of a digestion system described herein can 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 can 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 750WSGR Docket No. 63472-722.601gallons, 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.

[0235] Reactors can be maintained at different pH levels within a digestion system. Reactors can be maintained at the same pH levels within a digestion system. The pH of a reactor in a digestion system can be at least about 4.0, at least about 4.5, at least about 5.0, at least about 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 can be at most about 10.0, at most about 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.

[0236] In some embodiments, the pH of a reactor in a digestion system can be about 3 to about 9. In some embodiments, the pH of a reactor in a digestion system can 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 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 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.

[0237] In some embodiments, the reactors can 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 can be anaerobic, microaerobic, or aerobic. Without wishing to be bound by theory, the aerobic conditions of the reactors of the digestion system can enrich biocontrol-promoting microbes and / or metabolites with biocontrol capability in the microbial consortium of the system.Working Fluids and Microbial Consortia

[0238] A working fluid can 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 moreWSGR Docket No. 63472-722.601isolated 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 can allow for the expansion of microbes or act as a culture for an inoculum of a microbe to grow. A working fluid can 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 can comprise a first working fluid. In some embodiments, a working fluid in a second reactor can comprise a second working fluid. In some embodiments, a working fluid in a third reactor can comprise a third working fluid. In some embodiments, a working fluid in a fourth reactor can comprise a fourth working fluid. In some embodiments, a working fluid in a fifth reactor can comprise a fifth working fluid. In some embodiments, at least a portion of the second working fluid can be transferred to the third reactor. In some embodiments, at least a portion of the third working fluid can be transferred to the fourth reactor. In some embodiments, at least a portion of the fourth working fluid can be transferred to the fifth reactor. In some embodiments, a working fluid can be mixed in a reactor (e.g., chamber or container) prior to a first reactor. In some embodiments, the working fluid in each reactor can be distinct from the working fluid in other reactors in the digestion system. Distinct working fluids can comprise different microbial populations. The different microbial populations can include different microbes, (e.g., bacteria, fungi, algae, or any combination thereof). Distinct working fluids can comprise different concentrations of a target isolate. Distinct working fluids can comprise different concentrations of a carbon source and / or a nitrogen source. Distinct working fluids can 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 can be similar to a working fluid of a different reactor of the digestion system. The working fluid in each reactor can comprise different microbial populations. The different microbial populations can include different bacteria, fungi, algae, or any combination thereof.

[0239] The working fluid within a container of the bioreactor system can comprise one or more enzymes. The working fluid within one or more reactors (e.g., within each reactor) can comprise the same enzymes, which can be produced by microbes within the working fluid. The working fluid within one or more reactors (e.g., within each reactor) can comprise different enzymes, which can be produced by microbes within the working fluid. An enzyme within a working fluid can 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 arylsulphatase, 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 combinationWSGR Docket No. 63472-722.601thereof. An enzyme within a working fluid can comprise nitrogenase, 1 -aminocyclopropane- 1 -carboxylate deaminase (e.g., ACC-deaminase), quinoprotein glucose dehydrogenase (e.g., PQQ or quinone), gluconate 2-dehydrogenase, cellulase, endo-1,3(4)-β-glucanase, pectin lyase, or any combination thereof. In some embodiments, the enzyme can be a cellulase. The working fluid within each reactor can comprise different concentrations of enzymes. The working fluid within each reactor can comprise a different average abundance of an enzyme. An enzyme can be present at an average abundance of less than 0.001%. An enzyme can be present at an average abundance of greater than 1%. In some embodiments, an enzyme can 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 can 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 can comprise enzymes with different enzymatic activity. Enzymatic activity can include, but is not limited to, nitrogen fixation, ammonia production, phosphate solubilization, cell wall lysing, or any combination thereof.

[0240] A working fluid can comprise different digestion products from working fluid within other reactors of the system. In some embodiments, a working fluid can comprise digestion products from an aqueous organic feedstock and microbial consortium at least partially derived from a previous working fluid.

[0241] The pH of a working fluid within each reactor can be different from working fluid in other reactors. The pH of a working fluid within each reactor can be the same. The pH of a working fluid can be less than 6. The pH of a working fluid can be greater than 6. The pH of a working fluid can be in a range from 2 to 11. The pH of a working fluid can 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 can 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. In some embodiments, the pH of a working fluid with any one or more of the reactors can be from about about 5.0 to about 9.0, about 5.0 to about 8.0, about 5.0 to about 7.5, about 5.0 to about 7.0, about 5.5 to about 9.0, about 5.5 to about 8.0, about 5.5 to about 7.5, about 5.5 to about 7.0, about 6.0 to about 9.0, about 6.0 to about 8.0, about 6.0 to about 7.5, about 6.0 to about 7.0, about 6.5 to about 9.0, about 6.5 to about 8.0, about 6.5 to about 7.5, or from about 6.5 to about 7.0.

[0242] The microbial consortia disclosed herein can be stable. In a stable microbial consortium, the identity and relative abundance of bacteria does not appreciably change overtime, such as over a period 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, 6 weeks, 8 weeks, 12 weeks, or greater than about 15 weeks. In a stable microbial consortium, the identity and relative abundance of bacteria does not appreciably change overtime, such as over a period of at most about 12 weeks, 8 weeks, 6 weeks, 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. In some embodiments, in a stable microbial consortium, the identity and relative abundance of bacteria does not appreciably change overtime, such asWSGR Docket No. 63472-722.601over a period of from about 2 weeks to about 12 weeks, from about 2 weeks to about 8 weeks, from about 2 weeks to about 4 weeks, or for about 3-4 weeks.

[0243] In some embodiments, the microbial consortia can be characterized by population analysis. The population analysis can comprise a community analysis, determination of the core community, and computation of a microbial -community distance matrix. In some embodiments, the microbial consortia can be characterized in batches. Characterization of the microbial consortia can be measured in at least about 1, 2, 3, 4, 5, 6, 7, 8 or more batches. Characterization of the microbial consortia can 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 can be determined. The most abundant species of the microbial consortia can 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 can have microbial consortia with different species being the most abundant.

[0244] In some embodiments, a first microbial consortium can be established in a mixing chamber, in which various inputs can be mixed into a homogenous aqueous mixture to be input into a digestion reactor. In some embodiments, a digestion system described herein can comprise one or more mixing chambers in which a microbial consortium can be established. The first microbial consortium can 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 can 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 can 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 can 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 can 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 can 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 can be derived from inputs to a first reactor and can be present in a base product of a digestion system. A first microbial consortium can 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 can shift its microbial population and form a second microbial consortium. A second microbial consortium can 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 can shift its microbial population and form a third microbial consortium. A third microbial consortium can be present in a first reactor, a second reactor, a third reactor, or a clarifier. Without wishingWSGR Docket No. 63472-722.601to be bound by theory, a third microbial consortium in a working fluid can shift its microbial population and form a fourth microbial consortium. A fourth microbial consortium can 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 can shift its microbial population and form a fifth microbial consortium. A fifth microbial consortium can be present in a first reactor, a second reactor, a third reactor, or a clarifier. Microbial consortia of the digestion system described herein can 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.

[0245] A portion of a first working fluid can 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 can comprise a second working fluid. A portion of a second working fluid can 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 can comprise a third working fluid. A portion of a third working fluid can 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 can comprise a fourth working fluid. A portion of a fourth working fluid can 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 can comprise a fifth working fluid. A portion of a fifth working fluid can 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 can comprise a sixth working fluid.

[0246] The working fluid of a container in the digestion system can incubate in the container. A flow rate of the digestion system can increase or decrease a volume of working fluid. The working fluid of a first, second, third, fourth, fifth, or sixth container can increase in volume over a time period. The working fluid of a first, second, third, fourth, fifth, or sixth container can decrease in volume over a time period. The working fluid of a first, second, third, fourth, fifth, or sixth container cannot increase or decrease in volume over a time period. The volume of working fluid in each of the containers of a digestion system can be the same. The volume of working fluid in each of the containers of a digestion system can 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 can be constant (e.g., unchanging over a time period). A constant volume can comprise a volume that cannot 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.

[0247] As working fluid flows from each container of digestion system, the working fluid can comprise a flow rate. A first flow rate can comprise a flow rate of an aqueous feedstock inputted into a first container from a source outside the digestion system. A second flow rate can comprise a flow rate of a working fluid from a first container into a second container. A third flow rate can comprise a flow rate of a working fluid from a second container into a third container. A fourth flow rate can comprise a flow rate of a working fluid from a third container into a fourth container. A fifth flow rate can 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, thirdWSGR Docket No. 63472-722.601flow rate, fourth flow rate, fifth flow rate) can 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) can 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.

[0248] 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 in-putted into the digestion system can comprise a microbial consortium. Incubation in the digestion system can 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 can have a desired plant growth promotion property. The plant growth promotion property can comprise shoot biomass, root biomass, nutrient uptake, photosynthetic activity, crop yield, deaminase activity, acid production, leaf area, chlorophyll content, or total biomass.

[0249] Reactors of a digestion system can be fluidly connected. A portion of a working fluid in a first container can be transferred to a fluidly connected second container. A portion of a working fluid in a second container can be transferred to a fluidly connected third container. A portion of a working fluid in a third container can be transferred to a fluidly connected fourth container. A portion of a working fluid in a fourth container can be transferred to a fluidly connected fifth container. A portion of a working fluid in a fifth container can be transferred to a fluidly connected sixth container. In some embodiments, a transfer of working fluid between containers of a digestion system described herein can be continuous. A continuous flow of working fluid can 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) can 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) can have a second flow rate. In some embodiments, the first flow rate and the second flow rate are equal. A first flow rate can comprise a flow rate of fluid transferred from a source outside the digestion system into a first container. A second flow rate can 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.WSGR Docket No. 63472-722.601

[0250] 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 can 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 can be maintained at a constant volume. A constant volume can be maintained by a continuous flow of fluid through a digestion system described herein.

[0251] In some embodiments, a digestion system can be inoculated with an inoculum of a microbe (e.g., an inoculum of a microbial strain). The inoculum of a microbial strain can 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 can comprise a mixture of multiple isolated microbes. The inoculum of a microbe can 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 can 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.

[0252] In some cases, a digestion system cannot be reinoculated with an isolate (e.g., microbial strain) or combination of isolates following a first inoculation. Reinoculation of a digestion system can comprise providing a microbial strain following a previous inoculation. Reinoculation of a digestion system can 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 can 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 can 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 can 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 can be reinoculated with a microbial strain described herein after operating the digestion system for a time period. For example, a digestion system can 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 can 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.WSGR Docket No. 63472-722.601

[0253] 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% of 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) can comprise small particles from a working fluid of a digestion system. The biosolids (e.g., floc) can accumulate in a clarifier chamber overtime and separate from a supernatant (e.g., base product). In some embodiments, the population of the microbial strain can 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 can be retained in the floc (e.g., biosolids) of the digestion system. Floc can be generated at any point during operating of a bioreactor system as described herein. For example, floc can 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 can be generated in a clarifier chamber of a bioreactor system. In some embodiments, floc can comprise at least a portion of biocontrol-promoting microbes generated in a digestion system described herein.

[0254] In some embodiments, there can 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 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 can 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 can 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 can 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 toWSGR Docket No. 63472-722.601about 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 CFU / ml, about 2 logs CFU / ml to about 6 logs CFU / ml, about 2 logs CFU / ml to about 7 logs CFU / ml, about 2 logs CFU / ml to about 8 logs CFU / ml, about 3 logs CFU / ml to about 4 logs CFU / ml, about 3 logs CFU / ml to about 5 logs CFU / ml, about 3 logs CFU / ml to about 6 logs CFU / ml, about 3 logs CFU / ml to about 7 logs CFU / ml, about 3 logs CFU / ml to about 8 logs CFU / ml, about 4 logs CFU / ml to about 5 logs CFU / ml, about 4 logs CFU / ml to about 6 logs CFU / ml, about 4 logs CFU / ml to about 7 logs CFU / ml, about 4 logs CFU / ml to about 8 logs CFU / ml, about 5 logs CFU / ml to about 6 logs CFU / ml, about 5 logs CFU / ml to about 7 logs CFU / ml, about 5 logs CFU / ml to about 8 logs CFU / ml, about 6 logs CFU / ml to about 7 logs 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.

[0255] In some embodiments, there can 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 can 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 can 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 can 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 CFU / ml, about 2 logs CFU / ml to about 6 logs CFU / ml, about 2 logs CFU / ml to about 7 logs CFU / ml, about 2 logs CFU / ml to about 8 logs CFU / ml, about 3 logs CFU / ml to about 4 logs CFU / ml, about 3 logs CFU / ml to about 5 logs CFU / ml, about 3 logs CFU / ml to about 6 logs CFU / ml, about 3 logs CFU / ml to about 7 logs CFU / ml, about 3 logs CFU / ml to about 8 logs CFU / ml, about 4 logs CFU / ml to about 5 logs CFU / ml, about 4 logs CFU / ml to about 6 logs CFU / ml, about 4 logs CFU / ml to about 7 logs CFU / ml, about 4 logs CFU / ml to about 8 logs CFU / ml, about 5 logs CFU / ml to about 6 logs CFU / ml, about 5 logs CFU / ml to about 7 logs CFU / ml, about 5 logs CFU / ml to about 8 logs CFU / ml, about 6 logs CFU / ml to about 7 logs 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 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.WSGR Docket No. 63472-722.601

[0256] Incubation of a microbial consortium in the digestion system can enrich a microbial community with biocontrol properties and / or plant growth promotion properties (e.g., biocontrol-promoting microbes). Incubation of the inoculum of the microbe, the biocontrol-promoting microbes of the microbial consortium, or any combination thereof can generate metabolites with desired biocontrol properties and / or plant growth promotion properties (e.g., biocontrol-promoting metabolites. The inoculum of the microbe, biocontrolpromoting microbes of the microbial consortium, biocontrol-promoting metabolites, or any combination thereof can be biocontrol-promoting microbes in the working fluid of the system and / or in the output product (e.g., base product) of the digestion system. A concentration of biocontrol-promoting microbes can increase throughout a retention time of a digestion system described herein. The concentration of biocontrol-promoting microbes can increase from a first container to a second container of the digestion system. The concentration of biocontrol-promoting microbes can increase from a first container to a third container of the digestion system. The concentration of biocontrol-promoting microbes can increase from a first container to a fourth container of the digestion system. The concentration of biocontrol-promoting microbes can increase from a first container to a fifth container of the digestion system. The concentration of biocontrol -promoting microbes can increase from a first container to a sixth container of the digestion system. In some embodiments, an output product (e.g., base product) can have a higher concentration of biocontrol-promoting microbes than a concentration of biocontrol-promoting microbes in a first container of a digestion system.

[0257] In some embodiments, a concentration of biocontrol-promoting microbes can increase from a first container to a second container, a third container, a fourth container, a fifth container, and / or a sixth container of a digestion system described herein. In some embodiments, a concentration of biocontrolpromoting microbes in a second container, a third container, a fourth container, a fifth container, and / or a sixth container can be at least about 50x, at least about lOOx, at least about 200x, at least about 250x, at least about 300x, at least about 400x, at least about 500x, at least about 600x, at least about 700x, at least about an 800x, at least about 900x, at least about lOOOx, at least about I250x, at least about I500x, at least about 2000x, or greater than about 2000x increased from a concentration of biocontrol-promoting microbes in a first container of a digestion system described herein. In some embodiments, a concentration of biocontrol-promoting microbes in a second container, a third container, a fourth container, a fifth container, and / or a sixth container can be at most about 2000x, at most about I500x, at most about 125 Ox, at most about lOOOx, at most about 900x, at most about an 800x, at most about 700x, at most about 600x, at most about 500x, at most about 400x, at most about 300x, at most about 25 Ox, at most about 200x, at most about lOOx, at most about 50x, or less than about 50x increased from a concentration of biocontrol-promoting microbes in a first container of a digestion system described herein.

[0258] In some embodiments, a concentration of biocontrol-promoting microbes in a second container, a third container, a fourth container, a fifth container, and / or a sixth container can be from about 25x to about 2,500x increased from a concentration of biocontrol-promoting microbes in a first container of a digestion system described herein. In some embodiments, a concentration of biocontrol-promoting microbes in aWSGR Docket No. 63472-722.601second container, a third container, a fourth container, a fifth container, and / or a sixth container can be from about 25x to about 50x, about 25x to about lOOx, about 25x to about 150x, about 25x to about 200x, about 25x to about 250x, about 25x to about 500x, about 25x to about 750x, about 25x to about l,000x, about 25x to about l,500x, about 25x to about 2,000x, about 25x to about 2,500x, about 50x to about lOOx, about 5 Ox to about 15 Ox, about 5 Ox to about 200x, about 5 Ox to about 25 Ox, about 50x to about 500x, about 50xto about 750x, about 50xto about l,000x, about 50xto about l,500x, about 50xto about 2,000x, about 5 Ox to about 2,5 OOx, about lOOxto about 15 Ox, about lOOxto about 200x, about lOOxto about 25 Ox, about lOOx to about 500x, about lOOx to about 750x, about lOOx to about l,000x, about lOOx to about l,500x, about lOOx to about 2,000x, about lOOx to about 2,500x, about 150x to about 200x, about 150x to about 250x, about 150x to about 500x, about 150x to about 750x, about 150x to about l,000x, about 150x to about l,500x, about 150x to about 2,000x, about 150x to about 2,500x, about 200x to about 250x, about 200x to about 500x, about 200x to about 750x, about 200x to about l,000x, about 200x to about l,500x, about 200x to about 2,000x, about 200x to about 2,500x, about 250x to about 500x, about 250x to about 750x, about 250x to about l,000x, about 250x to about l,500x, about 250x to about 2,000x, about 250x to about 2,500x, about 500x to about 750x, about 500x to about l,000x, about 500x to about l,500x, about 500xto about 2,000x, about 500xto about 2,500x, about 750xto about l,000x, about 750xto about l,500x, about 750x to about 2,000x, about 750x to about 2,500x, about l,000x to about l,500x, about l,000x to about 2,000x, about l,000x to about 2,500x, about l,500x to about 2,000x, about l,500x to about 2,500x, or about 2,000x to about 2,5 OOx.

[0259] In some embodiments, a proportion of a concentration of biocontrol-promoting microbes relative to a total bacterial population count can increase across containers of a fluidly connected digestion system. In some embodiments, a proportion of a concentration biocontrol-promoting microbes relative to a total bacterial population count can increase from one container to another container of a digestion system described herein. In some embodiments, a proportion of a concentration biocontrol -promoting microbes relative to a total bacterial population count can increase from a first container to a second container of a digestion system described herein. The first container can be any container in a bioreactor system. In some embodiments, a proportion of a concentration biocontrol-promoting microbes relative to a total bacterial population count can increase from a first container to a third container of a digestion system described herein. In some embodiments, a proportion of a concentration biocontrol-promoting microbes relative to a total bacterial population count can increase from a first container to a fourth container of a digestion system described herein. In some embodiments, a proportion of a concentration biocontrol-promoting microbes relative to a total bacterial population count can increase from a first container to a fifth container of a digestion system described herein. In some embodiments, a proportion of a concentration biocontrolpromoting microbes relative to a total bacterial population count can increase from a first container to a sixth container of a digestion system described herein.

[0260] Population of the microbe can be measured using methods including but not limited to spectrophotometers, cell counting, measures of turbidity, hemocytometers, electronic enumeration,WSGR Docket No. 63472-722.601determination of nitrogen content, measures of cell mass, quantitative polymerase-chain reaction (qPCR), semi-quantitative PCR, and measures of cell activity.

[0261] The addition of the isolate (e.g., the microbial biocontrol agent) can have an added benefit in improving target functionality of working solution in a reactor of the digestion system and / or in the output base product of the digestion system. In some embodiments, addition of the inoculum of the microbial strain can improve the biocontrol capacity of working fluids and base product of a digestion system compared to working fluids and base product of a digestion system without an inoculum of the microbial.

[0262] A digestion system can be inoculated with a microbial strain at the start of a digestion system, which can allow for the microbial strain to flow through the system and working fluids of the reactors. Without wishing to be bound by theory, a digestion system inoculated with a microbial strain can increase a biocontrol capacity of a working fluid and / or a base product compared to a working fluid and / or base product of an otherwise identical digestion system with no inoculated microbial strain. Without wishing to be bound by theory, a digestion system inoculated with a microbial strain can increase a biocontrol capacity of a working fluid and / or a base product compared to a working fluid and / or base product of an otherwise identical digestion system with the microbial strain added (e.g., spiked) at the end of the system. Without wishing to be bound by theory, a digestion system inoculated with a microbial strain can increase a biocontrol capacity of a base product compared to a base product of an otherwise identical digestion system with the microbial strain added (e.g., spiked) at the end of the system. Incubation of the microbial strain in the digestion system can enrich the working fluid with biocontrol-promoting microbes and / or generate biocontrol-promoting metabolites.

[0263] In some embodiments, a system described herein can demonstrate enrichment of bacteria and / or enzymes. A working fluid from a container of a bioreactor system described herein can show increased abundance of one or more bacteria and / or enzymes compared to an abundance of the one or more bacteria and / or enzymes in a working fluid of a container that precedes the other container. For example, a working fluid from a container in a second stage of a bioreactor system (e.g., a multi-stage bioreactor system) can show increased abundance of one or more bacteria and / or enzymes compared to an abundance of the one or more bacteria and / or enzymes in a working fluid of a container in the first stage of the bioreactor system (e.g., the multi-stage bioreactor system).

[0264] In some embodiments, a working fluid from a second stage reactor described herein can show a different abundance of one or more bacteria and / or enzymes relative to a working fluid from a first stage container (e.g., primary clarifier) described herein. The abundance can be an increased abundance in the one or more bacteria and / or enzymes. The abundance can be a decreased abundance in the one or more bacteria and / or enzymes. In some embodiments, a working fluid from a second reactor or third reactor in a second stage of a bioreactor system (e.g., a multi-stage bioreactor system) can show a different abundance of one or more bacteria and / or enzymes relative to a working fluid of a first reactor in the second stage of the bioreactor system (e.g., the multi-stage bioreactor system. The abundance can be an increasedWSGR Docket No. 63472-722.601abundance in the one or more bacteria and / or enzymes. The abundance can be a decreased abundance in the one or more bacteria and / or enzymes.

[0265] There can be an enrichment of bacteria with biocontrol -related functional enzymatic abilities in a system described herein. Cellulase is an enzyme that can be produced by biocontrol agents. Cellular can help limit the spread of one or more pathogens in plants. Cellulase can be produced by biocontrol bacteria and can break down pathogens. For example, cellular can break down the cell wall, DNA, and / or proteins of one or more pathogen (e.g., plant pathogens, e.g., phytopathogens). Cellular can help manage plant pathogens and can (i) treat a plant infected by a pathogen, (ii) protect a plant against a plant pathogen, or (iii) any combination thereof. In some embodiments, along an assembly of container of a system described herein, there can be a greater abundance of bacteria with biocontrol-related functional enzymatic abilities (e.g., cellulase-active bacteria) in the working fluid of (i) a second container compared to that of a first container, (ii) a second container compared to that of a first container, (iii) a third container compared to that of a first container, (iv) a fourth container compared to that of a first container, (v) a fifth container compared to that of a first container, (vi) a sixth container compared to that of a first container, (vii) a seventh container compared to that of a first container, (viii) or any combination thereof. A first container, second container, third container, fourth container, fifth container, sixth container, seventh container, or any combination thereof can be present in the system or in a stage of a system (e.g. a stage of a multi-stage bioreactor system). As another example, in a system described herein, there can be a greater abundance of bacteria with biocontrol-related functional enzymatic abilities (e.g., cellulase-active bacteria) in the working fluid of (i) a first container of a second stage compared to that of a container in a first stage (e.g., a primary clarifier); (ii) a second container of a second stage compared to that of a container in a first stage (e.g., a primary clarifier); (iii) a third container of a second stage compared to that of a container in a first stage (e.g., a primary clarifier); (iv) a fourth container of a second stage compared to that of a container in a first stage (e.g., a primary clarifier); or any combination thereof.

[0266] In some embodiments, a product of a system described herein (e.g., a base product) can have an abundance of bacteria with biocontrol-related functional enzymatic abilities. Bacteria with biocontrol-related functional enzymatic abilities may be cellulase -active bacteria, chitinase -producing microbes, protease -producing microbes, or any combination thereof. In some embodiments, a product of a system described herein (e.g., a base product) can have greater abundance of bacteria with biocontrol-related functional enzymatic abilities (e.g., cellulase -active bacteria) compared to a working fluid of any container in the system. For example, a product of a system described herein (e.g., a base product) can have greater abundance of bacteria with biocontrol-related functional enzymatic abilities (e.g., cellulase-active bacteria) compared to a working fluid obtained from a container in a first stage of a bioreactor system (e.g., a primary clarifier) and / or a working fluid obtained from a container in a first stage of a bioreactor system (e.g., a first second-stage reactor, a second second-stage reactor, a third second-stage reactor, a fourth second-stage reactor, a secondary clarifier, or any combination thereof).WSGR Docket No. 63472-722.601

[0267] In some embodiments, a working fluid of a system described herein comprising a microbial strain (e.g., a microbial biocontrol agent) can show greater abundance of bacteria with biocontrol-related functional enzymatic abilities (e.g., cellulase -active bacteria) compared to a working fluid of a system described herein that cannot comprise the microbial strain (e.g., a microbial biocontrol agent). In some embodiments, a working fluid of a container of a bioreactor system can comprise an abundance of bacteria with biocontrol-related functional enzymatic abilities (e.g., cellulase-active bacteria), measured in colonyforming units (cfu / ml). In some embodiments, a working fluid of a container in a first stage (e.g., a primary clarifier) can comprise an abundance of bacteria with biocontrol-related functional enzymatic abilities (e.g., cellulase-active bacteria) of at least about 1.0E+03 cfu / ml, at least about 5.0E+03 cfu / ml, at least about 1.0E+04 cfu / ml, at least about 5.0E+04 cfu / ml, at least about 1.0E+05 cfu / ml, at least about 5.0E+05 cfu / ml, at least about 1.0E+06 cfu / ml, at least about 5.0E+06 cfu / ml, at least about 1.0E+07 cfu / ml, at least about 5.0E+07 cfu / ml, at least about 1.0E+08 cfu / ml, or greater than about 1.0E+08 cfu / ml. In some embodiments, a working fluid of a container in a first stage (e.g., a primary clarifier) can comprise an abundance of bacteria with biocontrol-related functional enzymatic abilities (e.g., cellulase-active bacteria) of at most about 1.0E+08 cfu / ml, at most about 5.0E+07 cfu / ml, at most about 1.0E+07 cfu / ml, at most about 5.0E+06 cfu / ml, at most about 1.0E+06 cfu / ml, at most about 5.0E+05 cfu / ml, at most about 1.0E+05 cfu / ml, at most about 5.0E+04 cfu / ml, at most about 1.0E+04 cfu / ml, at most about 5.0E+03 cfu / ml, at most about 1.0E+03 cfu / ml, or less than about 1.0E+03 cfu / ml. In some embodiments, a working fluid of a container in a second stage described herein (e.g., a first second-stage reactor, a second second-stage reactor, a third second-stage reactor, or any combination thereof) can comprise an abundance of bacteria with biocontrol-related functional enzymatic abilities (e.g., cellulase -active bacteria) of at least about 1.0E+03 cfu / ml, at least about 5.0E+03 cfu / ml, at least about 1.0E+04 cfu / ml, at least about 5.0E+04 cfu / ml, at least about 1.0E+05 cfu / ml, at least about 5.0E+05 cfu / ml, at least about 1.0E+06 cfu / ml, at least about 5.0E+06 cfu / ml, at least about 1.0E+07 cfu / ml, at least about 5.0E+07 cfu / ml, at least about 1.0E+08 cfu / ml, or greater than about 1.0E+08 cfu / ml. In some embodiments, a working fluid of a container in a second stage described herein (e.g., a first second-stage reactor, a second second-stage reactor, a third second-stage reactor, or any combination thereof) can comprise an abundance of bacteria with biocontrol-related functional enzymatic abilities (e.g., cellulase-active bacteria) of at most about 1.0E+08 cfu / ml, at most about 5.0E+07 cfu / ml, at most about 1.0E+07 cfu / ml, at most about 5.0E+06 cfu / ml, at most about 1.0E+06 cfu / ml, at most about 5.0E+05 cfu / ml, at most about 1.0E+05 cfu / ml, at most about 5.0E+04 cfu / ml, at most about 1.0E+04 cfu / ml, at most about 5.0E+03 cfu / ml, at most about 1.0E+03 cfu / ml, or less than about 1.0E+03 cfu / ml. In some embodiments, a product of a system described herein (e.g., a biocontrol product) can comprise an abundance of bacteria with biocontrol-related functional enzymatic abilities (e.g., cellulase -active bacteria) of at least about I.0E+03 cfu / ml, at least about 5.0E+03 cfu / ml, at least about 1.0E+04 cfu / ml, at least about 5.0E+04 cfu / ml, at least about I.0E+05 cfu / ml, at least about 5.0E+05 cfu / ml, at least about I.0E+06 cfu / ml, at least about 5.0E+06 cfu / ml, at least about 1.0E+07 cfu / ml, at least about 5.0E+07 cfu / ml, at least about 1.0E+08 cfu / ml, or greater than about 1.0E+08 cfu / ml.WSGR Docket No. 63472-722.601In some embodiments, a product of a system described herein (e.g., a biocontrol product) can comprise an abundance of bacteria with biocontrol-related functional enzymatic abilities (e.g., cellulase-active bacteria) of at most about 1.0E+08 cfu / ml, at most about 5.0E+07 cfu / ml, at most about 1.0E+07 cfu / ml, at most about 5.0E+06 cfu / ml, at most about 1.0E+06 cfu / ml, at most about 5.0E+05 cfu / ml, at most about 1.0E+05 cfu / ml, at most about 5.0E+04 cfu / ml, at most about 1.0E+04 cfu / ml, at most about 5.0E+03 cfu / ml, at most about 1.0E+03 cfu / ml, or less than about 1.0E+03 cfu / ml.

[0268] In some embodiments, a working fluid of a container in a system described herein can have a proportion of bacteria with biocontrol-related functional enzymatic abilities (e.g., cellulase-active bacteria) relative to a total bacterial population present in the working fluid. A working fluid of a container in a system described herein can have a greater proportion of bacteria with biocontrol-related functional enzymatic abilities (e.g., cellulase-active bacteria) compared to a proportion in the working fluid another container of the system. For example, a reactor (e.g., a second-stage reactor) of a system described herein can have a greater proportion of bacteria with biocontrol-related functional enzymatic abilities (e.g., cellulase-active bacteria) compared to a proportion in a working fluid of a clarifier (e.g., a primary clarifier described herein). As another example, a second reactor (e.g., a second second-stage reactor) of a system described herein can have a greater proportion of bacteria with biocontrol-related functional enzymatic abilities (e.g., cellulase-active bacteria) compared to a proportion in a working fluid of a first reactor (e.g., a first second-stage reactor). As another example, a third reactor (e.g., a third second-stage reactor) of a system described herein can have a greater proportion of bacteria with biocontrol-related functional enzymatic abilities (e.g., cellulase-active bacteria) compared to a proportion in a working fluid of a second reactor (e.g., a second second-stage reactor).

[0269] A proportion of bacteria with biocontrol-related functional enzymatic abilities (e.g., cellulaseactive bacteria) in a working fluid of a clarifier (e.g., a primary clarifier) described herein can be at least about 1%, 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%, at least about 9%, at least about 10%, at least about 15%, at least about 20%, or greater than about 20% relative to a total bacterial population in the working fluid. A proportion of bacteria with biocontrol-related functional enzymatic abilities (e.g., cellulase-active bacteria) in a working fluid of a clarifier (e.g., a primary clarifier) described herein can be at most about 20%, at most about 15%, at most about 10%, at most about 9%, 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%, at most about 1%, or less than about 1% relative to a total bacterial population in the working fluid. A proportion of bacteria with biocontrol-related functional enzymatic abilities (e.g., cellulase -active bacteria) in a working fluid of a reactor (e.g., a second-stage reactor) described herein can be at least about 5%, at least about 6%, at least about 7%, at least about 8%, at least about 9%, at least about 10%, at least about 15%, at least about 20%, at least about 25%, at least about 30%, at least about 40%, at least about 50%, at least about 60%, at least about 75%, or greater than about 75% relative to a total bacterial population in the working fluid. A proportion of bacteria with biocontrol-related functional enzymatic abilities (e.g., cellulase-active bacteria)WSGR Docket No. 63472-722.601in a working fluid of a clarifier (e.g., a primary clarifier) described herein can be at most about 75%, at most about 60%, at most about 50%, at most about 40%, at most about 30%, at most about 25%, at most about 20%, at most about 15%, at most about 10%, at most about 9%, at most about 8%, at most about 7%, at most about 6%, at most about 5%, or less than about 5% relative to a total bacterial population in the working fluid.

[0270] In some embodiments, a proportion of bacteria with biocontrol-related functional enzymatic abilities (e.g., cellulase-active bacteria) in a working fluid of a reactor (e.g., a second-stage reactor) can be a fold-change greater than a proportion of bacteria with biocontrol-related functional enzymatic abilities (e.g., cellulase-active bacteria) in a working fluid of a clarifier (e.g., a primary clarifier) described herein. In some embodiments, a proportion of bacteria with biocontrol-related functional enzymatic abilities (e.g., cellulase-active bacteria) in a working fluid of a reactor (e.g., a second-stage reactor) can be at least about 1.1-fold higher, at least about 1.2-fold higher, at least about 1.3-fold higher, at least about 1.4-fold higher, at least about 1.5-fold higher, at least about 1.6-fold higher, at least about 1.7-fold higher, at least about 1.8-fold higher, at least about 1.9-fold higher, at least about 2-fold higher, at least about 2.5-fold higher, at least about 3 -fold higher, at least about 4-fold higher, at least about 5 -fold higher, or greater than about 5-fold higher than a proportion of bacteria with biocontrol-related functional enzymatic abilities (e.g., cellulase-active bacteria) in a working fluid of a clarifier (e.g., a primary clarifier). In some embodiments, a proportion of bacteria with biocontrol-related functional enzymatic abilities (e.g., cellulase-active bacteria) in a working fluid of a clarifier (e.g., a primary clarifier) can be at most about 5 -fold higher, at most about 4-fold higher, at most about 3-fold higher, at most about 2.5-fold higher, at most about 2-fold higher, at most about 1.9-fold higher, at most about 1.8-fold higher, at most about 1.7-fold higher, at most about 1.6-fold higher, at most about 1.5-fold higher, at most about 1.4-fold higher, at most about 1.3-fold higher, at most about 1.2-fold higher, at most about 1.1-fold higher, or less than about 1.1-fold higher than a proportion of bacteria with biocontrol-related functional enzymatic abilities (e.g., cellulase-active bacteria) in a working fluid of a reactor (e.g., a second-stage reactor) described herein.

[0271] In some embodiments, a proportion of bacteria with biocontrol-related functional enzymatic abilities (e.g., cellulase-active bacteria) in a working fluid of a reactor (e.g., a second second-stage reactor and / or a third second-stage reactor) can be at least about 1.1 -fold higher, at least about 1.2-fold higher, at least about 1.3-fold higher, at least about 1.4-fold higher, at least about 1.5-fold higher, at least about 1.6-fold higher, at least about 1.7-fold higher, at least about 1.8-fold higher, at least about 1.9-fold higher, at least about 2-fold higher, at least about 2.5 -fold higher, at least about 3 -fold higher, at least about 4-fold higher, at least about 5 -fold higher, or greater than about 5 -fold higher than a proportion of bacteria with biocontrol-related functional enzymatic abilities (e.g., cellulase -active bacteria) in a working fluid of a reactor that precedes the other reactor (e.g., a first second-stage reactor). In some embodiments, a proportion of bacteria with biocontrol-related functional enzymatic abilities (e.g., cellulase-active bacteria) in a working fluid of a first reactor (e.g., a first second-stage reactor) can be at most about 5 -fold higher, at most about 4-fold higher, at most about 3-fold higher, at most about 2.5-fold higher, at most about 2-foldWSGR Docket No. 63472-722.601higher, at most about 1.9-fold higher, at most about 1.8-fold higher, at most about 1.7-fold higher, at most about 1.6-fold higher, at most about 1.5-fold higher, at most about 1.4-fold higher, at most about 1.3-fold higher, at most about 1.2-fold higher, at most about 1.1-fold higher, or less than about 1.1-fold higher than a proportion of bacteria with biocontrol-related functional enzymatic abilities (e.g., cellulase-active bacteria) in a working fluid of another reactor (e.g., a second second-stage reactor and / or a third second-stage reactor) described herein.

[0272] In some embodiments, a product (e.g., a biocontrol product or base product) of a system described herein can comprise a greater proportion of bacteria with biocontrol-related functional enzymatic abilities (e.g., cellulase -active bacteria) compared to a proportion in a working fluid of a container of the system. For example, a product (e.g., a biocontrol product or base product) of a system described herein can comprise a greater proportion of bacteria with biocontrol-related functional enzymatic abilities (e.g., cellulase-active bacteria) compared to a proportion in a working fluid of a clarifier (e.g., a primary clarifier) of the system. As another example, a product (e.g., a biocontrol product or base product) of a system described herein can comprise a greater proportion of bacteria with biocontrol -related functional enzymatic abilities (e.g., cellulase-active bacteria) compared to a proportion in a working fluid of a reactor (e.g., a first reactor (e.g., first second-stage reactor), second reactor (e.g., second second-stage reactor), third reactor (e.g., third second-stage reactor), or any combination thereof).

[0273] A proportion of bacteria with biocontrol-related functional enzymatic abilities (e.g., cellulaseactive bacteria) in a product (e.g., a biocontrol product) described herein can be at least about 5%, at least about 6%, at least about 7%, at least about 8%, at least about 9%, at least about 10%, at least about 15%, at least about 20%, at least about 25%, at least about 30%, at least about 40%, at least about 50%, at least about 60%, at least about 75%, or greater than about 75% relative to a total bacterial population in the working fluid. A proportion of bacteria with biocontrol-related functional enzymatic abilities (e.g., cellulase-active bacteria) in a product (e.g., a biocontrol product) described herein can be at most about 75%, at most about 60%, at most about 50%, at most about 40%, at most about 30%, at most about 25%, at most about 20%, at most about 15%, at most about 10%, at most about 9%, at most about 8%, at most about 7%, at most about 6%, at most about 5%, or less than about 5% relative to a total bacterial population in the working fluid.

[0274] In some embodiments, a proportion of bacteria with biocontrol-related functional enzymatic abilities (e.g., cellulase-active bacteria) in a product (e.g., a biocontrol product) described herein can be a fold-change greater than a proportion of bacteria with biocontrol-related functional enzymatic abilities (e.g., cellulase -active bacteria) in a working fluid of a clarifier (e.g., a primary clarifier) and / or reactor (e.g., second-stage reactor) described herein. In some embodiments, a proportion of bacteria with biocontrol-related functional enzymatic abilities (e.g., cellulase-active bacteria) in a product (e.g., a biocontrol product) described herein can be at least about 1.1-fold higher, at least about 1.2-fold higher, at least about 1.3-fold higher, at least about 1.4-fold higher, at least about 1.5-fold higher, at least about 1.6-fold higher, at least about 1.7-fold higher, at least about 1.8-fold higher, at least about 1.9-fold higher, at least about 2-WSGR Docket No. 63472-722.601fold higher, at least about 2.5-fold higher, at least about 3-fold higher, at least about 4-fold higher, at least about 5 -fold higher, or greater than about 5 -fold higher than a proportion of bacteria with biocontrol -related functional enzymatic abilities (e.g., cellulase-active bacteria) in a working fluid of a clarifier (e.g., a primary clarifier) and / or reactor (e.g., second-stage reactor). In some embodiments, a proportion of bacteria with biocontrol-related functional enzymatic abilities (e.g., cellulase -active bacteria) in a working fluid of a clarifier (e.g., a primary clarifier) and / or reactor (e.g., second-stage reactor) can be at most about 5-fold higher, at most about 4-fold higher, at most about 3-fold higher, at most about 2.5-fold higher, at most about 2-fold higher, at most about 1.9-fold higher, at most about 1.8-fold higher, at most about 1.7-fold higher, at most about 1.6-fold higher, at most about 1.5-fold higher, at most about 1.4-fold higher, at most about 1.3-fold higher, at most about 1.2-fold higher, at most about 1.1-fold higher, or less than about 1.1-fold higher than a proportion of bacteria with biocontrol-related functional enzymatic abilities (e.g., cellulase-active bacteria) in a product (e.g., a biocontrol product) described herein.

[0275] One or more enzymes can also be enriched in a bioreactor system described herein. For example, a relative abundance in bacteria with genomic capacity to create one or more enzymes with biocontrol abilities (e.g., cellulases, glucanases, chitinases, proteases, xylanases, amylases, lipases, or any combination thereof) may be increased in one container compared to another in the system. In some embodiments, one or more enzymes (e.g., enzymes with biocontrol abilities) that may be enriched in the system can be Beta glucosidase, Alpha-glucosidase, Alpha-amylase, Chitinase, Rhomboid-protease, Exo-1.4-beta-D-glucosaminidase, 6-phospho-beta-glucosidase, Oligo- 1.6-glucosidase, Oligosaccharide-reducing-end-xylanase, Chitosanase, Maltose-6.-phosphate-glucosidase, Glucan- 1,6-alpha-glucosidase, Glucuronoarabinoxylan-endo-1.4-beta-xylanase, Polygalacturonase, Cellulase, or any combination thereof.

[0276] For example, a relative abundance of one or more enzymes (e.g., enzymes with biocontrol abilities) can be greater in a product (e.g., a biocontrol product) compared to a relative abundance measured in working fluid of a container of the bioreactor system. For example, a relative abundance of one or more enzymes (e.g., enzymes with biocontrol abilities) can be greater in a product (e.g., a biocontrol product) compared to a relative abundance measured in working fluid from a clarifier (e.g., primary clarifier). As another example, a relative abundance of one or more enzymes (e.g., enzymes with biocontrol abilities) can be greater in a product (e.g., a biocontrol product) compared to a relative abundance measured in working fluid from a reactor (e.g., a first reactor (e.g., first second-stage reactor), second reactor (e.g., second second-stage reactor), third reactor (e.g., third second-stage reactor), or any combination thereof).

[0277] A relative abundance of one or more enzymes measured from a product (e.g., a biocontrol product) described herein can be at least about 1.1-fold higher, at least about 1.2-fold higher, at least about 1.3-fold higher, at least about 1.4-fold higher, at least about 1.5-fold higher, at least about 1.6-fold higher, at least about 1.7-fold higher, at least about 1.8-fold higher, at least about 1.9-fold higher, at least about 2-fold higher, at least about 2.5-fold higher, at least about 3-fold higher, at least about 4-fold higher, at least about 5 -fold higher, or greater than about 5 -fold higher than a relative abundance of the one or more enzymesWSGR Docket No. 63472-722.601measured from a working fluid of a clarifier (e.g., primary clarifier) and / or reactor (e.g., a first reactor (e.g., first second-stage reactor), second reactor (e.g., second second-stage reactor), third reactor (e.g., third second-stage reactor), or any combination thereof).Microbial Isolates

[0278] Certain microorganisms disclosed herein can have all of the identifying characteristics of the deposited strains and, in particular, the identifying characteristics of being able to promote plant growth, yield, biocontrol capacity, or any combination thereof as described herein. Microorganisms disclosed herein can refer to the deposited microorganisms as described herein, and strains derived therefrom.

[0279] In some embodiments, the bacterial strain is from Paenibacillus genus. In some embodiments, the bacterial strain is from a Paenibacillus ottowii species. In some embodiments, the Paenibacillus ottowii strain is the strain deposited under ATCC Accession No. PTA- 124703, or an isolated clone thereof. In some embodiments, the 16S rRNA gene of the microbial strain comprises the nucleotide sequence of SEQ ID NO: 1. In some embodiments, the microbial strain comprises a 16S rRNA gene comprising a nucleotide sequence that exhibits at least 80%, at least 85%, at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, at least 99%, at least 99.9%, or 100% sequence identity to a nucleotide sequence as set forth in SEQ ID NO: 1. In some embodiments, the gyrB gene of the microbial strain comprises the nucleotide sequence of SEQ ID NO: 2. In some embodiments, the microbial strain comprises a gyrB gene comprising a nucleotide sequence that exhibits at least 80%, at least 85%, at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, at least 99%, at least 99.9%, or 100% sequence identity to a nucleotide sequence as set forth in SEQ ID NO: 2. In some embodiments, the rpoB gene of the microbial strain comprises the nucleotide sequence of SEQ ID NO: 3. In some embodiments, the microbial strain comprises a rpoB gene comprising a nucleotide sequence that exhibits at least 80%, at least 85%, at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, at least 99%, at least 99.9%, or 100% sequence identity to a nucleotide sequence as set forth in SEQ ID NO: 3.

[0280] In some embodiments, the microbial strain is from a Bacillus genus. In some embodiments, the bacterial strain is from a Bacillus amyloliquefaciens species. In some embodiments, the Bacillus amyloliquefaciens strain is the strain deposited under ATCC Accession No. PTA-124702, or an isolated clone thereof. In some embodiments, the 16S rRNA gene of the microbial strain comprises the nucleotide sequence of SEQ ID NO: 4. In some embodiments, the microbial strain comprises a 16S rRNA gene comprising a nucleotide sequence that exhibits at least 80%, at least 85%, at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, at least 99%, at least 99.9%, or 100% sequence identity to a nucleotide sequence as set forth in SEQ ID NO: 4. In some embodiments, the gyrB gene of the microbial strain comprises the nucleotide sequence of SEQ ID NO: 5. In some embodiments, the microbial strain comprises a gyrB gene comprising a nucleotide sequence that exhibits at least 80%, at least 85%, at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, atWSGR Docket No. 63472-722.601least 95%, at least 96%, at least 97%, at least 98%, at least 99%, at least 99.9%, or 100% sequence identity to a nucleotide sequence as set forth in SEQ ID NO: 5. In some embodiments, the rpoB gene of the microbial strain comprises the nucleotide sequence of SEQ ID NO: 6. In some embodiments, the microbial strain comprises a rpoB gene comprising a nucleotide sequence that exhibits at least 80%, at least 85%, at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, at least 99%, at least 99.9%, or 100% sequence identity to a nucleotide sequence as set forth in SEQ ID NO: 6.

[0281] In some embodiments, the microbial strain is from a Bacillus genus. In some embodiments, the bacterial strain is from a Bacillus amyloliquefaciens species. In some embodiments, the Bacillus amyloliquefaciens strain is the strain deposited under ATCC Accession No. PTA-124708, or an isolated clone thereof. In some embodiments, the 16S rRNA gene of the microbial strain comprises the nucleotide sequence of SEQ ID NO: 7. In some embodiments, the microbial strain comprises a 16S rRNA gene comprising a nucleotide sequence that exhibits at least 80%, at least 85%, at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, at least 99%, at least 99.9%, or 100% sequence identity to a nucleotide sequence as set forth in SEQ ID NO: 7. In some embodiments, the gyrB gene of the microbial strain comprises the nucleotide sequence of SEQ ID NO: 8. In some embodiments, the microbial strain comprises a gyrB gene comprising a nucleotide sequence that exhibits at least 80%, at least 85%, at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, at least 99%, at least 99.9%, or 100% sequence identity to a nucleotide sequence as set forth in SEQ ID NO: 8. In some embodiments, the rpoB gene of the microbial strain comprises the nucleotide sequence of SEQ ID NO: 9. In some embodiments, the microbial strain comprises a rpoB gene comprising a nucleotide sequence that exhibits at least 80%, at least 85%, at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, at least 99%, at least 99.9%, or 100% sequence identity to a nucleotide sequence as set forth in SEQ ID NO: 9.

[0282] In some embodiments, the microbial strain is from a Bacillus genus. In some embodiments, the bacterial strain is from a Bacillus amyloliquefaciens species. In some embodiments, the Bacillus amyloliquefaciens strain is the strain deposited under ATCC Accession No. PTA-124707, or an isolated clone thereof. In some embodiments, the 16S rRNA gene of the microbial strain comprises the nucleotide sequence of SEQ ID NO: 10. In some embodiments, the microbial strain comprises a 16S rRNA gene comprising a nucleotide sequence that exhibits at least 80%, at least 85%, at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, at least 99%, at least 99.9%, or 100% sequence identity to a nucleotide sequence as set forth in SEQ ID NO: 10. In some embodiments, the gyrB gene of the microbial strain comprises the nucleotide sequence of SEQ ID NO: 11. In some embodiments, the microbial strain comprises a gyrB gene comprising a nucleotide sequence that exhibits at least 80%, at least 85%, at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, at least 99%, at least 99.9%, or 100% sequence identityWSGR Docket No. 63472-722.601to a nucleotide sequenc...

Claims

1. WSGR Docket No. 63472-722.6012.CLAIMS WHAT IS CLAIMED IS:

1. A method of making a product having a biocontrol property, the method comprising:4.(a) providing a bioreactor system comprising one or more containers, wherein the one or more containers comprise a working fluid and a microbial biocontrol agent; and (b) collecting the product from the bioreactor system, wherein the product has the biocontrol property, and5.wherein the microbial biocontrol agent is present in the product collected from the bioreactor system at a concentration of at least 1.0 x 104colony forming units per milliliter (cfu / ml).

2. The method of claim 1, wherein the microbial biocontrol agent is a bacteria or fungi.

3. The method of claim 1, wherein the microbial biocontrol agent is a bacteria.

4. The method of any one of claims 1-3, wherein the microbial biocontrol agent is a microbial strain of the genus Bacillus.

5. The method of any one of claims 1-4, wherein the microbial biocontrol agent is of the species Bacillus amyloliquefaciens.

6. The method of any one of claims 1-3, wherein the microbial biocontrol agent is a microbial strain of the genus Paenibacillus.

7. The method of claim 6, wherein the microbial biocontrol agent is of the species Paenibacillus ottowii.

8. The method of any one of claims 1-7, wherein the microbial biocontrol agent is the microbial strain deposited under ATCC Accession No. PTA- 124703 (MS 2379), ATCC Accession No. PTA- 124708 (MS2697), ATCC Accession No. PTA-124707 (MS2681), or ATCC Accession No. PTA- 124702 (MS2335).

9. The method of any one of claims 1-8, wherein the microbial biocontrol agent is the microbial strain deposited under ATCC Accession No. PTA-124703 (MS2379).

10. The method of any one of claims 1-9, wherein the one or more containers of the bioreactor system comprise an aqueous feedstock comprising a microbial consortium.

11. The method of claim 10, wherein the aqueous feedstock comprises an organic substrate.

12. The method of claim 11, wherein the organic substrate comprises seaweed, manure, or any combination thereof.

13. The method of claim 12, wherein the organic substrate comprises seaweed.

14. The method of claim 13, wherein the seaweed comprises kelp.

15. The method of claim 13, wherein the kelp is of the genus Ascophyllum.

16. The method of claim 15, wherein the kelp is of the species Ascophyllum nodosum.

17. The method of any one of claims 1-16, wherein the bioreactor system comprises chitin.WSGR Docket No. 63472-722.60118. The method of any one of claims 1-17, wherein the bioreactor system comprises yeast.

19. The method of any one of claims 1-18, wherein the bioreactor system comprises a bacterial growth medium.

20. The method of claim 19, wherein the bacterial media comprises rice flour, sucrose, soy flour, bran, micronutrients, or any combination thereof.

21. The method of any one of claims 1-20, wherein the bioreactor system comprises one or more carbon sources.

22. The method of claim 21, wherein the one or more carbon sources comprises sucrose.

23. The method of any one of claims 1-22, wherein the microbial biocontrol agent is not present in the aqueous organic feedstock or any other input into the bioreactor system at a concentration of greater than 100 cfu / ml.

24. The method of any one of claims 1-23, wherein the microbial biocontrol agent is not present in the aqueous organic feedstock or any other input into the bioreactor system.

25. The method of any one of claims 1-24, wherein the bioreactor system comprises a complete mix reactor (CMR).

26. The method of claim 25, further comprising introducing the aqueous organic feedstock into the CMR.

27. The method of claim 25 or 26, further comprising introducing a hydraulic source into the CMR.

28. The method of claim 27, wherein the hydraulic source is water.

29. The method of any one of claims 25-27, wherein the bioreactor system comprises a first clarifier, and the CMR is in fluidic communication with the first clarifier.

30. The method of claim 29, further comprising continuously flowing the working fluid from the CMR to the first clarifier.

31. The method of claim 29 or 30, wherein the first clarifier comprises one or more floc folding flights configured to agitate a portion of settled floc in the first clarifier.

32. The method of claim 30 or 31, wherein the working fluid comprises biosolids, and further comprising returning at least a portion of the biosolids in the working fluid from the first clarifier to the CMR.

33. The method of any one of claims 1-32, wherein the bioreactor system comprises at least six containers.

34. The method of any one of claims 29-32, wherein the bioreactor comprises a two-stage bioreactor, wherein a first stage of the two-stage bioreactor comprises the CMR and the first clarifier and a second stage of the two-stage bioreactor comprises one or more second stage containers.

35. The method of claim 34, wherein the one or more second stage containers comprise fluidized bed reactors.WSGR Docket No. 63472-722.60136. The method of claim 34 or 35, wherein the bioreactor system comprises a manifold air system, wherein the method further comprises continuously supplying air to the one or more second stage containers using the manifold air system.

37. The method of claim 36, wherein the continuously supplying air is at a rate from about 5 L / min to about 25 L / min.

38. The method of any one of claims 1-37, further comprising operating the bioreactor system under aerobic conditions.

39. The method of any one of claims 1-38, wherein the bioreactor system comprises a second clarifier.

40. The method of claim 39, wherein the working fluid comprises a supernatant portion and a floc portion, the method further comprising separating the supernatant portion of the working fluid from the floc portion of the working fluid within the second clarifier.

41. The method of claim 40, wherein the separating occurs via gravity separation.

42. The method of claim 40 or 41, wherein the second clarifier comprises one or more second floc folding flights configured to agitate a portion of settled floc in the second clarifier without resuspending solids in the floc portion into the supernatant portion.

43. The method of any one of claims 40-42, further comprising recycling the floc portion of the second clarifier to an earlier container in the bioreactor system via a floc return line.

44. The method of any one of claims 39-43, wherein the second clarifier comprises a product outflow port.

45. The method of any one of claims 1-44, further comprising maintaining a flow rate of the working fluid in the bioreactor system that results in a hydraulic retention time of at least 10 days.

46. The method of any one of claims 1-45, further comprising maintaining a flow rate of working fluid in the bioreactor system that results in a hydraulic retention time of at least 14 days.

47. The method of any one of claims 1-46, further comprising maintaining a flow rate of product from the bioreactor system that results in at least 5 gallons of product produced per day.

48. The method of any one of claims 1-47, wherein a total volume of working fluid in the bioreactor system is about 80 gallons.

49. The method of any one of claims 1-47, wherein a total volume of working fluid in the bioreactor system is about 105 gallons.

50. The method of any one of claims 1-47, further comprising providing the microbial biocontrol agent to a first container the bioreactor system at a concentration.

51. The method of claim 50, wherein the concentration of the microbial biocontrol agent in the first container is at least about 2.0 x 106cfu / ml.

52. The method of claim 50, wherein the concentration of the microbial biocontrol agent in the first container is at most about 2.0 x 106cfu / ml.WSGR Docket No. 63472-722.60153. The method of any one of claims 48-52, wherein a concentration of the microbial biocontrol agent in the product collected from the bioreactor system is from about 10 to about 1000-fold lower than a concentration of the microbial biocontrol agent in the first container of the bioreactor system.

54. The method of any one of claims 1-53, wherein a concentration of the microbial biocontrol agent in the product at a Day 0 is within about 10 to about 100-fold of a concentration of the microbial biocontrol agent in the product at a Day 30.

55. The method of any one of claims 1-54, wherein a concentration of the microbial biocontrol agent in the product at a Day 0 is within about 10 to about 100-fold of a concentration of the microbial biocontrol agent in the product at a Day 60.

56. The method of any one of claims 1-55, further comprising producing one or more microbial metabolites that directly or indirectly promote the biocontrol property in a plant.

57. The method of claim 56, wherein the product having the biocontrol property comprises the one or more microbial metabolites.

58. The method of any one of claims 1-57, wherein the biocontrol property comprises promoting resistance of a plant disease or pathogen, treating of a plant disease or pathogen, or any combination thereof.

59. The method of claim 58, wherein the pathogen is of the genus Botrytis cinerea, Alternaria, Pythium, Cercospora sojina, Rhizoctonia, Phomopsis, Colletotrichum orhiculare, Neopestalotiopsis, Phytophthora capsici, Phytophthora infestans, Pythium ultimum, Sclerotinia sclerotiorum, Corynespora Cassiicola, Cercospora sojina, Phakopsora pachirhizi, Puccina sorghi, Podospheara xanthii, or Fusarium.

60. The method of claim 57, wherein the pathogen is of the genus Botrytis.

61. The method of claim 58 or 59, wherein the pathogen is of the species Botrytis cinerea.

62. The method of any one of claims 1-61, wherein the product comprises an abundance of cellulaseactive bacteria of at least about 1.0E+03 cfu / mL.

63. The method of any one of claims 1-62, wherein the product comprises an abundance of cellulaseactive bacteria of at least about 5.0E+03 cfu / mL.

64. The method of any one of claims 1-63, wherein the product comprises an proportion of cellulaseactive bacteria relative to a total bacterial population, and wherein the proportion is at least about 10%.

65. The method of any one of claims 1-64, wherein the product comprises an proportion of cellulaseactive bacteria relative to a total bacterial population, and wherein the proportion is at least about 25%.

66. The method of any one of claims 1-63, wherein the product comprises an proportion of cellulaseactive bacteria relative to a total bacterial population, and wherein the proportion is from about 20% to 70%.

67. A method of making a product having a biocontrol property, the method comprising:WSGR Docket No. 63472-722.60171.(a) providing a bioreactor system comprising a first stage and a second stage, wherein the first stage comprises one or more first stage containers and the second stage comprises one or more second stage containers, and wherein the bioreactor system comprises an aqueous feedstock and a microbial biocontrol agent;72.(b) collecting the product from the bioreactor system having the biocontrol property; and wherein the microbial biocontrol agent is not present in the one or more first stage containers.

68. A method of making a product having a biocontrol property, the method comprising:73.(a) providing a bioreactor system comprising a first stage and a second stage, wherein the first stage comprises one or more first stage containers and the second stage comprises one or more second stage containers, and wherein the bioreactor system comprises an aqueous feedstock and a microbial biocontrol agent;74.(b) collecting the product from the bioreactor system having the biocontrol property; and wherein the microbial biocontrol agent is present in the product from the bioreactor system at a concentration of at most 100-fold less than a concentration in the one or more second stage containers of the bioreactor system.

69. The method of claim 67 or 68, wherein each of the one or more second stage containers comprises a volume of a working fluid.

70. The method of any one of claims 67-69, wherein the aqueous feedstock comprises an organic substrate and a microbial consortium.

71. The method of claim 70, wherein the organic substrate comprises seaweed, manure, or any combination thereof.

72. The method of claim 71, wherein the seaweed comprises kelp.

73. The method of claim 72, wherein the kelp is of the genus Ascophyllum.

74. The method of claim 72 or 73, wherein the kelp is of the species Ascophyllum nodosum.

75. The method of any one of claims 67-74, wherein the bioreactor system comprises chitin.

76. The method of any one of claims 67-75, wherein the bioreactor system comprises yeast.

77. The method of any one of claims 67-76, wherein the bioreactor system comprises a bacterial media.

78. The method of claim 77, wherein the bacterial media comprises rice flour, sucrose, soy flour, bran, micronutrients, or any combination thereof.

79. The method of any one of claims 67-78, wherein the bioreactor system comprises one or more carbon sources.

80. The method of claim 79, wherein the one or more carbon sources comprise sucrose.

81. The method of any one of claims 67-80, wherein the microbial biocontrol agent is a bacteria or fungi.

82. The method of any one of claims 67-81, wherein the microbial biocontrol agent is a bacteria.

83. The method of any one of claims 67-82, wherein the microbial biocontrol agent is a microbial strain of the genus Bacillus.WSGR Docket No. 63472-722.60184. The method of claim 81, wherein the microbial biocontrol agent is of the species Bacillus amyloliquefaciens.

85. The method of any one of claims 67-82, wherein the microbial biocontrol agent is a microbial strain of the genus Paenibacillus.

86. The method of claim 85, wherein the microbial biocontrol agent is of the species Paenibacillus ottowii.

87. The method of any one of claims 67-86, wherein the microbial biocontrol agent is the microbial strain deposited under ATCC Accession No. PTA-124708 (MS2697), ATCC Accession No. PTA- 124707 (MS2681), or ATCC Accession No. PTA-124702 (MS2335).

88. The method of claim 87, wherein the microbial biocontrol agent is the microbial strain deposited under ATCC Accession No. PTA-124703 (MS2379).

89. The method of any one of claims 67-88, wherein the microbial biocontrol agent is not present in the aqueous organic feedstock or any other input into the bioreactor system at a concentration of greater than 100 colony forming units per milliliter (cfii / ml).

90. The method of any one of claims 67-89, wherein the microbial biocontrol agent is not present in the aqueous organic feedstock or any other input into the bioreactor system.

91. The method of any one of claims 67-90, wherein the bioreactor system comprises a complete mix reactor (CMR).

92. The method of claim 91, wherein the CMR is present in the first stage of the bioreactor system.

93. The method of claim 92, further comprising introducing the aqueous organic feedstock into the CMR.

94. The method of any one of claims 91-93, further comprising introducing a hydraulic source into the CMR.

95. The method of any one of claims 91-94, wherein the CMR is in fluidic communication with a clarifier.

96. The method of claim 95, further comprising continuously flowing the working fluid from the CMR to the clarifier.

97. The method of claim 95 or 96, wherein the clarifier comprises one or more floc folding flights configured to agitate settled a floc portion in the clarifier.

98. The method of claim 96 or 97, further comprising returning at least a portion of bioso lids in the working fluid from the clarifier to the CMR.

99. The method of any one of claims 95-98, wherein the CMR and the clarifier comprise the first stage of the bioreactor system, wherein the first stage of the bioreactor system is configured to rehydrate the organic substrate of the aqueous feedstock.

100. The method of any one of claims 67-99, wherein the bioreactor system comprises at least six containers.WSGR Docket No. 63472-722.601101. The method of any one of claims 67-100, wherein the one or more second stage containers of the bioreactor system comprise fluidized bed reactors.

102. The method of any one of claims 67-101, wherein the bioreactor system comprises a manifold air system configured to continuously supply air to the one or more second stage containers of the bioreactor system.

103. The method of claim 102, wherein the manifold air system supplies air at a rate from about 5 L / min to 25 L / min to the one or more second stage containers of the bioreactor system.

104. The method of any one of claims 67-103, further comprising operating the bioreactor system under aerobic conditions.

105. The method of any one of claims 67-104, wherein the bioreactor system comprises a second clarifier.

106. The method of claim 105, further comprising separating a supernatant portion of the working fluid from a floc portion of the working fluid within the second clarifier.

107. The method of 106, wherein the separating occurs via gravity separation.

108. The method of claim 106 or 107, wherein the second clarifier comprises one or more second floc folding flights configured to agitate settled a floc portion in the clarifier without resuspending solids in the floc portion into the supernatant portion.

109. The method of any one of claims 106-108, further comprising recycling the floc portion of the second clarifier to an earlier container in the bioreactor system via a floc return line.

110. The method of any one of claims 105-109, wherein the second clarifier comprises a product outflow port.

111. The method of claim 110, wherein the product collected via the product outflow port comprises a final concentration of the microbial biocontrol agent of at least about 1 x 104cfu / ml.

112. The method of any one of claims 68-111, further comprising maintaining a flow rate of the working fluid in the bioreactor system that results in a hydraulic retention time of at least 10 days.

113. The method of any one of claims 68-112, further comprising maintaining a flow rate of working fluid in the bioreactor system that results in a hydraulic retention time of at least 14 days.

114. The method of any one of claims 67-113, further comprising maintaining a flow rate of product from the bioreactor system that results in at least about 5 gallons of product produced per day.

115. The method of any one of claims 67-114, further comprising providing a concentration of the microbial biocontrol agent to the bioreactor system.

116. The method of claim 115, wherein the concentration of the microbial biocontrol agent is at least about 2.0 x 106cfu / ml.

117. The method of claim 115 or 116, wherein the concentration of the microbial biocontrol agent is at most about 2.0 x 106cfu / ml.WSGR Docket No. 63472-722.601118. The method of any one of claims 67-117, wherein a concentration of the microbial biocontrol agent in the product is from about 10 to about 1000-fold lower than a concentration of the microbial biocontrol agent in the one or more second containers of the bioreactor system.

119. The method of any one of claims 67-118, wherein a concentration of the microbial biocontrol agent in the product at a Day 0 is within about 10 to about 100-fold of a concentration of the microbial biocontrol agent in the product at a Day 30.

120. The method of any one of claims 67-119, wherein a concentration of the microbial biocontrol agent in the product at a Day 0 is within about 10 to about 100-fold of a concentration of the microbial biocontrol agent in the product at a Day 60.

121. The method of any one of claims 67-120, further comprising producing microbial metabolites that directly or indirectly promote the biocontrol property in a plant.

122. The method of any one of claims 67-121, wherein the biocontrol property comprises promoting resistance of a plant disease or pathogen, treating of a plant disease or pathogen, or any combination thereof.

123. The method of claim 122, wherein the pathogen is of the genus Botrytis, Alternaria, or Fusarium.

124. The method of claim 122 or 123, wherein the pathogen is of the species Botrytis cinerea.

125. The method of any one of claims 67-124, wherein the product comprises an abundance of cellulase-active bacteria of at least about 1.0E+03 cfu / mL.

126. The method of any one of claims 67-125, wherein the product comprises an abundance of cellulase-active bacteria of at least about 5.0E+03 cfu / mL.

127. The method of any one of claims 67-126, wherein the product comprises an proportion of cellulase-active bacteria relative to a total bacterial population, and wherein the proportion is at least about 10%.

128. The method of any one of claims 67-127, wherein the product comprises an proportion of cellulase-active bacteria relative to a total bacterial population, and wherein the proportion is at least about 25%.

129. The method of any one of claims 67-126, wherein the product comprises an proportion of cellulase-active bacteria relative to a total bacterial population, and wherein the proportion is from about 20% to 70%.

130. A composition comprising the product produced by the method of any one of claims 1-129.

131. A method of treating a disease of a plant comprising contacting the plant, a seed, or a plant growth medium with the composition of claim 130.

132. A method of promoting resistance to a disease of a plant comprising contacting the plant, a seed, or a plant growth medium with the composition of claim 130.

133. The method of claim 131 or 132, wherein disease comprises a plant pathogen oi Botrytis cinerea, Fusarium, Alternaria, Phomopsis, or any combination thereof.WSGR Docket No. 63472-722.601134. The method of any one of claims 131-133, wherein the composition inhibits lesion growth in a leaf of the plant after contacting.

135. The method of any one of claims 131-134, wherein the plant growth medium comprises soil, a hydroponic medium, turface, or isolite.

136. The method of any one of claims 131-135, wherein the contacting is via foliar application.

137. The method of any one of claims 131-135, wherein the contacting is via in-furrow application.

138. The method of any one of claims 131-137, wherein the contacting increases an average leaf area of the plant by at least about 30% compared to an average leaf area of an otherwise identical plant administered water.

139. The method of any one of claims 131-138, wherein the contacting decreases a lesion diameter by at least 5 millimeters (mm) from a lesion diameter of a plant leaf administered Botrytis cinerea and treated with water.

140. A composition comprising:143.(a) a microbial consortium comprising one or more bacterial strains selected from MS2379 (ATCC Accession No. PTA-124703), MS2697 (ATCC Accession No. PTA-124708), MS2681 (ATCC Accession No. PTA-124707), and MS2335 (ATCC Accession No. PTA- 124702); and144.(b) metabolites produced by digestion of an organic substrate by microbes within the microbial consortium, and145.wherein the organic substrate comprises seaweed.

141. The composition of claim 140, wherein the seaweed is kelp.

142. The composition of claim 141, wherein the kelp is of the genus Ascophyllum.

143. The composition of claim 141 or 142, wherein the kelp is of the species Ascophyllum nodosum.

144. The composition of any one of claims 140-143, wherein the microbial consortium further comprises an enriched microbial community comprising one or more biocontrol properties.

145. The composition of any one of claims 140-144, wherein the microbial consortium comprises microbes derived from the seaweed.

146. A method of making a product having a biocontrol property, the method comprising:151.(a) providing a multistage bioreactor system comprising: (i) a first stage comprising a first stage container comprising a volume of organic feedstock, wherein the organic feedstock comprises a manure or a seaweed, and a second stage comprising a second stage container, wherein the volume of organic feedstock undergoes rehydration in the first stage container to generate an aqueous feedstock;152.(b) transferring a portion of the aqueous feedstock to the second stage container; and (c) collecting the product from the multistage bioreactor system, wherein the product has the biocontrol property.

147. A product having a biocontrol property, wherein the product is produced by:WSGR Docket No. 63472-722.601154.(a) providing a bioreactor system comprising:155.(i) one or more containers, wherein the one or more containers comprise a volume of a working fluid and a microbial biocontrol agent; and156.(b) collecting the product from the bioreactor system, wherein the product has the biocontrol property; and157.wherein the microbial biocontrol agent is present in the product collected from the bioreactor system at a concentration of at least 1.0 x 104colony forming units per milliliter (cfu / ml).

148. A product having a biocontrol property, wherein the product is produced by:158.(a) providing a multistage bioreactor system comprising: (i) a first stage comprising a first stage container comprising a volume of organic feedstock, wherein the organic feedstock comprises a manure or a seaweed, and a second stage comprising a second stage container, wherein the volume of organic feedstock undergoes rehydration in the first stage container to generate an aqueous feedstock;159.(b) transferring a portion of the aqueous feedstock to the second stage container; and (c) collecting the product from the multistage bioreactor system, wherein the product has the biocontrol property.

149. A method of treating a plant disease, the method comprising:161.(a) contacting to a plant or a soil a composition having a biocontrol property, wherein the composition is produced by:162.(i) providing a bioreactor system comprising one or more containers, wherein the one or more containers comprise a volume of a working fluid and a microbial biocontrol agent; and163.(ii) collecting a product from the bioreactor system, wherein the product has the biocontrol property; and164.wherein the composition comprises the product from the bioreactor system.

150. A method of treating a plant disease, the method comprising:166.(a) contacting to a plant or a soil a composition having a biocontrol property, wherein the composition is produced by:167.(i) providing a multistage bioreactor system comprising: (i) a first stage comprising a first stage container comprising a volume of organic feedstock, wherein the organic feedstock comprises a manure or a seaweed, and a second stage comprising a second stage container, wherein the volume of organic feedstock undergoes rehydration in the first stage container to generate an aqueous feedstock;168.(ii) transferring a portion of the aqueous feedstock to the second stage container;169.and WSGR Docket No. 63472-722.601170.(iii) collecting the product from the multistage bioreactor system, wherein the product has the biocontrol property.

151. A method of promoting resistance to a plant pathogen, the method comprising:172.(a) contacting to a plant or a soil a composition having a biocontrol property, wherein the composition is produced by:173.(i) providing a bioreactor system comprising one or more containers, wherein the one or more containers comprise a volume of a working fluid and a microbial biocontrol agent; and174.(ii) collecting a product from the bioreactor system, wherein the product has the biocontrol property; and175.wherein the composition comprises the product from the bioreactor system.

152. A method of promoting resistance to a plant pathogen, the method comprising:177.(a) contacting to a plant or a soil a composition having a biocontrol property, wherein the composition is produced by:178.(i) providing a multistage bioreactor system comprising: (i) a first stage comprising a first stage container comprising a volume of organic feedstock, wherein the organic feedstock comprises a manure or a seaweed, and a second stage comprising a second stage container, wherein the volume of organic feedstock undergoes rehydration in the first stage container to generate an aqueous feedstock;179.(ii) transferring a portion of the aqueous feedstock to the second stage container;180.and181.(iii) collecting the product from the multistage bioreactor system, wherein the product has the biocontrol property.

153. The method of any one of claims 149-152, wherein the contacting upregulates one or more biotic defense genes.

154. The method of claim 153, wherein the biotic defense genes belong to one or more pathways comprising defense response, defense response to bacterium, defense response to other organism, jasmonic acid metabolic process, defense response to oomycetes, regulation of defense response to fungus, regulation of salicylic acid biosynthetic process, systemic acquired resistance, innate immune response, jasmonic acid biosynthetic process, plant-pathogen interaction, response to biotic stimulus, killing of cells of other organism, defense response to fungus, chitin catabolic process, salicylic acid metabolic process, response to salicylic acid and regulation of salicylic acid mediated signaling pathway, or any combination thereof.

155. A bioreactor system comprising:WSGR Docket No. 63472-722.601185.(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 microbial biocontrol agent; (b) a second container arranged in a series with the first container, wherein the second container comprises a volume of a second working fluid, and wherein the second container comprises a product outflow stream port; and186.(c) a product outflow stream in fluid communication with the product outflow stream port, wherein the product outflow stream comprises a biocontrol product, wherein the biocontrol product comprises an amount of the microbial biocontrol agent, and wherein the amount of the microbial biocontrol agent promotes a biocontrol property of a plant administered the biocontrol product as compared to an otherwise identical plant not administered the biocontrol product.

156. A composition made by the system of claim 155.

157. A method of treating a disease of a plant comprising contacting a plant, seed, or plant growth medium with the composition of claim 156.

158. A method of promoting resistance to a disease of a plant comprising contacting a plant, seed, or plant growth medium with the composition of claim 156.

159. A method of enhancing biocontrol of a plant, comprising:191.(a) contacting a plant and / or plant growth medium in which the plant is growing with a composition comprising one or more compounds, wherein the one or more compounds is selected from the group consisting of Decyl octanoate, Tetradecanamide, 2-monopahnitin, Palmitoleic acid, 18,22,22-Trimethyl- 17,27,29,3 O-tetranor-c-homoolean- 14-ene- 3beta, 21 alpha-diol, 2-monoolein, Cyclopropanecarboxamide, N-octadecyl, Arachidonic acid, D-(-)-fructose, 2-methyl-4-(trimethylsilyl)methyl-5-hexen-3-one, Caprylic acid, 1- pentamethyldisilanyloxy-4-pentamethyldisilanylbenzene, 3 -hydroxypyridine, D-(-)- ribose, N-octadecyl, Protocatechuic acid, 5-methyl-3-hexenyltrimethylsilane, D-xylulose, Octanal, 7-methoxy-3,7-dimethyl, l-pentamethyldisilanyloxy-4- pentamethyldisilanylbenzene, Pentane, 2,2,4,4-tetramethyl, N-octadecyl, 5-methyl-3- hexenyltrimethylsilane, 7-Ethyl-cis-4a,trans-4b,cis-8a,trans-10a-perhydro-4b,trans-7,10a- trimethyl- 1 -phenanthrenone 2,4-dinitrophenylhydrazone, 10-methyl- 1 -dodecanol, Glucaric acid, 4-methyl-2-pentenoic acid trimethylsilyl ester, one or more derivatives thereof, and any combination thereof.

160. The method of claim 159, wherein the enhancing biocontrol of the plant comprises upregulating one or more biotic defense genes of the plant.

161. The method of claim 159 or 160, wherein the enhancing biocontrol of the plant comprises preventing a lesion caused by a plant pathogen or reducing a size of a lesion caused by a plant pathogen.WSGR Docket No. 63472-722.601162. The method of claim 161, wherein the plant pathogen is of a genera selected from the group consisting of Mycosphaerella, Colletotrichum, Puccinia, Botrytis, Fusarium, Alternaria, Blumeria, Ustilago, Melampsora, and any combination thereof.

163. The method of claim 161 or 162, wherein the plant pathogen is of a species selected from the group consisting of Mycosphaerella graminicola, Colletotrichum spp., Puccinia spp., Botrytis cinerea, Fusarium graminearum, Fusarium oxysporum, Blumeria graminis, Ustilago maydis, Melampsora lini, and any combination thereof.

164. The method of any one of claims 159-163, wherein the concentration of the one or more compounds in the composition is at least about 1 nanomolar (nM).

165. The method of any one of claims 159-164, 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.

166. The method of any one of claims 159-165, wherein the contacting comprises contacting the plant with the composition.

167. The method of any one of claims 159-166, wherein the contracting comprises contacting a plant seed with the composition.

168. The method of any one of claims 159-167, wherein the contacting comprises contacting a leaf of the plant with the composition.

169. The method of any one of claims 159-168, wherein the plant growth medium comprises soil, a hydroponic medium, turface, or isolite.

170. A method of enhancing biocontrol of a plant, comprising:202.(a) contacting a plant and / or plant growth medium in which the plant is growing with a composition comprising one or more compounds, wherein the one or more compounds is selected from the group consisting of Palmitoleic acid, 12-01eanen-3-yl acetate, (3.alpha.)-, Heptadecyl acetate, 5-Alpha-androstane-3, 17-dione 17-monooxime, Malic acid, Erucic acid, 1,5-Anhydro-D-glucitol, Palmitic acid, Eserine, Protocatechuic acid, 1- pentamethyldisilanyloxy-4-pentamethyldisilanylbenzene, 3-methylhistidine, 4-methyl-2- pentenoic acid trimethylsilyl ester, Caprylic acid, Octanal, 7-methoxy-3,7-dimethyl-, Beta-alanine, L-arginine, 3-methylhistidine, 4-methyl-2-pentenoic acid trimethylsilyl ester, 1 -pentamethyldisilanyloxy-4-pentamethyldisilanylbenzene, Beta-hydroxymyristic acid, Octanal, 7-methoxy-3,7-dimethyl-, Pentane, 2,2,4,4-tetramethyl-, 2-Benzyl-6- methyl-4(3H)-pyrimidinone, one or more derivatives thereof, and any combination thereof.

171. The method of claim 170, wherein the enhancing biocontrol of the plant comprises upregulating one or more biotic defense genes of the plant.

172. The method of claim 170 or 171, wherein the enhancing biocontrol of the plant comprises preventing a lesion caused by a plant pathogen or reducing a size of a lesion caused by a plant pathogen.WSGR Docket No. 63472-722.601173. The method of claim 172, wherein the plant pathogen is of a genera selected from the group consisting of Mycosphaerella, Colletotrichum, Puccinia, Botrytis, Fusarium, Alternaria, Blumeria, Ustilago, Melampsora, and any combination thereof.

174. The method of claim 172 or 173, wherein the plant pathogen is of a species selected from the group consisting of Mycosphaerella graminicola, Colletotrichum spp., Puccinia spp., Botrytis cinerea, Fusarium graminearum, Fusarium oxysporum, Blumeria graminis, Ustilago maydis, Melampsora lini, and any combination thereof.

175. The method of any one of claims 170-174, wherein the concentration of the one or more compounds in the composition is at least about 1 nanomolar (nM).

176. The method of any one of claims 170-175, 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.

177. The method of any one of claims 170-176, wherein the contacting comprises contacting the plant with the composition.

178. The method of any one of claims 170-177, wherein the contacting comprises contacting a plant seed with the composition.

179. The method of any one of claims 170-178, wherein the contacting comprises contacting a leaf of the plant with the composition.

180. The method of any one of claims 170-179, wherein the plant growth medium comprises soil, a hydroponic medium, turface, or isolite.

181. A composition for enhancing biocontrol of a plant, comprising:213.(a) at least one microbial strain selected from a Paenihacillus ottowii strain or a Bacillus amyloliquefaciens strain; and214.(b) one or more compounds selected from Decyl octanoate, Tetradecanamide, 2- monopalmitin, Palmitoleic acid, 18,22,22-Trimethyl-17,27,29,30-tetranor-c-homoolean- 14-ene-3beta,21alpha-diol, 2-monoolein, N-octadecyl, Arachidonic acid, D-(-)-fructose, 2-methyl-4-(trimethylsilyl)methyl-5-hexen-3-one, Caprylic acid, 1- pentamethyldisilanyloxy-4-pentamethyldisilanylbenzene, 3 -hydroxypyridine, D-(-)- ribose, Cyclopropanecarboxamide, N-octadecyl, Protocatechuic acid, 5-methyl-3- hexenyltrimethylsilane, D-xylulose, 7- Octanal, 7-methoxy-3,7-dimethyl, 1- pentamethyldisilanyloxy-4-pentamethyldisilanylbenzene, Pentane, 2,2,4,4-tetramethyl, N-octadecyl, 5-methyl-3-hexenyltrimethylsilane, 7-Ethyl-cis-4a,trans-4b,cis-8a,trans- 10a-perhydro-4b,trans-7, 1 Oa-trimethyl- 1 -phenanthrenone 2,4-dinitrophenylhydrazone, 10-methyl-l -dodecanol, Glucaric acid, 4-methyl -2 -pentenoic acid trimethylsilyl ester, one or more derivatives thereof, and any combination thereof.

182. The composition of claim 181, wherein the Paenihacillus ottowii strain comprises one or more of the following:216.(a) 16S rRNA gene sequence at least 95% identical to SEQ ID NO: 1; WSGR Docket No. 63472-722.601217.(b) a gyrB gene sequence at least 95% identical to SEQ ID NO: 2; or218.(c) a rpoB gene sequence at least 95% identical to SEQ ID NO: 3.

183. The composition of claim 181, wherein the Bacillus amyloliquefaciens strain comprises one or more of the following:220.(a) a 16S rRNA gene sequence at least 95% identical to SEQ ID NO: 4;221.(b) a gyrB gene sequence at least 95% identical to SEQ ID NO: 5; or222.(c) a rpoB gene sequence at least 95% identical to SEQ ID NO: 6.

184. The composition of claim 181, wherein the Bacillus amyloliquefaciens strain comprises one or more of the following:224.(a) a 16S rRNA gene sequence at least 95% identical to SEQ ID NO: 7;225.(b) a gyrB gene sequence at least 95% identical to SEQ ID NO: 8; or226.(c) a rpoB gene sequence at least 95% identical to SEQ ID NO: 9.

185. The composition of claim 181, wherein the Bacillus amyloliquefaciens strain comprises one or more of the following:228.(a) a 16S rRNA gene sequence at least 95% identical to SEQ ID NO: 10;229.(b) a gyrB gene sequence at least 95% identical to SEQ ID NO: 11; or230.(c) a rpoB gene sequence at least 95% identical to SEQ ID NO: 12.

186. The composition of any one of claims 181-185, wherein Decyl octanoate, Tetradecanamide, Caprylic acid, 2-methyl-4-(trimethylsilyl)methyl-5-hexen-3-one, Cyclopropanecarboxamide, 1- pentamethyldisilanyloxy-4-pentamethyldisilanylbenzene or any combination thereof is present in the composition at the highest relative abundance relative to a total dry weight of the composition.

187. The composition of any one of claims 181-186, further comprising a carrier.

188. The composition of claim 187, wherein the carrier is formulated for application to a plant and / or medium in which the plant is growing.

189. A composition for enhancing biocontrol of a plant, comprising:235.(a) at least one microbial strain selected from a Paenibacillus ottowii strain or a Bacillus amyloliquefaciens strain; and236.(b) one or more compounds selected from Palmitoleic acid, 12-01eanen-3-yl acetate, (3. alpha.)-, Heptadecyl acetate, 5 -Alpha-androstane-3, 17-dione 17-monooxime, Malic acid, Erucic acid, 1,5-Anhydro-D-glucitol, Palmitic acid, Eserine, Protocatechuic acid, 1- pentamethyldisilanyloxy-4-pentamethyldisilanylbenzene, 3-methylhistidine, 4-methyl-2- pentenoic acid trimethylsilyl ester, Caprylic acid, Octanal, 7-methoxy-3,7-dimethyl-, Beta-alanine, L-arginine, 3-methylhistidine, 4-methyl-2-pentenoic acid trimethylsilyl ester, 1 -pentamethyldisilanyloxy-4-pentamethyldisilanylbenzene, Beta-hydroxymyristic acid, Octanal, 7-methoxy-3,7-dimethyl-, Pentane, 2,2,4,4-tetramethyl-, 2-Benzyl-6- methyl-4(3H)-pyrimidinone, one or more derivatives thereof, and any combination thereof. WSGR Docket No. 63472-722.601190. The composition of claim 189, wherein the Paenibacillus ottowii strain comprises one or more of the following:238.(a) 16S rRNA gene sequence at least 95% identical to SEQ ID NO: 1;239.(b) a gyrB gene sequence at least 95% identical to SEQ ID NO: 2; or240.(c) a rpoB gene sequence at least 95% identical to SEQ ID NO: 3.

191. The composition of claim 189, wherein the Bacillus amyloliquefaciens strain comprises one or more of the following:242.(a) a 16S rRNA gene sequence at least 95% identical to SEQ ID NO: 4;243.(b) a gyrB gene sequence at least 95% identical to SEQ ID NO: 5; or244.(c) a rpoB gene sequence at least 95% identical to SEQ ID NO: 6.

192. The composition of claim 189, wherein the Bacillus amyloliquefaciens strain comprises one or more of the following:246.(a) a 16S rRNA gene sequence at least 95% identical to SEQ ID NO: 7;247.(b) a gyrB gene sequence at least 95% identical to SEQ ID NO: 8; or248.(c) a rpoB gene sequence at least 95% identical to SEQ ID NO: 9.

193. The composition of claim 189, wherein the Bacillus amyloliquefaciens strain comprises one or more of the following:250.(a) a 16S rRNA gene sequence at least 95% identical to SEQ ID NO: 10;251.(b) a gyrB gene sequence at least 95% identical to SEQ ID NO: 11; or252.(c) a rpoB gene sequence at least 95% identical to SEQ ID NO: 12.

194. The composition of any one of claims 189-193, wherein Palmitoleic acid, Protocatechuic acid, 3- methylhistidine, 4-methyl-2 -pentenoic acid trimethylsilyl ester, Beta-hydroxymyristic acid, or any combination thereof is present in the composition at the highest relative abundance relative to a total dry weight of the composition.

195. The composition of any one of claims 189-194, further comprising a carrier.

196. The composition of claim 195, wherein the carrier is formulated for application to a plant and / or medium in which the plant is growing.

197. A composition for enhancing biocontrol of a plant, comprising:257.(a) two or more compounds selected from the group consisting of Decyl octanoate, Tetradecanamide, 2-monopahnitin, Palmitoleic acid, 18,22,22-Trimethyl-17,27,29,30- tetranor-c-homoolean-14-ene-3beta,21 alpha-diol, 2-monoolein, N-octadecyl, Arachidonic acid, D-(-)-fructose, 2-methyl-4-(trimethylsilyl)methyl-5-hexen-3-one, Caprylic acid, 1- pentamethyldisilanyloxy-4-pentamethyldisilanylbenzene, 3 -hydroxypyridine, D-(-)- ribose, Cyclopropanecarboxamide, N-octadecyl, Protocatechuic acid, 5-methyl-3- hexenyltrimethylsilane, D-xylulose, 7- Octanal, 7-methoxy-3,7-dimethyl, 1- pentamethyldisilanyloxy-4-pentamethyldisilanylbenzene, Pentane, 2,2,4,4-tetramethyl, N-octadecyl, 5-methyl-3-hexenyltrimethylsilane, 7-Ethyl-cis-4a,trans-4b,cis-8a,trans- WSGR Docket No. 63472-722.601258.10a-perhydro-4b,trans-7, 1 Oa-trimethyl- 1 -phenanthrenone 2,4-dinitrophenylhydrazone, 10-methyl-l -dodecanol, Glucaric acid, 4-methyl -2 -pentenoic acid trimethylsilyl ester, one or more derivatives thereof, and any combination thereof; and259.(b) a carrier.

198. The composition of claim 197, wherein the carrier is formulated for application to a plant and / or medium in which the plant is growing.

199. The composition of claim 197 or 198, wherein the carrier comprises a fertilizer.

200. The composition of claim 199, wherein the fertilizer is a solid.

201. The composition of any one of claims 197-200, wherein the carrier is a liquid.

202. The composition of any one of claims 197-201, wherein the composition is configured to prevent a lesion caused by a plant pathogen or reduce a size of a lesion caused by a plant pathogen.

203. The composition of claim 202, wherein the plant pathogen is of a genera selected from the group consisting of Mycosphaerella, Colletotrichum, Puccinia, Botrytis, Fusarium, Alternaria, Blumeria, Ustilago, Melampsora, and any combination thereof.

204. The composition of claim 202 or 203, wherein the plant pathogen is of a species selected from the group consisting of Mycosphaerella graminicola, Colletotrichum spp., Puccinia spp., Botrytis cinerea, Fusarium graminearum, Fusarium oxysporum, Blumeria graminis, Ustilago maydis, Melampsora lini, and any combination thereof.

205. The composition of any one of claims 197-204, wherein the composition further comprises an adjuvant selected from a wetting agent, spreading agent, dispersing agent, sticking agent, dust control agent, and adhesive.

206. A composition for enhancing biocontrol of a plant, comprising:268.(a) two or more compounds selected from the group consisting of Palmitoleic acid, 12- Oleanen-3-yl acetate, (3.alpha.)-, Heptadecyl acetate, 5-Alpha-androstane-3, 17-dione 17- monooxime, Malic acid, Erucic acid, 1,5-Anhydro-D-glucitol, Palmitic acid, Eserine, Protocatechuic acid, l-pentamethyldisilanyloxy-4-pentamethyldisilanylbenzene, 3- methylhistidine, 4-methyl-2 -pentenoic acid trimethylsilyl ester, Caprylic acid, Octanal, 7- methoxy-3,7-dimethyl-, Beta-alanine, L-arginine, 3-methylhistidine, 4-methyl-2- pentenoic acid trimethylsilyl ester, l-pentamethyldisilanyloxy-4- pentamethyldisilanylbenzene, Beta-hydroxymyristic acid, Octanal, 7-methoxy-3,7- dimethyl-, Pentane, 2,2,4,4-tetramethyl-, 2-Benzyl-6-methyl-4(3H)-pyrimidinone, one or more derivatives thereof, and any combination thereof; and269.(b) a carrier.

207. The composition of claim 206, wherein the carrier is formulated for application to a plant and / or medium in which the plant is growing.

208. The composition of claim 206 or 207, wherein the carrier comprises a fertilizer.

209. The composition of claim 208, wherein the fertilizer is a solid.WSGR Docket No. 63472-722.601210. The composition of any one of claims 206-209, wherein the carrier is a liquid.

211. The composition of any one of claims 206-210, wherein the composition is configured to prevent a lesion caused by a plant pathogen or reduce a size of a lesion caused by a plant pathogen.

212. The composition of claim 211, wherein the plant pathogen is of a genera selected from the group consisting of Mycosphaerella, Colletotrichum, Puccinia, Botrytis, Fusarium, Alternaria, Blumeria, Ustilago, Melampsora, and any combination thereof.

213. The composition of claim 211 or 212, wherein the plant pathogen is of a species selected from the group consisting of Mycosphaerella graminicola, Colletotrichum spp., Puccinia spp., Botrytis cinerea, Fusarium graminearum, Fusarium oxysporum, Blumeria graminis, Ustilago maydis, Melampsora lini, and any combination thereof.

214. The composition of any one of claims 206-213, wherein the composition further comprises an adjuvant selected from a wetting agent, spreading agent, dispersing agent, sticking agent, dust control agent, and adhesive.

215. A method of treating a disease of a plant or promoting resistance to a disease of a plant, the method comprising:278.(a) contacting a plant and / or a growth medium in which the plant is growing with a composition comprising one or more compounds, wherein the one or more compounds is selected from the group consisting of Oleanolic acid, Myo-inositol, N-Heptadecanol-1, 1- (Trimethylsilyl)cyclopropyl phenyl sulfide, Vitexicarpin, 1,3-Benzenedicarboxylic acid, 5 -( 1, 1 -dimethylethyl)-, 1 -tridecanethiol, Trans-p-Dimethylaminocinnamonitrile, Stigmasteryl trimethylsilyl ether, Pentadecane, Methyl 5-methyl-3-keto-4-hexenoate, 1,1- Dichloro-l-sila-2,3-benzo-4,5-thiophenocyclopentadiene, Cis-4-octene, 7- hydroxycholesterol, 25-Methyl-21-tritriacontene-l,9,l 1-triol, Fosfomycin calcium, 2- chloroethanol, 2-Pyridyl hydroxymethane sulfonic acid, 4-(2,4- Dichlorophenoxyjbutanoic acid, 1-deoxynojirimycin, l,2-Diarachidoyl-sn-glycero-3- phosphocholine, 2,3,6-Trichlorobenzoic acid, L-serine, 3-methoxytyramine, 5-(4-Chloro- 3-hydroxy-l-butynyl)-2,2'-bithiophene, 27-norcholestanehexol, Dehydroabietamide, 2,4- dihydroxybenzophenone, 5 -Nonadecyl- 1,3 -benzenediol, Tiformin, Benzamide, N-(5- chloro-2-pyridinyl)-3 -(trifluoromethyl)-, Isoduartin methyl ether, 4-Bromo-l-((2- bromophenyl)sulfonyl)-lH-pyrazole, (3ar,4R,5R,6as)-5-Hydroxy-4-((S, E)-3-hydroxyoct- 1 -en- 1 -yl)hexahydro-2H-cyclopenta[b] furan-2-one, Ampiroxicam, 3 -(2,3 - Dihydroxyphenyljpropanoic acid, 1 -phenylpiperazine, 3-Oxazolidinecarboxylic acid, 2,2- dimethyl-4-( 1 -oxo-2 -hexadecyn-l-yl)-, 1,1 -dimethylethyl ester, (4S)-, Trenbolone acetate, Methyl thieno[3,2-d]thiadiazole-6-carboxylate, N-(2,2,2- trifluoroethyl)morpholine-4-carbothioamide, Butonate, 3, 5 -dinitrocatechol, 9- aminoacridine, Pyridinoline, Xanthotoxol, Gramine(l+), Lanosol, PG(22:6(4z,7z,10z,13z,16z,19z) / 20:2(l lz,14z)), 2-deoxystreptamine, (4-Chloro-3-nitro- WSGR Docket No. 63472-722.601279.benzoylamino)-acetic acid, Pentedrone, (S)-10,16-Dihydroxyhexadecanoic acid, 2-Amino-3-[4-hydroxy-3-(3-methylbut-2-enyl)phenyl]propanoic acid, (2S,4S)-1-Acetoxy-16-heptadecene-2,4-diol, Flutamide, 2-Aminobenzoic acid, Psilocin, (R)-2-Hydroxysterculic acid, Tg(16:0 / 16:0 / 16: l(9z)), 2-hydroxy-3-({3-[3-methoxy-4- (sulfooxy )phenyl]prop-2 -enoyl }oxy)butanedioic acid, Dimethyl adipate, Ps(22: 6(4z,7z, 1 Oz, 13z, 16z, 19z) / 20: 4(5z, 8z, 11 z, 14z)), Thr-tyr-glu, Pro-phe-lys, Ubiquinone-1, Methoxydihydrosorgoleone, (6S,8Z)-6-Hydroxy-3-oxotetradecenoic acid, (9z)-N-[(2s,3r,4e)-l-(Beta-D-Glucopyranosyloxy)-3-Hydroxyoctadec-4-En-2-Yl]octadec-9-Enamide, D-Glucono-l,5-lactone 6-phosphate, Hexadecanedioic acid, 6k-PGFld4, Brefeldin A, Nifenazone, Anethole, Alpha-Mangostin, Karbutilate, L-Asparaginyl-L-lysine, 4-Hydroxy-3-methoxybenzenemethanol, (1R,2R,3R,4R)-1-[(R)- 1.5 -Dimethyl- 1 -hydroxy-4-hexenyl] -4-methylcyclohexane- 1,2,3,4-tetrol, 2,3 ',4,5 '-tetramethoxystilbene, N4-(N-acetylaminopropyl)spermidine, Maltose, Ethion, 2,3,5-Triiodobenzoic acid, Isonicotinylglycine, (R*, S*)-4-[l-Ethyl-2-(4-fluorophenyl)butyl]phenol, 2,3-bisphosphoglycerate, 2',5'-Dichlorobiphenyl-3-ol, Artemisinin, Lys-tyr-gln-glu-ala, Prometon, Shogaol, Rolipram, Bis(2,3-dihydroxypropyl) phosphate, 4-Hydroxy-2 -oxoglutaric acid, Mesulfenfos, 3 -Sulfobenzoic acid, Athidathion, Novaluron, 5 -Bromo-7-methoxy-l-benzofuran-2 -carboxylic acid, 4-(Hydroxymethyl)-2-iodo-6-methoxyphenol, 5-(3',4',5'-Trihydroxyphenyl)-gamma-valerolactone-4'-O-sulphate, [Trpll] neurotensin (8-13), Dibutyl phthalate, Cavipetin C, Monobutyl phthalate, Lys-gly-his, Disulfoton sulfone, 3-Formylsalicylic acid, Dxtp, Hco3-, Sodium sulfate, 13-docosenamide, 6-acetoxydihydrotheaspirane, His-ala-gly, N-(5-methyl-l,3-thiazol-2-yl)-2-(phenylsulfanyl)acetamide, 8,8-Diethoxy-2,6-dimethyl-2-octanol, 13,14-dihydro-15-keto-tetranor Prostaglandin E2, 1-Deoxyvaleric-acid, 2-Propyl-2 -pentenoic acid, 6,8a-Seco-6,8a-deoxy-5-oxoavermectin"lb" aglycone, L-Tyrosyl-L-serine, Ciclopirox, 1 -ethenyl -4-methoxy-benzene, 5-Chloro-6-hydroxy-2-oxohexa-3, 5 -dienoic acid, Desalkyl verapamil D617, N-(Tetradecanoyl)-sphing-4-enine, 3.4.5 -trihydroxy-6-( { 8-hydroxy-2-oxo-2H-furo [2,3 -h]chromen-4-yl } oxy)oxane-2-carboxylic acid, Vitamin E, Phosphoadenosine phosphosulfate, Permethrin, Kenpaullone, Andrographolide, Neopikromycin, O, O-Diethyl hydrogen thiophosphate, Naringenin chaicone, Tris(2-chloroethyl) phosphate, Trimetazidine, 9,10-epome, 6-(2-Prop-2-ynoxyphenyl)hexanoic acid, Imperialine, 2,2,6,6-Tetramethyl-l,3-dithiane-4-thione, Ethyl 2-cyano-3-(lh-indol-3-yl)prop-2-enoate, 17alpha-Estradiol, [(6S,7S,10R)-4,10,11,1 l-tetramethyl-3-oxo-6-tricyclo[5.3.1.01, 5]undec-4-enyl] acetate, Monoisobutyl phthalate, Tris(2 -butoxyethyl) phosphate, l-(2-Bromophenyl)-3-(2-hydroxy-4-nitrophenyl)urea, Arg-pro-thr, Met-pro-tyr, 4-Hydroxyphenyl thiocyanate, 2-Amino-3-chloro-5-nitrobenzotrifluoride, Phosphoric acid, Fenethylline, WSGR Docket No. 63472-722.601280.Pc(20:5(5z,8z,l lz,14z,17z) / 18:4(6z,9z,12z,15z)), Thr-arg-gly, Heliocide H4, 2,4- diacetylphloroglucinol, N-[(R)-4-phosphopantothenoyl]-L-cysteine, 5,7- Dichlorokynurenic acid, Octyl -beta-d-glucopyranoside, 9,11 -methane -epoxy Prostaglandin flalpha, Betulinic acid, 2,2,4-Trimethyl-l,3-pentanediol diisobutyrate, 4,4'- Diaponeurosporen-4-al, Methyl (E,2R)-2-hydroxytritriacont-7-enoate, 3abeta,4,5,5a,6,7,8,9,9aalpha,9bbeta-Decahydro-8beta,9alpha-dihydroxy- 3alpha,5abeta,9-trimethylnaphtho[l,2-b]furan-2(3H)-one, 3-Methoxy-4- methyldotriacontane-9,ll-diol, Glycolithocholic acid, Val-gln-ile-asp, 5- hydroxyemedastine, Ethiprole, Propoxur, 7,7-Dimethyl-(5Z,8Z)-eicosadienoic acid, - octene, or any combination thereof.

216. A method of treating a disease of a plant or promoting resistance to a disease of a plant, the method comprising:282.(a) contacting a plant and / or a growth medium in which the plant is growing with a composition comprising one or more compounds, wherein the one or more compounds is selected from the group consisting of DG(20: 5 (5Z, 8Z, 11Z, 14Z, 17Z) / 22: 6(4Z,7Z, 10Z, 13Z, 16Z, 19Z) / 0: 0), Methylparaben, alpha-Neo-Endorphin (1-7), l-(2-Fluorophenyl)-3-(pyridin-4-ylmethyl)urea, (2S,3R)-4- methylidene-2-octyl-5-oxooxolane-3-carboxylic acid, Epsilon-caprolactam, Pyruvic Acid, Tyrosol, 16,16-dimethyl-6-keto Prostaglandin El, Todralazine, Crufomate, Methyl- D-erythritol Phosphate, LPE(16: 1 / 0:0), JWH 018 4-hydroxyindole metabolite-d9, 3,7- Dihydroxy-12-oxocholanoic acid, Arachidonoyl m-Nitroaniline, Pyrazinecarboxamide, N-(piperidinomethyl)-, LPC(O- 16: 0 / 2:0), Carvedilol, 9-Oxo-l l-(3-pentyloxiran-2- YL)undec- 10-enoic acid, 3 -Hydroxy-2 -phenylpropyl carbamate, Phe4Cl-His-OH, Zoledronic acid, 3 -Hydroxy dodecanoic acid, Dichlorprop-P, Acetylthiocholine, Oxasulfuron, L-Arabitol, Octodrine, Sodium l-[2-deoxy-5-O- (hydroxyphosphinato)pentofuranosyl]-5-fluoropyrimidine-2,4(lH,3H)-dione, 15-keto Latanoprost(free acid), Arg-Gly-Tyr-Val-Tyr-Gln-Gly-Leu, Ascorbate 2-sulfate, 1- pentadecanoyl-2-(9Z-tetradecenoyl)-glycero-3-phosphocholine, {[l-(6-hydroxy-7- methoxy-2-oxo-2H-chromen-8-yl)-3-methylbut-3-en-2-yl]oxy} sulfonic acid, (S)-5-oxo- 2,5-dihydro-2-furylacetic acid, Daphnetin, Sulfamonomethoxine, 8-[(2-O,4-O-Disulfo- beta-D-glucopyranuronosyl)oxy] -5,7-dihydroxy-2-(4-methoxyphenyl)-4H- 1 - benzopyran-4-one, 5 -Hydroxyisourate, 2-Amino-5-fluoro-3 -iodopyridine, (5Z,8Z,1 lZ,14Z)-N-(3-Furanylmethyl)-5,8,l 1,14-eicosatetraenamide, Niclosamide, Tiopronin, (3E,6Z)-3,6-Nonadien-l-ol, DL-Glyceraldehyde 2-Phosphate, Desaminotyrosine, Benzenebutanoic acid, Ibutilide, 4,4'-Methylenebis(2,6-DI-tert- butylphenol), Lyso-PAF C-16-d4, Swertianin, or any combination thereof. WSGR Docket No. 63472-722.601217. The method of claim 215 or 216, wherein the concentration of the one or more compound in the composition is at least about 1 nanomolar (nm).

218. The method of any one of claims 215-217, 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.

219. The method of any one of claims 215-218, wherein the contacting comprises contacting the plant with the composition.

220. The method of any one of claims 215-218, wherein the contracting comprises contacting a plant seed with the composition.

221. The method of any one of claims 215-218, wherein the contacting comprises contacting a leaf of the plant with the composition.

222. The method of any one of claims 215-221, wherein the growth medium comprises soil, a hydroponic medium, turface, or isolite.

223. The method of any one of claims 215-222, wherein the promoting resistance to the disease of the plant comprises upregulating one or more biotic defense genes of the plant.

224. The method of any one of claims 215-223, wherein the promoting resistance to the disease of the plant comprises preventing a lesion caused by a plant pathogen or reducing a size of a lesion caused by a plant pathogen.

225. The method of claim 224, wherein the plant pathogen is of a genera selected from the group consisting of Mycosphaerella, Colletotrichum, Puccinia, Botrytis, Fusarium, Alternaria, Blumeria, Ustilago, Melampsora, and any combination thereof.

226. The method of claim 224 or 225, wherein the plant pathogen is of a species selected from the group consisting of Mycosphaerella graminicola, Colletotrichum spp., Puccinia spp., Botrytis cinerea, Fusarium graminearum, Fusarium oxysporum, Blumeria graminis, Ustilago maydis, Melampsora lini, and any combination thereof.

227. The method of claim 215, wherein the composition comprises five or more of the compounds.

228. The method of claim 215, wherein the composition comprises ten or more of the compounds.

229. The method of claim 216, wherein the composition comprises five or more of the compounds.

230. The method of claim 216, wherein the composition comprises ten or more of the compounds.

231. The method of any one of claims 215-230, wherein the composition further comprises a carrier.

232. The method of claim 231, wherein the carrier is formulated for application to a plant and / or medium in which the plant is growing.

233. The method of claim 231, wherein the carrier comprises a fertilizer.

234. The method of claim 233, wherein the fertilizer is a solid.

235. A composition for treating a disease of a plant or promoting resistance to a disease of a plant, comprising:301.(a) at least one microbial strain selected from a Paenihacillus ottowii strain or a Bacillus amyloliquefaciens strain; and WSGR Docket No. 63472-722.601302.(b) one or more compounds selected from the group consisting of DG(20: 5 (5Z, 8Z, 11Z, 14Z, 17Z) / 22: 6(4Z,7Z, 1 OZ, 13Z, 16Z, 19Z) / 0: 0), Methylparaben, alpha-Neo-Endorphin (1-7), l-(2-Fluorophenyl)-3-(pyridin-4-ylmethyl)urea, (2S,3R)-4- methylidene-2-octyl-5-oxooxolane-3-carboxylic acid, Epsilon-caprolactam, Pyruvic Acid, Tyrosol, 16,16-dimethyl-6-keto Prostaglandin El, Todralazine, Crufomate, Methyl- D-erythritol Phosphate, LPE(16: 1 / 0:0), JWH 018 4-hydroxyindole metabolite-d9, 3,7- Dihydroxy-12-oxocholanoic acid, Arachidonoyl m-Nitroaniline, Pyrazinecarboxamide, N-(piperidinomethyl)-, LPC(O- 16: 0 / 2:0), Carvedilol, 9-Oxo-l l-(3-pentyloxiran-2- YL)undec- 10-enoic acid, 3 -Hydroxy-2 -phenylpropyl carbamate, Phe4Cl-His-OH, Zoledronic acid, 3 -Hydroxy dodecanoic acid, Dichlorprop-P, Acetylthiocholine, Oxasulfuron, L-Arabitol, Octodrine, Sodium l-[2-deoxy-5-O- (hydroxyphosphinato)pentofuranosyl]-5-fluoropyrimidine-2,4(lH,3H)-dione, 15-keto Latanoprost(free acid), Arg-Gly-Tyr-Val-Tyr-Gln-Gly-Leu, Ascorbate 2-sulfate, 1- pentadecanoyl-2-(9Z-tetradecenoyl)-glycero-3-phosphocholine, {[l-(6-hydroxy-7- methoxy-2-oxo-2H-chromen-8-yl)-3-methylbut-3-en-2-yl]oxy} sulfonic acid, (S)-5-oxo- 2,5-dihydro-2-furylacetic acid, Daphnetin, Sulfamonomethoxine, 8-[(2-O,4-O-Disulfo- beta-D-glucopyranuronosyl)oxy] -5,7-dihydroxy-2-(4-methoxyphenyl)-4H- 1 - benzopyran-4-one, 5 -Hydroxyisourate, 2-Amino-5-fluoro-3 -iodopyridine, (5Z,8Z,1 lZ,14Z)-N-(3-Furanylmethyl)-5,8,l 1,14-eicosatetraenamide, Niclosamide, Tiopronin, (3E,6Z)-3,6-Nonadien-l-ol, DL-Glyceraldehyde 2-Phosphate, Desaminotyrosine, Benzenebutanoic acid, Ibutilide, 4,4'-Methylenebis(2,6-DI-tert- butylphenol), Lyso-PAF C-16-d4, Swertianin, or any combination thereof.

236. The composition of claim 235, wherein the Paenibacillus ottowii strain comprises one or more of the following:304.(a) 16S rRNA gene sequence at least 95% identical to SEQ ID NO: 1;305.(b) a gyrB gene sequence at least 95% identical to SEQ ID NO: 2; or306.(c) a rpoB gene sequence at least 95% identical to SEQ ID NO: 3.

237. The composition of claim 235, wherein the Bacillus amyloliquefaciens strain comprises one or more of the following:308.(a) a 16S rRNA gene sequence at least 95% identical to SEQ ID NO: 4;309.(b) a gyrB gene sequence at least 95% identical to SEQ ID NO: 5; or310.(c) a rpoB gene sequence at least 95% identical to SEQ ID NO: 6.

238. The composition of claim 235, wherein the Bacillus amyloliquefaciens strain comprises one or more of the following:312.(a) a 16S rRNA gene sequence at least 95% identical to SEQ ID NO: 7;313.(b) a gyrB gene sequence at least 95% identical to SEQ ID NO: 8; or314.(c) a rpoB gene sequence at least 95% identical to SEQ ID NO:

9. WSGR Docket No. 63472-722.601239. The composition of claim 235, wherein the Bacillus amyloliquefaciens strain comprises one or more of the following:316.(a) a 16S rRNA gene sequence at least 95% identical to SEQ ID NO: 10;317.(b) a gyrB gene sequence at least 95% identical to SEQ ID NO: 11; or318.(c) a rpoB gene sequence at least 95% identical to SEQ ID NO: 12.

240. The composition of claim 235, wherein the at least one microbial strain is selected from the group consisting of MS2379 (ATCC Accession No. PTA-124703), MS2697 (ATCC Accession No. PTA- 124708), MS2681 (ATCC Accession No. PTA-124707), and MS2335 (ATCC Accession No. PTA- 124702).

241. The composition of any one of claims 235-240, wherein the composition comprises two or more microbial strains.

242. A composition for treating a disease of a plant or promoting resistance to a disease of a plant, comprising: one or more compounds is selected from the group consisting of Oleanolic acid, Myoinositol, N-Heptadecanol-1, l-(Trimethylsilyl)cyclopropyl phenyl sulfide, Vitexicarpin, 1,3- Benzenedicarboxylic acid, 5 -(1,1 -dimethylethyl)-, 1 -tridecanethiol, Trans-p- Dimethylaminocinnamonitrile, Stigmasteryl trimethylsilyl ether, Pentadecane, Methyl 5 -methyl - 3-keto-4-hexenoate, 1, l-Dichloro-l-sila-2,3-benzo-4,5-thiophenocyclopentadiene, Cis-4-octene, 7-hydroxycholesterol, 25-Methyl-21-tritriacontene-l,9,l 1-triol, Fosfomycin calcium, 2- chloroethanol, 2-Pyridyl hydroxymethane sulfonic acid, 4-(2,4-Dichlorophenoxy)butanoic acid, 1- deoxynojirimycin, l,2-Diarachidoyl-sn-glycero-3-phosphocholine, 2,3,6-Trichlorobenzoic acid, L-serine, 3-methoxytyramine, 5-(4-Chloro-3-hydroxy-l-butynyl)-2,2'-bithiophene, 27- norcholestanehexol, Dehydroabietamide, 2,4-dihydroxybenzophenone, 5 -Nonadecyl- 1,3- benzenediol, Tiformin, Benzamide, N-(5-chloro-2-pyridinyl)-3-(trifluoromethyl)-, Isoduartin methyl ether, 4-Bromo-l-((2-bromophenyl)sulfonyl)-lH-pyrazole, (3ar,4R,5R,6as)-5-Hydroxy-4- ((S, E)-3-hydroxyoct-l-en-l-yl)hexahydro-2H-cyclopenta[b]furan-2-one, Ampiroxicam, 3-(2,3- Dihydroxyphenyl)propanoic acid, 1 -phenylpiperazine, 3-Oxazolidinecarboxylic acid, 2,2- dimethyl-4-( 1 -oxo-2 -hexadecyn-l-yl)-, 1,1 -dimethylethyl ester, (4S)-, Trenbolone acetate, Methyl thieno[3,2-d]thiadiazole-6-carboxylate, N-(2,2,2-trifluoroethyl)morpholine-4-carbothioamide, Butonate, 3, 5 -dinitrocatechol, 9-aminoacridine, Pyridinoline, Xanthotoxol, Gramine(l+), Lanosol, PG(22:6(4z,7z,10z,13z,16z,19z) / 20:2(l lz,14z)), 2-deoxystreptamine, (4-Chloro-3-nitro- benzoylamino)-acetic acid, Pentedrone, (S)-10,16-Dihydroxyhexadecanoic acid, 2-Amino-3-[4- hydroxy-3-(3-methylbut-2-enyl)phenyl]propanoic acid, (2S,4S)-1 -Acetoxy- 16-heptadecene-2, 4- diol, Flutamide, 2-Aminobenzoic acid, Psilocin, (R)-2-Hydroxysterculic acid, Tg( 16:0 / 16:0 / 16: l(9z)), 2-hydroxy-3-({3-[3-methoxy-4-(sulfooxy)phenyl]prop-2- enoyl}oxy)butanedioic acid, Dimethyl adipate, Ps(22:6(4z,7z,10z,13z,16z,19z) / 20:4(5z,8z,l lz,14z)), Thr-tyr-glu, Pro-phe-lys, Ubiquinone-1, Methoxydihydrosorgoleone, (6S,8Z)-6-Hydroxy-3-oxotetradecenoic acid, (9z)-N-[(2s,3r,4e)-l-WSGR Docket No. 63472-722.601322.(Beta-D-Glucopyranosyloxy)-3-Hydroxyoctadec-4-En-2-Yl]octadec-9-Enamide, D-Glucono-1,5- lactone 6-phosphate, Hexadecanedioic acid, 6k-PGFld4, Brefeldin A, Nifenazone, Anethole, Alpha-Mangostin, Karbutilate, L-Asparaginyl-L-lysine, 4-Hydroxy-3-methoxybenzenemethanol, ( 1 R,2R,3R,4R)- 1 -[(R)- 1,5 -Dimethyl- 1 -hydroxy-4-hexenyl] -4-methylcyclohexane- 1,2,3,4-tetrol, 2,3',4,5'-tetramethoxystilbene, N4-(N-acetylaminopropyl)spermidine, Maltose, Ethion, 2,3,5- Triiodobenzoic acid, Isonicotinylglycine, (R*, S*)-4-[l-Ethyl-2-(4-fluorophenyl)butyl]phenol, 2,3 -bisphosphogly cerate, 2',5'-Dichlorobiphenyl-3-ol, Artemisinin, Lys-tyr-gln-glu-ala, Prometon, Shogaol, Rolipram, Bis(2, 3 -dihydroxypropyl) phosphate, 4-Hydroxy-2-oxoglutaric acid, Mesulfenfos, 3 -Sulfobenzoic acid, Athidathion, Novaluron, 5-Bromo-7-methoxy-l- benzofuran-2-carboxylic acid, 4-(Hydroxymethyl)-2-iodo-6-methoxyphenol, 5-(3',4',5'- Trihydroxyphenyl)-gamma-valerolactone-4'-O-sulphate, [Trpll] neurotensin (8-13), Dibutyl phthalate, Cavipetin C, Monobutyl phthalate, Lys-gly-his, Disulfoton sulfone, 3 -Formylsalicylic acid, Dxtp, Hco3-, Sodium sulfate, 13-docosenamide, 6-acetoxydihydrotheaspirane, His-ala-gly, N-(5-methyl-l,3-thiazol-2-yl)-2-(phenylsulfanyl)acetamide, 8,8-Diethoxy-2,6-dimethyl-2- octanol, 13,14-dihydro-15-keto-tetranor Prostaglandin E2, 1-Deoxyvaleric-acid, 2-Propyl-2- pentenoic acid, 6,8a-Seco-6,8a-deoxy-5-oxoavermectin"lb" aglycone, L-Tyrosyl-L-serine, Ciclopirox, 1 -ethenyl -4-methoxy-benzene, 5-Chloro-6-hydroxy-2-oxohexa-3,5-dienoic acid, Desalkyl verapamil D617, N-(Tetradecanoyl)-sphing-4-enine, 3,4,5-trihydroxy-6-({8-hydroxy-2- oxo-2H-furo[2,3-h]chromen-4-yl}oxy)oxane-2-carboxylic acid, Vitamin E, Phosphoadenosine phosphosulfate, Permethrin, Kenpaullone, Andrographolide, Neopikromycin, O, O-Diethyl hydrogen thiophosphate, Naringenin chaicone, Tris(2-chloroethyl) phosphate, Trimetazidine, 9,10-epome, 6-(2-Prop-2-ynoxyphenyl)hexanoic acid, Imperialine, 2,2,6,6-Tetramethyl-l,3- dithiane-4-thione, Ethyl 2-cyano-3-(lh-indol-3-yl)prop-2-enoate, 17alpha-Estradiol, [(6S,7S,10R)-4,10,ll,ll-tetramethyl-3-oxo-6-tricyclo[5.3.1.01,5]undec-4-enyl] acetate, Monoisobutyl phthalate, Tris(2-butoxyethyl) phosphate, l-(2-Bromophenyl)-3-(2-hydroxy-4- nitrophenyl)urea, Arg-pro-thr, Met-pro-tyr, 4-Hydroxyphenyl thiocyanate, 2-Amino-3-chloro-5- nitrobenzotrifluoride, Phosphoric acid, Fenethylline, Pc(20:5(5z,8z,l lz,14z,17z) / 18:4(6z,9z,12z,15z)), Thr-arg-gly, Heliocide H4, 2,4- diacetylphloroglucinol, N-[(R)-4-phosphopantothenoyl]-L-cysteine, 5,7-Dichlorokynurenic acid, Octyl-beta-d-glucopyranoside, 9,11-methane-epoxy Prostaglandin flalpha, Betulinic acid, 2,2,4- Trimethyl-l,3-pentanediol diisobutyrate, 4,4'-Diaponeurosporen-4-al, Methyl (E,2R)-2- hydroxytritriacont-7-enoate, 3abeta,4,5,5a,6,7,8,9,9aalpha,9bbeta-Decahydro-8beta,9alpha- dihydroxy-3alpha,5abeta,9-trimethylnaphtho[l,2-b]furan-2(3H)-one, 3-Methoxy-4- methyldotriacontane-9,ll-diol, Glycolithocholic acid, Val-gln-ile-asp, 5-hydroxyemedastine, Ethiprole, Propoxur, 7,7-Dimethyl-(5Z,8Z)-eicosadienoic acid, -octene, or any combination thereof.

243. The composition of any one of claims 235-241, further comprising a carrier.WSGR Docket No. 63472-722.601244. The composition of claim 243, wherein the carrier is formulated for application to a plant and / or medium in which the plant is growing.

245. The composition of claim 243, wherein the carrier comprises a fertilizer.

246. The composition of claim 245, wherein the fertilizer is a solid.

247. The composition of claim 243, wherein the carrier is a liquid.

248. The composition of any one of claims 235-247, wherein the composition is configured to prevent a lesion caused by a plant pathogen or reduce a size of a lesion caused by a plant pathogen.

249. The composition of claim 248, wherein the plant pathogen is of a genera selected from the group consisting of Mycosphaerella, Colletotrichum, Puccinia, Botrytis, Fusarium, Alternaria, Blumeria, Ustilago, Melampsora, and any combination thereof.

250. The composition of claim 248 or 249, wherein the plant pathogen is of a species selected from the group consisting of Mycosphaerella graminicola, Colletotrichum spp., Puccinia spp., Botrytis cinerea, Fusarium graminearum, Fusarium oxysporum, Blumeria graminis, Ustilago maydis, Melampsora lini, and any combination thereof.

251. The composition of any one of claims 235-250, wherein the composition further comprises an adjuvant selected from a wetting agent, spreading agent, dispersing agent, sticking agent, dust control agent, and adhesive.

252. A method of making a product having an enriched population of a microbial biocontrol agent, the method comprising:332.(a) providing a bioreactor system comprising two or more containers, wherein the two or more containers comprise a working fluid and the microbial biocontrol agent; and (b) collecting the product from the bioreactor system,333.wherein, relative to a total bacterial population, the product has a greater proportion of the microbial biocontrol agent relative to a proportion of the microbial biocontrol agent in at least one of the two or more containers.

253. The method of claim 252, wherein the microbial biocontrol agent is a cellulase-active bacteria.

254. The method of claim 252 or 253, wherein the product has a greater relative abundance of one or more enzymes associated with biocontrol activity relative to a relative abundance of the one or more enzymes associated with biocontrol activity in at least one of the two or more containers.

255. The method of claim 254, wherein the one or more enzymes associated with biocontrol activity comprise a cellulase, a glucanase, a chitinase, a protease, a xylanase, an amylase, or a lipase.

256. The method of any one of claims 252-255, wherein the product has a greater proportion of the microbial biocontrol agent relative to a proportion of the microbial biocontrol agent in a first container of the bioreactor system.

257. The method of any one of claims 252-256, wherein the product has a greater proportion of the microbial biocontrol agent relative to a proportion of the microbial biocontrol agent in at least two of the two or more containers.WSGR Docket No. 63472-722.601258. The method of any one of claims 252-257, wherein the one or more containers of the bioreactor system comprise an aqueous feedstock comprising a microbial consortium.

259. The method of claim 258 wherein the aqueous feedstock comprises an organic substrate.

260. The method of claim 259, wherein the organic substrate comprises seaweed, manure, or any combination thereof.

261. The method of claim 260, wherein the organic substrate comprises seaweed.

262. The method of claim 261, wherein the seaweed comprises kelp.

263. The method of claim 262, wherein the kelp is of the genus Ascophyllum.

264. The method of claim 262, wherein the kelp is of the species Ascophyllum nodosum.

265. The method of any one of claims 252-264, wherein the bioreactor system comprises chitin.

266. The method of any one of claims 252-265, wherein the bioreactor system comprises yeast.

267. The method of any one of claims 252-266, wherein the bioreactor system comprises a bacterial growth medium.

268. The method of claim 267, wherein the bacterial growth medium comprises rice flour, sucrose, soy flour, bran, micronutrients, or any combination thereof.

269. The method of any one of claims 252-268, wherein the bioreactor system comprises at least six containers.

270. The method of any one of claims 252-269, wherein the two or more containers comprise fluidized bed reactors.

271. The method of any one of claims 252-270, wherein the bioreactor system comprises a manifold air system, wherein the method further comprises continuously supplying air to the one or more second stage containers using the manifold air system.

272. The method of any one of claims 252-271, wherein the product comprises one or more microbial metabolites.

273. The method of any one of claims 252-272, wherein the product is configured to (i) promote resistance of a plant disease or a plant pathogen and / or (ii) treat a plant disease or a plant pathogen.

274. The method of claim 273, wherein the plant pathogen is of a genera selected from the group consisting of Mycosphaerella, Colletotrichum, Puccinia, Botrytis, Fusarium, Alternaria, Blumeria, Ustilago, Melampsora, and any combination thereof.

275. The method of claim 273 or 274, wherein the plant pathogen is of a species selected from the group consisting of Mycosphaerella graminicola, Colletotrichum spp., Puccinia spp., Botrytis cinerea, Fusarium graminearum, Fusarium oxysporum, Blumeria graminis, Ustilago maydis, Melampsora lini, and any combination thereof.

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