Physiological and molecular insights into the CO2-concentrating mechanism in Saccharina japonica: Implications for carbon fixation and sustainable bioengineering

The CO 2 -concentrating mechanism (CCM) in macroalgae enhances photosynthetic efficiency under limited inorganic carbon (Ci) conditions. In this study, the physiological and molecular characteristics of the CCM in Saccharina japonica were comprehensively examined. Physiological measurements showed that sporophytes of S. japonica retained 82.2% of their initial Fv/Fm (0.73 ± 0.003–0.60 ± 0.006) after 6 h in carbon-depleted seawater, with relatively stable ETRmax, α, and Ik values, indicating CCM effectiveness. However, all parameters significantly declined after 8 h, reflecting limitations of intracellular Ci reserves. Under varying CO 2 concentrations, photosynthetic performance peaked at 0.3% CO 2 , with maximal ETRmax, Ik, and pigment (Chl a, carotenoid) content, while 3% CO 2 caused feedback inhibition and pigment reduction. These trends aligned with seawater carbonate chemistry, where higher CO 2 led to increased dissolved inorganic carbon (DIC) and CO 2 (aq) but reduced pH. Transcriptomic analysis revealed extensive CO 2 -responsive gene expression. At 0.3% and 3% CO 2 , 2644 and 5406 differentially expressed genes (DEGs) were identified, respectively, many involved in carbon fixation and energy metabolism. Key CCM-related genes, such as Sjα-CA1 and Sjα-CA2, were downregulated under high CO 2 , whereas Sjγ-CA1, Sjγ-CA2, and C4-like genes SjPCK1 and MDH2 were upregulated. Subcellular localization using immunogold electron microscopy confirmed Sjα-CA3 in chloroplasts and SjPCK1 in the cytosol. These findings support the presence of a functional CCM in S. japonica , providing new insights into its carbon assimilation mechanisms. And such natural CCM may inform strategies for bioengineering algae with improved carbon fixation capabilities and contribute to the development of sustainable carbon management technologies. • Saccharina japonica exhibits a functional CO 2 -concentrating mechanism (CCM). • Optimal CO 2 level (0.3%) enhances carbon fixation and pigment biosynthesis efficiency. • Transcriptomic data reveal CO 2 -responsive regulation of CCM and C4-like pathway genes. • Key CCM components (Sjα-CA3, SjPCK1) are localized in chloroplasts and cytosol, respectively. • Findings guide the engineering of macroalgae bioreactors with improved carbon fixation.