Session 8 – Advancing Understanding of Lake, River and Coastal Marine System Dynamics Using Environmental DNA

Thursday, April 1, 10:00AM-12:00PM

Kristina Cammen, School of Marine Sciences, University of Maine
John Kocik, NOAA Fisheries, Northeast Fisheries Science Center
Heather Leslie, Darling Marine Center, School of Marine Sciences, University of Maine

Environmental DNA (eDNA) is a tool of recent interest, rapid development, and promising potential for monitoring and management of aquatic ecosystems. This approach is built on the premise that organisms slough cells containing DNA into the water they inhabit and we can extract that DNA from a water sample without ever handling, or even seeing, the organism. eDNA approaches have been used successfully in diverse aquatic ecosystems to detect species presence and characterize biodiversity. There is also growing interest in further pushing the boundaries of eDNA’s potential for quantitative assessment of species abundance and distribution, as well as characterization of genetic diversity of individuals in a system. These new approaches are appealing to scientists and managers alike, who hope to use eDNA to sample populations and ecosystems in a non-invasive, cost-efficient manner.

Session Overview

  • 10:00AM-10:05AMWelcome
    Kristina Cammen

eDNA as a Tool

eDNA in Freshwater Systems

eDNA in Estuarine and Marine Environments

Developing eDNA Knowledge with and for Coastal Communities


Introduction to Environmental DNA and the Maine-eDNA EPSCoR Program

Michael Kinnison1, David Emerson2, Heather Leslie3, Kate Beard-Tisdale4, Shane Moeykens5, Kody Varahramyan6
1. University of Maine, School of Biology and Ecology, Orono, ME
2. Bigelow Laboratory for Ocean Sciences, Boothbay, ME
3. University of Maine, School of Marine Sciences and Darling Marine Center, Walpole, ME
4. University of Maine, School of Computing and Information Sciences, Orono, ME
5. Maine EPSCoR Office, Orono, ME
6. University of Maine, Office of the Vice President for Research and Dean of the Graduate School, Orono, ME

A video of this presentation is available

Environmental DNA is rapidly becoming a widespread tool in environmental monitoring and research because of its ability to detect organisms with higher sensitivity, species breadth, ease of sampling, and less harm than many current sampling methods. It has the potential to revolutionize both how we study populations, communities and ecosystems, and who participates in that monitoring and research. The vision of the NSF EPSCoR RII Track-1 program Molecule to ecosystem: environmental DNA as a nexus of coastal ecosystem sustainability for Maine (Maine-eDNA) is to make Maine ‘the DNA Coast’ – a world leader in eDNA-based partnerships, understanding, and sustainability of coastal marine and freshwater ecosystems. To do so, the program harnesses the power of eDNA science to 1) advance ecological understanding crucial to the current needs of Maine’s marine and freshwater resources, while 2) building the Big Data and IP innovations, technical workforce, and partnership capacities to address the increasingly large-scale and complex sustainability challenges of changing coastal ecosystems. In this talk, we will provide an introduction to common applications of environmental DNA monitoring and introduce the Maine-eDNA program’s research themes, which seek to innovate new eDNA capacities through transdisciplinary team science. We will also outline Maine-eDNA’s broader impacts through investments in education, training, commercialization, and outreach to diverse communities.

Environmental DNA: A powerful Tool to Detect the Presence of Target Aquatic Species Across Different Ecosystems and Our Lessons Learned

Jacob W. Riley
Stantec, Topsham, ME

Sampling for environmental DNA (eDNA) has emerged as a reliable and cost-effective method for biomonitoring for species at risk and invasive species. As compared with conventional field surveys, sampling for eDNA is rapid, less labor-intensive, and provides an objective way to confirm species presence or absence. A field-based eDNA sampling and testing tool has recently emerged and provides real-time results in the field. We will compare the pros and cons of this new tool with conventional laboratory eDNA methods and results and eDNA sampling versus traditional aquatic sampling techniques. We will review the results of the proof-of-concept testing that has been conducted on pilot projects to confirm the presence of fish, mollusks, and salamanders in streams, lakes, and vernal pools, in Maine and the Northeast, along with the quality control measures that have been built into the tool to provide reliable results. eDNA is a powerful and sensitive new sampling technology with the ability to detect a single fish in a stream for only 17 hours and 5 fish 1,000 meters downstream in our caged studies, while minimizing costs and impacts to rare, threatened and endangered species and their habitat. We will review examples of how eDNA sampling has been incorporated into Stantec’s fisheries and aquatic monitoring projects to help answer research questions and augment conventional survey approaches to address research questions and lessons learned from these case studies projects.

Invasive Invertebrate Species Detection in Northeast Regional Lakes using Environmental DNA (eDNA)

Denise Blanchette1, Alison Watts2
1. Maine Department of Environmental Protection, Augusta, ME
2. University of New Hampshire, Durham, NH

A video of this presentation is available

In this study we developed and conducted a pilot environmental DNA (eDNA) sampling program for target invasive invertebrate species in northeastern lakes. This project provides proof of concept and initial eDNA data for two invasive invertebrates; Asian clam (Corbicula fluminea) and Zebra Mussel (Dreissena polymorpha). These species are present in some areas of the region and are considered at risk of spread. Improved early detection methods will support timely response and management actions.May through October 2019, samples from 16 sites in six New England Lakes were collected and analyzed. Samples were analyzed by University of New Hampshire using ddPCR.

  • Asian clam analysis successfully detected DNA near known infestations in three lakes, with the concentration decreasing with distance.
  • Zebra mussel analysis detected DNA in a lake with a viable population but detected very low or no signal at sites with smaller infestations, or where an infestation had been recently removed. Concentrations were higher in spring/early summer.
  • Zebra mussel signal in viable populations was highest in May, slightly lower in July, and lowest in October. Sampling in early spring will likely improve detection probability.
  • Asian clam concentration was highest in July and May, and lowest in October. The Asian clam signal may peak slightly later in the spring than zebra mussel.
  • Additional analysis will support the development of occupancy models to estimate sampling design detection probabilities. Re-sample low concentration sites in early spring, taking larger volume samples, and focusing on areas with known colonies to develop low concentration detection methods.

Integrating eDNA Community Analysis into Stream Assessment

Alison Watts, Devin Thomas
University of New Hampshire, Durham, NH

eDNA monitoring in aquatic systems is a potentially powerful tool for assessing fish community, biodiversity, and invasive species presence. In 2019 we sampled 40 stream locations as part of the New Hampshire Department of Environmental Services long term trend monitoring program. 1 liter water samples were filtered onsite, then the DNA was extracted and analyzed for broad eukaryote community (18S) and fish (12S). Attached algae samples were collected, extracted and analyzed for diatoms and other indicative species. We identified over 80 fish species, with up to 37 species in one sample. Replicate samples were highly variable, indicating the need for multiple samples to fully identify a community. Fish community, as identified by DNA, is a function of both the species present, sampling location, and stream transport properties. Smaller streams may retain DNA longer, although sunlight and warmth degrade the signal. Water quality, including natural tannins may inhibit DNA amplification. Once extracted the DNA can be re-run for additional species, and can be frozen for many years in case additional analyses are requested at a later date. We will evaluate the DNA-identified aquatic community represented in water and algal samples with respect to stream and watershed parameters, including temperature, nutrients, land use etc. and will provide recommendations on the use of eDNA-based surveys in stream assessments.

Using Environmental DNA for Endangered Atlantic Salmon Assessment in Streams: From Detection to Delineation

Zachary T. Wood1, Bradley F. Erdman1, Geneva York1, Joan G. Trial2, Michael T. Kinnison1
1. University of Maine, Orono, ME
2. Project SHARE, Eastport, ME

A video of this presentation is available

Managing freshwater ecosystems often requires that we understand the distribution and abundance of species on the landscape. However, this core monitoring need is often highly constrained and costly for endangered species like anadromous Atlantic salmon (Salmo salar). Traditional population monitoring relies on labor intensive capture, requires special permits, and thus can only be conducted by relatively few specially-trained personnel. Environmental DNA (eDNA) testing of stream water provides a promising alternative to survey aquatic species in a more cost-effective, less invasive, and potentially more sensitive way. Here, we use cage experiments with small numbers of Atlantic salmon to examine the relationships between eDNA detection rates and eDNA quantities and downstream distance from fish. We apply our eDNA distance relationships to selection of stream sampling intervals for detecting fish without known locations and find that even a single juvenile salmon can be reliably detected with intervals up to 400 m spacing. We then use these distance relationships to compare paired electrofishing and eDNA data from another stream, and demonstrate the power of eDNA to identify stream sections of highest conservation priority at resolutions < 1 km.

Piloting the Use of Environmental DNA in the Estuarine Environment

Laura Crane1, Jason Goldstein1, Jacob Aman1, Alison W. Watts2, Michael T. Kinnison3
1. Wells National Estuarine Research Reserve, Wells, ME
2. University of New Hampshire, Durham, NH
3. University of Maine, Orono, ME

A video of this presentation is available

Environmental monitoring programs are essential for effective estuarine management, but they are often time-consuming, expensive, and subject to technical and resource limitations. Traditional monitoring methods may also miss early detection of newly arrived invasive species or incorrectly confirm losses of rare native species. Environmental DNA (eDNA) provides a tool for detecting aquatic species and offers a potentially effective alternative (and complement) to traditional techniques that is cost effective and highly sensitive. The Wells NERR, in partnership with universities and other NERRs, is piloting the application of eDNA for monitoring invasive crabs, fish assemblages, and imperiled migratory fish species in Gulf of Maine estuaries. We present results from two case studies: 1) a comparison of eDNA and traditional methods for detecting fish species in the Webhannet Estuary and 2) eDNA detection of invasive green crabs. Results from the first study indicate that different sampling techniques yield variable outcomes and suggest that eDNA can complement traditional surveys to provide a more complete picture of fish assemblages. From our green crab study, we share challenges associated with detecting crab eDNA in estuaries, including laboratory-based results suggesting that life history is a critical consideration for eDNA detection of hard-shelled organisms. Overall, these studies demonstrate that availability of eDNA within the aquatic environment is subject to numerous biological and environmental factors and careful study design is critical for gathering reliable data. Our work illuminates the benefits and challenges of eDNA methods in estuaries and provides a model for adoption by researchers and resource managers alike.

Laying the Foundation for Understanding Sea Scallop Population Dynamics Using eDNA Techniques

Phoebe Jekielek1, Heather Leslie2, Nichole Price3
1. Hurricane Island Center for Science and Leadership, Rockland, ME
2. University of Maine Darling Marine Center, Walpole, ME
3. Bigelow Laboratory for Ocean Sciences, East Boothbay, ME

A video of this presentation is available

Aquaculture is the fastest growing agricultural sector in the world and in Maine, its total economic impact has almost tripled since 2017. Shellfish (bivalve) aquaculture is growing particularly quickly alongside established wild shellfisheries, generating $32.2M in landings for Maine communities in 2018. Unlike most other farmed shellfish in Maine, scallop production lacks a hatchery. Farms rely on successful reproduction and recruitment from the wild fishery, the dynamics of which are not well understood. This creates the potential for conflict but also opportunity to explore the possible contribution of farms to wild scallop populations. Opportunities with newly-developed environmental DNA (eDNA) tools may help elucidate the complex dynamics of larval supply. The Maine eDNA program is designed to engage with commercially important species and the communities they support by advancing ecological understanding of coastal macrosystems to inform ecosystem-based approaches for management. To be successful, it requires fishing and farming community engagement and interdisciplinary cooperation. As part of this effort and partnering with scallop farmers and wild harvesters throughout Maine, we plan to investigate the following questions – Q1: Can scallop aquaculture farms serve as population refugia and restoration areas for wild populations, and if so, how?; Q2: How do wild and farmed scallop populations respond to ecosystem variability and change? This talk will provide an overview of scallop aquaculture and wild harvesting in Maine, a review of previous relevant eDNA work, and propose a four-year research effort to address the questions above.

Communication and Team Science for Maine-eDNA

Bridie McGreavy1, Kaitlyn Haynal1,2, Heather Leslie2, Mike Kinnison3 Jennifer Smith-Mayo1 (Student), Jessica Reilly-Moman2 (Student)

1. Dept. of Communication and Journalism, University of Maine, Orono, ME
2. Darling Marine Center, University of Maine, Walpole, ME
3. School of Biology and Ecology, University of Maine, Orono, ME
4. Ecology and Environmental Studies, University of Maine, Orono, ME

A video of this presentation is available

One of the challenges with strengthening coastal resilience, or the ability for people who live and work in coastal communities to respond to changes in marine ecosystems and economies, is the number of data gaps. A host of partners in state agencies, tribal governments, non-profit organizations, and coastal communities have identified the need for environmental-DNA (e-DNA) to help fill these data gaps, especially for fisheries and water quality. For example, being able to detect the presence and extent of harmful algae blooms would help shellfish managers make informed decisions about the length and extent of “red tide” closures. However, eDNA is a new tool that requires multiple forms of knowledge to develop and apply it in scientifically-rigorous and socially-relevant ways. While eDNA offers unique opportunities to increase citizen participation in data collection and sharing, applying this tool also requires new forms of collaboration and relationships among partners. An engaged and solutions-oriented approach to eDNA applications also needs to fit partner decision-making needs, respond to questions that matter, use methods that fit the context, and share research products in ways that are timely, applicable, and accessible. The Maine-eDNA project recognizes that communication is at the heart of building such collaborations and we are using team science to work across disciplines and with diverse partners to build eDNA knowledge together and shape science-based tools so they are meaningful and applicable. In this presentation, we share key elements of our communication and team science research design and highlight initial insights from our ethnographic and engaged research that helps shape our collaborative approach to developing eDNA knowledge with and for coastal communities.