Temporal transcriptional regulation and genetic adaptation strategies in Nannochloropsis oceanica during long-term CO2 acclimation.

To overcome the limited tolerance of microalgal strains to high CO2 levels and the non-directional nature of traditional physicochemical mutagenesis, long-term multi-cycle acclimation under 10%-100% CO2 was employed to domesticate Nannochloropsis oceanica with the aim of elucidating its temporal transcriptional regulation and genetic adaptation strategies. Under multi-cycle acclimation at 55% CO2, chloroplast-associated genes underwent mutations that promoted accelerated chloroplast development, enhanced photosystem II efficiency, enhanced Calvin cycle activity, and reduced photodamage. The temporal sequence of adaptive gene regulation was characterized by (1) reduced respiratory energy expenditure, (2) accelerated chloroplast biogenesis, (3) enhancement of photoreaction, (4) increased dark reaction rates, and (5) stimulation of cell proliferation, ultimately promoting biomass accumulation. In contrast, acclimation under 100% CO2 resulted in increased DNA damage and the accumulation of harmful mutations. Key functions, including photosystem II stability factor, nucleotide excision, and mismatch repair, were impaired. This disruption of genetic stability and transcriptional regulation resulted in reduced biomass growth and carbon fixation. Compared to the wild-type strain, the 55% CO2-domesticated microalgae exhibited a 78% increase in biomass dry weight and a 3-fold increase in carbon fixation under a 95% CO2 environment. Expression levels of PSII core proteins, carbon fixation rate-limiting enzymes, and cyclin genes were significantly upregulated. These findings demonstrate that long-term 55% CO2 domestication promoted the enrichment of beneficial mutations in photosynthetic carbon fixation and cell division genes, conferring stable tolerance to high CO2. This cost-effective and simple strategy provides a viable approach for developing microalgal strains suitable for industrial flue-gas CO2 mitigation.