Microbiomes of a native threatened turtle and invasive turtles are impacted by land use in the San Francisco Bay Area

The environment has significant effects on species and the makeup of their microbiomes. As semi-aquatic, freshwater turtles and their microbiomes are especially sensitive to the negative impacts of habitat quality degradation. In this study, we use 16S rRNA amplicon sequencing to characterize the skin and cloacal microbiotas of freshwater turtles in the San Francisco Bay Area, California. While we captured mostly the native western pond turtle (Actinemys marmorata) across eight sites located in urban and rural environments, our sampling efforts included several individuals of the invasive red-eared slider (Trachemys scripta elegans). We assessed differences in diversity and composition among skin and cloacal samples, and evaluated how the alpha and beta diversity metrics were influenced by habitat quality. We found high taxonomic level turnover in the microbiota of freshwater turtles relative to the host tissue substrate samples. Our findings indicate that location elicits a high degree of lower taxonomic turnover, and we found that increased habitat quality directly results in richer communities on skin microbiotas and poorer communities on the cloacal microbiotas. In addition, internal and external microbiotas responded inversely to change in habitat quality. Finally, the skin and cloacal microbiotas of red-eared sliders overlapped with those of their native conspecifics suggesting the possible existence of microbial dispersal between these two species. Our results add to our current understanding of turtle microbiome ecology by establishing patterns of microbial variation in an urban to rural gradient.