Spatio-Temporal Reactive Transport Modeling of Microbially Induced Calcite Precipitation and Porosity Evolution in Porous Media

Cow urine as a source of nutrients for Microbial-Induced Calcite Precipitation in sandy soil

Microbially induced calcite precipitation (MICP) is a sustainable method of stabilizing (i.e., cementing) loose sandy deposits or creating an impervious barrier within the soil mass or both. MICP can occur through various biochemical pathways, and ‘Urea Hydrolysis’ (UH) is considered to be the most efficient of the MICP methods for biochemically inducing calcite precipitation. To date, the geotechnical engineering community that has investigated MICP has tended to focus on the hydromechanical behavior of the end product, i.e., MICP cemented sands; however, many biochemical factors that affect reaction-rate kinetics and MICP outcomes have been understudied or neglected. This study investigates the kinetics of UH and compares different sources of the urease enzyme—those microbially cultivated in the laboratory (i.e., Sporosarcina pasteurii) and those extracted from plants (i.e., Jack bean meal)—to investigate the influence of urea concentration, buffer capacity, and the cell harvesting method on UH. Through this study, an attempt has been made to arrive at an optimal concentration of urea, under the influence of the previously mentioned parameters and the buffering action of the soil, on urea hydrolysis. These results have implications for optimizing MICP and, in particular, for upscaling these methods to in situ applications.

BCH modelling studies on biocementation process in mitigating leaks from a CO2 sequestrated aquifer

Mineral precipitation via microbial activity is a well-known process with applications in various fields. This relevance of microbially induced calcite precipitation (MICP) has pushed researchers to explore various naturally occurring MICP capable bacterial strains. The present study was performed to explore the efficiency of microbially induced calcite precipitation (MICP) via locally isolated bacterial strains and role of guar gum, which is a naturally occurring polymer, on the MICP process. The strains were isolated from local soil and screened for urease activity Further, the urease positive strain was subjected to urea and calcium chloride based medium to investigate the efficacy of isolated strain for microbial induced precipitation. Among screened isolates, the soil bacterium that showed urease positive behaviour and precipitated calcium carbonate was subjected to 16S rRNA gene sequencing. This strain was identified as Bacillus velezensis. Guar gum-a natural polymer, was used as a sole carbon source to enhance the MICP process. It was observed that the isolated strain was able to breakdown the guar gum into simple sugars resulting in two-fold increase in calcium carbonate precipitate. Major bio-chemical activities of isolated strain pertaining to MICP such as ammonium ion concentration, pH profiling, and total reducing sugar with time were explored under four different concentrations of guar gum (0.25%, 0.5%, 0.75% and 1% w/v). Maximum ammonium ion concentration (17.5 μg/ml) and increased pH was observed with 1% guar gum supplementation, which confirms augmented MICP activity of the bacterial strain. Microstructural analysis of microbial precipitation was performed using scanning electron microscopy (SEM) and X-ray diffraction (XRD) techniques, which confirmed the presence of calcium carbonate in different phases. Further, XRD and SEM based studies corroborated that guar gum supplemented media showed significant increase in stable calcite phase as compared to media without guar gum supplementation. Significant diverse group of nitrogenous compounds were observed in guar gum supplemented medium when subjected to Gas Chromatography-Mass spectrometry (GC-MS) profiling.

Mineral precipitation via microbial activity is a well-known process with applications in various fields. This relevance of microbially induced calcite precipitation (MICP) has pushed researchers to explore various naturally occurring MICP capable bacterial strains. The present study was performed to explore the efficiency of microbially induced calcite precipitation (MICP) via locally isolated bacterial strains and role of guar gum, which is a naturally occurring polymer, on the MICP process. The strains were isolated from local soil and screened for urease activity Further, the urease positive strain was subjected to urea and calcium chloride based medium to investigate the efficacy of isolated strain for microbial induced precipitation. Among screened isolates, the soil bacterium that showed urease positive behaviour and precipitated calcium carbonate was subjected to 16S rRNA gene sequencing. This strain was identified as Bacillus velezensis. Guar gum—a natural polymer, was used as a sole carbon source to enhance the MICP process. It was observed that the isolated strain was able to breakdown the guar gum into simple sugars resulting in two-fold increase in calcium carbonate precipitate. Major bio-chemical activities of isolated strain pertaining to MICP such as ammonium ion concentration, pH profiling, and total reducing sugar with time were explored under four different concentrations of guar gum (0.25%, 0.5%, 0.75% and 1% w/v). Maximum ammonium ion concentration (17.5 μg/ml) and increased pH was observed with 1% guar gum supplementation, which confirms augmented MICP activity of the bacterial strain. Microstructural analysis of microbial precipitation was performed using scanning electron microscopy (SEM) and X-ray diffraction (XRD) techniques, which confirmed the presence of calcium carbonate in different phases. Further, XRD and SEM based studies corroborated that guar gum supplemented media showed significant increase in stable calcite phase as compared to media without guar gum supplementation. Significant diverse group of nitrogenous compounds were observed in guar gum supplemented medium when subjected to Gas Chromatography–Mass spectrometry (GC-MS) profiling.

SUMMARY Soil stabilization processes aim at enhancing soil's engineering properties. Although the concept is straightforward, it involves physical and chemical changes to the subsurface that could result in local environmental changes. Compared to conventional soil stabilization methods (such as cement grouting), bio-mediated soil stabilization, such as microbial-induced calcite precipitation (MICP), offers the opportunity to minimize environmental impact, but the underlying processes need to be well understood for proper applications. Accurate characterization and long-term monitoring are paramount for the success of soil improvement, especially MICP treatments. Spectral induced polarization (SIP), an established geophysical method, has shown to be sensitive to MICP processes and products (e.g. calcite). In this work, we performed a two-phase study to explore SIP's suitability as a monitoring tool. Phase 1 involved a laboratory scale MICP study under controlled conditions and phase 2 a pilot field scale study. In the laboratory, MICP was induced through the introduction of ureolytic microorganisms, while in the field, indigenous soil microbes were stimulated to promote ureolysis. In both cases, traditional geochemical monitoring, along with spatiotemporally dense SIP monitoring, were performed. Over the course of the laboratory study, SIP successfully tracked the MICP progress as well as the calcite precipitation behaviour. Similarly, the SIP results of the field scale study showed to be sensitive to the subsurface changes in response to MICP. SIP offered spatiotemporally rich information on the MICP progress and process status. The similarity between observed signal trends in the laboratory and field in this study clearly proved that SIP signals from MICP in controlled laboratory environments can be successfully used to study field MICP applications despite scale and complexity differences.

A coupled bio-chemo-hydraulic model to predict porosity and permeability reduction during microbially induced calcite precipitation

ABSTRACT: Caprock formation forms a natural barrier for geological storage of CO2, nuclear wastes, and hydrocarbon resources. Fault and natural/artificial fractures that crosscut the storage systems represent potential leakage pathways. Sealing of caprock fractures/faults is of great importance to ensure its long-term sealing integrity. In this study, we conduct microbial-induced-calcite-precipitation (MICP) experiments for sealing anhydrite fractures (artificially cut) with gouges. MICP involves a bio-chemical reaction for calcite precipitation using ureolytic microorganism – Sporosarcina pasteurii. The precipitated calcite, which occurs initially from finer pores to larger pores, induces a 10.7% decrease of porosity inside the fracture after the 1st 12 cycles of MICP treatment. After 18-21 cycles of MICP treatment, the fracture permeability of the two fractured core samples effectively decreases by 2-3 orders of magnitude. Our study also indicates that the MICP sealing efficiency could be improved by lowering the injection rate, optimizing fluid chemistry for a better bacteria retention inside the fracture. The study provides a baseline for using MICP technique to seal anhydrite fractures. 1. INTRODUCTION Caprocks with very low permeability and ultra-fine pores, consisting of massive consolidated clay-rich sediments (shale) and evaporites such as anhydrite and halite, create natural barriers for hydrocarbon resources, CO2 sequestration, disposal of radioactive wastes, hydrogen storage, etc. However, natural fractures/faults or injection-induced fractures that crosscut subsurface storage systems (Figure 1) could provide potential leakage pathways 1,2. Seeking an efficient technique to seal caprock fractures is crucial. Microbially induced calcite precipitation (MICP) has been considered as an environmentally sustainable grouting technology for soil improvement 3,4, fracture sealing 5-8, removal of contaminants in ground water 9,10, among others. It has several advantages over conventional cement grouting methods, including (1) the low viscosity of the bacterial solution and cementing solution (urea and calcium chloride), which allows to penetrate with relatively low pumping power; (2) micron-size microbes for sealing fine pores and fractures; and (3) potential low carbon footprint. MICP is a naturally occurring metabolic phenomenon that can be found in soil and marine environment 11. This bio-inspired grouting technique also have advantages over conventional chemical grouting method (such as acrylates, acrylamides, and polyurethanes, etc.) due to its lower cost of the raw materials and less toxicity to the environment 12.

The biogeochemical process known as microbially induced calcite precipitation (MICP) is being investigated for engineering and material science applications. To model MICP process behavior in porous media, computational simulators must couple flow, transport, and relevant biogeochemical reactions. Changes in media porosity and permeability due to biomass growth and calcite precipitation, as well as their effects on one another must be considered. A comprehensive Darcy-scale model has been developed by Ebigbo et al. (Water Resour. Res. 48(7), W07519, 2012) and Hommel et al. (Water Resour. Res. 51, 3695–3715, 2015) and validated at different scales of observation using laboratory experimental systems at the Center for Biofilm Engineering (CBE), Montana State University (MSU). This investigation clearly demonstrates that a close synergy between laboratory experimentation at different scales and corresponding simulation model development is necessary to advance MICP application to the field scale. Ultimately, model predictions of MICP sealing of a fractured sandstone formation, located 340.8 m below ground surface, were made and compared with corresponding field observations. Modeling MICP at the field scale poses special challenges, including choosing a reasonable model-domain size, initial and boundary conditions, and determining the initial distribution of porosity and permeability. In the presented study, model predictions of deposited calcite volume agree favorably with corresponding field observations of increased injection pressure during the MICP fracture sealing test in the field. Results indicate that the current status of our MICP model now allows its use for further subsurface engineering applications, including well-bore cement sealing and certain fracture-related applications in unconventional oil and gas production.

Studies on heavy metal bioremediation through microbial-induced calcite precipitation (MICP) typically involve bioaugmentation approaches that use low calcium-to-urea ratios and target single contaminants. We present an investigation on the efficiency of soils' autochthonous ureolytic bacteria to simultaneously remediate multiple heavy metals and sequester carbon through urea hydrolysis and MICP on an urban soil containing excess Pb, Zn, Mn, Sr, Ba and Al. Soils were treated at a fixed urea concentration of 333 mM and increasing calcium content of 0, 50 and 333 mM to provide a range of carbonation potential. Urea hydrolysis (Ca2+ = 0 mM) did not produce quantifiable soil carbonation and mobilised Mn into the exchangeable fraction. Ca2+ at 50 mM delayed soils' autochthonous ureolytic activity and produced limited carbon and heavy metal mineralisation (CaCO3 = 0-0.7 %). 333 mM of Ca2+ inhibited urea hydrolysis however, if applied following urea hydrolysis, both carbon (CaCO3 = 4-7 %) and heavy metal (Pb, Zn, Mn, Sr and Ba) mineralisation were maximised. Urea hydrolysis and MICP were most successful in removing Pb and Zn from the exchangeable fraction (>85 %). However, the higher pH induced by urea hydrolysis at Ca2+ = 0-50 mM (∼9) compared to 333 mM (∼8.5) favoured partition of Pb into the oxyhydroxide fraction. Instead, partition of Zn, Mn, Sr and Ba into the soil carbonate fraction increased with increasing calcium, whilst there was no evidence of Al carbonation. The results of this study evidence the feasibility of biostimulation approaches to remediate multiple contaminants simultaneously through MICP, provide insights into multiple element's behaviour during urea hydrolysis and MICP and demonstrate carbon and element mineralisation are maximised at equimolar calcium-to-urea ratio of 333 mM.

Microbially induced calcite precipitation (MICP) is an emerging ground improvement technique that uses microbes to induce cementation between soil particles. To date, the majority of research has focused on exploring MICP with silica-rich sands; however, the present study investigates the process and efficacy of MICP in a carbonate-rich natural soil, and a comparison is made with benchmark silica-rich sands. MICP column experiments were performed with a range of treatment formulations to optimize and understand the MICP process in carbonate-rich soil. Performance was quantified using chemical (pH, urea, and ammonium concentrations) and physical measurements (TGA and LOI tests). Micro-scale characterization of the cemented soils was performed with XRD, SEM, and EDS, while shear-wave velocity (Vs) and unconfined compressive strength tests were performed to evaluate the effect of precipitated calcite on macroscopic engineering properties. Natural carbonates were found to have a significant impact on the MICP process, resulting in an increase in MICP efficiency of 23% and increases in precipitated calcite contents by as much as 82% when compared to benchmark silica-rich soils receiving similar treatments. These results suggest that the presence of natural carbonate minerals within soils may lower the energy barrier and act as preferential sites for calcite precipitation during the MICP process. Furthermore, SEM images highlighted the association of bacterial cells with precipitated calcite crystals, differences in calcite morphologies and more widespread cementation bonds in carbonate-rich soil when compared to silica sand. Generated cementation also resulted in a linear increase in Vs with increases in precipitated calcite contents for MICP treated carbonate-rich soil, consistent with past results for silica sands. Lastly, differences in yeast extract concentrations applied in treatment solutions were also found to significantly impact the development of ureolytic microbial capacity and the efficiency of the MICP process in the considered soils.

Mineral precipitation reactions in porous media can change the porosity and permeability of the rock formations. Predicting the rate of reaction and impacts on formation properties is challenging due to a lack of understanding of mineral precipitation reaction kinetics and mechanisms in porous media. This is furthermore challenging due to the highly heterogeneous nature of natural porous media. Here, we aim to develop a novel experimental platform leveraging 3D printing to facilitate replicable mineral precipitation experiments in controlled, heterogenous porous media systems. This requires fundamental understanding of the kinetics of mineral precipitation on the polymer materials used to fabricate the 3D printed porous media. In this work, we manipulate (via sulfonation) material surfaces (high impact polystyrene, HIPS) to promote calcite precipitation from supersaturated solutions to inform the design of synthetic subsurface systems. Calcite precipitation on HIPS films of varied surface sulfonation is confirmed using X-ray diffraction (XRD) analysis and weight-based precipitation experiments where increased precipitation with increased surface functionalization and solution saturation index are observed. This approach is then applied to 3D-printed porous media to enhance understanding of geochemical reactions, specifically calcite precipitation. Three dimensional images of Bentheimer Sandstone are used as the basis for 3D-printed porous media samples. Two 3D-printed samples were functionalized with acid to activate the surface and promote mineral precipitation. Functionalized and unfunctionalized samples underwent calcite precipitation core flooding experiments with oversaturated calcite solutions for 96 hours. Three dimensional X-ray micro-CT imaging revealed calcite growth in functionalized samples, with a calcite volume fraction of approximately 2.6% and a substantial reduction in porosity. Unfunctionalized samples exhibited diminished calcite precipitation and porosity changes. These findings demonstrate that reactive 3D-printed porous media can provide a versatile geochemical modeling and experimentation platform. Functionalizing 3D printed samples enhances reactivity, allowing investigations of mineral precipitation processes in complex porous media. This research highlights the potential for further exploration of 3D-printed media in various geochemical contexts.

Microbially induced calcite precipitation (MICP) is widely gaining popularity as a bio-mediated technique for soil stabilisation and recycling in an eco-friendly way. In the present study, MICP was employed to enhance the geotechnical properties of coal mine waste, a heterogeneous waste material unsuitable for engineering applications. To ensure the field-scale applicability of MICP and to address the shortcomings of the uniform distribution of calcite precipitations in high-fines-content matrices, a novel bacterial incorporation strategy was developed. This approach employed a native ureolytic bacterium, Sporosarcina pasteurii PS3A cells, for calcium carbonate precipitation through urea hydrolysis, resulting in the formation of mineral bridges that improved particle binding and reduced permeability. The chemical composition of the biogenic precipitate under different treatment conditions was probed by X-ray photoelectron spectroscopy, and its morphology was assessed using field-emission scanning electron microscopy. A ~ 17-fold increase in unconfined compressive strength in samples containing 22% fines was observed post-treatment. Optimisation of bacterial concentrations and cementitious solution molarity enabled precise control over volumetric shrinkage, which was reduced to 1-5%, improving dimensional stability across treated soils. The ultrasonic pulse velocity testing confirmed cementation, with a strong empirical correlation to unconfined compressive strength. These findings establish the necessity and effectiveness of targeted methodologies for applying MICP to fine-grained industrial wastes, advancing its viability as a sustainable alternative to conventional stabilisation techniques within the framework of the circular economy and low-carbon geotechnical engineering.

Microbially Induced Calcite Precipitation (MICP) is a bio-mediated cementation process that can improve the engineering properties of granular soils through the precipitation of calcite. The process is made possible by soil microorganisms containing urease enzymes, which hydrolyze urea and enable carbonate ions to become available for precipitation. While most researchers have injected non-native ureolytic bacteria to complete bio-cementation, enrichment of native ureolytic microorganisms may enable reductions in process treatment costs and environmental impacts. In this study, a large-scale bio-cementation experiment involving two 1.7-meter diameter tanks and a complementary soil column experiment were performed to investigate biogeochemical differences between bio-cementation mediated by either native or augmented (Sporosarcina pasteurii) ureolytic microorganisms. Although post-treatment distributions of calcite and engineering properties were similar between approaches, the results of this study suggest that significant differences in ureolysis rates and related precipitation rates between native and augmented microbial communities may influence the temporal progression and spatial distribution of bio-cementation, solution biogeochemical changes, and precipitate microstructure. The role of urea hydrolysis in enabling calcite precipitation through sustained super-saturation following treatment injections is explored.

Microbially induced calcite precipitation (MICP) using ureolytic bacteria has been investigated to improve the engineering properties of soil. Urease, produced by ureolytic bacteria, can hydrolyse urea to drive the biogeochemical reaction in MICP. The goal of this study was to use changes in electrical conductivity (EC) and pH values from the urea hydrolysis test as an indicator to monitor the ureolytic activities of bacteria before the MICP process and using this indicator to maintain a consistent MICP treatment. Laboratory experiments were conducted to establish the relationship between the EC and pH values and unconfined compression strength (UCS) of MICP-treated soil. The EC and pH values of the mixed solution were measured after adding bacterial suspension into urea solution. Then, the bacterial suspension was mixed with a sand sample and cementation medium to drive the MICP process. The results showed that, once the bacterial suspension was mixed with urea, the EC and pH values of the mixed solution increased immediately due to urea hydrolysis. The optimum EC and pH values at 60 min were found to be 1·50–1·80 mS/cm and 8·82–9·02, respectively, to achieve consistent UCS performance of MICP-treated specimens with 0·25 M calcium (Ca) cementation medium.