PRJNA531014
Variability in the snake skin microbiome across spatial scales and disease states
Understanding how biological patterns translate into functional processes across different scales is a central question in ecology. Within a spatial context, extent is used to describe the overall geographic area of a study, whereas, grain describes the overall unit of observation. This study aimed to characterize the snake skin microbiome (grain) and to determine host-microbiome-pathogen effects across spatial extents within the Southern United States. The causative agent of snake fungal disease, Ophidiomyces ophiodiicola, is a fungal pathogen threatening snake populations. We hypothesized that the skin microbiome of snakes differs from its surrounding environment, by host species, spatial scale, season, and in the presence of O. ophiodiicola. We collected snake skin swabs, soil samples, and water samples across six states in the Southern U.S. (macroscale extent), four Tennessee ecoregions (mesoscale extent), and at multiple sites within each Tennessee ecoregion (microscale extent). These samples were subjected to DNA extraction and quantitative PCR to determine the presence/absence of O. ophiodiicola. High-throughput sequencing was also utilized to characterize the microbial communities. We concluded that the snake skin microbiome was partially distinct from environmental microbial communities. Snake host species was strongly predictive of the skin microbiome at macro-, meso- and microscale spatial extents, however, the effect was variable across geographic space and season. Lastly, the presence of the fungal pathogen O. ophiodiicola is predictive of the microbiome across macro- and meso-spatial extents and particular bacterial taxa associate with O. ophiodiicola pathogen load. Our results highlight the importance of scale regarding wildlife host-pathogen-microbiome interactions.