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RAPID VIRULENCE ANNOTATION OF THE SOIL METAGENOME UNDER DIFFERENT AGRICULTURAL PRODUCTION PRACTICES
Successful stewardship of the natural resource base requires an understanding of the connection between aboveground and belowground processes. Soil microbes are key players in nutrient cycling, and are involved in both beneficial and harmful interactions with crop plants. There is emerging evidence that the diversity of bacteria capable of positive and negative interactions with plants is greater than previously recognized, but tools to test this idea have been lacking. One likely result of this knowledge gap is gross underestimation of the extent of the soil pathosphere (total number of disease-causing organisms), including the reservoir from which important crop pathogens evolve. Our long-term goal is to determine whether organisms capable of causing disease in agricultural soils are more diverse than previously recognized. The objective of this application, which is the next logical step towards our long-term goal, is to develop high-throughput tools for screening potential disease genes, and recovering the organisms harboring these genes. We propose to achieve this objective by pursuing the following Specific Aims: 1. Develop a functional screen for disease genes (Rapid Virulence Annotation) using a model system of mixed microbial cultures 2. Recover cells from the model system using a magnetic tagging approach 3. Apply the functional screen and cell recovery approach to characterize both recognized and novel pathogens in natural microbial communities from agricultural soils 4. Determine the prevalence of tagged pathogens in soils subjected to different production approaches. The proposed project is innovative because Rapid Virulence Annotation has been applied previously only to single microbial strains, and has not been coupled to cell recovery approaches for the identification of new disease-causing organisms. The expected outcome is demonstration of the validity of these novel approaches. An additional outcome with more immediate positive impact will be a dataset that can be integrated with the results of a larger agricultural ecosystems research study, and contribute to the future development of more economically and environmentally sustainable practices in the Western High Plains and Intermountain regions.
USDA CRIS Project Information Link: 0221372