Cutaneous shedding in amphibians causes shifts in bacterial microbiomes

Considerable research has focused on microbes on amphibian skin, as they act as the first line of defense against invading pathogens. This effort has generated substantial data on patterns across species, space, time, and ontogeny, alongside a growing list of beneficial antifungal symbionts. Though there is evidence of stability in amphibian skin microbial communities, there is also an indication that regular skin shedding reduces cultivable bacteria, with regrowth and recolonization in the period between sheds. This suggests that skin communities are in constant flux, and we lack an understanding of how the membership and structure of those communities are affected by shedding events. In this study, we conducted experiments on cane toads (Rhinella marina) to investigate the influence of shedding on skin microbiomes. We first used quantitative PCR to verify a positive correlation between bacterial loads and time in the days after shedding. We then resampled individuals over time to describe changes in community composition in the 38 h after shedding using amplicon sequencing. Similar to trends of bacterial loads, we found increases in alpha diversity over time after shedding, suggesting that shedding reduces bacterial diversity as it knocks down bacterial loads. During the 38-h period, community structure became similar to pre-shed communities in some individuals, but there was no consistent pattern in structural changes among individuals. In light of the amphibian chytridiomycosis pandemic, understanding how physiological events such as skin shedding affect beneficial bacteria and communities on amphibians would provide important insight into amphibian ecology.