Microbiome varies by body site in the yellow mud turtle, Kinosternon flavescens, from the Chihuahuan Desert.

Microbiomes are important to the ecology and evolution of their associated animal hosts. These important functions range broadly from individual animal health to population-level adaptations. Turtle-associated microbiomes are under increasing investigation, given turtles' conservation status and the unique natural history of the shell as an evolutionary-developmental novelty. Many components of the turtle-microbiome interaction remain understudied, including how microbial communities assemble based on host and environmental factors. Here, we hypothesized that age, habitats, and body sites would exhibit significant differential effects on bacterial microbiomes in the Yellow Mud Turtle (Kinosternon flavescens) in the Chihuahuan Desert of West Texas, USA. We also hypothesized there would be differential abundance of specific bacterial taxa associated with a recently described, algae-mediated shell disease. Using 16S rRNA amplicon sequencing of 64 turtle samples, we found bacterial community differences among body sites (cloaca, carapace, plastron, and skin), but weaker trends associated with habitat types (ephemeral or permanent-water ponds), and over age gradients (age 4-12+ years). Specifically, the carapace and plastron hosted high bacterial richness compared to the skin and cloaca, and all body sites differed in their bacterial composition across habitat sites. In many individuals, including those with advanced stages of the algae-mediated shell disease (Stage 3 or 4; 25% of sampled turtles), we detected significant differential abundance of specific bacterial taxa, including Cyanobacteria strains. These results are important for informing sampling regimes in long-term studies related to K. flavescens ecology and evolution, and for continuing conservation and natural history work associated with turtles broadly.IMPORTANCEThis research addresses the role of host and environmental factors in shaping bacterial communities in turtles. Specifically, this study is the first to test the hypothesis that body and habitat sites drive microbial community structure and enrichment patterns in the Yellow Mud Turtle, Kinosternon flavescens. Turtle body site is shown to be a significant contributor to turtle bacterial community structure and enrichment. This includes the presence of specific taxa that may have a role in a specific algae-mediated shell disease, which is of interest to conservation efforts. Taxa associated with the cloaca across individuals are also identified, as these may have important evolutionary implications. This work will be important to generating hypotheses and guiding methods in future turtle microbiome studies and will also serve as important background information for turtle conservation efforts.