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Cyanobacteria are important players in the global carbon cycle, accounting for approximately 25% of global CO2 fixation. Their CO2-concentrating mechanisms (CCMs) are thought to play a key role in cyanobacterial calcification, but the mechanisms are not completely understood. In Synechocystis sp. strain PCC 6803, a single Ca2+/H+ exchanger (Slr1336) controls the Ca2+/H+ exchange reaction. We knocked out the exchanger and investigated the effects on cyanobacterial calcification and CCMs. Inactivation of slr1336 significantly increased the calcification rate and decreased the zeta potential, indicating a relatively stronger Ca2+-binding ability. Some genes encoding CCM-related components showed increased expression levels, including the cmpA gene, which encodes the Ca2+-dependent HCO3- transporter BCT1. The transcript level of cmpA in the mutant was 30 times that in wild type. A Western blot analysis further confirmed that protein levels of CmpA were higher in the mutant than the wild type. Measurements of inorganic carbon fluxes and O2 evolution proved that both the net HCO3- uptake rate and the BCT1 transporter supported photosynthetic rate in the slr1336 mutant were significantly higher than in the wild type. This would cause the mutant cells to liberate more OH- ions out of the cell and stimulate CaCO3 precipitation in the microenvironment. We conclude that the mutation of the Ca2+/H+ exchanger in Synechocystis promoted the cyanobacterial calcification process by upregulating CCMs, especially the BCT1 HCO3- transporter. These results shed new light on the mechanism by which CCM-facilitated photosynthesis promotes cyanobacterial calcification. [ABSTRACT FROM AUTHOR]