Wheat mycobiome dynamics driven by interseasonal crop-crop transfer and Fusarium head blight

Authors: Whitaker, Briana; Maccready, Kristi; Vaughan, Martha; McCormick, Susan; BECKER, TALON - University Of Illinois Urbana-Champaign

Submitted to: Frontiers in Microbiology
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 2/18/2026
Publication Date: 3/4/2026
Citation: Whitaker, B.K., Maccready, K.G., Vaughan, M.M., Mccormick, S.P., Becker, T. 2026. Wheat mycobiome dynamics driven by interseasonal crop-crop transfer and Fusarium head blight. Frontiers in Microbiology. https://doi.org/10.3389/fmicb.2026.1778987.
DOI: https://doi.org/10.3389/fmicb.2026.1778987

Interpretive Summary: Fusarium Head Blight (FHB) is a serious disease of wheat and other cereal crops in the United States. FHB costs farmers millions of dollars each year and results in grain contaminated with a toxin that makes it unsafe to eat. Traditional FHB control strategies can lead to soil erosion and fungicide-resistant pathogens. The crop microbiome could be leveraged as a more sustainable control strategy. However, translation of promising microbiome-based strategies is hampered by our limited understanding of how microbes interact with Fusarium in wheat. Therefore, ARS researchers in Peoria, Illinois, and Madison, Wisconsin, in collaboration with scientists from the University of Illinois at Urbana-Champaign, studied microbiome-Fusarium relationships across two locations and three wheat varieties in Illinois USA locations. Multiple potential modes of action for microbiome-based FHB control were identified, including multiple species of fungal yeasts that were more abundant when FHB disease was reduced. This work will allow industry partners to develop the next generation of FHB control strategies and will help U.S. farmers grow healthier wheat and keep harmful toxins out of our food.

Technical Abstract: Fusarium Head Blight (FHB) is a devastating disease of wheat that causes mycotoxin contamination in grains. Traditional FHB control strategies have led to soil erosion and fungicide-resistant pathogens. Leveraging the microbiome for more sustainable control is an alternative – however, translation of promising strategies is hampered by our limited understanding of crop microbiomes across plant development and tissue types. We planted three wheat varieties in replicated plots at two Illinois USA locations. The phyllosphere mycobiome was analyzed across five developmental timepoints in wheat leaves and heads, and in maize debris remaining from the previous season. Mycobiome composition varied strongly by tissue type, though site and developmental timepoint were also important contributors. Host variety conditionally explained mycobiome variation in wheat heads, but not in leaves or debris. We also identified debris as a major fungal source to leaves early in development, but not later – and found that leaves were never a large inoculum source to head mycobiomes. Taxa enriched under high FHB belonged to the Ascomycota, while taxa enriched under low FHB were primarily Basidiomycetous yeasts. Our research highlights the potential to leverage microbiome intervention strategies for specific tissues and developmental periods, with implications for pre-season control of mycotoxins and food safety.