When they embarked upon an experiment to swab leaves at Kibale National Park in Uganda in June 2022, Christina Lynggaard, Jan Gogarten and Patrick Omeja had little to no expectations.

The idea had stemmed from Lynggaard’s previous work in biodiversity monitoring with the help of DNA samples collected from the air. “If animal DNA is in the air all around us, perhaps it settles and gets stuck to sticky surfaces,” Lynggaard, a scientist at the Helmholtz Institute for One Health in Germany and the Global Institute at the University of Copenhagen, told Mongabay. “Could we simply collect the settling DNA from air on leaves?”

But rainforests are harsh and humid environments. Assuming that DNA might degrade there quickly, the team hadn’t harbored high hopes.

Until the results came in and left them “flabbergasted.”

The researchers identified 50 species of animals including mammals, birds and rodents, all detected from merely swabbing leaves for a little over an hour — 72 minutes, to be precise. In a study published in August in the journal Current Biology, the team described their quick and cost-effective technique of DNA sampling in a terrestrial environment.

“All it takes is a swab and some gloves with a collection tube filled with a liquid to fix the DNA; that and three minutes to swab some leaves,” co-author Gogarten, also from the Helmholtz Institute and the Applied Zoology and Nature Conservation Research Group at the University of Greifswald in Germany, told Mongabay in an email interview.

Environmental DNA, or eDNA, is the genetic material left behind by animals via their hair, excreta, fur and saliva. For a while now, scientists have collected, tested and analyzed eDNA to understand biodiversity that lives in different ecosystems, including oceans, rivers, air, forests, and even the world’s highest mountain. The methodology has become increasingly popular in recent years, thanks to its ability to survey large areas and its noninvasive nature. The boom in interest in eDNA has also spurred innovation in sampling techniques, from drones that collect water samples, to robotic rovers that gather leaf litter and soil.

However, environmental DNA testing has been used more to survey some ecosystems than others. “For aquatic systems, eDNA has clearly joined the toolkit of conservation biologists and fisheries managers,” Gogarten said. “People simply filter a volume of water and look for animal DNA. This approach has replaced very challenging survey techniques.”

In a terrestrial setting, however, it gets a little more complicated. Invertebrates that have come into contact with terrestrial animals have proven to be a reliable source of eDNA, as have soil and air samples, Gogarten said. But these sampling methods are yet to be widely adopted by researchers and wildlife managers.

“This is partially due to the fact that the collection of eDNA from sources like invertebrates or soil or air samples is time consuming and requires quite a bit of equipment and training,” he said. “The processing is also quite time consuming, which has ruled out the large samples that are frequently seen using water samples.”

It’s in this context that the team set out to test the feasibility of swabbing leaves to gather DNA.

As part of their experiment, the team used 24 swabs to collect samples from three locations at Kibale, best known for its chimpanzees and other primates. To ensure more diversity of species, they collected samples from vegetation closer to the ground as well as from ones above their heads.

“Sample collection was really simple — put on some gloves, unwrap a cotton bud, dip it in a solution that preserves DNA, and then swab all the leaves we could for three minutes,” study co-author Patrick Omeja, a senior research fellow and field director at Makerere University in Kampala, told Mongabay in an email interview. “If you have to leave the area quickly because elephants arrive on the scene, there is no equipment or heavy batteries to pack up and carry, which is another advantage.”

Back in the lab, Lynggaard found vertebrate DNA in every single swab they’d collected in the field, detecting an average of eight species per swab. This ranged from animals such as the mighty African elephant (Loxodonta africana), the usually elusive L’Hoest’s monkey (Allochrocebus Ihoesti), the endangered ashy red colobus (Piliocolobus tephrosceles), the hammer-headed fruit bat (Hypsignathus monstrosus), the forest giant squirrel (Protoxerus stangeri), and birds such as the great blue turaco (Corythaeola cristata) and the gray parrot (Psittacus erithacus).

It’s the high detection rate, complemented by the ease of sampling, that makes Lynggaard and the team confident about the immense potential in using the method for biodiversity monitoring. However, while the approach was effective in Kibale, the team still has unanswered questions about the efficacy of this approach in other ecosystems.

“Perhaps the sun in a savannah breaks down animal DNA more quickly on leaves, so it will not be as efficient,” Gogarten said. “Or in a place with a lot of rain where the leaves get cleaned off more regularly, and so it doesn’t work very well there.”

Additionally, they’re still unclear as to how long DNA persists on leaves in the tropics. “If an animal was at that spot in the forest a year ago, can we still detect its DNA on leaves a year later?” Gogarten said. “These are the types of questions that we are hoping to tackle next.”

As they work to answer these questions in the months and years ahead, Lynggaard said she hopes the field of eDNA also develops further to overcome the limitations that exist at the moment.

“These types of detections confirming that a species is present in an ecosystem are really neat, but a really big next step for eDNA is to move towards abundance estimates,” she said. “This would let us monitor a population through time or explore how populations vary across landscapes or in relation to environmental factors.”

The absence of comprehensive and adequate reference databases to which DNA sequences can be compared is also a hurdle. “There are big initiatives underway to barcode much more of animal life,” Lynggaard said. “But we are a long way from having a complete database.”

Banner image: Jan Gogarten and Christina Lynggaard swabbing leaves to collect vertebrate eDNA. Image by Andreas Sachse.

Abhishyant Kidangoor is a staff writer at Mongabay. Find him on 𝕏 @AbhishyantPK.

Scientists hope to tech the heck out of eDNA sampling with drones, robots

Citation:

Lynggaard, C., Calvignac-Spencer, S., Chapman, C. A., Kalbitzer, U., Leendertz, F. H., Omeja, P. A., … Gogarten, J. F. (2023). Vertebrate environmental DNA from leaf swabs. Current Biology, 33(16), R853-R854. doi: