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

This BIOAg progress report documents development of a high-throughput SmartChip qPCR platform to quantify soilborne pathogens and beneficial microbes in Washington cropping systems. The project aims to link farm management practices with microbial community composition across diversified organic vegetable systems and dryland cereal-legume-oilseed systems. In 2023, primer sets targeting key pathogenic fungi (Phytophthora, Pythium, Rhizoctonia, Verticillium, Fusarium), the protist Plasmodiophora brassicae, and arbuscular mycorrhizal fungi were assembled and DNA cultures prepared for validation. Work also includes developing optimized sampling strategies to address spatial variability of soilborne pathogens. Progress was slower than anticipated due to funding delays and personnel transitions, but laboratory validation and grower sampling are scheduled for 2024. The SmartChip platform is intended to provide cost-effective, high-throughput diagnostics to support soil health monitoring and management decisions.