Abstract:In this study, the fermentation protein yield of Auxenochlorella pyrenoidosa was aimed to be enhanced, and its amino acid quality was improved through combined mutagenesis. The high-protein, chlorophyll-deficient mutant strain CX41, previously obtained by the research team, was used as the original strain. Combined mutagenesis was conducted using ethyl mesylate (EMS) and atmospheric and room temperature plasma (ARTP), followed by high-throughput screening through microbial microdroplet culture system (MMC) and 48-well plate cultivation. Subsequently, after secondary screening via 250 mL shake flask cultivation, the mutant strain Y11 was ultimately obtained. It was shown that under dark fermentation conditions at 30 ℃ and 160 r·min-1 for 96 h in Basal medium containing 30 g·L-1 glucose and 3.75 g·L-1 sodium nitrate, the biomass, protein content, and yield of Y11 reached 9.05 g·L-1, 55.54 g/100 g dry weight and 1.26 g·L-1d-1, respectively, which were significantly higher than those of the original strain CX41 by 21.15%, 25.60%, and 51.81%, respectively. The amino acid score (94.41) and the total branched-chain amino acid content (6.96 g/100 g dry weight) were also improved by 3.49 points and 27.35%, respectively. Moreover, the lutein content (1.12 mg·g-1), yield (10.10 mg·L-1), and productivity (2.52 mg·(L·d)?1) were significantly increased by 4.67%, 26.88%, and 26.63%, respectively, compared to CX41. This study is regarded as having provided a theoretical basis and technical support for the breeding of high-quality microalgal strains using combined mutagenesis and high-throughput screening techniques.