Effects of host species and environment on the skin microbiome of Plethodontid salamanders

Environmental metadata for 100 Plethodon salamanders of three species sampled in the Central Appalachian Mountains. We conducted a general descriptive analysis of the bacterial OTUs identified from the three host species (n = 100), including description of their core microbiome. Then, we examined microbiome structure in two subsets of the data: a co-occurring species dataset (n = 62) and an elevational dataset (n = 50). Twelve individuals were included in both analyses. We characterized skin microbiome structure (alpha-diversity, beta-diversity and bacterial operational taxonomic unit [OTU] abundances) using 16S rRNA gene sequencing for co-occurring Plethodon salamander species (35 P. cinereus, 17 P. glutinosus, 10 P. cylindraceus) at three localities to differentiate the effects of host species from environmental factors on the microbiome. We sampled the microbiome of P. cinereus along an elevational gradient (n = 50, 700 – 1000 masl) at one locality to determine whether elevation predicts microbiome structure. Finally, we quantified prevalence and abundance of putatively anti-Bd bacteria to determine if Bd-inhibitory bacteria are dominant microbiome members. Pyrosequencing runs have been deposited in the National Center for Biotechnology Information Sequence Read Archive (www.ncbi.nlm.nih.gov/sra) under accession number SUB2660574