Shell Lesion Prevalence and Bacteriome Associations in Threatened Western Pond Turtles (Actinemys marmorata and Actinemys pallida) in California, USA.

Bacteriome characterization studies can provide insights into the microbial ecology associated with disease. We collected western pond turtles (Actinemys marmorata and Actinemys pallida) from six San Francisco Bay Area, California, US, ponds; assessed their shells for lesions; and collected shell swabs and keratin scrape samples to evaluate bacteriome differences between the whole shell (swabs) and the affected tissues (scrapes). We quantified shell lesion type and prevalence by using visual inspections of photographs collected of the plastron and carapace and then applied 16S rRNA amplicon sequencing to characterize the associated bacteriomes of shells that observed pits, ulcerations, or no lesions. We observed shell lesions at high frequencies throughout our sites, with larger individuals (>100-mm plastron length) more likely to possess injuries. We saw no differences in alpha diversities between shells presenting with lesions and those on which we did not observe lesions; however, swab samples showed higher bacterial richness than keratin scrapes. The bacterial composition within the scrapes was influenced by pond location and then lesion presence. We observed a higher relative abundance of Actinobacteriota, Bacteroidota, Cyanobacteria, and Deinococcota in the shell keratin microflora of turtles with shell lesions. Because western pond turtles are under consideration for listing under the Endangered Species Act of 1973 in the US, understanding patterns of shell disease pathologies and the bacteria associated with disease is imperative for the management of current populations.