Shedding Light On "microbial Dark Matter"

There are millions of species of bacteria and archaea on the Earth, but we know remarkably little about most of them. Now, researchers have mined the genomes of thousands of microorganisms preserved at the RIKEN BioResource Research Center (BRC) to find organisms that may be capable of capturing CO₂. BRC, located in Tsukuba-one of Japan's largest centers of scientific research-is a unique world-class research facility. Researchers there collect and carefully manage the quality of biological resources-such as mice, plants, cells, genes, and microorganisms-used in research and provide these resources to research institutions around the world. These high-quality biological resources help to ensure the reproducibility of experiments and support the credibility of science. The researchers involved in the current project, from the Microbe Division (also known as the Japan Collection of Microorganisms (JCM)), thoroughly analyzed the genomes of approximately 6,700 microbial strains and discovered that roughly 300 of them possess a set of genes involved in the fixation of CO₂. This finding could contribute to research aimed at reducing CO₂ emissions using microorganisms and slowing global warming.

From left: Postdoctoral Researcher Arisa Nishihara, Senior Research Scientist Shingo Kato, Microbe Division (RIKEN JCM), RIKEN BioResource Research Center © 2026 RIKEN

An enormous collection of strains

JCM staff collect and store microbial strains discovered and cultured by microbiologists from around the world. In addition to genomic information, they also collect data that is useful for experiments and culturing, such as the environments in which the microorganisms were found and the conditions under which they grow.

The collection contains over 32,000 microbial strains. Of these, approximately 21,000-those for which information has been published in scientific papers or as genetic sequence data-are made publicly available, and the center provides over 4,000 strains annually to researchers both in Japan and abroad. The current research was aimed at making full use of the JCM collection, and the group decided to focus their investigation on the CO₂ fixation capabilities of microorganisms.

Exploring the "Calvin-Benson Cycle"

"To be honest, this was the kind of research I'd been hoping someone else would take on," laughs Arisa Nishihara, a postdoctoral researcher on the team.

The project to discover CO₂ fixation capabilities turned out to be a painstaking two-year analysis process. Microorganisms are divided into eukaryotes-such as molds and yeasts-and prokaryotes, which include bacteria and archaea. Scientists estimate that millions of species of bacteria and archaea exist on Earth, yet only a small fraction have been formally described and given scientific names. Many have never even been grown in the laboratory. This vast realm of poorly understood microbial life is sometimes called "microbial dark matter."

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. There is also-separately-a vast literature on these prokaryotes, including some related to CO₂ fixation. However, the genomic data and literature have never been systematically linked, leaving a gap in concrete research in areas such as CO₂ fixation using microorganisms.

So where to start? Plants use photosynthesis to capture CO₂ from the atmosphere and convert it into organic compounds. At the heart of this process is a series of chemical reactions known as the Calvin-Benson cycle, the major pathway responsible for CO₂ fixation on Earth. But plants aren't the only organisms capable of this kind of carbon fixation. Many microorganisms can also use the cycle-or other carbon-fixation pathways-to capture CO₂, including in complete darkness. Given this, the researchers decided to the genomes of 6,749 JCM strains for genes associated with the Calvin-Benson cycle.

At the same time, the team worked to cross-reference this data with the vast literature to determine whether the microorganisms they were examining were actually performing CO₂ fixation (Fig. 1).

Figure 1: Search for candidate CO₂ fixation strains based on microbial resources

The photo on the left shows microbial strains stored at the JCM. In order to ensure long-term stable preservation, the microorganisms are either refrigerated (top left) or frozen (bottom left) and strictly managed by strain number.

Senior Research Scientist Shingo Kato explains, "While photosynthesis carried out by plants performs CO₂ fixation, it requires light. In contrast, there are many microorganisms that can fix CO₂ in the dark. We believed that if we could harness this ability in places where light doesn't reach, it would contribute to the realization of a low-carbon society."

Finding 306 candidates

Approximately two years have passed since the start of the research. The search identified 306 strains carrying genes associated with the Calvin-Benson cycle, and the 306 strains belonged to 147 genera-genus being a higher taxonomic rank. When the researchers searched the scientific literature, they found evidence of CO₂ fixation in 74 of those genera-but not in the other 73. "Among the 74 genera for which CO₂ fixation was reported, we found that some were already being utilized in both basic and applied research. The remaining 73 genera represent promising candidates for further research," says Nishihara (Table 1).

Moving forward, the research team decided to focus on the enzyme Rubisco, which catalyzes a key step in the Calvin-Benson cycle. They classified 306 strains based on their type, habitat, and metabolic properties. The results revealed significant differences in the energy sources they utilized and their habitats.

Using the genetic data, the team found 173 strains that had potential for CO₂ fixation, despite belonging to genera for which no CO₂ fixation had previously been reported. These results suggested that many prokaryotes may possess the potential ability to fix CO₂ using hydrogen or sulfur compounds.

Nishihara explains, "There are various types of microorganisms. Some prefer hydrogen, some prefer sulfur, and some thrive in oxygen-free environments. That means that by changing the culture conditions, we may be able to discover microorganisms that exhibit CO₂ fixation ability."

From microbial collection to predictive science

This painstaking research is helping to enhance the value of the microbial collection held by JCM, as it will make it possible to specifically note "CO₂ fixation" as a characteristic in the catalog. This could help researchers around the globe select microorganisms that are best suited to achieving their specific CO₂ fixation goals.

Looking at the future direction of the research, Nishihara states, "First, I'd like to find new microorganisms capable of CO₂ fixation. AI may be useful for that. 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."

RIKEN is currently carrying out the TRIP initiative, which aims to connect cutting-edge research infrastructure and various types of data across disciplines. Kato says, "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."

This article is a translation of the Japanese article "全ゲノム解析でCO₂固定能を持つ微生物300株を発掘".

Rate this article

Thank you!