Inventorying the plants in a tract of woods or fields or searching for invasive species can take days of hot, hard work slogging through thorny brush and tick-infested grass. Now, researchers have shown that simply capturing and analyzing the DNA plants release into the air can work as well as putting boots on the ground—and in some cases even better.
“Airborne DNA could be a game changer in our ability to monitor and study biodiversity,” says Kristine Bohmann, a molecular ecologist at the University of Copenhagen who was not involved with the work. The approach could help track how climate change is altering the makeup of plant communities, researchers say, and provide early warning of invading species.
Reported last month in BMC Ecology and Evolution, the work takes the study of environmental DNA (eDNA)—genetic material shed, defecated, coughed up, or otherwise released into the environment—into a new realm. Aquatic eDNA is now a proven tool for identifying fish and other marine and freshwater organisms, with no need to catch them. In soil, eDNA can reveal the presence of people and animals, current or ancient. “The time is right to look at another source,” says Elizabeth Clare, a molecular ecologist at York University who has tracked animal species with airborne eDNA.
Plants already emit airborne tracers that are familiar to anyone with allergies: windborne pollen. The grains’ distinctive shapes make it possible to identify unseen species simply by capturing their pollen. But pollen surveys have their limits. They only detect pollen that’s spread by wind (other types depend on pollinating insects and other animals), require well-trained experts, and don’t always produce species-specific identifications. Mark Johnson, a graduate student at Texas Tech University, wanted to know whether studying the eDNA shed into air as pollen or in minuscule fragments of leaves or flowers would work better.
He and his colleagues developed better ways to collect plant eDNA in dust traps, and in 2019 they demonstrated that the filters capture DNA-bearing traces from all sorts of plants. “We could find species not flowering, not pollinating, or when they are not active like in the winter,” Johnson says.
Now, he has shown how eDNA can inventory an entire plant community. He and his colleagues mounted dust traps in nine places across a well-studied short grass prairie owned by his university. They collected the dust every couple of weeks for 1 year, extracted the DNA, and sequenced a gene that varies among plant species, serving as a “DNA barcode” for identifying them. In the spring and again in the fall, his team also pulled on their boots and surveyed plants along 27 100-meter transects. They compared the results of the two kinds of surveys.
The traditional surveys detected 80 species and the air eDNA study 91, the team reported. Both surveys uncovered the same 13 grass species, but the eDNA work found an additional 13. Among nonwoody flowering plants, both approaches yielded a total of 60 species, but each detected 20 or so that the other missed. eDNA was better at finding easily overlooked species with small flowers, such as weakleaf bur ragweed. But people were better at spotting plants too rare to release much eDNA, particularly when they had showy flowers, such as the chocolate daisy.
Airborne DNA also revealed tree of heaven, an invasive plant not detected by the survey. That’s encouraging, says Loren Rieseberg, a plant evolutionary biologist at the University of British Columbia, Vancouver. “I think [airborne eDNA] will be especially useful for detecting invasive species before they become widespread and difficult to get rid of.”
The technique recorded how the abundance of different species changed through time: For example, the rapid bloom and growth of the tansy mustard in early spring, an event missed by ground surveys. “This [report] might encourage more researchers to take up dust traps to complement” other kinds of surveys, particularly at long-term study site, says Fabian Roger, an ecologist at ETH Zürich who was not involved with this work.
Along with plant DNA, the filters picked up DNA from fungi, and other researchers have picked out insect, earthworm, and slug DNA from the air. “Potentially air DNA is incredibly diverse and representative for the full diversity of living organisms,” Roger says. His own eDNA survey of insects in the wild detected just a fraction of the species known to be present, but he expects sensitivity to improve with a better understanding of how wind and other conditions affect DNA collection, and better technology.
Existing traps typically rely on natural air flow to carry in particles carrying eDNA, but the concentrations can be very low. More efficient filters, or traps equipped with fans to suck in air, could work better. “You need a good system to trap the air,” agrees Crystal Jaing, a molecular biologist at Lawrence Livermore National Laboratory who has been assessing high-altitude airborne microbes from specially equipped airplanes.
Joseph Craine, co-owner of Jonah Ventures, a company commercializing eDNA surveys, thinks the technology isn’t ready to be scaled up. “I can’t see the application,” he says. Finely tuned spectroscopic measurements from space are a better approach to surveying plants, he says.
But others point to how far aquatic eDNA studies have come in recent years and think air eDNA can do the same for monitoring terrestrial life. Roger says: “Air has the potential to be the ‘water’ over the land.”