Bacteria found in solid rock

Japanese researchers say they have found single-celled creatures living in tiny cracks inside volcanic rocks taken from deep beneath the seafloor.

They admit to being lucky and surprised, despite what they say was a decade of trial and error.

And success has left them somewhat visionary, suggesting this may inspire a new search for life on Mars.

“I am now almost over-expecting that I can find life on Mars,” says Yohey Suzuki from the University of Tokyo, first author of a paper in the journal Communication Biology.

“If not, it must be that life relies on some other process that Mars does not have, like plate tectonics.” 

And it’s not just a dream. Suzuki says his team is beginning a collaboration with NASA’s Johnson Space Centre to design a plan to examine rocks collected from the Martian surface by rovers.

“This discovery of life where no one expected it in solid rock below the seafloor may be changing the game for the search for life in space,” he says.

200403 core samples
A core sample solid rock from 122 metres beneath the seafloor. Image B is 1000 times greater magnification than Image A. In each, the left side was taken in normal light and the right using fluorescent light. Credit: Suzuki et all. 2020, CC by 4.0

Here’s the story to date.

Undersea volcanoes spew out red hot lava, which cools to become rock with cracks often smaller than a millimetre. Over millions of years, Suzuki says, these fill with clay minerals – and with bacteria that multiply.

The microbes identified in the cracks are aerobic bacteria, meaning they use a process similar to how human cells make energy, relying on oxygen and organic nutrients.

The researchers estimate that the communities they found have a density of about 10 billion bacterial cells per cubic centimetre – the same as the human gut. The average density in mud sediment on the seafloor is estimated to be just 100 cells per cubic centimetre.

“These cracks are a very friendly place for life,” Suzuki says. “Clay minerals are like a magic material on Earth; if you can find clay minerals, you can almost always find microbes living in them.”

Suzuki helped collect the rock samples in late 2010 as part of the ongoing Integrated Ocean Drilling Program (IODP). 

A research ship stopped three times on its trip between Tahiti and New Zealand, and core samples 6.2 centimetres wide were taken from down to 125 metres below the sea floor. There was 75 metres of mud sediment before they hit solid rock.

Depending on the location, the samples were estimated to be 13.5 million, 33.5 million and 104 million years old. 

Importantly, the collection sites were not near hydrothermal vents or sub-seafloor water channels, so the researchers are confident the bacteria arrived in the cracks independently rather than being forced in by a current. 

For years Suzuki and his team used traditional chipping and grinding methods to try to find bacteria in his samples, but without success. He then tried an approach he says was inspired by the way pathologists prepare ultrathin slices of body tissue samples to diagnose disease.

He coated the rocks in a special epoxy to support their natural shape so that they wouldn’t crumble when he sliced off thin layers. These were then washed with dye that stains DNA and placed under a microscope.

The bacteria appeared as glowing green spheres tightly packed into tunnels that glow orange, surrounded by black rock. That orange glow comes from clay mineral deposits, the “magic material” giving bacteria an attractive place to live.

Whole genome DNA analysis identified the different species of bacteria that lived in the cracks. Samples from different locations had similar, but not identical, species of bacteria. 

Rocks at different locations are different ages, which may affect what minerals have had time to accumulate and therefore what bacteria are most common in the cracks.

Suzuki and his colleagues speculate that the clay mineral-filled cracks concentrate the nutrients that the bacteria use as fuel. 

This might explain, they say, why the density of bacteria in the rock cracks is eight orders of magnitude greater than the density of bacteria living freely in mud sediment where seawater dilutes the nutrients.

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