Extreme microbial adaptations arise in one of America’s most polluted waterways

The industrially ravaged Gowanus Canal, long regarded as a symbol of urban environmental neglect, is being reimagined through the lens of scientific inquiry as a complex reservoir of microbial life shaped by intense selective pressures.

Research led by NYU Tandon School of Engineering has discovered microbes in Brooklyn’s Gowanus Canal that carry genes for breaking down industrial pollutants and neutralizing heavy metals. Genetic screening also uncovered resistance to multiple antibiotic classes and thousands of biosynthetic gene clusters with implications for developing new antibiotics, industrial enzymes, and bioactive compounds.

Built in the mid 1800s, the 2.9 km long industrial canal has experienced over 150 years of unregulated environmental abuse. As a hub of heavy industry, various mills, petroleum and chemical plants have lined the canal banks.

Unknown volumes of arsenic, heavy metals, polychlorinated biphenyls, coal tar, petroleum products, volatile organic compounds, chlorinated solvents and untreated sewage overflow have discharged into the small waterway.

Designated a Superfund site in 2010, the Gowanus Canal is one of the most contaminated waterways in the United States. When the EPA began evaluating the site for restoration, they discovered approximately two hundred previously unknown and unpermitted pipes that discharge directly into the canal.

So toxic are the sediments and extreme the environment that mere skin contact with the water poses a health hazard for humans. To microbiologists, such extreme environments are highly intriguing opportunities to see how life finds a way to adapt and even thrive. Microbial life has previously been discovered in similarly extreme contexts.

Discoveries in NASA clean rooms revealed microbes that lived off of paint and cleaning solutions. An enzyme that revolutionized early genomic research came from a bacterium found in the hot springs of Yellowstone National Park. Microorganisms discovered in contaminated environments have previously been used to degrade petroleum hydrocarbons and other pollutants.

While the Gowanus Canal is unquestionably an environmental disaster, it can also serve as a long-running experiment in microbial evolution.

In the study, “Metagenomic interrogation of urban Superfund site reveals antimicrobial resistance reservoir and bioremediation potential,” published in the Journal of Applied Microbiology, researchers performed a metagenomic analysis of microbial communities in the Gowanus Canal.

To assess the microbial diversity and functional potential of the Gowanus Canal biome, researchers collected sediment samples from 14 distinct locations spanning the length of the waterway.

A deep sediment core was extracted from one site at a depth of 3.5 meters, offering a vertical glimpse into historical microbial accumulation. Samples were collected at two separate timepoints to evaluate temporal variation and were immediately preserved at −80°C to maintain DNA integrity.

Sediment samples underwent high-throughput metagenomic sequencing on Illumina platforms, yielding over ~26.5 million sequencing read pairs per sample. Bioinformatic pipelines were used to assemble and annotate the raw reads, allowing for taxonomic classification of microbial species and functional gene identification, including genes involved in antibiotic resistance, pollutant degradation, and metal detoxification.

With a comprehensive dataset and in-depth profiling of Gowanus microbial communities, researchers were able to identify previously undocumented microbial lineages and assess their potential for environmental remediation.

Metagenomic analysis of sediment samples from the Gowanus Canal revealed a diverse microbial community comprising 455 distinct microbial species, including bacteria, archaea, and viruses.

Across both surface and core samples, researchers identified 64 metabolic pathways involved in the degradation of organic contaminants, alongside 1,171 genes associated with the detoxification of heavy metals such as iron, copper, and nickel. Researchers identified 2,319 biosynthetic gene clusters, many of which may be linked to the production of novel secondary metabolites with potential therapeutic or industrial value.

A comprehensive screening of antimicrobial resistance genes demonstrated the presence of 28 resistance genes across eight different antibiotic classes, including agents commonly used in clinical settings such as rifampin and aminoglycosides.

Coexistence of pollutant-degrading genes and antimicrobial resistance likely arises from ecological adaptations driven by prolonged exposure to urban and industrial waste. Microorganisms within the canal deploy multiple degradation pathways to metabolize pollutants like toluene and phenolic compounds, while simultaneously exhibiting traits that confer resilience to heavy metal stress.

Findings suggest that extreme urban ecosystems like the Gowanus Canal may act as reservoirs of both beneficial and hazardous genetic elements. Some of the antimicrobial resistance genes appear to originate from human gut-associated microbes, likely introduced through untreated sewage overflow, raising urgent new concerns around public health risks.

While not an experiment any scientist would have chosen to run, if future research findings lead to novel industrial or clinical insights, it could transform the Gowanus Canal from a symbol of urban neglect into that of a living laboratory. One where the pressures of prolonged contamination have forged a microbial community that has created the keys to future ecological restoration and molecular innovation.

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