Expanding Opportunities for Environmental DNA Sampling

by Daniel Chase and Patricia Valcarcel

The use of eDNA provides a unique and powerful non-invasive tool for biologists and natural resource managers.

The molecule that contains the genetic instructions for life, and is found in every species on the planet, is now opening new doors and providing a powerful tool for biologists and natural resource managers.  Deoxyribonucleic acid, more commonly known as DNA, is fundamental to life.  For decades, scientists have worked to understand, identify, and catalog DNA and their efforts have helped build an expansive database of genetic information for a multitude of species.  Research has also led to an improved ability to sample and detect DNA, allowing the use of the technology to expand outside of the laboratory setting.

Terrestrial and aquatic organisms such as this California red-legged frog leave traces of DNA in their environment.

Organisms in terrestrial and aquatic environments leave traces of DNA in the environment in a number of forms including tissue, hair, fecal/urine waste, saliva, blood, sluffing cells, etc.  Sampling DNA from the environment provides the ability to detect what species occur in the area, as each species’ DNA is unique.  Environmental DNA (eDNA) sampling is the process of collecting and filtering DNA from the environment so it can be analyzed in a lab to determine if a species’ (or community of organisms’) DNA occurs within an aquatic or terrestrial medium. In order to identify target species, an assay, or genetic marker, must first be developed to contain a segment of DNA specific to that species.

Sampling for eDNA has been used in fisheries science for several years by taking a water sample from a flowing stream, filtering the sample to extract DNA from the water, then comparing the DNA collected in the field to a genomic database to detect a target fish species in the area or immediately upstream.  Recently, sampling techniques and assays have been developed expanding this technique beyond flowing stream environments and to non-fish species.  This includes water samples in ponds to identify what composition of species occur in, and potentially adjacent to, the water body.  The use of eDNA is becoming a more common survey technique, and can be applied for such purposes as detecting a target species presence or absence, detecting hard to survey for species, refining or focusing collection or survey efforts, and deciphering between cryptic (i.e. morphologically similar) species.  Collecting and extracting DNA from a sample can also provide a unique timestamped sample that can be analyzed or reanalyzed weeks, months, or even years in the future.

WRA biologists Patricia Valcarcel and Nick Brinton sampling for eDNA.

WRA wildlife and fisheries biologists have been using eDNA to help detect species and supplement standard survey techniques.  The use of eDNA provides a unique and powerful non-invasive tool that does not require the direct capture or handling of a species.  WRA is currently using eDNA to identify potential biological constraints and opportunities and better inform clients and direct permitting strategies.  Potential applications for clients include use for land purchase due diligence when protocol surveys would be excessive and time consuming, pre-project planning phase, for parks and land trusts managing habitat for species, pre-construction surveys for biologically sensitive species, and assisting monitoring efforts in early detection of an invasive species’ entrance into new habitats and waterways.

In addition to field applications, WRA biologists have also assisted with the development of an eDNA assay to help detect the federally threatened California red-legged frog (Rana draytonii). The list of threatened and endangered species that eDNA has been used to detect continues to grow, and includes Delta smelt (Hypomesus transpacificus), green sturgeon (Acipenser medirostris), Chinook salmon (Oncorhynchus tshawytscha), steelhead (O. mykiss), tidewater goby (Eucyclogobius newberryi), California tiger salamander (Ambystoma californiense), giant garter snake (Thamnophis gigas), and San Joaquin kit fox (Vulpes macrotis mutica).

Contact Us

If you have questions about eDNA, or if using eDNA sampling can be used at your site and/or project, contact Daniel Chase at chase@wra-ca.com or 415.454.8868.