Something in the Air – Environmental DNA Update

DNA is the calling card of life. 

In and on our bodies, traces of DNA sequences other than our own announce the presence of many microbes, our microbiome.

DNA in Natural and Artificial Ecosystems

In the environment, snippets of environmental, or “e” DNA, are also abundant, yet more dynamic, constantly changing, compared to the more staid microbial communities inhabiting our skin folds, intestines, armpits, and elsewhere. Airborne eDNA sequences in natural ecosystems are particularly in flux, as species come and go. 

Human-made (artificial) ecosystems also have transient microbial residents that leave in their wake genetic material. One early study probed the short sequences of DNA mired in sticky goo scraped from banisters and stairways of a New York City subway stop, where millions of commuters regularly deposit the microoganisms on their skin.

The planet presents many ecosystems, natural or not, to probe. DNA Science has covered eDNA clinging to minerals to reconstruct a 2-million-year-old ecosystem from northern Greenland in the throes of climate change, and in the air surrounding two European zoos. That study picked up the genetic material of zoo residents as well as from animals in surrounding natural habitats, such as hedgehogs and red squirrels.

Analyzing eDNA is a little like Star Trek’s tricorder, a handheld sensor. Bones, the doc on the USS Enterprise, would dramatically hold the futuristic instrument aloft to scan the immediate environment to identify and analyze trace molecules in the air. The “tri” refers to the device’s sensing, recording, and computing.

From Air Over Dublin to a Florida Forest

A new paper published in Nature Ecology & Evolution reports the “hoovering” up of airborne DNA over Dublin and above a forest in Florida.

Team leader David Duffy, professor of wildlife disease genomics at the University of Florida‘s Whitney Laboratory for Marine Bioscience, was surprised at the ease of sampling and analyzing the eDNA. “It seemed like it would be hard to get intact large fragments of DNA from the air, but that’s not the case. We’re finding a lot of informative DNA. You can study species without directly having to disturb them, without ever having to see them. It opens up huge possibilities to study all the species in an area simultaneously, from microbes and viruses all the way up to vertebrates like bobcats and humans, and everything in between.”

Earlier, the research team analyzed eDNA from sea turtles, using classic tools from molecular genetics. They collected eDNA pieces using an air filter, deployed PCR to amplify the pieces, then overlapped the copies to reconstitute the genome sequence, a variation of the “shotgun” method Craig Venter’s team used to sequence the first human genome.

The team probed the air above Dublin for a “proof-of-concept,” which yielded genetic hints of hundreds of human pathogens. The approach can detect emerging infectious diseases like new flu or COVID variants, as well as track allergens. The air over Dublin also held DNA evidence of plants and fungi associated with human activity – cannabis, poppy, and magic mushrooms.

A second experiment that probed the air from a forest in Florida yielded genetic evidence of a golden silk orb weaver spider and a bobcat. Using the simple tools and technologies, the researchers painted a molecular portrait of the ecosystem without needing to collect excrement or track endangered species, older techniques.  

And the analysis is relatively easy and fast. An investigator can process and analyze DNA for every species in an area in just a day, thanks to compact, affordable equipment and software hosted in the cloud. “It seems like science fiction, but it’s becoming science fact. The technology is finally matching the scale of environmental problems,” Duffy said. Knowing the origins of a population is important in conservation biology.

“The level of information that’s available in environmental DNA is such that we’re only starting to consider what the potential applications can be, from humans, to wildlife to other species that have implications for human health,” said Duffy.

CODA

DNA tests can have repercussions, and tracking eDNA is no exception. The speed and ease of analyzing eDNA raises the bioethical issue of privacy when applied to DNA from people. That might be valuable for a forensic investigation that detects whiffs of a murder suspect’s DNA in a defined area, like a specific alleyway, forest trail, or building.

But a technology that localizes an individual without that person’s permission, then zaps it up to a cloud, might be reminiscent of a worried parent tracking a teen’s cell phone. To quote The Police, “Every breath you take, and every move you make, every bond you break, every step you take I’ll be watchin’ you.”