When geneticist Elizabeth Clare placed 70 small filters around England’s Hamerton Zoo Park last year, there was an air of hope. Clare intended for the traps to collect DNA from the sky, allowing scientists to identify the animals present in each enclosure. What she hadn't caught wind of yet, however, was that another team of scientists, more than 500 miles away, was conducting a similar experiment in the Copenhagen Zoo. Independently, and surprisingly, both teams succeeded.
Two new proof-of-concept studies published today in the journal Current Biology are among the first to show that tiny fragments of DNA in the air can be used to detect different species. The non-invasive approach could be especially useful for detecting rare, invasive and otherwise hard-to-find animals. The discovery was made simultaneously by the two independent research groups, one based in Denmark, and the other based in the United Kingdom and Canada.
Wild animals are usually studied by sight, or indirectly through clues that they leave behind, like fur, feathers or feces. That means certain animals—especially the small, fast and shy ones—are often missed in traditional wildlife surveys. Because all living organisms shed DNA into their environment, the two research groups hoped they could use those genetic traces to find out what animals frequent an area. “Both of us admit that this is a bit of a crazy idea—we're vacuuming DNA out of the sky,” says Clare, of York University, Canada, who was at Queen Mary University of London when she led the work. The complementing study was led by Kristine Bohmann, a genomicist from the Globe Institute, University of Copenhagen.
Research on environmental DNA, called eDNA, has developed rapidly over the past two decades, but most work has been limited to aquatic environments. Collecting DNA from the air presents different challenges than water, as the concentration of DNA in the air is often lower and more irregularly mixed. Because eDNA has proven to be an important tool for species detection in water, the research groups were eager to see if airborne eDNA could be used to find land-dwelling animals and approached their local zoos for help.
One of the biggest challenges of working with airborne eDNA is avoiding contamination from other sources, which could muddle results. "The zoo becomes this perfect environment where we know that everything that we're detecting or that we think we're going to detect has only one possible source," says Clare. "My lab doesn't handle tiger DNA ever, so if we’re detecting a tiger, there is no other source.”
To see if eDNA could be detected in the air, both teams placed filters in different zoo enclosures, including both indoor and outdoor exhibits. Bohmann’s group collected 40 air samples in three locations around the Copenhagen Zoo: the tropical rainforest house, the okapi stable and in the outdoor space between animal enclosures. They also tested three different air sampling apparatuses, including an adapted water-based vacuum cleaner, and two styles of blower fans and filters. Depending on the collection device, any free-floating genetic material from things like fur, saliva, and feces would get trapped, either in sterilized water or on a paper filter.
Clare’s group took a similar approach but instead used just one type of air pump that the team previously tested in a prior study on naked mole rats. They deployed the sampling devices in dozens of different locations around Hamerton Zoo Park. While Clare’s team operated their pumps for half-hour sessions, Bohmann’s group ran their filtering devices between 30 minutes and 30 hours. Both teams then brought the samples back to their respective labs and used a technique called polymerase chain reaction (PCR) to look at the DNA sequences. From there, they checked what they found against public databases. “We basically had libraries of what the sequences should look like for those animals, and then it becomes a bit like the card game Go Fish,” says Clare.
Though both groups were optimistic their idea could work, they were still shocked at their results. In the 40 samples that Bohmann’s group collected, they successfully found 49 species including mammals, birds, reptiles and fish. “We had no idea that this would actually work so well,” says Bohmann. When she saw results, she “could not believe it,” says Bohmann. “It was tears and laughter.” They were also able to find DNA from local species near the Copenhagen Zoo, like the water vole and red squirrel.
Clare’s team was able to identify DNA from more than two dozen different species of animals from their samples, including tigers, lemurs and dingoes. The researchers were also able to detect nearby native species like the endangered Eurasian hedgehog.
While doing their research, the teams had no knowledge of the other’s work, but after finding each other’s preprint proof-of-concept papers online, the two groups decided to submit their manuscripts for review together. “It's insane that two groups did such similar studies in two places, but it's also a very rare opportunity,” says Bohmann.
The fact the groups took different paths to find a similar result is particularly compelling, says Mark Johnson, who studies eDNA and Texas Tech University and was not involved in the work. “It's really exciting looking at how both of these papers, done independently of each other, have produced, really, the same results,” says Johnson. “It adds that extra little bit of validation that what we're seeing is real.” While hopeful about the future of airborne eDNA, Johnson notes huge leaps need to be made before the techniques used in the zoo can be applied in the field. Collecting eDNA in the wild adds a host of new variables, and enclosed spaces like caves may accumulate genetic material differently than open areas like grasslands. “The next step is to take it from the zoo into the natural environment and see what we find there,” says Johnson.
Clare and Bohmann anticipate that one of the best applications of airborne DNA could be to measure biodiversity in difficult-to-access places, such as burrows and caves. Fabian Roger, an eDNA researcher at ETH in Switzerland, is eager to see how the work could be applied to studying insects. “We have very little ways of monitoring them other than catching and killing them,” says Roger, who was not involved in the recent work. Using eDNA to detect insect species from a sample of air instead of trapping them could rapidly advance entomology research. The technique could also clue scientists into the presence or spread of an invasive species. Like Clare and Bohmann, Roger doesn’t see airborne eDNA as a replacement for traditional monitoring methods, but as another tool they can use. “Biodiversity science is sort of an all-hands-on-deck situation. It's not one over the other, or one or the other,” says Roger.
In a field growing as quickly as eDNA research, a lot of unknowns exist. Clare and Bohmann aren’t sure if eDNA captured from the air will ever be able to offer information about a species population, or even the total number of individual animals in an environment. Scientists also aren’t sure how quickly DNA degrades once it’s shed, or how long a species needs to be in an environment before it can be detected through airborne eDNA. Despite the challenges in front of them, both Bohmann and Clare are optimistic that airborne eDNA could revolutionize the study of biodiversity.
“It could be that this is how things go from now on, that people just go and collect filters of air and can diagnose a jungle,” says Clare. “To a certain extent, it's science fiction, but it's also now becoming science fact—and that's cool.”