Accelerated directed evolution of microbial consortia for the development of desirable plant phenotypic traits

1. A method for deriving a microbial community, enriched for spore-forming microbes that are associated with imparting a beneficial phenotypic trait to a plant, comprising:

a) growing a plurality of plants in a growth medium, in the presence of a first microbial community;

b) selecting at least one plant from said plurality, following step a), based upon a beneficial phenotypic trait exhibited by the plant relative to other plants of said plurality;

c) acquiring a second microbial community from the at least one plant selected in step b);

d) repeating steps a) to c) in an iterative manner, wherein the second microbial community acquired in step c) is used as an inoculum in step a) of any successive repeat; and

e) acquiring a microbial community enriched for spore-forming microbes that is associated with imparting a beneficial phenotypic trait to a plant,

wherein an enrichment procedure that ensures the selective survival of spore-forming microbes is applied to the first and/or second microbial community.

2. The method according to claim 1 , wherein the enrichment procedure that ensures the selective survival of spore-forming microbes comprises: exposing the first and/or second microbial community to an element or condition that is selective for the survival of spore-forming microbes and is deleterious to the survival of microbes that do not form spores.

3. The method according to claim 1 , wherein the enrichment procedure that ensures the selective survival of spore-forming microbes comprises: exposing the first and/or second microbial community to a solvent or sterilant that is selective for the survival of spore-forming microbes and is deleterious to the survival of microbes that do not form spores.

4. The method according to claim 1 , wherein the enrichment procedure that ensures the selective survival of spore-forming microbes comprises: exposing the first and/or second microbial community to an organic solvent that is selective for the survival of spore-forming microbes and is deleterious to the survival of microbes that do not form spores.

5. The method according to claim 1 , wherein the enrichment procedure that ensures the selective survival of spore-forming microbes comprises: exposing the first and/or second microbial community to an alcohol that is selective for the survival of spore-forming microbes and is deleterious to the survival of microbes that do not form spores.

6. The method according to claim 1 , wherein the enrichment procedure that ensures the selective survival of spore-forming microbes comprises: exposing the first microbial community of step a) to an alcohol.

7. The method according to claim 1 , wherein the enrichment procedure that ensures the selective survival of spore-forming microbes comprises: exposing the second microbial community of step c) to an alcohol.

8. The method according to claim 1 , wherein the enrichment procedure that ensures the selective survival of spore-forming microbes comprises: exposing the first microbial community of step a) to an alcohol and also exposing the second microbial community of step c) to an alcohol.

9. The method according to claim 5 , wherein the alcohol is applied to the growth medium in step a).

10. The method according to claim 5 , wherein the alcohol is applied to the inoculum in step d).

11. The method according to claim 1 , wherein the enrichment procedure that ensures the selective survival of spore-forming microbes comprises: exposing the first and/or second microbial community to ethanol.

12. The method according to claim 1 , wherein the enrichment procedure ensures the selective survival of Fungi, Firmicutes, and/or Actinomycetes.

13. The method according to claim 1 , wherein the enrichment procedure ensures the selective survival of members of the genus Bacillus.

14. The method according to claim 1 , wherein said first microbial community in step a) is obtained by a microbial capture step, comprising:

growing a plurality of plants in a growth medium, in the presence of a microbial community; and

acquiring said first microbial community from the plurality of plants, or growth medium surrounding the plurality of plants.

15. The method according to claim 1 , wherein said first microbial community in step a) is obtained by a microbial capture step, comprising:

growing a plurality of plants in a growth medium, in the presence of a microbial community; and

acquiring said first microbial community from the plurality of plants, or growth medium surrounding the plurality of plants; and

exposing the acquired first microbial community to an element or condition that is selective for the survival of spore-forming microbes and is deleterious to the survival of microbes that do not form spores.

16. The method according to claim 1 , wherein said first microbial community in step a) is obtained by a microbial capture step, comprising:

growing a plurality of plants in a growth medium, in the presence of a microbial community, wherein an enrichment procedure that ensures the selective survival of spore-forming microbes is applied to the growth medium; and

acquiring said first microbial community from the plurality of plants, or growth medium surrounding the plurality of plants.

17. The method according to claim 1 , wherein said first microbial community in step a) is obtained by a microbial capture step, comprising:

acquiring a first microbial community from a plurality of plants growing in natural soil; and

exposing the acquired first microbial community to an element or condition that is selective for the survival of spore-forming microbes and is deleterious to the survival of microbes that do not form spores.

18. The method according to claim 1 , further comprising: isolating at least one microbe from the microbial community acquired in step e).

19. The method according to claim 1 , further comprising: isolating at least one microbe from the microbial community acquired in step e) and utilizing a molecular technique to characterize the isolated microbe.

20. The method according to claim 1 , wherein the plurality of plants are members of the Poaceae family.