Scientists vacuum zoo animals' DNA out of the air

Geoff Brumfiel

January 09, 2022 / 4:00 am

caption: Researchers were able to detect DNA from elephants at the Copenhagen Zoo simply by sampling the air nearby.

A key part of protecting endangered species is figuring out where they're living. Now researchers say they have found a powerful new tool that could help: vacuuming DNA out of the air.

"This is a bit of a crazy idea," admits Elizabeth Clare, a molecular ecologist at York University in Toronto, Canada. "We are literally sucking DNA out of the sky."

But it works. Clare's group was one of two to publish papers in the journal Current Biology on Thursday showing that dozens of animal species could be detected by simply sampling the air.

A wild idea takes off

Using environmental DNA, or eDNA, to track species isn't new. For a few years now, researchers have been using DNA in water to track aquatic animals. They've also been able to pick up eDNA from plants floating in the air.

"One thing that we've discovered in eDNA research is really that any environmental medium (water, soil, snow, etc.) has the potential to harbor DNA that we can sample," Stephen F. Spear, a research biologist with the U.S. Geological Survey, wrote via email. Spear has used eDNA to track a species of aquatic salamander known as the hellbender.

But the idea of using eDNA from air to track a large land animal like a rhinoceros or a giraffe still seemed "crazy" to Kristine Bohmann, a researcher at the GLOBE Institute at the University of Copenhagen in Denmark, and the lead author on the second paper in Current Biology.

Bohmann and her team thought up the idea independently from Clare's group a few years ago. She was trying to come up with a wacky research idea for a Danish foundation that funds far-out science.

"In the end I got so frustrated that I just blurted out, 'No! It has to be crazier! It has to be, like, vacuuming animal DNA out of air!'" she recalls.

The idea stuck, and she eventually got funding and hired a postdoc named Christina Lynggaard. Lynggaard's first job was to figure out what kind of device the team could use to vacuum eDNA from the air.

"We tried three different devices, and one of them was a vacuum cleaner, a commercial one," Lynggaard says.

It worked. They could sample DNA simply by using it, although it was "super noisy." Lynggaard also used some home-made samplers that used a small fan, like a computer blower fan, mounted in a 3-D printed housing. They worked just as well and were far quieter and more power efficient. Bohmann suspects they will be more useful in actual sampling in the wild.

A tale of two zoos

To make the experiment successful, the team also needed a good place to look for animal DNA.

"We realized we are based in Copenhagen ... we had the Copenhagen Zoo," Bohmann recalls. It was almost like the zoo was custom-built for this experiment: Most of the animals are nonnative, so they really stick out in a DNA analysis.

"If we detect a flamingo, well we're sure that it's not coming from anywhere else but that flamingo enclosure," she says.

The team took samples from around the zoo. And they were shocked. They picked up 49 animal species including rhinos, giraffes and elephants.

"We even detected the guppy that was living in the pond in the rainforest house," Bohmann says. "It was just absolutely mind-blowing."

Meanwhile, Elizabeth Clare, who is also affiliated with Queen Mary University of London, was sampling at an outdoor zoo park in Cambridgeshire, U.K.

Her team was able to detect 25 species, even some non-zoo animals: "Things like the Eurasian hedgehog, which is critically endangered in the U.K.," Clare says. Zookeepers verified that hedgehogs have been seen wandering the area.

The two groups were nearing submission to a scientific journal when they learned of each other's work.

"I woke up to this flurry of text messages from my co-authors saying, 'There's another paper, have you seen this?'" Clare recalls.

Clare and Bohmann knew each other, and rather than compete to rush out a publication first, the two groups got in touch and decided to publish their findings as a pair.

"We are independently confirming this works to ourselves, and to everybody else," Clare says. "I think, we both thought, the papers are stronger together."

Could airborne DNA help track endangered species?

There are a lot of unanswered questions. For one thing, Clare says, researchers still aren't sure what the eDNA they're detecting actually is. It could be skin, saliva, or even urine or feces.

Also, "there were some species we simply never detected even though we know they were there," she notes. Her group missed maned wolves, even though she could smell them throughout the zoo park. Lynggaard says their team missed the Copenhagen Zoo's hippos.

"I see the current state of airborne eDNA as very similar to when the first papers on aquatic eDNA came out over a decade ago," says Stephen Spear, the USGS biologist who was not affiliated with either group.

He believes much more research will be needed to show just how air sampling of eDNA can be applied: "Will this technique work consistently for animals that are smaller or are more mobile? How does it compare to other methods such as camera traps? What's the best way to sample and collect eDNA from the air?"

For her part, Clare is eager to dive into answering these questions, and developing eDNA air sampling into a cornerstone technology for conservation.

"I have this vision of samplers that are deployed globally that can suck up the DNA from all these different sources, from soil and honey and rain and snow and air and water, sequence them on site, beam the data up to the servers," she says. The goal would be a global system of biomonitoring the world's animals. "We don't have a coordinated system for that."