In a first, scientists have revealed that animal and human DNA can be plucked straight out of thin air. The development heralds a promising new scientific technique with possible applications for ecology, forensics, and medicine, according to a new study.
Because animals shed cells into their environments, researchers can use water or soil samples to hunt for environmental DNA (eDNA), which provides a novel source of information about the lifeforms that inhabit any given area even if they are not present for DNA collection. The collection of eDNA has been pioneered in aquatic and underground environments, offering a data-rich and non-invasive way to examine species and their habitats.
Now, a team led by Elizabeth Clare, senior lecturer at Queen Mary University of London (QMUL), has provided the “first proof of concept demonstration that air samples are a viable source of DNA for the identification of species in the environment,” according to a study published on Wednesday in the journal PeerJ.
Plant and fungal eDNA has been snatched from the air before, but Clare was surprised to find that there were no analogous studies for animals in the scientific literature. She noted, though, that a pair of high school students from Japan presented a bird-focused eDNA concept at a science fair.
“There were a number of papers that speculated about it—that it will be the next thing that should be tried—but no one had done it,” Clare said in a call. “So, we gave it a try, and we just happened to have a really good experimental setup that allowed us to find a way that would give us the best possible chance of success early on.”
The setup for the DNA-grabbing experiment was a room containing “Colony Omega,” a group of naked mole-rats that have been studied and cared for by QMUL researchers for years. Naked mole-rats are fascinating animals for numerous reasons, but this colony also served as an ideal test subject for eDNA since they had lived in the same place for so long, allowing shed cells to build up in the environment. As the species’ name implies, naked mole-rats also don’t have fur or hair, which upped the odds that they would shed skin cells that are a better source of eDNA.
“They were just a really wonderful experimental system to start with,” Clare said.
Clare and her colleagues didn’t know what to expect from the experiment, so they used the same type of commercially available Sterivex-HV pressure filters that are common in aquatic eDNA studies. The filter component is located inside a plastic chamber that keeps samples sterile, and a pump attached to the equipment sucks air into the filter system to make collection more efficient.
To the team’s delight, the pressure filters successfully picked up naked mole-rat eDNA from the air inside the rodents’ burrows, and within the room itself, without needing to be adapted at all for a different medium.
What’s more, the experiment also picked up human eDNA that had been shed by researchers and caretakers of the rodents over time. At first, Clare’s team was disappointed by the presence of the human DNA, viewing it as a contaminant of the animal study. Soon, however, the researchers realized that there could be enormous implications for both sets of samples.
“That was the first thing we all discussed and said: ‘Well, isn't that terrible? It's so contaminated with human DNA,’” Clare recalled. “And then we thought: ‘No, that's a different form of DNA. We're just mammals in the environment as well.’”
The discovery of this exciting new eDNA source is bound to impact multiple scientific disciplines. Unlike DNA collected directly from one individual animal, eDNA samples can be gathered passively from an environment with no animals immediately present. These samples often contain a mixture of genetic fragments from multiple organisms that just happen to end up in filters at a certain place and time.
For this reason, eDNA is better suited for large-scale ecological studies of populations and biodiversity, such as tests for the presence of invasive species or making inventories of species that live in a selected habitat, as opposed to detecting and monitoring individuals.
Clare, who has extensively studied bats, sees special potential for ecologists hoping to non-invasively capture information about animals that live in inaccessible or potentially hazardous habitats such as caves, tree hollows, or subterranean burrows.
“We see it as another tool in the toolbox of being able to monitor different forms of life,” Clare said. “We have camera traps in forests, and we have different types of nets and aquatic filtering for waterways. We're hoping this is a way we could sample different forms of terrestrial life.”
The human eDNA also offers tantalizing possibilities for fields such as forensic anthropology or forensic archaeology, which involve data collection from human remains. For instance, specialists who study ancient remains, such as mummies, might be able to collect eDNA from within a tomb without invasively opening it, though this has not been tried yet.
Airborne eDNA could also complement existing techniques for studying the spread of pathogens, such as coronavirus. Pathogens have evolved to be robust and long-lived as they travel through the air—as opposed to shedded DNA, which quickly deteriorates—so scientists have already developed many ways to study infectious disease transmission. Still, eDNA from the air could help to contextualize the kinds of information gathered by more established techniques.
Clare and her colleagues are already busy with follow-up studies that will shed more light on the future applications and best practices for eDNA collection from the air.
“It's fun to speculate,” she said, “but we're also quite a long way from being able to know what this material will do. Step number two is to figure out under what conditions can we even collect it.”
“What we’ve done is show it’s possible,” Clare concluded. “Now we have to figure out under what context is it possible before we actually can apply it anywhere, in particular.”