bioRxiv2025
In a world of increasingly urbanized environments, it is critical to understand the impact of urbanization on microbial communities, including fungal communities, as a measure of ecosystem health, and to document how these environments are changing. Aquatic environments, in particular, can be highly sensitive to urbanization with removal of local habitat and inputs of wastewater and contaminants, leading to displacement or extinction of natural flora, fauna, and funga. Aquatic microbial communities, especially fungal communities, are extremely complex and far less characterized compared to their macro counterparts. Here, we characterized the fungal microbiome, i.e. "mycobiome", across multiple habitats-- water, sediment, and frog fecal matter from three species (American bullfrog (Lithobates catesbeianus), Green frog (Lithobates clamitans), and Pickerel frog (Lithobates palustris)) -- within the Tatnuck Brook waterway in Worcester, MA. The Tatnuck Brook waterway is a connected group of streams, ponds, and lakes that transition from protected areas at its headwaters, below the citys drinking water reservoir, to highly urbanized regions within Worcester. Using metabarcode sequencing, we found that water, sediment, and frog gut habitats harbor distinct fungal communities, but all exhibit parallel shifts in diversity along an urbanization gradient. In particular, we identified fungal taxa from the amphibian mycobiome and environmental samples that exhibited a range of sensitivities to urbanization. These taxa, including Basidiobolus, Cladosporium, and Lemonniera in fecal and sediment samples, as well as Candida, which was found in all habitats, are potential indicators of shifts in aquatic ecosystems due to urbanization. Their responses to urban stressors may serve as a baseline for further studies of aquatic fungal communities. IMPORTANCEAs cities grow, they can change nearby rivers, streams, and ponds in ways that affect plants, animals, and even tiny microbes. Fungi are an important part of these ecosystems because they help break down materials and can affect the health of animals like frogs. However, we still know very little about how fungi respond to urban environments. In this study, we looked at fungi living in water, sediment, and frog guts along a range of places from natural to highly developed areas in Worcester, Massachusetts. We found that some fungi were more common in cleaner, less developed sites, while others were more common in urban ones. These patterns suggest that fungi could be useful indicators of environmental health. Our work helps scientists better understand how urbanization affects nature and offers a new way to monitor and protect freshwater ecosystems.