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In a modern peritidal microbial mat from Qatar, both biomediated carbonates and Mg‐rich clay minerals (palygorskite) were identified. The mat, ca 5 cm thick, shows a clear lamination reflecting different microbial communities. The initial precipitates within the top millimetres of the mat are composed of Ca–Mg–Si–Al–S amorphous nanoparticles (few tens of nanometres) that replace the ultrastructure of extracellular polymeric substances. The extracellular polymeric substances are enriched in the same cations and act as a substrate for mineral nucleation. Successively, crystallites of palygorskite fibres associated with carbonate nanocrystals develop, commonly surrounding bacterial bodies. Micron‐sized crystals of low‐Mg calcite are the most common precipitates, together with subordinate aragonite, very high‐Mg calcite/dolomite and ankerite. Pyrite nanocrystals and framboids are present in the deeper layers of the …