Is it a Bird? Is it Batman? Filtering and Extracting DNA from the Air Can Provide a Clue

Featured Image Caption: DNA is composed of four building blocks; the distinct order of these building blocks is called a sequence. Scientists use sequences to match DNA to its living origin. Environmental DNA shed by organisms can be found in water, on land, and even in the air. Credit: Furiosa-L. Source: Pixabay

Reference: Clare, E. L., Economou, C. K., Bennett, F. J., Dyer, C. E., Adams, K., McRobie, B., … & Littlefair, J. E. (2022). Measuring biodiversity from DNA in the air. Current Biology 32, 693-700.

The air we breathe everyday contains more invisible particles than we care to acknowledge, but amongst these unseen particles is something that might seem rather unexpected: DNA! Living organisms of every shape and size possess DNA, a complex molecule made of smaller building blocks that encodes all genetic information, causing uniqueness amongst individuals. Some examples of materials that contain DNA are skin cells, feces, pollen, and fungal spores. DNA released by organisms into their surroundings is called environmental DNA or eDNA for short. Tiny pieces of this eDNA can become airborne, and Clare et al. demonstrates that sophisticated filtering can recapture eDNA for analysis. Analysis of DNA involves a process known as sequencing in which advanced machinery reads the order of each building block in a set length of DNA. Scientists are then presented with the distinct order, called a sequence. Then, this sequence can be compared to other known sequences that have been matched to their respective living origin.

DNA is composed of four building blocks that are each assigned a letter. Sequencing reads the order of each letter. Credit: National Human Genome Research Institute, by Darryl Leja, NHGRI. Source: Flickr

Pulling DNA from Thin Air

Sampling of eDNA in aquatic habitats has gained popularity in recent years, which has led to its use in biodiversity monitoring and invasive species management. However, airborne terrestrial eDNA has received less attention. Clare et al. set out to determine if vertebrate DNA was present in the air. If so, they wanted to develop a protocol for sampling and sequencing, as well as investigate how far the airborne vertebrate eDNA traveled. To accomplish this, they chose a zoological park in the United Kingdom that had a variety of animals in confined spaces. Capturing eDNA from the air was conducted using a filtering system. In short, the scientists used an apparatus that pumps air into a flexible tube. First however, the air passes through a filter with miniscule holes. The purpose of the filter is to catch particles that could contain eDNA, while allowing even smaller, non-target air components to pass through. Once back in the laboratory, the filter is removed from the pump, and the process of DNA extraction begins. Extraction involves the use of several chemicals to wash and remove DNA from the paper filter. The next step is amplification, where DNA is reproduced in large quantities. Reproduction of DNA is often employed to obtain many copies of a specific DNA segment of interest. This step is also a safeguard in case the original sample is damaged. After amplification, sequencing takes place.

The zoological park that served as the study site had animals kept in pens that varied in the amount of open air. For example, some were indoors with solid walls and little air movement. Other enclosures were outside and exposed to the air, with only fences as barriers. In total, Clare and her colleagues collected 72 air samples from different types of enclosures. Of these samples, 64 contained DNA that belonged to terrestrial vertebrates.

Here, There, Everywhere!

Using complex statistical modeling, the researchers found that more eDNA belonging to a specific vertebrate was found in its own respective enclosure, even if the spaces were open, with no air movement limitations. This could lead to the conclusion that eDNA does not travel large distances. Surprisingly, this is not the case. The authors demonstrated airborne eDNA was not restricted to the immediate area of its origin. When they sampled the air from a respective animal’s enclosure, they did indeed find its DNA. However, they also discovered DNA that did not belong to that animal. For instance, the scientists did not have access to some confined areas that housed birds. Regardless, they still detected the birds’ DNA in other enclosures nearby. Long-range dispersal was also indicated by the DNA analysis. DNA identified as meerkat was located 245 meters away from the meerkat enclosure. It was also detected at the gibbon enclosure which was 122 meters away.

Monitoring Species Presence and Ecological Relationships

Another exciting discovery from the DNA sequencing and analysis was revealed. Some unexpected DNA was found in 3 of the DNA samples: DNA belonging to a hedgehog that had been listed as a vulnerable to extinction. The zoo was surrounded by countryside, where wildlife roams. Hedgehog sightings had been reported, but these mammals usually aren’t active in the winter when sampling took place. This discovery opens a new facet to airborne eDNA sampling: detection of vulnerable or endangered species. The alternative is equally important, as airborne eDNA can be employed to detect the presence of invasive species. The UK scientists found evidence of an invasive deer in the eDNA sampling. Finally, a third category of eDNA was detected. Over 30% of the DNA recovered from the samples belonged to cows, pigs, or chickens. Long-range dispersal from the nearby countryside could have contributed to this finding, but the scientists theorize that this eDNA actually represented prey fed to the carnivorous zoo animals. Indeed, high levels of chicken were found in several carnivore enclosures. Human movement could also contribute; some prey DNA was also located in herbivore enclosures.

The presence of species vulnerable to extinction, such as the European hedgehog (Erinaceus europaeus), can be detected and tracked by sampling air for eDNA. Source: Wikimedia Commons

The robust report and analysis presented by Clare et al. opens the door for many new applications of terrestrial vertebrate surveillance. Predator/prey relationships can be studied in-depth, which provides information on ecosystem dynamics and food chains. In addition, analyzing DNA from the air can contribute to the monitoring of endangered and invasive species. Sampling air from a distance is non-invasive, as the author notes; this will reduce negatively impacting potential vulnerable species. Airborne eDNA sampling can be crucial to monitoring biodiversity in any given area as well. This is another attractive quality, as the environment continues to experience multiple stresses due to a changing climate, shifting food changes, and severe weather events. Reducing anthropogenic stresses by sampling eDNA from the air will have humans well on their way to discovering many intriguing facets of their environment and the organisms that inhabit it.

While this image uses the term ‘metabarcoding’, it is still depicting applications of Clare et al.’s work. Metabarcoding is simply a term used to describe the process of identifying the DNA of multiple species from one sample. Source: Wikimedia Commons

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Maria Marlin

I am a plant pathologist living in Oregon and working for Oregon State University extension. I study soilborne and foliar pathogens that attack ornamental crops, but the vast majority of my time is spent conducting outreach! I train nursery workers in scouting and detecting signs and symptoms of plant disease. I love to write and share my love of science with others! In my free time, I love to horseback ride and adventure through the magical Pacific Northwest that I am so fortunate to call home. Whether it is chasing mountain summits, exploring the rugged coast, or basking in the silence of the mossy, misty, and moody forests, I am my happiest and most inspired when surrounded by nature.

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