Whole cell evaluation and the enzymatic kinetic study of urease from ureolytic bacteria affected by potentially toxic elements

Understanding microbial biomineralization at the molecular level: recent advances

Microbial biomineralization is a phenomenon involving deposition of inorganic minerals inside or around microbial cells as a direct consequence of biogeochemical cycling. The microbial metabolic processes often create environmental conditions conducive for the precipitation of silicate, carbonate or phosphate, ferrate forms of ubiquitous inorganic ions. Till date the fundamental mechanisms underpinning two of the major types of microbial biomineralization such as, microbially controlled and microbially induced remains poorly understood. While microbially-controlled mineralization (MCM) depends entirely on the genetic makeup of the cell, microbially-induced mineralization (MIM) is dependent on factors such as cell morphology, cell surface structures and extracellular polymeric substances (EPS). In recent years, the organic template-mediated nucleation of inorganic minerals has been considered as an underlying mechanism based on the principles of solid-state bioinorganic chemistry. The present review thus attempts to provide a comprehensive and critical overview on the recent progress in holistic understanding of both MCM and MIM, which involves, organic-inorganic biomolecular interactions that lead to template formation, biomineral nucleation and crystallization. Also, the operation of specific metabolic pathways and molecular operons in directing microbial biomineralization have been discussed. Unravelling these molecular mechanisms of biomineralization can help in the biomimetic synthesis of minerals for potential therapeutic applications, and facilitating the engineering of microorganisms for commercial production of biominerals.

Genomic characterization of a novel ureolytic bacteria, Lysinibacillus capsici TSBLM, and its application to the remediation of acidic heavy metal-contaminated soil

Soil heavy metal contamination is an essential challenge in ecological and environmental management, especially for acidic soils. Microbially induced carbonate precipitation (MICP) is an effective and environmentally friendly remediation technology for heavy metal contaminated sites, and one of the key factors for its realization lies in the microorganisms. In this study, Lysinibacillus capsici TSBLM was isolated from heavy metal contaminated soil around a gold mine, and inferred to be a novel ureolytic bacteria after phylogenomic inference and genome characterization. The urease of L. capsici TSBLM was analyzed by genetic analysis and molecular docking, and further applied this bacteria to the remediation of Cu and Pb in solution and acidic soils to investigate its biomineralization mechanism and practical application. The results revealed L. capsici TSBLM possessed a comprehensive urease gene cluster ureABCEFGD, and the encoded urease docked with urea at the lowest binding energy site (ΔG = -3.43 kcal/mol) connected to three amino acids threonine, aspartic, and alanine. The urease of L. capsici TSBLM is synthesized intracellularly but mainly functions extracellularly. L. capsici TSBLM removes Cu/Pb from the solution by generating heavy metal carbonates or co-precipitating with CaCO3 vaterite. For acidic heavy metal-contaminated soil, the carbonate-bound states of Cu and Pb increased significantly from 7 % to 16 % and from 23 % to 35 % after 30 days by L. capsici TSBLM. Soil pH improved additionally. L. capsici TSBLM maintained the dominant status in the remediated soil after 30 days, demonstrating good environmental adaptability and curing persistence. The results provided new strain resources and practical application references for the remediation of acidic heavy metal contaminated soil based on MICP.

Effect of biopolymer chitosan on manganese immobilization improvement by microbial‑induced carbonate precipitation

Microbially induced carbonate precipitation (MICP), as an eco-friendly and promising technology that can transform free metal ions into stable precipitation, has been extensively used in remediation of heavy metal contamination. However, its depressed efficiency of heavy metal elimination remains in question due to the inhibition effect of heavy metal toxicity on bacterial activity. In this work, an efficient, low-cost manganese (Mn) elimination strategy by coupling MICP with chitosan biopolymer as an additive with reduced treatment time was suggested, optimized, and implemented. The influences of chitosan at different concentrations (0.01, 0.05, 0.10, 0.15 and 0.30 %, w/v) on bacterial growth, enzyme activity, Mn removal efficiency and microstructure properties of the resulting precipitation were investigated. Results showed that Mn content was reduced by 94.5 % within 12 h with 0.15 % chitosan addition through adsorption and biomineralization as MnCO3 (at an initial Mn concentration of 3 mM), demonstrating a two-thirds decrease in remediation time compared to the chitosan-absent system, whereas maximum urease activity increased by ∼50 %. Microstructure analyses indicated that the mineralized precipitates were spherical-shaped MnCO3, and a smaller size and more uniform distribution of MnCO3 is obtained by the regulation of abundant amino and hydroxyl groups in chitosan. These results demonstrate that chitosan accelerates nucleation and tunes the growth of MnCO3 by providing nucleation sites for mineral formation and alleviating the toxicity of metal ions, which has the potential to upgrade MICP process in a sustainable and effective manner. This work provides a reference for further understanding of the biomineralization regulation mechanism, and gives a new perspective into the application of biopolymer-intensified strategies of MICP technology in heavy metal contamination.

Statistical modelling, optimization, and mechanistic exploration of novel ureolytic Enterobacter hormaechei IITISM-SA3 in cadmium immobilization under microbial inclusive and cell-free conditions through microbially induced calcite precipitation

The study aimed to evaluate the potential of a novel isolated ureolytic Enterobacter hormaechei IITISM-SA3 in cadmium bioremoval through MICP. The optimization and modelling of the biotic and abiotic factors affecting the process of mineralization were also performed. In addition, the underlying mechanism of MICP-driven Cd mineralization under microbial-inclusive and cell-free conditions was revealed and supported through the characterization of the bio-precipitates obtained using various characterization techniques. The results indicated that the isolate could remove 97.18% Cd2+ of 11.4 ppm under optimized conditions of 36.86 h, pH 7.63, and biomass dose of 1.75 ml. Besides, the presence and absence of bacterial cells were found to influence both the morphologies and crystalline structures of precipitates. The precipitates obtained under microbial-inclusive conditions showed typical rhombohedral crystalline structures of the composition comprising CaCO3, CdCO3, and 0.67Ca0.33CdCO3. However, the crystalline nature of the precipitate reduced to a nano-sized granular structure in cell-free media. Unlike the cadmium mineralization process under microbial-inclusive media, where bacterial cells serve as nucleation sites for crystallization, the carbonate precipitation effectively captures Cd2+ through co-precipitation, chemisorption, or alternative mechanisms involving interactions between metal ions and CaCO3 under cell-free conditions. The findings presented suggest that using cell-free culture supernatant enriched with carbonate ions provides an avenue that could be harnessed for sustainable metal remediation.

Mobility, speciation of cadmium, and bacterial community composition along soil depths during microbial carbonate precipitation under simulated acid rain

An overexploitation of earth resources results in acid deposition in soil, which adversely impacts soil ecosystems and biodiversity and affects conventional heavy metal remediation using immobilization. A series of column experiments was conducted in this study to compare the cadmium (Cd) retention stability through biotic and abiotic carbonate precipitation impacted by simulated acid rain (SAR), to build a comprehensive understanding of cadmium speciation and distribution along soil depth and to elucidate the biogeochemical bacteria-soil-heavy metal interfaces. The strain of Sporosarcina pasteurii DSM 33 was used to trigger the biotic carbonate precipitation and cultivated throughout the 60-day column incubation. Results of soil pH, electrical conductivity (EC), and quantitative CdCO3/CaCO3 analysis concluded that the combination of biotic and abiotic soil treatment could reinforce soil buffering capacity as a strong defense mechanism against acid rain disturbance. Up to 1.8 ± 0.04 U/mg urease enzyme activity was observed in combination soil from day 10, confirming the sustained effect of urease-mediated microbial carbonate precipitation. Cadmium speciation and distribution analyses provided new insights into the dual stimulation of carbonate-bound and Fe/Mn-bound phases of cadmium immobilization under microbially induced carbonate precipitation (MICP). As confirmed by the microbial community analysis, outsourcing urea triggered diverse microbial metabolic responses, notably carbonate precipitation and dissimilatory iron metabolism, in both oxygen-rich topsoil and oxygen-depleted subsurface layers. The overall investigation suggests the feasibility of applying MICP for soil Cd remediation under harsh environments and stratagem by selecting microbial functionality to overcome environmental challenges.

Competitive Mn(II) removal occurs in Lysinibacillus sp. MHQ-1 through microbially-induced carbonate precipitation (MICP) and indirect Mn(II) oxidation

Biological Mn(II) removal usually involves adsorption and precipitation of Mn(II) in the form of various minerals. Manganese oxides (MnOx) formation through the activity of Mn(II) oxidation bacteria (MnOB) contributes to the majority of Mn(II) removal. However, whether other bacterial-mediated pathway could couple or competitive with Mn(II) oxidation during Mn(II) removal is scarcely reported. In this study, we reported a competitive Mn(II) removal occurred in nutrient-rich condition during the indirect Mn(II) oxidation of Lysinibacillus sp. MHQ-1, i.e., microbially-induced carbonate precipitation (MICP). In the presence of 1 mM Mn(II), 39.4% of free Mn(II) converted to MnCO3(s) quickly within 100 h, and then 11.6% of initial Mn(II) slowly oxidized to MnOx within 442 h. The urease activity assay and the genome sequencing confirmed the existence of urease and the absence of Mn(II)-oxidizing enzymes in the genome of strain MHQ-1. The urease catalyzed the formation of carbonate ion that reacts with Mn(II) and the formed ammonia raises the pH to initiate indirect Mn(II) oxidation. Genome survey suggests the urease widely exists in various Mn(II)-oxidizing bacteria (MnOB), emphasizing the importance to reconsider the composition, stability and environmental effects of biological Mn(II) removal products in nutrient-rich environment.