A decade ago, biologists and natural historians around the world launched ambitious goals to create inventories of our planet’s biodiversity. After all, they said, you can’t save what you don’t know exists. Even some high estimates suggest that only a quarter of Earth’s species have been described by science, raising concerns about the big picture amidst rising extinction rates.
As these projects have crept along with the painstaking work of collecting and describing species, a new line of attack has emerged for capturing the DNA of Earth’s unknown species for cataloguing purposes: pull it out of thin air.
The approach, which involves sequencing the genetic material in cells shed by organisms, or their environmental DNA (eDNA), is especially useful in sampling insects. It is less costly and faster than traditional sampling methods, and can capture data from many species at once without harming them.
A new poster, presented this week at the Ecology Across Borders conference, reports on a proof-of-concept effort to show how it works. While employed as a postdoctoral fellow at Lund University in Sweden, Fabian Roger collected airborne samples using a commercially available liquid cyclone contraption, which swirls air into a liquid-filled tube, thereby trapping DNA fragments previously borne in the air. He collected air samples at three locations in southern Sweden, where he also used traditional methods to survey insects for comparison.
Roger and his colleagues then extracted DNA segments from the samples for subsequent amplification and sequencing. To identify the taxa, the team relied on metabarcoding, a technique which enables the simultaneous detection of aggregates of species from short regions of genes found in a single sample. None of the identified species were new to science. The goal of the new work was to demonstrate that it would be possible to inventory insects by analyzing DNA collected from air samples.
The team found traces of DNA from 85 species, including butterflies, beetles, ants, flies and their close relatives. They also found nine species of frogs, birds and other vertebrates. Some of the identifications overlapped with the conventional survey results, but the eDNA method missed others. For example, 48 moth species were found in traps, but the air sampling method only identified nine. The work has not yet been peer-reviewed.
Roger, now at ETH in Switzerland, says he was inspired to try to sample eDNA in the air after monitoring aquatic ecosystems for new species. “It hit me how difficult it was to get good data on populations,” he says. “And with recent research showing a 70 percent reduction in insect biomass, we have a crucial lack of data.” He knew that some entomologists were already detecting insects’ eDNA in soil. If insect DNA ended up on terra firma, he reasoned, it could have started out elsewhere, such as the air above.
Researchers estimate that only one million of 5.5 million insect species have been formally described by scientists, so looking to the air to monitor species biodiversity is an exciting development that can speed up conservation efforts, says Kristine Bohmann, an evolutionary genomics researcher at the University of Copenhagen in Denmark. She was not involved in the new research but has recently done studies on sensing environmental DNA of mammals, birds, reptiles and amphibians in the air at the Copenhagen Zoo.
“The time is ready for environmental DNA to take on this new substrate,” she says, adding that she has worked on eDNA on fecal samples, and others have looked at soil, water and even flowers to discover which pollinating species have landed there. “So much has gone into developing the techniques and making sure they’re trustworthy, so it’s just amazing to see the results. Why didn’t we think about this before?”
Bohmann adds that when it comes to monitoring insects, it’s especially important to see a method that doesn’t require killing the creatures it’s trying to assess. Some DNA inventorying methods often involve catching and squishing up the species to create an insect blend.
Several eDNA and air issues remain hazy, says Elizabeth Clare, a molecular ecologist at York University in Canada, who has worked on similar air-sampling studies. For one, it’s unclear how long an individual insect’s DNA persists in the air after it has flitted away. Are researchers sensing a recent visit or one made months ago? Studies have found intact DNA in permafrost up to 10,000 years after organisms perished. But in other conditions, such as exposure to ultraviolet radiation from the sun, DNA may degrade quickly.
In aquatic environments like rivers and lakes, DNA can be trapped in sediments and then stirred up at some point later in time, Clare says. “I imagine something similar could happen on land where it’s in the soil and you disturb the soil, and suddenly it’s aerosolized again. So we really don’t know if the eDNA is from minutes, hours, or decades [ago].”
Another huge question involves abundance. Does a larger signal of a species’ DNA indicate the presence of a larger number of individuals? This is one of the hottest topics in eDNA research circles, Clare says. “The simple answer is no, you can’t know the abundance unless you have extremely controlled conditions,” she says. Some evidence in aquatic conditions suggests that the quantity of a species’ DNA is related to its environmental abundance—along with distance traveled to the sampling station, she adds. The signal may be larger when species are closer to the sampler.
Such an eDNA signal could reveal the existence of one butterfly right next to the air sampler or a vast kaleidoscope of lepidopterans farther away. And when something dies, the degrading body typically sloughs off more genetic material than it did alive, Clare says. “We don't know the answer to any of these questions.”
Once these questions are ironed out, Roger envisions a world of passive, instantaneous monitoring for insects—in biodiversity hotspots as well as in agricultural fields, where growers could be alerted to the first signs of an invading pest.
The potential research benefits for eDNA in the air are immense, says Brian Brown, who heads up Natural History Museum of Los Angeles County’s Entomology Department. He travels around the world using conventional approaches to sample insects and create taxonomic reference libraries—the kind of material that will be vital to understanding the genetic snippets from eDNA samplers. “I don’t think this will replace what I do,” he says, “but it’s exciting because it’s affordable and could be very little work to sequence the air. It’s fascinating to think that we live and move through a matrix of biological soup.”