Breathing without oxygen: How ancient microbes powered early life

Earth’s modern biosphere teems with plants, animals, and many other organisms that breathe oxygen to break down sugars into carbon dioxide and water. This process yields ATP – the universal “energy currency” essential for life’s biochemical reactions. 

But early in our planet’s history, oxygen was absent from the atmosphere, raising the question of how organisms generated ATP in those conditions.

New research now provides an answer by closely examining primordial microbes that inhabit present-day, oxygen-free ecosystems such as deep-sea hot springs. 

These ancient microbes illustrate a particular kind of respiration in which carbon dioxide and hydrogen are combined to form acetic acid, and the findings explain how that reaction is harnessed to generate ATP.

Significance of oxygen-free metabolism

Although life today often revolves around oxygen-based respiration, many habitats on early Earth – and even some modern extreme environments – lack this gas entirely. Instead, microorganisms living there rely on alternative energy-producing pathways, one of which uses CO₂ and hydrogen. 

Understanding such processes is vital for reconstructing how life might have functioned billions of years ago when oxygen did not exist in the atmosphere, and also for potentially developing new biotechnologies.

These ancient microbes perform a known reaction: combining carbon dioxide and hydrogen to yield acetic acid. 

The precise mechanism for producing ATP, however, remained unclear until a research team led by professor Volker Müller, Chair of molecular microbiology and bioenergetics at Goethe University Frankfurt, worked out the details.

An ion-based energy system

According to Müller, the team was able to show that the production of acetic acid itself activates a sophisticated mechanism as part of which sodium ions are pumped out of the bacterial cell into the environment.

“This reduces the sodium concentration inside the cell, whereby the cell envelope acts like a kind of dam for the ions. Once this dam is opened, the sodium ions flow back into the cell, driving a kind of molecular turbine that generates ATP,” explained Müller.

In essence, the ancient microbes devised an ion-based energy system. Instead of using oxygen to drive electron transport, they rely on a pathway that pumps sodium ions out, creating a gradient that can be exploited for ATP production. 

This approach parallels how many other organisms use proton gradients for ATP synthesis, underlining the remarkable plasticity of life’s energy strategies.

Protein network in ancient microbes

At the heart of the mechanism is a large, membrane-embedded collection of proteins called the Rnf complex. These proteins shunt electrons from hydrogen to carbon dioxide, forming acetic acid in the process. 

However, Rnf’s delicate structure made it extremely difficult to isolate. Researchers only managed to do so a few years ago, demonstrating just how challenging it is to study such ancient systems in the lab.

When carbon dioxide and hydrogen come together, electrons move through several intermediates. 

The Rnf complex mediates the final leg of that journey, ensuring that each electron is properly transferred. This procedure led to the question: how exactly is electron flow coupled to pumping out sodium ions?

Using cryo-electron microscopy, the scientists created detailed, high-resolution snapshots of the Rnf complex from the bacterium Acetobacterium woodii. 

During the imaging process, the purified complex was rapidly frozen, forming a thin film of ice that preserved it in near-native condition. 

By looking at Rnf from various angles, the team constructed 3D models that reveal which parts of the proteins physically interact to enable electron flow.

Sodium ion pumping in ancient microbes

Still, knowledge of the protein structures did not fully explain how moving electrons expels sodium ions. That puzzle was partially solved by a molecular dynamics simulation conducted by Professor Ville Kaila’s group at Stockholm University. 

The team’s simulation highlighted a crucial iron-sulfur cluster stationed in the middle of the membrane. As soon as the cluster takes on an electron, it becomes negatively charged, attracting sodium ions from within the cell like a magnet.

“The positively charged sodium ions from inside the cell are drawn to this cluster, just like a magnet,” said Jennifer Roth, a doctoral candidate in Müller’s research group. 

“This attraction in turn causes the proteins to shift around the iron-sulfur cluster, much like a rocker switch: they create an opening leading to the outside of the membrane, through which the sodium ions are once again released.”

That shift completes a full cycle: by “locking in” a sodium ion, toggling the cluster, and then releasing the ion externally, the cell effectively pumps sodium outward. 

An abundant sodium gradient accumulates, and the bacteria later allow ions to flow back in, spinning the molecular turbine (ATP synthase) that synthesizes ATP.

Understanding respiration without oxygen

Though the spotlight is on ancient metabolism, this discovery could have pragmatic uses in carbon capture. These microbes seize carbon dioxide to create acetic acid. 

With deeper understanding, industries may be able to harness bacteria to remove greenhouse gases from emissions or to produce high-value chemicals. 

“Once we know how the bacteria generate energy in the process, we may be able to optimize this process in a manner that would allow us to produce even higher-quality end products,” said Müller.

Furthermore, similar respiratory enzymes are found in some pathogens, raising the prospect of drug design that targets these crucial proteins to combat bacterial diseases.

By explaining a novel system for respiration without oxygen, the study has revealed another facet of life’s resilience. 

Such findings reveal how the earliest life forms innovated to harness energy, demonstrating the creative adaptations that allowed Earth’s diverse biosphere to flourish – even under seemingly inhospitable conditions.

The study is published in the journal Nature Communications.

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