Temperature variation underlies turnover of 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 seasonal variability affects structure and composition of skin bacterial communities, and in turn, promotes or limits the colonization of opportunistic pathogens. Here, we ask whether the loss of putatively beneficial bacteria predisposes hosts to subsequent infections. We report on a spatiotemporal study of three amphibian populations infected by the pathogenic fungus Batrachochytrium dendrobatidis (Bd). Our focal host species is a direct-developing frog (Eleutherodactylus coqui) 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 species. Increased frog body temperatures over time allowed the colonization of bacteria and recruitment of putatively beneficial bacteria. Our results underscore how natural fluctuations in temperature and precipitation can create opportunities for bacterial replacement, potentially attenuating pathogen transmission, and thus contributing to host persistence in E. coqui populations.