The Skin Microbiota of Eleutherodactylus Frogs: Effects of Host Ecology, Phylogeny, and Local Environment

Amphibian skin microbiota has a potential protective role against diseases. However, the effects of environmental and host factors on symbiotic bacterial communities are not well understood. Caribbean frogs in the genus Eleutherodactylus represent a case of congeneric species that differ in ecological specialization by the process of adaptive radiation. For a small clade of Eleutherodactylus from Puerto Rico, we investigated the role of local environments, host species, and microhabitat in the composition of their skin microbiome. The potential congruence between microbial communities in hosts that are most closely related phylogenetically was also addressed. We hypothesized that the skin microbiota of Eleutherodactylus frogs would be mostly associated to microhabitat use, but also differ according to locality, and to a lesser extent to host species. To test this hypothesis, we swabbed the skin of a total of 98 adult individuals of seven Eleutherodactylus species distributed in two nearby localities in Puerto Rico, and sequenced the V4 region of the 16S rRNA gene. Results showed that locality had the greatest effect on determining skin bacterial communities of amphibian hosts, but this effect was stronger on the composition (based on presence/absence) than on its structure (based on sequence abundance). The most ecologically distinct host, E. cooki, and the generalist E. coqui presented, respectively, the most dissimilar and similar microbiota compared to other hosts. Host phylogeny showed a weak influence on skin microbiota. Results suggest that both local environment and ecological specialization are structuring the skin bacterial community in these Eleutherodactylus species, but that characteristics intrinsic to species may also render unique hosts the ability to maintain distinct microbiotas.