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Oil in the Jarvis structure underlying the main Upper Jurassic reservoir at the Ettrick oilfield (Outer Moray Firth, UK northern North Sea) is present in Upper Permian (Zechstein) carbonates. The origin of this "Jarvis oil" is investigated in this paper using a multidisciplinary approach based on data from well‐logs and cores from wells 20/02‐2 and 20/02‐3. Reservoirs at the Jarvis structure consist of carbonates in the upper part of the Halibut Carbonate Formation (Ca2) and in the Carbonate Member of the Turbot Anhydrite Formation (Ca3). These carbonates are typical Zechstein dolomites composed of a range of facies from mudpackstones with storm beds deposited at moderate water depths to shoreface bioclastic‐oolitic packstones to shallow‐subtidal and intertidal microbial laminites. Interbedded anhydrites replace sabkha and lagoonal selenitic gypsum. Several shallowing‐upward units are recognised. Molecular analysis of the Jarvis oil, and comparisons with biomarker and other geochemical data from extracts of Zechstein cores and published data from different source rocks from the North Sea area, suggest that the oil was generated by marine, OM‐rich shales in the Upper Jurassic Kimmeridge Clay Formation. The oil was generated at peak oil window maturity and is characterised by high Pr/Ph, BNH/H and DBT/P ratios, and abundant C28 steranes and C28+29 monoaromatic and C26R + C27S triaromatic steroids. The molecular composition of organic material in extracts of core samples of Zechstein carbonates from wells in the Jarvis structure differs significantly from that of the Jarvis oil. Biomarkers such as BNH are absent in the core extracts, and there are different distributions and abundances of saturated and aromatic hydrocarbons, likely controlled by thermal maturity. [ABSTRACT FROM AUTHOR]

Abstract Carbonates from the Holkerian (Lower Carboniferous) Concretionary Beds of the Bristol area, the Upper Jurassic-Lower Cretaceous Purbeck Limestone Group of southern England and the Aptian Pre-salt succession of the South Atlantic exhibit spherulites and a range of related crystal shrubs and fibrous crusts. Some of these fabrics are associated with framework microbialites, including thrombolites, that developed under varying degrees of non-marine influence. Brackish or fresh waters affected the Holkerian and Purbeckian microbialites, although the Holkerian also experienced marine conditions. The South Atlantic Pre-salt microbialites were deposited under saline lacustrine conditions. The fabrics are a topic of intense discussion and disagreement over the role (if any) of microbes in spherulite formation. Whilst the case for microbial influences on the Holkerian and Purbeckian spherulites is strong, the alternative influence of Mg-Si gel or Mg-clay (particularly stevensite) is appraised in detail for the Aptian spherulites, including reference to studies of modern microbial analogues. Results of published laboratory experiments concerning such gels and studies on contemporaneous Aptian facies in the same basins lacking Mg-clay, but including spherulites, are considered in an attempt to resolve the abiotic-versus-biotic spherulite origin. That spherulites may be either initiated in suspension or reworked and resedimented provides an added dimension for all three cases. The evidence is strongly in favour of spherulite nuclei being directly created by microbial metabolism but the fibro-radial cortices may be entirely inorganic or passively controlled by microbial extracellular polymeric substances (EPS) which apparently occur as relatively abundant inclusions within the spherulite crystals. The body of evidence suggests that the spherulites and their associated shrubs and crusts are at least partly microbially or biotically influenced. [ABSTRACT FROM AUTHOR]

Biomarker, palaeontological and isotopic evidence suggests that the Late Permian carbonate seas, i.e. the Northern (NPB) and Southern (SPB) Permian basins of northern Pangea, were characterized by significant spatial and temporal variations in the palaeowater-column redox state. This is particularly the case with regard to the deposition of the Lopingian Zechstein cycle 2 carbonate rocks. A shelf to basin reconstruction of environmental conditions was achieved by analysing nearly 400 core samples from 49 wells. This allowed an evaluation of the spatial variations in facies and broad oceanographic conditions at the basin scale. Specifically, in the lower slope and shallow-basin facies of the northern margin of the SPB (present-day northern Poland and eastern Germany), highly variable concentrations of the green sulphur bacterial biomarkers chlorobactane and isorenieratane (and their likely degradation products, C 15 to C 31 2,3,6-aryl isoprenoids, indicative of photic zone euxinia) and homohopane indices (indicative of anoxia), combined with the presence of a benthic fauna and bioturbation, indicate a variable but occasionally anoxic/euxinic water column. Locally in lagoonal facies in the northern and southern margin of the SPB, euxinic conditions also developed but these were likely associated with localised conditions or benthic production in association with microbialites. The presence of gammacerane in the eastern SPB (south-eastern Germany and eastern Poland) suggests elevated salinities there, compatible with the restricted configuration of the basin. However, a lack of these signatures in basinal settings of the eastern SPB indicates that strongly reducing conditions were restricted to the lower slope and shallow-basin locations and restricted lagoons, and were not developed in the basin centre. Moreover, this anoxia/euxinia in marginal settings is restricted to the north-eastern part of the SPB. The south-eastern part of the SPB (SE Poland), in contrast, is devoid of evidence for PZE. The southern margin of the SPB is also characterized by generally oxic-suboxic conditions, with local anoxia limited to more restricted embayments, and elevated salinities limited to restricted oxic-anoxic lagoons. In the western SPB (NE England and adjacent offshore) and the NPB (Outer Moray Firth, offshore Scotland) the water columns were oxic-suboxic. Overall, it appears that high but episodic primary bioproductivity of organic matter was concentrated on (or even limited to) the lower slopes of the SPB's north-eastern margin and the restricted lagoons and shallow basin of its southern margin, leading to the formation of source rocks for petroleum in these areas. In addition, the temporal and geographical restriction of anoxia appears to have prevented the accumulation of large and more widespread quantities of organic matter; in fact TOC contents exhibit a poor correlation with ecological and anoxia indicators. Crucially, this work confirms that the strong evidence for PZE observed in shelf and lower slope/shallow-basin facies of the north-eastern SPB need not be associated with widespread, basin-scale anoxia; this conclusion has implications for organic matter burial, carbon cycling and biotic crises during other times in Earth history. [ABSTRACT FROM AUTHOR]

Crayfish produce small button‐like gastroliths in their stomachs. These curious calcitic objects are increasingly common in lakes and streams in the UK and Europe as the invasive American crayfish increase their domination of freshwater environments. These stomach stones are also present in the geological record. [ABSTRACT FROM AUTHOR]

Deposition of Middle Eocene carbonates in the Sirt Basin in Libya has been the subject of considerable study in recent years because of the importance of sediments of this age as hydrocarbon reservoirs. The Gialo Formation is an important gas-producing reservoir in the Assumood, Sahl and other nearby fields. The gas which is generated from the gas-prone Sirt Shale source rock of the northern Ajdabiya Trough probably migrated in to the Assumood Ridge from the northeast through late Cretaceous, Paleocene and early Eocene carbonates, before being trapped beneath the Augila Shale (Upper Eocene) which is the principal regional seal in the area. This integrated study has enhanced our understanding of reservoir heterogeneity and hydrocarbon potential of the Gialo carbonates and should lead to improved exploration in the future. Reservoir quality in the Gialo Formation is a function of grain types, pore types, grain size, sorting, cementation and compaction, and predicting areas of high reservoir quality has proved difficult; exploration should be oriented to positioning wells into the main trend of the mid-ramp, nummulite accumulation. Different nummulite facies can be reservoirs depending on their diagenetic history. A diagenetic reduction in porosity must be distinguished from a lack of porosity resulting from an unfavourable depositional environment, so that exploration alternatives can be assessed. This integrated study has demonstrated the presence of suitable reservoir rocks, hydrocarbon traps and the close proximity of potential source rocks. These features should encourage further hydrocarbon exploration in the area. [ABSTRACT FROM AUTHOR]

Abstract: Palmarito strata in the mid-Permian of the Venezuelan Andes show three different types of metre-scale cycle: Type A cycles are mixed clastic-carbonate, shallowing-upward peritidal cycles. The upper boundaries of the cycles are exposure surfaces with calcrete. This kind of cycle shows a significant degree of randomness in its thickness pattern and this is attributed to an autocyclic origin through tidal-flat progradation, and variations in carbonate productivity and clastic input to the depositional area. Type B cycles consist entirely of shallow subtidal facies with a shallowing-upward arrangement and an alternation between heterozoan and photozoan assemblages. Type C cycles were deposited in a middle to outer ramp setting and are characterized by a heterozoan assemblage and shallowing-upward trends that includes spiculitic wackestone–packstone passing up into neomorphic bioclastic wackestone or bioclastic crinoidal–bryozoan wackestone–packstone. All cycles are interpreted as 4th–5th order (104 to 105 years duration) and some can be linked to Milankovitch orbital rhythms, notably short eccentricity (~100,000years). Overall, the origin of the Palmarito cycles was a complex combination of autocyclic and allocyclic controls; however, the evidence suggests that cycles in the lower part of the succession were dominated more by autocyclic processes whereas those in the upper part were more the result of allocyclic controls. Climate-driven processes, such as migration of the intertropical convergence one and the waxing and waning of polar ice-caps, had significant effects on deposition of the Palmarito succession and the cycles therein, controlling the clastic sediment supply, nutrient availability and thus carbonate production, and sea-level change, and these factors determined the vertical stacking pattern of the cycles. [Copyright &y& Elsevier]

Abstract: Upper Palaeozoic strata in South America were deposited over cratonic areas and in intracratonic basins (e.g. Solimões, Amazonas, Paraná); however in many areas such as Venezuela and Colombia they are rarely exposed through dense vegetation and the nature of the terrain, so that the strata are poorly documented. However, these strata do have significant implications for the palaeogeography of the time. This article reports on a study of the Permian carbonates of the Palmarito Formation, exposed throughout the Venezuelan Andes, and discusses the succession of palaeoenvironments and the palaeogeography resulting from detailed field and lab work. Deposition took place on an extensive ramp which probably dipped gently northwards towards the open ocean. Much of the Palmarito succession shows a general transgressive trend, with a few thinner, more-regressive intervals, likely a response to glaciation–deglaciation cycles. Towards the end of the Permian in the Venezuelan Andes region, a major sea-level fall led to extensive uplift and erosion, resulting in a major disconformity between the Upper Guadalupian carbonates and overlying Jurassic red beds. The early Palmarito tidal-flat facies are noteworthy for their sub-metre-scale mud-to-sand cycles with incipient palaeosoil fabrics. Overlying mid-outer ramp carbonate facies are characterised by thin storm beds and bioclastic lenses, arranged into metre-scale coarsening-upward cycles. Succeeding shallow-marine inner-mid ramp, bioclastic grain–wacke-stones are dominated by an open-marine fauna of fusulinids, calcareous algae, crinoids, bryozoans and brachiopods. Outer-ramp facies are wacke–mud-stones with sponge spicules, radiolarians and brachiopod fragments. There are similarities between the Permian deposits of Venezuela and those recorded from Guatemala and México to the north, and from Colombia and Perú–Bolivia to the west and southwest, where carbonate systems also dominate. These facies were all part of a tropical foreland basin setting, the Mucuchachi Basin, which contrasts with the other Late Palaeozoic intracratonic basins in South America. Evidence provided here demonstrates that a seaway existed between Laurentia and Gondwana from the Early Permian through to the late Early Permian. [Copyright &y& Elsevier]

The reservoir quality of Middle Eocene carbonates in the intracratonic Sirt Basin is strongly influenced by depositional facies and various diagenetic processes. Based on data from core samples and well logs from five boreholes in the Assumood and Sahl gasfields in the subsurface of the north-central Sirt Basin, six major carbonate facies (and fourteen microfacies) are distinguished in the Middle Eocene Gialo Formation (thickness ∼1100 ft/335 m). Wackestones-packstones dominate the Gialo Formation with abundant grains of larger benthic foraminifera, especially nummulites, in a matrix composed mostly of finely comminuted bioclastic material. Sediments were deposited as a mosaic of facies on a broad carbonate ramp in moderate-energy nummulite-packstone banks, with locally restricted back-bank lagoons and fore-bank areas of foraminiferal debris passing to offshore lime mudstones. Marine diagenesis was minor with micritization of bioclasts and rare vadose marine fibrous cements. Sparry calcite cements are ubiquitous and were precipitated during shallow to moderate burial from seawater and/or meteoric water, the latter largely unaffected by surface-pedogenic processes. This is indicated by the fabrics and pre- and post-compaction precipitation of drusy spar and echinoderm overgrowths, and supported by their bright-to-dull luminescence and low negative δ18O signatures (-2.68 to -4.16%° PDB). Some early neomorphic alteration of calcitic bioclasts is suggested by bright CL and marine to low negative δ18O values (-1.06 to -3.93%° PDB). Bioclastic grains have δ13C values ranging between 0.76 and 1.19%° PDB, interpreted as marine signatures. Similar low positive δ13C values of the cements (0.9 to 1.05 %°) indicate a source of carbonate from dissolution of grains and/or seawater/meteoric water, but without any near-surface/soil effects. Dissolution of grains and matrix, notably originally aragonitic grains but also the originally high-Mg calcite nummulites, was a major porosity-enhancing process, and took place from shallow to moderate burial depths. Fractures may locally have increased porosity too. Shallow-water packstones/rudstones containing both primary intergranular and secondary biomouldic porosity have the best reservoir quality and these are concentrated in the upper parts (top ∼100 ft/30 m) of the wells, with porosity-permeability decreasing downwards. This trend relates to the broad, large-scale facies pattern of more mud-dominated facies giving way upwards to more grainy, nummulite-dominated facies as a result of an overall shallowing of the depositional environment. In addition, the influx of meteoric waters in the upper part of the Gialo platform, before drowning and deposition of the overlying Augila Shale, increased porosity through dissolution. This integrated study has helped in understanding the reservoir heterogeneity and hydrocarbon potential of the Gialo carbonates. [ABSTRACT FROM AUTHOR]

Molar-tooth (MT) structure is an enigmatic sedimentary structure consisting of variously-shaped cracks and voids filled with a characteristically uniform, equant calcite microspar. It is globally distributed but temporally restricted to rocks from Neoarchean to Neoproterozoic age. The origin of MT structures has been debated for more than a century and the topic continues to be highly contentious. Some features of MT structure occurring in micritic limestones of the Mesoproterozoic Gaoyuzhuang Formation (ca. 1500 Ma to ca. 1400 Ma), Jixian section, Tianjin City, North China show that: 1) there is a definite interface or lining, rich in organic material and pyrite, between the MT crack-filling calcite microspar and the micritic host rock, which is also rich in organic matter; 2) the micritic host rocks are notable for the absence of stromatolites and microbial laminites; 3) distinctive conglomeratic lag deposits made up of intraclasts of MT microspar result from storm reworking of the MT structures; 4) the MT structure is associated with possible algal megafossils such as Chuaria; 5) the MT microspar is made up of the larger calcite crystal and the MT crack is marked by the diversity of configurations; 6) both the TOC content and the carbon-isotopic value (δ13CPDB) among the host rock, the MT microspar and the possible algae fossil are obviously different. For the forming mechanism of the Gaoyuzhuang MT structure, these features can still indicate that: A) the MT microspar was formed by rapid precipitation and lithification; B) the MT microspar precipitated directly within the cracks; C) the decomposition of organic matter within the host micrite might be the chief mechanism producing gas bubbles; D) microscale gas-sediment interaction led to the generation of the MT cracks and the precipitation of microspar therein; E) the MT cracks might represent the track of migration and expansion of gas bubbles, and that the recrystallization of host micrites cannot be eliminated during forming process of the MT microspar; F) the MT structure is occurred in early diagenetic period; and G) the formation of MT microspars is a complex diagenetic process. Therefore, model of the microbially-induced gas-bubble expansion and migration is the best interpretation for the formation of the MT structure. Effectively, MT structures are a type of sedimentary structure that is formed in the early diagenetic period and is related to microbial activities and organic matter degradation. [ABSTRACT FROM AUTHOR]

Abstract: The mid-Carboniferous strata of northern England are characterised by mixed clastic–carbonate cycles (Yoredale cyclothems), attributed here to the short eccentricity Milankovitch rhythm. In a typical cycle, transgressive normal-marine shelf carbonates are succeeded by marine shales, then highstand prodelta mudstones and delta front-delta top sandstones with local coals. A detailed study of one cycle, the Great Limestone Cyclothem of the northern Pennines (Alston Block), reveals that within the transgressive carbonates, the beds, averaging 75 cm in thickness and defined by mm-shale partings or cm-mudrock layers, form two thinning-upward to thickening-upward bed-sets. Individual beds and the bed-sets can be correlated across the region. Oxygen isotope and strontium trace element data also reveal patterns of increasing and decreasing values through the limestone, which broadly correspond to the bed-thickness cycles. The beds are interpreted as millennial-scale cycles, the result of high-frequency, arid–humid climatic fluctuations. The bed-sets are interpreted as the response to a longer term arid–humid climate and sea-level cycle, driven by the precession rhythm. It is postulated that millennial-scale climatic changes, which are a well-known feature of the Quaternary and are here inferred for the Carboniferous, were responsible for the deposition of the beds that are a characteristic feature of many marine sedimentary successions in the geological record. The most likely over-riding control is fluctuations in solar output. [Copyright &y& Elsevier]

Two sequences (SFr, SFa), each 1–1.2 Myr in duration, are recognised in the strata across the Frasnian–Famennian (F–F) transition both in carbonate platform and interplatform basinal successions in South China. The sequence boundary between the two sequences is placed a little below the top of the Frasnian. The sequences are basically composed of coarsening-upward/bed-thickness increasing-upward cycles and shallowing-upward cycles (parasequences) in basinal and platform deposits respectively, which stack into cycle-sets (typically six to eight cycles). 10 and 12 cycle-sets are identified in sequences SFr and SFa respectively. These cycle-sets can be further grouped into larger-scale composite cycle-sets (herein termed mesocycle- and megacycle-sets with two and four cycle-sets respectively). This vertical cycle-stacking pattern and the hierarchy of cyclicity suggest a Milankovitch style of forcing such that the cycles and cycle-sets were formed in response to the orbital perturbations of precession (16–18 kyr) and eccentricity (∼100 kyr in duration), respectively. In the basinal cycles, smaller-scale rhythmic stratification beds (typically six to eight beds in a cycle) are extensive, and were likely caused by millennial-scale climatic forcing. In the lower sequence, SFr, the latest highstand deposits consist of calciturbidites and debrites in deep-water strata and fenestral limestones in shallow-water strata, representing a major (third-order) sea-level fall. Within these deposits, four cycle-sets are further identified in both coeval deep-water and platform successions. Succeeding deeper-water organic-rich facies, within which three cycles occur, are the transgressive deposits of the overlying Famennian sequence (SFa). These cycles represent three higher-frequency (16–18 kyr) sea-level fluctuations and accompanying anoxia, superimposed on a major third-order sea-level rise. The F–F boundary is placed at the top of the first cycle, based on conodont data. Thus, a major sea-level fall and then a rise occurred in the F–F transitional period. Faunal and sedimentological data reveal a massive biotic decline in concert with the major sea-level fall, and a further biotic demise coinciding with the major sea-level rise and its three superimposed higher-frequency sea-level fluctuations and accompanying anoxia. The F–F biotic crisis was therefore characterised by two episodes of step-down extinction. On the basis of Milankovitch orbital rhythms, the first major biotic extinction took place over ∼400 kyr, and the subsequent event was ∼50 kyr in duration, i.e. ∼450 kyr for the entire event. At the same time as the massive decline of normal-marine fossils during the latest Frasnian sea-level fall, there was widespread cyanobacterial growth and a thriving of planktonic calcispheres, suggesting eutrophic conditions. This situation could have caused a severe biotic loss, as a result of the deterioration of surface water clarity and formation of anoxic bottom waters due to over-consumption of oxygen through respiratory demands and decomposition by the cyanobacteria and phytoplankton. The subsequent rapid sea-level rise with superimposed higher-frequency sea-level fluctuations and accompanying anoxia could have caused rapid elevation of anoxic bottom waters and expansion of eutrophic surface waters over shallow-water platforms due to enhanced upwelling ocean currents and improved ocean circulation. This situation would have exerted further stresses upon the already-weakened biota, leading to a further biotic demise. However, a small number of organisms such as pelagic tentaculitids, small mud-adapted brachiopods and gastropods did survive into the Famennian, although with very low diversity. [Copyright &y& Elsevier]

ABSTRACT The depositional organization and architecture of the middle–late Devonian Yangdi rimmed carbonate platform margin in the Guilin area of South China were related to oblique, extensional faulting in a strike-slip setting. The platform margin shows two main stages of construction in the late Givetian to Frasnian, with a bioconstructed margin evolving into a sand-shoal system. In the late Givetian, the platform margin was rimmed with microbial buildups composed mainly of cyanobacterial colonies (mostly Renalcis and Epiphyton ). These grew upwards and produced an aggradational (locally slightly retrogradational) architecture with steep foreslope clinoforms. Three depositional sequences (S3–S5) are recognized in the upper Givetian strata, which are dominated by extensive microbialites. Metre-scale depositional cyclicity occurs in most facies associations, except in the platform-margin buildups and upper foreslope facies. In the latest Givetian (at the top of sequence S5), relative platform uplift (± subaerial exposure) and associated rapid basin subsidence (probably a block-tilting effect) caused large-scale platform collapse and slope erosion to give local scalloped embayments along the platform margin and the synchronous demise of microbial buildups. Subsequently, sand shoals and banks composed of ooids and peloids and, a little later, stromatoporoid buildups on the palaeohighs, developed along the platform margin, from which abundant loose sediment was transported downslope to form gravity-flow deposits. Another strong tectonic episode caused further platform collapse in the early Frasnian (at the top of sequence S6), leading to large-scale breccia release and the death of the stromatoporoid buildups. Siliceous facies (banded cherts and siliceous shales) were then deposited extensively in the basin centre as a result of the influx of hydrothermal fluids. The platform-margin sand-shoal/bank system, possibly with gullies on the slope,... [ABSTRACT FROM AUTHOR]

During the early Middle Devonian in South China, an extensive carbonate platform was broken up through extension to create a complex pattern of platforms, and interplatform basins. In Givetian and Frasnian carbonate successions, five depositional facies, including peritidal, restricted shallow subtidal, semi-restricted subtidal, intermediate subtidal and deep subtidal facies, and 18 lithofacies units are recognized from measured sections on three isolated platforms. These deposits are arranged into metre-scale, upward-shallowing peritidal and subtidal cycles. Nine third-order sequences are identified from changes in cycle stacking patterns, vertical facies changes and the stratigraphic distribution of subaerial exposure indicators. These sequences mostly consist of a lower transgressive part and an upper regressive part. Transgressive packages are dominated by thicker-than-average subtidal cycles, and regressive packages by thinner-than-average peritidal cycles. Sequence boundaries are transitional zones composed of stacked, high-frequency, thinner-than-average cycles with upward-increasing intensity of subaerial exposure, rather than individual, laterally traceable surfaces. These sequences can be further grouped into catch-up and keep-up sequence sets from the long-term (second-order) changes in accommodation and vertical facies changes. Catch-up sequences are characterized by relatively thick cycle packages with a high percentage of intermediate to shallow subtidal facies, and even deep subtidal facies locally within some individual sequences, recording long-term accommodation gain. Keep-up sequences are characterized by relatively thin cycle packages with a high percentage of peritidal facies within sequences, recording long-term accommodation loss. Correlation of long-term accommodation changes expressed by Fischer plots reveals that during the late Givetian to early Frasnian increased accommodation loss on platforms coincided with increased accommodation gain in interplatform basins. This suggests that movement on faults resulted in the relative uplift of platforms and subsidence of interplatform basins. In the early Frasnian, extensive siliceous deposits in most interplatform basins and megabreccias at basin margins correspond to exposure disconformities on platforms. [ABSTRACT FROM AUTHOR]

The effect of barium ions on the biomineralization of calcium and magnesium ions is often overlooked when utilizing microbial-induced carbonate precipitation technology for removing barium, calcium, and magnesium ions from oilfield wastewater. In this study, Bacillus licheniformis was used to bio-precipitate calcium, magnesium, and barium ions. The effects of barium ions on the physiological and biochemical characteristics of bacteria, as well as the components of extracellular polymers and mineral characteristics, were also studied in systems containing coexisting barium, calcium, and magnesium ions. The results show that the increasing concentrations of barium ions decreased pH, carbonic anhydrase activity, and concentrations of bicarbonate and carbonate ions, while it increased the contents of humic acids, proteins, polysaccharides, and DNA in extracellular polymers in the systems containing all three types of ions. With increasing concentrations of barium ions, the content of magnesium within magnesium-rich calcite and the size of minerals precipitated decreased, while the full width at half maximum of magnesium-rich calcite, the content of O-C=O and N–C=O, and the diversity of protein secondary structures in the minerals increased in systems containing all three coexisting ions. Barium ions does inhibit the precipitation of calcium and magnesium ions, but the immobilized bacteria can mitigate the inhibitory effect. The precipitation ratios of calcium, magnesium, and barium ions reached 81–94%, 68–82%, and 90–97%. This research provides insights into the formation of barium-enriched carbonate minerals and offers improvements for treating oilfield wastewater. [ABSTRACT FROM AUTHOR]

The diagenesis of carbonate platform sediments is controlled by the original facies and mineralogy, climate, sea-level changes and burial history; these controls are clearly seen in the diagenesis of the Urgonian platform carbonates of SE France. Early diagenesis in the Urgonian platform included the precipitation of marine cements, dissolution of rudist shells and minor karstification Diagenetic features produced during this phase were controlled by several falls in relative sea-level during the Barremian to mid-Aptian punctuating platform sedimentation, the original mineralogy of the sediment and the prevailing semi-arid/arid climate in the region at this time. Following a relative sea-level rise and further sedimentation, progressive burial of the platform led to minor compaction, followed by precipitation of coarse, equant, zoned to non-luminescent, calcite cement. This cement was cut by later stylolites, suggesting a relatively shallow-burial origin. Stable isotope (mean values - 7.94‰ δ[SUP18]O and 0.36‰ δ[SUP13]C) and trace element (mean values of Fe 334 ppm, Mn 92 ppm and Sr 213 ppm) data suggest that these cements precipitated from meteoric fluids at temperatures slightly elevated relative to depositional temperatures. A variable thickness of replacive dolomite which occurs preferentially within the shelf-margin facies of the lower part of the Urgonian post-dates mechanical fracturing and chemical compaction, but pre-dates the main phase of stylolitization. It is probable that the dolomitizing fluid was sourced by the early compactiondriven release of connote fluids held within the underlying muddy units. The burial history of these rocks suggests that calcite cementation and dolomitization took place at relatively shallow burial depths (1-1.5 km). The overall diagenetic history of the Urgonian Limestone Formation is a reflection of the pre-conditioning of the platform limestones by climate, sea level, tectonics and... [ABSTRACT FROM AUTHOR]

The Upper Triassic in South Wales is composed of up to 100 m of red, dolomitic mudstones of the Mercia Mudstone Group which overlie and are laterally equivalent to basin margin coarse clastic deposits. In the Sully island and Dines Powys areas, a series of carbonate deposits was laid down within small basins adjacent to the main Bristol Channel Basin. The rocks consist of dolomites containing replaced evaporites, overlain by perilittoral freshwater limestones. The limestones are fenestral intrasparites and contain abundant pedogenic and stromatolitic horizons, as well as locally developed travertines. Evidence for vadose diagenesis within the limestones is common. The travertines consist of sheets of fibrous calcite (flowstone) associated with pisoids and floe calcite. Most of the travertines consist of single sheets several millimetres in thickness although 'mounds' up to 1 m in height and 5 m in diameter are also present. The topmost metre of the limestones, which has been dolomitized, is deformed into tepee and megapolygonal structures. The carbon and oxygen stable isotopic composition of the limestones suggests that they were precipitated in low salinity waters. Successive samples from individual bands of flowstone show a covariance of δ[SUP18]O and δ[SUP13]C which is consistent with the mixing of resurgent groundwaters with pools of more evolved waters at the surface. The sedimentological and geochemical evidence suggests that the limestones were deposited in a small, enclosed basin fed by upwelling meteoric groundwaters in an environment distinct from that in which the laterally equivalent gypsiferous red mudstones were formed. [ABSTRACT FROM AUTHOR]

Two oolites in the Dinantian (Mississippian⁄Lower Carboniferous) of Glamorgan, SW Britain, were deposited in similar depositional environments but have contrasting diagenetic histories. The Brofiscin and Gully Oolites occur in the upper parts of shallowing-upward sequences, formed through strandplain progradation and sand shoal and barrier growth upon a southward-dipping carbonate ramp. The Brofiscin Oolite is characterized by a first-generation cement of equant calcite spar, preferentially located at grain-contracts and forming non-isopachous fringes around grains, interpreted as meteoric vadose and phreatic in origin. Isopachous fibrous calcite fringes of marine origin are rather rare and occur only at a few horizons. Burial compaction was not important and porosity was occluded by poikilotopic calcite spar. Fitted grain-grain contacts locally occur and could be the results of near-surface vadose dissolution compaction. Syntaxial overgrowth on echinoderm debris are common. Pre-compaction overgrowths are cloudy (inclusion-rich) and probably of meteoric origin, and post-compaction overgrowths are inclusion free. By contrast, the Gully Oolite has little first-generation cement. However, marine fibrous calcite is common in oolitic intraclasts, as isopachous fringes of acicular calcite crystals closely associated with peloidal internal sediment; and early equant, drusy calcite spar occurs in the uppermost part of the Gully, beneath a prominent palaeokarst where pedogenic cements also occur. The major feature of Gully diagenesis is burial compaction, resulting in extensive grain-grain dissolution and microstylolitic grain contacts, and post-compaction poikilotopic spar occluded remaining porosity. The Brofiscin Oolite is pervasively dolomitized up-dip but the Gully Oolite for the most part only contains scattered pre-compaction dolomite rhombs and late veins of baroque dolomite, with less pervasive dolomitization. The difference in diagenetic style if the two... [ABSTRACT FROM AUTHOR]

Reports on the occurrence of a variety of ooid types within the Siyeh and Snowslip Formations of the mid-Proterozoic Belt Supergroup, Montana. Composition of the cortical layers; Replacement of the aragonitic cortical layers by calcite spar which contains the relics of the original cortical structure; Suggestion of a high magnesium content of the calcitic cortical layers by probable microdolomite inclusions.

Devonian limestone turbidites from North Cornwall, composed mainly of crinoidal debris, are considered to have been derived from an oceanic rise or schwelle. Large-scale cross-bedding (representing division C) occurs in some limestone bands. The turbidites lack a pelitic division and there is usually a sharp contact with the shales above. Typical flutes are rare but broad grooves and channels are present on the soles. [ABSTRACT FROM AUTHOR]

Extensive carbonate crusts discovered forming on the slopes of seamounts in many parts of the world's oceans are providing extra stability to the volcanic edifices. These crusts are hardgrounds composed of mixtures of volcaniclastic debris and bioclastic material, in most cases cemented by calcite, in the form of isopachous coatings around grains and pore-filling spar. Such crusts, which have been collected by a remotely-operated vehicle (ROV), are described here from moderate-depth to deeper-water slopes (180–820 m) around the volcanic island of Montserrat in the Caribbean, and from the nearby Kick'em Jenny submarine volcano off Grenada. Radiogenic 87Sr/86Sr isotope ratios from the carbonates give an indication of age (up to 0.4 Ma years old) but they also demonstrate that some samples have been altered by hydrothermal-volcanic processes, to give ages much older than expected (14 to 18 Ma) based on the foraminifera present. Such alteration is also supported by carbon and oxygen isotope (δ13C and δ18O) ratios, although most samples retain typical marine values. In many cases δ18O is usually a little more positive than expected from modern Caribbean shallow-water carbonates, likely reflecting cooler water at their moderate depths of lithification. Just one sample, from Kick'em Jenny, has very negative δ13C (−42‰) indicating methanogenesis. Crusts are also reported here from the Mediterranean Sea, with an example described from Kolumbo submarine volcano, northeast of the Santorini volcanic complex in the Hellenic subduction zone, that are similar in many respects to those from the Caribbean. Typically, the biota of the crusts consists of calcareous red algae (commonly encrusting volcanic clasts), foraminifera (benthic, some also encrusting, and planktic), subordinate serpulids, bivalves, pteropods and heteropods, and rare deeper-water corals. Some bioclasts are derived from shallower water, others from the moderate depths of the slope itself, and planktic fallout. In addition, there is evidence for the former presence of microbes from the occurrence of calcified filaments and peloids in intragranular cavities. Several generations of sponge borings are usually present as well as calcite cement. Dissolution and calcite replacement of aragonitic bioclasts and cement, and sponge spicules (originally opaline silica), have taken place. The carbonate crusts are attributed to seawater circulating within the surficial sediment, in some cases mixing with hydrothermal fluid driven by geothermal and volcanic processes. Submarine volcanic slopes clearly provide a location for moderate-depth carbonate production and cementation, but a further significance of these hardgrounds is in stabilising seamounts, enabling their slopes to avoid frequent collapse, dissection and readjustment. However, when failure does occur, larger-scale submarine landslides involving coherent slabs are more likely. • Carbonate crusts have been recovered on the slopes of volcanic islands using remotely operated vehicles • Crusts consist of mixtures of volcaniclastic and biogenic fragments cemented together by calcite in various forms • Crusts are attributed to seawater circulating within the surficial sediment, in some cases mixing with hydrothermal fluids • Crusts provide increased stability of submarine slops by armoring surficial sediments [ABSTRACT FROM AUTHOR]

Microbially induced manganese carbonate precipitation has been utilized for the treatment of wastewater containing manganese. In this study, Virgibacillus dokdonensis was used to remove manganese ions from an environment containing 5% NaCl. The results showed a significant decrease in carbonic anhydrase activity and concentrations of carbonate and bicarbonate ions with increasing manganese ion concentrations. However, the levels of humic acid analogues, polysaccharides, proteins, and DNA in EPS were significantly elevated compared to those in a manganese-free environment. The rhodochrosite exhibited a preferred growth orientation, abundant morphological features, organic elements including nitrogen, phosphorus, and sulfur, diverse protein secondary structures, as well as stable carbon isotopes displaying a stronger negative bias. The presence of manganese ions was found to enhance the levels of chemical bonds O–C=O and N–C=O in rhodochrosite. Additionally, manganese in rhodochrosite exhibited both + 2 and + 3 valence states. Rhodochrosite forms not only on the cell surface but also intracellularly. After being treated with free bacteria for 20 days, the removal efficiency of manganese ions ranged from 88.4 to 93.2%, and reached a remarkable 100% on the 10th day when using bacteria immobilized on activated carbon fiber that had been pre-cultured for three days. The removal efficiency of manganese ions was significantly enhanced under the action of pre-cultured immobilized bacteria compared to non-pre-cultured immobilized bacteria. This study contributes to a comprehensive understanding of the mineralization mechanism of rhodochrosite, thereby providing an economically and environmentally sustainable biological approach for treating wastewater containing manganese. [ABSTRACT FROM AUTHOR]

The discovery of cyanobacteria fossils in microbialite prompts the investigation of carbonate biomineralization using cyanobacteria. However, the impact of coexisting magnesium and iron in microbialite on carbonate biomineralization has been overlooked. Here, Synechocystis sp. PCC 6803 was used to induce calcium carbonate in the presence of coexisting magnesium and ferric ions. The findings demonstrate that cell concentration, pH, carbonic anhydrase activity, and carbonate and bicarbonate concentrations decreased with increasing concentrations of magnesium and calcium ions. Ferric ions yielded a contrasting effect. The levels of deoxyribonucleic acid, protein, polysaccharides, and humic substances in extracellular polymeric substances increased in the presence of separated or coexisting calcium, magnesium, and ferric ions. Magnesium ions inhibited calcium ion precipitation, whereas ferric ions exhibited the opposite effect. Protein secondary structures became more abundant and O-C=O and N-C=O contents increased with increasing ion concentrations by Fourier transform infrared spectroscopy and X-ray photoelectron spectroscopy analyses. Scanning electron microscopy revealed that ferric ions lead to rougher surfaces and incomplete rhombohedral structures of calcite, whereas magnesium ions promoted greater diversity in morphology. Magnesium ions enhanced the incorporation of ferric ions. This work aims to further understand the effect of magnesium and ferric ions on calcium carbonate biomineralization induced by cyanobacteria. [ABSTRACT FROM AUTHOR]

Microbialites can be important oil and gas reservoirs because of their high initial porosity and they may well be source rocks too. However, the formation mechanisms of calcimicrobes in microbialites are still not fully understood, and further research is needed. Herein, microbialites (thrombolites, dendrolites, and oncolites) from the Cambrian successions of Shandong Province, China, are examined for their microbial fabrics and comparisons are made with the results of laboratory biomineralization experiments using the modern cyanobacterium Synechocystis sp. PCC6803 and the halophilic Bacillus licheniformis SRB2. The thrombolites show mosaic, meshed, and spotted textures, each with a different microbial clot morphology, and Epiphyton is the dominant calcimicrobe. Dendrolitic buildups consist of a lower gray core dominated by the chambered Renalcis, and an upper orange part dominated by dendritic Epiphyton, suggesting a transition of the microbial community across the color change, related to an increase in iron content. Oncolites occur in beds up to 10-cm-thick with spherical to ellipsoidal oncoids containing Girvanella developed around a bioclast nucleus. Scanning electron microscopy observations distinguish the calcimicrobes with their rough, peloidal surface morphology from adjacent cement; aggregated spheroidal and or filamentous calcimicrobes can be recognized, the latter with hollow centers in some cases. The results of the laboratory biomineralization experiments show that the two modern microbes can induce the precipitation of carbonate minerals, mostly of calcite. These biominerals are commonly granular and have a complex microscopic structure including spherical and dumbbell shapes. The microbes are commonly encrusted with calcite and after decomposition of the bacteria, hollow mineral crusts are produced; these are the result of the nucleation and growth of nano-minerals on the extracellular polymeric substances (EPS) present around the microbes. The bio-precipitates induced by modern microbes in the laboratory experiments are similar in many respects to the calcimicrobes in the Cambrian microbialites; biomineralization processes clearly play an important role in the formation of carbonate minerals and lithification of microbial mats. [ABSTRACT FROM AUTHOR]

Abstract A key problem of how to distinguish between biotic and abiotic carbonate minerals in nature and/or in the laboratory has confused researchers for some time. Although numerous studies have been performed to explore the formation mechanism and the unique characteristics of biotic minerals, the issue needs to be studied further. Here, biotic calcite precipitation was induced by the microorganism Bacillus cereus MRR2 (GenBank KY810857), while organogenic and inorganogenic calcite was investigated in parallel. The results indicate that carbonic anhydrase (CA, a common enzyme of bacteria) promoted carbon dioxide hydration to release HCO 3 − and CO 3 2− in the process of calcite precipitation; the pH increased from 7.2 to 8.9 as a result of the combination effect of the released ammonia by B. cereus MRR2 and the HCO 3 − and CO 3 2− ions originating from the CA reaction. Glutamic acid is the most abundant amino acid in the extracellular polymeric substances of the bacteria, and its free carboxyl ions with a large number of negative charges in the alkaline environment facilitated the adsorption of calcium ions. The biotic calcite has a series of unique characteristics different from the organogenic and inorganogenic calcites, such as particular morphologies, P element composition and a variety of organic functional groups. Intracellular amorphous nanospheres without any crystal structure are also recorded. Stable carbon isotope analyses show that the biotic calcite (−20.9‰) has more negative δ13C values than the organogenic calcite (−15.6‰) and inorganogenic calcite (−11.7‰), indicating that microbial activity strongly affected the carbon isotope composition of biotic calcite. More importantly, the crystallinity and activation energy of the biotic calcite are clearly higher than those of organogenic calcite, suggesting that the thermal stability of biotic calcite is much higher. Thus, this study provides important insights into understanding the mechanisms of microbial biomineralization and the processes of biotic calcite formation, especially the roles microbes played in mineral nucleation and growth, as well as the unique characteristics of the resulting minerals. This study may provide useful evidence for further recognizing biotic and abiotic calcite in the geological record. Graphical abstract The model of biotic, organogenic and inorganogenic calcite. Unlabelled Image Highlights • The pH increase is caused by the combination effect of ammonia and CA. • Biotic calcite has higher thermal stability than abiotic calcite. • Biotic calcite has more negative δ13C values than abiotic calcite. • Glutamic acid is the most abundant amino acid in EPS. • The intracellular amorphous nanospheres are found. [ABSTRACT FROM AUTHOR]

Travertines, which precipitate from high temperature water saturated with calcium carbonate, are generally considered to be dominated by physico-chemical and microbial precipitates. Here, as an additional influence on organomineral formation, metagenomic data and microscopic analyses clearly demonstrate that highly diverse viral, bacterial and archaeal communities occur in the biofilms associated with several modern classic travertine sites in Europe and Asia, along with virus-like particles. Metagenomic analysis reveals that bacteriophages (bacterial viruses) containing icosahedral capsids and belonging to the Siphoviridae, Myoviridae and Podoviridae families are the most abundant of all viral strains, although the bacteriophage distribution does vary across the sampling sites. Icosahedral shapes of capsids are also the most frequently observed under the microscope, occurring as non-mineralized through to mineralized viruses and virus-like particles. Viruses are initially mineralized by Ca-Si amorphous precipitates with subordinate Mg and Al contents; these then alter to nanospheroids composed of Ca carbonate with minor silicate 80–300 nm in diameter. Understanding the roles of bacteriophages in modern carbonate-saturated settings and related organomineralization processes is critical for their broader inclusion in the geological record and ecosystem models. [ABSTRACT FROM AUTHOR]

Biomineralization has become a research focus in wastewater treatment due to its much lower costs compared to traditional methods. However, the low sodium chloride (NaCl)-tolerance of bacteria limits applications to only water with low NaCl concentrations. Here, calcium ions in hypersaline wastewater (10% NaCl) were precipitated by free and immobilized Halovibrio mesolongii HMY2 bacteria and the differences between them were determined. The results show that calcium ions can be transformed into several types of calcium carbonate with a range of morphologies, abundant organic functional groups (C-H, C-O-C, C=O, etc), protein secondary structures (β-sheet, α-helix, 3 10 helix, and β-turn), P=O and S-H indicated by P2p and S2p, and more negative δ13C PDB (‰) values (-16.8‰ to -18.4‰). The optimal conditions for the immobilized bacteria were determined by doing experiments with six factors and five levels and using response surface method. Under the action of two groups of immobilized bacteria prepared under the optimal conditions, by the 10th day, Ca2+ ion precipitation ratios had increased to 79%-89% and 80%-88% with changes in magnesium ion cencentrations. Magnesium ions can significantly inhibit the calcium ion precipitation, and this inhibitory effect can be decreased under the action of immobilized bacteria. Minerals induced by immobilized bacteria always aggregated together, had higher contents of Mg, P, and S, lower stable carbon isotope values and less well-developed protein secondary structures. This study demonstrates an economic and eco-friendly method for recycling calcium ions in hypersaline wastewater, providing an easy step in the process of desalination. [ABSTRACT FROM AUTHOR]

Microbially-induced calcium carbonate precipitation (MICP) has been studied extensively. However, the effect of different sources of magnesium ions on calcium carbonate biomineralization has rarely been examined. In this study, Lysinibacillus xylanilyticus DB1-12 bacteria isolated from petroleum samples were used to biomineralize calcium ions under the action of different sources of magnesium (magnesium chloride and magnesium sulfate). The results show that calcium ion precipitation ratios were much higher in MgSO4 group experiments than in the MgCl2 group (p < 0.01). The mineral phases in the MgCl2 group experiments were the same as those in MgSO4 group at each Mg/Ca ratio. Minerals with a 'twisted' shape were much more common in the MgSO4 group; the protein secondary structures hidden in minerals were much more abundant in the MgCl2 group, and the activation energy of biotic monohydrocalcite at a Mg/Ca ratio of 11 was also much higher in the MgCl2 group than in the MgSO4 group. The main reasons for these differences are closely related to the lower magnesium content and the more common protein secondary structures in the monohydrocalcite in the MgCl2 group. The shift of Mg1s XPS spectra suggests that the chemical interactions occurring on the monohydrocalcite surfaces in the MgCl2 group were different from those in the MgSO4 group. The δ13CPDB values of the biominerals in the MgSO4 group are in the range of −16.93 to −18.87‰, lower than those in the MgCl2 group (-15.77 to −18.69‰). The morphology of L. xylanilyticus DB1-12 became deformed and some rod-shaped protrusions developed on the cell surface during the process of biomineralization. This study not only contributes to the understanding of biomineralization mechanisms generally, but is also helpful in the interpretations of paleo-environmental conditions. [ABSTRACT FROM AUTHOR]

Ca2+, Mg2+, and Sr2+ are elements with similar ionic and hydrochemical characteristics, yet the microbial mineralization behavior in their coexisting environments is seldomly explored. In this study, the cyanobacterium Synechocystis sp. PCC6803 was used to induce the precipitation of minerals in mediums with various Mg/Ca and Sr/Ca ratios (Ca2+ = 0.01 M). The medium hydrochemistry, including cell density, solution pH, and alkalinity, was recorded periodically. The bio-precipitates were characterized with X-ray diffraction (XRD), scanning and transmission electron microscopy (SEM and TEM), Fourier Translation Infrared spectroscopy (FT-IR), and Thermal Gravimetric Analyzer (TGA). The results show the growth of Synechocystis sp. PCC6803 was inhibited by increasing ionic strength, although the final alkalinity and pH values of the medium were not affected. Two crystalline minerals, calcite (CaCO3) and strontianite (SrCO3) were precipitated in the mediums with low ionic strength; these were transformed from early amorphous precipitates by a dissolution and re-precipitation mechanism. The morphology of the precipitated cyanobacterial strontianite changed from columnar to dumbbell shape and finally into a spherulite shape. High concentrations of Sr2+, like Mg2+, prolonged the stabilization of amorphous carbonate precipitates. The acidic amino acids (Glu and Asp) in the EPS of Synechocystis sp. PCC6803 cultured in mediums with high Sr2+ and high Mg2+ concentrations increased significantly, compared to those cultured in a medium with no Sr2+ or Mg2+ (p < 0.005) ions. The negative binding energy calculated by Density Functional Theory (DFT) on the binding between the two acidic amino acids (Glu and Asp) and ion-H2O complexes (Ca[H2O]62+, Mg[H2O]62+, and Sr[H2O]62+), indicating that they are all thermodynamically-favored processes. Consequently, lower energy was needed in their subsequent precipitation and nucleation within the EPS of Synechocystis sp. PCC6803. This inferred process was also supported by the appearance of amorphous particles in the EPS of Synechocystis sp. PCC6803. [ABSTRACT FROM AUTHOR]

Hypersaline wastewater has been widely used in industrial processes in some countries short of freshwater, but calcium ions in such wastewater should be removed due to the danger of limescale being produced. In this study, calcium ions in hypersaline (sodium chloride: 5%) wastewater was biomineralized into different carbonate minerals under the action of free and immobilized Virgibacillus dokdonensis WLR1 bacteria. The results show that the calcium ion precipitation rate was much higher under the conditions of immobilized bacteria (p<0.01), and that there was a significant difference in the mineral phases, the diversity of protein secondary structures and morphologies, and chemical characteristics of the mineral surfaces between the free and the immobilized bacteria based on XRD, FTIR, SEM-EDS, and XPS analyses. TG, DTG, and DSC results show that with increasing calcium ion concentrations, the thermal stability of calcium carbonate under the conditions of free bacteria decreased due to the decline in crystallinity. The stable carbon isotope values (d13CPDB) of calcium carbonate formed by free bacteria changed from -16.80‰ to -18.17‰; the much more negative d13CPDB values suggest that the calcium carbonate minerals are biotic. From ultrathin slices analyzed by HRTEM-mapping-SAED, it was observed that calcite is formed inside the cell, thus also facilitating calcium ion removal. Research concerning intracellular calcite has rarely been reported. This study helps to further understand the mechanisms of biomineralization, and also provides an environmentally friendly method to remove calcium ions from hypersaline wastewater. [ABSTRACT FROM AUTHOR]

The study evaluates pore systems in samples of tight Upper Permian Zechstein 2 Carbonate (Z2C) facies from widely dispersed locations in the eastern and western parts of the Southern Permian Basin, NW Europe. Samples of Z2C drill cores comprising platform to shallow-basin deposits were examined by petrographic techniques, porosity measurement and SEM analysis, in order to acquire a better understanding of porosity development and pore microstructure. Four carbonate lithofacies were identified by core-scale and thin-section analyses: subtidal / intertidal planar stromatolites and thrombolites; slope facies (laminated dolo- and lime-mudstones and grain-dominated turbidites); toe-of-slope / lower slope facies (laminated lime mudstones with turbidite beds); and shallow-basin (embayment) facies (laminated lime mudstones and hemipelagic deposits). Porosity ranges from 0.08% to 9.6% and is lowest in the subtidal / intertidal planar and columnar stromatolites. The highest porosities, in the slope and shallow-basin (embayment) lithofacies, probably resulted from catagenetic processes and microbial activity. High porosity in subtidal thrombolites is related to the original pore network. SEM analyses showed that pores are present within organic matter, pyrite framboids and microfossils, and between crystals. Subtidal / intertidal planar and columnar stromatolites and thrombolites have a high proportion of nanopores, probably resulting from microbial activity. Although porosity development is a combined function of the presence of organic matter and mineral components, together with sediment fabric and fractures, it is mostly a result of the early diagenetic transformation of mineral phases, microbial activity, and evaporite and carbonate dissolution. [ABSTRACT FROM AUTHOR]

The sequence development and evolution of latest Devonian–earliest Carboniferous Fairfield Group in the Canning Basin have been established through integration of detailed sedimentological analysis of core, petrophysical data, existing biostratigraphic data and new seismic interpretations. The Fairfield Group on the Lennard Shelf was deposited on a mixed carbonate–siliciclastic distally-steepened ramp with a broad inner ramp, narrow mid ramp and steepened outer ramp. The majority of facies associations (FA1–FA8) were formed in intertidal–shallow subtidal conditions in proximal to distal inner ramp including siliciclastic tidal flats (FA1), carbonate intertidal flats (FA2), tidal flats and channels (FA3), lagoons (FA4–FA5), and shallow subtidal (FA6), backshoal (FA7) and fore-shoal areas (FA8). Bioclastic muddy sandstone (FA9) and bioclastic mudstone (FA10) are the dominant mid-ramp facies. Recognition of turbiditic facies of middle to lower slope of the outer ramp (FA11–FA13) led to the identification of a distally-steepened ramp. Antecedent topography exerted a significant control on platform morphology and the development of the widespread inner-ramp facies on the Lennard Shelf. A sequence-stratigraphic analysis reveals that the Fairfield Group ramp deposits consists of four third-order sequences (S1–S4) that were largely deposited during sea-level highstands (HST) characterized by progradational trends and dominant shallow subtidal inner-ramp facies associations. Transgressive systems tracts (TST) are well developed in S1 and S3 and have a retrogradational facies pattern with dominant deep subtidal mid-outer ramp facies associations. Lowstand systems tracts, characterized by lowstand wedges and turbiditic facies, are identified in the lower parts of S2 and S3. Coarse and fine-grained siliciclastic facies are mixed with carbonate facies as a result of coeval deposition on the inner and mid ramp, and reciprocal deposition on the outer ramp. A temporal variation in the types of carbonate grains and the amount of siliciclastic facies, from the mixed peloidal-skeletal carbonate–siliciclastic ramp in S1 and S2, to the mixed skeletal carbonate–siliciclastic ramp in S3 and a siliciclastic-dominated ramp in S4, is interpreted as the change from a greenhouse to an icehouse state. [ABSTRACT FROM AUTHOR]

The shale-gas potential of mid-Carboniferous mudrocks in the Bowland-Hodder unit in the Cleveland Basin (Yorkshire, northern England) was investigated through the analysis of a cored section from the uppermost part of the unit in the Malton-4 well using a multidisciplinary approach. Black shales are interbedded with bioturbated and bedded sandstones, representing basinal-offshore to prodelta - delta-front lithofacies. The total organic carbon (TOC) content of the shales ranges from 0.37 to 2.45 wt %. Rock-Eval pyrolysis data indicate that the organic matter is mainly composed of Type III kerogen with an admixture of Type II kerogen. Tmax (436-454°C), 20S/(20S+20R) C29 sterane ratios, and vitrinite reflectance values indicate that organic matter is in the mid- to late- mature (oil) stage with respect to hydrocarbon generation. Sedimentological and geochemical redox proxies suggest that the black shales were deposited in periodically oxic-dysoxic and anoxic bottom waters with episodic oxic conditions, explaining the relatively low TOC values. The Rock-Eval parameters indicate that the analysed mudrocks have a limited shale-gas potential. However, burial and thermal history modelling, and VRr data from other wells in the region, indicate that where they are more deeply-buried, the Bowland-Hodder shales will be within the gas window with VRr > 1.1 % at depths in excess of 2000 m. Therefore although no direct evidence for a high shale-gas potential in the Cleveland Basin has been found, this cannot be precluded at greater depths especially if deeper horizons are more organic rich. [ABSTRACT FROM AUTHOR]

Remnants of some of the planet's most ancient life forms, stromatolites in the late Mesoproterozoic sea of the Chattisgarh Basin, India, preserve a conspicuous sinuous pattern. They occur as successive biostromes, 10–30 cm thick, separated by 2–5-cm-thick marly layers and discrete bioherms up to several metres thick and 20 m across. Stromatolite columns in the Chandi Formation are 5–10 cm high, sinuous, inclined and straight, with both branched and non-branched types. These stromatolites are composed of calcite micrite and show well defined light and dark laminae with evidence of erosion between lamina sets. The column sinuosity probably originated as a response to changes in direction and strength of currents. Successive flat beds of stromatolite (biostromes), separated by marl/clay horizons, impart a rhythmic pattern to the succession. The Chandi sinuous stromatolite columns resemble those occurring in China, North America and Siberia, of a comparable age, suggesting that similar marine conditions of stromatolite formation might have been operating in the late Mesoproterozoic seas worldwide. However, the petrographic and sedimentological analyses of these stromatolites indicate their development through in situ production of carbonate with some trapping and binding of detrital sediment. As a result of the presence of terrigenous material within the stromatolites, whole-rock geochemical analyses for trace elements and rare earth elements cannot be used for interpretation of seawater chemistry and the redox conditions at the time. [ABSTRACT FROM AUTHOR]

A modern lithifying biofilm, associated with fluvial calcareous tufa in southern Italy, is composed of a complex community of micro‐organisms including autotrophic and heterotrophic bacteria, together with likely viruses (bacteriophages) and bacterial vesicles. Produced by most of the bacterial forms, extracellular polymeric substances are widespread and are the main sites of mineral precipitation, rather than the microbial cells themselves, but viruses and vesicles also appear to be mineralized. Neoformed biominerals replace these organic substrates starting with an amorphous phase rich in Ca, Si and several other cations followed by two different types of proto‐crystal: a granular−irregular Ca‐rich type and a lamellar/fibrous Si‐Al‐Mg‐rich type. Their growth leads to the formation of Ca‐carbonate and Mg‐silicate crystals that preserve their initial different habits. The coeval precipitation of silicate and carbonate at the initial stage of bio‐mediated mineral formation is a process common within freshwater and saline to hypersaline‐water calcareous microbialites. This is most probably related to the initial formation of poorly‐crystallized Mg‐Si phases that precipitate within the extracellular polymeric substances, related to the rise of pH in the zone of active oxygenic photosynthesis, and the mineralization of viruses, associated with the successive nucleation of Ca‐carbonate in close proximity to bacterial degradation of organic matter. [ABSTRACT FROM AUTHOR]

This study investigates the co-precipitation of calcium and barium ions in hypersaline wastewater under the action of Bacillus licheniformis using microbially induced carbonate precipitation (MICP) technology, as well as the bactericidal properties of the biomineralized product vaterite. The changes in carbonic anhydrase activity, pH, carbonate and bicarbonate concentrations in different biomineralization systems were negatively correlated with variations in metal ion concentrations, while the changes in polysaccharides and protein contents in bacterial extracellular polymers were positively correlated with variations in barium concentrations. In the mixed calcium and barium systems, the harvested minerals were vaterite containing barium. The increasing concentrations of calcium promoted the incorporation and adsorption of barium onto vaterite. The presence of barium significantly increased the contents of O-C O, N-C O, and Ba-O in vaterite. Calcium promoted barium precipitation, but barium inhibited calcium precipitation. After being treated by immobilized bacteria, the concentrations of calcium and barium ions decreased from 400 and 274 to 1.72 and 0 mg/L (GB/T15454–2009 and GB8978–1996). Intracellular minerals were also vaterite containing barium. Extracellular vaterite exhibited bactericidal properties. This research presents a promising technique for simultaneously removing and recycling hazardous heavy metals and calcium in hypersaline wastewater. [Display omitted] • Probiotic B. licheniformis simultaneously removed Ba2+ and Ca2+ in hypersaline fluid. • Ca2+ promoted Ba2+ precipitation, but Ba2+ inhibited Ca2+ precipitation. • Hydrochemical index and EPS components changed greatly in Ba2+-Ca2+ fluid. • Intracelluar vaterite containing Ba was also beneficial to the Ba2+ and Ca2+ removal. • Ba-vaterite exhibited bactericidal activity against E.coli. [ABSTRACT FROM AUTHOR]

Manganese (Mn) is a common trace element in dolomite, yet its precise role in dolomite precipitation, if any, has not been explored. This study aims to investigate carbonate mineral formation in the presence of extracellular polymeric substances produced by Bacillus licheniformis Y 1 in 14 cross-over experiments within the MgCl 2 -CaCl 2 -MnCl 2 system. The study involved the analysis and comparison of water chemistry, mineralogy and bacterial metabolites. The findings indicate that B. licheniformis Y 1 induces the formation of Mg-free calcite and low-Mg calcite in Mn-free solutions (Mg/Ca < 2). The addition of 0.001 mol/L Mn2+ results in the precipitation of Mg-rich calcite. In the presence of a relatively high Mg2+ content in the solution (Mg/Ca > 6), B. licheniformis Y 1 in a Mn-free solution induces the formation of aragonite and dypingite, whereas the addition of 0.001 mol/L Mn2+ leads to the formation of Mn-bearing dolomite in the precipitate. Notably, at Mg/Ca = 6, an increase in Mn2+ content of the fluid to 0.002 and 0.003 mol/L yields Mn-rich dolomite. The Mn-bearing dolomite exhibits a regular spherical aggregate morphology with diameters ranging from 15 to 60 μm. The 2θ position of the (104) crystal face is close to that of dolomite, and the thermal decomposition temperature is lower than that of calcite. XPS results show that Mn O bonds exist on the mineral surface. Acidic amino acids such as glutamic acid as well as humic acid in EPS, especially fulvic acid analogues, actually rise with increasing Mn2+ concentration and contain a large number of functional groups including carboxyl groups. Molecular dynamics simulations show that fulvic acid can effectively promote the dehydration of Mg-water complexes, thus promoting the formation of dolomite. These experiments indicate that the presence of Mn ions in the solution, along with bacteria and EPS, promote the precipitation of protodolomite. [Display omitted] [ABSTRACT FROM AUTHOR]

The assembly process of Organic Matter (OM) from single molecules to polymers and the formation process of Ca– CO 3 ion-pairs are explored at the micro-scale, and then the relationship between OM and carbonate based on the results of microbially-induced carbonate precipitation (MICP) laboratory experiments is established at the macro-scale. Molecular dynamics (MD) is used to model the assembly of OM (a) in an aqueous solution, (b) on surfaces of calcite (10 1 ‾ 4) crystals and (c) on defective calcite (10 1 ‾ 4) crystal surfaces. From the MICP experiments, carbonate minerals containing abundant OM were precipitated and were characterized by Scanning Electron Microscopy (SEM), X-Ray Diffractometry (XRD) and Fourier Transform Infrared Spectroscopy (FTIR). The results of the MD show that OM is assembled into polymers in all three simulation systems. Although the Ca–CO 3 ion-pairs and OM were briefly combined, the aggregation assembly of OM molecules and the precipitation of carbonate calcium are not related in the long run. The highly specific surface area of the defective calcite shows an increase in the adsorption of OM. The van der Waals forces, which are primarily responsible for controlling the assembly of OM molecules, increase with the degree of aggregation. According to the MICP experiments, OM is enriched on the mineral surfaces, and more OM is found at the steps of defective crystals with their larger surface areas. Through MD and MICP laboratory experiments, this work systematically describes the interaction of OM and carbonate minerals from the micro to the macro scales, and this provides insight into the interaction between OM and carbonates and biogeochemical processes related to the accumulation of OM in sediments. • The interaction between organic matter and carbonate during sedimentation is examined from the micro to macro scale • The assembly of OM and the formation of Ca–CO 3 ion pairs in an aqueous solution are transitory • The adsorption of organic matter is increased by surface defects in the calcite [ABSTRACT FROM AUTHOR]

Microalgae are one of the important sources of organic matter which, if preserved well in sediments, can generate hydrocarbons during burial diagenesis. However, the preservation mode of microalgal organic matter within product aggregates induced by marine microalgae has rarely been examined. Herein, a strain of eukaryotic marine microalgae, Chlorella sp. MASCC-0008, was used to conduct biomineralization experiments in an f/2 medium with a 0.02 mol/L Ca2+ ion concentration and various Mg2+ ion concentrations of 0.05, 0.06, 0.07 and 0.10 mol/L. It was found that the soluble organic matter of the microalgae contains amino acids and fulvic acids which can attract and absorb cations. With an increase in Mg2+ ion concentration in the experimental group with Chlorella sp., the aragonite content of the mineral precipitates increased whereas the calcite content decreased. In contrast, calcite was the sole mineral precipitated in the control experiments with no Chlorella sp.. Due to the porous structure of minerals, their organic matters were preferred to be preserved in aragonite aggregates compared to calcite aggregates. The TOC content of the minerals aggregates is the highest (0.45%) and the hydrocarbon generation potential (S 1 + S 2) of organic matter is the greatest (3.66 mg/g) in those precipitated in the medium with a Mg2+ ion concentration of 0.10 mol/L. Microalgal organic matter has significant hydrocarbon generation potential due to its effective preservation in the product aggregates formed by the microalgal biomineralization. Squalene is the most abundant alkene detected in the pyrolytic products. These results suggest that microalgae can induce precipitation of carbonate minerals, a process that facilitates the sequestration of organic matter within the product aggregates precipitated, thus potentially preserving this microalgal organic matter into the burial diagenetic realm where, if conditions are appropriate, hydrocarbons may be developed. [ABSTRACT FROM AUTHOR]

Abstract: Three sites of actively-forming tufa, two barrage systems and one terraced slope system, located in northern Calabria (Italy) and in north-east England, have been investigated with the purpose of studying the neo-formed carbonate minerals at the interface with the organic components that compose the associated biofilms. Several depositional facies are distinguished, notably peloidal to aphanitic, laminar and dendrolitic fabrics composed of micrite and microsparite, and isolated botryoids and continuous crusts composed of sparite. All fabrics occurring in all depositional facies are organized into layers with a more or less well-developed seasonal cyclicity. Low-Mg calcite precipitates more or less constantly during all seasons within the active depositional zone. This extends for a few hundred microns upon the external surface of the deposits, where the biofilm occurs. The latter is composed of a heterogeneous community of green algae, filamentous cyanobacteria and other types of prokaryotes, Actinobacteria and fungi, with a variable amount of extracellular polymeric substances (EPS). Porous micro-columns (50 to 150μm in size), separated by interstitial spaces, characterize the active depositional zone. Here precipitation always begins with organomineral nanospheres (10 to 20nm diameter), both along the external surfaces and within internal cavities of the micro-columns, by replacing degraded organic matter, and at point-sites suspended within living cyanobacterial tufts along the external surface of their sheaths, indicating that the biological activities of the biofilm are crucial, with its living organisms and non-living organic matter. Organomineral nanospheres successively agglutinate to form irregular to rod-shaped crystal aggregates, 100–200nm in size, that with their further agglutination create two basic types of larger, more ordered, crystal structure: polyhedrons in the range of 1–2μm, and minute triads of calcite fibres varying in length from ~0.4 (short triads) to ~1μm (long triads). Basic crystal structures coalesce to form larger crystals (mainly tetrahedrons tens of microns in size) that constitute the micro-columns. [Copyright &y& Elsevier]

In a multi-scale approach to the study of the organic and mineral components in an active barrage-type tufa system of southern Italy, neo-formed deposits, in both natural depositional sites and on inorganic substrates placed in the stream for this study, were observed and compared through one year of monitoring. Dams and lobes representing the basic morpho-facies of the deposits are composed of two depositional facies: vacuolar tufa (a mixture of phytoclastic and framestone tufa) and stromatolitic tufa (phytoherm boundstone tufa). Three petrographic components comprise both facies: micrite and microsparite, often forming peloidal to aphanitc, laminar and dendrolitic fabrics, and sparite, which occurs as isolated to coalescent fan-shaped crystals forming botryoids or continuous crusts. All fabrics occurring in all depositional facies are organized into layers with a more or less well-developed cyclicity, which has its best expression in stromatolitic lamination. The precipitation of all types of calcite (with Mg 1·0 to 3·2 mole % and Sr 0·5 to 0·8 mole %) takes place more or less constantly during all seasons, in spite of the low saturation state of the water (the saturation index range is 0·75 to 0·89) within the active depositional zone; the latter extends for a few hundred microns through the external surface of the deposit. The active depositional zone has a particular micro-morphology composed of porous micro-columns (50 to 150 μm in size), separated by interstitial channels. Mineral precipitation occurs upon both external surfaces and within internal cavities of the micro-columns, while further point sites of precipitation occur suspended within the masses of cyanobacterial tufts. Sub-spherical mineral units, 'nano-spheres' (10 to 20 nm in diameter) are the basic biotic neo-precipitate; they commonly form by replacing non-living degrading organic matter and at point sites along the external surface of living cyanobacterial sheaths. Nano-spheres agglutinate to form first rod-shaped aggregates (100 to 200 nm) which then evolve into triads of fibres or polyhedral structures. Successively, both triads and polyhedral solids coalesce to form larger calcite crystals (mainly tetrahedrons tens of microns in size) that represent the fundamental bricks for the construction of the micro-columns in the active depositional zone. Precipitation is attributed to the presence of a widespread biofilm that occurs in the active depositional zone; this is composed of a heterogeneous community comprising epilithic and endolithic filamentous cyanobacteria, green algae, unicellular prokaryotes, actinobacteria and fungi, with a variable amount of extracellular polymeric substances. No precipitation takes place where the biofilm is absent, indicating that the biological activities of the biofilm are crucial, with its living organisms and non-living organic matter. Basic aggregates of neo-precipitates do not form in association with any one particular type of organic matter substrate, but appear to be related to the seasonal temperature variation: polyhedral micro-crystals mainly precipitate in the colder season, short triads in the intermediate seasons, and long triads in the warmest conditions. These three basic crystal aggregates have a petrographic counterpart, respectively, in the spar, microspar and micrite. [ABSTRACT FROM AUTHOR]

Even though biomineralization induced by bacteria has been studied for many years, some unsolved problems are still present in the biomineralization, especially the intracellular biomineralization, which should be further explored. In this study, the Bacillus subtilis Daniel-1 strain was identified by 16S rDNA homology, used to induce calcium carbonate biomineralization at various Mg/Ca molar ratios (0, 2, 4, 6, and 8). The results showed that pH still increased at the decline stage in the bacterial growth process, and could increase to about 8.69, resulting from the influence of carbonic anhydrase activity and ammonia. X-ray diffraction (XRD) results showed that calcite, Mg-rich calcite, and aragonite minerals were induced in the extracellular biomineralization process. The diversified morphologies and the presence of fatty acids, protein, and other organic substances in calcium carbonate analyzed by scanning electron microscopy-energy dispersive X-ray spectroscopy (SEM-EDS), Fourier transform infrared spectroscopy (FTIR), and X-ray photoelectron spectroscopy (XPS) proved the biogenesis of these minerals. The stable carbon isotope values (–19.37‰ to −19.79‰) and oxygen isotope values (–6.37‰ to −8.91‰) presented in this study were relatively negative, also confirmed the biogenesis of the minerals. Magnesium carbonate contents in Mg-rich calcite increased from 8.79% to 25.71% with increasing Mg/Ca ratios. Aragonite could be grown not only in cell surface but also inside the cell by analyzing ultrathin slices of bacteria with HRTEM-EDS-SAED. Aragonite in cell surface was elongated whereas intracellular aragonite was granular. To the best of our knowledge, the intracellular biotic crystalline aragonite has rarely been reported. This study is helpful to further understand the mechanism of carbonate mineral biomineralization, and may also provide useful evidence for further studies on intracellular crystal structures. [ABSTRACT FROM AUTHOR]

Spectacularly developed lower Eocene chert in the Corones platform carbonates of the Spanish Pyrenees is concentrated within a restricted, brackish-water, laminated ostracod-rich facies, which also contains abundant sponge spicules. The chert occurs as nodular, bedded and mottled varieties, and four petrographic types of quartz are developed: microquartz; length-fast (LF) chalcedony; megaquartz; and microspheres. δ18O values of chert range from 29·6‰ to 30·9‰ (SMOW), which correspond to a broad isotope rank common for biogenic and diagenetic replacement cherts. Calcian dolomite crystals with high Fe and Na are disseminated within the microquartz and LF-chalcedony, but are absent from the megaquartz and host carbonate. The chert is closely associated with desiccation cracks and with interstratal dewatering structures. Load casts are silicified, and laminae rich in sponge spicules are convoluted. Early cracks related to dewatering are filled by microquartz and quartz cements. Ostracod shells within chert are locally fractured; those in the host carbonate are commonly flattened. Late fractures are filled by LF-chalcedony and megaquartz. There is much evidence for the dissolution of sponge spicules and their calcitization in the carbonate host rock. Silica for the Corones cherts was derived from sponges during early diagenesis and shallow burial. Early mechanical compaction and sediment dewatering played a major role in sponge spicule dissolution, migration of silica-rich fluids and the consequent precipitation of chert. Quartz cements continued to be precipitated into the burial environment. [ABSTRACT FROM AUTHOR]

Although it has been suggested that viruses may induce precipitation of carbonate, the exact mechanisms involved and the roles they might play in the nucleation of carbonates are still unknown. Experimental evidence is reported here demonstrating that bacteriophages are an important factor in calcium carbonate formation. Short-term experiments were designed to induce viral-mediated mineral precipitation at different fluid compositions. The precipitates obtained, analysed with fluorescence and electron microscopes and X-Ray diffraction, and evaluated by statistics, clearly show that bacteriophages strongly affect the process of carbonate precipitation. We demonstrate that as a result of the coalescence of the phages, the carbonate precipitates form large aggregates consisting of spheroids. The spheroids are constructed of angular nanoparticles resembling viral-like particles. In control experiments spheroids were also observed; however, they consist of irregular nanoparticles and additionally they do not form large aggregates. We also demonstrate that bacteriophages strongly influence the mineral composition of the precipitates, with vaterite being the dominant form, and they likely control vaterite stability. [ABSTRACT FROM AUTHOR]

The halophilic bacterium Halomonas smyrnensis from a modern salt lake used in experiments to induce biomineralization has resulted in the precipitation of monohydrocalcite and other carbonate minerals. In this study, a Halomonas smyrnensis WMS-3 (GenBank:MH425323) strain was identified based on 16S rDNA homology comparison, and then cultured in mediums with 3% NaCl concentration to induce monohydrocalcite at different Mg/Ca molar ratios of 0, 2, 5, 7, and 9. The growth curve of WMS-3 bacteria, pH values, NH4+ concentration, HCO3− and CO32− concentration, carbonic anhydrase (CA) activity, and the changes in Ca2+ and Mg2+ ion concentration were determined to further explore the extracellular biomineralization mechanism. Moreover, the nucleation mechanism of monohydrocalcite on extracellular polymeric substances (EPS) was analyzed through studying ultrathin slices of the WMS-3 strain by High resolution transmission electron microscopy (HRTEM), Selected area election diffraction (SAED), Scanning transmission electron microscopy (STEM), and elemental mapping, besides this, amino acids in the EPS were also analyzed. The results show that pH increased to about 9.0 under the influence of ammonia and CA activity. The precipitation ratio (%, the ratio of the mass/volume concentration) of the Ca2+ ion was 64.32%, 62.20%, 60.22%, 59.57%, and 54.42% at Mg/Ca molar ratios of 0, 2, 5, 7, and 9, respectively, on the 21st day of the experiments, and 6.69%, 7.10%, 7.74%, 8.09% for the Mg2+ ion concentration at Mg/Ca molar ratios 2, 5, 7, and 9, respectively. The obtained minerals were calcite, Mg-rich calcite, aragonite, and hydromagnesite, in addition to the monohydrocalcite, as identified by X-ray diffraction (XRD) analyses. Monohydrocalcite had higher crystallinity when the Mg/Ca ratio increased from 7 to 9; thus, the stability of monohydrocalcite increased, also proven by the thermogravimetry (TG), derivative thermogravimetry (DTG) and differential scanning calorimetry (DSC) analyses. The C=O and C–O–C organic functional groups present in/on the minerals analyzed by Fourier transform infrared spectroscopy (FTIR), the various morphologies and the existence of P and S determined by scanning electron microscope-energy dispersive spectrometer (SEM-EDS), the relatively more negative stable carbon isotope values (−16.91‰ to −17.91‰) analyzed by a carbon isotope laser spectrometer, plus the typical surface chemistry by XPS, all support the biogenesis of these mineral precipitates. Moreover, Ca2+ ions were able to enter the bacterial cell to induce intracellular biomineralization. This study is useful to understand the mechanism of biomineralization further and may provide theoretical reference concerning the formation of monohydrocalcite in nature. [ABSTRACT FROM AUTHOR]

Extensive studies have led to a common understanding of how organic molecules affect the phase, morphology and crystal structure of carbonate minerals. However, further analyses of crystal structures and the unique thermal decomposition characteristics of calcite affected by glycine have rarely been reported. Here, glycine was added as an additive to investigate the biomimetic mineralization of calcites at different glycine concentrations and pH values by virtue of the titration method. The sample characteristics were first analyzed by scanning electron microscopy (SEM), X-ray diffraction (XRD) and laser grain size analysis to investigate the morphology, crystal structure and grain size distribution, respectively. The results indicate that the precipitates are calcites, although SEM and XRD analyses indicated significant differences regarding surface morphology, cell density and cell volume. In addition, taking into account the complexation of Ca2+ with glycine, the samples removed from the precipitation system at different time intervals also confirm the presence of vaterite. More importantly, comparative studies of thermal decomposition between calcites under different conditions were carefully investigated using thermogravimetric analysis at different heating rates of 5, 10, 20, and 30 °C min−1 from 100 to 1000 °C. The kinetic parameters of average activation energy (E) and pre-exponential factor (A) were calculated by the Flynn–Wall–Ozawa and Kissinger–Akahira–Sunose methods to verify that the calcite has a lower crystallinity, activation energy and enthalpy change (ΔH) with glycine incorporation. Thus, this study provides important new insight into the effects of glycine in inducing the biomimetic mineralization of calcite, especially the crystal structural and thermodynamic characteristics. [ABSTRACT FROM AUTHOR]

The interaction between bacteria and minerals is very complicated and has been intensively studied in the laboratory and the field in the last few decades, but the processes and mechanisms of biomineralization and mineral precipitation are still not fully understood and need to be explored further. In the present work, biomineralization experiments were undertaken using Klebsiella pneumoniae LH1, collected from a natural surface environment in an area of outcrops of Cambrian dolomite, in a culture medium with various Mg/Ca molar ratios (0, 3, 6 and 12). The mineral precipitates obtained were analyzed by X-ray diffraction (XRD), scanning electron microscope (SEM), energy dispersive spectrometer (EDS), Fourier transform infrared spectrometer (FTIR), laser scanning confocal microscopy (LSCM) and X-ray photoelectron spectroscopy (XPS). Cells were analyzed with a scanning transmission electron microscope (STEM), high resolution transmission electron microscope (HRTEM) and selected area electron diffraction (SAED). The composition of amino acids in extracellular polymeric substances (EPS) was also determined. In the experiments it was found that the production of ammonia and the presence of carbonate anhydrase promoted the increase of the medium pH and that minerals are nucleated on the EPS, which consist chiefly of amino acids and negatively-charged organic functional groups. With increasing Mg/Ca ratios, the mineral phases changed, including calcite (100%) at Mg/Ca molar ratio of 0, monohydrocalcite (36.05%) + dypingite (63.95%) at Mg/Ca molar ratio of 3, monohydrocalcite (29.72%) + dypingite (15.48%) + nesquehonite (54.80%) at Mg/Ca molar ratio of 6, and monohydrocalcite (14.2%) + dypingite (1.0%) + nesquehonite (84.80%) at Mg/Ca molar ratio of 12. Some intracellular amorphous calcium- and magnesium-rich inclusions were also detected in K. pneumoniae LH1, suggesting intracellular biomineralization accompanying the extracellular mineral precipitation. This study provides further understanding of the biomineralization processes of microorganisms. [ABSTRACT FROM AUTHOR]

In this study, a facultative anaerobic strain isolated from marine sediments and identified as Citrobacter freundii, was used to induce the precipitation of carbonate and phosphate minerals in the laboratory under anaerobic conditions. This is the first time that the ability of C. freundii ZW123 to precipitate carbonate and phosphate minerals has been demonstrated. During the experiments, carbonic anhydrase, alkaline phosphatase and ammonium released by the bacteria not only promoted an increase in pH, but also drove the supersaturation and precipitation of carbonate and phosphate minerals. The predominant bio-mediated minerals precipitated at various Mg/Ca molar ratios were calcite, vaterite, Mg-rich calcite, monohydrocalcite and struvite. A preferred orientation towards struvite was observed. Scanning transmission electron microscopy (STEM) and elemental mapping showed the distribution of magnesium and calcium elements within Mg-rich calcite. Many organic functional groups, including C=O, C-O-C and C-O, were detected within the biominerals, and these functional groups were also identified in the associated extracellular polymeric substances (EPS). Fifteen kinds of amino acid were detected in the biotic minerals, almost identical to those of the EPS, indicating a close relationship between EPS and biominerals. Most amino acids are negatively charged and able to adsorb cations, providing an oversaturated microenvironment to facilitate mineral nucleation. The X-ray photoelectron spectroscopy (XPS) spectrum of struvite shows the presence of organic functional groups on the mineral surface, suggesting a role of the microorganism in struvite precipitation. The ZW123 bacteria provided carbon and nitrogen for the formation of the biotic minerals through their metabolism, which further emphasizes the close relationship between biominerals and the microorganisms. Thermal studies showed the enhanced thermal stability of biotic minerals, perhaps due to the participation of the bacteria ZW123. The presence of amino acids such as Asp and Glu may explain the high magnesium content of some calcites. Molecular dynamics simulations demonstrated that the morphological change and preferred orientation were likely caused by selective adsorption of EPS onto the various struvite crystal surfaces. Thus, this study shows the significant role played by C. freundii ZW123 in the bioprecipitation of carbonate and phosphate minerals and provides some insights into the processes involved. [ABSTRACT FROM AUTHOR]