Accidental DNA collection by air sensors could revolutionize wildlife tracking

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An air-quality monitoring station in Lodon is near a deer park, so it picks up DNA from species such as fallow deer (Dama dama) in its filters.Credit: Robert Knell

Scientists might be able to keep tabs on the world's flora and fauna by analysing DNA floating through the air. That's the conclusion of a study published on 5 June in Current Biology1, in which a team identified more than 180 types of organism, including plants, fungi, insects and animals, using DNA captured by filters from air-pollution monitoring stations. The researchers say that, because of the ubiquity of such stations, the method could transform the monitoring of biodiversity on Earth, and might even be able to detect rare species.

Global biodiversity is plummeting — some estimates suggest a 69% drop in wildlife populations since 1970. Scientists struggle to keep track of changes in ecosystems and rates of species decline because they lack infrastructure to measure biodiversity on large scales. Typically, researchers or conservation volunteers monitor a few terrestrial species in small regions using labour-intensive methods such as camera surveillance, in-person observations and examining traces including footprints and faeces. Over large scales, only very general measurements are possible, such as assessments of forest cover.

Source: Ref. 1

But environmental DNA (eDNA) — small amounts of genetic material shed by living things — that is collected automatically using air-pollution tracking networks could help solve this problem, says Elizabeth Clare, a molecular ecologist at York University in Toronto, Canada, and lead author of the study.

Scientists have been collecting and sequencing eDNA from soil and water samples for about 20 years to track rare or endangered species, such as the great crested newt (Triturus cristatus) in the United Kingdom and Gouldian finches (Erythrura gouldiae) in Australia. Regulatory agencies have used eDNA to detect invasive species; for example, the US Fish and Wildlife Service uses it to monitor silver carp (Hypophthalmichthys molitrix) in the Great Lakes system. But it wasn't until last year that scientists, including Clare, reported that eDNA can be captured from air samples and used to explore terrestrial biodiversity2. The DNA probably comes from cells shed by organisms, researchers say.

In the latest research, Clare and her colleagues ran a pilot study in which they got access to existing UK air-quality monitoring stations in London and near Edinburgh, to see whether they could trap airborne eDNA from the local flora and fauna. Both are designed to monitor atmospheric pollutants such as lead in particulate matter that becomes trapped in the devices’ filters. The Edinburgh station is part of a UK-wide network that is run in part by the National Physical Laboratory (NPL) in Teddington.

The US Fish and Wildlife Service uses eDNA to monitor silver carp (Hypophthalmichthys molitrix), an invasive species.Credit: Jason Lindsey/Alamy

The researchers set up the London station, which is next to a deer park, to take samples over various time intervals, from one hour to one week, allowing them to test whether sampling time is important. They also explored how long samples could be preserved by analysing the Edinburgh station's filters, which had collected DNA for a week before being stored for eight months.

The research team, which included scientists from the NPL, extracted and sequenced eDNA from one-quarter of each filter. The scientists then compared the sequences with those available in DNA databases such as GenBank, run by the US National Institutes of Health.

The researchers were surprised to find DNA from so many groups of organism on the filters. These included 34 species of bird, such as wrens (Troglodytes troglodytes) and great tits (Parus major), as well as ash trees (of the genus Fraximus), nettles (of the genus Soleirolia) and pathogenic Septoriella fungi (see ‘Keeping tabs on taxa’).

The advantage of using existing air-monitoring stations is that this infrastructure is already set up in many countries around the world, including across North and Central America, Europe, Asia and the Southern Hemisphere, the researchers say. They urge monitoring-station operators to preserve filters after air-quality analysis so ecologists can use them.

"Until we truly understand their ecological value, we’ve got to stop throwing them away," Clare says.

Researchers retrieved wildlife DNA from the Auchencorth Moss air-quality monitoring station near Edinburgh.Credit: National Physical Laboratory/Local Site Operator

Eily Allan, a molecular biologist and chief scientist of the eDNA Collaborative, a research programme at the University of Washington in Seattle, says the automated collection of airborne eDNA using existing networks of air-monitoring stations could "push environmental monitoring into the twenty-first century". It moves the research community from disjointed sampling to regular, repeated, long-term data collection, she adds.

But before the monitoring method can be rolled out widely, researchers need to work out some details, including the optimal sampling time to ensure broad eDNA collection. The team says its data suggest that a day is too short for sampling, but a week is too long — there is a sweet spot between collecting enough DNA and keeping it for so long that the material degrades.

Other unknowns include how far eDNA travels in air, which will determine how large an area this method can monitor. Study co-author Joanne Littlefair, a molecular ecologist at Queen Mary University of London, says the team is also still working out what ecological information eDNA can provide beyond identifying species. For example, she suggests it is unlikely that the method will be able to measure species abundance. But it could monitor bird migrations and how they are changing in response to climate change.

"We don't know really what you can reliably look at yet," she says.

doi: https://doi.org/10.1038/d41586-023-01850-z

Littlefair, J. E. et al. Curr. Biol. https://doi.org/10.1016/j.cub.2023.04.036 (2023).

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Clare, E. L. et al. Curr. Biol. 32, 693–700 (2022).

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