Native Bacterial Community Convergence in Augmented and Stimulated Ureolytic MICP Biocementation

Microbiologically induced calcite precipitation (MICP) in situ remediated heavy metal contamination in sludge nutrient soil

Microbiologically induced calcite precipitation (MICP), as a newly developing bioremediation technology, could redeem heavy metal contamination in diverse scenarios. In this study, MICP bacterium Sporosarcina ureilytica ML-2 was employed to suppress the pollution of Pb, Cd and Zn in municipal sludge nutrient soil. After MICP remediation, the exchangeable Cd and Zn in sludge nutrient soil were correspondingly reduced by 31.02 % and 6.09 %, while the carbonate-bound Pb, Cd and Zn as well as the residual fractions were increased by 16.12 %, 6.63 %, 13.09 % and 6.10 %, 45.70 %, 3.86 %, respectively. In addition, the extractable Pb, Cd and Zn either by diethylenetriaminepentaacetic acid (DTPA) or toxicity characteristic leaching procedure (TCLP) in sludge nutrient soil were significantly reduced. These results demonstrated that the bio-calcite generated via MICP helped to immobilize heavy metals. Furthermore, MICP treatment improved the abundance of functional microorganisms related to urea cycle, while reduced the overall abundance of metal resistance genes (MRGs) and antibiotic resistance genes (ARGs). This work confirmed the feasibility of MICP in remediation of heavy metal in sludge nutrient soil, which expanded the application field of MICP and provided a promising way for heavy metal pollution management.

Microbially induced calcium carbonate precipitation through CO2 sequestration via an engineered Bacillus subtilis

BACKGROUND

Microbially induced calcium carbonate precipitation has been extensively researched for geoengineering applications as well as diverse uses within the built environment. Bacteria play a crucial role in producing calcium carbonate minerals, via enzymes including carbonic anhydrase-an enzyme with the capability to hydrolyse CO2, commonly employed in carbon capture systems. This study describes previously uncharacterised carbonic anhydrase enzyme sequences capable of sequestering CO2 and subsequentially generating CaCO3 biominerals and suggests a route to produce carbon negative cementitious materials for the construction industry.

RESULTS

Here, Bacillus subtilis was engineered to recombinantly express previously uncharacterised carbonic anhydrase enzymes from Bacillus megaterium and used as a whole cell catalyst allowing this novel bacterium to sequester CO2 and convert it to calcium carbonate. A significant decrease in CO2 was observed from 3800 PPM to 820 PPM upon induction of carbonic anhydrase and minerals recovered from these experiments were identified as calcite and vaterite using X-ray diffraction. Further experiments mixed the use of this enzyme (as a cell free extract) with Sporosarcina pasteurii to increase mineral production whilst maintaining a comparable level of CO2 sequestration.

CONCLUSION

Recombinantly produced carbonic anhydrase successfully sequestered CO2 and converted it into calcium carbonate minerals using an engineered microbial system. Through this approach, a process to manufacture cementitious materials with carbon sequestration ability could be developed.

Synergistic biocementation: harnessing Comamonas and Bacillus ureolytic bacteria for enhanced sand stabilization

Biocementation, driven by ureolytic bacteria and their biochemical activities, has evolved as a powerful technology for soil stabilization, crack repair, and bioremediation. Ureolytic bacteria play a crucial role in calcium carbonate precipitation through their enzymatic activity, hydrolyzing urea to produce carbonate ions and elevate pH, thus creating favorable conditions for the precipitation of calcium carbonate. While extensive research has explored the ability of ureolytic bacteria isolated from natural environments or culture conditions, bacterial synergy is often unexplored or under-reported. In this study, we isolated bacterial strains from the local eutrophic river canal and evaluated their suitability for precipitating calcium carbonate polymorphs. We identified two distinct bacterial isolates with superior urea degradation ability (conductivity method) using partial 16 S rRNA gene sequencing. Molecular identification revealed that they belong to the Comamonas and Bacillus genera. Urea degradation analysis was performed under diverse pH (6,7 and 8) and temperature (15 °C,20 °C,25 °C and 30 °C) ranges, indicating that their ideal pH is 7 and temperature is 30 °C since 95% of the urea was degraded within 96 h. In addition, we investigated these strains individually and in combination, assessing their microbially induced carbonate precipitation (MICP) in silicate fine sand under low (14 ± 0.6 °C) and ideal temperature 30 °C conditions, aiming to optimize bio-mediated soil enhancement. Results indicated that 30 °C was the ideal temperature, and combining bacteria resulted in significant (p ≤ 0.001) superior carbonate precipitation (14-16%) and permeability (> 10- 6 m/s) in comparison to the average range of individual strains. These findings provide valuable insights into the potential of combining ureolytic bacteria for future MICP research on field applications including soil erosion mitigation, soil stabilization, ground improvement, and heavy metal remediation.

Composite biomediated engineering approaches for improving problematic soils: Potentials and opportunities

Several conventional chemical stabilizers are used for soil stabilization, among which cement is widely adopted. However, the high energy consumption and environmental challenges associated with these stabilizers have necessitated the transition toward the adoption/deployment of eco-friendly approaches for soil stabilization. Biomediated techniques are sustainable soil improvement methods adopting less toxic microorganisms, enzymes, or polymers for cementing soil. However, these processes also have several drawbacks, such as slow hardening, environmental impact, high cost, and lack of compatibility with different types of soils. It is hypothesized that these limitations may be overcome by exploring the prospects and opportunities offered by hybrid technological approaches involving the integration of nontraditional stabilizers and microbial-induced biomineralization processes for improving problematic soils. This paper discusses selected previous studies integrating different technologies and their benefits and challenges. The emerging fungi-based bio-mediation techniques and the possibility of forming sustainable fungal-based biocomposites to improve problematic soils are also highlighted.

State-of-the-art review of soil erosion control by MICP and EICP techniques: Problems, applications, and prospects

In recent years, the application of microbially induced calcite precipitation (MICP) and enzyme-induced carbonate precipitation (EICP) techniques have been extensively studied to mitigate soil erosion, yielding substantial achievements in this regard. This paper presents a comprehensive review of the recent progress in erosion control by MICP and EICP techniques. To further discuss the effectiveness of erosion mitigation in-depth, the estimation methods and characterization of erosion resistance were initially compiled. Moreover, factors affecting the erosion resistance of MICP/EICP-treated soil were expounded, spanning from soil properties to treatment protocols and environmental conditions. The development of optimization and upscaling in erosion mitigation via MICP/EICP was also included in this review. In addition, this review discussed the limitations and correspondingly proposed prospective applications of erosion control via the MICP/EICP approach. The current review presents up-to-date information on the research activities for improving erosion resistance by MICP/EICP, aiming at providing insights for interdisciplinary researchers and guidance for promoting this method to further applications in erosion mitigation.

Effect of surfactant on urease-producing flora from waste activated sludge using microbially induced calcite precipitation technology to suppress coal dust

The wettability of microbially induced calcite precipitation (MICP) is a challenge in dust suppression. Herein, the tolerance of urease-producing flora to surfactants was investigated. The optimal tolerance concentrations of the urease-producing flora to sodium dodecylbenzene sulfonate (SDBS, anionic surfactant), alkyl polyglycoside (APG, non-ionic surfactant), and cocamidopropyl betaine (CAB, zwitterionic surfactant), and were 0.2%, 0.1%, and 0.05%. The cetyltrimethylammonium bromide (CTAB, cationic surfactant) inhibited urease production by urease-producing flora. The mineralization products of SDBS, APG, and CAB treatments were all transformed into calcite. The wind resistance test showed that the mass loss of all samples is less than 0.1%. The rain resistance and hardness tests showed that 0.2% SBDS had the best effect, followed by 0.1% APG and 0.05% CAB, and finally, No surfactants. Microbiome analysis showed that the abundance of Sporosarcina and Unclassified_bacillaceae reduced, and the intense competition between Paenalcaligenes and Sporosarcina are essential reasons for reducing urease activity. SDBS and APG could reduce the pathogenic risk of microbial dust suppressants. This study will facilitate the practical application of microbial dust suppressants.

Identification of coastal pesticide pollutants as potent inhibitors of Bacillus pasteurii urease mediated calcium carbonate precipitation: a computational approach

Microbially induced calcite precipitation (MICP) through urease enzyme has attained a lot of recognition in various fields of civil engineering and geotechnology for stabilizing the strength of soil and various concrete materials. The activity of urease has been found to be affected by various factors like temperature, substrate concentrations, pH of the medium, presence of inhibitors, etc. Through this study, the outcome of the interaction of pesticides (commonly found in Indian coastal regions) on Bacillus pasteurii urease, a major organism reported for MICP studies has been investigated in silico. The results from the study revealed that the enzyme has higher interactions of -4.1, -3.2, and -3.4 kJ/mol with common pesticides like dichloro diphenyl dichloro ethane(DDD), dichloro diphenyl trichloroe thane (DDT), and methyl parathion of organochlorides and organophosphates class. From the molecular dynamics simulation analysis, complex 1 (DDD -receptor) has been found to have the highest and more compact structure followed by methyl parathion -receptor. Prime MM-GBSA analysis also revealed the highest binding energy of -27.8 kcal/mol with the protein and DDD. Thus, it can be inferred from the current study that pesticides, particularly, DDD, DDT, and methyl parathion present in the coastal areas may have an impact on urease. This interaction can result in the inhibition of the urease activity of B. pasteurii, thus preventing the biomineralization process. This study would be the first report on the computational approach to understanding the interaction of prominent pesticides on the coastal region and B. pasteurii urease.Communicated by Ramaswamy H. Sarma.

Microbial functionalities and immobilization of environmental lead: Biogeochemical and molecular mechanisms and implications for bioremediation

The increasing environmental and human health concerns about lead in the environment have stimulated scientists to search for microbial processes as innovative bioremediation strategies for a suite of different contaminated media. In this paper, we provide a compressive synthesis of existing research on microbial mediated biogeochemical processes that transform lead into recalcitrant precipitates of phosphate, sulfide, and carbonate, in a genetic, metabolic, and systematics context as they relate to application in both laboratory and field immobilization of environmental lead. Specifically, we focus on microbial functionalities of phosphate solubilization, sulfate reduction, and carbonate synthesis related to their respective mechanisms that immobilize lead through biomineralization and biosorption. The contributions of specific microbes, both single isolates or consortia, to actual or potential applications in environmental remediation are discussed. While many of the approaches are successful under carefully controlled laboratory conditions, field application requires optimization for a host of variables, including microbial competitiveness, soil physical and chemical parameters, metal concentrations, and co-contaminants. This review challenges the reader to consider bioremediation approaches that maximize microbial competitiveness, metabolism, and the associated molecular mechanisms for future engineering applications. Ultimately, we outline important research directions to bridge future scientific research activities with practical applications for bioremediation of lead and other toxic metals in environmental systems.

Microbially induced calcium precipitation driven by denitrification: Performance, metabolites, and molecular mechanisms

Microbially induced calcium precipitation (MICP) driven by denitrification has attracted extensive attention due to its application potential in nitrate removal from calcium-rich groundwater. However, little research has been conducted on this technique at the molecular level. Here, Pseudomonas WZ39 was used to explore the molecular mechanisms of nitrate-dependent MICP and the effects of Ca²⁺ on bacterial transcriptional regulation and metabolic response. The results exhibited that appropriate Ca²⁺ concentration (4.5 mM) can promote denitrification and the production of ATP, EPSs, and SMPs. Genome-wide analysis showed that the nitrate-dependent MICP was accomplished through heterotrophic denitrification and CO₂ capture. During this process, EPS biosynthesis and Ca²⁺ signaling regulation were involved in the nucleation template supply and Ca²⁺ homeostasis balance. Untargeted transcriptome- and metabolome-association analyses revealed that the addition of Ca²⁺ triggered the significant up-regulation in several key pathways, such as transmembrane transporter and channel activities, amino acid metabolism, fatty acid biosynthesis, and carbon metabolism, which played a momentous role in the mineral nucleation and energy provision. The detailed information provided novel insights for understanding the active control of bacteria on MICP, and has great significance for deepening the cognition of groundwater remediation using nitrate-dependent MICP technique.

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.

Efficient bio-cementation between silicate tailings and biogenic calcium carbonate: Nano-scale structure and mechanism of the interface

Biogenic calcium carbonate (bio-CaCO₃) cementing tailings is an efficient technology to immobilize heavy metals in waste tailings. However, the underlying mechanism of interface cementation has not yet been clearly established, which limits the technological development. In this study, we used advanced techniques, including atomic force microscopy-based Lorentz contact resonance (AFM-LCR) spectroscopy, AFM-based nanoscale infrared (AFM-IR) spectroscopy, and solid-state nuclear magnetic resonance (ssNMR) spectroscopy, to reveal the structural, mechanical, and chemical properties of the interface on the nanoscale. Ureolytic bacteria produced bio-CaCO₃ to fill in pore space and to bind cement tailings particles, which prevented the formation of leachate containing heavy metals. After cementation, a strong 40-300 nm thin interface was formed between the taillings and bio-CaCO₃ particles. Unlike chemically synthesized CaCO₃, bio-CaCO₃ is strongly negatively charged, which gives it better adhesion ability. Fourier transform infrared (FTIR), AFM-IR, and ²⁹Si ssNMR spectra indicated that the Si-OH and Si-O-Si groups on the silicate surface were converted to deprotonated silanol groups (≡Si-O^-) at a high pH and they formed strong chemical bonds of Si-O-Ca on the interface through a Ca ion bridge. In addition, hydrogen bonding with Si-OH also played a role at the cementation interface. These findings provide the nano-scale interfacial structure and mechanism of bio-CaCO₃ cementing silicate tailings and accelerate the development of tailings disposal technology.

Heavy metal bioremediation using microbially induced carbonate precipitation: Key factors and enhancement strategies

With the development of economy, heavy metal (HM) contamination has become an issue of global concern, seriously threating animal and human health. Looking for appropriate methods that decrease their bioavailability in the environment is crucial. Microbially induced carbonate precipitation (MICP) has been proposed as a promising bioremediation method to immobilize contaminating metals in a sustainable, eco-friendly, and energy saving manner. However, its performance is always affected by many factors in practical application, both intrinsic and external. This paper mainly introduced ureolytic bacteria-induced carbonate precipitation and its implements in HM bioremediation. The mechanism of HM immobilization and in-situ application strategies (that is, biostimulation and bioaugmentation) of MICP are briefly discussed. The bacterial strains, culture media, as well as HMs characteristics, pH and temperature, etc. are all critical factors that control the success of MICP in HM bioremediation. The survivability and tolerance of ureolytic bacteria under harsh conditions, especially in HM contaminated areas, have been a bottleneck for an effective application of MICP in bioremediation. The effective strategies for enhancing tolerance of bacteria to HMs and improving the MICP performance were categorized to provide an in-depth overview of various biotechnological approaches. Finally, the technical barriers and future outlook are discussed. This review may provide insights into controlling MICP treatment technique for further field applications, in order to enable better control and performance in the complex and ever-changing environmental systems.

Coupled effect of microbiologically induced calcium carbonate and biofilms in leachate

Fouling and clogging are persistent challenges to the collection and treatment of leachate. The main components of fouling and clogging are calcium carbonate (CaCO₃) and biofilms. However, the relationships between CaCO₃ and biofilms remain to be clarified. In this study, the interaction between microbially induced CaCO₃ precipitation (MICP) and biofilms was investigated using Luria-Bertani (LB) or urea media. Results showed that the bacteria promoted the precipitation of CaCO₃ and the formation of a complex mixture of biofilms. The amount of formed CaCO₃ in the urea medium was 12.9 times of that in the LB medium. The high MICP potential in the urea medium was associated with increased pH and alkalinity. In addition, the clogging materials exhibited a layered structure and uneven distribution over the clogging width and depth profile. These results indicated the presence of nucleation sites of CaCO₃ on the surface of and inside the bacteria. This research provides insights into the regulation of MICP and biofilms through dynamic control of clogging and fouling.

Enhanced removal of fluoride, nitrate, and calcium using self-assembled fungus-flexible fiber composite microspheres combined with microbially induced calcium precipitation

Self-assembled fungus-flexible fiber composite microspheres (SFFMs) were firstly combined with microbially induced calcium precipitation (MICP) in a continuous-flow bioreactor and achieved the efficient removal of fluoride (F^-), nitrate (NO₃^-), and calcium (Ca²⁺). Under the influent F^- of 3.0 mg L^-1, pH of 7.0, and HRT of 8 h, the average removal efficiencies reached 77.54%, 99.39%, and 67.25% (0.29, 2.03, and 8.34 mg L^-1 h^-1), respectively. Fluorescence spectrum and flow cytometry analyses indicated that F^- content significantly affected the metabolism and viability of bacteria. SEM images showed that flexible fibers and intertwined hyphae provided effective locations for bacterial colonization in SFFMs. The precipitated products were characterized by XRD and FTIR, which revealed that F^- was mainly removed in the form of calcium fluoride and calcium fluorophosphate (CaF₂ and Ca₅(PO₄)₃F). High-throughput analysis at different levels demonstrated that Pseudomonas sp. WZ39 acted as the core strain, which played a crucial role in the bioreactor. The mechanism of enhanced denitrification was attributed to minor F^- stress and bioaugmentation technology. This study highlighted the superiorities of SFFMs and MICP combined remediation and documented a promising option for F^-, NO₃^-, and Ca²⁺ removal.

Effect of cell density on decrease in hydraulic conductivity by microbial calcite precipitation

The effect of number of cells deposited on decrease in hydraulic conductivity of porous media using CaCO₃ precipitation induced by Sporosarcina pasteurii (ATCC 11,859) was examined in columns packed with glass beads in the range of 0.25 mm and 3 mm in diameter. After resting Sporosarcina pasteurii cells were introduced into the columns, a precipitation solution, which consisted of 500 mM CaCl₂ and 500 mM urea, was introduced under continuous flow conditions. It was shown that hydraulic conductivity was decreased by formation of microbially induced CaCO₃ precipitation from between 8.37 * 10⁻¹ and 6.73 * 10⁻² cm/s to between 3.69 * 10⁻¹ and 1.01 * 10⁻² cm/s. The lowest hydraulic conductivity was achieved in porous medium consisting of the smallest glass beads (0.25 mm in diameter) using the highest density of cell suspension (OD₆₀₀ 2.25). The number of the deposited cells differed depending on the glass bead size of the columns. According to the experiments, 7 * 10⁻⁹ g CaCO₃ was produced by a single resting cell. The urease activity, which led CaCO₃ precipitation, depended on presence of high number of cells deposited in the column because the nutrients were not included in the precipitation solution and consequently, the amount of CaCO₃ precipitated was proportional with the cell number in the column. A mathematical model was also developed to investigate the experimental results, and statistical analysis was also performed.

Sporosarcina pasteurii, which is an ecologically friendly bacterium for environmental biotechnology, produces urease to form CaCO₃ precipitation

CaCO₃ precipitation decreases the hydraulic conductivity of porous media

The urease activity depends on the presence of high number of Sporosarcina pasteurii

A critical review on microbial carbonate precipitation via denitrification process in building materials

The naturally occurring biomineralization or microbially induced calcium carbonate (MICP) precipitation is gaining huge attention due to its widespread application in various fields of engineering. Microbial denitrification is one of the feasible metabolic pathways, in which the denitrifying microbes lead to precipitation of carbonate biomineral by their basic enzymatic and metabolic activities. This review article explains all the metabolic pathways and their mechanism involved in the MICP process in detail along with the benefits of using denitrification over other pathways during MICP implementation. The potential application of denitrification in building materials pertaining to soil reinforcement, bioconcrete, restoration of heritage structures and mitigating the soil pollution has been reviewed by addressing the finding and limitation of MICP treatment. This manuscript further sheds light on the challenges faced during upscaling, real field implementation and the need for future research in this path. The review concludes that although MICP via denitrification is an promising technique to employ it in building materials, a vast interdisciplinary research is still needed for the successful commercialization of this technique.