Fungicides on wheat reshape fungal communities and shift mycotoxin risks

Fungicide sprays used against Fusarium head blight in wheat do not simply lower mycotoxin risk, according to a new field study: they redistribute it. In two wheat field trials run under distinct fungicide programmes, treatment consistently cut levels of the well-known toxins deoxynivalenol and zearalenone by 2.7 to 4.4-fold, yet at the same time raised the sum of the toxins T-2 and HT-2 roughly threefold and increased emerging metabolites such as enniatins and beauvericin.

The study, published open access in the journal Environmental Microbiome, combined several complementary measurements on the same plots. The researchers profiled fungal communities on wheat ears using ITS-based sequencing, ran targeted Luminex assays for selected Fusarium markers and biosynthetic genes, and quantified 47 different mycotoxins, allowing them to link chemical disease control to both community composition and multi-toxin outcomes.

Multivariate ordination showed clear treatment-associated shifts in mycobiome composition at both sites. Fungicide application explained a measurable proportion of the variation in community structure, with PERMANOVA returning R-squared values of 0.078 to 0.092 and a P value of 0.001. In other words, the chemical treatment left a statistically detectable imprint on which fungi were present on the ears, even though it accounted for only a modest share of total community variation.

The treatment was also associated with reassembly of conservative Fusarium ITS lineages, the fungal groups most directly tied to head blight.

Responses for other targeted markers were more variable and site-specific, underscoring that the fungal community does not respond uniformly across locations. This heterogeneity matters for interpretation: the same fungicide programme can suppress one set of toxin-producing fungi while opening ecological space for others, and the balance appears to depend on local conditions.

At the community level, fungicide treatment shifted the trophic composition of the mycobiome towards taxa assigned as pathotrophs, organisms classified as plant pathogens. The number of inferred co-occurrence associations among fungi also increased after treatment, suggesting that the fungal network on treated ears was not merely reduced but restructured into a denser, differently organised set of relationships.

The toxin trade-offs had a regulatory dimension as well. When the measured concentrations were benchmarked against the current European Union maximum level for unprocessed wheat grain, exceedance of the 50 micrograms per kilogram limit for the sum of T-2 and HT-2 occurred more frequently in treated plots than in untreated ones. This means that a control measure aimed at one regulatory threshold can push contamination closer to, or over, another.

The authors frame these results as evidence that fungicide programmes do not simply suppress mycotoxin risk but can redistribute it through fungal-community restructuring, generating reproducible toxin trade-offs. Because the findings come from two field trials with distinct fungicide programmes, they demonstrate consistent directional patterns across those settings rather than a universal outcome for every product, dose, or wheat-growing region.

The implications reach into food-safety surveillance, regulation, and cereal disease management. Monitoring programmes that track only deoxynivalenol and zearalenone could miss the rises in T-2 and HT-2 and in emerging metabolites such as enniatins and beauvericin observed here, while multi-toxin profiling of both treated and untreated grain would give a more complete picture of what fungicide use actually does to the mycotoxin burden in wheat.

The study also highlights the value of pairing chemical measurements with community profiling. By combining quantitative data on 47 mycotoxins with sequencing-based mycobiome analysis and targeted Fusarium assays, the work connects the ecological effect of fungicides on wheat-ear fungi to the practical question of which toxins end up in the grain, offering a template for evaluating disease-control programmes by their full toxin profile rather than by any single target.

Subject of Research: How fungicide programmes restructure the wheat ear fungal community and redistribute mycotoxin contamination

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

Article References: Kolawole, O., van Diepeningen, A. D., Martens, J. G., Larrañaga, A. A., Black, L., & van Overbeek, L. (2026). Fungicide-induced restructuring of the wheat ear mycobiome redistributes mycotoxin profiles. Environmental Microbiome. https://doi.org/10.1186/s40793-026-00950-3

Image Credits: AI Generated

DOI: 10.1186/s40793-026-00950-3

Keywords: wheat, fungicides, mycotoxins, mycobiome, Fusarium head blight, deoxynivalenol, T-2 and HT-2, enniatins, beauvericin, food safety, fungal communities, Environmental Microbiome