Strain-specific ureolytic microbial calcium carbonate precipitation

Diversity pattern and antibiotic activity of microbial communities inhabiting a karst cave from Costa Rica

The studies of cave bacterial communities worldwide have revealed their potential to produce antibiotic molecules. In Costa Rica, ~400 caves have been identified; however, their microbial diversity and biotechnological potential remain unexplored. In this work, we studied the chemical composition and microbial diversity of a Costa Rican cave (known as the Amblipigida cave) located in Puntarenas, Costa Rica. Additionally, through culture-dependent methods, we evaluated the potential of its microbiota to produce antibiotic molecules. Mineralogical and elemental analyses revealed that the Amblipigida cave is primarily composed of calcite. However, small variations in chemical composition were observed as a result of specific conditions, such as light flashes or the input of organic matter. The 16S rRNA gene metabarcoding revealed an extraordinarily high microbial diversity (with an average Shannon index of ~6.5), primarily comprising bacteria from the phyla Pseudomonadota, Actinomycetota, Firmicutes and Acidobacteriota, with the family Pseudomonadaceae being the most abundant. A total of 93 bacteria were isolated, of which 15% exhibited antibiotic activity against at least one Gram-positive or yeast strain and were classified within the genera Lysobacter, Streptomyces, Pseudomonas, Brevundimonas and Bacillus. These findings underscore the highly diverse nature of cave microbiota and their significant biotechnological potential, particularly in the production of antibiotic compounds.

Carbonate precipitation and phosphate trapping by microbialite isolates from an alkaline insular lake (Bagno dell'Acqua, Pantelleria Island, Italy)

The Bagno dell'Acqua lake is characterized by CO2 emissions, alkaline waters (pH = 9) and Eh values which indicate strongly oxidizing conditions. A typical feature of the lake is the presence of actively growing microbialites rich in calcium carbonates and silica precipitates. Mineralogy, petrography and morphology analyses of the microbialites were coupled with the analysis of the microbial community, combining molecular and cultivation approaches. The DNA sequencing revealed distinct patterns of microbial diversity, showing pronounced differences between emerged and submerged microbialite, with the upper layer of emerged samples exhibiting the most distinctive composition, both in terms of prokaryotes and eukaryotes. In particular, the most representative phyla in the microbial community were Proteobacteria, Actinobacteriota, and Bacteroidota, while Cyanobacteria were present only with an average of 5%, with the highest concentration in the submerged intermediate layer (12%). The role of microorganisms in carbonate mineral formation was clearly demonstrated as most of the isolates were able to precipitate calcium carbonate and five of them were characterized at molecular level. Interestingly, when microbial isolates were cultivated only in filtered water, the precipitation of hazenite was observed (up to 85%), opening new prospective in P (phosphate) recovery from P depleted environments.

Investigating the influence of the gut microbiome on cholelithiasis: unveiling insights through sequencing and predictive modeling

BACKGROUND

Cholelithiasis is one of the most common disorders of hepatobiliary system. Gut bacteria may be involved in the process of gallstone formation and are, therefore considered as potential targets for cholelithiasis prediction.

OBJECTIVE

To reveal the correlation between cholelithiasis and gut bacteria.

METHODS

Stool samples were collected from 100 cholelithiasis and 250 healthy individuals from Huzhou Central Hospital; The 16S rRNA of gut bacteria in the stool samples was sequenced using the third-generation Pacbio sequencing platform; Mothur v.1.21.1 was used to analyze the diversity of gut bacteria; Wilcoxon rank-sum test and linear discriminant analysis of effect sizes (LEfSe) were used to analyze differences in gut bacteria between patients suffering from cholelithiasis and healthy individuals; Chord diagram and Plot-related heat maps were used to analyze the correlation between cholelithiasis and gut bacteria; six machine algorithms were used to construct models to predict cholelithiasis.

RESULTS

There were differences in the abundance of gut bacteria between cholelithiasis and healthy individuals, but there were no differences in their community diversity. Increased abundance of Costridia, Escherichia flexneri, and Klebsiella pneumonae were found in cholelithiasis, while Bacteroidia, Phocaeicola, and Phocaeicola vulgatus were more abundant in healthy individuals. The top four bacteria that were most closely associated with cholelithiasis were Escherichia flexneri, Escherichia dysenteriae, Streptococcus salivarius, and Phocaeicola vulgatus. The cholelithiasis model based on CatBoost algorithm had the best prediction effect (sensitivity: 90.48%, specificity: 88.32%, and AUC: 0.962).

CONCLUSION

The identification of characteristic gut bacteria may provide new predictive targets for gallstone screening. As being screened by the predictive model, people at high risk of cholelithiasis can determine the need for further testing, thus enabling early warning of cholelithiasis.

Use of buffer treatment to utilize local non-alkali tolerant bacteria in microbial induced calcium carbonate sedimentation in concrete crack repair

Concrete often suffers cracks due to its low tensile strength. The repair process can vary ranging from surface coating, grouting, and strengthening. Microbial induced calcium carbonate sedimentation process (MICP) is a process of utilizing non-pathogenic bacteria to produce calcium carbonate through its urease activity in crack repair (filling). It is known as an alternative crack repair method that does not utilize Portland cement. In general, the bacteria used in MICP are alkali tolerant bacteria that have a higher chance of surviving the high alkalinity environment in concrete. However, in some regions, alkali tolerant bacteria are difficult to acquire and unavailable locally. This study introduced a technique to utilize non-alkali tolerant bacteria in MICP using buffer treatment. Instead of injecting bacteria directly onto the crack surface, the buffer solution was applied onto the crack surface prior to the bacteria injection. Results from the laboratory indicated a higher bacteria survival rate when the buffer treatment was applied to the medium. For the crack filling, with the buffer treatment, the crack was completely filled within 21-28 days. The microstructure results also showed that the crystal deposits from both laboratory and crack surface were similar in both physical appearance and phase composition.

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 carbonate precipitation in fossil consolidation treatments: Preliminary results inducing exogenous Myxococcus xanthus bacteria in a miocene Cheirogaster richardi specimen

This research paper proposes Microbially Induced Calcium Carbonate Precipitation (MICP) as an innovative approach for palaeontological heritage conservation, specifically on deteriorated carbonate fossils. Due to its efficiency in bioconsolidation of carbonate ornamental rocks, Myxococcus xanthus inoculation on carbonate fossils was studied in this research. Treatment was tested on nine fossil samples from decontextualized fragments of Cheirogaster richardi specimens (Can Mata site, Hostalets de Pierola, Catalonia, Spain). The main objective was to evaluate whether treatment with Myxococcus xanthus improved fossil surface cohesion and hardness and mechanical strength without significant physicochemical and aesthetic changes to the surface. Chemical compatibility of the treatment, penetration capacity and absence of noticeable changes in substrate porosity were considered as important issues to be evaluated. Samples were analysed, before and after treatment, by scanning electron microscopy, weight control, spectrophotometry, X-ray diffraction analysis, water absorption analysis, pH and conductivity control, Vickers microindentation and tape test. Results show that hardness increases by a factor of almost two. Cohesion also increases and surface disaggregated particles are bonded together by a calcium carbonate micrometric layer with no noticeable changes in surface roughness. Colour and gloss variations are negligible, and pH, conductivity and weight hardly change. Slight changes in porosity were observed but without total pore clogging. To sum up, results indicate that Myxococcus xanthus biomineralisation is an effective consolidation treatment for carbonate fossils and highly compatible with carbonate substrates. Furthermore, bacterial precipitation of calcium carbonate is a safe and eco-friendly consolidation treatment.

Study on the Performance of Recycled Coarse and Fine Aggregates as Microbial Carriers Applied to Self-Healing Concrete

The contradiction between the scarcity of natural resources and the demand for construction materials has given rise to the application of recycled aggregates. Microbial self-healing concrete (SHC) is a clean and smart material, and its carrier has a great influence on repair performance. In this paper, recycled coarse aggregate (RCA) and recycled fine aggregate (RFA) were used as carriers, and their different repair effects over time were intensively investigated. The results showed that the RCA carrier had a better repair effect compared with that of RFA, and the maximum healing width could reach 0.27 mm by 28 day. The microbial repair efficiency was significantly influenced by the distribution of old mortar, with the RFA specimen having a small volume and wide distribution of repair products, while the RCA repair showed a centralized tendency. In addition, SEM, MIP and XRD characterization were used to analyze the repair mechanism. The time-dependent repair model was developed, and the applicability of the model for concrete enhancement under microbial repair was verified through experimental results. The research results could promote industrial applications by giving intelligent and green properties to recycled aggregates.

Effects of Al2O3, SiO2 nanoparticles, and g-C3N4 nanosheets on biocement production from agricultural wastes

Environmental issues are brought up concerning the production of Portland cement. As a result, biocement serves as a reliable substitute for Portland cement in green construction projects. This study created a brand-new technique to create high-quality biocement from agricultural wastes. The technique is based on nanomaterials that improve and accelerate the "Microbially Induced Calcite Precipitation (MICP)" process, which improves the quality of the biocement produced. The mixture was further mixed with the addition of 5 mg/l of graphitic carbon nitride nanosheets (g-C₃N₄ NSs), alumina nanoparticles (Al₂O₃ NPs), or silica nanoparticles (SiO₂ NPs). The cement: sand ratio was 1:3, the ash: cement ratio was 1:9, and water: cement ratio was 1:2. Cubes molds were prepared, and then cast and compacted. Subsequent de-molding, all specimens were cured in nutrient broth-urea (NBU) media until testing at 28 days. The medium was replenished at an interval of 7 days. The results show that the addition of 5 mg/l of g-C₃N₄ NSs with corncob ash delivered the highest "Compressive Strength" and the highest "Flexural Strength" of biocement mortar cubes of 18 and 7.6 megapascal (MPa), respectively; and an acceptable "Water Absorption" (5.42%) compared to all other treatments. This treatment delivered a "Compressive Strength", "Flexural Strength", and "Water Absorption" reduction of 1.67, 1.26, and 1.21 times the control (standard Portland cement). It was concluded that adding 5 mg/l of g-C₃N₄ NSs to the cementitious mixture enhances its properties, where the resulting biocement is a promising substitute for conventional Portland cement. Adding nanomaterials to cement reduces its permeability to ions, increasing its strength and durability. The use of these nanomaterials can enhance the performance of concrete infrastructures. The use of nanoparticles is an effective solution to reduce the environmental impact associated with concrete production.

Immobilization of Cd2+ and Pb2+ by biomineralization of the carbonate mineralized bacterial consortium JZ1

Microbially induced carbonate precipitation (MICP) has been proven to effectively immobilize Cd²⁺ and Pb²⁺ using a single bacterium. However, there is an urgent need for studies of Cd²⁺ and Pb²⁺ immobilized by a bacterial consortium. In this study, a stable consortium designated JZ1 was isolated from soil that was contaminated with cadmium and lead, and the dominant genus Sporosarcina (99.1%) was found to have carbonate mineralization function. The results showed that 91.52% and 99.38% of Cd²⁺ and Pb²⁺ were mineralized by the consortium JZ1 with 5 g/L CaCl₂ at an initial concentration of 5 mg/L Cd²⁺ and 150 mg/L Pb²⁺, respectively. The bioprecipitates were characterized using X-ray diffraction (XRD), Fourier-transform infrared spectroscopy (FTIR), scanning electron microscopy (SEM), and energy dispersive X-ray spectroscopy (EDS). Moreover, the kinetic studies indicated that the urea hydrolysis reaction fit well with the Michaelis-Menten equation, and the kinetic parameters K_m and V_max were estimated to be 38.69 mM and 58.98 mM/h, respectively. When the concentration of urea increased from 0.1 to 0.3 M, the mineralization rate increased by 1.58-fold. This study can provide a novel microbial resource for the biomineralization of Cd and Pb in soil and water environments.

Correlation tests between relative light unit and colony forming unit for improving adenosine triphosphate bioluminescence analysis in bacterial consolidation treatments on palaeontological heritage

In this article bacterial carbonate mineralization treatments are proposed as a novel strategy for decayed fossils and palaeontological heritage conservation; specifically, by means of inoculation of Myxococcus xanthus, a bacterium of proven effectiveness in ornamental stone bioconsolidation. Bioconsolidation treatments can be very effective, stable, nontoxic, environmentally friendly, and chemically compatible with fossil heritage. The method reproduces what nature has been doing for millennia with fossils that have been permineralized by bacterial calcium carbonate precipitation. There is, however, some concern that bacterial inoculation could lead to the growth of undesirable microbiota, which could subsequently damage the fossil substrate. Because of this, the use of bacteria on heritage items must be meticulously monitored and analysis strategies should be carried out to detect bacteria viability during and after treatments. For this purpose, adenosine triphosphate assay is proposed in this article as a fast, affordable, portable, and easy-to-use system for conservators. as ATP assay results are relative and difficult to relate to colony forming unit, this study aims to improve their applicability by examining the correlation between ATP analysis and total viable bacteria count in the specific case of M. xanthus. This research provides reference and correlatable data to obtain an approximate estimation of M. xanthus viable bacterial colonies based on relative light unit data.

Insight on bacteria communities in outdoor bronze and marble artefacts in a changing environment

Epilithic bacteria play a fundamental role in the conservation of cultural heritage (CH) materials. On stones, bacterial communities cause both degradation and bioprotection actions. Bronze biocorrosion in non-burial conditions is rarely studied. Only few studies have examined the relationship between bacteria communities and the chemical composition of patinas (surface degradation layers). A better comprehension of bacterial communities growing on our CH is fundamental not only to understand the related decay mechanisms but also to foresee possible shifts in their composition due to climate change. The present study aims at (1) characterizing bacterial communities on bronze and marble statues; (2) evaluating the differences in bacterial communities' composition and abundance occurring between different patina types on different statues; and (3) providing indications about a representative bacterial community which can be used in laboratory tests to better understand their influence on artefact decay. Chemical and biological characterization of different patinas were carried out by sampling bronze and marble statues in Bologna and Ravenna (Italy), using EDS/Raman spectroscopy and MinION-based 16SrRNA sequencing. Significant statistical differences were found in bacterial composition between marble and bronze statues, and among marble patinas in different statues and in the same statue. Marble surfaces showed high microbial diversity and were characterized mainly by Cyanobacteria, Proteobacteria and Deinococcus-Thermus. Bronze patinas showed low taxa diversity and were dominated by copper-resistant Proteobacteria. The copper biocidal effect is evident in greenish marble areas affected by the leaching of copper salts, where the bacterial community is absent. Here, Ca and Cu oxalates are present because of the biological reaction of living organisms to Cu ions, leading to metabolic product secretions, such as oxalic acid. Therefore, a better knowledge on the interaction between bacteria communities and patinas has been achieved.

Characterization and applicability of novel alkali-tolerant carbonatogenic bacteria as environment-friendly bioconsolidants for management of concrete structures and soil erosion

Cracking and erosion are critical factors that reduce the mechanical properties and stability of concrete structures and soil, respectively. They are recognized worldwide as severe disasters causing the collapse of many structures including stone heritage and dams, and landslides. Therefore, it is essential to propose effective and environment-friendly management methods to prevent them. Carbonatogenesis has recently received considerable attention as a reliable biological process for remediating cracks in calcareous structures, stabilizing loose soils, and sequestering CO₂ in the environment. Isolating and characterizing carbonatogenic bacteria with excellent performance is crucial for applying this process to the field of environmental and civil engineering. The aim of this study was to isolate new CaCO₃-precipitating bacteria and investigate various properties for their use as bioconsolidants. Furthermore, the possibility of restoring damaged structures and stabilizing loose sandy soil using isolated strain was investigated. Strain LC13 with urease and CaCO₃-precipitating activity was isolated from limestone cave soil in Korea and identified as Arthrobacter sulfureus by phenotypic characterization and 16S rRNA gene analysis. Although cell growth was observed after an adaptation period at pH 11, strain LC13 grew well at pH 7-11, indicating alkali tolerance. The optimal conditions for CaCO₃ precipitation were 1.0% yeast extract, 2.5% urea, 0.35% NaHCO₃, and 400 mM CaCl₂, with an initial pH of 6.5 at 30 °C. Under optimized conditions, maximal CaCO₃ (22.92 ± 0.14 g/l) precipitated after 3 days, which was 10.8-fold higher than the value in a urea-CaCl₂ medium. CaCO₃ precipitation by strain LC13 was associated with an increased pH due to ureolysis and protein deamination. Using an optimized medium as a cementation solution, strain LC13 completely remediated 340-760 μm wide cracks over 3 days, and also restored the spalling of concrete surfaces. Furthermore, the sand treated with LC13 solidified with a surface strength of 14.9 kPa. Instrumental analysis confirmed that the crystals precipitated were a mixture of CaCO₃ polymorphs composed of rhombohedral calcite and spherical vaterite. These results suggest that A. sulfureus LC13 may be useful for implementing sustainable biorestoration and environmental management technologies such as the in situ remediation of structural cracks and in situ prevention of soil erosion.

Integrated application of bacterial carbonate precipitation and silicon nanoparticles enhances productivity, physiological attributes, and antioxidant defenses of wheat (Triticum aestivum L.) under semi-arid conditions

The use of calcium carbonate-precipitating bacteria (CCPB) has become a well-established ground-improvement technique. However, the effect of the interaction of CCPB with nanoparticles (NPs) on plant performance is still meager. In this study, we aimed at evaluating the role of CCPB and/or silicon NPs (Si-NPs) on the growth, physio-biochemical traits, and antioxidative defense of wheat (Triticum aestivum L.) under semi-arid environmental conditions. A 2-year pot experiment was carried out to determine the improvement of the sandy soil inoculated with CCPB and the foliar application of Si-NPs on wheat plants. We tested the following treatments: spraying plants with 1.0 or 1.5 mM Si-NPs (control = 0 mM Si-NPs), soil inoculated with Bacillus lichenforms (MA16), Bacillus megaterium (MA27), or Bacillus subtilis (MA34), and the interaction of individual Bacillus species with Si-NPs. Our results showed that soil inoculation with any of the three isolated CCPB and/or foliar application of Si-NPs at the rates of 1.0 or 1.5 mM significantly improved (p ≤ 0.05) the physiological and biochemical attributes as well as the enzymatic antioxidant activities of wheat plants. Therefore, the combined treatments of CCPB + Si-NPs were more effective in enhancing physio-biochemical characteristics and enzymatic antioxidant activities than the individual treatments of CCPB or Si-NPs, thus achieving the best performance in the treatment of MA34 + 1.5 mM Si-NPs. Our results demonstrated that the co-application of CCPB and Si-NPs, particularly MA34 + 1.5 mM Si-NPs, considerably activated the antioxidant defense system to mitigate the adverse effects of oxidative stress, thus increasing tolerance and enhancing the production of wheat plants in sandy soils under semi-arid environmental conditions.

Evaluation of gallstone classification and their diagnosis through serum parameters as emerging tools in treatment: a narrative review

The treatment of gallstones is a matter of real concern as they may cause gallbladder cancer if not properly attended to. Evaluating the classification of gallstones can give major clues in their treatment as it will decide their aetiology, chemical composition, and pathogenesis. Also, serum parameters have emerged as an efficient tool for diagnosing gallstones. They can be probed to evaluate different biochemicals and the changes in their levels in gallstone patients which can be correlated with early prediction of the formation of gallstones. In the present review, a thorough search of the available literature was done starting from the earliest approaches for the classification of gallstones up to the recent advancements. The alteration in the level of serum parameters was also studied in gallstone patients so that it can act as a potential diagnostic tool for early detection of gallstone formation. The earliest classification of gallstones was done in 1896 by Nauyn. He classified them into pure cholesterol stones, laminated cholesterol stones, ordinary gallbladder stones, mixed bilirubin stones, and rare forms. The most recent classification of gallstones was done by Peter et al in 2020 and they classified them as pure, mixed, composite cholesterol, carbonate stones, black and brown pigment stones. The altered of levels of serum parameters was analyzed by Reuben (1985) and in recent times by Peter et al (2020). The various serum parameters studied were as RDW-CV test (red blood cell distribution width), PCT (prolactin) test, MPV (mean platelet count), LYM (lymphocyte) test, and EOS (eosinophil and eosinophil count test). Also, we discussed some practical considerations for gallstones that can be taken into account for gallstone prevention and diagnosis. Further research is required to detect gallstone type in the gallbladder by using the alteration in the levels of serum parameters.

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.

A quantitative, high-throughput urease activity assay for comparison and rapid screening of ureolytic bacteria

Urease is a dinickel enzyme commonly found in numerous organisms that catalyses the hydrolysis of urea into ammonia and carbon dioxide. The microbially induced carbonate precipitation (MICP) process mediated by urease-producing bacteria (UPB) can be used for many applications including, environmental bioremediation, soil improvement, healing of cracks in concrete, and sealing of rock joints. Despite the importance of urease and UPB in various applications, a quantitative, high-throughput assay for the comparison of urease activity in UPB and rapid screening of UPB from diverse environments is lacking. Herein, we reported a quantitative, 96-well plate assay for urease activity based on the Christensen's urea agar test. Using this assay, we compared urease activity of six bacterial strains (E. coli BL21, P. putida KT2440, P. aeruginosa PAO1, S. oneidensis MR-1, S. pasteurii DSM 33, and B. megaterium DSM 319) and showed that S. pasteurii DSM 33 exhibited the highest urease activity. We then applied this assay to quantify the inhibitory effect of calcium on urease activity of S. pasteurii DSM 33. No significant inhibition was observed in the presence of calcium at concentrations below 10 mM, while the urease activity decreased rapidly at higher concentrations. At a concentration higher than 200 mM, calcium completely inhibited urease activity under the tested conditions. We further applied this assay to screen for highly active UPB from a wastewater enrichment and identified a strain of S. pasteurii exhibiting a substantially higher urease activity than DSM 33. Taken together, we established a 96-well plate-based quantitative, high-throughput urease activity assay that can be used for comparison and rapid screening of UPB. As UPB and urease activity are of interest to environmental, civil, and medical researchers and practitioners, we envisage wide applications of the assay reported in this study.

New Biocalcifying Marine Bacterial Strains Isolated from Calcareous Deposits and Immediate Surroundings

Marine bacterial biomineralisation by CaCO3 precipitation provides natural limestone structures, like beachrocks and stromatolites. Calcareous deposits can also be abiotically formed in seawater at the surface of steel grids under cathodic polarisation. In this work, we showed that this mineral-rich alkaline environment harbours bacteria belonging to different genera able to induce CaCO3 precipitation. We previously isolated 14 biocalcifying marine bacteria from electrochemically formed calcareous deposits and their immediate environment. By microscopy and µ-Raman spectroscopy, these bacterial strains were shown to produce calcite-type CaCO3. Identification by 16S rDNA sequencing provided between 98.5 and 100% identity with genera Pseudoalteromonas, Pseudidiomarina, Epibacterium, Virgibacillus, Planococcus, and Bhargavaea. All 14 strains produced carbonic anhydrase, and six were urease positive. Both proteins are major enzymes involved in the biocalcification process. However, this does not preclude that one or more other metabolisms could also be involved in the process. In the presence of urea, Virgibacillus halodenitrificans CD6 exhibited the most efficient precipitation of CaCO3. However, the urease pathway has the disadvantage of producing ammonia, a toxic molecule. We showed herein that different marine bacteria could induce CaCO3 precipitation without urea. These bacteria could then be used for eco-friendly applications, e.g., the formation of bio-cements to strengthen dikes and delay coastal erosion.

Revealing the Enhancement and Degradation Mechanisms Affecting the Performance of Carbonate Precipitation in EICP Process

Given that acid-rich rainfall can cause serious damage to heritage buildings in NW China and subsequently accelerate their aging problem, countermeasures to protect their integrity and also to preserve the continuity of Chinese culture are in pressing need. Enzyme-induced carbonate precipitation (EICP) that modifies the mechanical properties of the soil through enhancing the interparticle bonds by the precipitated crystals and the formation of other carbonate minerals is under a spotlight in recent years. EICP is considered as an alternative to the microbial-induced carbonate precipitation (MICP) because cultivating soil microbes are considered to be challenging in field applications. This study conducts a series of test tube experiments to reproduce the ordinary EICP process, and the produced carbonate precipitation is compared with that of the modified EICP process subjected to the effect of higher MgCl₂, NH₄Cl, and CaCl₂ concentrations, respectively. The modified EICP, subjected to the effect of higher MgCl₂ concentrations, performs the best with the highest carbonate precipitation. The enhancement mechanism of carbonate precipitation is well interpreted through elevating the activity of urease enzyme by introducing the magnesium ions. Furthermore, the degradation of carbonate precipitation presents when subjected to the effect of higher NH₄Cl concentration. The decreasing activity of urease enzyme and the reverse EICP process play a leading role in degrading the carbonate precipitation. Moreover, when subjected to the effect of higher CaCl₂ concentrations, the slower rate of urea hydrolysis and the decreasing activity of urease enzyme are primarily responsible for forming the "hijacking" phenomenon of carbonate precipitation. The findings of this study explore the potential use of the EICP technology for the protection of heritage buildings in NW China.

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.

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.

Biostimulation of sulfate-reducing bacteria used for treatment of hydrometallurgical waste by secondary metabolites of urea decomposition by Ochrobactrum sp. POC9: From genome to microbiome analysis

Sulfate-reducing bacteria (SRB) are key players in many passive and active systems dedicated to the treatment of hydrometallurgical leachates. One of the main factors reducing the efficiency and activity of SRB is the low pH and poor nutrients in leachates. We propose an innovative solution utilizing biogenic ammonia (B-NH₃), produced by urea degrading bacteria, as a pretreatment agent for increasing the pH of the leachate and spontaneously stimulating SRB activity via bacterial secondary metabolites. The selected strain, Ochrobactrum sp. POC9, generated 984.7 mg/L of ammonia in 24 h and promotes an effective neutralization of B-NH₃. The inferred metabolic traits indicated that the Ochrobactrum sp. POC9 can synthesize a group of vitamins B, and the production of various organic metabolites was confirmed by GC-MS analysis. These metabolites comprise alcohols, organic acids, and unsaturated hydrocarbons that may stimulate biological sulfate reduction. With the pretreatment of B-NH₃, sulfate removal efficiency reached ~92.3% after 14 days of incubation, whereas SRB cell count and abundance were boosted (~10⁷ cell counts and 88 OTUs of SRB) compared to synthetic ammonia (S-NH₃) (~10³ cell counts and 40 OTUs of SRB). The dominant SRB is Desulfovibrio in both S-NH₃ and B-NH₃ pretreated leachate, however, it belonged to two different clades. By reconstructing the ecological network, we found that B-NH₃ not only directly increases SRB performance but also promotes other strains with positive correlations with SRB.

Influence of native ureolytic microbial community on biocementation potential of Sporosarcina pasteurii

Microbially induced calcium carbonate precipitation (MICP)/Biocementation has emerged as a promising technique for soil engineering applications. There are chiefly two methods by which MICP is applied for field applications including biostimulation and bioaugmentation. Although bioaugmentation strategy using efficient ureolytic biocementing culture of Sporosarcina pasteurii is widely practiced, the impact of native ureolytic microbial communities (NUMC) on CaCO₃ mineralisation via S. pasteurii has not been explored. In this paper, we investigated the effect of different concentrations of NUMC on MICP kinetics and biomineral properties in the presence and absence of S. pasteurii. Kinetic analysis showed that the biocementation potential of S. pasteurii is sixfold higher than NUMC and is not significantly impacted even when the concentration of the NUMC is eight times higher. Micrographic results revealed a quick rate of CaCO₃ precipitation by S. pasteurii leading to generation of smaller CaCO₃ crystals (5-40 µm), while slow rate of CaCO₃ precipitation by NUMC led to creation of larger CaCO₃ crystals (35-100 µm). Mineralogical results showed the predominance of calcite phase in both sets. The outcome of current study is crucial for tailor-made applications of MICP.

The complex role of microbial metabolic activity in fossilization

Bacteria play an important role in the fossilization of soft tissues; their metabolic activities drive the destruction of the tissues and also strongly influence mineralization. Some environmental conditions, such as anoxia, cold temperatures, and high salinity, are considered widely to promote fossilization by modulating bacterial activity. However, bacteria are extremely diverse, and have developed metabolic adaptations to a wide range of stressful conditions. Therefore, the influence of the environment on bacterial activity, and of their metabolic activity on fossilization, is complex. A number of examples illustrate that simple, general assumptions about the role of bacteria in soft tissue fossilization cannot explain all preservational pathways: (i) experimental results show that soft tissues of cnidaria decay less in oxic than anoxic conditions, and in the fossil record are found more commonly in fossil sites deposited under oxic conditions rather than anoxic environments; (ii) siderite concretions, which often entomb soft tissue fossils, precipitate due to a complex mixture of sulfate- and iron reduction by some bacterial species, running counter to original theories that iron reduction is the primary driver of siderite concretion growth; (iii) arthropod brains, now widely accepted to be preserved in many Cambrian fossil sites, are one of the first structures to decay in taphonomic experiments, indicating that their fossilization processes are complex and influenced by bacterial activity. In order to expand our understanding of the complex process of bacterially driven soft tissue fossilization, more research needs to be done, on fossils themselves and in taphonomic experiments, to determine how the complex variation in microbial metabolic activity influences decay and mineralization.

Isolation, Screening and Characterization of Ureolytic Bacteria from Cave Ornament

<b>Background and Objective:</b> Ureolytic bacteria are bacteria capable of hydrolyzing urea. In construction, these bacteria are known to help improve soil stability. One of the habitats of ureolytic bacteria is cave ornaments such as gourdam, flowstone, stalagmite and stalactite. This study aims to find isolates and characterization of ureolytic bacteria in cave ornaments. <b>Materials and Methods:</b> Urea-CaCl<sub>2</sub> was used as the isolation medium and urea agar medium was used as a qualitative urease test for cave ornament bacteria isolate. This study applied a survey method and tested for gram staining, spore staining, mannitol test, catalase test and lactose test for characterization. <b>Results:</b> There were 17 isolates positive for urease from 30 isolates from the isolates of cave ornament bacteria. The characteristics of 17 ureolytic bacteria isolates were 2 isolates gram-negative basil with negative lactose test and 1 isolate positive glucose and 1 isolate negative glucose. Total 15 isolates gram-positive basil with spore staining results, 14 isolates spore-positive with 2 isolates positive mannitol and 12 isolates negative mannitol and 1 isolate spore-negative with negative catalase. <b>Conclusion:</b> Total 17 ureolytic bacteria isolates were found from cave ornaments. Biochemical characterization showed 1 isolate of <i>Proteus</i> spp., 1 isolate of <i>Pseudomonas</i> spp, 2 isolates suspected of being <i>Bacillus megaterium</i> or <i>Bacillus subtilis</i>, 12 isolates of <i>Bacillus cereus</i> and 1 isolate of <i>Lactobacillus</i> spp.

Density-dependent microbial calcium carbonate precipitation by drinking water bacteria via amino acid metabolism and biosorption

Drinking water plumbing systems appear to be a unique environment for microorganisms as they contain few nutrients but a high mineral concentration. Interactions between mineral content and bacteria, such as microbial calcium carbonate precipitation (MCP) however, has not yet attracted too much attention in drinking water sector. This study aims to carefully examine MCP behavior of two drinking water bacteria species, which may potentially link scaling and biofouling processes in drinking water distribution systems. Evidence from cell density evolution, chemical parameters, and microscopy suggest that drinking water isolates can mediate CaCO₃ precipitation through previously overlooked MCP mechanisms like ammonification or biosorption. The results also illustrate the active control of bacteria on the MCP process, as the calcium starts to concentrate onto cell surfaces only after reaching a certain cell density, even though the cell surfaces are shown to be the ideal location for the CaCO₃ nucleation.

Insights into the influence of cell concentration in design and development of microbially induced calcium carbonate precipitation (MICP) process

Microbially induced calcium carbonate precipitation (MICP) process utilising the biogeochemical reactions for low energy cementation has recently emerged as a potential technology for numerous engineering applications. The design and development of an efficient MICP process depends upon several physicochemical and biological variables; amongst which the initial bacterial cell concentration is a major factor. The goal of this study is to assess the impact of initial bacterial cell concentration on ureolysis and carbonate precipitation kinetics along with its influence on the calcium carbonate crystal properties; as all these factors determine the efficacy of this process for specific engineering applications. We have also investigated the role of subsequent cell recharge in calcium carbonate precipitation kinetics for the first time. Experimental results showed that the kinetics of ureolysis and calcium carbonate precipitation are well-fitted by an exponential logistic equation for cell concentrations between optical density range of 0.1 OD to 0.4 OD. This equation is highly applicable for designing the optimal processes for microbially cemented soil stabilization applications using native or augmented bacterial cultures. Multiple recharge kinetics study revealed that the addition of fresh bacterial cells is an essential step to keep the fast rate of precipitation, as desirable in certain applications. Our results of calcium carbonate crystal morphology and mineralogy via scanning electron micrography, energy dispersive X-ray spectroscopy and X-ray diffraction analysis exhibited a notable impact of cell number and extracellular urease concentration on the properties of carbonate crystals. Lower cell numbers led to formation of larger crystals compared to high cell numbers and these crystals transform from vaterite phase to the calcite phase over time. This study has demonstrated the significance of kinetic models for designing large-scale MICP applications.

The effect of an acidified-gypsum mixture on broiler litter urease-producing bacteria and nitrogen mineralization

Ammonia (NH₃ ) volatilization from broiler (Gallus gallus domesticus) litter is a microbially mediated process that can decrease bird productivity and serves as an environmental pollutant. The release of NH₃ is strongly influenced by the pH of litter. Flue-gas desulfurization gypsum (FGDG) has been suggested as a potential amendment to reduce NH₃ volatilization due to the pH buffering capacity of calcium carbonate (CaCO₃ ) precipitation. However, its effect on litter pH is not as pronounced as acidifying agents, such as aluminum sulfate (alum). The main objective of our study was to develop an acidified-FGDG amendment that has a more pronounced effect on litter pH and NH₃ volatilization than FGDG alone. We conducted a 33-d incubation in which litter pH, NH₃ volatilization, nitrogen mineralization, PLUP-ureC gene abundance, and CaCO₃ precipitation were measured. Treatments in the study included: broiler litter (BL), broiler litter + 20% FGDG (BL+FGDG), broiler litter + FGDG-alum mixture (BL+FGDG+A6), broiler litter + 6% alum (BL+A6), and broiler litter + 10% alum (BL+A10). Our FGDG+alum amendment decreased litter pH (0.68 pH units) and PLUP-ureC gene abundance (>1 log) compared with FGDG alone and the control (p < .05). This led to a 25% decrease in cumulative NH₃ loss after 33 d. The addition of FGDG alone did not have an effect on litter pH (p = .36) or cumulative NH₃ loss (p = .29) due to a lack of significant CaCO₃ precipitation. Treating litter with 6 and 10% alum was the most effective amendment for reducing pH and cumulative NH₃ loss.

Immobilization of cadmium by Burkholderia sp. QY14 through modified microbially induced phosphate precipitation

Microbially induced phosphate precipitation (MIPP) is an advanced bioremediation technology to immobilize heavy metals. An indigenous bacterium QY14 with the function of mineralization isolated from Cd contaminated farmland soil was identified as Burkholderia ambifaria. The minimum inhibitory concentration value for QY14 was 550 mg/L for soluble Cd concentration. This study found that the addition of 10 mM Ca²⁺ during MIPP process could significantly increase the removal ratio of Cd, and the maximum removal ratio of Cd with 10 mM Ca²⁺ and without Ca²⁺ in solution was 99.97% and 76.14%, respectively. The increase of acid phosphatase activity and the formation of precipitate containing calcium caused by 10 mM Ca²⁺ addition contributed the increase of Cd removal efficiency. The results of SEM-EDS, FTIR and XRD showed that Cd was removed by forming Cd containing hydroxyapatite (Cd-HAP). In addition, the dissolution experiment showed the Cd release ratio of Cd-HAP (0.01‰ at initial pH 3.0 of solution) was lower than Cd-absorbed HAP, indicating that Cd was more likely removed by the formation of Ca_10-xCd_x(PO₄)₆(OH)₂ solid solution. Our findings revealed MIPP-based bioremediation supplied with 10 mM Ca²⁺ could increase the Cd removal and could potentially be applied for Cd remediation.

Design Service Life of RC Structures with Self-Healing Behaviour to Increase Infrastructure Carbon Savings

Corrosion of reinforced concrete (RC) structures costs the UK GBP 23b annually and is one of the main durability problems contributing to the development of rust, spalling, cracking, delamination, and structural deterioration. This paper intends to demonstrate the benefit of using tailored self-healing bacteria-based concrete for RC corrosion minimisation and service life increase. The purpose was to evaluate the enhancement in the lifespan of the structure exposed to a harsh marine microenvironment by utilising a probabilistic performance-based method. Comparison is made with the performance of a commercially available solution and in terms of embodied carbon impact. Three different concretes, using CEM I 52.5N, CEM II/A-D, and CEM III/A, were tested with and without an iron-respiring bioproduct (BIO) and an added admixture corrosion inhibitor (AACI). Results show that bioproduct significantly contributes to service life increase of RC structures with CEMIII/A. The repair solution with self-healing behaviour not only increases RC service life, but also enables us to decrease the required cover thickness from 60 mm to 50 mm in an XS2 chloride environment. In both XS2 and XS3 environments, a comparison of CEMIII/A+BIO and CEMII/A-D+AACI concrete shows the benefit of using bioproduct in corrosion inhibition context, besides contributing to an embodied carbon reduction of more than 20%.

Tuning Polymorphs and Morphology of Microbially Induced Calcium Carbonate: Controlling Factors and Underlying Mechanisms

Microbially precipitated calcium carbonate (CaCO₃) has drawn broad attention due to its potential applications in various areas, for example, biocementation, medicine, and soil reinforcement. Sporosarcina pasteurii (S. pasteurii), formerly known as Bacillus pasteurii, has been investigated for CaCO₃ biomineralization due to its high ureolytic activity. A high degree of supersaturation with respect to the presence of bacterial cell wall, extracellular polymeric substances, and organic byproducts of bacterial activity plays an important role in the formation and stabilization of CaCO₃ polymorphs. Although microbially induced CaCO₃ and its polymorphs have been investigated broadly, the mechanisms of polymorph selection and morphological evolution are not well understood. This study employs ex situ approaches to address the complication of biomineralization in the presence of living organisms and to elucidate how solution chemistry, bacterial activity, and precipitation kinetics alter the polymorphism and morphology of CaCO₃ induced by S. pasteurii. The results indicate that in the presence of enough calcium ions and urea (as a carbonate source), the bacterial activity favors the formation and stabilization of vaterite. The morphological observations also provide valuable information on the particles' microstructure. The morphology of calcite evolves from single crystal to polycrystalline structures, and the morphology of vaterite evolved from spherical to oval-shaped structures on increasing the organic material concentration. Specific functional groups also exert morphological control on CaCO₃ polymorphs. However, the sensitivity of the calcite polymorph to the composition and orientation of these functional groups is higher compared to that of the vaterite polymorph. These findings offer important insights that can be used to constrain a set of experimental conditions for synthesizing a certain polymorph ratio for vaterite/calcite or a particular morphology of each polymorph and shed light on the crystallization and phase transformation mechanisms in such complicated bioenvironments.

Whey as an Alternative Nutrient Medium for Growth of Sporosarcina pasteurii and Its Effect on CaCO3 Polymorphism and Fly Ash Bioconsolidation

Whey in large quantities can cause environmental problems when discarded, because it reduces dissolved oxygen and aquatic life. Nonetheless, it could be used as an easily available and economical alternative to reduce culture medium costs in microbially induced calcium carbonate precipitation (MICP). In this work, a native Sporosarcina pasteurii was isolated and then cultured by using different proportions of whey (W) in nutrient broth (NB). The solids were characterized by XRD, FT-IR, TGA, and SEM. The potential applications in bioconsolidation were also studied. Whey concentration was directly related to CaCO3 production. Higher whey concentrations reduced calcium carbonate purity to nearly 80%. All experiments showed calcite and vaterite fractions, where a whey increment in the media increased calcite content and decreased vaterite content, causing a decrease in crystal size. MICP improved compressive strength (CS) in sand and fly ash. The best CS results were obtained by fly ash treated with 25 W-75 NB (37.2 kPa) and sand with 75 W-25 NB (32.1 kPa). Whey changed crystal polymorphism in biogenic CaCO3 production. Material bioconsolidation depends on the CaCO3 polymorph, thus fly ash was effectively bioconsolidated by crystallization of vaterite and sand by crystallization of calcite.

Bio-mineralisation, characterization, and stability of calcium carbonate containing organic matter

The composition of organic matter in biogenic calcium carbonate has long been a mystery, and its role has not received sufficient attention. This study is aimed at elucidating the bio-mineralisation and stability of amorphous calcium carbonate (ACC) and vaterite containing organic matter, as induced by Bacillus subtilis. The results showed that the bacteria could induce various structural forms of CaCO3, such as biogenic ACC (BACC) or biogenic vaterite (BV), using the bacterial cells as their template, and the carbonic anhydrase secreted by the bacteria plays an important role in the mineralisation of CaCO3. The effects of Ca2+ concentration on the crystal structure of CaCO3 were ascertained; when the amount of CaCl2 increased from 0.1% (m/v) to 0.8% (m/v), the ACC was transformed to polycrystalline vaterite. The XRD results demonstrated that the ACC and vaterite have good stability in air or deionised water for one year, or even when heated to 200 °C or 300 °C for 2 h. Moreover, the FTIR results indicated that the BACC or BV is rich in organic matter, and the contents of organic matter in biogenic ACC and vaterite are 39.67 wt% and 28.47 wt%, respectively. The results of bio-mimetic mineralisation experiments suggest that the protein secreted by bacterial metabolism may be inclined to inhibit the formation of calcite, while polysaccharide may be inclined to promote the formation of vaterite. Our findings advance our knowledge of the CaCO3 family and are valuable for future research into organic-CaCO3 complexes.

MICP as a potential sustainable technique to treat or entrap contaminants in the natural environment: A review

In the last two decades, developments in the area of biomineralization has yielded promising results making it a potentially environmentally friendly technique for a wide range of applications in engineering and wastewater/heavy metal remediation. Microbially Induced Carbonate Precipitation (MICP) has led to numerous patented applications ranging from novel strains and nutrient sources for the precipitation of biominerals. Studies are being constantly published to optimize the process to become a promising, cost effective, ecofriendly approach when compared with the existing traditional remediation technologies which are implemented to solve multiple contamination/pollution issues. Heavy metal pollution still poses a major threat towards compromising the ecosystem. The removal of heavy metals is of high importance due to their recalcitrance and persistence in the environment. In that perspective, this paper reviews the current and most significant discoveries and applications of MICP towards the conversion of heavy metals into heavy metal carbonates and removal of calcium from contaminated media such as polluted water. It is evident from the literature survey that although heavy metal carbonate research is very effective in removal, is still in its early stages but could serve as a solution if the microorganisms are stimulated directly in the heavy metal environment.

Field Application of Microbial Self-Healing Cement Slurry in Chunguang 17-14 Well

Due to the inappropriate treatment of dairy wastewater, which can easily cause underground water pollution, there is an increasing need for a novel approach to reuse dairy wastewater. The technology of microbially induced calcium carbonate precipitation with environmentally friendly characteristics and high efficiency has been widely used for underground infrastructure remediation. However, there is a lack of in-depth research on the application of this technology under extreme underground environments, such as the borehole of oil wells with high temperature, high pressure, alkaline, and aerobic conditions. In addition, to reduce the cost of this technology when applied on a large scale, we adopted dairy wastewater to cultivate bacteria. Then, we put the bacterial solution into cement slurry in the borehole to improve the cementing quality. In this paper, the rheology properties, mechanical strength, permeability, porosity, and pore distribution of microbial cementing slurry were studied. Moreover, we applied this microbial cement slurry in the Chunguang 17-14 well of China, and the sealing channeling ability of cement sheath on site was evaluated. The results showed that dairy wastewater could serve as an alternative medium to provide nutrients and energy for the growth of bacteria with low cost. Additionally, the microbial cement slurry exhibited a good right-angle thickening performance and high mechanical strength. The field application displayed an anti-gas channeling ability after microbial remediation. The application of dairy wastewater incubated bacteria to cement slurry not only provides an alternative method for the reuse of dairy wastewater but is also conducive to prolonging the lifespan of oil wells.

Study on the simultaneous removal of fluoride, heavy metals and nitrate by calcium precipitating strain Acinetobacter sp. H12

The removal properties and mechanisms of fluoride (F^-) and nickel (Ni²⁺) were studied by biomineralizing bacteria (Acinetobacter sp. H12). The results showed that the removal ratio of F^-, Ca²⁺ and Ni²⁺ reached 75% (0.031 mg·L^-1·h^-1), 84.96% (2.123 mg·L^-1·h^-1), and 56.67% (0.024 mg·L^-1·h^-1) after 72 h, respectively. The removal ratio of nitrate (NO₃^-) reached 100% (0.686 mg·L^-1·h^-1) after 24 h. SEM and XRD images indicated that bioprecipitation of CaF₂, Ca₅(PO₄)₃F, Ca₅(PO₄)₃(OH), NiCO₃, CaCO₃ and Ni were formed, and some of these precipitation used bacteria as nucleation sites to form biological crystal seeds. N₂ was the primary product in gas chromatography analysis. Meanwhile, both the fluorescence spectroscopy and fourier transform near-infrared spectroscopy analysis proved that strain H12 had good ability to remove fluoride and nickel ions simultaneously.

Formulation of an exoskeleton degrading bacterial consortium from seafood processing effluent for the biocontrol of crustacean parasite Alitropus typus

Parasitic infestations on cultured fish due to the crustacean isopod Alitropus typus has been on the rise in recent years, causing large scale mortality, leading to significant economic loss to the farmer. Crustaceans are encased by an exoskeleton composed of chitin, protein and lipid microfibril frameworks, in which calcium carbonate is deposited. A strategy focused on the degradation of the exoskeletal framework utilizing nonpathogenic microorganisms that produce a wide variety of hydrolytic enzymes may be an environment-friendly and safe alternative to control these pests. The present study was aimed to formulate a microbial consortium having chitinase, protease, lipase and urease producing bacteria from seafood processing effluents that can potentially degrade the exoskeleton of A. typus. Based on the qualitative and quantitative assessment of the extracellular enzymes produced by the isolates, a novel consortium was prepared with three strains that were not antagonistic to each other and were nonpathogenic. The chitinase producing - Stenotrophomonas maltophilia and Bacillus altitudinis that produced protease and lipase as well; and non-chitinase producing Klebsiella pneumoniae were taken in the ratio of 1:1:2 respectively (10⁹ CFU/mL). The result showed 100 % mortality of the isopods within five days when applied at a concentration of 2% (v/v) of 10⁷ CFU/mL without any adverse effect on the fish host Oreochromis niloticus. Analysis of the ultrastructural alterations of the parasites by Environmental Scanning Electron microscopy (ESEM) showed noticeable exoskeletal damages. The microbial members of the consortium displayed remarkable chemotactic properties towards A. typus. The results suggest that the microbial consortium acts as a potential parasiticide that can be used for the control of A. typus infestation in aquaculture ponds., thus benefitting the aquaculture industry especially the small-scale farmers.

Microbially induced carbonate precipitation via methanogenesis pathway by a microbial consortium enriched from activated anaerobic sludge

AIMS

Various applications of microbially induced carbonate precipitation (MICP) has been proposed. However, most studies use cultured pure strains to obtain MICP, ignoring advantages of microbial consortia. The aims of this study were to: (i) test the feasibility of a microbial consortium to produce MICP; (ii) identify functional micro-organisms and their relationship; (iii) explain the MICP mechanism; (iv) propose a way of applying the MICP technique to soil media.

METHODS AND RESULTS

Anaerobic sludge was used as the source of the microbial consortium. A laboratory anaerobic sequencing batch reactor and beaker were used to perform precipitation experiment. The microbial consortium produced MICP with an efficiency of 96·6%. XRD and SEM analysis showed that the precipitation composed of different-size calcite crystals. According to high-throughput 16S rRNA gene sequencing, the functional micro-organisms included acetogenic bacteria, acetate-oxidizing bacteria and archaea Methanosaeta and Methanobacterium beijingense. The methanogenesis acetate degradation provides dissolved inorganic carbon and increases pH for MICP. A series of reactions catalysed by many enzymes and cofactors of methanogens and acetate-oxidizers are involved in the acetate degradation.

CONCLUSION

This work demonstrates the feasibility of using the microbial consortium to achieve MICP from an experimental and theoretical perspective.

SIGNIFICANCE AND IMPACT OF THE STUDY

A method of applying the microbial-consortium MICP to soil media is proposed. It has the advantages of low cost, low environmental impact, treatment uniformity and less limitations from natural soils. This method could be used to improve mechanical properties, plug pores and fix harmful elements of soil media, etc.

Influence of Fraction Particle Size of Pure Straw and Blends of Straw with Calcium Carbonate or Cassava Starch on Pelletising Process and Pellet

The aim of this study was to investigate the pressure agglomeration process of wheat straw (WS) and the blends of WS with calcium carbonate (CC) or cassava straw (CS) with a ratio of 6% wt./wt. from seven separate fractions with sizes in the range of 0.21-2.81 mm. The agglomeration was performed at a moisture of 30% wb and a material temperature of 78 °C, with a dose of 0.1 g, in a die of diameter 8 mm and height 80 mm. The effects of the process were evaluated based on the compaction parameters and the pellets' density, tensile strength, and water absorption. The incorporation of additives into the WS improved the pellet process and quality. Refined results were achieved after adding CC, as compared to those achieved after adding CS, and the preferred particle size was in the range of 1.00-1.94 mm. This was because, under the given conditions, the back pressure in the die chamber significantly increased, allowing the achievement of a single pellet density of 800 kg·m^-3. The pellets were resistant to compressive loads and cracked only at tensile strength of 6 MPa and a specific compression work of 6.5 mJ·mm^-2. The addition of CC to the WS improved the strength of the adhesive and the cohesive bonds between the particles. The water absorption for the uncrushed pellets was considerably less than that for crushed pellets, which results in the safer storage of uncrushed pellets and excellent moisture absorption of crushed pellets. The addition of CC to the WS offers benefits in the form of pellet strength with a high water absorption capability. Notably, a study of crushed pellet litter under broiler rearing conditions and an analysis of the operational costs of using WS additives are required for implementing this study.

Characterisation of Wheat Straw Pellets Individually and in Combination with Cassava Starch or Calcium Carbonate under Various Compaction Conditions: Determination of Pellet Strength and Water Absorption Capacity

This study aimed to optimise the production conditions of wheat straw (WS) pellets and pellets with the additives of cassava starch (CS) or calcium carbonate (CC) based on the criteria of pellet strength and water absorption by crushed pellets. The pellets produced using a 2-10%-wt/wt additive ratio, material moisture of 10-30% w.b., die height of 66-86 mm, and material temperature of 78-108 °C were tested. The influence these factors on the strength parameters of pellets was different than on the water absorption by the crushed pellets. The pellets made of WS blended with CC additive were characterised by better strength parameters and the compressed pellets were characterised by better water absorption than those with CS. High and positive correlation among specific pellet compression work, elasticity modulus for pellet compression, and tensile strength values were observed. As the strength parameters of pellets showed high correlation with single pellet density, for the consistency of conclusions, the optimal conditions for pellet production were assumed based on the density. For optimal conditions at 4% wt/wt additive ratio, 23% w.b. material moisture, 78 mm die height, and 80 °C material temperature, the specific pellet compression work was 3.22 mJ·mm-2, elasticity modulus was 5.78 MPa, and maximum tensile strength of the pellets was 2.68 MPa; moreover, the water absorption by crushed pellets amounted to 2.60 g H2O·g-1 of dry matter.

Applications of Bacillus subtilis Spores in Biotechnology and Advanced Materials

The bacterium Bacillus subtilis has long been an important subject for basic studies. However, this organism has also had industrial applications due to its easy genetic manipulation, favorable culturing characteristics for large-scale fermentation, superior capacity for protein secretion, and generally recognized as safe (GRAS) status. In addition, as the metabolically dormant form of B. subtilis, its spores have attracted great interest due to their extreme resistance to many environmental stresses, which makes spores a novel platform for a variety of applications. In this review, we summarize both conventional and emerging applications of B. subtilis spores, with a focus on how their unique characteristics have led to innovative applications in many areas of technology, including generation of stable and recyclable enzymes, synthetic biology, drug delivery, and material sciences. Ultimately, this review hopes to inspire the scientific community to leverage interdisciplinary approaches using spores to address global concerns about food shortages, environmental protection, and health care.

Bioimmobilization of toxic metals by precipitation of carbonates using Sporosarcina luteola: An in vitro study and application to sulfide-bearing tailings

Metal release from mining wastes is a major environmental problem affecting ecosystems that requires effective, low-cost strategies for prevention and reclamation. The capacity of two strains (UB3 and UB5) of Sporosarcina luteola was investigated to induce the sequestration of metals by precipitation of carbonates in vitro and under microcosm conditions. These strains carry the ureC gene and have high urease activity. Also, they are highly resistant to metals and have the capacity for producing metallophores and arsenophores. SEM, EDX and XRD reveal that the two strains induced precipitation of calcite, vaterite and magnesian calcite as well as several (M²⁺)CO₃ such as hydromagnesite (Mg²⁺), rhodochrosite (Mn²⁺), cerussite (Pb²⁺), otavite (Cd²⁺), strontianite (Sr²⁺), witherite (Ba²⁺) and hydrozincite (Zn²⁺) in vitro. Inoculation of the mixed culture of UB3+UB5 in tailings increased the pH and induced the precipitation of vaterite, calcite and smithsonite enhancing biocementation and reducing pore size and permeability slowing down the oxidation of residual sulfides. Results further demonstrated that the strains of S. luteola immobilize bioavailable toxic elements through the precipitation and coprecipitation of thermodynamically stable (M²⁺)CO₃, Fe-Mn oxyhydroxides and organic chelates.

Characterisation of CaCO3 phases during strain-specific ureolytic precipitation

Numerous microbial species can selectively precipitate mineral carbonates with enhanced mechanical properties, however, understanding exactly how they achieve this control represents a major challenge in the field of biomineralisation. We have studied microbial induced calcium carbonate (CaCO₃) precipitation (MICP) in three ureolytic bacterial strains from the Sporosarcina family, including S. newyorkensis, a newly isolated microbe from the deep sea. We find that the interplay between structural water and strain-specific amino acid groups is fundamental to the stabilisation of vaterite and that, under the same conditions, different isolates yield distinctly different polymorphs. The latter is found to be associated with different urease activities and, consequently, precipitation kinetics, which change depending on pressure-temperature conditions. Further, CaCO₃ polymorph selection also depends on the coupled effect of chemical treatment and initial bacterial concentrations. Our findings provide new insights into strain-specific CaCO₃ polymorphic selection and stabilisation, and open up promising avenues for designing bio-reinforced geo-materials that capitalise on the different particle bond mechanical properties offered by different polymorphs.

Efficient option of industrial wastewater resources in cement mortar application with river-sand by microbial induced calcium carbonate precipitation

The industrial wastewater disposal has been growing attention for environmental protection and resource substitution, current decades. Similarly, the durability enhancement of concrete has increased attention by microbial induced CaCO₃ precipitation (MICP) process (biocalcification). However, ecofriendly utilization of industrial wastewater in concrete formation is unstudied so far. The present study was carried out to evaluate the effect of industrial wastewater on the formation of cement mortar, compressive strength and water absorption. The biocement mortar strength (y) increased (y = 0.5295ײ + 1.6019×+251.05; R² = 0.9825) with increasing percentage of organic wastewater (x) (BM₀ – BM₁₀₀) by MICP, where highest strength (280.75 kgf/cm²) was observed on BM₁₀₀ (100% wastewater), compared to control (252.05 kgf/cm²). The water absorption (y) of biocement mortar decreases (y = −0.0251ײ–0.103× + 15.965; R²= 0.9594) with increment of wastewater (x) (%) (BM₀ – BM₁₀₀), where a minimum-water-absorption (14.42%) observed on BM₁₀₀, compared to control (15.89%). SEM micrograph and XRD shows the formation of most-distinctive CaCO₃ crystallization (aragonite/calcite) (acicular, brick shape, massive and stacked structure) inside biocement mortar (BM₁₀₀), which fills the pores within cement mortar to form a denser structure, by microbial organic wastewater. Thus, present findings implied a cost-effective of MICP technology to improve the concrete properties along with the mitigation of industrial wastewater pollution, which goes some way towards solving the problem of industrial wastewater pollution.

The performance and mechanism of simultaneous removal of fluoride, calcium, and nitrate by calcium precipitating strain Acinetobacter sp. H12

A calcium precipitating and denitrifying bacterium H12 was used to investigate the F^- removal performance and mechanism. The results showed that the strain H12 reduced 85.24% (0.036 mg·L^-1·h^-1) of F^-, 62.43% (0.94 mg·L^-1·h^-1) of Ca²⁺, and approximately 100% of NO₃^- over 120 h in continuous determination experiments. The response surface methodology analysis demonstrated that the maximum removal efficiency of F^- was 88.98% (0.062 mg·L^-1·h^-1) within 72 h under the following conditions: the initial Ca²⁺ concentration of 250.00 mg·L^-1, pH of 7.50, and the initial C₄H₄Na₂O₄·6H₂O concentration of 800.00 mg·L^-1. The scanning electron microscopy images, the X-ray photoelectron spectroscopy, and X-ray diffraction results suggested the following removal mechanism of F^-: (1) the bacteria, as the nucleation site, were encapsulated by bioprecipitation to form biological crystal seeds; (2) Biological crystal seeds adsorbed F^- to form Ca₅(PO₄)₃F and CaF₂; (3) Under the induction of bacteria, calcium, fluoride and phosphate coprecipitated to form Ca₅(PO₄)₃F and CaF₂. In addition, the gas chromatography data indicated that F^- had little or no effect on the gas composition during denitrification, and the fluorescence spectroscopy analysis also proved that the extracellular polymeric substance (protein) is the site of bioprecipitation nucleation.

Life and its traces in Antarctica's McMurdo Dry Valley paleolakes: a survey of preservation

The extremely cold and arid conditions of Antarctica make it uniquely positioned to investigate fundamental questions regarding the persistence of life in extreme environments. Within the McMurdo Dry Valleys and surrounding mountain ranges are multiple ancient relict lakes, paleolakes, with lacustrine deposits spanning from thousands to millions of years in age. Here we present data from light microscopy, scanning electron microscopy, electron dispersive x-ray spectroscopy, and radiocarbon dating to catalog the remarkable range of life preserved within these deposits. This includes intact microbes and nanobacteria-sized cocci, CaCO₃ precipitations consistent with biogenic calcium, previously undescribed net-like structures, possible dormant spores, and long-extinct yet exquisitely preserved non-vascular plants. These images provide an important reference for further microbiome investigations of Antarctic paleolake samples. In addition, these findings may provide a visual reference for the use of subsurface groundwater microbial communities as an analog for paleolake subsurface water on planets such as Mars.