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Environmental DNA (eDNA)

Environmental DNA (eDNA) refers to DNA collected not directly from the tissue of an organism, as is normally done, but filtered from an environmental sample such as stream water. While microbial DNA predominates in most environmental samples, it is nonetheless possible to detect minute amounts that come from larger organisms such as vertebrate and invertebrate animals, by amplifying diagnostic DNA sequences. These eDNA molecules ultimately comes from cells that are sloughed off from the organism or excreted with wastes, and the methods to detect this DNA are very sensitive and specific. eDNA has become the basis for innovative surveillance methods that can identify whether otherwise difficult-to-monitor species inhabit a study area, e.g. species that are rare, nocturnal, or live in inaccessible habitats, or are alien to that environment. Ongoing research seeks to increase the power of the method, for example by quantifying the number of animals contributing to the detected sequences and whether they were living or, alternatively, detected from the waste products of predators. Utilizing eDNA has the potential to provide resource managers with early notice that a species no longer uses a particular habitat or that a species is expanding its range into geographic areas where it is not previously known.


Molecular Detection of Vertebrates in Stream Water: A Demonstration Using Rocky Mountain Tailed Frogs and Idaho Giant Salamanders
Photo: Filtering stream water to collect environmental DNA from stream amphibians. Photo credit: by Matthew Laramie, USGS.

Photo: Filtering stream water to collect environmental DNA from stream amphibians. Photo credit: Matthew Laramie, USGS.

Photo: Idaho Giant Salamander (Dicamptodon aterrimus). Photo credit: Robert Arkle, USGS.

Photo: Idaho Giant Salamander (Dicamptodon aterrimus). Photo credit: Robert Arkle, USGS.

Stream ecosystems harbor many secretive and imperiled species, and studies of vertebrates in these systems face the challenges of relatively low detection rates and high costs. Environmental DNA (eDNA) has recently been confirmed as a sensitive and efficient tool for documenting aquatic vertebrates in wetlands and in a large river and canal system. However, it was unclear whether this tool could be used to detect low-density vertebrates in fast-moving streams where shed cells may travel rapidly away from their source. To evaluate the potential utility of eDNA techniques in stream systems, researchers designed targeted primers to amplify a short, species-specific DNA fragment for two secretive stream amphibian species in the northwestern region of the United States (Rocky Mountain tailed frogs, Ascaphus montanus, and Idaho giant salamanders, Dicamptodon aterrimus). Three DNA extraction and five PCR protocols were tested to determine whether eDNA could be detected from these species in filtered water samples from five streams with varying densities of these species in central Idaho, USA.
Findings included successful amplification and sequencing of the targeted DNA regions for both species from stream water filter samples. C.S. Goldberg, D.S. Pilliod, Robert Arkle, Lisette Waits.
PLoS ONE 6(7): e22746. doi:10.1371/journal.pone.0022746

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