Airborne DNA can now be used to detect rare and endangered species

Airborne DNA can now be used to detect rare and endangered species



The discovery of environmental DNA has altered the way environmentalists monitor biodiversity. Scientists can examine entire ecosystems or find unusual animals that are too elusive to trace using traditional methods by sequencing the genetic material contained in water and soil samples.

Environmental DNA, or eDNA, has been utilized by teams to catalog everything from viruses and bacteria to plants and animals, from the slopes of Mount Everest to the depths of the ocean.

New research is now opening up even more possibilities. Several research groups have recently demonstrated that eDNA may be retrieved from thin air and used to identify adjacent plants and animals.

This approach is potentially a valuable new tool for monitoring the terrestrial environment, the researchers say. Airborne DNA could be used to detect rare and endangered species and to track shifts in the makeup of species assemblages due to climate change. It could also provide early warning of invading species moving into novel environments and might even be a handy way of sleuthing wildlife trafficking.

“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,” Elizabeth Clare, a biologist at York University in Canada who led one of the research groups, said in a statement. The animals “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.”

As organisms move through their environment, they shed genetic fingerprints in the form of skin, fur, scales, pollen and secretions. Typical eDNA surveys developed over the past few decades sample water, soils or surfaces for these genetic clues. However, new studies show that DNA-containing material is also circulating in the air all around us and can be readily collected and sequenced. The findings are a “huge step forward in the eDNA field,” Tracie Seimon, director of the Wildlife Conservation Society’s molecular laboratory in New York, told Mongabay in an email.

Dingos at Hamerton Zoo in the U.K. eye the air sampling equipment with curiosity. Photo courtesy of Elizabeth Clare
Dingos at Hamerton Zoo in the U.K. eye the air sampling equipment with curiosity. Photo courtesy of Elizabeth Clare

From theory to proof of concept

The recent proof-of-concept studies have each independently demonstrated the effectiveness of airborne DNA to identify a variety of life forms. Last month, two separate research groups published studies in the journal Current Biology showing that sampling air from a zoo yields enough DNA to identify nearby animals.

The research teams — one in Denmark sampling at Copenhagen Zoo, and one in the U.K. at Hamerton Zoo Park — had no knowledge of each other’s work until the studies were completed. The fact that the two teams have independently demonstrated the efficacy of the technique adds to the strength of their results, the researchers say.

“When you’re doing something that’s a little bit crazy, it’s nice to have someone else that’s done it as well,” Clare, who led the U.K.-based team while she was a senior lecturer at Queen Mary University of London, told Mongabay in an interview. “Because two teams have done this and independently found the same things, it makes you realize it was an idea that was ready to happen.”

Both teams chose to test the technique in zoos because of the high density of a variety of precisely located exotic animals. “We could go to the countryside and detect [DNA from] cows. But we wouldn’t know whether it was from cows in front of us, or manure on fields, or cows hundreds of miles away,” Clare said. “The zoo is perfect, because all of those animals are only found in one location. If I detect tiger DNA, there is only one possible source in the English countryside — the tiger in front of me; it cannot be mixed up with any other signal in the environment.”

The research groups used similar methods to collect and process the airborne DNA samples. The U.K.-based team employed low-powered vacuum pumps and the Denmark-based team used blow fans to collect DNA onto filters at various locations around their respective zoos, both indoors and outdoors. Each team then amplified the tiny fragments of DNA using polymerase chain reaction (PCR) and compared the sequences to a reference database to identify the species present. In total, the U.K. team identified 25 vertebrate species and the Denmark team found 49.

Christina Lynggaard and Kristine Bohmann collect air samples at the Copenhagen Zoo. Photo courtesy of Christian Bendix
Christina Lynggaard and Kristine Bohmann collect air samples at the Copenhagen Zoo. Photo courtesy of Christian Bendix

“We were astonished when we saw the results,” Kristine Bohmann, a biologist at the University of Copenhagen and lead investigator of the Denmark study, said in a statement. “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.”

While both teams detected many of the zoo animals, they also detected several wild species from nearby natural surroundings. For instance, squirrels, brown rats and mice showed up in the Danish samples, and the U.K. team picked up the increasingly scarce Eurasian hedgehog, clearly demonstrating the potential for airborne DNA in monitoring rare wildlife.

In addition to the exhibits and local wild animals, both studies also picked up DNA from the species used as feed. The Danish team identified salmon and roach that were on the menu of Copenhagen Zoo’s seals, polar bears and crocodiles, and the U.K. team detected cows, pigs and chickens — all prime fodder for the tigers, cheetahs and wolves housed at Hamerton Zoo Park.

The detection of DNA from inert meat suggests airborne DNA technology could also be used to sniff out contraband in the illegal wildlife trade. However, Ross McEwing, a project officer at the U.N. Office on Drugs and Crime (UNODC), who has led efforts to use forensic science in the investigation of wildlife crime in many parts of the world, expressed skepticism. Wildlife crime labs typically employ simple and standardized DNA sequencing techniques, he said, so processing highly fragmented air DNA samples would not be realistic. Furthermore, processed and preserved wildlife products in trade, such as tiger bone paste, preserved skins, or powdered rhino horn are unlikely to contain detectable DNA.

Nonetheless, McEwing said air DNA sniffing devices could be a “useful tool” in wet markets or around shipping containers to verify whether wildlife items being sold or imported were what they claimed to be rather than a trade-restricted species.

Elizabeth Clare sampling air at Hammerton Zoo Park in the U.K. to collect airborne DNA. Photo courtesy of Elizabeth Clare
Elizabeth Clare sampling air at Hammerton Zoo Park in the U.K. to collect airborne DNA. Photo courtesy of Elizabeth Clare

Not just big animals

Meanwhile, scientists at Lund University in Sweden have shown that it’s not just large vertebrates that can be detected from air samples. A research team led by Fabian Roger, an entomologist now at ETH Zürich in Switzerland, detected 85 species of invertebrates, including bees, moths, flies, beetles, wasps and ants, from air sampled in a variety of outdoor settings. The research group reported its findings in December 2021 at the Ecology Across Borders online conference.

Airborne DNA sampling for invertebrates could be particularly useful to keep tabs on commercially important crop pests and disease vectors. It would also help to gauge the overall health and diversity of insect assemblages suffering from climate change, overuse of pesticides, and agricultural intensification.

“In the face of the biodiversity crisis, we desperately need better information on the status and distribution of species,” Roger said in a statement. Airborne DNA sampling “opens many exciting possibilities for species monitoring and detection, which could allow us to comprehensively monitor biodiversity at large spatial and temporal scales.”

The approach has also proved an effective means of monitoring entire plant communities. A recent U.S.-based study published in BMC Ecology and Evolution showed that airborne DNA inventorying is comparable to traditional visual botanical surveys. Researchers used dust traps mounted across a grassland area in Texas to collect plant pollen and fragments of leaves and flowers carried in the natural air flow. In total, DNA sequencing revealed 91 plant species, compared to 80 species identified through visual surveys.

Although field botanists recorded more rare species with showy flowers, the genetic approach detected more grasses and also picked up an inconspicuous invasive species that had slipped past the human surveyors. This finding, in particular, highlights airborne DNA’s potential for early detection of harmful invasive species, allowing timely action for eradication, according to the study.

WCS Vietnam veterinarian, Long Nguyen, using a ‘Biomeme’ portable eDNA PCR field kit developed by the WCS Molecular Lab to detect the Yangtze giant softshell turtle in Vietnam. Photo courtesy of Tracie Seimon
WCS Vietnam veterinarian, Long Nguyen, using a ‘Biomeme’ portable eDNA PCR field kit developed by the WCS Molecular Lab to detect the Yangtze giant softshell turtle in Vietnam. Photo courtesy of Tracie Seimon

Real-world applications

Airborne DNA sampling has three major potential applications, according to Clare. First, DNA sniffing devices could be employed as a way of passively monitoring the composition of species in the environment. Second, it could be used for early detection of invasive species moving into an environment. And lastly, it could be used to study very sensitive or endangered species that are otherwise hard to monitor due to their scarcity.

In some cases, it might even be possible to use eDNA to study the genetic diversity of populations on the brink of extinction that scientists cannot risk disturbing. “That is very powerful, especially when we are dealing with rare and endangered species,” Clare said. “Anything that is non-invasive that allows us to estimate their population genetic health would be massively important.”

Although eDNA offers a powerful alternative to traditional ways of monitoring terrestrial ecosystems, such as direct observations or camera traps, experts don’t view it as a substitute. Rather, they see its potential as an additional tool that can be used in combination with other methods.

For instance, eDNA is increasingly incorporated into flagship conservation projects, according to Seimon of WCS. In Vietnam, conservation teams are searching for the critically endangered saola ox (Pseudoryx nghetinhensis) and Yangtze giant softshell turtle (Rafetus swinhoei) using traditional methods in combination with eDNA sampling of dung and lake water, respectively. The new airborne DNA research “shows how air sample eDNA should be explored as a new potential application for wildlife biology and ecology, population genetics, and conservation,” Seimon said.

While the new research is a “useful first step,” follow-up studies will be needed to hone the method before it can be used as a way of monitoring wildlife in the field, according to Seimon. Learning more about how DNA moves through and persists in the air will be critical.

“We know that some species shed eDNA differently, and many environmental variables can impact eDNA degradation in the field such as temperature, ultraviolet radiation and humidity,” Seimon said. “Determining how well eDNA can be detected from air in a forest, mountainous, or desert environment, where animals are moving … will be important questions to answer.”

Clare agrees that further development is required to optimize the technique and understand more about its sensitivity and reliability. But the fact that aquatic eDNA sampling has come so far in recent years offers a huge pool of resources from which to accelerate the technique’s development. And according to Clare, the journey of discovery itself is a reward.

“We’re now working on a set of experiments [to test] where we are going to be able to use it,” Clare said. “We don’t know yet. But that’s part of the fun at the moment, trying different things to see what might work.”

Citations:

Clare, E. L., Economou, C. K., Bennett, F. J., Dyer, C. E., Adams, K., McRobie, B., … Littlefair, J. E. (2021). Measuring biodiversity from DNA in the air. Current Biology. doi: 10.1016/j.cub.2021.11.064

Lynggaard, C., Bertelsen, M. F., Jensen, C. V., Johnson, M. S., Guldberg Frøslev, T., Olsen, M. T., & Bohmann, K. (2021). Airborne environmental DNA for terrestrial vertebrate community monitoring. doi:10.1016/j.cub.2021.12.014

Clare, E. L., Economou, C. K., Faulkes, C. G., Gilbert, J. D., Bennett, F., Drinkwater, R., & Littlefair, J. E. (2021). eDNAir: Proof of concept that animal DNA can be collected from air sampling. PeerJ, 9, e11030. doi:10.7717/peerj.11030

Roger, F., Ghanavi, H., Danielsson, N., Wahlberg, N., Löndahl, J., Pettersson, L.B., … Clough, Y. (2021) Airborne environmental DNA metabarcoding for the monitoring of terrestrial insects — a proof of concept. bioRxiv, 2021.07.26.453860. doi:10.1101/2021.07.26.453860

Johnson, M. D., Fokar, M., Cox, R. D., & Barnes, M. A. (2021). Airborne environmental DNA metabarcoding detects more diversity, with less sampling effort, than a traditional plant community survey. BMC Ecology and Evolution, 21(1). doi:10.1186/s12862-021-01947-x

This article by Carolyn Cowan was first published by Mongabay.com on 11 February 2022. Lead Image: A Toco toucan (Ramphastos toco), one of the species detected via airborne DNA sampling at Copenhagen Zoo. Image by Rhett A. Butler for Mongabay.


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