Analysis: You're certainly getting more than oxygen as DNA captured from the atmosphere shows exactly what's in the air in the capital city
By Jenny Whilde, University of Florida
It turns out that the air of the capital city also contains cats, dogs, rats, cannabis, poppy, and even magic mushrooms, or at least their DNA. This is the result of a new study that found DNA floating in the air in the city provides ample information to simultaneously identify not just larger plants and animals, but tiny insects, fungi, bacteria and even viruses.
The research, led by Dr David Duffy, at the University of Florida's Whitney Laboratory for Marine Bioscience, involved taking air samples in Trinity College Dublin, in the heart of the city centre. There, two floors above the hustle and bustle of urban life, a small machine sucked city air through a tube like a vacuum cleaner. A week later, the machine is switched off and a small three-inch-long filter is detached from the end of the tube. The machine is then run again in rural locations in the Wicklow Mountains and at Wildlife Rehabilitation Ireland in the Boyne Valley Estuary.
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The filters were brought back to the Trinity College Zoology Department and University College Dublin's Systems Biology Ireland. Originally pristine white, the filters now looked grey and dirty, but didn’t appear to have caught anything that might be useful in identifying organisms. However, invisible to the naked eye, they hold the genetic code to thousands of species from each area.
This code is environmental DNA (eDNA), DNA that has been shed naturally into the environment by the living things in the area. The scuff of a paw in the earth, a gust of wind blowing leaves from a tree or a cough or sneeze all release microscopic fragments that contain enough DNA to identify the source.
Traditional approaches can only examine very short pieces of eDNA from a pre-selected subset of species. But a technique known as shotgun metagenomic sequencing allows scientists to rapidly sequence the genomes or partial genomes of a whole range of species in an area, rather than just one species of interest.
The study, published in Nature Ecology and Evolution, was also able to determine the ancestry of bobcats (lynx) and venomous spiders whose DNA was hoovered up from air in a Florida forest. With little more than an air filter, and within a couple of days, scientists can identify endangered species and identify where they came from, without having to see, capture or stress the species being studied. Previously, eDNA was thought to consist of only low-quality degraded short fragments. The recovery of intact DNA from air enables much deeper, faster, and more affordable study of the animals, plants, fungi, bacteria and viruses, in all environments.
Unsurprisingly, the research team found that the genetic ancestry of humans in the city centre was more diverse than in remote rural locations. A high amount of bumble bee DNA indicated the Trinity College Campus Pollinator Plan was working well. There was also plenty of cow and pig DNA in the city air – perhaps from burgers and ham sandwiches? What they hadn't expected to find was DNA from cannabis, poppy and even magic mushrooms.
The animals, plants, fungi, biodiversity, pathogens (human, animal and crop), disease vectors, allergens, antimicrobial resistance genes and genetic diversity in an area can all be easily monitored and compared. The researchers identified different human pathogens from the air, including viruses and bacteria, with far more pathogens present in urban areas. Such surveillance could help scientists easily and rapidly track emerging diseases.
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The implications are huge for many different fields of research, including conservation, health and agriculture: surveying species that are difficult to observe; tracking changes in biological diversity over time; early identification of pest species and disease spread; screening for antimicrobial and pesticide resistance. Simultaneous and rapid surveillance of pathogens (such as Covid-19, potato blight, crayfish plague, wildlife viruses), invasive species (Japanese knotweed), endangered species, pest species, disease-vector species (such as mosquitoes), allergens and plant- and fungal-derived narcotics are all possible from air eDNA shotgun metagenomic sequencing.
This technology does not come without concerns, especially when sampling in areas frequented by humans. We shed our DNA into the air just like other animal species. The study highlights ethical issues such as individual privacy, potential beneficial applications of eDNA technology for law enforcement purposes or worrying applications by surveillance states. These ethical issues need to be taken into serious consideration by the scientific and legislative communities, and guidelines around the safe and appropriate use of information gleaned from eDNA will need to be put in place.
As technology that only existed in the sci-fi fantasies of our childhoods becomes a reality, it seems that we are closer than ever to developing a lifeform detection device as envisaged by Star Trek’s tricorder.
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Dr Jenny Whilde is Environmental Grant Coordinator at the Whitney Laboratory for Marine Bioscience at the University of Florida.
The views expressed here are those of the author and do not represent or reflect the views of RTÉ
