Mechanism of carbonate mineralization induced by microbes: Taking Curvibacter lanceolatus strain HJ-1 as an example

The effect of extracellular polymeric substances on MICP solidifying rare earth slags and stabilizing Th and U

Microbially induced carbonate precipitation (MICP) has been used to cure rare earth slags (RES) containing radionuclides (e.g. Th and U) and heavy metals with favorable results. However, the role of microbial extracellular polymeric substances (EPS) in MICP curing RES remains unclear. In this study, the EPS of Lysinibacillus sphaericus K-1 was extracted for the experiments of adsorption, inducing calcium carbonate (CaCO3) precipitation and curing of RES. The role of EPS in in MICP curing RES and stabilizing radionuclides and heavy metals was analyzed by evaluating the concentration and morphological distribution of radionuclides and heavy metals, and the compressive strength of the cured body. The results indicate that the adsorption efficiencies of EPS for Th (IV), U (VI), Cu2+, Pb2+, Zn2+, and Cd2+ were 44.83%, 45.83%, 53.7%, 61.3%, 42.1%, and 77.85%, respectively. The addition of EPS solution resulted in the formation of nanoscale spherical particles on the microorganism surface, which could act as an accumulating skeleton to facilitate the formation of CaCO3. After adding 20 mL of EPS solution during the curing process (Treat group), the maximum unconfined compressive strength (UCS) of the cured body reached 1.922 MPa, which was 12.13% higher than the CK group. The contents of exchangeable Th (IV) and U (VI) in the cured bodies of the Treat group decreased by 3.35% and 4.93%, respectively, compared with the CK group. Therefore, EPS enhances the effect of MICP curing RES and reduces the potential environmental problems that may be caused by radionuclides and heavy metals during the long-term sequestration of RES.

Insight into biomolecular interaction-based non-classical crystallization of bacterial biocement

In an attempt to draw a correlation between calcium carbonate (CaCO3) precipitation and biomacromolecules such as extracellular polymeric substances and enzyme activity in biomineralizing microbe, this report aims to elucidate the ureolytic and ammonification route in Paenibacillus alkaliterrae to explore the possible role of organic biomolecule(s) present on cell surface in mediating nucleation and crystallization of biogenic CaCO3. After 168 h of biomineralization in ureolysis and ammonification, 2.2 g/l and 0.87 g/l of CaCO3 precipitates were obtained, respectively. The highest carbonic anhydrase activity (31.8 µmoles/min/ml) was evidenced in ammonification as opposed to ureolysis (24.8 µmoles/min/ml). Highest urease activity reached up to 9.26 µmoles/min/ml in ureolytic pathway. Extracellular polymeric substances such as polysaccharides and proteins were found to have a vital role not only in the nucleation and crystal growth but also in addition direct polymorphic fate of CaCO3 nanoparticles. EPS production was higher during ammonification (3.1 mg/ml) than in ureolysis (0.72 mg/ml). CaCO3 nanoparticle-associated proteins were found to be 0.82 mg/ml in ureolysis and 0.56 mg/ml in ammonification. After 30 days of biomineralization, all the polymorphic forms stabilized to calcite in ureolysis but in ammonification vaterite predominated. In our study, we showed that organic template-mediated prokaryotic biomineralization follows the non-classical nucleation and varying proportions of these organic components causes selective polymorphism of CaCO3 nanoparticles. Overall, the findings are expected to further the fundamental understanding of enzymes, EPS-driven non-classical nucleation of CaCO3, and we foresee the design of fit-for-purpose futuristic biominerals arising from such renewed understanding of biomineralization. KEY POINTS: • Organic-inorganic interface of cell surface promote crystallization of biominerals • Carbohydrate and proteins in the interface results selective polymorphism of CaCO3 • Calcite stabilized at 30 days in ureolysis, vaterite-calcite mix in ammonification.

Direct Biocatalytic Processes for CO2 Capture as a Green Tool to Produce Value-Added Chemicals

Direct biocatalytic processes for CO₂ capture and transformation in value-added chemicals may be considered a useful tool for reducing the concentration of this greenhouse gas in the atmosphere. Among the other enzymes, carbonic anhydrase (CA) and formate dehydrogenase (FDH) are two key biocatalysts suitable for this challenge, facilitating the uptake of carbon dioxide from the atmosphere in complementary ways. Carbonic anhydrases accelerate CO₂ uptake by promoting its solubility in water in the form of hydrogen carbonate as the first step in converting the gas into a species widely used in carbon capture storage and its utilization processes (CCSU), particularly in carbonation and mineralization methods. On the other hand, formate dehydrogenases represent the biocatalytic machinery evolved by certain organisms to convert CO₂ into enriched, reduced, and easily transportable hydrogen species, such as formic acid, via enzymatic cascade systems that obtain energy from chemical species, electrochemical sources, or light. Formic acid is the basis for fixing C₁-carbon species to other, more reduced molecules. In this review, the state-of-the-art of both methods of CO₂ uptake is assessed, highlighting the biotechnological approaches that have been developed using both enzymes.

Microbially induced calcium precipitation coupled with medical stone-coated sponges: A targeted strategy for enhanced nitrate and fluoride removal from groundwater

The coexistence of nitrate and fluoride in groundwater is of high concern due to its potential environmental impacts and health risks. Medical stone-coated sponges, as a microbial activity promoter and slow-release calcium source, were introduced into an immobilized bioreactor for enhanced removal of nitrate and fluoride. Under the hydraulic retention time of 3 h, nitrate, fluoride, and calcium contents of 16.5, 3.0, and 100 mg L^-1, the average removal efficiencies of nitrate, fluoride, and calcium reached 99.49%, 74.26%, and 70.43%, respectively. Co-precipitation and chemisorption were the mechanisms for fluoride and calcium removal. Medical stone load improved the competitiveness of dominant bacteria and electron transport activity, accelerated the denitrification process, and stimulated biofilm formation. High fluoride level (5.0 mg L^-1) inhibited the nitrate removal and aromatic protein production. The fluoride content changes altered the carbon source preference of the microbial community, which preferred to use amino acids and carbohydrates under a higher fluoride content. The introduction of medical stones significantly accelerated the fluoride and nitrate removal, providing a new insight for the application of microbially induced calcium precipitation technique in the remediation of low-calcium groundwater.

Microbial-induced carbonate precipitation prevents Cd2+ migration through the soil profile

Cadmium (Cd)-containing wastewater has been used to irrigate agricultural land. However, long term usage has resulted in the accumulation of Cd in the soil systems, which can eventually leach into the aquifer, contaminating groundwater. Microbial-induced carbonate precipitation (MICP), an economical and effective method, was used to block the in situ migration of Cd²⁺ in the soil profile. The results of the laboratory experiments showed that the maximum Cd²⁺ adsorption capacity of the soil exposed to MICP (8.92 mg/g) was higher than that of soil without MICP (7.12 mg/g). The Thomas model provided a good fit for the Cd²⁺ migration process in soil exposed to MICP (R² > 0.96), and Cd²⁺ was trapped more effectively by soil exposed to MICP than by soil alone. Further testing showed that the Cd²⁺ retention time in the MICP soil column increased with increasing soil urea content and pH but decreased with increasing flow rate. Soil physico-chemical properties showed that the MICP process increased the soil particle size and Cd capacity and decreased the proportion of exchangeable Cd in the soil. Scanning electron microscopy and X-ray diffraction analyses confirmed the generation of CdCO₃ in the MICP soil column. The findings of this study indicate that MICP can be effectively used to immobilize Cd²⁺ and prevent its migration in the soil profile.

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.

Role of subterranean microbiota in the carbon cycle and greenhouse gas dynamics

Subterranean ecosystems play an active role in the global carbon cycle, yet only a few studies using indirect methods have focused on the role of the cave microbiota in this critical cycle. Here we present pioneering research based on in situ real-time monitoring of CO₂ and CH₄ diffusive fluxes and concurrent δ¹³C geochemical tracing in caves, combined with 16S microbiome analysis. Our findings show that cave sediments are promoting continuous CH₄ consumption from cave atmosphere, resulting in a significant removal of 65% to 90%. This research reveals the most effective taxa and metabolic pathways in consumption and uptake of greenhouse gases. Methanotrophic bacteria were the most effective group involved in CH₄ consumption, namely within the families Methylomonaceae, Methylomirabilaceae and Methylacidiphilaceae. In addition, Crossiella and Nitrosococcaceae wb1-P19 could be one of the main responsible of CO₂ uptake, which occurs via the Calvin-Benson-Bassham cycle and reversible hydration of CO₂. Thus, syntrophic relationships exist between Crossiella and nitrifying bacteria that capture CO₂, consume inorganic N produced by heterotrophic ammonification in the surface of sediments, and induce moonmilk formation. Moonmilk is found as the most evolved phase of the microbial processes in cave sediments that fixes CO₂ as calcite and intensifies CH₄ oxidation. From an ecological perspective, cave sediments act qualitatively as soils, providing fundamental ecosystem services (e.g. nutrient cycling and carbon sequestration) with direct influence on greenhouse gas emissions.

The effect of Bacillus cereus LV-1 on the crystallization and polymorphs of calcium carbonate

The study of CaCO₃ polymorphism is of great significance for understanding the mechanism of carbonate mineralization induced by bacteria and the genesis of carbonate rock throughout geological history. To investigate the effect of bacteria and shear force on CaCO₃ precipitation and polymorphs, biomineralization experiments with Bacillus cereus strain LV-1 were conducted under the standing and shaking conditions. The results show that LV-1 induced the formation of calcite and vaterite under the standing and shaking conditions, respectively. However, the results of mineralization in the media and the CaCl₂ solution under both kinetic conditions suggest the shear force does not affect the polymorphs of calcium carbonate in abiotic systems. Further, mineralization experiments with bacterial cells and extracellular polymeric substances (EPS) were performed under the standing conditions. The results reveal that bacterial cells, bound EPS (BEPS), and soluble EPS (SEPS) are favorable to the formation of spherical, imperfect rhombohedral, and perfect rhombohedral minerals, respectively. The increase in the pH value and saturation index (SI) caused by LV-1 metabolism under the shear force played key roles in controlling vaterite precipitation, whereas bacterial cells and EPS do not play roles in promoting vaterite formation. Furthermore, we suggest that vaterite formed if pH > 8.5 and SI_ACC > 0.8, while calcite formed if pH was between 8.0–9.0 and SI_ACC < 0.8. Bacterial cells and BEPS are the main factors affecting CaCO₃ morphologies in the mineralization process of LV-1. This may provide a deeper insight into the regulation mechanism of the polymorphs and morphologies during bacterially induced carbonate mineralization.

The study of CaCO₃ polymorphism is of great significance for understanding the mechanism of bacterial carbonate mineralization and the genesis of carbonate rock formation throughout geological history.