Scientists can detect animal species by vacuuming their DNA out of the air

Scientists have found a way to identify animals that have passed by and are already gone or are hiding too well to find — by sucking their DNA fingerprints out of the air.

Environmental DNA fingerprints could be used to find, monitor rare species

Elizabeth Clare, now a professor at York University in Toronto, uses a vacuum pump to sample the air for environmental DNA. In new research, two different teams of scientists found the technique could detect and identify species up to hundreds of metres away. (Submitted by Elizabeth Clare)

Scientists have found a way to identify animals that have passed by and are already gone or are hiding too well to find – by vacuuming their DNA fingerprints out of the air.

Environmental DNA or "eDNA" is shed by organisms into their surroundings from things such as dead skin cells or feces. It has already been used to monitor biodiversity of animals that live in water or soil, from fish to microbes. 

Now biologists and ecologists are excited about the invention of a way to use eDNA in the air to monitor land animals such as birds and mammals — especially vulnerable species.

"It's just gobsmacking," said Jennifer Sunday, an assistant professor of ecology and evolution at McGIll University. She wasn't involved in the study, but uses eDNA to study the biodiversity of aquatic species.

The technique was developed independently by two groups of researchers, one led by Kristine Bohmann, an associate professor of evolutionary genomics at the Globe Institute at the University of Copenhagen and the other by Elizabeth Clare, who is now at York University in Toronto.

"If you're working with a critically endangered or very rare population that's very sensitive, you may never see them in the environment, even if you know they're there," said Clare.

"Or alternatively, you may not be able to get near them because they're so sensitive or so protected."

With eDNA detection, she said, the animal doesn't have to be physically present. It may have left some time ago. "And so when you're looking for something rare, that is a big advantage."

Two scientific papers describing how animals can be detected from DNA in the air, one by Clare and her collaborators and the other from Bohmann and her team were published this week in the journal Current Biology.

How it works

Clare started by testing the air in her lab, which was at the time at Queen Mary University of London in the U.K., where she was a senior lecturer. The lab was home to a colony of animals called naked mole rats.

A juvenile naked mole rat is seen at the Bronx Zoo in New York. Clare's lab had a colony of mole rats, and mole rat DNA was one of the first kinds detected in the air in her first experiments to see if the vacuuming technique could work. (Julie Larsen Maher/The Associated Press)

She and her team set up a vacuum pump that would pull air through a piece of filter paper — similar to the kind used to brew coffee — in her lab. The next step was to extract any DNA that might be on the paper and make extra copies of it using a technique called PCR, which is also used in COVID-19 testing, so it could be more easily detected and analyzed. The DNA was then compared to known databases of different species.

"To our delight and probably surprise, every sample we took had DNA in it," she recalled. "We had naked mole rat DNA. We had human DNA. We had dog DNA." 

The last one was a surprise and a puzzle, since there were no dogs in the lab — until the team realized that one of the animal care technicians had been looking after his mother's dog on the weekend and was probably bringing its DNA into the lab somehow on his clothing.

"And so suddenly, we realized not only was this going to work — it was actually way more sensitive than we expected," said Clare, whose research was funded by the Engineering and Physical Sciences Research Council in the U.K.

What happened next — at the zoo

Clare decided that the next step was to try a less controlled environment, but one where the researchers could clearly identify the source of DNA and how far away it was.

So they headed to the Hamerton Zoo Park in England and collected more than 70 air samples from different locations, both inside and outside.

Dingoes eye the air sampling equipment at the Hamerton Zoo Park in the U.K. with curiosity. Clare and her team detected all kinds of DNA on the grounds, including that of a hedgehog that had wandered through the grounds and the types of meat fed to the zoo's animals. (Submitted by Elizabeth Clare)

The researchers managed to detect the nearest animals, but also some that were hundreds of metres away.

"We found dingo DNA in the gibbon enclosure and we found zebra finch DNA in the primate house," Clare said.

That's not all. They also detected DNA from the chicken and beef in the animals' feed, and from local wildlife such as squirrels and even the European hedgehog, a critically endangered species that zoo staff confirmed they had spotted wandering the grounds.

"There's something that we really, really want to be able to detect with this kind of technology because they need more ways we can biomonitor for rare species," Clare said. "So I think that was probably our most exciting detection."

Scientific minds thinking alike

As the team prepared to publish their zoo study, some journalists who were covering their earlier lab work asked if they could see it. Clare obliged by posting it as a preprint online before publication.

Two days later, she received a flurry of text messages from her research team — another group of scientists from Denmark had seen the paper, and put up their own paper featuring a very similar experiment at the Copenhagen Zoo, funded by a philanthropic foundation called the Villum Fonden that supports scientific and technical research.. 

Christina Lynggaard and Kristine Bohmann, members of another research team that made similar findings, collect air samples at the Copenhagen Zoo. Their team and Clare's both submitted their findings to a research journal at the same time as evidence of independent scientific replication. (Christian Bendix)

That team, led by Bohmann, used a different commercial water-based vacuum and collected air samples from three different locations. 

"In just 40 samples, we detected 49 species spanning mammal, bird, amphibian, reptile and fish. In the Rainforest House we even detected the guppies in the pond, the two-toed sloth and the boa," Bohmann said in a news release.

She and Clare got in touch and decided to submit their two papers to the same journal for publication at the same time, arguing that this was a great idea because it showed independent scientific replication. It was something they had never heard of anyone trying before, but it worked.

This sloth, which lives at the Rainforest House in the Copenhagen Zoo, was detected in eDNA identified by Bohmann and her team. (Christian Bendix)

How it could become a valuable conservation tool

Clare said the next step in the research is to figure out how long DNA hangs around in the air and what environmental conditions cause it to accumulate or degrade.

In the future, she hopes the technique will be a valuable tool not just for rare species, but as an early warning system for invasive species or a tool for detecting species in hard-to-reach places such as caves or burrows.

She said eDNA is already routinely used as a tool by regulators to monitor biodiversity and populations in aquatic environments. She hopes, similarly, eDNA from the air becomes equally valuable.

When asked if eDNA from air could potentially be used in forensic investigations of crimes, Clare said, "I suppose theoretically." But she noted that the DNA analysis procedure would be quite different from theirs, which is intended to differentiate among species.

A hedgehog baby walks in Frankfurt. Clare was most excited about finding the DNA from a hedgehog, which is as species at risk in the U.K. She thinks the air eDNA technique could be used to monitor rare species. (Michael Probst/The Associated Press)

Canadian researchers who use eDNA as a biomonitoring tool for marine and aquatic conservation were excited by the development.

"I'm actually quite excited to read this paper," said Mehrdad Hajibabaei, an associate professor at the Centre for Biodiversity Genomics at the University of Guelph.

Hajibabaei, who is also the founder of eDNAtec, a consulting firm that provides eDNA-based ecological and biomonitoring to clients such as offshore energy and fisheries, called it an "important step" that has the potential for monitoring species such as large predators that are rare, elusive and move through huge territories. 

What he hopes to see next is whether it can be scaled up, and in natural environments and be developed into a tool that can be used by groups such as regulatory agencies, as Clare suggested.

Jennifer Sunday of McGill University said she thought it was amazing that the technique seemed to work.

She said traditional methods of tracking biodiversity, such as trapping, photographing or listening for species, are difficult and laborious.

One of her research areas is tracking how the distribution of species changes with human-caused climate change. That's very challenging.

"And so one reason to be excited about eDNA technology is that it can transform how we track biodiversity change at much larger scale [and] faster so that it can be more like tracking the weather," Sunday said.

"And that's going to totally change if we do it and we do it well. I think we could be much more proactive and [gain a better] understanding." 

Add some “good” to your morning and evening.

A variety of newsletters you'll love, delivered straight to you.

Sign up now