Ecosystem in a Bottle

Every ounce of water teems with affirmation of life. All aquatic plants, animals, and microbes leave genetic traces wherever they go as a natural byproduct of their life and death. This environmental DNA, or eDNA, has the potential to provide scientists with a wealth of data about the organisms, how they interact, and their environment.

Scientists from Bigelow Laboratory and University of Maine are leading a $20 million National Science Foundation project to pioneer technology to harness this eDNA and make discoveries about pressing issues – from economically important and potentially harmful species to ecosystems shifting in the face of climate change.

With the help of collaborators in education, government, industry, and community groups, as well as a large cohort of UMaine graduate students, the research team aims to develop a DNA-based toolset that enables states to better monitor life in their coastal waters.

“One of the powers of eDNA is this integrative ability to look across all organisms – literally from bacteria to whales – within a single sample,” said Dave Emerson, senior research scientist at Bigelow Laboratory and co-principal investigator on the project. “When you start putting lots of that data together, you can look at associations between different organisms and see what kinds of patterns come to light.”

For smaller organisms like microbes, eDNA can come from the whole organism. For larger ones, it typically comes from shed skin cells, reproductive cells, or waste products. eDNA is collected through water samples and even a small bottle of water provides the potential to find traces of a particular species or to construct a snapshot of an ecosystem.

“We hope that eDNA will enable us to see associations that we didn't understand before because now we can look much more broadly across a community,” said Emerson, who is also leading a project team examining the use of eDNA to understand distribution patterns of marine microbes and their responses to environmental changes. “Because microbes respond most quickly, using eDNA could give us an early warning about changes that may be occurring in an ecosystem.”

Maine is being reshaped by the shifting of existing species and the introduction of new ones, some of which can be harmful. Senior Research Scientists Pete Countway and Doug Rasher are leading teams to monitor some of these changes and how they will impact species diversity and movement into new habitats.

In recent years, Maine has experienced toxic blooms of algae and cyanobacteria with increasing frequency, duration, and variety. When these toxins become concentrated in shellfish, for example, they can be passed up the food chain. Countway is leading a team using eDNA to discover where different species are located, how they may impact environments, and how to identify the biogeochemical processes and microbial interactions that may lead to toxic blooms.

Information from eDNA can be used in two main ways. The first is to create a snapshot of the organisms in an ecosystem by matching up DNA sequences from a water sample to libraries of known DNA sequences. Alternatively, eDNA can be used to find one particular organism and estimate its abundance, from a mixture of millions of other genetic signatures. Countway’s project is using both approaches. He first examines a broad swath of the ecosystem from microbes to fish, and then identifies the potentially toxic species. He can then design a genetic assay for a particular species, much like a COVID test, that can quickly detect that species in future water samples.

“Normally we don't see a bloom coming, we just notice it suddenly one day when we drive past the water and it's bright green, or the harbor is red from a marine algal bloom,” Countway said. “These eDNA techniques are so sensitive that oftentimes we can detect the DNA signature from just one cell in a liter of water.”

Many environmental changes are not as visible as red algal blooms and can easily go unnoticed, while creating serious consequences for the ecosystem. Senior Research Scientist Doug Rasher is working with Countway on one such issue – the changing ecology of kelp forests on the seafloor.

“Maine's kelp forests provide essential habitat and refuge to a variety of marine species, including economically important fish and shellfish,” Rasher said. “However, these forests are threatened by a variety of stressors, and their declining health is now recognized as a sentinel of ocean change.”

As the Gulf of Maine warms, temperatures are becoming too high for some of Maine’s native species, and the region is becoming more habitable for species that are historically from further south. Even compared to surveys from 2018, Rasher said ecosystems are rapidly changing and it is important to implement these tools as soon as possible.

“We're going to see a reshuffling of communities in the kelp forest ecosystem, some of which will be detrimental to the ecosystem and its associated fisheries, and some of which will create new economic opportunities,” Rasher said. “In both cases, we need to be able to observe species range shifts as they're unfolding, and understand their causes.”

He and his colleagues are working to use eDNA to gather information on new species that arrive to an ecosystem but are not yet abundant enough to show up with traditional sampling methods. Even if newly arrived species are still too rare to spot on a dive survey, they may leave genetic fingerprints behind.

While powerful, eDNA has limitations. For example, it can tell researchers if an organism’s DNA is in the water, but it can’t reveal the organism’s age or if it is still alive. Part of the Maine eDNA project is to find solutions to these sorts of problems. At the same time, Rasher, a self-described “muddy boots ecologist,” believes that traditional methods will long continue to provide valuable information.

“Traditional methods still do the best job at telling us what the ecosystem looks like,” he said. “But when you pair them with eDNA, you can develop a more comprehensive picture of what's happening in the ecosystem, as well as what’s new and may be missed by old-school methods.”

Neither approach is a panacea. However, Senior Research Scientist Nichole Price thinks eDNA could be the efficient, large-scale tool that has long been needed. She is leading a team using eDNA to understand the movement and dispersal of larvae that are key to the health of commercial fisheries.

Seaweeds, scallops, mussels, and other organisms that stick to the bottom of nearshore environments begin life as microscopic plankton with limited swimming ability. They are carried around by currents until they find a suitable spot to attach and grow.

“Harvesters of these really lucrative organisms are depending on natural pulses of them to just show up when and where we expect them to,” Price said. “It makes fisheries management for these kinds of species really tricky, especially in the face of climate change, which is making these settlement patterns even less predictable.”

Price hopes that eDNA tools can help scientists better understand the size and location of these species. This is something that traditional sampling methods have struggled to do, especially in cases where organisms are too small or similar to differentiate.

“eDNA allows us to start looking for these pulses of otherwise invisible larvae by screening the water for the DNA fingerprints of those species,” she said. “We want to develop unique tools that can help us differentiate between the adult and larval stages of these organisms, which is key to ecosystem and fisheries management.”

From larval development to shifting species, the true power of eDNA is in its applied opportunities. Senior Research Scientist Nick Record is working with many of the project’s research teams to actualize that potential. He specializes in machine learning and big data. And, if anything constitutes big data, eDNA is it – it's not uncommon to get 20,000 individual DNA sequences from a liter of water.

Record is working with researchers to sort through this trove of information and create forecasting tools that can serve communities around Maine. They hope to identify signatures that are precursors to events like algal blooms and species shifts, similar to how meteorologists know that a drop in atmospheric pressure can signal a storm is coming. The resulting early warning systems could be beneficial to all those who work and play on the water.

“If farmers can be informed of a harmful bloom developing in a sensitive area, they could either perform their harvest a little bit early or move their shellfish out of harm's way,” Countway said.

Ultimately, the project aims to develop tools that can be used by community scientists and stakeholders. Many eDNA techniques are relatively inexpensive and accessible, and Countway is working with communities around New England to build their capacity for eDNA research.

“At the end of the project, I'd like to look back and say we've trained up a cohort of community scientists that have the capability to analyze a water sample taken nearby and don’t have to wait for the gatekeepers of the technology to give them an answer,” he said.

If communities were able to conduct monitoring on their own, the amount of data would feed enormous possibilities. Researchers hope the technology can be leveraged in ways to engage communities, expand research, and democratize science.

“There could be a thousand other people around the area contributing measurements in different places,” Record said. “The data could be integrated and visualized in near real-time and empower people to observe and monitor their environment in a scientifically rigorous way.”

This kind of public-oriented, multidisciplinary science is at the core of the project. One of the researchers’ main goals is to share and integrate the data with other monitoring efforts in Maine’s coastal communities. Using eDNA to answer fundamental science questions will help validate it as a tool to gauge the health of coastal ecosystems during a time of significant environmental changes.

“One of the cool things about it is that it brings together these different disciplines and allows you to think about other groups of not only organisms, but research disciplines in a more common way,” Emerson said. “And, to me, that's pretty powerful.”