CO2 metabolism and energy acquisition mechanisms of Rhodococcus ruber lz1 under autotrophic conditions

In this study, a strain capable of autotrophic growth, Rhodococcus ruber lz1, was isolated from the activated sludge of propylene oxide saponification wastewater. Genomic and transcriptomic analyses revealed the absence of canonical carbon fixation pathways, but identified a complete [NiFe]-hydrogenase maturation system. Notably, hydrogenase subunits (hyaA and hyaB) were significantly upregulated under autotrophic conditions, suggesting the use of trace atmospheric H₂ as an electron donor. The strain is proposed to fix CO₂ via a non-canonical C₁ assimilation pathway proceeding through CO₂ → formate → formaldehyde → CH₂-THF → serine → pyruvate. Genes involved in gluconeogenesis, the TCA cycle, and pyruvate/propionate metabolism were also upregulated, indicating a coordinated metabolic network supporting carbon flux and energy homeostasis. These findings offer new insights into alternative CO₂ fixation strategies in non-classical autotrophic bacteria.