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These microbial communities have learned to live at Earth’s most extreme reaches

Brown fungus colonies growing in a Petri dish.

A culture of Eurotium herbariorum fungus, often retrieved from ocean-floor sediments.Credit: Tom Kleindinst/Woods Hole Oceanographic Institution (WHOI)

At the bottom of the Indian Ocean, in one of the deepest layers of Earth’s crust ever explored, researchers are finding life. An analysis of rock samples from Atlantis Bank, part of a seafloor mountain where deep crustal rock is exposed close to the surface, has revealed microbes adapted to life within nutrient-poor, hairline fractures in the earth.

These single-celled survivors seem to be able to live and grow — albeit slowly — despite having extremely limited access to resources. The research1, published in Nature on 11 March, is the latest instalment in a quest to define the extreme edges of Earth’s habitable space.

A team led by marine microbiologist Virginia Edgcomb at Woods Hole Oceanographic Institution in Massachusetts found several species of bacteria, fungi and archaea that live in the rocks and feed on carbon from fragments of amino acids and other organic molecules carried in deep ocean currents.

“It is exciting that there is a community of microbes alive down there,” says Edgcomb. “They are surviving using strategies that rely on intensive recycling of carbon.”

These types of microorganism were once considered ‘extreme’ forms of life, but research over the past couple of decades has shown that as much as 70% of all microbes on Earth live in similarly harsh environments. Other studies have shown that life is abundant in places long deemed inhospitable, such as deep sediments under the oceans, the cold deserts of Antarctica and even the stratosphere.

A transmission light micrograph of a rock thin section: a pattern of colours on a dark background.

A thin slice of rock from oceanic crust at Atlantis Bank in the Indian Ocean, where slow-living bacteria have been found.Credit: Frieder Klein/WHOI

And these scavenging microbes have evolved diverse ways to survive the challenges their habitats present. Some are able to breathe metals, even radioactive ones such as uranium. Some capture nutrients from trace gases in the air. And others, like those found buried deep in the sludgy ocean floor, live so incredibly slowly that they might survive to be hundreds or thousands of years old, eating and reproducing infrequently.

“They are like finely tuned, apocalyptic machines. And they love scarcity,” says Karen Lloyd, a geomicrobiologist at the University of Tennessee, Knoxville, who has scoured the globe for these rarely-seen life forms.

Life in the slow lane

Early hints that life existed deep within Earth’s crust first surfaced in the 1920s, when oil prospectors noticed that groundwater around their oil fields was laced with hydrogen sulfide and bicarbonate, which are both made by bacteria. In the 1980s, microbiologists began counting the microbes in cores brought back from the Deep Sea Drilling Project — a large-scale effort to explore the sea floor — and were astounded by the numbers.

It wasn’t until the early 2000s, with the launch of an expedition devoted solely to exploring life in the deep biosphere, that scientists started to understand the biology of these deep-sea-dwelling microbes. The JOIDES Resolution, a drill ship equipped with a floating lab, left San Diego, California, with a team of scientists led by Bo Jørgensen, a geomicrobiologist from Aarhus University in Denmark, and Steven D’Hondt, an oceanographer from the University of Rhode Island. It sailed to the eastern Pacific Ocean, where the team sampled rock cores as deep as 5,300 metres off the coast of Peru, capturing sediment up to 35 million years old2.

The team confirmed that the sediments contained an abundance of microbes. And despite having little to feast on — the organic carbon available to them represents about 1% of the carbon that is fixed by photosynthesizing organisms on the surface — these microorganisms seemed to be surviving.

Early experiments on the JOIDES showed that these microbes were carrying out basic biological function at a much slower rate than microbes on the surface, an adjustment necessary when food sources are not replenished for millennia. Some scientists even wondered whether these microbes were truly alive, or whether they were just slowly starving to death.

Jørgensen is convinced that the microbes in these environments are living, and points to subsequent research showing they have active protein and DNA repair mechanisms3.

“We always expect that bacteria are growing fast — this is what you see in the laboratory — but I found that most of them are growing extremely slowly,” says Jørgensen. “What we used to think was extreme is the normal."

Too wild for the lab

Most of these edge dwellers can’t be studied in a lab: they simply don’t grow in culture. And even the ones that do act differently under artificial conditions from how they would in the wild. Because of this, studying their survival strategies has proved difficult. But that is now changing thanks to the advent of metagenomic techniques, which allow scientists to track gene expression in whole communities simultaneously.

These methods have allowed researchers to identify genes that are involved in low-energy protein and DNA repair processes, as well as energy-efficient metabolic strategies. They have even found genes that allow bacteria to survive off trace gases such as carbon monoxide and hydrogen.

The findings from Edgcomb’s team “extend what we are learning about how microbes live in fractured rocks that make up much of Earth’s subsurface”, says Rick Colwell, a microbial ecologist at Oregon State University in Corvallis. “We are gaining more evidence that the things they subsist on — like hydrogen as a source of energy — create a different tempo for life.”

doi: https://doi.org/10.1038/d41586-020-00697-y

References

  1. 1.

    Li, J. et al. Nature 579, 250–255 (2020).

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  2. 2.

    D’Hondt, S. et al. Science 306, 2216-2221 (2004).

    PubMed  Article  Google Scholar 

  3. 3.

    Mhatre, S. S. et al. FEMS Microbiol. Ecol. 95, fiz068 (2019).

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