Effect of flooding on spring wheat mycobiota

Flooding affects both above- and below-ground ecosystem processes, representing a substantial threat for cereal productivity under climate change. Plant-associated fungi play important roles in agriculture, but their response to extreme weather is unclear. Here, we established a pot experiment to determine the effects of flooding stress on the spring wheat-microbiota complex inducing flooding at different plant growth stages.We monitored the wheat-mycobiota response to flooding characterizing the fungal community associated with the phyllosphere, root and rhizosphere using a metabarcoding approach. Several soil and plant traits were measured through the whole experiment to correlate edaphic and physiological plant changes with shifts in fungal community assemblage.Flooding caused a significant reduction in wheat fitness and induced dramatic shifts in fungal assembly across the whole plant. Notably, we observed a functional transition, consisting of a decline in mutualist abundance and richness, and a concomitant increase in the abundance and richness of pathogenic taxa.We conclude that flooding stress had a detrimental effect on the spring wheat-microbiota complex. Our findings provide a baseline for future studies, and highlighted the urgent need to understand how these extreme climate events affect the biodiversity and function of the fungal populations associated with cereal crop in agroecosystems.