Detecting Invasive and Rare Species with the National Streamflow Network

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Two recently published papers suggest the integration of environmental DNA, or eDNA, sampling at select National Streamflow Network streamgages in the U.S. Northwest is feasible.

Proper management of the Nation’s riverine ecosystems requires extensive data relating to their physical, chemical, and biological characteristics and processes. The two papers provide a proof-of-concept to see if the existing local streamgage network configuration and protocols were adequate to detect rare or invasive aquatic species.

Large Boulders Detroit

Dreissenid mussels coat the river bottom. Photo by USGS

One study, published in Ecosphere, evaluated the efficacy of adding eDNA surveillance to USGS streamgages downstream of reservoirs to detect the presence of dreissenid mussels, specifically quagga and zebra mussels. Researchers consistently detected dreissenid mussel DNA in waters downstream of reservoirs in Arizona and Minnesota known to harbor them. Dreissenid mussels were not detected below eight Columbia River Basin reservoirs in Idaho, Oregon, and Washington that are considered to have moderate to high suitability for invasive dreissenid mussels. They did detect two fish species at these same gages, Kokanee salmon and yellow perch, which are known to occur in the reservoirs.

The other study, published in the Journal of the American Water Resources Association, determined that eDNA analyses using the current streamgage configuration could provide useful information about distribution and habitat associations for rainbow and bull trout, two species with different distribution and environmental tolerances. However, occasional sampling between streamgages may be necessary to meet regulatory requirements for species that occur at very low density, have restricted distributions, or have narrow environmental tolerances or habitat preferences. This study collected samples from five streamgages in southwest Idaho for an entire water year - October to September. Samples were also collected at equallyspaced intervals between streamgages during three sampling events to determine whether the spacing of existing gages was adequate.

Management Implications
  • Integration of eDNA sampling and analyses as a biological component, along with existing physical and chemical monitoring within the USGS streamgage network, could provide an invasive and rare species early detection-surveillance network.
  • eDNA collection and analysis could be added to an existing streamgage site, using existing infrastructure and workflows, at a reasonable cost per site.


Sepulveda, A.J., Schmidt, C.G., Amberg, J.J., Hutchins, P.R., Stratton, C., Mebane, C.A., Laramie, M.B., Pilliod, D.S., 2019, Adding invasive species biosurveillance to the U.S. Geological Survey streamgage network: Ecosphere, p. e02843,


Pilliod, D.S., Laramie, M.B., McCoy, D., Maclean, S., 2019, Integration of eDNA-based Biological Monitoring within the USGS National Streamgage Network: Journal of the American Water Resources Association, v. 1, no. 14, p. online,


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Date published: January 1, 2019

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thumbnail image of Pilliod-Sepulveda-eDNA-streamgage pub brief
October 1, 2019

Pilliod, et al. 2019 and Sepulveda, et al. 2019 Publication Brief

Plain language summary of:

Sepulveda, et al. 2019, Adding invasive species biosurveillance to the U.S. Geological Survey streamgage network

Pilliod, et al. 2019, Integration of eDNA-based Biological Monitoring within the USGS National Streamgage Network