Imagine being able to get a “DNA report” that, based on traces of genetic material in the environment, lists all the plants and animals in the area, the way a daily weather forecast tallies precipitation, wind, and temperature. A pipe dream, scientists might once have said. But a paper published today shows that routine, remote biodiversity monitoring may soon be a reality. By tapping into existing air quality monitoring sensors, researchers have discovered a cheap way to census nearby species.
“This paper is impressive because of its ingenuity,” says Chris Jerde, an ecologist at the University of California, Santa Barbara who was not involved with the work. Julie Lockwood, an ecologist at Rutgers University, another outside expert, says the study “presents a very good opportunity to do large-scale biodiversity monitoring,” something countries have agreed to perform as part of an international treaty called the Convention on Biological Diversity.
The new research builds on growing evidence that environmental DNA, or eDNA, is a powerful shortcut for cataloging species, reducing the need for labor-intensive traditional sampling methods such as trapping or directly observing individual plants or animals. “We are starting to see [that] eDNA is left everywhere,” says Kristine Bohmann, a molecular ecologist at the University of Copenhagen. Larger animals slough off DNA in skin, scales, and feathers, and researchers have also detected eDNA from mussels, sponges, dung beetles, spiderwebs, and even carnivorous plants, on land and in water. Over the past 2 years, several research teams, including Bohmann’s, have demonstrated they could even find DNA from plants, insects, and mammals suspended in thin air.
James Allerton suspected that airborne DNA sampling might already be taking place as an accidental byproduct of pollution monitoring. A physicist at the National Physical Laboratory in England, he helps oversee a 60-year-old effort by the U.K. government to monitor air quality by tracking heavy metals and other particles using hundreds of air samplers across the country. Allerton contacted Elizabeth Clare, a York University biologist whose team had shown that eDNA samples from air in a zoo captured the animal diversity within. Together with biologist Joanne Littlefair from Queen Mary University of London, the scientists agreed to see whether the country’s air quality monitor filters had collected eDNA in addition to air pollutants.
The team extracted and sequenced DNA from a monitor at the National Physical Laboratory in suburban London. They also gathered 8-month-old filters from a monitoring station in Scotland.
“We had no expectation that it would work,” Clare recalls. And yet, the eDNA revealed the presence of 180 plants, fungi, insects, mammals, and amphibians, including 34 species of birds across the two sites, the team reports today in Current Biology. The samples included DNA from threatened species such as hedgehogs and songbirds; ash, linden, and oak trees; and crops such as wheat and cabbage. “The fact that filters originally collected for other purposes can be repurposed for sensitive eDNA studies is astonishing,” says Naiara Rodríguez-Ezpeleta, an eco-evolutionary geneticist at AZTI in Sukarrieta, Spain.
When it came to the number and kinds of species identified, “There was little difference at the two locations,” Clare says, even though the Scottish samples had been in storage for 8 months. Researchers had thought the DNA would degrade over that period; its preservation “raises intriguing possibilities for eDNA analysis,” Rodriguez-Ezpeleta says. Providing old filters are kept dry, which helps maintain the DNA’s integrity, it might be possible to go back in time to track changes in biodiversity by looking at archived filters, Clare says.
That’s exactly what Per Stenberg, a geneticist at Umeå University, has done in work yet to be published. His team has obtained DNA from 30 years’ worth of archived air filters, removed weekly from sensors set up to detect radioactive fallout from nuclear explosions across Sweden. These samplers collected huge volumes of air and thus are very sensitive to low concentrations of contaminants, he explains. He and his colleagues found the DNA documented changes in the relative abundances of all types of organisms through time—trends that “correlate well with more traditional monitoring data,” he says, changes that could reflect the influence of climate, he says.
Whether the many thousands of air filters monitoring pollution around the world can be a consistent and reliable way to detect changes in biodiversity isn’t clear. “Detecting some species sometimes is not the same as detecting a signal of biodiversity change representative for a larger area,” says Fabian Roger, an ecologist at ETH Zürich, who is testing the potential of air samplers to detect insects that may cause crop or tree damage Researchers don’t know how far from a sensor an organism can be and still be detected, or whether some organisms are easier to detect. “The devil is in the details,” Einar Eg Nielsen, a molecular ecologist at the Technical University of Denmark who was not involved with the study, says.
“The potential could be great,” Roger adds. “But it’s still to be demonstrated.”