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DOE OSTI2020

Addressing wellbore integrity and thief zone permeability using microbially-induced calcium carbonate precipitation (MICP): A field demonstration

Microbially-induced calcium carbonate precipitation (MICP) is an emerging biotechnology for wellbore integrity applications including sealing defects in wellbore cement and modifying the permeability of rock formations. The goal of this field demonstration was to characterize a failed waterflood injection well and provide proof of principle that MICP can reduce permeability in the presence of oil using conventional oilfield fluid delivery methods. Here we compared well logs performed at the time the well was drilled with ultrasonic logs, sonic cement evaluation, and temperature logs conducted after the well failed. Analysis of these logs suggested that, rather than entering the target waterflood formation, injectate was traveling through defects in the well cement to a higher permeability sandstone layer above the target formation. Sporosarcina pasteurii cultures and urea-calcium media were delivered 2290 ft (698 m) below ground surface using a 3.75 gal (14.2 L) slickline dump bailer to promote mineralization in the undesired flow paths. By Day 6 and after 25 inoculum and 49 calcium media injections, the injectivity [gpm/psi] had decreased by approximately 70%. This demonstration shows that 1) common well logs can be used to identify scenarios where MICP can be employed to reduce system permeability, remediate leakage pathways, and improve waterflood efficiency, and 2) MICP can occur in the presence of hydrocarbons.

42 ENGINEERING↗

DOE OSTI2020

Microbial and Geochemical Dynamics of an Aquifer Stimulated for Microbial Induced Calcite Precipitation (MICP)

Microbially induced calcite precipitation (MICP) is an alternative to existing soil stabilization techniques for construction and erosion. As with any biologically induced process in soils or aquifers, it is important to track changes in the microbial communities that occur as a result of the treatment. Our research assessed how native microbial communities developed in response to injections of reactants (dilute molasses as a carbon source; urea as a source of nitrogen and alkalinity) that promoted MICP in a shallow aquifer. Microbial community composition (16S rRNA gene) and ureolytic potential (ureC gene copy numbers) were also measured in groundwater and artificial sediment. Aquifer geochemistry showed evidence of sulfate reduction, nitrification, denitrification, ureolysis, and iron reduction during the treatment. The observed changes in geochemistry corresponded to microbial community succession in the groundwater and this matched parallel geophysical and mineralogical evidence of calcite precipitation in the aquifer. We detected an increase in the number of ureC genes in the microbial communities at the end of the injection period, suggesting an increase in the abundance of microbes possessing this gene as needed to hydrolyze urea and stimulate MICP. We identify geochemical and biological markers that highlight the microbial community response that can be used along with geophysical and geotechnical evidence to assess progress of MICP.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2020

Controls on reservoir properties in organic-matter-rich shales: Insights from MICP analysis

Mercury injection capillary pressure (MICP) analysis was used to study organic-matter-rich Devonian shales varying in maturity from marginally mature to postmature to discuss controls on drainage and imbibition in shale reservoirs. Six samples come from the New Albany Shale; their total organic carbon (TOC) ranged from 3.3–8.4 % and vitrinite reflectance (R o ) from 0.54–1.42 %. One Marcellus Shale sample with R o 2.50 % was used to extend the maturity range to the advanced dry gas window. Three coal samples of varying rank were also included for comparison. Porosity of the shales ranges from 1.5–5.0 %, and MICP-derived permeability ranges from 0.17–9.9 mD. Injection capillary pressure curves have a range of entry pressures from 0.055 to0.421 MPa, and no relationship of entry pressure with maturity was revealed. Maturity, however, has an influence on pore size distribution, with the higher-maturity samples having significantly lower volumes of pores with throats less than 10 nm in diameter. Withdrawal capillary pressure curves document a wide range of withdrawal efficiencies from 55 % to almost 100 %, and pores having throats between 3–50 nm in diameter play a major role in the ability of mercury to be released from the pore system. The obtained data provide valuable information about shale properties and their behavior not only in the air-mercury system but also under reservoir conditions.

02 PETROLEUM↗

DOE OSTI2020

Project Methods to Enhance Wellbore Cement Integrity with Microbially-Induced Calcite Precipitation (MICP) (Final Scientific/Technical Report)

The goal of this project was to develop improved methods for sealing compromised wellbore cement in leaking oil and gas wells, thereby reducing the risk of unwanted upward fluid migration. Novel methods for improving wellbore integrity, such as microbially induced calcite precipitation (MICP), can reduce leakage potential, improve the safety of fossil fuel extraction, improve the public perception of hydraulic fracturing, and promote environmentally-prudent unconventional oil and gas development. Microbes, with the urease enzyme, can catalyze the chemical reaction of urea hydrolysis to induce the precipitation of calcium carbonate which can be used as a cementitious material to seal leakage pathways. In this project, methods to promote robust bio-composite cementitious materials were designed and tested in the laboratory. Scale-up of those methods were tested in meso-scale reactor systems and in field applications. In this report, in Section One, we describe laboratory efforts to develop injection strategies to promote precipitation in wellbore analogs and determine the strength of the bio-composite cements as compared to fine cement. In Section Two, we describe the efforts to scale up the work and study the use of materials that can be used in field application, for example exploring the use of calcium chloride ice melt or urea fertilizer as source chemicals. In Section Three, the three field trials (methods and results) performed as part of the project are described and summarized. At the end of the report is a comprehensive summary and conclusion section which highlights the key findings of the project. The work performed during this project significantly advanced the technology readiness level (TRL) of the MICP wellbore sealing strategy.

02 PETROLEUM↗

DOE OSTI2020

Methods to Enhance Wellbore Cement Integrity with Microbially-Induced Calcite Precipitation (MICP) (Final Scientific/ Technical Report)

03 NATURAL GAS↗

DOE OSTI2022

Citizen Green #1 Well: MICP and Pycnometry Data, Sidewall Cores

This submission includes information on helium pycnometry & MICP measurements conducted on sidewall sub-samples from the Citizen Green #1 well drilled on King Island, CA (API 07720688) as part of the WESTCARB partnership basin characterization effort. Cores were acquired with a rotary sidewall tool at a range of depths. See the sidewallCore submission for additional formation data.

Citizen Green↗

DOE OSTI2024

Beyond the Surface: Non-Invasive Low-Field NMR Analysis of Microbially-Induced Calcium Carbonate Precipitation in Shale Fractures

Microbially-induced calcium carbonate precipitation (MICP) is a biological process in which microbially-produced urease enzymes convert urea and calcium into solid calcium carbonate (CaCO 3 ) deposits. MICP has been demonstrated to reduce permeability in shale fractures under elevated pressures, raising the possibility of applying this technology to enhance shale reservoir storage safety. For this and other applications to become a reality, non-invasive tools are needed to determine how effectively MICP seals shale fractures at subsurface temperatures. In this study, two different MICP strategies were tested on 2.54 cm diameter and 5.08 cm long shale cores with a single fracture at 60 °C. Flow-through, pulsed-flow MICP-treatment was repeatedly applied to Marcellus shale fractures with and without sand (“proppant”) until reaching approximately four orders of magnitude reduction in apparent permeability, while a single application of polymer-based “immersion” MICP-treatment was applied to an Eagle Ford shale fracture with proppant. Low-field nuclear magnetic resonance (LF-NMR) and X-Ray computed microtomography (micro-CT) techniques were used to assess the degree of biomineralization. With the flow-through approach, these tools revealed that while CaCO 3 precipitation occurred throughout the fracture, there was preferential precipitation around proppant. Without proppant, the same approach led to premature sealing at the inlet side of the core. In contrast, immersion MICP-treatment sealed off the fracture edges and showed less mineral precipitation overall. This study highlights the use of LF-NMR relaxometry in characterizing fracture sealing and can help guide NMR logging tools in subsurface remediation efforts.

MICP↗

DOE OSTI2026

Multi-omic characterization of a soil microbial consortium reveals critical role of succinate and glutamate metabolism during calcium carbonate precipitation

Microbially induced calcium carbonate precipitation (MICP) holds potential for use in soil stabilization and carbon sequestration, with the overall efficiency of the process being a major determinant for use in many environmental and civil engineering applications. While the biogeochemical pathways and enzymes driving MICP are known, the microbial metabolic networks and community dynamics underlying such precipitation remain poorly characterized. To address this gap, we developed a four-member consortium of soil bacteria (Curtobacterium flaccumfaciens, Rhodococcus qingshengii, Microbacterium sp., and Bacillus toyonensis), termed carbon storing consortium - A (CSC-A), that is capable of MICP. Prior work shows that MICP production is higher in CSC-A compared to the sum of carbonate produced by each member, suggesting carbonate production is driven by consortium dynamics. To that end we used a multi-omic integration approach of genomics, transcriptomics, and metabolomics to investigate potential inter-species interactions that may influence the MICP phenotype. Genomic life history characterizations identified evidence of niche specialization by B. toyonensis and Microbacterium, while metatranscriptomic analysis suggests R. qingshengii is a keystone species during growth in urea. By comparing individual species’ metabolomes to the metabolic profile of a shared well of precipitated metabolites, we identified over 200 metabolites predicted to be produced or consumed by CSC-A members. Integrating both data types to search the KEGG reactome highlighted a network centered around glutamine metabolism and branched chain amino acid biosynthesis under regulation during CSC-A growth in urea. Succinate metabolism was also a major node in this network and laboratory assays confirmed that increasing the amount of succinate in the growth medium leads to increased carbonate precipitation by CSC-A, a critical confirmation of our modeling approach. By isolating and identifying the interconnected metabolic components underlying MICP in CSC-A, we identified keystone taxa, metabolites, and pathways important for future optimization of the application of this consortia to carbonate precipitation.

carbon storing consortium - A (CSC-A)↗

DOE OSTI2024

Meta-omics reveals role of photosynthesis in microbially induced carbonate precipitation at a CO2-rich geyser

Abstract Microbially induced carbonate precipitation (MICP) is a natural process with potential biotechnological applications to address both carbon sequestration and sustainable construction needs. However, our understanding of the microbial processes involved in MICP is limited to a few well-researched pathways such as ureolytic hydrolysis. To expand our knowledge of MICP, we conducted an omics-based study on sedimentary communities from travertine around the CO2-driven Crystal Geyser near Green River, Utah. Using metagenomics and metaproteomics, we identified the community members and potential metabolic pathways involved in MICP. We found variations in microbial community composition between the two sites we sampled, but Rhodobacterales were consistently the most abundant order, including both chemoheterotrophs and anoxygenic phototrophs. We also identified several highly abundant genera of Cyanobacteriales. The dominance of these community members across both sites and the abundant presence of photosynthesis-related proteins suggest that photosynthesis could play a role in MICP at Crystal Geyser. We also found abundant bacterial proteins involved in phosphorous starvation response at both sites suggesting that P-limitation shapes both composition and function of the microbial community driving MICP.

Violette, Marlene J.↗

DOE OSTI2020

Direct Injection of Biomineralizing Agents to Restore Injectivity and Wellbore Integrity

Summary In this manuscript, we describe the second of two field demonstrations of microbially induced calcium carbonate precipitation (MICP) performed in a failed waterflood injection well in Indiana. In 2012, fracture-related flow pathways developed in the wellbore cement, causing injection water to bypass the oil-bearing formation and enter a high-permeability sandstone thief zone, thereby substantially decreasing injection pressure. In the first field demonstration, our study team characterized the well's mode of failure and successfully applied MICP to decrease flow through the defective cement. However, because the MICP treatment was conducted using a bailer delivery system, the degree of permeability reduction achievable was not adequate to fully restore the historic injection pressure of 1,400 psi at 1 gal/min. For the second field demonstration (reported herein), a direct injection system was developed that substantially increased the injection volume of MICP-promoting fluids. Two strategies were implemented to produce more ureolytic microbes: resuspending concentrated frozen cells immediately before injection and scaling up the bioreactor growth capacity. Multiple pulses of microbes and urea-calcium media were pumped into a string of 1-in.-diameter tubing separated by brine spacers and injected continuously at a flow rate of 3.4 to 1.4 gal/min. During the third day of injection, an injection pressure of 1,384 psi at a flow rate of 1.4 gal/min was achieved, and the experiment was terminated. This study demonstrates that MICP can be successfully used in large-volume applications where the time frame for the delivery of reactants is limited. This finding has significant relevance for commercialization of the MICP biotechnology in the oil and gas industry.

Engineering↗

DOE OSTI2024

Multi-scale Simulation, Calibration, and Optimization of Calcium Carbonate Precipitation in Microbial Communities

Ensuring the efficient engineering of microbially induced calcium carbonate precipitation (MICP) is crucial for a variety of environmental and civil engineering applications, such as soil stabilization and carbon sequestration. Addressing this need, we present a comprehensive multi-scale workflow that begins with the isolation of calcium carbonate-producing microbes from soil samples, followed by metagenomic sequencing and metabolic reconstruction. We then characterize microbial growth phenotypes under diverse nutrient conditions, compare observed growth with metabolic model predictions, and apply the Consistent Reproduction of Phenotype (CROP) algorithm to refine these models. Furthermore, we analyze metabolite consumption and production, and develop a consumer-resource model that is calibrated using time-series measurements of growth rates, pH levels, and calcium carbonate precipitation. The primary benefit of our approach lies in its ability to predict and control MICP outcomes, facilitated by a Bayesian methodology that incorporates priors on initial conditions and parameters. This allows us to compute posteriors by integrating experimental data, and to solve a risk optimization problem under uncertainty to identify nutrient conditions that maximize calcium carbonate production. In contrast to non-Bayesian methods, which fail to quantify uncertainty accurately, our approach provides a more reliable pathway to optimizing nutrient conditions, enhancing the likelihood of achieving desired MICP outcomes. This positions our method as a superior alternative in the quest to improve MICP through engineered microbial consortia.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2020

A Numerical Model for Enzymatically Induced Calcium Carbonate Precipitation

Enzymatically induced calcium carbonate precipitation (EICP) is an emerging engineered mineralization method similar to others such as microbially induced calcium carbonate precipitation (MICP). EICP is advantageous compared to MICP as the enzyme is still active at conditions where microbes, e.g., Sporosarcina pasteurii , commonly used for MICP, cannot grow. Especially, EICP expands the applicability of ureolysis-induced calcium carbonate mineral precipitation to higher temperatures, enabling its use in leakage mitigation deeper in the subsurface than previously thought to be possible with MICP. A new conceptual and numerical model for EICP is presented. The model was calibrated and validated using quasi-1D column experiments designed to provide the necessary data for model calibration and can now be used to assess the potential of EICP applications for leakage mitigation and other subsurface modifications.

42 ENGINEERING↗

DOE OSTI2023

Using Low-Field Nuclear Magnetic Resonance and X-Ray Computed Microtomography Imaging to Explore Potential of Microbially-Induced Calcium Carbonate Precipitation Treatment to Seal Shale Fractures

Microbially-induced calcium carbonate precipitation (MICP) is a biological process in which microbially produced urease enzymes convert urea and calcium into solid calcium carbonate (CaCO 3 ) deposits. Studies have shown that MICP can be used to seal fractures in shale, raising the possibility of applying this technology to restimulate fracking wells by plugging underperforming fractures. For this and other applications to become a reality, non-invasive tools are needed to determine how effectively MICP seals shale fractures under subsurface conditions. In this study, a 2.54 cm wide and 5.08 cm long Marcellus shale core with a single, ~1 mm wide fracture held open by sand "proppant" underwent MICP-treatment at 60°C until reaching three orders of magnitude permeability reduction. Low-field nuclear magnetic resonance (LF-NMR) and X-Ray computed microtomography (μ-CT) techniques were used to assess the extent of biomineralization within the fracture. These tools revealed that while CaCO 3 precipitation occurred throughout the fracture, there was preferential precipitation around proppant, and the core sealed at the effluent end before filling most of the fracture. Both tools were able to independently calculate of the amount of solid biomineral formed inside the fracture. Furthermore, this study found that the distribution of proppant within the shale fracture was an important parameter controlling the degree of biomineralization.

clastic rock↗

DOE OSTI2021

Pore accessibility and trapping of methane in Marcellus shale

Accessibility of pore space in unconventional reservoirs is an important factor influencing both methane storage capacity and the kinetics of methane desorption. The determination of open (accessible) versus closed (inaccessible) porosity is therefore vital for the prediction of gas production potential. This study investigates accessibility of pores to methane in overmature middle Devonian Marcellus shale samples (cut parallel and perpendicular to bedding) using small and ultra-small neutron scattering (SANS and USANS) with contrast matching (CM), supplemented by other complementary techniques, such as mercury injection capillary pressure (MICP) and low pressure gas (N2 and CO2) adsorption. Our results demonstrate that for the samples studied, only about 6 % of pores with diameter 25-500 nm are accessible to methane. The accessibility fraction for pores larger than 500 nm is 35%. For nanopores smaller than 25 nm, pore accessibility could not be quantitatively determined due to increased methane density and condensation effects in confinement. Our observations indicate that methane penetrates the accessible small mesopores and micropores down to at least 1 nm in diameter, and the density of confined deuterated methane (CD4) is 0.68 g/cm3 for pores of diameter 25 nm and gradually increases with the decreased pore size. Moreover, elevated gas pressure causes formation of additional high-density methane nano-clusters. These clusters have a form of slightly anisotropic polydisperse discs oriented along bedding plane, about 1-12 nm in diameter and with average thickness of 3.6 nm. Utilizing samples cut parallel and perpendicular to the bedding, this study also briefly addresses anisotropy of pores. Based on the iso-size intensity ratio R, our SANS and USANS results demonstrate anisotropy in the out-of-bedding direction and suggest that the degree of anisotropy depends on the pore size. Specifically, for pore diameters ~2.5 to 250 nm, the extent of anisotropy is smaller than for pores ~500 nm to 6 µm in diameter. Finally, comparison of pore size distribution results calculated from SANS/USANS to those obtained using MICP shows good agreement at low pressures, but large difference at pressures above 1000 bar. Here, this discrepancy requires further testing; it is possible that the high mercury pressure used in MICP alters the mesopore and micropore structure of shales.

03 NATURAL GAS↗

DOE OSTI2020

Mineralogy of microbially induced calcium carbonate precipitates formed using single cell drop-based microfluidics

Microbe-mineral interactions are ubiquitous and can facilitate major biogeochemical reactions that drive dynamic Earth processes such as rock formation. One example is microbially induced calcium carbonate precipitation (MICP) in which microbial activity leads to the formation of calcium carbonate precipitates. A majority of MICP studies have been conducted at the mesoscale but fundamental questions persist regarding the mechanisms of cell encapsulation and mineral polymorphism. Here, we are the first to investigate and characterize precipitates on the microscale formed by MICP starting from single ureolytic E. coli MJK2 cells in 25 µm diameter drops. Mineral precipitation was observed over time and cells surrounded by calcium carbonate precipitates were observed under hydrated conditions. Using Raman microspectroscopy, amorphous calcium carbonate (ACC) was observed first in the drops, followed by vaterite formation. ACC and vaterite remained stable for up to 4 days, possibly due to the presence of organics. The vaterite precipitates exhibited a dense interior structure with a grainy exterior when examined using electron microscopy. Autofluorescence of these precipitates was observed possibly indicating the development of a calcite phase. The developed approach provides an avenue for future investigations surrounding fundamental processes such as precipitate nucleation on bacteria, microbe-mineral interactions, and polymorph transitions.

58 GEOSCIENCES↗

DOE OSTI2022

Capillary Pressure to Relative Permeability: Task 7.3.4 Relative Permeability Analysis Final Report

Surface tension affects all aspects of fluid flow in porous media. Through measurements of surface tension interaction under multiphase conditions, a relative permeability relationship can be determined. Relative permeability is a numerical description of the interplay between two or more fluids and the porous media they flow through. It is a critical parameter for various tools used to characterized subsurface multiphase flow systems, such as numerical simulation for oil and gas development, carbon sequestration, and groundwater contamination remediation. Therefore, it is critical to get a good statistic distribution of relative permeability in the porous media under study. Empirical relationships for determining relative permeability from capillary pressure are already well established but do not provide the needed flexibility required to match laboratory derive relative permeability relationships. By expanding the existing methods for calculating relative permeability from capillary pressure data, it is possible to create both two and three-phase relative permeability relationships. Existing laboratory-measured relative permeability data along with mercury intrusion capillary (MICP) data coupled with interfacial tension and contact angle measurements were used to determine the efficacy of this approach to relative permeability curve creation. The relative permeability relationships determined with this method were fit to existing laboratory data to elucidate common fitting parameters that were then used to create relative permeability relationships from MICP data that does not have an associated laboratory-measured relative permeability relationship.

58 GEOSCIENCES↗

DOE OSTI2024

An integrated approach to derive relative permeability from capillary pressure

Surface tension affects all aspects of fluid flow in porous media. Through measurements of surface tension interaction under multiphase conditions, a relative permeability curve can be determined. Relative permeability is a numerical description of the interaction between two or more fluids and the porous media. It is a critical parameter for various tools that characterize subsurface multiphase flow systems, such as numerical simulation for carbon sequestration, oil and gas development, and groundwater contamination remediation. Therefore, it is critical to get a good statistical distribution of relative permeability in the porous media under study. Empirical formula for determining relative permeability from capillary pressure are already well established but do not provide the needed flexibility that is required to match laboratory-derived relative permeability curves. By expanding the existing methods for calculating relative permeability from capillary pressure data, it is possible to create both two and three-phase relative permeability curves. Mercury intrusion capillary pressure (MICP) data from the Morrow 'B' Sandstone coupled with interfacial tension and contact angle measurements were used to create a suite of relative permeability curves. Furthermore, these curves were then calibrated to a small sample of existing laboratory curves to elucidate common fitting parameters for the formation that were then used to create relative permeability curves from MICP data that does not have an associated laboratory-measured relative permeability curve.

58 GEOSCIENCES↗

DOE OSTI2022

Multiscale petrophysical characterization and flow unit classification of the Minnelusa eolian sandstones

Integration of petrophysical and geological information is critical to simulation of subsurface carbon storage (GCS). In this sense, two depositional facies were identified from the core description and well-log interpretation, namely massive (MS) and cross-bedded (CB) facies groups. Additionally, pore-scale characteristics were studied by a combination of techniques, e.g. Nuclear Magnetic Resonance (NMR) and mercury intrusion capillary pressure (MICP). Scanning electron microscope (SEM) and petrographic analyses show that the pore structure is dominantly controlled by the depositional environment and dolomite cementation. NMR-T 2 distributions of MS and CB facies show triple and quadruple modes, respectively. In addition, MICP of high- and low-permeability MS facies samples, and their CB facies group mixtures were collected. The MS sample pore-throat size distribution is uni-modal, while the triple-modal characteristic of the mixtures indicates heterogeneous pore structures at the sub-core scale for CB facies. The reliably estimates of porosity and permeability for both facies groups via NMR techniques and the MLR (Multiple Linear Regression) approach demonstrate the applicability of these techniques to eolian sandstone. Moreover, irreducible water saturation via the T 2 -cutoff method correlates strongly with T 2LM instead of porosity. Finally, the rock quality index and flow zone indicator were calculated based on Combinable Magnetic Resonance (CMR) log interpretations. This provides direct connection to properties measured in the well. Four flow units were classified for both facies groups. Finally, results show that better reservoir quality with significant heterogeneities is observed in the CB facies. This study highlights the importance integrating multiscale petrophysical properties including facies, pore architecture and diagenesis analysis with core- to log-scale property characterization. The results herein validate our reservoir characterization and flow unit classification in eolian reservoirs.

58 GEOSCIENCES↗