Engineered Marine Bacteria Supercharge Rock Weathering to Pull Carbon from the Air

Rock weathering is one of the planet’s oldest climate regulators, a slow-motion thermostat that has kept Earth’s temperatures within habitable bounds for billions of years. When silicate minerals are exposed to water and air, they gradually dissolve, releasing magnesium, iron, and silicate ions while pulling carbon dioxide out of the atmosphere and locking it away as bicarbonate dissolved in water. That bicarbonate eventually washes into the ocean, where the captured carbon remains harmlessly buffered for vast stretches of time. The trouble, from a climate perspective, is speed: the natural cycle operates on timescales of hundreds of thousands of years, far too leisurely to counteract the rapid accumulation of greenhouse gases from human activity. Now a team of synthetic biologists and earth scientists believes it has found a way to compress geological time into something closer to an industrial process, using genetically engineered marine bacteria to accelerate the very chemistry that nature performs at a glacial pace.

The research, a collaboration between the Wyss Institute for Biologically Inspired Engineering at Harvard University, Harvard Medical School’s Department of Systems Biology, and the Stanford Doerr School of Sustainability, was led by Wyss Founding Core Faculty member Pamela Silver and Associate Faculty member Michael Springer. First author and chemical engineer Neil Dalvie, who spearheaded the project as a postdoctoral fellow in Silver’s laboratory, and his colleagues genetically engineered Alteromonas macleodii, a bacterium widespread in marine environments, to produce far greater quantities of molecules called siderophores. These compounds are the bacterial world’s iron-scavenging tools, and it turns out they are also remarkably effective at stripping iron from the surfaces of silicate minerals. In customized bioreactors flushed with a continuous flow of seawater, the engineered microbe accelerated the weathering of the silicate mineral olivine by 2.6-fold, measurably increasing the amount of atmospheric carbon dioxide drawn into the water. The findings were published in Nature Biotechnology.

To understand why bacteria can speed up rock dissolution, it helps to look closely at what actually happens on a weathering mineral surface. When olivine and similar silicates dissolve, they release magnesium, iron, and silicate, and the chemistry of that dissolution simultaneously traps atmospheric carbon dioxide in the surrounding water as bicarbonate. But the released iron presents a problem: exposed to oxygen in the atmosphere, it is not soluble and instead precipitates as rust, coating the mineral surface and slowing the entire weathering process to a crawl. Bacteria that produce siderophores can capture, solubilize, and import that oxidized iron to satisfy their own nutritional needs. In doing so, they effectively de-rust the mineral surface, exposing fresh reactive material to seawater and allowing dissolution to continue. It is a subtle biological intervention with outsized geochemical consequences, and it is precisely this natural mechanism the Harvard team set out to amplify.

The first obstacle the researchers encountered was regulatory rather than chemical. Using custom bioreactors to dissect when natural bacteria produce siderophores, they discovered that even a small amount of iron-containing mineral completely shut down siderophore production. Wild bacteria, it seems, are thrifty: once they have accumulated enough iron to support growth, they stop investing energy in making the scavenging molecules altogether. That built-in thriftiness is a disaster for anyone hoping to harness siderophores for industrial-scale carbon removal, because the whole point is to have the bacteria continuously attack mineral surfaces regardless of how much iron is already available. Once wild bacteria have enough iron to grow, they stop making siderophores completely, Dalvie explained. To enable enhanced weathering at scale, the team engineered A. macleodii to always produce siderophores, essentially decoupling production from environmental iron levels and converting a self-regulating survival mechanism into a relentless industrial workhorse.

Engineering the microbes took roughly a month, but the far harder task was proving that the modification actually translated into faster weathering and greater carbon uptake. For that validation, Dalvie teamed up with Amogh Jalihal, a postdoctoral fellow in Springer’s group at the Wyss Institute and Harvard Medical School. The two researchers concluded that the most rigorous measurement would be made at steady state, with seawater and bacteria continuously flowing over the minerals rather than sitting in batch cultures where conditions drift unpredictably. Fortunately, Springer’s group had recently acquired an entire room of eVOLVER bioreactors, small-scale devices originally designed by Ahmad Khalil, another Wyss Associate Faculty member and professor at Harvard University. The eVOLVER platform, with its modular, automated control of growth conditions, proved ideal for the small-scale studies that would establish whether the engineered strain genuinely outperformed its wild-type ancestor on real rock.

Those early experiments showed promise, and the team escalated to pilot-scale bioreactors loaded with several kilograms of green olivine sand submerged under gallons of raw seawater drawn from Boston Harbor. Working at pilot scale forced the researchers to confront the practical questions that separate laboratory demonstrations from deployable technology: how often cells needed to be added, how they should be fed, and how the system could be kept running continuously. Eventually the team was able to measure actual uptake of 0.5 grams of atmospheric carbon dioxide into the reactors each day, a modest absolute quantity but a compelling proof of principle for a process that could, in principle, be replicated across enormous basins. The result demonstrated that engineered bacteria could survive and function in unprocessed seawater, on unrefined mineral feedstock, under conditions far closer to the open environment than a sterile laboratory flask.

Quantifying the climate value of any proposed carbon removal technology requires more than measuring uptake in a reactor, however. To that end, Dalvie and Jalihal collaborated with Abigail Fitzgibbon, a doctoral student working with Steven Davis, Professor of Earth System Science at the Stanford Doerr School of Sustainability, whose group develops models to quantify the carbon emissions of industrial and agricultural processes and their effects on air quality and human wellbeing. Together the teams carried out a Life Cycle Analysis, an accounting framework that captures all carbon emitted or sequestered by the entire system over time, including its living, geological, and chemical components. The collaboration enabled the researchers to calculate the net carbon balance of their system precisely and to identify which process parameters would be decisive in making the technology efficient at industrial scale. Such analyses are essential for distinguishing genuinely negative-emission technologies from those that merely shuffle carbon from one reservoir to another.

The path from pilot reactor to planetary impact still runs through substantial scale-up work. The team notes that further studies are needed to identify economically viable sources of feedstocks and silicate minerals, since the cost and carbon footprint of mining, crushing, and transporting rock could easily erode the climate benefit if chosen poorly. Intriguingly, the researchers are also investigating whether valuable metals could be extracted from the silicate minerals alongside carbon sequestration, potentially creating a co-product revenue stream that improves the economics of deployment. Dalvie recently received a fellowship from the Burroughs Wellcome Career Awards at the Scientific Interface program, which will fund continued work on microbial siderophore production and mineral processing, providing momentum for the next phase of development.

Springer’s vision for deployment is strikingly pragmatic. The most straightforward way to create environmental impact, he suggested, would be to grow the bacterial strains with adequate food sources in large basins resembling those found at sewage treatment plants, continuously pumping unprocessed seawater in and releasing alkaline seawater back into the ocean, where the bound carbon would be completely harmless and buffered away. Such a design would piggyback on existing industrial infrastructure and established engineering practices, avoiding the need to invent novel containment systems from scratch. Because the carbon ends up as bicarbonate dissolved in seawater, the approach avoids many of the permanence and monitoring concerns that complicate other carbon removal strategies, and the alkalinity released to the ocean may itself help counteract acidification, though the team’s published claims rest on the weathering and carbon uptake results rather than on ocean alkalinity benefits.

Silver framed the work as an embodiment of biologically inspired engineering, demonstrating how synthetic biology can enhance natural climate-regulating processes with potentially positive planetary impact. She and her colleagues believe the strategy is easily applicable and low-risk, and could be implemented in many locations with real-world decarbonization outcomes. Whether engineered bacteria can weather rock fast enough to matter for the global carbon balance remains to be proven at scale, and the jump from half a gram of carbon dioxide per day to gigatonne-relevant removal is enormous. But the study, supported by the Wyss Institute Director’s Fund, the Synthetic Biology Hive at Harvard Medical School, Harvard’s Climate and Sustainability Translational Fund, the Salata Institute for Climate and Sustainability, a Garden Grant from the Homeworld Collective, and a Schmidt Science Fellowship, establishes a credible new entry in the growing portfolio of ocean-based carbon removal approaches. Other authors on the study include Jan-Tobias Böhnke, Mohammed Hijaz, and Quincey Justman. If the numbers scale as hoped, the humble chemistry of rusting iron and dissolving stone, accelerated by reprogrammed microbes, could become one of the more elegant tools in humanity’s decarbonization arsenal.

Subject of Research: Synthetic biology enhancement of marine bacterial siderophore production to accelerate silicate rock weathering for atmospheric carbon dioxide removal

Article Title: Pulling carbon into seawater using engineered bacteria

Article References: Pulling carbon into seawater using engineered bacteria. (n.d.). Original publication

Image Credits: AI Generated

DOI: Not provided

Keywords: carbon removal, rock weathering, synthetic biology, siderophores, Alteromonas macleodii, olivine, ocean alkalinity, enhanced weathering, climate change, bioreactors, life cycle analysis, marine bacteria