A systematic overview of CO2-fixing microorganisms in the JCM collection

2026/09/07

A systematic overview of CO₂-fixing microorganisms in the JCM collection

To deepen our understanding of microorganisms and to utilize them effectively as biological resources, it is important to integrate genome information with cultivation data.

To this end, we examined the presence of Calvin–Benson–Bassham (CBB) cycle–related genes and CO₂ fixation capabilities among approximately 6,700 genome-sequenced microbial strains maintained in the Japan Collection of Microorganisms (JCM) [Nishihara A, et al. 2026]. Our analysis revealed a lack of experimental confirmation of the ability to fix CO₂ in many cultured microbial strains.

The analysis found that 147 genera (approximately 300 strains) harbored CBB cycle–related genes. Among these, CO₂ fixation has been reported in 74 genera. In contrast, the remaining 73 genera consist of strains for which CO₂ fixation capability has not yet been reported in the literature or has not yet been verified experimentally. In particular, several lineages within Actinomycetota (Streptosporangiales) and Deinococcota (Thermales) contain strains that may possess CO₂ fixation potential but their autotrophic growth has not yet been reported.

Therefore, we systematically organized the data based on literature surveys and genome analyses by integrating gene information with cultivation conditions, including oxygen concentration, temperature, pH, energy sources (electron donors), and isolation environments. The dataset we put together gives a foundation for research on CO₂ fixation using microbial resources from JCM.

CO₂ fixation, the process by which carbon dioxide is incorporated into organic compounds, is a fundamental biological activity that supports global biogeochemical cycles. The CBB cycle is one of the most widespread mechanisms of CO₂ fixation and is estimated to account for approximately 95% of carbon fixation on Earth. With growing interest in technologies that utilize CO₂ as a resource, microorganisms possessing the CBB cycle are attracting attention not only for understanding the carbon cycle but also for potential
applications in environmentally sustainable production processes and bio-manufacturing.

Several representative microorganisms capable of CO₂ fixation via the CBB cycle are listed below.

•Cupriavidus necator (e.g., JCM 36303)
Formerly known as Ralstonia eutropha, Wautersia eutropha, or Alcaligenes eutrophus.
This hydrogen-oxidizing bacterium is a well-established model organism and is widely used in industrial applications such as the production of the bioplastic polyhydroxyalkanoate (PHA) [e.g., Pohlmann A, et al. 2006]. Nine strains, including the type strain, are preserved in the JCM.

• Acidithiobacillus thiooxidans (e.g., JCM 3867)
Formerly known as Thiobacillus thiooxidans.
This species oxidizes sulfur and sulfur compounds in acidic environments. It is utilized in bioleaching, a technology that uses microorganisms to recover metals from ores [e.g., Wang J, et al. 2014]. Five strains, including the type strain, are preserved in the JCM.

• Hydrogenovibrio marinus (JCM 7688)
A hydrogen-oxidizing autotrophic bacterium isolated from marine environments. It exhibits high oxygen tolerance and has been reported to grow under relatively high oxygen concentrations (up to 40%) [Nishihara H, et al. 1991].　This organism possesses two types of RuBisCO enzyme which involved in the CBB cycle.

• Cereibacter sphaeroides (JCM 6121)
Formerly known as Rhodobacter sphaeroides or Rhodopseudomonas sphaeroides. This purple non-sulfur bacterium is a widely used model organism in studies of photosynthesis and the CBB cycle and possesses two forms of RuBisCO enzyme [e.g.,Tabita FR. 1988].

References
Nishihara A, et al. 2026.
Exploring the diversity and metabolic potential of CO₂ fixation mediated by RubisCO in prokaryotes in the Japan Collection of Microorganisms.
Microbes and Environments 41: ME25035.
DOI: 10.1264/jsme2.ME25035

Pohlmann A, et al. 2006.
Genome sequence of the bioplastic-producing “Knallgas” bacterium Ralstonia eutropha H16.
Nature Biotechnology 24: 1257–1262.
DOI: 10.1038/nbt1244

Wang J, et al. 2014.
Bioleaching of low-grade copper sulfide ores by Acidithiobacillus ferrooxidans and Acidithiobacillus thiooxidans.
Journal of Central South University 21: 728–734.
DOI: 10.1007/s11771-014-1995-3

Nishihara H, et al. 1991.
Growth characteristics and high cell-density cultivation of a marine obligately chemolithoautotrophic hydrogen-oxidizing bacterium Hydrogenovibrio marinus strain MH-110 under a continuous gas-flow system.
Journal of Fermentation and Bioengineering 72: 358–361.
DOI: 10.1016/0922-338X(91)90087-W

Tabita FR. 1988.
Molecular and cellular regulation of autotrophic carbon dioxide fixation in microorganisms.
Microbiological Reviews 52: 155–189.
DOI: 10.1128/mr.52.2.155-189.1988

Freeze-dried microbial strains in glass ampoules

JCM accession number
JCM:

Example: JCM = 12345 (Exact match search)

Scientific name 1
Genus: Species:

Example 1: Genus = Micromonospora Example 2: Species = aurantiaca Example 3: Genus = %monospo, Species = %ensis (Prefix match search at each box. Inside match or suffix match search can be performed by using "%" as a wild-card character like Example 3. Case-insensitive)

Scientific name 2
Scientific name:

Example 1: Scientific name = Micromonospora chalcea Example 2: Scientific name = Lactobacillus paracasei subsp. paracasei (Prefix match search. Inside match or suffix match search can be performed by using "%" as a wild-card character. Case-insensitive)

Culture medium
JCM Medium No.: Name of Medium:

Example 1: JCM Medium No. = 58 Example 2: Name of Medium = malt extract (Exact match search for "JCM Medium No." and inside match search for "Name of Medium". Case-insensitive)