To find rare snakes, we can look to the soil

FORT COLLINS, Colo., Jan. 15, 2024— Scientists have developed a new method to monitor the elusive eastern indigo snake, the longest native snake in the United States. This innovative approach looks for traces of environmental DNA in soil samples and can significantly bolster efforts to conserve this threatened species.

Eastern indigo snakes are notoriously difficult to find in the wild, making management of the species and their habitats challenging. More accurate distribution information can focus habitat restoration and management efforts for more targeted and effective conservation. A team of researchers, funded by the Department of Defense’s Legacy Resource Management Program, have now shown that eDNA – a method that detects the genetic material that organisms shed into their environments – can be used to identify the presence of eastern indigo snakes without the need to observe them directly.  

“This is an exciting development for eastern indigo snake conservation,” said Dr. Houston Chandler of The Orianne Society. “It adds another tool to the toolbox that can now be used to make better conservation decisions for this charismatic species.” The findings highlight the potential of eDNA to improve population monitoring for many difficult-to-find species, ensuring that conservation efforts are more effective and better informed.

Scientists found that eastern indigo snakes leave detectible DNA in the soil in less than two minutes – and the snakes sometimes continue to be detectable for up to 10 days. “This method increases the time window available for biologists to detect snakes in their natural habitats,” said lead author Leah Samuels of the USDA Forest Service Rocky Mountain Research Station. “One of the challenges of eastern indigo snake monitoring is that the animals are highly mobile. When used in conjunction with active searches, soil samples could let you know not just if snakes are using the habitat right now, but if they have in recent history.”

Eastern indigo snakes live in dry sandhills during winter months across most of their range. Until now, it has been unclear whether eDNA-based monitoring methods would work in these conditions, since the genetic traces degrade over time. To answer this question, the scientists studied captive snakes in sandy enclosures to mimic real-world conditions. They placed snakes into four different enclosures for different time periods and collected soil samples after each round. Then, they used a novel DNA extraction method to identify the eDNA left by the snake in the soil. Ultimately, this research showed that, yes, soil sampling for eastern indigo snakes is likely a good option and can complement other monitoring methods.

This research may have implications for monitoring other species as well. “Environmental DNA sampling was really pioneered in aquatic systems, but this study is an example of the power of these tools in terrestrial systems as well,” said co-author Taylor Wilcox of the Rocky Mountain Research Station. “This approach will be attractive to land management agencies working to conserve the species.” He added “We appreciate the Department of Defense’s support for this research as part of its ongoing commitment to preserving species and habitats under their stewardship.”

This research was led by Leah Samuels, ORISE fellow, and Dr. Taylor Wilcox, research geneticist, both with the Rocky Mountain Research Station, along with Dr. Houston Chandler and Benjamin Stegenga of The Orianne Society, Michelle Hoffman and Dr. James Bogan of the Central Florida Zoo, Dr. Michele Elmore and Dr. Robert Aldredge of the U.S. Fish and Wildlife Service, Stephanie Hertz of Texas A&M University, Dr. Mark Davis of the University of Illinois Urbana-Champaign, and John Kronenberger and Dr. Michael Schwartz of the Rocky Mountain Research Station.  This work was funded by the Department of Defense Legacy Resource Management Program. You can find more information in the research paper published in Environmental DNA.

The Rocky Mountain Research Station is one of five Forest Service research stations serving federal and state agencies, international organizations, Tribes, academia, non-profit groups, and the public. RMRS researchers work in a range of biological, physical, and social science fields to promote sustainable management of the nation's diverse forests and rangelands. The station develops and delivers scientific knowledge and innovative technologies with a focus on informing policy and land-management decisions. Working out of 15 laboratories across the Western U.S., RMRS researchers work in collaboration with a range of partners, including other agencies, academia, nonprofit groups, and industry.