An oilfield chemistry with a biotechnology twist is reprogramming stranded petroleum resources to produce both the promise of commercial scale and the potential for reducing industry’s carbon footprint. Now, Eclipse Energy wants to turn those wells into a distributed hydrogen production system by introducing native microbes to eat any remaining hydrocarbons and produce hydrogen without drilling new wells.
How Microbes Make Hydrogen Below the Ground
In concept, the company’s approach is simple but in execution it is intricate. Naturally occurring microbial communities reside at the oil–water interface within reservoir fluids. Eclipse screens and grows such organisms, and then returns the best-performing strains to the reservoir. As the bugs chow down on long-chain hydrocarbons, they release a steady flow of hydrogen and carbon dioxide up through existing wellbores.
The low density of hydrogen allows it to be moved through pipelines far more easily than by energy-intensive artificial lift, which is often needed to deliver thick oil. At the surface, common separation methods – like membranes or pressure swing adsorption – can separate out hydrogen from CO₂. A large fraction of the CO₂ is still stored in the formation under pressure, solubility and mineral trapping, with what’s left sequestered or used. It will be very important to have independent measurement, reporting and verification of those carbon balances.
From Liability to a Low-Carbon Asset for Idle Wells
Idle wells are everywhere and expensive. Estimates from the Department of the Interior indicate that the U.S. has hundreds of thousands of orphaned wells requiring remediation and up to several million idle or abandoned wells total. Among the other issues: The Bipartisan Infrastructure Law includes billions of dollars to plug and monitor, reflecting knowledge of methane leakage and risks to groundwater. Converting some of these wells into hydrogen sources could reduce stewardship costs even as it provides a cleaner fuel.
Eclipse is aiming for hydrogen at around $0.50 per kilogram, which would bring it in line or below “gray” hydrogen manufactured from natural gas with no carbon capture. For context, the U.S. Department of Energy’s Hydrogen Shot is targeting $1 per kilogram by the end of this decade, and many electrolytic “green” hydrogen projects today are in the $3 to $6 per kilogram cost range (depending on power prices and capacity factor). If Eclipse’s field economics pan out, microbial hydrogen would undercut the incumbent supply for refiners, ammonia producers and petrochemical consumers struggling to decarbonize.
Lifecycle emissions will establish whether the product meets new standards as low-carbon hydrogen. The DOE’s Clean Hydrogen Production Standard establishes a level of 4 kg CO₂e per kilogram of hydrogen. Real-world carbon intensity of microbial hydrogen will be influenced by the integrity of wells, underground retention of CO₂, efficiency of capture at the surface and control on fugitive emissions.
Oilfield Muscle Meets Microbiology for Project Scale
For scale, Eclipse is turning to an oilfield services expert. For downhole sampling, microbial deployment and production services it has selected Weatherford as its operating partner. That’s important because — while converting an idle well into a source of hydrogen is relatively known territory technically — doing so effectively prompts the need for careful reservoir characterization, materials that can withstand hydrogen and robust safety systems up to and including gas detection and blowout prevention.
Site selection is the silent make-or-break factor. The performance of microorganisms and the amount of hydrogen produced are affected by temperature, salinity, permeability, and the type of oil. Eclipse says it is working on “native” microbes (as opposed to engineered ones that are built to withstand tough conditions or shape themselves according to regulatory dictums). The playbook is reminiscent of enhanced oil recovery campaigns, but rather than chemical floods or steam, it uses selective biology.
Market Context and Competition in Hydrogen Production
Global demand for hydrogen is about 95–100 million metric tons a year, as per the International Energy Agency, but most of it comes from high-carbon sources. Microbial “gold hydrogen” is a new pathway to add to electrolyzers, natural hydrogen (“white hydrogen”) prospecting and methane reforming with carbon capture. Other start-ups are working on similar subsurface bioprocessing ideas, a sign of a wider ethos of retrofitting fossil worldviews to produce cleaner molecules instead of erecting every asset anew.
If the microbial hydrogen can be produced near enough to end users — refineries, or ammonia plants, or future fueling hubs — projects could skirt some transportation costs and losses in converting it into carriers such as ammonia. That geographic advantage may well be relevant as regional standards for clean hydrogen and tax credits emerge.
Key Risks to Watch as Hydrogen Pilots Scale Up
The model still has hurdles. Lost circulation and other drilling-related complications can result in lower production per well as the feed depletes reservoirs. Hydrogen embrittlement may impact some steels; old wells could require retrofitting. Reservoir heterogeneity can reduce yields, and microbial activity may diminish over time (requiring re-inoculation). Regulators will seek clear assurances on CO₂ permanence and groundwater protections. Clear third-party validation—potentially to an ISO greenhouse gas accounting standard — will be critical for securing low-carbon certification and offtake contracts.
But the upside is difficult to resist. Subsurface biomanufacturing capitalizes on sunk investment, transforms stranded hydrocarbons into cleaner fuel and dovetails with existing oilfield operations. With a real path to low-cost, low-carbon hydrogen and an extensive pipeline of candidate wells, Eclipse’s microbes could breathe new life into legacy reservoirs during the energy transition.
