Rising levels of atmospheric carbon dioxide (CO2) represent an urgent global issue, with communities already experiencing more extreme weather because of a changing climate. One strategy that companies are exploring to reduce the level of this greenhouse gas is to capture it and store it deep underground.
Byung-Kwan Cho and his group identify novel acetogens and explore their metabolic mechanisms to find those that could provide climate solutions.
Seulgi Kang
“That's not an ultimate solution to solve this CO2 problem, so we have to convert CO2 into other forms of things,” said Byung-Kwan Cho, a synthetic biologist at the Korean Advanced Institute of Science and Technology. One way to do this would be to take advantage of acetogenic bacteria, which use CO2 and hydrogen to generate energy and produce byproducts like acetate. These bacteria could serve as biocatalysts to metabolize and remove CO2 from the atmosphere. However, differences in metabolic strategies and regulatory mechanisms among various acetogenic bacteria lead to differences in their rates of CO2 fixation.
Cho and his team recently isolated and characterized a new acetogen, Sporomusa sphaeroides KIAC (KIAC), that rapidly consumes CO2. Using multiple genomic analyses, the team demonstrated that this isolate contains several different hydrogenase enzymes, pointing to these proteins as important mediators in the rate of CO2 fixation.1 The findings, published in mSystems, offer important insights into leveraging acetogenic bacteria to address the climate crisis.
Although their new isolate was most genetically similar to S. sphaeroides, Cho and his team saw that KIAC grew faster and consumed CO2 more rapidly than its relative. To explore what could be contributing to KIAC’s rapid CO2 fixation, the researchers compared the genes in its metabolic pathways to a closely related and well-characterized species in the same genus, S. ovata. While these two species shared many genes, KIAC’s genome included genes for different hydrogenases, as well as unique formate dehydrogenase genes, which is an enzyme tied to CO2 metabolism, suggesting potential versatility in metabolic capacity in this bacterium.
“I’m not entirely convinced if this microbe is now really faster [than most other acetogens],” said Jo Philips, a biotechnologist and microbiologist at Aarhus University who was not involved in the study. “They did a lot of genomic comparisons, but the real comparison of the rates [between KIAC and S. ovata] there, I think that is missing.”
To study the regulation of these genes in CO2 fixation further, the team identified transcriptional start sites and studied these regions for promoter motifs. They identified six sequences used by distinct sigma factors. They observed that the expression of one sigma factor, SigH, increased in hydrogen and CO2 conditions. Additionally, many genes involved in energy production and acetogenesis contained binding sites for this sigma factor. While several other acetogens, including those from the Sporomusa genus, contained the motif for SigH, it was not universal among acetogens, highlighting a potential novel regulatory role.
Next, the team used RNA sequencing to study KIAC’s gene expression when given four different carbon sources for energy. They showed that KIAC constitutively expressed some energy-producing genes as well as four hydrogenases. “That, I think, is surprising. That was not really what I expected,” Philips said, adding that since the hydrogenases are expressed in the absence of hydrogen, it could indicate they have other functions. Cho’s team also saw that KIAC expressed genes related to formate dehydrogenase differently depending on the carbon substrates available.
To study the role of these different hydrogenases in CO2 fixation, Cho’s team expressed three of these genes individually in another acetogen, Eubacterium limosum, which typically encodes one hydrogenase. Each KIAC hydrogenase increased the growth rate and consumption of hydrogen and CO2 as well as the production of acetate in E. limosum compared to a control strain. The metabolism of formate occurred faster in KIAC hydrogenase-expressing strains compared to the original E. limosum.
Researchers from Cho's team use anaerobic fermenters to grow acetogenic bacteria.
Seulgi Kang
Cho’s team concluded that diverse hydrogenases increase a bacteria’s metabolic capacity, possibly through their unique pathways available to produce and conserve energy, leading to improved CO2 fixation. “There is a kind of regulatory network to more efficiently utilize those hydrogenases because the energy level outside changes a lot,” Cho said.
Philips said that the hypothesis was interesting but added that subsequent studies removing these hydrogenase genes from the KIAC strain to see how it affects its growth and CO2 fixation rates would add more support to it. However, she acknowledged that, given the constraints of working with anaerobic bacteria, this is a difficult experiment to conduct.
Cho and his team plan to explore using KIAC in larger fermentation reactions to determine its industrial potential in CO2 conversion.
- Bae J, et al. Multi-omics analysis reveals the genetic basis for rapid CO2 utilization in the acetogenic bacterium Sporomusa sphaeroides KIAC. mSystems. 2025;10(9):00451-25.
