Host phylogeny and environment shape the diversity of the salamander skin microbiome

Abstract The composition and diversity of animal-associated microbial communities are shaped by multiple ecological and evolutionary processes acting at different spatial and temporal scales. Skin microbiomes are thought to be strongly influenced by the environment due to the direct interaction of the host’s skin with the external media. As expected, the diversity of amphibian skin microbiomes is shaped by climate and host habitats, whereas phylogenetic effects appear to be weak. However, the relative strength of phylogenetic and environmental effects on amphibian skin microbiomes remains poorly understood. Here, we analysed sequence data from 1,091 adult salamanders in 41 species to characterise and compare the diversity and composition of skin bacteria. We assessed the relative contribution of climate, host habitat, and host phylogeny to the observed patterns of bacterial diversity. We found that microbial alpha was mainly associated with host habitat and climate, but that microbial beta diversity was more strongly associated with host taxonomy and phylogeny. This phylogeny effect predominantly occurred at intermediate levels of host divergence (0–50 Mya). Our results support the importance of environmental factors shaping the diversity of amphibian skin microbiomes, but also support host phylogenetic history as a major factor shaping these microbial communities.