Scientists want to track the world’s biodiversity using DNA in the air
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Scientists want to track the world’s biodiversity using DNA in the air
Scientists want to track the world’s biodiversity using DNA in the air. Elizabeth Clare: “We don’t know what lives on planet Earth” Clare wanted to see whether we could measure biodiversity on the scale of an entire country. In a preprint article published on bioRxiv, she and her colleagues say they’ve done just that. “How to measure everything at once — there’s no way of doing that in our toolbox of tools at the moment,” she says. “Snatching out a few DNA out of the air is not the same as snatching out an entire species of organism” in the wild”Biodiversity” has never been recognized by science,” says Clare. “This is the problem of biodiversity. How do you describe this? I mean, Idon’t know.” It’s a question that’s become ever more urgent to answer given how many species around the world are in danger of winking out due to habitat loss, climate change, and other disruptions. “We need to be able to monitor whether conservation plans are working,” Clare says.
toggle caption Luis Echeverría for NPR
Outside her cabin in northern Belize, Elizabeth Clare, a biodiversity scientist at York University, walks along a path. Everywhere she looks, it’s teeming with life.
“There’s hibiscus flowers over there,” she says. “One of my favorite things to find in this part of the world is leaf-cutter ants.” She points out the kingfisher birds that can be spotted flying overhead and the iguanas populating the trees.
“You can look at a couple square feet of ground here and never possibly describe all the things that are in it,” Clare says. “This is the problem of biodiversity. How do you describe this? I mean, I don’t know. No one knows.”
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It’s a question that’s become ever more urgent to answer given how many species around the world are in danger of winking out due to habitat loss, climate change, and other disruptions.
“We don’t know what lives on planet Earth,” says Clare. “Most things in the world have never been recognized by science. So we wanted to see whether we could measure biodiversity on the scale of an entire country — actually monitor it over and over again to tell us how things are changing.”
In a preprint article published on bioRxiv that hasn’t yet been peer reviewed, she and her colleagues say they’ve done just that — by pulling DNA out of the air.
The parts of ourselves we can’t help but leave behind
To help explain the approach, Nina Garrett, a biology PhD student at York University, approaches a colossal guanacaste tree erupting out of the ground not too far from that path Clare was pacing. A good half of it is in the grip of a strangler fig tree. But at the base of the trunk is a hole that Garrett can just peek inside.
“Now you can hear them chittering,” says Garrett, referring to a group of common vampire bats that she knows reside in this tree. In fact, she spots a baby on the inner back wall of the trunk. “It’s not uncommon to see a pup without a mom inside the roost,” she says.
But Garrett is curious if there might also be white-winged vampire bats inside — a different species. “It’s never been caught here physically,” she says, “but it’s always been suspected to be in the area just based on habitat type and range maps.”
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The problem is that bats are elusive and skittish. Most techniques would likely spook any animals roosting here. So how can Garrett tell what’s inside this tree?
It turns out that even if the bats themselves are out of reach, they can’t conceal themselves completely. That’s because they cast small fragments of their DNA into the environment. Clare says all creatures big and small are forever “losing little bits of themselves. It’s what we do by being alive.” She says to think of it like a footprint that all of life leaves behind.
“They are shedding hair, could be little skin cells, it could be saliva,” says Garrett. “Anything that they are putting out into the environment — even when they breathe out.”
Garrett wants to collect this environmental DNA, or eDNA, from inside the tree to deduce who’s here. She lays a piece of filter paper atop a small fan, places the apparatus inside the tree, and flips the switch.
The fan draws the internal air across the filter, trapping free-floating DNA, which Garrett can analyze later for the presence of not just white-winged vampire bats, but any mammal. If she wanted, she could survey the genetic material for different species of plants and fungi too. This is the power of the technique: It can catalog the breadth of life crammed into a place like this little tree hollow.
toggle caption Luis Echeverría for NPR
The problem is that a single tree doesn’t tell you how species are doing on a grander scale. And most techniques that operate over broader areas don’t allow you to focus on many kinds of organisms at once.
Clare wanted to think bigger, at the level of a nationwide census of all living things. It’s something that she says is needed urgently given the number of species threatened with extinction — “to be able to monitor whether conservation plans have any effect” and whether remediation efforts after some large environmental disruption are actually working.
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But Clare didn’t know how she’d even attempt such a thing. “How to measure everything everywhere all at once — there’s no way of doing that in our toolbox of tools at the moment.”
Snatching DNA out of the air across an entire country
Then, a few years ago, a group of British chemists and physicists from the National Physical Laboratory (NPL) got in touch with Clare. This group monitors pollution levels across the U.K. using a network of stations that continuously draw air from the environment across little discs of filter paper to capture, among other pollutants, heavy metals. In other words, the basic setup mirrors the one in that guanacaste tree.
“We soon realised that the large number of filters we analyze for the air quality networks might contain some hidden information about species abundance,” says Andrew Brown, an air quality scientist with the NPL. “So we got in touch with Beth.”
Clare and her colleagues took about a year’s worth of these filters from across the U.K. When they analyzed them for DNA, they were astonished by what they found: hundreds upon hundreds of different insects and spiders, a heap of plants and fungi, and more than a hundred species of birds and mammals.
“It’s like a treasure hunt for biodiversity scientists,” she says. “Those same systems, it turns out, have been accidentally capturing this airborne DNA that we want.”
The approach may not be as detailed as a fleet of human observers, but sometimes it identifies organisms that people would miss.
“Compared to large-scale citizen science programs with thousands to tens of thousands observations,” writes Orianne Tournayre, a molecular ecologist at York University and lead author on the manuscript, “airborne eDNA recovered fewer taxa overall, but detected species that are harder to spot or identify visually.”
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Each filter disc on its own stored just a morsel of information, “but when you have hundreds of them being collected all the time, over and over again, at spatially distributed scales,” says Clare, “and you step back, all of those dots coalesce into a picture.”
It is a picture of the biodiversity of a nation — and how that picture changes as species invade a new area or disappear altogether. “These advances could also be used to identify pathogens and agricultural pests,” adds Brown.
“If filter storage is optimized for DNA preservation, this could pave the way for a highly standardized, scalable, and cost-effective monitoring system that operates almost continuously,” writes Tournayre. “It would be like turning our air quality network into a global wildlife monitoring system: the same network designed to protect human health could become a system for protecting wildlife as well.”
Ryan Kelly is a marine scientist at the University of Washington who studies environmental DNA and wasn’t involved in the research.
“What I think is really cool here,” he says, “is we can see the whole living world based on the DNA in the air, and we can do it all without any new infrastructure.”
Kelly says it’s not yet clear over what area or timeframe these pollution monitoring stations are sampling the DNA. He remains enthusiastic, however, about what the approach can facilitate. “If we have biodiversity management questions, all sorts of environmental impact questions, things that we’ve never really known how to do at scale before,” he says, “I think this paper points the way to doing that.”
Clare argues this may be just the beginning of bigger things to come.
“If we can do it at the level of a country,” she says, “we can do it at a level of a continent, we can do it at multiple continents. This is something that truly could scale to huge, almost planetary measurements.”
Scientists want to track the world’s biodiversity using DNA in the air
Scientists say they’ve developed an alternate method of tracking biodiversity. It relies on the DNA that animals release into the environment, known as eDNA. The technique can catalog the breadth of life crammed into a place like this little tree hollow. It can also identify species of plants and fungi too, which could be used to protect species in other parts of the world, scientists say.”You can look at a couple square feet of ground here and never possibly describe all the things that are in it,” says Elizabeth Clare, a biodiversity scientist at York University. “This is the problem of biodiversity. How do you describe this? I mean, I don’t know. No one knows,” Clare says. “Most things in the world have never been recognized by science””We wanted to see whether we could measure biodiversity on the scale of an entire country,” says Clare. “To be able to monitor whether conservation plans have any effect” on conservation efforts, Clare says, “it’s something that needs to be done”
Outside her cabin in northern Belize, Elizabeth Clare, a biodiversity scientist at York University, walks along a path. Everywhere she looks, it’s teeming with life.
“There’s hibiscus flowers over there,” she says. “One of my favorite things to find in this part of the world is leaf-cutter ants.” She points out the kingfisher birds that can be spotted flying overhead and the iguanas populating the trees.
“You can look at a couple square feet of ground here and never possibly describe all the things that are in it,” Clare says. “This is the problem of biodiversity. How do you describe this? I mean, I don’t know. No one knows.”
It’s a question that’s become ever more urgent to answer given how many species around the world are in danger of winking out due to habitat loss, climate change, and other disruptions.
“We don’t know what lives on planet Earth,” says Clare. “Most things in the world have never been recognized by science. So we wanted to see whether we could measure biodiversity on the scale of an entire country — actually monitor it over and over again to tell us how things are changing.”
In a preprint article published on bioRxiv that hasn’t yet been peer reviewed, she and her colleagues say they’ve done just that — by pulling DNA out of the air.
The parts of ourselves we can’t help but leave behind
To help explain the approach, Nina Garrett, a biology PhD student at York University, approaches a colossal guanacaste tree erupting out of the ground not too far from that path Clare was pacing. A good half of it is in the grip of a strangler fig tree. But at the base of the trunk is a hole that Garrett can just peek inside.
“Now you can hear them chittering,” says Garrett, referring to a group of common vampire bats that she knows reside in this tree. In fact, she spots a baby on the inner back wall of the trunk. “It’s not uncommon to see a pup without a mom inside the roost,” she says.
But Garrett is curious if there might also be white-winged vampire bats inside — a different species. “It’s never been caught here physically,” she says, “but it’s always been suspected to be in the area just based on habitat type and range maps.”
The problem is that bats are elusive and skittish. Most techniques would likely spook any animals roosting here. So how can Garrett tell what’s inside this tree?
It turns out that even if the bats themselves are out of reach, they can’t conceal themselves completely. That’s because they cast small fragments of their DNA into the environment. Clare says all creatures big and small are forever “losing little bits of themselves. It’s what we do by being alive.” She says to think of it like a footprint that all of life leaves behind.
“They are shedding hair, could be little skin cells, it could be saliva,” says Garrett. “Anything that they are putting out into the environment — even when they breathe out.”
Garrett wants to collect this environmental DNA, or eDNA, from inside the tree to deduce who’s here. She lays a piece of filter paper atop a small fan, places the apparatus inside the tree, and flips the switch.
The fan draws the internal air across the filter, trapping free-floating DNA, which Garrett can analyze later for the presence of not just white-winged vampire bats, but any mammal. If she wanted, she could survey the genetic material for different species of plants and fungi too. This is the power of the technique: It can catalog the breadth of life crammed into a place like this little tree hollow.
Nina Garrett, a biology PhD student at York University, sets up devices in northern Belize that collect DNA floating in the ambient air.
The problem is that a single tree doesn’t tell you how species are doing on a grander scale. And most techniques that operate over broader areas don’t allow you to focus on many kinds of organisms at once.
Clare wanted to think bigger, at the level of a nationwide census of all living things. It’s something that she says is needed urgently given the number of species threatened with extinction — “to be able to monitor whether conservation plans have any effect” and whether remediation efforts after some large environmental disruption are actually working.
But Clare didn’t know how she’d even attempt such a thing. “How to measure everything everywhere all at once — there’s no way of doing that in our toolbox of tools at the moment.”
Snatching DNA out of the air across an entire country
Then, a few years ago, a group of British chemists and physicists from the National Physical Laboratory (NPL) got in touch with Clare. This group monitors pollution levels across the U.K. using a network of stations that continuously draw air from the environment across little discs of filter paper to capture, among other pollutants, heavy metals. In other words, the basic setup mirrors the one in that guanacaste tree.
“We soon realised that the large number of filters we analyze for the air quality networks might contain some hidden information about species abundance,” says Andrew Brown, an air quality scientist with the NPL. “So we got in touch with Beth.”
Clare and her colleagues took about a year’s worth of these filters from across the U.K. When they analyzed them for DNA, they were astonished by what they found: hundreds upon hundreds of different insects and spiders, a heap of plants and fungi, and more than a hundred species of birds and mammals.
“It’s like a treasure hunt for biodiversity scientists,” she says. “Those same systems, it turns out, have been accidentally capturing this airborne DNA that we want.”
The approach may not be as detailed as a fleet of human observers, but sometimes it identifies organisms that people would miss.
“Compared to large-scale citizen science programs with thousands to tens of thousands observations,” writes Orianne Tournayre, a molecular ecologist at York University and lead author on the manuscript, “airborne eDNA recovered fewer taxa overall, but detected species that are harder to spot or identify visually.”
Each filter disc on its own stored just a morsel of information, “but when you have hundreds of them being collected all the time, over and over again, at spatially distributed scales,” says Clare, “and you step back, all of those dots coalesce into a picture.”
It is a picture of the biodiversity of a nation — and how that picture changes as species invade a new area or disappear altogether. “These advances could also be used to identify pathogens and agricultural pests,” adds Brown.
“If filter storage is optimized for DNA preservation, this could pave the way for a highly standardized, scalable, and cost-effective monitoring system that operates almost continuously,” writes Tournayre. “It would be like turning our air quality network into a global wildlife monitoring system: the same network designed to protect human health could become a system for protecting wildlife as well.”
Ryan Kelly is a marine scientist at the University of Washington who studies environmental DNA and wasn’t involved in the research.
“What I think is really cool here,” he says, “is we can see the whole living world based on the DNA in the air, and we can do it all without any new infrastructure.”
Kelly says it’s not yet clear over what area or timeframe these pollution monitoring stations are sampling the DNA. He remains enthusiastic, however, about what the approach can facilitate. “If we have biodiversity management questions, all sorts of environmental impact questions, things that we’ve never really known how to do at scale before,” he says, “I think this paper points the way to doing that.”
Clare argues this may be just the beginning of bigger things to come.
“If we can do it at the level of a country,” she says, “we can do it at a level of a continent, we can do it at multiple continents. This is something that truly could scale to huge, almost planetary measurements.”
India gears to use eDNA to identify, track wildlife
The Zoological Survey of India is testing new technology to assess biodiversity using environmental DNA (eDNA) Technology can aid researchers in quantifying wildlife, flora and fauna and even explore elusive species. The new technology may also be able to provide much-needed data on invasive alien species in India. Researchers collect scat (fecal) material from animals and take them for identification. This is done in the areas they are studying. The DNA of the particular targeted species is then sorted out for population estimation. A study by scientists from the United Kingdom has stated that air-quality networks collect environmental DNA with the potential to measure biodiversity at continental scales. These samples have ‘surprisingly stable DNA’, and it is the best possible method to ascertain terrestrial biodiversity, according to the study. The technology is currently being used in the United States and Europe to monitor biodiversity and assess the flora andfauna of a region. “The new methodology can even help the scientific community in finding elusive species that lived in a particular region, but haven’t been discovered by anyone to date,” said a scientist.
eDNA technology can aid researchers in quantifying wildlife, flora and fauna and even explore elusive species.
The new technology may also be able to provide much-needed data on invasive alien species in India. See All Key Ideas
The Zoological Survey of India (ZSI) has set up a pilot project to use eDNA (environmental DNA), to study and monitor wildlife.
At present, researchers collect scat (fecal) material from animals and take them for identification. This is done in the areas they are studying. The DNA of the particular targeted species is then sorted out for population estimation.
However, a study by scientists from the United Kingdom has stated that air-quality networks collect environmental DNA with the potential to measure biodiversity at continental scales and that these samples have ‘surprisingly stable DNA’, and it is the best possible method to ascertain terrestrial biodiversity.
ZSI’s pilot project, based on this study, will do this through air quality monitoring stations, set up by various government authorities, that are used to identify and collect particulate matter present in the air. These stations have two filters, PM 10 and PM 2.5, which collect air particles to quantify levels of pollution in the air. “These filters are changed in eight hours, in the case of PM 10 and 24 hours for PM 2.5 respectively, said Rajender Kumar, a scientific officer with the Himachal Pradesh Pollution Control Board. Based on the particulate matter present or collected on filters, the levels of pollution in the air are determined after processing and analysing filters in the lab.”
The study also added that “air monitoring networks are in fact gathering eDNA data reflecting local biodiversity on a continental scale, as a result of their routine function. In some regions, air quality samples are stored for decades, presenting the potential for high-resolution biodiversity time series. With minimal modification of current protocols, this material provides the best opportunity to date for detailed monitoring of terrestrial biodiversity using an existing, replicated transnational design and it is already in operation.”
Lalit Kumar Sharma, a scientist with the Kolkata-based Zoological Survey of India, told Mongabay-India that they have started a pilot project in North Bengal to collect animals’ eDNA and monitor wildlife by using air filters or air quality monitoring stations. “For eDNA collection, we will make use of particulate materials collected on filters at the air quality monitoring station for ascertaining wild population and flora and fauna of the region,” he said. “The new methodology can even help the scientific community in finding elusive species that lived in a particular region, but haven’t been discovered by anyone to date.”
He added that the technology is currently being used in the United States and Europe to monitor biodiversity and assess the flora and fauna of a region.
Illustration by Rupsy Khurana.
eDNA for biodiversity monitoring
Ajay Bijoor, a programme coordinator with Nature Conservation Foundation (NCF) said the present methodology used to estimate wildlife, especially the International Union for Conservation of Nature (IUCN)-designated species, is a sort of trial and error method.
He explained that whenever a researcher or scientist goes for population estimation, one has to form small teams with local forest officials or volunteers to trap the targeted species or collect fecal matter. The next steps involve carefully preserving the samples and sending them to DNA labs for analysis.
“It costs around Rs. 1,000 to Rs. 1,500 per sample for processing at labs and takes around one or two weeks to complete the process,” ZSI’s Lalit Sharma added. He highlighted that ZSI has its own labs to process and analyse DNA but “for independent researchers or scientists at state departments, finding labs and processing the samples can be tough and time-consuming”.
“The eDNA has tremendous potential to develop our understanding of biodiversity science and provide implications for conservation practices with census data of species present at a comprehensive scale in real-time,” noted a May 2022 study on using environmental DNA as a tool for biodiversity monitoring in aquatic systems.
The authors, Manisha Ray and Govindhaswamy Umapathy note that environmental DNA (eDNA) was introduced in the field of microbiology for the detection of microbial communities in sediments in 1987. “DNA extracted non-invasively from environmental sources like soil, air, or water is termed environmental DNA (eDNA),” says the study. Aggregates of eDNA greater than 0.2 µm are termed as particulate DNA (P-DNA) while those lesser than 0.2 µm are termed as dissolved DNA (D-DNA).
The origin of eDNA can be several sources such sloughed cells, fecal matter, spores, slimy coating (in amphibians), or dead carcasses.
The study says “the traditional practices of estimating biodiversity are biased towards the sampling of particular species or can also pose a risk to sensitive organisms”.
The eDNA technique has also been used in the aquatic system to either detect the presence or absence of a species or for quantitative estimation of a particular species. “Its application varies between lotic and lentic ecosystems as their nature varies,” the study added. “The lotic ecosystem is flowing and can transport eDNA directionally downstream from the correct location of the target organism, whereas the lentic ecosystem is stagnant. eDNA is released into the environment and subsequently undergoes progressive decay due to many biotic and abiotic factors.”
Umapathy told Mongabay-India that the particulate matter collected for eDNA established that it not only contains DNA of wildlife, flora, and fauna of a particular region, but also information on fungi and even various viruses.
“Our analyses have shown that eDNA tech can accurately predict and quantify biodiversity and wildlife in a particular area or region,” Umapathy added.
Read more: Environmental DNA analysis: Detecting invasive fish with a cup of water
eDNA can prepare for better conservation
Umapathy’s study noted that there are many applications in which eDNA ranging can be used for conservation purposes. It can help in the “detection of invasive species, elusive species or any other ecologically important or threatened species to unravel community dynamics and their response to changing spatial-temporal changes.”
For instance, a few years ago, a study in the U.S. used the eDNA technique to study the “introduction and spread” of silver carp (Hypophthalmichthys molitrix), which is an invasive species. For a biodiversity-rich country such as India, which is battling conservation issues including a massive problem of invasive species threatening natural and agricultural landscapes, it can contribute significantly.
It is estimated that India has lost $127.3 billion (Rs 8.3 trillion) in the last 60 years due to 10 invasive alien species. The frightening part is that a lot of research is still required regarding the impact of invasive alien species, but that is hampered by lack of data.
The eDNA technology can help organisations, whether government or independent, in preparing “better conservation focus on regions or species of special importance. In this era of unprecedented climate change and concerns possessed by it, eDNA can help assist in the monitoring of biodiversity alongside other conventional methods to yield better results”, added the study.
Read more: Privacy concerns rise as wildlife surveillance tech ‘watches’ people
Banner image: Red panda in Darjeeling. Photo by Tomayank29/Wikimedia Commons.
Source: https://www.npr.org/2025/05/22/g-s1-67081/environmental-dna-edna-air-track-biodiversity