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

Abstract

Fusarium head blight (FHB) is a devastating disease of wheat that causes mycotoxin contamination in grains. Diseases like FHB have traditionally been managed with integrated strategies; but this has led to a proliferation of fungicide-resistant pathogens and soil erosion while full disease control has remained elusive. Leveraging the microbiome for more sustainable management is an alternative – however, translation of promising strategies is hampered by our limited understanding of crop microbiome differences across plant development and tissue types. Therefore, we used amplicon sequencing to analyze the phyllosphere mycobiome differences across five developmental timepoints in wheat leaves and heads, and in maize debris remaining from the previous season at two Illinois USA locations. 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 at either developmental stage tested. Taxa enriched under high FHB conditions in wheat heads belonged to the Ascomycota (Cladosporium, Pseudopithomyces), while taxa enriched under low FHB conditions primarily belonged to the Basidiomycota (Filobasidium, Sporobolomyces, Tilletiopsis, Entyloma). Fusarium spp. were important nodes in wheat head and maize debris microbiome networks. Our research highlights the potential to leverage microbiome intervention strategies for specific tissues and developmental periods, with implications for pre-season management targeting crop debris.