Introduction. Bicarbonate and CO₂ are important substrates for carboxylation reactions in bacterial central metabolism. In the opportunistic pathogen Staphylococcus aureus, the bicarbonate transporter, MpsABC (membrane potential-generating system), is the only uptake system of the membrane-impermeant bicarbonate, which is crucial for growth in ambient air. The S. aureus ΔmpsABC mutant's growth deficit in ambient air, could be rescued by 5% CO₂. Goals. We aimed to investigate the impact of bicarbonate depletion on the phenotypic and genotypic changes that enable the ΔmpsABC mutant to counteract CO2/bicarbonate deficiency. Material & Methods.We compared WT and mutant by electron microscopy (EM), analyzed the cell wall (CW) composition by HPLC and mass spectrometry (MS), investigated the susceptibility to cell wall lytic enzymes, and carried out comparative RNAseq analysis for gene expression. Results. EM revealed that the CW of ΔmpsABC was twice as thick compared to the parent strain. The mutant was largely resistant to lysostaphin due to the incorporation of L-alanine in the interpeptide bridge. The RNAseq profiling revealed that particularly genes encoding CW-hydrolases were highly upregulated; while genes encoding CW-anchored proteins, wall teichoic acid biosynthesis, secreted proteins, transporters and toxins were downregulated. Conclusion. Bicarbonate depletion in S. aureus induces major changes in cell wall composition and global gene expression. The changes may indicate general survival strategies adopted by bacteria which face CO₂/bicarbonate limitation.