Skin microbiome (16S and ITS) profiles of Southern Corroborree frogs during rewildling

The amphibian skin microbiome largely consists of bacterial and fungal taxa, and together this community is hypothesized to be important for mediating host immunity and pathogen defence. However, whilst there is substantial evidence that the skin microbiome is sensitive to captivity, there remains little understanding of how the rewilding and diet supplementation of captive-bred individuals together influence bacterial and fungal microbiome composition and their interactions during microbiome restructuring. This study investigated the effect of field release and dietary beta-carotene supplementation on the bacterial and fungal microbiome of the critically endangered Southern Corroboree frog (Pseudophryne corroboree). Consistent with previous studies on bacterial microbiomes, we found large-scale restructuring and diversification of both bacterial and fungal skin communities post-release, with these shifts occurring at the individual level. Post-release, the fungal mycobiome was more transient and demonstrated stronger temporal and spatial fluctuations than the bacterial microbiome, suggesting that fungal communities are more sensitive to localised transmission and microbial invasion than bacterial communities. After accounting for the effect of temporal and spatial restructuring, we found strong residual associations between bacterial members, yet limited evidence for residual inter-domain associations or associations between fungal members, suggesting that co-occurrence patterns between bacteria and fungi are largely a result of shared responses to the environment rather than direct interactions. Lastly, we found manipulation of dietary beta-carotene concentrations had no impact on microbiome diversity but was associated with approximately 15% of common genera, with affected taxa differing between pre- and post-release frogs. Further research on the functional importance of bacterial and fungal dynamics upon rewilding will be crucial for developing strategies to support the health and survival of endangered amphibian species.