The Salamander Bacterial Microbiome: Composition, Ecology, and Anti-Chytrid Utility

Abstract

The chytrid fungi Batrachochytrium dendrobatidis and B. salamandrivorans recently emerged as epizootic pathogens with rapidly expanding geographic and host ranges, and they have caused mass mortality events in amphibian populations on five continents. Bioaugmentation of antifungal bacteria on the skin of amphibians to curb growth of the pathogens and mitigate disease has been attempted; however, few if any bioaugmentation-based treatments have been effective. This project aimed to pinpoint the best candidates for bioaugmentation by describing the structures of both the entire skin-bacterial community and the antifungal, culturable fraction of the skin-bacterial community of plethodontid salamanders. The entire bacterial community was characterized from skin swab samples (n = 249) using high-throughput sequencing of the 16S rRNA gene. Differences in community structures across three genera of plethodontid salamanders, three ecoregions of Tennessee, and two seasons were assessed. Core members of the communities were identified using indicator species analysis, core community analysis, and ecological interaction networks. The culturable, anti-chytrid fraction of the bacterial community was described using traditional microbiological techniques, Sanger sequencing of the 16S rRNA gene of isolates (n = 104), and co-culture challenge assays with a strain of B. dendrobatidis. Candidates for bioaugmentation-based treatments were evaluated based on 1) amenability to isolation from skin swabs, 2) ubiquity in skin communities of a broad range of salamander hosts, and 3) consistency in inhibition of B. dendrobatidis across multiple bacterial strains. Lastly, surveys for the presence of B. salamandrivorans in Appalachian plethodontid salamander populations were conducted at ten sites in Tennessee