Tracking the prevalence of a fungal pathogen, Batrachochytrium dendrobatidis (chytrid fungus), using environmental DNA

Chytridiomycosis, a primary disease driving widespread and unprecedented amphibian declines, is caused by the fungal pathogen Batrachochytrium dendrobatidis (Bd). Tracking Bd through space and time requires monitoring protocols that efficiently and reliably assess pathogen prevalence and intensity, which in turn requires an understanding of environment–pathogen dynamics. Environmental DNA (eDNA) was used to track Bd prevalence and intensity in 95 waterbodies in southern Ontario, Canada, and assess zoospore counts relative to biotic, abiotic, and geographic factors. Bd was also monitored on a semi‐weekly basis in 10 waterbodies to better understand patterns of temporal variability. Bd showed variable prevalence, with 47% and 29% of waterbodies having zoospores detected in May and July, respectively. Patterns of prevalence were markedly variable both within and across waterbodies, indicating high spatio‐temporal heterogeneity. Bd prevalence was not related to environmental factors, geographic variables, or amphibian species richness, but intensity was negatively related to estimated canopy cover. In intensively sampled waterbodies, Bd counts were highly variable through time, with some sites switching from detection to non‐detection (and vice versa) across 2‐week intervals. We conclude that eDNA can be a useful tool for monitoring Bd zoospores in wetlands but emphasize the need for additional research into environmental and methodological factors affecting zoospore detection and abundance before this method should be widely adopted. Chytridiomycosis, caused by the fungus Batrachochytrium dendrobatidis (Bd), is a significant threat to amphibian populations worldwide. We used eDNA to sample for Bd in waterbodies in Ontario Canada, and correlated these results with environmental and habitat variables at the time of sampling. We found that there was a significant correlation between Bd abundance in water samples and canopy cover at a given waterbody, and also note high variation in Bd presence and abundance in a waterbody over relatively short time scales.