What do an extinct Brazilian frog, illicit fish in a Hong Kong wet market and a slimy algae called “rock snot” have in common? Answer: They were all recently detected by scientists searching for traces of elusive species in a sample of water. The developing field of environmental DNA (or eDNA) is revolutionizing wildlife studies.
Environmental DNA represents the biological soup of cells — hair, skin, feces, blood, semen, urine, viruses and bacteria — shed by creatures as they go about their daily lives.
Traditionally, field biologists have spent months, years, even lifetimes combing the wilderness for rare and cryptic species, sometimes to no avail. But by identifying the eDNA collected from a sample of water or soil, it’s possible for scientists to swiftly complete their quests in the laboratory.
Finding an endangered species or detecting the early arrival of a harmful invasive species “can be like finding a needle in a haystack,” says Kellie Carim, an aquatic research biologist with the National Genomics Center for Wildlife and Fish Conservation at the U.S. Forest Service’s Rocky Mountain Research Station in Missoula, Mont. “eDNA is the tool that allows us to find that needle.”
When Carim surveys a Northwestern stream for the presence of bull trout, an endangered species, her tools are a plastic cup fitted with a water filter, attached by a long skinny hose to a battery-powered pump. For each eDNA sample, she pumps about five liters of water through the filter. Then, she removes the filter from the cup and places it in a Ziplock bag to preserve the eDNA for analysis back in the lab.
Confirming the presence of bull trout in the stream relies on the same technology that medical professionals are now using to test nose swab samples for the coronavirus. Known as quantitative PCR (polymerase chain reaction), the analysis uses specific genetic markers that attach to the target DNA when it is present.
She runs a different type of analysis called DNA metabarcoding if she wants to study all the animals in the stream. The metabarcoding method queries all of the DNA from the sample for comparison against a database of known species. Matching the DNA sequences reveals the identity of every creature present, such as microscopic bacteria, small crustaceans, salmon and even bears that fish in the river.
Recently, Carim’s lab has been using eDNA sampling in an effort to detect the presence of bobcats, lynx and wolverines from snow tracks found on forest lands. Instead of filtering water samples, the researchers collect scoops of snow to be thawed and filtered in the lab.
“When my colleagues were first talking about their plans, I have to admit, I had my doubts,” she says. “But it’s amazingly accurate and efficient at identifying these animals.”
Wildlife managers are finding eDNA to be an increasingly valuable tool for monitoring invasive species that can harm habitats and native wildlife, including Asian carp, zebra mussels and Didymosphenia geminata, an algae nicknamed rock snot or didymo, which spreads between waterways by boot soles and boat bottoms.
“Didymo . . . can be easily overlooked in general,” says Aaron Henning, a fisheries biologist with the Susquehanna River Basin Commission in Harrisburg, Pa. But even the hint of a rock snot invasion is alarming because “it can choke a streambed and kill other aquatic life,” Henning says.
In 2016, an eDNA study revealed the beginning of a rock snot invasion in the Susquehanna River system. This early warning allowed the agency to put out signs to remind people to clean their boots and gear. Fortunately, the outbreak has so far been contained to one area.
The difficulty of removing invasive species is what makes early detection so important, Henning says, and eDNA is incredibly useful for sampling large areas in short amounts of time. Recently, his small team of four biologists surveyed 60 sites in the Susquehanna watershed for invasive snakehead fish and blue catfish.
“We did the eDNA survey in two days,” he says. “If we were doing it traditionally [with electroshocking equipment and fishing nets], it would have taken two months.”
Recently, scientists were excited when eDNA metabarcoding analysis revealed likely traces of a Brazilian frog believed to be extinct for more than 50 years. The missing frog, Megaelosia bocainensis, was last seen in the Atlantic Forest biome in Serra da Bocaina National Park.
“This species was known only from a few specimens collected in 1968,” says Kelly Zamudio, a Cornell University ecologist who collaborated on the study with biologists in Brazil. “We didn’t have a DNA sequence from it — we still don’t — because nobody took tissue samples back then. But there are other species of Megaelosia, and we had sequences for all of those in our extensive database.”
When the scientists took water samples from a mountain waterfall where Megaelosia bocainensis was last spotted, they found an unknown DNA sequence that matched the Megaelosia genus.
“We infer that it must be Megaelosia bocainensis because it’s the only Megaelosia species ever found there,” Zamudio says. “That’s as far as you can get if you don’t have the sequence of the real animal.”
The next step will be confirming the discovery by catching a live specimen. Plans have been made to return to the area with nets and poles.
Scientists working in Hong Kong, a major hub for illegal wildlife trading, are now experimenting with using eDNA as a forensic tool for investigating wildlife crimes. Researchers at the Hong Kong University Conservation Forensics laboratory recently conducted a pilot study in seafood markets where protected fish species have been sold illegally. They tested the eDNA collected from market drainage systems and found 144 marine creatures represented, including three internationally protected species: two sharks and a close shark relative, the blackchin guitarfish.
“From previous research, we knew that endangered species were being traded all the time at the markets,” says molecular biologist Jonathan Richards, who worked on the study as a Hong Kong University research assistant collecting field samples and analyzing the eDNA.
While market vendors might have been reluctant to talk to scientists asking questions about endangered fish, no one paid much attention to scientists collecting water samples from drains.
“It was a grimy job,” Richards says. “The drains are full of blood and guts and dirt and waste.”
After sieving out the large particles, they filtered the water to collect the eDNA. The analysis took about a month, Richards says, which is why the technique is not yet ready for prime-time use in criminal investigations.
With a lot more research, however, scientists say that eDNA could be promising as an investigative tool for law enforcement agents trying to identify where protected species are being sold.
“Finding probable cause — that’s where I see the greatest value. But you still need to go and physically look for and find the species to arrest a suspected trafficker,” says Mary Burnham-Curtis, supervisory senior forensic scientist with the U.S. Fish and Wildlife Service’s Forensic Laboratory in Ashland, Ore.
In an era when wildlife species are increasingly vanishing because of habitat destruction, climate change, poaching and other threats, scientists say eDNA may hold the key to finding animals while there’s still time to save species and habit.