Exploring the Diversity and Metabolic Potential of CO₂ fixation Mediated by RubisCO in Prokaryotes in the Japan Collection of Microorganisms

Abstract

A genome anal­ysis is essential for identifying valuable microbial resources for future applications. In the present study, we exami­ned potential CO₂-fixing microorganisms based on the presence of the Calvin–Benson–Bassham (CBB) cycle using 6,262 bacterial and 487 archaeal genomes from available cultures in the Japan Collection of Microorganisms (JCM), a well-established culture collection, in October 2023. A total of 306 strains (147 genera, eight phyla) carried CBB cycle genes, and a literature survey showed that 74 genera had experimental evidence of autotrophic growth while 73 lacked supporting information. A phylogenetic anal­ysis of the large subunit of ribulose-1,5-bisphosphate carboxylase/oxygenase (RbcL) identified diverse forms (IA, IB, IC, IE, I+α, II, and III) with distinct metabolic associations; IA was associated with sulfur species oxidation and formed IC with hydrogen oxidation. Genome-based metabolic predictions identified the potential for CO₂ fixation in numerous species lacking experimental evidence. Our anal­yses indicate that members of Actinomycetota harboring IE RbcL were generally associated with hydrogen oxidation, possibly by using oxygen or nitrate as an electron acceptor. Additionally, 12 species in Pseudomonadota contained photosystem II reaction center proteins (PufL and PufM), suggesting phototrophic capabilities. However, the prediction of electron donors failed in some of these species. They may use the CBB cycle to regulate the intracellular redox balance under photoheterotrophic growth. The present results reveal unrecognized autotrophic potential in JCM strains and broaden our knowledge of the diversity of CO₂-fixing microorganisms. Experimental validation will clarify their roles in the global carbon cycle and their potential for biotechnological applications towards environmental sustainability.