Rock-eating Microbes Have a Chemical Machine That Turns CO2 Into Life Without Sunlight

Take any enzyme that turns one molecule into another. Add the right ingredients, and it does its job. That’s just how they work – reliable molecular machines, driven by chemistry alone.

Inside a rock-eating sulfur bacterium, there’s a carbon-capture enzyme unlike any other. Load it with CO2, give it water – it just sits there. Only the cell membrane’s electrical charge can make it react.

Microbes without sunlight

These organisms have a name that sounds borrowed from a tabloid: rock-eating microbes. Scientifically they’re chemolithoautotrophs.

Instead of sunlight, they harvest energy by chewing through inorganic chemistry – hydrogen, sulfur compounds, iron, ammonia.

They live where almost everything else would die: hot vents, sulfide-rich sediments, rock kilometers below the surface. Collectively, they make up a vast slice of Earth’s microbial life.

Two German labs took the puzzle apart together. Dr. Jan Schuller’s group at the University of Marburg (Uni Marburg) and Dr. Sven Stripp’s at the University of Potsdam (Uni Potsdam) targeted a sulfur-loving species called Halothiobacillus neapolitanus.

CO2 and bicarbonate

Carbon dioxide drifts through cell membranes easily. That’s not the hard part. The hard part is what happens next. Cells can’t use CO2 directly for carbon fixation – they need it converted into bicarbonate.

Bicarbonate is electrically charged, and it doesn’t cross the membrane on its own. Most organisms burn ATP, the cell’s energy currency, to pump it inside.

Rock-eaters can’t afford that. Energy is so scarce in their world that every molecule of ATP is spoken for. A system that burns through it just to import bicarbonate would leave nothing for growth.

A 2019 study identified a two-piece protein called DAB2 in H. neapolitanus‘s membrane that seemed to pull CO2 inside and convert it to bicarbonate without burning ATP. The mechanism was a mystery.

Mapping the machine

Schuller’s team used cryo-electron microscopy – a technique that flash-freezes proteins and images them at near-atomic detail – to get a close look at DAB2. They caught it in three snapshots: empty, gripping CO2, and holding bicarbonate.

Weeks of trouble. The protein kept falling apart during preparation. The team fused the two subunits together and dropped the construct into a tiny lipid disc that mimicked a cell membrane.

What they saw was a two-piece complex: one subunit in the cell’s interior, one embedded in the membrane.

The interior piece, DabA2, resembled carbonic anhydrase – an enzyme that swaps CO2 and bicarbonate. But a strange version.

A buried active site

Normal carbonic anhydrases sit wide open – their reaction chamber sits near the surface, easy for CO2 to wander in and out.

This one is built differently. Its chamber is buried deep inside the protein, reachable only by squeezing through two narrow tunnels.

At the bottom of that chamber sits a zinc atom. Around it, the frozen image revealed something no standard carbonic anhydrase has ever shown – two CO2 molecules packed in side by side.

Stranger still, the building block thought to trigger the reaction in every other carbonic anhydrase is absent here. Leucine sits in its place – and leucine can’t do that job.

Power from gradients

That missing piece was the clue. To investigate, Stripp’s group ran infrared spectroscopy – a method that tracks chemical reactions in real time by detecting how molecules absorb light – as CO2 was added to the protein.

Unexpected result. The protein grabbed CO2 tightly – about ten times more strongly than a non-catalytic control – but produced no bicarbonate. Just binding. Nothing more.

Alone, the complex is inert. It appears to need a charge difference across the membrane to activate – the same electrical gradient that drives ATP synthesis everywhere else in biology.

Now they had a mechanism in hand. Rock-eaters appear to tap that same charge gradient, but route it through a custom enzyme instead of spending ATP, Stripp said.

Trapping bicarbonate inside

Until this study, no one had directly observed how rock-eating bacteria connect proton flow to carbon capture. Most carbonic anhydrases work both directions – they can turn CO2 into bicarbonate, or split bicarbonate back into CO2. DAB2 doesn’t.

Structural maps show that bicarbonate can’t fit in the active site in reverse. Only one direction works: CO2 in, bicarbonate out, no going back.

That’s the trick. When protons move through the membrane, the tunnels appear to open. The active site only forms bicarbonate, never undoes it. Every CO2 molecule that enters gets locked in, accumulating far above the outside concentration.

Where it leads

The rock-eaters’ trick is now in view. Schuller and Stripp’s teams showed for the first time that a buried, gated pump inside a sulfur bacterium runs carbon fixation on the cell membrane’s charge alone. No ATP spent.

It’s a mechanism unlike the cyanobacterial carbon pumps we already knew. That finding also explains how vast slices of microbial life survive in low-energy habitats, including the deep subsurface – where recent research puts a huge fraction of Earth’s biomass.

The implications stretch beyond basic biology. Close relatives of DAB2 turn up in human pathogens like Bacillus anthracis and Vibrio cholerae, where carbon scavenging supports their virulence.

Targeting these pumps could give microbiologists a new antibiotic angle. The same blueprint, in friendlier hands, could help engineers build ATP-free carbon concentrators into crops or industrial microbes.

The study is published in Nature Communications.