Bacteria DNA has evolved to withstand copper
Copper-based coatings are often used to slow bacterial growth on marine surfaces — but bacteria have adapted
American Institute of Physics
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Coated and uncoated PVC panels (top), which encountered bacterial growth after being placed in the Chesapeake Bay (bottom, left). The bacteria were then assayed and their genetics studied (bottom, center and right).
view moreCredit: Kenan P. Fears
WASHINGTON, Oct. 13, 2026 — Marine bacteria have evolved to bypass the copper-based coatings placed under ships to stop the growth of barnacles, algae, and other marine life. This necessitates new methods for managing biofouling — the unwanted accumulation of marine organisms — on ship hulls.
In Biointerphases, an AVS journal published by AIP Publishing, researchers from the U.S. Naval Research Laboratory and Duke University studied the genetic characteristics of various bacteria species responsible for their survival on copper surfaces, a step toward inhibiting these copper-resistant genes.
“We have observed increasing copper resistance in some of the ports our team frequents over the past decade, particularly in ports with heavy tourist [or] industry shipping activity,” said author Kenan Fears. “We wanted to identify the resistance pathways across a diverse microbial community to provide insight into how members of a complex community could be acting symbiotically to resist toxic environments.”
The researchers placed pieces of PVC panels in the Chesapeake Bay, some coated with a copper-based coating and some left uncoated. After two weeks, they extracted the DNA and sequenced the genomes of the bacterial colonies that grew on the panels to identify the copper-resistant genes and tested each colony’s tolerance against copper-based water treatments.
Surprisingly, the bacteria species had a lot in common regardless of whether they grew near the copper-based coating. The bacteria from the control colonies — the ones that did not initially grow on the copper-coated surfaces — were just as copper-resistant and could thrive at copper concentrations above 70 milligrams per liter.
“To put that in perspective, the U.S. Environmental Protection Agency limit in seawater for a short-term spike in copper is 18 micrograms per liter,” Fears said.
This is a likely marker of evolution and bacteria adapting to their new environments.
“Copper was not always in a water-soluble state; it only became so after oxygen accumulated in Earth’s atmosphere,” Fears said. “However, as environmental copper loading has increased, the bacteria with the best defense mechanisms continued to reproduce.”
The researchers hope to use their findings to target the molecular pathways that help bacteria express copper-resistant genes, weakening their ability to survive in copper-rich environments.
“Our research suggests the smarter path moving forward is to design antifouling coatings that select microbial communities that either help deter macrofouler settlement — like barnacles or tubeworms — or do not impede the release of biocidal compounds,” Fears said. “With increasing regulatory pressure on copper use in antifouling coatings, there is an urgent need for alternatives.”
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The article “Extreme copper tolerance and genomic adaptation in early-stage marine biofilms” is authored by Kailey N. Richard, Sara M. Tuck, Sophie M. Colston, Maryssa A. Beasley, W. Judson Hervey, Kevin Le, Sean Brown, Katherine J. Franz, and Kenan P. Fears. It will appear in Biointerphases on Oct. 13, 2026 (DOI: 10.1116/6.0005640). After that date, it can be accessed at https://doi.org/10.1116/6.0005640.
ABOUT THE JOURNAL
Biointerphases, an AVS journal published by AIP Publishing, emphasizes quantitative characterization of biomaterials and biological interfaces. As an interdisciplinary journal, a strong foundation of chemistry, physics, biology, engineering, theory, and/or modelling is incorporated into originated articles, reviews, and opinionated essays. See https://pubs.aip.org/avs/bip.
ABOUT AVS
AVS is an interdisciplinary, professional society with some 4,500 members worldwide. Founded in 1953, AVS hosts local and international meetings, publishes five journals, serves members through awards, training and career services programs, and supports networking among academic, industrial, government, and consulting professionals. Its members come from across the fields of chemistry, physics, biology, mathematics, engineering, and business and share a common interest in basic science, technology development and commercialization related to materials, interfaces, and processing.
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Journal
Biointerphases
Article Title
Extreme copper tolerance and genomic adaptation in early-stage marine biofilms
Article Publication Date
13-Oct-2026
Newly discovered antiviral system in bacteria is ‘strangest of its kind’
The complex Rube Goldberg-like molecular machinery could inspire novel technology to study and treat disease
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Gladstone scientists, including Karen Zhang, uncovered a counterintuitive class of bacterial defense systems, known as type VI retrons, that can be adapted to engineer more efficient gene editing tools.
view moreCredit: Michael Short/Gladstone Institutes
SAN FRANCISCO—Researchers at Gladstone Institutes have uncovered an extraordinarily unusual bacterial immune system that operates in reverse of known defenses.
The discovery, published in Molecular Cell, details the mechanics of "type VI retrons"—a uniquely counterintuitive class of bacterial defenses. More than just a biological curiosity, decoding these complex systems provides a molecular blueprint that scientists can adapt to engineer more efficient DNA-editing tools for human health and therapies.
“This is, by far, the strangest of the retron systems that we or anyone else has come across,” says Gladstone Investigator Seth Shipman, PhD, senior author of the new study. “These retrons operate with Rube Goldberg-level complexity, using molecular mechanisms that we would never have thought to invent, but that we’ll use in future technologies.”
Bacteria have long evolved specialized defenses to destroy phages, which are viruses that target bacterial cells. A particularly powerful line of defense, known as retrons, recognize viral attacks and trigger self-destruction to protect the broader bacterial colony.
Because retrons can also efficiently modify and deliver single-stranded DNA, researchers including Shipman and his team are working to harness them to rewrite disease-causing mutations inside human cells with unprecedented precision.
Inverted Expectations
Many types of retron systems exist, but they all follow the same basic principle: they sense when a specific strain of phage has attacked the bacterial cell, and they then unleash a toxic protein to kill the cell. This self-destruction stops the phage before it has a chance to multiply and spread to neighboring cells in the same colony.
Decades of research have led to the general understanding that all retrons produce a toxin that, in uninfected cells, is constantly present but deliberately repressed by small, single-stranded DNA molecules. When a phage invades, it perturbs the DNA and causes it to release the toxin.
“The way we typically detect retrons inside uninfected cells is by looking for this single-stranded DNA,” says Karen Zhang, a PhD student in Shipman’s lab and lead author of the study. “But type VI retrons caught our attention because they didn’t appear to have this signature. It was very odd, and we wondered if they might be broken.”
But when the scientists tested certain bacteria containing type VI retrons, they found that the retrons were still able to successfully defend their cells against phages.
“That kicked off a long molecular odyssey,” Shipman says. “Whenever we tried the experiments we normally use to study retrons, they would fail, so we kept having to think of new ways to figure out how these retrons work.”
The experimental saga ultimately revealed that, unlike other retrons, type VI retrons do not produce noticeable levels of single-stranded DNA nor toxin in uninfected cells. Instead, the entry of a phage into a cell is needed to trigger the retron to start producing single-stranded DNA.
Once it builds up, the DNA then interacts with an RNA that has been blocking production of the toxin. This interaction releases the block, allowing toxin production to ramp up.
The toxin appears to be a tiny protein that embeds itself into the membrane surrounding the cell, which destabilizes the cells and kills it.
“It’s almost the mirror-image version of how we traditionally view retrons, because the DNA switches on toxin production instead of inhibiting an already-produced toxin,” Zhang says. “It would be fascinating to explore how bacterial evolution could have resulted in such a complex molecular system—whether type VI retrons are older or newer than other retrons, or whether they’re a stepping stone between different types.”
Rethinking Retron Research
To decipher the unique machinery of type VI retrons, the team had to concoct novel experiments and repurpose existing methods in new ways. One early breakthrough, for instance, arose from the repeated, mysterious failure of standard methods to detect DNA made by type VI retrons in uninfected cells.
The researchers turned to a different tool called Spacer-seq previously developed in Shipman’s lab. This tool harnesses the molecular components of another kind of bacterial immune system, CRISPR-Cas, to create a record of gene activity inside a cell.
“We had just about given up hope that any DNA was being made when this approach finally revealed a very, very low level of production in uninfected cells,” Zhang says.
The finding motivated the team to keep digging, and further experiments showed that the DNA only ramps up to defensive levels after the phage enters.
Nature-Inspired Tools and Treatments
The unique machinery of type VI retrons is already inspiring the development of novel tools in Shipman’s lab, including new synthetic sensors and switches that can control gene activity.
“This system represents a unique way to potentially build a molecular sensor and switch encoded in DNA and RNA, that no one has thought of before,” Zhang says. “Synthetic sensors and switches have many possible applications, both in treating disease and in designing experiments to better understand how certain diseases operate.”
The tiny, highly potent toxins produced by the type VI retrons could also prove useful in a medical context. The scientists are working on ways to incorporate these toxins into new types of antimicrobial therapies, which could target and kill bacteria that cause human disease.
“This study highlights why it’s so important for a molecular technology development lab like ours to keep looking to nature for inspiration,” Shipman says. “We can use what evolution has given us as starting points to build complex machines that would have been tremendously hard to even conceptualize.”
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About the Study
The study, “Reverse transcribed ssDNA derepresses translation of a retron antiviral protein,” was published in Molecular Cell on October 13, 2026. In addition to Shipman and Zhang, authors are Matías Rojas-Montero, Darshini Poola, and Alejandro González-Delgado of Gladstone; Josepha Klas, Arturo Carabias, Dennis Zhang, Mario Mestre, Ruiliang Zhao, Ana Dávila-Hidalgo, Guillermo Montoya, and Rafael Pinilla-Redondo of the University of Copenhagen; and Lieza Chan and Kliment Verba of UC San Francisco.
The work was supported by the National Science Foundation, the Robert J. Kleeberg Jr. and Helen C. Kleberg Foundation, the Gordon and Betty Moore Foundation, the Lundbeck Foundation, the Fulbright U.S. Student Program, the Junta de Castilla y León and European Social Fund Plus, the European Molecular Biology Organization, the Novo Nordisk Foundation, the European Research Council, and the Villum Foundation.
About Gladstone Institutes
Gladstone Institutes is an independent, nonprofit life science research organization that uses visionary science and technology to overcome disease. Established in 1979, it is located in the epicenter of biomedical and technological innovation, in the Mission Bay neighborhood of San Francisco. Gladstone has created a research model that disrupts how science is done, funds big ideas, and attracts the brightest minds.
Journal
Molecular Cell
Article Title
Reverse transcribed ssDNA derepresses translation of a retron antiviral protein
Article Publication Date
13-Oct-2026
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