Summary
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?

Microbial carbonates: the geological record of the calcified bacterial-algal mats and biofilms

/pdf/processes-of-carbonate-precipitation-in-modern-microbial-176vfhaypi.pdf

Processes of carbonate precipitation in modern microbial mats

Dolomite: occurrence, evolution and economically important associations

1. Weathering and Soils 2. Transport and Deposition of Siliciclastic Sediment 3. Sedimentary Textures 4. Sedimentary Structures 5. Siliciclastic Sedimentary Rocks 6. Carbonate Sedimentary Rocks 7. Other Chemical/Biochemical and Carbonaceous Sedimentary Rocks 8. Continental (Terrestrial) Environments 9. Marginal-Marine Environments 10. Siliciclastic Marine Environments 11. Carbonate and Evaporite Environments 12. Lithostratigraphy 13. Seismic, Sequence, and Magnetic Stratigraphy 14. Biostratigraphy 15. Chronostratigraphy and Geologic Time 16. Basin Analysis, Tectonics, and Sedimentation

Principles of Sedimentology and Stratigraphy

3.3.7. Nucleation of Calcium Carbonate 357 3.4. Dissolution Reactions 359 3.4.1. Calcite Dissolution Kinetics 359 3.4.2. Aragonite Dissolution 360 3.4.3. Magnesian Calcite Dissolution Kinetics 360 3.5. Biominerals and Nanophase Carbonates 361 3.5.1. General Considerations 361 3.5.2. Biomineralization 361 3.5.3. Biogeochemistry, Geomicrobiology 361 3.5.4. Nanophase Carbonates 362 3.6. Calcium Carbonate−Organic Matter Interactions 363

Calcium Carbonate Formation and Dissolution

DOLOMITE (CaMg(CO3)2) is a common carbonate mineral which is found in much greater abundance in ancient rocks than in modern carbonate environments. Why this is so remains a mystery. Over the past 30 years, dolomite formation has been observed in several modern environments, and various thermodynamic, kinetic and hydrological factors have been proposed to explain its formation1,2. But attempts to precipitate dolomite at low temperatures in the laboratory have been unsuccessful3,4, and the 'dolomite problem' remains a source of controversy in sedimentary geology5-7. Here we describe experiments in which a ferroan dolomite with a fairly high degree of cation order was precipitated in the presence of sulphate-reducing bacteria from the Desulfovibrio group. We propose that the direct mediation of these anaerobes can overcome the kinetic barrier to dolomite nucleation, and that they may play an active role in the formation of this mineral in natural environments.

Microbial mediation as a possible mechanism for natural dolomite formation at low temperatures

Dolomite, despite its thermodynamic stability and abundance in the ancient rock record, is rarely found forming in Holocene environments. This enigma is frequently called the Dolomite Problem. The recent discovery of modern dolomite formation in Lagoa Vermelha, a shallow-water isolated coastal lagoon east of Rio de Janeiro, Brazil, provides a new environment to investigate the factors promoting dolomite precipitation under earth surface conditions. Lagoa Vermelha serves as a natural laboratory in which the dolomite formation process was studied using an integrated hydrologic, geochemical, and sedimentological approach. The results of this study indicate that Ca-dolomite precipitation occurs under anoxic hypersaline conditions within a black sludge layer directly overlying the water/se iment interface. With deposition, the dolomite undergoes an "ageing" process, whereby increased ordering of the crystal structure occurs. Both the initial precipitation and subsequent early diagenesis are strongly mediated by microbial activity. In fact, using sulfate-reducing bacteria cultured from Lagoa Vermelha samples, a highly ordered dolomite has been produced in the laboratory at low temperatures. These experimental results combined with the study of the natural environment mandate that a microbial factor be added to the list of factors capable of causing dolomite precipitation. Considering the Lagoa Vermelha system, we propose a new actualistic model for dolomite formation, which we call the microbial dolomite model.

Microbial Mediation of Modern Dolomite Precipitation and Diagenesis Under Anoxic Conditions (Lagoa Vermelha, Rio de Janeiro, Brazil)

ABSTRACT Dolomite, despite its thermodynamic stability and abundance in the ancient rock record, is rarely found forming in Holocene environments. This enigma is frequently called the Dolomite Problem. The recent discovery of modern dolomite formation in Lagoa Vermelha, a shallow-water isolated coastal lagoon east of Rio de Janeiro, Brazil, provides a new environment to investigate the factors promoting dolomite precipitation under earth surface conditions. Lagoa Vermelha serves as a natural laboratory in which the dolomite formation process was studied using an integrated hydrologic, geochemical, and sedimentological approach. The results of this study indicate that Ca-dolomite precipitation occurs under anoxic hypersaline conditions within a black sludge layer directly overlying the water/se iment interface. With deposition, the dolomite undergoes an \"ageing\" process, whereby increased ordering of the crystal structure occurs. Both the initial precipitation and subsequent early diagenesis are strongly mediated by microbial activity. In fact, using sulfate-reducing bacteria cultured from Lagoa Vermelha samples, a highly ordered dolomite has been produced in the laboratory at low temperatures. These experimental results combined with the study of the natural environment mandate that a microbial factor be added to the list of factors capable of causing dolomite precipitation. Considering the Lagoa Vermelha system, we propose a new actualistic model for dolomite formation, which we call the microbial dolomite model.

Microbial mediation of modern dolomite precipitation and diagenesis under anoxic conditions

To study the process of microbial-mediated dolomite formation, growth experiments were carried out with selected bacterial cultures under anoxic environmental conditions simulating those found in Lagoa Vermelha, a hypersaline lagoon in Brazil where dolomite precipitation occurs. Specifically, we report the isolation of a particular strain of sulfate-reducing bacteria, LVform6, from Lagoa Vermelha sediment, which apparently promotes the formation of nonstoichiometric dolomite. Sulfate-reducing bacteria grown in a synthetic liquid medium produced dolomite during 30 days incubation at 30 °C. The precipitates have morphologies similar to those observed in Lagoa Vermelha sediment. Our results demonstrate that sulfate-reducing bacteria can influence dolomite precipitation under controlled lowtemperature, anoxic conditions, and imply that anaerobic microorganisms can play an important role in carbonate sedimentation. They may have been particularly significant in Earth's earliest history when a more reducing atmosphere existed.

Bacterially induced dolomite precipitation in anoxic culture experiments

Decades of various and numerous isotopic studies to interpret the environmental conditions of dolomite formation proved to be inconclusive because the temperature-dependent oxygen isotope fractionation factor between dolomite and the solution from which it precipitated could not be determined experimentally at low temperatures. With the discovery of bacteria that mediate the precipitation of dolomite, it is now possible to overcome kinetic barriers and precipitate dolomite under controlled temperature conditions in culture experiments. Herein we report on the results of microbial experiments that have enabled us to calibrate the dolomite-water oxygen isotope fractionation factor and provide a paleothermometer to evaluate conditions of ancient dolomite formation. The temperature (T) dependence of the fractionation is defined by the equation: 1000 In α d o l o m i t e - w a t e r = 2.73 X 10 6 T - 2 + 0.26.

Crisogono Vasconcelos

Papers

Microbial mediation as a possible mechanism for natural dolomite formation at low temperatures

Microbial Mediation of Modern Dolomite Precipitation and Diagenesis Under Anoxic Conditions (Lagoa Vermelha, Rio de Janeiro, Brazil)

Microbial mediation of modern dolomite precipitation and diagenesis under anoxic conditions

Bacterially induced dolomite precipitation in anoxic culture experiments

Calibration of the δ18O paleothermometer for dolomite precipitated in microbial cultures and natural environments