3 days ago
Scanning the air for life
We are a step closer to the legendary Star Trek tricorder, a fictional device that enabled the intrepid crew of the Starship Enterprise to scan an alien planet for signs of life.
A
recent paper
by Nousias and colleagues shows how the instructions of life, contained in
DNA
, can be detected and analysed in greater detail than ever before from air samples.
While environmental DNA has been collected before from water, soil, sand and even air, the team combined air samples with deep sequencing methods that recover much more detailed information on the genetic code of animals, plants, humans and microbes in the environment.
This paper has a fascinating Irish connection. Some of the tiny air pumps used to collect samples were located at the zoology building in
Trinity College Dublin
, the Boyne estuary in Meath and Croghan mountain in Wicklow.
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These samples were contrasted with air samples from Florida coastal and forest locations. Notable species detections in Dublin city centre included dust mites, high bacterial diversity and a substantial amount of bumblebee DNA – perhaps related to the success of Trinity's recent campuswide actions for pollinators.
DNA was also detected from plants that may be largely consumed rather than grown in the area, including peanuts, cannabis, opium poppy and the fungus psilocybe – 'magic mushrooms'.
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Organisms in the environment, including humans, shed DNA into the air through the flaking of skin, production of pollen or saliva and all manner of other materials that are produced as they go about their daily lives. The materials we use and consume also shed DNA. The air is therefore a veritable genetic soup which can be sampled and the DNA sequenced.
Modern genetic sequencing called 'shotgun sequencing' enables sequences of DNA to be produced without an initial template, so genetic surprises may be found by comparing the sequences with databases of known species.
Methods such as 'genetic barcoding' require that you fish in the genetic soup with a specific set of organisms in mind, and your detections are therefore limited by what you are looking for. 'Shotgun sequencing' also enables you to quantify how much DNA of a particular genetic sequence is in the air sample, which means you can compare sites for the relative abundance of a particular animal, plant or microbe.
Of course human DNA is also detectable. An astonishing level of detail on the genetics of human populations can be retrieved from sampling the air alone. DNA from Dublin was characteristic of a diverse international city, whereas there were much fewer genetic types in the rural samples. While individual humans were not identified in this study, the technology now undoubtedly exists to enable individual human genomes to be analysed and identified from non-invasive samples, such as the air you have recently walked through.
As with many technological leaps there are risks and opportunities for the deployment of deep sequenced environmental DNA analysis from air samples. Rapid biodiversity assessment is urgently needed to identify, monitor and manage the health of our environment. Difficult to study and detect species such as nocturnal bats and moths, low-density predators and microscopic species can be sampled using these methods.
Environmental monitoring for detection of harmful pathogens is possible, with the potential for early-warning signals of disease outbreaks. In one week of sampling in Dublin city, 221 species with disease potential for humans were detected. Air can be scanned for the presence of allergens such as peanuts or for illegal narcotics.
It will also be possible to deploy this technology for harmful purposes, including military use, monitoring and targeting of particular human populations or individuals and the illicit sampling of natural resources in the search for new medicinal drugs. There are profound ethical consequences of large-scale genomic analysis of human populations and individuals that need to be urgently addressed and regulated.
While the lure of the tricorder is strong, there is still a lot of work to be done to ensure that the methods are robust and representative of the abundance and presence of particular species in the sample area.
International and national-level policy and regulation needs to be developed to ensure that the benefits of rapid biodiversity assessment can be achieved with guardrails in place to prevent potentially damaging uses.
Yvonne Buckley is co-director of the Co-Centre for Climate + Biodiversity + Water and professor of zoology at Trinity College Dublin
