Scientists figured out how to use engineered bacteria to dissolve rocks faster and capture carbon dioxide

Engineered ocean bacteria kept rust off olivine sand and sped up rock weathering, a slow process that pulls carbon dioxide into seawater.

As rock slowly wears away, it releases compounds that trap carbon dioxide and take it out of the atmosphere. The trouble is speed. Left alone, the process takes thousands of years, partly because iron in the rock turns to rust and coats the surface.

Now, a team led by Harvard researchers has engineered a common ocean bacterium to keep that rust from building up. In tanks of real harbor water, the microbes made crushed rock dissolve about three times faster than plain seawater did.

That's a big jump for a process that has looked too slow to matter. So far the researchers have tested it only in lab reactors and a few glass tanks, not in the open ocean.

Neil Dalvie, a synthetic biology fellow in systems biology at Harvard Medical School, led the study with colleagues at the Wyss Institute and the Stanford Doerr School of Sustainability.

Dalvie told Earth.com he wanted to highlight the interdisciplinary nature of the work.

"We learned about alkalinity and mineral measurements from geochemists in the rock weathering industry," he said. "Very few people have both the skillsets for molecular biology, microbial engineering, and mineral processing."

"Some people describe rock weathering as a silver bullet for climate change," said Dalvie. "The problem is that it's too slow."

Rust slows the rock down

The team worked with olivine, a common mineral, in the form of sand. When olivine dissolves in seawater, it gives off magnesium, silicon and iron.

The magnesium is the useful part. It makes seawater more alkaline, and alkaline seawater takes up carbon dioxide from the air. This is held as bicarbonate, a form of carbon dissolved in water.

Because magnesium stays in the ocean for a very long time, the authors count that carbon as stored for good.

Iron is the problem. It doesn't stay dissolved. It forms a layer of rust on the rock, and that layer slows any further dissolving.

The rust is one reason that natural rock weathering takes so long. Spreading crushed rock on farm fields or coastlines helps, but the authors note that the carbon captured that way has been hard to measure.

Natural bacteria stop helping

Many microbes already have a way to deal with rust. When they run low on iron, they release molecules that grab iron and make it dissolve in water. Biologists call them siderophores.

Once a microbe has enough iron, though, it stops making these molecules. And a microbe doesn't need much.

The team tested this with Alteromonas macleodii, a marine bacterium that makes its own siderophore. The researchers ran 16 small lab reactors with different amounts of olivine sand and different flow rates.

The bacteria made large amounts of the molecule only when there was little rock and the water moved fast.

With more rock, the bacteria had iron to spare and quit. The authors concluded that the bacterium's natural settings rule out steady siderophore production in a tank big enough for industrial use.

Engineered bacteria kept rock dissolving

So the team rewired the bacterium. They replaced the genetic switch that turns siderophore production on only when iron runs short with one that keeps it on all the time.

Dalvie said the change itself was fairly easy. Showing that it worked was the hard part.

"The bacteria keep growing, the cells keep making siderophores, the rock keeps dissolving - it's very hard to measure all these things at the same time," Dalvie said.

In the small reactors, the engineered strain produced more than 100 times as much of the siderophore as the natural strain. Olivine dissolved about 2.6 times faster with the engineered cells than in reactors with no cells at all, while the natural strain made no clear difference.

Harbor water tanks removed carbon

Then came a bigger test. The researchers placed more than 8.8 pounds (4 kilograms) of construction-grade olivine sand in the bottom of 3-gallon (11-liter) glass fish tanks.

Unfiltered seawater from Boston Harbor flowed through each tank at about 1.6 quarts (1.5 liters) a day. Some tanks got a slow drip of nutrients, and two of those also got a fresh dose of the engineered bacteria once a week.

In those two tanks, magnesium came off the rock 3.1 times faster. The water also became more alkaline, which the team calculated as about 0.018 ounce (0.50 grams) of carbon dioxide removed from the air each day.

That's about half the weight of a paper clip. The amount is small, but it was measured directly in the water rather than estimated from a model.

Engineered bacteria survive in rock biofilms

In earlier small reactors fed raw seawater, the engineered strain held steady for about a week before its numbers fell. That's why the pilot tanks got a fresh dose weekly.

The strain's staying power surprised the team. "We were actually surprised that our originally engineered strains were able to survive and perform for over a week in unfiltered seawater," Dalvie said.

"We think that biofilms may help protect the bacteria from growth competition and viruses in the seawater."

Feeding the bacteria costs carbon

Bacteria have to eat, and making their food releases carbon dioxide too. So the team ran a life-cycle analysis, an accounting of the emissions from building and running a full-size version.

Sugar failed on both counts. Making it emits too much, and in the lab, feeding it to the bacteria left the water less alkaline, likely because of acidic byproducts. The researchers switched to acetate, a simple food that some companies now make from carbon dioxide itself.

Ordinary bacteria failed the accounting too. Feeding wild microbes enough to keep them hungry for iron would release far more carbon dioxide than the faster weathering captured.

With engineered bacteria and a carbon-neutral acetate feed, the model predicted 74 percent more net carbon removal than a tank of rock and seawater alone. The researchers assumed the 2.6-fold speedup from the lab would hold at that scale.

"We've found a way that it could work and, maybe more importantly, now we have a model to calculate what it would look like to implement this at scale," he said.

Four of the authors, Dalvie among them, have filed a patent application on strains of bacteria engineered for siderophore production that keep rust off rock.

Biofilms built up on rocks

The pilot tanks didn't stay fast. After about three weeks of feeding, dissolving and carbon uptake dropped in every tank.

Slimy films of microbes had built up on the glass and on top of the sand, especially in the tanks that got the engineered bacteria.

The films appeared to keep the water from mixing, and the researchers suspect they blocked the rock. A thin crust had also formed, and most of the dissolving probably happened in the top 0.4 inch (1 centimeter) of sand.

The authors suggest that breaking up that top layer from time to time could keep the rock working, but they haven't tested it. Dalvie and his colleagues say the next steps are larger experiments, better nutrient mixes and more efficient bacteria.

What remains unknown

Dalvie said a real coastline or mine would need "some sort of enclosure or tank" to make enough of the iron-grabbing molecules. Such a tank "would resemble existing wastewater processes," he said.

The bigger hurdle, he said, is the food for the bacteria. "Green feedstocks like this need to be available at large scales," Dalvie said, referring to the acetate made from carbon dioxide and electricity.

The study did not analyze the economics of capturing carbon dioxide. "The price of carbon needs to be high enough to justify a new biochemical process," he stressed.

The full study was published in the journal Nature Biotechnology.

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