Natural Hydrogen and Subsurface Microbiology: How Do Bacteria Influence Geological Accumulations?
In just nine days, a sulfate-reducing bacterium consumed 32.9% of the hydrogen present in a porous silicon micromodel during a laboratory experiment [4]. Carried out under conditions favorable to microbial activity, this result doesn't directly represent the behavior of a natural reservoir, but it illustrates the influence certain microorganisms can have on subsurface gases.
Natural hydrogen, also known as geological hydrogen or white hydrogen, is drawing growing interest as a potential low-carbon energy resource. Its presence and evolution in the subsurface result from the interaction of several geological, chemical, and biological processes. Microorganisms are part of this system: depending on environmental conditions, they can produce, consume, or transform hydrogen within geological formations.
Where Does Natural Hydrogen in the Subsurface Come From?
Natural hydrogen forms in the Earth's crust without human intervention. It can arise through several mechanisms and occur across a wide range of geological settings, including volcanic and geothermal systems, ultramafic rocks, and alkaline igneous complexes.
Hydrogen formation underground relies on two broad families of mechanisms: abiotic processes, which result from physical or chemical reactions with no involvement of living organisms, and biotic processes, which depend on microbial activity [1].
Abiotic mechanisms have been studied extensively, since they can generate hydrogen across a variety of geological environments and over long timescales. Among the best known and most studied are:
Serpentinization, a set of reactions between water and certain iron- and magnesium-rich rocks. These transformations alter the minerals present in the rock and can release hydrogen [1].
Water radiolysis, which occurs when radiation emitted by the decay of radioactive elements such as uranium, thorium, or potassium splits water molecules apart, contributing to hydrogen formation [1].
Biotic processes follow a different logic. In environments where conditions are compatible with life, certain microorganisms can also take part in hydrogen production through various metabolic pathways [1]. Their role isn't limited to production, though, since they can also consume or transform the hydrogen already present in geological formations. These interactions are explored further below.
Table 1 — Main Sources of Natural Hydrogen in the Subsurface
| Process | Type | Associated Geological Context |
|---|---|---|
| Serpentinization | Abiotic | Mafic and ultramafic rocks |
| Water radiolysis | Abiotic | Crystalline basement and sediments containing radioactive elements |
| Microbial fermentation | Biotic | Subsurface environments with sufficient organic carbon |
| Nitrogen fixation | Biotic | Oxic or anoxic environments |
Source: Data drawn from Gregory et al. (2019) [1]
An Active Subsurface Biosphere Despite Harsh Conditions
The deep subsurface isn't a sterile place. Despite limited nutrient availability and sometimes difficult conditions, microbial communities live in rock fractures, aquifers, and other underground formations. Their activity is favored whenever certain chemical reactions can supply them with energy. In these settings, natural hydrogen can act as an electron donor, meaning it serves as an energy source for some microorganisms [1].
A study conducted across 14 aquifers in Alberta, drawing on 138 groundwater samples, illustrates this relationship between geology and microbiology. The analyses revealed diverse, productive microbial communities, including in ancient groundwater, and showed that hydrogen is an important energy source for many of them [5].
These findings show that hydrogen generated underground can also feed into biological processes. Depending on the conditions of the environment and the microorganisms present, it may then be consumed or transformed through different microbial metabolisms.
To learn more: "Natural Hydrogen: What's the Difference Between a Diffuse Surface Flux and a Trapped Geological Reservoir?"
How Do Microorganisms Consume Hydrogen in the Subsurface?
In the subsurface, natural hydrogen can become an energy source for various microorganisms. Its low redox potential allows it to act as an electron donor in several biological reactions. Even at low concentrations, it can support diverse metabolisms as long as a suitable electron acceptor is available [1].
The main hydrogenotrophic metabolisms include:
methanogenesis, which converts H₂ and CO₂ into methane;
acetogenesis, which produces acetate from H₂ and CO₂;
sulfate reduction, which can generate hydrogen sulfide (H₂S), along with other pathways such as iron(III) reduction or denitrification [1].
In deep, nutrient-poor environments, these microorganisms may compete for a limited supply of hydrogen, so their activity varies with geochemical conditions and the communities present.
Measurable Losses in the Laboratory
In a porous silicon micromodel, a sulfate-reducing bacterium caused gaseous H₂ saturation to drop by 29.4% after two days, compared with 3.7% in the sterile control [4]. These results, obtained under conditions favorable to microbial activity, can't be extrapolated directly to a real reservoir.
Tests on brines collected from European storage sites also revealed rapid hydrogen loss in several porous reservoir samples. By contrast, most salt cavern brines showed negligible activity after twelve months. Consumption was most often linked to methanogenesis [3].
The Role of Methanogenic Archaea
Methanogenic archaea use hydrogen and CO₂ to produce methane. At several sites in the Vienna Basin, archaea made up 20 to 58% of the communities detected in groundwater, with methanogens the dominant group. Some samples from surface facilities reached as much as 87% methanogens [2].
This conversion can reduce the amount of recoverable hydrogen. The same mechanism is also being studied in Power-to-Methane technologies, where hydrogen and CO₂ are biologically converted into methane [2].
Microorganisms Can Also Produce Hydrogen
The relationship between microorganisms and subsurface hydrogen isn't one-directional. While some microbes consume this gas, others produce it, feeding into the broader hydrogen cycle within geological formations.
Metabolic Pathways of Microbial Hydrogen Production
Microorganisms can generate hydrogen through several distinct metabolic pathways:
Fermentation of organic matter
Fixation of atmospheric nitrogen
Anaerobic oxidation of carbon monoxide
Oxidation of phosphite [1]
Microbial hydrogen production generally involves hydrogenases. H₂ generation is mainly associated with [FeFe]-hydrogenases, typical of many anaerobic bacteria and some eukaryotes, though certain [NiFe]-hydrogenases can also play a role [1].
Fermentation of organic matter is particularly important in subsurface environments where sufficient organic carbon is available. That said, hydrogen produced through fermentation is generally a transient compound: it has to be removed quickly for fermentation to continue, since its buildup inhibits the process itself [1]. In other words, microbial hydrogen production often depends on other organisms consuming the gas as it's generated.
Microbiology into the Exploration and Assessment of Natural Hydrogen
Subsurface microbiology can shape the fate of hydrogen in geological formations. Certain microorganisms can consume it, transform it, or alter conditions in the surrounding environment, which can affect how much gas is available, its composition, and certain reservoir properties.
Current knowledge comes mainly from studies on underground storage of injected hydrogen. Even so, these studies help explain why microbial activity is also a relevant factor to weigh when assessing natural accumulations.
Possible Effects on Reservoirs
Depending on geochemical conditions and the communities present, microbial activity can lead to:
a decrease in the amount of hydrogen available through biological consumption;
a potential change in injectivity or wettability when microbial growth affects pores and rock surfaces;
an alteration of gas composition through the production of hydrogen sulfide (H₂S), which can degrade gas quality; sulfate-reducing bacteria are also linked to risks of microbiologically influenced corrosion [2][4].
These effects don't show up the same way in every setting. How significant they are depends largely on temperature, fluid composition, nutrient availability, and the microorganisms present.
Conclusion: A Constraint, but Also a Potential
The presence of microorganisms isn't just something to monitor. Some communities can also drive useful transformations. Methanogens, for instance, convert hydrogen and CO₂ into methane, a mechanism being studied in Power-to-Methane technologies [2].
More broadly, the microbiology of the hydrogen cycle also matters for carbon storage, energy gas storage, and other subsurface applications [1]. It is therefore an important factor in understanding how hydrogen evolves within geological formations and how biological and geochemical processes interact.
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Note: This article is presented for informational and educational purposes. The data and scientific results mentioned come from the cited sources and don't represent research carried out by Squatex.
References
[1] Gregory, Simon P., et al. "Subsurface Microbial Hydrogen Cycling: Natural Occurrence and Implications for Industry." Microorganisms, vol. 7, no. 2, 2019, p. 53. MDPI, https://doi.org/10.3390/microorganisms7020053.
[2] Hanišáková, Nikola, et al. "Microbiological Insight into Various Underground Gas Storages in Vienna Basin Focusing on Methanogenic Archaea." Frontiers in Microbiology, vol. 14, 2023, article 1293506. Frontiers Media SA, https://doi.org/10.3389/fmicb.2023.1293506.
[3] Černá, K., et al. "Assessment of Potential Microbial Hydrogen Consumption in European Hydrogen Underground Storage Sites." Sixth EAGE Global Energy Transition Conference & Exhibition Proceedings, 2025, pp. 1-5. European Association of Geoscientists and Engineers, https://doi.org/10.3997/2214-4609.202521032.
[4] Liu, Na, et al. "Pore-Scale Study of Microbial Hydrogen Consumption and Wettability Alteration During Underground Hydrogen Storage." Frontiers in Energy Research, vol. 11, 2023, article 1124621. Frontiers Media SA, https://doi.org/10.3389/fenrg.2023.1124621.
[5] Ruff, S. Emil, et al. "Hydrogen and Dark Oxygen Drive Microbial Productivity in Diverse Groundwater Ecosystems." Nature Communications, vol. 14, 2023, article 3194. https://doi.org/10.1038/s41467-023-38523-4.
