Researchers can now collect and sequence DNA from the air

We leave DNA all over the place, including in the air, and for the first time, researchers have collected animal DNA from mere air samples, according to a new study. 

The DNA that living things, human and otherwise, shed into the environment is called environmental DNA (eDNA). Collecting eDNA from water to learn about the species living there has become fairly common, but until now, no one had attempted to collect animal eDNA from the air. 

"What we wanted to know was whether we could filter eDNA from the air to track the presence of terrestrial animals," study author Elizabeth Clare, an ecologist at Queen Mary University of London, said in a video abstract for the study, published Mar. 31 in the journal PeerJ. "We were interested in whether we could use this 'airDNA' as a way to assess what species were present in a burrow or a cave where we could not easily see or capture them," she added.

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As a proof-of-concept experiment, Clare and her colleagues tried collecting DNA from the air in an animal facility housing a model organism, the naked mole rat. The researchers detected both human and mole rat DNA in air from both the mole rat enclosures and the room where the enclosures are housed.  

"The demonstration that the DNA from relatively large animals can also be detected in air samples dramatically expands the potential for airborne eDNA analysis," said Matthew Barnes, an ecologist at Texas Tech University, in Lubbock, who was not involved in the new study. 

In the last decade, the collection and analysis of eDNA to study and manage plant and animal populations has taken off, Barnes said. "The analogy that I use is like the detective at the crime scene, finding a cigarette butt and swabbing it for DNA to place the criminal at the crime scene. We do that with eDNA except for instead of looking for criminals, we're looking for a rare or elusive species," Barnes said. The species might be endangered or an invasive species new to an environment, he said. 

Prior to this study, some researchers had collected plant DNA from the air, but most of those experiments involved plants that were "expected to intentionally release plumes of DNA into the air in the form of pollen and dispersing seeds," Barnes said. Animals, on the other hand, don't do that. "We had no idea if this would work," Clare told Live Science.

But while animals don't shoot pollen spores into the air, they do shed DNA in the forms of saliva and dead skin cells, for example. To see if animal eDNA from these sources could be collected, Clare and her colleagues vacuumed air from an enclosure of naked mole rats and from the room housing the enclosures through filters similar to the HEPA filters commonly found in heating and ventilation systems. The researchers then extracted DNA from the filters and sequenced it. To identify the species the DNA came from, the researchers compared the sequences to reference sequences in a database. 

The finding of human DNA within the animal enclosure at first surprised the researchers, Clare told Live Science. However, given that humans care for the mole rats, it made sense in retrospect, Clare said.

The presence of human DNA in nearly every sample from the study is "a major hurdle," Barnes said. On one hand, it encouragingly shows that the detection method is sensitive, Barnes said. But "this could also suggest that airborne samples are particularly easy to contaminate with DNA from the research team, especially when mammals are the target of analysis," he added. 

To avoid such contamination, researchers might have to use clean room techniques — think air filters, gowns and hair nets — to avoid adding their DNA to the environments they're studying or to DNA samples they're working with, he said.

In the future, scientists hope to use the technique to monitor animal species in hard-to-reach dwellings. "I can envision sticking a tube into a roost or down a tunnel system and sucking the air from that system rather than having to try and track the animals to figure out what's present," Clare told Live Science. 

It might also be a good way to detect species that are present but rare in a given environment, such as an endangered species, she added. And it could help detect a species without interacting with it, which could have advantages, Barnes said. "[The method might] give us an opportunity to survey for organisms without having to handle them and stress them out," he said.

Whether eDNA analysis would allow scientists to estimate population sizes, or the number of animals living in a dwelling, is a subject of debate, but Clare said that she doesn't think it's good for that. "There are too many steps in the procedure that can cause the amount of DNA you collect to vary," she said. 

Now Clare and colleagues are studying how far airDNA can travel and how the size of space affects how much eDNA can be detected, Clare said in the video abstract. 

Another important step in the study of animal airDNA will be to try to collect airDNA from animals outdoors, rather than in a research lab, Barnes said. 

Originally published on Live Science.