This paper provides evidence of the role of the proteinaceous constituents of the sedimentary organic matter in the control of (Ca, Mg) carbonate precipitation within recent stromatolitic sediments belonging to the kopara-type (Rangiroa, Tuamotu Archipelago, French Polynesia). Millimeter- to cm-thick alternating carbonate-rich and carbonate-poor layers allow the separation by hand of these two contrasted types of layers (with respect to carbonate content). The study aims, (1) to decipher the potential compartments (cyanobacterially derived and dissolved organic matter) for proteins that interact with divalent cations, to compare their biochemical composition with those of the intramineral organic matrices that incorporate fine authigenic micrites when they form; (2) to discriminate the ageing processes of organic matter, including OM mineralized by CaCO₃; (3) to correlate the biochemical features of protein-rich molecules dissolved in natural pore waters, extracted from different sediment layers (either carbonate-rich or carbonate-poor), with experimental tests of the efficiency of these same protein-rich molecules in the role of calcium carbonate inhibitors. The extracted natural macromolecules definitely control the rate of in vitro calcium carbonate precipitation: they exert an inhibiting effect, which strength depends on the type of layer–carbonate-rich or carbonate-poor–out of which they have been extracted. The quality (with respect to their aspartic and/or glutamic acid contents), as well as the amount of soluble protein-rich macromolecules present in the pore waters in each layer, plays a key role in active calcification processes. As a matter of fact, pore waters of carbonate-poor layers deliver high concentrations of dissolved, aspartic-rich macromolecules that are shown to inhibit strongly calcium carbonate precipitation in experimental conditions.

The consequence of such experimentally based results, as well as the correlation with the actual intensity of calcification in natural sediment layers, is crucial for discussing calcium carbonate balance or the formation of laminations in paleoenvironments.