Subscribed Content Calcium Carbonate Precipitation by Ureolytic Subsurface Bacteria

Coprecipitation in carbonate minerals offers a means of slowing the transport of divalent radionuclides and contaminant metals (e.g.,⁹⁰Sr²⁺, UO²⁺, Co²⁺) in the subsurface. It may be possible to accelerate this process by stimulating the native microbial community to generate chemical conditions favoring carbonate precipitation. In a preliminary evaluation of this approach, we investigated the ability of ureolytic subsurface bacteria to produce alkaline conditions conducive to calcium carbonate precipitation. Groundwater samples from the Eastern Snake River Plain (ESRP) aquifer in Idaho were screened for urea-hydrolyzing microorganisms; three isolates were selected for further evaluation. Analysis of 16S rRNA gene sequences indicated that two of the ESRP isolates were of the genus Pseudomonas , and the other was a Variovorax sp. The specific urease activities of the ESRP isolates appeared to be similar to each other but less than that of Bacillus pasteurii , a known urease-positive organism. However, calcium carbonate was rapidly precipitated in all cultures that were supplied with urea and calcium, and X-ray diffraction analyses indicated that calcite was always the predominant carbonate polymorph produced. The correspondence between measured calcium concentrations and equilibrium predictions suggested that the rate of calcite precipitation was directly linked to the rate of urea hydrolysis. These results are promising with respect to the potential utility of this approach for in situ remediation and indicate that further evaluation of this approach under conditions more closely simulating environmental conditions is warranted.     

Microbial Carbonate Precipitation as a Soil Improvement Technique

In order to evaluate MCP as a soil strengthening process, a five meter sand column was treated with bacteria and reagents under conditions that were realistic for field applications. The injection and reaction parameters were monitored during the process and both bacteria and process reagents could be injected over the full column length at low pressures (hydraulic gradient < 1; a flow rate of approximately 7 m/day) without resulting in clogging of the material. After treatment, the column was subjected to mechanical testing, which indicated a significant improvement of strength and stiffness over several meters. Calcium carbonate was precipitated over the entire five meter treatment length. Improvement of the load bearing capacity of the soil without making the soil impermeable to fluids was shown with microbial carbonate precipitation, and this is a unique property compared to alternative soil treatment methods that are currently available for use in the subsurface.     

Formate Oxidation-Driven Calcium Carbonate Precipitation by Methylocystis parvus OBBP

Microbially induced carbonate precipitation (MICP) applied in the construction industry poses several disadvantages such as ammonia release to the air and nitric acid production. An alternative MICP from calcium formate by Methylocystis parvus OBBP is presented here to overcome these disadvantages. To induce calcium carbonate precipitation, M. parvus was incubated at different calcium formate concentrations and starting culture densities. Up to 91.4% ± 1.6% of the initial calcium was precipitated in the methane-amended cultures compared to 35.1% ± 11.9% when methane was not added. Because the bacteria could only utilize methane for growth, higher culture densities and subsequently calcium removals were exhibited in the cultures when methane was added. A higher calcium carbonate precipitate yield was obtained when higher culture densities were used but not necessarily when more calcium formate was added. This was mainly due to salt inhibition of the bacterial activity at a high calcium formate concentration. A maximum 0.67 ± 0.03 g of CaCO₃ g of Ca(CHOOH)₂⁻¹ calcium carbonate precipitate yield was obtained when a culture of 10⁹ cells ml⁻¹ and 5 g of calcium formate liter⁻¹ were used. Compared to the current strategy employing biogenic urea degradation as the basis for MICP, our approach presents significant improvements in the environmental sustainability of the application in the construction industry.     

Carbonate Mineral Precipitation for Soil Improvement Through Microbial Denitrification

Microbially induced carbonate precipitation (MICP) and associated biogas production may provide sustainable means of mitigating a number of geotechnical challenges associated with granular soils. MICP can induce interparticle soil cementation, mineral precipitation in soil pore space and/or biogas production to address geotechnical problems such as slope instability, soil erosion and scour, seepage of levees and cutoff walls, low bearing capacity of shallow foundations, and earthquake-induced liquefaction and settlement. Microbial denitrification has potential for improving the mechanical and hydraulic properties of soils because it promotes precipitation of calcium carbonate (CaCO₃) and produces nitrogen (N₂) gas without generating toxic by-products. We evaluated the potential for inducing carbonate precipitation in soil via bacterial denitrification using bench-scale experiments with the facultative anaerobe Pseudomonas denitrificans. Bench-scale experiments were conducted (1) without calcium in an N-rich bacterial growth medium in 2.0 L glass batch reactors and (2) with a source of calcium in sand-filled acrylic columns. Changes of pH, alkalinity, NO₃^? and NO₂^? in the batch reactors and columns, quantification of biogas production and observations of calcium-carbonate precipitation in the sand-filled columns indicate that denitrification led to carbonate precipitation and particle cementation in the pore water as well as a substantial amount of biogas production in both systems. These results document that bacterial denitrification has potential as a soil improvement mechanism.     

Bacterial Calcium Carbonate Precipitation in Cave Environments: A Function of Calcium Homeostasis

To determine if microbial species play an active role in the development of calcium carbonate (CaCO ₃ ) deposits (speleothems) in cave environments, we isolated 51 culturable bacteria from a coralloid speleothem and tested their ability to dissolve and precipitate CaCO ₃ . The majority of these isolates could precipitate CaCO ₃ minerals; scanning electron microscopy and X-ray diffractrometry demonstrated that aragonite, calcite and vaterite were produced in this process. Due to the inability of dead cells to precipitate these minerals, this suggested that calcification requires metabolic activity. Given growth of these species on calcium acetate, but the toxicity of Ca ²⁺ ions to bacteria, we created a loss-of-function gene knock-out in the Ca ²⁺ ion efflux protein ChaA. The loss of this protein inhibited growth on media containing calcium, suggesting that the need to remove Ca ²⁺ ions from the cell may drive calcification. With no carbonate in the media used in the calcification studies, we used stable isotope probing with C ¹³ O ₂ to determine whether atmospheric CO ₂ could be the source of these ions. The resultant crystals were significantly enriched in this heavy isotope, suggesting that extracellular CO ₂ does indeed contribute to the mineral structure. The physiological adaptation of removing toxic Ca ²⁺ ions by calcification, while useful in numerous environments, would be particularly beneficial to bacteria in Ca ²⁺ -rich cave environments. Such activity may also create the initial crystal nucleation sites that contribute to the formation of secondary CaCO ₃ deposits within caves.     

Microbially Induced Calcium Carbonate Precipitation on Surface or in the Bulk of Soil

Microbial precipitation of calcium carbonate takes place in nature by different mechanisms. One of them is microbially induced carbonate precipitation (MICP), which is performed due to bacterial hydrolysis of urea in soil in the presence of calcium ions. The MICP process can be adopted to reduce the permeability and/or increase the shear strength of soil. In this paper, a study on the use of Bacillus sp., which was isolated from tropical beach sand, to perform MICP either on the surface or in the bulk of sand is presented. If the level of calcium salt solution was below the sand surface, MICP took place in the bulk of sand. On the other hand, if the level of calcium salt solution was above the sand surface, MICP was performed on the sand surface and formed a thin layer of crust of calcium carbonate. After six sequential batch treatments with suspension of urease-producing bacteria and solutions of urea and calcium salt, the permeability of sand was reduced to 14 mm/day (or 1.6×10^?7 m/s) in both cases of bulk and surface MICP. Quantities of precipitated calcium after six treatments were 0.15 and 0.60 g of Ca per cm² of treated sand surface for the cases of bulk or surface MICP, respectively. The stiffness of the MICP treated sand also increased considerably. The modulus of rupture of the thin layer of crust was 35.9 MPa which is comparable with limestone.     

Microbially Mediated Calcium Carbonate Precipitation: Implications for Interpreting Calcite Precipitation and for Solid-Phase Capture of Inorganic Contaminants

Microbial degradation of urea was investigated as a potential geochemical catalyst for Ca carbonate precipitation and associated solid phase capture of common groundwater contaminants (Sr, UO₂, Cu) in laboratory batch experiments. Bacterial degradation of urea increased pH and promoted Ca carbonate precipitation in both bacterial control and contaminant treatments. Associated solid phase capture of Sr was highly effective, capturing 95% of the 1 mM Sr added within 24 h. The results for Sr are consistent with solid solution formation rather than discrete Sr carbonate phase precipitation. In contrast, UO₂ capture was not as effective, reaching only 30% of the initial 1 mM UO₂ added, and also reversible, dropping to 7% by 24 h. These results likely reflect differing sites of incorporation of these two elements-Ca lattice sites for Sr versus crystal defect sites for UO₂. Cu sequestration was poor, resulting from toxicity of the metal to the bacteria, which arrested urea degradation and concomitant Ca carbonate precipitation. Scanning electron microscopy (SEM) indicated a variety of morphologies reminiscent of those observed in the marine stromatolite literature. In bacterial control treatments, X-ray diffraction (XRD) analyses indicated only calcite; while in the presence of either Sr or UO₂, both calcite and vaterite, a metastable polymorph of Ca carbonate, were identified. Tapping mode atomic force microscopy (AFM) indicated differences in surface microtopography among abiotic, bacterial control, and bacterial contaminant systems. These results indicate that Ca carbonate precipitation induced by passive biomineralization processes is highly effective and may provide a useful bioremediation strategy for Ca carbonate-rich aquifers where Sr contamination issues exist.     

Biomediated Precipitation of Calcium Carbonate Metastable Phases in Hypogean Environments: A Short Review

Natural precipitates of metastable polymorphs of CaCO 3 , such as vaterite, are rarely found in nature however, they have been widely synthesized in laboratory under particular conditions (ie, supersaturated solutions, relative high temperatures, etc.). By SEM and XRD we recognize vaterite spherulites from culturable microbial colonies isolated from hypogean environments. Spherical bodies (∽10μin diameter), probably composed of vaterite, occur in submilimetric microbial mats and biofilms on volcanic substrates (Saint Callixtus Catacombs, Rome, Italy) and karstic caves (Altamira, Candamo, and Tito Bustillo caves, Spain, and Grotta dei Cervi, Italy) where cyanobacteria and actinomycetes are the major microbial components. These particles form beneath dense biofilms, where particular physicochemical conditions are developed by the microbial activity. Natural biofilms seems to generate microenvironments favoring the formation and preservation of metastable CaCO 3 polymorphs. This also shows a major role of microbes in processes of low-temperature alteration of different hypogean rock-substrates.     

Nanoparticle Accumulation in Microbial Induced Carbonate Precipitation: The Crucial Role of Extracellular Polymeric Substance

Abstract

Microbes and their secreted extracellular polymeric substance (EPS) could regulate the mineral phases, morphologies and structure of the microbial induced carbonate precipitates (MICPs). Here, two groups of mineralization experiments were carried out respectively to investigate the mechanism of the microbial induced carbonate precipitation (MICP) using Arthrobacter sp. MF-2 strain and its EPS. X-ray diffraction (XRD) were used to characterize the mineral species and scanning electron microscopy (SEM) was used to investigate the morphologies of the precipitates. Besides, focused ion beam (FIB) was used to prepare calcified bacterial slice for transmission electron microscopy (TEM) analysis. Meanwhile, the temporal change of bacterial density, pH value, conductivity, weight of precipitates, Ca²⁺ concentration and EPS content were also recorded. The results of this paper showed EPS could serve as the stabilizer of unstable phases and the scaffold for the accumulation of nanoparticles.     

GFP Facilitates Native Purification of Recombinant Perlucin Derivatives and Delays the Precipitation of Calcium Carbonate

Insolubility is one of the possible functions of proteins involved in biomineralization, which often limits their native purification. This becomes a major problem especially when recombinant expression systems are required to obtain larger amounts. For example, the mollusc shell provides a rich source of unconventional proteins, which can interfere in manifold ways with different mineral phases and interfaces. Therefore, the relevance of such proteins for biotechnological processes is still in its infancy. Here we report a simple and reproducible purification procedure for a GFP-tagged lectin involved in biomineralization, originally isolated from mother-of-pearl in abalone shells. An optimization of E. coli host cell culture conditions was the key to obtain reasonable yields and high degrees of purity by using simple one-step affinity chromatography. We identified a dual functional role for the GFP domain when it became part of a mineralizing system in vitro. First, the GFP domain improved the solubility of an otherwise insoluble protein, in this case recombinant perlucin derivatives. Second, GFP inhibited calcium carbonate precipitation in a concentration dependent manner. This was demonstrated here using a simple bulk assay over a time period of 400 seconds. At concentrations of 2 µg/ml and higher, the inhibitory effect was observed predominantly for HCO₃ ⁻ as the first ionic interaction partner, but not necessarily for Ca²⁺ _. The interference of GFP-tagged perlucin derivatives with the precipitation of calcium carbonate generated different types of GFP-fluorescent composite calcite crystals. GFP-tagging offers therefore a genetically tunable tool to gently modify mechanical and optical properties of synthetic biocomposite minerals.     

Amorphous Calcium Carbonate Precipitation by Cellular Biomineralization in Mantle Cell Cultures of Pinctada fucata

The growth of molluscan shell crystals is generally thought to be initiated from the extrapallial fluid by matrix proteins, however, the cellular mechanisms of shell formation pathway remain unknown. Here, we first report amorphous calcium carbonate (ACC) precipitation by cellular biomineralization in primary mantle cell cultures of Pinctada fucata. Through real-time PCR and western blot analyses, we demonstrate that mantle cells retain the ability to synthesize and secrete ACCBP, Pif80 and nacrein in vitro. In addition, the cells also maintained high levels of alkaline phosphatase and carbonic anhydrase activity, enzymes responsible for shell formation. On the basis of polarized light microscopy and scanning electron microscopy, we observed intracellular crystals production by mantle cells in vitro. Fourier transform infrared spectroscopy and X-ray diffraction analyses revealed the crystals to be ACC, and de novo biomineralization was confirmed by following the incorporation of Sr into calcium carbonate. Our results demonstrate the ability of mantle cells to perform fundamental biomineralization processes via amorphous calcium carbonate, and these cells may be directly involved in pearl oyster shell formation.     

Microbial Geochemical Calcium Cycle

The participation of microorganisms in the geochemical calcium cycle is the most important factor maintaining neutral conditions on the Earth. This cycle has profound influence on the fate of inorganic carbon, and, thereby, on the removal of CO₂ from the primitive atmosphere. Most calcium deposits were formed in the Precambrian, when the prokaryotic biosphere predominated. After that, calcium recycling based on biogenic deposition by skeletal organisms became the main process. Among prokaryotes, only a few representatives, e.g. cyanobacteria, exhibit a special calcium function. The geochemical calcium cycle is made possible by the universal features of bacteria involved in biologically mediated reactions and is determined by the activities of microbial communities. In the prokaryotic system, the calcium cycle begins with the leaching of igneous rocks, predominantly through the action of the community of organotrophic organisms. The release of carbon dioxide to the soil air by organotrophic aerobes leads to leaching with carbonic acid and soda salinization. Under anoxic conditions, of major importance is the organic acid production by primary anaerobes (fermentative microorganisms). Calcium carbonate is precipitated by secondary anaerobes (sulfate reducers) and to a smaller degree by methanogens. The role of the cyanobacterial community in carbonate deposition is recorded by stromatolites, which are the most common organo–sedimentary Precambrian structures. Deposition of carbonates in cyanobacterial mats as a consequence of photoassimilation of CO₂ does not appear to be a significant process. It is argued that carbonates were deposited at the boundary between the soda continent, which emerged as a result of subaerial leaching with carbonic acid, and the ocean containing Ca²⁺. Such ecotones provided favorable conditions for the development of the benthic cyanobacterial communities, which were the precursors of stromatolites.     

Process of Carbonate Precipitation by Deleya halophila

Scanning electron microscopy and X-ray dispersive energy microanalysis were used to investigate the formation of carbonate crystals by Deleya halophila. The formation of calcium carbonate crystals (polymorphous aragonite) by D. halophila is a sequential process that commences with a nucleus formed by the aggregation of a few calcified bacterial cells and the subsequent accumulation of more calcified cells and carbonate, which acts to weld the bacteria together. The process leads to the formation of spherical bioliths measuring approximately 50 μm in diameter. The mechanism of carbonate precipitation by D. halophila under our working conditions represents a process of induced biomineralization.     

Carbonate and Phosphate Precipitation by Chromohalobacter marismortui

The ability of Chromohalobacter marismortui to precipitate carbonate and phosphate minerals has been demonstrated for the first time. Mineral precipitation in both solid and liquid media at different salts concentrations and different magnesium/calcium ratios occurred whereas crystal formation was not observed in the control. The precipitated minerals were studied by X-ray diffraction, scanning electron microscopy and EDX, and were different in liquid and solid media. In liquid media aragonite, struvite, vaterite and monohydrocalcite were precipitated forming crystals and bioliths. Bioliths accreted preferentially close to organic pellicles, whereas struvite preferentially grows in microenvironments free of such pellicles. Magnesian calcite, calcian-magnesian kutnahorite, “proto-dolomite” and huntite were formed in solid media. The Mg content of the magnesian calcite and of Ca-Mg kutnahorite also varied depending on the salt concentration of the culture media. This is the first report on bacterial precipitation of Ca-Mg kutnahorite and huntite in laboratory cultures. The results of this research show the active role played by C. marismortui in mineral precipitation, and allow us to compare them with those obtained previously using other taxonomic groups of moderately halophilic bacteria.     

Manganese Carbonate Precipitation Induced by Calcite-Forming Bacteria

Abstract

Several dissimilatory metal-reducing bacteria and a halophilic bacterium are able to induce manganese carbonate (rhodochrosite) precipitation. In this study, it was revealed that Ensifer adhaerens JCM 21105^T, Microbacterium testaceum JCM 1353^T, Pseudomonas protegens DSM 19095^T, and Rheinheimera texasensis DSM 17496^T, which are calcite-forming bacteria, were able to aerobically induce the precipitation of manganese carbonate crystals on an agar medium. In the case of all four strains, the principal morphology of the precipitated manganese carbonate crystals was that of micro-sized spheres, when they were aerobically cultivated over the entire surface of the agar medium at 28?°C for 7?days.     

Microbial Metal Tolerance in Bermuda Carbonate Sediments

The recovery of aerobic heterotrophic bacteria from Bermuda carbonate sediments on metal-supplemented media varied as much as 44-fold over a 15-cm depth. Distributional relationships with sulfate-reducing bacteria and sediment character indicated that metal tolerance was a function of metal bioavailability.     

A Transferable Interatomic Potential for Calcium Carbonate

Abstract

The development of an interatomic potential for calcium carbonate is described. The potential is fitted to calcite and then transferred to aragonite. The calculated structure and trend in lattice energies are both compared with experimental values.     

Induction of Calcium Carbonate by Bacillus cereus

The purpose of this research was to study how the bacteria Bacillus cereus (DCB1) utilizes calcium ions in a culture medium with carbon dioxide (CO₂) to yield calcium carbonate (CaCO₃). The bacteria strain DCB1 was a dominant strain isolated from dolomitic surfaces in areas of Karst topographies. The experimental method was as follows: a modified beef extract-peptone medium (beef extract 3.0 g, peptone 10 g, NaCl 5.0 g, CaCl₂ 2.0 g, glass powder 2.0 g, distilled water 1 L, and a pH between 6.5 and 7.5) was inoculated with B. cereus to attempt to induce the synthesis of CaCO₃. The sample was then processed by centrifugation every 24 h during the 7-day cultivation period. The pH, carbonic anhydrase (CA) activity, and the concentrations of both HCO^- ₃ and Ca²⁺ in the supernatant fluid were measured. Subsequently, precipitation in the culture medium was analyzed to confirm, or otherwise, the presence and if present, the formation, of CaCO₃. Methods used included X-ray diffraction (XRD), Scanning Electron Microscopy (SEM), Transmission Electron Microscopy (TEM), and Energy Dispersive Spectroscopy (EDS). Meanwhile, the carbon source in the carbonate was classified by its isotope composition. Results showed that B. cereus can improve its pH value in this culture medium; concentrations of HCO^- ₃ and Ca²⁺ showed a significant decline over the duration of the cultivation period. CA activity reached its maximum during the second day; XRD, SEM, TEM, and isotope analysis all revealed the presence of CaCO₃ as a precipitate. Additionally, these results did not occur in an aseptic control group: no detectable level of CaCO₃ was produced therein. In conclusion: B. cereus can metabolize active materials, such as secretase, by its own growth and metabolism, and can either utilize atmospheric CO₂, or respire, to induce CaCO₃ production. Experimental evidence is offered for a concomitant CO₂ reduction and CaCO₃ induction by microorganisms.