Promote Carbonate Precipitation Research Articles

Recognizing microbial manganese reduction in lacustrine carbonate and its linkage to terrestrial biogeochemical processes

Carbonate authigenesis, the in situ precipitation of carbonate minerals within the sediment porewaters, is a key pathway for carbonate deposition and plays a crucial role in global biogeochemical cycles. Heterotrophic microorganisms are essential in regulating authigenic carbonate formation, primarily through the consumption of organic matter. Although bacterial manganese reduction is known to influence the formation of rhodochrosite and dolomite, its role in limestone deposition is unclear. Here, we present a systematic investigation of mixed calcareous siliciclastic rocks from a Paleogene freshwater lake to identify the formation of authigenic carbonate, decode the role of microbial Mn reduction, and understand the microbial response to ancient lacustrine environmental changes. The positive correlation between carbonate fraction in bulk samples (Carb%) and Mn content in carbonate minerals (Mncarb) suggests that carbonate precipitation is stimulated by Mn2+ enrichment. The dissimilarity between Mncarb and Fecarb, along with the synergic variations of Mncarb and diagenetic indicators, support an authigenic rather than a hydrogenetic origin for the carbonates. Using a one-dimensional diffusion–advection-reaction model, we quantify the impact of Mn reduction on promoting carbonate precipitation. Furthermore, correlations between Pcarb and other values–positive with the chemical index alteration (CIA), negative with Mncarb, and none with TOC–suggest that nitrogen availability, regulated by continental weathering, is likely the primary factor limiting both the primary productivity and the bacterial reduction intensity at the study site. Overall, this study uncovers the role of microbial Mn reduction in stimulating authigenic carbonate precipitation, and reveals the modulation mechanism of Mn-reducing microorganisms in an ancient lake. These findings shed new light on the authigenic limestone formation mechanisms and provide a new perspective on interpreting the authigenic impacts on carbonate chemistry.

Simulation Study of the Solidification on the Outcrop Caused by Microbial Dynamics

Algae on/in outcrops induce calcium carbonate precipitation. The calcium carbonate protects surface of the outcrops and improves their mechanical properties. Therefore, if this phenomenon can be artificially reproduced and applied to real environments, weathered outcrops could be restored in a self-organized manner. However, it is difficult to directly observe the dynamic changes of carbonate precipitation on the surface of outcrops in experiments because the active zone of algae is very small. In this study, we propose a simulation technique that can evaluate the growth of algae and the carbonate deposition process on/in the surface layer of outcrops. The results of the numerical analysis indicate that photoautotroph move in the direction perpendicular to the outcrop and promote carbonate precipitation. The spatial distribution of algae obtained by the simulation was very similar to that in a real environment. The proposed method has the potential to accurately evaluate algae growth and carbonate precipitation processes and is considered to be a promising tool for predicting this phenomenon.

Potential role for microbial ureolysis in the rapid formation of carbonate tufa mounds.

Modern carbonate tufa towers in the alkaline (~pH 9.5) Big Soda Lake (BSL), Nevada, exhibit rapid precipitation rates (exceeding 3cm/year) and host diverse microbial communities. Geochemical indicators reveal that carbonate precipitation is, in part, promoted by the mixing of calcium-rich groundwater and carbonate-rich lake water, such that a microbial role for carbonate precipitation is unknown. Here, we characterize the BSL microbial communities and evaluate their potential effects on carbonate precipitation that may influence fast carbonate precipitation rates of the active tufa mounds of BSL. Small subunit rRNA gene surveys indicate a diverse microbial community living endolithically, in interior voids, and on tufa surfaces. Metagenomic DNA sequencing shows that genes associated with metabolisms that are capable of increasing carbonate saturation (e.g., photosynthesis, ureolysis, and bicarbonate transport) are abundant. Enzyme activity assays revealed that urease and carbonic anhydrase, two microbial enzymes that promote carbonate precipitation, are active in situ in BSL tufa biofilms, and urease also increased calcium carbonate precipitation rates in laboratory incubation analyses. We propose that, although BSL tufas form partially as a result of water mixing, tufa-inhabiting microbiota promote rapid carbonate authigenesis via ureolysis, and potentially via bicarbonate dehydration and CO2 outgassing by carbonic anhydrase. Microbially induced calcium carbonate precipitation in BSL tufas may generate signatures preserved in the carbonate microfabric, such as stromatolitic layers, which could serve as models for developing potential biosignatures on Earth and elsewhere.

Mechanism of carbonate mineralization induced by microbes: Taking Curvibacter lanceolatus strain HJ-1 as an example

Microbial-induced carbonate precipitation is important in the global carbon cycle, especially in fixing atmospheric CO2. Many simulation experiments have shown that microbes can induce carbonate precipitation, although there is no established understanding of the mechanism. In this study, several mineralization experiments were performed using Curvibacter lanceolatus strain HJ-1, including its secreted extracellular polymeric substances (EPS) and carbonic anhydrase (CA). We found that strain HJ-1, EPS, and CA could promote carbonate precipitation if compared with the respective control experiments (CK). Also, both HJ-1 and EPS1 experiments contained calcite and aragonite, whereas CA experiments formed calcite only. Therefore, HJ-1 and EPS is favorable for carbonate precipitation, especially for aragonite. Besides, the formation of calcite in the EPS2 experiments indicated that EPS contains a trace amount of CA, which might promote CO2 hydration and eventually lead to carbonate precipitation. It was suggested that CA only provide CO32− for the formation of carbonate minerals. In the absence of exogenous HCO3-, the optimized calcification rate followed the order: HJ-1(49.5 %) > CA(6.6 %) > EPS2(4.1 %). In addition, MICP mechanisms was studied, an increase in pH and CO2 hydration by CA play synergetic roles in providing supersaturated alkaline conditions in the system with bacteria. Finally, bacterial cells and EPS promote the formation of calcite and aragonite by acting as nucleation sites.

Atmospheric dust stimulated marine primary productivity during Earth’s penultimate icehouse

The importance of dust as a source of iron (Fe) for primary production in modern oceans is well studied but remains poorly explored for deep time. Vast dust deposits are well recognized from the late Paleozoic and provisionally implicated in primary production through Fe fertilization. Here, we document dust impacts on marine primary productivity in Moscovian (Pennsylvanian, ca. 307 Ma) and Asselian (Permian, ca. 295 Ma) carbonate strata from peri-Gondwanan terranes of Iran. Autotrophic contents of samples, detected by both point-count and lipid-biomarker analyses, track concentrations of highly reactive Fe, consistent with the hypothesis that dust stimulated primary productivity, also promoting carbonate precipitation. Additionally, highly reactive Fe tracks the fine-dust fraction. Dust-borne Fe fertilization increased organic and inorganic carbon cycling in low- and mid-latitude regions of Pangaea, maintaining low pCO2.

Molecular biosignatures reveal common benthic microbial sources of organic matter in ooids and grapestones from Pigeon Cay, The Bahamas.

Ooids are sedimentary grains that are distributed widely in the geologic record. Their formation is still actively debated, which limits our understanding of the significance and meaning of these grains in Earth's history. Central questions include the role played by microbes in the formation of ooids and the sources of ubiquitous organic matter within ooid cortices. To address these issues, we investigated the microbial community composition and associated lipids in modern oolitic sands at Pigeon Cay on Cat Island, The Bahamas. Surface samples were taken along a transect from the shallow, turbulent surf zone to calmer, deeper water. Grains transitioned from shiny and abraded ooids in the surf zone, to biofilm-coated ooids at about 3m water depth. Further offshore, grapestones (cemented aggregates of ooids) dominated. Benthic diatoms and Proteobacteria dominated biofilms. Taxa that may promote carbonate precipitation were abundant, particularly those associated with sulfur cycling. Compared to the lipids associated with surface biofilms, relict lipids bound within carbonate exhibited remarkably similar profiles in all grain types. The enhanced abundance of methyl-branched fatty acids and β-hydroxy fatty acids, 1-O-monoalkyl glycerol ethers and hopanoids bound within ooid and grapestone carbonate confirms a clear association of benthic sedimentary bacteria with these grains. Lipids bound within ooid cortices also contain molecular indicators of microbial heterotrophic degradation of organic matter, possibly in locally reducing conditions. These included the loss of labile unsaturated fatty acids, enhanced long-chain fatty acids/short-chain fatty acids, enriched stable carbon isotopes ratios of fatty acids, and very high stanol/stenol ratios. To what extent some of these molecular signals are derived from later heterotrophic endolithic activity remains to be fully resolved. We speculate that some ooid carbonate forms in microbial biofilms and that early diagenetic degradation of biofilms may also play a role in early stage carbonate precipitation around ooids.

The origin of bedding-parallel fibrous calcite veins in the Lower Permian Chihsia Formation in western Hubei Province, South China

Bedding-parallel fibrous veins occurring as lenticular to flattened intercalations were found in the organic-rich marlstone/calcareous shale of the upper Lower Permian Chihsia Formation in western Hubei Province, South China. They dominantly consist of fibrous calcite crystals with smooth and tight boundaries, forming fence-like inward, syntaxial growth clusters toward the vein center along which a median suture line generally occurs. Petrographic evidence indicates that these veins may form at relatively shallow burial depth, where fluid overpressures would have incrementally created the bed-parallel vein space, resulting in displacive growth of fibrous calcite. On the other hand, the C, O and S isotopic data across the vein reveal slightly depleted δ13Ccarb values (−3.32‰ to +0.19‰ VPDB) and moderately depleted δ18Ocarb values (−9.6‰ to −7.3‰ VPDB) with respect to those of coeval seawaters and slightly heavier δ34Spyrite values (−7.88% CDT) with respect to those of ambient rocks. Stable isotope evidence consistently suggests significant contribution of bacterial sulfate reduction (BSR) to the formation of the fibrous calcite cements in the vein. The BSR could have been intensive with the availabilities of residual sulfate and abundant organic matters in the Chihsia sediments during shallow burial, increasing the alkalinity of pore waters and further promoting carbonate precipitation. Thus, the bedding-parallel fibrous calcite vein in the upper Lower Permian Chihsia Formation is an important time-specific petrographic capsule, providing clues for understanding the diagenetic process in organic-rich sediments.

Concretions as Agents of Soft-Tissue Preservation: A Review

Carbonate concretions may preserve exceptional soft-tissue fossils. Organismal decay in sediment can produce HCO3−faster than it diffuses away, creating a local microenvironment of high alkalinity around the decaying organism that promotes carbonate precipitation. Infilling of sediment pore-space around the decaying organism decreases permeability and inhibits decay, thus increasing preservation potential within the concretion and promoting soft-tissue preservation. Different patterns of concretion growth may promote different mechanisms of soft-tissue preservation. Other factors such as shifting salinity and clay mineral chemistry, which increase preservation potential in the depositional environment, also promote soft tissue preservation within concretions. The rate of concretion nucleation and growth affects preservation; the faster concretions nucleate and grow, the better the preservation. Concretionary preservation is biased both by concretion-promoting environments and organism size effects on concretion formation.

Study of Mineral Trapping of CO2 and Seal Leakage Mitigation

Abstract Mineral trapping of carbon dioxide is the safest and the most permanent sequestration mechanism. Brine composition, brine pH, system temperature and pressure have been reported to have significant effects on mineral trapping of CO2 in brines. It has also been reported that iron cation in brine could cause pH instability that may lead to lower carbonation conversion rate. This study aims to investigate whether ferric or ferrous iron caused this pH instability. pH stability studies and high temperature/high pressure carbonation experiments (150 °C,100 bar) with the addition of 1.0 M KOH were conducted using different synthetic brines with Fe3+, Fe2+, and without Fe. It can be concluded from this study that ferrous iron causes pH instability. However, ferrous iron might promote carbonate precipitation in non-pure CO2 streams in iron oxyhydroxide-containing saline aquifers as seal leakage mitigation.

Isotopic fingerprints of microbial respiration in aragonite from Bahamian stromatolites

Authigenic aragonite preserves a carbon isotopic record of heterotrophic microbial influences on dissolved inorganic carbon (DIC) in microenvironments within shallow subtidal stromatolites from Highborne Cay, Bahamas. A greater amount of aragonite precipitates when and where respiration, rather than photosynthesis, influences local DIC, which is consistent with sulfate reduction promoting carbonate precipitation and calcium release during decay of exopolymeric substances. Thus, heterotrophs play a more direct role than phototrophs in stromatolite lithification. Cyanobacteria are spatially associated with aragonite containing heterotrophic isotopic signatures. Hence, the absence of an autotrophic isotopic signature in the rock record does not imply the absence of photosynthetic organisms.

Bacterial diversity and carbonate precipitation in the giant microbialites from the highly alkaline Lake Van, Turkey

Lake Van harbors the largest known microbialites on Earth. The surface of these huge carbonate pinnacles is covered by coccoid cyanobacteria whereas their central axis is occupied by a channel through which neutral, relatively Ca-enriched, groundwater flows into highly alkaline (pH approximately 9.7) Ca-poor lake water. Previous microscopy observations showed the presence of aragonite globules composed by rounded nanostructures of uncertain origin that resemble similar bodies found in some meteorites. Here, we have carried out fine-scale mineralogical and microbial diversity analyses from surface and internal microbialite samples. Electron transmission microscopy revealed that the nanostructures correspond to rounded aragonite nanoprecipitates. A progressive mineralization of cells by the deposition of nanoprecipitates on their surface was observed from external towards internal microbialite areas. Molecular diversity studies based on 16S rDNA amplification revealed the presence of bacterial lineages affiliated to the Alpha-, Beta- and Gammaproteobacteria, the Cyanobacteria, the Cytophaga-Flexibacter-Bacteroides (CFB) group, the Actinobacteria and the Firmicutes. Cyanobacteria and CFB members were only detected in surface layers. The most abundant and diverse lineages were the Firmicutes (low GC Gram positives). To the exclusion of cyanobacteria, the closest cultivated members to the Lake Van phylotypes were most frequently alkaliphilic and/or heterotrophic bacteria able to degrade complex organics. These heterotrophic bacteria may play a crucial role in the formation of Lake Van microbialites by locally promoting carbonate precipitation.

Stratigraphic and palaeoenvironmental significance of microbial carbonates in the Asbian Sandy Craig Formation of Fife

Synopsis This study concentrates on Viséan Strathclyde Group microbial carbonates from the eastern Midland Valley of Scotland. In the largely non-marine Sandy Craig and West Lothian Oil-Shale formations persistent lithostratigraphical marker horizons, such as distinct microbial carbonates, are used to aid correlation of sequences where conventional biostratigraphy is limited to the identification of infrequent marine bands. In the newly described Rosyth core, microbial carbonates above the Burdiehouse Limestone are correlated with microbial horizons at Kingswood (Fife) and Inchkeith (Firth of Forth), a correlation supported by the presence of the bivalve Curvirimula scotica. The revised position of the Inchkeith microbial horizon to 20–30 m above the Burdiehouse Limestone contradicts earlier correlations of the Inchkeith sequences with the Burdiehouse Limestone. The microbial carbonates represent littoral and sublittoral zone stromatolites growing in <20 m of water. The best modern analogues are stromatolites forming in East African Rift Valley lakes. These microbial carbonates formed in volcanically isolated shallow sub-basins or in association with delta progradation. Lavas and tuffs provided stable substrates free of clastic sediment for stromatolite nucleation, and their weathering may have enhanced Ca 2+ ion activity to promote carbonate precipitation. These lacustrine microbial carbonates cannot be implicitly linked with climatic events or basin-wide regression as has been proposed for a regionally persistent microbial carbonate below the Burdiehouse Limestone.

The role of bacteria in the formation of cold seep carbonates: geological evidence from Monferrato (Tertiary, NW Italy)

Abstract Methane-derived carbonate rocks (Lucina limestone and Marmorito limestone) crop out in Monferrato (NW Italy) and represent one of the first described examples of rocks produced at fossil cold seeps. These rocks, of Miocene age, consist of strongly carbonate-cemented siliciclastic sediments ranging in grain size from mud to coarse sand. The methane-related origin of Monferrato carbonates is based on: (a) outcrop-scale evidence: patchiness of cementation, chemosymbiotic fossil communities, presence of a network of polyphase carbonate-filled veins not related to tectonics; (b) isotope geochemistry: very depleted δ13C values, as low as −50‰ PDB; (c) peculiar petrographic features. Diverse microbial communities have been observed in present-day cold seeps. These communities include sulphate-reducing, sulphur-oxidizing and methane-oxidizing bacteria. The present work is focused on the identification and description of fossil evidence of such microbial activity in the Monferrato carbonates. Examples of fossilization of microbial structures are probably represented by pyritic rods and dolomite tubes referable to sulphur-oxidizing and to unspecified bacteria, respectively. Less direct but more abundant evidence has been found through petrographic and SEM studies of seep carbonates. Many features point to the presence of organic clumps or mats capable of trapping sediment and promoting carbonate precipitation: microcrystalline calcite peloids; dolomite crystals with irregular hollow cores; dolomite spheroids with dumbbell-shaped cores; laminated internal sediments lining cavities completely. All these features are interpreted to result from bacterially mediated, sedimentary and diagenetic processes and can therefore be considered as an additional evidence of ancient methane seeps.

Organic matter oxidation and sediment chemistry in mixed terrigenous-carbonate sands of Ningaloo Reef, Western Australia

Abstract The oxidation of organic matter in relation to porewater and solid-phase element chemistry was examined in mixed terrigenous-carbonate sediments in sheltered and exposed lagoons of Ningaloo Reef, Western Australia. Rates of O2 consumption and CO2 release were faster in the very fine sand (41–43% CaCO3 content) of the sheltered lagoon of Mangrove Bay (means = 10.5 mmolm−2day−1 O2 and 9.4mmolm−2day−1 CO2) than in the carbonate-rich (73% CaCO3) sand of the exposed back-reef lagoon of Ningaloo Reef (means = 2.1 mmolm−2 day−1 O2 and 3.5 mmolm−2 day−1 CO2). Rates of sulfate reduction (ΣSRR) were similarly faster in the Mangrove Bay sediments (6.1–25.3 mmolm−2day−1 S), sufficient to account for all of the organic matter mineralization. In Ningaloo reef sands, ΣSRR rates (1.0 mmol m−2 day−1 S) accounted for a significant fraction (57%) of total organic carbon oxidation. In Mangrove Bay, in contrast to previous measurements of sulfate reduction in tropical sediments, most (mean = 64%) of the reduced 35S was incorporated into the acid-volatile sulflde fraction with a buildup of iron sulfides. In contrast to most carbonate-bearing sediments, the production and accumulation of Fe sulfides (most evident in Mangrove Bay) increased pH to levels promoting carbonate precipitation. Higher decomposition rates in Mangrove Bay are attributed to restricted water circulation, a richer benthic community, and geomorphology conducive to greater input and retention of mangrove- and macroalgae-derived detritus. At both sites, the lack of a clear zonational sequence of porewater solutes, discrepancies between depth profiles of solutes and solid-phase elements, and high core-to-core variation in conservative element concentrations and in rates of bacterial activity, suggest non-steady state diagenesis. Non-steady state conditions may be fostered by a combination of factors, such as physical disturbances, temporal changes in rates and quality of organic sedimentation, and tidal advection.