Fungicide-induced restructuring of the wheat ear mycobiome redistributes mycotoxin profiles

Abstract Fungicides are widely used to control Fusarium head blight in cereals, yet their effects on mycotoxin contamination remain inconsistent and poorly understood. Here, we combined ITS-based fungal community profiling, targeted Luminex assays for selected Fusarium markers and biosynthetic gene, and quantitative measurement of 47 mycotoxins across two wheat field trials employing distinct fungicide programmes. We examined how chemical disease control reshapes wheat-ear mycobiomes and multi-toxin outcomes. Fungicide application consistently reduced deoxynivalenol and zearalenone by 2.7–4.4-fold but simultaneously increased the sum of T-2 and HT-2 by approximately 3-fold and elevated emerging metabolites, including enniatins and beauvericin. Multivariate ordination revealed clear treatment-associated shifts in mycobiome composition at both sites, with fungicide explaining a measurable proportion of community variation (PERMANOVA (R^2 = 0.078–0.092), ( P = 0.001)). Fungicide treatment was also associated with reassembly of conservative Fusarium ITS lineages. Targeted assays showed lower F. graminearum signals in treated plots at both sites, alongside site-specific and more variable responses for other targeted markers. At the community level, fungicide treatment altered trophic composition towards pathotroph-assigned taxa and increased the number of inferred co-occurrence associations. When benchmarked against the current European Union maximum level for unprocessed wheat grain, exceedance of the 50 µg kg⁻¹ limit for the sum of T-2 and HT-2 occurred more frequently in treated plots. Together, these results show that fungicide programmes do not simply suppress mycotoxin risk but can redistribute it through fungal-community restructuring, generating reproducible toxin trade-offs with implications for food-safety surveillance, regulation, and cereal disease management.