Strain-specific ureolytic microbial calcium carbonate precipitation

Microbial induced solidification and stabilization of municipal solid waste incineration fly ash with high alkalinity and heavy metal toxicity

This paper presents an experimental study on the applicability of microbial induced carbonate precipitation (MICP) to treat municipal solid waste incineration (MSWI) fly ash with high alkalinity and heavy metal toxicity. The experiments were carried out on fly ashes A and B produced from incineration processes of mechanical grate furnace and circulating fluidized bed, respectively. The results showed that both types of fly ashes contained high CaO content, which could supply sufficient endogenous Ca for MICP treatment. Moreover, S. pasteurii can survive from high alkalinity and heavy metal toxicity of fly ash solution. Further, the unconfined compressive strength (UCS) of MICP treated fly ashes A and B reached 0.385MPa and 0.709 MPa, respectively. The MICP treatment also resulted in a reduction in the leaching toxicity of heavy metals, especially for Cu, Pb and Hg. MICP had a higher solidification and stabilization effect on fly ash B, which has finer particle size and higher Ca content. These findings shone a light on the possibility of using MICP technique as a suitable and efficient tool to treat the MSWI fly ash.

Controlling the Distribution of Microbially Precipitated Calcium Carbonate in Radial Flow Environments

Bacterially driven reactions such as ureolysis can induce calcium carbonate precipitation, a well-studied process called microbially induced calcium carbonate precipitation (MICP). MICP is of interest in subsurface applications such as sealing leaks around wells. For effective field deployment, it is important to study MICP under radial flow conditions, which are relevant to near-well environments. In this study, a laboratory-scale radial flow reactor of 23 cm diameter, with a 1 mm glass bead monolayer serving as a porous medium, was used to investigate the effects of fluid flow rates and calcium concentrations on the mass and distribution of MICP by the ureolytic bacterium Sporosarcina pasteurii. Experiments were performed at hydraulic residence times of 14, 7, and 3.5 min and calcium to urea molar ratios of 0.5:1, 1:1, and 2:1. The total amount of CaCO₃ precipitated in the reactor increased with increasing residence time and with decreasing Ca²⁺ to urea molar ratios. Increased bacterial attachment and increased CaCO₃ precipitation were observed with distance from the center inlet of the reactor in all experiments. More uniform calcium distribution was achieved at lower flow rates. The relationship between reaction and transport rate (i.e., the Damköhler number) is identified as a useful parameter for the prediction of MICP in radial flow environments.

Sporosarcina pasteurii can form nanoscale calcium carbonate crystals on cell surface

The bacterium Sporosarcina pasteurii (SP) is known for its ability to cause the phenomenon of microbially induced calcium carbonate precipitation (MICP). We explored bacterial participation in the initial stages of the MICP process at the cellular length scale under two different growth environments (a) liquid culture (b) MICP in a soft agar (0.5%) column. In the liquid culture, ex-situ imaging of the cellular environment indicated that S. pasteurii was facilitating nucleation of nanoscale crystals of calcium carbonate on bacterial cell surface and its growth via ureolysis. During the same period, the meso-scale environment (bulk medium) was found to have overgrown calcium carbonate crystals. The effect of media components (urea, CaCl₂), presence of live and dead in the growth medium were explored. The agar column method allows for in-situ visualization of the phenomena, and using this platform, we found conclusive evidence of the bacterial cell surface facilitating formation of nanoscale crystals in the microenvironment. Here also the bulk environment or the meso-scale environment was found to possess overgrown calcium carbonate crystals. Extensive elemental analysis using Energy dispersive X-ray spectroscopy (EDS) and X-ray powder diffraction (XRD), confirmed that the crystals to be calcium carbonate, and two different polymorphs (calcite and vaterite) were identified. Active participation of S. pasteurii cell surface as the site of calcium carbonate precipitation has been shown using EDS elemental mapping with Scanning transmission electron microscopy (STEM) and scanning electron microscopy (SEM).

Environmental safety and biosafety in construction biotechnology

The topics of Construction Biotechnology are the development of construction biomaterials and construction biotechnologies for soil biocementation, biogrouting, biodesaturation, bioaggregation and biocoating. There are known different biochemical types of these biotechnologies. The most popular construction biotechnology is based on precipitation of calcium carbonate initiated by enzymatic hydrolysis of urea which follows with release of ammonia and ammonium to environment. This review focuses on the hazards and remedies for construction biotechnologies and on the novel environmentally friendly biotechnologies based on precipitation of hydroxyapatite, decay of calcium bicarbonate, and aerobic oxidation of calcium salts of organic acids. The use of enzymes or not living bacteria are the best options to ensure biosafety of construction biotechnologies. Only environmentally safe construction biotechnologies should be used for such environmental and geotechnical engineering works as control of the seepage in dams, channels, landfills or tunnels, sealing of the channels and the ponds, prevention of soil erosion and soil dust emission, mitigation of soil liquefaction, and immobilization of soil pollutants.

Study on the Remediation of Cd Pollution by the Biomineralization of Urease-Producing Bacteria

Cadmium (Cd) is a highly toxic metal that can affect human health and environmental safety. The purpose of this study was to research the removal of Cd from an environmental perspective. In this article, four highly urease-active strains (CZW-2, CZW-5, CZW-9 and CZW-12) were isolated from an abandoned mine and their phylogenetic trees were analyzed. The maximum enzyme activities, the mineralized precipitate and the removal rates of these strains were compared. The results showed that CZW-2 had the highest urease activity at 51.6 U/mL, and the removal rates of CZW-2, CZW-5, CZW-9 and CZW-12 after 120 h were 80.10%, 72.64%, 76.70% and 73.40%, with an initial concentration of Cd of 2 mM in the Cd precipitation experiments. XRD (X-ray diffractometer), EDS (Energy dispersive spectrometer) and FTIR (Fourier transform infrared spectroscopy) analysis indicated that the mineralized precipitate was CdCO₃. SEM (Scanning electron microscopy) analysis revealed that the diameter of the oval-shaped mineralized product ranked from 0.5 to 2 μm. These strains were used to remedy Cd-contaminated soil, and five different fractions of Cd were measured. Compared with the control, the results of spraying pre-cultured strains containing 2% urea to remove Cd from contaminated soils showed that the exchangeable fraction of Cd decreased by 53.30%, 27.78%, 42.54% and 53.80%, respectively, whereas the carbonate-bound fraction increased by 55.42%, 20.27%, 39.67% and 34.36%, respectively, after one month. These data show that these strains can effectively reduce the bioavailability and mobility of Cd in contaminated soils. The results indicate that biomineralization based on the decomposition of substrate urea can be applied to remedy heavy contaminated soil and water.

The Complete Genome and Physiological Analysis of the Eurythermal Firmicute Exiguobacterium chiriqhucha Strain RW2 Isolated From a Freshwater Microbialite, Widely Adaptable to Broad Thermal, pH, and Salinity Ranges

Members of the genus Exiguobacterium are found in diverse environments from marine, freshwaters, permafrost to hot springs. Exiguobacterium can grow in a wide range of temperature, pH, salinity, and heavy-metal concentrations. We characterized Exiguobacterium chiriqhucha strain RW2 isolated from a permanently cold freshwater microbialite in Pavilion Lake, British Columbia using metabolic assays, genomics, comparative genomics, phylogenetics, and fatty acid composition. Strain RW2 has the most extensive growth range for temperature (4–50°C) and pH (5–11) of known Exiguobacterium isolates. Strain RW2 genome predicts pathways for wide differential thermal, cold and osmotic stress using cold and heat shock cascades (e.g., csp and dnaK), choline and betaine uptake/biosynthesis (e.g., opu and proU), antiporters (e.g., arcD and nhaC Na⁺/K⁺), membrane fatty acid unsaturation and saturation. Here, we provide the first complete genome from Exiguobacterium chiriqhucha strain RW2, which was isolated from a freshwater microbialite. Its genome consists of a single 3,019,018 bp circular chromosome encoding over 3,000 predicted proteins, with a GC% content of 52.1%, and no plasmids. In addition to growing at a wide range of temperatures and salinities, our findings indicate that RW2 is resistant to sulfisoxazole and has the genomic potential for detoxification of heavy metals (via mercuric reductases, arsenic resistance pumps, chromate transporters, and cadmium-cobalt-zinc resistance genes), which may contribute to the metabolic potential of Pavilion Lake microbialites. Strain RW2 could also contribute to microbialite formation, as it is a robust biofilm former and encodes genes involved in the deamination of amino acids to ammonia (i.e., L-asparaginase/urease), which could potentially boost carbonate precipitation by lowering the local pH and increasing alkalinity. We also used comparative genomic analysis to predict the pathway for orange pigmentation that is conserved across the entire Exiguobacterium genus, specifically, a C₃₀ carotenoid biosynthesis pathway is predicted to yield diaponeurosporene-4-oic acid as its final product. Carotenoids have been found to protect against ultraviolet radiation by quenching reactive oxygen, releasing excessive light energy, radical scavenging, and sunscreening. Together these results provide further insight into the potential of Exiguobacterium to exploit a wide range of environmental conditions, its potential roles in ecosystems (e.g., microbialites/microbial mats), and a blueprint model for diverse metabolic processes.

Alkaliphiles: The Emerging Biological Tools Enhancing Concrete Durability

Concrete is one of the most commonly used building materials ever used. Despite it is a very important and common construction material, concrete is very sensitive to crack formation and requires repair. A variety of chemical-based techniques and materials have been developed to repair concrete cracks. Although the use of these chemical-based repair systems are the best commercially available choices, there have also been concerns related to their use. These repair agents suffer from inefficiency and unsustainability. Most of the products are expensive and susceptible to degradation, exhibit poor bonding to the cracked concrete surfaces, and are characterized by different physical properties such as thermal expansion coefficients which are different to that of concrete. Moreover, many of these repair agents contain chemicals that pose environmental and health hazards. Thus, there has been interest in developing concrete crack repair agents that are efficient, long lasting, safe, and benign to the environment and exhibit physical properties which resemble that of the concrete. The search initiated by these desires brought the use of biomineralization processes as tools in mending concrete cracks. Among biomineralization processes, microbially initiated calcite precipitation has emerged as an interesting alternative to the existing chemical-based concrete crack repairing system. Indeed, results of several studies on the use of microbial-based concrete repair agents revealed the remarkable potential of this approach in the fight against concrete deterioration. In addition to repairing existing concrete cracks, microorganisms have also been considered to make protective surface coating (biodeposition) on concrete structures and in making self-healing concrete.Even though a wide variety of microorganisms can precipitate calcite, the nature of concrete determines their applicability. One of the important factors that determine the applicability of microbes in concrete is pH. Concrete is highly alkaline in nature, and hence the microbes envisioned for this application are alkaliphilic or alkali-tolerant. This work reviews the available information on applications of microbes in concrete: repairing existing cracks, biodeposition, and self-healing. Moreover, an effort is made to discuss biomineralization processes that are relevant to extend the durability of concrete structures. Graphical Abstract.

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.

Effect of divalent ions and a polyphosphate on composition, structure, and stiffness of simulated drinking water biofilms

The biofilm chemical and physical properties in engineered systems play an important role in governing pathogen transmission, fouling facilities, and corroding metal surfaces. Here, we investigated how simulated drinking water biofilm chemical composition, structure, and stiffness responded to the common scale control practice of adjusting divalent ions and adding polyphosphate. Magnetomotive optical coherence elastography (MM-OCE), a tool developed for diagnosing diseased tissues, was used to determine biofilm stiffness in this study. MM-OCE, together with atomic force microscopy (AFM), revealed that the biofilms developed from a drinking water source with high divalent ions were stiffer compared to biofilms developed either from the drinking water source with low divalent ions or the water containing a scale inhibitor (a polyphosphate). The higher stiffness of biofilms developed from the water containing high divalent ions was attributed to the high content of calcium carbonate, suggested by biofilm composition examination. In addition, by examining the biofilm structure using optical coherence tomography (OCT), the highest biofilm thickness was found for biofilms developed from the water containing the polyphosphate. Compared to the stiff biofilms developed from the water containing high divalent ions, the soft and thick biofilms developed from the water containing polyphosphate will be expected to have higher detachment under drinking water flow. This study suggested that water chemistry could be used to predict the biofilm properties and subsequently design the microbial safety control strategies.

A variety of analytical techniques are revealing the complex influences of ions in drinking water supplies on the structure of biofilms. Such biofilms often contaminate water supply pipes and machinery. Yun Shen and colleagues at the University of Illinois at Urbana-Champaign in the USA investigated the effects of ions with a double positive charge – ‘divalent cations’ – and polyphosphate ions. Divalent cations, especially calcium and magnesium ions, are abundant in drinking water in many regions, promoting the formation of limescale deposits. Polyphosphates are commonly added to water supplies to reduce limescale formation, inhibit corrosion and discourage biofilm formation. The research revealed that divalent cations increase biofilm stiffness, while polyphosphates promote softer but thicker biofilms that are more easily removed. The results will help optimize water treatment procedures to control both microbial contamination and limescale problems.

Physiological and genetic characterization of calcium phosphate precipitation by Pseudomonas species

Microbial biomineralization is a widespread phenomenon. The ability to induce calcium precipitation around bacterial cells has been reported in several Pseudomonas species but has not been thoroughly tested. We assayed 14 Pseudomonas strains representing five different species for the ability to precipitate calcium. Calcium phosphate precipitated adjacent to the colonies of all the Pseudomonas strains tested and also precipitated on the surface of colonies for several of the Pseudomonas strains assayed. The precipitate was commonly precipitated as amorphous calcium phosphate, however seven of the 14 Pseudomonas strains tested precipitated amorphous apatite in agar adjacent to the colonies. Out of the seven Pseudomonas strains that precipitated amorphous apatite, six are plant pathogenic. The formation of amorphous apatite was commonly observed in the area of the agar where amorphous calcium phosphate had previously formed. A transposon mutagenesis screen in Pseudomonas syringae pv. tomato DC3000 revealed genes involved in general metabolism, lipopolysaccharide and cell wall biogenesis, and in regulation of virulence play a role in calcium precipitation. These results shed light on the common ability of Pseudomonas species to perform calcium precipitation and the underlying genetic regulation involved in biomineralization.

Ureolytic Prokaryotes in Soil: Community Abundance and Diversity

Although the turnover of urea is a crucial process in nitrogen transformation in soil, limited information is currently available on the abundance and diversity of ureolytic prokaryotes. The abundance and diversity of the soil 16S rRNA gene and ureC (encoding a urease catalytic subunit) were examined in seven soil types using quantitative PCR and amplicon sequencing with Illumina MiSeq. The amplicon sequencing of ureC revealed that the ureolytic community was composed of phylogenetically varied prokaryotes, and we detected 363 to 1,685 species-level ureC operational taxonomic units (OTUs) per soil sample, whereas 5,984 OTUs were site-specific OTUs found in only one of the seven soil types.

Diversity of Sporosarcina-like Bacterial Strains Obtained from Meter-Scale Augmented and Stimulated Biocementation Experiments

Microbially Induced Calcite Precipitation (MICP) is a biomediated soil cementation process that offers an environmentally conscious alternative to conventional geotechnical soil improvement technologies. This study provides the first comparison of ureolytic bacteria isolated from sand cemented in parallel, meter-scale, MICP experiments using either biostimulation or bioaugmentation approaches, wherein colonies resembling the augmented strain ( Sporosarcina pasteurii ATCC 11859) were interrogated. Over the 13 day experiment, 47 of the 57 isolates collected were strains of Sporosarcina and the diversity of these strains was high, with 20 distinct strains belonging to 5 species identified. Although the S. pasteurii inoculant used for augmentation was recovered immediately after introduction in the augmented specimen, the strain was not recovered after 8 days in either augmented or stimulated soils, suggesting that it competes poorly with indigenous bacteria. Past studies on the physiological properties of S. pasteurii ATCC 11859 suggest that close relatives may have selective advantages under the biogeochemical conditions employed during MICP; however, the extent to which these properties apply to isolates of the current study is unknown. Whole cell urease kinetic properties were investigated for representative isolates and suggest up to 100-fold higher rates of carbonate production when compared to other biomediated processes proposed for MICP.

A Low-Tech Bioreactor System for the Enrichment and Production of Ureolytic Microbes

Ureolysis-driven microbially induced carbonate precipitation (MICP) has recently received attention for its potential biotechnological applications. However, information on the enrichment and production of ureolytic microbes by using bioreactor systems is limited. Here, we report a low-tech down-flow hanging sponge (DHS) bioreactor system for the enrichment and production of ureolytic microbes. Using this bioreactor system and a yeast extract-based medium containing 0.17 M urea, ureolytic microbes with high potential urease activity (> 10 μmol urea hydrolyzed per min per ml of enrichment culture) were repeatedly enriched under non-sterile conditions. In addition, the ureolytic enrichment obtained in this study showed in vitro calcium carbonate precipitation. Fluorescence in situ hybridization analysis showed the existence of bacteria of the phylum Firmicutes in the bioreactor system. Our data demonstrate that this DHS bioreactor system is a useful system for the enrichment and production of ureolytic microbes for MICP applications.

Current challenges and future directions for bacterial self-healing concrete

Microbially induced calcium carbonate precipitation (MICP) has been widely explored and applied in the field of environmental engineering over the last decade. Calcium carbonate is naturally precipitated as a byproduct of various microbial metabolic activities. This biological process was brought into practical use to restore construction materials, strengthen and remediate soil, and sequester carbon. MICP has also been extensively examined for applications in self-healing concrete. Biogenic crack repair helps mitigate the high maintenance costs of concrete in an eco-friendly manner. In this process, calcium carbonate precipitation (CCP)-capable bacteria and nutrients are embedded inside the concrete. These bacteria are expected to increase the durability of the concrete by precipitating calcium carbonate in situ to heal cracks that develop in the concrete. However, several challenges exist with respect to embedding such bacteria; harsh conditions in concrete matrices are unsuitable for bacterial life, including high alkalinity (pH up to 13), high temperatures during manufacturing processes, and limited oxygen supply. Additionally, many biological factors, including the optimum conditions for MICP, the molecular mechanisms involved in MICP, the specific microorganisms suitable for application in concrete, the survival characteristics of the microorganisms embedded in concrete, and the amount of MICP in concrete, remain unclear. In this paper, metabolic pathways that result in conditions favorable for calcium carbonate precipitation, current and potential applications in concrete, and the remaining biological challenges are reviewed.

Urea Hydrolysis and Calcium Carbonate Precipitation in Gypsum-Amended Broiler Litter

Broiler () litter is subject to ammonia (NH) volatilization losses. Previous work has shown that the addition of gypsum to broiler litter can increase nitrogen mineralization and decrease NH losses due to a decrease in pH, but the mechanisms responsible for these effects are not well understood. Therefore, three laboratory studies were conducted to evaluate the effect of gypsum addition to broiler litter on (i) urease activity at three water contents, (ii) calcium carbonate precipitation, and (iii) pH. The addition of gypsum to broiler litter increased ammonium concentrations ( < 0.0033) and decreased litter pH by 0.43 to 0.49 pH units after 5 d ( < 0.0001); however, the rate of urea hydrolysis in treated litter only increased on Day 0 for broiler litter with low (0.29 g HO g) and high (0.69 g HO g) water contents, and on Day 3 for litter with medium (0.40 g HO g) water content ( < 0.05). Amending broiler litter with gypsum also caused an immediate decrease in litter pH (0.22 pH units) due to the precipitation of calcium carbonate (CaCO) from gypsum-derived calcium and litter bicarbonate. Furthermore, as urea was hydrolyzed, more urea-derived carbon precipitated as CaCO in gypsum-treated litter than in untreated litter ( < 0.001). These results indicate that amending broiler litter with gypsum favors the precipitation of CaCO, which buffers against increases in litter pH that are known to facilitate NH volatilization.

Isolation, differentiation and biodiversity of ureolytic bacteria of Qatari soil and their potential in microbially induced calcite precipitation (MICP) for soil stabilization

Biomineralization plays a key role in modifying the geological properties of soil, thereby stabilizing it against wind erosion, especially in areas characterized by harsh weather and harsh soil (calcareous and arid); i.e. Arabic Gulf region. Among soil microorganisms, ureolytic bacteria are capable of modifying soil characteristics and thus, inducing biomineralization. This research investigated the occurrence and diversity of ureolytic bacteria in Qatari soils, specifically to study their acquired potential to adapt to harsh conditions exhibiting ureolytic activity. Soil samples were collected from various locations in Qatar and were used to isolate the indigenous ureolytic bacteria. It was noticed that most of the ureolytic bacteria in Qatari soil belong to the genus Bacillus mainly Bacillus cereus. Identification and differentiation of 18 ureolytic isolates were performed using MALDI-TOF MS techniques while ribotyping (16S rRNA) molecular technique was used mainly for 6 selected strains. This study not only shows the diversity of species of ureolytic bacteria in Qatari soil but also shows the diversity in their protein profiles, which confirms that bacteria have adapted well to the harsh environment. In addition, the strains were evaluated based on a newly modified screening method in this work; i.e. production of arbitrary urease activity (AUA). Thus, the strains showing the highest AUA, exhibited the highest capability to produce urease enzymes induced by urea. Analysis of calcium carbonate precipitation utilizing SEM-EDX showed that the ureolytic bacteria also play a significant role in the precipitation of minerals such as CaCO₃, in the presence of urea in soil. Therefore, this research showed a high occurrence of indigenous Bacillus bacteria in Qatari soil that can perform biomineralization and thus can be helpful, if properly stimulated, in enhancing soil stabilization, and for other local applications as well, since they are adapted to these soil and weather conditions.

Biomineralization plays a key role in modifying the geological properties of soil, thereby stabilizing it against wind erosion, especially in areas characterized by harsh weather and harsh soil (calcareous and arid); i.e. Arabic Gulf region.

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

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

Isolation and Potential Biocementation of Calcite Precipitation Inducing Bacteria from Colombian Buildings

Microbiological induced calcium carbonate or calcite precipitation (MICP) has become a highly researched issue due to its multiple applications in the construction industry, being a promising alternative with a great biotechnological importance. In this work, potential calcite precipitation inducing bacteria were isolated from mortar and concrete samples of different buildings at the National University of Colombia. Eighteen crystal-precipitating strains were recovered in Urea-CaCl₂ solid medium. The 16S rRNA gene sequencing identified isolates as Arthrobacter, Psychrobacillus and Rhodococcus genera. It is reported, for the first time, the calcite precipitation by P. psycrodurans and R. qingshengii. Optical microscopy and Scanning Electron Microscopy showed crystals with irregular and spherical shapes, and beige and white colours. Furthermore, crystals formation appeared to be strain-specific. X-Ray diffraction analysis confirmed crystals composition as CaCO₃. Biocementation tests showed that MICP treatments of mortar cubes using P. psycrodurans caused an increase in their compressive strength compared to control samples. The positive action of a native MICP strain in mortar blocks biomineralization is shown, which is of great interest and potential for the construction industry.

Bacterial Community Dynamics and Biocement Formation during Stimulation and Augmentation: Implications for Soil Consolidation

Microbially-induced CaCO₃ precipitation (MICP) is a naturally occurring process wherein durable carbonates are formed as a result of microbial metabolic activities. In recent years, MICP technology has been widely harnessed for applications in civil engineering wherein synthesis of calcium carbonate crystals occurs at ambient temperature paving way for low energy biocement. MICP using pure urease (UA) and carbonic anhydrase (CA) producing bacteria has been promising in laboratory conditions. In the current study we enriched ureolytic and carbonic anhydrase communities in calcareous soil under biostimulation and bioaugmentation conditions and investigated the effect of microbial dynamics on carbonate precipitation, calcium carbonate polymorph selection and consolidation of biological sand column under nutrient limited and rich conditions. All treatments for stimulation and augmentation led to significant changes in the composition of indigenous bacterial population. Biostimulation as well as augmentation through the UA route was found to be faster and more effective compared to the CA route in terms of extracellular enzyme production and carbonate precipitation. Synergistic role of augmented cultures along with indigenous communities was recorded via both the routes of UA and CA as more effective calcification was seen in case of augmentation compared to stimulation. The survival of supplemented isolates in presence of indigenous bacterial communities was confirmed through sequencing of total diversity and it was seen that both UA and CA isolate had the potential to survive along with native communities under high nutrient conditions. Nutrient conditions played significant role in determining calcium carbonate polymorph fate as calcitic crystals dominated under high carbon supplementation. Finally, the consolidation of sand columns via stimulation and augmentation was successfully achieved through both UA and CA route under high nutrient conditions but higher consolidation in short time period was noticed in UA route. The study reports that based upon the organic carbon content in native soils, stimulation can be favored at sites with high organic carbon content while augmentation with repeated injections of nutrients can be applied on poor nutrient soils via different enrichment routes of microbial metabolism.

Non-ureolytic calcium carbonate precipitation by Lysinibacillus sp. YS11 isolated from the rhizosphere of Miscanthus sacchariflorus

Although microbially induced calcium carbonate precipitation (MICP) through ureolysis has been widely studied in environmental engineering fields, urea utilization might cause environmental problems as a result of ammonia and nitrate production. In this study, many non-ureolytic calcium carbonate-precipitating bacteria that induced an alkaline environment were isolated from the rhizosphere of Miscanthus sacchariflorus near an artificial stream and their ability to precipitate calcium carbonate minerals with the absence of urea was investigated. MICP was observed using a phase-contrast microscope and ion-selective electrode. Only Lysinibacillus sp. YS11 showed MICP in aerobic conditions. Energy dispersive X-ray spectrometry and X-ray diffraction confirmed the presence of calcium carbonate. Field emission scanning electron microscopy analysis indicated the formation of morphologically distinct minerals around cells under these conditions. Monitoring of bacterial growth, pH changes, and Ca²⁺ concentrations under aerobic, hypoxia, and anaerobic conditions suggested that strain YS11 could induce alkaline conditions up to a pH of 8.9 and utilize 95% of free Ca²⁺ only under aerobic conditions. Unusual Ca²⁺ binding and its release from cells were observed under hypoxia conditions. Biofilm and extracellular polymeric substances (EPS) formation were enhanced during MICP. Strain YS11 has resistance at high pH and in high salt concentrations, as well as its spore-forming ability, which supports its potential application for self-healing concrete.

Non-ureolytic calcium carbonate precipitation by Lysinibacillus sp. YS11 isolated from the rhizosphere of Miscanthus sacchariflorus

Although microbially induced calcium carbonate precipitation (MICP) through ureolysis has been widely studied in environmental engineering fields, urea utilization might cause environmental problems as a result of ammonia and nitrate production. In this study, many non-ureolytic calcium carbonate-precipitating bacteria that induced an alkaline environment were isolated from the rhizosphere of Miscanthus sacchariflorus near an artificial stream and their ability to precipitate calcium carbonate minerals with the absence of urea was investigated. MICP was observed using a phase-contrast microscope and ion-selective electrode. Only Lysinibacillus sp. YS11 showed MICP in aerobic conditions. Energy dispersive X-ray spectrometry and X-ray diffraction confirmed the presence of calcium carbonate. Field emission scanning electron microscopy analysis indicated the formation of morphologically distinct minerals around cells under these conditions. Monitoring of bacterial growth, pH changes, and Ca²⁺ concentrations under aerobic, hypoxia, and anaerobic conditions suggested that strain YS11 could induce alkaline conditions up to a pH of 8.9 and utilize 95% of free Ca²⁺ only under aerobic conditions. Unusual Ca²⁺ binding and its release from cells were observed under hypoxia conditions. Biofilm and extracellular polymeric substances (EPS) formation were enhanced during MICP. Strain YS11 has resistance at high pH and in high salt concentrations, as well as its spore-forming ability, which supports its potential application for self-healing concrete.

Screening for Urease-Producing Bacteria from Limestone Caves of Sarawak

Urease is a key enzyme in the chemical reaction of microorganism and has been found to be associated withcalcification, which is essential in microbially induced calcite precipitation (MICP) process. Three bacterialisolates (designated as LPB19, TSB31 and TSB12) were among twenty-eight bacteria that were isolated fromsamples collected from Sarawak limestone caves using the enrichment culture technique. Isolates LPB19, TSB31and TSB12 were selected based on their quick urease production when compared to other isolates. Phenotypiccharacteristics indicate all three bacterial strains are gram-positive, rod-shaped, motile, catalase and oxidasepositive. Urease activity of the bacterial isolates were measured through changes in conductivity in the absence ofcalcium ions. The bacterial isolates (LPB19, TSB12 and TSB31) showed urease activity of 16.14, 12.45 and 11.41mM urea hydrolysed/min respectively. The current work suggested that these isolates serves as constitutiveproducers of urease, potentially useful in inducing calcite precipitates.

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.

Metagenomic Analysis Suggests Modern Freshwater Microbialites Harbor a Distinct Core Microbial Community

Modern microbialites are complex microbial communities that interface with abiotic factors to form carbonate-rich organosedimentary structures whose ancestors provide the earliest evidence of life. Past studies primarily on marine microbialites have inventoried diverse taxa and metabolic pathways, but it is unclear which of these are members of the microbialite community and which are introduced from adjacent environments. Here we control for these factors by sampling the surrounding water and nearby sediment, in addition to the microbialites and use a metagenomics approach to interrogate the microbial community. Our findings suggest that the Pavilion Lake microbialite community profile, metabolic potential and pathway distributions are distinct from those in the neighboring sediments and water. Based on RefSeq classification, members of the Proteobacteria (e.g., alpha and delta classes) were the dominant taxa in the microbialites, and possessed novel functional guilds associated with the metabolism of heavy metals, antibiotic resistance, primary alcohol biosynthesis and urea metabolism; the latter may help drive biomineralization. Urea metabolism within Pavilion Lake microbialites is a feature not previously associated in other microbialites. The microbialite communities were also significantly enriched for cyanobacteria and acidobacteria, which likely play an important role in biomineralization. Additional findings suggest that Pavilion Lake microbialites are under viral selection as genes associated with viral infection (e.g CRISPR-Cas, phage shock and phage excision) are abundant within the microbialite metagenomes. The morphology of Pavilion Lake microbialites changes dramatically with depth; yet, metagenomic data did not vary significantly by morphology or depth, indicating that microbialite morphology is altered by other factors, perhaps transcriptional differences or abiotic conditions. This work provides a comprehensive metagenomic perspective of the interactions and differences between microbialites and their surrounding environment, and reveals the distinct nature of these complex communities.

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

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

Soil Bacteria Population Dynamics Following Stimulation for Ureolytic Microbial-Induced CaCO3 Precipitation

Microbial-induced CaCO3 precipitation (MICP) via urea-hydrolysis (ureolysis) is an emerging soil improvement technique for various civil engineering and environmental applications. In-situ application of MICP in soils is performed either by augmenting the site with ureolytic bacteria or by stimulating indigenous ureolytic bacteria. Both of these approaches may lead to changes in the indigenous bacterial population composition and to the accumulation of large quantities of ammonium. In this batch study, effective ureolysis was stimulated in coastal sand from a semiarid environment, with low initial ureolytic bacteria abundance. Two different carbon sources were used: yeast-extract and molasses. No ureolysis was observed in their absence. Ureolysis was achieved using both carbon sources, with a higher rate in the yeast-extract enrichment resulting from increased bacterial growth. The changes to the indigenous bacterial population following biostimulation of ureolysis were significant: Bacilli class abundancy increased from 5% in the native sand up to 99% in the yeast-extract treatment. The sand was also enriched with ammonium-chloride, where ammonia-oxidation was observed after 27 days, but was not reflected in the bacterial population composition. These results suggest that biostimulation of ureolytic bacteria can be applied even in a semiarid and nutrient-poor environment using a simple carbon source, that is, molasses. The significant changes to bacterial population composition following ureolysis stimulation could result in a decrease in trophic activity and diversity in the treated site, thus they require further attention.

Microbial composition of biofilms associated with lithifying rubble of Acropora palmata branches

Coral reefs are among the most productive ecosystems on the planet, but are rapidly declining due to global-warming-mediated changes in the oceans. Particularly for the Caribbean region, Acropora sp. stony corals have lost ∼80% of their original coverage, resulting in vast extensions of dead coral rubble. We analyzed the microbial composition of biofilms that colonize and lithify dead Acropora palmata rubble in the Mexican Caribbean and identified the microbial assemblages that can persist under scenarios of global change, including high temperature and low pH. Lithifying biofilms have a mineral composition that includes aragonite and magnesium calcite (16 mole% MgCO(3)) and calcite, while the mineral phase corresponding to coral skeleton is basically aragonite. Microbial composition of the lithifying biofilms are different in comparison to surrounding biotopes, including a microbial mat, water column, sediments and live A. palmata microbiome. Significant shifts in biofilm composition were detected in samples incubated in mesocosms. The combined effect of low pH and increased temperature showed a strong effect after two-week incubations for biofilm composition. Findings suggest that lithifying biofilms could remain as a secondary structure on reef rubble possibly impacting the functional role of coral reefs.

Microbial ureolysis in the seawater-catalysed urine phosphorus recovery system: Kinetic study and reactor verification

Our previous study has confirmed the feasibility of using seawater as an economical precipitant for urine phosphorus (P) precipitation. However, we still understand very little about the ureolysis in the Seawater-based Urine Phosphorus Recovery (SUPR) system despite its being a crucial step for urine P recovery. In this study, batch experiments were conducted to investigate the kinetics of microbial ureolysis in the seawater-urine system. Indigenous bacteria from urine and seawater exhibited relatively low ureolytic activity, but they adapted quickly to the urine-seawater mixture during batch cultivation. During cultivation, both the abundance and specific ureolysis rate of the indigenous bacteria were greatly enhanced as confirmed by a biomass-dependent Michaelis-Menten model. The period for fully ureolysis was decreased from 180 h to 2.5 h after four cycles of cultivation. Based on the successful cultivation, a lab-scale SUPR reactor was set up to verify the fast ureolysis and efficient P recovery in the SUPR system. Nearly complete urine P removal was achieved in the reactor in 6 h without adding any chemicals. Terminal Restriction Fragment Length Polymorphism (TRFLP) analysis revealed that the predominant groups of bacteria in the SUPR reactor likely originated from seawater rather than urine. Moreover, batch tests confirmed the high ureolysis rates and high phosphorus removal efficiency induced by cultivated bacteria in the SUPR reactor under seawater-to-urine mixing ratios ranging from 1:1 to 9:1. This study has proved that the enrichment of indigenous bacteria in the SUPR system can lead to sufficient ureolytic activity for phosphate precipitation, thus providing an efficient and economical method for urine P recovery.

The Micro-mechanism Involved and Wollastonite Signature in the Calcareous Precipitates of Marine Isolates

Micro-mechanical studies connecting the influence of extrinsic factors over intrinsic factors on 30 calcareous isolates obtained from marine sediment biofilms of the Bay of Bengal (Indian Ocean) revealed that the fate of calcareous crystal precipitation is highly dependent on factors like extracellular polysaccharides (EPS), organic carbon and nutrition. Further studies exemplified that EPS and the organic carbon secreted by the isolates controlled the dissemination of the calcareous crystals precipitated. From the study, it is evident that an EPS concentration of 7-15 mg l(-1) was found to enhance the dissemination of the calcareous crystals. Atomic force micrographs explain the nucleation behaviour and morphology of the calcareous crystals precipitated. X-ray diffraction (XRD) and energy-dispersive X-ray spectroscopy (EDAX) showed that the crystals were mainly composed of calcite and partially wollastonite.

Biogenic concrete protection driven by the formate oxidation by Methylocystis parvus OBBP

The effectiveness of Microbiologically Induced Carbonate Precipitation (MICP) from the formate oxidation by Methylocystis parvus OBBP as an alternative process for concrete protection was investigated. MICP was induced on Autoclaved Aerated Concrete (AAC), the model material, by immersing the material in 10⁹M. parvus cells mL⁻¹ containing 5 g L⁻¹ of calcium formate. A 2 days immersion of the material gave the maximum weight increase of the specimens (38 ± 19 mg) and this was likely due to the deposition of calcium carbonate, biomass, and unconverted calcium formate. The solid deposition mainly occurred in the micropores of the specimen, close to the outer surface. A significantly lower water absorption was observed in the bacterially treated specimens compared to the non-treated ones (up to 2.92 ± 0.91 kg m⁻²) and this could be attributed to the solid deposition. However, the sonication test demonstrated that the bacterial treatment did not give a consolidating effect to the material. Overall, compared to the currently employed urea hydrolysis process, the formate-based MICP by M. parvus offers a more environmentally friendly approach for the biotechnological application to protect concrete.

Formate oxidation-driven calcium carbonate precipitation by Methylocystis parvus OBBP

Microbially induced carbonate precipitation (MICP) applied in the construction industry poses several disadvantages such asammonia release to the air and nitric acid production. An alternative MICP from calcium formate by Methylocystis parvus OBBP is presented here to overcome these disadvantages. To induce calcium carbonate precipitation, M. parvus was incubated at different calcium formate concentrations and starting culture densities. Up to 91.4% ± 1.6% of the initial calcium was precipitated in the methane-amended cultures compared to 35.1% ± 11.9% when methane was not added. Because the bacteria could only utilize methane for growth, higher culture densities and subsequently calcium removals were exhibited in the cultures when methane was added. A higher calcium carbonate precipitate yield was obtained when higher culture densities were used but not necessarily when more calcium formate was added. This was mainly due to salt inhibition of the bacterial activity at a high calcium formate concentration. A maximum 0.67 ± 0.03 g of CaCO3 g of Ca(CHOOH)2(-1) calcium carbonate precipitate yield was obtained when a culture of 10(9) cells ml(-1) and 5 g of calcium formate liter(-)1 were used. Compared to the current strategy employing biogenic urea degradation as the basis for MICP, our approach presents significant improvements in the environmental sustainability of the application in the construction industry.

Biomineralization processes of calcite induced by bacteria isolated from marine sediments

Biomineralization is a known natural phenomenon associated with a wide range of bacterial species. Bacterial-induced calcium carbonate precipitation by marine isolates was investigated in this study. Three genera of ureolytic bacteria, Sporosarcina sp., Bacillus sp. and Brevundimonas sp. were observed to precipitate calcium carbonate minerals. Of these species, Sporosarcina sp. dominated the cultured isolates. B. lentus CP28 generated higher urease activity and facilitated more efficient precipitation of calcium carbonate at 3.24 ± 0.25 × 10⁻⁴ mg/cell. X-ray diffraction indicated that the dominant calcium carbonate phase was calcite. Scanning electron microscopy showed that morphologies of the minerals were dominated by cubic, rhombic and polygonal plate-like crystals. The dynamic process of microbial calcium carbonate precipitation revealed that B. lentus CP28 precipitated calcite crystals through the enzymatic hydrolysis of urea, and that when ammonium ion concentrations reached 746 mM and the pH reached 9.6, that favored calcite precipitation at a higher level of 96 mg/L. The results of this research provide evidence that a variety of marine bacteria can induce calcium carbonate precipitation, and may influence the marine carbonate cycle in natural 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.

Genetically-enriched microbe-facilitated self-healing concrete – a sustainable material for a new generation of construction technology

Genetically modified spore formingB. subtilisbacterial cells for eco-friendly sustainable self-healing bio-concrete.

A mineralogical characterization of biogenic calcium carbonates precipitated by heterotrophic bacteria isolated from cryophilic polar regions

Precipitation of calcium carbonate (CaCO3(s) ) can be driven by microbial activity. Here, a systematic approach is used to identify the morphological and mineralogical characteristics of CaCO3(s) precipitated during the heterotrophic growth of micro-organisms isolated from polar environments. Focus was placed on establishing mineralogical features that are common in bioliths formed during heterotrophic activity, while in parallel identifying features that are specific to bioliths precipitated by certain microbial phylotypes. Twenty microbial isolates that precipitated macroscopic CaCO3(s) when grown on B4 media supplemented with calcium acetate or calcium citrate were identified. A multimethod approach, including scanning electron microscopy, high-resolution transmission electron microscopy, and micro-X-ray diffraction (μ-XRD), was used to characterize CaCO3(s) precipitates. Scanning and transmission electron microscopy showed that complete CaCO3(s) crystal encrustation of Arthrobacter sp. cells was common, while encrustation of Rhodococcus sp. cells did not occur. Several euhedral and anhedral mineral formations including disphenoid-like epitaxial plates, rhomboid-like aggregates with epitaxial rhombs, and spherulite aggregates were observed. While phylotype could not be linked to specific mineral formations, isolates tended to precipitate either euhedral or anhedral minerals, but not both. Three anhydrous CaCO3(s) polymorphs (calcite, aragonite, and vaterite) were identified by μ-XRD, and calcite and aragonite were also identified based on TEM lattice-fringe d value measurements. The presence of certain polymorphs was not indicative of biogenic origin, although several mineralogical features such as crystal-encrusted bacterial cells, or casts of bacterial cells embedded in mesocrystals are an indication of biogenic origin. In addition, some features such as the formation of vaterite and bacterial entombment appear to be linked to certain phylotypes. Identifying phylotypes consistent with certain mineralogical features is the first step toward discovering a link between these crystal features and the precise underlying molecular biology of the organism precipitating them.