Environmental DNA

Using genetic information to inform restoration efforts

In 2019, MCWC received funds from the Oregon Wildlife Foundation and worked with partners at the Bureau of Land Management, US Forest Service, and the Xerces Society to begin a pilot project collecting environmental DNA (eDNA) samples across our working area, with the goal of filling in large gaps in species distribution information for lamprey and freshwater mussels.

While lamprey and freshwater mussel species have been recognized for their ecological and cultural values by tribes for thousands of years, they are understudied within the scientific community. The lack of recognition and ecological understanding of both freshwater mussels and lamprey in restoration projects that target endangered salmon is of concern both for sustaining populations of these species, as well as for the benefits that they can provide to salmon in intact systems. By determining the presence of these species in our working area, MCWC and are partners increasing our capability to effectively conduct holistic restoration projects and implement Best Management Practices that protect the myriad ways that native species depend on one another.

Explore the species frequently identified through environmental DNA

Why lamprey?

Lamprey are some of the oldest vertebrate species in the world, and are in decline. Tribal fisheries and other co-managers began noting declining returns of these anadromous species in the 1950’s. As a result, in Oregon, Pacific lamprey (Lampetra tridentate) were listed as a sensitive species in 1993, with greater protected status being attained in 1996.

Like freshwater mussels, they are sensitive to habitat degradation, such as poor water quality, low flows, and river channelization. The parasitic behavior of some lamprey species couples them to the status of other native fish populations (Kostow, 2002).

Lamprey larvae (ammoceotes), which spend 4-6 years in freshwater, purify water via filter feeding (Close et al, 2002). They are an important food source for salmon fry and many other species, and help buffer salmon adults and smolts from predation pressure. A 1984 study found that the most abundant dietary item in seals and sea lions was lamprey, and in a 1995 study, lamprey made up 71% of the diet of California gulls, ringbill gulls, western gulls, and Foster terns in the Columbia River.

Lamprey are also an important traditional food source for many Tribes of the Pacific Northwest, and are valued, in part, for being extremely nutritionally dense: caloric values for lamprey range from 5.92 to 6.34 kcal/g wet weight, whereas salmon average 1.26-2.87 kcal/g.

Why Freshwater Mussels?

Freshwater mussels represent one of the most endangered and quickly declining groups of organisms on earth (Dysthe et al, 2018). They are long-lived organisms, with some individuals aged at over 100 years. Throughout their lifetime, freshwater mussels perform the valuable ecosystem service of water purification via filter feeding, which in turn provides clean habitats for other aquatic organisms. In 2014, it was found that floater mussels (genus Anodonta or Sinanodonta) could remove pharmaceuticals from water, and in 2015, bacterial populations, such as E. coli, that otherwise contribute to fish mortality. The cleaning activities of Western pearlshell mussels (Margaritifera falcate) allow for increased populations of other macroinvertebrates, which in turn provide a food source for juvenile salmonids. Further, lamprey can grow faster when found near western pearlshell mussel beds. In addition, freshwater mussels serve as a food source for river otters when other prey is scarce. Freshwater mussels are also an example of a traditional food source for Tribes in the Pacific Northwest, notably in the Columbia Basin, where shells were also used for cultural items such as wampum necklaces (Blevin et al, 2019). Unfortunately, their sedentary and filter feeding nature makes them vulnerable to anthropogenic activities that degrade water quality beyond their tolerance, especially increased sedimentation inputs to streams. And because freshwater mussels require native fish as hosts for reproduction and dispersal as larvae (called glochidia), they are also impacted by the status of native fish populations, namely salmonids. Their declines have earned them listings as vulnerable and near threatened on the IUCN Red List, however, regulatory listings have yet to be made.

Why environmental DNA?

eDNA sampling in aquatic environments has been recognized as an effective tool for determining species presence, especially for a wide range of taxa and for rare or otherwise difficult to survey species, including mollusks and lamprey. eDNA sampling is a less time-intensive way to determine freshwater mussel species distribution than traditional surveys that require specialized expertise for quality results. This newer technology is vital to filling in distribution data and to improve an existing database of sightings maintained by the Xerces Society. For instance, the only entry that existed in the database for freshwater mussels in the North Fork Yachats River before our sampling in 2019 was taken 60 years prior. In a similar vein, lamprey are difficult to reliably identify in freshwater surveys, as they are most frequently observed during their juvenile phase as ammocoetes, when physical characteristics that allow for species differentiation to be made have not yet developed. Further, their observance is generally only collected incidentally during salmonid monitoring efforts, which, although more up to date than some of the recorded freshwater mussel sightings, is nowhere near comprehensive.

2019 Results

So far, laboratory analysis for Pacific Lamprey has taken place on all the 57 sites sampled by MCWC, a contracted crew from the Lincoln Soil and Water Conservation District, and the BLM in 2019. At right is a map showing where Pacific Lamprey were confirmed (green stars), and where eDNA collections did not detect any Pacific Lamprey (black diamonds).

What’s Next?

Samples collected in 2019 will continue to be stored so that analysis of additional species of lamprey, freshwater mussels, or other aquatic organisms may take place in the future.

For any species being targeted in eDNA sampling, the detection of species present at a particular collection site means that the species' range extends further upstream from where that sample was taken. With this in mind, MCWC plans to build off of the 2019 pilot project results to work our way upstream mainstem and tributary streams in the major basins of our working area, including the Salmon, Siletz, Yaquina, Alsea, and Yachats. Of great interest will be to collect samples above perceived natural fish passage barriers (such as the falls in the upper Siletz River and South Fork Alsea), which often receive less attention in conservation and restoration projects.

best management practices

For more information on how in-stream restoration projects can be conducted to minimize impacts to lamprey and freshwater mussels, click on the buttons below.