Comparing Herpetofauna Microbiome Diversity Across Northern New York

Abstract

Several threats to herpetofaunal species such as habitat loss and the increase of diseases have decreased their global populations. Climate change is projected to shift many species of plants and animals into cooler regions. Within the last century there has been an ~80% decline in species due to habitat loss, climate change, and disease. Most notably is chytrid fungus, Batrachochytrium dendrobatidis, which keratinized the skin of herpetofauna. Microhabitat complexity is linked to their microbiome diversity and fitness. Our study was designed to evaluate the influence of both macro- and microhabitat on herpetofaunal epidermal microbiome. At three sites (Rugar Woods, Paul Smiths Visitor’s Interpretive Center, and Lewis Preserve Wildlife Management Area), we surveyed herpetofauna using hand capture techniques and collected microbial samples by swabbing the skin of individuals. Bacteria were plated to determine morphotype richness and serial dilutions were made in order to isolate the most prominent colonies. Microbial DNA was extracted, followed by a 16s rRNA polymerization chain reaction (PCR), and Sanger sequencing to confirm microbial species. Herpetofauna epithelial microbiome included Serratia sp., Pantoea sp., Pseudomonas sp., and Sphingobacteria. Herpetofaunal richness was the same across all macro-sites (S=3), with red-backed salamanders (Plethodon cinereus) being ubiquitous and spotted salamanders (Ambystoma maculatum), leopard frogs (Lithobates pipiens), spring peepers (Pseudacris crucifer), American toads (Anaxyrus americanus), and garter snakes (Thamnophis sirtalis) being rare. The most common microhabitat under which herpetofauna were found was coarse woody debris (CWD) and in terms of silviculture, single tree cuts and control sites had more animals than did other treatments such as clearcuts. Bacterial morphotype richness was greatest at Lewis Preserve and among red-backed salamanders and leopard frogs. Our bacterial species were common to herpetofaunal microbiomes and many support antifungal activity. Our findings suggested that a minimally managed wildlife management area with mature mixed forest, extensive floodplain, and riparian edge will support a diverse herpetofaunal community with high bacterial morphotype richness, affording greater defense against disease.