Dingoes at Hamerton Zoo in the UK look curiously at the air sampling equipment. (Image: Elizabeth Clare)
The zoo's air is filled with smells of fish used as fodder and the smell of herbivores' droppings, but we now know that it is also full of DNA from the animals that live here. In the Jan. 6 issue of the journal Current Biology, two different research teams each published an independent proof-of-concept study showing that by taking air samples from local zoos, enough DNA can be collected to identify animal species near the sampling site. The technology may prove to be a valuable and non-intrusive tool for tracking biodiversity.
Kristine Bohmann, team leader and researcher at the University of Copenhagen, said: "By capturing the air-environment DNA of vertebrates, we can even detect animals that we can't see. ”
Terrestrial animals can be monitored by direct observation, such as camera shooting and on-site observation, and indirect observation, by observing traces of terrestrial pathway processes, such as footprints or feces. But the disadvantages of these methods are that they require researchers to conduct frequent field trips and the need to know that the animals have indeed been present. For example, monitoring an animal through a camera requires knowing the animal's route in advance, in order to place the camera on the corresponding road, and finally sifting through thousands of photos to select the photos of the target animal, but this usually requires a little luck.
Bohmann laments: "Early in my career, I wanted to conduct research on lemurs in Madagascar. But it was actually whimsical, I hardly ever saw them, and more often than not I could hear them moving through the canopy. For many species, detection through direct observation is extremely labor-intensive, especially for those living in isolated or inaccessible habitats. ”
Elizabeth Clare, lead researcher at queen Mary University of London's research team (now working at York University in Toronto), said: "Compared with the water-like environmental DNA obtained in rivers and lakes before, the concentration of DNA in the air is extremely low, and monitoring is even more difficult. But our studies in zoos were effective on different samples, genes, locations, and variables of experimental methods, and the results were surprising. ”
Christina Lynggaard and Kristine Bohmann collect air samples at Copenhagen Zoo. (Image: Christian Bendix)
Bohmann and Clare, who have previously collected samples of shedding DNA from animals such as hair or tissue, have drawn a great deal of experience from surveillance studies of these wild animals. This technology, known as "environmental DNA, or eDNA," is well established and is most commonly used to sequence eDNA in water bodies to monitor the biodiversity of aquatic organisms.
Bohmann says: "Everything is surrounded by air, so we wanted to avoid contamination of the samples while optimizing our dna-to-life detection techniques for animals. Our latest study on air eDNA includes previous work on working with eDNA samples, with only minor tweaks. ”
Each team collected air samples from different parts of the zoo for experiments, including walled environments such as houses and indoor stables that mimic tropical environments, as well as open-air chamber perimeter bars. Christina Lynggaard, postdoc at the University of Copenhagen and lead author of the article, said: "We collected DNA from the air by running a fan that resembled a computer heatsink, and we also added a filter to the fan. ”
The fan filters air from zoos and their surroundings, and although researchers don't yet know exactly where the genetic material in the air comes from, they may be diverse, such as from small molecules carried by the breath, saliva, fur, or feces. Lynggaard said: "Any tiny particle that can float in the air can be collected. After the air is filtered, we can extract DNA from the filter and increase the copy number of the animal's DNA using PCR amplification technology. After DNA sequencing, we processed millions of DNA sequences and eventually compared those sequences with DNA reference data to identify animal species. ”
"It's a sublimation of belief, because when you're dealing with regular tissue samples or watery DNA, you can explicitly measure the amount of DNA that's extracted, but the samples we're dealing with now are very small," Clare says. In many cases, concentrations cannot be detected when an air sample is collected for only a few minutes, so we must jump straight to the next step in pcrography to detect the presence of DNA. When we spend hours collecting air samples, we can obviously get more DNA, but there is a balance between the time of collection and the amount of DNA acquired. ”
Elizabeth Clarezai collects DNA in the air. (Image: Elizabeth Clare)
In each study, the researchers were able to detect animals from zoos and wildlife from nearby areas. Clare's team from Queen Mary University of London detected DNA from 25 species of mammals and birds, and even the DNA of eurasian hedgehogs endangered in the UK. The University of Copenhagen's Bohmann team detected 49 species of non-human vertebrates, including mammals, birds, reptiles, amphibians and fish. These species detected included zoo animals such as the mammoth and the armadillo, as well as peacock fish in tropical house ponds, squirrels of local species and harmful animals such as brown rats and house rats. In addition, they detected fish used as feed in zoos. Both teams went out of their way to ensure that the samples were not contaminated, including by DNA present in the lab.
The researchers chose the zoo as the study site because it gave them a clear picture of the location of many of the non-native species in the park, and this information could help them distinguish which were true signals and which were pollutants. "We originally wanted to set the site of the study on the farm, but if you collected the DNA of the cows, you would definitely ask, 'Is this DNA from the farm cows, or is it from a cow a hundred miles away, or is it in someone's lunch?'" Says Clare said. ’。 However, if we take the zoo as a model, we cannot detect other tigers except the tigers in the zoo. This limiting factor truly reflects detection rates. ”
"Both of our labs have developed and applied new tools, so it's not surprising that we might come up with the same idea at the same time," Clare says. ”
However, it is no coincidence that the two research teams published papers in the journal Current Biology at the same time. Both groups had seen each other's articles on the preprint server platform and decided to contribute to the magazine together. "We decided we'd rather gamble than compete on this project," Clare said. In fact, this is a very crazy idea, and we would do well if our respective experiments can be effectively independently tested. Both teams are very eager to see the technology evolve. ”
Translation: Huang Junman
Reviewer: Bingying Zhao
Source of introduction: Physicists Organization Network
This article is from: China Digital Science and Technology Museum