Establishing Maine as a leader in environmental genetics

Awarded in 2019, the NSF EPSCoR RII Track-1 Maine-eDNA project has reached the conclusion of its NSF funding. The program, which investigated Maine’s coast, inland lakes and the waterways in between, championed environmental DNA (eDNA) as a powerful and cost-effective approach to monitoring an environment as small as a stream to as large as Maine’s coastline. Maine-eDNA Co-PI Michael Kinnison, University of Maine professor of evolutionary applications remarked, “The real power that we were seeing for eDNA is being able to look at the biology of the Maine coast at not just local but by very large scales that span habitats. That sort of snapshot of the coastal system is broadly something that’s really hard to get a handle on with other approaches.”

Bigelow Laboratory for Ocean Sciences Senior Research Scientist and Geomicrobiologist David Emerson served as a Co-PI for Maine-eDNA and authored the white paper that developed into the project’s proposal. “There are three things that really excite me about eDNA. Scientifically, it is the opportunity to study all organisms, from microbes to whales, within an ecosystem to see how they interconnect; collaboratively, it is the opportunity to work together with researchers from many different disciplines using a common language, DNA, and practically, it is the opportunity to develop an important new tool for ecosystem management and sustainability,” explained Emerson.

This genetic tool leverages the DNA shed by organisms in their environment. Researchers take a sample from the environment, in the case of Maine-eDNA as little as a liter of water, and, depending on method, identify the likely presence of a specific species or range of species in the vicinity. While like any technology there are tradeoffs, this allows researchers to accurately detect species presence in a relatively unobtrusive manner that does not rely on visual identification.

Researchers across Maine saw potential in the technology. “We saw an opportunity to push an emerging technology forward, become a leader in the field and benefit the lives of Mainers,” explained Kody Varahramyan, Maine-eDNA PI and UMaine Vice President for Research and Graduate Studies. “Maine-eDNA’s achievements exemplify the power of partnership and collaboration.”

eDNA technology has developed quickly over the past decade. When the original proposal for Maine-eDNA was in its infancy, researchers were exploring the capabilities of eDNA and interested in finding more applications, but the depth of real-world applications was limited. Fast-forward to 2024 and the President’s Office of Science and Technology Policy released their National Aquatic Environmental DNA Strategy which directs government offices to invest resources in the technology. During the interim years it was projects like Maine-eDNA that pushed the technology forward by improving methodologies, standardizing approaches, making data accessible to others, and pushing the scope of application into new areas.

Maine in many ways was a perfect testing ground as the technology offered a way for researchers to survey the vast expanse of Maine’s waters over the course of several years at a fraction of the price presented by other approaches. A survey of this size also demands the standardization and ground truthing the technology needed. Maybe most importantly, the project put eDNA technology in the hands of students, researchers, resource managers, businesses and other stakeholders through outreach and collaboration.

While the COVID-19 pandemic created new barriers to performing research, it likely increased adoption of eDNA. On mass, people were seeing the proliferation of DNA testing and learning what the technology was capable of as it became the gold-standard for COVID detection. Suddenly, people were familiar with the notion that PCR testing could detect small amounts of DNA from organisms we couldn’t directly see, which made adoption of the technology easier.

One avenue of uptake was through community groups concerned with harmful algae blooms (HABs). Many Maine communities have lakes that serve as water supplies or centers for recreation. When an algae bloom appears it can be hard for these small community groups to identify the bloom and determine if it is a HAB and if so what type in order to react to it. Working with Maine-eDNA researchers at the Bigelow Laboratory for Ocean Sciences, groups such as Wolfeboro Waters were able to purchase and use eDNA testing equipment to monitor blooms in their communities.

Mentorship was a feature of the Maine-eDNA program. With over 30 graduate students, primarily seeking Ph.D.s, their research enriched nearly every aspect of the project. Graduate students conducted their own research, drove Maine-eDNA’s vast coastal sample collection efforts, and helped guide the project’s undergraduate interns as they entered the world of eDNA for the first time. These students’ research was helping define eDNA’s strengths and weaknesses through trial, error and innovation. Kinnison reflected, “You don’t always learn what you set out to learn, but you learn something.” While this can be frustrating, it is a crucial element to developing as a researcher and pushing an emerging technology forward.
Recognizing that powerful new technologies can come with unintended consequences, Maine-eDNA researchers found common interest in advocating for ethical principles in this emerging field. Anticipating the possible ethical pitfalls presented by a transformative technology is critical to utilizing it equitably. While it is a time consuming pursuit to look at such potential problems from multiple angles, it is also an essential one, especially given the historic misuse of genetics in ways that sometimes harmed marginalized peoples. This work took the form of classes, working groups and investment in data sovereignty principles in collaboration with international programs like Local Contexts.

In addition to developing new eDNA tools and insights into the Maine’s coast that will be used for many years to come, one of the greatest achievements of Maine-eDNA was to set a genetic sample and data baseline for Maine’s coast.. Maine-eDNA’s Index Site samples and data of lake, estuary, and coastal environments across Maine will be the genetic reference point to which Maine’s changing coastal systems will be compared for the foreseeable future.

This work will be continued by the Maine Center for Genetics in the Environment (MCGE), one of Maine-eDNA’s primary outcomes. Kinnison, MCGE’s director, explained, “MCGE marries Maine’s long term, well-established natural resource industries to modern data, technology, genetic technology, biotechnology, type tools.” The center serves as a steward of the technology and a place people know they can turn to when they seek insights from eDNA.
The Maine-eDNA project in some ways only scratched the surface of what eDNA can do. Focusing on aquatic environments leaves the vast terrestrial world to explore through the lens of countless disciplines where eDNA is also emerging. MCGE hopes to bridge that gap. “The center is something that could bring people from all across the UMaine campus and across institutions in Maine together,” remarked Kinnison. “We are building and nurturing a community of people who see these opportunities.”

So while Maine-eDNA has completed its work, there is so much more to do. The program established eDNA as a powerful tool for understanding Maine’s aquatic ecosystems. These new insights are helping resource managers, communities and other stakeholders make informed decisions about the environments they work with. The MCGE will continue to be a resource for partner organizations like the Gulf of Maine Research Institute who were able to stand up their own molecular lab by drawing on the expertise within the larger Mainee-eDNA program. “The community of practitioners that has arisen as a result of Me-eDNA will continue to be a force multiplier for propelling the technique into the future of coastal and fisheries management in the Gulf of Maine,” said Graham Sherwood, a senior scientist at the Gulf of Maine Research Institute], Maine-eDNA’s work will carry forward through the work of MCGE and everyone involved with Maine-eDNA throughout its length.

If you are interested in potential applications of eDNA for your business, community, or education, please reach out to the Maine Center for Genetics in the Environment at MCGE@maine.edu.