Nanoscale detection of organic signatures in carbonate microbialites

Effects of trehalose and sodium alginate on microbially induced carbonate precipitation

The process of altering the microbial-induced carbonate precipitation (MICP) by adding additives has been extensively studied. The impact of polysaccharides, as an important component of bacteria, still requires deeper exploration on MICP. This work thus focuses on two types of sugars, sodium alginate (SA) and trehalose (Tre), to explore their effects on biomineralization of carbonate induced by Bacillus pumilus Z6. The results show that B. pumilus Z6 can raise the environmental pH and increase the supersaturation of carbonate and bicarbonate ions through carbonic anhydrase. The presence of organic functional groups and the negative carbon isotope signatures in minerals provide evidence of microbial involvement. Tre and SA do not change the mineral phase, which mainly consists of hollow rice-like granular vaterite and irregular calcite. Tre is conducive to the formation of calcite, whereas the carboxyl groups in SA contribute to the stability of vaterite. Both Tre and SA enhance the removal rate of calcium ions; however, SA is more effective for this purpose. Furthermore, mineralization experiments with calcium alginate gel tablets indicate that SA can attract calcium carbonate to nucleate on its surface. This research offers significant insights into biomineralization processes and introduces novel perspectives for advancing MICP technology.

Passivation of metal sulfides by a marine bacterium for acid mine drainage control

Acid mine drainage originates from metal sulfides oxidation, which results in acidic metal-rich leachate. In this study, a novel and environmentally friendly approach was demonstrated to passivate pyrite and lead-zinc tailings, respectively. The key to this approach is to develop biofilms of the marine bacterium Qipengyuania flava S1. Biofilms can induce biomineralization, thereby isolating metal sulfides from air and water. The stability and biological toxicity of the bio-passivation layers were evaluated by leaching bio-passivated pyrite or tailings in initially acidic H2O2 solutions with shaking for 180 days and then cultivating Brassica chinensis and Allium cepa with the leachates. Our results showed that after passivation, the amount of iron released by pyrite decreased by at least 99.2 ± 0.2 (in wt%). For lead-zinc tailings after passivation, the released metal ions (Fe+Al+Pb+Zn) decreased by at least 52.0 ± 3.2 (in wt%). The bio-passivation layers also maintained the pH of the leachate in the range of 7.5-8.0. Before bio-passivation, compared with mineral water, the pyrite leachate significantly inhibited the growth of the two plants, and the tailings leachate significantly inhibited the growth of A. cepa, whereas the bio-passivated pyrite or tailings leachate did not show any inhibitory effect.

Interfacial Interaction in MeOx/MWNTs (Me-Cu, Ni) Nanostructures as Efficient Electrode Materials for High-Performance Supercapacitors

Due to their unique physical and chemical properties, complex nanostructures based on carbon nanotubes and transition metal oxides are considered promising electrode materials for the fabrication of high-performance supercapacitors with a fast charge rate, high power density, and long cycle life. The crucial role in determining their efficiency is played by the properties of the interface in such nanostructures, among them, the type of chemical bonds between their components. The complementary theoretical and experimental methods, including dispersion-corrected density functional theory (DFT-D3) within GGA-PBE approximation, scanning electron microscopy (SEM), X-ray diffraction (XRD), Raman, X-ray photoelectron, and X-ray absorption spectroscopies, were applied in the present work for the comprehensive investigation of surface morphology, structure, and electronic properties in CuOx/MWCNTs and NiOx/MWCNTs. As a result, the type of interfacial interaction and its correlation with electrochemical characteristics were determined. It was found that the presence of both Ni-O-C and Ni-C bonds can increase the contact between NiO and MWCNTs, and, through this, promote electron transfer between NiO and MWCNTs. For NiOx/MWCNTs, better electrochemical characteristics were observed than for CuOx/MWCNTs, in which the interfacial interaction is determined only by bonding through Cu-O-C bonds. The electrochemical properties of CuOx/MWCNTs and NiOx/MWCNTs were studied to demonstrate the effect of interfacial interaction on their efficiency as electrode materials for supercapacitor applications.

Bacterial templated carbonate mineralization: insights from concave-type crystals induced by Curvibacter lanceolatus strain HJ-1

The elucidation of carbonate crystal growth mechanisms contributes to a deeper comprehension of microbial-induced carbonate precipitation processes. In this research, the Curvibacter lanceolatus HJ-1 strain, well-known for its proficiency in inducing carbonate mineralization, was employed to trigger the formation of concave-type carbonate minerals. The study meticulously tracked the temporal alterations in the culture solution and conducted comprehensive analyses of the precipitated minerals' mineralogy and morphology using advanced techniques such as X-ray diffraction, scanning electron microscopy, focused ion beam, and transmission electron microscopy. The findings unequivocally demonstrate that concave-type carbonate minerals are meticulously templated by bacterial biofilms and employ calcified bacteria as their fundamental structural components. The precise morphological evolution pathway can be delineated as follows: initiation with the formation of bacterial biofilms, followed by the aggregation of calcified bacterial clusters, ultimately leading to the emergence of concave-type minerals characterized by disc-shaped, sunflower-shaped, and spherical morphologies.

Production of carbon-containing pyrite spherules induced by hyperthermophilic Thermococcales: a biosignature?

Thermococcales, a major order of hyperthermophilic archaea inhabiting iron- and sulfur-rich anaerobic parts of hydrothermal deep-sea vents, are known to induce the formation of iron phosphates, greigite (Fe3S4) and abundant quantities of pyrite (FeS2), including pyrite spherules. In the present study, we report the characterization of the sulfide and phosphate minerals produced in the presence of Thermococcales using X-ray diffraction, synchrotron-based X ray absorption spectroscopy and scanning and transmission electron microscopies. Mixed valence Fe(II)-Fe(III) phosphates are interpreted as resulting from the activity of Thermococcales controlling phosphorus-iron-sulfur dynamics. The pyrite spherules (absent in abiotic control) consist of an assemblage of ultra-small nanocrystals of a few ten nanometers in size, showing coherently diffracting domain sizes of few nanometers. The production of these spherules occurs via a sulfur redox swing from S0 to S-2 and then to S-1, involving a comproportionation of (-II) and (0) oxidation states of sulfur, as supported by S-XANES data. Importantly, these pyrite spherules sequester biogenic organic compounds in small but detectable quantities, possibly making them good biosignatures to be searched for in extreme environments.

Ice-nucleating agents in sea spray aerosol identified and quantified with a holistic multimodal freezing model

Sea spray aerosol (SSA) is a widely recognized important source of ice-nucleating particles (INPs) in the atmosphere. However, composition-specific identification, nucleation processes, and ice nucleation rates of SSA-INPs have not been well constrained. Microspectroscopic characterization of ambient and laboratory-generated SSA confirms that water-borne exudates from planktonic microorganisms composed of a mixture of proteinaceous and polysaccharidic compounds act as ice-nucleating agents (INAs). These data and data from previously published mesocosm and wave channel studies are subsequently used to further develop the stochastic freezing model (SFM) producing ice nucleation rate coefficients for SSA-INPs. The SFM simultaneously predicts immersion freezing and deposition and homogeneous ice nucleation by SSA particles under tropospheric conditions. Predicted INP concentrations agree with ambient and laboratory measurements. In addition, this holistic freezing model is independent of the source and exact composition of the SSA particles, making it well suited for implementation in cloud and climate models.

Precipitation of calcium carbonate in the presence of rhamnolipids in alginate hydrogels as a model of biomineralization

This paper reports the effects of rhamnolipids presence in the alginate hydrogel and CO₃^2- solution, on the precipitation of CaCO₃ in the Ca²⁺ loaded alginate hydrogel. Characteristics of the formed particles are discussed. Model conditions containing alginate hydrogel and rhamnolipids were used in order to mimic the natural environment of biomineralization in biofilms. It has been shown that rhamnolipids affect the characteristics of precipitated calcium carbonate effect of using these biosurfactants depends on their concentration as well as whether they are directly present in the hydrogel matrix or the carbonate solution surrounding the hydrogel. The greatest effect compared to the control samples was found for the rhamnolipids in the form of micelles directly present in the hydrogel with the CaCl₂ cross-linked solution at concentration of 0.05 M. These conditions result in the highest increase in vaterite content, specific surface area, and pore volume. The mechanism of CaCO₃ precipitation in alginate hydrogel containing rhamnolipids has been proposed.

Contrasting Modes of Carbonate Precipitation in a Hypersaline Microbial Mat and Their Influence on Biomarker Preservation (Kiritimati, Central Pacific)

Microbial mats represented the earliest complex ecosystems on Earth, since fossil mineralized examples (i.e., microbialites) date back to the Archean Eon. Some microbialites contain putative remains of organic matter (OM), however the processes and pathways that lead to the preservation of OM within microbialite minerals are still poorly understood. Here, a multidisciplinary study is presented (including petrographic, mineralogical and organic geochemical analyses), focusing on a modern calcifying mat from a hypersaline lake in the Kiritimati atoll (Central Pacific). The results show that this mat has a complex history, with two main growth phases under hypersaline conditions, separated by an interruption caused by desiccation and/or freshening of the lake. The mineral precipitates of the mat are predominantly aragonitic and two contrasting precipitation modes are observed: the main growth phases of the mat were characterized by the slow formation of irregular micritic particles with micropeloidal textures and subspherical particles, linked to the degradation of the exopolymer (EPS) matrix of the mat; whereas the interruption period was characterized by the rapid development of a thin but laterally continuous crust composed of superposed fibrous aragonite botryoids that entombed their contemporaneous benthic microbial community. These two precipitation modes triggered different preservation pathways for the OM of the mat as the thin crust shows a particular lipid biomarker signature, different from that of other layers and the relatively rapid precipitation of the crust protecting the underlying lipids from degradation, causing them to show a preservation equivalent to that of a modern active microbial community, despite them being >1100 years old. Equivalent thin mineral crusts occur in other microbialite examples and, thus, this study highlights them as excellent targets for the search of well-preserved biomarker signatures in fossil microbialites. Nevertheless, the results of this work warn for extreme caution when interpreting complex microbialite biomarker signatures, advising combined petrographic, mineralogical and geochemical investigations for the different microbialite layers and mineral microfabrics.

Successive Modes of Carbonate Precipitation in Microbialites along the Hydrothermal Spring of La Salsa in Laguna Pastos Grandes (Bolivian Altiplano)

Interpreting the paleoecosystems of ancient microbialites relies on our understanding of how modern microbialites form in relation with the bio-physico-chemical conditions of their environment. In this study, we investigated the formation of modern carbonate microbialites in the hydrothermal system of La Salsa in Laguna Pastos Grandes (Bolivia), which spans a wide range of physicochemical conditions and associated microbial communities. By combining dissolved inorganic carbon (DIC) isotope mass balance modeling, analysis of carbonates solubility diagram, and imaging of the microorganisms–mineral assemblages within microbial mats, we found that several modes of carbonate precipitation dominate in distinct portions of the hydrothermal system. (1) In high-[DIC] waters, undersaturated to slightly saturated with respect to calcite, cyanobacterial calcification is promoted by CO2 degassing and photosynthetic activity within the microbial mats. (2) In alkaline waters undergoing sustained evaporation, the precipitation of an amorphous calcium carbonate phase seems to control the water a(Ca2+)/a(CO32−) ratio and to serve as a precursor to micritic calcite formation in microbial mats. (3) In saline ephemeral ponds, where the carbonate precipitation is the highest, calcite precipitation probably occurs through a different pathway, leading to a different calcite texture, i.e., aggregates of rhombohedral crystals.

Nested Formation of Calcium Carbonate Polymorphs in a Bacterial Surface Membrane with a Graded Nanoconfinement: An Evolutionary Strategy to Ensure Bacterial Survival

It is the intention of this study to elucidate the nested formation of calcium carbonate polymorphs or polyamorphs in the different nanosized compartments. With these observations, it can be concluded how the bacteria can survive in a harsh environment with high calcium carbonate supersaturation. The mechanisms of calcium carbonate precipitation at the surface membrane and at the underlying cell wall membrane of the thermophilic soil bacterium Geobacillus stearothermophilus DSM 13240 have been revealed by high-resolution transmission electron microscopy and atomic force microscopy. In this Gram-positive bacterium, nanopores in the surface layer (S-layer) and in the supporting cell wall polymers are nucleation sites for metastable calcium carbonate polymorphs and polyamorphs. In order to observe the different metastable forms, various reaction times and a low reaction temperature (4 °C) have been chosen. Calcium carbonate polymorphs nucleate in the confinement of nanosized pores (⌀ 3–5 nm) of the S-layer. The hydrous crystalline calcium carbonate (ikaite) is formed initially with [110] as the favored growth direction. It transforms into the anhydrous metastable vaterite by a solid-state transition. In a following reaction step, calcite is precipitated, caused by dissolution of vaterite in the aqueous solution. In the larger pores of the cell wall (⌀ 20–50 nm), hydrated amorphous calcium carbonate is grown, which transforms into metastable monohydrocalcite, aragonite, or calcite. Due to the sequence of reaction steps via various metastable phases, the bacteria gain time for chipping the partially mineralized S-layer, and forming a fresh S-layer (characteristic growth time about 20 min). Thus, the bacteria can survive in solutions with high calcium carbonate supersaturation under the conditions of forced biomineralization.

Calcite Nanotuned Chitinous Skeletons of Giant Ianthella basta Marine Demosponge

Marine sponges were among the first multicellular organisms on our planet and have survived to this day thanks to their unique mechanisms of chemical defense and the specific design of their skeletons, which have been optimized over millions of years of evolution to effectively inhabit the aquatic environment. In this work, we carried out studies to elucidate the nature and nanostructural organization of three-dimensional skeletal microfibers of the giant marine demosponge Ianthella basta, the body of which is a micro-reticular, durable structure that determines the ideal filtration function of this organism. For the first time, using the battery of analytical tools including three-dimensional micro—X-ray Fluorescence (3D-µXRF), X-ray diffraction (XRD), infra-red (FTIR), Raman and Near Edge X-ray Fine Structure (NEXAFS) spectroscopy, we have shown that biomineral calcite is responsible for nano-tuning the skeletal fibers of this sponge species. This is the first report on the presence of a calcitic mineral phase in representatives of verongiid sponges which belong to the class Demospongiae. Our experimental data suggest a possible role for structural amino polysaccharide chitin as a template for calcification. Our study suggests further experiments to elucidate both the origin of calcium carbonate inside the skeleton of this sponge and the mechanisms of biomineralization in the surface layers of chitin microfibers saturated with bromotyrosines, which have effective antimicrobial properties and are responsible for the chemical defense of this organism. The discovery of the calcified phase in the chitinous template of I. basta skeleton is expected to broaden the knowledge in biomineralization science where the calcium carbonate is regarded as a valuable material for applications in biomedicine, environmental science, and even in civil engineering.

Treated wastewater reuse in micro-irrigation: effect of shear stress on biofilm development kinetics and chemical precipitation

Treated wastewater in micro-irrigation is a promising approach that could be used to decrease the pressure on good quality water resources. However, the clogging of such systems due to biofilm development and chemical precipitation constitute a constraint with the use of treated wastewater (TWW) and lead to lower irrigation system performance. The objective of this work is to study the development of biofilm and composition of fouling due to TWW under shear stresses of 0.7, 2.2 and 4.4 Pa detected along micro-irrigation systems. For this purpose, a Taylor-Couette reactor (TCR) was specifically calibrated for the cultivation of biofilm. The analysis of fouling composition samples (organic and inorganic) shows that biofilm tends to develop under the highest shear stress value (4.4 Pa). Precipitation of calcium carbonate in the form of calcite was observed in conjunction with biofilm growth using X-ray diffractometry (XRD) and thermogravimetric analysis (TGA). These results can be used to ascertain the origins of chemical and biological clogging of drippers and fouling of pipes related to reclaimed water- irrigation.

Substrate-Dependent Study of Chain Orientation and Order in Alkylphosphonic Acid Self-Assembled Monolayers for ALD Blocking

For years, many efforts in area selective atomic layer deposition (AS-ALD) have focused on trying to achieve high-quality self-assembled monolayers (SAMs), which have been shown by a number of studies to be effective for blocking deposition. Herein, we show that in some cases where a densely packed SAM is not formed, significant ALD inhibition may still be realized. The formation of octadecylphosphonic acid (ODPA) SAMs was evaluated on four metal substrates: Cu, Co, W, and Ru. The molecular orientation, chain packing, and relative surface coverage were evaluated using near-edge X-ray absorption fine structure (NEXAFS), Fourier transform infrared (FTIR) spectroscopy, and electrochemical impedance spectroscopy (EIS). ODPA SAMs formed on Co, Cu, and W showed strong angular dependence of the NEXAFS signal whereas ODPA on Ru did not, suggesting a disordered layer was formed on Ru. Additionally, EIS and FTIR spectroscopy confirmed that Co and Cu form densely packed, "crystal-like" SAMs whereas Ru and W form less dense monolayers, a surprising result since W-ODPA was previously shown to inhibit the ALD of ZnO and Al₂O₃ best among all the substrates. This work suggests that multiple factors play a role in SAM-based AS-ALD, not just the SAM quality. Therefore, metrological averaging techniques (e.g., WCA and FTIR spectroscopy) commonly used for evaluating SAMs to predict their suitability for ALD inhibition should be supplemented by more atomically sensitive methods. Finally, it highlights important considerations for describing the mechanism of SAM-based selective ALD.

Core microbial communities of lacustrine microbialites sampled along an alkalinity gradient

Microbialites are usually carbonate-rich sedimentary rocks formed by the interplay of phylogenetically and metabolically complex microbial communities with their physicochemical environment. Yet, the biotic and abiotic determinants of microbialite formation remain poorly constrained. Here, we analysed the structure of prokaryotic and eukaryotic communities associated with microbialites occurring in several crater lakes of the Trans-Mexican volcanic belt along an alkalinity gradient. Microbialite size and community structure correlated with lake physicochemical parameters, notably alkalinity. Although microbial community composition varied across lake microbialites, major taxa-associated functions appeared quite stable with both, oxygenic and anoxygenic photosynthesis and, to less extent, sulphate reduction, as major putative carbonatogenic processes. Despite interlake microbialite community differences, we identified a microbial core of 247 operational taxonomic units conserved across lake microbialites, suggesting a prominent ecological role in microbialite formation. This core mostly encompassed Cyanobacteria and their typical associated taxa (Bacteroidetes, Planctomycetes) and diverse anoxygenic photosynthetic bacteria, notably Chloroflexi, Alphaproteobacteria (Rhodobacteriales, Rhodospirilalles), Gammaproteobacteria (Chromatiaceae) and minor proportions of Chlorobi. The conserved core represented up to 40% (relative abundance) of the total community in lakes Alchichica and Atexcac, displaying the highest alkalinities and the most conspicuous microbialites. Core microbialite communities associated with carbonatogenesis might be relevant for inorganic carbon sequestration purposes.

Solubility investigations in the amorphous calcium magnesium carbonate system

Amorphous precursors are known to occur in the early stages of carbonate mineral formation in both biotic and abiotic environments. Although the Mg content of amorphous calcium magnesium carbonate (ACMC) is a crucial factor for its temporal stabilization, to date little is known about its control on ACMC solubility. Therefore, amorphous Ca x Mg1-x CO3·nH2O solids with 0 ≤ x ≤ 1 and 0.4 ≤ n ≤ 0.8 were synthesized and dispersed in MgCl2-NaHCO3 buffered solutions at 24.5 ± 0.5 °C. The chemical evolution of the solution and the precipitate clearly shows an instantaneous exchange of ions between ACMC and aqueous solution. The obtained ion activity product for ACMC (IAPACMC = "solubility product") increases as a function of its Mg content ([Mg]ACMC = (1 - x) × 100 in mol%) according to the expression: log(IAPACMC) = 0.0174 (±0.0013) × [Mg]ACMC - 6.278 (±0.046) (R 2 = 0.98), where the log(IAPACMC) shift from Ca (-6.28 ± 0.05) to Mg (-4.54 ± 0.16) ACMC endmember, can be explained by the increasing water content and changes in short-range order, as Ca is substituted by Mg in the ACMC structure. The results of this study shed light on the factors controlling ACMC solubility and its temporal stability in aqueous solutions.

Organization of Bone Mineral: The Role of Mineral–Water Interactions

The mechanism (s) that drive the organization of bone mineral throughout the bone extracellular matrix remain unclear. The long-standing theory implicates the organic matrix, namely specific non-collagenous proteins and/or collagen fibrils, while a recent theory proposes a self-assembly mechanism. Applying a combination of spectroscopic and microscopic techniques in wet and dry conditions to bone-like hydroxyapatite nanoparticles that were used as a proxy for bone mineral, we confirm that mature bone mineral particles have the capacity to self-assemble into organized structures. A large quantity of water is present at the surface of bone mineral due to the presence of a hydrophilic, amorphous surface layer that coats bone mineral nanoparticles. These water molecules must not only be strongly bound to the surface of bone mineral in the form of a rigid hydration shell, but they must also be trapped within the amorphous surface layer. Cohesive forces between these water molecules present at the mineral–mineral interface not only hold the mature bone mineral particles together, but also promote their oriented stacking. This intrinsic ability of mature bone mineral particles to organize themselves without recourse to the organic matrix forms the foundation for the development of the next generation of orthopedic biomaterials.

Sub-micron level investigation reveals the inaccessibility of stabilized carbon in soil microaggregates

Direct evidence-based approaches are vital to evaluating newly proposed theories on the persistence of soil organic carbon and establishing the contributions of abiotic and biotic controls. Our primary goal was to directly identify the mechanisms of organic carbon stabilization in native-state, free soil microaggregates without disrupting the aggregate microstructure using scanning transmission x-ray microscopy coupled with near edge x-ray absorption fine structure spectroscopy (STXM-NEXAFS). The influence of soil management practices on microaggregate associated-carbon was also assessed. Free, stable soil microaggregates were collected from a tropical agro-ecosystem in Cruz Alta, Brazil. The long-term experimental plots (>25 years) comparing two tillage systems: no-till and till with a complex crop rotation. Based on simultaneously collected multi-elemental associations and speciation, STXM-NEXAFS successfully provided submicron level information on organo-mineral associations. Simple organic carbon sources were found preserved within microaggregates; some still possessing original morphology, suggesting that their stabilization was not entirely governed by the substrate chemistry. Bulk analysis showed higher and younger organic carbon in microaggregates from no-till systems than tilled systems. These results provide direct submicron level evidence that the surrounding environment is involved in stabilizing organic carbon, thus favoring newly proposed concepts on the persistence of soil organic carbon.

Coupled X-ray Fluorescence and X-ray Absorption Spectroscopy for Microscale Imaging and Identification of Sulfur Species within Tissues and Skeletons of Scleractinian Corals

Identifying and mapping the wide range of sulfur species within complex matrices presents a challenge for understanding the distribution of these important biomolecules within environmental and biological systems. Here, we present a coupled micro X-ray fluorescence (μXRF) and X-ray absorption near-edge structure (XANES) spectroscopy method for determining the presence of specific sulfur species in coral tissues and skeletons at high spatial resolution. By using multiple energy stacks and principal component analysis of a large spectral database, we were able to more accurately identify sulfur species components and distinguish different species and distributions of sulfur formerly unresolved by previous studies. Specifically, coral tissues were dominated by more reduced sulfur species, such as glutathione disulfide, cysteine, and sulfoxide, as well as organic sulfate as represented by chondroitin sulfate. Sulfoxide distributions were visually correlated with the presence of zooxanthellae endosymbionts. Coral skeletons were composed primarily of carbonate-associated sulfate (CAS) along with minor contributions from organic sulfate and a separate inorganic sulfate likely in the form of adsorbed sulfate. This coupled XRF-XANES approach allows for a more accurate and informative view of sulfur within biological systems in situ and holds great promise for pairing with other techniques to allow for a more encompassing understanding of elemental distributions within the environment.

Characterization of Pustular Mats and Related Rivularia-Rich Laminations in Oncoids From the Laguna Negra Lake (Argentina)

Stromatolites are organo-sedimentary structures that represent some of the oldest records of the early biosphere on Earth. Cyanobacteria are considered as a main component of the microbial mats that are supposed to produce stromatolite-like structures. Understanding the role of cyanobacteria and associated microorganisms on the mineralization processes is critical to better understand what can be preserved in the laminated structure of stromatolites. Laguna Negra (Catamarca, Argentina), a high-altitude hypersaline lake where stromatolites are currently formed, is considered as an analog environment of early Earth. This study aimed at characterizing carbonate precipitation within microbial mats and associated oncoids in Laguna Negra. In particular, we focused on carbonated black pustular mats. By combining Confocal Laser Scanning Microscopy, Scanning Electron Microscopy, Laser Microdissection and Whole Genome Amplification, Cloning and Sanger sequencing, and Focused Ion Beam milling for Transmission Electron Microscopy, we showed that carbonate precipitation did not directly initiate on the sheaths of cyanobacterial Rivularia, which dominate in the mat. It occurred via organo-mineralization processes within a large EPS matrix excreted by the diverse microbial consortium associated with Rivularia where diatoms and anoxygenic phototrophic bacteria were particularly abundant. By structuring a large microbial consortium, Rivularia should then favor the formation of organic-rich laminations of carbonates that can be preserved in stromatolites. By using Fourier Transform Infrared spectroscopy and Synchrotron-based deep UV fluorescence imaging, we compared laminations rich in structures resembling Rivularia to putatively chemically-precipitated laminations in oncoids associated with the mats. We showed that they presented a different mineralogy jointly with a higher content in organic remnants, hence providing some criteria of biogenicity to be searched for in the fossil record.

Experimental and visual research on the microbial induced carbonate precipitation by Pseudomonas aeruginosa

Microbial induced carbonate precipitation (MICP) is a common occurrence of geochemistry influences in many fields, such as biological, geographical, and engineering systems. However, the processes that control interactions between carbonate biomineralization and biofilm properties are poorly understood. We develop a method for real time, in situ and nondestructive imaging with confocal scanning microscopy. This method provides a possible way to observe biomineralization process and the morphology of biomineralized deposits within biofilms. We use this method to show calcite biominerals produced by Pseudomonas aeruginosa biofilms which extremely change biofilm structures. The distribution of calcite precipitation produced in situ biomineralization is highly heterogeneous in biofilms and also to occur primarily on the bottom of biofilms. It is distinct from those usual expectations that mineral started to precipitate from surface of biofilm. Our results reveal that biomineralization plays a comprehensive regulation function on biofilm architecture and properties.

Nucleation and Growth of Mg-Calcite Spherulites Induced by the Bacterium Curvibacter lanceolatus Strain HJ-1

Calcite spherulites have been observed in many laboratory experiments with different bacteria, and spherulitic growth has received much interest in mineralogy research. However, the nucleation and growth mechanism, as well as geological significance of calcite spherulites in solution with bacteria is still unclear. Herein, spherulites composed of an amorphous core, a Mg-calcite body and an organic film were precipitated by the Curvibacter lanceolatus HJ-1 bacterial strain in a solution with a molar Mg/Ca ratio of 3. Based on the results, we provide a possible mechanism for the biomineralization of Mg-calcite spherulites. First, amorphous calcium carbonate particles are deposited and aggregated into a stable sphere-like core in combination with organic molecules. The core then acts as the nucleus of spherulitic radial growth. Finally, the organic film grows on the surface of Mg-calcite spherulites as a result of bacterial metabolism and calcification. These findings provide insight into the growth mode and crystallization of biogenic spherulites during biomineralization, and are of significance in the application of novel biological materials.

Spatially Resolved Distribution of Fe Species around Microbes at the Submicron Scale in Natural Bacteriogenic Iron Oxides

Natural bacteriogenic iron oxides (BIOS) were investigated using local-analyzable synchrotron-based scanning transmission X-ray microscopy (STXM) with a submicron-scale resolution. Cell, cell sheath interface (EPS), and sheath in the BIOS were clearly depicted using C-, N-, and O- near edge X-ray absorption fine structure (NEXAFS) obtained through STXM measurements. Fe-NEXAFS obtained from different regions of BIOS indicated that the most dominant iron mineral species was ferrihydrite. Fe(II)- and/or Fe(III)-acidic polysaccharides accompanied ferrihydrite near the cell and EPS regions. Our STXM/NEXAFS analysis showed that Fe species change continuously between the cell, EPS, and sheath under several 10-nm scales.

Microbial Extracellular Polymeric Substances (EPSs) in Ocean Systems

Microbial cells (i.e., bacteria, archaea, microeukaryotes) in oceans secrete a diverse array of large molecules, collectively called extracellular polymeric substances (EPSs) or simply exopolymers. These secretions facilitate attachment to surfaces that lead to the formation of structured 'biofilm' communities. In open-water environments, they also lead to formation of organic colloids, and larger aggregations of cells, called 'marine snow.' Secretion of EPS is now recognized as a fundamental microbial adaptation, occurring under many environmental conditions, and one that influences many ocean processes. This relatively recent realization has revolutionized our understanding of microbial impacts on ocean systems. EPS occur in a range of molecular sizes, conformations and physical/chemical properties, and polysaccharides, proteins, lipids, and even nucleic acids are actively secreted components. Interestingly, however, the physical ultrastructure of how individual EPS interact with each other is poorly understood. Together, the EPS matrix molecules form a three-dimensional architecture from which cells may localize extracellular activities and conduct cooperative/antagonistic interactions that cannot be accomplished efficiently by free-living cells. EPS alter optical signatures of sediments and seawater, and are involved in biogeomineral precipitation and the construction of microbial macrostructures, and horizontal-transfers of genetic information. In the water-column, they contribute to the formation of marine snow, transparent exopolymer particles (TEPs), sea-surface microlayer biofilm, and marine oil snow. Excessive production of EPS occurs during later-stages of phytoplankton blooms as an excess metabolic by product and releases a carbon pool that transitions among dissolved-, colloidal-, and gel-states. Some EPS are highly labile carbon forms, while other forms appear quite refractory to degradation. Emerging studies suggest that EPS contribute to efficient trophic-transfer of environmental contaminants, and may provide a protective refugia for pathogenic cells within marine systems; one that enhances their survival/persistence. Finally, these secretions are prominent in 'extreme' environments ranging from sea-ice communities to hypersaline systems to the high-temperatures/pressures of hydrothermal-vent systems. This overview summarizes some of the roles of exopolymer in oceans.

Comparative metagenomics unveils functions and genome features of microbialite-associated communities along a depth gradient

Modern microbialites are often used as analogs of Precambrian stromatolites; therefore, studying the metabolic interplay within their associated microbial communities can help formulating hypotheses on their formation and long-term preservation within the fossil record. We performed a comparative metagenomic analysis of microbialite samples collected at two sites and along a depth gradient in Lake Alchichica (Mexico). The community structure inferred from single-copy gene family identification and long-contig (>10 kb) assignation, consistently with previous rRNA gene surveys, showed a wide prokaryotic diversity dominated by Alphaproteobacteria, Gammaproteobacteria, Cyanobacteria, and Bacteroidetes, while eukaryotes were largely dominated by green algae or diatoms. Functional analyses based on RefSeq, COG and SEED assignations revealed the importance of housekeeping functions, with an overrepresentation of genes involved in carbohydrate metabolism, as compared with other metabolic capacities. The search for genes diagnostic of specific metabolic functions revealed the important involvement of Alphaproteobacteria in anoxygenic photosynthesis and sulfide oxidation, and Cyanobacteria in oxygenic photosynthesis and nitrogen fixation. Surprisingly, sulfate reduction appeared negligible. Comparative analyses suggested functional similarities among various microbial mat and microbialite metagenomes as compared with soil or oceans, but showed differences in microbial processes among microbialite types linked to local environmental conditions.

X-ray spectromicroscopy of nanoparticulate iron oxide phases

Soft x-ray spectromicroscopy techniques have seen great amount of development in the recent years, and with the development of new diffraction limited synchrotron source, many new nanoscale and mesoscale characterization opportunities of applied materials are foreseen. In this perspective, the authors present some examples that illustrate the capabilities of spectromicroscopy techniques, namely, 2D and 3D spatially resolved chemical quantification, surface and bulk sensitive measurements, and polarization dependent measurements as applied to iron oxide nanoparticulate materials of biological, geological, and other origins.

Molecular preservation of 1.88 Ga Gunflint organic microfossils as a function of temperature and mineralogy

The significant degradation that fossilized biomolecules may experience during burial makes it challenging to assess the biogenicity of organic microstructures in ancient rocks. Here we investigate the molecular signatures of 1.88 Ga Gunflint organic microfossils as a function of their diagenetic history. Synchrotron-based XANES data collected in situ on individual microfossils, at the submicrometre scale, are compared with data collected on modern microorganisms. Despite diagenetic temperatures of ∼150–170 °C deduced from Raman data, the molecular signatures of some Gunflint organic microfossils have been exceptionally well preserved. Remarkably, amide groups derived from protein compounds can still be detected. We also demonstrate that an additional increase of diagenetic temperature of only 50 °C and the nanoscale association with carbonate minerals have significantly altered the molecular signatures of Gunflint organic microfossils from other localities. Altogether, the present study provides key insights for eventually decoding the earliest fossil record.

Thermal diagenesis is generally seen as detrimental to the preservation of organic biosignatures. Using synchrotron-based XANES data, Alleon et al. find preservation of the molecular signatures of organic microfossils from the 1.88 Ga Gunflint cherts.

In Situ Biomineralization and Particle Deposition Distinctively Mediate Biofilm Susceptibility to Chlorine

Microbial biofilms and mineral precipitation commonly co-occur in engineered water systems, such as cooling towers and water purification systems, and both decrease process performance. Microbial biofilms are extremely challenging to control and eradicate. We previously showed that in situ biomineralization and the precipitation and deposition of abiotic particles occur simultaneously in biofilms under oversaturated conditions. Both processes could potentially alter the essential properties of biofilms, including susceptibility to biocides. However, the specific interactions between mineral formation and biofilm processes remain poorly understood. Here we show that the susceptibility of biofilms to chlorination depends specifically on internal transport processes mediated by biomineralization and the accumulation of abiotic mineral deposits. Using injections of the fluorescent tracer Cy5, we show that Pseudomonas aeruginosa biofilms are more permeable to solutes after in situ calcite biomineralization and are less permeable after the deposition of abiotically precipitated calcite particles. We further show that biofilms are more susceptible to chlorine killing after biomineralization and less susceptible after particle deposition. Based on these observations, we found a strong correlation between enhanced solute transport and chlorine killing in biofilms, indicating that biomineralization and particle deposition regulate biofilm susceptibility by altering biocide penetration into the biofilm. The distinct effects of in situ biomineralization and particle deposition on biocide killing highlight the importance of understanding the mechanisms and patterns of biomineralization and scale formation to achieve successful biofilm control.

Spatial patterns of carbonate biomineralization in biofilms

Microbially catalyzed precipitation of carbonate minerals is an important process in diverse biological, geological, and engineered systems. However, the processes that regulate carbonate biomineralization and their impacts on biofilms are largely unexplored, mainly because of the inability of current methods to directly observe biomineralization within biofilms. Here, we present a method for in situ, real-time imaging of biomineralization in biofilms and use it to show that Pseudomonas aeruginosa biofilms produce morphologically distinct carbonate deposits that substantially modify biofilm structures. The patterns of carbonate biomineralization produced in situ were substantially different from those caused by accumulation of particles produced by abiotic precipitation. Contrary to the common expectation that mineral precipitation should occur at the biofilm surface, we found that biomineralization started at the base of the biofilm. The carbonate deposits grew over time, detaching biofilm-resident cells and deforming the biofilm morphology. These findings indicate that biomineralization is a general regulator of biofilm architecture and properties.

Metagenome-based diversity analyses suggest a significant contribution of non-cyanobacterial lineages to carbonate precipitation in modern microbialites

Cyanobacteria are thought to play a key role in carbonate formation due to their metabolic activity, but other organisms carrying out oxygenic photosynthesis (photosynthetic eukaryotes) or other metabolisms (e.g., anoxygenic photosynthesis, sulfate reduction), may also contribute to carbonate formation. To obtain more quantitative information than that provided by more classical PCR-dependent methods, we studied the microbial diversity of microbialites from the Alchichica crater lake (Mexico) by mining for 16S/18S rRNA genes in metagenomes obtained by direct sequencing of environmental DNA. We studied samples collected at the Western (AL-W) and Northern (AL-N) shores of the lake and, at the latter site, along a depth gradient (1, 5, 10, and 15 m depth). The associated microbial communities were mainly composed of bacteria, most of which seemed heterotrophic, whereas archaea were negligible. Eukaryotes composed a relatively minor fraction dominated by photosynthetic lineages, diatoms in AL-W, influenced by Si-rich seepage waters, and green algae in AL-N samples. Members of the Gammaproteobacteria and Alphaproteobacteria classes of Proteobacteria, Cyanobacteria, and Bacteroidetes were the most abundant bacterial taxa, followed by Planctomycetes, Deltaproteobacteria (Proteobacteria), Verrucomicrobia, Actinobacteria, Firmicutes, and Chloroflexi. Community composition varied among sites and with depth. Although cyanobacteria were the most important bacterial group contributing to the carbonate precipitation potential, photosynthetic eukaryotes, anoxygenic photosynthesizers and sulfate reducers were also very abundant. Cyanobacteria affiliated to Pleurocapsales largely increased with depth. Scanning electron microscopy (SEM) observations showed considerable areas of aragonite-encrusted Pleurocapsa-like cyanobacteria at microscale. Multivariate statistical analyses showed a strong positive correlation of Pleurocapsales and Chroococcales with aragonite formation at macroscale, and suggest a potential causal link. Despite the previous identification of intracellularly calcifying cyanobacteria in Alchichica microbialites, most carbonate precipitation seems extracellular in this system.

Probing carbonate in bone forming minerals on the nanometre scale

To devise new strategies to treat bone disease in an ageing society, a more detailed characterisation of the process by which bone mineralises is needed. In vitro studies have suggested that carbonated mineral might be a precursor for deposition of bone apatite. Increased carbonate content in bone may also have significant implications in altering the mechanical properties, for example in diseased bone. However, information about the chemistry and coordination environment of bone mineral, and their spatial distribution within healthy and diseased tissues, is lacking. Spatially resolved analytical transmission electron microscopy is the only method available to probe this information at the length scale of the collagen fibrils in bone. In this study, scanning transmission electron microscopy combined with electron energy-loss spectroscopy (STEM-EELS) was used to differentiate between calcium-containing biominerals (hydroxyapatite, carbonated hydroxyapatite, beta-tricalcium phosphate and calcite). A carbon K-edge peak at 290 eV is a direct marker of the presence of carbonate. We found that the oxygen K-edge structure changed most significantly between minerals allowing discrimination between calcium phosphates and calcium carbonates. The presence of carbonate in carbonated HA (CHA) was confirmed by the formation of peak at 533 eV in the oxygen K-edge. These observations were confirmed by simulations using density functional theory. Finally, we show that this method can be utilised to map carbonate from the crystallites in bone. We propose that our calibration library of EELS spectra could be extended to provide spatially resolved information about the coordination environment within bioceramic implants to stimulate the development of structural biomaterials.

Viruses Occur Incorporated in Biogenic High-Mg Calcite from Hypersaline Microbial Mats

Using three different microscopy techniques (epifluorescence, electronic and atomic force microscopy), we showed that high-Mg calcite grains in calcifying microbial mats from the hypersaline lake "La Salada de Chiprana", Spain, contain viruses with a diameter of 50-80 nm. Energy-dispersive X-ray spectrometer analysis revealed that they contain nitrogen and phosphorus in a molar ratio of ~9, which is typical for viruses. Nucleic acid staining revealed that they contain DNA or RNA. As characteristic for hypersaline environments, the concentrations of free and attached viruses were high (>10(10) viruses per g of mat). In addition, we showed that acid treatment (dissolution of calcite) resulted in release of viruses into suspension and estimated that there were ~15 × 10(9) viruses per g of calcite. We suggest that virus-mineral interactions are one of the possible ways for the formation of nano-sized structures often described as "nanobacteria" and that viruses may play a role in initiating calcification.

Characterization of environmental conditions during microbial Mg-carbonate precipitation and early diagenetic dolomite crust formation: Brejo do Espinho, Rio de Janeiro, Brazil

For many years, sedimentary dolomite rocks have been considered to be primarily a replacement product of the calcium carbonate components comprising the original limestone, a process known as secondary replacement dolomitization. Although numerous dolomite formations in the geological record are composed of fine-grained crystals of micritic dolomite, an alternative process, that is, direct precipitation, is often excluded because of the absence of visible or geochemical indicators supporting primary precipitation. In this research, we present a study of a modern coastal hypersaline lagoon, Brejo do Espinho, Rio de Janeiro State, Brazil, which is located in a special climatic regime where a well-defined seasonal cycle of wet and dry conditions occur. The direct precipitation of modern high-Mg calcite and Ca-dolomite mud from the lagoonal waters under low-temperature hypersaline conditions is associated with the activity of microbial organisms living in this restricted environment. The mud undergoes an early diagenetic transformation into a 100% dolomite crust on the margins of the lagoon. The biomineralization process, characterized by the variations of the physico-chemical conditions in this environment during the annual hydrological cycle, is integrated with isotopic analysis to define the early diagenetic processes responsible for the formation of both dolomitic mud and crust. The carbon isotope values indicate a contribution of respired organic carbon, which is greater for the crust (δ13C=−9.5‰ Vienna Pee Dee Belemnite (VPDB)) than mud (δ13C=−1.2‰ VPDB). The oxygen isotope values reflect a moderate degree of evaporation during mud formation (δ18O=1.1‰ VPDB), whereas it is greatly enhanced during early diagenetic crust formation (δ18O=4.2‰ VPDB). The clumped isotope formation temperature derived for the Brejo do Espinho mud is 34 °C, whereas it is 32 °C for the crust. These temperatures are consistent with the upper range of measured values during the dry season when the lagoon experiences the most hypersaline conditions.

Organic and mineral imprints in fossil photosynthetic mats of an East Antarctic lake

Lacustrine microbial mats in Antarctic ice-free oases are considered modern analogues of early microbial ecosystems as their primary production is generally dominated by cyanobacteria, the heterotrophic food chain typically truncated due to extreme environmental conditions, and they are geographically isolated. To better understand early fossilization and mineralization processes in this context, we studied the microstructure and chemistry of organo-mineral associations in a suite of sediments 50-4530 cal. years old from a lake in Skarvsnes, Lützow Holm Bay, East Antarctica. First, we report an exceptional preservation of fossil autotrophs and their biomolecules on millennial timescales. The pigment scytonemin is preserved inside cyanobacterial sheaths. As non-pigmented sheaths are also preserved, scytonemin likely played little role in the preservation of sheath polysaccharides, which have been cross-linked by ether bonds. Coccoids preserved thylakoids and autofluorescence of pigments such as carotenoids. This exceptional preservation of autotrophs in the fossil mats argues for limited biodegradation during and after deposition. Moreover, cell-shaped aggregates preserved sulfur-rich nanoglobules, supporting fossilization of instable intracellular byproducts of chemotrophic or phototrophic S-oxidizers. Second, we report a diversity of micro- to nanostructured CaCO3 precipitates intimately associated with extracellular polymeric substances, cyanobacteria, and/or other prokaryotes. Micro-peloids Type 1 display features that distinguish them from known carbonates crystallized in inorganic conditions: (i) Type 1A are often filled with globular nanocarbonates and/or surrounded by a fibrous fringe, (ii) Type 1B are empty and display ovoid to wrinkled fringes of nanocrystallites that can be radially oriented (fibrous or triangular) or multilayered, and (iii) all show small-size variations. Type 2 rounded carbonates 1-2 μm in diameter occurring inside autofluorescent spheres interpreted as coccoidal bacteria may represent fossils of intracellular calcification. These organo-mineral associations support organically driven nanocarbonate crystallization and stabilization, hence providing potential markers for microbial calcification in ancient rocks.

16S rDNA-based analysis reveals cosmopolitan occurrence but limited diversity of two cyanobacterial lineages with contrasted patterns of intracellular carbonate mineralization

Cyanobacteria are mainly thought to induce carbonate precipitation extracellularly via their photosynthetic activity combined with the nucleation potential of exopolymeric substances. The discovery in microbialites of the alkaline lake Alchichica (Mexico) of Candidatus Gloeomargarita lithophora, a cyanobacterium forming large amounts of intracellular Mg-Ca-Sr-Ba carbonate spherules, showed that intracellular biomineralization in cyanobacteria is also possible. A second cyanobacterium isolated from the same environment, Candidatus Synechococcus calcipolaris G9, has been recently shown to also form intracellular calcium carbonates at the cell poles, a capability shared by all cultured species of the Thermosynechococcus clade, to which it belongs. To explore the diversity of these two distant cyanobacterial lineages representing two different patterns of intracellular calcification, we designed specific primers against their 16S rRNA genes and looked for their occurrence in a wide variety of samples. We identified the presence of members of the Gloeomargarita and Thermosynechococcus/S. calcipolaris lineages in microbialites collected from Lake Alchichica and three other neighboring Mexican lakes. The two clades also occurred in karstic areas and in some thermophilic or hypersaline microbial mats collected in South America and/or Southern Europe. Surprisingly, the within-group diversity in the two clades was low, especially within the S. calcipolaris clade, with all 16S rRNA gene sequences retrieved sharing more than 97% identity. This suggests that these clades are composed of a limited number of operational taxonomic units (OTUs) with cosmopolitan distribution. Moreover, scanning electron microscopy coupled with energy dispersive x-ray spectrometry showed the presence of intracellularly calcifying Gloeomargarita-like cyanobacteria in fresh samples where this clade was relatively abundant, suggesting that these cyanobacteria do precipitate carbonates intracellularly under natural conditions.

Microbial mediated formation of Fe-carbonate minerals under extreme acidic conditions

Discovery of Fe-carbonate precipitation in Rio Tinto, a shallow river with very acidic waters, situated in Huelva, South-western Spain, adds a new dimension to our understanding of carbonate formation. Sediment samples from this low-pH system indicate that carbonates are formed in physico-chemical conditions ranging from acid to neutral pH. Evidence for microbial mediation is observed in secondary electron images (Fig. 1), which reveal rod-shaped bacteria embedded in the surface of siderite nanocrystals. The formation of carbonates in Rio Tinto is related to the microbial reduction of ferric iron coupled to the oxidation of organic compounds. Herein, we demonstrate for the first time, that Acidiphilium sp. PM, an iron-reducing bacterium isolated from Rio Tinto, mediates the precipitation of siderite (FeCO₃) under acidic conditions and at a low temperature (30°C). We describe nucleation of siderite on nanoglobules in intimate association with the bacteria cell surface. This study has major implications for understanding carbonate formation on the ancient Earth or extraterrestrial planets.

Laboratory activity to effectively teach introductory geomicrobiology concepts to non-geology majors

We have designed a three-week experiment that can complement any microbiology course, to teach main geomicrobiology concepts for non-geology majors. One of the most difficult concepts for non-geology majors to comprehend is how bacteria serve as a platform for different mineralization reactions. In our three-week laboratory practice, students learn the main principles and conditions required for an induced bacterial mineralization. Upon completion of the laboratory experience, students will: 1) learn how microbial-induced mineralization (such as calcium carbonate formation) is affected by differential media and growth conditions; 2) understand how bacterial physiology affects any induced in situ or in vitro mineralization; 3) comprehend how growing conditions and bacterial physiologies interrelate, resulting in differential crystal formation. The teaching-learning process was assessed using a pre-/posttest with an increase from 26% to 76% in the number of positive answers from the students. We also measured the students' proficiency while conducting specific technical tasks, revealing no major difficulties while conducting the experiments. A final questionnaire was provided with satisfactory evaluations from the students regarding the organization and content of the practices. 84-86% of the students agreed that the exercises improved their knowledge in geomicrobiology and would like to attend similar laboratories in the future. Such response is the best indicator that the laboratory practice can be implemented in any undergraduate/graduate microbiology course to effectively teach basic geomicrobiology concepts to non-geology majors.

Stromatolitic knobs in Storr's Lake (San Salvador, Bahamas): a model system for formation and alteration of laminae

The initial lamination in young, metabolically active Scytonema knobs developing in Storr's Lake (Bahamas) results from the iterative succession of two different stages of microbial growth at the top of this microbialite. Stage 1 is dominated by vertically oriented cyanobacterial filaments and is characterized by a high porosity of the fabric. Stage 2 shows a higher microbial density with the filaments oriented horizontally and with higher carbonate content. The more developed, dense microbial community associated with Stage 2 of the Scytonema knobs rapidly degrades extracellular organic matter (EOM) and coupled to this, precipitates carbonate. The initial nucleation forms high-Mg calcite nanospheroids that progressively replace the EOM. No precipitation is observed within the thick sheath of the Scytonema filaments, possibly because of strong cross-linking of calcium and EOM (forming EOM-Ca-EOM complexes), which renders Ca unavailable for carbonate nucleation (inhibition process). Eventually, organominerals precipitate and form an initial lamina through physicochemical and microbial processes, including high rates of photosynthetic activity that lead to (13) C-enriched DIC available for initial nucleation. As this lamina moves downward by the iterative production of new laminae at the top of the microbialite, increased heterotrophic activity further alters the initial mineral product at depth. Although some rare relic preservation of 'Stage 1-Stage 2' laminae in subfossil knobs exists, the very fine primary lamination is considerably altered and almost completely lost when the knobs develop into larger and more complex morphologies due to the increased accommodation space and related physicochemical and/or biological alteration. Despite considerable differences in microstructure, the emerging ecological model of community succession leading to laminae formation described here for the Scytonema knobs can be applied to the formation of coarse-grained, open marine stromatolites. Therefore, both fine- and coarse-grained extant stromatolites can be used as model systems to understand the formation of microbialites in the fossil record.

Biomineralization of calcium carbonates and their engineered applications: a review

Microbially induced calcium carbonate precipitation (MICCP) is a naturally occurring biological process in which microbes produce inorganic materials as part of their basic metabolic activities. This technology has been widely explored and promising with potential in various technical applications. In the present review, the detailed mechanism of production of calcium carbonate biominerals by ureolytic bacteria has been discussed along with role of bacteria and the sectors where these biominerals are being used. The applications of bacterially produced carbonate biominerals for improving the durability of buildings, remediation of environment (water and soil), sequestration of atmospheric CO2 filler material in rubbers and plastics etc. are discussed. The study also sheds light on benefits of bacterial biominerals over traditional agents and also the issues that lie in the path of successful commercialization of the technology of microbially induced calcium carbonate precipitation from lab to field scale.

Specific carbonate-microbe interactions in the modern microbialites of Lake Alchichica (Mexico)

The role of microorganisms in microbialite formation remains unresolved: do they induce mineral precipitation (microbes first) or do they colonize and/or entrap abiotic mineral precipitates (minerals first)? Does this role vary from one species to another? And what is the impact of mineral precipitation on microbial ecology? To explore potential biogenic carbonate precipitation, we studied cyanobacteria-carbonate assemblages in modern hydromagnesite-dominated microbialites from the alkaline Lake Alchichica (Mexico), by coupling three-dimensional imaging of molecular fluorescence emitted by microorganisms, using confocal laser scanning microscopy, and Raman scattering/spectrometry from the associated minerals at a microscale level. Both hydromagnesite and aragonite precipitate within a complex biofilm composed of photosynthetic and other microorganisms. Morphology and pigment-content analysis of dominant photosynthetic microorganisms revealed up to six different cyanobacterial morphotypes belonging to Oscillatoriales, Chroococcales, Nostocales and Pleurocapsales, as well as several diatoms and other eukaryotic microalgae. Interestingly, one of these morphotypes, Pleurocapsa-like, appeared specifically associated with aragonite minerals, the oldest parts of actively growing Pleurocapsa-like colonies being always aragonite-encrusted. We hypothesize that actively growing cells of Pleurocapsales modify local environmental conditions favoring aragonite precipitation at the expense of hydromagnesite, which precipitates at seemingly random locations within the biofilm. Therefore, at least part of the mineral precipitation in Alchichica microbialites is most likely biogenic and the type of biominerals formed depends on the nature of the phylogenetic lineage involved. This observation may provide clues to identify lineage-specific biosignatures in fossil stromatolites from modern to Precambrian times.

Calcification and silicification: fossilization potential of cyanobacteria from stromatolites of Niuafo'ou's Caldera Lakes (Tonga) and implications for the early fossil record

Calcification and silicification processes of cyanobacterial mats that form stromatolites in two caldera lakes of Niuafo'ou Island (Vai Lahi and Vai Si'i) were evaluated, and their importance as analogues for interpreting the early fossil record are discussed. It has been shown that the potential for morphological preservation of Niuafo'ou cyanobacteria is highly dependent on the timing and type of mineral phase involved in the fossilization process. Four main modes of mineralization of cyanobacteria organic parts have been recognized: (i) primary early postmortem calcification by aragonite nanograins that transform quickly into larger needle-like crystals and almost totally destroy the cellular structures, (ii) primary early postmortem silicification of almost intact cyanobacterial cells that leave a record of spectacularly well-preserved cellular structures, (iii) replacement by silica of primary aragonite that has already recrystallized and obliterated the cellular structures, (iv) occasional replacement of primary aragonite precipitated in the mucopolysaccharide sheaths and extracellular polymeric substances by Al-Mg-Fe silicates. These observations suggest that the extremely scarce earliest fossil record may, in part, be the result of (a) secondary replacement by silica of primary carbonate minerals (aragonite, calcite, siderite), which, due to recrystallization, had already annihilated the cellular morphology of the mineralized microbiota or (b) relatively late primary silicification of already highly degraded and no longer morphologically identifiable microbial remains.