Deposits produced by microbial growth and metabolism have been important components of carbonate sediments since the Archaean. Geologically best known in seas and lakes, microbial carbonates are also important at the present day in fluviatile, spring, cave and soil environments. The principal organisms involved are bacteria, particularly cyanobacteria, small algae and fungi, that participate in the growth of microbial biofilms and mats. Grain-trapping is locally important, but the key process is precipitation, producing reefal accumulations of calcified microbes and enhancing mat accretion and preservation. Various metabolic processes, such as photosynthetic uptake of CO2 and/or HCO3– by cyanobacteria, and ammonification, denitrification and sulphate reduction by other bacteria, can increase alkalinity and stimulate carbonate precipitation. Extracellular polymeric substances, widely produced by microbes for attachment and protection, are important in providing nucleation sites and facilitating sediment trapping.
Microbial carbonate microfabrics are heterogeneous. They commonly incorporate trapped particles and in situ algae and invertebrates, and crystals form around bacterial cells, but the main component is dense, clotted or peloidal micrite resulting from calcification of bacterial cells, sheaths and biofilm, and from phytoplankton-stimulated whiting nucleation. Interpretation of these texturally convergent and often inscrutable fabrics is a challenge. Conspicuous accumulations are large domes and columns with laminated (stromatolite), clotted (thrombolite) and other macrofabrics, which may be either agglutinated or mainly composed of calcified or spar-encrusted microbes. Stromatolite lamination appears to be primary, but clotted thrombolite fabrics can be primary or secondary. Microbial precipitation also contributes to hot-spring travertine, cold-spring mound, calcrete, cave crust and coated grain deposits, as well as influencing carbonate cementation, recrystallization and replacement. Microbial carbonate is biologically stimulated but also requires favourable saturation state in ambient water, and thus relies uniquely on a combination of biotic and abiotic factors. This overriding environmental control is seen at the present day by the localization of microbial carbonates in calcareous streams and springs and in shallow tropical seas, and in the past by temporal variation in abundance of marine microbial carbonates. Patterns of cyanobacterial calcification and microbial dome formation through time appear to reflect fluctuations in seawater chemistry.
Stromatolites appeared at ∼3450 Ma and were generally diverse and abundant from 2800 to 1000 Ma. Inception of a Proterozoic decline variously identified at 2000, 1000 and 675 Ma, has been attributed to eukaryote competition and/or reduced lithification. Thrombolites and dendrolites mainly formed by calcified cyanobacteria became important early in the Palaeozoic, and reappeared in the Late Devonian. Microbial carbonates retained importance through much of the Mesozoic, became scarcer in marine environments in the Cenozoic, but locally re-emerged as large agglutinated domes, possibly reflecting increased algal involvement, and thick micritic reef crusts in the late Neogene. Famous modern examples at Shark Bay and Lee Stocking Island are composite coarse agglutinated domes and columns with complex bacterial–algal mats occurring in environments that are both stressed and current-swept: products of mat evolution, ecological refugia, sites of enhanced early lithification or all three?