Aquatic fungi drive important ecosystem processes, which may be affected by anthropogenic stressors, including changes in water quality. However, due to the great diversity of aquatic fungi, our understanding of the relationships among water quality variables, fungal community composition, and ecosystem function remains incomplete. Here, we show that aquatic fungal community structure and functional diversity correlate strongly with water quality. We used a multi-marker survey of environmental DNA and long-term water quality data to survey 17 stream, pond, and tidal creek sites within a coastal drainage network in southeastern Virginia, USA, targeting both the ITS2 and LSU barcoding regions. The community composition of Chytridiomycota and Ascomycota (fungal phyla) and aquatic hyphomycetes (a functional group) were strongly correlated with habitat type and water quality variables. Functional diversity of aquatic fungi decreased with warmer water, due mainly to the reduced richness of saprotrophic groups, and increased with total particulate phosphorus, due to the richness of algal parasites. Community dissimilarity analyses of samples using both ITS2 and LSU yielded consistent results, but per-sample alpha diversity differed. This work reveals a surprising degree of local variation in aquatic fungal community composition and functional diversity within a coastal watershed, which was coupled with variation in water quality variables. Furthermore, eDNA sampling is an effective and efficient means to accurately characterize diverse aquatic fungal communities with exciting implications for addressing basic and applied research questions. Our work supports the prediction that community composition and functional diversity of aquatic fungi are impacted by impaired water quality and global change.
