Biomineralization of Monohydrocalcite Induced by the Halophile Halomonas smyrnensis WMS‐3

Co-removal and recycling of Ba2+ and Ca2+ in hypersaline wastewater based on the microbially induced carbonate precipitation technique: Overlooked Ba2+ in extracellular and intracellular vaterite

This study investigates the co-precipitation of calcium and barium ions in hypersaline wastewater under the action of Bacillus licheniformis using microbially induced carbonate precipitation (MICP) technology, as well as the bactericidal properties of the biomineralized product vaterite. The changes in carbonic anhydrase activity, pH, carbonate and bicarbonate concentrations in different biomineralization systems were negatively correlated with variations in metal ion concentrations, while the changes in polysaccharides and protein contents in bacterial extracellular polymers were positively correlated with variations in barium concentrations. In the mixed calcium and barium systems, the harvested minerals were vaterite containing barium. The increasing concentrations of calcium promoted the incorporation and adsorption of barium onto vaterite. The presence of barium significantly increased the contents of O-CO, N-CO, and Ba-O in vaterite. Calcium promoted barium precipitation, but barium inhibited calcium precipitation. After being treated by immobilized bacteria, the concentrations of calcium and barium ions decreased from 400 and 274 to 1.72 and 0 mg/L (GB/T15454-2009 and GB8978-1996). Intracellular minerals were also vaterite containing barium. Extracellular vaterite exhibited bactericidal properties. This research presents a promising technique for simultaneously removing and recycling hazardous heavy metals and calcium in hypersaline wastewater.

Carbonate chimneys at the highly productive point Dume methane seep: Fine-scale mineralogical, geochemical, and microbiological heterogeneity reflects dynamic and long-lived methane-metabolizing habitats

Methane is a potent greenhouse gas that enters the marine system in large quantities at seafloor methane seeps. At a newly discovered seep site off the coast of Point Dume, CA, ~ meter-scale carbonate chimneys host microbial communities that exhibit the highest methane-oxidizing potential recorded to date. Here, we provide a detailed assessment of chimney geobiology through correlative mineralogical, geochemical, and microbiological studies of seven chimney samples in order to clarify the longevity and heterogeneity of these highly productive systems. U-Th dating indicated that a methane-driven carbonate precipitating system at Point Dume has existed for ~20 Kyr, while millimeter-scale variations in carbon and calcium isotopic values, elemental abundances, and carbonate polymorphs revealed changes in carbon source, precipitation rates, and diagenetic processes throughout the chimneys' lifespan. Microbial community analyses revealed diverse modern communities with prominent anaerobic methanotrophs, sulfate-reducing bacteria, and Anaerolineaceae; communities were more similar within a given chimney wall transect than in similar horizons of distinct structures. The chimneys represent long-lived repositories of methane-oxidizing communities and provide a window into how carbon can be transformed, sequestered, and altered over millennia at the Point Dume methane seep.

Effect of Ba2+ on the biomineralization of Ca2+ and Mg2+ ions induced by Bacillus licheniformis

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

Difference in calcium ion precipitation between free and immobilized Halovibrio mesolongii HMY2

Biomineralization has become a research focus in wastewater treatment due to its much lower costs compared to traditional methods. However, the low sodium chloride (NaCl)-tolerance of bacteria limits applications to only water with low NaCl concentrations. Here, calcium ions in hypersaline wastewater (10% NaCl) were precipitated by free and immobilized Halovibrio mesolongii HMY2 bacteria and the differences between them were determined. The results show that calcium ions can be transformed into several types of calcium carbonate with a range of morphologies, abundant organic functional groups (C-H, C-O-C, C=O, etc), protein secondary structures (β-sheet, α-helix, 3₁₀ helix, and β-turn), P=O and S-H indicated by P2p and S2p, and more negative δ¹³C_PDB (‰) values (-16.8‰ to -18.4‰). The optimal conditions for the immobilized bacteria were determined by doing experiments with six factors and five levels and using response surface method. Under the action of two groups of immobilized bacteria prepared under the optimal conditions, by the 10^th day, Ca²⁺ ion precipitation ratios had increased to 79%-89% and 80%-88% with changes in magnesium ion cencentrations. Magnesium ions can significantly inhibit the calcium ion precipitation, and this inhibitory effect can be decreased under the action of immobilized bacteria. Minerals induced by immobilized bacteria always aggregated together, had higher contents of Mg, P, and S, lower stable carbon isotope values and less well-developed protein secondary structures. This study demonstrates an economic and eco-friendly method for recycling calcium ions in hypersaline wastewater, providing an easy step in the process of desalination.

Mineralogy of Bioprecipitate Evolution over Induction Times Mediated by Halophilic Bacteria under Various Mg/Ca Molar Ratios

In microbial mineralization experiments, the induction time of mineral precipitation is ambiguous, and this may lead to difficulties in reproducing and confirming the test results. To explore the link between induction time and microbially mediated carbonate precipitation, we report here the mineralogy and morphology of carbonate precipitates induced by the halophilic Halomonas utahensis WMS2 bacterium in media with various Mg/Ca molar ratios over a range of induction times. The results show that the biominerals are formed in an alkaline environment affected by ammonia secreted by H. utahensis WMS2 bacteria. The content of dissolved inorganic carbon increased as a result of carbonic anhydrase catalyzing the hydration of carbon dioxide to release bicarbonate and carbonate ions. The X-ray diffraction (XRD) results show that the phase of mineral precipitated gradually changes from an unstable Mg-rich calcite to metastable monohydrocalcite and then to stable hydromagnesite with an increase in the Mg²⁺ ion concentration and induction time. The scanning electron microscopy (SEM), energy-dispersive X-ray spectroscopy (EDS), and Fourier transform infrared spectroscopy (FTIR) results show that minerals mostly change from single particles/crystallites to aggregations under the action of the microorganisms at different Mg²⁺ ion concentrations and induction times. Our experiments demonstrate that the carbonate minerals produced in the presence of microbes change significantly with the induction time, in addition to the influence of the hydrochemical factors; this indicates that the induction time is significant in determining the mineralogy of biominerals.

Biomineralization of Carbonates Induced by Mucilaginibacter gossypii HFF1: Significant Role of Biochemical Parameters

Although the precipitation of carbonate minerals induced by various bacteria is widely studied, the changes in the biochemical parameters, and their significant role in the biomineralization processes, still need further exploration. In this study, Mucilaginibacter gossypii HFF1 was isolated, identified, and used to induce carbonate minerals at various Mg/Ca ratios. The biochemical parameters were determined in order to explore the biomineralization mechanisms, including cell concentration, pH, ammonia, carbonic anhydrase activity, and alkaline phosphatase activity. The characteristics of extracellular minerals and intracellular inclusions were both analyzed. In addition, the amino acid composition of the extracellular polymeric substance was also tested. Results show that the biochemical parameters provide an alkaline environment for precipitation, due to the combined effect of ammonia, carbonic anhydrase, and alkaline phosphatase. Biotic minerals are characterized by preferred orientation, specific shape, and better crystalline and better thermal stability, indicating their biogenesis. Most of the amino acids in the extracellular polymeric substance are negatived charged, and facilitate the binding of magnesium and calcium ions. The particles with weak crystalline structure in the EPS prove that it acts as a nucleation site. Intracellular analyses prove the presence of the intracellular amorphous inclusions. Our results suggest that the changes in the biochemical parameters caused by bacteria are beneficial to biomineralization, and play a necessary role in its process. This offers new insight into understanding the biomineralization mechanism of the bacteria HFF1.

High Mg/Ca Molar Ratios Promote Protodolomite Precipitation Induced by the Extreme Halophilic Bacterium Vibrio harveyi QPL2

Bacterial activities have been demonstrated as critical for protodolomite precipitation in specific aqueous conditions, whereas the relationship between the various hydrochemical factors and bacterial activity has not been fully explored. In this study, biomineralization experiments were conducted using a newly isolated extreme halophilic bacterium from salina mud, Vibrio harveyi QPL2, under various Mg/Ca molar ratios (0, 3, 6, 10, and 12) and a salinity of 200‰. The mineral phases, elemental composition, morphology, and crystal lattice structure of the precipitates were analyzed by XRD, SEM, and HRTEM, respectively. The organic weight and functional groups in the biominerals were identified by TG-DSC, FTIR, and XPS analysis. The amounts of amino acids and polysaccharides in the EPS of QPL2 cultured at various Mg/Ca molar ratios were quantified by an amino acid analyzer and high-performance liquid chromatography. The results confirm that disordered stoichiometric protodolomite was successfully precipitated through the activities of bacteria in a medium with relatively high Mg/Ca molar ratios (10 and 12) but it was not identified in cultures with lower Mg/Ca molar ratios (0, 3, and 6). That bacterial activity is critical for protodolomite formation as shown by the significant bacterial relicts identified in the precipitated spherulite crystals, including pinhole structures, a mineral coating around cells, and high organic matter content within the crystals. It was also confirmed that the high Mg/Ca molar ratio affects the composition of the organic components in the bacterial EPS, leading to the precipitation of the protodolomite. Specifically, not only the total EPS amount, but also other facilitators including the acidic amino acids (Glu and Asp) and polysaccharides in the EPS, increased significantly under the high Mg/Ca molar ratios. Combined with previous studies, the present findings suggest a clear link between high Mg/Ca molar ratios and the formation of protodolomite through halophilic bacterial activity.

New Biocalcifying Marine Bacterial Strains Isolated from Calcareous Deposits and Immediate Surroundings

Marine bacterial biomineralisation by CaCO3 precipitation provides natural limestone structures, like beachrocks and stromatolites. Calcareous deposits can also be abiotically formed in seawater at the surface of steel grids under cathodic polarisation. In this work, we showed that this mineral-rich alkaline environment harbours bacteria belonging to different genera able to induce CaCO3 precipitation. We previously isolated 14 biocalcifying marine bacteria from electrochemically formed calcareous deposits and their immediate environment. By microscopy and µ-Raman spectroscopy, these bacterial strains were shown to produce calcite-type CaCO3. Identification by 16S rDNA sequencing provided between 98.5 and 100% identity with genera Pseudoalteromonas, Pseudidiomarina, Epibacterium, Virgibacillus, Planococcus, and Bhargavaea. All 14 strains produced carbonic anhydrase, and six were urease positive. Both proteins are major enzymes involved in the biocalcification process. However, this does not preclude that one or more other metabolisms could also be involved in the process. In the presence of urea, Virgibacillus halodenitrificans CD6 exhibited the most efficient precipitation of CaCO3. However, the urease pathway has the disadvantage of producing ammonia, a toxic molecule. We showed herein that different marine bacteria could induce CaCO3 precipitation without urea. These bacteria could then be used for eco-friendly applications, e.g., the formation of bio-cements to strengthen dikes and delay coastal erosion.

Using electromagnetic fields to inhibit biofouling and scaling in biogas slurry drip irrigation emitters

Reusing biogas slurry (BS) in agricultural drip irrigation systems may provide a solution to deal with the adverse environmental impacts of applying BS. Biofouling and scaling are two leading issues in drip irrigation emitters. This study investigated a practice that applied electromagnetic fields (EMFs) to control biofilms and scales. The bacterial communities and mineral precipitations in the clogging substances of emitters were determined. Results showed that EMFs inhibited the growth of microbes, and influenced BS physicochemical parameters. Consequently, EMFs shifted the bacterial communities with reduced diversities. Network analyses revealed that bacterial species under EMFs treatments showed lower average connectivities and simpler interactions, which were responsible for the decreases of extracellular polymers substances (EPS). Moreover, EMFs treatments not only reduced the carbonates in emitters, but also prevented the depositions of phosphates, silicates, and quartzes. EMFs also had impacts on the lattice parameters and crystal volumes of carbonates. In addition, the changes in bacterial communities and EPS contents were associated with the reductions of various minerals. Accordingly, EMFs effectively mitigated biofilms and scales with the fixed clogging substances reduced by 29.1-53.8 %. These findings demonstrated that applying EMFs is an effective anti-biofouling and anti-scaling treatment with potential applications in BS irrigation systems.

Carbonate biomineralization differentially induced by two psychrophilic Pseudomonas psychrophila strains isolated from an alpine travertine landform

Besides geography and climate, biological factors play an important role in shaping travertine landforms, but the biochemical mechanisms of microbial processes in travertine formation have been rarely studied. Two psychrophilic bacterial strains, A20-18 and B21-3 of Pseudomonas psychrophila, isolated from travertine pools of Huanglong, a typical alpine travertine landform, were investigated for their roles in calcium carbonate mineralization, including the deposition process and products. X-ray diffraction, Fourier-transform infrared spectroscopy, and scanning electron microscopy were used to characterize the crystal phase and morphology of CaCO₃ precipitation. The results showed that there were no significant differences between the two strains in CaCO₃ deposition rate. Extracellular polymeric substances (EPS)-free cells significantly inhibited calcification, compared with a control. Irregular crystals and polyhedral structures are common to all treatments using the two strains. These complex polycrystals were the result of the synergistic effect of homogeneous nucleation and heterogeneous nucleation. EPS and cells of strain B21-3 formed ring-like structures of calcium carbonate, which was possibly from the amphiphilic polymer forming a circular arrangement in water. These results are significant for understanding the microbial factor in Huanglong travertine deposition and providing new insights into the morphological control of the biomineralization mechanism at low temperatures.

Calcium carbonate crystals induced by two Pseudomonas psychrophila strains and their organic compounds were studied.

Incorporating Far-Infrared Data into Carbonate Mineral Analyses

Polycrystalline carbonate minerals (including calcite, Mg-calcite, and aragonite) can show distinctive variations in their far-infrared (FIR) spectra. We describe how to identify mixed-phase samples by correlating FIR spectral changes with mid-infrared spectra, X-ray diffraction data, and simple peak overlap simulations. Furthermore, we show how to distinguish portlandite-containing (Ca(OH) 2 ) mixtures that are common in heated calcium carbonate samples. Ultimately, these results could be used for tracking how minerals are formed and how they change during environmental exposure or processing after extraction.

Biomineralization of Carbonate Minerals Induced by The Moderate Halophile Staphylococcus Warneri YXY2

Although biomineralization of minerals induced by microorganisms has been widely reported, the mechanisms of biomineralization and the characteristics of the biominerals precipitated needs to be studied further. In this study, Staphylococcus warneri YXY2, a moderate halophile, was used to induce the precipitation of carbonate minerals at various Mg/Ca molar ratios. To investigate the biomineralization mechanism, the growth curve, pH changes, ammonia test, the concentration of bicarbonate and carbonate ions, and the activity of carbonic anhydrase (CA) and alkaline phosphatase (ALP) were determined. X-ray powder diffraction (XRD), scanning electron microscopy - energy disperse spectroscopy (SEM-EDS), Fourier transform infrared spectroscopy (FTIR), X-ray photoelectron spectroscopy (XPS), scanning transmission electron microscopy (STEM), and stable carbon isotope analyses were used to characterize the minerals. The obtained biotic minerals were calcite, vaterite, Mg-rich calcite, and aragonite crystals. The crystallinity of aragonite decreased with increasing Mg/Ca ratios. The preferred orientation, diverse morphologies, organic substances, and more negative stable carbon isotope values proved the biogenesis of these carbonate minerals. The presence of Mg in the biotic aragonite crystals was likely related to the acidic amino acids which also facilitated the nucleation of minerals on/in the extracellular polymeric substances (EPS). Mg2+ and Ca2+ ions were able to enter into the YXY2 bacteria to induce intracellular biomineralization. Dynamics simulation using Material Studio software proved that different adsorption energies of Glutamic acid (Glu) adsorbed onto different crystal planes of aragonite led to the preferred orientation of aragonite. This study helps to deepen our understanding of biomineralization mechanisms and may be helpful to distinguish biotic minerals from abiotic minerals.

Bio-Precipitation of Carbonate and Phosphate Minerals Induced by the Bacterium Citrobacter freundii ZW123 in an Anaerobic Environment

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