Composition of the North American wood frog (Rana sylvatica) skin microbiome and seasonal variation in community structure

Abstract

While a number of amphibian microbiomes have been characterized, it is unclear how microbial communities might vary in response to seasonal changes in the environment and the behaviors which many amphibians exhibit. Given recent studies demonstrating the importance of the skin microbiome in frog innate immune defenses against pathogens, investigating how changes in the environment impact the microbial species present, and thus their potential contribution to skin host defense, will provide a better understanding of conditions that may alter host susceptibility to pathogens in their environment. We sampled the skin microbiome of North American wood frogs (Rana sylvatica) from two breeding ponds in the spring, along with the microbial community present in their vernal breeding pools, and frogs from the nearby forest floor in the summer and fall to determine whether the microbial composition differs by sex, vernal pond site, or temporally across season (spring, summer, fall). Taxon abundance data reveals a profile of bacterial phyla similar to those previously described on anuran skin, with Proteobacteria, Bacteroidetes, and Actinobacteria dominating the wood frog skin microbiome. Our results indicate that sex had no significant effect on skin microbiota diversity, however, this may be due to our limited female sample size. Vernal pool site had a small but significant effect on skin microbiota, but skin-associated communities were more similar to each other than to the communities observed in the frogs respective pond water. Across seasons, diversity analyses suggest there are significant differences between the skin microbiome of frogs from spring and summer/fall groups while the average -diversity per frog remained consistent. Bacterial genera known to have antifungal properties such as Pseudomonas spp. and Rhizobium spp. were prevalent, and several were considered core microbiota during at least one season. These results illustrate seasonal variation in wood frog skin microbiome structure and highlight the importance of considering temporal trends in an amphibian microbiome, particularly for species whose life history requires recurrent shifts in habitat and behavior.