​Microbes in Brooklyn Superfund site teach lessons on fighting industrial pollution

Using advanced DNA sequence analysis, a research team led by NYU Tandon School of Engineering’s Assistant Professor Elizabeth Hénaff has discovered that tiny organisms in Brooklyn’s highly contaminated Gowanus Canal have developed a comprehensive collection of pollution-fighting genes.

The findings were published in the Journal of Applied Microbiology on April 15, 2025.

The team identified 455 species of microorganisms wielding 64 different biochemical pathways to degrade pollutants and 1,171 genes to process heavy metals. This suggests the potential of a cheaper, more sustainable, and less disruptive method for cleaning contaminated waterways than the current oft-used dredging operations.

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The researchers also discovered 2,300 novel genetic sequences that could enable microbes to produce potentially valuable biochemical compounds for medicine, industry, or environmental applications.

Nature’s toxic clean-up manual

“We found what amounts to nature’s own toxic cleanup manual, but with a crucial warning,” said Hénaff, who sits in NYU Tandon’s Technology, Culture and Society Department and is a member of Tandon’s Center for Urban Science + Progress. “These microbes have stories to tell that go beyond scientific data.”

To communicate these stories effectively, Hénaff and colleagues created CHANNEL, an immersive installation at BioBAT Art Space in Brooklyn, New York featuring sculpture, prints, sound, and projections alongside over 300 gallons of native Gowanus sediment and water that has been growing over the last 9 months. The Living Interfaces Lab, Hénaff’s research group, uses methods from sciences and arts to address pressing urban issues.

“While more research is needed to understand how to cooperate with these organisms effectively, the discovery of such genetic tools for pollution cleanup may offer valuable lessons for environmental restoration worldwide,” Hénaff said. “I consider artistic research to be a key component in not just illustrating but also informing our scientific research.” The work is on view at the exhibit’s closing event on April 18, 2025.

Resistance to antibiotics

The team discovered genes for resistance to eight different classes of antibiotics in the canal microbes, with some coming from human gut bacteria that enter the canal during Combined Sewer Overflows – when heavy rainfall causes stormwater and untreated sewage to discharge directly into waterways. Other resistance genes were found in native aquatic species.

“The long-term coexistence of microbial communities from sewage and the natural canal environment is expected to enhance the rates of horizontal transfer of a wide array of genetic elements, and as such merits our attention for public health monitoring and surveillance as environmental ‘superbug’ reservoirs,” said Sergios-Orestis Kolokotronis, a study co-author and assistant professor of epidemiology and infectious diseases at SUNY Downstate Health Sciences University.

Despite these concerns, the study also reveals promising potential benefits. While the pollutant-degrading microbes in the canal can break down contaminants, their natural processes are too slow for practical cleanup. Understanding their genetic adaptations could help scientists develop faster methods, either by isolating specific microbes for treatment or enhancing their abilities.

Potential for resource recovery

Some classes of contaminants such as heavy metals are also valuable materials for industry, and bioremediation methods could be adapted to resource recovery for re-use, not just removal.

To make its discoveries, the team collected samples from 14 locations along the canal’s 1.8- mile length, gathering both surface sediment and deep core samples reaching 11.5 feet below the canal floor. They found microbes capable of breaking down many historical pollutants, including petroleum products, PCBs, and industrial solvents.

The findings come as the Environmental Protection Agency continues its $1.5 billion dredging and capping operation at the canal, removing contaminated sediment and sealing remaining pollution under clean material.

Gowanus Canal microbiome

The team’s current study builds on prior research spanning a decade to understand the Gowanus Canal microbiome. The project began in 2014 when the current study’s co-authors Ian Quate of Fruit Studio and Matthew Seibert of the University of Virginia led the first sediment sampling, processing samples at community bio lab Genspace with study co-author Ellen Jorgensen of Biotech without Borders.

The DNA was sequenced in the lab of study co-author Christopher Mason – WorldQuant Professor of Genomics and Computational Biomedicine at Weill Cornell Medicine – as part of the Pathomap Project, now expanded to cities around the world in the metagenomics of subways and urban biomes (MetaSUB) project.

“The hardy microbial organisms of the Gowanus Canal have a unique genetic catalog of survival, which provides a roadmap for adaptation and directed evolution that we can use in polluted sites around the world,” said Mason, who serves as co-founder and Director of the MetaSUB Consortium.

Secrets in the sediment

Later, lead author Hénaff’s team collected more samples through the BKBioReactor project while study co-author Kolokotronis gathered core samples. Bioinformatic approaches implemented by study co-authors Chandrima Bhattacharya of Weill Cornell Medicine and Rupobrata Panja of Rutgers University allowed the team to identify microbes breaking down industrial pollutants in the canal’s thick sediment.

This research was supported by funding from WorldQuant Foundation, the Pershing Square Foundation, National Aeronautics and Space Administration, National Institutes of Health, National Science Foundation and NYU Tandon.