Biocalcifying Potential of Ureolytic Bacteria Isolated from Soil for Biocementation and Material Crack Repair

Microbial Carbonate Mineralization: A Comprehensive Review of Mechanisms, Applications, and Recent Advancements

Microbial carbonate mineralization, the process by which microorganisms (Bacillus sp., Sporosarcina sp., Penicillium sp., Cyanobacteria, etc.) directly mediate or indirectly influence mineral formation and deposition, represents the next frontier in technology with vast potential across scientific disciplines, including construction, environmental remediation, and carbon sequestration. This review explores the fundamental aspects of microbial carbonate mineralization, focusing on key mechanisms such as photosynthesis, methane oxidation, sulfate reduction, ureolysis, denitrification, carbonic anhydrase activity, iron reduction, and EPS mediation, all of which influence carbonate saturation and mineral nucleation. Additionally, it highlights critical regulatory factors that enhance biomineralization for bio-inspired material development in heavy metal remediation, wastewater treatment, self-healing concrete, biomedical applications, nanoscale technologies, and 3D printing. A major focus is microbial-induced calcite precipitation (MICP), an emerging and cost-efficient biomineralization technique, with an in-depth analysis of its molecular mechanisms and expanding applications. Furthermore, this review discusses current challenges, including process scalability, long-term stability, and environmental and safety considerations, while identifying future research directions to improve the efficacy and sustainability of microbial carbonate mineralization in advanced technological applications.

Removal of high concentrations of zinc, cadmium, and nickel heavy metals by Bacillus and Comamonas through microbially induced carbonate precipitation

Heavy metal pollution in urban freshwater, driven by anthropogenic activities, poses significant risks to aquatic ecosystems and human health due to its toxicity and persistence. Recently, urease-producing bacteria have gained attention for their ability to remove heavy metals through microbial-induced carbonate precipitation (MICP). In this study, eight urease-producing bacteria were exposed to individual solutions of zinc (Zn2+), cadmium (Cd2+), and nickel (Ni2+) at concentrations ranging from 0 to 6 mM to assess their resistance. Three strains-Bacillus subtilis HMZC1 (B2), Bacillus sp. HMZCSW (B6), and Comamonas sp. HMZC (B11)-survived at 4 mM and 6 mM, while most others could not tolerate 4 mM. Their urea-degrading ability was tested at different pH levels, identifying an optimal pH of 7 for MICP. Heavy metal carbonate precipitation experiments at 4 mM and 6 mM revealed that all three strains achieved > 93% removal of Zn2+, Ni2+, and Cd2+ within 72 h. Comamonas sp. HMZC exhibited the highest efficiency, achieving > 95% removal of certain heavy metals at 6 mM. Statistical analysis using one-way ANOVA revealed significant differences (p < 0.05) in heavy metal removal efficiencies among the strains for certain treatment conditions (Cd2+ and Zn2+ at 4 mM), although not all comparisons reached statistical significance. Scanning Electron Microscopy and X-ray Diffraction confirmed the morphology and composition of the precipitated heavy metal carbonates. Our findings demonstrate that urease-producing bacteria can effectively immobilize multiple heavy metals, highlighting the MICP process as a practical and sustainable biological approach for ecological restoration and wastewater treatment.

Application of Sporosarcina pasteurii for the biomineralization of calcite in the treatment of waste concrete fines

In this study, we explored and described various parameters of microbially induced calcite precipitation (MICP) using the alkaliphilic bacterium Sporosarcina pasteurii DSM 33, which exhibits ureolytic activity, to stabilize and strengthen waste concrete fines (WCF). Bacterial cell concentration, single and repeated addition of bacterial suspension, and pH adjustment were tested in stage 1 of the experimental agenda in order to tune parameters for sample preparation in stage 2 focused on the effect of MICP treatment duration (14, 30, 60, and 90 days). Two types of WCF materials differing in their physicochemical properties were used for the stabilization. The results of the EDS and XRD analyses confirmed the presence of CaCO3 crystals, which increased by about 10-12% over time, affecting the porosity, compactness, and strength of the formed composites. The XRD results also indicated that the WCF properties significantly influence the formation of the type of CaCO3 crystals, supported also by microscopy observations. This study highlights the potential of MICP technology to make concrete recycling more sustainable, aligning with the concept of a circular economy; however, the interplay between the WCF materials of various properties and bacterial activity must be further scrutinized.

Genomic and biochemical investigations in the biomineralizing potential of an isolated marine ureolytic Bacillus sp. N₉

Microbially Induced Calcium Carbonate Precipitation (MICP) plays a significant role in coastal soil stabilization and erosion prevention. In the present study, the biomineralizing potential of a newly isolated Bacillus sp. N₉ was investigated through MICP. The isolated Bacillus sp. N₉ induced calcium carbonate (CaCO3) precipitation in broth, agar, and real beach rock was evaluated by X-ray Fluorescence, Scanning Electron Microscopy, and X-ray Diffraction. The visual appearance of calcites as white crystals on the rock and the sealing of cracks in the beach sand cubes confirmed the CaCO3 precipitation by the isolated strain. The pH changes, soluble calcium (Ca2+) concentration levels and urease activity during the growth of the isolated Bacillus sp. N₉ were studied. High urease activity was observed, resulting in an increased production of carbonate (CO32-) ions, which in turn promoted a higher rate of CaCO₃ precipitation. Further, the assembly of the 3.27 Mb genome of the isolated Bacillus sp. N₉ was evaluated using Nanopore sequencing technology, and various extracellular proteins, including urease, were identified. The gene annotation through PROKKA and RAST predicted 6700 and 7317 protein-coding sequences. The pathway annotation analysis through gene ontology, KEGG, and COG inferred the presence of genes in proteolytic characteristics, carbohydrate metabolism, and amino acid derivatives. The present study provides valuable insights into the isolated native Bacillus sp. N₉, demonstrating its potential to produce high urease activity and calcite precipitation through combined genomics and in vitro techniques.

Microbially Induced Calcium Carbonate Precipitation Using Lysinibacillus sp.: A Ureolytic Bacterium from Uttarakhand for Soil Stabilization

Microbially induced calcium carbonate precipitation (MICP) is a soil remediation method that has emerged as a viable and long-term solution for enhancing soil mechanical qualities. The technique of MICP that has been extensively researched is urea hydrolysis, which occurs naturally in the environment by urease-producing bacteria as part of their fundamental metabolic processes. The objectives of the current study include screening and identifying native ureolytic bacteria from soil in Uttarakhand, optimizing growth factors for increased urease activity, and calcite precipitation by the bacteria using response surface methodology. Additionally, it was assessed how well the isolated bacteria in the medium biomineralized when using synthetic media and cheaper alternatives such as cow urine and eggshell as sources of urea and Ca2+, respectively. The isolated strain identified as Lysinibacillus sp. was found to be the very active strain after soil samples were screened for ureolytic bacteria. It was discovered that optimization studies with values of pH 8, urea concentration (0.8 M), inoculum concentration (3%), and incubation time (48 h) yielded a higher activity of 33.7 U/mL (threefold increase), and a higher calcium carbonate precipitation (enzyme activity: 10.96 U/mL, pH: 8.92, soluble Ca2⁺: 25.53 mM and insoluble Ca2⁺: 0.856 g). The calcite precipitation in broth media supplemented with ready-made substrates and alternative sources demonstrated a similar result of increased pH and ammonia release. Thus, the current study successfully paves the way for several possibilities to stabilize the slopy soils prone to landslides and erosion in Uttarakhand and pinpoint an economic approach through biomineralization.

Microbial Ecology of an Arctic Travertine Geothermal Spring: Implications for Biosignature Preservation and Astrobiology

Jotun springs in Svalbard, Norway, is a rare warm environment in the Arctic that actively forms travertine. In this study, we assessed the microbial ecology of Jotun's active (aquatic) spring and dry spring transects. We evaluated the microbial preservation potential and mode, as well as the astrobiological relevance of the travertines to marginal carbonates mapped at Jezero Crater on Mars (the Mars 2020 landing site). Our results revealed that microbial communities exhibited spatial dynamics controlled by temperature, fluid availability, and geochemistry. Amorphous carbonates and silica precipitated within biofilm and on the surface of filamentous microorganisms. The water discharged at the source is warm, with near neutral pH, and undersaturated in silica. Hence, silicification possibly occurred through cooling, dehydration, and partially by a microbial presence or activities that promote silica precipitation. CO2 degassing and possible microbial contributions induced calcite precipitation and travertine formation. Jotun revealed that warm systems that are not very productive in carbonate formation may still produce significant carbonate buildups and provide settings favorable for fossilization through silicification and calcification. Our findings suggest that the potential for amorphous silica precipitation may be essential for Jezero Crater's marginal carbonates because it significantly increases the preservation potential of putative martian organisms.

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.

Microbial Biomineralization of Alkaline Earth Metal Carbonates on 3D-Printed Surfaces

The biomineralizing bacterium Sporosarcina pasteurii has attracted considerable interest in the area of geotechnical engineering due to its ability to induce extracellular mineralization. The presented study investigated S. pasteurii's potential to induce the mineralization of alkali-earth metal carbonate coatings on different polymeric 3D-printed flat surfaces fabricated by different additive manufacturing methods. The use of calcium, barium, strontium, or magnesium ions as the source resulted in the formation of vaterite (CaCO3), witherite (BaCO3), strontianite (SrCO3), and nesquehonite MgCO3·3H2O, respectively. These mineral coatings generally exhibit a compact, yet variable, thickness and are composed of agglomerated microparticles similar to those formed in solution. However, the mechanism behind this clustering remains unclear. The thermal properties of these biologically induced mineral coatings differ from their inorganic counterpart, highlighting the unique characteristics imparted by the biomineralization process. This work seeks to capitalize on the bacterium S. pasteurii's ability to form an alkali-earth metal carbonate coating to expand beyond its traditional use in geoengineering applications. It lays the ground for a novel integration of biologically induced mineralization of single or multilayered and multifunctional coating materials, for example, aerospace applications.

Microbial induced carbonate precipitation for remediation of heavy metals, ions and radioactive elements: A comprehensive exploration of prospective applications in water and soil treatment

Improper disposal practices have caused environmental disruptions, possessing by heavy metal ions and radioactive elements in water and soil, where the innovative and sustainable remediation strategies are significantly imperative in last few decades. Microbially induced carbonate precipitation (MICP) has emerged as a pioneering technology for remediating contaminated soil and water. Generally, MICP employs urease-producing microorganisms to decompose urea (NH2CONH2) into ammonium (NH4+and carbon dioxide (CO2), thereby increasing pH levels and inducing carbonate precipitation (CO32-), and effectively removing remove contaminants. Nonetheless, the intricate mechanism underlying heavy metal mineralization poses a significant challenge, constraining its application in contaminants engineering, particularly in the context of prolonged heavy metal leaching over time and its efficacy in adverse environmental conditions. This review provides a comprehensive idea of recent development of MICP and its application in environmental engineering, examining metabolic pathways, mineral precipitation mechanisms, and environmental factors as well as providing future perspectives for commercial utilization. The use of ureolytic bacteria in MICP demonstrates cost-efficiency, environmental compatibility, and successful pollutant abatement over tradition bioremediation techniques, and bio-synthesis of nanoparticles. limitations such as large-scale application, elevated Ca2+levels in groundwater, and gradual contaminant release need to be overcome. The possible future research directions for MICP technology, emphasizing its potential in conventional remediation, CO2 sequestration, bio-material synthesis, and its role in reducing environmental impact for long-term economic benefits.

Duckweed-associated bacteria as plant growth-promotor to enhance growth of Spirodela polyrhiza in wastewater effluent from a poultry farm

Duckweed has been highlighted as an invaluable resource because of its abilities to remove nitrogen and phosphorus from wastewater coupling with the production of high starch/protein-containing plant biomass. Duckweed recruits microbes and particularly forms a stable "core" bacterial microbiota, which greatly reduces the colonization efficiency of plant growth-promoting bacteria (PGPB). In this study, natural duckweeds were enriched in a sterilized-partially treated wastewater effluent from a poultry farm. After 24 days of cultivation, the duckweed-associated bacteria (DAB) were isolated and evaluated for their plant growth-promoting (PGP) potentials by co-cultivation with axenic Spirodela polyrhiza. Ten species were found in more than one location and could be considered candidates for the stable "core" DAB. Among them, all isolates of Acinetobacter soli, Acidovorax kalamii, Brevundimonas vesicularis, Pseudomonas toyotomiensis, and Shinella curvata increased duckweed growth in Hoagland medium. The highest PGP ability was observed in Sh. curvata W12-8 (with EPG value of 208.72%), followed by Paracoccus marcusii W7-16 (171.31%), Novosphingobium subterraneum W5-13 (156.96%), and Ac. kalamii W7-18 (156.96%). However, the highest growth promotion in the wastewater was observed when co-cultured with W7-16, which was able to increase biomass dry weight and root length of duckweed by 3.17 and 2.26 folds, respectively.

Characterization and genome analysis of Neobacillus mesonae NS-6, a ureolysis-driven strain inducing calcium carbonate precipitation

In this study, a highly promising bacterium was isolated from sandstone oil in the Ordos Basin, named strain NS-6 which exhibited exceptional urease production ability and demonstrated superior efficiency in inducing the deposition of calcium carbonate (CaCO3). Through morphological and physiochemical characteristics analysis, as well as 16S rRNA sequencing, strain NS-6 was identified as Neobacillus mesonae. The activity of urease and the formation of CaCO3 increased over time, reaching a maximum of 7.9 mmol/L/min and 184 mg (4.60 mg/mL) respectively at 32 h of incubation. Scanning Electron Microscopy (SEM) revealed CaCO3 crystals ranging in size from 5 to 6 μm, and Energy Dispersive X-ray (EDX) analysis verified the presence of calcium, carbon, and oxygen within the crystals. X-ray Diffraction (XRD) analysis further confirmed the composition of these CaCO3 crystals as calcite and vaterite. Furthermore, the maximum deposition of CaCO3 by strain NS-6 was achieved using response surface methodology (RSM), amounting to 193.8 mg (4.845 mg/mL) when the concentration of calcium ions was 0.5 mmol/L supplemented with 0.9 mmol/L of urea at pH 8.0. Genome-wide analysis revealed that strain NS-6 possesses a chromosome of 5,736,360 base pairs, containing 5,442 predicted genes, including 3,966 predicted functional genes and 1,476 functionally unknown genes. Genes like ureA, ureB, and ureC related to urea catabolism were identified by gene annotation, indicating that strain NS-6 is a typical urease-producing bacterium and possesses a serial of genes involved in metabolic pathways that mediated the deposition of CaCO3 at genetic level.

Enzymes and Biocatalysis

Enzymes, also known as biocatalysts, are proteins produced by living cells and found in a wide range of species, including animals, plants, and microorganisms [...]