Document Type

Master's Research

Degree Name

Master of Science




Frank V. Paladino and Tanya T. Soule

Date of Award



Animal microbiomes have become increasingly regarded as a system responsible for supporting vital functions, such as digestion, amino acid production, and immune response. Despite their importance, there is limited understanding of the microbiome of sea turtles and the effect it has on their overall health. Green turtles (Chelonia mydas) provide an interesting model of change in these microbial communities since they undergo a pronounced shift from a surface-pelagic distribution and omnivorous diet to a more shallow coastal distribution and herbivorous diet. We investigated the cloacal microbiomes of juvenile green turtles before and after this recruitment to neritic waters to characterize and assess any changes in their microbial community structure. Green turtles were captured among the pelagic Sargassum habitat in the Gulf of Mexico, and within the neritic foraging grounds of St. Joseph Bay and St. Andrew Bay, FL, USA. Additionally, we captured turtles in the surf zone of Santa Rosa Island (SRI), FL, USA with the expectation that the site may harbor an intermediate stage within the shift from pelagic habitats to shallow bays since this is a relatively understudied neritic habitat for green turtles. Cloacal swabs were taken from each turtle and the DNA was isolated for analysis of the 16S rRNA gene sequences using high-throughput Illumina sequencing. One fecal sample was also collected opportunistically from a pelagic individual. We found that pelagic and neritic juvenile green turtle bacterial communities were significantly different. However, samples from SRI were more similar to those from the pelagic habitat (ANOSIM; R2 = 0.556) than the bays (ANOSIM; R2 = 0.988). These results suggest that the environment and dietary resources in neritic habitats support different bacterial communities in green turtles than pelagic habitats. Furthermore, the relative similarity between microbial communities from the cloaca of pelagic juvenile green turtles and those from SRI may be due to the beachfront serving as an intermediate habitat during the turtle’s recruitment to coastal bays. This is the first study to characterize the cloacal microbiome of the green sea turtle in the context of their ontogenic dietary shift. Understanding how the microbiome of green turtles can change throughout their ontogeny could provide valuable insight into the origins of their gut bacteria and how the microbial community supports their shift to herbivory.