Two research teams independently used vacuums to measure biodiversity

Just as the pandemic hit, Christina Islas Lynggaard—a postdoc researcher at the University of Copenhagen’s Globe Institute—sat in her apartment surrounded by vacuums and filters. She tested them, eventually landing on a water vacuum, which was, for her purposes, pretty good. The rest didn’t quite make the cut—they had good suction, but the second you put a filter in them, it messed with their power supplies. “It just dies, and then the motor comes to overheat, and it was very difficult,” Lynggaard said.

All this testing was done for an interesting case, one that seems obvious in hindsight but could have valuable ecological applications. In short, Lynggaard and other researchers on her team were looking for a way to collect environmental DNA (eDNA) from the air to measure biodiversity or look for the presence of rare or invasive species.

Out of thin air

“We had no idea the best way to collect DNA from air,” Kristine Bohmann told Ars. Bohmann is an associate professor at the Globe Institute and one of the researchers involved in the effort.

As it turns out, it appears you can gather eDNA from the air by sucking it through a vacuum (or something similar), catching it in an attached filter, and analyzing it. Bohmann, Lynggaard, and other researchers recently published the results of their work in Current Biology. The study's publication coincides with a different piece of research showing largely the same conclusions using a slightly different method developed by a team in the UK and Canada.

In the past, trying to measure biological diversity or check for the presence of a species was grunt work that often involved setting up cameras or going out and waiting to spot the species. More recently, however, researchers have been using eDNA for this purpose, as it can be easier. According to a paper from last February, the most common form of eDNA testing involves filtering environmental water through a membrane and studying the accumulated materials—often DNA-carrying bits of skin, feces, mucus, etc.

“Air is the equivalent of water in that it surrounds everything on land, just as water surrounds everything in a lake or in the ocean,” Bohmann said. However, these two papers describe something that, by and large, hasn’t been done before: measuring eDNA from the air. The concept isn’t wholly new; one piece of research from last year used air, water, and soil to detect big brown bats. All the same, the Danish researchers believe they’re onto something with this work.

“I had a very good gut feeling about this. I just knew I had to do this study.” Bohmann said, recalling the first grant application she wrote for this project, which was denied.

Proofs of concept

In 2019, though, Bohmann and Lynggaard's second attempt to get a grant came through. To test their ideas, the team went out to the Copenhagen Zoo armed with the water vacuum and—by the suggestion of one of their coauthors—two blower fans. The fans were like the ones found in laptops but with a 3D-printed housing so filters could be attached to them. Lynggaard tested out a lot of filters before landing on class F8 filters, which are good at collecting and retaining particles.

From there, the team wandered around the zoo and collected samples from three different areas: a stable, which contained okapi and a tiger; the outdoor holding area; and inside the “Rainforest House,” which featured birds, reptiles, sloths, etc. The vacuums sucked up air in these areas, and bits of animal detritus got caught in the filters or, in the case of the water vacuum, in the water. Back in the lab, the water could also be run through a filter.

The lab itself was thoroughly cleaned and had strict rules about entry to avoid contaminating the samples. The team also collected air samples from the lab to get a sense of the ambient DNA present.

At first, they weren’t sure what kinds of DNA, if any, they would find. From the 40 samples they took, the team members identified 49 different species, from a rhino down to the guppies in the Rainforest Room. Each sample had DNA from between six and 21 creatures. Some of the detected species—such as the water vole and red squirrel—weren’t even zoo animals; they were just nearby. “We were absolutely falling off the chair amazed, surprised, shocked,” Bohmann said.

The Canadian/UK researchers took a similar approach, but they headed to the Hamerton Zoo Park, UK, said Elizabeth Clare. Clare is an author of the paper and is currently an assistant professor at York University’s Department of Biology. Her team used vacuum pumps fitted with sensitive filters and collected more than 70 air samples from various areas around the zoo, both in and outside animal sleeping areas. She compared the device they used to a coffee machine, except the filter catches DNA rather than grounds. From there, much like the Danish researchers, she took the samples and analyzed them. “We have a great deal of experience working with environmental DNA,” she told Ars.

After the analysis, her team found DNA from 25 species, such as dingoes and tigers. Seventeen were known zoo species, while the rest were non-zoo animals nearby, such as the Eurasian hedgehog, which is endangered in the UK. The researchers also found that they could capture DNA from an animal even when collecting it from outside a sealed building, and—like the Danish team—detected DNA from animal-based foods like chicken in an area with an animal that eats chicken. “We’re almost certainly detecting their food as well as them,” Clare said.

Questions remain

The teams became aware of each other's work and say they are encouraged that the studies came to similar conclusions through different approaches. “I’ve never seen such identical experiments put together at exactly the same time… that didn’t have any knowledge of each other,” Clare said. “When you’re doing something a little bit crazy—vacuuming DNA out of the sky—it’s really nice when someone else has also been able to do the same thing and independently confirm that [it] works.”

Beyond the potential it has for biodiversity monitoring and checking for the presence of rare or invasive species, the approach is likely to be a lot less disruptive than going into a terrestrial ecosystem and actively seeking out a target species. According to Clare, the process also negates the need to actually physically see a creature, either in-person or using a camera trap, which animals can simply walk behind. “They’re leaving a trace of themselves. The animal can move on and be gone, and you can still detect them,” she said.

However, both teams agree that it's still early days for this area of research. Clare noted that the researchers don't know how things like wind, sunlight, and other factors—some of which might degrade the DNA in the air—could impact the approach's efficacy. And its sensitivity is unclear. The Danish researchers said that terrain—say, a rainforest versus an open field—may also impact results. The optimal way to collect the DNA, which likely varies from setting to setting, is yet another area that needs more exploration. “It’s very, very early in this… But the potential is enormous,” Clare said.

Current Biology (2021). DOI: 10.1016/j.cub.2021.11.064
Current Biology (2021). DOI: 10.1016/j.cub.2021.12.014

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