Multiple microorganism influences and interactions limit the reliability of underground hydrogen and carbon storage simulation models at the reservoir scale
Abstract
The various types of microorganisms encountered in subsurface reservoirs are identified, and their consequences for underground hydrogen storage and carbon dioxide storage are described. In underground hydrogen storage reservoirs, most microorganism activities have negative consequences (pore clogging, reduction in permeability, corrosion, change in composition and loss of stored gas). In underground carbon dioxide storage most of those negative consequences also apply, but transforming some of the stored CO2 into methane by the biomethanation process can be beneficial and potentially exploited. Although laboratory studies and simplified-system simulations have qualitatively explained the microorganism processes involved at the pore scale in underground hydrogen storage and underground carbon dioxide storage reservoirs, it is difficult to model these processes quantitatively at the reservoir scale. The simplifying assumptions, scales and dimensions of the majority of bioreactive transport models fail to take adequate account of reservoir heterogeneities, biofilm development complexities, periodic fluctuations in fluid-flow and nutrient supply. These limitations mean that most of the existing bioreactive transport models are unable to reliably quantify changes in gas composition, gas loss, permeability, or the degree of corrosion likely to occur across heterogeneous underground hydrogen storage or underground carbon dioxide storage reservoirs. However, several opportunities exist to improve field-scale bioreactive transport model performance for underground hydrogen storage and underground carbon dioxide storage in the coming years. These include building on the knowledge gained from the existing simplified models by incorporating new modelling techniques and more detailed reservoir scale information. Exploiting DNA sequencing offers the capability to better characterize the properties of reservoir microorganism communities. Physics-informed machine learning techniques could be tailored to provide efficient surrogate models for simulations of heterogeneous reservoirs. Such improvements should lead to simulation models capable of accommodating more complex reservoir-scale assumptions.
Document Type: Review
Cited as: Wood, D. Multiple microorganism influences and interactions limit the reliability of underground hydrogen and carbon storage simulation models at the reservoir scale. Sustainable Earth Resources Communications, 2025, 1(2): 53-68.
https://doi.org/10.46690/serc.2025.02.04
DOI:
https://doi.org/10.46690/serc.2025.02.04Keywords:
Microorganism H2/CO2 transformations, gas storage reservoir heterogeneities, bioreactive transport complexities, biofilm characteristics, biomethanationReferences
Ahmadi, M. Physics-informed neural modeling of inter-facial tension in hydrogen-rich systems using atten-tion-based learning. International Journal of Hy-drogen Energy, 2025, 163: 150829.
Ahn, A. C., Hidalgo-Ulloa. A., Pererva Y, et al. Review of the window of viability of the different microbial metabolisms relevant for subsurface H2 storage ap-plication. www.hyuspre.eu (accessed on 20 De-cember 2025).
Ali, M., Arif, M., Sedev, R., et al. Underground hydrogen storage: The microbiotic influence on rock wettabil-ity. Journal of Energy Storage, 2023,72: 108405
Ansari, S., Safaei-Farouji, M., Atashrouz, S., et al. Predic-tion of hydrogen solubility in aqueous solutions: Comparison of equations of state and advanced machine learning-metaheuristic approaches. Inter-national Journal of Hydrogen Energy, 2022, 47: 37724–37741.
Ahmadzadegan, A., Wang, S., Vlachos, P. P., et al. Hy-drodynamic attraction of bacteria to gas and liquid interfaces. Physical Review E, 2019, 100: 062605.
Bosu, S., Rajamohan, N. Recent advancements in hy-drogen storage - Comparative review on methods, operating conditions and challenges. International Journal of Hydrogen Energy, 2024 52: 352–370.
Belcour, A., Megy, L., Stephant, S., et al. Predicting coarse-grained representations of biogeochemical cycles from metabarcoding data, Bioinformatics, 2025: 41(1): i49–i57.
Bijay, K. C., Frash, L. P., Creasy, N. M., et al. Laboratory study of cyclic underground hydrogen storage in porous media with evidence of a dry near-well zone and evaporation induced salt precipitation, Interna-tional Journal of Hydrogen Energy, 2024, 71: 515-527.
Black, M. E., Fei, C., Alert, R., et al. Capillary interac-tions drive the self-organization of bacterial colo-nies. Nature Physics, 2025, 21:1444–1450.
Boon, M., Buntic, I., Ahmed, K., et al. Microbial induced wettability alteration with implications for under-ground hydrogen storage. Scientific Reports,2024, 14: 8248.
Cai, J., Wood, D. A., Hajibeygi, H., et al. Multiscale and multiphysics influences on fluids in unconventional reservoirs: modeling and simulation. Advances in Geo-Energy Research, 2022, 6 (2): 91-94.
Černá, K., Fadrhonc, K., Říha, J., et al. Towards stand-ardized microbial hydrogen consumption testing in the subsurface: harmonized field sampling and en-richment approaches. World Journal of Microbi-ology and Biotechnology,2025, 41: 342.
Chang, Q., Huang, L., McKenzie, K., et al. Influence of hydrogen sulfide on gas-water interface in under-ground hydrogen storage: A molecular dynamics study. Journal of Energy Storage, 2024, 97: 112766.
Davoodi, S., Al-Shargabi, M., Wood, D. A., et al. Review of technological progress in carbon dioxide capture, storage, and utilization. Gas Science and Engineer-ing, 2023, 117: 205070.
Davoodi, S., Al-Shargabi, M. A., Wood, D. A., et al. Car-bon dioxide sequestration through enhanced oil re-covery: a review of storage mechanisms and tech-nological applications. Fuel, 2024, 366: 131313.
Davoodi, S., Al-Shargabi, M. A., Wood, D. A., et al. Un-derground hydrogen storage: a review of techno-logical developments, challenges, and opportunities. Applied Energy, 2025, 381: 125172.
Davoodi, S., Wood, D. A., Al-Shargabi, M., et al. Emerg-ing applications of physics-informed and phys-ics-guided machine learning in geoenergy science: A review. Communications in Nonlinear Science and Numerical Simulation, 2026 (In Press).
Dawi, M. A., Starnoni, M., Porta, G., et al. Pore‐scale coupling of flow, biofilm growth, and nutrient transport: a microcontinuum approach. Water Re-sources Research,2024, 60 (11): e2024WR038393.
Du, Q., Wei, Y., Zhang, L. et al. An improved CRISPR and CRISPR interference (CRISPRi) toolkit for en-gineering the model methanogenic archaeon Methanococcus maripaludis. Microbial Cell Facto-ries, 2024, 23: 239.
Dopffel, N., Jansen, S., Gerritse, J. Microbial side effects of underground hydrogen storage – Knowledge gaps, risks and opportunities for successful imple-mentation. International Journal of Hydrogen En-ergy, 2021, 46: 8594–8606.
Eddaoui, N., Panfilov, M., Ganzer, L., et al. Impact of pore clogging by bacteria on underground hydrogen storage. Transp Porous Media, 2021, 139(1): 89–108.
Ferrando, N., Cacas-Stentz, M. C., Patacchini, F. et al. Numerical simulation of hydrogen phase equilib-rium and migration at basin scale, in Natural Hy-drogen Systems: Properties, Occurrences, Genera-tion Mechanisms, Exploration, Storage and Trans-portation, edited by Rezaee, R., Evans, B. J., De Gruyter, : pp. 385-416, 2025.
Gbadamosi, A., Adamu, H., Usman, J., et al. New-generation machine learning models as predic-tion tools for modeling interfacial tension of hy-drogen-brine system. International Journal of Hy-drogen Energy, 2024, 50: 1326–1337.
Ghaedi, M., Gholami, R., Bellas, S., et al. Evapora-tion-induced salt precipitation and dry-out evolu-tion during hydrogen storage in geological porous media. International Journal of Hydrogen Energy, 2025, 102: 1306-1314.
Haddad, P. G., Mura, J., Castéran, F., et al. Biological, geological and chemical effects of oxygen injection in underground gas storage aquifers in the setting of biomethane deployment. Science of The Total En-vironment 2022, 806: 150690.
Hagemann, B., Rasoulzadeh, M., Panfilov, M., et al. Hydrogenization of underground storage of natural gas. Computers & Geosciences, 2016, 20(3): 595–606.
Hagemann, B., Hogeweg, S., Strobel, G. Application of analytical solutions of the reactive transport equa-tion for underground methanation reactors. Transport in Porous Media, 2024, 151: 2601-2623.
Hassan, I. A., Ramadan, H. S., Saleh, M. A., et al. Hy-drogen storage technologies for stationary and mo-bile applications: Review, analysis and perspectives. Renewable and Sustainable Energy Reviews, 2021, 149: 111311.
Hassannayebi, N., Jammernegg, B., Schritter, J., et al. Relationship between microbial growth and hy-draulic properties at the sub-pore scale. Transp Po-rous Media, 2021, 139: 579–593.
Hassanpouryouzband, A., Adie, K., Cowen, T., et al. Geological hydrogen storage: geochemical reactivi-ty of hydrogen with sandstone reservoirs. ACS En-ergy Letter, 2022, 7: 2203–2210.
Hogeweg, S., Hagemann, B., Bobrov, V., et al. Devel-opment and calibration of a bio-geo-reactive transport model for UHS. Frontiers in Energy Re-search, 2024, 12:1385273.
Imani, G., Zhang, L., Thaysen, E. M., et al. Microbial reactions at gas–liquid and solid–liquid interfaces in underground hydrogen storage. Advances in Colloid and Interface Science, 2026, 349:103762.
Khajooie, S., Gaus, G., Seemann, T., et al. Methanogenic activity in water-saturated reservoir analogues for underground hydrogen storage: The role of surface area. International Journal of Hydrogen Energy, 2024, 90: 171-190.
Kapellos, G. E., Alexiou, T. S., Pavlou, S. Fluid-Biofilm Interactions in Porous Media, in Heat transfer and fluid flow in biological processes, edited by S. M. Becker and A. V. KuznetsovAcademic Press, pp. 207-238, 2015.
Krsmanovic, M., Biswas, D., Ali, H., et al. Hydrodynam-ics and surface properties influence biofilm prolif-eration. Advances In Colloid And Interface Science, 2021, 288: 102336.
Kurz, D. L., Secchi, E., Carrillo, F. J., et al. Competition between growth and shear stress drives intermitten-cy in preferential flow paths in porous medium bio-films. Proceedings of the National Academy of Sciences of the United States of America, 2022, 119: e2122202119.
Li, X., Yang X. Pore-scale modeling of biofilm formation and biofilm-induced anomalous transport features in heterogenous porous media. Advances In Water Resources, 2025, 195: 104877.
Liu, E., Lu, X., Wang, D., et al. A Systematic Review of Carbon Capture, Utilization and Storage: Status, Progress and Challenges. Energies, 2023a, 16: 2865.
Liu, N., Kovscek, A. R., Fernø. M. A., et al. Pore-scale study of microbial hydrogen consumption and wettability alteration during underground hydrogen storage. Frontiers in Energy Research, 2023b, 11: 1-10.
Liu, N., Ostertag-Henning, C., Fernø, M. A., et al. Growth on hydrogen by the sulfate-reducing Oleidesul-fovibrio alaskensis induces biofilm dispersion and detachment ─ implications for underground hy-drogen storage. Environmental Science & Technol-ogy, 2025. 59(14): 7095–7105.
Longe, P., Davoodi, S., Mehrad, M., et al. Combined deep learning and optimization for hydro-gen-solubility prediction in aqueous systems appro-priate for underground hydrogen storage reservoirs. Energy & Fuels, 2024, 38(22): 22031–22049.
Longe. P., Davoodi, S., Makarov, N., et al. Hybrid deep learning predictions of interfacial tension in hydro-gen-brine-cushion-gas systems: implications for underground hydrogen storage. Chemical Engi-neering Science, 2026 (In Press).
Lysyy, M., Ersland, G., Fernø, M. Pore-scale dynamics for underground porous media hydrogen storage. Advances In Water Resources, 2022, 163:104167.
Minougou, J. D., Azizmohammadi, S., Gholami, R., et al. A bio-reactive transport model for bio-methanation in hydrogen underground storage sites. Greenhouse Gases: Science and Technology, 2024, 14(6): 977-994.
Muñoz-Duarte, L., Chakraborty, S., Grøn, L. V., et al. H2 consumption by acetogenic bacteria follows first-order kinetics. BoiRxrv, 2024.
Ng, C. S. W., Djema, H., Nait Amar. M., et al. Modeling interfacial tension of the hydrogen-brine system using robust machine learning techniques: Implica-tion for underground hydrogen storage. Interna-tional Journal of Hydrogen Energy, 2022, 47:39595–39605.
Omeke, J., Misra, S., Retnanto, A. Dynamic response modeling in underground hydrogen storage using a Fourier-integrated hybrid neural framework. Inter-national Petroleum Technology Conference, Kuala Lumpur, Malaysia, February 2025.
Orgogozo, L., Golfier, F., Buès, M. A., et al. A du-al-porosity theory for solute transport in bio-film-coated porous media, Advances in Water Re-sources, 2013, 62(B): 266-279.
Pal, M. K., Lavanya, M. Microbial influenced corrosion: understanding bioadhesion and biofilm formation. Journal of Bio- and Tribo-Corrosion, 2022, 8: 76.
Park, T., Yoon, S., Jung, J., et al. Effect of fluid–rock interactions on in situ bacterial alteration of interfa-cial properties and wettability of CO2–brine–mineral systems for geologic carbon storage. Envi-ronmental Science & Technology, 2020, 54: 15355–15365.
Pinto, Y., Bhatt, A. S. Sequencing-based analysis of mi-crobiomes. Nature Reviews Genetics,2024, 25: 829–845.
Pizzi, F., Peters, F., Sorribes, E., et al. Modulation of bio-film growth by shear and fluctuations in turbulent environments. Scientific Reports, 2025, 15: 1–21.
Rumah, B. L., Claxton Stevens, B. H., Yeboah, J. E., et al. In vivo genome editing in Type I and II metha-notrophs using a CRISPR/Cas9 system. ACS Syn-thetic Biology, 2023, 12(2): 544-554.
Safari, A., Sugai, Y., Salgar-Chaparro, S. J., et al. Hydro-gen-consuming bacteria in underground hydrogen storage: Bacterial diversity and mathematical modeling of their impacts on storage efficiency. Journal of Energy Storage, 2025, 113: 115519.
Sekar, L. K., Kiran, R., Okoroafor, E. R., et al. Review of reservoir challenges associated with subsurface hy-drogen storage and recovery in depleted oil and gas reservoirs. Journal of Energy Storage, 2023, 72: 108605.
Shojaee, A., Ghanbari, S., Wang, G., et al. Interplay be-tween microbial activity and geochemical reactions during underground hydrogen storage in a sea-water-rich formation. International Journal of Hy-drogen Energy, 2024, 50: 1529–1541.
Starnoni, M., Sanchez-Vila, X. Pore-scale modelling of subsurface biomineralization for carbon mineral storage. Advances In Water Resources, 2024, 185: 104641.
Strobel, G., Hagemann, B., Huppertz, T. M., Ganzer, L. Underground bio-methanation: Concept and po-tential. Renewable and Sustainable Energy Reviews, 2020, 123,109747.
Strobel, G., Zawallich, J., Hagemann, B., et al. Experi-mental and numerical investigation of microbial growth in two-phase saturated porous media at the pore-scale. Sustainable Energy and Fuels, 2023a, 7: 3939–3948.
Strobel, G., Hagemann, B., Lüddeke, C. T., et al. Cou-pled model for microbial growth and phase mass transfer in pressurized batch reactors in the context of underground hydrogen storage. Frontiers in Mi-crobiology, 2023b, 14: 1150102.
Subbiahdoss, G., Reimhult, E. Biofilm formation at oil-water interfaces is not a simple function of bac-terial hydrophobicity. Colloids Surfaces B Bioin-terfaces, 2020, 194: 111163.
Takai, K., Nakamura, K., Toki, T., et al. Cell proliferation at 122 degrees C and isotopically heavy CH4 pro-duction by a hyperthermophilic methanogen under high-pressure cultivation. Proceedings of the Na-tional Academy of Sciences of the United States of America, 2008, 105(31): 10949-10954.
Tan, Y. Wang, Z.-X., Schneider, R. P., et al. Modelling microbial growth: A statistical thermodynamic ap-proach. Journal of Biotechnology, 1994, 32 (2): 97-106.
Thaysen, E. M., Mcmahon, S., Strobel, G. J., et al. Esti-mating microbial growth and hydrogen consump-tion in hydrogen storage in porous media. Renewa-ble and Sustainable Energy Reviews, 2021, 151: 111481.
Thaysen, E. M., Armitage, T., Slabon, L., et al. Microbial risk assessment for underground hydrogen storage in porous rocks. Fuel, 2023, 352: 128852.
Tremosa, J., Jakobsen, R., Le Gallo, Y. Assessing and modeling hydrogen reactivity in underground hy-drogen storage: a review and models simulating the Lobodice town gas storage. Frontiers in Energy Re-search, 2023, 11: 1141975
Tyne, R. L., Barry, P. H., Lawson, M., et al. Rapid mi-crobial methanogenesis during CO2 storage in hy-drocarbon reservoirs. Nature, 2021, 600(7890): 670–674.
Vasile, N. S. A Comprehensive Review of Biogeochemi-cal Modeling of Underground Hydrogen Storage: A Step Forward in Achieving a Multi-Scale Approach. Energies, 2024, 17: 6094.
Vo Thanh, H., Rahimi, M., Dai, Z., et al. Predicting the wettability rocks/minerals-brine-hydrogen system for hydrogen storage: Re-evaluation approach by multi-machine learning scheme. Fuel, 2023, 345: 128183.
Vo Thanh, H. V. Physics informed machine learning for prediction hydrogen solubility in aqueous solution to implication for underground hydrogen storage formations. Renewable Energy, 2026, 256(Part G): 124460.
Vu, H. P., Black, J. R., Haese, R. R. The geochemical effects of O2 and SO2 as CO2 impurities on flu-id-rock reactions in a CO2 storage reservoir. Interna-tional Journal of Greenhouse Gas Control, 2018, 68: 86–98.
Wang, G., Pickup, G., Sorbie, K., et al. Bioreaction cou-pled flow simulations: Impacts of methanogenesis on seasonal underground hydrogen storage. Inter-national Journal of Hydrogen Energy, 2024, 55: 921–931.
Wheeler, J. D., Secchi, E., Rusconi, R., Stocker, R. Not just going with the flow: The effects of fluid flow on bacteria and plankton. Annual Review of Cell and Developmental Biology, 2019, 35:213–237.
Wood, D. A. Microbial improved and enhanced oil re-covery (MIEOR): Review of a set of technologies diversifying their applications. Advances in Geo-Energy Research, 2019, 3(2): 122-140.
Wood, D. A. Biodiesel from microalgae, in 3rd Genera-tion Biofuel: Disruptivetechnologies to enable commercial production, edited by E. Jacob-Lopes, L. Q. Zepka, I. A. Severo, and M. M. Maronese, (Woodhead Publishing Series in Energy (Elsevier), pp. 417-438, 2022.
Wood, D. A. Well integrity for underground gas storage relating to natural gas, carbon dioxide, and hydro-gen, in Sustainable Natural Gas Drilling: Technolo-gies and Case Studies for the Energy Transition, ed-ited by D. A. Wood and J. Cai, Elsevier, pp. 551-576, 2024a.
Wood, D. A. Natural hydrogen resource exploitation must confront the issue that certain gas composi-tions are undesirable in terms of environmental sustainability. Advances in Geo-Energy Research, 2024, 15(3): 185-189.
Wood, D. A. Critical review of development challenges for expanding hydrogen-fuelled energy systems. Fuel, 2025, 287: 134394.
Wood, D. A., Rezaee, R. Environmental impacts of hy-drogen production and usage, in Natural Hydro-gen Systems: Properties, Occurrences, Generation Mechanisms, Exploration, Storage and Transporta-tion, edited by R. Rezaee, B. J. Evans, De Gruyter, pp. 607-644, 2025.
Wu, L., Hou, Z., Luo, Z., et al. Efficiency assessment of underground biomethanation with hydrogen and carbon dioxide in depleted gas reservoirs: A bioge-ochemical simulation. Energy, 2023, 283:128539.
Wu, L., Hou, Z.-M., Luo, Z.-F., et al. Impacts of microbi-al interactions on underground hydrogen storage in porous media: A comprehensive review of experi-mental, numerical, and field studies. Petroleum Science, 2024, 21: 4067–4099.
Xu, D., Gu, T., Lovley, D. R. Microbially mediated metal corrosion. Nature Reviews Microbiology, 2023, 21: 705–718.
Zhao, N., Ding, H., Zhou, X., et al. Dissimilatory iron-reducing microorganisms: The phylogeny, physiology, applications and outlook. Critical Re-views in Environmental Science and Technology, 2024, 55(2): 73–98.
Zheng, S., Bawazir, M., Dhall, A., et al. Implication of surface properties, bacterial motility, and hydro-dynamic conditions on bacterial surface sensing and their initial adhesion. Frontiers in Bioengineer-ing and Biotechnology, 2021, 9: 1–22.
Zhu, Y., Wang, H., Vano, K. Applying the wavelet neural network to estimate hydrogen dissolution in under-ground sodium chloride solutions. International Journal of Hydrogen Energy, 2022, 47: 22720–22730.
Downloads
Additional Files
Published
How to Cite
Issue
Section
License
Copyright (c) 2025 Author(s)
This work is licensed under a Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International License.