{"id":5750,"date":"2026-09-07T11:57:27","date_gmt":"2026-09-07T02:57:27","guid":{"rendered":"http:\/\/jcm.brc.riken.jp\/en\/?page_id=5750"},"modified":"2026-09-07T11:57:27","modified_gmt":"2026-09-07T02:57:27","slug":"resource_news_e_vol13","status":"publish","type":"page","link":"http:\/\/jcm.brc.riken.jp\/en\/resource_news_e\/resource_news_e_vol13","title":{"rendered":"A systematic overview of CO2<\/sub>-fixing microorganisms in the JCM collection"},"content":{"rendered":"
2026\/09\/07<\/font>\n<\/div>\n

A systematic overview of CO2<\/sub>-fixing microorganisms in the JCM collection<\/font><\/p>\n

To deepen our understanding of microorganisms and to utilize them effectively as biological resources, it is important to integrate genome information with cultivation data.<\/font><\/p>\n

To this end, we examined the presence of Calvin\u2013Benson\u2013Bassham (CBB) cycle\u2013related genes and CO2<\/sub> fixation capabilities among approximately 6,700 genome-sequenced microbial strains maintained in the Japan Collection of Microorganisms (JCM) [Nishihara A, et al<\/i>. 2026]. Our analysis revealed a lack of experimental confirmation of the ability to fix CO2<\/sub> in many cultured microbial strains.<\/font><\/p>\n

The analysis found that 147 genera (approximately 300 strains) harbored CBB cycle\u2013related genes. Among these, CO2<\/sub> fixation has been reported in 74 genera. In contrast, the remaining 73 genera consist of strains for which CO2<\/sub> fixation capability has not yet been reported in the literature or has not yet been verified experimentally. In particular, several lineages within Actinomycetota<\/i> (Streptosporangiales<\/i>) and Deinococcota<\/i> (Thermales<\/i>) contain strains that may possess CO2<\/sub> fixation potential but their autotrophic growth has not yet been reported.<\/font><\/p>\n

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<\/sub> fixation using microbial resources from JCM.<\/font><\/p>\n

CO2<\/sub> 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<\/sub> fixation and is estimated to account for approximately 95% of carbon fixation on Earth. With growing interest in technologies that utilize CO2<\/sub> as a resource, microorganisms possessing the CBB cycle are attracting attention not only for understanding the carbon cycle but also for potential
\napplications in environmentally sustainable production processes and bio-manufacturing.<\/font><\/p>\n

Several representative microorganisms capable of CO2<\/sub> fixation via the CBB cycle are listed below.<\/font><\/p>\n

•Cupriavidus necator<\/i> (e.g.<\/i>, JCM 36303<\/a>)
\nFormerly known as Ralstonia eutropha<\/i>, Wautersia eutropha<\/i>, or Alcaligenes eutrophus<\/i>.
\nThis 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.<\/i>, Pohlmann A, et al<\/i>. 2006]. Nine strains, including the type strain, are preserved in the JCM.
\n<\/font><\/p>\n

• Acidithiobacillus thiooxidans<\/i> (e.g.<\/i>, JCM 3867<\/a>)
\nFormerly known as Thiobacillus thiooxidans<\/i>.
\nThis 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.<\/i>, Wang J, et al<\/i>. 2014]. Five strains, including the type strain, are preserved in the JCM.<\/font><\/p>\n

• Hydrogenovibrio marinus<\/i> (JCM 7688<\/a>)
\nA 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<\/i>. 1991].\u3000This organism possesses two types of RuBisCO enzyme which involved in the CBB cycle.<\/font><\/p>\n

• Cereibacter sphaeroides<\/i> (JCM 6121<\/a>)
\nFormerly known as Rhodobacter sphaeroides<\/i> or Rhodopseudomonas sphaeroides<\/i>. 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.<\/i>,Tabita FR. 1988].<\/font><\/p>\n

 
\nReferences
\nNishihara A, et al<\/i>. 2026.
\nExploring the diversity and metabolic potential of CO2<\/sub> fixation mediated by RubisCO in prokaryotes in the Japan Collection of Microorganisms.
\nMicrobes and Environments 41: ME25035.
\nDOI: 10.1264\/jsme2.ME25035<\/a><\/font><\/p>\n

Pohlmann A, et al<\/i>. 2006.
\nGenome sequence of the bioplastic-producing “Knallgas” bacterium Ralstonia eutropha<\/i> H16.
\nNature Biotechnology 24: 1257\u20131262.
\nDOI: 10.1038\/nbt1244<\/a><\/font><\/p>\n

Wang J, et al<\/i>. 2014.
\nBioleaching of low-grade copper sulfide ores by Acidithiobacillus<\/i> ferrooxidans<\/i> and Acidithiobacillus thiooxidans<\/i>.
\nJournal of Central South University 21: 728\u2013734.
\nDOI: 10.1007\/s11771-014-1995-3<\/a><\/font><\/p>\n

Nishihara H, et al<\/i>. 1991.
\nGrowth characteristics and high cell-density cultivation of a marine obligately chemolithoautotrophic hydrogen-oxidizing bacterium Hydrogenovibrio marinus<\/i> strain MH-110 under a continuous gas-flow system.
\nJournal of Fermentation and Bioengineering 72: 358\u2013361.
\nDOI: 10.1016\/0922-338X(91)90087-W<\/a><\/font><\/p>\n

Tabita FR. 1988.
\nMolecular and cellular regulation of autotrophic carbon dioxide fixation in microorganisms.
\nMicrobiological Reviews 52: 155\u2013189.
\nDOI: 10.1128\/mr.52.2.155-189.1988<\/a><\/font><\/p>\n

 <\/p>\n\n\n\n
<\/td>\n<\/tr>\n
Freeze-dried microbial strains in glass ampoules<\/td>\n<\/tr>\n<\/table>\n","protected":false},"excerpt":{"rendered":"

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\u2013Benson\u2013Bassham (CBB) cycle\u2013related 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\u2013related 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. […]<\/p>\n","protected":false},"author":17,"featured_media":0,"parent":4527,"menu_order":0,"comment_status":"closed","ping_status":"closed","template":"","meta":{"_seopress_titles_title":"","_seopress_titles_desc":"","_seopress_robots_index":"","_seopress_robots_follow":"","_seopress_robots_imageindex":"","_seopress_robots_snippet":"","_seopress_robots_primary_cat":"","_seopress_robots_breadcrumbs":"","_seopress_robots_freeze_modified_date":"","_seopress_robots_custom_modified_date":"","_seopress_robots_canonical":"","_seopress_social_fb_title":"","_seopress_social_fb_desc":"","_seopress_social_fb_img":"","_seopress_social_fb_img_attachment_id":0,"_seopress_social_fb_img_width":0,"_seopress_social_fb_img_height":0,"_seopress_social_twitter_title":"","_seopress_social_twitter_desc":"","_seopress_social_twitter_img":"","_seopress_social_twitter_img_attachment_id":0,"_seopress_social_twitter_img_width":0,"_seopress_social_twitter_img_height":0,"_seopress_redirections_value":"","_seopress_redirections_enabled":"","_seopress_redirections_enabled_regex":"","_seopress_redirections_logged_status":"","_seopress_redirections_param":"","_seopress_redirections_type":0,"_seopress_analysis_target_kw":"","footnotes":"","_wp_rev_ctl_limit":""},"class_list":["post-5750","page","type-page","status-publish","hentry"],"_links":{"self":[{"href":"http:\/\/jcm.brc.riken.jp\/en\/wp-json\/wp\/v2\/pages\/5750","targetHints":{"allow":["GET"]}}],"collection":[{"href":"http:\/\/jcm.brc.riken.jp\/en\/wp-json\/wp\/v2\/pages"}],"about":[{"href":"http:\/\/jcm.brc.riken.jp\/en\/wp-json\/wp\/v2\/types\/page"}],"author":[{"embeddable":true,"href":"http:\/\/jcm.brc.riken.jp\/en\/wp-json\/wp\/v2\/users\/17"}],"replies":[{"embeddable":true,"href":"http:\/\/jcm.brc.riken.jp\/en\/wp-json\/wp\/v2\/comments?post=5750"}],"version-history":[{"count":1,"href":"http:\/\/jcm.brc.riken.jp\/en\/wp-json\/wp\/v2\/pages\/5750\/revisions"}],"predecessor-version":[{"id":5751,"href":"http:\/\/jcm.brc.riken.jp\/en\/wp-json\/wp\/v2\/pages\/5750\/revisions\/5751"}],"up":[{"embeddable":true,"href":"http:\/\/jcm.brc.riken.jp\/en\/wp-json\/wp\/v2\/pages\/4527"}],"wp:attachment":[{"href":"http:\/\/jcm.brc.riken.jp\/en\/wp-json\/wp\/v2\/media?parent=5750"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}