How scientists can identify rare animals by vacuuming 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 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.

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.

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 looked 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.