Soil Reservoirs of Antifungal-Resistant Fungi: Implications for Plant Disease Management with a Focus on Fusarium

Crop losses driven by fungal pathogens remain a major constraint to global food production, reinforcing agriculture’s dependence on fungicide-based disease control. Soil acts as a long-term reservoir and key hotspot for the evolution and persistence of antifungal-resistant Fusarium. The intensive, prolonged use of overlapping single-site fungicides in agriculture strongly selects for both intrinsic and acquired resistance in soilborne Fusarium populations, contributing to major crop losses, food insecurity, and One Health concerns. This review synthesizes current knowledge on (i) target-site (CYP51, β-tubulin, cytochrome b, SDH, myosin-5) and non-target-site (ABC/MFS efflux, multidrug resistance, epigenetic regulation) resistance mechanisms across the genus Fusarium; (ii) the influence of management practices and fungicide characteristics and behaviour in soil in reshaping microbial communities and selecting for resistant Fusarium; (iii) the consequences for plant disease management and the limitations of practices like cultural and biological control; and (iv) innovative strategies for plant disease management, as well as the monitoring and detection of antifungal resistance in soils. These aspects show that soil reservoirs of antifungal-resistant Fusarium are compromising fungicide-based control and increasing risks across sectors, highlighting the urgent need for sustainable, multi-layered, integrated pest management strategies combined with robust, molecularly informed resistance monitoring.