Vacuuming DNA Out Of The Air : Short Wave A few years ago, ecologist Elizabeth Clare had an idea--what if she could study rare or endangered animals in the wild without ever having to see or capture them? What if she could learn about them by only pulling data out of thin air? It turns out, the air's not so thin. There are bits of DNA floating around us, and Elizabeth figured out how to collect it. She talks to guest host Lauren Sommer about testing her collection method in a zoo, how another science team simultaneous came up with and tested the same idea and how DNA taken from the environment could revolutionize the field of ecology.

Read about the study here.

Vacuuming DNA Out Of The Air

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EMILY KWONG, BYLINE: You're listening to SHORT WAVE...

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KWONG: ...From NPR.

LAUREN SOMMER, HOST:

Hi, SHORT WAVErs. Lauren Sommer here. Elizabeth Clare took a really unusual trip to Hamerton Zoo in England a few years ago.

ELIZABETH CLARE: They have a lot of really lovely outdoor enclosures, but probably the nicest scene was all the dingoes.

SOMMER: Elizabeth is an ecologist at York University in Toronto.

CLARE: And this entire pack of dingoes lined up, watching us out of total curiosity and jumping up and down trying to get closer to find out what it was we were doing.

SOMMER: That's because she and her team were standing next to the enclosure holding up a weird kind of vacuum.

CLARE: We had a very tiny filter. It's about 2 inches long. And it's attached to a long hose. And the hose runs to a pump. It's kind of analogous if you're making coffee and you had the water dripping through and the grounds of coffee are caught on the filter paper, but the water goes through.

SOMMER: What her team was doing was collecting DNA from the zoo animals without touching them because the DNA was floating in the air. It's called environmental DNA, or eDNA.

CLARE: Environmental DNA is any DNA that you capture that doesn't come directly from the source. So if I went to those animals and I took a skin sample or a saliva sample, that's a direct DNA sample.

SOMMER: But this DNA is airborne. It drifted off the animal - though what part, they're not really sure.

CLARE: It could very well be bits of dead skin cells that are being lost or fragments of hair. It could be saliva. It could be urine or feces that's tossed up into the air and becomes particlized and aerosolized and then can float around.

SOMMER: Because animals are always shedding DNA, and the molecules can end up in a lot of places.

CLARE: They've been found in the soil and the water and permafrost and snow and rain, and now we're able to collect them directly from the air.

SOMMER: That makes it a powerful scientific tool that could change the way researchers study animals and even entire ecosystems. Today on the show, we talk about the invisible bits of DNA floating in the air all around us and how it could help rare and endangered species around the world. I'm Lauren Sommer, and you're listening to SHORT WAVE, the daily science podcast from NPR.

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SOMMER: When biology textbooks talk about DNA, they usually talk about it hanging out inside cells. That's not the kind of DNA Elizabeth Clare studies. I talked to her about DNA that's shed by living things into the environment.

So, you know, ever since the discovery of DNA, have scientists known or guessed that this eDNA could kind of just be around everywhere? Was eDNA kind of discovered at a certain point?

CLARE: The first report of environmental DNA, as we discuss it now, really comes from about 2003, and it was found in ice cores, in permafrost, some of it going back tens of thousands, hundreds of thousands of years. And in fact, some of the very first studies of environmental DNA were reconstructing paleo environments, finding extinct animals. A lot of people didn't believe it was real when they actually managed to find hundred-thousand-year-old fragments of DNA floating in a bit of ice. And then it kind of carried on in that area of research for a couple of years.

And then where it really became important was in water, but we've also found it almost everywhere we've looked. So people have found DNA in the footprints left in snow or in the water that runs off foliage. Honey has been found as a source of DNA - that you can look at insect and plant communities from honey samples. So it really is everywhere.

SOMMER: It's a really interesting idea to think we're all walking around in a big soup of DNA (laughter) all around us.

CLARE: Well, exactly. And from a research perspective, it's a marvelous idea that there's literally information hanging in front of me, and I just figure out how I can get it, then I can use that information. But then you sort of think - when I go for a walk with my dog or with my kids as I'm playing at the park and I take a deep breath, and I think, what have I just breathed in? What bit of information has just entered my body? You know, there's all these - this sort of soup of everything and everybody in every organism that's been through an environment, leaving behind this little trace.

SOMMER: Where did your idea come from to look in the air?

CLARE: My university at the time actually offered some funding available for what they described as sort of high-risk but potentially transformative or really high-impact ideas. And so I pitched this idea, and I said, I think I can vacuum DNA out of the sky. And I said, you know, if it's successful - the aquatic community has shown us the power of this technology. If we can do it with air, we can do on land what has now become almost universally applied in water. And so they funded the research to let us try it.

SOMMER: And so you ran your experiment in a zoo, which makes sense, right? You kind of know what's there, at least based on the map of all the animals. Did you find the eDNA of everything that was on that map in terms of each animal that was there?

CLARE: Sort of yes and sort of no. The zoo is a wonderful place to run the experiment on land because you have this colony of non-native species, and you can't mix them up with anything. If I detect tiger DNA in the British countryside, there's only one source for that DNA. It'll be the tiger in front of me.

But also, one of the real big questions is how far the material could move. And so we know with absolute certainty where those animals are at the zoo. If we detect their DNA somewhere else, we can at least give a minimum estimate of how far it went. We detected about half of the animals we were sort of targeting to detect.

We then detected a lot of things we didn't expect. We detected other zoo animals that we weren't specifically targeting because their DNA was moving towards us through the zoo. We also detected the stuff they were eating. So we detected chicken DNA amongst the pens where animals are fed mostly chicken. We detected cow and pig and horse and deer specific to the enclosures where that's the preferred food of the animals.

And then we detected some of the native British wildlife, and that's really exciting 'cause, ultimately, that's exactly what we want to be able to do.

And we also, excitingly, found hedgehogs. And the European hedgehog is actually endangered in the U.K. So being able to detect its DNA in that environment where we know they probably should exist is a really good indicator of the kind of sensitivity of this to local wildlife and things that are potentially the real targets of this - the endangered species.

SOMMER: So it really is just a proof of concept. Were you surprised at the number of things or how far the DNA was traveling?

CLARE: Yes. I mean, we had no preconceived idea of what we might find. And we're very seriously concerned we would find nothing, that it just wouldn't be viable outside. I think we were shocked at how well it worked.

SOMMER: And you had to get a menu readout from the zoo about everything they were serving, basically.

(LAUGHTER)

CLARE: Well, that's where it became fun, saying things like, well, am I correct that you feed the dingoes this? And they'd go, yes. And, you know...

(LAUGHTER)

CLARE: And then it becomes almost like magic. It's so exciting to be able to do those kind of things.

SOMMER: And kind of in the middle of this process - right? - you learned that someone else was working on a similar idea. Can you tell me what happened?

CLARE: Yeah, this is my favorite part of the whole story, I think, beyond the excitement of the science. We put our paper on an open-access preprint server, and it turns out, completely independently, a group of scientists in Denmark had done exactly the same thing at the Copenhagen Zoo, and they had basically found all the same things we had found. They had written their paper up. They had submitted it to the same journal we had. And then they saw our paper and they put their paper up on the same preprint server.

I have never heard of this happening before. And so the PI of the other paper, Kristen Bowman (ph), and I talked to our teams and to the other authors, and we decided as two groups that we were not willing to engage in a scientific race. We wrote to editors of those journals directly, saying we really think these papers should appear together - perfect scientific replication, completely independent and totally simultaneous. You get both or neither. We want them to be together.

SOMMER: And as you said, science is competitive. It's not that common to kind of collaborate in this way. But is there a real strength in doing it like this?

CLARE: Absolutely. Science is supposed to be replicable, and you couldn't get better replication than having two people perform the same experiment with no knowledge of each other.

SOMMER: So in ecology - right? - a huge part of the field is just trying to figure out what's out there - right? - monitoring species, trying to figure out their habitats. Is eDNA actually making a difference in the field right now in terms of knowing what endangered species are out there or conservation - stuff like that?

CLARE: Absolutely. When you work with environmental DNA, you can target a particular thing you want to survey for, but you're going to get everything else at the same time. So like in our case, we were targeting zoo species. We also got native wildlife, and we got diet, all at once. And so for the same effort of collecting material and analyzing it, rather than getting one baseline assessment of whether something is present, you'll get hundreds at the same time. Environmental DNA is massively speeding up the process of doing environmental monitoring.

The other amazing thing about it is you don't have to be a specialist to do this. Knowing what to do with it afterwards requires fairly highly specialized facilities, but actually collecting the information to begin with doesn't turn out to be that hard.

SOMMER: And is there a sense of how long eDNA can hang out? Like, if a tiger walked through six months ago, is there still a chance you would pick up its DNA?

CLARE: In air, we simply don't know. That - these are literally the first experiments that have ever shown it's even possible. And beyond that, it's - this is the kind of question we have to ask now. You know, how far away do I have to be to detect it? How many have to be there for me to detect them? Is wind going to change that scenario - or temperature or humidity or solar radiation?

SOMMER: Are there any specific examples of endangered species that are kind of like the poster species for using eDNA?

CLARE: Yes. In aquatic systems, the biggest and most famous example of doing this are the great crested newts in the U.K. Environmental DNA monitoring is now part of the basic requirements for doing an assessment for the presence of the great crested newt. And so that's actually one of the most famous examples.

SOMMER: I guess, what are you most excited about for this field in the years and decades ahead? I mean, do you see this as being really revolutionary for conservation?

CLARE: I think so. The two things that really excite me, the potentials for this are - No. 1 is sort of invasive species. We probably can use this as a sort of early warning system. If something is newly moving into an area, we might detect it with DNA long before there's enough of them that you would see them in a camera trap or catch them in your net or your trap.

The other end of the spectrum on rare species are the endangered species or the highly, highly sensitive species that you can't get near because they're so sensitive. This is a very, very noninvasive technique, and I think it'll be really good at allowing us to assess whether something that is rare is still present in an area.

SOMMER: You know, we know there's a biodiversity crisis out there, and so it is a really interesting idea of could we have an assessment and track it over time to really get a picture of how that's happening?

CLARE: Yes. And this is being done in water, and it's the kind of thing we want to replicate on land. If you're going out to survey the tiny, little things that actually make ecosystems functional - the insects and all the nematodes and the things that do the real functions of ecosystems - most of them have never been seen and never been recorded. And DNA is one of the great levelers for this. It's a fundamental problem for all of biodiversity science that we do not have a good estimate about what lives in any ecosystem on the planet. And that's a disaster. You cannot measure if something is disappearing if you've never recorded its presence.

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SOMMER: That was Elizabeth Clare, professor at York University in Toronto.

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SOMMER: This episode was produced by Berly McCoy, edited by Gisele Grayson and fact-checked by Katherine Sypher. The audio engineer for this episode was Patrick Murray. I'm Lauren Sommer. Thanks for listening to SHORT WAVE from NPR.

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