Amphithéâtre Marguerite de Navarre, Site Marcelin Berthelot
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The synthesis of carbonate skeletons by biological organisms also influences the acid-base balance of seawater. To form, calcium carbonate consumes dissolved ions, notably carbonate ions CO32-. To compensate for this loss, HCO3- ions (bicarbonates or hydrogen carbonates) are converted into CO32- ions and dissolvedCO2.

The precipitation of solid CaCO3 thus shifts the acid-base equilibrium and leads to a drop in seawater pH. If the pCO2 of surface water is in equilibrium with that of the overlying atmosphere, the excessCO2 linked to calcification will diffuse from the ocean into the atmosphere. This phenomenon is often referred to as the carbonate "counter-pump", to underline the fact that calcification tends to increaseatmospheric pCO2, unlike the organic biological pump described above.

After the death of organisms, carbonate skeletons sediment in the water column and pile up on the ocean floor to form calcareous sludge. Some of the carbonates will redissolve in the form of carbonate and calcium ions. Dissolution takes place during the fall in the water column, as well as in the interstitial water of surface sediments. The reaction is favored because limestone solubility increases with pressure and decreases with temperature. High pressures and low temperatures on the ocean floor therefore favor the dissolution of carbonates formed in the surface layers of the ocean. What's more, as the degradation of organic matter lowers the pH of deep waters, the effect of limestone undersaturation is further enhanced, particularly in the North Pacific where aged water masses are characterized by high TCO2, low pH and low CO32- levels.