Science

DNA pulled from thin air identifies nearby animals

This kingfisher stunning its prey may spread DNA of both species into the air.

Kevin Elsby/FLPA/Minden Pictures

DNA is everywhere, even in the air. That’s no surprise to anyone who suffers allergies from pollen or cat dander. But two research groups have now independently shown the atmosphere can contain detectable amounts of DNA from many kinds of animals. Their preprints, posted on bioRxiv last week, suggest sampling air may enable a faster, cheaper way to survey creatures in ecosystems.

The work has impressed other scientists. “The ability to detect so many species in air samples using DNA is a huge leap,” says Matthew Barnes, an ecologist at Texas Tech University. “It represents an exciting potential addition to the toolbox.”

“The surprising part is that you’re able to get birds and mammals—wow,” says Julie Lockwood, a molecular ecologist at Rutgers University, New Brunswick. The new studies suggest “there’s more than just spores; there’s cells and hair and all kinds of interesting things that float through the air.”

For more than a decade, researchers have analyzed those disparate sources of DNA in water to identify elusive organisms. Researchers’ sampling of environmental DNA (eDNA) in lakes, streams, and coastal waters has let them identify invasive species like lionfish as well as rare organisms such as the great crested newt. More recently, some scientists have tracked insects by eDNA on leaves, and also found soil eDNA apparently left by mammals loping along a trail.

Far fewer studies have been done on animal eDNA in air. It’s not obvious how much tissue wafts off animals or how long the genetic contents of those cells persist in air. Some earlier studies used metagenomic sequencing—an approach to identify mixtures of DNA—to detect microorganisms including bacteria and fungi that are abundant in air. And a 2015 study of air monitors for pathogens in the Washington, D.C., area found traces of eDNA from many kinds of vertebrates and arthropods. But it wasn’t obvious how useful the technique would be, and it’s not clear how terrestrial animals shed cells that float away.

Earlier this year, Elizabeth Clare, a molecular ecologist now at York University, reported in PeerJ that eDNA from naked mole rats could be detected in air samples taken in the laboratory. To find out whether animal eDNA could be detected outdoors, she and colleagues from Queen Mary University of London went to a zoo: There, the species are known and absent from the surrounding landscape, so the team could determine the source of airborne eDNA they found. In December 2020, Clare set up vacuum pumps with filters in 20 locations in Hamerton Zoo Park and let each run for 30 minutes.

Clare collected 72 air samples from both outside and inside zoo buildings. She used polymerase chain reaction to amplify the scant genetic fragments left on the filters into enough DNA for sequencing. “We had to take a leap of faith that it was there because it wasn’t something you can measure,” she says. After sequencing the eDNA, she matched the snippets to known sequences in a database. The team identified 17 species kept at the zoo and others living near and around it, such as hedgehogs and deer. Some zoo animal DNA was found nearly 300 meters from the animals’ enclosures. She also detected airborne DNA likely from the meat of chicken, pig, cow, and horse fed to captive predators indoors. All told, the team detected 25 species of mammals and birds.

Meanwhile, researchers in Denmark had pursued the same idea. Kristine Bohmann, a molecular ecologist at the University of Copenhagen, recalls inspiration struck while brainstorming proposals for a high-risk grant program. “I remember saying, it has to be crazier—like vacuuming DNA from air, that would be insane.” They won the grant and sucked up air from three locations in the Copenhagen Zoo with vacuums and fans in three types of samplers. They consistently detected animals—a total of 49 species of vertebrate.

“These preprints are exciting and show some great data,” says Kristy Deiner, a conservation ecologist at ETH Zürich. She leads an XPRIZE Rainforest team to develop airborne DNA technology for monitoring biodiversity.

Airborne DNA may help reveal the presence of otherwise hard to detect animals, such as those in dry environments, burrows, or caves, and those that fly out of sight of wildlife cameras, like some birds, Lockwood says.

She cautions that many questions remain about the approach, including the key issue of how far eDNA travels on air, which will influence how well the method can pinpoint the recent location of animals. That distance will depend on many factors, including the environment; eDNA will probably waft farther in a grassland than in a forest. Another question is how exactly animals shed the DNA. It could be when cells are freed as they scratch or rub their skin, sneeze, or do any vigorous activity like fighting or subduing prey. But even sloth eDNA turned up, says molecular ecologist Christina Lynggaard, a postdoc at the University of Copenhagen who did the sampling at the zoo.

Preventing contamination—always an issue with eDNA studies—is particularly thorny. Sampling eDNA in air, Barnes says, is like “pipetting underwater.” One problem, Clare says, is how to find a negative control, or a test sample with no DNA in it. “I don’t know where to buy a balloon of sterile air.”

Despite the unknowns, Barnes and others have high hopes. Lockwood, who studies forest pests and has identified eDNA traces on bark and leaves, is already hoping to identify insect pests from air. “I can’t wait to try it,” she says. 

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