Biomineralization of carbonate and phosphate by moderately halophilic bacteria

Phenolate-thiazole based reversible "turn-on" chemosensor for the selective detection of carbonate anion: X-ray crystallography, DFT/TDFT, and cell study

A new phenolate-thiazole derivative (L) has been synthesized and structurally characterized.The chemo-sensing activity of L is detected by the naked eye for the aqueous carbonate anion in the pH range of 4 to 8. The selective 'turn-on' fluorescence occurs through the formation of a stable intermediate L∙CO32-(1) following the PET mechanism. The limit of detection (LOD) is found 0.18 µM based on the absorbance-based assay.The quinonoid form of bromophenol unit binds strongly with CO32- through thiazole nitrogen and hydrazinic nitrogen. Further, the selective holding of CO32- anion over other planar tetranuclear anions (e.g., SO32-, NO3-) happens with several intra and intermolecular hydrogen bonds as envisaged by the DFT/TDFT study. The formation mechanism of L∙CO32- is proposed based on experimental and theoretical studies. The biological experiments (MTT and cell imaging)reveal the non-cytotoxicity nature of L and the biocompatible uptake of L mostly in the cytoplasm at physiological pH.

Searching for microbial contribution to micritization of shallow marine sediments

Micritization is an early diagenetic process that gradually alters primary carbonate sediment grains through cycles of dissolution and reprecipitation of microcrystalline calcite (micrite). Typically observed in modern shallow marine environments, micritic textures have been recognized as a vital component of storage and flow in hydrocarbon reservoirs, attracting scientific and economic interests. Due to their endolithic activity and the ability to promote nucleation and reprecipitation of carbonate crystals, microorganisms have progressively been shown to be key players in micritization, placing this process at the boundary between the geological and biological realms. However, published research is mainly based on geological and geochemical perspectives, overlooking the biological and ecological complexity of microbial communities of micritized sediments. In this paper, we summarize the state-of-the-art and research gaps in micritization from a microbial ecology perspective. Since a growing body of literature successfully applies in vitro and in situ 'fishing' strategies to unveil elusive microorganisms and expand our knowledge of microbial diversity, we encourage their application to the study of micritization. By employing these strategies in micritization research, we advocate promoting an interdisciplinary approach/perspective to identify and understand the overlooked/neglected microbial players and key pathways governing this phenomenon and their ecology/dynamics, reshaping our comprehension of this process.

Preliminary indication of the role of AHL-dependent quorum sensing systems in calcium carbonate precipitation in Gram-negative bacteria

Numerous microbial species participate in precipitation of carbonates in various natural environments, including soils, geological formations, freshwater biofilms and oceans. Despite the geochemical interest of such a biomineralization process, its molecular mechanisms and adaptive aspects remain poorly known. Many Gram-negative bacteria use cell-to-cell communication systems relying on N-acylhomoserine lactone (AHLs) signal molecules to express certain phenotypic traits in a density-dependent manner, a phenomenon referred as to quorum-sensing (QS). In this work, bacterial isolates collected from cave and rhizosphere soil were analyzed to study the occurrence of the AHL-mediated QS in bacterial calcium carbonate (CaCO3) precipitation. To test the production of AHLs signal molecules, we cross-streaked Gram-negative calcifying strains, selected among the environmental strains studied, with the AHL-negative mutant Chromobacterium subtsugae strain CV026. Only Burkholderia ambifaria LMG 11351 was able to restore violacein production in CV026 among the tested strains. The constructed AHL-negative mutant of B. ambifaria LMG 11351 could not precipitate CaCO3 on B-4 agar. Scanning Electron Microscopy (SEM) analysis on CaCO3 crystals obtained in vitro shows crystals of different morphologies, calcified biofilms and bacteria in close contact with the precipitated crystals. In the inner layers of the bioliths deposited by B. ambifaria LMG 11351, a stream-like organization of the Burkholderia imprints was not detected by SEM. Our data provide preliminary evidence that the activation of AHL-regulated genes may be a prerequisite for in vitro bacterial carbonatogenesis, in some cases, confirming the specific role of bacteria as CaCO3 precipitating agents. We enhance the understanding of bacterial CaCO3 biomineralization and its potential biotechnology implications for QS-based strategies to enhance or decrease CaCO3 precipitation through specific bacterial processes. The AHL-negative mutant of B. ambifaria LMG 11351 (a well-known plant growth-promoting bacterium) could also be used to study plant-bacteria interactions. The adaptive role of bacterial CaCO3 biomineralization was also discussed.

Biologically-induced synthetic manganese carbonate precipitate (BISMCP) for potential applications in heavy metal removal

Heavy metal pollution of water is a burning issue of today's world. Among several strategies involved for heavy metal remediation purpose, biomineralization has shown great potential. Of late, research has been focused on developing effective mineral adsorbents with reduced time and cost consumption. In this present paper, the Biologically-Induced Synthetic Manganese Carbonate Precipitate (BISMCP) was produced based on the biologically-induced mineralization method, employing Sporosarcina pasteurii in aqueous solutions containing urea and MnCl₂. The prepared adsorbent was characterized using Fourier transform infrared spectroscopy (FTIR), scanning electron microscopy (SEM), SEM-energy dispersive X-ray spectroscopy (SEM-EDX), X-ray diffraction (XRD) and BET surface area analyzer. EDX analysis showed the elements in the crystal BISMCP were Mn, C, and O. XRD result of BISMCP determined the crystal structure, which is close to rhodochrosite (MnCO₃). Spectral peaks of FTIR at 1641.79 cm^-1 confirmed the appearance of C[bond, double bond]O binding, with strong stretching of CO₃^2- in Amide I. From the six kinds of BISMCP produced, sample MCP-6 has the higher specific surface area by BET analysis at 109.01 m²/g, with pore size at 8.76 nm and higher pore volume at 0.178 cm³/g. These specifications will be suitable as an adsorbent for heavy metal removal by adsorption process. This study presents a preliminary analysis of the possibility of BISMCP for heavy metals adsorption using ICP multi-element standard solution XIII (As, Cr, Cd, Cu, Ni, and Zn). BISMCP formed from 0.1 MnCl₂ and 30 ml of bacteria volume (MCP-6) produced a better adsorbent material than others concentrations, with the adsorption efficiency of total As at 98.9%, Cr at 97.0%, Cu at 94.7%, Cd at 88.3%, Zn at 48.6%, and Ni at 29.5%. Future work could be examined its efficiency adsorbing individual heavy metals.

Inhibited and Retarded Behavior by Ca2+ and Ca2+/OD Loading Rate on Ureolytic Bacteria in MICP Process

The estimation of optical density (OD) with viable cells is challenging for engineering purposes. In this study, the OD conversion based on previous study was used. The inhibited and retarded behavior of the microbially induced carbonate precipitation (MICP) process was examined. The experimental results showed that high Ca²⁺ drastically influences the inhibited and retarded behavior on MICP processes. The analysis showed that the inhibition and retardation effects occurred when the Ca²⁺/OD loading rate exceeded 8.46 M. The critical value was equal to the proportional constant for obtaining carbonate precipitation rate (CPR) from OD. Due to this, the blending design of materials became possible, with no risk of inhibition. In conclusion, the inhibition and retardation of the MICP process are governed by the Ca²⁺ load and the linear standard line (LSL), which may be attributed to the capacity or tolerance of viable cells, i.e., CPR/OD = 8.46 M or Ca²⁺/OD = 8.46 M.

Phosphorus biogeochemistry regulated by carbonates in soil

Phosphates are the dominant phosphorus (P) source on Earth. The phosphates govern available P in soil, or even the complete ecosystem. The common deficiency of available P in carbonate-enriched soils suggests the tight correlation between P and C biogeochemistry, although the two elements have diverse abundance in soil. The influences of carbonates on P cycle were reviewed in this study, via both abiotic and biotic pathways. The abiotic processes at geochemical scale include element release, transport, sorption, desorption, weathering, precipitation, etc. The sorption of P on carbonate and buffering ability of carbonates were particularly addressed. Biotic factors are ascribed to various microorganisms in soil. As the most active P pool in soil, microorganisms prefer to consume abundant P, and then accumulate it in their biomass. Carbonates, however, are usually utilized by microorganisms after conversion to organic C. Meanwhile, extracellular precipitation of Ca-P phases significantly regulates the transportation of P in/out the cells. Moreover, they boost and complexify both carbonates and P turnover in soil via bioweathering and biomineralization, i.e., the intense interactions between biosphere and lithosphere. Based on this review, we proposed that carbonates may negatively affect P supply in soil system. This comprehensive review regarding the regulation by carbonates on P biogeochemistry would shed a light on predicting long-term P availability influenced by C biogeochemistry.

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.

Recognition and mechanistic investigation of anion sensing by ruthenium(II) arene complexes and bio-imaging application

In this work, four new ruthenium complexes [Ru(η⁶-p-cymene)(L1)Cl] 1, [Ru(η⁶-p-cymene)(L2)Cl] 2, [Ru(η⁶-p-cymene)(L3)Cl] 3 and [Ru(η⁶-p-cymene)(L4)Cl] 4 [HL1 = (2-cyanophenyl)glycine; HL2 = (5-chloro-2-cyanophenyl)glycine; HL3 = (2-cyano-3-fluorophenyl)glycine; HL4 = (4-cyanophenyl)glycine] were synthesized and well characterized by several spectroscopic and analytical techniques. Complexes 1 and 3 were found to be fluorescent in most of the solvents; however, 2 and 4 were found to be fluorescent mostly in EtOAc, DMF and ethanol. Amongst these four complexes, 3 has shown selective sensing against CO₃^2- and SO₄^2- anions by quenching of fluorescence. The LOD values are found to be in the sub-micromolar range. Investigations of the sensing mechanism performed by computation and NMR studies indicate a possible adduct formation between the NH group of the ligand and the anion(s) through hydrogen bond formation, which ultimately might lead to proton transfer to the bi-negative anion. The quantum yield of the complex 3 was found to decrease on addition of CO₃^2- and SO₄^2- anions from 0.46 to 0.13 and 0.12, respectively. The Job's plot indicates the binding between the probe and anion in a 1 : 1 ratio for both CO₃^2- and SO₄^2- anions. Along with that, all the complexes were found to be biocompatible when tested against several cell lines showing very high IC₅₀ values. It can also be observed that 1 is capable of penetrating within the cells and can act as a cell imaging agent showing fluorescence, and thus can be used for bio-imaging purposes.

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.

Characterization of bio-adsorptive removal performance of strontium through ureolysis-mediated bio-mineralization

The adsorptive removal performance of strontium (Sr) through bio-mineralization metabolism under various parameters was evaluated in this study. The primary mechanism of bio-mineralization used in this study was the urea hydrolysis process through bacterial enzymatic catalysis. Bacillus sp, which was isolated from river sediment, was used as a ureolytic bacteria. Various environmental conditions were set as different initial concentrations of Sr (10, 50, 100, 200, and 500 mg/L), and various ratios of Mg/Ca (4, 2, 1, 0.5, and 0.25). The concentrations of Sr²⁺, Ca²⁺, and Mg²⁺ in the solution of the batch experiment were measured to identify the bio-mineralization performance and the removal rate of Sr. In addition, the main Sr removal mechanism of ureolytic bacteria was identified. As a result, for Sr removal of bacteria, the bio-mineralization mechanism was more predominant than the adsorption of Sr. The rapid growth and high nucleation site production were observed when the initial concentration of Sr²⁺ increased and the Mg/Ca ratio was lowered, resulting in high biomineralization performance and Sr removal rate. The main phases of carbonate minerals formed in the presence of Sr, Ca, and Mg were SrCO₃ and SrCa(CO₃)₂. Mg²⁺ could retard the bacterial growth and participate in the formation of carbonate minerals, when a large amount of Mg²⁺ was present. Furthermore, the desorption rate of Sr²⁺ from bacterial pastes containing the carbonate minerals increased as the concentration of HCl increased, although the carbonate minerals were in a stable state.

Improvement of Biomineralization of Sporosarcina pasteurii as Biocementing Material for Concrete Repair by Atmospheric and Room Temperature Plasma Mutagenesis and Response Surface Methodology

Microbially induced calcium carbonate precipitation (MICP) has recently become an intelligent and environmentally friendly method for repairing cracks in concrete. To improve on this ability of microbial materials concrete repair, we applied random mutagenesis and optimization of mineralization conditions to improve the quantity and crystal form of microbially precipitated calcium carbonate. Sporosarcina pasteurii ATCC 11859 was used as the starting strain to obtain the mutant with high urease activity by atmospheric and room temperature plasma (ARTP) mutagenesis. Next, we investigated the optimal biomineralization conditions and precipitation crystal form using Plackett-Burman experimental design and response surface methodology (RSM). Biomineralization with 0.73 mol/l calcium chloride, 45 g/l urea, reaction temperature of 45°C, and reaction time of 22 h, significantly increased the amount of precipitated calcium carbonate, which was deposited in the form of calcite crystals. Finally, the repair of concrete using the optimized biomineralization process was evaluated. A comparison of water absorption and adhesion of concrete specimens before and after repairs showed that concrete cracks and surface defects could be efficiently repaired. This study provides a new method to engineer biocementing material for concrete repair.

Microbially induced calcite precipitation performance of multiple landfill indigenous bacteria compared to a commercially available bacteria in porous media

Microbially Induced Carbonate Precipitation (MICP) is currently viewed as one of the potential prominent processes for field applications towards the prevention of soil erosion, healing cracks in bricks, and groundwater contamination. Typically, the bacteria involved in MICP manipulate their environment leading to calcite precipitation with an enzyme such as urease, causing calcite crystals to form on the surface of grains forming cementation bonds between particles that help in reducing soil permeability and increase overall compressive strength. In this paper, the main focus is to study the MICP performance of three indigenous landfill bacteria against a well-known commercially bought MICP bacteria (Bacillus megaterium) using sand columns. In order to check the viability of the method for potential field conditions, the tests were carried out at slightly less favourable environmental conditions, i.e., at temperatures between 15-17°C and without the addition of urease enzymes. Furthermore, the sand was loose without any compaction to imitate real ground conditions. The results showed that the indigenous bacteria yielded similar permeability reduction (4.79 E-05 to 5.65 E-05) and calcium carbonate formation (14.4–14.7%) to the control bacteria (Bacillus megaterium), which had permeability reduction of 4.56 E-5 and CaCO₃ of 13.6%. Also, reasonably good unconfined compressive strengths (160–258 kPa) were noted for the indigenous bacteria samples (160 kPa). SEM and XRD showed the variation of biocrystals formation mainly detected as Calcite and Vaterite. Overall, all of the indigenous bacteria performed slightly better than the control bacteria in strength, permeability, and CaCO₃ precipitation. In retrospect, this study provides clear evidence that the indigenous bacteria in such environments can provide similar calcite precipitation potential as well-documented bacteria from cell culture banks. Hence, the idea of MICP field application through biostimulation of indigenous bacteria rather than bioaugmentation can become a reality in the near future.

Selective, pH sensitive, "turn on" fluorescence sensing of carbonate ions by a benzimidazole

Anions play crucial roles in the sustenance of life on earth in many ways. Selective detection of specific anions is important in developing new diagnostic tools and therapeutics. A pH-sensitive & selective benzimidazole-based fluorescent sensor has been developed for rapid detection of carbonate ions which can detect carbonate ions in low nanomolar concentrations. NMR based experiments indicate direct interaction of benzimidazole imino protons with the carbonate ions leading to 1:1 ligand carbonate ion complexation events. This is one of the first reports of benzimidazole sensing carbonate ions with high selectivity which may have implications in disease prevention and toxicity assessment.

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.

Bacteria-induced mineral precipitation: a mechanistic review

Micro-organisms contribute to Earth's mineral deposits through a process known as bacteria-induced mineral precipitation (BIMP). It is a complex phenomenon that can occur as a result of a variety of physiological activities that influence the supersaturation state and nucleation catalysis of mineral precipitation in the environment. There is a good understanding of BIMP induced by bacterial metabolism through the control of metal redox states and enzyme-mediated reactions such as ureolysis. However, other forms of BIMP often cannot be attributed to a single pathway but rather appear to be a passive result of bacterial activity, where minerals form as a result of metabolic by-products and surface interactions within the surrounding environment. BIMP from such processes has formed the basis of many new innovative biotechnologies, such as soil consolidation, heavy metal remediation, restoration of historic buildings and even self-healing concrete. However, these applications to date have primarily incorporated BIMP-capable bacteria sampled from the environment, while detailed investigations of the underpinning mechanisms have been lagging behind. This review covers our current mechanistic understanding of bacterial activities that indirectly influence BIMP and highlights the complexity and connectivity between the different cellular and metabolic processes involved. Ultimately, detailed insights will facilitate the rational design of application-specific BIMP technologies and deepen our understanding of how bacteria are shaping our world.

MICP as a potential sustainable technique to treat or entrap contaminants in the natural environment: A review

In the last two decades, developments in the area of biomineralization has yielded promising results making it a potentially environmentally friendly technique for a wide range of applications in engineering and wastewater/heavy metal remediation. Microbially Induced Carbonate Precipitation (MICP) has led to numerous patented applications ranging from novel strains and nutrient sources for the precipitation of biominerals. Studies are being constantly published to optimize the process to become a promising, cost effective, ecofriendly approach when compared with the existing traditional remediation technologies which are implemented to solve multiple contamination/pollution issues. Heavy metal pollution still poses a major threat towards compromising the ecosystem. The removal of heavy metals is of high importance due to their recalcitrance and persistence in the environment. In that perspective, this paper reviews the current and most significant discoveries and applications of MICP towards the conversion of heavy metals into heavy metal carbonates and removal of calcium from contaminated media such as polluted water. It is evident from the literature survey that although heavy metal carbonate research is very effective in removal, is still in its early stages but could serve as a solution if the microorganisms are stimulated directly in the heavy metal environment.

Morphogenesis and evolution mechanisms of bacterially-induced struvite

Bacteria are able to induce struvite precipitation, and modify struvite morphology, leading to the mineral with various growth habits. However, the relevant work involving the morphogenesis is limited, thereby obstructing our understanding of bacterially mediated struvite mineralization. Here, an actinomycete Microbacterium marinum sp. nov. H207 was chosen to study its effect on struvite morphology. A combination of bacterial mineralization and biomimetic mineralization techniques was adopted. The bacterial mineralization results showed that strain H207 could induce the formation of struvite with grouping structure (i.e., a small coffin-like crystal grown on a large trapezoid-like substrate crystal), and the overgrowth structure gradually disappeared, while the substrate crystal further evolved into coffin-like, and quadrangular tabular morphology with time. The biomimetic experiments with different organic components confirmed that the soluble macromolecules rich in electronegative carboxyl groups secreted by strain H207 dominate the formation of the struvite grouping. The time-course biomimetic experiments with supernatant testified that the increase in pH and NH₄⁺ content promoted the evolution of crystal habits. Moreover, the evolution process of substrate crystal can be divided into two stages. At the first stage, the crystal grew along the crystallographic b axis. At the later stage, coupled dissolution–precipitation process occurred, and the crystals grew along the corners (i.e., [110] and [1-10] directions). In the case of dissolution, it was also found that the (00-1) face of substrate crystal preferentially dissolved, which results from the low initial phosphate content and high PO₄³⁻ density on this face. As a result, present work can provide a deeper insight into bio-struvite mineralization.

In Situ Growth of Halophilic Bacteria in Saline Fracture Fluids from 2.4 km below Surface in the Deep Canadian Shield

Energy derived from water-rock interactions such as serpentinization and radiolysis, among others, can sustain microbial ecosystems deep within the continental crust, expanding the habitable biosphere kilometers below the earth's surface. Here, we describe a viable microbial community including sulfate-reducing microorganisms from one such subsurface lithoautotrophic ecosystem hosted in fracture waters in the Canadian Shield, 2.4 km below the surface in the Kidd Creek Observatory in Timmins, Ontario. The ancient groundwater housed in fractures in this system was previously shown to be rich in abiotically produced hydrogen, sulfate, methane, and short-chain hydrocarbons. We have further investigated this system by collecting filtered water samples and deploying sterile in situ biosampler units into boreholes to provide an attachment surface for the actively growing fraction of the microbial community. Scanning electron microscopy, energy-dispersive X-ray spectroscopy, and DNA sequencing analyses were undertaken to classify the recovered microorganisms. Moderately halophilic taxa (e.g., Marinobacter, Idiomarina, Chromohalobacter, Thiobacillus, Hyphomonas, Seohaeicola) were recovered from all sampled boreholes, and those boreholes that had previously been sealed to equilibrate with the fracture water contained taxa consistent with sulfate reduction (e.g., Desulfotomaculum) and hydrogen-driven homoacetogenesis (e.g., Fuchsiella). In contrast to this "corked" borehole that has been isolated from the mine environment for approximately 7 years at the time of sampling, we sampled additional open boreholes. The waters flowing freely from these open boreholes differ from those of the long-sealed borehole. This work complements ongoing efforts to describe the microbial diversity in fracture waters at Kidd Creek in order to better understand the processes shaping life in the deep terrestrial subsurface. In particular, this work demonstrates that anaerobic bacteria and known halophilic taxa are present and viable in the fracture waters presently outflowing from existing boreholes. Major cations and anions found in the fracture waters at the 2.4 km level of the mine are also reported.

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.

Isolation and characterization of phosphate solubilizing bacteria from rhizosphere soils of the Yeyahu Wetland in Beijing, China

Phosphate solubilizing bacteria (PSB) can convert insoluble forms of phosphorus (P) to accessible forms. 11 strains of PSB, including five inorganic phosphate solubilizing bacteria (IPSBs) and six organic phosphate solubilizing bacteria (OPSBs), were isolated from rhizosphere soils of three plants Scirpus planiculmis, Zizania latifolia, and Phrnagmites australis in the Yeyahu Wetland of Beijing, China to investigate P-solubilizing activities. In addition, the distributions of P fractions in soil samples were also observed. All strains evaluated above 1.0 by the ratio of transparent circle diameter to colony diameter (D/d) on Ca₃(PO₄)₂ or lecithin plates were identified by 16S rRNA sequencing. Results showed that Ca-bound P (Ca-P) was the main species of inorganic P (IP), and highly resistant organic P (HR-OP) accounted for the most part of organic P (OP). These strains were identified as bacterial species of Enterobacter asburiae, Acinetobacter sp., Bacillus cereus strain, and so on. The most efficient IPSB strain could convert over 430 mg L^-1 orthophosphate, while the equivalent OPSB strain only liberated less than 4 mg L^-1 in liquid culture, which indicated that IPSBs have a better P-solubilizing ability than OPSBs in rhizosphere soils of the Yeyahu Wetland and IPSBs are likely to regulate the P transformation process in this wetland. Graphical abstract ᅟ.

Deciphering Biosignatures in Planetary Contexts

Microbial life permeates Earth's critical zone and has likely inhabited nearly all our planet's surface and near subsurface since before the beginning of the sedimentary rock record. Given the vast time that Earth has been teeming with life, do astrobiologists truly understand what geological features untouched by biological processes would look like? In the search for extraterrestrial life in the Universe, it is critical to determine what constitutes a biosignature across multiple scales, and how this compares with "abiosignatures" formed by nonliving processes. Developing standards for abiotic and biotic characteristics would provide quantitative metrics for comparison across different data types and observational time frames. The evidence for life detection falls into three categories of biosignatures: (1) substances, such as elemental abundances, isotopes, molecules, allotropes, enantiomers, minerals, and their associated properties; (2) objects that are physical features such as mats, fossils including trace-fossils and microbialites (stromatolites), and concretions; and (3) patterns, such as physical three-dimensional or conceptual n-dimensional relationships of physical or chemical phenomena, including patterns of intermolecular abundances of organic homologues, and patterns of stable isotopic abundances between and within compounds. Five key challenges that warrant future exploration by the astrobiology community include the following: (1) examining phenomena at the "right" spatial scales because biosignatures may elude us if not examined with the appropriate instrumentation or modeling approach at that specific scale; (2) identifying the precise context across multiple spatial and temporal scales to understand how tangible biosignatures may or may not be preserved; (3) increasing capability to mine big data sets to reveal relationships, for example, how Earth's mineral diversity may have evolved in conjunction with life; (4) leveraging cyberinfrastructure for data management of biosignature types, characteristics, and classifications; and (5) using three-dimensional to n-D representations of biotic and abiotic models overlain on multiple overlapping spatial and temporal relationships to provide new insights.

Microbial Communities in Sediments From Four Mildly Acidic Ephemeral Salt Lakes in the Yilgarn Craton (Australia) - Terrestrial Analogs to Ancient Mars

The Yilgarn Craton in Australia has a large number of naturally occurring shallow ephemeral lakes underlain by a dendritic system of paleodrainage channels. Processes like evaporation, flooding, erosion, as well as inflow of saline, often acidic and ion-rich groundwater contribute to the (dynamic) nature of the lakes and the composition of the sediments. The region has previously been described as an analog environment for early Mars due to its geological and geophysical similarities. Here, we investigated sediment samples of four lake environments aimed at getting a fundamental understanding of the native microbial communities and the mineralogical and (bio)chemical composition of the sediments they are associated with. The dominant mineral phases in the sediments were quartz, feldspars and amphiboles, while halite and gypsum were the only evaporites detected. Element analysis revealed a rich and complex image, in which silicon, iron, and aluminum were the dominant ions, but relative high concentrations of trace elements such as strontium, chromium, zirconium, and barium were also found. The concentrations of organic carbon, nitrogen, and phosphorus were generally low. 16S amplicon sequencing on the Illumina platform showed the presence of diverse microbial communities in all four lake environments. We found that most of the communities were dominated by extremely halophilic Archaea of the Halobacteriaceae family. The dynamic nature of these lakes appears to influence the biological, biochemical, and geological components of the ecosystem to a large effect. Inter- and intra-lake variations in the distributions of microbial communities were significant, and could only to a minor degree be explained by underlying environmental conditions. The communities are likely significantly influenced by small scale local effects caused by variations in geological settings and dynamic interactions caused by aeolian transport and flooding and evaporation events.

Biocalcification by Piezotolerant Bacillus sp. NIOTVJ5 Isolated from Deep Sea Sediment and its Influence on the Strength of Concrete Specimens

Biocalcification or microbially induced carbonate precipitation (MICP) is gaining attention from the research fraternity, primarily ascribed to their eco-friendly applications. Bacterial strains have been isolated from various sources and their ability to precipitate carbonate has been studied extensively. In spite of the fact that the deep-sea environment is a potential source for bioprospecting, meager reports exist on the isolation of biocalcifying bacterial strains from deep-sea. In this study, a deep-sea sediment sample obtained from off-Barren Island coast in the Andaman Sea was investigated for biocalcifying strains. Based on the urease activity and the ability to produce calcite crystals, the strain NIOTVJ5 was chosen for further investigations. The strain showed a similarity to Bacillus thuringiensis through 16S rRNA sequencing and was shown to possess positive urease, protease, amylase, catalase, and oxidase activities. The isolate was found to be piezotolerant as it was able to survive at 100 bar pressure with significant changes in the spore morphology. The strain was able to produce strong monoxenic biofilms as well. Maximum urease activity was 554.03 U/mL and it precipitated 1.80 g/L of carbonate crystals. Scanning electron microscopy coupled with energy dispersive X-ray spectroscopy confirmed the presence of calcium carbonate. The carbonate polymorph was identified as calcite using X-ray powder diffraction. The impact of biocalcification by NIOTVJ5 on concrete specimens indicated an increase of 30.91% in their compressive strength. This is the first report of a biocalcifying strain from a deep-sea sediment around the Indian subcontinent region. This study indicates the potential of the strain NIOTVJ5, which can be employed for various biotechnological applications.

Microbial Mg-rich Carbonates in an Extreme Alkaline Lake (Las Eras, Central Spain)

This paper provides strong evidence for the contribution of the phylum Firmicutes in mediating the primary precipitation of Mg-rich carbonates (hydromagnesite, dolomite, magnesite, and nesquehonite) in recent microbialites from a highly alkaline and ephemeral inland lake (Las Eras, Central Spain). The carbonate mineral precipitation occurs sequentially as the microbial mats decay. Scanning electron microscopy (SEM) provided solid proof that hydromagnesite nucleation is initiated on the exopolymeric substances (EPS) and the microbial cells associated to the microbial mat degradation areas. The progressive mineralization of the EPS and bacterial cells by hydromagnesite plate-like crystals on their surface, results in the entombment of the bacteria and formation of radiating aggregates of hydromagnesite crystals. The hydrous phases, mostly hydromagnesite, were produced at a high percentage in the first stages of the microbial degradation of organic matter. When the availability of organic substrates declines, the heterotrophs tend to reduce their number and metabolic activity, remain dormant. At this stage, the anhydrous phases, dolomite and magnesite, nucleate on bacterial nanoglobules and/or collapsed cells. Evidence for the sequential formation of the Mg-rich carbonates trough the decay of organic matter by a fermentative EPS-forming bacterium isolated from the microbialites, Desemzia incerta, is drawn through a comparative analysis of carbonate formation in both natural and experimental settings. This study will help to constrain potential mechanisms of carbonate formation in natural systems, which are of fundamental importance not only for understanding modern environments but also as a window into the geologic past of Earth and potentially Mars.

Bioprospecting of Ureolytic Bacteria From Laguna Salada for Biomineralization Applications

The processes of biomineralization, mediated by ureolytic bacteria, possess a wide range of technological applications, such as the formation of biocements and remediation of water and soil environments. For this reason, the bioprospecting of new ureolytic bacteria is interesting for its application to these technologies, particularly for water treatment. This study demonstrates the isolation, selection, and identification of halotolerant ureolytic bacteria from Laguna Salada (inland from Atacama Desert) and the evaluation of their ability to precipitate calcium carbonate crystals in freshwater in the presence of calcium ions, as well as the ability to induce the precipitation of crystals from different ions present in seawater. Twenty-four halotolerant ureolytic bacteria whose molecular identification gives between 99 and 100% identity with species of the genus Bacillus, Porphyrobacter, Pseudomonas, Salinivibrio, and Halomonas were isolated. When cultivated in freshwater, urea, and calcium chloride, all species are able to biomineralize calcium carbonate in different concentrations. In seawater, the strains that biomineralize the highest concentration of calcium carbonate correspond to Bacillus subtilis and Halomonas sp. SEM–EDX and XRD analyses determined that both bacteria induce the formation of 9–33% halite (NaCl), 31–66% monohydrocalcite (CaCO₃ × H₂O), and 24–27% struvite (MgNH₄PO₄ × 6H₂O). Additionally, B.subtilis induces the formation of 7% anhydrite (CaSO₄). In seawater, B.subtilis and Halomonas sp. were able to precipitate both calcium (96–97%) and magnesium (63–67%) ions over 14 days of testing. Ion removal assays with B.subtilis immobilized in beads indicate a direct relationship between the urea concentration and a greater removal of ions with similar rates to free cells. These results demonstrate that the biomineralization mediated by bacterial urea hydrolysis is feasible in both freshwater and seawater, and we propose its application as a new technology in improving water quality for industrial uses.

The Significant Roles of Mg/Ca Ratio, Cl− and SO42− in Carbonate Mineral Precipitation by the Halophile Staphylococcus epidermis Y2

Carbonate precipitation induced by microorganisms has become a hot topic in the field of carbonate sedimentology, although the effects of magnesium on biomineral formation have rarely been studied. In experiments described here, magnesium sulfate and magnesium chloride were used to investigate the significant role played by Mg2+ on carbonate precipitation. In this study, Staphylococcus epidermidis Y2 was isolated and identified by 16S ribosomal DNA (rDNA) homology comparison and ammonia, pH, carbonic anhydrase, carbonate, and bicarbonate ions were monitored during laboratory experiments. The mineral phase, morphology, and elemental composition of precipitates were analyzed by XRD and SEM-EDS. Ultrathin slices of bacteria were analyzed by HRTEM-SAED and STEM. The results show that this bacterium releases ammonia and carbonic anhydrase to increase pH, and raise supersaturation via the large number of carbonate and bicarbonate ions that are released through carbon dioxide hydration catalyzed by carbonic anhydrase. The crystal cell density of monohydrocalcite is lower in a magnesium chloride medium, compared to one of magnesium sulfate. Crystals grow in the mode of a spiral staircase in a magnesium sulfate medium, but in a concentric circular pattern in a magnesium chloride medium. There was no obvious intracellular biomineralization taking place. The results presented here contribute to our understanding of the mechanisms of biomineralization, and to the role of Mg2+ in crystal form.

Biomineralisation performance of bacteria isolated from a landfill in China

We report an investigation of microbially induced carbonate precipitation by seven indigenous bacteria isolated from a landfill in China. Bacterial strains were cultured in a medium supplemented with 25 mmol/L calcium chloride and 333 mmol/L urea. The experiments were carried out at 30 °C for 7 days with agitation by a shaking table at 130 r/min. Scanning electron microscopic and X-ray diffraction analyses showed variations in calcium carbonate polymorphs and mineral composition induced by all bacterial strains. The amount of carbonate precipitation was quantified by titration. The amount of carbonate precipitated in the medium varied among isolates, with the lowest being Bacillus aerius rawirorabr15 (LC092833) precipitating around 1.5 times more carbonate per unit volume than the abiotic (blank) solution. Pseudomonas nitroreducens szh_asesj15 (LC090854) was found to be the most efficient, precipitating 3.2 times more carbonate than the abiotic solution. Our results indicate that bacterial carbonate precipitation occurred through ureolysis and suggest that variations in carbonate crystal polymorphs and rates of precipitation were driven by strain-specific differences in urease expression and response to the alkaline environment. These results and the method applied provide benchmarking and screening data for assessing the bioremediation potential of indigenous bacteria for containment of contaminants in landfills.

Understanding the growth of the bio-struvite production Brevibacterium antiquum in sludge liquors

Biological struvite (bio-struvite) production through biomineralization has been suggested as an alternative to chemically derived struvite production to recover phosphorus from wastewater streams. In this study, statistical experimental design techniques were used to find the optimal growth rate (μ) of Brevibacterium antiquum in sludge liquors. Acetate, oleic acid, NaCl, NH₄-N, and Ca₂₊ were shown to affect the growth rate of B. antiquum. The growth rate reached 3.44 1/d when the bacteria were supplemented with 3.0% w/v NaCl and 1124 mg chemical oxygen demand/L as acetate. However, NaCl was found to hinder the biomineralization of bio-struvite. A two-stage experiment demonstrated that bio-struvite was produced in the presence of acetate. Bio-struvite production was confirmed with X-ray spectroscopy and crystal morphology (prismatic, tabular, and twinned crystal habit) through electron microscope analysis. The bio-struvite production was estimated by measuring phosphate content of the recovered precipitates, reaching 9.6 mg P/L as bio-struvite. Overall, these results demonstrated the optimal conditions required to achieve high growth rates as well as bio-struvite production with B. antiquum. The results obtained in this study could be used to develop a process to grow B. antiquum in wastewater streams in mixed cultures and recover phosphorus-rich products such as struvite.

The role of pH on the biological struvite production in digested sludge dewatering liquors

Struvite production mediated by bacteria has opened up a new route for phosphorus recovery from wastewater streams but its application to digested sludge dewatering liquors is not yet well understood. This study investigates the growth and biological struvite production of selected bacteria in wastewater liquors with pHs between 5.7 to 9.1. The bacterial growth was assessed through flow cytometry. Bacillus pumilus, Halobacterium salinarum and Brevibacterium antiquum remained viable at pHs between 5.7 to 9.1 but B. antiquum was able to grow at pHs between 7.3 to 7.8. Further analysis allowed the identification of crystals as struvite in tests between pH 7.3 to 8.3. All strains were capable of producing struvite at a range of pHs, but the highest production of 135-198 mg/L was observed for pHs between 7.3 to 8.3. At pHs > 8.3, precipitation of struvite and calcium compounds was observed in inoculated and non-inoculated tests. This study demonstrates that biological struvite production can occur at a wide range of pHs, hence significantly different from chemical struvite precipitation that occurs at pH > 8.3, making it a potentially viable process for phosphorus recovery as struvite from wastewater streams and sludge liquors without strict pH control.

Microbial Diversity and Mineralogical-Mechanical Properties of Calcitic Cave Speleothems in Natural and in Vitro Biomineralization Conditions

Natural mineral formations are a window into important processes leading to carbon storage and mineralized carbonate structures formed through abiotic and biotic processes. In the current study, we made an attempt to undertake a comprehensive approach to characterize the mineralogical, mechanical, and microbial properties of different kinds of speleothems from karstic caves; with an aim to understand the bio-geo-chemical processes in speleothem structures and their impact on nanomechanical properties. We also investigated the biomineralization abilities of speleothem surface associated microbial communities in vitro. Mineralogical profiling using techniques such as X-ray powder Diffraction (XRD) and Tescan Integrated Mineral Analyzer (TIMA) demonstrated that calcite was the dominant mineral in the majority of speleothems with Energy Dispersive X-ray Analysis (EDS) indicating a few variations in the elemental components. Differing proportions of polymorphs of calcium carbonate such as aragonite and vaterite were also recorded. Significant variations in trace metal content were recorded through Inductively Coupled Plasma Mass Spectrometer (ICP-MS). Scanning Electron Microscopy (SEM) analysis revealed differences in morphological features of the crystals which varied from triangular prismatic shapes to etched spiky forms. Microbial imprints and associations were seen in a few sections. Analysis of the associated microbial diversity showed significant differences between various speleothems at Phylum level; although Proteobacteria and Actinobacteria were found to be the predominant groups. Genus level microbial associations showed a relationship with the geochemistry, mineralogical composition, and metal content of the speleothems. The assessment of nanomechanical properties measured by Nanoindentation revealed that the speleothems with a dominance of calcite were stronger than the speleothems with mixed calcium carbonate polymorphs and silica content. The in vitro metabolic activity of the microbial communities associated with the surfaces of the speleothems resulted in calcium carbonate crystal precipitation. Firmicutes and Proteobacteria dominated these populations, in contrast to the populations seen in natural systems. The precipitation of calcium carbonate crystals in vitro indicated that microbial metabolic activity may also play an important role in the synthesis and dissociation of biominerals in the natural environment. Our study provides novel evidence of the close relationship between mineralogy, microbial ecology, geochemistry, and nanomechanical properties of natural formations.

Biomineralisation of carbonate and sulphate by the halophilic bacterium Halomonas maura at different manganese concentrations

The ability of Halomonas maura to bioprecipitate carbonate and sulphate crystals in solid media at different manganese concentrations has been demonstrated in this study for the first time. The precipitated minerals were studied by X-ray diffraction, scanning and transmission electron microscopy, and energy-dispersive X-ray spectroscopy. The precipitated minerals were different based on the manganese concentration present in the medium and the incubation time. In the absence of manganese, H. maura formed pseudokutnahorite crystals; in the presence of manganese, the concentration in the culture medium determined the precipitation carbonates, such as rhodochrosite and dolomites. However, in the presence of low concentrations of manganese chloride (MnCl₂) (5 g/l), kutnohorite crystals were also formed. Finally, when H. maura was grown in the presence of manganese, small amounts of sulphate crystals (such as bassanite and gypsum) were detected. Our study of the precipitated minerals showed an active role of H. maura in the biomineralisation process, but the geochemical conditions, and the manganese concentrations in particular, were clearly influential.

Removal of Soluble Strontium via Incorporation into Biogenic Carbonate Minerals by Halophilic Bacterium Bacillus sp. Strain TK2d in a Highly Saline Solution

Radioactive strontium (⁹⁰Sr) leaked into saline environments, including the ocean, from the Fukushima Daiichi Nuclear Power Plant after a nuclear accident. Since the removal of ⁹⁰Sr using general adsorbents (e.g., zeolite) is not efficient at high salinity, a suitable alternative immobilization method is necessary. Therefore, we incorporated soluble Sr into biogenic carbonate minerals generated by urease-producing microorganisms from a saline solution. An isolate, Bacillus sp. strain TK2d, from marine sediment removed >99% of Sr after contact for 4 days in a saline solution (1.0 × 10^-3 mol liter^-1 of Sr, 10% marine broth, and 3% [wt/vol] NaCl). Transmission electron microscopy and energy-dispersive X-ray spectroscopy showed that Sr and Ca accumulated as phosphate minerals inside the cells and adsorbed at the cell surface at 2 days of cultivation, and then carbonate minerals containing Sr and Ca developed outside the cells after 2 days. Energy-dispersive spectroscopy revealed that Sr, but not Mg, was present in the carbonate minerals even after 8 days. X-ray absorption fine-structure analyses showed that a portion of the soluble Sr changed its chemical state to strontianite (SrCO₃) in biogenic carbonate minerals. These results indicated that soluble Sr was selectively solidified into biogenic carbonate minerals by the TK2d strain in highly saline environments.IMPORTANCE Radioactive nuclides (¹³⁴Cs, ¹³⁷Cs, and ⁹⁰Sr) leaked into saline environments, including the ocean, from the Fukushima Daiichi Nuclear Power Plant accident. Since the removal of ⁹⁰Sr using general adsorbents, such as zeolite, is not efficient at high salinity, a suitable alternative immobilization method is necessary. Utilizing the known concept that radioactive ⁹⁰Sr is incorporated into bones by biomineralization, we got the idea of removing ⁹⁰Sr via incorporation into biominerals. In this study, we revealed the ability of the isolated ureolytic bacterium to remove Sr under high-salinity conditions and the mechanism of Sr incorporation into biogenic calcium carbonate over a longer duration. These findings indicated the mechanism of the biomineralization by the urease-producing bacterium and the possibility of the biomineralization application for a new purification method for ⁹⁰Sr in highly saline environments.

Biogenic Hydroxyapatite: A New Material for the Preservation and Restoration of the Built Environment

Ordinary Portland cement (OPC) is by weight the world's most produced man-made material and is used in a variety of applications in environments ranging from buildings, to nuclear wasteforms, and within the human body. In this paper, we present for the first time the direct deposition of biogenic hydroxyapatite onto the surface of OPC in a synergistic process which uses the composition of the cement substrate. This hydroxyapatite is very similar to that found in nature, having a similar crystallite size, iron and carbonate substitution, and a semi-crystalline structure. Hydroxyapatites with such a structure are known to be mechanically stronger and more biocompatible than synthetic or biomimetic hydroxyapatites. The formation of this biogenic hydroxyapatite coating therefore has significance in a range of contexts. In medicine, hydroxyapatite coatings are linked to improved biocompatibility of ceramic implant materials. In the built environment, hydroxyapatite coatings have been proposed for the consolidation and protection of sculptural materials such as marble and limestone, with biogenic hydroxyapatites having reduced solubility compared to synthetic apatites. Hydroxyapatites have also been established as effective for the adsorption and remediation of environmental contaminants such as radionuclides and heavy metals. We identify that in addition to providing a biofilm scaffold for nucleation, the metabolic activity of Pseudomonas fluorescens increases the pH of the growth medium to a suitable level for hydroxyapatite formation. The generated ammonia reacts with phosphate in the growth medium, producing ammonium phosphates which are a precursor to the formation of hydroxyapatite under conditions of ambient temperature and pressure. Subsequently, this biogenic deposition process takes place in a simple reaction system under mild chemical conditions and is cheap and easy to apply to fragile biological or architectural surfaces.

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.

Bioprecipitation of Calcium Carbonate Crystals by Bacteria Isolated from Saline Environments Grown in Culture Media Amended with Seawater and Real Brine

The precipitation of calcium carbonate and calcium sulphate by isolated bacteria from seawater and real brine obtained in a desalination plant growth in culture media containing seawater and brine as mineral sources has been studied. However, only bioprecipitation was detected when the bacteria were grown in media with added organic matter. Biomineralization process started rapidly, crystal formation taking place in the beginning a few days after inoculation of media; roughly 90% of total cultivated bacteria showed. Six major colonies with carbonate precipitation capacity dominated bacterial community structure cultivated in heterotrophic platable bacteria medium. Taxonomic identification of these six strains through partial 16S rRNA gene sequences showed their affiliation with Gram-positive Bacillus and Virgibacillus genera. These strains were able to form calcium carbonate minerals, which precipitated as calcite and aragonite crystals and showed bacterial fingerprints or bacteria calcification. Also, carbonic anhydrase activity was observed in three of these isolated bacteria. The results of this research suggest that microbiota isolated from sea water and brine is capable of precipitation of carbonate biominerals, which can occur in situ with mediation of organic matter concentrations. Moreover, calcium carbonate precipitation ability of this microbiota could be of importance in bioremediation of CO₂ and calcium in certain environments.

Biotic and abiotic effects on CO2 sequestration during microbially-induced calcium carbonate precipitation

In this study, CO2 sequestration was investigated through the microbially-induced calcium carbonate precipitation (MICP) process with isolates obtained from a cave called 'Cave Without A Name' (Boerne, TX, USA) and the Pamukkale travertines (Denizli, Turkey). The majority of the bacterial isolates obtained from these habitats belonged to the genera Sporosarcina, Brevundimonas, Sphingobacterium and Acinetobacter. The isolates were investigated for their capability to precipitate calcium carbonate and sequester CO2. Biotic and abiotic effects of CO2 sequestration during MICP were also investigated. In the biotic effect, we observed that the rate and concentration of CO2 sequestered was dependent on the species or strains. The main abiotic factors affecting CO2 sequestration during MICP were the pH and medium components. The increase in pH led to enhanced CO2 sequestration by the growth medium. The growth medium components, on the other hand, were shown to affect both the urease activity and CO2 sequestration. Through the Plackett-Burman experimental design, the most important growth medium component involved in CO2 sequestration was determined to be urea. The optimized medium composition by the Plackett-Burman design for each isolate led to a statistically significant increase, of up to 148.9%, in CO2 uptake through calcification mechanisms.

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

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

Precipitation of phosphate minerals by microorganisms isolated from a fixed-biofilm reactor used for the treatment of domestic wastewater

The ability of bacteria isolated from a fixed-film bioreactor to precipitate phosphate crystals for the treatment of domestic wastewater in both artificial and natural media was studied. When this was demonstrated in artificial solid media for crystal formation, precipitation took place rapidly, and crystal formation began 3 days after inoculation. The percentage of phosphate-forming bacteria was slightly higher than 75%. Twelve major colonies with phosphate precipitation capacity were the dominant heterotrophic platable bacteria growing aerobically in artificial media. According to their taxonomic affiliations (based on partial sequencing of the 16S rRNA), the 12 strains belonged to the following genera of Gram-negative bacteria: Rhodobacter, Pseudoxanthobacter, Escherichia, Alcaligenes, Roseobacter, Ochrobactrum, Agromyce, Sphingomonas and Paracoccus. The phylogenetic tree shows that most of the identified populations were evolutionarily related to the Alphaproteobacteria (91.66% of sequences). The minerals formed were studied by X-ray diffraction, scanning electron microscopy (SEM), and energy dispersive X-ray microanalysis (EDX). All of these strains formed phosphate crystals and precipitated struvite (MgNH4PO4·6H2O), bobierrite [Mg3(PO4)2·8H2O] and baricite [(MgFe)3(PO4)2·8H2O]. The results obtained in this study show that struvite and spherulite crystals did not show any cell marks. Moreover, phosphate precipitation was observed in the bacterial mass but also near the colonies. Our results suggest that the microbial population contributed to phosphate precipitation by changing the media as a consequence of their metabolic activity. Moreover, the results of this research suggest that bacteria play an active role in the mineral precipitation of soluble phosphate from urban wastewater in submerged fixed-film bioreactors.

CO2concentration and pH alters subsurface microbial ecology at reservoir temperature and pressure

Molecular ecology techniques are utilized to determine the impact of CO₂concentrations on microbial communities under reservoir temperature and pressure simulating geological carbon sequestration.

Carbonate precipitation under pressure for bioengineering in the anaerobic subsurface via denitrification

A number of bioengineering techniques are being developed using microbially catalyzed hydrolysis of urea to precipitate calcium carbonate for soil and sand strengthening in the subsurface. In this study, we evaluate denitrification as an alternative microbial metabolism to induce carbonate precipitation for bioengineering under anaerobic conditions and at high pressure. In anaerobic batch culture, the halophile Halomonas halodenitrificans is shown to be able to precipitate calcium carbonate at high salinity and at a pressure of 8 MPa, with results comparable to those observed when grown at ambient pressure. A larger scale proof-of-concept experiment shows that, as well as sand, coarse gravel can also be cemented with calcium carbonate using this technique. Possible practical applications in the subsurface are discussed, including sealing of improperly abandoned wells and remediation of hydraulic fracturing during shale gas extraction.

Influence of zinc on the calcium carbonate biomineralization of Halomonas halophila

BACKGROUND

The salt tolerance of halophilic bacteria make them promising candidates for technical applications, like isolation of salt tolerant enzymes or remediation of contaminated saline soils and waters. Furthermore, some halophilic bacteria synthesize inorganic solids resulting in organic-inorganic hybrids. This process is known as biomineralization, which is induced and/or controlled by the organism. The adaption of the soft and eco-friendly reaction conditions of this formation process to technical syntheses of inorganic nano materials is desirable. In addition, environmental contaminations can be entrapped in biomineralization products which facilitate the subsequent removal from waste waters. The moderately halophilic bacteria Halomonas halophila mineralize calcium carbonate in the calcite polymorph. The biomineralization process was investigated in the presence of zinc ions as a toxic model contaminant. In particular, the time course of the mineralization process and the influence of zinc on the mineralized inorganic materials have been focused in this study.

RESULTS

H. halophila can adapt to zinc contaminated medium, maintaining the ability for biomineralization of calcium carbonate. Adapted cultures show only a low influence of zinc on the growth rate. In the time course of cultivation, zinc ions accumulated on the bacterial surface while the medium depleted in the zinc contamination. Intracellular zinc concentrations were below the detection limit, suggesting that zinc was mainly bound extracellular. Zinc ions influence the biomineralization process. In the presence of zinc, the polymorphs monohydrocalcite and vaterite were mineralized, instead of calcite which is synthesized in zinc-free medium.

CONCLUSIONS

We have demonstrated that the bacterial mineralization process can be influenced by zinc ions resulting in the modification of the synthesized calcium carbonate polymorph. In addition, the shape of the mineralized inorganic material is chancing through the presence of zinc ions. Furthermore, the moderately halophilic bacterium H. halophila can be applied for the decontamination of zinc from aqueous solutions.

Phenotypic characterization and 16S rDNA identification of culturable non-obligate halophilic bacterial communities from a hypersaline lake, La Sal del Rey, in extreme South Texas (USA)

BACKGROUND

La Sal del Rey ("the King's Salt") is one of several naturally-occurring salt lakes in Hidalgo County, Texas and is part of the Lower Rio Grande Valley National Wildlife Refuge. The research objective was to isolate and characterize halophilic microorganisms from La Sal del Rey. Water samples were collected from the lake and a small creek that feeds into the lake. Soil samples were collected from land adjacent to the water sample locations. Sample salinity was determined using a refractometer. Samples were diluted and cultured on a synthetic saline medium to grow halophilic bacteria. The density of halophiles was estimated by viable plate counts. A collection of isolates was selected, gram-stained, tested for catalase, and characterized using API 20E® test strips. Isolates were putatively identified by sequencing the 16S rDNA. Carbon source utilization by the microbial community from each sample site was examined using EcoPlate™ assays and the carbon utilization total activity of the community was determined.

RESULTS

Results showed that salinity ranged from 4 parts per thousand (ppt) at the lake water source to 420 ppt in water samples taken just along the lake shore. The density of halophilic bacteria in water samples ranged from 1.2 × 102 - 5.2 × 103 colony forming units per ml (cfu ml-1) whereas the density in soil samples ranged from 4.0 × 105 - 2.5 × 106 colony forming units per gram (cfu g-1). In general, as salinity increased the density of the bacterial community decreased. Microbial communities from water and soil samples were able to utilize 12 - 31 carbon substrates. The greatest number of substrates utilized was by water-borne communities compared to soil-based communities, especially at lower salinities. The majority of bacteria isolated were gram-negative, catalase-positive, rods. Biochemical profiles constructed from API 20E® test strips showed that bacterial isolates from low-salinity water samples (4 ppt) showed the greatest phenotypic diversity with regards to the types and number of positive tests from the strip. Isolates taken from water samples at the highest salinity (420 ppt) tended to be less diverse and have only a limited number of positive tests. Sequencing of 16S DNA displayed the presence of members of bacterial genera Bacillus, Halomonas, Pseudomonas, Exiguobacterium and others. The genus Bacillus was most commonly identified. None of the isolates were members of the Archaea probably due to dilution of salts in the samples.

CONCLUSIONS

The La Sal del Rey ecosystem supports a robust and diverse bacterial community despite the high salinity of the lake and soil. However, salinity does appear to a limiting factor with regards to the density and diversity of the bacterial communities that inhabit the lake and surrounding area.

Bacterially mediated mineralisation processes lead to biodeterioration of artworks in Maltese catacombs

Mineral structures formed by bacterial and microalgal biofilms growing on the archaeological surface in Maltese hypogea were studied using Energy Dispersive X-Ray Spectroscopy (EDS) coupled to Environmental Scanning Electron Microscopy (ESEM), X-ray micro-diffraction (XRD) and X-ray fluorescence (XRF). These techniques have shown that mineral structures having different morphologies and chemical composition were associated with the microorganisms in the subaerophytic biofilm. Salt efflorescences and mineral deposits on the archaeological surface were often formed from gypsum (CaSO(4)∙2H(2)O), halite (NaCl) and calcite (CaCO(3)). Biogenic carbonates produced by microbial activities were a common occurrence. These assumed different forms, such as the production of mineral coats around cyanobacterial sheaths and the occurrence of calcite fibres with different morphologies on the surface of the biofilms. Moreover, vaterite (CaCO(3)) spherulites which appeared hollow in cross-section were observed. The presence of struvite was recorded from one catacomb site. These investigations have facilitated the study of the neoformation of metastable minerals by microbially mediated processes, which potentially contribute to a better understanding of the biodeterioration of artworks in Maltese palaeo-Christian catacombs.

Characterization of phosphate solubilizing bacteria in sediments from a shallow eutrophic lake and a wetland: isolation, molecular identification and phosphorus release ability determination

The transformation of phosphorus (P) is a major factor of lake eutrophication, and phosphate releasing bacteria play an important role in the release process. Experiments were conducted to investigate P content and characterize phosphate solubilizing bacterial composition at the molecular level in a shallow eutrophic lake and a wetland. Results showed that P concentrations were relatively high and derived from agricultural runoff and domestic or industrial pollution. Enumeration and molecular identification of these strains indicated that these bacterial groups were abundant in the ecosystem and various kinds of bacteria participated in the phosphorus release process. Twelve phosphate solubilizing bacteria, including eight organic P-solubilizing bacteria (OPBs) and four inorganic P-solubilizing bacteria (IPBs), which belonged to three different families, were isolated and identified. Cupriavidus basilensis was found for the first time to have the ability to mineralize organic P (OP). Laboratory tests on P release ability revealed that IPBs were more effective at releasing P than OPBs. The most efficient IPB strain could accumulate over 170 mg·L^-1 orthophosphate, while the equivalent OPB strain only liberated less than 4 mg·L^-1 orthophosphate in liquid culture. The results obtained from this investigation should help clarify the roles of microorganisms in aquatic systems and the mechanisms of eutrophication.