Hidden Ecosystems of an Endangered Giant: Microbiomes of Leatherback Sea Turtles

Abstract

The leatherback sea turtle (Dermochelys coriacea) is a migratory, globally endangered marine species whose associated microbiota remain understudied. Characterizing these communities may inform animal health and conservation. We hypothesized that different turtle body sites and nests host distinct microbial communities. To test this, we analyzed 76 samples from five animals and seven nests, comprising nest sand (surface and bottom layers), eggs, and turtle-associated microbiota from the cloaca, mouth, tears, and carapace, collected during the nesting and hatching periods. The microbiota of sand and eggs were similar regardless of collection period but differed significantly from that of the turtle (p. adj ≤ 0.009). Composition also differed among turtle body sites, although this analysis is exploratory given the small number of animals sampled; between the nesting period and post-hatching nests (p = 0.001); among egg stages (deposited, unhatched/false, or hatched; p = 0.012); and between nest sand depths (surface versus bottom; p = 0.032). Human pathogen-associated taxa inferred using FAPROTAX tended to be more abundant in sand and egg samples than in turtle-associated samples, although this pattern was not statistically significant. Alpha diversity did not differ among sample types, egg stages, or turtle body sites, but was higher in nest sand during the hatching period than during nesting. These findings provide evidence of spatial and temporal variation in microbial communities associated with leatherback turtles and their nesting environments, and one of the first microbiome baselines for Caribbean leatherbacks, against which future change at this site can be assessed.