Wild animal species can be monitored with airborne DNA – studies

Great minds think alike. In Denmark and the United Kingdom, two independent groups of researchers studied environmental DNA (eDNA) of zoo animals, collected from the air as a non-invasive method of determining which species are in a certain area.

The two groups came across each others’ work on a preprint server and decided to join their forces and publish simultaneously. Their findings were reported in Current Biology in the same January 2022 issue, one titled ‘Airborne environmental DNA for terrestrial vertebrate community monitoring’, and the other, ‘Measuring biodiversity from DNA in the air’.

“Capturing airborne environmental DNA from vertebrates makes it possible for us to detect even animals that we cannot see are there,” says Kristine Bohmann, researcher and head of the team at the University of Copenhagen.

According to a news release, terrestrial animals can be monitored by many methods, including camera traps, analysis of the environment for footprints or faeces, or in-person observation. Yet these methods “can involve intensive fieldwork and require the animal to be physically present.”

However, eDNA can be more accurate because it traps the DNA of many animals which are then extracted in the lab and sequenced to determine the animals present, even if they cannot be directly observed.

“Earlier in my career, I went to Madagascar hoping to see lots of lemurs. But in reality, I rarely saw them. Instead, I mostly just heard them jumping away through the canopy.” says Bohmann. “So, for many species it can be a lot of work to detect them by direct observation, especially if they are elusive and live in very closed or inaccessible habitats.”

“Compared to what people find in rivers and lakes, monitoring airborne DNA is really, really hard, because the DNA seems super diluted in the air,” says Elizabeth Clare, who was lead researcher of the Queen Mary University of London team and is now at York University in Toronto. “But our zoo studies have yet to fail for different samplers, genes, locations, and experimental approaches. All of it worked and surprisingly well.”

Two independent groups of researchers, one in Denmark and the other based in the UK and Canada, tried to determine if airborne eDNA could be used to detect terrestrial animal species. They collected air samples from two European zoos – Copenhagen Zoo, Denmark, and  Hamerton Zoo Park, UK.

The method of extracting eDNA is generally used for aquatic creatures, but researchers wanted to see if it would work for terrestrial animals.

 “Air surrounds everything, and we wanted to avoid contamination in our samples while optimising true detection of animal DNA,” says Bohmann. “Our newest work with airborne eDNA involves what we usually do when processing eDNA samples, just tuned up a little bit.”

Each research group went to a local zoo and collected samples throughout, including “inside walled-in enclosures like the tropical house and indoor stables, as well as outdoor enclosures in the open air.”

“To collect airborne eDNA, we used a fan, like one you would use to cool down a computer, and attached a filter to it. We then let it run for some time,” says Christina Lynggaard, first author and postdoctoral fellow at the University of Copenhagen.

The fan ingests air from the zoo and its surroundings, which could contain genetic material from “anything that can become airborne and is small enough to continue floating in the air,” says Lynggaard. “After air filtration, we extracted the DNA from the filter and used PCR amplification to make a lot of copies of the animal DNA. After DNA sequencing, we processed the millions of sequences and ultimately compared them to a DNA reference database to identify the animal species.”

The results were extraordinary: “When we analysed the collected samples, we were able to identify DNA from 25 different species of animals, such as tigers, lemurs and dingoes, 17 of which were known zoo species. We were even able to collect eDNA from animals that were hundreds of metres away from where we were testing without a significant drop in the concentration, and even from outside sealed buildings. The animals were inside, but their DNA was escaping,” says Clare.

“We were astonished when we saw the results,” says Bohmann. “In just 40 samples, we detected 49 species spanning mammal, bird, amphibian, reptile and fish. In the Rainforest House we even detected the guppies in the pond, the two-toed sloth and the boa. When sampling air in just one outdoor site, we detected many of the animals with access to an outdoor enclosure in that part of the zoo, for example kea, ostrich and rhino.”

The researchers chose zoos because of the uniqueness of the collection of animals housed there, and also because they would be able to prevent contamination. “We had originally thought of going to a farm, but if you pick up cow DNA you must ask ‘Is that cow here or is it some cow a hundred miles away or in someone’s lunch?’” says Clare. “But by using the zoo as a model there's no other way I would detect DNA from a tiger, except for the zoo’s tiger. It lets us really test the detection rates.”

The scientists detected species not only in zoos but also from surrounding areas: “We also identified food items from air sampled in enclosures and detected taxa native to the local area, including the Eurasian hedgehog, endangered in the United Kingdom,” the British team write. “Of these 49 species [detected by eDNA sampling], five species were wild or domestic non-zoo species known to occur in or around the zoo (e.g., Eurasian red squirrel and water vole),” the Danish team reports.

The two teams also detected DNA from food items for zoo animals, such as chicken, cow, horse and fish. The capability of eDNA sampling of picking up a wide range of species means that the process could be used for detecting and monitoring terrestrial animal species in the wild. By using eDNA sampling, scientists could bolster global conservation efforts.

“The non-invasive nature of this approach makes it particularly valuable for observing vulnerable or endangered species as well as those in hard-to-reach environments, such as caves and burrows. They do not have to be visible for us to know they are in the area if we can pick up traces of their DNA, literally out of thin air,” says Clare. “Air sampling could revolutionise terrestrial biomonitoring and provide new opportunities to track the composition of animal communities as well as detect invasion of non-native species.”