Metabolism-Induced CaCO3 Biomineralization During Reactive Transport in a Micromodel: Implications for Porosity Alteration

A comprehensive review of recent advancements in microbial-induced mineralization: biosynthesis and mechanism, with potential implementation in various environmental, engineering, and medical sectors

Biomineralization has garnered profuse attention in multidisciplinary fields. Using this strategy, living things, including eukaryotes or prokaryotes, mediate the uptake of ions from the surrounding environment, followed by assembling and depositing them as greatly configured structures inside the organic matrix. The generated biominerals, including nanomaterials, possess outstanding hierarchical structures that exceed their chemically synthesized counterparts. Despite the significant progress achieved in microbial-mediated mineralization, several key knowledge gaps remain, including mechanisms controlling biomineralization pathways and the impact of environmental factors on mineral morphology, crystallinity, and stability. This review provides a comprehensive description of this biomineralization, which can be categorized into controlled, influenced, and induced biomineralization. Interestingly, we highlighted biologically-induced mineralization approaches, such as photosynthesis, methane oxidation, and nitrogen-based metabolic pathways, and identified various chemical interactions during mineral production following analytical chemistry. This review also extensively delineates updates on application of biominerals across all fields, commencing with the remediation of deleterious pollutants and biominerals exploited in industrial sectors, moving on to using them to reinforce soil, generate biocement for construction, and delving into their utilization in pharmaceutical applications to deliver drugs, repair teeth and bones, and combat cancer and pathogenic microorganisms. Moreover, the review outlines the drawbacks and adequate solutions for biomineralization, particularly CaCO₃-mediated processes, such as the generation of ammonium and nitrate during the CaCO₃ precipitation process and the relatively slow rate of microbial-mediated mineralization. Biomineralization inspired the fabrication of smart biomaterials, which combine biological advantages. Overall, this comprehensive review discusses updated research and highlights potential approaches to future studies.

A review of microfluidic approaches for carbon capture and storage research

The reliance on fossil fuels for the increasing global energy demand necessitates the advancement of carbon capture and storage technologies to mitigate anthropogenic CO2 emissions. However, conventional experimental platforms have reached their practical limitations, stagnating further advancements in optimizing carbon capture and storage (CCS) processes. Microfluidic technologies have emerged as promising tools for investigating and optimizing CCS processes at the microscale, offering precise control over gas-liquid interactions, reaction kinetics, and multiphase flow dynamics, which would be very challenging with conventional macroscale platforms. This review uniquely consolidates carbon capture and storage advancements, providing a structured approach that starts from fundamental mechanisms and systematically progresses to advanced microfluidic-assisted CCS strategies. Unlike prior reports, this review demonstrates how microfluidics complements conventional macroscale approaches and outperforms in certain aspects for studying CO2 capture and storage through specific experimental examples. The carbon capture section explores microfluidic approaches for physical absorption, chemical absorption, and adsorption, highlighting their advantages over conventional methods. The discussion extends to key mass transfer models, microchannel geometries, and flow regimes that dictate CO2 dissolution rates and interfacial transport phenomena. The carbon storage section examines microfluidic investigations into carbon mineralization and geological sequestration, providing insights into pore-scale trapping mechanisms, mineralization kinetics, and enhanced storage efficiency. The integration of real-time analytical techniques has further facilitated high-resolution quantification of CO2 transport and reaction dynamics. Despite significant progress, challenges remain in scaling microfluidic findings to field applications, accurately mimicking reservoir conditions, and developing reactive microfluidic platforms for in situ mineralization studies. This review aims to show the pivotal role of microfluidics in accelerating CCS innovation.

Modeling the Migration and Growth of Shewanella Oneidensis MR-1 in a Diffusion-Dominated Microfluidic Gradient Chamber Under the Influence of an Antibiotic Concentration Gradient

Motility and chemotaxis allow bacteria to migrate from areas that become depleted in energy yielding substrates to more favorable locations, possibly enhancing the biodegradation of pollutants in soil and groundwater. However, in some cases substrates are co-mingled with one or more toxic solutes that inhibit pollutant degradation and/or microbial growth, and the impacts on motility and chemotaxis represent a knowledge gap. In this study, a one-dimensional diffusion reaction model is developed and used to simulate dissimilatory biological reduction of nitrate to ammonia (DNRA) presented in a previously published microfluidic gradient chamber (MGC) experiment, where spatial abundances of Shewanella oneidensis MR-1 cells were recorded over 5 days in a diffusion limited porous media domain as it degraded nitrate and lactate introduced from opposite boundaries, and at one boundary co-mixed with the antibiotic ciprofloxacin. The model considers S. oneidensis chemotaxis toward nitrate and nitrite, random motility, and growth inhibition by ciprofloxacin. Parameters were adjusted within ranges commonly reported in the literature to obtain results that agreed with the data. Simulation results indicate that motility and not chemotaxis, in combination with inhibition of cell growth by ciprofloxacin, controls the distribution of cells in the toxic region (containing ciprofloxacin) of the MGC. This suggests that cell motility may facilitate nitrate removal in soil and groundwater by enabling microorganisms to migrate toward nitrate contaminated regions with elevated antibiotic concentrations.

Microfluidics for studying the deep underground biosphere: from applications to fundamentals

In this review, selected examples are presented to demonstrate how microfluidic approaches can be utilized for investigating microbial life from deep geological environments, both from practical and fundamental perspectives. Beginning with the definition of the deep underground biosphere and the conventional experimental techniques employed for these studies, the use of microfluidic systems for accessing critical parameters of deep life in geological environments at the microscale is subsequently addressed (high pressure, high temperature, low volume). Microfluidics can simulate a range of environmental conditions on a chip, enabling rapid and comprehensive studies of microbial behavior and interactions in subsurface ecosystems, such as simulations of porous systems, interactions among microbes/microbes/minerals, and gradient cultivation. Transparent microreactors allow real-time, noninvasive analysis of microbial activities (microscopy, Raman spectroscopy, FTIR microspectroscopy, etc.), providing detailed insights into biogeochemical processes and facilitating pore-scale analysis. Finally, the current challenges and opportunities to expand the use of microfluidic methodologies for studying and monitoring the deep biosphere in real time under deep underground conditions are discussed.

Statistical and machine learning analysis for the application of microbially induced carbonate precipitation as a physical barrier to control seawater intrusion

Seawater intrusion in coastal aquifers is a significant problem that can be addressed through the construction of subsurface dams or physical cut-off barriers. An alternative method is the use of microbially induced carbonate precipitation (MICP) to reduce the hydraulic conductivity of the porous medium and create a physical barrier. However, the effectiveness of this method depends on various factors, and the scientific literature presents conflicting results, making it challenging to generalise the findings. To overcome this challenge, a statistical and machine learning (ML) approach is employed to infer the causes for the reduction in hydraulic conductivity and identify the optimum MICP parameters for preventing seawater intrusion. The study involves data curation, exploratory analysis, and the development of various models to fit the input data (k-Nearest Neighbours - kNN, Support Vector Regression - SVR, Random Forests - RF, Gradient Boosting - XgBoost, Linear model with interaction terms, Ensemble learning algorithms with weighted averages - EnL-WA and stacking - EnL-Stack). The models performed reasonably well in the region where permeability reduction is sensitive to carbonate increase capturing the permeability reduction profile with respect to cementation level while demonstrating that they can be used in initial assessments of the specific conditions (e.g., soil properties). The best performing algorithms were the EnL-Stack and RF followed by XgBoost and SVR. The MICP method is effective in reducing hydraulic conductivity provided that the various biochemical parameters are optimised. Critical biochemical parameters for successful MICP formulations are the bacterial optical density, the urease activity, calcium chloride concentration and flow rate as well as the interaction terms across the properties of the porous media and the biochemical parameters. The models were used to identify the optimum MICP formulation for various porous media properties and the maximum permeability reduction profiles across cementation levels have been derived.

Unveiling the role of pore characteristics in sludge dewatering: Visualization by Nano-CT and micromodel study

The solid-liquid separation is an indispensable and primary link in the process of sludge treatment and disposal. The past research was focused primarily on the technique explorations of sludge dewatering and always disregarded the internal pore structure and water migration behavior in sludge. In this work, the real three-dimensional pore structure of sludge was obtained by Nano-CT. Based on this, a pore-scale heterogeneous sludge micromodel was firstly presented, and the water flooding experiment was carried out to visualize the water migration behavior. The results showed that the sludge structure transformed from sheet-like floc to microsphere particles, and then agglomerated into large globular granules during anaerobic ammonia oxidation. And the equivalent pore size increases from 342 μm to 617 μm, improving the sludge dewaterability characterized by capillary suction time (CST). The most significant implication of this work was revealing the critical role of invalid connected pore in sludge dewatering. Such pore was not contributed to fluid flow but the circulating vortex in it even induced energy dissipation, thus deteriorated the sludge dewaterability. This work may be helpful to understand the critical role of pore characteristic in water migration and shed light on the new dewatering techniques from the perspective of regulating sludge structure.

Steerable artificial magnetic bacteria with target delivery ability of calcium carbonate for soil improvement

The microbial-induced carbonate precipitation (MICP) has acquired significant attention due to its immense potential in sustainable engineering applications, particularly in soil improvement. However, the precise control of microbial-induced calcium carbonate precipitation remains a formidable challenge in engineering practices, owing to the uncertain movement paths of bacteria and the nonuniform distribution of soil pores. Taking inspiration from targeted therapy in medicine, this paper presents novel research on the development and validation of magnetically responsive bacteria. These bacteria demonstrate the ability to target calcium carbonate precipitation in a microfluidic chip, thereby promoting an environmentally friendly and ecologically sustainable biomineralization paradigm. The study focuses on investigating the migration of magnetite nanoparticles (MNPs) in aqueous solutions and enhancing the stability of MNP culture liquids. A specially designed microfluidic chip is utilized to simulate natural sand particles and their pores, while an external magnetic field is applied to precisely control the movement path of the artificial magnetic bacteria, enabling targeted precipitation of calcium carbonate at the micron-scale. Verification of the engineered artificial magnetic bacteria and their ability to induce calcium carbonate precipitation is conducted through SEM-EDS analysis, microfluidic chip observations, and the application of the K-means algorithm and ImageJ software to analyze calcium carbonate formation. The influence of the concentration of magnetic nanoparticles on the calcium carbonate production rate was also studied. The results confirm the potential of the artificial magnetic bacteria for future engineering applications. KEY POINTS: • Sporosarcina pasteurii is first time successfully engineered into artificial magnetic bacteria. • The artificial magnetic bacteria show excellent performance of targeted transportation and directional deposition of CaCO3 in microfluidic chip. • The emergence of artificial magnetic bacteria promotes paradigm shift of next generation environmentally friendly biomineralization.

Controlling pore-scale processes to tame subsurface biomineralization

Microorganisms capable of biomineralization can catalyze mineral precipitation by modifying local physical and chemical conditions. In porous media, such as soil and rock, these microorganisms live and function in highly heterogeneous physical, chemical and ecological microenvironments, with strong local gradients created by both microbial activity and the pore-scale structure of the subsurface. Here, we focus on extracellular bacterial biomineralization, which is sensitive to external heterogeneity, and review the pore-scale processes controlling microbial biomineralization in natural and engineered porous media. We discuss how individual physical, chemical and ecological factors integrate to affect the spatial and temporal control of biomineralization, and how each of these factors contributes to a quantitative understanding of biomineralization in porous media. We find that an improved understanding of microbial behavior in heterogeneous microenvironments would promote understanding of natural systems and output in diverse technological applications, including improved representation and control of fluid mixing from pore to field scales. We suggest a range of directions by which future work can build from existing tools to advance each of these areas to improve understanding and predictability of biomineralization science and technology.

Microfluidics as an Emerging Platform for Exploring Soil Environmental Processes: A Critical Review

Investigating environmental processes, especially those occurring in soils, calls for innovative and multidisciplinary technologies that can provide insights at the microscale. The heterogeneity, opacity, and dynamics make the soil a "black box" where interactions and processes are elusive. Recently, microfluidics has emerged as a powerful research platform and experimental tool which can create artificial soil micromodels, enabling exploring soil processes on a chip. Micro/nanofabricated microfluidic devices can mimic some of the key features of soil with highly controlled physical and chemical microenvironments at the scale of pores, aggregates, and microbes. The combination of various techniques makes microfluidics an integrated approach for observation, reaction, analysis, and characterization. In this review, we systematically summarize the emerging applications of microfluidic soil platforms, from investigating soil interfacial processes and soil microbial processes to soil analysis and high-throughput screening. We highlight how innovative microfluidic devices are used to provide new insights into soil processes, mechanisms, and effects at the microscale, which contribute to an integrated interrogation of the soil systems across different scales. Critical discussions of the practical limitations of microfluidic soil platforms and perspectives of future research directions are summarized. We envisage that microfluidics will represent the technological advances toward microscopic, controllable, and in situ soil research.

Effect of poly(acrylic acid) on crystallization of calcium carbonate in a hydrogel

As carbonate ions are diffused into an agarose hydrogel containing calcium ions and poly(acrylic acid), elliptical and spherical calcites are controllably formed depending on the concentration of poly(acrylic acid) and the position of the hydrogel.

Review of Microfluidic Devices and Imaging Techniques for Fluid Flow Study in Porous Geomaterials

Understanding transport phenomena and governing mechanisms of different physical and chemical processes in porous media has been a critical research area for decades. Correlating fluid flow behaviour at the micro-scale with macro-scale parameters, such as relative permeability and capillary pressure, is key to understanding the processes governing subsurface systems, and this in turn allows us to improve the accuracy of modelling and simulations of transport phenomena at a large scale. Over the last two decades, there have been significant developments in our understanding of pore-scale processes and modelling of complex underground systems. Microfluidic devices (micromodels) and imaging techniques, as facilitators to link experimental observations to simulation, have greatly contributed to these achievements. Although several reviews exist covering separately advances in one of these two areas, we present here a detailed review integrating recent advances and applications in both micromodels and imaging techniques. This includes a comprehensive analysis of critical aspects of fabrication techniques of micromodels, and the most recent advances such as embedding fibre optic sensors in micromodels for research applications. To complete the analysis of visualization techniques, we have thoroughly reviewed the most applicable imaging techniques in the area of geoscience and geo-energy. Moreover, the integration of microfluidic devices and imaging techniques was highlighted as appropriate. In this review, we focus particularly on four prominent yet very wide application areas, namely “fluid flow in porous media”, “flow in heterogeneous rocks and fractures”, “reactive transport, solute and colloid transport”, and finally “porous media characterization”. In summary, this review provides an in-depth analysis of micromodels and imaging techniques that can help to guide future research in the in-situ visualization of fluid flow in porous media.

Aerobic and anaerobic removal of lead and mercury via calcium carbonate precipitation mediated by statistically optimized nitrate reductases

The nonbiodegradability nature of heavy metals renders them resident in food chain and subsequently, destructing the entire ecosystem. Therefore, this study aimed to employ nitrate reduction-driven calcium carbonate precipitation in remediation of lead and mercury aerobically and anaerobically by Proteus mirabilis 10B, for the first time. Initially, Plackett-Burman design was employed to screen of 16 independent variables for their significances on periplasmic (NAP) and membrane-bound (NAR) nitrate reductases. The levels for five significant variables and their interaction effects were further optimized by central composite design. The maximum activities of NAP and NAR recorded 2450 and 3050 U/mL by 2-fold enhancement, comparing with non-optimized medium. Under aerobic and anaerobic optimized remediation conditions, the changes in media chemistry revealed positive correlation among bacterial growth, nitrate reductase activity, pH, NO₃^- and NO₂^- consumption and removal of Ca²⁺, Pb²⁺ and Hg²⁺. Subsequently, the remediated precipitates were subjected to mineralogical analysis; energy dispersive X-ray patterns exhibited characteristic peaks of C, O and Ca in addition to Pb and Hg. Scanning electron microscope depicted the presence of bacterial imprints and protrusions on rough and smooth surface bioliths. However, X-ray diffraction indicated entrapment of PbCO₃, Pb₂O, CaPbO₃, Hg and Hg₂O in calcite lattice. Interestingly, such approach is feasible, efficient, cost-effective and ecofriendly for heavy metals remediation.

Studying key processes related to CO2 underground storage at the pore scale using high pressure micromodels

Micromodels experimentation for studying and understanding CO₂ geological storage mechanisms at the pore scale.

Pore-Scale Analysis of Calcium Carbonate Precipitation and Dissolution Kinetics in a Microfluidic Device

In this work, we have characterized the calcium carbonate (CaCO₃) precipitates over time caused by reaction-driven precipitation and dissolution in a micromodel. Reactive solutions were continuously injected through two separate inlets, resulting in transverse-mixing induced precipitation during the precipitation phase. Subsequently, a dissolution phase was conducted by injecting clean water (pH = 4). The evolution of precipitates was imaged in two and three dimensions (2-, 3-D) at selected times using optical and confocal microscopy. With estimated reactive surface area, effective precipitation and dissolution rates can be quantitatively compared to results in the previous works. Our comparison indicates that we can evaluate the spatial and temporal variations of effective reactive areas more mechanistically in the microfluidic system only with the knowledge of local hydrodynamics, polymorphs, and comprehensive image analysis. Our analysis clearly highlights the feedback mechanisms between reactions and hydrodynamics. Pore-scale modeling results during the dissolution phase were used to account for experimental observations of dissolved CaCO₃ plumes with dissolution of the unstable phase of CaCO₃. Mineral precipitation and dissolution induce complex dynamic pore structures, thereby impacting pore-scale fluid dynamics. Pore-scale analysis of the evolution of precipitates can reveal the significance of chemical and pore structural controls on reaction and fluid migration.

Real rock-microfluidic flow cell: A test bed for real-time in situ analysis of flow, transport, and reaction in a subsurface reactive transport environment

Physical, chemical, and biological interactions between groundwater and sedimentary rock directly control the fundamental subsurface properties such as porosity, permeability, and flow. This is true for a variety of subsurface scenarios, ranging from shallow groundwater aquifers to deeply buried hydrocarbon reservoirs. Microfluidic flow cells are now commonly being used to study these processes at the pore scale in simplified pore structures meant to mimic subsurface reservoirs. However, these micromodels are typically fabricated from glass, silicon, or polydimethylsiloxane (PDMS), and are therefore incapable of replicating the geochemical reactivity and complex three-dimensional pore networks present in subsurface lithologies. To address these limitations, we developed a new microfluidic experimental test bed, herein called the Real Rock-Microfluidic Flow Cell (RR-MFC). A porous 500μm-thick real rock sample of the Clair Group sandstone from a subsurface hydrocarbon reservoir of the North Sea was prepared and mounted inside a PDMS microfluidic channel, creating a dynamic flow-through experimental platform for real-time tracking of subsurface reactive transport. Transmitted and reflected microscopy, cathodoluminescence microscopy, Raman spectroscopy, and confocal laser microscopy techniques were used to (1) determine the mineralogy, geochemistry, and pore networks within the sandstone inserted in the RR-MFC, (2) analyze non-reactive tracer breakthrough in two- and (depth-limited) three-dimensions, and (3) characterize multiphase flow. The RR-MFC is the first microfluidic experimental platform that allows direct visualization of flow and transport in the pore space of a real subsurface reservoir rock sample, and holds potential to advance our understandings of reactive transport and other subsurface processes relevant to pollutant transport and cleanup in groundwater, as well as energy recovery.

Toward Reservoir-on-a-Chip: Fabricating Reservoir Micromodels by in Situ Growing Calcium Carbonate Nanocrystals in Microfluidic Channels

We introduce a novel and simple method to fabricate calcium carbonate (CaCO₃) micromodels by in situ growing a thin layer of CaCO₃ nanocrystals with a thickness of 1-2 μm in microfluidic channels. This approach enables us to fabricate synthetic CaCO₃ reservoir micromodels having surfaces fully covered with calcite, while the dimensions and geometries of the micromodels are controllable on the basis of the original microfluidic channels. We have tuned the wettability of the CaCO₃-coated microchannels at simulated oil reservoir conditions without introducing any chemical additives to the system; thus the resulting oil-wet surface makes the micromodel more faithfully resemble a natural carbonate reservoir rock. With the advantage of its excellent optical transparency, the micromodel allows us to directly visualize the complex multiphase flows and geochemical fluid-calcite interactions by spectroscopic and microscopic imaging techniques. The CaCO₃-coated microfluidic channels provide new capabilities as a micromodel system to mimic real carbonate reservoir properties, which would allow us to perform a water-oil displacement experiment in small-volume samples for the rapid screening of candidate fluids for enhanced oil recovery (EOR). The immiscible fluid displacement process within carbonate micromodels has been demonstrated showing the water-oil-carbonate interactions at pore-scale in real time by fluorescence microscopic imaging.

Impact of Mineral Precipitation on Flow and Mixing in Porous Media Determined by Microcomputed Tomography and MRI

Precipitation reactions influence transport properties in porous media and can be coupled to advective and dispersive transport. For example, in subsurface environments, mixing of groundwater and injected solutions can induce mineral supersaturation of constituents and drive precipitation reactions. Magnetic resonance imaging (MRI) and microcomputed tomography (μ-CT) were employed as complementary techniques to evaluate advection, dispersion, and formation of precipitate in a 3D porous media flow cell. Two parallel fluids were flowed concentrically through packed glass beads under two relative flow rates with Na₂CO₃ and CaCl₂ in the inner and outer fluids, respectively. CaCO₃ became supersaturated and formed a precipitate at the mixing interface between the two solutions. Spatial maps of changing local velocity fields and dispersion in the flow cell were generated from MRI, while high resolution μ-CT imaging visualized the precipitate formed in the porous media. Formation of a precipitate minimized dispersive and advective transport between the two fluids and the shape of the precipitation front was influenced by the relative flow rates. This work demonstrates that the combined use of MRI and μ-CT can be highly complementary in the study of reactive transport processes in porous media.