As the home to more than 250 species of fish, amphibians and reptiles, West Virginia’s waterways are literally teeming with life. However, the effects of anthropogenic disturbances on the biodiversity of aquatic life and habitats in West Virginia and Appalachia is an environmental concern. Recent advances in non-invasive genetic sampling has facilitated methods that allow researchers to collect environmental DNA (eDNA) and detect organisms that might have been previously challenging to observe.
Some species are difficult to detect and monitor because of location, behavioral characteristics, and low population densities. In the past, cataloging the presence these species involved sampling the aquatic community in streams using electrofishing and other techniques in a process that was both time and resource intensive, and that was limited by sampling errors and bias.
Environmental DNA represents free-floating DNA that has been excreted or shed by organisms into aquatic or terrestrial environments and provides a relatively new approach to detect and monitor species in freshwater environments. The analysis eDNA has also been shown to be relatively sensitive - such that a single strand of DNA is required to identify the presence of a species, and is not affected by misidentification.
“All animals that live in water leave eDNA behind via their feces, urine or skin cells,” said Dr. Eric Merriam, a post-doctoral researcher at West Virginia University. “By taking water samples and analyzing them for eDNA, it is possible to show the presence of a species without actually needing to catch individuals or even see them.
“Using eDNA for this purpose involves simply obtaining a water sample from the aquatic environment, he added. “This sample is then taken back to the lab, where DNA, if present, is extracted and analyzed using a series of genetic techniques, ultimately providing a list of the species that are present, as well as the amount of DNA in each sample that came from each species.”
Merriam is currently working with Drs. Jim Anderson, Todd Petty and Yvette Halley to develop eDNA capabilities within the state, particularly its use in the state’s wetlands, as part of the Appalachian Freshwater Initiative (AFI), a National Science Foundation (NSF) Experimental Program to Stimulate Competitive Research (EPSCoR) project (NSF Award Number 1458952).
“The NSF EPSCoR program was created to build capacity in science and engineering so research related eDNA was a natural fit for the West Virginia project.” said Merriam. “Our eDNA research creates capacity at West Virginia University and within the state.”
Environmental DNA research has been done mostly in western streams to look for non-native species. Initial samples have allowed the team to develop and refine existing field and laboratory techniques for use in West Virginia.
To date, the WVU team has developed and tested field and lab methods for collecting, extracting and analyzing eDNA from diverse organisms and systems, including successfully using eDNA to identify the presence of cryptic species, the Eastern Hellbender, within pristine streams in West Virginia. The team has also utilized eDNA samples and assess fish and amphibian community composition in streams with a range of chemical conditions and complex pollution mixtures.
“As part of our research, we had to adapt methods that were developed for pristine waters to allow filtering of often extremely polluted water,” said Merriam. “So far, these adapted methodologies appear to be successfully characterizing aquatic communities within the state. Moreover, our success in these diverse systems suggest that eDNA will be valuable across the range of water quality conditions within West Virginia as there was some concern that significant pollution, such as acid mine drainage, wastewater effluent, and agricultural runoff might degrade eDNA, limiting its use in those systems.”
The team has also been successful in developing methods to assess wetland communities using eDNA as past research has been largely conducted in pristine streams, with essentially no previous work in wetland or heavily degraded systems.
“Surprisingly, there has been very limited research utilizing eDNA in wetland systems, which represents a significant advancement in the science of wetland assessment and management,” said Anderson, who is spearheading the University’s eDNA research in wetlands. “Our goals are to use environmental DNA to monitor Appalachian streams and wetlands in the state, streamline current eDNA collection and analysis methodology, and contribute to methodical understandings of the scientific community and society. We’re committed to the idea of using eDNA to advance the management of aquatic environments throughout West Virginia.”
The research highlighted in this story is based upon work supported by the National Science Foundation under Award Number 1458952. Any opinions, findings, and conclusions or recommendations expressed in this material are those of the author/researcher(s) and do not necessarily reflect the views of the National Science Foundation.