Deposits produced by microbial growth and metabolism have been important co
mponents 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 organi
sms involved are bacteria, particularly cyanobacteria, small algae and fung
i, that participate in the growth of microbial biofilms and mats. Grain-tra
pping 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 o
f CO2 and/or HCO3- by cyanobacteria, and ammonification, denitrification an
d sulphate reduction by other bacteria, can increase alkalinity and stimula
te carbonate precipitation. Extracellular polymeric substances, widely prod
uced by microbes for attachment and protection, are important in providing
nucleation sites and facilitating sediment trapping.
Microbial carbonate microfabrics are heterogeneous. They commonly incorpora
te trapped particles and in situ algae and invertebrates, and crystals form
around bacterial cells, but the main component is dense, clotted or peloid
al micrite resulting from calcification of bacterial cells, sheaths and bio
film, 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 (str
omatolite), clotted (thrombolite) and other macrofabrics, which may be eith
er agglutinated or mainly composed of calcified or spar-encrusted microbes.
Stromatolite lamination appears to be primary, but clotted thrombolite fab
rics can be primary or secondary. Microbial precipitation also contributes
to hot-spring travertine, cold-spring mound, calcrete, cave crust and coate
d grain deposits, as well as influencing carbonate cementation, recrystalli
zation 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 e
nvironmental control is seen at the present day by the localization of micr
obial carbonates in calcareous streams and springs and in shallow tropical
seas, and in the past by temporal variation in abundance of marine microbia
l carbonates. Patterns of cyanobacterial calcification and microbial dome f
ormation through time appear to reflect fluctuations in seawater chemistry.
Stromatolites appeared at similar to 3450 Ma and were generally diverse and
abundant from 2800 to 1000 Ma. Inception of a Proterozoic decline, various
ly identified at 2000, 1000 and 675 Ma, has been attributed to eukaryote co
mpetition 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 import
ance 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 Isla
nd are composite coarse agglutinated domes and columns with complex bacteri
al-algal mats occurring in environments that are both stressed and current-
swept: products of mat evolution, ecological refugia, sites of enhanced ear
ly lithification or all three?