In-Depth Profiling of Calcite Precipitation by Environmental Bacteria Reveals Fundamental Mechanistic Differences with Relevance to Application

Ancient and remote quartzite caves as a novel source of culturable microbes with biotechnological potential

Quartzite caves located on table-top mountains (tepuis) in the Guyana Shield, are ancient, remote, and pristine subterranean environments where microbes have evolved peculiar metabolic strategies to thrive in silica-rich, slightly acidic and oligotrophic conditions. In this study, we explored the culturable fraction of the microbiota inhabiting the (ortho)quartzite cave systems in Venezuelan tepui (remote table-top mountains) and we investigated their metabolic and enzymatic activities in relation with silica solubilization and extracellular hydrolytic activities as well as the capacity to produce antimicrobial compounds. Eighty microbial strains were isolated with a range of different enzymatic capabilities. More than half of the isolated strains performed at least three enzymatic activities and four bacterial strains displayed antimicrobial activities. The antimicrobial producers Paraburkholderia bryophila CMB_CA002 and Sphingomonas sp. MEM_CA187, were further analyzed by conducting chemotaxonomy, phylogenomics, and phenomics. While the isolate MEM_CA187 represents a novel species of the genus Sphingomonas, for which the name Sphingomonas imawarii sp. nov. is proposed, P. bryophila CMB_CA002 is affiliated with a few strains of the same species that are antimicrobial producers. Chemical analyses demonstrated that CMB_CA002 produces ditropolonyl sulfide that has a broad range of activity and a possibly novel siderophore. Although the antimicrobial compounds produced by MEM_CA187 could not be identified through HPLC-MS analysis due to the absence of reference compounds, it represents the first soil-associated Sphingomonas strain with the capacity to produce antimicrobials. This work provides first insights into the metabolic potential present in quartzite cave systems pointing out that these environments are a novel and still understudied source of microbial strains with biotechnological potential.

Self-healing microcapsule - a way towards futuristic cement: an-up-to-date-review

This article provides a brief description of microcapsule self-healing technique and its potential use in concrete structures. Because concrete is readily available and reasonably priced, it is widely utilised in the building industry globally, despite its susceptibility to the formation of cracks. The longevity and security of concrete buildings are greatly impacted by the existence of cracks and other deterioration occurring during the course of their use. Through the encapsulation of healing material inside microcapsules, which shows rupture upon cracking in cement-based materials, the microcapsule exhibits promise in accomplishing self-healing and increasing durability and strength in the structures. The article first explains the basic ideas behind the science of microcapsule self-healing and then looks at different ways to prepare microcapsules. It also looks into how adding microcapsules affects the basic characteristics of the concrete building. A summary of the efficiency and self-healing mechanisms of microcapsules is also provided.

Mimicking nature to develop halide perovskite semiconductors from proteins and metal carbonates

Halide perovskite (HPs) nanostructures have recently gained extensive worldwide attentions because of their remarkable optoelectronic properties and fast developments. However, intrinsic instability against environmental factors-i.e., temperature, humidity, illumination, and oxygen-restricted their real-life applications. HPs are typically synthesized as colloids by employing organic solvents and ligands. Consequently, the precise control and tuning of complex 3D perovskite morphologies are challenging and have hardly been achieved by conventional fabrication methods. Here, we combine the benefits of self-assembly of biomolecules and an ion exchange reaction (IER) approach to customize HPs spatial shapes and composition. Initially, we apply a biomineralization approach, using biological templates (such as biopolymers, proteins, or protein assemblies), modulating the morphology of MCO3 (M = Ca2+, Ba2+) nano/microstructures. We then show that the morphology of the materials can be maintained throughout an IER process to form surface HPs with a wide variety of morphologies. The fabricated core-shell structures of metal carbonates and HPs introduce nano/microcomposites that can be sculpted into a wide diversity of 3D architectures suitable for various potential applications such as sensors, detectors, catalysis, etc. As a prototype, we fabricate disposable humidity sensors with an 11-95% detection range by casting the formed bio-templated nano/micro-composites on paper substrate.

Key energy metabolisms in modern living microbialites from hypersaline Andean lagoons of the Salar de Atacama, Chile

Microbialites are organosedimentary structures formed mainly due to the precipitation of carbonate minerals, although they can also incorporate siliceous, phosphate, ferric, and sulfate minerals. The minerals' precipitation occurs because of local chemical changes triggered by changes in pH and redox transformations catalyzed by the microbial energy metabolisms. Here, geochemistry, metagenomics, and bioinformatics tools reveal the key energy metabolisms of microbial mats, stromatolites and an endoevaporite distributed across four hypersaline lagoons from the Salar de Atacama. Chemoautotrophic and chemoheterotrophic microorganisms seem to coexist and influence microbialite formation. The microbialite types of each lagoon host unique microbial communities and metabolisms that influence their geochemistry. Among them, photosynthetic, carbon- and nitrogen- fixing and sulfate-reducing microorganisms appear to control the main biogeochemical cycles. Genes associated with non-conventional energy pathways identified in MAGs, such as hydrogen production/consumption, arsenic oxidation/reduction, manganese oxidation and selenium reduction, also contribute to support life in microbialites. The presence of genes encoding for enzymes associated with ureolytic processes in the Cyanobacteria phylum and Gammaproteobacteria class might induce carbonate precipitation in hypersaline environments, contributing to the microbialites formation. To the best of our knowledge, this is the first study characterizing metagenomically microbialites enriched in manganese and identifying metabolic pathways associated with manganese oxidation, selenium reduction, and ureolysis in this ecosystem, which suggests that the geochemistry and bioavailability of energy sources (As, Mn and Se) shapes the microbial metabolisms in the microbialites.

A review of biomineralization in healing concrete: Mechanism, biodiversity, and application

Concrete is the main ingredient in construction, but it inevitably fractures during its service life, requiring a large amount of cement and aggregate for maintenance. Concrete healing through biomineralization can repair cracks and improve the durability of concrete, which is conducive to saving raw materials and reducing carbon emissions. This paper reviews the biodiversity of microorganisms capable of precipitating mineralization to repair the concrete and their mineralization ability under different conditions. To better understand the mass transfer process of precipitates, two biomineralization mechanisms, microbially-controlled mineralization and microbially-induced mineralization, have been briefly described. The application of microorganisms in the field of healing concrete, comprising passive healing and intrinsic healing, is discussed. The key insight on the interaction between cementitious materials and microorganisms is the main approach for developing novel self-healing concrete in the future to improve the corrosion resistance of concrete. At the same time, the limitations and challenges are also pointed out.

The Evaluation of the Effectiveness of Biomineralization Technology in Improving the Strength of Damaged Fiber-Reinforced LWAC

Concrete cracks and local damage can affect the bond performance between concrete and steel bars, thereby reducing the durability of reinforced concrete structures. Compared with general concrete crack repair methods, biomineralization repair not only has effective bonding capabilities but is also particularly environmentally friendly. Therefore, this study aimed to apply biomineralization technology to repair damaged fiber-reinforced lightweight aggregate concrete (LWAC). Two groups of LWAC specimens were prepared. The experimental group used lightweight aggregates (LWAs) containing bacterial spores and nutrient sources, while the control group used LWAs without bacterial spores and nutrient sources. These specimens were first subjected to compression tests and pull-out tests, respectively, and thus were damaged. After the damaged specimen healed itself in different ways for 28 days, secondary compression and pull-out tests were conducted. The self-healing method of the control group involved placing the specimens in an incubator. The experimental group was divided into experimental group I and experimental group II according to the self-healing method. The self-healing method of experimental group I was the same as that of the control group. The self-healing method of experimental group II involved soaking the specimen in a mixed solution of urea and calcium acetate for two days, and then taking it out and placing it in an incubator for two days, with a cycle of four days. The test results show that in terms of the relative bond strength ratio, the experimental group II increased by 17.9% compared with the control group. Moreover, the precipitate formed at the cracks in the sample was confirmed to be calcium carbonate with the EDS and XRD analysis results, which improved the compressive strength and bond strength after self-healing. This indicates that the biomineralization self-healing method used in experimental group II is more effective.

New insights into Saccharomyces cerevisiae induced calcium carbonate precipitation

Our previous study reported that Saccharomyces cerevisiae could induce calcium carbonate (CaCO3) precipitation, but the associated mechanism was unclear. In the present study, Saccharomyces cerevisiae was cultured under various conditions, including the presence of different organic acids and initial pH, and the yields of CaCO3 formation induced by the different organic acids were compared. The metabolism of organic acid by the metabolites of S. cerevisiae was also assessed in vitro. The SEM-EDS and XRD results showed that only acetate acid, pyruvic acid, and α-ketoglutaric acid could induce CaCO3 formation, and the weight order of the produced CaCO3 was pyruvic acid, acetate acid, α-ketoglutaric acid. In addition, the presence of only yeast metabolites and the initial neutral or alkaline environment also limited the CaCO3 formation. These results illustrated that organic acid oxidation intracellularly, especially the tricarboxylic acid cycle, was the major mechanism, and the CaCO3 yield was related to the amount of CO2 produced by the metabolism of organic acids. These findings will deepen the knowledge of the mineralization capacity of S. cerevisiae and provide a theoretical basis for the future application of yeast as an alternative microorganism in MICP.

Microbially Induced Calcium Carbonate Precipitation by Sporosarcina pasteurii: a Case Study in Optimizing Biological CaCO3 Precipitation

Current production of traditional concrete requires enormous energy investment that accounts for approximately 5 to 8% of the world's annual CO2 production. Biocement is a building material that is already in industrial use and has the potential to rival traditional concrete as a more convenient and more environmentally friendly alternative. Biocement relies on biological structures (enzymes, cells, and/or cellular superstructures) to mineralize and bind particles in aggregate materials (e.g., sand and soil particles). Sporosarcina pasteurii is a workhorse organism for biocementation, but most research to date has focused on S. pasteurii as a building material rather than a biological system. In this review, we synthesize available materials science, microbiology, biochemistry, and cell biology evidence regarding biological CaCO3 precipitation and the role of microbes in microbially induced calcium carbonate precipitation (MICP) with a focus on S. pasteurii. Based on the available information, we provide a model that describes the molecular and cellular processes involved in converting feedstock material (urea and Ca2+) into cement. The model provides a foundational framework that we use to highlight particular targets for researchers as they proceed into optimizing the biology of MICP for biocement production.

Effect of microbially induced calcium carbonate precipitation treatment on the solidification and stabilization of municipal solid waste incineration fly ash (MSWI FA) - Based materials incorporated with metakaolin

Microbially induced calcium carbonate precipitation (MICP) has been considered as a potential treatment method for the solidification and stabilization of municipal solid waste incineration fly ash (MSWI-FA).The main obstacle for MICP treatment of MSWI-FA is the harsh environment which causes the bacteria fail to maintain their urease activity effectively, thus decreases the solidification effect and material properties. Currently, there is no research on blending metakaolin (MK) as a protective carrier for the bacteria into the MSWI-FA. The effect of the MICP process on the curing properties of MSWI FA-based cementing materials in the MK and MSWI-FA reaction system is largely unknown. In this study, different mixing ratios of MK were used to adjust the Ca/Si/Al ratio in the mixture, and the properties of the cementing material (MSWI-FA mixed with MK and water) and the MICP-treated material (MSWI-FA mixed with MK and bacterial solution) were investigated. This study contributes to find suitable additives to promote effect of MICP on the solidification of MSWI-FA and the improvement of material properties. The results showed when the mixing ratio of MSWI FA was 90 wt %, the MICP treatment was able to increase the compressive strength of the samples up to 0.99 Mp, and the compressive strength of samples reached 1.46 MPa, when the mixing ratio of MSWI FA was 80 wt %. Though the metakaolin did not show inhibitory effect on the urease activity, the compressive strength of the MICP-treated samples did not further show a significant increase when the mixture of MK was increased from 20 wt% to 30 wt%. Further investigation suggested that MICP activities of bacteria utilizing calcium sources could have an impact on the formation/deformation of calcium-containing hydration products in the reaction system, thus affecting the mechanical and chemical properties of MSWI based materials. MICP treatment is effective in the immobilization of certain heavy metals of MSWI FA, especially for Pb, Cd and Zn. This research shows the potential of using MICP to treat the MSWI fly ash, meanwhile, it is necessary to find suitable reaction system with the proper additives in order to further improve the properties of the MSWI FA based material in terms of mechanical performance.

Application of Biomineralization Technology to Self-Healing of Fiber-Reinforced Lightweight Concrete after Exposure to High Temperatures

In the field of civil engineering, concrete self-healing technology plays an important role. Concrete self-healing should be able to effectively heal cracks, not only improving the internal structure, but also improving the mechanical properties and durability of the concrete structure. The biomineralization-repair method is characterized by its potential for long-lasting, rapid, and active crack repair potential. Biomineralization repair has an effective bond ability, is compatible with concrete components, and is also environmentally friendly. This study used biomineralization to explore the self-healing of fiber-reinforced lightweight concrete after its exposure to high temperatures. Concrete specimens of a control group (using lightweight aggregate without bacterial spores and a nutrient source) and an experimental group (using lightweight aggregate containing bacterial spores and a nutrient source) were prepared. The repair effect of the microbial self-healing concrete after the exposure to high temperature was observed by a crack-width gauge, field-emission scanning electron microscopy (FESEM), energy-dispersive spectroscopy (EDS), and X-ray diffraction (XRD). According to the EDS and XRD analyses, the precipitate formed at the crack was calcium carbonate. After 28 days of self-healing, the water absorption rate of the experimental group was lower than that of the control group. This is because the specimens of the penetration test were taken from the middle of the concrete cylinder after high temperature, and their bacterial survival rate was higher, which made the mineralization more significant. However, the mechanical test results of the control and experimental groups after the self-healing in the water were not substantially different, which indicated that the bacterial mineralization in the experimental group was slow in the absence of an adequate source of nutrients.

Highlighting Bacteria with Calcifying Abilities Suitable to Improve Mortar Properties

Biomineralization, the use of microorganisms to produce calcium carbonate, became a green solution for application in construction materials to improve their strength and durability. The calcifying abilities of several bacteria were investigated by culturing on a medium with urea and calcium ions. The characterization of the precipitates from bacterial cultures was performed using X-ray diffraction, Fourier transform infrared spectroscopy, and thermogravimetric analysis. The formation of carbonate crystals was demonstrated by optical and scanning electron microscopy. Water absorption and compressive strength measurements were applied to mortars embedded with sporal suspension. The efficiency of the supplementation of mortar mixtures with bacterial cells was evaluated by properties, namely the compressive strength and the water absorption, which are in a relationship of direct dependence, the increase in compressive strength implying the decrease in water absorption. The results showed that Bacillus subtilis was the best-performing bacterium, its introduction into the mortar producing an increase in compressive strength by 11.81% and 9.50%, and a decrease in water absorption by 11.79% and 10.94%, after 28 and 56 days of curing, respectively, as compared to standards. The exploitation of B. subtilis as a calcifying agent can be an interesting prospect in construction materials.

Strain Screening and Particle Formation: a Lysinibacillus boronitolerans for Self-Healing Concrete

Microbial-induced calcite precipitation is a promising technology to solve the problem of cracks in soil concrete. The most intensively investigated microorganisms are urease-producing bacteria. Lysinibacillus that is used as urease-producing bacteria in concrete repair has rarely been reported. In this study, Lysinibacillus boronitolerans with a high urease activity was isolated from soil samples. This strain is salt- and alkali-tolerance, and at pH 13, can grow to ~OD₆₀₀ 2.0 after 24 h. At a salt concentration of 6%, the strain can still grow to ~OD₆₀₀ 1.0 after 24 h. The feasibility of using this strain in self-healing concrete was explored. The data showed that cracks within ~0.6 mm could be repaired naturally with hydration when spores and substrates were added to the concrete in an appropriate proportion. Moreover, the number and morphology of CaCO₃ crystals that were produced by bacteria can be influenced by the concrete environment. An efficiency method to elucidate the process of microbial-induced calcium carbonate crystal formation was established with Particle Track G400. This study provides a template for future studies on the theory of mineralization based on microorganisms. IMPORTANCE The formation of calcium carbonate crystals in concrete by urease-producing bacteria is not understood fully. In this study, a Lysinibacillus boronitolerans strain with a high urease activity was isolated and used to analyze the counts and sizes of the crystals and the relationship with time. The data showed that the number of crystal particles increases exponentially in a short period with sufficient substrate, after which the crystals grow, precipitate or break. In concrete, the rate-limiting steps of calcium carbonate crystal accumulation are spore germination and urease production. These results provided data support for the rational design of urease-producing bacteria in concrete repair.

Relationship between Bacterial Contribution and Self-Healing Effect of Cement-Based Materials

The civil research community has been attracted to self-healing bacterial-based concrete as a potential solution in the economy 4.0 era. This concept provides more sustainable material with a longer lifetime due to the reduction of crack appearance and the need for anthropogenic impact. Regardless of the achievements in this field, the gap in the understanding of the importance of the bacterial role in self-healing concrete remains. Therefore, understanding the bacterial life cycle in the self-healing effect of cement-based materials and selecting the most important relationship between bacterial contribution, self-healing effect, and material characteristics through the process of microbiologically (bacterially) induced carbonate precipitation is just the initial phase for potential applications in real environmental conditions. The concept of this study offers the possibility to recognize the importance of the bacterial life cycle in terms of application in extreme conditions of cement-based materials and maintaining bacterial roles during the self-healing effect.

Bacterial community structure and metabolic potential in microbialite-forming mats from South Australian saline lakes

Microbialites are sedimentary rocks created in association with benthic microorganisms. While they harbour complex microbial communities, Cyanobacteria perform critical roles in sediment stabilisation and accretion. Microbialites have been described from permanent and ephemeral saline lakes in South Australia; however, the microbial communities that generate and inhabit these biogeological structures have not been studied in detail. To address this knowledge gap, we investigated the composition, diversity and metabolic potential of bacterial communities from different microbialite-forming mats and surrounding sediments in five South Australian saline coastal lakes using 16S rRNA gene sequencing and predictive metagenome analyses. While Proteobacteria and Bacteroidetes were the dominant phyla recovered from the mats and sediments, Cyanobacteria were significantly more abundant in the mat samples. Interestingly, at lower taxonomic levels, the mat communities were vastly different across the five lakes. Comparative analysis of putative mat and sediment metagenomes via PICRUSt2 revealed important metabolic pathways driving the process of carbonate precipitation, including cyanobacterial oxygenic photosynthesis, ureolysis and nitrogen fixation. These pathways were highly conserved across the five examined lakes, although they appeared to be performed by distinct groups of bacterial taxa found in each lake. Stress response, quorum sensing and circadian clock were other important pathways predicted by the in silico metagenome analysis. The enrichment of CRISPR/Cas and phage shock associated genes in these cyanobacteria-rich communities suggests that they may be under selective pressure from viral infection. Together, these results highlight that a very stable ecosystem function is maintained by distinctly different communities in microbialite-forming mats in the five South Australian lakes and reinforce the concept that 'who' is in the community is not as critical as their net metabolic capacity.

Evaluation of Cyclic Healing Potential of Bacteria-Based Self-Healing Cementitious Composites

At present, little evidence exists regarding the capability of bacteria-based self-healing (BBSH) cementitious materials to successfully re-heal previously healed cracks. This paper investigates the repeatability of the self-healing of BBSH mortars when the initially healed crack is reopened at a later age (20 months) and the potential of encapsulated bacterial spores to heal a new crack generated at 22 months after casting. The results show that BBSH cement mortar cracks that were successfully healed at an early age were not able to successfully re-heal when cracks were reformed in the same location 20 months later, even when exposed to favourable conditions (i.e., high humidity, temperature, calcium source, and nutrients) to promote their re-healing. Therefore, it is likely that not enough bacterial spores were available within the initially healed crack to successfully start a new self-healing cycle. However, when entirely new cracks were intentionally generated at a different position in 22-month-old mortars, these new cracks were able to achieve an average healing ratio and water tightness of 93.3% and 90.8%, respectively, thus demonstrating that the encapsulated bacterial spores remained viable inside the cementitious matrix. The results reported in this paper provide important insights into the appropriate design of practical self-healing concrete and, for the first time, show limitations of the ability of BBSH concrete to re-heal.

High level of calcium carbonate precipitation achieved by mixed culture containing ureolytic and non-ureolytic bacterial strains

This study demonstrates a remarkably high level of microbial-induced calcium carbonate precipitation (MICP) using a mixed culture containing TBRC 1396 (Priestia megaterium), TBRC 8147 (Neobacillus drentensis), and ATCC 11859 (Sporosarcina pasteurii) bacterial strains. The mixed culture produced CaCO₃ weights 1.4 times higher than those obtained from S. pasteurii, the gold standard for efficient MICP processes. The three strains were selected after characterization of various Bacillus spp. and related species for their ability to induce the MICP process, especially in an alkaline and high temperature environment. Results showed that TBRC 1396 and TBRC 8147 strains, as well as TBRC 5949 (Bacillus subtilis) and TBRC 8986 (Priestia aryabhattai) strains, could generate calcium carbonate at pH 9-12 and temperature 30-40 °C, which is suitable for construction and consolidation purposes. The TBRC 8147 strain also exhibited CaCO₃ precipitation at 45 °C. The TBRC 8986 and TBRC 8147 strains are non-ureolytic bacteria capable of MICP in the absence of urea, which can be used to avoid the generation of undesirable ammonia associated with the ureolytic MICP process. These findings facilitate the successful use of MICP as a sustainable and environmentally friendly technology for the development of various materials, including self-healing concrete and soil consolidation.

New Insights Into Microbial Induced Calcium Carbonate Precipitation Using Saccharomyces cerevisiae

Saccharomyces cerevisiae plays an important role in the mineralization of many metal ions, but it is unclear whether this fungus is involved in the mineralization of calcium carbonate. In this study, S. cerevisiae was cultured under various conditions to explore its ability to perform microbially induced calcium carbonate precipitation (MICP). Organic acids, yeast extract, and low-carbon conditions were the factors influencing the biomineralization of calcium carbonate caused by S. cerevisiae, and biomolecules secreted by the fungus under different conditions could change the morphology, size, and crystal form of the biosynthesized mineral. In addition, transcriptome analysis showed that the oxidation of organic acids enhanced the respiration process of yeast. This implied that S. cerevisiae played a role in the formation of calcium carbonate through the mechanism of creating an alkaline environment by the respiratory metabolism of organic acids, which could provide sufficient dissolved inorganic carbon for calcium carbonate formation. These results provide new insights into the role of S. cerevisiae in biomineralization and extend the potential applications of this fungus in the future.

Genetic optimisation of bacteria-induced calcite precipitation in Bacillus subtilis

Background

Microbially induced calcite precipitation (MICP) is an ancient property of bacteria, which has recently gained considerable attention for biotechnological applications. It occurs as a by-product of bacterial metabolism and involves a combination of chemical changes in the extracellular environment, e.g. pH increase, and presence of nucleation sites on the cell surface or extracellular substances produced by the bacteria. However, the molecular mechanisms underpinning MICP and the interplay between the contributing factors remain poorly understood, thus placing barriers to the full biotechnological and synthetic biology exploitation of bacterial biomineralisation.

Results

In this study, we adopted a bottom-up approach of systematically engineering Bacillus subtilis, which has no detectable intrinsic MICP activity, for biomineralisation. We showed that heterologous production of urease can induce MICP by local increases in extracellular pH, and this can be enhanced by co-expression of urease accessory genes for urea and nickel uptake, depending on environmental conditions. MICP can be strongly enhanced by biofilm-promoting conditions, which appeared to be mainly driven by production of exopolysaccharide, while the protein component of the biofilm matrix was dispensable. Attempts to modulate the cell surface charge of B. subtilis had surprisingly minor effects, and our results suggest this organism may intrinsically have a very negative cell surface, potentially predisposing it for MICP activity.

Conclusions

Our findings give insights into the molecular mechanisms driving MICP in an application-relevant chassis organism and the genetic elements that can be used to engineer de novo or enhanced biomineralisation. This study also highlights mutual influences between the genetic drivers and the chemical composition of the surrounding environment in determining the speed, spatial distribution and resulting mineral crystals of MICP. Taken together, these data pave the way for future rational design of synthetic precipitator strains optimised for specific applications.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12934-021-01704-1.

Controlling the calcium carbonate microstructure of engineered living building materials

The fabrication of responsive soft materials that enable the controlled release of microbial induced calcium carbonate (CaCO3) precipitation (MICP) would be highly desirable for the creation of living materials that can be used, for example, as self-healing construction materials. To obtain a tight control over the mechanical properties of these materials, needed for civil engineering applications, the amount, location, and structure of the forming minerals must be precisely tuned; this requires good control over the dynamic functionality of bacteria. Despite recent advances in the self-healing of concrete cracks and the understanding of the role of synthesis conditions on the CaCO3 polymorphic regulation, the degree of control over the CaCO3 remains insufficient to meet these requirements. We demonstrate that the amount and location of CaCO3 produced within a matrix, can be controlled through the concentration and location of bacteria; these parameters can be precisely tuned if bacteria are encapsulated, as we demonstrate with the soil-dwelling bacterium Sporosarcina pasteurii that is deposited within biocompatible alginate and carboxymethyl cellulose (CMC) hydrogels. Using a competitive ligand exchange mechanism that relies on the presence of yeast extract, we control the timing of the release of calcium ions that crosslink the alginate or CMC without compromising bacterial viability. With this novel use of hydrogel encapsulation of bacteria for on-demand release of MICP, we achieve control over the amount and structure of CaCO3-based composites and demonstrate that S. pasteurii can be stored for up to 3 months at an accessible storage temperature of 4 °C, which are two important factors that currently limit the applicability of MICP for the reinforcement of construction materials. These composites thus have the potential to sense, respond, and heal without the need for external intervention.

Bacillus subtilis biofilm formation and social interactions

Biofilm formation is a process in which microbial cells aggregate to form collectives that are embedded in a self-produced extracellular matrix. Bacillus subtilis is a Gram-positive bacterium that is used to dissect the mechanisms controlling matrix production and the subsequent transition from a motile planktonic cell state to a sessile biofilm state. The collective nature of life in a biofilm allows emergent properties to manifest, and B. subtilis biofilms are linked with novel industrial uses as well as probiotic and biocontrol processes. In this Review, we outline the molecular details of the biofilm matrix and the regulatory pathways and external factors that control its production. We explore the beneficial outcomes associated with biofilms. Finally, we highlight major advances in our understanding of concepts of microbial evolution and community behaviour that have resulted from studies of the innate heterogeneity of biofilms.

Comprehensive Profiling of Microbiologically Induced CaCO3 Precipitation by Ureolytic Bacillus Isolates from Alkaline Soils

Microbiologically induced CaCO3 precipitation (MICP) is a well-known bio-based solution with application in environmental, geotechnical, and civil engineering. The significance of the MICP has increased explorations of process efficiency and specificity via natural bacterial isolates. In this study, comprehensive profiling of five soil ureolytic Bacillus strains was performed through a newly formed procedure that involved six steps from selection and identification, through kinetic study, to the characterization of the obtained precipitates, for the first time. To shorten the whole selection procedure of 43 bioagents with the MICP potential, Standard Score Analysis was performed and five selected bacteria were identified as Bacillus muralis, B. lentus, B. simplex, B. firmus, and B. licheniformis by the MALDI-TOF mass spectrometry. Despite following the targeted activity, kinetic studies were included important aspects of ureolysis and the MICP such as cell concentration, pH profiling, and reduction in calcium ion concentration. At the final step, characterization of the obtained precipitates was performed using FTIR, XRD, Raman, DTA/TGA, and SEM analysis. Although all tested strains showed significant potential in terms of precipitation of calcite or calcite and vaterite phase, the main differences in the MICP behavior can be observed at the bacterial strain level. B. licheniformis showed favorable behavior compared to the reference Sporosarcina pasteurii DSM 33.

Isolation of alkaliphilic calcifying bacteria and their feasibility for enhanced CaCO3 precipitation in bio-based cementitious composites

Microbially induced calcite precipitation (MICP), secreted through biological metabolic activity, secured an imperative position in remedial measures within the construction industry subsequent to ecological, environmental and economical returns. However, this contemporary recurrent healing system is susceptible to microbial depletion in the highly alkaline cementitious environment. Therefore, researchers are probing for alkali resistant calcifying microbes. In the present study, alkaliphilic microbes were isolated from different soil sources and screened for probable CaCO3 precipitation. Non-ureolytic pathway (oxidation of organic carbon) was adopted for calcite precipitation to eliminate the production of toxic ammonia. For this purpose, calcium lactate Ca(C3 H5 O3 )2 and calcium acetate Ca(CH3 COO)2 were used as CaCO3 precipitation precursors. The quantification protocol for precipitated CaCO3 was established to select potent microbial species for implementation in the alkaline cementitious systems as more than 50% of isolates were able to precipitate CaCO3 . Results suggested 80% of potent calcifying strains isolated in this study, portrayed higher calcite precipitation at pH 10 when compared to pH 7. Ten superlative morphologically distinct isolates capable of CaCO3 production were identified by 16SrRNA sequencing. Sequenced microbes were identified as species of Bacillus, Arthrobacter, Planococcus, Chryseomicrobium and Corynebacterium. Further, microstructure of precipitated CaCO3 was inspected through scanning electron microscopy (SEM), X-ray diffraction (XRD) and thermal gravimetric (TG) analysis. Then, the selected microbes were investigated in the cementitious mortar to rule out any detrimental effects on mechanical properties. These strains showed maximum of 36% increase in compressive strength and 96% increase in flexural strength. Bacillus, Arthrobacter, Corynebacterium and Planococcus genera have been reported as CaCO3 producers but isolated strains have not yet been investigated in conjunction with cementitious mortar. Moreover, species of Chryseomicrobium and Glutamicibacter were reported first time as calcifying strains.

Bacteria-induced mineral precipitation: a mechanistic review

Micro-organisms contribute to Earth's mineral deposits through a process known as bacteria-induced mineral precipitation (BIMP). It is a complex phenomenon that can occur as a result of a variety of physiological activities that influence the supersaturation state and nucleation catalysis of mineral precipitation in the environment. There is a good understanding of BIMP induced by bacterial metabolism through the control of metal redox states and enzyme-mediated reactions such as ureolysis. However, other forms of BIMP often cannot be attributed to a single pathway but rather appear to be a passive result of bacterial activity, where minerals form as a result of metabolic by-products and surface interactions within the surrounding environment. BIMP from such processes has formed the basis of many new innovative biotechnologies, such as soil consolidation, heavy metal remediation, restoration of historic buildings and even self-healing concrete. However, these applications to date have primarily incorporated BIMP-capable bacteria sampled from the environment, while detailed investigations of the underpinning mechanisms have been lagging behind. This review covers our current mechanistic understanding of bacterial activities that indirectly influence BIMP and highlights the complexity and connectivity between the different cellular and metabolic processes involved. Ultimately, detailed insights will facilitate the rational design of application-specific BIMP technologies and deepen our understanding of how bacteria are shaping our world.

Calcifying Bacteria Flexibility in Induction of CaCO3 Mineralization

Microbially induced CaCO₃ precipitation (MICP) is considered as an alternative green technology for cement self-healing and a basis for the development of new biomaterials. However, some issues about the role of bacteria in the induction of biogenic CaCO₃ crystal nucleation, growth and aggregation are still debatable. Our aims were to screen for ureolytic calcifying microorganisms and analyze their MICP abilities during their growth in urea-supplemented and urea-deficient media. Nine candidates showed a high level of urease specific activity, and a sharp increase in the urea-containing medium pH resulted in efficient CaCO₃ biomineralization. In the urea-deficient medium, all ureolytic bacteria also induced CaCO₃ precipitation although at lower pH values. Five strains (B. licheniformis DSMZ 8782, B. cereus 4b, S. epidermidis 4a, M. luteus BS52, M. luteus 6) were found to completely repair micro-cracks in the cement samples. Detailed studies of the most promising strain B. licheniformis DSMZ 8782 revealed a slower rate of the polymorph transformation in the urea-deficient medium than in urea-containing one. We suppose that a ureolytic microorganism retains its ability to induce CaCO₃ biomineralization regardless the origin of carbonate ions in a cell environment by switching between mechanisms of urea-degradation and metabolism of calcium organic salts.

Field detection of urease and carbonic anhydrase activity using rapid and economical tests to assess microbially induced carbonate precipitation

Microbial precipitation of calcium carbonate is a widespread environmental phenomenon that has diverse engineering applications, from building and soil restoration to carbon sequestration. Urease-mediated ureolysis and CO2 (de)hydration by carbonic anhydrase (CA) are known for their potential to precipitate carbonate minerals, yet many environmental microbial community studies rely on marker gene or metagenomic approaches that are unable to determine in situ activity. Here, we developed fast and cost-effective tests for the field detection of urease and CA activity using pH-sensitive strips inside microcentrifuge tubes that change colour in response to the reaction products of urease (NH3 ) and CA (CO2 ). The urease assay proved sensitive and useful in the field to detect in situ activity in biofilms from a saline lake, a series of calcareous fens, and ferrous springs, finding relatively high urease activity in lake samples. Incubations of lake microbes with urea resulted in significantly higher CaCO3 precipitation compared to incubations with a urease inhibitor, showing that the rapid assay indicated an on-site active metabolism potentially mediating carbonate precipitation. The CA assay, however, showed less sensitivity compared to the urease test. While its sensitivity limits its utility, the assay may still be useful as a preliminary indicator given the paucity of other means for detecting CA activity in the field. Field urease, and potentially CA, activity assays complement molecular approaches and facilitate the search for carbonate-precipitating microbes and their in situ activity, which could be applied toward agriculture, engineering and carbon sequestration technologies.

Novel method to achieve crystallinity of calcite by Bacillus subtilis in coupled and non-coupled calcium-carbon sources

Bacteria mineralization is a promising biotechnological approach to apply in biomaterials development. In this investigation, we demonstrate that Bacillus subtilis 168 induces and influences CaCO₃ composites precipitation. Crystals were formed in calcium-carbon non-coupled (glycerol + CaCl₂, GLY; or glucose + CaCl₂, GLC) and coupled (calcium lactate, LAC; or calcium acetate, ACE) agar-sources, only maintaining the same Ca²⁺ concentration. The mineralized colonies showed variations in morphology, size, and crystallinity form properties. The crystals presented spherulitic growth in all conditions, and botryoidal shapes in GLC one. Birefringence and diffraction patterns confirmed that all biogenic carbonate crystals (BCC) were organized as calcite. The CaCO₃ in BCC was organized as calcite, amorphous calcium carbon (ACC) and organic matter (OM) of biofilm; all of them with relative abundance related to bacteria growth condition. BCC-GLY presented greatest OM composition, while BCC-ACE highest CaCO₃ content. Nucleation mechanism and OM content impacted in BCC crystallinity.