DNA extracted from the air helps identify nearby animals | Science

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This kingfisher stuns its prey can shed the DNA of both species in the air.

Photos by Kevin Elsby / FLPA / Minden

By Erik Stokstad

DNA is everywhere, even in the air. This is no surprise to anyone who suffers from allergies to pollen or cat dander. But two research groups have now independently shown that the atmosphere can contain detectable amounts of DNA from many types of animals. Their preprints, published on bioRxiv last week, suggest that air sampling may provide a faster and cheaper way to study creatures in ecosystems.

The work impressed other scientists. “The ability to detect so many species in air samples using DNA is a huge step forward,” says Matthew Barnes, an environmentalist at Texas Tech University. “This represents an exciting potential addition to the toolkit. “

“What’s surprising is that you are able to get birds and mammals – wow,” says Julie Lockwood, molecular ecologist at Rutgers University in New Brunswick. The new studies suggest “it’s not just spores; there are cells, hair, and all kinds of interesting things floating around in the air.

For more than a decade, researchers have analyzed these disparate sources of DNA in water to identify elusive organisms. The researchers’ sampling of environmental DNA (eDNA) in lakes, streams and coastal waters allowed them to identify invasive species like lionfish as well as rare organisms like the crested newt. . More recently, some scientists have been tracking insects by eDNA on leaves, and have also found eDNA in soil apparently left behind by mammals sneaking along a trail.

Far fewer studies have been done on animal DNA in the air. It is not clear how much tissue is released from animals or how long the genetic content of these cells lasts in the air. Some previous studies have used metagenomic sequencing – an approach to identify mixtures of DNA – to detect microorganisms, including bacteria and fungi abundant in the air. And a 2015 study of air monitors for pathogens in the Washington, DC area found traces of eDNA from many types of vertebrates and arthropods. But it was not clear how useful the technique would be, and it is not clear how land animals get rid of the flying cells.

Earlier this year, Elizabeth Clare, a molecular ecologist now at York University, reported in PairJ that the DNA of hairless mole rats could be detected in air samples taken in the laboratory. To find out if animal eDNA could be detected outdoors, she and her colleagues from Queen Mary University in London visited a zoo: there the species are known and absent from the surrounding landscape, so that the team was able to determine the source of the airborne eDNA they found. . In December 2020, Clare installed vacuum pumps with filters at 20 locations in Hamerton Zoo and let each run for 30 minutes.

Clare collected 72 air samples outside and inside the zoo buildings. She used the polymerase chain reaction to amplify the rare genetic fragments left on the filters into enough DNA for sequencing. “We must have believed it was there because it wasn’t something you can measure,” she says. After sequencing the eDNA, she matched the snippets to known sequences in a database. The team identified 17 species kept at the zoo and others living nearby and around, such as hedgehogs and deer. DNA from zoo animals has been found nearly 300 meters from the animal enclosures. It also detected airborne DNA likely from the meat of chicken, pork, cows and horses fed inside captive predators. In total, the team detected 25 species of mammals and birds.

Meanwhile, researchers in Denmark had pursued the same idea. Kristine Bohmann, a molecular ecologist at the University of Copenhagen, recalls the inspiration she got when thinking about proposals for a high-risk grants program. “I remember saying, it must be crazier, like sucking DNA out of the air, that would be crazy.” They won the grant and sucked air from three locations in the Copenhagen Zoo with vacuums and fans in three types of samplers. They systematically detected animals – a total of 49 species of vertebrates.

“These preprints are exciting and show great data,” says Kristy Deiner, conservation ecologist at ETH Zürich. She is leading an XPRIZE Rainforest team to develop airborne DNA technology for biodiversity monitoring.

Airborne DNA can help reveal the presence of otherwise hard-to-detect animals, such as those that live in dry environments, burrows or caves, and those that fly out of sight of wildlife cameras, such as certain birds. , explains Lockwood.

She cautions that many questions remain about the approach, including the key question of how far eDNA travels in the air, which will influence how the method can pinpoint the recent locations of animals. This distance will depend on many factors, including the environment; The DNA will likely float further in a meadow than in a forest. Another question is how exactly do animals get rid of DNA. This can be when cells are released as they scratch or rub their skin, sneeze, or do some vigorous activity like fighting or subduing prey. But even the sloth’s eDNA appeared, says molecular ecologist Christina Lynggaard, a postdoctoral fellow at the University of Copenhagen who carried out the sampling at the zoo.

Preventing contamination, always an issue with eDNA studies, is particularly tricky. Sampling eDNA in air, Barnes says, is like “pipetting underwater.” One problem, says Clare, is how to find a negative control or a test sample without DNA. “I don’t know where to buy a sterile air balloon.”

Despite the unknowns, Barnes and others have high hopes. Lockwood, who studies forest pests and has identified traces of eDNA on bark and leaves, is already hoping to identify insect pests from the air. “I can’t wait to try it,” she says.

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