Mycobiome Simplification in Wheat Is Associated With the Pathogen Parastagonospora nodorum

Plant mycobiomes are essential to plant health, yet their assembly under biotic stressors such as pathogen infection remains poorly understood. Plant pathogens can influence microbial community composition through direct antagonism and suppression of host immune responses, potentially altering mycobiome composition in ways that could affect plant performance. We investigated how the wheat (Triticum aestivum L.) foliar mycobiome was associated with inoculation with the fungal pathogen Parastagonospora nodorum (Berk.) Quaedvlieg, Verkley & Crous, which can cause substantial loss of yield and grain density throughout its range. To address this, we studied inoculation effects in four wheat cultivars planted in a randomized block design at two North Carolina field sites. We used ITS amplicon metagenomics to characterize wheat mycobiome richness, composition, and structure. We found that P. nodorum inoculation reduced fungal richness by up to 38.5%. We also found simplified foliar fungal networks for plants inoculated with P. nodorum, with up to 13.1% fewer taxa present and up to 41.2% fewer associations among those taxa. As part of these changes, increasing P. nodorum absolute abundance was correlated with increasing proportional representation of pathogens in wheat leaves due to loss of non-pathogenic taxa. Fewer fungal taxa and reduced network connectivity were particularly evident in reportedly susceptible cultivars and at one of the two sites where conditions favoured pathogen success. Based on these results, we suggest that pathogen infection plays a significant role in mycobiome assembly and has implications for disease management and mycobiome-based interventions in agricultural systems.