Audio long read: The air is full of DNA — here’s what scientists are using it for

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Airborne DNA Introduction

1:39This is an audio long read from Nature. In this episode, the air is full of DNA. Here's what scientists are using it for. Written by Aisling Irwin and read by me, Benjamin Thompson. Ryan Kelly is in awe of what floats invisibly in the air. It is completely mind-blowing, says Kelly, who studies environmental DNA, or eDNA, at the University of Washington in Seattle.

2:15We are absolutely surrounded by information in the form of DNA and RNA at all times. Scientists have long pulled DNA from water and soil, but they have only just started to see the air as a source of genetic information. Over the past decade or so, researchers have been learning how to measure airborne DNA, study its abundance, and use it to put together a picture of an ecosystem's inhabitants and health. Airborne DNA is being used to monitor individual species, and being trialled as a way to detect invasive species or attacks with biological weapons.

2:55It is also being tested as a way to judge the success of conservation efforts. The technique promises to link, quote, the whole of biodiversity, the whole world together, with a single assay that's really rapid and that can even be done in the field and analysed in the cloud. Says David Duffy, a researcher who specialises in wildlife disease genomics at the University of Florida in St. Augustine. But there is still a lot to pin down, such as how fast DNA decays in the air and how far it travels.

3:29Some genetic material pulled from the air comes from humans, and several scientists are concerned that when using the technique for conservation research, it could inadvertently reveal people's ethnicity or whether a person has a genetic disorder, and even be used to identify individuals.

3:50Scratch your head and you'll release DNA-rich cellular material into the air. There, it will mingle with DNA from myriad other sources, your own and others' exhalations and exfoliations, fragments of hair, feathers, excrement, pollen and spores, and microorganisms such as viruses and microalgae. This DNA, which can include segments that are tens of thousands of base pairs long, will then wander the air for perhaps a few days, often clinging to dust particles.

4:24It can travel distances that range from a few metres to several thousand. Although eDNA is already collected routinely from water, snow and soil to gather information about biodiversity or to track contaminants or viruses, scientists have not typically monitored sources of DNA in air, other than pollen and spores, robust packages designed to travel on the breeze. But in the early 2010s, various ecologists began to wonder whether air might contain useful DNA traces,

5:01beyond those wrapped in such wind-borne bundles. In 2013, biologists Matt Clarke at the Natural History Museum in London and Richard Leggett at the Erlim Institute in Norwich, UK, took air samples in a greenhouse and outside it. We were just wondering whether we would get anything, says Clarke. Actually, we got dozens, hundreds of things turning up. Meanwhile, at Texas Tech University in Lubbock, ecologist Matthew Barnes analysed air samples using techniques developed for collecting water-borne eDNA

5:38and discovered they were teeming with DNA from leaves and flowers, as well as types of pollen not designed to be wind-borne. He realised then the potential for understanding whole plant communities, using air. But it was the discovery of tiger DNA near Cambridge, UK, that alerted the wider community to airborne DNA's potential. Elizabeth Clare at York University in Toronto, Canada, and Joanne Littlefair at University College London wanted to know whether they could find animal DNA in the air.

6:14They collected samples at a small zoo in Cambridge, UK, reasoning that they would know the origin of any DNA they found because the exotic animals were confined to the park. In the laboratory, the researchers extracted the DNA from the samples and amplified and sequenced it. They found that they could sniff out tigers 200 metres away from their enclosure, as well as many of the zoo's other animals, their food, including chicken, horse and pig,

6:47and wildlife such as hedgehogs, bats and squirrels. In total, the samples contained DNA from 25 species of mammal and bird, including 17 kept at the zoo. Another study near Copenhagen Zoo, published at the same time, had similar findings.

7:07Airborne animal DNA has always been there, it's just that we've never looked for it, says Simon Correa, who studies molecular ecology at Bangor University, UK. But it was a physicist who found a way to scale the method up. James Allerton, at the National Physical Laboratory in London, suggested that Clare examined samples taken by the UK Heavy Metals Monitoring Network, which has 25 air pumps, located in cities, in the countryside and at industrial sites.

7:40The researchers studied samples from 15 of the network sites and, last year, published what they say is the world's first national survey of terrestrial biodiversity using airborne eDNA. They found common UK animals, as well as exotic pets such as parrots, and an invasive fish species, the silver carp, that had not previously been reported in the region. From vertebrates to single-celled protists, they picked up 1,100 taxa.

8:14To check the reliability of their method, the researchers compared their results with data from massive databases, such as iNaturalist, in which citizen scientists record what they see.

8:27iNaturalist had failed to pick up half of what the team found. In turn, eDNA did not reflect 43% of the iNaturalist observations.

8:40Citizen science tended to find more birds and other charismatic visible species near human habitation. Airborne DNA picked up more of the small, the invisible, and the nocturnal, including fungi, lichens, invertebrates, and plants other than trees, says Littlefair. Quote, These are really the powerhouses of ecosystem function. End quote. The method, says the team, is, quote, a realistic solution to monitoring

9:11the dynamics of life on land. End quote. Now, the researchers are helping countries with similar monitoring networks to do the same. But what if you could harness a network that pumps huge amounts of air through its filters, and that has records stretching back decades? In 2015, molecular biologist Per Stenberg at Umea University in Sweden heard about just such a possibility. A 70-year-old history of biodiversity,

9:42told in wisps of DNA, caught on tens of thousands of filters, and stored at the Swedish Defense Research Agency in Stockholm. He was at a seminar about Sweden's radionuclide detection network, built in the late 1950s,

Ecological History and Monitoring

10:00to detect nuclear weapons tests. The 25 stations suck in hundreds of cubic metres of air per hour, and the contents are then stored on glass fibre filters.

10:13Stenberg set about analysing the filters from a station north of the Arctic Circle. Whereas Littlefair's team searched for short marker regions of DNA that identify individual species, known as DNA meta-barcoding, Stenberg used shotgun sequencing, in which DNA is broken down into tiny pieces, sequenced and matched to known reference genomes using a computer. The shotgun approach consumes more time and energy,

10:44and requires more complex statistical techniques than does the meta-barcoding technique, but the results are more detailed. It was four years before he and his collaborator, Mats Forsman, the agency's research director, got results. Viruses, bacteria, fungi, plants, animals, birds, fish, the intestinal parasites of moose, recounts Stenberg. I mean, whatever was out there and had a reference to match it, we could see every single organism

11:15that is not extremely rare in the ecosystem. The results indicated that the technique could be trusted, he says. Quote, so then it was like, wow, this is something we need to explore. End quote.

11:29Ecologists are doing just that, documenting weekly, seasonal, and cyclic fluctuations in the abundance of many species and matching these to climate variations. They have uncovered long-term community changes, the rise and fall in the abundance of pine trees because of changing forestry management, and a concomitant decline in other trees, mosses, lichens, and fungi. They have tracked over time well-known covariance between several species,

11:59such as those between flies and some bacteria, and found new ones. Europe is dotted with radionuclide detection stations, which could provide, quote, an unprecedented opportunity to reconstruct ecological history and detect ongoing changes, says Stenberg and his co-authors. Such networks are, however, in fixed locations. Some scientists are experimenting with more flexible monitoring.

12:30Erin Hahn, who studies conservation genetics at the Australian National Wildlife Collection in Canberra, has designed and 3D-printed passive samplers which don't need an energy supply and given them to landholders across New South Wales. Her team is still at the pilot stage. There's heaps of variables around airflow, light exposure, proximity to game trails, says Hahn. We're just starting to chip away at them to better understand how DNA moves around.

13:00What Hahn ultimately wants is a nimble network that can pinpoint change quickly, flagging invasive species or crashing populations that need management. For governments, companies, scientists and conservationists aiming to track the health of ecosystems, airborne DNA could provide a comprehensive, regular readout of biodiversity on land. It means that we can rapidly assess environments before, during and after mitigation

13:30and not just think we improve biodiversity but really have a quantitative measure, says Duffy, who is evaluating its potential for tracking forest restoration. DNA readouts could also help to chronicle ecosystem vitality by tracking pathogen load and the genetic diversity of individual species, an indicator of health. There are other enduring ecological questions that airborne DNA could help to solve. Stenberg's group is developing models that aim to understand

14:01cause and effect in ecosystems. We know that foxes eat rabbits and rabbits eat some plants and so on, Stenberg says, but the full ecosystem, when we talk about the bacteria, the nematodes, the insects, the plants, the animals, we basically have no idea. Uncovering more detail could provide practical information on how ecosystems respond to damage. But there's a lot of troubleshooting to do first. Why, for example,

14:32did cod DNA turn up in a Swedish forest sample taken 160 kilometres from the sea? Stenberg has solved this one by matching its appearance to the arrival of strong northerly winds. And what does it mean, asks Hahn, if a farmer's sample contains rat DNA? Did the animal trot past yesterday? Or did century-old fragments of rat excrements blow in from a decayed midden? There are four key questions

15:03that will determine how airborne DNA is interpreted, says Crea. How does the DNA get into the environment? What state is it in? How long does it take to degrade? And how is it transported? Andrew Nisbet is also wrestling with these questions. He leads the development of innovative monitoring technologies at Natural England, a UK government advisory body in York that helps to protect and restore England's natural environment. If we put out

15:34one sampler, he says, does that give us a picture of a whole nature reserve? Or should we be putting out ten? If we run it for a day, is that enough?

15:45Nisbet thinks that airborne DNA is currently less useful than are techniques such as acoustic fingerprinting, which uses sound to identify animal species and satellite data.

15:58Airborne DNA strengths could initially lie in fields in which, quote, even one verified discovery of a thing answers your question, like that an invasive species or pathogen has arrived, end quote. That application is a focus for Clark and Leggett. Since their first discovery of plant DNA blowing in the air, they have developed technology that can detect known crop pathogens weeks before they cause visible damage. Information that could enable

16:29more judicious spraying of pesticides, they say. Clark and Leggett launched a spin-off company this year that deploys a technology, AirSeq, which they say could be used to track human and animal diseases or antimicrobial resistance, for example. We are interested to see what people might do with it, says Clark.

16:52One advantage of such systems is that they can suck up everything in an environment and provide an overall readout, rather than search for specific pathogens. This feature is useful in defence, says Jamie Marseille, an engineer at detector manufacturer Chromec in Sedgefield, UK, because you might want to discover new pathogens or engineered biological weapons. Initially, in collaboration with Clark and Leggett, he is developing a shoebox-sized device that can

17:22continuously sample the air, extract the DNA, and feed information into an algorithm that then identifies sequences associated with virulence or with the potential to cause respiratory diseases. But the idea of continuously collecting airborne DNA in public spaces troubles some scientists, who raise concerns similar to those about the sampling of DNA in wastewater. Breathe out on an evening walk and your DNA could waft

17:54into a discreetly placed urban sampler. Shotgun sequencing, using rapidly emerging cheap portable techniques that can generate the type of readout that helps to identify individuals, could produce results in the field in near real time, says Duffy. His team has shown this to be possible by sampling the air and unwashed window panes in Dublin and in Florida, from which they could distinguish between individuals of the same animal species. For ethical reasons,

18:24they did not try this type of sequencing for the human DNA that wound up in their samples, which is known as human genomic bycatch. But short-read analysis revealed human ancestries and some genetic diseases.

Ethical Concerns and Future Directions

18:39Many in the field are wary of the implications of such bycatch. If breathing is putting your DNA out into the air, how does that bump up against how we think of privacy, says Kelly, who co-wrote an article in 2023 that calls for a moratorium on the study of human DNA from environmentally sourced samples, until global principles are agreed. Some journals already have a moratorium, such as Environmental DNA, for which Crea is an editor-in-chief.

19:11Crea and others are hoping to create a multidisciplinary group to assess the ethics. Researchers in other sectors are intrigued by the possibilities. Peter Gill, a forensic geneticist at the University of Oslo and his colleagues, have been assessing airborne DNA caught in offices and air conditioning units for its potential as a forensic tool. Quote, people who have been recently in a building within a day or so, you can certainly pick up their DNA,

19:41end quote, from the air, says Gill. For a longer-term record, he says, there is airborne DNA on surfaces. You can take the dust from on top of a door sill where people don't normally clean, and then you'll have a sort of mini-historical record of people who have been there. Gill says that airborne DNA could be useful in forensics, provided its limitations are taken into account. These are similar to those of established techniques for analysing DNA from surfaces that have been touched.

20:13You need a human DNA database with which to compare your sample, and a correlation is a probability, not a match. What some scientists fear most is a backlash that triggers restrictions on their work. It's important to tread carefully, says Crear, quote, so it doesn't damage the really exciting and progressive world of biodiversity discovery using environmental DNA, end quote.

20:41To read more of nature's long-form journalism, head over to nature.com slash news.

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