“Every day I see something bubbling up that didn’t occur to me.”
Peter Andrey Smith at Singularity Hub:In the late 1980s, at a federal research facility in Pensacola, Florida, Tamar Barkay used mud in a way that proved revolutionary in a manner she could never have imagined at the time: a crude version of a technique that is now shaking up many scientific fields. Barkay had collected several samples of mud—one from an inland reservoir, another from a brackish bayou, and a third from a low-lying saltwater swamp. She put these sediment samples in glass bottles in the lab, and then added mercury, creating what amounted to toxic sludge.
At the time, Barkay worked for the Environmental Protection Agency and she wanted to know how microorganisms in mud interact with mercury, an industrial pollutant, which required an understanding of all the organisms in a given environment—not just the tiny portion that could be successfully grown in petri dishes in the lab. But the underlying question was so basic that it remains one of those fundamental driving queries across biology. As Barkay, who is now retired, put it in a recent interview from Boulder, Colorado: “Who is there?” And, just as important, she added: “What are they doing there?”
Such questions are still relevant today, asked by ecologists, public health officials, conservation biologists, forensic practitioners, and those studying evolution and ancient environments—and they drive shoe-leather epidemiologists and biologists to far-flung corners of the world.
The 1987 paper Barkay and her colleagues published in the Journal of Microbiological Methods outlined a method—“Direct Environmental DNA Extraction”—that would allow researchers to take a census. It was a practical tool, albeit a rather messy one, for detecting who was out there. Barkay used it for the rest of her career.
Today, the study gets cited as an early glimpse of eDNA, or environmental DNA, a relatively inexpensive, widespread, potentially automated way to observe the diversity and distribution of life. Unlike previous techniques, which could identify DNA from, say, a single organism, the method also collects the swirling cloud of other genetic material that surrounds it. In recent years, the field has grown significantly. “It’s got its own journal,” said Eske Willerslev, an evolutionary geneticist at the University of Copenhagen. “It’s got its own society, scientific society. It has become an established field.”
eDNA serves as a surveillance tool, offering researchers a means of detecting the seemingly undetectable. By sampling eDNA, or mixtures of genetic material—that is, fragments of DNA, the blueprint of life—in water, soil, ice cores, cotton swabs, or practically any environment imaginable, even thin air, it is now possible to search for a specific organism or assemble a snapshot of all the organisms in a given place. Instead of setting up a camera to see who crosses the beach at night, eDNA pulls that information out of footprints in the sand. “We’re all flaky, right?” said Robert Hanner, a biologist at the University of Guelph in Canada. “There’s bits of cellular debris sloughing off all the time.”
As a method for confirming the presence of something, eDNA isn’t failproof. For instance, the organism detected in eDNA might not actually live in the location where the sample was collected; Hanner gave the example of a passing bird, a heron, that ate a salamander and then pooped out some of its DNA, which could be one reason signals of the amphibian are present in some areas where they’ve never been physically found.
Still, eDNA has the ability to help sleuth out genetic traces, some of which slough off in the environment, offering a thrilling—and potentially chilling—way to collect information about organisms, including humans, as they go about their everyday business.
