Catalytic biomineralization of fluorescent calcite by the thermophilic bacterium Geobacillus thermoglucosidasius

Insight into biomolecular interaction-based non-classical crystallization of bacterial biocement

In an attempt to draw a correlation between calcium carbonate (CaCO3) precipitation and biomacromolecules such as extracellular polymeric substances and enzyme activity in biomineralizing microbe, this report aims to elucidate the ureolytic and ammonification route in Paenibacillus alkaliterrae to explore the possible role of organic biomolecule(s) present on cell surface in mediating nucleation and crystallization of biogenic CaCO3. After 168 h of biomineralization in ureolysis and ammonification, 2.2 g/l and 0.87 g/l of CaCO3 precipitates were obtained, respectively. The highest carbonic anhydrase activity (31.8 µmoles/min/ml) was evidenced in ammonification as opposed to ureolysis (24.8 µmoles/min/ml). Highest urease activity reached up to 9.26 µmoles/min/ml in ureolytic pathway. Extracellular polymeric substances such as polysaccharides and proteins were found to have a vital role not only in the nucleation and crystal growth but also in addition direct polymorphic fate of CaCO3 nanoparticles. EPS production was higher during ammonification (3.1 mg/ml) than in ureolysis (0.72 mg/ml). CaCO3 nanoparticle-associated proteins were found to be 0.82 mg/ml in ureolysis and 0.56 mg/ml in ammonification. After 30 days of biomineralization, all the polymorphic forms stabilized to calcite in ureolysis but in ammonification vaterite predominated. In our study, we showed that organic template-mediated prokaryotic biomineralization follows the non-classical nucleation and varying proportions of these organic components causes selective polymorphism of CaCO3 nanoparticles. Overall, the findings are expected to further the fundamental understanding of enzymes, EPS-driven non-classical nucleation of CaCO3, and we foresee the design of fit-for-purpose futuristic biominerals arising from such renewed understanding of biomineralization. KEY POINTS: • Organic-inorganic interface of cell surface promote crystallization of biominerals • Carbohydrate and proteins in the interface results selective polymorphism of CaCO3 • Calcite stabilized at 30 days in ureolysis, vaterite-calcite mix in ammonification.

Novel Focused Ion Beam Liftouts for Spatial Characterization of Spherical Biominerals With Transmission Electron Microscopy

Focused ion beam (FIB) is frequently used to prepare electron- and X-ray-beam-transparent thin sections of samples, called lamellae. Typically, lamellae are prepared from only a subregion of a sample. In this paper, we present a novel approach for FIB lamella preparation of microscopic samples, wherein the entire cross-section of the whole sample can be investigated. The approach was demonstrated using spherical, porous, and often hollow microprecipitates of biologically precipitated calcium carbonate. The microprecipitate morphology made these biogenic samples more fragile and challenging than materials commonly investigated using FIB lamellae. Our method enables the appropriate orientation of the lamellae required for further electron/X-ray analyses after attachment to the transmission electron microscopy (TEM) grid post and facilitates more secure adhesion onto the grid post. We present evidence of autofluorescence in bacterially precipitated vaterite using this lamella preparation method coupled with TEM selected area diffraction. This innovative approach allows studying biomineralization at the micro to nano scales, which can provide novel insights into bacterial responses to microenvironmental conditions.

Mg-rich amorphous to Mg-low crystalline CaCO3 pathway in foraminifera

Calcium carbonate minerals produced by marine organisms play a central role in the global carbon cycle and carbonate sedimentation, which influence the climate by regulating atmospheric CO₂ levels. Foraminifera are important marine single-celled organisms that have produced calcite shells for over 300 million years. Here, we present new observations promoting our understanding for foraminiferal biocalcification by studying Amphistegina lessonii. We integrated in vivo confocal autofluorescence and dye fluorescence imaging with elemental analysis of the cell supporting the concept that the calcite shells of foraminifera are produced via deposition of intracellularly formed Mg-rich amorphous calcium carbonate (Mg-ACC) particles that transform into a stable mineral phase. This process is likely accompanied by the activity of endosymbiotic microalgae and seawater-derived endocytic vesicles that provide calcification substrates such as DIC, Ca²⁺, and Mg²⁺. The final transformation of semi-liquid amorphous nanoparticles into a crystalline shell was associated with Mg²⁺ liberation.

Matrix is everywhere: extracellular DNA is a link between biofilm and mineralization in Bacillus cereus planktonic lifestyle

To date, the mechanisms of biomineralization induced by bacterial cells in the context of biofilm formation remain the subject of intensive studies. In this study, we analyzed the influence of the medium components on the induction of CaCO₃ precipitation by the Bacillus cereus cells and composition of the extracellular matrix (ECM) formed in the submerged culture. While the accumulation of extracellular polysaccharides and amyloids appeared to be independent of the presence of calcium and urea during the growth, the accumulation of extracellular DNA (eDNA), as well as precipitation of calcium carbonate, required the presence of both ingredients in the medium. Removal of eDNA, which was sensitive to treatment by DNase, did not affect other matrix components but resulted in disruption of cell network formation and a sixfold decrease in the precipitate yield. An experiment with a cell-free system confirmed the acceleration of mineral formation after the addition of exogenous salmon sperm DNA. The observed pathway for the formation of CaCO₃ minerals in B. cereus planktonic culture included a production of exopolysaccharides and negatively charged eDNA lattice promoting local Ca²⁺ supersaturation, which, together with an increase in the concentration of carbonate ions due to pH rise, resulted in the formation of an insoluble precipitate of calcium carbonate. Precipitation of amorphous CaCO₃ on eDNA matrix was followed by crystal formation via the ACC-vaterite-calcite/aragonite pathway and further formation of larger mineral aggregates in complex with extracellular polymeric substances. Taken together, our data showed that DNA in extracellular matrix is an essential factor for triggering the biomineralization in B. cereus planktonic culture.

Highlighting Bacteria with Calcifying Abilities Suitable to Improve Mortar Properties

Biomineralization, the use of microorganisms to produce calcium carbonate, became a green solution for application in construction materials to improve their strength and durability. The calcifying abilities of several bacteria were investigated by culturing on a medium with urea and calcium ions. The characterization of the precipitates from bacterial cultures was performed using X-ray diffraction, Fourier transform infrared spectroscopy, and thermogravimetric analysis. The formation of carbonate crystals was demonstrated by optical and scanning electron microscopy. Water absorption and compressive strength measurements were applied to mortars embedded with sporal suspension. The efficiency of the supplementation of mortar mixtures with bacterial cells was evaluated by properties, namely the compressive strength and the water absorption, which are in a relationship of direct dependence, the increase in compressive strength implying the decrease in water absorption. The results showed that Bacillus subtilis was the best-performing bacterium, its introduction into the mortar producing an increase in compressive strength by 11.81% and 9.50%, and a decrease in water absorption by 11.79% and 10.94%, after 28 and 56 days of curing, respectively, as compared to standards. The exploitation of B. subtilis as a calcifying agent can be an interesting prospect in construction materials.

Thermoluminescence studies of calcite conducted by bacterial CaCO3 precipitation in organic soil

In this study, the thermoluminescence (TL) properties of the calcite conducted by bacterial calcium carbonate (CaCO₃) precipitation (BCCP) in organic soils were investigated. The bacterial calcium carbonate (CaCO₃) precipitation (BCCP) is a popular technique and has been applied in a variety of civil and geotechnical engineering applications. For example, bacterial calcium carbonate precipitation fills the gaps on the organic ground and makes cementing it with the biological method using bacteria. The study reveals that the calcium carbonate mineral called as calcite has a clear TL glow curve with four main peaks located around 90, 140, 210 and 240 °C, a wide linear dose response region between 140Gy and 2.3 kGy is observed. In addition, a good reusability is seen in the high temperature peaks. The TL glow curve peaks are not affected by reusability. Although the dosimetric peaks at 210 and 240 °C appear to be nearly constant, the TL peak intensities at 90 °C and 140 °C completely faded after 24 and 336 h storage time, respectively. The activation energies (E_a) and frequency factors (s) for peaks at 90 °C, 140 °C, 210 °C and 240 °C were evaluated via variable heating rate (VHR). The activation energy of the peaks in the TL glow curve is lying between 0.57eV and 1.04 eV.

Continuous and efficient immobilization of heavy metals by phosphate-mineralized bacterial consortium

Traditional sewage treatment technology cannot remove heavy metals, which needs to be improved urgently. Lysinibacillus with the function of bio-mineralization was screened and loaded on granular sludge to form a phosphate-mineralized bacterial consortium, which demonstrated the ability of self-regulating pH and automatic solid-liquid separation. Heavy metals could be fixed on the bacterial consortium to produce stable and harmless phosphate minerals. The highest removal efficiency of Pb(Ⅱ), Cd(Ⅱ), and Ni(Ⅱ) were 97.9%, 70%, and 40%, respectively. Organic matter and other metal ions in actual polluted water had little effect on the Pb(Ⅱ) removal efficiency. Mechanism analysis was conducted through 3D-EEM, XRD, SEM-EDS, XPS, FTIR, and high-throughput sequencing analyses. The bacterial consortium was a multi-species coexistence system, but Lysinibacillus played a major role in removing Pb(Ⅱ). C-O and O-H bonds of tyrosine and phosphorous organics were broken by enzyme catalysis and the metal-oxygen bond (Pb-O) was formed. Mineral crystals in the reactor accumulated, transforming from the initial phase non-crystalline structure to the metaphase Pb₃(PO₄)₂ and eventually to the Pb₅(PO₄)₃OH. This research obtained a promising technique for immobilizing Pb(Ⅱ) or other hazardous metals continuously and efficiently.

Characterization of a Novel CaCO3-Forming Alkali-Tolerant Rhodococcus erythreus S26 as a Filling Agent for Repairing Concrete Cracks

Biomineralization, a well-known natural phenomenon associated with various microbial species, is being studied to protect and strengthen building materials such as concrete. We characterized Rhodococcus erythreus S26, a novel urease-producing bacterium exhibiting CaCO₃-forming activity, and investigated its ability in repairing concrete cracks for the development of environment-friendly sealants. Strain S26 grown in solid medium formed spherical and polygonal CaCO₃ crystals. The S26 cells grown in a urea-containing liquid medium caused culture fluid alkalinization and increased CaCO₃ levels, indicating that ureolysis was responsible for CaCO₃ formation. Urease activity and CaCO₃ formation increased with incubation time, reaching a maximum of 2054 U/min/mL and 3.83 g/L, respectively, at day four. The maximum CaCO₃ formation was achieved when calcium lactate was used as the calcium source, followed by calcium gluconate. Although cell growth was observed after the induction period at pH 10.5, strain S26 could grow at a wide range of pH 4–10.5, showing its high alkali tolerance. FESEM showed rhombohedral crystals of 20–60 µm in size. EDX analysis indicated the presence of calcium, carbon, and oxygen in the crystals. XRD confirmed these crystals as CaCO₃ containing calcite and vaterite. Furthermore, R. erythreus S26 successfully repaired the artificially induced large cracks of 0.4–0.6 mm width.

Field detection of urease and carbonic anhydrase activity using rapid and economical tests to assess microbially induced carbonate precipitation

Microbial precipitation of calcium carbonate is a widespread environmental phenomenon that has diverse engineering applications, from building and soil restoration to carbon sequestration. Urease-mediated ureolysis and CO2 (de)hydration by carbonic anhydrase (CA) are known for their potential to precipitate carbonate minerals, yet many environmental microbial community studies rely on marker gene or metagenomic approaches that are unable to determine in situ activity. Here, we developed fast and cost-effective tests for the field detection of urease and CA activity using pH-sensitive strips inside microcentrifuge tubes that change colour in response to the reaction products of urease (NH3 ) and CA (CO2 ). The urease assay proved sensitive and useful in the field to detect in situ activity in biofilms from a saline lake, a series of calcareous fens, and ferrous springs, finding relatively high urease activity in lake samples. Incubations of lake microbes with urea resulted in significantly higher CaCO3 precipitation compared to incubations with a urease inhibitor, showing that the rapid assay indicated an on-site active metabolism potentially mediating carbonate precipitation. The CA assay, however, showed less sensitivity compared to the urease test. While its sensitivity limits its utility, the assay may still be useful as a preliminary indicator given the paucity of other means for detecting CA activity in the field. Field urease, and potentially CA, activity assays complement molecular approaches and facilitate the search for carbonate-precipitating microbes and their in situ activity, which could be applied toward agriculture, engineering and carbon sequestration technologies.

Mineralogy of microbially induced calcium carbonate precipitates formed using single cell drop-based microfluidics

Microbe-mineral interactions are ubiquitous and can facilitate major biogeochemical reactions that drive dynamic Earth processes such as rock formation. One example is microbially induced calcium carbonate precipitation (MICP) in which microbial activity leads to the formation of calcium carbonate precipitates. A majority of MICP studies have been conducted at the mesoscale but fundamental questions persist regarding the mechanisms of cell encapsulation and mineral polymorphism. Here, we are the first to investigate and characterize precipitates on the microscale formed by MICP starting from single ureolytic E. coli MJK2 cells in 25 µm diameter drops. Mineral precipitation was observed over time and cells surrounded by calcium carbonate precipitates were observed under hydrated conditions. Using Raman microspectroscopy, amorphous calcium carbonate (ACC) was observed first in the drops, followed by vaterite formation. ACC and vaterite remained stable for up to 4 days, possibly due to the presence of organics. The vaterite precipitates exhibited a dense interior structure with a grainy exterior when examined using electron microscopy. Autofluorescence of these precipitates was observed possibly indicating the development of a calcite phase. The developed approach provides an avenue for future investigations surrounding fundamental processes such as precipitate nucleation on bacteria, microbe-mineral interactions, and polymorph transitions.

Effect of Target Gene Silencing on Calcite Single Crystal Formation by Thermophilic Bacterium Geobacillus thermoglucosidasius NY05

Geobacillus thermoglucosidasius NY05 catalyzes calcite single crystal formation at 60 °C by using acetate and calcium. Endospores are embedded at the central part of the calcite single crystal and carbon atoms in the calcite lattice are derived from acetate carbon. Here, we synthesized 21-mer antisense DNA oligonucleotides targeting sporulation transcription factor, acetate-CoA ligase, isocitrate lyase, and malate synthase G mRNAs and evaluated the effect of these oligonucleotides on calcite formation in G. thermoglucosidasius NY05. G. thermoglucosidasius NY05 cells containing antisense DNA oligonucleotides targeting sporulation transcription factor, acetate-CoA ligase, isocitrate lyase, and malate synthase G mRNAs had reduced calcite single crystal formation by 18.7, 50.6, 55.7, and 82.3%, respectively, compared with cells without antisense DNA oligonucleotides. These results support that calcite formation needs endospores as the nucleus to grow, and carbon dioxide generated from acetate, which is metabolized via the glyoxylate pathway and glucogenesis, is supplied to the crystal lattice.

Lead removal by phosphate solubilizing bacteria isolated from soil through biomineralization

Microorganisms with the function of biological mineralization were isolated from a soil. The bacteria were identified by 16S rRNA as Bacillus sp and possessed a significant lead removal ability. Lead removal experiment indicated that the mathematical model of η=η_max-η_ce^t/k fit the variation of removal rate with time well. Different from the previous studies, this work discovered that the culture medium had the ability to remove aqueous lead (Pb²⁺). At the same dosage, the removal rates of Pb²⁺ followed the order of: cells < culture medium < metabolites < bacterial suspension. The lead removal mechanism was further explored using the techniques of XRD, FTIR, and SEM. The results showed that during the fermentation, the bacteria decomposed phosphate-containing organic compounds in the culture medium to generate a large amount of phosphate groups on the surface of the bacterial cells. Pb²⁺ was precipitated in the form of Pb₃(PO₄)₂ stable minerals.

Urease-aided calcium carbonate mineralization for engineering applications: A review

Inducing calcium carbonate precipitation is another important function of urease in nature. The process takes advantage of the supply of carbonate ions derived from urea hydrolysis and of an increase in pH generated by the reaction, effects that in the presence of Ca²⁺ ions lead to the precipitation of CaCO₃. Further to its importance in nature, if performed in a biomimetic manner, the urease-aided CaCO₃ mineralization offers enormous potential in innovative engineering applications as an eco-friendly technique operative under mild conditions, to be used for remediation and cementation/deposition in field applications in situ. These include among others, the strengthening and consolidation of soil/sand, the protection and restoration of stone and concrete structures, conservation of stone cultural heritage materials, cleaning waste- and groundwater of toxic metals and radionuclides, and plugging geological formations for the enhancement of oil recovery and geologic CO₂ sequestration. In view of the potential of this newly emerging interdisciplinary branch of engineering, this article presents the principles of urease-aided calcium carbonate mineralization apposed to other biomineralization processes, and reviews the advantages and limitations of the technique compared to the conventional techniques presently in use. Further, it presents areas of its existing and potential applications, notably in geotechnical, construction and environmental engineering, and its future perspectives.

Genomic and Transcriptomic Insights into Calcium Carbonate Biomineralization by Marine Actinobacterium Brevibacterium linens BS258

Calcium carbonate (CaCO3) biomineralization has been investigated due to its wide range of scientific and technological implications, however, the molecular mechanisms of this important geomicrobiological process are largely unknown. Here, a urease-positive marine actinobacterium Brevibacterium linens BS258 was demonstrated to effectively form CaCO3 precipitates. Surprisingly, this bacterium could also dissolve the formed CaCO3 with the increase of the Ca2+ concentration. To disclose the mechanisms of biomineralization, the genome of B. linens BS258 was further completely sequenced. Interestingly, the expression of three carbonic anhydrases was significantly up-regulated along with the increase of Ca2+ concentration and the extent of calcite dissolution. Moreover, transcriptome analyses revealed that increasing concentration of Ca2+ induced KEGG pathways including quorum sensing (QS) in B. linens BS258. Notably, most up-regulated genes related to QS were found to encode peptide/nickel ABC transporters, which suggested that nickel uptake and its associated urease stimulation were essential to boost CaCO3 biomineralization. Within the genome of B. linens BS258, there are both cadmium and lead resistance gene clusters. Therefore, the sequestration abilities of Cd2+ and Pb2+ by B. linens BS258 were checked. Consistently, Pb2+ and Cd2+ could be effectively sequestered with the precipitation of calcite by B. linens BS258. To our knowledge, this is the first study investigating the microbial CaCO3 biomineralization from both genomic and transcriptomic insights, which paves the way to disclose the relationships among bacterial metabolisms and the biomineralization.

Magnesium-Calcite Crystal Formation Mediated by the Thermophilic Bacterium Geobacillus thermoglucosidasius Requires Calcium and Endospores

Fresh Geobacillus thermoglucosidasius cells grown on soybean-casein digest nutrient agar were inoculated as a parent colony 1 cm in diameter on the surface of an agar gel containing acetate and calcium ions (calcite-promoting hydrogel) and incubated at 60 °C for 4 days, after which magnesium-calcite single crystals of 50-130 µm in size formed within the parent colony. Addition of EDTA, polyacrylic acid or N,N-dicyclohexylcarbodiimide to the calcite-forming hydrogel inhibited the parent colony from forming magnesium-calcite crystals. Inoculation of G. thermoglucosidasius on calcite-forming hydrogel containing 5 µM cadmium and 20 µM zinc resulted in a decrease in the sporulation rate from 55 to 7-8 %. Magnesium-calcite synthesis decreased relative to the sporulation rate. G. thermoglucosidasius exhibited higher adsorption/absorbance of calcium than other Geobacillus sp. that do not mediate calcite formation and higher levels of magnesium accumulation. Calcium ions contained in the calcite-promoting hydrogel and magnesium ions concentrated in G. thermoglucosidasius cells serve as the elements for magnesium-calcite synthesis. The observed decreases in sporulation rate and magnesium-calcite formation support the hypothesis that endospores act as nuclei for the synthesis of magnesium-calcite single crystals.

Induced calcium carbonate precipitation using Bacillus species

Microbially induced calcium carbonate precipitation is an emerging process for the production of self-healing concrete. This study was aimed to investigate the effects and optimum conditions on calcium carbonate biosynthesis. Bacillus licheniformis, Bacillus sphaericus, yeast extract, urea, calcium chloride and aeration were found to be the most significant factors affecting the biomineralization of calcium carbonate. It was noticed that the morphology of microbial calcium carbonate was mainly affected by the genera of bacteria (cell surface properties), the viscosity of the media and the type of electron acceptors (Ca²⁺). The maximum calcium carbonate concentration of 33.78 g/L was achieved at the optimum conditions This value is the highest concentration reported in the literature.

Fracture Sealing with Microbially-Induced Calcium Carbonate Precipitation: A Field Study

A primary environmental risk from unconventional oil and gas development or carbon sequestration is subsurface fluid leakage in the near wellbore environment. A potential solution to remediate leakage pathways is to promote microbially induced calcium carbonate precipitation (MICP) to plug fractures and reduce permeability in porous materials. The advantage of microbially induced calcium carbonate precipitation (MICP) over cement-based sealants is that the solutions used to promote MICP are aqueous. MICP solutions have low viscosities compared to cement, facilitating fluid transport into the formation. In this study, MICP was promoted in a fractured sandstone layer within the Fayette Sandstone Formation 340.8 m below ground surface using conventional oil field subsurface fluid delivery technologies (packer and bailer). After 24 urea/calcium solution and 6 microbial (Sporosarcina pasteurii) suspension injections, the injectivity was decreased (flow rate decreased from 1.9 to 0.47 L/min) and a reduction in the in-well pressure falloff (>30% before and 7% after treatment) was observed. In addition, during refracturing an increase in the fracture extension pressure was measured as compared to before MICP treatment. This study suggests MICP is a promising tool for sealing subsurface fractures in the near wellbore environment.

Transcriptomics provides insight into Mytilus galloprovincialis (Mollusca: Bivalvia) mantle function and its role in biomineralisation

The mantle is an organ common to all molluscs and is at the forefront of the biomineralisation process. The present study used the Mediterranean mussel (Mytilus galloprovincialis) as a model species to investigate the structural and functional role of the mantle in shell formation. The transcriptomes of three regions of the mantle edge (umbo to posterior edge) were sequenced using Illumina technology which yielded a total of 61,674,325 reads after adapter trimming and filtering. The raw reads assembled into 179,879 transcripts with an N50 value of 1086bp. A total of 1363 transcripts (321, 223 and 816 in regions 1, 2 and 3, respectively) that differed in abundance in the three mantle regions were identified and putative function was assigned to 54% using BLAST sequence similarity searches (cut-off less than 1e(-10)). Morphological differences detected by histology of the three mantle regions was linked to functional heterogeneity by selecting the top five most abundant Pfam domains in the annotated 1363 differentially abundant transcripts across the three mantle regions. Calcium binding domains dominated region two (middle segment of the mantle edge). Candidate biomineralisation genes were mined and tested by qPCR. This revealed that Flp-like, a penicillin binding protein potentially involved in shell matrix maintenance of the Pacific oyster (Crassostrea gigas), had significantly higher expression in the posterior end of the mantle edge (region one). Our findings are intriguing as they indicate that the mantle edge appears to be a heterogeneous tissue, displaying structural and functional bias.

Formations of calcium carbonate minerals by bacteria and its multiple applications

Biomineralization is a naturally occurring process in living organisms. In this review, we discuss microbially induced calcium carbonate precipitation (MICP) in detail. In the MICP process, urease plays a major role in urea hydrolysis by a wide variety of microorganisms capable of producing high levels of urease. We also elaborate on the different polymorphs and the role of calcium in the formation of calcite crystal structures using various calcium sources. Additionally, the environmental factors affecting the production of urease and carbonate precipitation are discussed. This MICP is a promising, eco-friendly alternative approach to conventional and current remediation technologies to solve environmental problems in multidisciplinary fields. Multiple applications of MICP such as removal of heavy metals and radionuclides, improve the quality of construction materials and sequestration of atmospheric CO₂ are discussed. In addition, we discuss other applications such as removal of calcium ions, PCBs and use of filler in rubber and plastics and fluorescent particles in stationary ink and stationary markers. MICP technology has become an efficient aspect of multidisciplinary fields. This report not only highlights the major strengths of MICP, but also discusses the limitations to application of this technology on a commercial scale.

Carbonate Precipitation through Microbial Activities in Natural Environment, and Their Potential in Biotechnology: A Review

Calcium carbonate represents a large portion of carbon reservoir and is used commercially for a variety of applications. Microbial carbonate precipitation, a by-product of microbial activities, plays an important metal coprecipitation and cementation role in natural systems. This natural process occurring in various geological settings can be mimicked and used for a number of biotechnologies, such as metal remediation, carbon sequestration, enhanced oil recovery, and construction restoration. In this study, different metabolic activities leading to calcium carbonate precipitation, their native environment, and potential applications and challenges are reviewed.

Lacustrine Nostoc (Nostocales) and associated microbiome generate a new type of modern clotted microbialite

Microbialites are mineral formations formed by microbial communities that are often dominated by cyanobacteria. Carbonate microbialites, known from Proterozoic times through the present, are recognized for sequestering globally significant amounts of inorganic carbon. Recent ecological work has focused on microbial communities dominated by cyanobacteria that produce microbial mats and laminate microbialites (stromatolites). However, the taxonomic composition and functions of microbial communities that generate distinctive clotted microbialites (thrombolites) are less well understood. Here, microscopy and deep shotgun sequencing were used to characterize the microbiome (microbial taxa and their genomes) associated with a single cyanobacterial host linked by 16S sequences to Nostoc commune Vaucher ex Bornet & Flahault, which dominates abundant littoral clotted microbialites in shallow, subpolar, freshwater Laguna Larga in southern Chile. Microscopy and energy-dispersive X-ray spectroscopy suggested the hypothesis that adherent hollow carbonate spheres typical of the clotted microbialite begin development on the rigid curved outer surfaces of the Nostoc balls. A surface biofilm included >50 nonoxygenic bacterial genera (taxa other than Nostoc) that indicate diverse ecological functions. The Laguna Larga Nostoc microbiome included the sulfate reducers Desulfomicrobium and Sulfospirillum and genes encoding all known proteins specific to sulfate reduction, a process known to facilitate carbonate deposition by increasing pH. Sequences indicating presence of nostocalean and other types of nifH, nostocalean sulfide:ferredoxin oxidoreductase (indicating anoxygenic photosynthesis), and biosynthetic pathways for the secondary products scytonemin, mycosporine, and microviridin toxin were identified. These results allow comparisons with microbiota and microbiomes of other algae and illuminate biogeochemical roles of ancient microbialites.

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.

Geobacillus thermoglucosidasius endospores function as nuclei for the formation of single calcite crystals

Geobacillus thermoglucosidasius colonies were placed on an agar hydrogel containing acetate, calcium ions, and magnesium ions, resulting in the formation of single calcite crystals (calcites) within and peripheral to the plating area or parent colony. Microscopic observation of purified calcites placed on the surface of soybean casein digest (SCD) nutrient medium revealed interior crevices from which bacterial colonies originated. Calcites formed on the gel contained [1-(13)C]- and [2-(13)C]acetate, demonstrating that G. thermoglucosidasius utilizes carbon derived from acetate for calcite formation. During calcite formation, vegetative cells swam away from the parent colony in the hydrogel. Hard-agar hydrogel inhibited the formation of calcites peripheral to the parent colony. The calcite dissolved completely in 1 M HCl, with production of bubbles, and the remaining endospore-like particles were easily stained with Brilliant green dye. The presence of DNA and protein in calcites was demonstrated by electrophoresis. We propose that endospores initiate the nucleation of calcites. Endospores of G. thermoglucosidasius remain alive and encapsulated in calcites.

Augmented Topological Descriptors of Pore Networks for Material Science

One potential solution to reduce the concentration of carbon dioxide in the atmosphere is the geologic storage of captured CO2 in underground rock formations, also known as carbon sequestration. There is ongoing research to guarantee that this process is both efficient and safe. We describe tools that provide measurements of media porosity, and permeability estimates, including visualization of pore structures. Existing standard algorithms make limited use of geometric information in calculating permeability of complex microstructures. This quantity is important for the analysis of biomineralization, a subsurface process that can affect physical properties of porous media. This paper introduces geometric and topological descriptors that enhance the estimation of material permeability. Our analysis framework includes the processing of experimental data, segmentation, and feature extraction and making novel use of multiscale topological analysis to quantify maximum flow through porous networks. We illustrate our results using synchrotron-based X-ray computed microtomography of glass beads during biomineralization. We also benchmark the proposed algorithms using simulated data sets modeling jammed packed bead beds of a monodispersive material.

Influence of substrate mineralogy on bacterial mineralization of calcium carbonate: implications for stone conservation

The influence of mineral substrate composition and structure on bacterial calcium carbonate productivity and polymorph selection was studied. Bacterial calcium carbonate precipitation occurred on calcitic (Iceland spar single crystals, marble, and porous limestone) and silicate (glass coverslips, porous sintered glass, and quartz sandstone) substrates following culturing in liquid medium (M-3P) inoculated with different types of bacteria (Myxococcus xanthus, Brevundimonas diminuta, and a carbonatogenic bacterial community isolated from porous calcarenite stone in a historical building) and direct application of sterile M-3P medium to limestone and sandstone with their own bacterial communities. Field emission scanning electron microscopy (FESEM), atomic force microscopy (AFM), powder X-ray diffraction (XRD), and 2-dimensional XRD (2D-XRD) analyses revealed that abundant highly oriented calcite crystals formed homoepitaxially on the calcitic substrates, irrespective of the bacterial type. Conversely, scattered spheroidal vaterite entombing bacterial cells formed on the silicate substrates. These results show that carbonate phase selection is not strain specific and that under equal culture conditions, the substrate type is the overruling factor for calcium carbonate polymorph selection. Furthermore, carbonate productivity is strongly dependent on the mineralogy of the substrate. Calcitic substrates offer a higher affinity for bacterial attachment than silicate substrates, thereby fostering bacterial growth and metabolic activity, resulting in higher production of calcium carbonate cement. Bacterial calcite grows coherently over the calcitic substrate and is therefore more chemically and mechanically stable than metastable vaterite, which formed incoherently on the silicate substrates. The implications of these results for technological applications of bacterial carbonatogenesis, including building stone conservation, are discussed.