How many rats are in New York City? Scientists find new clues in the East River.

With just a plastic bucket—the kind you’d get from the hardware store—environmental geneticist Mark Stoeckle hauled a treasure trove of information out of New York City's East River.

His water samples painted a surprisingly detailed picture of New York City, revealing when fish visit, foreshadowing pest problems, and even showing signs of what people were eating.

Stoeckle, a researcher at The Rockefeller University in New York, spent a year working with his team to take weekly one-liter samples and test for bits of DNA lingering in the environment, referred to by scientists as eDNA. The data revealed that once-rare fish such as skilletfish and feather blennies, which typically live in oyster beds, are flourishing. Stoeckle suggests this could be due to a healthier ecosystem thanks to local restoration efforts, such as the Billion Oyster project, which is replanting oyster beds along New York City’s coastline.

Since the 1970s, levels of sewage and industrial pollution in the river have improved. Stoeckle says that aquatic life has increased—“fishermen will tell you they catch more striped bass than they used to”—and this food sometimes even brings whales and dolphins in to forage in the harbor mouth. “Our study adds to evidence that the harbor is cleaner,” he says.

Stoeckle and his coauthors suggest this simple technique could be used to easily monitor environments all around the world, even in places that might usually be challenging to sample. Their findings are published in the journal PLOS One.

There’s something in the water

The technology that allows scientists to sample and analyze DNA in the environment has been available for more than a decade, but as eDNA technology has improved, it’s now allowing scientists to get more detailed genetic analyses from only small bits of an animal such as skin cells, hair, or waste.

“It turns out there's DNA all around us,” Stoeckle explains. Animals are shedding cells, mucus, and feces all the time. When they do, “they're leaving little traces of DNA behind.”

Sampling for wildlife in this way is also typically quicker, cheaper, and easier to use than traditional research techniques that require more manual labor, he adds.

“You can only send so many divers down or put so many nets in the water,” says Elizabeth Andruszkiewicz Allan, an eDNA scientist at private biotech company Wilderlab, who wasn’t involved in the study.

In the rocky, fast-running East River, nets get caught on rocks, and traps can be washed away by the strong current. Stoeckle says the year-long study cost around $15,000: “If you want to put a boat in water with a net, that will cost you $15,000 a day.”

The data revealed a surprising amount of wildlife diversity in the East River. The scientists found 71 local fish species, each with their own seasonally varied behavioral patterns. During summer, for instance, there was a 10-fold increase in species. “It's like Times Square of fish, but they have different work schedules,” says Stoeckle.

Detecting DNA in water, soil, or air samples can reveal which species were in the area recently—usually within a few days, depending on the environmental and weather conditions. It’s like crime scene technology, he explains, except scientists are looking for creatures, not criminals. “It's just a wonderful way to learn about nature,” he says. “You can learn things that otherwise would be very difficult to know.”

A window into life on land

These weekly water samples also gave the scientists a glimpse into the city’s urban wildlife, including squirrels, raccoons, beavers, and rats.

Stoeckle wasn’t surprised by their presence. He notes that DNA from terrestrial animals washes into the river through wastewater that overflows into the East River. “It's a much bigger picture of the environment than we realize,” he says.

By monitoring how rat DNA fluctuates in the river, the study authors suggest pest control might be able to detect the early signs of an infestation.

The team also detected DNA from cows, pigs, and chickens. Similar to the traces of the city’s rats, the researchers think these DNA signatures may show up in the water when heavy rain causes sewage to overflow into the river.

After detecting these livestock traces, the scientists compared the proportion of food animal DNA with U.S. consumption statistics and found a surprisingly close match.

The study authors suggest sampling for eDNA could be a useful public health tool, for example, helping to monitor whether people are eating less red meat in response to the climate crisis—and say this is the first time eDNA in wastewater has been used to report on human diets.

“What this does with the DNA analysis is actually give you much more granular information on the type of foodstuffs out there,” says Willie Wilson, chief executive of the Marine Biological Association in England, who wasn’t involved in the study.

Both Wilson and Andruszkiewicz Allan were excited by potentially using eDNA to monitor public health trends.

A cheaper, easier conservation tool

eDNA can’t tell scientists the exact population sizes of local wildlife, but it can show whether a particular species is increasing or decreasing. The study authors say this can make effective environmental monitoring as routine as a blood test.

It can also protect habitats from harmful non-native species, which can take hold incredibly quickly. If gathering data is too slow, “you missed the boat,” says Andruszkiewicz Allan. “In many cases with invasive species, by the time it's there, the remediation is really expensive and probably not very likely to be successful.”

eDNA is “a perfect early warning system for detecting them,” says Wilson.

This method is becoming more popular around the world: from tracking elusive Canadian lynx to detecting butterflies from puddles of meltwater up Mount Everest.

However, the many benefits of eDNA don’t mean traditional methods will be wiped out. “I don't think we should forget about all the other tools in our toolbox,” adds Andruszkiewicz Allan. “We just added a new fitting to our drill.”