Western Fisheries Science News, April 2018 | Issue 6.4

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Using Environmental DNA (eDNA) to Detect Lamprey

Scientist collecting eDNA samples

WFRC scientist collecting eDNA samples. Credit: Jeff Duda, USGS. (Public domain.)

The ability to detect aquatic species by using environmental DNA (eDNA) has recently emerged as a technique offering great potential for studies in conservation biology and ecology. eDNA refers to DNA extracted from genetic material obtained from environmental samples such as water or sediment. eDNA-based methods provide an alternative to traditional sampling methods for detecting and monitoring a wide range of aquatic species, including fish, amphibians, insects, and mollusks. These methods are based on the premise that genetic material is shed into the aquatic environment from source organisms through waste products (feces and urine), mucous, skin cells, tissues, and gametes. This genetic material can be collected from environmental samples, allowing target species residing in aquatic habitats to be detected by using molecular genetic methods.

eDNA has application as a monitoring tool for species conservation and management. It is effective for identifying species that are otherwise difficult to detect with traditional sampling methods and may have increased detection probabilities relative to traditional sampling methods even when species are rare or occur at low densities. eDNA can be used to detect invasive species, monitor translocation and re-introduction programs, track recolonization following barrier removal or habitat improvement projects, and can be applied to occupancy modeling. In addition, eDNA sampling does not require the permitting challenges associated with capturing endangered species.

Conducting surveys for lamprey in 18 Puget Sound watersheds

Pacific Lamprey are culturally important to Native American tribes. Once found in abundance throughout North Pacific drainages from Mexico to Japan, Pacific lamprey populations have declined and are now a “species of concern.” Lamprey population prominence within many Puget Sound areas are unknown, therefore occupancy information is needed for advancing conservation goals.

In a recent study conducted by the USGS Western Fisheries Research Center (Ostberg et al. 2018), scientists developed two eDNA assays, one to target Pacific Lamprey and one to target both Western River Lamprey and Western Brook Lamprey (Lampetra spp). The assays were applied to water samples collected from 18 Puget Sound watersheds to characterize the spatial and temporal distribution of lamprey eDNA. Water samples were collected in fall and spring to compare eDNA detection between seasons. Data collected from the eDNA study was compared to lamprey data collected by Hayes et al. (2013) who used traps designed for sampling juvenile salmonids to capture lamprey. Research findings indicated that occupancy results from eDNA were consistent with known lamprey distributions and detection of lamprey eDNA differed between spring and fall, likely due to differences in stream flow rate and life history events between seasons. These eDNA assays will be an effective and valuable tool for resource managers and the scientists demonstrated that certain periods yield better eDNA detections than others, which can ultimately influence cost effective sampling strategies for target organisms.

Environmental DNA as another lamprey detection tool

To advance the conservation goals for Pacific lamprey it is necessary to know their distribution and occupancy. Targeted sampling methods such as electrofishing and trapping have been successful methods for detection. Through their eDNA research Ostberg, et al. (2018) found that the assays they created provide an additional approach that can be used by resource managers to survey for Pacific Lamprey and Lampetra spp. It is important that resource managers understand that eDNA-based methods, like other species detection methods, are sensitive to environmental conditions. For example, DNA could be transferred from one site to another, which could produce a false positive result (i.e. eDNA detection when the species is actually not present). eDNA detection may also be more effective by sampling water in areas containing the substrate type preferred by larvae.

Current research and future applications

As the use of eDNA increases for detecting aquatic species, analytical techniques will improve. However, for now eDNA is a complement rather than replacement for traditional surveying methods. eDNA research provides a valuable non-invasive tool for detecting aquatic species. Its application is useful for studies addressing threatened and endangered species, cryptic species, species that are difficult to sample, and for early detection of invasive species.

WFRC is taking advantage of this new tool and advancing its application. Scientists have been combining field and laboratory studies to develop assays and answer research questions. Some recent examples include monitoring the recolonization of salmon in the Elwha River following dam removal, evaluating the utility of eDNA for estimating relative or absolute abundance of salmon (e.g., Tillotson et al. 2018), investigating the use of sediment for detecting larval lamprey, and detecting invasive macrophyte species (Eurasian watermilfoil and Brazilian Elodea) in lakes and reservoirs which could allow for rapid assessment and response to aquatic invasions.

For more information, contact Dr. Carl Ostberg, costberg@usgs.gov, 206-526-2535.

Newsletter Author: Debra Becker

 

Research

USGS Hosts Scientist from Tunisa: Dr. Nadia Cherif from the National Institute of Sea Sciences and Technologies in Tunisia visited the WFRC for 10 days as part of a U.S. Agency for International Development Partnerships for Enhanced Engagement in Research (PEER) program administered by the U.S. National Academy of Sciences. The project titled “Enhanced Research Capacity and Fish Health Infrastructure to Assist Tunisian Aquaculture” will be important in gaining a better understanding of the global distribution of fish diseases and in developing novel methods to reduce their impact in Tunisia and other countries of the Mediterranean region. Such efforts ultimately will also benefit the U.S. by helping to reduce the global spread of diseases that can affect both commercial aquaculture and native species. The role of the WFRC will be to provide technical assistance in the creation and validation of novel methods for the detection of fish diseases. For more information, contact Jim Winton, jwinton@usgs.gov, Seattle, WA.

Events

USGS at Salish Sea Ecosystem Conference: USGS scientist Theresa Liedtke gave a presentation at the 2018 Salish Sea Ecosystem Conference (SSEC), on April 4-6, 2018, at the Washington State Convention Center in Seattle, WA. Liedtke presented new research on the maternal transfer of PCB loads in sand lance, a forage fish in Puget Sound. Forage fish like sand lance play a central role in the marine food web, and PCBs in these fish will transfer up the food web and contribute to PCB loads in salmon, birds, and marine mammals. The research is part of the USGS Coastal Habitats in Puget Sound (CHIPS) Program, an interdisciplinary collaboration to coordinate, integrate, and link studies with Puget Sound Nearshore Ecosystem Recovery goals. The CHIPS team was the first to report PCB contamination in sand lance, making a direct contribution to the USGS Environmental Health Mission Area by advancing the understanding of how contaminants in the environment affect the health of biota. This new research expands the initial finding by detailing that eggs and larval stages of sand lance have significant PCB loads due to offloading of PCBs by females during reproductive processes. The SSEC assembles scientists, First Nations, resource managers, community and business leaders, policy makers, and educators to present the latest scientific research on the state of the ecosystem, and to guide future actions for protecting and restoring the Salish Sea ecosystem. For more information, contact Theresa Liedtke, tliedtke@usgs.gov, Cook, WA.

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Western Fisheries Science News, April 2018 | Issue 6.4
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Western Fisheries Science News, April 2018 | Issue 6.4 (pdf)

Western Fisheries Science News, April 2018 | Issue 6.4 (pdf)