Microbes that extract rare earth elements can also capture carbon

A small but mighty microbe that can safely extract the rare earth and other critical elements for building everything from satellites to solar panels has another superpower: capturing carbon dioxide.

Three papers published in the last month by Cornell researchers explore new strategies to recruit the bacteria Gluconobacter oxydans (G. oxydans) to more efficiently dissolve rocks to not only extract metals needed for advanced technologies but also to speed natural processes that capture carbon dioxide from the air.

Buz Barstow, Ph.D. ’09, associate professor of biological and environmental engineering in the College of Agriculture and Life Sciences, and Esteban Gazel, the Charles N. Mellowes Professor in Cornell Engineering in the Department of Earth and Atmospheric Sciences, have been collaborating on this work for the past seven years. The pair has made breakthroughs in the basic science of how microbes interact with metals and minerals, and in engineering microorganisms that can extract metals from minerals and separate them.

“More metals will have to be mined in this century than in all of human history, but traditional mining technologies are enormously environmentally damaging,” Barstow said. “Currently, the U.S. has to obtain almost all of these elements from foreign sources, including China, creating a risk of supply-chain disruption.”

In nature, metals such as magnesium, iron and calcium can react with CO₂ in the atmosphere to form new minerals that permanently sequester the climate-warming compound. Custom-designed microbes increase the efficiency of this process by weathering rock and exposing those metals to CO₂ in the air.

“What we’re trying to do,” Gazel said, “is take advantage of processes that already exist in nature but turbocharge their efficiency and improve sustainability.”

In the new papers, the researchers have:

Significantly improved bioleaching of rare earth elements: Earlier work by the research group identified genes that contribute to acidification: G. oxydans B58 can survive and thrive in very acidic conditions, and the acidic byproducts the bacteria produce aid bioleaching of rare earth elements from rock.

In a paper published in Communications Biology, researchers made two simultaneous edits to the bacteria’s genome: one that directly accelerates acid production; and a second that “takes the brakes off acid production,” Barstow said. These edits increased bioleaching of rare earth elements by up to 73%.

The first author is Alexa Schmitz, Ph.D. ’18, a former Cornell Energy Systems Institute postdoctoral fellow in Barstow’s lab and now CEO of REEgen, an Ithaca-based private company that is using G. oxydans to extract rare earth elements.

Improved extraction efficiency of G. oxydans by up to 111%: As they worked with G. oxydans, Barstow and Gazel’s teams realized that the microbe was using more than acids to get metals out of rocks. Understanding and harnessing these abilities would make biomining much more efficient.

The researchers studied the genome of a high-performing variant of G. oxydans, B58, and systematically knocked out pieces of the genome to directly understand which genes increased biomining efficiency and which reduced it. The paper, published in Communications Biology, identified 89 genes important for bioleaching, 68 of which had not been identified for this use before. The first author is Sabrina Marecos Ortiz, a Ph.D. candidate in Barstow’s lab.

“We discovered that different genes in G. oxydans are involved in the carbon capture process as opposed to the genes that influence extraction of rare earth elements,” Marecos Ortiz said. “This understanding enables us to engineer microbes that are best designed for the task we want them to do. Specifically, engineered strains that we generate in the future may lead to other applications, as well.”

Demonstrated that biomining microbes effectively weather rock to accelerate the natural process of carbon capture by 58 times: As rocks are worn down by rain, they release calcium and magnesium. In the presence of water, these elements react with CO₂ to form limestone, which permanently pulls CO₂ from the atmosphere.

The paper, published in Scientific Reports, is the first to characterize how G. oxydans interacts with ultramafic minerals (rocks high in magnesium and iron). The first author is Joseph Lee, a Ph.D. student in Barstow’s lab.

“This process can occur in ambient conditions, at low temperatures, and it doesn’t involve the use of harsh chemicals,” Lee said. “It naturally draws down CO₂ and stores it permanently as minerals. We’re also recovering other energy-critical metals like nickel as byproducts. It’s a two-fold solution.”

Scientists have known for many years that microbes can interact with minerals and metals, and today up to 20% of the world’s copper supply can come from microbial processes, Barstow said. But there are no known microbes for mining any other metal, so Barstow and Gazel’s labs are building custom biomining microbes, via genetic engineering.