Microbial consortia for soil improvement
Provided herein is technology relating to functional microbial consortia and particularly, but not exclusively, to methods and systems for producing a microbial consortium possessing a desired function and microbial consortia produced according to such methods. The microbial consortia may be used to improve soil, e.g., for agricultural uses.
1 . A method of producing a living microbial consortium that accumulates nitrogen in an agricultural medium, the method comprising:
(a) providing an input sample produced from an environmental sample comprising a plurality of microbes; and
(b) proceeding, starting with the input sample, to produce a microbial consortium using an iterative process comprising:
(i) inoculating a fixed carbon-free and fixed nitrogen-free growth medium with the input sample to produce a culture;
(ii) incubating the agricultural medium culture in the presence of nitrogen gas (N 2 ) and carbon dioxide (CO 2 ) gas and with illumination by a light source to produce an incubated culture; and
(iii) measuring a phenotype of the incubated culture,
with a portion of the incubated culture acting as the input sample for a next iteration of the iterative process until the phenotype is stable,
wherein the microbial consortium comprises a plurality of living organisms comprising a cyanobacterium and the cyanobacterium abundance in the microbial consortium is greater than an abundance of the cyanobacterium abundance in the environmental sample; and
wherein the microbial consortium fixes nitrogen.
2 . The method of claim 1 , wherein said microbial consortium comprises one photosynthetic microbe.
3 . The method of claim 2 , wherein said microbial consortium comprises a photosynthetic bacterium or a photosynthetic alga.
4 . The method of claim 3 , wherein said photosynthetic alga is a member of a genus that is Tetraselmis, Chlorella, Coleochaete, Gonium, Paradoxia, Cymbomonas, Palmaria, Characiochloris, Marvania, Chlamydomonas, Parachlorella, Coccomyxa, Trebouxia, Cyanidium, Treubaria, Dangeardinia, Galdieria, Nyholmiella, Porphyra, Chara, Ankistrodesmus, Picochlorum, Cyanophora, Chondrus, Pseudochloris, Interfilum, Gelidium, Symphyogyna, Chlorosarcina , or Cyanothece.
5 . The method of claim 2 , wherein said microbial consortium comprises two or more photosynthetic microbes.
6 . The method of claim 1 , wherein the phenotype is a functional phenotype.
7 . The method of claim 6 , wherein the functional phenotype comprises nitrogen fixation.
8 . The method of claim 7 , wherein the functional phenotype further comprises carbon sequestration and/or phosphate mobilization.
9 . The method of claim 1 , wherein the microbial consortium comprises one microbe that sequesters carbon.
10 . The method of claim 9 , wherein the microbial consortium comprises two or more microbes that sequester carbon.
11 . The method of claim 1 , wherein said microbial consortium comprises one nitrogen-fixing microbe.
12 . The method of claim 11 , wherein said microbial consortium comprises two or more nitrogen-fixing microbes.
13 . The method of claim 1 , wherein said cyanobacterium abundance in the microbial consortium is at least 1%.
14 . The method of claim 1 , wherein the microbial consortium comprises a microbe of a phylum that is Proteobacteria.
15 . The method of claim 1 , wherein the microbial consortium comprises a microbe of an order that is Cyanobacteriales, Cyanobacteriota, Nostocales, Pseudoanabaenales, Spirulinales, or Oscillatoriales.
16 . The method of claim 1 , wherein the microbial consortium comprises a microbe from a genus that is Variovorax, Caulobacter , and/or Pseudomonas.
17 . The method of claim 1 , wherein the microbial consortium comprises a microbe from a genus that is Acaryochloris, Aliinostoc, Aliterella, Amazonocrinis, Anabaena, Anabaenopsis, Aphanizomenon, Atlanticothrix, Aulosira, Calenema, Calothrix, Camptylonemopsis, Chlorogloeopsis, Chroococcidiopsis, Chrysosporum, Compactonostoc, Constrictifilum, Crocosphaera, Cyanobacterium, Cyanocohniella, Cylindrospermopsis, Cylindrospermum, Dendronalium, Desikacharya, Desmonostoc, Dolichospermum, Erythrobacter, Fischerella, Fortiea, Fremyella, Geitlerinema, Gloeocapsa, Gloeocapsopsis, Gloeothece, Gloeotrichia, Goleter, Hapalosiphon, Hydrocoryne, Jaaginema, Johanseniella, Kamptonema, Komarekiella, Leptolyngbya, Lyngbya, Macrochaete, Mastigocoleus, Microchaete, Nodosilinea, Nodularia, Nostoc, Nostocaceae, Nostochopsis, Oligotropha, Oscillatoria, Pantanalinema, Pelatocladus, Planktothrichoides, Planktothrix, Polymorphum, Porphyrobacter, Prochlorococcus, Prochlorothrix, Pseudanabaena, Pseudoaliinostoc, Raphidiopsis, Richelia, Rivularia, Roholtiella, Rubidibacter, Scytonema, Spirulina, Synechococcus, Synechocystis, Thermosynechococcus, Tolypothrix, Trichormus, Violetonostoc, Wollea , or Xenococcus.
18 . The method of claim 1 , wherein a microbe of the microbial consortium has a ribosomal RNA gene nucleotide sequence that is at least 90% identical to SEQ ID NO: 1, 3, 7, 10, 13, 19, 22, 26, 30, 32, 34, 35, 39, 42, 45, 51, 54, 57, 61, 63, 66, 70,74, 84, 89, 99, 103, 108, 116, 122, 123, 125, or 127.
19 . The method of claim 1 , wherein the microbial consortium sequesters carbon.
20 . The method of claim 1 , wherein said microbial consortium comprises a microbe capable of metabolizing carbon-containing compounds produced by the cyanobacterium.
21 . The method of claim 1 , wherein the microbial consortium comprises a photosynthetic microbe that is a member of a genus that is Nodularia, Chrysosporum, Gloeocapsopsis, Richelia, Mastigocoleus, Hapalosiphon, Gloeothece, Acaryochloris, Kamptonema, Raphidiopsis, Crocosphaera, Macrochaete, Thermosynechococcus, Pseudanabaena, Chroococcidiopsis, Prochlorothrix, Anabaena, Leptolyngbya, Calothrix, Cylindrospermopsis, Dolichospermum, Scytonema, Lyngbya, Tolypothrix, Fischerella, Fortiea, Aliterella, Hydrocoryne, Prochlorococcus, Planktothrichoides, Geitlerinema, Xenococcus, Jaaginema, Nostochopsis, Pantanalinema, Oscillatoria, Spirulina, Pelatocladus, Nodosilinea, Aphanizomenon, Chlorogloeopsis, Gloeocapsa, Calenema, Rivularia, Trichormus, Synechococcus, Synechocystis, Cylindrospermum, Planktothrix, Bosea, Shinella, Novosphingobium or Rubidibacter.
22 . The method of claim 1 , wherein said light source provides light having wavelengths from approximately 380 nm to 750 nm.
23 . The method of claim 1 , wherein the cyanobacterium is a Nostoc species, a Trichormus species, or an Amazonocrinis species.
24 . The method of claim 1 , wherein the microbial consortium comprises an alpha-proteobacterium or a gamma-proteobacterium.
25 . The method of claim 1 , wherein the phenotype is microbial community membership and/or microbial community abundance.