Longitudinal patterns in the skin microbiome of wild, individually marked frogs from the Sierra Nevada, California

The amphibian skin microbiome has been the focus of numerous studies because of the protective effects that some bacteria provide against the pathogenic fungus Batrachochytrium dendrobatidis, which has caused a global panzootic among amphibians. However, the mechanisms driving community structure and function in the amphibian skin microbiome are still poorly understood, and longitudinal analyses of the skin microbiome have not yet been conducted in wild populations. In this study, we investigate longitudinal patterns in the skin microbiome of 19 individually marked adult frogs from two wild populations of the endangered Sierra Nevada yellow-legged frog (Rana sierrae), sampled over the course of 2 years. We found that individuals with low bacterial diversity (dominated by order Burkhorderiales) had significantly more stable bacterial communities than those with higher diversity. Amplicon sequence variants (ASVs) with high relative abundance were significantly less transient than those with low relative abundance, and ASVs with intermediate-level relative abundances experienced the greatest volatility over time. Based on these results, we suggest that efforts to develop probiotic treatments to combat B. dendrobatidis should focus on bacteria that are found at high relative abundances in some members of a population, as these strains are more likely to persist and remain stable in the long term.