Host and Environmental Factors Outweigh Pathogen in Shaping Skin Microbiome of a Threatened Andean Amphibian Community.

The fungal pathogen Batrachochytrium dendrobatidis (Bd) has driven severe amphibian declines across the Neotropics, yet some species persist under enzootic pathogen conditions following epizootics. We investigated whether skin bacterial communities and host mucosome activity contributed to the persistence of seven amphibian species in a once megadiverse Chocó-Andean community that experienced drastic Bd-associated declines. Across dry and wet seasons, we characterized skin bacterial communities using 16S rRNA metabarcoding and assessed mucosome-mediated inhibition of a local Bd lineage using in vitro challenge assays. Host species identity was the strongest predictor of bacterial community composition, while season and reproductive mode, which were strongly associated with habitat use, also contributed to microbiome structure. Host phylogeny was associated with broad-scale bacterial community patterns, whereas Bd infection status and intensity explained little variation. Putative Bd-inhibitory bacteria were detected in all host species and occurred at greater relative abundance during the dry season and in species with aquatic larvae, but neither their richness nor abundance was associated with Bd infection or load. Mucosome assays showed little to no inhibition of Bd growth in most species; only Pristimantis laticlavius, one of the few species whose abundance increased following the historical Bd epizootic, exhibited slight inhibition. Overall, host identity, seasonality, and habitat-associated reproductive mode, rather than current Bd infection, were the principal drivers of amphibian skin bacterial community composition. The widespread occurrence of putative Bd-inhibitory bacteria and their enrichment in some persistent hosts are consistent with a potential microbiome-mediated response, but limited mucosome activity indicates that the microbiome alone is unlikely to explain host persistence. Integrating host immune traits, pathogen characteristics, and environmental conditions will be necessary to understand long-term host-pathogen coexistence in this threatened amphibian community.