Living microbes found sealed inside a sealed 2-billion-year-old rock - a 'very exciting discovery'

Crack open a piece of volcanic rock that formed roughly 2.05 billion years ago, and you might expect nothing but minerals, and certainly not living microbes. However, scientists tend to think outside-the-box.

A team from the University of Tokyo decided to ask a different question: could tiny microbes be living inside the rock’s hairline cracks, and could those cells be native to the stone rather than modern hitchhikers?

The answer points to an underground world that runs on chemistry instead of sunlight.

Earth’s deep subsurface hosts slow, sparse communities that survive on tiny energy trickles released when water reacts with minerals.

If those reactions can power life over long spans of time, then ancient, stable rock should be a good place to look.

That idea led researchers to an enormous igneous formation in South Africa and a careful test of whether the signals they found were real rather than contamination.

Searching for microbes in rocks

The Bushveld Igneous Complex is one of the largest bodies of ancient magma on the planet. It cooled into hard, dark mafic rock and has stayed relatively calm for eons, without dramatic heating or tearing.

That stability matters. If deep rocks can support life, a steady setting gives microbes a chance to persist at a crawl and leave faint traces behind.

There’s a practical hurdle, though. Drilling can drag modern cells into a core sample.

Any claim about life inside a rock has to prove the sample stayed clean. The team designed their work to deal with that from the start.

Only after lining up and thoroughly vetting the evidence did the lead scientist step forward to describe what it means for the field.

Yohey Suzuki, an associate professor at the Graduate School of Science at the University of Tokyo, led the study and explained why the signals inside the rocks caught his eye and how they were verified.

“We didn’t know if 2-billion-year-old rocks were habitable,” Suzuki explained. “Until now, the oldest geological layer in which living microorganisms had been found was a 100-million-year-old deposit beneath the ocean floor, so this is a very exciting discovery.”

How the core stayed clean

At a mine site near Burgersfort, the team drilled a short core from a shallow depth. Before any analysis, they sterilized the outer surface.

They also spiked the drilling fluid with fluorescent plastic microspheres – tiny beads that act as tracers. If fluid leaked into internal cracks, the beads would ride along and reveal the breach under ultraviolet light.

The fluid lit up with beads, as expected. The interior of the rock did not.

That result indicated the core’s interior stayed sealed during drilling, clearing the way to hunt for native signals without crushing the sample and losing location information.

Micron-scale fingerprints of life

With contamination controls in place, the researchers turned to optical photothermal infrared (O-PTIR) spectroscopy.

This high-resolution method maps chemical fingerprints at the micron scale, including amide peaks that indicate proteins. Thin slices of the rock showed narrow veins glowing at protein-related wavelengths.

Only then did they stain the slice with a DNA-binding dye and check the same spots by fluorescence microscopy.

In the protein-rich veins, they saw cell-shaped specks – many less than a micron across – clustered in the same places.

That co-location of protein signals and DNA, in a core interior that passed the bead test, built a strong case for truly indigenous microbes tucked inside microveins of the rocks.

Understanding the microveins

Electron microscopy and elemental analysis pointed to saponite, a magnesium-rich clay in the smectite family, filling those veins.

Clay minerals can hold water, and organic molecules and can form where water alters volcanic minerals.

That kind of alteration can release hydrogen gas, which is a valuable energy source for many deep microbes that make a living without sunlight.

The clay did something else helpful too. It packed the veins so tightly that it likely acted as a seal.

That kept the fluorescent beads – and any microbes from the drilling fluid – from getting in, and it probably limited how far the native cells could move, leaving them clustered along the clay-filled cracks.

Repetition is crucial in science

The study’s workflow is as important as the discovery itself.

Instead of crushing rock and losing context, the team kept location information at every step: dry, clean cutting to avoid adding organics; in-place checks for fluorescent beads to confirm the interior stayed sealed; infrared mapping to find protein signatures at single-cell resolution; and only then DNA staining as a final confirmation.

That layered approach gives future projects a path to separate true subsurface life from modern contamination with more confidence.

Hidden microbes in Earth’s rocky interior

Put the pieces together and a picture emerges: small, quiet communities perched along clay-filled cracks inside ancient igneous rock.

They live on a tiny energy budget – hydrogen here, traces of oxidants and organic compounds there. Growth is slow. Movement is limited.

Yet they persist, shielded by minerals and fed by steady rock-water chemistry that doesn’t depend on the sun.

This widens the map of where life can exist and for how long. Ancient volcanic rocks are not sterile museum pieces.

Under the right conditions, they can host cells that endure, sealed away from surface flux and nourished by reactions that churn on in the dark.

Microbes inside Martian rocks

“I am very interested in the existence of subsurface microbes not only on Earth, but also the potential to find them on other planets,” Suzuki shared.

NASA’s Mars Perseverance rover is slated to return rock samples, and some could be similar in age to the Bushveld rocks examined here.

If methods can reliably confirm ancient, native cells on Earth, that raises the bar – and the hope – for what could be found in returned Martian samples.

“Finding microbial life in samples from Earth from 2 billion years ago and being able to accurately confirm their authenticity makes me excited for what we might be able to now find in samples from Mars,” Suzuki enthused.

Finding more living microbes in rocks

The work opens a practical to-do list. Collect more cores from different depths and rock types. Identify which microbes are present.

Reconstruct when the clay veins formed and how long the communities have occupied them. Track how nutrients and waste move in such tight spaces.

Each answer will sharpen the picture of Earth’s deep biosphere and refine search strategies for life in extreme settings elsewhere.

Ancient igneous rocks can shelter life. The signals line up: clean cores, protein fingerprints, DNA staining, and clay-sealed veins that both protect and support tiny cells.

The study shows how to tell native life from modern contamination and points to a style of living that is slow, steady, and persistent – life that whispers from within the rock.

The full study was published in the journal Microbial Ecology.

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