Engineered Bacteria Capture Carbon in Seawater

By Benjamin Boettner

(BOSTON) — Rock weathering, the breakdown and dissolving of rocks and minerals caused by their exposure to water, air, and biological life, is a major regulator of Earth's atmospheric CO₂ levels and climate. Throughout Earth's history, rock weathering has been faster during warm periods with increased atmospheric CO₂ levels. Dissolved minerals ultimately wash into the ocean, where they draw CO₂ from the atmosphere and cool the planet again. While this thermostat is responsible for the temperate climate we enjoy on Earth, the weathering cycle occurs over hundreds of thousands of years.

In search of climate solutions, scientists have asked if the rock weathering cycle could be sped up, resulting in a number of new companies pursuing Enhanced Rock Weathering (ERW). By scattering crushed silicate rocks on agricultural surfaces or into water, they aim to pull excess CO₂ out of the atmosphere. Although this strategy is generally safe and environmentally friendly, it is still too slow to affect the global carbon balance or to be economically viable at industrial scale.

Now, a collaborative research team at the Wyss Institute at Harvard University , Harvard Medical School (HMS)'s Department of Systems Biology , and the Stanford Doerr School of Sustainability , led by Wyss Institute Founding Core Faculty member Pamela Silver , Ph.D. and Wyss Institute Associate Faculty member Michael Springer , Ph.D., has engineered a potential solution to this problem. The research team, spearheaded by first-author and chemical engineer Neil Dalvie , Ph.D., genetically engineered Alteromonas macleodii, a widespread marine bacterium, to produce much higher amounts of so-called siderophores, molecules that extract iron from silicate minerals. In customized bioreactors with a continuous flow of seawater, the engineered bacterium sped up the weathering of the silicate mineral olivine by 2.6-fold, boosting the amount of CO₂ that was removed from air. Their findings are published in Nature Biotechnology.

"Our study embraces the concept of biologically inspired engineering and how synthetic biology can be applied to enhance normal climate-regulating processes, which ultimately could have a positive impact on our planet," said Silver, who also is the Elliot T. and Onie H. Adams Professor of Biochemistry and System Biology at HMS and, together with Springer, founded the Synthetic Biology Hive at HMS. "We believe this easily applicable, risk-free environmental engineering strategy could be implemented at many places with real-world decarbonization outcomes."

Fast-tracking geology with synthetic biology

During natural rock weathering, silicate minerals like olivine dissolve to release primarily magnesium (Mg), iron (Fe) and silicate (SiO₄), trapping atmospheric CO₂ in the water as bicarbonate (HCO₃^-). Specifically, the released iron is not soluble when exposed to the atmosphere. Instead, it covers the mineral surface as rust, slowing down the whole process. By producing siderophores, bacteria can capture, solubilize, and take up oxidized (rusted) iron to sustain their own growth. Conveniently, this effectively de-rusts the mineral surface, speeding up rock weathering.

Researchers used custom bioreactors to tease apart when natural bacteria produce siderophores. They found that even a small amount of iron-containing mineral completely inhibited siderophore production, posing a big problem for siderophore production at industrial scales. "Once wild bacteria have enough iron to grow, they stop making siderophores completely," said the study's first and co-corresponding author Neil Dalvie, Ph.D., who spearheaded the project as a postdoctoral fellow in Silver's lab. "To enable enhanced weathering at scale, we engineered A. macleodii to always produce siderophores. We essentially decoupled siderophore production from environmental iron levels."

Proof-of-principle in rock-seawater bioreactors

While it took the team roughly one month to engineer the microbes, the real challenge was showing that they sped up rock weathering and removed more CO₂ from the atmosphere. To get a handle on this validation, Dalvie teamed up with co-author Amogh Jalihal , Ph.D., a postdoctoral fellow in Springer's group at the Wyss Institute and HMS. "We put our heads together and decided that the measurement would be best at steady state. We needed seawater and bacteria to be continuously flowing over the minerals," said Dalvie. Conveniently, Springer's group had recently acquired an entire room full of eVOLVERs, small-scale bioreactors that were originally designed by Ahmad (Mo) Khalil , Ph.D., another Associate Faculty Member at the Wyss Institute and the Hok Lam and Kathleen Kam Wong Professor of Bioengineering and Professor of Molecular and Cellular Biology at Harvard University.

After small-scale studies showed promise, the team constructed pilot-scale bioreactors, loaded with several kilograms of green olivine sand submerged under gallons of raw seawater from the Boston Harbor. "Operating at pilot scale allowed us to start solving scale-up problems: How often to we need to add cells? How do we feed them? Eventually we were able to measure actual uptake of 0.5 g of atmospheric CO₂ into our reactors each day, which was a compelling end result."

The team also carried out a Life Cycle Analysis (LCA), which accounts for all carbon captured or emitted by the entire system over time, including all living, geological, and chemical parts. Dalvie and Jalihal collaborated with Abigail Fitzgibbon , a Ph.D. student working with Steven Davis , Ph.D. Professor of Earth System Science at the Stanford Doerr School of Sustainability at Stanford University. Davis' group has developed models to quantify the carbon emissions of industrial or agricultural processes and the effects on air quality on human wellbeing. "Our collaboration with the Stanfort group enabled us to precisely calculate the net carbon balance in our system. We could see which process parameters were key to make it an efficient environmental technology when used at industrial scale."

Looking to the future

Dalvie recently received a fellowship from the Burroughs Wellcome Career Awards at the Scientific Interface (CASI) program, which will fund further work on microbial siderophore production and mineral processing. For bio-weathering, more scale-up studies are needed to identify economically viable sources of feedstocks and silicate minerals. The team is also investigating if valuable metals could be extracted from silicate minerals alongside CO₂ sequestration. "We are currently thinking that the most straight-forward way of creating environmental impact would be to grow our bacterial strains with adequate food sources in large basins resembling those in sewage 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," said Springer, who is studying how evolution has shaped and constrained the interactions of organisms with their environments.

Other authors on the study are Jan-Tobias Böhnke, Mohammed Hijaz, and Quincey Justman. The study was supported by the Wyss Institute Director's Fund, Synthetic Biology Hive at Harvard Medical School, Harvard Climate and Sustainability Translational Fund from Harvard's Office of Technology Development, the Salata Institute for Climate and Sustainability, a Garden Grant from Homeworld Collective, and a Schmidt Science Fellowship.