Cornell Unlocks Bacteria’s Power for Enhanced Rock Weathering

The ability to capture carbon dioxide is one of the notable traits of a small but effective microbe that can also help extract rare earth and other essential elements used in manufacturing products such as solar panels and satellites.

In three studies published last month, Cornell researchers explored new methods to encourage the bacterium Gluconobacter oxydans (G. oxydans) to break down rocks more efficiently. This could accelerate natural processes that both absorb atmospheric carbon dioxide and extract metals needed for advanced technologies.

For the past seven years, Esteban Gazel, the Charles N. Mellowes Professor in the Department of Earth and Atmospheric Sciences, and Buz Barstow, Ph.D. '09, Associate Professor of Biological and Environmental Engineering, have collaborated on this research.

In addition to engineering microbes that can isolate and extract metals from minerals, their work has advanced the basic understanding of how bacteria interact with metals and mineral surfaces.

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

Buz Barstow, Ph.D, Associate Professor, Biological and Environmental Engineering, Cornell University

Metals such as magnesium, iron, and calcium can react with atmospheric CO₂ to form new minerals that permanently store the gas. Custom-engineered microbes enhance this process by breaking down rocks and helping expose these metals to CO₂.

What we are trying to do is to take advantage of processes that already exist in nature but turbocharge their efficiency and improve sustainability.

Esteban Gazel, Charles N. Mellowes Professor, Department of Earth and Atmospheric Sciences, Cornell University

In the latest studies, researchers have:

Significantly improved bioleaching of rare earth elements

In earlier work, the research team identified genes that support acid production in Gluconobacter oxydans B58. This strain can survive and grow in highly acidic conditions, and its acidic byproducts aid in extracting rare earth elements from rock through a process called bioleaching.

In a study published on May 27, 2025, in Communications Biology, researchers made two genetic modifications to G. oxydans. One directly increased acid production, while the other removed regulatory limits that suppressed acid output. According to Buz Barstow, these changes led to a bioleaching improvement of up to 73 %.

The study’s first author is Alexa Schmitz, Ph.D. '18, a former postdoctoral researcher at the Cornell Energy Systems Institute in Barstow’s lab. She is now the CEO of REEgen, an Ithaca-based company that uses G. oxydans to extract rare earth elements.

Improved extraction efficiency of G. oxydans by up to 111 %

While working with Gluconobacter oxydans, the research teams led by Barstow and Gazel found that the microbe uses more than just acid to extract metals from rocks. Understanding these additional mechanisms could lead to significant improvements in biomining efficiency.

To explore this, the researchers analyzed the genome of a high-performing strain, G. oxydans B58. They systematically deleted sections of its genome to identify which genes increased or decreased the microbe’s ability to extract metals.

The study, published on April 30^th, 2025, in Communications Biology, identified 89 genes required for effective bioleaching. Of these, 68 had not previously been linked to this process. The study's 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. 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.

Sabrina Marecos Ortiz, Study First Author and Ph.D. Student, Cornell University

Demonstrated that biomining microbes effectively weather rock to accelerate the natural process of carbon capture by 58 times

Rain breaks down rocks, releasing elements like calcium and magnesium. When these elements react with CO₂ in the presence of water, they form limestone. This process removes CO₂ from the atmosphere and stores it permanently.

A study published in Scientific Reports on April 30, 2025, is the first to examine how Gluconobacter oxydans interacts with ultramafic rocks, minerals rich 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 temperature, and it does not involve the use of harsh chemicals. It naturally draws down CO₂ and stores it permanently as minerals. We are also recovering other energy-critical metals like nickel as byproducts. It is a two-fold solution.

Joseph Lee, Study First Author and Ph.D. Student, Cornell University

According to Barstow, scientists have long known that microbes can interact with minerals and metals. Microbial processes are already responsible for producing up to 20 % of the world’s copper supply. However, no known microbes are currently used to extract other metals.

To address this gap, Barstow and Gazel’s teams are using genetic engineering to develop specialized bacteria for biomining a wider range of metals.