When Mark Stoeckle went fishing in New York City’s East River, he caught a lot more than he was expecting.
The scientist from The Rockefeller University was focused on testing whether DNA floating in the water could shed light on which fish were living in the notoriously polluted stretch of water that separates Manhattan from Brooklyn and Queens.
But the buckets of water he hauled up from the eastern edge of Manhattan contained evidence of a lot more than just aquatic life. They also illuminated New Yorker’s eating habits and the abundance of classic urban wildlife such as rats and pigeons, according to a paper appearing today in PLOS One. In other words, each bucket of water was a little window into the Anthropocene.
“Environmental DNA doesn’t just tell us what lives in the water, it reveals insights into the entire ecosystem surrounding it, including the city itself,” says Stoeckle.
Beyond just being a curiosity (Who knew you could find DNA from tropical tilapia in the river?), the findings could help people track a plethora of interesting and important phenomena: changes in fish populations, the effectiveness of environmental restoration, trends in what people are eating, and whether New Yorker’s are making any headway in their war on rats.
“Urban biodiversity monitoring could expand dramatically and inexpensively using minimal equipment at relatively low cost,” said Stoeckle. “This ability to integrate environmental and human signals positions eDNA as a powerful tool for understanding the Anthropocene – the era defined by human influence on Earth’s systems.”
The primary focus of this research was to see if environmental DNA, or eDNA, testing could be used to gauge fish populations near a city. This DNA, shed by organisms into the environment, has been hailed as a potentially powerful tool that could alert people to the presence of particular species even if they never set eyes on the creature. Scientists have repurposed air quality monitors to detect dozens of species, counted species in zoos from sniffs of the air, and used air and water samples to assemble a surprisingly detailed picture of who and what were nearby.
But there have been obstacles to making good on the technology’s promise. It’s one thing to tell if a species is there. It’s another, more complicated thing to use DNA to estimate the size of a population. Then there’s the possibility that a flush of DNA in a crowded place like New York City might drown out the signals from fish, especially when rainstorms overwhelm the city’s sewer system, sending 18 billion gallons of raw sewage into nearby waterways each year.
“After a heavy rain, the DNA of almost everything that makes the city tick—and squawk and squeak—ends up in the East River,” said coauthor Jesse Ausubel, who heads The Rockefeller University’s Program for the Human Environment.
“Genetically speaking, a rainstorm turns the river into something akin to Times Square on New Year’s Eve: crowded, noisy, and full of signals.”
To test what could be seen amid this chaos, each week between May 2024 and May 2025 the scientists collected two buckets of water from the same spot on the Manhattan side of the river and hauled it back to a lab. There, they ran the water through a filter much like a coffee filter. They took the residue left in the filter and put it through a series of treatments to see what DNA was there and compare it to a library of known DNA patterns.
When it comes to fish, the results revealed a number of fascinating patterns. The scientists didn’t claim to be able to produce counts of individual species populations. But they found that the amount of DNA from one species compared to another tracked closely with the comparative numbers that turned up in traditional net surveys. That means changes in DNA levels of different fish species over months or years probably reflects real rises and declines in their relative abundance.
That connection was buttressed by seasonal changes in the amount of fish DNA in the water. During the winter months, when fish numbers are lowest, so is their DNA. Their DNA surges tenfold during the warmer summer months, in line with population patterns.
The study also turned up evidence suggesting that efforts to rebuild reefs of oysters starting in 2015 are attracting fish. They turned up lots of DNA from skilletfish and feather blenny, which both are drawn to oyster reefs. A similar DNA survey in 2016 found little sign of those species. That matches results from nearby fish traps, where the species began appearing in 2020.
The more unexpected results were about what was happening on the surrounding land. The levels of DNA from different commonly eaten meats aligned with what New Yorkers are eating. Chicken came out on top, followed by beef and then pork. They also found traces of sheep, goat, turkey, salmon and tilapia.
They also found traces of city-dwelling wildlife. Top billing there, in terms of the concentration of their DNA in samples, went to Norway rats, followed by pigeons, Canada geese and ring-billed gulls. But it also turned up some less urban critters, including white-tailed deer and beavers.
The results show that a relatively simple, low-cost method could be used around the world to monitor the wild and not-so-wild pulse of cities, says Ausubel. A year’s worth of monitoring cost $15,000 and a slice of someone’s time, far less than traditional fishing surveys.
“Urban waterways worldwide could become distributed observatories of ecological change, reporting almost real-time what lives in and near them, not only fish but bats, beavers, and foxes,” Ausubel said. “With the right coordination, this approach could become the backbone of urban coastal monitoring.”
Stoeckle, et. al. “Biomonitoring in the Anthropocene: Urban estuary environmental DNA tracks marine fish, terrestrial wildlife, and human diet.” PLOS One. April 15, 2026.
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