His work in Maine exists at the intersection of different industries, working to understand how Maine’s communities interact with one another. In addition to working on the NSF EPSCor Maine-FOREST project, he is also a trainee in the NSF National Research Traineeship: 3D Ecosystem Science program. 

“I’ve gained experience in Maine’s local industries, first on waterfronts and now in forests. It’s important to understand the differences between coastal and forestry-based communities, and how they interact with each other,” said Colbert Stone. 

Colbert Stone, a self-described “convener,” focuses on bringing people and organizations together to best support one another and create meaningful change. Originally from Ohio, Colbert Stone began his academic career at Denison University, earning a bachelor’s degree in Black Studies and Women’s and Gender studies. He joined 91±¬ÁĎ’s Anthropology and Environmental Policy Master’s program to merge his past interests with his future career goals in the environmental sector. 

While in Maine, Colbert Stone has been involved with multiple organizations that work to increase environmental stewardship across the state while supporting local communities. As a research assistant with Maine-FOREST, he is currently involved with research on rural communities and youth education. Working with Dr. Lydia Horne and Dr. Sandra De Urioste Stone, he researches rural and tribal communities and how they can educate students for the future. The research team partners with Rural Aspirations Project, a Maine nonprofit that empowers students in rural schools to engage in their communities with place-based projects. 

The goal is to support forest communities by strengthening educational opportunities and student community engagement through the Rural Aspirations Project. He is currently interviewing community partners, teachers and administrators involved with the Rural Aspirations Project and the Maine Forest Collaborative to better understand rural education and environmental stewardship. 

“Their theory of change is that rural schools are one of the only places that rural communities have left to get together as a community and have real outcomes and change. So using the school as an avenue for rural vitality, empowering kids to know that they have a future here in Maine and don’t have to leave to attain their goals. It’s been really nice getting to work with them,” said Colbert Stone. 

Beyond his work as a researcher, Colbert Stone has further contributed to the Rural Aspirations Project through his own connections. As a recipient of a Changemakers Fellowship from the Maine Environmental Education Association, he received funding for a community project of his choice. He directed those funds to support a new school participating in the Maine Forest Collaborative, a program of Rural Aspirations Project. This program allows students to create place-based community projects relating to sustainability and forest management. 

Working with an eighth-grade class at Piscataquis Community Secondary School, he helped expand a project on maple tree awareness. Building on students’ experience with maple tapping, the class is planning a community event to highlight the cultural and historical significance of maple trees, including connections to Wabanaki traditions.

“It felt like a win for everybody,” Colbert Stone said. “The students receive the funding directly and gain experience managing a project themselves.”

This work is part of Colbert Stone’s mission to engage with Maine’s vital industries, such as the forest and marine sectors. After graduating this spring, Colbert Stone will become a community engagement associate with the Maine Women’s Lobby, focusing on research coordination and community organizing. 

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 91±¬ÁĎ 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 91±¬ÁĎ 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.

Even though the award period of the NSF EPSCoR Track-1 Maine-eDNA project comes to completion on December 31, 2024, the researchers involved remain as busy as ever going through data samples. One of these researchers is Yasmina Shah Esmaeili, a postdoctoral fellow bringing together previously collected data to reveal how kelp forest biodiversity has changed through space and time. Shah Esmaeili spent her undergraduate and master’s program studying in Belgium before heading to Brazil to earn her Ph.D. After completing a position at the Smithsonian Environmental Research Center in Maryland, Shah Esmaeili joined Maine-eDNA as part of Douglas Rasher’s lab at Bigelow Laboratory for Ocean Sciences.

Shah Esmaeili is developing a manuscript examining the overlap between eDNA and visual census data. The research brings together observations, eDNA data, and environmental data to reveal changes in kelp biodiversity and discover the emergence of “species on the move,” the forced movement of species due to human-caused climate change. Shah Esmaeili is also looking at how well four DNA primers helped detect species and which taxonomic groups are represented in the survey methods. These primers, or eDNA markers, are single-stranded DNA fragments used as a laboratory tool for detecting species. Each primer Maine-eDNA used is suited to detect a particular taxonomic group, a category of organisms based on shared characteristics. “Using a combination of multiple primers results in a clearer and more comprehensive picture of the overall diversity in an ecosystem,” Shah Esmaeili explained. These methods allow researchers to detect more species than traditional visual surveys. However, visual surveys are still needed to validate eDNA findings, and to identify some ecologically and economically important species that evade eDNA detection. Using multiple primers is costly, which makes Shah Esmaeili’s work more essential. She hopes her studies will validate the use of eDNA in biodiversity assessments, find what drives regional patterns in biodiversity across species, and identify which primers are essential to capture the majority of biodiversity in an area.

For eDNA to be effective, it must be matched to a species identified by taxonomists. As long as these references are publicly available on databases such as GenBank, researchers can use them. However, despite their importance, references are not always accessible to scientists, proving a challenge to finishing research, one Shah Esmaeili has faced.

“Applied research is becoming more and more important over the years since research is being used as a foundation for management decisions,” Shah Esmaeili remarked. Especially as climate change forces people and companies to change their behavior, research such as what Shah Esmaeili and Maine-eDNA are doing becomes increasingly relevant and crucial. “People commonly assume Maine’s kelp forests are species-poor, but eDNA has revealed that Maine’s kelp forests are quite speciose,” Shah Esmaeili said. However, as this diversity declines in the gulf and worldwide, the loss has serious consequences that are beginning to impact humans. Kelp are foundation species that provide food and shelter to many species, fueling the coastal food web, and as it begins to change, other species begin to drop out of the ecosystem. These changes can be seen in the data sets collected by Maine-eDNA and in previous data available through the Rasher Lab’s work.

The changes to the Gulf of Maine ecosystems are happening in real time, emphasizing the importance of Shah Esmaeili’s work with long-term data sets. “We need to understand how and why changes are occurring before we can come up with solutions,” Shah Esmaeili said. “That is the baseline of the work we are doing.” As Shah Esmaeili continues to go through the data sets, she expects to find more interesting revelations that will hopefully contribute to knowledge of, and a solution for, Gulf of Maine biodiversity.

River herring have and continue to play an economically, ecologically and culturally important role in Maine. These fish are anadromous, meaning that they migrate from saltwater to freshwater to spawn. Through their annual migration, river herring help drive the exchange of nutrients between fresh and marine waters. By studying their migration patterns and their favored zooplankton species, researchers such as Bengs can predict the preferred migration regions of river herring through their eating habits. 

As part of her research, Bengs works with Maine-eDNA’s partner the Gulf of Maine Research Institute (GMRI) and their Casco Bay Aquatic Systems Survey (CBASS) to assess juvenile fish populations from the Presumpscot River to the West Cod ledges in Cumberland County, using a variety of sampling methods. CBASS is a long-term ongoing aquatic surveying project that GMRI has conducted for over 10 years. Bengs collects environmental DNA (eDNA) samples to assess the presence of the river herring and zooplankton in the area and conducts gut content analysis of juvenile river herring to understand their preferred species of zooplankton. eDNA is the genetic material that is extracted from a water sample of a specific region in order to detect the presence of a species without handling or seeing the species itself. This sampling method allows Bengs to compare the location of river herring populations to concentrations of different species of zooplankton. Across Maine, researchers like Bengs are using eDNA methods to better understand the recovery of river herring but the approach is not without its limitations.

“It’s important to understand the limitations of any sampling method” explained Bengs. “With eDNA you can get a snapshot at some point in time which can work well for some situations, but if you are looking for a longer time series you would want to explore other options.” One solution that Bengs is experimenting with is 3D-printed metaprobes that can collect eDNA passively at various steps for hours at a time. These metaprobe devices are being tested by Bengs to see if they can increase the odds of detecting river herring eDNA signals so they can estimate in-and-out migration behavior more effectively. Bengs’ research with metaprobes can be used to improve eDNA testing efficiency for researchers across Maine. 

Bengs’ research elucidates river herring’s migrations and diets which allows us to understand their recent recovery as a species and helps ensure the previous conditions that contributed to their initial decline are not repeated. By understanding where and when they migrate, communities can take steps to make the migration easier and help restore their local ecosystems. 

As the Gulf of Maine warms, new species, invasive and not, are moving in. The delimitation between invasive and noninvasive species can be difficult to discern. At a simple level, it can be the level of human involvement in the species movement. For example, the European green crab made its way via ship from coastal Europe and North Africa to the Gulf of Maine, where they tear up eelgrass beds, posing a threat to the species that rely on them. Contrary to this is the blue crab which while new to the Gulf of Maine is native to the United States’ eastern coast. This species began migrating northwards into Maine as the Gulf of Maine and surrounding waters warmed rapidly. 

As a member of the National Science Foundation EPSCoR RII Track-1 Maine-eDNA project, recent doctoral graduate Emily Lancaster set out to determine the temperature ranges where these organisms of interest thrive. Based at the University of New England (UNE), and advised by Markus Frederich (UNE, professor of Marine Sciences) and Damian Brady (91±¬ÁĎ, Agatha B. Darling professor of oceanography), Lancaster explored the physiology, specifically thermal tolerance of both the European green crab and the Asian shore crab, as well as the development of environmental DNA (eDNA) detection technology for nine species of interest in the region. Using eDNA, the genetic material shed by an organism in the environment, helps researchers like Lancaster detect species without having to physically see them. 

The research began by testing the two crabs’ biological limits such as their heart rates within the maximum and minimum temperatures that these crabs can survive. Through these experiments, Lancaster found evidence that might be contributing to both species’ adaptation to the temperatures here in the Gulf of Maine. She discovered that the crabs shift the temperatures that they thrive at down in the wintertime so that they’re able to be a bit more flexible with their physiology. Using this information, Lancaster was able to determine each species’ ability to thrive in Maine’s coastal waters. “To thrive in this context is to reproduce, grow, and go about their daily activity,” explained Lancaster.

Invasive species like these can be highly destructive to Maine’s ecosystems and fisheries economy. The Asian shore crab is an opportunistic omnivore and feeds on just about anything it can get its claws on, including other crabs, posing a threat to native species. Early detection is crucial for eradication, containment, or long-term management of an invasive species. Lancaster’s work lays the groundwork for future investigation into the spread of invasive species, their adaptation to new environments, and their impact on the surrounding ecosystem. Studying the temperature ranges at which an invasive species can thrive, researchers like Lancaster could predict who will arrive in Maine next.

In addition to her work with crabs, Lancaster investigated the use of eDNA tools to detect nine species of interest. Lancaster found that eDNA detection tools for invertebrates must be carefully validated in the laboratory before deploying them in the field. These invertebrates could be divided along a textural line. Lancaster split them into two groups, squishy and crunchy. The squishy species, with little to no exoskeleton and exposed flesh, could generally be detected using eDNA data. The crunchy species, with harder exoskeletons and little to no exposed flesh, were in contrast far less detectable using eDNA. Researchers have long understood eDNA as a tool that in tandem with other methods can be incredibly powerful for species detection. Her work with invertebrates helps make researchers’ understanding of that more robust as they try to understand the plethora of new and existing species moving in and out of the Gulf of Maine.

Lancaster defended her dissertation on May 15, 2024 and is the most recent Maine-eDNA graduate student to achieve this, with more successful defenses expected in Maine-eDNA’s final months. During her tenure with Maine-eDNA, Lancaster became increasingly involved in the program’s outreach mission in addition to her research, teaching courses at Southern Maine Community College and UNE as well as leading and participating in a number of K-12 STEM experiences. This fall, Lancaster will begin her post Maine-eDNA career at Eckerd College in Florida, teaching invertebrate zoology and starting her own eDNA lab. 

While not as expansive as the renowned kelp forests of California and other parts of the world, the Gulf of Maine (GoM) is also home to a diverse kelp forest ecosystem on its rocky reefs. These out-of-sight underwater forests are known to foster biodiversity, providing vital resources and habitats for various marine organisms. Unfortunately, the GoM has been warming at a rapid rate. Because kelp thrives in cool, nutrient-rich water, the warming waters have led the once-thriving, three-meter-tall kelp forests to be replaced by red filamentous turf algae, which only stands a few centimeters tall. This ecosystem shift is analogous to a forest being flattened to grassland. 

Researchers at Bigelow Laboratory for Ocean Sciences are working to explore the effects of this transformation in the GoM as part of the NSF EPSCoR RII Track 1 Maine eDNA project. These researchers include Shane Farrell, a Ph.D. student studying Marine Biology at the 91±¬ÁĎ, Orono who is co-advised by Damian Brady (Agatha B. Darling Professor of Oceanography, 91±¬ÁĎ) and Doug Rasher (Senior Research Scientist, Bigelow Laboratory). For the past three years, Farrell has been focusing on how this habitat transition from kelp-dominated to turf-dominated reefs impacts the ecosystem. His research is a part of the Maine-eDNA “Species on the Move” theme, which, in part, examines the effects of range shifts in foundational taxa, such as kelp, on ecologically linked processes along the coast.

To document changes in these ecosystems, Farrell integrated both visual SCUBA surveys and environmental DNA. “By merging visual surveys and environmental DNA (eDNA) sampling, it allows us to infer the most out of the system,” Farrell explained. For the past three summers, Farrell and the Rasher lab conducted visual SCUBA surveys, observing changes in the algal, fish, and invertebrate communities, along Maine’s coast. During those dives, they also collected eDNA which allows Farrell to identify the presence of species that are overlooked during traditional visual surveys, including cryptic and invasive species. Additionally, he has been gathering samples of benthic microbial biofilms and water samples for chemical analysis to try and understand how microbial communities and chemical landscapes change on turf-dominated reefs. Ultimately, he is trying to identify possible chemical cues that could have detrimental impacts on the recruitment and settlement of kelp in these turf-dominated ecosystems.

While Farrell’s research is ongoing, it has already revealed some key takeaways. Firstly, he has observed that this shift from kelp-dominated to turf-dominated reefs is happening much more rapidly than anticipated. He has also noticed that these shifts are occurring further East than ever before. “We are seeing this shift happening as far East as Penobscot Bay now. Just five years ago, it was confined to Casco Bay,” he highlighted. A second key finding is that this transition has led to significant differences in the microbial and chemical communities. Farrell observed that as kelp declines, there is a proliferation of red turf algae. According to Farrell, “In other systems, like coral reefs, it has been shown that when macroalgae and red turf algae proliferate, it is detrimental for the ecosystem.” This is because red turf algae are known to produce organic chemical compounds known as exudates. As the abundance of red turf algae increases, so does the release of these chemical exudates. “These exudates have the potential to limit the settlement and survival of kelp on the reef, ultimately limiting their recovery and resilience,” he elaborated. This creates feedback loops that perpetuate the shift towards turf dominance. Farrell’s research highlights a potential new mechanism known as “chemical warfare” creating these feedbacks. Farrell is interested in exploring this mechanism further and understanding what this means for the ecosystem. 

This research has implications for marine ecosystems worldwide. As Farrell noted, “These habitat shifts on reefs are not just happening here in Maine, but around the globe.” The observed transition to turf dominance is a common thread among various ecosystems, as exemplified by occurrences in Norway, the Northwest Atlantic, and parts of Australia. “We need to understand here in Maine, and globally, what the implications of this shift are,” he emphasized. This is a central focus of the Rasher Lab, with research spanning the kelp forest fish communities and population genetics of kelp, to investigating the role of chemicals and microbes.

Farrell’s research has opened up numerous avenues for future research. There are still many questions that he has yet to answer, such as the driving forces behind the spread of red turf algae. While increased nutrients, warming waters, and faster growth rates are potential factors, he points out that there is a lack of studies investigating the effects of environmental conditions on turf spread. Moreover, there is a pressing need to identify chemicals and their sources on these reefs. “We are finding almost 20,000 unique chemicals from various sources, but we only know the identity of 2.5% of the chemicals there,” said Farrell. Exploring and identifying new chemicals is crucial in understanding species interactions and ecological dynamics. There are also some human applications for identifying new chemicals. For instance, Farrell mentioned that when it comes to the pharmaceutical field, many antibiotics and anti-cancer drugs on the market today come from marine ecosystems like coral reefs, while temperate systems are still underexplored. 

This habitat shift is not only altering the landscape of the GoM but also the landscape of rocky reefs all over the globe. As we strive to understand and mitigate the effects of climate change on marine ecosystems, Farrell’s work underscores the urgency of addressing these habitat shifts and identifying their implications for the health and resilience of rocky reefs worldwide.

In the vast expanse of the Earth’s ocean, our planet’s largest ecosystem, lie countless mysteries that have yet to be explored. Dedicated to uncovering such mysteries is Jamie Fogg, a sophomore studying Marine Science at the 91±¬ÁĎ.

Fogg began exploring marine biology during high school when she was involved in a program that selected her to go to Mount Desert Rock and develop her own research project. She documented wounded seals and presented her research at the Maine Science Fair, where she was awarded the Maine Top Scholar Award.

She was introduced to the world of environmental DNA (eDNA) during her first year at 91±¬ÁĎ under the mentorship of Kristina Cammen, associate professor of marine mammal science. “I had no idea what eDNA was before,” Fogg explained. “But the Cammen Lab mostly focuses on utilizing genetics to understand marine ecosystems, and eDNA is a significant part of it.” In the Cammen Lab, Fogg has engaged in a diverse array of research activities, contributing her expertise to ongoing projects exploring various aspects of genetics and eDNA analysis for marine species.

Working in the lab opened the door to opportunities with the NSF EPSCoR RII Track-1 Maine-eDNA project. This past summer Fogg completed a Maine-eDNA internship that split her time between 91±¬ÁĎ and Hurricane Island near Vinalhaven, Maine. In this position, she worked alongside Maine-eDNA Ph.D. Candidate Phoebe Jekielek, who aims to develop eDNA tools to help researchers better understand population dynamics, such as the reproductive and larval ecology of scallops, both in aquaculture and wild populations along the coast of Maine. 

Fogg and Jekielek collected both physical plankton samples, as well as eDNA water samples. In the lab, they counted how many scallop larvae were present in the plankton samples, while also conducting eDNA extractions and then performing qPCR analysis from the extractions to detect and quantify the presence of scallop larvae DNA in the sample. By following this procedure, they will be able to compare the number of scallop larvae in the water, as determined by the plankton samples, with the results of the qPCR data, which allowed them to assess the accuracy of the eDNA analysis in detecting the presence of scallop larvae. In addition to the physical plankton samples and eDNA water samples, they collected environmental data, including water turbidity, temperature, depth, and other measurements. Fogg is currently finishing her scallop enumerations. 

While their data analysis is not yet complete, Fogg emphasized the potential implications of the research findings. “I think a big part of this project’s goal is producing research that is tangible to local fishermen,” explained Fogg.  Jekielek’s work is inspired by the emerging scallop aquaculture industry. Her goal is to use findings to engage with and better inform members of the aquaculture industry, to ensure the industry’s long-term sustainability and adaptability.

One dimension of this they are exploring is how different types of seabed substrates impact scallop spawning. “We compared samples from two distinct sites: a soft bottom area and a rocky bottom site,” Fogg explained. One of these areas was near an aquaculture farm, representing cultivated scallop beds, while the other resembled natural scallop habitats. This comparison allows them to gain valuable insights into the differences between aquaculture and natural environments and how they may impact scallop populations. These insights could range from variations in scallop growth rates to differences in shell density or nutrient availability. Such discoveries hold the potential to inform and enhance aquaculture practices.

Fogg’s Maine-eDNA internship has been a rewarding experience. She appreciates the hands-on learning experience and has developed new technical skills,  and the experience led her to be more confident as a researcher. Fogg shared her personal growth experience, stating, “It has helped me really nail down that this is where I want to be, as well as visualize a future for myself in this field.” Fogg was the only Maine-eDNA intern assisting Jekielek in 2023, and while Jekielek is based at Hurricane Island, Fogg spent much of her summer stationed at the lab at 91±¬ÁĎ. “Phoebe would come to the lab and teach me a protocol, such as how to do a DNA extraction, and then I would repeat it independently the next day,” Fogg explained. “That definitely helped me gain more independence, as well as confidence.”

In addition to her work with the Cammen Lab and Maine-eDNA, Fogg’s scholarly pursuits have been recognized with a prestigious grant from 91±¬ÁĎ’s Center for Undergraduate Research (CUGR). Through her CUGR-funded research, Fogg is investigating the oceanographic aspects of marine ecology, with a specific focus on gray seal eDNA. She aims to determine the limitations of this technology for detecting the animals in coastal waters, facilitating the non-invasive monitoring of marine mammal populations. This research provides valuable insight into the conservation and management of marine ecosystems and the capabilities of eDNA technologies. “It is really cool how relatively new these methodologies are, and how we are still developing and improving them,” Fogg expressed. She finds herself drawn toward eDNA because of its non-invasive factors, and she emphasizes its crucial role in revolutionizing environmental monitoring. Fogg recently presented her CUGR research at the 91±¬ÁĎ’s annual student symposium and achieved first place in the natural science category. Additionally, she has recently been awarded the NOAA Hollings Scholarship, which will provide further research opportunities. She expressed that her experiences with the Cammen Lab and Maine-eDNA have undoubtedly helped prepare her for this prestigious scholarship. As Fogg looks ahead to her journey in research, fueled by her fascination with marine ecosystems and the innovative potential of eDNA technologies, she envisions pursuing a Ph.D. and continuing to contribute to the advancement of marine science.

The Gulf of Maine (GoM) is warming rapidly, and ecosystems contained within, including Maine’s rocky reefs, are undergoing significant changes. The kelp forest habitats along Maine’s coast are transitioning to red algae turf reefs. These kelp forests stand from one to a few meters tall that fish and other organisms swim through, hide in, and gain nutrients from. When these forests disappear they are replaced by red algae which only stands a few centimeters tall.

Researchers at Bigelow Laboratory for Ocean Sciences with the NSF EPSCoR RII Track-1 Maine-eDNA project are trying to understand this transformation in the GoM. One of those researchers is Dara Yiu, a 91±¬ÁĎ Ph.D. candidate in Marine Biology advised by Bigelow Senior Research Scientist Doug Rasher and Associate Professor of Marine Mammal Science Kristina Cammen. Her research focuses on the ecological role of fish communities in these rocky reefs and how these communities are impacted by this habitat transition.

Explaining, Yiu said, “We know that these reef ecosystems are changing in the GoM, but we need to evaluate how much they are changing, and the impact of this change on both energy channels and ecological niches of reef communities.”

Essential to this is understanding the importance of Maine’s kelp forests on its animal communities. However, most existing research on kelp forests is based in the Eastern Pacific. The relationship between fish and kelp forests in the North Atlantic is far less studied. Kelp forests in the Eastern Pacific differ structurally from those in the North Atlantic, so we cannot assume that their ecological importance or roles in their communities are the same. Yiu explained, “We know from other kelp forest systems that kelp is really important for fish as habitat, but no one really knows if that’s true for kelp forests in the Gulf of Maine.”

Based at Bigelow Laboratory, Yiu is working to quantify the degree to which this habitat change is impacting Gulf of Maine reef fishes, to determine if the loss of kelp and change in reef habitat is affecting the structure of these fish communities or the ecological niches they occupy.

To quantify the change in the reef communities, Yiu assessed reef communities along the coast of Maine using visual surveys and environmental DNA (eDNA) metabarcoding to estimate fish species diversity. The visual surveys, conducted via scuba diving, identified a low species diversity, with cunner and pollock being the main species found across the coast and in both kelp forests and turf reefs. eDNA metabarcoding complemented these surveys by detecting unseen or rare species. This combined approach gives a more multifaceted representation of the fish present at these study sites. Comparing the fish species in kelp-dominated to that of turf-dominated reefs will demonstrate if these two distinct habitats host different fish communities, which can help us understand how this habitat transition impacts communities and species diversity.

The loss of kelp forests can impact fish communities by shaping the species that live there if the fish directly use kelp for habitat. But it may also indirectly impact the ecology and energy dynamics of reef fishes if fish depend on kelp forests for their food or energy. To assess the possible effects of the habitat change on the reef community ecology, Yiu collected fish and invertebrates from places with robust kelp forests in Downeast Maine, as well as from places like Casco Bay, that have turned into turf reefs. Currently, Yiu is working to analyze these samples in various ways, to understand fish prey communities, fish diets, the ecological niche spaces fish use, and the proportion of energy they are getting from the kelp compared to other sources.

Recently, Yiu worked with collaborators at the University of New Mexico Center for Stable Isotopes to use stable isotopes to help address these questions. As primary producers such as kelp and red algae take carbon dioxide out of the environment to fix it into their tissues, they use different ratios of carbon-13 to carbon-12 (carbon isotopes). These physiological differences leave a subtle chemical signature in the molecules in producer tissues. When a consumer eats a primary producer, they assimilate the molecules from it, so this carbon moves up through the food web. Therefore, isotopic signatures in animal tissues contain clues about the food they eat, the energy channels they use, and the ecological niches they occupy. The preliminary stable isotope data is suggesting that fishes in kelp forests and turf reefs occupy different ecological niches and use different sources of energy. In kelp forests, a large proportion of fishes’ energy looks like it is coming from kelp, but when kelp disappears, they change to use more energy from both phytoplankon and red algae. We are still working on analyzing fish diets and invertebrate communities to try to understand if these differences between habitats are due to their prey availability, prey selection, or the energy channels that their invertebrate prey species are using.

As the GoM continues to warm, understanding the implications for fish communities and their habitats becomes increasingly crucial. The loss of kelp forests could have far-reaching consequences, not only for the diversity of fish species but also for the fisheries dependent on these ecosystems. For instance, the transformation of kelp forests to turf reefs may have consequences for important commercial species, as their larval and juvenile stages depend on kelp forests as a refuge from predators. In addition to evaluating the ecological impacts of these changing reef communities, Yiu’s work can also help inform models that help predict how species distributions might shift in response to changing reef communities. This is crucial for anticipating and managing future ecological shifts in the face of climate change.

Throughout the past four years, Yiu has observed firsthand how this habitat change can shape food webs and influence fish communities. As Yiu stated, “Our preliminary data shows that the kelp forests are definitely changing the way that fish either interact with their environment, or each other, or their resources.” But there are still questions left to untangle. “There are lots of intricacies, and now I have a lot more questions” remarked Yiu.

White sharks are one of the most iconic species in the sea. While they have gained a fearsome reputation, researchers like Patrick Tardie, a Maine-eDNA undergraduate intern, argue they should instead be recognized for their vital role as apex predators in marine ecosystems. While white shark populations faced a decline in Northwestern Atlantic waters in the past, they are experiencing a rebound in recent years. This recent resurgence has sparked the interest of researchers like Tardie.

Tardie is a junior studying marine biology at Maine Maritime Academy in Castine, Maine. He spent the past summer working as an intern for the NSF EPSCoR RII Track-1 Maine-eDNA project at the Bigelow Laboratory for Ocean Sciences under the mentorship of 91±¬ÁĎ Ph.D. candidates, Kyle Oliveira and Dara Yiu. They worked to detect the presence of white sharks along the coast of Maine to better our understanding of white shark movements. 

To do so, they used environmental DNA (eDNA) sampling, a method that involves analyzing genetic material that organisms shed into their environment. The researchers collected water samples from seven different testing locations along the coast of Maine, spanning from Cape Elizabeth to Ram Island. They then analyzed the samples to determine the presence of and quantify the white shark DNA. They tested for the validity of their qPCR assay with numerous tests and proved it was effective in detecting white shark DNA in water samples.

Despite applying an effective assay, no white sharks were detected in the samples. This led Tardie to the conclusion that random eDNA sampling may not be the most efficient way to detect white sharks and further experiments were needed. It’s worth considering that the water samples were collected from open waters.  Tardie explained, “We can kind of extrapolate that eDNA is not a good method for detecting white sharks in open ocean waters.” This could be, as he suggested, because of the overall scarcity of white sharks along the coast of Maine.

This outcome prompted questions about a more efficient sampling approach, suggesting that obtaining samples from areas where white shark eDNA is more likely to be present in higher concentrations might be beneficial for validating the team’s methods. “With this type of study, I would have liked to work at some sites and get some samples where maybe, the day of at best, there was a white shark in the area,” he remarked. “I think that would help reach a better conclusion about the strengths or weaknesses of our approach.”

Tardie’s research is a part of Maine-eDNA’s “Species on the Move” project, which explores the movement of species throughout the Gulf of Maine. Although his focus is on white sharks, his research contributes to the larger effort to understand how and why species are shifting in response to the rapidly changing climate. Tardie highlighted the potential of eDNA, stating, “Using eDNA, we can potentially track the presence of certain animals in certain areas, which, if done with every species, offers an easier, less invasive, and less expensive method for tracking species.” Despite the absence of white shark eDNA in the results, this study is far from a failure. Tardie emphasized, “Just because my research didn’t bring out positive results, it doesn’t mean that it didn’t work. eDNA is on the rise, and there are a lot of questions regarding it. My part is just one aspect.” 

While they may not have detected white sharks, it underscores the iterative nature of scientific research and the lessons that can be learned from what might initially seem like setbacks. Tardie’s work contributes to findings that will impact the state of Maine and its ecosystems. Researchers can use these insights to study this topic further and experiment with other methods and sampling approaches. 

Research experiences like Tardie’s have long been the focus of EPSCoR programs in Maine like the NSF EPSCoR RII Track-1 Maine-eDNA project. Tardie and other students are placed at leading research institutions across the state like the 91±¬ÁĎ and the Bigelow Laboratory for Ocean Sciences. NSF EPSCoR funding makes these experiences accessible. These internships are made available statewide, including to students at emerging research institutions like the Maine Maritime Academy, providing students with the opportunity to learn from renowned researchers and develop both academically and professionally, while also making real contributions to research initiatives of importance to Maine and the country. 

Amid Maine’s watersheds reside countless microorganisms that many do not take the time to consider. These organisms, while small in size, play a crucial role in their ecosystems. Scientists have harnessed the power of environmental DNA (eDNA) when it comes to understanding the world of microscopic organisms.

ÉtaĂ­n Cullen, an undergraduate botany major at the 91±¬ÁĎ (91±¬ÁĎ), explores the capabilities of eDNA technology as part of the NSF EPSCoR RII Track-1 Maine-eDNA project. Cullen also serves on the Maine-DNA Diversity, Equity and Inclusion Advisory Committee. Collaborating with the Maine Chytrid Lab, under the supervision of Peter Avis (Maine-eDNA undergraduate coordinator), Erin Grey (91±¬ÁĎ School of Biology and Ecology assistant professor of aquatic genetics), and Joyce Longcore (91±¬ÁĎ School of Biology and Ecology associate research professor), Cullen’s research offers a fascinating glimpse into the biodiversity of aquatic organisms in Maine’s watersheds. 

Among these aquatic organisms are chytrids and thraustochytrids. Chytrids, fungi that inhabit freshwater environments, and thraustochytrids, protists associated with marine habitats, play pivotal roles in their respective ecosystems. They act as decomposers, returning nutrients to aquatic carbon sinks over time. Despite their ecological importance, these organisms are not widely understood. “There is so much that people want to use them for, but they don’t really know what they do or how they’re related to each other,” Cullen emphasized. 

One known use of thraustochytrids is in the production of omega-3 fatty acids, which are used, for example, in dietary supplements. This has led some to see potential for other uses in these organisms. “Not knowing much about them could be detrimental or prevent us from using them to their fullest potential,” expressed Cullen.

It is important to understand these organisms broadly. “A lot of thraustochytrid [species] can be easily cultured and investigated but a lot of research is only focusing on the small few that produce the fatty acids that they want without looking at the larger picture more or less,” explained Cullen. She described how chytrids are experiencing a similar phenomenon, where research has been heavily focused on the one species that is killing off frog populations, before taking a step back to investigate chytrids in general and how they work.

“Learning more about what they do and how they work in general could help with further applications to benefit the environment as a whole.” Her findings have the potential to help address pressing issues such as algal blooms, where these organisms could play an important role as parasites that counteract the harmful algae population. Furthermore, she described how thraustochytrids are a known parasite to hard shell clams in Canada and the New England area in the past.

In this study, water samples were collected from Maine-eDNA’s Index Sites across the state, ranging from freshwater to estuarine and marine sites. Then, Cullen combined culturing and eDNA metabarcoding to identify and classify the organisms. Using this data, Cullen is also able to estimate ecosystem biodiversity. 

Her preliminary data suggests that the metabarcoding technique is effective in detecting chytrids and thraustochytrids. She has successfully cultured and classified organisms from these samples, constructing a phylogenetic tree that showcases the intricate relationships among chytrids and thraustochytrids.

Before working with Maine-eDNA, Cullen had little knowledge of the potential and capabilities of this emerging technology. Projects like this, “Really show how far we’ve come,” said Cullen. She has learned just how versatile eDNA is. “eDNA can be used for a lot of different things that I didn’t even think were really possible.” Looking forward, Cullen plans to continue her research, further developing the phylogenetic tree and expanding her knowledge of these aquatic organisms.