Diversity of Root Rot Associated Fungi and Oomycetes in Organic Dry Bean Production Systems in Northeast United States Under Different Tillage, Cover Cropping, and Nitrogen Management

Root rot is a major constraint to organic dry bean ( Phaseolus vulgaris L.) production, caused by diverse soilborne fungal and oomycete species. Despite the growing importance of organic dry beans in the Northeastern United States, the composition and responsiveness of these pathogens’ communities to management remain poorly understood. This study characterized root rotting fungal and oomycete communities in organic dry bean production in Maine (ME) and New York (NY) under different tillage, cover cropping, and nitrogen treatments across two seasons and assessed legacy effects in a subsequent barley crop using soil-based root bioassays. A total of 353 isolates representing 13 genera were recovered from dry bean roots with Fusarium, Pythium, Rhizoctonia, and Macrophomina comprising ~88% of the isolates. Species composition varied significantly by location and year with M. phaseolina only in NY and P. ultimum dominant in ME. Significant annual variation was also observed, with M. phaseolina isolated more frequently in 2024 and Pythium spp. in 2025. Tillage and nitrogen management had limited effects on isolation frequencies, with site-year-specific responses detected for Fusarium and Rhizoctonia . Root bioassays using soil from the subsequent barley crop confirmed persistence of viable inoculum, with Fusarium , Pythium , and Rhizoctonia accounting for ~94% of isolates. In these bioassays, disease severity was greater in soil from NY than ME, although species diversity was similar. While isolation frequency was not affected by tillage, cover cropping, or nitrogen, it was primarily affected by spatial and temporal factors indicating the need for site-specific management strategies.