In a proof-of-concept study, scientists from Queen Mary University of London have collected and sequenced animal DNA from the air. Their research is published in the journal PeerJ.1
Where there is life, there is DNA
The ability to collect and sequence DNA that has been shed into the environment – known as environmental DNA, or "eDNA" – is a fairly novel concept that is emerging as a useful tool for the study of ecosystems and biosurveillance. It can be collected from samples such as soil, sediment and water, and "has many uses," says Dr Elizabeth Clare, molecular ecologist at Queen Mary University of London (QMUL). "The most common research is to collect eDNA to study aquatic populations like fish," she adds.
Clare is interested in using DNA to solve ecological problems, primarily working with bats. Her colleague Dr Chris Faulkes is a reader in evolutionary ecology at QMUL and studies subterranean mammals, such as the African mole-rats of the family Bathyergidae. Clare and Faulkes face a similar hurdle in their research areas. Bats and mole-rats are alike in the fact that their natural environments, such as caves and burrows, can be hard to access for research purposes.
Together, the researchers began to question whether air might be a carrier of eDNA from animals and birds, just as water carries eDNA from fish. If so, it could offer a solution for studying hard-to-reach species in a burrow or a cave, amongst other applications. "We are also interested in the general applications. Can we sample in other environments for all sorts of mixed species? Can this be another tool in the toolbox to monitor global biodiversity?" Clare says.
Scientists had speculated on this phenomenon previously, Clare explains. However, the literature did not reveal any published cases of testing animal DNA collected from the air. Consequently, Clare and colleagues embarked on a new research project to determine whether it was possible.
It was, and their research is the first proof-of-concept publication outlining the successful collection and sequencing of eDNA from air.
Proof-of-concept: DNA can be collected from air
The study analyzed air from a dedicated animal housing room that had been home to naked mole-rats (Heterocephalus glaber) for a year. The room had been accessed by researchers that were caring for the animals.
"We collected samples 'paired' from within the main room with the filter pointing away from the colony and then with the filter inside one artificial burrow, 'Colony Omega' which contained 29 individuals within a system of acrylic boxes (3.6m3) with tubing 4.4m in length and 45mm in internal diameter," the authors write in the publication.
Following a protocol by Crauaud et al., Clare and colleagues extracted the DNA before amplifying it using PCR and conducting high-throughput sequencing.2 Mole-rat DNA was recovered from both the burrows and regular air samples, which demonstrates that airDNA is able to move beyond the burrow system of the mole-rats.
Unexpectedly, human DNA was also detected in all samples, including the controls. Clare recalls feeling a mixture of frustration followed by intrigue at this point in the study: "At first we were just thinking of it as a contamination. Now we are thinking of this as a new avenue of research."
Human DNA in the air: Potential applications
A new-found ability to collect and sequence human DNA from air samples opens many doors of opportunity, such as novel tools for human forensic analysis to unlocking secrets from the past. "What started off as an attempt to see if this approach could be used for ecological assessments has now become much more," says Clare. "We are really still speculating at this stage, but we are talking about all sorts of ideas from the world of ancient DNA to degraded material."
The research study is proof-of-concept, and when asked what challenges may be incurred when sampling airDNA going forward, Clare says there are many questions here. "We don’t really know yet for airDNA. Based on the extensive work from water, we can speculate that it will be finding enough of the airDNA that is not degraded in a large air volume… it may be very diluted. But this was also a worry about water and has not been the case. We need more investigation to find out."
More investigation is certainly encouraged by the team at QMUL, as Clare notes: "The eDNA work in water has given us a really good idea of how to further validate this technique but it will require extensive study by many research groups with different approaches and expertise."
For Clare and her team, the next step in developing their finding from this piece of work will be to repeat the studies using more challenging cases, including locations where the airDNA may have been degraded, or could be more diluted. "That is the next big step," Clare concludes.
Elizabeth Clare was speaking to Molly Campbell, Science Writer for Technology Networks.
1. Clare E, Economou C, Faulkes C et al. eDNAir: proof of concept that animal DNA can be collected from air. PeerJ. doi:10.7717/peerj.11030.
2. Cruaud P, Vigneron A, Fradette M-S, et al. Open the SterivexTM casing: An easy and effective way to improve DNA extraction yields. Limnology and Oceanography: Methods. 2017;15(12):1015-1020. doi:10.1002/lom3.10221.