Ongoing habitat loss, increased transportation and transmission pathways, and a changing climate will facilitate invasive species and disease expansion in the coming decades. The ecological impacts of invasive species and disease are often irreversible and far-reaching, and include reductions in the distribution, abundance, and diversity of native species. Moreover, invasive species and disease outbreaks have significant impacts on local and regional economies via losses in recreational value and the enormous costs to mitigate their effects. The USGS is committed to providing science and tools for preservation or control of invasive species and wildlife disease outbreaks, including advancing new innovative technologies such as examining environmental DNA, or eDNA, from aquatic environments to determine whether a particular species is present in the water.

Montana’s coldwater fisheries are the headwaters that feed the ecologically and economically vital Columbia and Missouri River Basins. In 2016, fisheries managers in Montana faced two natural resource emergencies that cost millions. The first was a detection of invasive dreissenid mussel larvae in the state. The second was a parasite-caused fish kill that shut down a popular fishery. Expertise at USGS Northern Rocky Mountain Science Center (NOROCK) in eDNA detection technologies was sought out by state partners to respond to both events. Our goals are to develop early detection and risk assessment approaches that inform better resource management decisions and assist resource managers in applying these tools.

Montana was one of few states in the West still free of invasive quagga and zebra mussels until 2016, when quagga mussel larvae were discovered in the Tiber Reservoir in northern Montana. The State activated a rapid response team to contain the invasion. NOROCK scientists serve as experts on aquatic invasives and dreissenids on the Monitoring Implementation Team, assisting managers in determining the best tool for early detection. Specifically, we are working with Montana Fish, Wildlife, and Parks on a comparative study of traditional aquatic invasive species (AIS) detection methods and eDNA in Tiber Reservoirs. We are also developing lab and field protocols for dreissenid mussel monitoring and dreissenid risk assessment criteria to prioritize sampling efforts. Working with the State and partners at the USGS eDNA lab at the Upper Missouri Ecological Science Center (UMESC), we are developing quality control methods to ensure comparable results among different sampling approaches.

Additional work with Tribal partners to get ahead of future mussel invasions involves piloting the use of USGS and Confederated Salish and Kootenai Tribe (CSKT) streamgage network as sites for eDNA surveillance, as well as training CKST partners in eDNA survey methods.

Also in 2016, Montana officials closed recreational activities in almost 200 miles of the Yellowstone River below Yellowstone National Park and its tributaries because of unprecedented mortality of mountain whitefish and trout due to proliferative kidney disease (PKD) caused by the parasite Tetracapsuloides bryosalmonae. Low stream flows and high temperatures are thought to have contributed to the massive scale of fish mortality. The closure had enormous economic impacts on the communities that depend upon summer tourism for much of their income. Our scientists assisted Montana Fish, Wildlife, and Parks and the U.S. Fish and Wildlife Service in developing  a new early detection eDNA method for T. bryosalmonae, and describing the distribution of T. bryosalmonae in Montana waters. In addition, we are helping managers understand and predict what conditions are likely to result in PKD fish kills across the state.

In late August, 2017, another fish die-off occurred along the Yellowstone River. The USGS assisted by using new methods to sample at the mortality location and assisted the State in counting dead fish. These methods use a new eDNA marker for superior early detection. The marker is being used to detect the presence of T. bryosalmonae in the Yellowstone River every two kilometers from Gardiner, MT to Big Timber, MT. Crews experimented with sampling at different locations in the river, such as near the surface and at the bottom, and concluded that DNA from the parasite is not evenly distributed in the river. They also determined that increased sampling intensity at a site is likely more informative at determining presence than increased sampling intensity over space. This sampling strategy may help to elucidate the relationship between abundance, stream temperature, flow, and when outbreaks occur, with a goal of improving predictive ability. Predictive ability is important to state officials who are making critical decisions about stream closures.  

Innovative eDNA capabilities allow NOROCK to rapidly respond to management needs in combating invasive species and disease, and mitigating impacts on livelihoods, ecosystems, and the economy. Our approaches will ultimately increase the cost-effectiveness of invasive species and disease management, preserving cold water fisheries in the West.