Agricultural fungicides shape soil and sediment reservoirs of multidrug-resistant fungi

Fungicide resistance in environmental fungi represents a growing One Health challenge, yet its ecological extent and clinical relevance remain poorly studied. Here, we integrate residue monitoring, community profiling, large-scale culture isolation, and mechanistic assays to investigate the resistance of fungi in agricultural soils and adjacent river sediments. The results indicate that fungicides are widely detected in environmental samples and pose substantial ecological risks, particularly carbendazim and tebuconazole. Resistant fungi are also widespread and account for a large proportion of the genera detected in fungal communities. Among >3,900 resistant isolates, we recover 358 multidrug-resistant (MDR) strains showing cross-resistance to multiple agricultural fungicides. Transcriptomic, qPCR, and molecular docking analyses suggest that environmental MDR phenotypes arise from synergistic effects of target-gene alterations, efflux pump overexpression, and adaptive stress responses. Notably, triazole exposure coordinately upregulates virulence genes and mycotoxin biosynthetic clusters, indicating transcriptional activation of genes associated with virulence and secondary metabolism. Together, these findings highlight agricultural landscapes as reservoirs of fungicide-resistant fungi and underscore the need to re-evaluate fungicide practices to protect crop health, ecosystem stability, and the effectiveness of clinical antifungals. The extent of fungicide resistance within the agricultural sector, specially across soil and river sediments, remains unclear. Here, the authors present a large-scale sampling effort, combined with transcriptomics, that identifies agricultural landscapes as reservoirs for multidrug-resistant fungal species.