Location matters: variations in gut microbiota composition of spatially separated freshwater turtles

Background The gut microbiota of vertebrates is malleable and may be shaped by both intrinsic and extrinsic factors. Here, the effect that geography has on the gut microbiota of two species of Australian freshwater chelonians, eastern longneck turtle (Chelodina longicollis) and Macquarie River turtle (Emydura macquarii), captured from waterbodies with different levels of anthropogenic pressure was investigated. We analysed the microbiota composition, structure and diversity through 16S rRNA gene amplicon sequencing. It was hypothesized that animals from less disturbed environments would harbour a more diverse gut microbial population. Results The gut microbiotas from 93 turtles (C. longicollis n = 78; E. macquarii n = 15), from five locations, were analysed. For both species the most predominant phylum was Proteobacteria. Gut microbiota alpha diversity varied significantly between the C. longicollis from all locations, but no differences were found for E. macquarii. In C. longicollis, turtles from wetlands within the centre of Melbourne had the lowest alpha diversity metrics, while the highest alpha diversity values were seen in turtles captured from an undisturbed rural waterbody. Beta diversity, obtained by weighted UniFrac distance, showed significant differences between location of capture for both species of turtles in this investigation. For C. longicollis, 91 biomarkers were identified responsible for explaining differences between locations, and in E. macquarii 40 biomarkers were found. Core community analysis revealed 49 and 36 ASVs shared between populations of C. longicollis and E. macquarii respectively. Conclusions The study showed that gut microbiota composition of freshwater turtles was significantly influenced by locality and that the disrupted environments may reduce microbial diversity in C. longicollis. The results highlight the need to interpret chelonian microbiota data in the context of geography and human disturbance of the environment.