I am certainly no expert, but I think I should better
explain methanogenesis for this multiple-part post. Methanogenesis refers to
biologically produced methane and is also referred to as bio-methanization. In
my oil & gas studies and work, I came to understand the two main sources of
subsurface methane generation: biogenic and thermogenic. Methane in drilled
natural gas fields may be of either type or a combination, but the bulk of it
is thermogenic, produced by the heat and pressure in deeply buried rock that is
rich in organic matter, typically decomposed algal matter. The PT conditions
influence the chemical “cracking” of heavier hydrocarbons into methane. Dry
natural gas occurs when the “wetter” liquids that make up crude oil are used up
in the process. Dry natural gas occurs where hydrocarbons are said to be
thermally mature. There is also abiotic methane produced by the interaction of
seawater and magmatic olivine in the process known as serpentinization. This
has recently been shown to be more prevalent at deep-sea trenches than thought.
According to a 2019 release from Woods Hole Oceanographic Institution:
“…seawater, moving through the deep oceanic crust, is
trapped in magma-hot olivine. As the mineral cools, the water
trapped inside undergoes a chemical reaction, a process called serpentinization
that forms hydrogen and methane. The authors demonstrate that in otherwise
inhospitable environments, just two ingredients—water and olivine—can form methane.”
According to Wikipedia:
“Methanogenesis or biomethanation is the formation of
methane coupled to energy conservation by microbes known as methanogens. It is
the fourth and final stage of anaerobic digestion. Organisms capable of
producing methane for energy conservation have been identified only from the
domain Archaea, a group phylogenetically distinct from both eukaryotes and
bacteria, although many live in close association with anaerobic bacteria. The
production of methane is an important and widespread form of microbial metabolism.
In anoxic environments, it is the final step in the decomposition of biomass.
Methanogenesis is responsible for significant amounts of natural gas
accumulations, the remainder being thermogenic.”
Marine sediments are an
important habitat for methane-generating microbial communities. In the most
common pathway, the microbes consume acetate, which comprises two-thirds of
global methane production. The abbreviated reactions are CO2 + 4 H2 → CH4 + 2
H2O and CH3COOH → CH4 + CO2. The pathways are shown in more detail below.
Both carbon and hydrogen
isotopes can be used to fingerprint methane. An August 2025 paper in Science
explores the main enzyme in methanogenesis, methyl–coenzyme M reductase (MCR),
and how modulating it with CRISPR alters the isotopic composition of microbial
methane, showing that a similar modulation pathway exists in nature. Jonathan
Gropp, the paper’s lead author, notes:
“…for methane, large uncertainties in fluxes exist --
within tens of percents for some of the fluxes -- that challenge our ability to
precisely quantify the relative importance and changes in time of the sources.
To quantify the actual sources of methane, you need to really understand the
isotopic processes that are used to constrain these fluxes. Microbes
respond to the environment by manipulating their gene expression, and then the
isotopic compositions change as well. This should cause us to think more
carefully when we analyze data from the environment."
Co-author Dipti Nayak, UC
Berkeley assistant professor of molecular and cell biology, added:
"It is well understood that methane levels are
rising, but there is a lot of disagreement on the underlying cause. This study
is the first time the disciplines of molecular biology and isotope
biogeochemistry have been fused to provide better constraints on how the
biology of methanogens controls the isotopic composition of methane. I think
what's unique about the paper is, we learned that the isotopic composition of
microbial methane isn't just based on what methanogens eat. What you 'eat'
matters, of course, but the amount of these substrates and the environmental
conditions matter too, and perhaps more importantly, how microbes react to
those changes.”
Geochemist and co-author
Daniel Stolper, UC Berkeley associate professor of earth and planetary science,
explained isotopic signatures and variation in methanogenesis pathways:
"Over the last 70 years, people have shown that
methane produced by different organisms and other processes can have
distinctive isotopic fingerprints. Natural gas from oil deposits often looks
one way. Methane made by the methanogens within cow guts looks another way.
Methane made in deep sea sediments by microorganisms has a different
fingerprint. Methanogens can consume or 'eat', if you will, a variety of
compounds including methanol, acetate or hydrogen; make methane; and generate
energy from the process. Scientists have commonly assumed that the isotopic
fingerprint depends on what the organisms are eating, which often varies from
environment to environment, creating our ability to link isotopes to methane
origins."
The researchers used CRISPR
to reduce the activity of the enzyme and found that when they did, the isotopic
composition of the methane changed. They also discovered that changes in the
availability of food sources for the microbes result in changes in gene
expression that lead to changes in isotopic signatures. These archaean microbes consume
acetate (essentially vinegar), methanol (the simplest alcohol), or molecular
hydrogen (H2) and produce methane, CH4, with a ratio of hydrogen and
carbon isotopes different from the ratios observed in the environment. They
found that the microbes, which normally get hydrogen from what they consume,
can also get it from the water in the environment if their food source becomes
scarce.
According to Science Daily
and the authors, using CRISPR in similar isotope/enzyme studies can help
increase understanding:
“Beyond this study, the CRISPR technique for tuning
production of enzymes in methanogens could be used to manipulate and study
isotope effects in other enzyme networks broadly, which could help researchers
answer questions about geobiology and the Earth's environment today and in the
past.”
"This opens up a pathway where modern molecular
biology is married with isotope-geochemistry to answer environmental
problems," Stolper said. "There are an enormous number of isotopic
systems associated with biology and biochemistry that are studied in the
environment; I hope we can start looking at them in the way molecular
biologists now are looking at these problems in people and other organisms --
by controlling gene expression and looking at how the stable isotopes respond."
Another potential benefit
could be using the knowledge gained to one day use it to reduce the methane
output to the atmosphere, but this is likely far off.
References:
Methanogenesis.
Wikipedia. Methanogenesis
- Wikipedia
Scientists
just found a hidden factor behind Earth’s methane surge: Using CRISPR to dial
down enzyme helps to understand the isotope signatures of methane from
different environments. Sceince Daily. University of California at Berkeley. August
17, 2025. Scientists
just found a hidden factor behind Earth’s methane surge | ScienceDaily
Modulation
of methyl–coenzyme M reductase expression alters the isotopic composition of
microbial methane. Jonathan Gropp, Markus Bill, Max K. Lloyd, Rebekah A. Stein,
Dipti D. Nayak, and Daniel A. Stolper. Science. 14 Aug 2025. Vol 389, Issue
6761. pp. 711-715. Modulation
of methyl–coenzyme M reductase expression alters the isotopic composition of
microbial methane | Science
Origin
of Massive Methane Reservoir Identified. Woods Hole Oceanographic Institution.
August 20, 2019. Origin
of Massive Methane Reservoir Identified – Woods Hole Oceanographic Institution
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