Approximately 300 of the 6,700 microbial strains analyzed at the RIKEN BioResource Research Center (BRC) in Tsukuba possess genes involved in CO2 fixation. RIKEN JCM staff collect and store microbial strains discovered and cultured by microbiologists from around the world, providing a unique resource for reproducing experiments and advancing microbiological research worldwide.

“To be honest, this was the kind of research I’d been hoping someone else would take on,” says postdoctoral researcher Arisa Nishihara, whose team completed a two-year analysis process to discover CO2 fixation capabilities. This finding may contribute to efforts aimed at reducing CO2 emissions through microbial means.

RIKEN BioResource Center Enables Genome-Scale Microbial CO2 Research

This extensive library proved central to a recent investigation into microbial carbon dioxide fixation, yielding the discovery of roughly 300 strains possessing a set of genes involved in the fixation of CO2. This detailed metadata allows researchers to understand where these microbes originated and how they thrive, potentially unlocking further insights into their CO2 fixation mechanisms. “First, I’d like to find new microorganisms capable of CO2 fixation.

Artificial intelligence might be useful for that,” explains postdoctoral researcher Arisa Nishihara, highlighting the potential for using artificial intelligence in future searches. “That said, pursuing applied research myself is a bit outside my area of expertise. I want to focus entirely on gathering high-quality primary data on microbial habitats, culture conditions, and other factors.” Among the 74 genera for which CO2fixation was reported, researchers found that some were already being utilized in both basic and applied research.

This discovery could significantly aid global efforts to select microorganisms best suited for specific CO2 fixation goals, potentially accelerating the development of microbial solutions for reducing atmospheric carbon. Shingo Kato, a senior research scientist, emphasizes the broader implications.

The TRIP initiative has three pillars: organizing high-quality data; achieving breakthroughs in quantum chemical calculations through the integration of mathematical sciences and AI; and creating predictive science. The role of our research is involved in compiling high-quality primary data, but we don’t want to stop there, we also want to use AI to add value and even make predictions about how these microorganisms can be used in specific research areas and industries. I strongly believe that we, too, will be able to make a contribution to the TRIP initiative.
Shingo Kato, Senior Research Scientist, RIKEN JCM

73 Microbial Genera Show Promise for Novel CO2 Fixation

This discovery stems from a painstaking two-year analysis process. Researchers classified 306 strains based on type, habitat, and metabolic properties, uncovering significant variations in energy sources and environments preferred by these microbes. The team identified 173 strains possessing potential for CO2 fixation, suggesting many prokaryotes may possess the potential ability to fix CO2 using hydrogen or sulfur compounds.

Of the 15,000 prokaryotic strains that JCM makes available, the full genomic data for 6,749 (6,262 bacteria and 487 archaea) has already been analyzed, representing a significant portion of what scientists term “microbial dark matter.” Arisa Nishihara explains the potential for manipulating microbial growth conditions to unlock CO2 fixation capabilities, stating, “There are various types of microorganisms.

By changing the culture conditions, we may be able to discover microorganisms that exhibit CO2fixation ability.” The BRC provides over 4,000 strains annually to researchers both in Japan and abroad, and approximately 21,000 strains, those with published data, are publicly available, positioning the center as a resource for advancing microbial CO2 research. These results suggest a broader potential for harnessing microbial processes in efforts to reduce atmospheric carbon dioxide.

Rubisco Analysis Reveals Potential in Hydrogen and Sulfur Metabolism

Analysis of Rubisco within the RIKEN BioResource Center’s (BRC) collection revealed that 173 strains, despite originating from genera not previously known to fix carbon dioxide, possess the genetic potential for CO2 fixation. This finding expands understanding of prokaryotic metabolism beyond established pathways and suggests a wider prevalence of CO2 fixation capabilities than previously recognized. The team’s systematic approach focused on the enzyme Rubisco, central to the Calvin-Benson cycle, to identify these previously uncharacterized strains.

The center provides over 4,000 strains annually to researchers both in Japan and abroad, and its catalog will now specifically note this characteristic, facilitating targeted research and resource reproduction for scientists worldwide.