Environmental DNA detection of an amphibian pathogen across an urbanization gradient in Atlanta

Chytridiomycosis, an infectious disease of amphibians, is caused by several species of pathogenic fungi. Chytridiomycosis affects amphibians by damaging the keratin layer of their skin, which is responsible for regulating respiration, intake of water and electrolytes such as sodium. The most geographically widespread fungal pathogen, Batrachochytrium dendrobatidis (Bd), is common in amphibians across Eastern North America. Previous work suggests that Bd may be more abundant in natural than urbanized habitats. Possible explanations could include differences in amphibian diversity and abundance, as well as microhabitat suitability for the pathogen (eg: chemical contamination and altered thermal profiles). Traditionally, scientists have tested for Bd by swabbing amphibian skin and using polymerase chain reaction (PCR) or quantitative PCR (qPCR) as a molecular test to detect the fungus. More recently, scientists have also developed environmental DNA (eDNA) methods to detect Bd from water samples collected from waterbodies. Here, we used a PCR-based eDNA method to survey for Bd in water collected from 25 sites across an urbanization gradient in Atlanta’s Peachtree Creek drainage. We included a serial dilution of a positive control to estimate the limit of detection and negative control to evaluate for laboratory contamination. We scored the presence of Bd by the presence of an amplicon of ~250 bp using gel electrophoresis. We analyzed how Bd prevalence varied by degree of disturbance and we interpreted our results in the context of previous research conducted on Bd prevalence linked to urbanization. In the future, this protocol could be optimized by using qPCR, which is more sensitive and able to detect Bd at very low concentrations