Ashlynn Canode
Department of Wildlife Ecology and Conservation, University of Florida
October 2025
Background
Emerging diseases represent a growing challenge for snake conservation across North America, but relatively little is known about how pathogens affect species in intact, fire-maintained longleaf pine ecosystems. As part of my master’s thesis research at the University of Florida, I am conducting a pathogen surveillance study at Tall Timbers in the Red Hills region of northern Florida and southern Georgia.
Key findings
Snakes were sampled as part of an ongoing drift-fence array study using 21 arrays distributed across three major habitat types (upland pine, field, and bottomland forest). Each array consisted of four 50-meter silt fence arms radiating from a central box trap with funnel traps at each end. Traps were checked daily for three weeks out of each month during the 2024–2025 active seasons (March–October), and all captured snakes were processed in the lab.
During processing, I collected oral–cloacal, cloacal, and skin swabs for pathogen screening. Skin swabs were rotated across the dorsal and ventral surfaces, with special attention to any abnormal areas, while oral–cloacal and cloacal swabs were collected for detection of Cryptosporidium serpentis and Raillietiella orientalis. Fecal samples were collected opportunistically and preserved for parasite examination. Each individual also received a health assessment, including inspection for ectoparasites, lesions, abnormal shedding, swelling, or deformities, which helped identify individuals for priority testing.
Over the course of the 2024–2025 field season, I sampled more than 750 snakes, representing fourteen species, to screen for three important pathogens: snake fungal disease (Ophidiomyces ophidiicola), cryptosporidiosis (Cryptosporidium serpentis), and the invasive pentastome (Raillietiella orientalis). This effort provides the first baseline of pathogen presence for snake populations in the Red Hills in a relatively undisturbed longleaf pine ecosystem.
Across all samples analyzed to date, 201 swabs from 120 individual snakes were screened for pathogen presence using qPCR assays. Thanks to support from The Orianne Society, I was able to increase my sample size by sending an additional set of skin swabs specifically for snake fungal disease analysis.
Across all swabs analyzed, 19 individuals tested positive for O. ophidiicola. Most detections were from body swabs, with a few from oral–cloacal swabs. Positive detections occurred primarily in Southern Black Racers and Florida Cottonmouths, which together accounted for over half of the positive results and were also among the most frequently captured species. Additional positives were found in Corn Snakes, Eastern Mud Snakes, Eastern Diamondbacks, and Eastern Garter Snakes, while Banded Water Snakes and Gray Rat Snakes were negative.
These results suggest that snake fungal disease persists at low levels within the Tall Timbers snake community but does not appear to be causing widespread outbreaks. The concentration of detections in cottonmouths may reflect species-specific susceptibility, habitat use, or behavioral factors, but further monitoring will be needed to understand species-specific risk.
We also sent 159 cloacal swabs to be tested for Raillietiella orientalis, and all were negative, suggesting that this invasive pentastome parasite has not yet established in the Red Hills region. However, two fecal samples examined microscopically revealed nematodes, cestodes, and trematodes, indicating that other endoparasites are present. No individuals tested positive for Cryptosporidium serpentis, suggesting that this gastrointestinal pathogen was absent or present at undetectable levels in the sampled population during the study period.
Discussion and future directions
This project highlights the importance of long-term ecological research stations like Tall Timbers and underscores the role of fire-maintained longleaf pine ecosystems in supporting healthy wildlife populations. Continued surveillance, particularly during the active summer months, will help track changes through time and provide early warning of emerging disease threats. By establishing this baseline, my research lays the foundation for understanding how habitat management, seasonal activity, and species behavior shape pathogen dynamics in native snake communities. I am grateful to The Orianne Society for supporting this work and helping to advance our understanding of snake health in southeastern ecosystems.