Platform for developing soil-borne plant pathogen inhibiting microbial consortia

Patent metadata

Field	Value
Publication number	US-2021251237-A1
Application number	US-201917262541-A
Country	US
Kind code	A1
Filing date	Jul 25, 2019
Priority date	Jul 25, 2018
Publication date	Aug 19, 2021
Grant date	—

Abstract

The disclosure relates to a systemic platform for developing soil-borne plant pathogen inhibiting microbial consortia. The platform utilizes multivariate computer modelling and multidimensional ecological function balancing (MEFB) nodal analysis to develop microbial consortia, consortia, and inoculants. The disclosure further relates to a prescriptive biocontrol system that will enable farmers to have site-specific agricultural biologics developed for their specific site and crop of interest.

First claim

1 . A method for creating a soil-borne plant pathogen inhibiting microbial consortia, comprising:
a) accessing or creating a soil-borne plant pathogen suppressive microbial library; b) utilizing microbes from the library of step a) to access or create one or more ecological function balancing nodal microbial libraries, selected from the group consisting of: a mutual inhibitory activity microbial library, a carbon nutrient utilization complementarity microbial library, an antimicrobial signaling capacity and responsiveness microbial library, a plant growth promotion ability microbial library, and an antimicrobial resistance to clinical antimicrobials library; c) performing a multi-dimensional ecological function balancing (MEFB) nodal analysis utilizing said one or more nodal microbial libraries; and d) selecting at least two microbes from the soil-borne plant pathogen suppressive microbial library based on the MEFB nodal analysis, thereby producing a soil-borne plant pathogen inhibiting microbial consortia having a targeted ecological function in at least one dimension.

2 . A method for creating a soil-borne plant pathogen inhibiting microbial consortia, comprising:
a) accessing or creating a soil-borne plant pathogen suppressive microbial library; b) utilizing microbes from the library of step a) to access or create one or more ecological function balancing nodal microbial libraries, selected from the group consisting of: a mutual inhibitory activity microbial library, a carbon nutrient utilization complementarity microbial library, an antimicrobial signaling capacity and responsiveness microbial library, a plant growth promotion ability microbial library, and an antimicrobial resistance to clinical antimicrobials library; c) performing a multi-dimensional ecological function balancing (MEFB) nodal analysis utilizing said one or more nodal microbial libraries; d) assembling a library of microbial consortia, each microbial consortia comprising at least two microbes from the soil-borne plant pathogen suppressive microbial library, selected based on the MEFB nodal analysis; e) screening microbial consortia from the library of microbial consortia in the presence of a plurality of soil-borne plant pathogens to produce a soil-borne plant pathogen suppressive profile for each screened microbial consortia; f) optionally ranking microbial consortia from the library of screened microbial consortia based upon at least one dimension of the soil-borne plant pathogen suppressive profile of each microbial consortia; and g) selecting a soil-borne plant pathogen inhibiting microbial consortia having the desired soil-borne plant pathogen suppressive profile from the library.

3 . The method of claim 2 , comprising: repeating steps a) through e) one or more times.

4 . The method of claim 2 , comprising: repeating steps a) through f) one or more times.

5 . The method of claim 2 , comprising: repeating steps b) through e) one or more times.

6 . The method of claim 2 , comprising: repeating steps b) through f) one or more times.

7 . The method of claim 2 , comprising: repeating steps d) through e) one or more times.

8 . The method of claim 2 , comprising: repeating steps d) through f) one or more times.

9 . The method of claim 1 , wherein the step of creating a soil-borne plant pathogen suppressive microbial library comprises creating the soil-borne plant pathogen suppressive microbial library, comprising:
i) screening a population of microbial isolates in the presence of the soil-borne plant pathogen identified and/or cultured in step (a), to create a soil-borne plant pathogen suppressive profile for each individual microbial isolate in said population,
wherein said plant pathogen suppressive profile indicates each microbial isolate's ability to suppress the soil-borne plant pathogen identified and/or cultured in step (a).

10 . The method of claim 1 , wherein the step of creating a mutual inhibitory activity microbial library comprises the steps of:
i) assembling a library of test microbial consortia, each test consortia comprising a combination of at least two microbial isolates from the soil-borne plant pathogen suppressive microbial library; ii) screening test microbial consortia of the assembled library for the relative degree of mutual inhibitory activity displayed by each microbial isolate towards every other microbial isolate within its own test microbial consortia; and iii) developing an n-dimensional mutual inhibitory activity matrix for test microbial consortia based on the mutual inhibitory activities screened in step (i).

11 . The method of claim 1 , wherein the step of creating a carbon nutrient utilization complementarity microbial library comprises the step of: i) screening a population of microbial isolates from the soil-borne plant pathogen suppressive microbial library for carbon nutrient utilization by growing said microbial isolates in a plurality of different nutrient media that each comprise a distinct single carbon source to create a carbon nutrient utilization profile for each individual microbial isolate in said population.

12 . The method of claim 1 , wherein the step of creating an antimicrobial signaling capacity and responsiveness microbial library comprises the steps of:
i) screening a population of microbial isolates from the soil-borne plant pathogen suppressive microbial library for the ability of each microbial isolate to signal and modulate the production of antimicrobial compounds in other microbial isolates from the population of microbial isolates; and/or screening a population of microbial isolates from the soil-borne plant pathogen suppressive microbial library for the ability of each microbial isolate to be signaled and have their production of antimicrobial compounds modulated by other microbial isolates from the population of microbial isolates; thereby creating an antimicrobial signaling capacity and responsiveness profile for each screened individual microbial isolate.

13 . The method of claim 1 , wherein the step of creating an antimicrobial resistance to clinical antimicrobials library comprises the steps of:
i) screening microbial isolates from the soil-borne plant pathogen suppressive microbial library for resistance to a plurality of antibiotics to create an n-dimensional antibiotic resistance profile.

14 . The method of claim 1 , wherein the step of creating a plant growth promotion ability microbial library comprises the steps of:
i) applying microbial isolates from the soil-borne plant pathogen suppressive microbial library to a test plant, ii) cultivating the test plant to maturity, and iii) comparing the growth of the test plant against that of a control plant that did not receive the microbial isolate;
wherein differences in the growth between the test plant and the control plant demonstrate a microbial isolate's plant growth promotion ability.

15 . The method of claim 1 , wherein the soil-borne pathogen is selected from the group consisting of: species of Colletotrichum, Fusarium, Verticillium, Phytophthora, Cercospora, Rhizoctonia, Septoria, Pythium, or Stagnospora. In some embodiments, target soil-born plant pathogens include fungi and fungi-like organisms, including members of Plasmodiophoromyces, Zygomycetes, Oomycetes, Ascomycetes, and Basidiomycetes. In some embodiments, fungi and fungi-like soil-borne plant pathogens include species of Aphanomyces, Bremia, Phytophthora, Pythium, Monosporascus, Sclerotinia, Rusarium Rhizoctonia, Verticillium, Plasmodiophora brassicae, Spongospora subterranean, Macrophomina phaseolina, Mon

Assignees

• Univ Minnesota

Inventors

• Kinkel Linda L

Classifications

• C12R2001/465

  Streptomyces · CPC title

• C12R2001/07

  Bacillus · CPC title

• C12N1/205

  Bacterial isolates · CPC title

• A01H3/00

  Processes for modifying phenotypes {, e.g. symbiosis with bacteria} (A01H4/00 takes precedence) · CPC title

• A01N63/22 Primary

  Bacillus · CPC title