Handheld Device Creates Genetic Profiles From Airborne DNA With Astounding Speed

A majestic bobcat sauntered through the Florida coastal forests. Nearby, diamondback rattlesnakes slithered across muddy terrain, alligator “swamp puppies” patrolled the waters, and venomous spiders waited for prey. Meanwhile, trekkers explored the grand oaks, slapped away mosquitos, and looked for bats and ospreys.

This may sound like an episode of Planet Earth—but there were no cameras. Instead, scientists collected microscopic snippets of airborne DNA with a vacuum. They documented the animals by running this environmental DNA, or eDNA, through a cutting-edge device about the size of a deck of cards. The device can do more. Halfway around the world in the city of Dublin—known for its pubs, music, and cheer—the team used it to detect DNA traces from weed, poppy, and magic mushrooms wafting on the breeze. They assembled genomic profiles with astounding speed, capturing whole genetic landscapes in just two days.

“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 study author David Duffy at the University of Florida in a press release.

The device is a powerful tool that can be used to monitor biodiversity, emerging viruses, and illicit drugs, but it can also detect the genetic heritage of people traipsing about nearby. Although it wasn’t used to identify individuals in the study, the authors warned that airborne eDNA “could provide seriously powerful potential for individual-level surveillance for…humans.”

Nevertheless, “It is boundary-pushing work,” Ryan Kelly at the  University of Washington, who was not involved in the study, told Science.

A Trove of Data

Living creatures shed genetic material. Fungi, plants, animals, humans, bacteria, viruses—all leave invisible genetic fingerprints as they roam the world.

As technologies to read DNA—known as genetic sequencing—have advanced, scientists have begun capturing DNA in the ambient environment to take a census of the living creatures there.

Some have found thousands of bacterial species in the depths of our oceans. Others are tracking ocean species using DNA “sponges” or land-based creatures by analyzing ingested eDNA from dung beetles. These studies can also monitor emerging viruses from animals—such as those in wildlife markets—by capturing and analyzing genetic molecules.

Duffy believes eDNA could invigorate conservation efforts. In 2022, his team devised a way to monitor endangered sea turtles on the Florida coast. These animals are difficult to track. They roam multiple habitats, including the open sea, coastal ecosystems, and beaches.

Though originally developed to track microbes, Duffy and team showed eDNA can be used to detect small chunks of genetic material from hair, skin, scales, and fluids left behind in sand and water. The team also picked up dangerous sea-turtle pathogens, including a virus that causes tumors in the turtles. Since then, they’ve captured human eDNA from oceans, rivers, and sand—and can identify individual volunteers based on their footprints on the beach.

Although eDNA samples are usually picked up from water and land, they also float in the breeze. This led the team to ask: How much information can we gather from air?

Bring in the Shotgun

Most eDNA studies use a technology called metabarcoding. Here, scientists extract DNA from a sample—say, water from a Florida swamp or a Dublin pub—and sequence the DNA. To detect which species are present, each DNA snippet is matched to a barcode in a data library. The method can be accurate, but it has some shortcomings.

For one, the approach can only identify eDNA sequences already in the database. The barcodes are a little like those on produce at the grocery, only instead of apples or onions, they’re small snippets of DNA unique to a species. You can only detect organisms with existing primers. That is, when the system scans a piece of DNA, it won’t register unless there’s already a barcode present. The method is also costly and takes days, if not weeks, to process a single sample.

Duffy and team turned to a method called shotgun sequencing, which randomly chops DNA sequences into billions of snippets called “reads.” Though the approach is powerful, it’s languished in the past due to the cost and time to piece together individual genetic snippets and match them to a group of organisms. The hardware was also bulky, roughly the size of a refrigerator, making it difficult to bring into the field. It was mostly used to study microbes—not animals or humans.

Thanks to cloud computing and deep sequencing—a type of DNA sequencing where the same DNA region is read many times—it’s now possible to do shotgun sequencing in the wild.

The team used a handheld device with a vacuum tube to suck DNA from the air. For two years, they collected samples across a range of urban and rural locations and produced 78 shotgun sequencing datasets.

“When we started, 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 actually finding a lot of informative DNA,” said Duffy.

In one experiment, they tracked bobcats by gathering eDNA near animal tracks for a week. They found it contained bobcat DNA from a wild population and a zoo-based one, suggesting the tech could be used to monitor animal lineages. They also collected airborne DNA near venomous spiders and found their genomes differ from those in the Caribbean or South America. Without having to lay eyes on the animals, the team painted a picture of species thriving in Florida’s coastal forests.

Meanwhile, Dublin had a completely different eDNA profile. The device identified 63 viruses in air samples across the city alongside a slew of allergens, such as those from peanuts and tree pollen. It also found evidence of illicit drugs, including magic mushrooms.

A Genetic Quandary

The technology isn’t an all-seeing eye, and it’s possible to over-interpret results.

It relies on algorithms to stitch DNA back together and some could just be random DNA floating in the air. Also, some applications, like those related to human DNA, could be beneficial but also risk unexpected negative consequences, wrote the authors. In Florida and Dublin, they could identify the genetic ancestry of people walking through a location. The team intentionally refrained from identifying individual people in the study—although it has already been done.

“As with artificial intelligence technologies, the human eDNA genie cannot be returned to the bottle,” wrote the team. The technology can be used for good or nefarious purposes. For now, the team is hoping to bring eDNA back to its roots, to save and conserve wildlife.

“It seems like science fiction, but it’s becoming science fact,” said Duffy.