The role of microbiology in natural hydrogen exploration and exploitation

Understanding natural hydrogen 

Natural hydrogen, often referred to as white or geologic hydrogen, is molecular hydrogen (H₂) that forms naturally within the Earth’s crust. Unlike industrial hydrogen, which must be produced via electrolysis or fossil fuel reforming, natural hydrogen is generated underground through geological processes such as water-rock reactions and mantle-derived gas migration. It can move through porous rock formations, accumulate in subsurface traps, and in some cases reach the surface via natural seeps. 

While early attention centered on isolated discoveries abroad, exploration has now accelerated in Europe. In France, dedicated exploration campaigns are underway in the Lorraine basin, where recent drilling programs by companies such as La Française de l’Énergie aim to quantify potentially significant hydrogen accumulations. Geological assessments suggest that parts of northeastern France could host large-scale subsurface hydrogen systems, shifting the concept from scientific curiosity to emerging energy opportunity. 

Natural hydrogen represents a fundamentally different energy concept: instead of manufacturing hydrogen, it may be possible to extract it directly from geological systems. 

And the potential scale is extraordinary. Early geological assessments suggest quantities so large they rival today’s global hydrogen demand many times over. If scalable production is confirmed, natural hydrogen would not simply decarbonize an industry, it could underpin a new, abundant, low-carbon energy era. 

(Blay-Roger et al 2024, https://doi.org/10.1016/j.rser.2023.113888.) 

Why natural hydrogen is gaining attention 

Hydrogen plays a central role in decarbonization strategies, particularly in sectors that are difficult, or in some cases nearly impossible, to electrify directly. The steel industry is a prime example: replacing coal-based blast furnaces with hydrogen-based direct reduction requires vast, continuous volumes of affordable hydrogen at industrial scale. Without abundant, low-cost hydrogen, deep decarbonization in heavy industry remains structurally constrained.  

Natural hydrogen is attracting attention because it may offer several strategic advantages. 

1. In some geological environments, hydrogen appears to be generated continuously over long timescales. This raises the possibility that certain accumulations could behave as dynamically replenished systems rather than strictly finite resources. 

2. As a primary geological resource, natural hydrogen would not require energy-intensive production processes. If recoverable at scale, it could lower the carbon footprint associated with hydrogen supply. 

3. Hydrogen has unique physical properties. It is the smallest and lightest molecule, diffuses rapidly, and stores high energy per unit mass. These characteristics influence how it migrates underground and how it must be handled in infrastructure systems. 

4. Hydrogen is not only an energy carrier for industry; it also fuels subsurface microbial life, making natural hydrogen scientifically distinct from conventional hydrocarbons. 

What is truly driving attention, however, is scale. Geological assessments suggest that hydrogen generation within the Earth’s crust could amount to billions, potentially trillions, of tonnes globally. Even a small recoverable fraction would dwarf today’s hydrogen market. 

Natural hydrogen is gaining attention because the resource potential is enormous. 

Geological systems that generate hydrogen 

Natural hydrogen forms through large-scale water–rock interactions and long-term geological processes. The most important mechanism is serpentinization, in which ultramafic, iron-rich rocks react with water to form serpentine minerals and release hydrogen. This reaction can persist for millions of years wherever reactive rocks are exposed to circulating fluids. 

Hydrogen can also be generated through iron oxidation in mafic rocks and through radiolysis, where natural radioactive decay in crystalline basement rocks splits water molecules into hydrogen and oxidants. 

Tectonic activity plays a critical role. Faults and fracture networks enable water to penetrate deep, reactive formations and provide pathways for hydrogen to migrate upward. 

For hydrogen to become commercially relevant, several geological factors must align: 

• A reactive source rock capable of sustained hydrogen generation 

• Active fluid circulation 

• Permeable pathways that allow hydrogen to migrate 

• Geological conditions that either limit rapid escape or enable continuous recharge 

Unlike methane, hydrogen does not necessarily require a large, conventional porous reservoir to accumulate. In some settings, production may tap into dynamically recharged systems, where hydrogen is continuously generated and flows through fracture networks rather than being stored in a static trap. 

Because hydrogen molecules are extremely small, highly diffusive, and biologically reactive, understanding migration dynamics, loss mechanisms, and recharge rates is central to exploration. 

The most important sources of H2 based on geological deposits (Wang et al., 2023, Klein et al., 2013). 

Hydrogen and the deep biosphere 

Hydrogen is a key energy source for microorganisms living deep underground. Entire microbial ecosystems rely on hydrogen as an energy carrier in environments where sunlight or oxygen are absent. 

Microbial communities in hydrogen-rich systems can: 

• Consume hydrogen 

• Produce methane, acetate or hydrogen sulfide 

• Form biofilms and syntrophic communities 

• Alter the chemical conditions of the reservoir 

From a resource perspective, microbial activity can reduce recoverable hydrogen volumes or change gas composition. From a scientific perspective, these ecosystems provide insight into life in extreme environments and the coupling between geology and biology. 

Assessing natural hydrogen reservoirs therefore requires not only geological evaluation but also geomicrobiological understanding. 

Microbiology and hydrogen infrastructure 

Microbiology does not stop being relevant once hydrogen is extracted. It continues to play a role in pipelines, storage facilities, and subsurface storage sites. 

Hydrogen can influence microbial growth conditions by changing redox environments and serving as an energy source for certain organisms. In infrastructure systems, this can lead to several challenges. 

One major concern is microbiologically influenced corrosion (MIC). Certain microbes can form biofilms on metal surfaces and produce corrosive byproducts. This may accelerate material degradation, reduce pipeline lifespan, and increase maintenance costs. In some cases, hydrogen sulfide formation can create additional safety and integrity risks. 

Underground hydrogen storage, such as in salt caverns or depleted gas fields, introduces further considerations. Microorganisms present in subsurface formations may consume stored hydrogen or alter its composition. The level of risk depends strongly on site conditions such as salinity, temperature, nutrient availability, and existing microbial populations. 

At the same time, understanding microbial behavior allows for better monitoring strategies, targeted mitigation measures, and informed site selection. 

Opportunities and challenges ahead 

Natural hydrogen has the potential to become a complementary pillar of the hydrogen economy. Its appeal lies in its geological origin, possible long-term generation, and compatibility with existing subsurface expertise from the oil and gas sector. 

However, its development faces uncertainties: 

• Exploration models are still evolving. 

• Retention efficiency remains difficult to predict. 

• Microbial processes may influence both reservoirs and storage systems. 

• Infrastructure must address combined risks of corrosion and hydrogen-specific material challenges. 

  
  

Natural hydrogen is therefore not simply another gas resource. It is a multidisciplinary challenge that requires integrating geology, geomicrobiology, reservoir engineering, and industrial microbiology. 

If these dimensions are understood and managed effectively, natural hydrogen could represent a significant and low-carbon addition to the future global energy system.