Staphylococcus spp. a salt-tolerant bacterium, exhibits a favorable flavor-enhancing effect during the soy sauce fermentation, especially at higher salt concentrations. To investigate the salt tolerance mechanism of staphylococci in the high-salt environment of soy sauce fermentation, a combined physiological and genomic research method was used to study three Staphylococcus strains (Staphylococcus carnosus CS1.21, S. piscifermentans CS1.22, and S. debuckii CS1.23) that were isolated from moromi. As the NaCl concentration increased from 40 to 180 g/L compared to the control, the contents of intracellular osmotic regulatory substances, such as soluble proteins and proline, increased significantly in all three Staphylococcus strains. Corresponding gene annotations revealed an abundance of protein synthesis genes and a complete proline synthesis pathway. Additionally, Na+/K+-ATPase activity increased significantly by 2.51–9.82 U/L (P < 0.05), and the Na+/K+ regulation genes have also been annotated. Catalase (CAT) activity and the rate of reactive oxygen species (ROS) scavenging were significantly enhanced by 0.75–2.51 U/mL and 28.13–62.98%, respectively, corresponding catalase synthesis genes have been annotated in all three strains. These genes form a synergistic regulatory network that, along with physiological adaptations, enhances the strains' salt tolerance under stress. The explanation of the salt tolerance mechanisms of the three staphylococci, which are based on maintaining osmotic balance and increasing ROS scavenging rates, laid the foundation for the complete utilization of the three strains in high-salt liquid fermentation.
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