Learning from the life living in Superfund sites

On a cool December day in Brooklyn, New York, in 2014, a group of academic and citizen scientists set off onto one of the most polluted 3 km stretches of water in the US. They’d soon find a thriving community of microbes living in toxic sludge about a meter below the water.

One of those keen researchers was Elizabeth Hénaff, who had just joined Chris Mason’s laboratory at Weill Cornell Medicine as a postdoctoral fellow. Several months earlier, two members of the Brooklyn community biology lab Genspace had approached Mason with an intriguing proposal. They wanted to study the bottom of the Gowanus Canal, an infamously toxic body of water, before the US Environmental Protection Agency dredged its bottom and covered it with an impermeable layer.

When she heard about the plan, Hénaff was hooked.

Decked out in hazmat suits and rubber boots, Hénaff and the team paddled out into the canal, three people to a boat. When they reached their first sampling location, the person in the back operated a 4 m long polyvinyl chloride pipe, “our super scientific sampling device,” from a big-box hardware store, Hénaff says.

After plunging the pipe into the soft sediment of muck below the water and capping the top with a gloved hand, the person at the stern gently pulled it out while maintaining the vacuum. The person at the front of the boat, ready for collection with a 50 mL centrifuge tube in hand, guided the black slop from pipe to tube once the vacuum was released.

Back in the lab, the research team extracted and sequenced DNA found in that sludge. “At first it came as a surprise to me that there was anything living in there,” says Hénaff, now an assistant professor in computational biology at New York University. “Now I know. Of course there are microbes there; there are microbes everywhere.”

Since 2014, Hénaff has studied the unseen microbiology of the Gowanus Canal. She and her team recently identified a community of more than 400 different species of bacteria, archaea, and viruses living in that sludge, and more than 1,000 genes that encode for proteins that process heavy metals (J. Appl. Microbiol. 2025, DOI: 10.1093/jambio/lxaf076).).

The Gowanus Canal is a particularly contaminated area that the EPA declared a Superfund cleanup site in 2010. The origins of that designation are at Love Canalin Niagara Falls, New York, where during the 1970s, residents experienced high rates of birth defects, pregnancy losses, and cancer as a result of industrial dumping of contaminants like chlorinated hydrocarbons in a local landfill.

The disaster brought the impacts of dumping hazardous waste to the forefront of the environmental movement and garnered widespread attention. To address the environmental and health concerns of hazardous waste sites such as Love Canal, the US Congress passed the Comprehensive Environmental Response, Compensation,and Liability Act in 1980. Part of that act established a $1.6 billion trust to clean up old waste sites, informally called Superfund sites.

Abandoned industrial sites contaminated with petroleum chemicals, nuclear waste, pesticides, heavy metals, and other anthropogenic pollutants are poisoning the environment and wreaking havoc on public health.

But while most organisms die off in such extreme environments, some microorganisms thrive. “These extremophiles have specific adaptations that let them tolerate the particular conditions they are in,” says Jeffrey Morris, an associate professor in microbiology at the University of Alabama at Birmingham. And in the case of polluted environments, those adaptations allow microbes to tolerate and degrade or otherwise detoxify environmental contaminants.

“Bacteria grow really fast and can adapt to almost any kind of environment you throw at them, anything that doesn’t just kill them out right,” Morris says. “If you give them time around a pollutant, they’ll come up with solutions to grow better in its presence.”

As researchers focused on hazardous waste sites, they began leveraging these microbes for cleanup, a process known as bioremediation. Early uses relied on microbes to clean up oil spills, such as the 1989 Exxon Valdez spill and the 2010 BP Deepwater Horizon spill. Because oil exists naturally in the environment, microbial communities that know how to consume components of oil already exist: Oceanospirillales bacteria, which use hydrocarbons as a source of carbon and energy, are one example. Microbes in sites full of human-made pollution have more pressure to evolve.

Each Superfund site is unique, with a distinct pollution history and dominant contaminants that offer scientists a “window into the process of evolution itself,” Morris says. What’s more, Morris and other researchers say, as they find new bacteria that survive in polluted sites, they can perhaps put those microbes to work. One day they may clean up pollution and do important, more sustainable chemistry. At some sites, bioremediation efforts are already under way.

In New York, Hénaff’s team identified 455 freshwater and saltwater species of bacteria, archaea, and viruses, and identified 64 ways microbes degrade organic pollutants and 1,171 genes that encode for proteins that use or detoxify heavy metals.

Hénaff identified microbes that can live in extremely salty environments, like sulfate-reducing Desulfobacterium autotrophicum, and heavy metal–contaminated environments, like Microbacterium laevaniformans. Her team also observed bacteria typically found in the human gut, which aligns with the frequent sewage overflows into the canal.

Hénaff says you can see, via the microbes that the team detected, how the Gowanus Canal was plagued by industrial waste dumping and commercial shipping activities, resulting in a chemical soup of infamous pollutants. “One interesting takeaway is this idea of microbial memory that’s maintained by these nonhuman organisms,” Hénaff says. “It’s a memory of the history of human intervention in a site.”

As a kid growing up in Brooklyn, just a few miles away from the Gowanus Canal, Lesley-Ann Giddings knew to avoid the notoriously toxic water. Years later, as a biochemistry professor at Middlebury College, Giddings set out to explore a different Superfund site, one plagued not by urban industrial pollution but by the legacy of mining that has left a microbial mark.

The Ely Copper Mine located in the old Copper Belt region of Vermont is home to abandoned mining-waste piles that are packed with rocks rich in metal sulfides. The rock piles drain acidic water into surrounding groundwater and sediment, a process known as acid rock drainage. Water in this region is contaminated with toxic levels of copper, iron, magnesium, zinc, and lead, and in 2001, the EPA designated it a Superfund site. Intrigued by the possible microbial communities thriving in the hyperacidic environment, Giddings decided to go microbe hunting.

The bright orange soil that clung to her boots as she stepped out of her car and made her way past the mine tailings, a by-product of mining, made it “very clear that we were at this mine with a lot of oxidized metals,” says Giddings, now a professor at Smith College. Giddings focused on a brook near the mine’s entrance and, like Hénaff, relied on a DIY approach to collect samples for DNA sequencing.

On a sunny summer day in 2015, Giddings and a small team hooked up a peristaltic pump to an old car battery, allowing them to pump water from the brook through filters that captured DNA. They later returned to the site a few more times over the next 4 years, in the winter and summer.

“The acid rock drainage environment is very nutrient deficient,” Giddings says, so to identify the acid-loving microbes surviving in this inhospitable environment, her team used shotgun metagenomic sequencing, an analysis that sequences all microbial genomes in a sample.

Hénaff’s team relied on the same sort of genetic analysis to make sense of the Gowanus sludge. To prepare samples for sequencing, the cellular membranes of the cells are cut open to release their DNA, which is then separated from cellular debris and chopped into pieces short enough for a sequencing instrument to handle.

Hénaff describes the process as taking a “mixed bag of bacteria and their genes,” from a site sample and processing it down to “a mixed bag of small pieces of DNA, each 150 base pairs long.” After that, a DNA-sequencing instrument turns molecules into data ready for computational analysis, comparing data from the mixed bag of DNA fragments with those in databases listing the unique genetic material specific to a certain microbe or assigning function to specific genes.

The Ely Brook microbiome that Giddings pieced together revealed a community of acid-tolerant bacteria, including Proteobacteria and Actinobacteria commonly found in metal-rich environments (PLOS One 2020, DOI: 10.1371/journal.pone.0237599). The team also identified bacteria that oxidize iron and sulfur, which are in high concentrations in the brook, as well as others, like Bradyrhizobium species, which produce nutrients for plants by reducing nitrogen gas to usable ammonia. Other researchers have found Bradyrhizobium bacteria at a former nuclear weapons production facility, the Savannah River Superfundsite.

But Giddings notes that the environment could have more microbes and genes that she wasn’t able to identify. Metagenomic analyses rely on previous research catalogued in existing databases to identify microbes and assign function to genes in a given sample, and because acid rock drainage environments are understudied, Giddings thinks there may be genes or microbes the analysis wasn’t able to label.

Beyond identifying these pollution-gobbling microbes, understanding what they actually do in the presence of pollutants could pave the way for their use in bioremediation.

In the 1990s, scientists discovered that waste- and groundwater contaminated with a common industrial solvent, trichloroethylene (TCE), contained Dehalococcoides bacteria. These bacteria dechlorinate TCE, now a known human carcinogen that the EPA recently banned, and convert it to nontoxic ethene.

Dehalococcoides species “use chlorinated solvents as their electron acceptor, the same way that you and I use oxygen,” says David Freedman, an environmental engineering professor at Clemson University. “We now understand there are dechlorinating bacteria that breathe hundreds of different types of chlorinated organics,” he says, including chlorinated methanes and polychlorinated biphenyls. Dehalococcoides cultures are now commercially available for bioremediation projects that need to break down toxic chlorinated ethenes.

Unlike organic pollutants, heavy metals can’t be fully degraded, but they can be isolated and even transformed into less toxic versions.

Certain microbes get rid of toxic metals by using proteins to pump out unwanted materials, “so if the metal ends up inside the cellular membrane of the microbes, they have the capacity to pump it back out” Hénaff says.

Other microbes immobilize the metals by absorbing them into bacterial cell surfaces or binding them inside cell walls with proteins. Microbes that hyperaccumulate heavy metals could one day be used to capture precious metals like lithium from the environment for reuse. “What’s considered a contaminant in this environment is a resource in other environments,” Hénaff says.

Microbes can also manipulate the oxidation state of metals to convert them into insoluble, immobile, and nontoxic states. “Oxidation states mean everything with respect to the mobility and toxicity of heavy metals,” Freedman says.

For example, iron-reducing microbes like Geobacter metallireducens can convert hexavalent chromium, a carcinogenic industrial compound shown to cause lung cancer, into insoluble, nontoxic trivalent chromium. Other microbial species dump waste electrons onto pentavalent arsenic, reducing it to soluble and more toxic trivalent arsenic. Giddings identified certain microbial genes in the Ely Brook that reduce sulfates into sulfides.

Several strategies exist for cleaning up contaminated Superfund sites, but Freedman says bioremediation is a favored approach for several reasons. One in particular stands out: “If you can accomplish remediation using biology, it’s going to be cheaper than using physical or chemical processes,” he says.

Ideally, remediation experts could just monitor how native microbial communities are dealing with pollutants on their own, but microbes can be slow, especially if their environment isn’t set up to maximize pollution degradation. So that’s when they step in to help.

Remediation specialists can encourage microbes to move faster by pumping in nutrients to create the ideal conditions for cleanup. At the East Tennessee Technology Park, Roger Petrie and Sam Scheffler from the US Department of Energy’s Oak Ridge Office of Environmental Management are focused on doing just that.

Part of the Oak Ridge Reservation Superfund site, the park was once home to enriched uranium production for the Manhattan Project and the commercial nuclear power industry before its closure in 1987. During its operation, the facility “used TCE as a degreaser and solvent,” Scheffler says. Now it’s the main contaminant of concern for groundwater remediation at the site.

Petrie and Scheffler’s goal is to reduce contaminant levels of TCE and related products in the most-polluted plumes on the site, which vary from 9 to 30 m in diameter. They hope to introduce a mixture of microbe-supporting components into the contaminated plumes via injection wells to help boost microbial productivity of TCE-chomping Dehalococcoides bacteria that live there.

The composition of the mixtures will depend on the geochemical characteristics of each plume, but they will all include some mix of emulsified vegetable oil, a microbial food source. Scheffler says the mix may also include a pH buffer, “since we know that Dehalococcoides runs the dechlorination mechanism at 6 to 8 pH,” zero-valent iron “to enhance anaerobic conditions,” and possibly even extra Dehalococcoides cultures to increase the rate of the remediation.

The team is still in the early phases of the project, and it is unclear how successful it will be. “We’re relying on living organisms to do the work for us,” Petrie says. “We do the best we can as far as identifying what would be ideal conditions for the microbes, but that information could still be flawed.”

Giddings says it’s a long road from her lab’s work—sampling sites and identifying the microbes—to downstream work by others that can lead to bioremediation applications. After genetic analysis comes the difficult task of growing microbes in the lab to study their function further, and recreating the extreme conditions extremophiles grow in within the confines of a pristine lab is nearly impossible. “Most microbes are unculturable,” Giddings says.

Still, the untapped potential of microbes in toxic environments makes them impossible to ignore, she says. Giddings hopes to find possible bioactive natural products or biocatalysts in the Vermont mine microbiome.

In New York City, Hénaff is similarly investigating how to use genes isolated from the Gowanus Canal to develop affordable biosensors to detect heavy metal contamination in sediment.

Hénaff says we have a lot to learn from microbes about what it means to live on a damaged planet. “We’ve never not lived in a microbial world,” she says. “I think they’re the ones who are going to get us through the rapid changes our planet is experiencing.”