Fracture permeability reduction and sealing mechanisms of microbial cementation in underground fractured media: Application to low-permeability reservoirs
Abstract
Microbially induced calcium precipitation is a promising method for sealing fractures in low-permeability reservoirs, yet the role of anaerobic indigenous microorganisms under reservoir conditions remains unclear. In this study, reservoir samples were anaerobically enriched, and a urease-producing indigenous strain identified as Bacillus megaterium was isolated. Its growth, environmental tolerance, stimulation response, biomineralization products, and fracture-sealing performance were systematically evaluated. The strain showed good adaptability to fractured reservoir conditions and produced extracellular polymeric substances that promoted calcium enrichment and calcite formation. Visual fracture experiments demonstrated that microbial cementation significantly reduced fracture permeability and achieved effective sealing. The results further indicate that the dominant sealing mechanism depends on fracture aperture: surface adsorption controls sealing in narrow fractures, whereas particle deposition, settling, and migration become increasingly important in wider fractures. These findings clarify the fracture-sealing mechanisms of indigenous anaerobic microorganisms and support their potential application in subsurface permeability control.
Document Type: Original article
Cited as: He, Y., An, S., Babadagli, T., Liu, K., Bai, L., Huang, H. Fracture permeability reduction and sealing mechanisms of microbial cementation in underground fractured media: Application to low-permeability reservoirs. Advances in Geo-Energy Research, 2026, 20(1): 85-97. https://doi.org/10.46690/ager.2026.04.07
DOI:
https://doi.org/10.46690/ager.2026.04.07Keywords:
Microbial enhanced oil recovery, microbially induced calcium precipitation , indigenous microorganisms, Bacillus megateriumReferences
Achal, V. and Pan, X. Influence of calcium sources on microbially induced calcium carbonate precipitation by Bacillus sp. CR2. Applied Biochemistry and Biotechnology, 2014, 173: 307-317.
Al Imran, M., Shinmura, M., Nakashima, K., et al. Effects of various factors on carbonate particle growth using ureolytic bacteria. Materials Transactions, 2018, 59(9): 1520-1527.
Almajed, A., Tirkolaei, H. K., Kavazanjian Jr, E., et al. Enzyme induced biocementated sand with high strength at low carbonate content. Scientific Reports, 2019, 9(1): 1135.
Chen, X., Li, Y., Liu, Z., et al. Investigation on matching relationship and plugging mechanism of self-adaptive micro-gel (SMG) as a profile control and oil displacement agent. Powder Technology, 2020, 364: 774-784.
Chen, Y., Wang, S., Tong, X., et al. Crystal transformation and self-assembly theory of microbially induced calcium carbonate precipitation. Applied Microbiology and Biotechnology, 2022, 106(10): 3555-3569.
Choi, S., Chang, I., Lee, M., et al. Review on geotechnical engineering properties of sands treated by microbially induced calcium carbonate precipitation (MICP) and biopolymers. Construction and Building Materials, 2020, 246: 118415.
Dhami, N, Reddy, S., and Mukherjee, A. Biomineralization of calcium carbonate polymorphs by the bacterial strains isolated from calcareous sites. Journal of Microbiology and Biotechnology, 2013, 23(5): 707-714.
Dong, H., Zhang, F., Xu, T., et al. Culture-dependent and culture-independent methods reveal microbe-clay mineral interactions by dissimilatory iron-reducing bacteria in an integral oilfield. Science of The Total Environment, 2022, 840: 156577.
Ferris, G., Phoenix, V., Fujita, Y., et al. Kinetics of calcite precipitation induced by ureolytic bacteria at 10 to 20 ℃ in artificial groundwater. Geochimica et Cosmochimica Acta, 2004, 68(8): 1701-1710.
He, Y., Liu, K., Huang, T., et al. Microbial community assembly and functional adaptation of urease-producing bacteria in oil reservoirs: Driven by phase heterogeneity and selective enrichment. Journal of Environmental Chemical Engineering, 2025, 13(6): 120521.
Hoang, T., Alleman, J., Cetin, B., et al. Sand and silty-sand soil stabilization using bacterial enzyme–induced calcite precipitation (BEICP). Canadian Geotechnical Journal, 2019, 56(6): 808-822.
Hu, W., Wei, Y., and Bao, J. Development of the theory and technology for low permeability reservoirs in China. Petroleum Exploration and Development, 2018, 45(4): 646-656.
Intarasoontron, J., Pungrasmi, W., Nuaklong, P., et al. Comparing performances of MICP bacterial vegetative cell and microencapsulated bacterial spore methods on concrete crack healing. Construction and Building Materials, 2021, 302: 124227.
Jain, S., Arnepalli, D. Biochemically induced carbonate precipitation in aerobic and anaerobic environments by Sporosarcina pasteurii. Geomicrobiology Journal, 2019, 36(5): 443-451.
Jiang, N., Tang, C., Yin, L., et al. Applicability of microbial calcification method for sandy-slope surface erosion control. Journal of Materials in Civil Engineering, 2019, 31(11): 04019250.
Jiang, N., Yoshioka, H., Yamamoto, K., et al. Ureolytic activities of a urease-producing bacterium and purified urease enzyme in the anoxic condition: Implication for subseafloor sand production control by microbially induced carbonate precipitation (MICP). Ecological Engineering, 2016, 90: 96-104.
Jin, A., Park, E., Li, C., et al. Geological CO2 storage in heterogeneous saline aquifers: Insights into the mechanisms of thermal and density effects. Advances in Geo-Energy Research, 2026, 19(3): 216-230.
Jongvivatsakul, P., Janprasit, K., Nuaklong, P., et al. Investigation of the crack healing performance in mortar using microbially induced calcium carbonate precipitation (MICP) method. Construction and Building Materials, 2019, 212: 737-744.
Kong, H., Kassim, K., Umar, M., et al. Microbially induced carbonate precipitations to improve residual soil at various temperatures. Bulletin of the Geological Society of Malaysia, 2019, 67: 75-81.
Lai, H., Cui, M., Wu, S., et al. Retarding effect of concentration of cementation solution on biocementation of soil. Acta Geotechnica, 2021, 16(5): 1457-1472.
Lei, Q., Wong, D., Luo, J., et al. Achievemensts and future work of oil and gas production engineering of CNPC. Petroleum Exploration and Development, 2019, 46(1): 139-145.
Li, M., Cheng, X., Guo, H., et al. Biomineralization of carbonate by Terrabacter tumescens for heavy metal removal and biogrouting applications. Journal of Environmental Engineering, 2016, 142(9): C4015005.
Lin, H., Zhou, M., Li, B., et al. Mechanisms, application advances and future perspectives of microbial-induced heavy metal precipitation: A review. International Biodeterioration & Biodegradation, 2023, 178: 105544.
Liu, Y., Zou, C., Zhou, D., et al. Novel Chemical Flooding System Based on Dispersed Particle Gel Coupling In-Depth Profile Control and High Efficient Oil Displacement. Energy & Fuels, 2019, 33(4): 3123-3132.
Kakelar, M., Meybodi, A., Sanjideh, S., et al. Cost-Effective Optimization of Bacterial Urease Activity Using a Hybrid Method Based on Response Surface Methodology and Artificial Neural Networks. Environmental Processes, 2022, 9(1): 1-24.
Martin, D., Dodds, K., Ngwenya, B., et al. Inhibition of Sporosarcina pasteurii under anoxic conditions: implications for subsurface carbonate precipitation and remediation via ureolysis. Environmental Science & Technology, 2012, 46(15): 8351-8355.
Minto, J., MacLachlan, E., El Mountassir, G., et al. Rock fracture grouting with microbially induced carbonate precipitation. Water Resources Research, 2016, 52(11): 8827-8844.
Mitchell, A., Dideriksen, K., Spangler, L., et al. Microbially enhanced carbon capture and storage by mineral-trapping and solubility-trapping. Environmental Science & Technology, 2010, 44(13): 5270-5276.
Mountassir, G., Lunn, R., Moir, H., et al. Hydrodynamic coupling in microbially mediated fracture mineralization: Formation of self-organized groundwater flow channels. Water Resources Research, 2014, 50(1): 1-16.
Peng, J., Liu, Z. Influence of temperature on microbially induced calcium carbonate precipitation for soil treatment. PLoS One, 2019, 14(6): e0218396.
Phillips, A., Troyer, E., Hiebert, R. et al. Enhancing wellbore cement integrity with microbially induced calcite precipitation (MICP): A field scale demonstration. Journal of Petroleum Science and Engineering, 2018, 171: 1141-1148.
Safdel, M., Anbaz, M., Daryasafar, A., et al. Microbial enhanced oil recovery, a critical review on worldwide implemented field trials in different countries. Renewable and Sustainable Energy Reviews, 2017, 74: 159-172.
Shi, W., Wang, M., Wu, L., et al. Study of Concrete Crack Repair using Bacillus megaterium. Advances in Materials Science and Engineering, 2022, 2022: 1-13.
Song, Z., Wu, C., Shen, D., et al. Microbially induced carbonate precipitation under high temperature and high pressure: Implications for geological CO2 storage. Journal of Rock Mechanics and Geotechnical Engineering, 2025, 17(6): 3872-3882.
Sun, S., Luo, Y., Zhou, Y., et al. Application of Bacillus spp. in Pilot Test of Microbial Huff and Puff to Improve Heavy Oil Recovery. Energy & Fuels, 2017, 31(12): 13724-13732.
Sun, X., Miao, L., Tong, T., et al. Study of the effect of temperature on microbially induced carbonate precipitation. Acta Geotechnica, 2019, 14: 627-638.
Sun, X., Miao, L., Wu, L., et al. Improvement of bio-cementation at low temperature based on Bacillus megaterium. Appl Microbiol Biotechnol, 2019, 103(17): 7191-7202.
Tang, C., Yin, L., Jiang, N., et al. Factors affecting the performance of microbial-induced carbonate precipitation (MICP) treated soil: a review. Environmental Earth Sciences, 2020, 79(5): 94
Turner, R., Castro, G., Minto, J., et al. Treatment of fractured concrete via microbially induced carbonate precipitation: From micro-scale characteristics to macro-scale behaviour. Construction and Building Materials, 2023, 384: 131467.
Wang, X., Dang, H., and Gao, T. Method of moderate water injection and its application in ultra-low permeability oil reservoirs of Yanchang Oilfield, NW China. Petroleum Exploration and Development, 2018, 45(6): 1094-1102.
Wang, X., Yang, Y., and Xi, W. Microbial enhanced oil recovery of oil-water transitional zone in thin-shallow extra heavy oil reservoirs: A case study of Chunfeng Oilfield in western margin of Junggar Basin, NW China. Petroleum Exploration and Development, 2016, 43(4): 630-635.
Wang, Z. and Bai, B. Preformed-particle-gel placement and plugging performance in fractures with tips. SPE Journal, 2018, 23(6): 2316-2326.
Wen, K., Li, Y., Amini, F., et al. Impact of bacteria and urease concentration on precipitation kinetics and crystal morphology of calcium carbonate. Acta Geotechnica, 2020, 15: 17-27.
Whiffin, V., Paassen, L., Harkes, M. Microbial carbonate precipitation as a soil improvement technique. Geomicrobiology Journal, 2007, 24(5): 417-423.
Wu, C., Chu, J., Wu, S., et al. 3D characterization of microbially induced carbonate precipitation in rock fracture and the resulted permeability reduction. Engineering Geology, 2019, 249: 23-30.
Xie, D., Zhang, R., and Wang, J. The influence of environmental factors and precipitation precursors on enzyme-induced carbonate precipitation (EICP) process and its application on modification of recycled concrete aggregates. Journal of Cleaner Production, 2023, 136444.
Zhang, K., Tang, C., Jiang, N., et al. Microbial‑induced carbonate precipitation (MICP) technology: a review on the fundamentals and engineering applications. Environmental Earth Sciences, 2023, 82(9): 229.
Zhang, L., Ni, J., Wang, C., et al. Study on Plugging the Multiscale Water Channeling in Low-Permeability Heterogeneous Porous Media Based on the Growth of Bacteria. SPE Journal, 2024, 29(8): 4248-4265.
Downloads
Downloads
Published
How to Cite
Issue
Section
License
Copyright (c) 2026 Yanlong He, Shizi An, Tayfun Babadagli, Keyi Liu, Lu Bai, Hai Huang
This work is licensed under a Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International License.