Biogeochemical Interactions and Their Role in European Underground Hydrogen Storage

Abstract

Integrating renewable energy requires robust, large-scale storage solutions to balance intermittent supply. Underground hydrogen storage (UHS) in geological formations, such as salt caverns, depleted hydrocarbon reservoirs, or aquifers, offers a promising way to store large volumes of energy for seasonal periods. This review focuses on the biological aspects of UHS, examining the biogeochemical interactions between H₂, reservoir minerals, and key hydrogenotrophic microorganisms such as sulfate-reducing bacteria, methanogens, acetogens, and iron-reducing bacteria within the gas–liquid–rock–microorganism system. These microbial groups use H₂ as an electron donor, triggering biogeochemical reactions that can affect storage efficiency through gas loss and mineral dissolution–precipitation cycles. This review discusses their metabolic pathways and the geochemical interactions driven by microbial byproducts such as H₂S, CH₄, acetate, and Fe²⁺ and considers biofilm formation by microbial consortia, which can further change the petrophysical reservoir properties. In addition, the review maps 76 ongoing European projects focused on UHS, showing 71% target salt caverns, 22% depleted hydrocarbon reservoirs, and 7% aquifers, with emphasis on potential biogeochemical interactions. It also identifies key knowledge gaps, including the lack of in situ kinetic data, limited field-scale monitoring of microbial activity, and insufficient understanding of mineral–microbe interactions that may affect gas purity. Finally, the review highlights the need to study microbial adaptation over time and the influence of mineralogy on tolerance thresholds. By analyzing these processes across different geological settings and integrating findings from European research initiatives, this work evaluates the impact of microbial and geochemical factors on the safety, efficiency, and long-term performance of UHS.

1. Introduction

The transition to clean energy systems has emerged as a central global objective in response to the increasingly evident impacts of climate change [1]. Renewable energies, such as solar, wind, hydropower, and geothermal, are considered key to this transition. However, the stability of renewable energy can be affected by seasonal and geographical factors, which may limit a continuous supply [2,3]. To bridge the gap between energy demand and supply, an urgent need for extensive research in identification and exploration of economically feasible energy storage methods is required. Among the various options, hydrogen (H₂) has attracted significant attention as a clean energy carrier and potential energy source, prompting intensive efforts to advance its efficient production, storage, and utilization. H₂ is an inherently energy dense carrier, with a gravimetric energy content of approximately 33.3 kWh·kg⁻¹. When it is produced by water electrolysis using renewable electricity, commonly referred to as green H₂, it combines this energy density with minimal emissions, making it an attractive option for sustainable energy storage and delivery [4]. However, its low volumetric energy density (approximately 3 kWh·m⁻³) poses a major challenge, as storing sufficient volumes to match conventional energy outputs requires substantial infrastructure and advanced storage solutions [5]. By 2050, Europe’s H₂ storage demand is projected to reach 63–180 billion standard m³, assuming a total H₂ demand of 780–2251 TWh and 24% storage capacity [6,7].

Due to their large storage capacity, low environmental impact, and minimal social impact, underground geological structures such as depleted oil and gas fields, saline and freshwater aquifers, and salt caverns are some of the most promising alternatives for storage, reaching TWh energy scales in terms of underground hydrogen storage (UHS) [8]. In Europe, current UHS projects primarily utilize artificially constructed salt caverns such as the HyUnder project [9], which have demonstrated suitability for short- to medium-term energy storage. For long-term, large-scale UHS, depleted hydrocarbon reservoirs and deep saline aquifers are particularly attractive, as they have a well-characterized geology due to past exploration and production activities [10]. However, injecting H₂ into subsurface reservoirs can stimulate the growth of hydrogenotrophic microbes, which can negatively impact storage efficiency and gas withdrawal [11]. Recent reviews highlight microbial risks in UHS, including H₂ consumption, changes in gas composition, reservoir clogging, corrosion, and microbial methanation [4,12,13,14,15,16,17]. Low-salinity and low-temperature reservoirs are particularly vulnerable, underscoring the critical sulfate-reducing bacteria (SRB) consummation of H₂ to reduce SO₄ and the need to monitor and control microbial activity in subsurface environments [18]. Additionally, microbial processes can generate corrosive metabolites such as hydrogen sulfide (H₂S), which alter pore wettability, mechanical properties, and relative permeability of the host reservoir [19]. These biogeochemical interactions can detrimentally affect H₂ transport during injection and withdrawal as well as its retention during storage.

Experience with UHS remains limited to a few pilot studies in salt caverns, depleted gas fields, and town gas storage in aquifers. Consequently, a thorough understanding of biogeochemical interactions and their influence on multiphase flow and reactive transport is critical for advancing UHS technologies. This knowledge is vital not only for optimizing hydrogen storage efficiency but also for assessing and managing potential risks, such as microbial-induced gas loss, corrosion, and reservoir clogging, particularly in European basins targeted for large-scale hydrogen storage projects [12,20]. Despite growing interest in UHS, a systematic understanding of how mineralogical variability across different geological structures influences H₂-driven biogeochemical reactions remains lacking, not to mention the countless mineralogical compositions within these same rocks that can vary over time due to the presence of microorganisms and fluids. These trigger metabolic processes, causing mineral precipitation and dissolution, with hydrogen acting as the main catalyst. This discrepancy complicates the reliable prediction of storage performance and integrity under real-world conditions.

This review consolidates current knowledge on the biogeochemical dynamics relevant to UHS in European basins, with a particular emphasis on microbial activity. It explores the roles of specific microbial groups, their metabolic pathways, and the potential geochemical interactions triggered by microbial byproducts (e.g., biofilm formation and mineral alteration). Comparing these processes across different geological structures and highlighting insights from European research initiatives, the review aims to assess how gas, liquid, rock, and microorganism (GLRM) interactions influence storage safety and performance. To address the remaining knowledge gaps, the present study (1) examines key GLRM interactions in representative geological structures and (2) summarizes possible risk cases related to biogeochemical processes in European Union projects.

2. Microbial Risk During UHS

UHS are subject to a range of biogeochemical interactions that can significantly impact their performance and long-team viability. One of the key concerns is the extreme reactivity of the injected H₂ gas, which can initiate both abiotic (mineral chemical processes) and biotic (microbially chemical process) reactions within subsurface reservoirs. While current major research indicates that abiotic reactions typically occur over extended timescales and under extreme conditions of pressure and temperature [21,22,23,24], biotic reactions are recognized as the dominant drivers of H₂ loss and pore clogging during storage [12].

This is primarily due to the role of H₂ as a highly attractive electron donor for various subsurface microbial species. These microorganisms metabolize hydrogen, leading to the production of reactive byproducts such as hydrogen sulfide (H₂S), which can degrade gas quality and induce geochemical reactions and biocorrosion of infrastructure. Biofilm formation can cause bioclogging, altering fluid flow pathways and enhancing localized geochemical reactions. These processes are embedded within the broader framework of gas–liquid–rock–microorganism (GLRM) interactions, where microbial metabolism influences geochemical equilibria in the reservoir. The resulting changes in reservoir properties—such as porosity, permeability, and mineral composition—pose challenges to the integrity and efficiency of UHS systems.

This section examines the physiochemical properties of H₂ and identifies key microbial taxa and metabolic pathways involved in subsurface interactions.

2.1. Physicochemical Properties of H₂ Gas

The physical properties of H₂ as an energy carrier determine how it is stored in geological structures. Its low molecular weight and small kinetic diameter confer a very high aqueous H₂ diffusivity, roughly 4.0 × 10⁻⁹ m²·s⁻¹ in pure water at 25 °C (and 10 bar) compared with about 1.88 × 10⁻⁹ m²·s⁻¹ for methane under same conditions, making H₂ an exceptionally mobile gas in subsurface environments [25,26]. This high mobility poses a significant challenge for UHS, particularly during stationary phases when containment stability is critical. Its small size and non-polar nature enable H₂ to diffuse rapidly through porous geological media, both in the gas phase and when dissolved in formation water, increasing the risk of leakage and its bioavailability to microbial communities even in low-permeability formations [27].

Hydrogen’s high reactivity and availability make it a central electron donor in anaerobic microbial processes within subsurface reservoirs. In deep, oxygen-deprived geological formations, microorganisms harness hydrogen to power their metabolism, coupling its oxidation to the reduction of alternative electron acceptors such as carbon dioxide, sulfate, or metal oxides. This hydrogen-driven metabolism supports key biogeochemical cycles, including sulfate reduction, methanogenesis, acetogenesis, and iron reduction, and plays a fundamental role in the long-term evolution of geochemical environments.

While hydrogen’s biochemical role is well established, its physical behavior in porous media also critically influences microbial accessibility and the overall UHS storage efficiency. The extent to which H₂ can reach and sustain microbial populations depends not only on its reactivity but also on its transport characteristics within the reservoir. These physical properties, in turn, shape the spatial distribution of microbial activity and the zones where biogeochemical transformations are most likely to occur. Parameters such as the flow velocity and mixing strength of the fluids in the medium affect the presence of bacteria in the pores [28]. Despite H₂′s high diffusivity, its low molecular density and viscosity reduce its effectiveness in transporting essential substrates to microbial communities, particularly in stagnant or low-flow zones. The injection of H₂ into porous media can lead to unstable fluid displacement due to the significant viscosity contrast between hydrogen and the resident fluids, such as brine or hydrocarbons [29,30]. This instability often results in non-uniform or preferential flow paths, creating zones of excess or limited hydrogen availability [4,31]. Such spatial variability can produce microbial “hotspots” where localized processes like hydrogen sulfide (H₂S) production or biofilm formation are intensified. These concentrated activities may alter geochemical conditions and contribute to issues such as corrosion, pore clogging, and compromised reservoir integrity.

Additionally, because of the low density, H₂ tends to accumulate at the top of the geological formation [32]. While this can reduce cushion gas requirements, it also raises the risk of lateral migration and containment loss [20]. This vertical segregation of hydrogen can lead to the development of stratified microbial ecosystems within the reservoir [33]. Microbial communities become spatially differentiated in response to local redox conditions and hydrogen availability. This stratification is further influenced by lithology, as rock type governs gas–liquid–rock–microbe (GLRM) interactions and shapes the composition of dominant microbial populations. These spatially separated communities drive heterogeneous biogeochemical processes, influencing byproduct distribution, corrosion patterns, and the long-term geochemical evolution of the reservoir.

2.2. Key Microbial Groups Involved in UHS

Four primary groups of microorganisms, sulfate-reducing bacteria (SRB), methanogens archaea, acetogens bacteria, and iron-reducing bacteria (IRB), engage in competition for H₂ gas in subsurface reservoirs. Each group metabolizes hydrogen via distinct biochemical pathways, leading to different byproducts that can adversely affect UHS operations. These microorganisms are widely distributed in sedimentary basins and aquifers, and their metabolic products can alter hydrogen purity, promote mineral precipitation, and disrupt the geochemical stability of storage formations.

Table 1. Major biogeochemical reactions and their adverse impact during UHS.

Hydrogenotrophic Microorganisms	Reaction	Byproduct(s)	Impact
Sulfate-reducing bacteria (SRB) (e.g., Oleidesulfovibrio alaskensis)	$\mathrm{S}{\mathrm{O}}_4^{2-}+4{\mathrm{H}}_2+2{\mathrm{H}}^{+}\rightleftharpoons {\mathrm{H}}_2\mathrm{S}+4{\mathrm{H}}_2\mathrm{O}$	H2S	Gas loss [19]; H2S production [12]; wettability alternation [19,34]; pH changes [15]; sulfide precipitation and biofilm formation [19].
Methanogens (e.g., Methanocalculus halotolerans)	$\mathrm{H}\mathrm{C}{\mathrm{O}}_3^{-}+4{\mathrm{H}}_2+{\mathrm{H}}^{+}\rightleftharpoons {\mathrm{C}\mathrm{H}}_4+3{\mathrm{H}}_2\mathrm{O}$	CH4	Gas contamination [18,35,36]; reducing reservoir pressure [37]; carbonate dissolution and precipitation [38].
Acetogenic bacteria (e.g., Clostridium scatologenes)	$2\mathrm{H}\mathrm{C}{\mathrm{O}}_3^{-}+4{\mathrm{H}}_2+{\mathrm{H}}^{+}\rightleftharpoons {\mathrm{C}\mathrm{H}}_4\mathrm{C}\mathrm{O}{\mathrm{O}}^{-}+4{\mathrm{H}}_2\mathrm{O}$	Acetate	Mineral dissolution [39]; pH changes [18].
Iron-reducing bacteria (IRB) (e.g., Geobacter metallireducens)	${\mathrm{H}}_2+4{\mathrm{H}}^{+}+2\mathrm{F}\mathrm{e}\mathrm{O}\mathrm{O}\mathrm{H}\to 2{\mathrm{F}\mathrm{e}}^{2+}+4{\mathrm{H}}_2\mathrm{O}$	Fe2+	Gas loss [40]; production of Fe2+ [41]; clogging [10].

summarizes key reactions and their impacts.

SRBs are among the most efficient hydrogenotrophs in sulfate-rich environments, where they reduce sulfate to H₂S, a highly corrosive and toxic compound. SRBs such as Desulfovibrio [42] are frequently detected in deep aquifers, depleted gas reservoirs, and marine sediments. Their activity is often associated with reservoir souring and infrastructure degradation [43]. Methanogens, strictly anaerobic archaea, can reduce carbon dioxide to methane using hydrogen as an electron donor. Genera such as Methanocalculus are commonly found in sulfate-depleted environments, including deep sedimentary formations and organic-rich shales [44]. Methanogenesis leads to hydrogen loss and the formation of methane, potentially impacting reservoir pressure and gas composition. Acetogens (e.g., Clostridium aceticum) use hydrogen to reduce carbon dioxide into acetate. They are known to have maximum activity at the same temperature and pressure as methanogens [40]. IRBs (e.g., Geobacter metallireducens) reduce ferric iron (Fe³⁺) to ferrous iron (Fe²⁺), which are known for their role in metal cycling and mineral transformation. IRB activity can alter reservoir properties by inducing changes in porosity, promoting mineral precipitation, and mobilizing trace metal processes that may significantly impact subsurface fluid flow and long-term reservoir performance.

The specific metabolic pathways, competitive interactions, and environmental controls governing these microbial processes are explored in detail in the following section.

3. Biogeochemical Interactions by Different Microbial Groups

Microbial activity is affected by various factors, including temperature, pH, pressure, and salinity. This section details their distinct electron acceptors, metabolic products, and geochemical consequences within the reservoir.

3.1. Sulfate-Reducing Bacteria (SRB)

SRBs are one of the most abundant microorganisms, found in environments ranging from marine sediments to the human gastrointestinal tract [45]. They can survive across a wide pH range, from highly acidic (~0.8) to alkaline (~11.5) conditions. Although they typically prefer temperatures around 38 °C and near-neutral pH conditions [46], some strains remain active at high salinity of 240 g NaCl·L⁻¹ [47] and temperatures above 100 °C [48]. Moreover, some piezophilic strains of SRBs [49] have demonstrated metabolic activity under high-pressure subsurface conditions [49,50], allowing them to function in deep geological environments relevant to UHS [51,52].

The sulfate-reduction metabolism increases the alkalinity [53], which plays a significant role in mineral precipitation, particularly carbonate minerals [53,54]. Han et al. [55] evaluated mineral precipitation of SRBs using different electron donors, including H₂. The results show that using H₂ in acetate medium, minerals such as Mg-phosphates hydrate (Mg₃(PO₄)₂ 10H₂O), calcite (CaCO₃), baricite ((MgFe²⁺)₃ (PO₄)₂ 8H₂O), and elemental sulfur precipitate. This mineralization may be linked to slight increases in the saturation index (SI), defined as the ion-activity product of dissolved species over the mineral’s solubility product, as well as to concurrent rises in carbonate alkalinity [54]. Also, Gallagher et al. [53] simulated an increase in pH in seawater caused by SRBs with different electron donors. This shows that H₂, as a metabolic resource, is one of the most significant elements that affect pH and the calcite saturation index, stimulating the precipitation of carbonate minerals, which may change the petrophysical properties such as porosity, which can be reduced by 15% by carbonates precipitation [56].

H₂S, produced by the SRB metabolic pathway, readily reacts with dissolved metals to form insoluble metal sulfides, which with the suitable conditions (pH > 6.5) [4,18] can lead to the formation of minerals (mackinawite|FeS, sphalerite|ZnS, galena|PbS, and covellite|CuS) [55]. H₂S can also promote metal corrosion, releasing ions like Fe²⁺, Zn²⁺, Pb²⁺, and Cu²⁺ from infrastructures into the fluid, which can alter pH of the fluid [18], creating an ionic imbalance that may further trigger the precipitation of minerals.

Sulfuric components are usually present in most geological formations, enabling ongoing cycles of mineral precipitation and dissolution involving sulfide minerals during UHS. Geological structures formed by sedimentary rocks contain a variety of minerals [57] that can interact with SRBs to promote mineral production under the right conditions, especially during hydrogen storage operations, and this makes it necessary to consider possible underground storage sites.

3.2. Methanogens

Subsurface methanogens are commonly found in anoxic, low-redox environments depleted in alternative electron acceptors such as sulfate and nitrate [58]. Methanogens exhibit a broad range of temperature and salinity tolerances that reflect their diverse ecological niches [10,59]. Methanogens exhibit wide physiological adaptability, with mesophilic species favoring 30–40 °C, thermophiles thriving at 50–65 °C, and hyperthermophiles tolerating up to 80–110 °C. They can withstand salinities ranging from approximately ~0.77 to ~3.4 M NaCl (equivalent to 45–200 g·L⁻¹) and pressures in the region of ~0.1 to ~75 MPa. Optimal growth occurs at a pH of 6.0–7.5, though they remain viable between pH 4.5 and 9; beyond this range, their activity is strongly inhibited [18].

Experience from hydrogen-rich gas storage operations—such as the Underground Sun Storage and Sun Conversion projects in Austria [60,61,62] and the HyChico project in Argentina—shows that methanogenic archaea consume hydrogen at rates of 0.01 to 0.2 mmol H₂·L⁻¹·day⁻¹, with activity strongly influenced by environmental conditions. In the H₂-rich underground gas storage facility at Lobodice, Czech Republic, methanogens were responsible for hydrogen losses of up to 17% over seven months, highlighting the significant impact of methanogenesis on microbial hydrogen consumption in engineered subsurface systems [63].

Methanogenesis in subsurface reservoirs can significantly alter the geochemical balance by leading to methane accumulation and shifts in redox conditions, which potentially promote the precipitation or dissolution of carbonate minerals [64]. Elevated methane levels also impact gas composition and pore pressure, influencing reservoir dynamics. Methane can be further consumed through anaerobic oxidation of methane (AOM) by SRB (see Figure 1), generating bicarbonate and H₂S [65]. The production of H₂S lowers the pH, while the bicarbonate increases alkalinity, together disturbing carbonate equilibrium and enhancing carbonate mineral precipitation (e.g., CaCO₃ and MgCO₃) if sufficient ion concentrations are present [17]. These microbial processes also influence mineral stability and porosity by affecting reactions like ferric iron reduction and authigenic clay formation. Collectively, these microbe–mineral interactions are crucial for long-term carbon sequestration and subsurface diagenesis, linking microbial metabolism to changes in reservoir chemistry and physical properties.

3.3. Acetogens

Acetogens typically thrive under mesophilic temperatures with an optimum around 20–30 °C and can tolerate salinities below 40 g·L⁻¹. Their optimal pH range is moderately neutral, between 6.0 and 7.5, with critical limits extending from 3.6 to 10.7 [18]. While their hydrogen consumption rates are lower compared to methanogens, some acetogens have been estimated to consume between 0.01 and 0.05 mmol H₂·L⁻¹·day⁻¹, depending on CO₂ concentrations and the availability of other nutrients [18].

Since methanogens and acetogens metabolize almost identical substrates, there may be strong competition between them, depending on environmental conditions and microbial populations [67]. Under certain thermodynamic conditions, acetate produced by acetogens can be converted back into H₂ and CO₂ [68]. Oxidation of acetate generates bicarbonate, which increases local alkalinity and alters carbonate equilibria, thereby promoting either precipitation or dissolution of carbonate minerals such as calcite (CaCO₃), magnesite (MgCO₃), and siderite (FeCO₃), depending on the availability of ions and the chemistry of the surrounding fluid. Moreover, acetate serves as an essential carbon and energy source for SRB, linking acetogenic activity to sulfate-reduction pathways that often result in the precipitation of sulfate minerals like anhydrate (CaSO₄) and pyrite (FeS₂) [40].

The metabolic interplay among methanogens, acetogens, and SRB is highly sensitive to environmental parameters such as temperature, salinity, and pH. Thaysen et al. [18] provided a comprehensive review highlighting the effects of reservoir conditions on these microbial groups, identifying preliminary optimal and critical thresholds for each. Accurate determination of these parameters is essential for effective site selection and management of subsurface reservoirs, enabling mitigation of microbial energy losses and maximizing hydrogen storage efficiency.

3.4. Iron-Reducing Bacteria (IRB)

IRB usually grow optimally at 0–30 °C but can survive temperatures up to 90 °C and an optimal pH around 6–7.5, but some strains can survive in wide range like 1.6 to 9. In addition to carbon sources, they require iron oxides, which are prevalent in aquifers and depleted gas and oil reservoirs. These geological structures are mainly composed of sedimentary rocks and contain clay minerals such as smectite (e.g., nontronite, (Na,Ca)_0.3(Fe,Al)₂(Si,Al)₄O₁₀(OH)₂ nH₂O) [69] and chlorite (e.g., clinochlore, (Mg,Fe³⁺)₅Al((OH)₈/AlSi₃O₁₀)) [70]. These minerals incorporate metal ions (Fe) into their crystal structure, providing a key source of reactive metal ions for microbial activity. The metabolic pathway requires relatively low activation energy (−114 to −228.3 ΔG°′ (kJ·mol⁻¹ H₂)) [18] compared with the other reactions to reduce Fe³⁺ (ferric), which oxides to Fe²⁺ (ferrous) [71]. Fe²⁺ can then precipitate as FeS when combined with SRB activity or as siderite (FeCO₃) if HCO₃⁻ is available and the pH near neutral to slightly alkaline [17].

Figure 2 presents a simplified diagram of geochemical and microbial interactions (GLRM), emphasizing the role of IRB during UHS. In this process, H₂ serves as an electron donor, reducing the insoluble Fe³⁺ to soluble Fe²⁺. This microbial reduction destabilizes the mineral structure, releasing Fe²⁺ into the aqueous phase. The mobilized Fe²⁺ can then interact with dominant anions such as carbonate (CO₃²⁻), phosphate (PO₄³⁻), or sulfide (S²⁻), leading to mineral precipitation. Fe²⁺ accumulates until ionic saturation is reached [18,71]. Once the saturation threshold is exceeded, heterogeneous nucleation occurs, often on cell surfaces acting as preferential sites for mineral aggregation. Crystalline growth and maturation follow with successive incorporation of Fe²⁺ and anions into the forming mineral structure [72]. Depending on the geochemical environment, this can consolidate minerals such as siderite (FeCO₃) in carbonate-rich environments, vivianite (Fe₃(PO₄)₂8H₂O) when phosphate is available, and mackinawite (FeS) and pyrite (FeS₂) in the presence of sulfide [72,73,74]. These biogenically precipitated ferrous minerals accumulate on rock surfaces and induce measurable changes in key petrophysical properties, such as permeability, porosity, and wettability [75]. This is a parameter of great importance in the context of UHS and working gas extraction.

Thus, the influence of these microorganisms on the geochemistry of geological formations is significant, as they can induce mineral precipitation cycles that generate secondary minerals unrelated to the mineralogy of the geological structure. These alterations can modify the original petrophysical properties, leading to H₂ loss and reducing their flow during injection and withdrawal process. Figure 3 presents a schematic of the biogeochemical cycles that may occur during subsurface H₂ storage in the presence of microbial activity.

3.5. Biofilms

In addition to inducing mineral precipitation, biofilm formation can significantly modify the geophysical properties of the porous medium by reducing permeability, altering wettability [19], triggering further mineral precipitation [38], blocking pore throats, and/or redirecting fluid flow toward larger pores or alternative channels [42]. Biofilms are defined as complex biological systems, which are commonly formed by microbial communities adhered to the surface by producing a matrix of extracellular polymeric substances (EPS), proteins, and extracellular DNA [78,79]. The biofilm growth cycle generally includes the following stages (Figure 4): (i) initial adhesion of planktonic cells to a surface; (ii), induction of irreversible adhesion by accumulation of microorganism; (iii), early structural development with generation of EPS coverage; (iv), maturation of the biofilm; (v) detachment of cells from the biofilm matrix; and (vi) regrowth in old and new places [4,13,80]. In the first phase, individual microorganisms encounter and firmly attach to the surface through specific surface interactions and adhesive structures. Once anchored, they multiply and secrete EPS, establishing the nascent biofilm matrix and driving its initial expansion. Then, as the biofilm develops, the EPS scaffold thickens and diversifies, creating chemically and physically distinct microniches (heterogeneous matrix); cells adopt varied physiological states: some enter dormant or stress-tolerant modes, while cooperative and competitive behaviors emerge, stabilizing the community’s architecture. Finally, in the last stage, the established EPS network undergoes targeted remodeling, triggering dispersal mechanisms. Clusters of cells detach, either as single cells or as aggregates, and return to the planktonic phase, ready to colonize new surfaces and perpetuate the biofilm life cycle.

The EPS matrix is primarily composed of polysaccharides, proteins, lipids, and nucleic acids, which serve to protect the embedded microbial cells from environmental virulence, stress factors and stripping [81]. These biofilm-mediated processes are of particular interest in subsurface hydrogen storage applications, where biofilm growth and EPS production can influence H₂ migration, retention, and potential bioreactivity within the reservoir.

Biofilm formation may lead to bioclogging, primarily observed in proximity to the fresh nutrient supply, promoting microbial growth and reduction in H₂ injectivity and altering the subsurface transport properties [19]. Despite its negative impact on H₂ injectivity, the effect of bioclogging during H₂ storage is not entirely detrimental. In fact, it was discovered that biofilms forming in areas of high H₂ saturation can impede the vertical rise of H₂ gas and facilitate more uniform radial gas penetration into the reservoir, which makes bioclogging beneficial for UHS [82]. However, biofilms vary significantly in their characteristics, which are shaped by the specific microorganisms involved and their interactions with the surrounding biogeochemical environment within the porous medium. In recent work, Liu et al. [42] reported that the sulfate-reducing bacterium Oleidesulfovibrio alaskensis G20 poses a low risk of bioclogging during cyclic UHS operations due to its increased cell motility and reduced biofilm attachment.

Nevertheless, biofilm formation is tightly regulated by nutrient availability, flow conditions, and environmental parameters including pH, temperature, and salinity. For instance, SRB activity increases mildly acidic pH (~5), where sulfide production can be 60% higher compared to neutral conditions [83]. High flow rates enhance nutrient supply but may shear off biofilm biomass, altering EPS output [80]. Consequently, in environments where microbes compete, the accumulation of metabolic by-products may modulate the activation of other species, establishing dynamic feedback loops among microbial communities. Table 1 summarizes the type of biofilms and the possible products for most relevant microorganisms in the UHS process.

Biofilm formation on rock surfaces alters surface characteristics and can lead to changes in wettability [42]. In a silicon pore network at 35 bar and 37 °C, Liu et al. [19] showed that growth of the halophilic sulfate-reducing bacterium Desulfohalobium retbaense in the presence of H₂ shifted surface wettability from water-wet to neutral-wet, reducing capillary pressure and enhancing gas recovery. Boon et al. [14] investigated the impact of surface roughness on two substrates (Bentheimer sandstone and quartz). In Bentheimer sandstone, which had a roughness of ~0.03 mm, biofilms tended to accumulate in deeper topographic depressions without significantly altering wettability. By contrast, on polished quartz (with a roughness of ~0.003 mm), the biofilm formed a uniform coating across the surface, modifying the contact angle and increasing hydrophilicity. This behavior can be explained by Wenzel’s model, which states that increased roughness amplifies a surface’s intrinsic hydrophilic or hydrophobic characteristics.

Biofilm formation is not solely determined by physical properties but also by the chemical composition of the rock [76,84]. In rocks with high clay content or complex porous structures, the high water retention capacity promotes the formation of organo-mineral aggregates, which serve as ideal microhabitats for microorganisms [76,85]. This facilitates biofilm development due to the availability of water, organic matter, and metallic substrates, such as potassium (K⁺), sodium (Na⁺), and nitrogen compounds. Crystalline structures such as kaolinite and smectite/montmorillonite (clay minerals of the 1:1 and 1:2 types, respectively) have different cation exchange capacities (10–80 milliequivalents 100 g⁻¹), a feature that is key for nutrient transport within biofilms. Consequently, smectite/montmorillonite is considered one of the most favorable clays for microbial anchoring due to its capacity to absorb organic molecules within its interlayer spaces (see Figure 5) [76]. It regulates the mobility of ions and the kinetics of nucleation, causing reactive solutes to precipitate and determining the spatial distribution and texture of all subsequent microbially induced precipitates.

Biofilm-induced microbiologically influenced corrosion (MIC) poses a significant risk to metal infrastructure and reservoir rocks in potential UHS sites. Biofilms accelerate corrosion by concentrating corrosive agents, facilitating electron transfer, and reducing the effectiveness of mitigation strategies [86,87]. Biofilms promote uneven bacterial colonization, forming differential aeration cells where thicker, oxygen-depleted colonies become anodic, and thinner ones become cathodic, thereby facilitating localized corrosion [88]. More severe corrosion has been observed in multispecies biofilms, where microbial interactions may trigger cascades of corrosive biochemical reactions. Diverse microbial communities, including sulfate-reducing, iron-oxidizing, iron-reducing, and acid-producing bacteria, are involved, with SRB identified as key contributors [89]. In UHS systems, molecular H₂ acts as an electron donor for SRB, enhancing hydrogen sulfide production and subsequent metal sulfide precipitation through electrochemical reactions. Biofilms can also promote differential aeration and localized corrosion, especially in multispecies communities. Conversely, some biofilms may offer protective effects by serving as diffusion barriers or by outcompeting corrosive species. Understanding and managing these biofilm-related processes is critical for ensuring the long-term integrity of UHS infrastructure.

4. Potential Storage Sites

Biogeochemical processes play a central role in the behavior of H₂ stored underground, reflecting the interaction between the host rock, reservoir fluids, and microbial communities. The outcome of these effects depends on the type of geological formation. This section outlines the key microbial and geochemical processes influencing H₂ behavior across different geological formations including salt caverns, depleted hydrocarbon reservoirs, and aquifers [12].

4.1. Salt Caverns

The high salinity of salt caverns, typically ranging between 2.5 and 5.2 M NaCl, creates intense osmotic stress, which only extreme halophilic microorganisms can tolerate [18]. Due to the low availability of sulfate, the presence of SRB in salt caverns is limited [18]. Nevertheless, some halophilic strains such as Desulfovibrio oxyclinae and Desulfohalobium retbaense, which are capable of tolerating highly saline conditions (up to 4.2 M NaCl), may still be present in these types of structures [18]. Most other microbial groups may become inactive at salinities above 4.7–8.1 M NaCl, and SRBs are likely the most active microorganisms in such high-salinity environments. In highly saline environments, water activity can drop below 0.75, whereas an optimal level for microbial growth is around 0.98 even for halophilic microorganisms [18]. This low water activity creates a hostile environment that inhibits microbial activity both in the short and long term.

In salt caverns used for H₂ storage, SRBs consume H₂ to reduce SO₄²⁻ to S²⁻, precipitating sulfides such as mackinawite and pyrite in the presence of Fe²⁺ or Mn²⁺. Simultaneously, IRBs reduce Fe³⁺ to Fe²⁺, promoting the bioprecipitation of siderite and magnetite under high CO₂ concentrations [90]. Acetogens and methanogens compete for H₂ and CO₂ [91], generating alkalization that promotes the dissolution of gypsum and the reprecipitation of carbonates (calcite and magnesite) on cell surfaces and in interstitial spaces [16].

Table 2. Common minerals in salt caves, including their chemical formulas, their classification as primary components, common impurities, secondary minerals, trace impurities, and the biogeochemical reaction pathways in the presence of H₂ and microorganisms [92,93,94].

Mineral	Chemical Formula	Classification	Interaction
Halite	NaCl	Primary component	-
Anhydrite	CaSO4	Common impurity	SRB and A|M
Gypsum	CaSO4·2H2O	Common impurity	SRB and A|M
Sylvite	KCl	Secondary mineral	-
Carnallite	MgCl2 KCl·6H2O	Secondary mineral	A|M
Polyhalite	K2Ca2Mg(SO4)4·2H2O	Secondary mineral	SRB and A|M
Quartz	SiO2	Trace impurity	-
Calcite	CaCO3	Trace impurity	A|M

(-) → Inert: do not participate in transformations even in the presence of H₂. (SRB) → Sulfate-reducing bacteria: use H₂ to reduce SO₄²⁻ to HS⁻|S²⁻, precipitating sulfides when metals such as Fe²⁺ or Mn²⁺ are present. (A|M) → Acetogens|Methanogens: consume H₂ and CO₂, raise the local pH, and promote carbonate precipitation (CaCO₃ or MgCO₃). (IRB) → Iron-reducing bacteria: do not act directly on these anhydrous or halide minerals, only on iron oxides.

lists the most common minerals found in salt caverns that can promote biogeochemical reactions.

4.2. Depleted Hydrocarbon Reservoirs (DHR)

Depleted hydrocarbon reservoirs (DHR) are geological structure with intergranular storage spaces and a large energy storage capacity (1.5–600 TWh) [95]. Compared to salt caverns, which hold only about 10% of the capacity of porous reservoirs [96], DHR offers a more cost-effective option for large scale storage. Their viability depends on the presence of rocks with high porosity and permeability, along with an effective seal rock to prevent gas leakage. However, residual hydrocarbons (occupying at least 10%–40% of the storage space) [97] can serve as carbon sources for various microorganisms. The injection of H₂ can then trigger multiple chemical reactions with both the microbes and the host rock. Hydrocarbon reservoirs can be classified according to the type of hydrocarbon they store or their structural component [98]. However, considering the focus on GLRM interactions, a non-usual classification is used, which is based on the type of rock, emphasizing its mineralogical component. Accordingly, hydrocarbon reservoirs can be classified into three main groups: sandstone, shale, and carbonates (see

Table 3. Primary mineralogical compositions of target reservoir lithologies and associated H₂-driven biogeochemical reactions in hydrocarbon reservoir minerals (sandstone, shale, and carbonate), considering only dominant minerals [99,100,101,102,103].

Rock Type	Minerals	Chemical Formula	Quantity in Rock (%)	Interaction
Sandstone	Quartz	SiO2	~45–50	-
	Feldspar	(K, Ca, Na, Ba)AlSi2O8	~35–40	- °
	Clay	(Fe, Mg, Ca, K, N)Al2O3 2SiO2·2H2O	~10–20	- °°
Shale	Clay	(Fe, Mg, Ca, K, N)Al2O3 2SiO2·2H2O	~58	- °°
	Quartz	SiO2	~28	-
	Feldspar	(K, Ca, Na, Ba)AlSi2O8	~6	- °
	Carbonates	CO32−	~5	A|M
	Iron Oxides	Fe2O3	~2	SRB and IRB
Carbonate	Calcite	CaCO3	~50–60	A|M
	Dolomite	CaMg(CO3)2		A|M
	Quartz	SiO2	~5–40	-
	Clay	(Fe, Mg, Ca, K, N)Al2O3 2SiO2 2H2O		- °°

- °: crystalline aluminosilicate framework remains unchanged under biogenic H₂ consumption; - °°: phyllosilicate structures do not precipitate or dissolve in response to microbial H₂ oxidation and may act as adsorption sites of free ions on the surface or in the laminar spaces.

). These rocks are in turn composed of a wide variety of minerals with the ability to react with the new working gas (H₂). However, for the purposes of this study, the most representative minerals are considered since accessory minerals such as sulfates, carbonates, and iron oxides may also be present, and the exact mineralogical makeup can vary significantly between different reservoirs.

The presence of organic components in the reservoir would mean a reduction in GLRM interactions; however, thermodynamically, there is a preference of H₂ over CH₄ due to the energy gain: sulfate reduction with H₂ releases up to ~−152 kJ per mole of SO₄²⁻ (≈−38 kJ·mol⁻¹·H₂⁻¹), whereas anaerobic oxidation of methane (AOM) coupled with sulfate yields only approximately −20 kJ·mol⁻¹·CH₄⁻¹, which is close to the minimum threshold required to sustain microbial respiration (threshold ΔG_(min) ≈ −20 kJ·mol⁻¹). This difference is why bacteria prioritize using H₂, thereby maximizing both their energy yield and the production of mineral precipitates in the reservoir [104].

The minerals that can precipitate under the influence of microorganisms vary depending on the type of microorganism as well as the thermodynamic conditions of the deposits and the availability of metal cations in the aqueous phase. SRB can precipitate secondary sulfides when Cu²⁺ or Ni²⁺ are available, such as chalcopyrite (CuFeS₂), cubanite (CuFe₂S₃), and pentlandite ((Fe,Ni)₉S₈) [105,106,107]. These are commonly found in environments with organic matter such as shale or, to a lesser extent, sandstone [108,109,110]. IRB release Fe²⁺, which can react with dissolved phosphate, forming vivianite (Fe₃(PO₄)₂8H₂O). In the presence of Ca²⁺ and Mg²⁺, it can then crystallize in ankerite (Ca(Fe,Mg)(CO₃)₂) [74]. Vivianite is mainly found in porphyry or granitoids but can also be present in sedimentary rocks like slate and shale through diagenetic processes [111]. Additionally, alkalinization generated by acetogens and methanogens in Mg²⁺-rich microenvironments promotes the nucleation of magnesite (MgCO₃), and in the presence of Mn²⁺, rhodochrosite (MnCO₃) can also precipitate [112].

The presence of new mineralogical structures, such as biogeochemistry-precipitated minerals, changes the flow patterns of the working gas (H₂), increasing the uncertainty about the gas dynamics in the geological structures. Combined with the physical properties of this gas, which has a clear tendency toward capillary interdigitation [4] due to high interfacial tensions between the displacing and displaced fluid because capillary forces are superimposed on viscous forces [4,30,113,114], this adds instability during drainage and imbibition processes.

4.3. Aquifers

Subsurface aquifers are geological formations that store and supply groundwater. They are classified by their lithological characteristics: (i) unconsolidated sedimentary aquifers, represented by loose sand and gravel deposits; (ii) consolidated sedimentary aquifers, such as sandstone and limestone formations; (iii) fractured-rock aquifers, comprising fissured igneous and metamorphic bedrock; and (iv) karst aquifers, developed within soluble carbonate lithologies like limestone and dolomite [115].

Since most aquifer host rocks are sedimentary in nature, their mineral composition is similar to that of depleted oil and gas reservoirs, as discussed in the previous section. Table 4 shows the predominant mineral composition of underground aquifers, categorized by rock type into four main groups. Quartz and feldspar are the main minerals found in unconsolidated sand and gravel as well as sandstone aquifers. They are highly resistant to chemical and physical breakdown, allowing them to survive transport and accumulate in high-porosity deposits. Despite their stability, certain microorganisms, including archaea, can interact with these minerals in ways that promote the formation of carbonates [85].

Clay minerals (e.g., illite, montmorillonite, and kaolinite) are also abundant in these siliciclastic settings. Their fine grain size and platy morphology allow clay minerals to settle in low-energy environments and provide vast surface area for adsorption [85]. This structure is particularly attractive to bacteria because clays with 2:1 structure (illite, montmorillonite, vermiculite, and chlorite) can retain water between their layers, making them ideal for biofilm formation and cationic nutrient exchange due to their overall negative charge [76,84,116]. When this divalent metal cation exchange occurs between its layers, it acts as a catalyst between the bacteria that take refuge in the clays, facilitating biogeochemical interactions such as mineral precipitation. Moreover, in this bidirectional interaction (microorganism → rock and rock → microorganism), once the biofilm is anchored to the clay, microorganisms such IRB can reduce the structural Fe³⁺ present in clay minerals, particularly in the octahedral and tetrahedral layers, transforming it into Fe²⁺ via microbial reduction. This process is closely linked to reservoir integrity, as a reduction of more than 33% in the amount of structural Fe³⁺ can lead to significant reductive mineral dissolution [76]. This weakens the rock matrix and increases the risk of H₂ leakage as well as the formation of secondary minerals such as amorphous silica, siderite, and illite [76,84].

In contrast, carbonate aquifers (limestone/dolomite karst) inherit their high calcite and dolomite content directly from primary marine or lacustrine precipitation, making re-precipitation of these same phases the path of least resistance under microbial alkalinization [117,118]. Fractured igneous and metamorphic rocks expose fresh minerals that contain Fe (e.g., primary Fe-oxides and pyrite) along fracture walls, so IRB-mediated reduction readily liberates Fe²⁺ and fosters secondary siderite, magnetite, and vivianite growth precisely where reactive surfaces are most accessible [119,120].

Table 4. Mineral composition of the rocks that make up the different types of aquifers and their interaction with the most representative bacteria in UHS processes [115,121,122,123].

Aquifer Type	Rock Type	Minerals	Interaction
Unconsolidated sedimentary	Sand and gravel	Qz, Or, Ab, Ill, Mt, Kln	A|M, IRB
Consolidated sedimentary	Sandstone	Qz, Or, Ab, Ill, Mt, Kln	IRB, A|M
	Limestone	Cal, Dol, Py	A|M
Fractured rock	Igneous (granite/gneiss)	Qz, Or, Ab, Py	IRB
	Metamorphic (schist/gneiss)	Qz, Or, Ab, Py	IRB
Karst	Carbonate (limestone/dolomite)	Cal, Dol	A|M, IRB (indirect)

Qz—quartz (SiO₂); Or—orthoclase (K-feldspar) (KAlSi₃O₈); Ab—albite (Na-feldspar) (NaAlSi₃O₈); Ill—illite (K_0.65Al_2.0–3.5Si_3.5–2.0O₁₀(OH)₂); Mt—montmorillonite (Smectite) ((Na,Ca)_0.33(Al,Mg)₂Si₄O₁₀(OH)₂·nH₂O); Kln—kaolinite (Al₂Si₂O₅(OH)₄); Cal—calcite (CaCO₃); Dol—dolomite (CaMg(CO₃)₂); Py (FeS₂).

Table 4. Mineral composition of the rocks that make up the different types of aquifers and their interaction with the most representative bacteria in UHS processes [115,121,122,123].

Aquifer Type	Rock Type	Minerals	Interaction
Unconsolidated sedimentary	Sand and gravel	Qz, Or, Ab, Ill, Mt, Kln	A|M, IRB
Consolidated sedimentary	Sandstone	Qz, Or, Ab, Ill, Mt, Kln	IRB, A|M
	Limestone	Cal, Dol, Py	A|M
Fractured rock	Igneous (granite/gneiss)	Qz, Or, Ab, Py	IRB
	Metamorphic (schist/gneiss)	Qz, Or, Ab, Py	IRB
Karst	Carbonate (limestone/dolomite)	Cal, Dol	A|M, IRB (indirect)

Qz—quartz (SiO₂); Or—orthoclase (K-feldspar) (KAlSi₃O₈); Ab—albite (Na-feldspar) (NaAlSi₃O₈); Ill—illite (K_0.65Al_2.0–3.5Si_3.5–2.0O₁₀(OH)₂); Mt—montmorillonite (Smectite) ((Na,Ca)_0.33(Al,Mg)₂Si₄O₁₀(OH)₂·nH₂O); Kln—kaolinite (Al₂Si₂O₅(OH)₄); Cal—calcite (CaCO₃); Dol—dolomite (CaMg(CO₃)₂); Py (FeS₂).

However, porous wet sandstones have demonstrated great stability in UHS due to a characteristic behavior where brine remains confined to the corners and throats of the porous system, slightly reducing GLRM interaction due to configuring a characteristic displacement behavior known as capillary fingering [124,125,126], which in the long term may be beneficial to the UHS process. Furthermore, these interactions are bidirectional: while the reservoir environment influences the activity of microorganisms, these microorganisms impact the petrophysical properties of the host rock, such as wettability, porosity, and permeability. Thoroughly understanding these interactions is essential for developing UHS over extended timeframes, as this enables risks to be minimized and capital investment to be protected in these projects.

5. European Union Projects

A total of ~140 hydrogen storage projects are underway across Europe, with capital investments varying greatly in scale from around EUR 9 million at TH2ICINO_LHYFE in Italy to EUR 40 billion at NEOM GREEN HYDROGEN in Saudi Arabia [127]. Additionally, an annual production ranging from 90 to 1,000,000 t H₂·yr⁻¹ is expected in projects like Hydrogen Valley South Tyrol (Italy) and Europe’s Hydrogen Hub: H₂ Proposition Zuid-Holland/Rotterdam (Rotterdam, The Netherlands), respectively. While these projects are at different stages of development, some, such as ZEV (Zero Emission Valley, Auvergne Rhône, France), HyBalance (Hobro, Denmark), Green Hysland (Mallorca, Spain), and eFarm (Nordfriesland, Germany), are already operational [127,128,129]. These projects cover the entire value chain, including primary energy integration, hydrogen production, storage, transport, and distribution. Additionally, the application areas include supplying hydrogen to gas-fired power stations, injecting hydrogen into existing gas networks, and powering stationary fuel cells for distributed generation [127].

According to H₂ Valley Map, the projects included in its database encompass a total of 76 storage projects, where 38 plan to use surface cylinder-based storage systems; 29 have not yet chosen their storage technology, or the information is not available; and 11 of them focus specifically on UHS, where the focus is salt cavern (CAV) structures [127]. Additionally, HyUSPRe and REPowerEU Plan show a new perspective where CAV, depleted hydrocarbon reservoirs (DHRs), and aquifers (AQUs) are considered in the UHS process [122].

Table 5. Overview of European hydrogen projects targeting UHS in salt caverns, aquifers, and depleted hydrocarbon reservoirs.

Project Name	Lead Developer	Location	Type Storage
Amber Hydrogen Valley	Orlen S.A.	Poland	CAV [127]
Basque Hydrogen Corridor (BH2C)	Petronor (Repsol Group)	Spain	CAV [130]
Clean Hydrogen Coastline	EWE AG	Germany	CAV [131]
Cluster NortH2	Evida and Gas Storage Denmark	Denmark	CAV [132,133]
HEAVENN	New Energy Coalition	The Netherlands	CAV [134]
Hydrogen Delta	Smart Delta Resources	The Netherlands	CAV [135]
Hydrogen Valley Estonia	Participating in Hansa Hydrogen Hubs	Estonia	CAV [136]
HyNet North West	Progressive Energy	The UK	CAV [137]
Ulster Hydrogen Valley	B9 Energy Storage Ltd.	The UK	CAV [127]
ZEV–Zero Emission Valley	Auvergne-Rhône-Alpes Regional Council	France	CAV [127]
Rehden Storage Facility	Astora|SEFE Storage GmbH	Germany	CAV [138]
H2RENGRID–Carrico UGS	REN	Portugal	CAV [139]
H2Burgos	Hidrogeno de Burgos	Spain	CAV [129]
H2 storage North-2	Enagás Infraestructuras de Hidrógeno	Spain	CAV [140]
HySoW storage	Terega SA	France	CAV [141]
GEOGAZ H2	Geogaz Lavera	France	CAV [129]
Masshylia	ENGIE	France	CAV [129]
GeoH2	Storengy SAS, Geomethane	France	CAV [129]
HyManosque	GEOSEL Manosque	France	CAV [129]
Extension Aura	Storengy SAS	France	CAV [129]
HyPSTER (1st, 2nd, and 3rd phase)	Storengy SAS	France	CAV [129]
StorgrHYn (1st, 2nd, and 3rd phase)	Storengy SAS	France	CAV [129]
Green Hydrogen Hub Zuidwending	Corre Energy BV	The Netherlands	CAV [142]
Hystock Opslag H2	N.V. Nederlandse Gasunie	The Netherlands	CAV [143]
Green Hydrogen Hub Drenthe	Corre Energy BV	The Netherlands	CAV [142]
HyCAVmobil	EWE AG et al.	Czechia	CAV [129]
Damaslawek Hydrogen Storage	GAZ-SYSTEM S.A.	Poland	CAV [144]
Aldbrough Hydrogen Storage	Equinor, SSE Thermal	The UK	CAV [145]
H2 storage@Kish	ESB et al.	Ireland	CAV [129]
Green Octopus Mitteldeutschland	VNG Gasspeicher	Germany	CAV [146]
RWE H2 Storage Staßfurt	RWE Gas Storage West GmbH	Germany	CAV [147]
EWE Hydrogen Storage Rüdersdorf	EWE GASSPEICHER	Germany	CAV [129]
UHS Peckensen I and II	Storengy Deutschland GmbH	Germany	CAV [129]
Green Hydrogen Hub Moeckow	Corre Energy BV	Germany	CAV [142]
UST Hydrogen Storage Epe	Uniper Energy Storage GmbH	Germany	CAV [129]
GET H2 IPCEI	RWE Gas Storage West GmbH	Germany	CAV [147]
Green Hydrogen Hub Ahaus-Epe	Corre Energy BV	Germany	CAV [142]
RWE Gronau (1st, 2nd, 3rd expansion)	RWE Gas Storage West GmbH	Germany	CAV [147]
Green Hydrogen Hub Harsefeld	Corre Energy BV	Germany	CAV [142]
SaltHy Harsefeld (1st, IIA, IIB phase)	Storengy Deutschland GmbH	Germany	CAV [148]
UHS Bremen-Lesum	Storengy Deutschland GmbH	Germany	CAV [129]
CHC Hydrogen Storage Huntorf ICPEI	EWE GASSPEICHER	Germany	CAV [149]
Green Hydrogen Hub Leer	Corre Energy BV	Germany	CAV [142]
CHC Hydrogen Storage Jemgum	EWE GASSPEICHER	Germany	CAV [129]
JemgumH2	SEFE Storage GmbH	Germany	CAV [150]
CHC Hydrogen Storage Nüttermoor	EWE GASSPEICHER	Germany	CAV [129]
Green Hydrogen Hub Drenthe	Corre Energy BV	Germany	CAV [142]
Hystock Opslag H2	N.V. Nederlandse Gasunie	Germany	CAV [143]
Green Hydrogen Hub Zuidwending	Corre Energy BV	Germany	CAV [142]
UST Hydrogen Storage Krummhörn	Uniper Energy Storage GmbH	Germany	CAV [151]
Green Hydrogen Hub Etzel	Corre Energy BV	Germany	CAV [142]
SpHyGer (GSE)	Gasunie Energy Development GmbH	Germany	CAV [129]
H2CAST	Storag Etzel	Germany	CAV [152]
NWKG H2 Storage	NWKG	Germany	CAV [153]
US Conversion	RAG	Austria	DHR [154]
USS 2030	RAG	Austria	DHR [154]
USS Scale-Up	RAG	Austria	DHR [154]
Aquamarine	HGS	Hungary	DHR [154]
Green Hydrogen	dCarbonX	Ireland	DHR [154]
UGS Velke Kapusany	Nafta	Slovakia	DHR [154]
H21-S&D	Nafta	Slovakia	DHR [154]
Aljarafe Project	Trinity Energy Storage SL	Spain	DHR [155]
Fiume Trieste UHS pilot test	SNAM/STOGIT	Italy	DHR [129]
Sergnano H2 storage	SNAM/STOGIT	Italy	DHR [129]
HyUS-Pre	HyUs-Pre	Hungary	DHR [128,155]
South Kavala UGS facility	HRADf	Greece	DHR [129]
Cretan H2SF–Development of Green H2	EUNICE	Greece	DHR [129]
UGS Lab-H2	NAFTA a.s.	Slovakia	DHR [129]
Project Kestrel	ESB, dCarbonX, Snam partnership	Ireland	DHR [129]
HyStorage	Uniper Energy Storage GmbH	Germany	DHR [151]
H2 Umstellung UGS Kirchheilingen	Thüringer Energie AG et al.	Germany	DHR [156]
H2 Readiness	RWE	Czechia	AQU [154]
Lacq Hydrogen	Terega	France	AQU [154]
HyPSTER	Storengy	France	AQU [154]
H2SS Latvia	Conexus	Latvia	AQU [154]
Yela H2 storage	Enagás Infraestructuras de Hidrógeno	Spain	AQU [140]

summarizes the projects targeting underground storage with the available data. The geological structures used for this purpose include the three structures mentioned above.

In line with projects proposed in Europe, there is a clear preference for some structures, such as CAVs. These dominate UHS projects, making up roughly 71% of schemes. Meanwhile, DHRs are the next most common choice, accounting for around 22% of projects, particularly in regions underlain by mature oil and gas fields (e.g., parts of Italy, Spain, and Austria). Otherwise, AQU storage remains a niche solution (around 7%), largely due to greater uncertainties in geological and hydrodynamic behavior, with only a few demonstration projects having been developed in France mainly.

Currently, most EU countries have underground gas storage facilities, providing prior experience in this area. However, biogeochemical interactions have received little or no study, creating a knowledge gap that must be addressed to improve the safety of UGS. In particular, interactions in GLRM systems have not been studied in isolation, yet they must be considered due to their potential to alter the physical properties of the reservoir and the working gas chemistry.

Salt caverns are the most common geological setting for current UHS (Table 5) due to their low degree of contamination, low risk of leakage, and low cushion gas requirements [12,38,157]. In Europe, this technology has been considered in regions with widespread salt formations from the Permian and Triassic periods [158]. These include large parts of the United Kingdom, the Netherlands, Germany, Poland, Denmark, and Lithuania, where salt domes and salt mantles are found at depths of up to 1000 m [158,159].

Despite salt caverns’ favorable conditions, GLRM interactions still pose risks under suitably moderated salinity and water activity conditions. If brine infiltrates through microfractures, localized acidification may occur via Fe³⁺ reduction by iron-reducing bacteria (IRB, e.g., Shewanella spp.), leading to dissolution of gypsum and anhydrite and mobilizing Ca²⁺ [16]. Similarly, trace pyrite may oxidize when redox conditions shift, releasing iron and sulfate [72]. Precipitation reactions occur when reductants and reactants are simultaneously available. If CO₂ is used as a cushion gas, IRB can induce siderite (FeCO₃) and magnetite (Fe₃O₄) formation from dissolved Fe²⁺ or Mn²⁺. Sulfate-reducing bacteria (SRB) may precipitate mackinawite (FeS) and pyrite (FeS₂). Acetogens and methanogens can form carbonate minerals—calcite, magnesite (MgCO₃), and rhodochrosite (MnCO₃)—in alkaline microniches [160]. These processes depend on environmental thresholds—salinity, water activity, temperature, and cushion gas type—all of which must fall within the tolerance range of halophilic microbial communities.

Salt caverns can only support about 3% of Europe’s projected 2500 TWh annual hydrogen demand [161]. Recent research about the possibles sites to use in UHS process reveal that including aquifers and depleted hydrocarbon reservoirs (DHR) achieves 20% of the annual energy demand, where 86% of that storage capacity is added by depleted hydrocarbon fields, making necessary increases in the storage sites [161].

HyUSPRe [128] evaluated Europe’s underground hydrogen potential across 140 aquifers and identified four regional capacities: (1) Southern Europe leads with 138 TWh·yr⁻¹ (71% in depleted hydrocarbon reservoirs, DHR); (2) Northwestern Europe follows at 127 TWh·yr⁻¹ (72% DHR); (3) Eastern Europe offers 86 TW·yr⁻¹ (over 90% DHR); and (4) Central Europe has the lowest at 64 TWh·yr⁻¹ but the highest DHR share (95%) [154,161]. The decision to focus on DHRs to incorporate UHS processes into the into existing natural gas pipeline networks necessitates detailed research on gas H₂ interactions, especially the risk of H₂S formation by sulfate-reducing bacteria in the presence of SO₄²⁻, which can compromise pipeline integrity. According to HyUSPRe, the heavy decision of using DHR is incorporated at those UHS sites in the natural gas storage; this requires extensive analysis of the influence of external gases on H₂ due to the possible incompatibility that could damage the pipeline, as in the case of H₂S produced by SRB interacting with SO₄²⁻.

Recognizing the influence of microbial agents and the fact that DHR offers the greatest storage capacity, the type of host rock is one of the most important factors to consider in GLRM interactions. In both DHRs and aquifers, sandstone is the predominant reservoir rock, with a smaller number of carbonate formations also present [154]. Because microbial activity can significantly alter reservoir integrity, it is important to mitigate its effects. High salinity (up to 240,000 ppm (4.0 M NaCl)) [18] and elevated reservoir temperatures (above 122 °C) can effectively sterilize the environment. The Underground Sun Storage project operating at high salinity has not recorded any significant H₂ loss to microbial consumption [51,162]. However, most European reservoirs sit at 24–97 °C, with a typical geothermal gradient of 30 °C·km⁻¹. Only a few sites, mainly in Central and Eastern Europe, reach temperatures close to the sterilization threshold [154].

As many high-capacity clusters do not meet these sterility conditions, microbial activity may influence the efficiency of UHS. Although these reservoirs are dominated by quartz-rich sandstones, their biogeochemical reactivity can be substantial where accessory minerals are present. Clay minerals, carbonates, sulfates, and iron oxides can supply electron acceptors, adsorptive surfaces, and pH buffering, thus promoting microbial metabolism in the presence of H₂ [163]. Consequently, the extent of biogeochemical activity in sandstone storage formations depends critically on their local mineralogical composition. While silicate-rich rocks reduce microbial influence, moderate reservoir temperatures around 30 °C, typical in many regions, can promote carbonate precipitation by methanogens and acetogens, especially in carbonate-bearing systems [154].

All things considered, UHS designs must explicitly account for biogeochemical processes, as GLRM interactions can alter reservoir integrity. As mentioned above, most of the predicted reserve sites consist of sandstone or carbonate rock, which are susceptible to microbially driven reactions. These microbial metabolisms not only generate new mineral phases but can also trigger cycles of localized dissolution, mobilization, and reprecipitation of secondary phases in pore throats and fracture networks. These dynamic dissolution–precipitation cycles can lead to progressive porosity loss, permeability reduction, and even mechanical weakening of the host rock. Therefore, integrating geomicrobiological insights into site selection, monitoring, and operational protocols is essential for reliable, long-term H₂ storage.

6. Methodological Framework Approaches: Experiments to Simulations

Understanding the biogeochemical behavior of hydrogen in the context of UHS requires a combination of experimental and computational approaches. Experimental techniques provide insights into reaction mechanisms and kinetics under controlled conditions, while simulation tools enable the extrapolation of these findings to field-relevant scales. This section outlines the current methodologies used to investigate microbial and geochemical processes in UHS systems, highlighting both laboratory-based experiments and modeling frameworks.

6.1. Experimental Methodologies for Investigating Biogeochemical Processes

Accurately determining biogeochemical reaction kinetics remains a significant challenge in UHS research [164]. The complexity of GLRM interactions, combined with the difficulty of replicating representative reservoir conditions, limits the availability of experimental tools capable of delivering precise kinetic data. Various experimental methodologies have been developed to approximate these conditions at different scales [164,165,166], incorporating technologies from diverse research disciplines.

Batch experiments provide a controlled setting to investigate the thermodynamics and kinetics of heterogeneous GLRM reactions over extended timescales [15]. Sterile powdered or cored rock samples are typically exposed to pure hydrogen or hydrogen-containing gas mixtures in saturated formation brines within pressurized vessels [167,168]. Following experimentation, solid phases are retrieved and analyzed to identify mineralogical transformations. Due to their relative simplicity and cost effectiveness, batch systems are well suited for testing multiple conditions and materials, often serving as a foundation for the design of more advanced experimental setups such as flow-through systems [169].

Flow-through and column experiments enable continuous sampling of effluent fluids under constant chemical conditions, thereby facilitating the assessment of reaction kinetics, such as mineral dissolution and precipitation rates. In these systems, hydrogen or hydrogen mixtures are injected into a pressurized chamber containing microbial solution with powdered or crushed rock [170,171]. Periodic fluids (gas and liquid) sampling under fixed temperature and pressure provides insights into evolving biogeochemical conditions [167]. Core flooding experiments extend this approach by introducing gases into intact or fractured rock cores at constant flow rates [168,171]. Maintaining reservoir-relevant pressure and temperature allows direct observation of reactions occurring within pore networks (intact cores) or along fracture apertures (fractured cores). These experiments closely mimic natural porous media systems and are particularly valuable for evaluating the impacts of biogeochemical reactions on rock transport properties, including changes in porosity and permeability.

At the pore scale, microfluidic devices with engineered geometries and surface chemistries have emerged as powerful tools to study flow dynamics and reactive transport under simulated subsurface conditions [19,29]. Conventional chips, however, often lack the complexity of natural pore structures and mineral compositions, limiting their ability to capture real reservoir behavior. Recent advances have enabled the development of functionalized microfluidic chips with tailored mineralogical and surface properties [172], permitting real-time monitoring of aqueous chemistry, microbial activity, mineral dissolution, and biofilm formation under reservoir conditions coupled with spectroscopic techniques. In addition, micromodels fabricated from natural mineral substrates and unconventional “real-rock” microfluidic chips [173] integrate genuine pore geometries and mineralogy, offering enhanced fidelity for investigating microbial growth, redox processes, and geochemical reactions at the microscale.

A variety of analytical and imaging methods are used to assess the effects of bio-geochemical reactions on rock properties. Bulk mineralogy is characterized before and after experiments using X-ray diffraction (XRD) [174] and scanning electron microscopy (SEM-EDS) [175], while fluid chemistry is monitored via high-performance liquid chromatography (HPLC) [176] and inductively coupled plasma atomic emission spectroscopy (ICP-OES) [177]. Potential gas products are analyzed with gas chromatography–mass spectrometry (GC-MS) [15]. Structural changes in intact or fractured cores are captured with X-ray micro-computed tomography (µCT) [178], and ultrasonic velocity measurements [179] provide information on evolving elastic properties. Magnetic resonance imaging (MRI) and spectroscopy [180] enable spatial mapping of biofilm growth, gas consumption/release, and mineral surface wetting in porous media under reservoir conditions. Petrographic analyses of thin sections using light microscopy and cathodoluminescence allow detailed evaluation of mineral assemblages, coatings, and porosity [181]. Magnetic susceptibility measurements provide a sensitive means to detect subtle mineralogical transformations (e.g., hematite to magnetite and pyrite to pyrrhotite) induced by hydrogen–rock interactions [23].

6.2. Modeling Microbial and Geochemical Interactions: From Laboratory Data to Field-Scale Simulations

To understand GLRM interactions in porous media, it is essential to extend experimental observations to scales that are representative of geological structures. Simulation tools play a crucial role in this process, serving as a bridge between laboratory data and field applications. The Monod model [182] (Equation (1)) is one of the most reliable approaches for simulating microbial growth in UHS systems and has been widely implemented in simulators designed to reproduce these processes. Its formulation can be adapted to incorporate key variables such as substrate type and concentration, the coexistence of multiple microbial populations, and microbial density. These extensions and parameter variations have been extensively reported in the literature [17,182], reinforcing the model’s versatility for biogeochemical applications. The simplified form of the Monod equation is presented below:

$$\mu \left(s\right)={\mu }_{max }{\displaystyle \frac{\left(S\right)}{K_s+S}}$$

(1)

where the specific growth rate (μ) depends on the concentration of available substrate (S), approaching a maximum value (μ_max) when nutrients are abundant. A key parameter is the half-saturation constant (K_s), which is defined as the substrate concentration at which μ reaches half of μ_max. Therefore, when substrate concentrations are low (S < K_s), growth is limited, and the relationship between μ and S is almost linear. In contrast, at high concentrations (S > K_s), the growth rate stabilizes at its maximum value. Thus, K_s reflects the microorganism’s affinity for the substrate; low values indicate high utilization efficiency.

By coupling different software tools (

Table 6. Summary of simulation tools for coupled GLRM interactions in UHS.

Software	MNS	RPR	PT	SP	Key Input Variables	Applicable Scale	Dimension
PHREEQC (v3.8.6)	✓	✓	✓	✓	Initial water chemistry, temperature, pressure, mineral solubility constants (Ksp), ion-activity product (IAP), and user-scripted microbial rate laws	Batch reactor, 1-D column	0-D/1-D
DuMuX (v3)	✓	✓	✓	✓	Porosity, permeability, reaction kinetics (mineral and microbial), and boundary conditions for flow	Pore to reservoir scale	1-D/2-D/3-D
Flownex (v9.0.1)	×	✓	×	×	Fluid properties (density and viscosity), network topology (nodes and conduits), and boundary conditions	System/network scale	0-D/1-D
CoFlow (2024.2)	✓	✓	×	×	Phase properties, user-defined reaction rates, and pore geometry	Reservoir domain scale	2-D/3-D
Lattice Boltzmann Model	✓	✓	×	×	Porous medium geometry (mesh), fluid properties, and kinetic parameters	Pore-scale	2-D/3-D
CMG GEM (v2024.10)	✓	✓	✓	✓	Reservoir properties (porosity and permeability), PVT data, component balances, and reaction definitions	Field scale	3-D
MATLAB (R2023b)	✓	✓	✓	✓	Kinetic equations, growth parameters, and initial conditions	Batch reactor/plug-flow	0-D/1-D
MRST (2024a)	✓	✓	×	×	Reservoir grids, rock/fluid properties, and user-defined flow and reaction laws	Reservoir scale	2-D/3-D
TOUGHREACT (v3.0)	✓	✓	✓	✓	Porosity, permeability, thermal properties, and reaction kinetic parameters	Pore to reservoir scale	1-D/2-D/3-D
COMSOL Multiphysics (v6.1)	✓	✓	✓	✓	Fluid/solid properties, user-defined PDEs for kinetics, and boundary and initial conditions	Lab to field scale	1-D/2-D/3-D
OpenFOAM (v11)	✓	✓	×	×	Geometry and mesh, fluid properties, user-defined and reaction mechanisms	Pore-scale	2-D/3-D
ANSYS Fluent (2024 R2)	✓	✓	×	×	Geometry, mesh, fluid properties, and user-defined reaction kinetics	Pore-scale	2-D/3-D
OpenGeoSys-Eclipse (e300)	×	✓	×	×	Reservoir data, PVT tables, component balances, and user-defined reaction rates	Field scale	3-D

Multi-nutrient support (MNS); reactions per run (RPR); population types (PT); simultaneous populations (SP).

), biochemical reactions occurring during UHS can be simulated, enabling the scaling of processes from laboratory results to field-scale applications. In this context, the summary considers four key modeling capabilities: the inclusion of multiple nutrients or electron donors/acceptors for microbial growth, the maximum number of simultaneous abiotic and biotic reaction pathways supported in a single run, the representation of distinct microbial functional groups or species, and the ability to simulate multiple microbial populations concurrently with independent kinetics. The following table summarizes the most commonly used simulation tools for UHS, with particular emphasis on GLRM interactions.

DuMuX and COMSOL stand out for their high extensibility and robust capabilities in multiphase, multicomponent simulations. PHREEQC also performs strongly in reaction handling and usability, although it is limited by its reduced native support for microbial diversity. MATLAB and Flownex are well suited for rapid kinetic prototyping but lack built-in functionalities for multiphase reactive transport. By contrast, lattice Boltzmann models are highly effective for pore-scale flow analysis, though they require substantial coding effort to incorporate complex biogeochemical reactions. Finally, the choice of software depends on the project’s objectives: whether the priority is rapid kinetic prototyping, detailed pore-scale studies, or field-scale multiphase reactive transport involving complex microbial communities.

7. Knowledge Gaps and Research Priorities

Despite advances in understanding the role of biogeochemical interactions in UHS processes, considerable gaps remain that limit our ability to forecast and manage these interactions under real-world operational settings. The current synthesis of existing knowledge highlights numerous unresolved challenges in the context of GLRM interactions.

First, quantitative data on the kinetics and yields of hydrogen-driven biogeochemical reactions under in situ reservoir conditions remain scarce. Several numerical simulation studies have taken into account one or more predominant hydrogenotrophic metabolisms in their deep ecosystems (i.e., methanogenesis, acetogenesis, and sulfate reduction) [183,184]. Laboratory experiments typically focus on selected strains, with limited data from reservoir formation water or native microbial communities. While microbial hydrogen consumption rates have been studied under controlled conditions, mineral dissolution and precipitation driven by microbial activity are rarely quantified or reported. The absence of kinetic parameters measured directly at reservoir conditions introduces uncertainty in predicting whether these reactions proceed at rates sufficient to affect hydrogen storage over operational timescales, which can span years to decades.

Second, CO₂ or CH₄ released during dissolution of specific minerals can dilute stored hydrogen, whereas reactions such as serpentinization in ultramafic lithologies can produce additional H₂ over long timescales, potentially increasing reserves [185]. While dissolution and re-precipitation of mineral phases have been documented as drivers for porosity and permeability variations, the role of pH changes induced by bacterial metabolic byproducts has not been systematically investigated. When hydrogenotrophic microorganisms activate their metabolic pathways, the production of byproducts alters the initial pH equilibrium of the system. These pH shifts can initiate cycles of mineral dissolution and precipitation within the porous medium, where dissolution may release additional gases into the surrounding environment, thereby reducing the purity of the working gas. The contribution of gases generated through mineral dissolution driven by microbially induced pH changes within a single microorganism–mineral–gas system remains largely unexplored. Understanding the net balance between gas-consuming and gas-producing reactions in these dynamic, pH-driven mineralogical cycles is essential for maintaining hydrogen purity during storage.

Third, current data on the environmental limits for key hydrogenotrophic microorganisms remain incomplete. Equally important is the limited understanding of microbial adaptation over extended storage periods, including how microbial communities mature or adjust under long-term operational conditions. Shifts in metabolic pathways, competitive dynamics, or tolerance thresholds in response to repeated injection events remain largely undocumented, particularly in mixed communities where synergistic or antagonistic interactions may alter these thresholds. Many target reservoirs, especially sandstones and carbonates, contain heterogeneous accessory minerals that can act as electron acceptors, catalysts, or nucleation sites. The mineral composition can vary significantly between different sites and even within the same location, making it more difficult to predict how biogeochemical processes will occur. Moreover, the influence of minerals on microbial adaptability must be considered. As observed in controlled experiments, certain bacteria can absorb mineral components and modify their DNA [186], thereby acquiring resistance to consecutive change conditions, which could increase their population. Consequently, the minerals present in geological formations where microorganisms are attached could alter their initial environmental thresholds during H₂ storage cycles.

Finally, biofilm formation is well known to reduce injectivity under cyclic injection–withdrawal operations, yet the specific conditions controlling this process, including associated changes in wettability, have not been thoroughly investigated. Even less is known about how these conditions influence the selective colonization of bacteria on specific pore geometries [187,188] or mineral surfaces, such as the preferential growth observed on swellable clay minerals [73]. Microbial activity within porous media is further shaped by flow patterns, nutrient availability, and mineralogical variability; however, spatial mapping of these activity “hotspots” in real reservoirs remains limited, making it difficult to accurately predict localized risks such as pore clogging or corrosion.

8. Conclusions

Biogeochemical interactions between microorganisms, minerals, and H₂ gas critically influence the safety, efficiency, and longevity of UHS. Microorganisms, including SRB, methanogens, acetogens, and IRB, can use the stored H₂ as an electron donor, which leads to gas consumption and biofilm formation. Additionally, their metabolic by-products may induce mineral reactions that further affect reservoir integrity and storage performance. The interaction between microorganisms and minerals in the geochemical environment depends on local physicochemical conditions. Each microorganism has their preference for certain types of minerals, but they are not exclusive to a single metabolic pathway. The coexistence of multiple microbial groups in reservoirs may trigger a symbiotic process that increases the risk of UHS processes. Therefore, the mineralogical composition of storage sites must be analyzed alongside the indigenous bacteria present since the presence of certain minerals, such as clays, favors the proliferation of microbial communities and the formation of biofilms, thereby increasing the risk of GLRM interactions during UHS processes. Quantitative data on the kinetics and yields of H₂-driven biogeochemical reactions under in situ conditions remain limited. Future research is essential to determine reaction rates and their significance for storage integrity and performance over operational timescales.

Salt caverns in eight European countries provide conditions of salinity that should suppress microbial activity; however, localized microenvironments can still host extremophiles that trigger sulfate and iron cycling. Depleted hydrocarbon fields and saline aquifers, which constitute the majority of Europe’s long-term storage capacity, have extensive pore networks with varying mineralogy (e.g., sandstone, shale, and carbonate) that support diverse hydrogenotrophic communities, thereby increasing the risk of long-term H₂ storage. European initiatives, from pilot salt-cavern projects to large-scale aquifer and reservoir programs, should integrate geomicrobiological risk assessments to anticipate mineral precipitation (e.g., siderite, calcite, and pyrite) and dissolution events that affect petrophysical properties. Coupling site-specific geological characterization with microbial threshold data enables policymakers and engineers to optimize site selection, monitor reactive transport, and develop operational protocols that safeguard storage integrity and realize Europe’s hydrogen infrastructure goals.