Data from: Temperature variation, bacterial diversity, and fungal infection dynamics in the amphibian skin

Host-associated bacterial communities on the skin act as the first line of defense against invading pathogens. Yet, for most natural systems, we lack a clear understanding of how temperature variability affects structure and composition of skin bacterial communities, and in turn, promotes or limits the colonization of opportunistic pathogens. Here, we examine how natural temperature fluctuations change skin bacterial diversity over time in three amphibian populations infected by the pathogenic fungus Batrachochytrium dendrobatidis (Bd). Our focal host species (Eleutherodactylus coqui) is a direct-developing frog that has suffered declines at some populations in the last 20 years, while others have not experienced any changes. We quantified skin bacterial alpha and beta diversity at four sampling time points, a period encompassing two seasons and ample variation in natural infections and environmental conditions. Despite the different patterns of infection across populations, we detected an overall increase in bacterial diversity through time, characterized by the replacement of bacterial OTUs. Increased frog body temperatures allowed the colonization of bacteria and the recruitment of a subset of indicator species that drove the changes in diversity patterns. Our results underscore how natural environmental fluctuations can create opportunities for bacterial replacement, potentially attenuating pathogen transmission, and thus contributing to host persistence in E. coqui populations.