Environmental DNA Can Be Pulled from the Air
Environmental DNA Can Be Pulled from the Air

Environmental DNA Can Be Pulled from the Air

A proof-of-concept study uses eDNA in the air to detect mammals, expanding the technique beyond aquatic sampling.

Amanda Heidt
Amanda Heidt
Apr 7, 2021

ABOVE: In the researchers’ experimental setup, a naked mole rat burrow is equipped with a tube that passes through a peristaltic pump, which forces air through a DNA-capturing filter. 
ELIZABETH CLARE

Researchers in the UK have successfully isolated airborne mammalian DNA, showing that in air, just as in water, animals leave behind invisible but useful traces of themselves that scientists can monitor. The results, published March 31 in PeerJ, represent a new direction for environmental DNA (eDNA) research that could one day lead to advances in forensic science and public health, in addition to ecological surveillance.

“This is really the first time airborne samples have been used to look at mammals, and it’s very exciting,” says Mark Johnson, an ecologist at Texas Tech University who has used airborne DNA to study plants and was not involved in the current work. Through his own research, Johnson adds, “we’ve learned that airborne DNA is a lot broader than what we originally gave it credit for, and I think this paper opens the door for expanding into new areas.”

Environmental DNA is one of the fastest growing ecological tools for biomonitoring in aquatic systems, according to study coauthor Elizabeth Clare, a molecular ecologist at Queen Mary University of London. Its use is premised on the fact that all organisms leave genetic fingerprints wherever they go in the environment. That DNA can yield valuable information about what species frequent an area. 

In the last few years, eDNA has helped scientists monitor endangered species, such as the highly protected great crested newt, as well as species such as the white shark that are difficult to track using conventional methods. As the tool has been further refined, researchers have also started pushing eDNA into new territories, including the detection of pathogens in the aquaculture industry and even the monitoring of terrestrial organisms, including mammals. But in all of these instances, the samples have come from water sources such as lakes or rivers, or in rare cases, moist soil. 

See “Researchers Detect Land Animals Using DNA in Nearby Water Bodies

To see whether eDNA could be detected in air, Clare started by designing a simple experiment looking for airborne mammalian eDNA in a small, three-meter by four-meter room housing a colony of 225 naked mole rats. “They had been established for a very long time in that room . . . so if DNA does accumulate [in air], it would be there,” Clare tells The Scientist.

Drawing on existing aquatic eDNA procedures, Clare rigged a pump to draw air, rather than a water sample, through either a 45- or 22-micrometer filter. Because eDNA can come in a variety of forms—pieces of hair, skin, or free-floating, naked DNA—it was likely that she would capture particles of many different sizes. The team also tested different filtering times to see if the quantity of DNA differed after 5, 10, or 20 minutes. In total, the experiment generated a total of 12 samples (six from the air trapped within the mole rats’ system of burrows and six from the open room) plus two positive and two negative controls.

Elizabeth Clare, a molecular ecologist at Queen Mary University of London, discusses how she pulled from techniques developed to sample environmental DNA, or eDNA, in water to search for genetic traces of mammals in the air.
PEERJ

All but two samples yielded mole rat sequences. Neither the filter size nor the time (and thus the volume of air being filtered) led to significant differences in DNA yield, although the burrows generated a stronger signal than the larger room did.

“It surprised us that it worked as well as it did right away,” Clare says. “We had actually anticipated a bunch of things we were going to modify . . . that we never had to use. It worked the first time with the first thing we tried.”

See “No Place to Hide

The current study is a solid foundation for future work, says University of Amsterdam evolutionary ecologist Kathryn Stewart, who works with eDNA and was not involved in the current research. Clare sees a role for airborne DNA in spaces that can be difficult to access, such as burrows, caves, and hollows. Johnson had previously applied for a grant to use airborne eDNA to noninvasively monitor for white nose syndrome in bats, but at the time, the project was deemed too experimental.

After the successes of eDNA in aquatic science, “it’s exhilarating to see somebody take it one step further and ask what other kinds of media we can extract DNA from,” Stewart tells The Scientist. “The only claim that they make is that you can accurately collect DNA from the air, but we need that forward thinking momentum for the field. I think the challenges that lie ahead are also exciting opportunities.”

One such challenge will be the issue of contamination. Despite carrying out their extractions in a clean hood, the team was surprised to find human DNA, but not mole rat DNA, in the study’s negative controls, suggesting that the contamination is coming from the scientists themselves. In some samples, the human component was as strong as that of the mole rats’, even within their burrows. For researchers targeting nonmammals, this is less of a concern, as the sequencing tools they use pick out only their species of interest. But for sampling aimed at detecting mammalian DNA, contamination is going to be “one of the biggest challenges,” Stewart says.

Clare has already started to brainstorm possible means for addressing contamination, either by having researchers collect samples while wearing suits that include respirators, deploying dust traps in the field for days or weeks to passively collect airborne material—as Johnson does for his studies on plant airborne DNA—or by using so-called blocking probes during sequencing that keep human DNA from amplifying. She is also designing studies to better understand how genetic material behaves and persists in the air’s changing environment. All of this is a push to validate airborne eDNA using the same rigorous standards applied to aquatic research.

The silver lining of human contamination, Clare says, is that it made her realize that airborne DNA could have forensic or public health applications. DNA from crime scenes is often degraded or sparse, but she was able to pull minute traces of the nucleic acid from the air and produce usable results.

Any such uses remain speculative, and Clare is quick to point out how much remains unknown. “In terms of what we could do with it, we’re very much at the speculatory stage of this,” she tells The Scientist. “Is extracting airborne DNA possible? Yes. Can we say anything beyond that? No.”

See “Researchers Track Sharks and Whales Using DNA in Seawater Samples

E.L. Clare et al., “eDNAir: proof of concept that animal DNA can be collected from air sampling,” PeerJ, doi:10.7717/peerj.11030, 2021.