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A Data-Driven Deep Learning Framework for Microbial Reaction Prediction for

Hydrogen Underground Storage

Conference Paper · March 2023

DOI: 10.2118/212187-MS

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SPE-212187-MS

A Data-Driven Deep Learning Framework for Microbial Reaction Prediction

for Hydrogen Underground Storage

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Klemens Katterbauer, Abdallah Al Shehri, Abdulaziz Qasim, and Ali Yousif, Saudi Aramco

Copyright 2023, Society of Petroleum Engineers DOI 10.2118/212187-MS

This paper was prepared for presentation at the SPE Reservoir Simulation Conference held in Galveston, Texas, USA, 28–30 March 2023.

This paper was selected for presentation by an SPE program committee following review of information contained in an abstract submitted by the author(s). Contents
of the paper have not been reviewed by the Society of Petroleum Engineers and are subject to correction by the author(s). The material does not necessarily reflect
any position of the Society of Petroleum Engineers, its officers, or members. Electronic reproduction, distribution, or storage of any part of this paper without the written
consent of the Society of Petroleum Engineers is prohibited. Permission to reproduce in print is restricted to an abstract of not more than 300 words; illustrations may
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Abstract
As the use of hydrogen gas (H2) as a renewable energy carrier experiences a major boost, one of the key
challenges for a constant supply is safe and cost-efficient storage of surplus H2 to bridge periods with low
energy demand. For this purpose, underground gas storage (UGS) in salt caverns, deep aquifers and depleted
oil-/gas reservoirs has been proposed, which provide suitable environments with potentially high microbial
abundance and activity. Subsurface microorganisms can use H2 in their metabolism and thus may lead to
a variety of undesired side effects such as H2 loss into formation, H2S build up, methane formation, acid
formation, clogging and corrosion.
We present a new AI framework for the determination of metabolism processes of subsurface
microorganisms in hydrogen underground storage. The AI framework enables to determine the potential
microbial related processes and reactions in order to optimize storage strategies as well as incorporate
potential remediating actions to ensure efficient and safe underground hydrogen storage and minimize
related side effects.
We evaluated the framework on investigating potential microbial reactions for hydrogen storage in the
Pohokura gas field in New Zealand. The framework evaluates reservoir parameters, such as temperature,
pressure, salinity and hydrogen injection volumes as well as duration, and then classifies which reactions
may take place as well as indicates the likelihood of the reaction taking place. For the deep learning
framework, an optimized random forest algorithm was implemented and compared to other multi-class
classification problems. The results demonstrated the ability to determine the microbial reactions that may
take place with hydrogen storage reservoir as well as its severity, which enhances the optimization of
injection strategy as well as suitability of a reservoir.
This framework represents an innovative approach to microbial reaction prediction for underground
hydrogen storage. The framework allows potential reservoirs to be efficiently evaluated and optimization
strategies to be utilized in order to maximize the efficiency of underground hydrogen storage.

Introduction
Hydrogen gas has become an important energy carrier to support the energy transition. For hydrogen
combutions, there are no harmful substances that are released and based on the gravimetric energy content
2 SPE-212187-MS

is more than 140 MJ/kg, which embodies a high energy density. This makes hydrogen an attractive reactant
for many chemical processes, specifically for the production of fertilizers, such as ammonia. Given the
significant growth of hydroge production technology and the increasing end-use, questions arise to what
extent hydrogen can be efficiently stored in order to be able to provide it when needed. Electricity supply
from renewable sources may experience natural variations, and also there may be various occurrences where
electricity demand may peak within short period of times, large scale energy storage is essential in order
to solve potential mismatches (Dawood, Anda, & Shafiullah, 2020). Underground storage in geological
formation is a major option for large scale hydrogen storage and has several benefits. The first is that

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the safety of the storage sistes are not susceptible to fire, extreme weather, military actions or terrorist
attackes. Secondly, the storage volumes range from a few million cubic meter to hundreds of million
cubic meter. Thirdly, the storage costs are relatively low as compared to large scale surface tanks, which
require significant investments. Furthermore, suitable geological storage sites are abundantly available,
which enables a decentralized storage (Ursua, Gandia, & Sanchis, 2011). There are various potential sites
for hydrogen storage, such as depleted gas and oil reservoirs, artificial salt caverns and deep aquifers, hard
rock caverns and abandoned mines. All of these environments harbor a variety of different and diverse
microbial organisms, which have to be taken into account for the assessment of the storage process. These
microbes may significantly influence and interact with the hydrogen and pose a challenge to storage quality
of hydrogen (Al Zahrani & Dincer, 2017).
Microbes play a crucial role in the earth's crust and subsurface, and includes two major single
cellular groups. These two groups are responsible for several biochemical and geochemical reactions.
Microorganisms can be easily encountered several kilometers in deep rock structures and may even
represent 104 to 108 cells per gram of rock. Such a critical biodiversity may have a significant impact
on its behavior, and human activity in the form of drilling, pumping and mining may lead to changes.
Short and long-term effects on these natural microbial communities are still at an early stage, but will
represent a key aspect in determining the impact on the storage quality. Microbes need basic substances
and certain environmental parameters in order to be active. This implies, water, energy source and essential
elements such as carbon, nitrogen, phosphorous and trace elements. These conditions may change in extreme
conditions where the cell numbers and diversity is generally lower. Temperature limits vary between 15
Celsius and more than 121 Celsius, but this threshold may differ for both pressure and brine salinity
(Pourrahmani & Moghimi, 2019).
pH ranges differ significantly, and high concentrations of toxic chemicals, and low water activity and high
radiation, the influence on microbes may be significant. These factors need to be taken into account when
analyzing the microbial activity (Turner, 2004).
Microbes gain energy via the oxidation of electron donors and experience a concurrent reduction of
an electron acceptor. Electron donors are in the water and rock, and can be simple or complex organic
compounds. Furthermore, inorganic compounds may be also present. Molecular hydrogen is a crucial
electron donor for microbial respiration in the subsurface. Hence, hydrogen may be used by different groups
of organisms metabolically. Within the cells, the specific enzymes catalyze the splitting of hydrogen into
protons and electrons. These can be used to chemically store the cellular energy. These can be used to drive
reactions within the cell (Tursunov, Kustov, & Kustov, 2017).
Microbial hydrogen oxidation leads to a depletion of hydrogen surrounding the cells. There is significant
hydrogen related hydrogenases, such as for the hydrogen affinities and properties to natural occurring
hydrogen containing environments. Oxygen, nitrate and iron reduction delivers high energy gain for the
cells. For example, the nitrate-reducing microbes use the electron donors faster and more efficiently than the
sulphate reducing microbes. If there is sufficient sulphate, the sulphate reducers outcompete methanogens
and acetate formers. If the hydrogen is stored in high concentrations, the hydrogen consuming terminal
electron accepting processes are possible and may take place simultaneously. Mineralogical and transport
induced differences and specific syntrophic microbial communities that may lead to multiple metabolisms,
SPE-212187-MS 3

which can be active at the same time. This has been observed at high temperatures, such as 90 Celisus and
high salinities (Heinemann, Alcalde, Miocic, & Hangx, 2021).
There are several side effects for underground hydrogen storage. Hydrogen may be utilized by microbes
within the metabolism, which may decrease the hydrogen content. Furthermore, it may lead to an increase
in other gases such as methane or H2S and can both decrease or increase CO2 concentrations. The resulting
re-produced hydrogen may be significantly affected in terms of quality, and such small concentrations of
H2S may affect the material integrity, safety and health and require additional gas treatment (Khan, et
al., 2021). This may even lead to a decrease in the overall hydrogen concentration. The degradation may

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be increasing with the injection and production cycles in contrast to the initial hydrogen loss caused by
diffusion. Diffusion will be most significant in the first cycle and then decrease over time. The existing
CO2 decline in any such mixture would be an indication of microbial activity, typically acetogenesis or
methanogensis. Methanogenesis leads to an increase in the methane concentration in the produced mix and
would lead to a change in the microbial community towards the domain of Archaea. There are several
field trials where industrial CO2 and hydrogen are converted into CH4 by methanogens, utilizing the above
described metabolism. Additionallly, acetogenesis may lead to additional hydrogen loss and an increase in
the acetate in the produced fluids with a higher presence of bacteria. This may also lead to a drop in pH,
which may be masked by a strong buffer potential (Chi & Yu, 2018).
Another key challenge is the souring of the hydrogen gas within the formation. Specifically, active
microbial sulphate reduction may lead to the formation of toxic and corrosive H2S gases. Sulphate may
be either in the presence of dissolved sulphate in water or may arise due to sulphidic minerals. Sulphidic
minerals are gypsum or anhydride that may occur in the microbial process (Chi & Yu, 2018). Additionally,
a decline in the suplhate content in the produced fluid is measurable and will lead to a sulphate reduction
process that can lead to significant amounts of H2S. In case there are dissolved iron or ferrous iron minerals
present, the H2S will lead to a precipitation wit hthe available Fe2b (Balachandar, Varanasi, Singh, Singh,
& Das, 2020).
Another challenge that arises is the steel corrosion by microbes and H2S. Corrosion caused by microbes
is a commong problem for water, oil and subsurface installations. These exhibit a complex interplay between
abiotic and biotic corrosion reactions that can lead to equipment failures. Specificially, it leads to the
formation of microbial biofilms on the surfaces of the steel. Biofilms are common in their appearance for
microorganisms in the environment. This implies that a biofilm consists of cells that surround the matrix
of exopolymeric substances such as sugar, protein and nucleic acids (Ranjekar & Yadav, 2021; Sadeghi
& Ghandehariun, 2020). The environment provides a protective surrounding as the physical and chemical
stresses are reduced. Sulphate reducing microorganisms, methanogens and acid producing microbes are
primarily associated with the biofilms and the associated corrosion problems. Microbial corrosion is hard to
distinguish from chemical corrosion rate, but represents an important part for hydrogen storage and ensuring
that the wellbore and the hydrogen gas quality is not significantly affected. Microbially formed H2S may
increase corrosion rates and even lead to stress cracking (Chen, Pei, & Gong, 2019).
Another critical challenge is the microbial induced plugging of the pore space in the rock, or
affecting even the pipelines. This may be in the form of microbial biomass, exopolymers, and microbial
induced mineral precipitations. Plugging is caused by the rapid growth and proliferation of cells and
the biofilmstructures. The decrease in pore space will reduce permeability, and subsequently may reduce
injectivity and the ability to produce from the reservoir. This is especially relevant given that the areas most
affected are those close to the injection or production wells as the nutrient and cell content is highest. As
the microbes catalyze redox reactions, different mineral precipitations may be triggered, which leads to
a plugging and declining well productivity (Pourrahmani & Moghimi, 2019). Sulphate reduction causes
H2S and this may lead to dissolved ferrous iron and other minerals. Iron-oxidizing microbes may lead to
ferric iron mineral precipitation, which may take on the form of ferrihydrite, goethite, magnetite and other
associated materials. Such microaerophilic iron-oxidizers represent a significant amount of biofilms and
4 SPE-212187-MS

minerals, which may affect oxygen ingress. Microbial induced carbonate precipitation is another challenge,
which are formed by chemical changes inducted by different metabolisms. Nitrate and sulphate reduction
may lead to precipitation if the carbon source is degraded. This may form CO2 in addition to an increase of
the pH. This can be associated with biofilms and enhances localized conditions for precipitation. This will
decrease the injectivity or increase the injection pressure. Long term severe effects may arise from such a
precipitation (Sivaramakrishnan, et al., 2021).
The drop of pH may be another challenge as this leads to the dissolution of carbonate and other minerals.
This leads to the release of CO2 and HCO3 and would be accompanied by an increase in the dissolved CO2

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for the reproduced fluid. The dissolved carbonate may be utilized as a carbon source for the microbes and
lead to enhanced growth and activity. The minerals will lead to change in the permeability and porosity, as
well as modify the flow behavior. Furthermore, heat may be released due to exothermic enzymatic reactions.
This may even lead to a slight temperature increase in the hydrogen storage site due to the microbial activity
(Sun & Nesic, 2009; Toghyani, Baniasadi, & Afshari, 2019).
Another key factor is the leakage of gas which may result due to operational failures, well integrity losses
and the diffusion through the cap rock or caused by geological cracks. Given that hydrogen exhibits a higher
diffusion coefficient, it may enter higher geological horizons including groundwater and the surface. These
effects may lead to impact the soil/ and groundwater microbial communities and nutrient cycles. While
the reaction within groundwater would be significant, which may enable to trace efficiently any hydrogen
leakage.

Pohokura field
The Pohokura gas field is located in the north-east of New Plymouth in the Taranaki Basin that is close
to the Methanex Motunui site in Waitara (Figure 1). The Taranaki Basin covers more than 100,000 km2,
primarily beneath the self and the continental slop that is offshore or in central-western of the North Island
in New Zealand. The land sections are beneath the Taranaki Peninsula and in the northwest of the South
Island. The basin incorporates a late Cretaceous to Quaternary sedimentary fill up that may be up to 8
km thick. The basin comprises an undeformed block and a heavily deformed area (Islam, Yunsi, Qadri,
Shalaby, & Haque, 2021). The heavily deformed area contains the Taranaki Fault that leads to a Miocene
basement overthrusting into the basin. The sedimentary fill of the Taranaki Basis may have arisen due to an
intracontinental manifestation of a transform fault offsetting or a failed-rift (Three-Dimensional Structural
and Petrophysical Modeling for Reservoir Characterization of the Mangahewa Formation, Pohokura Gas-
Condensate Field, Taranaki Basin, New Zealand). There were several tectonic episodes that influenced the
generation of the Taranaki Basin, which included the rifting between the cretaceous – Eocene period, the
compression within the Eocene period and an extension that arose from the late Miocene (Knox, et al.,
2008). The Pohokura files is the largest gas-condensate field and is a low-relief N-S trending anticline in
the Northern Graben. The boundaries of the field are supported by the Taranaki Fault Zone in the east and
the Cape Egmont Fault Zone in the west. The reservoir underwent compressional and extensional stress
regimes and most of the drilling was in the northern part of the Pohokura Field. The petroleum play is a
transgressive marginal marine sand within an inverted anticline. The coal seams of the Rakopi Formation
are the main sources for the hydrocarbons in the pohakura field. The Rakopi Formation represents the
deepest stratigraphic unit within the Taranaki Basin, and represents the major source for oil and gas fields
within the basin. The Rakopi Formation is heavily dominated by fluvial-to-marginal marine lithofacies.
The Mangahewa Formation from the Eocene Epoch is the primary reservoir zone, being the most prolific
and thickest. The Mangahewa Formation contains interbedded sandstone, siltstone, mudstone and coal. The
Turi Formation represents a top seal for the Pohokura Field and arose from Paleocene to the Eocene. The
top seal is composed of non-calcareous, dark colored, micaceous and carbonaceous marine mudstone that
is distributed throughout the Taranaki Basin (Sim & Adam, 2016).
SPE-212187-MS 5

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Figure 1—Map of central and southern Taranaki basin with the Maui and Pohokura fields indicated in orange.

The water depth is around 35 m in the block PMP 38154. The Taranaki Basin has several reservoirs that
range from the Paleocene to Pliocene and is a gas-condensate field in a low-relief anticline, that is north-
south elongated. The reservoir is 16 km long, and 5 km wide.

Figure 2—Map of the oil and gas fields in New Zealand.

6 SPE-212187-MS

The Pohokura-1 well (Figure 3) targeted the the Kapuni group Mangahewa Formation sands in the
Pohokura structure, where in total 700 meter of shallow marine sands were encountered. The overall gas
column extended to 130 m in the upper part of the Mangahewa structure. A deepening of the well was
performed in order to potentially access the lower Mangahewa formation and reach the TD in the Mid-
Eocene shales of the Omata formation. The lower part of the formation was not economically viable, and
never produced gas condensates (Knox, et al., 2008).

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Figure 3—Pohokura-1 gas well.

In order to measure the gas production performance, two drill stem tests were conducted in the upper
section within the interval of 3,625 to 3,634 m MD and between 3,553 to 3,570 m MD. The flow
measurements for the first interval were 3.5 MMSCF/D, and 16.5 MMSCF/D for the second interval. The
well was rather valuable in mapping the reservoir with seismic and have a control point for determine the
overall structure of the Pohokura field.
Given the existing infrastructure and beneficial reservoir properties, the Pohokura reservoir is an
attractive option to store efficiently large volumes of hydrogen within the reservoir formation. A key
challenge besides the injection and productivity potential is to what extent microbial effects have an impact
on longer term hydrogen storage.

AI Framework and Results

We evaluated the impact of microbial effects on hydrogen storage on the Pohokura field as outlined in
Figure 4. For the hydrogen storage assessment, we assumed that only the southern part of the reservoir
that is connected to the Pohokura Production Station, and the infrastructure of the Pohokura South station
SPE-212187-MS 7

are utilized. Specifically, POH-01 and POH-02 are monitoring wells equipped with sensors that monitor
the reservoir, and POS-01B and POW-3 are injector wells. The hydrogen is produced from POW-02 and
POW-01 that are connected to the existing Pohokura production station. The assumption for the reservoir
was that the injected hydrogen is sufficiently injected, and based on demand produced from the reservoir
via the two producer wells.

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Figure 4—Pohokura field and wells (Source: Shell Exploration NZ).

For the reservoir, each well measures pressure, temperature, salinity levels, the microbial growth rate,
concentrations of H2S and CO2 as well as the corrosion rate, and the amount of inhibitors present.
Additionally, the hydrogen injection and production rates are recorded. The measurement timeframe was
assumed to last five years, which provides sufficient time to experience the effect of microbial growth and
impact on the incorporation of inhibitors to reduce its impact.
We present in Figure 5 the hydrogen production profile and measured degree of microbes measured for
each of the wells. Hydrogen production oscillates depending on the energy demands with several trends of
lower and higher demand being clearly observable in the data.
8 SPE-212187-MS

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Figure 5—Hydrogen production profiles and the measured degree of microbes.

The first challenge that arises is to estimate microbial growth within the reservoir in order to determine
remedial actions. The measurement well data outline an increase in the microbial growth rate towards the end
of the timeperiod. This partially exponential behavior is commonplace for microbial growth and represents
a significant challenge for hydrogen storage quality. Specifically, the exponential growth rate requires early
intervention in the reservoir in order to prevent accelerated deterioration of the hydrogen quality and more
generally reservoir quality. Therefore, the first step is to establish a model to estimate and forecast the
microbial growth based on the reservoir parameters. We have developed a random forest framework for the
estimation of the microbial growth rate from the pressure, temperature, salinity, injection and production
rates for hydrogen. The results as outlined in Figure 6 show strong estimation performance in the training
stage, while simultaneously performing well on the test data set. The coefficient of determination is 0.88
for the training data, which represents a well-matched model. Likewise, the performance on the test data
set is equally strong with a high coefficient of determination. Additionally, uncertainty in the estimates is
relatively low given by the narrow distance of the points to the measurement points.

Figure 6—Microbial growth rate estimation versus actual recorded within the reservoir.

The final step for the framework was to evaluate the provide a methodology for the prediction of hydrogen
production from the reservoir. As outlined in Figure 7, both the prediction performance during the training
period for around 4 years and testing period of 1 year exhibited strong forecasting performance for the
hydrogen production.
SPE-212187-MS 9

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Figure 7—Estimated versus actual hydrogen production from the reservoir.

Conclusion
As the use of hydrogen gas (H2) as a renewable energy carrier experiences a major boost, one of the key
challenges for a constant supply is safe and cost-efficient storage of surplus H2 to bridge periods with low
energy demand. For this purpose, underground gas storage (UGS) in salt caverns, deep aquifers and depleted
oil-/gas reservoirs has been proposed, which provide suitable environments with potentially high microbial
abundance and activity. Subsurface microorganisms can use H2 in their metabolism and thus may lead to
a variety of undesired side effects such as H2 loss into formation, H2S build up, methane formation, acid
formation, clogging and corrosion.
We evaluated the framework on investigating potential microbial reactions for hydrogen storage in the
Pohokura gas field in New Zealand. The results demonstrated the ability to determine the microbial reactions
that may take place with hydrogen storage reservoir as well as its severity, which enhances the optimization
of injection strategy as well as suitability of a reservoir.
This framework represents an innovative approach to microbial reaction prediction for underground
hydrogen storage. The framework allows potential reservoirs to be efficiently evaluated and optimization
strategies to be utilized in order to maximize the efficiency of underground hydrogen storage. This will play
a critical role in enhancing hydrogen storage efficiency.

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