Location: Emerging Pests and Pathogens Research
Project Number: 8062-22410-007-023-A
Project Type: Cooperative Agreement
Start Date: Oct 1, 2021
End Date: May 31, 2025
The objective of this project is to investigate microbial communities associated with soils suppressive to the Soybean Cyst Nematode (SCN) in order to identify nematophagous fungi with potential for biological control of this invasive nematode pathogen or as sources of novel biopesticides. The specific aims/objectives are to: Objective 1: Identify genes and secondary metabolite biosynthetic clusters (SMBCs) enriched or upregulated in microbial communities in bulk soil, rhizosphere soil and SCN cysts of soybean in SCN suppressive soils. This project will focus on a known SCN suppressive soil, located in Waseca, MN, which shows much lower SCN densities than surrounding fields and a paired nearby non-suppressive field. Shotgun metagenomic and meta-transcriptomic approaches will be used to profile the diversity and abundance of taxa, gene families, and metabolic pathways involved in nematode parasitism (e.g. proteases, carbohydrate degrading enzymes, and SMBCs). Microbes will also be cultured from suppressive soils or identified within a large collection of fungi previously cultured by the ARS lab. Objective 2: Identify interactions between species, genes, and metabolic pathways using co-occurrence networks. Metagenome and metatranscriptome data collected in Obj. 1. will be analyze using co-occurrence networks to identify differences between suppressive and non-suppressive soils. We will test whether fungi directly antagonize nematodes (e.g. parasitism) or through production of secondary metabolites incidentally toxic to nematodes. Objective 3: Test hypotheses of species interactions in microbial consortia. Taxa comprising microbial consortia will be grown alone and in microbial consortia by systematically adding or removing taxa in the presence and absence of the nematode host. We will use several in-vitro bioassays as a high-throughput screen for production of metabolites active against nematodes.
Shotgun metagenomic and meta-transcriptomic approaches will be used to profile the diversity and abundance of taxa, gene families, and metabolic pathways involved in nematode parasitism (e.g. proteases, carbohydrate degrading enzymes, and SMBCs). Microbes will also be cultured from suppressive soils or identified within a large collection of fungi previously cultured by the Bushley lab. (Obj 1) These fungi and bacteria will be tested in bioassays to determine their ability for direct parasitism or production of toxic metabolites (Obj 2). Data from the first two objectives will be used to select consortia of microbes alone or in combination with their metabolites that can be tested in greenhouse trials for biocontrol efficacy against soybean cyst nematode. Collaborators at University of Minnesota will participate in project by 1) planting, maintaining, and sampling SCN suppressive and non-suppressive plots at the field sites at the Southern Outreach and Research Center (Waseca, MN) (Obj 1)and in 2) analyzing extracts from fungi and bacteria identified in the project to identify bioactive compounds with potential for development as bionematicides (Obj 2 and 3).