From Detection to Prediction: AI-Enabled Molecular Epidemiology for Precision Soybean Disease Management

Soilborne disease prediction remains one of the most persistent unmet challenges in soybean production. Soilborne diseases continue to constrain soybean yield stability across the United States, yet current management strategies rely largely on reactive diagnostics that fail to capture the ecological complexity underlying disease outcomes. Increasing evidence indicates that soybean diseases emerge from interactions among fungal pathogens, plant-parasitic nematodes, and surrounding microbial communities, creating disease complexes that are difficult to predict using organism-specific approaches. Improved predictive frameworks are needed to support timely and cost-effective management decisions for U.S. producers. This postdoctoral fellowship will develop a community-centered molecular epidemiology framework integrating molecular diagnostics, microbiome sequencing, and AI-assisted modeling to improve prediction of soybean disease risk. The research will (1) quantify pathogen guild structure using scalable molecular diagnostics and (2) identify microbial community signatures associated with disease outcomes across agricultural environments and cropping systems. These approaches will generate predictive models linking microbial community composition with plant health outcomes, advancing precision agriculture and disease management strategies. The proposed fellowship will provide advanced training in microbiome methodologies, bioinformatics, and predictive modeling, supporting the fellow’s transition from quantitative plant pathology toward independent leadership in plant–microbiome systems science. Professional development activities include mentoring undergraduate trainees, participation in teaching and extension activities, and dissemination of results to scientific and agricultural stakeholder communities. This fellowship integrates research, training, and workforce development activities aligned with USDA AFRI Education and Workforce Development program goals. By moving soybean disease management from detection toward prediction, this project advances USDA priorities in plant health, agricultural sustainability, and workforce development while preparing a future research leader equipped to address emerging challenges in U.S. crop production systems.