Watershed urbanization alters aquatic plant mycobiomes through the loss of rare taxa.

Urban expansion, projected to triple globally from 2000 to 2030, significantly impacts biodiversity and ecosystem processes, including those of microbial communities. Microbes are key drivers of many ecosystem processes and affect the fitness and resilience of plants and animals, but research on the biotic effects of urbanization has focused primarily on macroorganisms. This study investigates host-associated fungal communities in the pollution-tolerant aquatic plant along an urbanization gradient in the Provo River, Utah, USA, a rapidly urbanizing region. We collected plant and adjacent water samples from 10 locations along the river, spanning from rural to urbanized areas within a single watershed, and conducted DNA amplicon sequencing to characterize fungal community composition. Our results show a significant decline in fungal alpha diversity correlated with increased urbanization metrics such as impervious surface area and developed land cover. Specifically, fungal richness and Shannon diversity decreased as urbanization intensified, driven primarily by a reduction in rare taxa. Despite a stable core microbiome dominated by a few taxa, the overall community structure varied significantly along the urbanization gradient, with notable shifts in dominant fungal taxa. Contrary to expectations, no detectable levels of heavy metals were found in water samples at any location, suggesting that other urbanization-related factors, potentially including organic pollutants or plant stress responses, influence fungal endophyte communities. Our findings underscore the need for further investigation into the mechanisms driving these patterns, particularly the roles of organic pollution, nutrient loads, and plant stress. As global urbanized watershed area grows, the fate of aquatic plant life is tied to their fungal community. Understanding these interactions is crucial for predicting the impacts of continued urbanization on freshwater ecosystems.