Different Paths To Carbon Capture In Methanogens

Methane-producing microbes solve one of biology's most energy-demanding challenges: converting carbon dioxide into methane by using an energy-boosting trick called electron bifurcation. Now Researchers at the Max Planck Institute of Biophysics and the Max Planck Institute for Terrestrial Microbiology discovered that different microorganisms link these two reactions in different ways. The findings open up a new understanding of the diversity of molecular architectures that allow methanogens to thrive in different environments.

Methanogens are microorganisms that thrive in oxygen-free environments such as digesters, animal guts, and sediments. They convert CO₂ and hydrogen into methane, a process that plays a major role in the global carbon cycle and is widely used in biogas plants to produce renewable energy. But this conversion comes with a challenge: hydrogen alone does not carry enough energy to power the crucial first step, fixing CO₂. To get around this, methanogens rely on a biochemical process called electron bifurcation, in which an enzyme called heterodisulfide reductase (Hdr) splits a pair of electrons, sending one on an energy-releasing path while boosting the other to a higher energy level. This separation results in enough energy to drive CO₂ fixation by a partner enzyme called formylmethanofuran dehydrogenase (Fmd).

Two microbes, two solutions
In 2021, teams led by Bonnie Murphy and Seigo Shima, from the Max Planck Institute of Biophysics and the Max Planck Institute for Terrestrial Microbiology, discovered that in one methanogen species, called Methanospirillum hungatei, these two enzymes are physically locked together in a ring-shaped complex, allowing electrons to travel directly between them. Their new study, however, examined a different methanogenic organism, Methanothermobacter marburgensis, and found a completely different structure: instead of a ring, two Hdr units pair with four Fmd units, linked by a newly identified protein, MvhB, that transfers electrons between them at a high speed.

"This shows that different methanogens can solve the same energetic challenge with different molecular arrangements," says lead author Pablo San Segundo-Acosta. By comparing gene sequences across various methanogen species, the team traced the evolutionary history of the protein complex and found that the paired arrangement was likely present in the ancestor of all methanogens. San Segundo-Acosta adds: "Our analysis suggests this arrangement actually evolved first, with the ring-shaped form arising later in a separate lineage."

Bundling these enzymes together into a single complex has a clear advantage: electrons can travel directly from one enzyme to the other without leaking away into unwanted side reactions. But this efficiency comes at a cost, since it makes it harder for the microbe to adjust if conditions change. In their publication in Science Advances, the authors highlight that this trade-off may explain why two different architectures evolved.

Reading a microbe's strategy from its genes
These new findings offer a tool for exploring a large number of methanogens that remain poorly studied. "Linking these architectures to specific sequence features means we can now recognise them in genomes from organisms nobody has ever grown in the lab," says co-corresponding author Bonnie Murphy. "The study gives us a way to predict which arrangement a methanogen likely uses directly from its genome sequence — including species from digesters, animal guts and sediments that have never been isolated."

Since methanogens play a central role in natural and industrial carbon cycling, understanding the diverse architecture of their molecular machinery may ultimately help researchers harness these processes more effectively, turning a billion-year-old survival strategy into a tool for a more sustainable future.