Exploration on the Biotechnological Aspect of the Ureolytic Bacteria for the Production of the Cementitious Materials—a Review

Accelerated Reinforcement of Calcareous sand via Biomineralization with Aluminum Ion Flocculant

Microbially induced calcium carbonate precipitation (MICP) is an immensely growing technique that utilizes the metabolic pathways of bacteria to form calcite precipitation throughout the soil matrix, leading to improve geotechnical engineering properties. However, the excessive number of treatments limited the application of MICP for strengthening calcareous sand. To reduce the number of treatments and develop efficiencies, this paper investigates the optimized treatment protocol of adding aluminum ion flocculants to the cementing solution to accelerate the curing rate of the MICP and its effect. The results show that adding a certain concentration of AlCl3 to the cementing solution can resulted in a rapid increase in strength of the calcareous sand column. When 0.02 M aluminum chloride was added to the cementing solution, the unconfined compressive strength of the sand column reached 827 kPa after three treatments, and it reached 2 MPa after five treatments, while the control group needed to be treated 10 and 15 times, respectively, to reach equivalent strengths. In this paper, the unconfined compressive strength of the sand column formed using the proposed method was 27-40 times that of the control group at the same calcium carbonate content. The presented experimental approach can be used as a tool to design the treatment protocol for the engineering application of MICP-reinforced calcareous sand in practice.

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.

Microbial Concrete-a Sustainable Solution for Concrete Construction

In the ever-increasing demand of construction and construction materials worldwide, concrete is the most extensively used material for construction purposes almost next to the water. Therefore, there is a dire need of clean, green and durable concrete. Recently, an environmentally friendly strategy has been employed to manufacture bio-concrete by the usage of microorganisms in the traditional concrete to enhance its durability and compressive strength. In this review, we discuss the role of microbes in influencing the various properties of concrete such as compressive strength, flexural strength and tensile strength by reducing the concrete porosity and diminishing water absorption. The mechanism of microbial-induced calcium carbonate precipitation (MICP) in the traditional concrete by the action of microbes which resulted in the formation of bio-concrete as an improved building material has also been discussed. Additionally, an in-depth comparative analysis of the performance of bio-concrete with the traditional concrete synthesized from various industrial wastes such as silica fume, rice husk ash and metakaolin in terms of different properties such as compressive strength, flexural strength and percentage water absorption has been presented. This review highlights the impact of usage of microbes in the conventional concrete to produce novel and eco-friendly bio-concrete in construction technology.

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.

Smart soil grouting using innovative urease-producing bacteria and low cost materials

AIMS

Calcium carbonate is a biomineral whose precipitation could be mediated by ureolytic bacteria and contributes in strengthening of sandy soils. The type of bacteria and grade of reagents have significant influence on microbially induced calcite precipitation (MICP). In the present study, factorial experiments based on these two factors were designed to determine their potential on MICP process, taking into consideration the economic advantages while giving quality results as well.

METHODS AND RESULTS

For the first time, Alkalibacterium iburiense strain EE1 (GenBank accession no. MF355369.1) is reported for its biogrouting activity. Optimum growth conditions for MICP treatments were pH (9·56 ± 0·021), EC (44·7 ± 0·057 mS cm^-1 ), OD₆₀₀ (2·04 ± 0·015), NH₄ ⁺ concentration (487·06 ± 1·021 mmol l^-1 ), and urease activity (20·0 ± 0·75 mmol l^-1 urea hydrolysed min^-1 ) after 72-h incubation. Statistical analysis comparing the growth in technical-grade medium prepared in tap water and analytical-grade medium prepared in deionized water showed no significant differences (P = 1·0) in biomass and urease activity. In contrast to previous studies, the current approach could reduce the bacterial culture and cementation solution ratio by about 50%, using a simple surface percolation method with staged injection instead of parallel injection to treat different sand columns. Using fixation solution could immobilize the bacteria over the full length of columns for better strength improvement. The unconfined compressive strength ranged between 0·64 to 2·11 kg cm^-2 , and the corresponding CaCO₃ contents 5·7-38·5%. The scanning electron microscope images indicated that the precipitated CaCO₃ by bacteria was stable calcite.

CONCLUSIONS

Alkalibacterium iburiense and technical-grade reagents under nonsterile conditions are satisfactory consolidating agents for sandy soils.

SIGNIFICANCE AND IMPACT OF THE STUDY

This approach is considered eco-friendly and cost-effective for future scale-up applications in various geotechnical engineering.

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.

Investigating mechanical properties and biocement application of CaCO3 precipitated by a newly-isolated Lysinibacillus sp. WH using artificial neural networks

A newly-isolated Lysinibacillus sp. strain WH could precipitate CaCO₃ using calcium acetate (Ca(C₂H₃O₂)₂), calcium chloride (CaCl₂) and calcium nitrate (Ca(NO₃)₂) via non-ureolytic processes. We developed an algorithm to determine CaCO₃ crystal structures by fitting the simulated XRD spectra to the experimental data using the artificial neural networks (ANNs). The biogenic CaCO₃ crystals when using CaCl₂ and Ca(NO₃)₂ are trigonal calcites with space group R3c, while those when using Ca(C₂H₃O₂)₂ are hexagonal vaterites with space group P6₅22. Their elastic properties are derived from the Voigt–Reuss–Hill (VRH) approximation. The bulk, Young's, and shear moduli of biogenic calcite are 77.812, 88.197, and 33.645 GPa, respectively, while those of vaterite are 67.082, 68.644, 25.818 GPa, respectively. Their Poisson’s ratios are ~ 0.3–0.33, suggesting the ductility behavior of our crystals. These elastic values are comparable to those found in limestone cement, but are significantly larger than those of Portland cement. Based on the biocement experiment, the maximum increase in the compressive strength of Portland cement (27.4%) was found when Ca(NO₃)₂ was used. An increased strength of 26.1% was also found when Ca(C₂H₃O₂)₂ was used, implying the transformation of less-durable vaterite to higher-durable calcite. CaCO₃ produced by strain WH has a potential to strengthen Portland cement-based materials.

Harnessing the sponge microbiome for industrial biocatalysts

Within the marine sphere, host-associated microbiomes are receiving growing attention as prolific sources of novel biocatalysts. Given the known biocatalytic potential of poriferan microbial inhabitants, this review focuses on enzymes from the sponge microbiome, with special attention on their relevant properties and the wide range of their potential biotechnological applications within various industries. Cultivable bacterial and filamentous fungal isolates account for the majority of the enzymatic sources. Hydrolases, mainly glycoside hydrolases and carboxylesterases, are the predominant reported group of enzymes, with varying degrees of tolerance to alkaline pH and growing salt concentrations being common. Prospective areas for the application of these microbial enzymes include biorefinery, detergent, food and effluent treatment industries. Finally, alternative strategies to identify novel biocatalysts from the sponge microbiome are addressed, with an emphasis on modern -omics-based approaches that are currently available in the enzyme research arena. By providing this current overview of the field, we hope to not only increase the appetite of researchers to instigate forthcoming studies but also to stress how basic and applied research can pave the way for new biocatalysts from these symbiotic microbial communities in a productive fashion. KEY POINTS: • The sponge microbiome is a burgeoning source of industrial biocatalysts. • Sponge microbial enzymes have useful habitat-related traits for several industries. • Strategies are provided for the future discovery of microbial enzymes from sponges.

Feasibility Study of Native Ureolytic Bacteria for Biocementation Towards Coastal Erosion Protection by MICP Method

In recent years, traditional material for coastal erosion protection has become very expensive and not sustainable and eco-friendly for the long term. As an alternative countermeasure, this study focused on a sustainable biological ground improvement technique that can be utilized as an option for improving the mechanical and geotechnical engineering properties of soil by the microbially induced carbonate precipitation (MICP) technique considering native ureolytic bacteria. To protect coastal erosion, an innovative and sustainable strategy was proposed in this study by means of combing geotube and the MICP method. For a successful sand solidification, the urease activity, environmental factors, urease distribution, and calcite precipitation trend, among others, have been investigated using the isolated native strains. Our results revealed that urease activity of the identified strains denoted as G1 (Micrococcus sp.), G2 (Pseudoalteromonas sp.), and G3 (Virgibacillus sp.) relied on environment-specific parameters and, additionally, urease was not discharged in the culture solution but would discharge in and/or on the bacterial cell, and the fluid of the cells showed urease activity. Moreover, we successfully obtained solidified sand bearing UCS (Unconfined Compressive Strength) up to 1.8 MPa. We also proposed a novel sustainable approach for field implementation in a combination of geotube and MICP for coastal erosion protection that is cheaper, energy-saving, eco-friendly, and sustainable for Mediterranean countries, as well as for bio-mediated soil improvement.

Genomics of Urea Transport and Catabolism in Cyanobacteria: Biotechnological Implications

Cyanobacteria are widely-diverse prokaryotes that colonize our planet. They use solar energy to assimilate huge amounts of atmospheric CO₂ and produce a large part of the biomass and oxygen that sustain most life forms. Cyanobacteria are therefore increasingly studied for basic research objectives, as well as for the photosynthetic production of chemicals with industrial interests. One potential approach to reduce the cost of future bioproduction processes is to couple them with wastewater treatment, often polluted with urea, which in any case is cheaper than nitrate. As of yet, however, research has mostly focused on a very small number of model cyanobacteria growing on nitrate. Thus, the genetic inventory of the cyanobacterial phylum is still insufficiently employed to meaningfully select the right host for the right purpose. This review reports what is known about urea transport and catabolism in cyanobacteria, and what can be inferred from the comparative analysis of the publicly available genome sequence of the 308 cyanobacteria. We found that most cyanobacteria mostly harbor the genes encoding the urea catabolytic enzymes urease (ureABCDEFG), but not systematically, together with the urea transport (urtABCDE). These findings are consistent with the capacity of the few tested cyanobacteria that grow on urea as the sole nitrogen source. They also indicate that urease is important for the detoxification of internally generated urea (re-cycling its carbon and nitrogen). In contrast, several cyanobacteria have urtABCDE but not ureABCDEFG, suggesting that urtABCDE could operate in the transport of not only urea but also of other nutrients. Only four cyanobacteria appeared to have the genes encoding the urea carboxylase (uc) and allophanate hydrolase (ah) enzymes that sequentially catabolize urea. Three of these cyanobacteria belongs to the genera Gloeobacter and Gloeomargarita that have likely diverged early from other cyanobacteria, suggesting that the urea carboxylase and allophanate hydrolase enzymes appeared in cyanobacteria before urease.

Microbially induced calcium carbonate precipitation: a widespread phenomenon in the biological world

Biodeposition of minerals is a widespread phenomenon in the biological world and is mediated by bacteria, fungi, protists, and plants. Calcium carbonate is one of those minerals that naturally precipitate as a by-product of microbial metabolic activities. Over recent years, microbially induced calcium carbonate precipitation (MICP) has been proposed as a potent solution to address many environmental and engineering issues. However, for being a viable alternative to conventional techniques as well as being financially and industrially competitive, various challenges need to be overcome. In this review, the detailed metabolic pathways, including ammonification of amino acids, dissimilatory reduction of nitrate, and urea degradation (ureolysis), along with the potent bacteria and the favorable conditions for precipitation of calcium carbonate, are explained. Moreover, this review highlights the potential environmental and engineering applications of MICP, including restoration of stones and concrete, improvement of soil properties, sand consolidation, bioremediation of contaminants, and carbon dioxide sequestration. The key research and development questions necessary for near future large-scale applications of this innovative technology are also discussed.

Alkaliphiles: The Emerging Biological Tools Enhancing Concrete Durability

Concrete is one of the most commonly used building materials ever used. Despite it is a very important and common construction material, concrete is very sensitive to crack formation and requires repair. A variety of chemical-based techniques and materials have been developed to repair concrete cracks. Although the use of these chemical-based repair systems are the best commercially available choices, there have also been concerns related to their use. These repair agents suffer from inefficiency and unsustainability. Most of the products are expensive and susceptible to degradation, exhibit poor bonding to the cracked concrete surfaces, and are characterized by different physical properties such as thermal expansion coefficients which are different to that of concrete. Moreover, many of these repair agents contain chemicals that pose environmental and health hazards. Thus, there has been interest in developing concrete crack repair agents that are efficient, long lasting, safe, and benign to the environment and exhibit physical properties which resemble that of the concrete. The search initiated by these desires brought the use of biomineralization processes as tools in mending concrete cracks. Among biomineralization processes, microbially initiated calcite precipitation has emerged as an interesting alternative to the existing chemical-based concrete crack repairing system. Indeed, results of several studies on the use of microbial-based concrete repair agents revealed the remarkable potential of this approach in the fight against concrete deterioration. In addition to repairing existing concrete cracks, microorganisms have also been considered to make protective surface coating (biodeposition) on concrete structures and in making self-healing concrete.Even though a wide variety of microorganisms can precipitate calcite, the nature of concrete determines their applicability. One of the important factors that determine the applicability of microbes in concrete is pH. Concrete is highly alkaline in nature, and hence the microbes envisioned for this application are alkaliphilic or alkali-tolerant. This work reviews the available information on applications of microbes in concrete: repairing existing cracks, biodeposition, and self-healing. Moreover, an effort is made to discuss biomineralization processes that are relevant to extend the durability of concrete structures. Graphical Abstract.

In Situ Real-Time Study on Dynamics of Microbially Induced Calcium Carbonate Precipitation at a Single-Cell Level

Ureolytic microbially induced calcium carbonate precipitation (MICP) is a promising green technique for addressing a variety of environmental and architectural concerns. However, the dynamics of MICP especially at the microscopic level remains relatively unexplored. In this work, by applying a bacterial tracking technique, the growth dynamics of micrometer-sized calcium carbonate precipitates induced by Sporosarcina pasteurii were studied at a single-cell resolution. The growth of micrometer-scale precipitates and the occurrence and dissolution of many unstable submicrometer calcium carbonate particles were observed in the precipitation process. More interestingly, we observed that micrometer-sized precipitated crystals did not grow on negatively charged cell surfaces nor on other tested polystyrene microspheres with different negatively charged surface modifications, indicating that a negatively charged surface was not a sufficient property for nucleating the growth of precipitates in the MICP process under the conditions used in this study. Our observations imply that the frequently cited model of bacterial cell surfaces as nucleation sites for precipitates during MICP is oversimplified. In addition, additional growth of calcium carbonates was observed on old precipitates collected from previous runs. The presence of bacterial cells was also shown to affect both morphologies and crystalline structures of precipitates, and both calcite and vaterite precipitates were found when cells physically coexisted with precipitates. This study provides new insights into the regulation of MICP through dynamic control of precipitation.

Subsurface Endospore-Forming Bacteria Possess Bio-Sealant Properties

Concrete is a strong and fairly inexpensive building substance, but has several disadvantages like cracking that allows corrosion, thus reducing its lifespan. To mitigate these complications, long-lasting microbial self-healing cement is an alternative that is eco-friendly and also actively repairs cracks. The present paper describes the detailed experimental investigation on compressive strength of cement mortars, mixed with six alkaliphilic bacteria, isolated from subsurface mica mines of high alkalinity. The experiments showed that the addition of alkaliphilic isolates at different cell concentrations (10⁴ and 10⁶ cells/ml) enhanced the compressive strength of cement mortar, because the rapid growth of bacteria at high alkalinity precipitates calcite crystals that lead to filling of pores and densifying the concrete mix. Thus, Bacillus subtilis (SVUNM4) showed the highest compressive strength (28.61%) of cement mortar at 10⁴ cells/ml compared to those of other five alkaliphilic isolates (Brevibacillus sp., SVUNM15-22.1%; P. dendritiformis, SVUNM11-19.9%; B. methylotrophicus, SVUNM9-16%; B. licheniformis, SVUNM14-12.7% and S. maltophilia, SVUNM13-9.6%) and controlled cement mortar as well. This method resulted in the filling of cracks in concrete with calcite (CaCO₃), which was observed by scanning electron microscopy (SEM). Our results showed that the alkaliphilic bacterial isolates used in the study are effective in self-healing and repair of concrete cracks.

Study of the Interaction of Eu3+ with Microbiologically Induced Calcium Carbonate Precipitates using TRLFS

The microbial induced biomineralization of calcium carbonate using the ureolytic bacterium Sporosarcina pasteurii in the presence of trivalent europium, a substitute for trivalent actinides, was investigated by time-resolved laser-induced fluorescence spectroscopy (TRLFS) and a variety of physicochemical techniques. Results showed that the bacterial-driven hydrolysis of urea provides favorable conditions for CaCO₃ precipitation and Eu³⁺ uptake due to subsequent increases in NH₄⁺ and pH in the local environment. Precipitate morphologies were characteristic of biogenically formed CaCO₃ and consistent with the respective mineral phase compositions. The formation of vaterite with some calcite was observed after 1 day, calcite with some vaterite after 1 week, and pure calcite after 2 weeks. The presence of organic material associated with the mineral was also identified and quantified. TRLFS was used to track the interaction and speciation of Eu³⁺ as a molecular probe with the mineral as a function of time. Initially, Eu³⁺ is incorporated into the vaterite phase, while during CaCO₃ phase transformation Eu³⁺ speciation changes resulting in several species incorporated in the calcite phase either substituting at the Ca²⁺ site or in a previously unidentified, low-symmetry site. Comparison of the biogenic precipitates to an abiotic sample shows mineral origin can affect Eu³⁺ speciation within the mineral.

Carbonate Precipitation through Microbial Activities in Natural Environment, and Their Potential in Biotechnology: A Review

Calcium carbonate represents a large portion of carbon reservoir and is used commercially for a variety of applications. Microbial carbonate precipitation, a by-product of microbial activities, plays an important metal coprecipitation and cementation role in natural systems. This natural process occurring in various geological settings can be mimicked and used for a number of biotechnologies, such as metal remediation, carbon sequestration, enhanced oil recovery, and construction restoration. In this study, different metabolic activities leading to calcium carbonate precipitation, their native environment, and potential applications and challenges are reviewed.

The Micro-mechanism Involved and Wollastonite Signature in the Calcareous Precipitates of Marine Isolates

Micro-mechanical studies connecting the influence of extrinsic factors over intrinsic factors on 30 calcareous isolates obtained from marine sediment biofilms of the Bay of Bengal (Indian Ocean) revealed that the fate of calcareous crystal precipitation is highly dependent on factors like extracellular polysaccharides (EPS), organic carbon and nutrition. Further studies exemplified that EPS and the organic carbon secreted by the isolates controlled the dissemination of the calcareous crystals precipitated. From the study, it is evident that an EPS concentration of 7-15 mg l(-1) was found to enhance the dissemination of the calcareous crystals. Atomic force micrographs explain the nucleation behaviour and morphology of the calcareous crystals precipitated. X-ray diffraction (XRD) and energy-dispersive X-ray spectroscopy (EDAX) showed that the crystals were mainly composed of calcite and partially wollastonite.

Influence of calcium sources on microbially induced calcium carbonate precipitation by Bacillus sp. CR2

Stimulation of microbially induced calcium carbonate precipitation (MICCP) is likely to be influenced by calcium sources. In order to study such influences, we performed MICCP using Bacillus sp. CR2 in nutrient broth containing urea, supplemented with different calcium sources (calcium chloride, calcium oxide, calcium acetate and calcium nitrate). The experiment lasted 7 days, during which bacterial growth, urease activity, calcite production and pH were measured. Our results showed that calcium chloride is the better calcium source for MICCP process, since it provides higher urease activity and more calcite production. The influences of calcium sources on MICCP were further studied using Fourier transform-infrared (FTIR) spectroscopy, scanning electron microscopy (SEM) and X-ray diffraction (XRD) analyses. These analyses confirmed that the precipitate formed was CaCO3 and composed of predominantly calcite crystals with a little amount of aragonite and vaterite crystals. The maximum yield of calcite precipitation was achievable with calcium chloride followed by calcium nitrate as a calcium source. The results of present study may be applicable to media preparation during efficient MICCP process.