AGRICULTURE VIROMES IN FARMING SYSTEMS: EFFECTS ON MICROBIOME ASSEMBLY, FUNCTION AND CROP PRODUCTION

The overarching goal of this research is to assess how viruses function as part of agriculture soil microbiomes and how those functions impact soil health and crop productivity. This work will investigate the role of viruses within the soil microbiome (bacteria, archaea and fungi) under different farming practices (conventional, conservation, and organic, defined below) through field sampling and greenhouse experiments. To date, there has been very limited research on the soil virome regarding its composition, interactions with other soil microbes, and its potential impacts on agriculture. We hypothesize that the composition, distribution, and functions of the agriculture virome have important consequences for structuring soil microbiomes, manipulating the associated soil processes and functions, as well as for long term soil health and sustainable agriculture.Specific goals include:Objective 1: Characterize soil microbiome community structures, focusing on bacteria, archaea, fungi and viruses. DNA-based molecular techniques and high-throughput sequencing will be applied to characterize soil microbial communities and integrate viruses as part of the soil microbiome. Interaction networks, host prediction analyses, and characterization of virus-encoded auxiliary metabolic genes will be used to assess the role of viruses in soil microbiomes.Objective 2: Investigate the temporal effects and interaction of agricultural management practices on soil microbiomes and crop production. Physical and chemical properties of soil samples at two depths will be examined from fields with different management practices (conventional, conservation, organic) over two growing seasons. Management will be linked with soil properties (including bulk density, aggregate stability, pH, cation exchange capacity, extractable nutrients) as well as microbiome structure and function (e.g., nitrogen transformation potential, active carbon, and viral auxiliary metabolic genes).Objective 3: Determine the impacts of viral predation on soil microbiome structure and function, including crop production. Microcosm approaches will be used to assess the direct impacts of viral infection and lysis on soil microbiomes and ultimately plant growth and productivity over one growing season.Objective 4: Develop a conceptual model for how viruses impact soil microbiomes, respond to soil management practices, and ultimately impact system productivity. The collective data generated by these endeavors will be integrated into a conceptual model that accounts for the roles of viruses within agriculture soil microbiomes, including direct and indirect impacts on soil health and crop productivity.