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Sunday, May 19, 2024

Scientists Capture Airborne Animal DNA for the First Time

As a graduate student, Kristine Bohmann made a few sacrifices to obtain her academic pedigree, like wading into a leech-infested stream in Madagascar to collect genetic clues about nearby wildlife by examining the parasites’ guts. To do so, she first had to allow them to cling to her bare skin. “I acted as human bait,” says Bohmann, an associate professor of evolutionary genomics at the University of Copenhagen. “These leeches would actually have fed on animals in the rainforest, drawn their blood, and are excellent preservers of DNA.”

Now, Bohmann and a second group of researchers have come up with a much easier way to sample for environmental DNA, or “eDNA.” They rigged up a few air filters in and around two zoos to capture microscopic bits of genetic material floating along on the breeze. After removing the tiny filters and amplifying the DNA with a sequencer, they were able to find genetic markers for dozens of individual captive animal species, as well as the free-roaming creatures that live nearby, like squirrels, cats, and hedgehogs. While scientists have been using similar eDNA sampling techniques to detect genetic material from fish and other creatures in rivers and the ocean, this is the first time it’s been used for mammalian DNA collected from the air. “The next step is to figure out how to take this method into nature and how to adapt it to the different types of habitats and ecosystems,” Bohmann says. “It’s quite exciting.”

The results of these two zoo-based experiments were published last week in the journal Current Biology. The first paper is from Bohmann’s team at the University of Copenhagen; the second report is from a group at Queen Mary University in London and York University in Toronto.

The Danish researchers set up three air filters for 30 hours at a time and were able to identify 49 vertebrates, including 30 mammals, 13 birds, four fish, one amphibian, and one reptile. They found DNA from captive zoo animals like the okapi and an armadillo, a guppy living in a pond in the rainforest house, and even pests like the brown rat and house mouse. Tiny bits of DNA from fish used to feed other animals in the zoo were also lofted skyward and detected by the filter.

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In comparison, the UK group only sampled the air around the Hamerton Zoo Park near Cambridge, England for 30 minutes at a time, but they moved the filters from place to place in order to see if they could track the animals’ movements. The team took 72 samples and used a lab technique called polymerase chain reaction to amplify the tiny amount of material so they would have enough to identify genetic markers for individual species, according to Elizabeth Clare, the lead researcher and an assistant professor of biology at York University. She says the DNA filter worked like a coffee filter: “You've got the air going through, and anything that's particulate should get caught, the same way your coffee grounds get caught but the water rushes through. What we're trying to do is trap DNA or cells or microscopic fragments of tissue that's in the air on this filter. Then we can go back to a sterile lab, crack open the tube, withdraw this tiny filter, and extract DNA directly from that.”

The UK group identified 25 animal species, including 17 captive animals, such as gibbons, dingoes, meerkats, sloths, and donkeys. They also found random visitors, like squirrels and a hedgehog that was likely prowling around the park looking for food. The team detected movement of the zoo animals through space, not just their presence in one part of their enclosures. Clare expects that air sampling will soon be used in the field—which would be a huge deal for biologists trying to figure out where endangered animals live, breed, or migrate and to protect those areas from human development.

Wildlife researchers have been looking for a better way to track animals for years. Some set up “camera traps” along known wildlife trails to get images of shy creatures who might only come out rarely or at night. Others look for signs of scat, or feces, that might indicate the presence of the animal and what it’s been eating. There’s also the old standby: footprints left along a muddy riverbank, snowbank, or sandy desert.

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But for many biologists, tracking mammals that move miles each day and are wary of humans can be nearly impossible. Enter eDNA. “If we want to restore ecosystems, we need to understand how our conservation actions influence threatened and endangered species. But to do that we need to be able to detect even the rarest, shyest, and most cryptic species,” Michael Schwartz, senior scientist at the US Forest Service’s National Genomics Center for Wildlife and Fish Conservation in Missoula, Montana, wrote in an email to WIRED. “We need new technologies, like the ability to detect airborne environmental DNA.”

Schwartz, who was not involved in the two new studies, has been using air, water, and soil samples to track big brown bats (Eptesicus fuscus), whose numbers have been devastated by white-nose syndrome, a fungus-borne disease that arrived in the United States in 2006. Schwartz and his colleagues published a study in September in the journal Biological Conservation that examined eDNA samples from soil and water outside the caves where the bats roost. They also used an air sampler as part of the project to see if they could capture airborne DNA from a bat enclosure in Ohio. Six of the seven filtered air samples successfully detected their eDNA in the air, the study reported, but the concentrations were low, despite the 30 bats being housed in the room.

Schwartz says his colleagues are refining their air sampling techniques and working on a method of collecting small amounts of DNA from snow. This not only allows the USFS team to detect which mammal species recently traveled over the snowpack, but digging into it also lets them find evidence that a specific kind of animal traveled through the area months earlier. Schwarz’s group published some results on this project in the journal Biological Conservation in 2019. Using snow tracks to detect shy predators like the lynx is cost-effective, efficient, and definitive, he says.

Would the air-DNA sampling technique work for tracking genetic material from individual people? Hypothetically yes, but practically no, says one expert. “It's possible, but it would be a bit more challenging,” says Melania Cristescu, an associate professor in ecological genomics at McGill University, who uses eDNA to sample aquatic habitats. Bits of human DNA from hair, saliva, blood, or other genetic material left behind on surfaces are easier to analyze than the air. (Swiss researchers recently resolved a family ancestry mystery using DNA from postage stamps stuck on a postcard from World War I, demonstrating the stability of the molecule in certain conditions.) But it would take longer to get a big enough sample of airborne genetic material, and researchers would have to take great care not to allow their own DNA to contaminate the filter.

With airborne DNA, weather is also a factor. Sampling might not work as well if it's rainy or windy, for example, because these conditions might clear the air of particles carrying DNA. It’s also not clear how well the molecule will hold up under heat or bright sunlight. “Does solar radiation degrade DNA? Probably, but we don't know at what rate,” Clare says. “We don't know how far wind can disperse DNA. We don't know how temperature might affect its degradation rates. These are all really interesting questions.”

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Both Bohmann and Clare say their zoo-based experiments are just a start, and they hope to continue research to improve both sampling techniques and the technologies involved. The whole field of eDNA is moving quickly, and scientists foresee a time when they can use it to determine whether, say, invasive plant or animal species are moving into an area, or whether a certain patch of jungle or forest needs protection because wild animals use it to migrate or feed. 

Detecting an animal’s movement patterns over time, rather than just knowing its present position, is key to protecting its habitat from development and preserving the planet’s biodiversity, the researchers say. “Almost everything that exists requires the animal to be present when you are. So if you've got a camera trap, it has to walk in front of the camera trap. And if it goes behind, you’ll never know it was there,” Clare says. “DNA is a non-invasive method—so the animal may have been there yesterday or the day before, and you can actually still detect it. It's more like a footprint that's left behind.”


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