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Silent signals
A team of Smithsonian scientists is investigating subtle environmental clues to build a clearer picture of biodiversity in two important aquatic ecosystems.
By Michelle Z. Donahue
You don’t need to see a skunk to confirm its presence—one whiff of its particular perfume and you know. It’s been there.
Though they’re not all as recognizable as a skunk’s, all living organisms leave signs and signals of their presence and passing. Sometimes it’s urine, sometimes hair, sometimes a smear of mucus. But all living things leave behind a far more subtle clue to their presence: DNA.
Taken collectively across a region, a library of such DNA samples builds a snapshot of the biodiversity of that area or ecosystem.
A new initiative at the Smithsonian National Museum of Natural History (NMNH) seeks to create a representative catalog of environmental DNA, or eDNA, from two of the United States’ most important estuarine ecosystems: the Indian River Lagoon along Florida’s Atlantic coast, and the Chesapeake Bay of the Mid-Atlantic. It is one of the first major undertakings of the museum’s larger Ocean DNA project, an effort to develop genomic tools to rapidly assess ocean health as well as create a genetic reference library of Earth’s marine life, from massive to miniscule.
“What’s a consistent habitat through which we can monitor ocean change?” asked Chris Meyer, a research biologist at the museum and manager of the Ocean DNA initiative. “The one constant in these systems is the water column.”
Half a liter of water is all that is required to acquire eDNA. This is an especially savvy approach for detecting animals too small or too fast to be caught in nets. It also eliminates the need to capture an organism and take blood, hair or other material for analysis. Samples are drawn from more than a dozen sites across the Indian River Lagoon and the Chesapeake, two regions where the Smithsonian has been involved in long-term ecological monitoring programs for decades.
Once any genetic material in the water samples has been extracted and sequenced, scientists can begin the process of cataloging known organisms, and the tougher work of identifying unknowns which turn up in the samples. Because of the simplicity of the method, biologists will be able to monitor change over time far more effectively and efficiently. Updated snapshots require only water samples, giving researchers the ability to compare “ecosystem versions” over timeframes of days to years to decades.
eDNA detection methods have been increasingly used across the Smithsonian in recent years: to find elusive wood turtles in Virginia, and to measure fish biodiversity on a Panamanian coral reef, for example. The NMNH project differs in its scale: it seeks to enable an ecosystem-level picture of biodiversity. The goal is to be able to use the data for broad as well as targeted research, but also create a comprehensive baseline of biodiversity that can be used to track changes in these ecosystems over time.
Long-term, the eDNA project will also update and modernize NMNH’s biological collections. Because DNA information can be digitized and samples stored indefinitely in deep freezers, researchers both present and future can draw upon the information over and over.
Proof and protocols
In Fort Pierce, Florida, Holly Sweat runs the Benthic Ecology Lab at the Smithsonian Marine Station and conducts quarterly sampling of the communities that live in the lagoon’s sandy-silty bottom, adding to more than 16 years of data for a project to improve water quality management and restore the Florida Everglades watershed. At the Smithsonian Environmental Research Center (SERC) in Edgewater, Maryland, Matt Ogburn leads the Fisheries Conservation Lab which conducts sampling activities for three projects that have been running since the late 1970s and early 1980s.
With the new eDNA project, Sweat and Ogburn’s teams now also take samples of the water column at several of their established sampling sites.
A major advantage to using established sites in well-known ecosystems is that the teams have a good understanding of what should show up in the samples, which helps to validate the approach. Absences will be obvious; unidentified outliers even more so.
For example, Ogburn leads the Chesapeake Bay Barcode Initiative, which has collected new specimens and DNA sequences for more than 80 percent of fish species and more than 50 percent of larger invertebrate species in Chesapeake Bay. And Sweat and her colleagues have recently sequenced dozens of sediment-dwelling invertebrates that are key components of Indian River Lagoon ecosystems.
“This is potentially exciting for expanding on some of our long-term sampling—SERC has 50 years of data on a variety of things,” Ogburn said. He and his team go out three times a month and pull nets through the water, but only catch a portion of what is there—the big things can swim away, while the small creatures slip through the nets. “eDNA is sampling all of those, from small to large, independent of the size of your net or boat,” Ogburn noted.
“This project will show us what we are missing, and what we should be doing a better job of looking for,” Meyer said. This is an important step for demonstrating the approach’s utility as a model that other marine labs or large-scale efforts such as the Smithsonian-led MarineGEO and Tennenbaum Marine Observatories Network can adopt.
In their first year of sampling, the NMNH and SERC marine eDNA teams collected 192 water samples. Though the data are still brand-new and still undergoing analysis, several surprises have already emerged. A total of 94 vertebrate species have been identified, including grey squirrel, raccoon, wild boar, mahi-mahi and cownose ray.
One notable animal that the team expected to turn up in the samples but didn’t: manatees. Though they are typically common throughout in the Indian River Lagoon, and their numbers can fluctuate depending on the season, manatees did suffer a widespread die-off in 2021.
Amping up conservation
eDNA offers a potentially powerful tool for shaping conservation and habitat restoration approaches.
In the southern Indian River Lagoon, where the St. Lucie River estuary has been impacted by periodic freshwater releases from Lake Okeechobee, regional stakeholders work to restore the St. Lucie River’s hydrologic function. With the freshwater releases, and a high degree of inland runoff carrying polluted sediments to the lagoon bottom, the system experiences booms and busts in the biodiversity of tiny, burrowing benthic organisms like clams, worms and copepods. These watery canaries in the proverbial coal mine can signal distressing shifts in the lagoon’s water quality but are difficult to sample and analyze. DNA-based signals of community shifts can nudge management decisions in the right direction.
Similarly, in the Chesapeake Bay, Eastern oysters (Crassostrea virginica) and seagrass habitats have been a focus of restoration efforts. Though they’ve been dwindling for so long that what a well-functioning system looks like is lost to time, Ogburn and graduate fellow Laura Givens, a Ph.D. student at Duke University, are using eDNA as a new tool to evaluate restoration of these habitats. Biological technician Carmen Ritter at SERC has been responsible for the ongoing seasonal sampling of sediment cores and now, water samples.
Monitoring the different kinds of fish, invertebrates and even microbial species that take up residence at various sites can offer clues to more- and less-successful conservation approaches.
“Plankton, microbes and bacteria react a lot quicker to environmental shifts, and if we’re able to act slightly faster when we see these things changing, that could buy us more time to make good decisions,” said Steve Canty, the principal investigator on the eDNA project, and coordinator of the Marine Conservation Program at the Smithsonian Marine Station. As a monitoring tool, paired with goals for what communities should be seeing if conservation strategies are effective, “eDNA can help show if you’re moving towards that,” Canty said.
eDNA sampling could also offer clues for specific management of economically important fishery stocks. The day-to-day implementation of fisheries management has long fallen to fishermen and women: to reduce impacts and avoid overfishing, the main strategy is to reduce the days available in the fishing season or limit harvest in other ways. In the Chesapeake Bay, for example, the diets of striped bass and summer flounder differ drastically depending on where in the bay they’re caught, knowing more about what their prey species are and how to improve prey species habitat can improve fisheries from the bottom up.
“That is an alternate management tool to increase the production of fishery species, as opposed to just regulating fishing,” Ogburn said.
Additionally, this eDNA approach expands the pool of people who can participate in environmental and ecological research. With a limited number of scientists able to study massive systems of land and water, research is often incredibly time consuming and slow. A major thrust of the current work is to test several methods and filter sizes in order to standardize and simplify sampling protocols, which will enable scientists, fishing crews and schoolchildren to use the approach at sites virtually anywhere in the world.
A new age of museum research
Museum specimen collections and even fieldwork have historically been limited to the very visual: specimens big enough to see. eDNA now gives scientists the ability to perceive what cannot be seen—but also to re-investigate past datasets in the future.
“As techniques to analyze DNA improve into the future, we can go back in time to look at our ecosystem snapshots again, and compare,” Canty said. Through a philanthropic grant from the William H. Donner Foundation, Canty was able to sample and analyze a suite of new eDNA collections, which can be used by many different researchers. “You get more information, but it’s from the same snapshot,” Canty added.
Similarly, investigators can conduct multiple angles of research from one sample, just by shifting what they’re looking for within that sample.
“You can quickly switch the lens for the research you want to do,” Meyer said. “You could work on detecting invasive species one year, or do an analysis of a whole community, or have a wholly boutique approach if you know what you’re looking for.”
Meyer added that overall, the eDNA project and Ocean DNA program are helping to re-imagine the role of the Smithsonian’s natural history museum as it considers its future.
“It’s an extension of our role as a natural history museum – we’ve always had libraries of life; now we’re building libraries of systems, as well,” Meyer said. “At our core, our role has been to say: what is this thing? And compare it to specimens we have on our shelves to determine if it’s different, or what its name is. This DNA work helps us to expand on this concept to track global change across entire communities and strategically build our reference libraries so we don’t have unknowns in our collections.”