Characterization and genome analysis of Neobacillus mesonae NS-6, a ureolysis-driven strain inducing calcium carbonate precipitation
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ABSTRACT:
SUBMITTER: Xu R
PROVIDER: S-EPMC10646308 | biostudies-literature | 2023 Jan
REPOSITORIES: biostudies-literature
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Project description:During a study of ureolytic microbial calcium carbonate (CaCO(3)) precipitation by bacterial isolates collected from different environmental samples, morphological differences were observed in the large CaCO(3) crystal aggregates precipitated within bacterial colonies grown on agar. Based on these differences, 12 isolates were selected for further study. We hypothesized that the striking differences in crystal morphology were the result of different microbial species or, alternatively, differences in the functional attributes of the isolates selected. Sequencing of 16S rRNA genes showed that all of the isolates were phylogenetically closely related to the Bacillus sphaericus group. Urease gene diversity among the isolates was examined by using a novel application of PCR-denaturing gradient gel electrophoresis (DGGE). This approach revealed significant differences between the isolates. Moreover, for several isolates, multiple bands appeared on the DGGE gels, suggesting the apparent presence of different urease genes in these isolates. The substrate affinities (K(m)) and maximum hydrolysis rates (V(max)) of crude enzyme extracts differed considerably for the different strains. For certain isolates, the urease activity increased up to 10-fold in the presence of 30 mM calcium, and apparently this contributed to the characteristic crystal formation by these isolates. We show that strain-specific calcification occurred during ureolytic microbial carbonate precipitation. The specificity was mainly due to differences in urease expression and the response to calcium.
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Project description:Patterned calcium carbonate materials with controlled morphologies have broad applications in both environmental and engineering fields. However, how to fabricate such materials through environmental-friendly methods under ambient conditions is still challenging. Here, we report a green approach for fabricating patterned calcium carbonate materials. This eco-friendly approach is based on template-assisted microbially induced calcium carbonate precipitation. As a proof of concept, by varying the templates and optimizing fabrication parameters, different patterned calcium carbonate materials were obtained. The optimized parameters include C Ca2+ = 80 mM, T i = 15 °C, and templates made of small-sized CaCO3 particles with a concentration of 1.5 mg mL-1, under which better and more sharp patterns were obtained. Materials with periodic patterns were also fabricated through a periodic template, showing good scalability of this approach. The results of this study could mean great potential in applications where spatially controlled calcium carbonate depositions with user-designed patterns are needed.
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Project description:Calcium carbonate is an important component in exoskeletons of many organisms. The synthesis of calcium carbonate was performed by mixing dimethyl carbonate and an aqueous solution of calcium chloride dihydrate. The precipitation product was characterized by means of scanning electron microscopy (SEM), transmission electron microscopy (TEM), X-ray diffraction (XRD), and Fourier transform infrared spectroscopy (FTIR) measurements. In addition, the turbidity of the reaction solution was acquired to monitor the kinetics of the calcium carbonate structure's growth in the investigated system. In this study, samples of CaCO₃ particles obtained with individual proteins, such as ovalbumin, lysozyme, and a mixture of the proteins, were characterized and compared with a control sample, i.e., synthesized without proteins. The obtained data indicated that the addition of ovalbumin to the reaction changed the morphology of crystals from rhombohedral to 'stack-like' structures. Lysozyme, however, did not affect the morphology of calcium carbonate, yet the presence of the protein mixture led to the creation of more complex composites in which the calcium carbonate crystals were constructed in protein matrices formed by the ovalbumin-lysozyme interaction. It was also observed that in the protein mixture, ovalbumin has a major influence on the CaCO₃ formation through a strong interaction with calcium ions, which leads to the coalescence and creation of a steric barrier reducing particle growth. The authors proposed a mechanism of calcium carbonate grain growth in the presence of both proteins, taking into account the interaction of calcium ions with the protein.
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Project description:The use of additives has generated significant attention due to their extensive application in the microbially induced calcium carbonate precipitation (MICP) process. This study aims to discuss the effects of Na-montmorillonite (Na-MMT) on CaCO3 crystallization and sandy soil consolidation through the MICP process. Compared with the traditional MICP method, a larger amount of CaCO3 precipitate was obtained. Moreover, the reaction of Ca2+ ions was accelerated, and bacteria were absorbed by a small amount of Na-MMT. Meanwhile, an increase in the total cementing solution (TCS) was not conducive to the previous reaction. This problem was solved by conducting the reaction with Na-MMT. The polymorphs and morphologies of the CaCO3 precipitates were tested by using X-ray diffraction and scanning electron microscopy. Further, when Na-MMT was used, the morphology of CaCO3 changed from an individual precipitate to agglomerations of the precipitate. Compared to the experiments without Na-MMT in the MICP process, the addition of Na-MMT significantly reduced the hydraulic conductivity (HC) of sandy soil consolidated.
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Project description:Bacteria that are resistant to high temperatures and alkaline environments are essential for the biological repair of damaged concrete. Alkaliphilic and halotolerant Bacillus sp. AK13 was isolated from the rhizosphere of Miscanthus sacchariflorus. Unlike other tested Bacillus species, the AK13 strain grows at pH 13 and withstands 11% (w/v) NaCl. Growth of the AK13 strain at elevated pH without urea promoted calcium carbonate (CaCO3) formation. Irregular vateritelike CaCO3 minerals that were tightly attached to cells were observed using field-emission scanning electron microscopy. Energy-dispersive X-ray spectrometry, confocal laser scanning microscopy, and X-ray diffraction analyses confirmed the presence of CaCO3 around the cell. Isotope ration mass spectrometry analysis confirmed that the majority of CO32- ions in the CaCO3 were produced by cellular respiration rather than being derived from atmospheric carbon dioxide. The minerals produced from calcium acetate-added growth medium formed smaller crystals than those formed in calcium lactate-added medium. Strain AK13 appears to heal cracks on mortar specimens when applied as a pelletized spore powder. Alkaliphilic Bacillus sp. AK13 is a promising candidate for self-healing agents in concrete.
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Project description:Many challenges related to carbon-dioxide ([Formula: see text]) sequestration in subsurface rock are linked to the injection of fluids through induced or existing fracture networks and how these fluids are altered through geochemical interactions. Here, we demonstrate that fluid mixing and carbonate mineral distributions in fractures are controlled by gravity-driven chemical dynamics. Using optical imaging and numerical simulations, we show that a density contrast between two miscible fluids causes the formation of a low-density fluid runlet that increases in areal extent as the fracture inclination decreases from 90[Formula: see text] (vertical fracture plane) to 30[Formula: see text]. The runlet is sustained over time and the stability of the runlet is controlled by the gravity-driven formation of 3D vortices that arise in a laminar flow regime. When homogeneous precipitation was induced, calcium carbonate covered the entire surface for horizontal fractures (0[Formula: see text]). However, for fracture inclinations greater than 10[Formula: see text], the runlet formation limited the areal extent of the precipitation to less than 15% of the fracture surface. These insights suggest that the ability to sequester [Formula: see text] through mineralization along fractures will depend on the fracture orientation relative to gravity, with horizontal fractures more likely to seal uniformly.
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Project description:The evolution of multicellularity in animals required the production of extracellular matrices that serve to spatially organize cells according to function. In corals, three matrices are involved in spatial organization: (i) an organic ECM, which facilitates cell-cell and cell-substrate adhesion; (ii) a skeletal organic matrix (SOM), which facilitates controlled deposition of a calcium carbonate skeleton; and (iii) the calcium carbonate skeleton itself, which provides the structural support for the 3D organization of coral colonies. In this report, we examine the production of these three matrices by using an in vitro culturing system for coral cells. In this system, which significantly facilitates studies of coral cell physiology, we demonstrate in vitro excretion of ECM by primary (nondividing) tissue cultures of both soft (Xenia elongata) and hard (Montipora digitata) corals. There are structural differences between the ECM produced by X. elongata cell cultures and that of M. digitata, and ascorbic acid, a critical cofactor for proline hydroxylation, significantly increased the production of collagen in the ECM of the latter species. We further demonstrate in vitro production of SOM and extracellular mineralized particles in cell cultures of M. digitata. Inductively coupled plasma mass spectrometry analysis of Sr/Ca ratios revealed the particles to be aragonite. De novo calcification was confirmed by following the incorporation of (45)Ca into acid labile macromolecules. Our results demonstrate the ability of isolated, differentiated coral cells to undergo fundamental processes required for multicellular organization.
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Project description:Simple plugging of the high-permeability "thief zones" of oil reservoirs is the most plausible and also the most straightforwardly achievable approach to enhance sweep efficiency and oil recovery. Sporosarcina pasteurii is a representative microorganism with the ability to precipitate calcium carbonate (CaCO3) via enzymatic hydrolysis of urea in the presence of calcium ions. Microbially induced calcium carbonate precipitation (MICP) can cement and seal the granular and fractured media and thus can be used as a potential microbial plugging agent for the high-permeability zones of oil reservoirs. The following investigated the microscopic characteristics of MICP plugging and its efficacy in permeability reduction. The columns of near-spherical silica sand and angular silica sand with three separate granularities (40/60, 60/80, and 80/120 mesh) were used as artificial rock cores representing distinct pore sizes and pore characteristics to investigate the efficacy and microprocess of MICP plugging with different biotreatment periods. The results indicated that permeability is reduced significantly after only short periods of biotreatment. After eight cycles of MICP treatments, the permeability for each type of cores dropped by 54-90% of individual initial permeabilities. The measured CaCO3 content indicated that the decreasing rate in permeability with the increasing CaCO3 content experiences three contrasting stages, namely, slow decline, speedy decline, and plateauing. X-ray diffraction indicated that most of the generated CaCO3 crystals occur as vaterite with only a small amount of calcite. Imaging by scanning electron microscopy further revealed the microprocess of MICP plugging. Microorganisms first concentrate on the pore wall to secrete CaCO3, forming a thin and large uniform layer of CaCO3. Then, some nucleation sites of CaCO3 crystals will experience further preferential growth, resulting in large, dominant crystals that act as a plugging agent within the pore space. Compared to extracellular polymeric substances, which are currently the primary microbial plugging agent used to enhance sweep efficiency of oil reservoirs, bio-CaCO3 appears more effective in plugging in terms of its morphology, size, and growth characteristics.
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Project description:Saccharomyces cerevisiae plays an important role in the mineralization of many metal ions, but it is unclear whether this fungus is involved in the mineralization of calcium carbonate. In this study, S. cerevisiae was cultured under various conditions to explore its ability to perform microbially induced calcium carbonate precipitation (MICP). Organic acids, yeast extract, and low-carbon conditions were the factors influencing the biomineralization of calcium carbonate caused by S. cerevisiae, and biomolecules secreted by the fungus under different conditions could change the morphology, size, and crystal form of the biosynthesized mineral. In addition, transcriptome analysis showed that the oxidation of organic acids enhanced the respiration process of yeast. This implied that S. cerevisiae played a role in the formation of calcium carbonate through the mechanism of creating an alkaline environment by the respiratory metabolism of organic acids, which could provide sufficient dissolved inorganic carbon for calcium carbonate formation. These results provide new insights into the role of S. cerevisiae in biomineralization and extend the potential applications of this fungus in the future.
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Project description:Phosphorus (P) is a vital micronutrient element for all life forms. Typically, P can be extracted from phosphate rock. Unfortunately, the phosphate rock is a nonrenewable resource with a limited reserve on the earth. High levels of P discharged to water bodies lead to eutrophication. Therefore, P needs to be removed and is preferably recovered as an additional P source. A possible way to achieve this goal is by electrochemically induced phosphate precipitation with coexisting calcium ions. Here, we report a new concept of phosphate removal and recovery, namely a CaCO3 packed electrochemical precipitation column, which achieved improved removal efficiency, shortened hydraulic retention time, and substantially enhanced stability, compared with our previous electrochemical system. The concept is based on the introduction of CaCO3 particles, which facilitates calcium phosphate precipitation by buffering the formed H+ at the anode, releases Ca2+, acts as seeds, and establishes a high pH environment in the bulk solution in addition to that in the vicinity of the cathode. It was found that the applied current, the CaCO3 particle size, and the feed rate affect the removal of phosphate. Under optimized conditions (particle size, <0.5 mm; feed rate, 0.4 L/d; current, 5 mA), in a continuous flow system, the CaCO3 packed electrochemical precipitation column achieved 90 ± 5% removal of phosphate in 40 days and >50% removal over 125 days with little maintenance. The specific energy consumptions of this system lie between 29 and 61 kWh/kg P. The experimental results demonstrate the promising potential of the CaCO3 packed electrochemical precipitation column for P removal and recovery from P-containing streams.
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