Urban watercourses can reveal a surprising amount about life in water and in the city. This is the conclusion of a study that analyzed environmental DNA samples from the East River in New York over a year. The original aim was simply to track the development of fish stocks in the light of conservation efforts. But as the researchers found, the DNA traces in the water also provide information that goes far beyond that, for example about the populations of urban animals and even the population’s diet. Water samples therefore offer a cost-effective and effective option for biomonitoring.
The East River, a long strait in New York City, is traditionally heavily polluted. To this day, urban wastewater is discharged into the estuary. At the same time, environmental protection efforts ensure that fish populations in the urban waters recover. Regular surveys of fish stocks are important to monitor progress, but the strong currents and rocky ground make traditional methods such as traps and trawls difficult to use.
Searching for clues in water samples
In search of a simple and reliable method to obtain information about the fish in the East River, environmental scientists Mark Stoeckle and Jesse Ausubel from Rockefeller University in New York came up with the idea of studying the animal world in the water based on their remains: feces, mucus, skin cells and carcasses release DNA strands into the water that can be detected in the laboratory. Every week from May 2024 to May 2025, they took a liter of water from the banks of the East River, passed it through a filter and examined the DNA in what was stuck in the filter.
And indeed: The so-called environmental DNA (eDNA) not only provided information about which fish species were represented in the East River, but the proportions of the respective DNA traces also matched well with the population sizes that had been estimated from trawl surveys. “We can convert raw DNA sequence data into reliable estimates of population size,” reports Stoeckle. There was a positive development: the researchers identified a total of 71 local marine fish, including two species that were apparently newly represented in large numbers compared to previous studies.
Seasonal fluctuations were also noticeable. Because some species only live in the East River in the summer, the concentration of fish DNA increased tenfold during those months. The eDNA therefore reflects biological dynamics reliably and accurately and can offer an easy-to-perform supplement to trawl surveys.
Information about the whole city
But the insights that can be gained from the water samples go far beyond recording fish stocks. Stoeckler and Ausubel also found DNA traces from 60 terrestrial vertebrates, including wild animals such as rats, pigeons, beavers and raccoons, but also domestic animals such as dogs and cats as well as farm animals such as chickens, cattle and pigs. The respective DNA concentrations correlated strongly with the concentration of human DNA in the water samples. From the researchers’ perspective, this pattern suggests a common source: urban wastewater, which is discharged unfiltered into the East River when the sewage system is overloaded.
“After a heavy rainstorm, the DNA of almost everything that keeps the city running—and making it croak and squeak—ends up in the East River,” Ausubel says. “Genetically speaking, a downpour turns the river into something akin to Times Square on New Year’s Eve: crowded, noisy and full of signals.” These signals revealed surprising insights: “We found that the amount of animal DNA in the East River correlates closely with national sales data,” reports Ausubel. “We therefore believe that DNA in urban rivers can provide a fairly good insight into the dietary habits of local city dwellers.” For example, the most common livestock DNA in the water samples came from chickens, which also top the list of animals consumed most in New York.
Cost-effective monitoring
“Environmental DNA not only tells us what lives in the water, but also gives us insights into the entire ecosystem that surrounds it, including the city itself,” says Stoeckle. From the researchers’ perspective, it could represent a simple and cost-effective instrument for gaining important insights into the state of urban ecosystems. “We hope that our work will inspire authorities or civil society organizations to study eDNA in the waters around them. You learn a lot and it’s not that expensive.” The weekly examinations of the water samples for the study cost a total of only $15,000 over twelve months – significantly less than many other monitoring measures. “This approach promises to make environmental monitoring as easy and routine as a blood test,” says Stoeckle.
Source: Mark Stoeckle and Jesse Ausubel (Rockefeller University, New York, USA) et al., PLoS One, doi: 10.1371/journal.pone.0332676