Simultaneous Detection of Missing Amphibians and Their Fungal Pathogen in a Biodiversity Hotspot Using eDNA

Since the 1970s, striking amphibian declines in population abundances and presumed extinctions have been recorded globally. The chytrid fungus Batrachochytrium dendrobatidis (Bd) is one of the key drivers of these declines. To investigate the potential role of Bd in the decline of Brazil's amphibians, we first used eDNA metabarcoding to survey for DNA traces of 10 threatened amphibian species from the Southern Brazilian Atlantic forest (SBAF). Using the eDNA samples of this survey, along with eDNA samples from previous surveys of 32 threatened amphibian species from the Northern Brazilian Atlantic forest (NBAF), we examined the relationships between the presence or absence of targeted amphibians with the presence or absence of Bd lineages. We detected DNA traces of two of the 10 targeted species in the survey of SBAF, including one species that was missing for over 40 years (Cycloramphus cedrensis). We also detected DNA traces of two Bd lineages (Bd-GPL and Bd-Brazil) at nine of the 12 sampling sites where community-level amphibian declines were first reported in the late 1970s. Our results support a post-panzootic scenario, where some threatened amphibian species are coping to persist in the presence of enzootic Bd. Our research also provides novel insights into simultaneous eDNA surveys targeting both hosts and pathogens, offering important methodological contributions to tropical ecology and conservation.