A SmartChip for Pathogenic and Beneficial Microbes Underlying Soil Health: Final Report

This BIOAg-funded project developed and tested a high-throughput qPCR SmartChip platform to detect soilborne pathogens and beneficial microbes influencing soil health across Washington cropping systems. The work focused on optimizing primer sets and molecular protocols to quantify key pathogens such as Phytophthora, Pythium, Rhizoctonia, Fusarium, and Verticillium, along with beneficial arbuscular mycorrhizal fungi. Soil and culture samples were collected from diversified organic vegetable farms in western Washington and long-term research systems, including Cook Farm. Primer sets were validated using pure cultures and infected plant material, and DNA extraction and amplification protocols were refined. Although SmartChip runs were delayed due to equipment issues, the project established the necessary inputs and workflows for high-throughput diagnostics. The tool is intended to link farm management practices with microbial populations, supporting more informed decisions about soil health, disease management, and input use. Long-term, this approach aims to enable routine, cost-effective microbial monitoring for producers and researchers.