Using Microbes to Help Save Endangered Turtles

Microbes—the right microbes—might be the newest tool in the increasingly sophisticated work of saving endangered species.

That’s why members of Shedd Aquarium’s Microbiome Project team were called to Washington state to help solve a mystery surrounding the recovery of an iconic freshwater turtle.

New threat from unidentified disease
For more than 25 years, western pond turtles (Actinemys marmorata) have been the focus of a conservation coalition led by the Washington Department of Fish and Wildlife (WDFW), along with Seattle’s Woodland Park Zoo and the Oregon Zoo, which, like Shedd, are accredited members of the Association of Zoos and Aquariums (AZA).

Western pond turtles once ranged from Puget Sound to Baja California. But by the mid-1990s, overhunting, habitat loss and predation by introduced animals had reduced the Washington state population to about 150 animals. Since then, the population has slowly rebounded to more than 1,000 turtles at six sites, in large part through a head-start program in which zoo-reared yearlings are released into the wild.

But the success of these efforts has been hampered in recent years by the appearance of a mysterious fungal shell disease among the introduced turtles. The unidentified fungus has infected up to half the examined turtles in each population. The disease appears as shell lesions that can go through the outer layer of the shell to the underlying bone and body tissues, killing the afflicted turtles.

Conservation efforts were bolstered when AZA named the western pond turtle as one of the species for its intensive SAFE (Saving Animals From Extinction) program in 2015 and initiated a conservation action plan for the turtles that includes the Unidentified Shell Disease Project, in which Shedd is a partner.

Something in the water?
Chrissy Cabay, director of Shedd’s Microbiome Project, and Dr. Matt O’Connor, one of our staff veterinarians (and a turtle aficionado), traveled to Washington to investigate a hypothesis that the fungus got a shell-hold on the zoo-raised turtles because their controlled environment is missing critical beneficial microorganisms that are present in their native waters.

The first step was to collect water samples at several sites where the pond turtles naturally occur and head-started individuals have been released. Working from a small kayak, Chrissy took samples from across the habitats to learn what microbial communities the turtles interact with as they swim, break the water’s surface and bask.

Dr. Matt performed health assessments on the turtles to try to determine what environmental, dietary and developmental factors might be associated with the onset of the disease.

Back at Shedd, Chrissy and her team are doing DNA sequencing on the samples. It’s the same process researchers in the Microbiome Lab apply to monitoring the microbial communities in the aquarium’s habitats and tweaking bacterial balances for the animals’ optimal health.

Since Chrissy's initial trip with Dr. Matt, the Aquarium Microbiome Project has been awarded a two-year grant for a graduate project in partnership with the University of Illinois. Under the supervision of veterinarians with WDFW, Shedd and the university will collect and analyze more than 600 environmental and animal-associated samples. The data they obtain will help inform how head-start habitats might be augmented to incorporate beneficial microbes, boosting the turtles' chances of success.

Meanwhile, veterinarians with the University of Illinois Zoological Pathology Program, another partner in the disease detective work, are sequencing DNA to identify the fungus attacking the turtles’ shells.

Once the microorganisms, bad and beneficial, are known, the research partners in the Unidentified Shell Disease Project hope to address why the turtles have it, what environmental factors are contributing to it, how it might be treated and how it might be prevented.