For terrestrial amphibians, habitat conditions have been identified as one of the key drivers of skin bacterial diversity. Therefore, factors that alter local habitat condition, such as land use change, likely impact microbial community structure by leading to changes in soil characteristics (pH, soil nutrients, moisture), ultimately impacting which microbial species live there and are available to colonize salamander skin. However, understanding which aspects of the environment and host interact to contribute to microbiome assembly is still largely unknown—especially across small changes in micro-habitat conditions. To address this, we sampled over 150 Plethodon cinereus salamanders in two seasons and across eight sites in the greater New York metropolitan area and paired these with soil cores. Swab and soil bacterial DNA were extracted, amplified, and sequenced using a 16S high-throughput approach and then analyzed in QIIME2. A subset of swabs were tested for Bd presence using a Taqman assay. Additionally, soils were analyzed for over 50 characteristics including pH, moisture, CHN, and metals. We hypothesized that the soil would act as a regional pool supplying colonists to amphibian skin and that changes in skin microbiomes would match those seen in the soil.
Results/Conclusions
We found that salamanders share many microbes with their soil environment, but these two microbiomes are not identical with skin communities showing changes in the relative abundances of Acidobacteria, Actinobacteria, and Proteobacteria. As predicted, soil bacteria community composition varied with changes in pH, moisture, and heavy metals all of which associated with site and season. This in turn correlated with the compositional changes seen in the skin microbiome of salamander hosts. However, this correlation was weaker for individuals who tested positive for Bd infection—with pairwise comparisons showing a significant difference in the skin communities of Bd-positive vs. Bd-negative individuals at half of the sites. Together, these observations suggest that there are both stochastic (environmental) and deterministic (host) mechanisms guiding assembly of bacteria onto amphibian skin, with likely consequences in disease preventative function. In the future, we plan to combine these parameters into a computational model that can be used to predict how environmental changes in soil communities might alter assembly of beneficial microbes onto amphibian skin.