Maine Environmental DNA initiative advances coastal ecosystem sustainability

University of Maine researchers and collaborators are leading the way in an emerging field that combines environmental science and genetics, revolutionizing how scientists understand and monitor our state’s 3,500 miles of coastline that our marine ecosystems depend on.

Through a $20 million EPSCoR Research Infrastructure (RII) Track 1 award from the National Science Foundation in 2019, UMaine established the Maine Environmental DNA (Maine-eDNA) initiative.

The five-year initiative is co-led by researchers from UMaine and the Bigelow Laboratory alongside local industry leaders and collaborators in education and government agencies across the state.

“Maine-eDNA is a state-wide, multi-institutional initiative establishing Maine as a national leader in environmental monitoring, ecological understanding and sustainability of coastal ecosystems through research, education and outreach,” says principal investigator Kody Varahramyan, UMaine vice president for research and dean of the graduate school. “It addresses the statewide workforce needs in critically important areas including biotechnology, ecology, environmental and data sciences.” Co-PIs include Kate Beard-Tisdale, David Emerson, Michael Kinnison and Heather Leslie.

Organisms leave traces of DNA, the universal code for life, wherever they go. These fragments are called environmental DNA, or eDNA. Much like a genetic fingerprint of an ecosystem, these traces can be collected, identified and linked to those species.

Analyzing tiny fragments of DNA in the air, water and soil provides scientists with information that can help inform policymakers and industry leaders of rapid changes to critical ecosystems. The state’s fisheries and other resources in the Gulf of Maine have faced significant challenges due to harvesting, dams and climate change. 

The new program focuses on two pressing issues for the coast of Maine: sustainable fisheries and harmful species. Sustainable fisheries research includes studying the outcomes of large-scale restoration efforts and unraveling the complex early life cycles of economically important species like lobster. Work on harmful species includes developing early warning systems for toxic algal blooms and forecasting the spread and impacts of invasive species.

Researchers quickly identified the need for advanced testing services that serve academic, government, industry and non-governmental organizations and leveraged the RII Track-1 award to establish the Environmental DNA Laboratory through UMaine’s Coordinated Operating Research Entities (CORE).

“The lab plays a major and enduring role in the eDNA analysis pipeline that can support data sharing and reanalysis for current and future research. Establishing the pipeline is a major step to not only achieving the project’s goals but also for eDNA to achieve its long-term potential,” explains Kinnison, a professor of Evolutionary Applications at UMaine’s School of Biology and Ecology.

Kinnison also serves as the director of the Maine Center for Genetics in the Environment (MCGE). The center was established to provide infrastructure for interdisciplinary research, innovation and training. Collaborations and partnerships built under the Maine-eDNA program now have a permanent home. 

“The Maine Center for Genetics in the Environment is first and foremost a community of researchers and others who see the transformative value of genetics and genomics in environmental sciences,” Kinnison says. “Environmental genetics can do a lot to support Maine’s current natural resources industries, from fisheries to forestry, agriculture, energy production and tourism, while at the same time building Maine’s capacity in biotechnology and information technology.  In that sense, MCGE is a bridge between the old and the new, and I think we bring something exciting to the table for most Mainers.” 

The center is establishing a growing reputation for translating cutting-edge science into real-world applications. Recently MCGE was awarded funding that moves beyond their typical marine research—monitoring mosquito expansion and disease outbreaks through eDNA. “We are Maine’s environmental genetics resource,” Kinnison says.

Through its robust network, the program has also created opportunities for statewide outreach. Members with expertise in K-12 education work to deliver eDNA curriculum toolkits for teachers to use in classrooms and help to educate students about STEM career pathways. Over the course of the five-year grant, thousands of Maine students will be engaged.

Heather Leslie, professor in the School of Marine Sciences and director of the Darling Marine Center, noted that the prominent role of social science research within the Maine-eDNA Project has not only been exciting for the team but also for the National Science Foundation. 

“From the very beginning of this project, the social sciences and social scientists have been integral to how we have formulated our research projects, student training, and also engagement with community, government and private sector partners,” Leslie observed. “NSF noted that this explicit social science research component was unusual for previous Track 1 awards and that this was one of the reasons our project was deemed worthy of support.”

Kate Beard-Tisdale says, “For Maine-eDNA we have developed a comprehensive metadata database that tracks information covering field sampling, wet lab processing, sequencing and bioinformatics analysis steps. We did not find any similarly comprehensive metadatabases in the field so we feel this is a key contribution not just to Maine-eDNA but to the broader community.” Beard-Tisdale is a professor in the School of Computing and Information Science and a research faculty member with the Spatial Data Science Institute.

This year, researchers partnered with the New England Aquarium to analyze eDNA in a controlled setting. Their findings offer new insights into the effectiveness of eDNA methods and suggest that they can not only describe which species are present but also how their population sizes vary over time.

With these tools, researchers can study the structure and function of marine food webs, and shifts in species, and evaluate fisheries stocks and restoration efforts around the state. These findings set the stage for many future studies of commercially, recreationally and culturally important species in the Gulf of Maine.  

In just three years, the Maine-eDNA grant has had a profound impact. The new program has brought greater focus to sustaining coastal ecosystems and provided opportunities for new collaborations with organizations such as the Environmental Protection Agency, Maine Department of Transportation, Maine Department of Inland Fisheries and Wildlife and Wells Estuarine Research Reserve. “I think the most exciting thing about Maine-eDNA is that it brings together institutions that have similar aspirations to learn more about the environment,” says Peter Countway, a senior research scientist at the Bigelow Laboratory for Ocean Sciences.

The program has also had a significant impact on workforce development. It is currently supporting 30 faculty, nine technical staff, three postdoctoral fellows, 26 graduate students, and 35 undergraduate students, located at research sites across the state.

“Maine-eDNA is equipping the next generation of environmental researchers and the coastal industry’s workforce with advanced DNA technologies and skills,” says Shane Moeykens, director of Maine EPSCoR and associate project director of Maine-eDNA.

The program reflects a major interdisciplinary research achievement uniting educators, researchers and students. It sets the stage for long-term monitoring of biodiversity patterns and changes along the coast, a vital part of Maine’s economy.

Visit the Maine-eDNA website to learn more. 

RII Track-1: Molecule to Ecosystem: Environmental DNA as a Nexus of Coastal Ecosystem Sustainability for Maine (Maine-eDNA) is supported by National Science Foundation award #OIA-1849227 to Maine EPSCoR at the University of Maine.


Written by Ally Cooper and Tilan Copson