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Animal diversity can be monitored through DNA in the air

In an unprecedented move, two independent teams of scientists that conducted studies on the same topic have decided to publish their results in the same journal, simultaneously. Both research groups carried out proof-of-concept investigations to show that, by sampling air from surroundings where animals live, they can collect enough DNA to identify the species present. They suggest that this sampling method may be very useful for non-invasive animal diversity studies, especially in environments where it is difficult to observe resident species. 

The team from Denmark collected air samples from the Copenhagen Zoo while the UK team sampled air from different locations in the Hamerton Zoological Park in Huntingdonshire. This method helped them to determine the validity of their findings since most of the species in zoos are exotic and could not have come from anywhere other than within the boundaries of the zoo. Their results are published today in the journal Current Biology.

DNA is shed from all animals. It settles in the environment, in aquatic surroundings, in the air of terrestrial environments, and on surfaces such as leaves, snow and soil. Such DNA present in the surroundings is known as environmental DNA, or eDNA.

Sampling and sequencing eDNA from water samples is a well-established technique used to monitor aquatic organisms. But both current studies stress the potential usefulness of eDNA to identify the presence of different animal species in terrestrial environments as well, especially during investigations into biodiversity.

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

Traditional methods of monitoring terrestrial animals include using cameras, making personal observations, or analyzing tracks and feces left behind. These methods can involve laborious and intensive fieldwork and often don’t return very much data. 

“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.”

Although a few studies already exist showing that vertebrate species can be identified through eDNA filtered from air, the use of airborne eDNA for studying and monitoring vertebrate populations has not been explored before. 

“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, lead researcher of the UK team and scientist at Mary University of London (Clare 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.”

The research groups conducted their studies at the local zoos by collecting samples at various places in the zoo, 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 draws in air from the zoo and its surroundings, which could contain genetic material from any number of sources, like breath, saliva, fur, or feces, though the researchers have not determined the exact sources. “It could be 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,” explained Lynggaard.

“There’s a leap of faith component to some of this because when you deal with regular tissue or even aquatic DNA samples, you can measure how much DNA you have, but with these samples we’re dealing with forensically tiny amounts of DNA,” says Clare. “In many cases, when we only sample for a few minutes we can’t measure the DNA, and so we have to jump to the next stage of PCR where we find out whether there’s any in it or not. When we sample for hours, we get more but there is a trade-off.”

In each study, the researchers detected animals inside the zoo as well as wildlife from the natural areas nearby. Clare’s team from Queen Mary University of London detected DNA from 25 species of mammals and birds, and even DNA belonging to the Eurasian hedgehog, which is endangered in the UK. Bohmann’s team from the University of Copenhagen detected 49 non-human vertebrate species, including mammals, birds, reptiles, amphibians, and fish. These included zoo animals, like okapis and armadillos and even the guppy in a pond in the tropical house, locally occurring animals like squirrels, and pest animals like the brown rat and house mouse. 

The University of Copenhagen team even detected airborne DNA from fish species that were used as feed for other animals in the zoo. They also found that animals that were larger or were closer to the air filtering device had a greater probability of being detected using this method.

The Queen Mary University team also found that eDNA is most concentrated in areas that have been recently inhabited by animals, but that it disperses away from these sources and can be detected hundreds of meters away from them. This indicates that sampling of airborne eDNA can potentially be used to monitor animal populations from a distance.

Both teams were meticulous about not contaminating their samples with DNA, particularly from their own laboratories. By choosing a zoo for the location of their studies, the researchers knew the position of a large collection of non-native species, so they could tell the difference between a real DNA signal and a contaminant. 

“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.”

“One thing both our labs do is develop and apply new tools, so perhaps it’s not so surprising that we both ended up with the same idea at the same time,” says Clare.

However, the fact that both research groups are publishing at the same time is far from coincidental. After seeing each other’s articles on a preprint server, the two groups decided to submit their manuscripts to the journal together. “We decided we would rather take a bit of a gamble and say we’re not willing to compete on this,” says Clare. “In fact, it’s such a crazy idea, we’re better off having independent confirmations that this works. Both teams are very eager to see this technique develop.”

By Alison Bosman, Staff Writer

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