Identifying Animals Through Airborne DNA
In recent years, the technique of eDNA—environmental DNA, or samples taken from the environment, as opposed to from a specific animal—has changed ecology research. Scientists have learned how to obtain eDNA from water samples, soil, and even the intestinal tract of other animals. Writing recently in the journal Current Biology, two different groups report that air samples collected with filters in a zoo can provide enough DNA to paint a partial picture of the species living in and around the zoo.
After taking over 72 samples from 20 sites around a zoo in the UK, Dr. Elizabeth Clare and colleagues brought their trove back to the lab, and were able to identify 25 different species living in and around the zoo. Some were expected zoo inhabitants, and others were surprises—including DNA from a species of endangered European hedgehog. At the same time, a separate group of researchers performed a similar analysis on a Danish zoo, and achieved similar results.
Dr. Clare joins Ira Flatow to talk about the research, and what the technique of eDNA might be able to bring to the world of conservation ecology.
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Elizabeth Clare is an assistant professor in the Department of Biology at York University in Toronto, Ontario, Canada.
IRA FLATOW: This is Science Friday. I’m Ira Flatow. This hour has sort of an animal theme. We’re going to be singing the praises of pigeons. I know you’re going to want to stay with us for that one. And we’re going to scratch our head at an acrobatic beetle. But our first story, well, it’s all happening at the zoo. Suppose you want to know what species live in your local zoo. Well, you could look at the zoo’s website, maybe ask people coming out of the zoo what they saw or listen for the noises you hear. Or maybe you could sniff the DNA out of the air.
Writing in the journal, Current Biology, two research groups report that they’ve been able to do just that– detect what animals live in the zoo by sniffing the air with a fan and a filter and sampling the DNA they trap– eDNA, as it’s called. Joining me is Dr. Elizabeth Clare. She’s an assistant professor in the Department of Biology at York University in Toronto, Canada, and a member of one of the research groups. Welcome to Science Friday.
ELIZABETH CLARE: Thanks for the invitation.
IRA FLATOW: Is it really as simple as setting up a fan and a filter and getting an air sample and sequencing what you find there?
ELIZABETH CLARE: Pretty much. We’re vacuuming the DNA out of the sky now, and no one was more surprised than me that it actually worked.
IRA FLATOW: Tell us about your setup, please.
ELIZABETH CLARE: We have a long history of working with this environmental DNA. It’s any of the DNA that’s shed into the environment. You don’t take it directly from an animal source. And we’ve been filtering this out of water. We’ve collected it from things like soils, from the gut tract of another animal to figure out what they’re eating. And so we took the apparatus we actually use to filter water, and we aimed it at the air. It’s a really simple device. It’s a tiny little capsule with a very, very fine filter in it.
And it’s kind of like the way you make coffee. When you’re making coffee, the water goes through and the grounds get trapped in the filter. It’s the same idea, only this time, we’re pulling air through. And anything that’s in the air is being trapped on this tiny, tiny little filter. And then I can take it back to my lab. I can crack that open, take this really tiny, fine filter out, and use it like a tissue source. And it turns out it’s absolutely full of DNA, and it’s just floating around us.
IRA FLATOW: That’s amazing. And I know you looked at a zoo in the UK with this technique. What could you identify in the air?
ELIZABETH CLARE: Well, the great thing about a zoo as a place to test this kind of technology is that the animals are this collection of non-native species. Had we gone to a farm and detected, for instance, a cow, we really do not know whether it’s the cow in front of us or a manure on the fields or cows hundreds of miles away. The zoo, there’s only one source for that animal DNA in that environment. So if I pick up tiger, it’s the tiger in front of me. There’s no other signal I could confuse it with in the British countryside. So that’s one of the reasons to pick a zoo in the first place.
We took samples at their enclosures, where they sleep, outside, where they roam around freely, and almost all of our samples turned up DNA. We picked up about 25 different species of mammal and bird. About half of them were zoo residents that we expected to get because we were right there looking at them. The other half were this mixture of other zoo species that we were nowhere near that had the DNA had sort of drifted towards us. We also picked up the things they were being fed. So if you’re near a carnivore cage, we were able to determine their favorite food from the DNA in the air, the thing they ate the most of.
And then we picked up some of the native British wildlife, like ducks and squirrels and even the European hedgehog, which is endangered in the UK and of serious environmental concern and just exactly the kind of target we should be able to pick up DNA from, something we want to be able to determine if it’s present or absent and track it. And there was its DNA, floating around the zoo.
IRA FLATOW: Did some animals not show up that you expected to show up?
ELIZABETH CLARE: Yes, both research teams, our team and the team in Denmark, picked up animals they expected to, but also missed some. So in our case, for instance, there were several species of lemur at the zoo. One of them, we never detected. One of them was the most common thing we detected. And at this point, we have no idea why that difference should exist. The Danish team, I think they missed hippopotamuses that were there.
IRA FLATOW: Wow, that’s something big to miss.
ELIZABETH CLARE: Yeah, and we don’t know. And that’s true of many forms of environmental DNA. When you detect something, you can be pretty sure it was there. When you miss it, it’s not always clear why you miss it.
IRA FLATOW: And is the whole point of this to do a census of what is at the zoo?
ELIZABETH CLARE: Well, it was a test bed for us. The whole point of this is to be able to go out into an environment, sample the air, and determine biodiversity without ever actually seeing the animals. Most of the techniques we have for doing an environmental survey require that the animal be present when you are.
If you’re using a camera trap, it has to walk in front of your camera trap. It goes behind, you’ll never know it was there. If you’re doing a visual survey, it has to be there when you’re there. But environmental DNA is more like a footprint. They leave it behind. And so you can detect things that were there yesterday or the day before that. It gives you a longer period to sample. And it’s one of the powers of environmental DNA that hangs around.
And so the real thing we want to do with this is to go out into the wild, be able to take air samples, and add this to our toolbox of things to do an environmental survey. So, yep, biodiversity, we want to be able to count things in the environment and know they’re present. But probably the greater application is with rare things. Environmental DNA has been uniquely good at finding stuff that’s rare that you miss on the traditional surveys.
And so the sort of immediate applications I can think of are invasive species, things that are moving into an area that you haven’t picked up on your traditional surveys yet– you might get their DNA first– or the rare species, the endangered species that are so sensitive that you can’t interfere with them. This is a totally non-invasive way of taking a sample. And you might be able to determine that they’re still present, even when they’re so rare, you don’t see them very often. So we really think the true application is going to be looking for rare things.
IRA FLATOW: That makes me want to ask how far away– if you take it out into the wild, how far away, how good is it at detecting stuff in the wild?
ELIZABETH CLARE: That’s a really good question. The distance that the DNA travels is something we’re trying to determine. And that’s the other reason why the zoo was picked as our place to test this out as a viable method. We know where all those animals are spatially in the zoo. So if we pick their DNA up somewhere different, we can at least measure the minimum it traveled.
We found dingo DNA at the gibbon enclosure. We found zebra finch DNA at the primate house. And so it allows us to measure at least how far it could have gone. And in our case, we know it was going a few hundred meters at least. We don’t know the upper limit on that. There is some anecdotal evidence it might be traveling a lot further than that. But from our experiment at the zoo, at least 250 to 300 meters is reasonable.
IRA FLATOW: Tell us about the DNA a bit more. Is it coming from the skin or the breath or something else? All kinds of possibilities.
ELIZABETH CLARE: Well, we really don’t know the source. We know that environmental DNA is shed all the time. It’s been found in almost every substance we’ve looked at. Strange things like honey traps environmental DNA, rain, snow, soil. People even spray the surfaces of leaves and collect the water that runs off to get DNA that settled.
Where it comes from is more complicated. It’s probably every source you can think of– bits of skin cells being shed, tiny fragments of hair, urine, feces, maybe even breath being breathed out carrying DNA with it. It might even be the fragments of DNA that are left behind when a cell dies and dumps its contents into the environment. So it could be absolutely anything. Any way that you draw up a tiny little piece of yourself behind is going to leave this trace that we can now collect.
IRA FLATOW: Hmm, interesting. What about this other team? There’s another paper that goes right alongside with yours.
ELIZABETH CLARE: Well, this is the wonderful thing about this story. We had finished our paper, and we put it up on an online server to share with the scientific community. And then another paper appeared that was absolutely identical. Same experiment, a different zoo, a different group of people. And it appeared within 48 hours of ours. And so we contacted the other team and discovered that we had both done the same experiment at the same time, perfectly replicating each other’s data, with no knowledge. It’s the biggest scientific coincidence I think I’ve ever heard of.
And so we contacted the other group, and rather than getting into some sort of race to see who could publish their paper first, we started to coordinate. And over the course of a couple of weeks, we contacted editors of the scientific journals directly and said, we think you’re stronger to have two. If you’ve got some crazy idea, it’s nice to have someone else who’s done the same thing and shown it works. And so we worked with the other team to get them published on the same day at the same time. And the other team found the same things we did and total coincidence.
But it’s really how science is supposed to work. We’re supposed to replicate each other’s data. And this is an incredible case where two groups, our group in England and the group in Denmark, did the same experiment in the same way at the same time and found the same thing and have managed to publish them in the same journal on the same day.
IRA FLATOW: We’ve got these rapid tests for various diseases like COVID. Do you think it’d be possible to design a rapid test for DNA in air, a sort of a paper that turns color if a certain species is nearby?
ELIZABETH CLARE: That’s possible. I’m not sure how widely applicable it would be. If there’s something in particular you’re looking for, you can do that. And I know those sort of assays exist. But in general, the sort of DNA is being used for finding everything. And we do have mobile labs that can do this. I have gone out into the middle of a jungle and sequenced DNA with no internet and no lab and no source of even a cell phone signal.
We’ve been able to do that. It’s not very practical. It still takes a couple of days. But it’s certainly possible. This sort of technology is advancing so quickly that I think very soon, my lab and others like them will be doing just that. Go to an environment and do all your collection and sequencing on-site, never go back to your lab at all.
IRA FLATOW: Well, would you be just as excited if you found and collected DNA that you have never seen before?
ELIZABETH CLARE: Absolutely. I started off my career as a taxonomist describing new species and doing that using DNA as a primary source of information. And so if we find something that’s never been seen before, that’s not uncommon in the world of biodiversity science. Most animals don’t have a name attached to them. Most of the biodiversity of the planet is unknown. So if we can collect DNA and start saying, well, we think we’ve got something new here, it’ll tell us where to focus our other sources of information gathering to learn about it.
I’m part of a very big global consortium that is trying to document biodiversity with DNA called BioScan, and that’s exactly one of our objectives, is to try and document the unknown things in environments.
IRA FLATOW: Am I thinking too big in thinking that the end goal of your research and other research is to have a census of the whole planet?
ELIZABETH CLARE: No, that is the end goal. And it’s surprising to most people that we don’t have that. When I lecture my students about biodiversity, I usually point out to them that biodiversity scientists struggle to even estimate the number of species on the planet to an order of magnitude. Somewhere between 10 and 100 million species currently, but we don’t know which end of the spectrum we’re closer to. So we can’t even estimate how many species are there, let alone count them and actually know what they are. And about 90% of that has never been seen by science.
And so that’s a huge problem for us trying to document global biodiversity. We don’t even have a good estimate of how many things are yet to be found, let alone have an inventory we can use to identify things. And so we need all these new technologies to help us advance that goal quickly at a time when species are going extinct very, very fast. To not even know they exist before they disappear is, to me, a real problem in science.
IRA FLATOW: Very, very interesting. We wish you great luck in your efforts to find out.
ELIZABETH CLARE: Thank you.
IRA FLATOW: Dr. Elizabeth Clare, assistant professor in the Department of Biology at York University in Toronto, Canada.