Microbial consortia
Disclosed herein are microbial consortia and compositions including microbes for example for use in agricultural or biodegradation applications. In some embodiments, soil, plants, and/or plant parts (such as seeds, seedlings, shoots, roots, leaves, fruit, stems, or branches) are contacted with a disclosed microbial consortia or composition including microbes. The microbial consortia or microbe-containing compositions may be applied to soil, plant, and/or plant parts alone or in combination with additional components (such as chitin, chitosan, glucosamine, amino acids, and/or liquid fertilizer). In additional embodiments, the disclosed microbial consortia or compositions including microbes are used in methods of degrading biological materials, such as chitin-containing biological materials.
1. A method comprising:
mixing a chitin-containing biological source with a composition comprising cells of five or more microbial species selected from Bacillus spp., Lactobacillus spp., Clostridium spp., Streptomyces spp., Virgibacillus spp., Brevibacillus spp., Paenibacillus spp., Oceanobacillus spp., Lysinibacillus spp., Acetobacter spp., Rummeliibacillus spp., and Candida spp., wherein each of the five or more microbial species has a 16S rDNA sequence with at least 99% sequence identity to one of SEQ ID NOs: 1-17 to form a mixture;
fermenting the mixture; and
separating the fermented mixture into solid, aqueous, and lipid fractions.
2. The method of claim 1 , wherein the chitin-containing biological source comprises a marine animal or marine animal by-product, an insect, or a fungus.
3. A method comprising contacting soil, plants, or plant parts with a composition comprising cells of five or more microbial species selected from Bacillus spp., Lactobacillus spp., Clostridium spp., Streptomyces spp., Virgibacillus spp., Brevibacillus spp., Paenibacillus spp., Oceanobacillus spp., Lysinibacillus spp., Acetobacter spp., Rummeliibacillus spp., and Candida spp., wherein each of the five or more microbial species has a 16S rDNA sequence with at least 99% sequence identity to one of SEQ ID NOs: 1-17.
4. The method of claim 3 , further comprising contacting the soil, plants, or plant parts with:
one or more of chitin, chitosan, glucosamine, and amino acids;
a liquid fertilizer; and/or
one or more pesticides, one or more fungicides, one or more herbicides, one or more insecticides, one or more plant hormones, one or more plant elicitors, or combinations of two or more thereof.
5. The method of claim 1 , wherein the composition comprises cells of ten or more microbial species selected from Bacillus spp., Lactobacillus spp., Clostridium spp., Streptomyces spp., Virgibacillus spp., Brevibacillus spp., Paenibacillus spp., Oceanobacillus spp., Lysinibacillus spp., Acetobacter spp., Rummeliibacillus spp., and Candida spp.
6. The method of claim 1 , wherein the composition comprises cells of five or more microbial species having 16S rDNA sequences comprising any one of SEQ ID NOs: 1-17.
7. The method of claim 1 , wherein the composition comprises cells of microbial species selected from each of Bacillus spp., Lactobacillus spp., Clostridium spp., Streptomyces spp., Virgibacillus spp., Brevibacillus spp., Paenibacillus spp., Oceanobacillus spp., Lysinibacillus spp., Acetobacter spp., Rummeliibacillus spp., and Candida spp.
8. The method of claim 1 , wherein:
the Bacillus spp. comprises one or more of Bacillus flexus, Bacillus circulans, Bacillus subtilis, Bacillus pumilus, Bacillus licheniformis, Bacillus amyloliquefaciens, Bacillus pocheonensis , and Bacillus clausii;
the Lactobacillus spp. comprises Lactobacillus vini and/or Lactobacillus buchneri;
the Clostridium spp. comprises one or more of Clostridium nitrophenolicum, Clostridium beijerinckii , and Clostridium pasteurianum;
the Paenibacillus spp. comprises one or more of Paenibacillus brevis, Paenibacillus cookii, Paenibacillus lautus, Paenibacillus, chibensis, Paenibacillus anaericanus , and Paenibacillus agaridevorans;
the Oceanobacillus spp. comprises Oceanobacillus oncorhynchi subsp. incaldanensis;
the Lysinibacillus spp. comprises Lysinibacillus xylanilyticus;
the Acetobacter spp. comprises Acetobacter pasteurianum;
the Rummeliibacillus spp. comprises Rummeliibacillus pycnus ; and/or
the Candida spp. comprises Candida ethanolica.
9. The method of claim 1 , wherein the composition further comprises cells of one or more of Bacillus subterraneus, Bacillus oceanisediminis, Bacillus firmus, Virgibacillus halophilus, Brevibacillus brevis, Paenibacillus validus, Paenibacillus timonensis, Paenibacillus cineris, Paenibacillus rhizoospherae, Paenibacillus favisporus, Clostridium tyrobutyricum, Clostridium sphenoides, Lysinibacillus fusiformis , and Rummeliibacillus stabekisii.
10. The method of claim 1 , wherein the composition further comprises cells of one or more of Azotobacter spp. and Rhizobium spp.
11. The method of claim 10 , wherein the Azotobacter spp. comprises Azotobacter vinelandii and/or Azotobacter chroococcum or the Rhizobium spp. comprises Rhizobium japonicus and/or Rhizobium leguminosarum.
12. The method of claim 3 , wherein the composition comprises cells of ten or more microbial species selected from Bacillus spp., Lactobacillus spp., Clostridium spp., Streptomyces spp., Virgibacillus spp., Brevibacillus spp., Paenibacillus spp., Oceanobacillus spp., Lysinibacillus spp., Acetobacter spp., Rummeliibacillus spp., and Candida spp.
13. The method of claim 3 , wherein the composition comprises cells of five or more microbial species having 16S rDNA sequences comprising any one of SEQ ID NOs: 1-17.
14. The method of claim 3 , wherein the composition comprises cells of microbial species selected from each of Bacillus spp., Lactobacillus spp., Clostridium spp., Streptomyces spp., Virgibacillus spp., Brevibacillus spp., Paenibacillus spp., Oceanobacillus spp., Lysinibacillus spp., Acetobacter spp., Rummeliibacillus spp., and Candida spp.
15. The method of claim 3 , wherein:
the Bacillus spp. comprises one or more of Bacillus flexus, Bacillus circulans, Bacillus subtilis, Bacillus pumilus, Bacillus licheniformis, Bacillus amyloliquefaciens, Bacillus pocheonensis , and Bacillus clausii;
the Lactobacillus spp. comprises Lactobacillus vini and/or Lactobacillus buchneri;
the Clostridium spp. comprises one or more of Clostridium nitrophenolicum, Clostridium beijerinckii , and Clostridium pasteurianum;
the Paenibacillus spp. comprises one or more of Paenibacillus brevis, Paenibacillus cookii, Paenibacillus lautus, Paenibacillus, chibensis, Paenibacillus anaericanus , and Paenibacillus agaridevorans;
the Oceanobacillus spp. comprises Oceanobacillus oncorhynchi subsp. incaldanensis;
the Lysinibacillus spp. comprises Lysinibacillus xylanilyticus;
the Acetobacter spp. comprises Acetobacter pasteurianum;
the Rummeliibacillus spp. comprises Rummeliibacillus pycnus ; and/or
the Candida spp. comprises Candida ethanolica.
16. The method of claim 3 , wherein the composition further comprises cells of one or more of Bacillus subterraneus, Bacillus oceanisediminis, Bacillus firmus, Virgibacillus halophilus, Brevibacillus brevis, Paenibacillus validus, Paenibacillus timonensis, Paenibacillus cineris, Paenibacillus rhizoospherae, Paenibacillus favisporus, Clostridium tyrobutyricum, Clostridium sphenoides, Lysinibacillus fusiformis , and Rummeliibacillus stabekisii.
17. The method of claim 3 , wherein the composition further comprises cells of one or more of Azotobacter spp. and Rhizobium spp.
18. The method of claim 17 , wherein the Azotobacter spp. comprises Azotobacter vinelandii and/or Azotobacter chroococcum or the Rhizobium spp. comprises Rhizobium japonicus and/or Rhizobium leguminosarum.
19. The method of claim 1 , wherein the microbial composition comprises the microbes in ATCC deposit number PTA-122728.
20. The method of claim 3 , wherein the microbial composition comprises the microbes in ATCC deposit number PTA-122728.