Exploring the diversity and physiological characteristics of RubisCO-mediated carbon fixation in culturable prokaryotes

The utilization of microbial resources requires their relevant reproducible characteristics, and genome analysis plays a crucial role in discovering valuable strains for future applications. In this study, we analyzed potential carbon-fixing microorganisms via Calvin-Benson-Bassham (CBB) cycle using 6,262 bacterial and 487 archaeal genomes from available cultures in Japan Collection of Microorganisms (JCM), one of the well-established culture collections today. A total of 306 strains (147 genera, eight phyla) carried CBB cycle genes and a literal survey showed that 74 genera had reported evidence of their autotrophic growth, although 73 lacked supporting information. Phylogenetic analysis of RubisCO large subunit (RbcL) identified diverse forms (IA, IB, IC, IE, I+, II, and III) with distinct metabolic associations: form IA associated with sulfur oxidation and form IC with hydrogen oxidation. Genome-based metabolic predictions suggested potential carbon fixation in numerous strains lacking experimental evidence. Our analyses showed members of Actinomycetota harboring form IE RubisCO tend to associate with hydrogen oxidation possibly using oxygen or nitrate as an electron acceptor. Additionally, 12 strains in Pseudomonadota contained pufL and pufM genes, suggesting possible phototrophic capabilities, although some failed to predict their electron donors and they possibly use CBB cycle to regulate intracellular redox balance under photoheterotrophic growth. Our findings highlight unrecognized autotrophic potentials in JCM strains and expand our knowledge of carbon fixation diversity. Future experimental validation will deepen our understanding of these microbes roles in the global carbon cycle, with potential applications in carbon sequestration and environmental sustainability.