Of Hosts and Habitats: The Ecological and Evolutionary Patterns of the Amphibian Skin Microbiome

The skin microbiome of amphibian hosts can inhibit growth of pathogenic fungi, contribute to anti-predator compounds in newts, and is linked with sex-specific scents in frogs. However, despite growing evidence of symbiont importance to amphibians, how symbionts are acquired and maintained on hosts remains poorly resolved. Microbiomes exist on a dynamic spectrum from casual assemblages to intricate systems, and community members vary in fidelity and association to hosts. The establishment of these communities involves complex interactions between symbionts, host traits, and source communities. I seek to enhance our understanding by assessing the spatial-temporal patterns of the salamander skin microbiome relative to their cover objects which are likely an important, but rarely investigated source of microbes for colonization onto host skin. In Chapter 1, I investigate small-scale similarity and differentiation between host species and cover objects along an aquatic and terrestrial interface to determine the effects of host species, habitat, and microhabitat. I find that bacterial communities associated with salamanders display differentiation according to host species, which is matched in cover object communities suggesting microhabitat rather than host traits determine bacterial presence and community composition in heavily divergent communities. To understand patterns of dissimilarity, in Chapter 2, I test whether heterogeneity between salamander hosts, other salamander hosts, and their cover objects can be explained by priority effects, host selection, or stochastic dispersal in aquatic or terrestrial habitats and find differences between salamander-associated communities are consistent with stochastic colonization and extinction of environmental microbes. In Chapter 3, I use the phenology of E. cf. wilderae to understand the temporal variability by sampling hosts seasonally for one year as hosts move between aquatic and terrestrial habitats. Host-associated communities show turnover seasonally that is exacerbated with habitat changes. However, a small subset shows evidence of non-random associations, some of which can produce antifungal metabolites, potentially providing a defensive function for hosts. These results that suggest stochastic processes dominate the amphibian skin microbiome with little evidence for deterministic structuring. Despite this high heterogeneity between hosts, we identify a few microbial taxa as candidates for investigating mechanisms that promote persistence on amphibian skin.