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In many contexts, microbial reactions are studied in batch-type reactors to identify conditions necessary for active microbial metabolism and to determine reaction rates or kinetics of selected reactions. One example is the microbial oxidation of hydrogen (e.g. Dohrmann & Krüger, 2023; Dopffel et al 2023) in the context of subsurface storage of hydrogen as energy carrier.
Within batch-type reactors (or serum bottle experiments), a single large gas-fluid interface may limit the replenishment of dissolved hydrogen by mass transfer from the gas phase (cf. Strobel et al 2023). In addition, the single static interface present in the batch-type reactors and the analysis of bulk fluid or gas samples only prevents investigation of spatial chemical gradients of e.g. dissolved hydrogen concentrations or dissolved redox-acceptor concentrations developing on the micrometre scale in subsurface porous rocks. There these gradients most likely will govern growth rates, overall rates of biofilm formation - and more important, its localization with respect to pore throats (Hassannayebi et al 2021). This in turn will affect the overall microbial growth, hence microbial oxidation of hydrogen and formation of by-products, and changes in permeability. First attempts to assess the importance of localized biofilm formation used either packed column experiments (cf. Mushabe et al. 2025) without spatial resolution or were confined to the spatially resolved optical observation of biofilm growth (Liu et al. 2025) without information on chemical gradients.
Therefore we started to develop methods combining optical and Raman spectroscopic techniques enabling us to quantify the concentrations of dissolved ions in the aqueous phase with microbial cells and the partial pressure of gases in adjacent gas phase in microfluidic chips on the micrometre scale. We present data for a first example, the spatially resolved observation of changes in sulphate concentration and hydrogen partial pressure due to microbial oxidation of hydrogen by sulphate-reducing bacteria (strain Oleidesulfovibrio alaskensis) inside a microfluidic chip. It was possible to quantify the decrease of the concentration of sulphate down to 5 mM and hence determine the localized rate of microbial sulphate reduction. In adjacent gas pockets in the pore space, the decrease of the hydrogen partial pressure could be quantified down to 0.01 MPa. The ability to constrain the chemical composition within the chip with high spatial resolution enables addressing the above-mentioned questions of governing effects of evolving chemical gradients on microbial growth, biofilm formation and localization in the pore space - even under (stopped) flow conditions. We outline the next steps towards assessing in chip effective microbial rates in the context of factors as local sulphate concentration, limitations of e.g. hydrogen supply, influence of fluid velocity etc. - necessarily including parallel pore-scale modelling of the systems investigated.
| References | Dohrmann, A. B., & Krüger, M. (2023). Microbial H2 Consumption by a Formation Fluid from a Natural Gas Field at High-Pressure Conditions Relevant for Underground H2 Storage. Environ Sci Technol, 57(2), 1092–1102. https://doi.org/10.1021/acs.est.2c07303 Dopffel, N., Mayers, K., Kedir, A., Alagic, E., An-Stepec, B. A., Djurhuus, K., Boldt, D., Beeder, J., & Hoth, S. (2023). Microbial hydrogen consumption leads to a significant pH increase under high-saline-conditions: implications for hydrogen storage in salt caverns. Sci Rep, 13(1), 10564. https://doi.org/10.1038/s41598-023-37630-y Hassannayebi, N., Jammernegg, B., Schritter, J., Arnold, P., Enzmann, F., Kersten, M., Loibner, A. P., Fernø, M., & Ott, H. (2021). Relationship Between Microbial Growth and Hydraulic Properties at the Sub-Pore Scale. Transport in Porous Media, 139(3), 579–593. https://doi.org/10.1007/s11242-021-01680-5 Liu, N., Ostertag-Henning, C., Fernø, M. A., & Dopffel, N. (2025). Growth on Hydrogen by the Sulfate-Reducing Oleidesulfovibrio alaskensis Induces Biofilm Dispersion and Detachment ─ Implications for Underground Hydrogen Storage. Environ Sci Technol, 59(14), 7095–7105. https://doi.org/10.1021/acs.est.4c13893 Mushabe, R., Liu, N., Dopffel, N., Ersland, G., & Fernø, M. A. (2025). Experimental Study of Microbial Hydrogen Consumption Rates by Oleidesulfovibrio Alaskensis in Porous Media. InterPore Journal, 2(2), IPJ040625–3. https://doi.org/10.69631/1.15 Strobel, G., Hagemann, B., Lüddeke, C. T., & Ganzer, L. (2023). Coupled model for microbial growth and phase mass transfer in pressurized batch reactors in the context of underground hydrogen storage. Front Microbiol, 14, 1150102. https://doi.org/10.3389/fmicb.2023.1150102 |
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| Country | Germany |
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