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A litre of water from a water body every week for a year has helped scientists to capture a snapshot of life in and around New York City, including human food consumption habits, urban wildlife and its seasonal shifts.
Scientists collected the samples from the East River, a lower Hudson River estuary surrounding the city, the largest and most densely populated coastal city in North America. They then used the vertebrate environmental DNA (eDNA) metabarcoding to analyse the water samples.
The findings indicate that urban waterways anywhere can serve as continuous biosensors, enable biodiversity tracking, influence habitat restoration outcomes and human impacts in real time, the team of scientists said.
eDNA traces are found in water through biological expulsion from fish and wildlife via shedding skin cells, waste and other biological products. These waterborne traces are collected to identify species, estimate their population and other insights.
To collect data, scientists picked a litre of shoreline water between May 2024 and May 2025 and passed it through something similar to a small coffee filter. Through the sediment on the filter along with 12S metabarcoding primers, the scientists found vital information on seasonal fish abundance.
Researchers detected 71 local marine fish species with more than 60 terrestrial animals, including rats, raccoons, squirrels, and common city birds. The species abundance reflected that only 16 species, amounting to 23 per cent of the total samples, accounted for 95 per cent of the fish eDNA.
Moreover, there was a 10-fold increase in local marine fish eDNA during the summer, which closely paralleled seasonal changes in water temperature. Comparison with a 2016 survey revealed that two species — skilletfish and feather blenny — have become newly abundant at the site, likely due to local oyster reef restoration efforts.
The findings, according to researchers, supported the hypothesis that eDNA accurately indexes local fish populations, with top species findings overlapping broadly with traditional mechanical gear-based surveys conducted over the last 35 years.
The sewage water released into the river also disclosed crucial information. When conduits are overloaded, as frequently occurs in New York City after even modest rainfall, the effluent empties at combined sewer overflow (CSO) outfalls into waterways. CSO outfalls in New York City currently discharge about 18 billion gallons of untreated wastewater into the estuary annually, the study said.
“Wastewater remains an inextricable constituent of urban waterways. Incorporating wastewater eDNA analysis in habitat assessments may provide a more complete picture of the local Anthropocene biosphere,” it noted.
The study found that human eDNA was the most abundant vertebrate category found in the samples. The levels of other vertebrate eDNA—such as domesticated animals, non-fish wildlife, and dietary fish—were directly correlated with human eDNA levels, indicating they share a wastewater source.
Lead author Mark Y Stoeckle at the Rockefeller University’s Program for the Human Environment in a press statement said the most unexpected findings included the detection of food animals’ DNA in proportions closely aligned with human diet patterns – genetic traces of chicken, beef, pork, turkey, lamb, goat, and commonly consumed fish such as salmon and European sea bass.
The proportions of eDNA documented in the water closely matched with the national US consumption statistics suggesting that urban wastewater eDNA can help assess the diet of local human populations.
Stoeckle added that using eDNA, municipal authorities could potentially assess, for example, whether rat populations are increasing or decreasing, that is, whether rat control programs are working.
“Instead of obscuring ecological data, these readings provide a unique window into eating patterns and public health trends,” Stoeckle said.
The statement said eDNA can serve as a reliable platform for future monitoring, enabling cities to track ecosystem and health continuously. “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,” it added.
