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These microbes live more than 2 kilometers below the sea floor off the coast of Japan.

These microbes live more than 2 kilometers below the sea floor off the coast of Japan.

Hiroyuki Imachi/JAMSTEC

'It's like going to Pluto and seeing McDonald's'

If you want to find some weird, undiscovered organisms, the sediments more than 2 kilometers below the ocean floor should be a good place to look. The heat and pressure are intense, and food is in short supply. But researchers have now obtained the first samples of microorganisms from these depths, and they turn out to be surprisingly ordinary. The cells are similar to microbes that live in a less demanding habitat on land: the soils in forests.

Microbes tough out some inauspicious environments, from searing hot springs to lakes beneath Antarctic ice. How far below the ocean bottom organisms can survive isn’t clear. Researchers have pulled up cells from more than 1900 meters under the sea floor, and they’ve detected chemical signs of life from about 4 kilometers down.

To search for other deeply buried microbes, an international team of researchers drilled more than 2400 meters into sediments off the northeast coast of Japan. About 23 million years ago the area was a coastal environment containing wetlands and lagoons, probably similar to parts of Florida, says co-author Kai-Uwe Hinrichs, a biogeochemist at the University of Bremen in Germany. But as the continents shifted position, the area gradually sank and was covered by sediment. Now, this deep layer is rich in coal.

The researchers took several precautions to try to eliminate contaminating microbes from their samples. Aboard the drilling ship, they scrutinized the sediment cores with an x-ray CT scanner and picked the ones that were the most solid. They removed sediment samples for analysis from the middle of the cores. Back in the lab, the scientists sequenced genes from the microbes and from microorganisms that were likely to contaminate the samples. They then used a statistical technique to correct their measurements for the presence of these interlopers.

As the researchers report online today in Science, their analysis showed small numbers of microbes even in the deepest sediments, which came from 2466 meters below the ocean floor. A cubic centimeter of deep-sea sediment contained about 10 to 10,000 microbial cells. In comparison, the same amount of dirt from your backyard would contain billions of microorganisms, Hinrichs says. “There is life, but there is very little life” at these depths, he says.

When the researchers incubated some of the microbes at 40°C and threw in a little coal dust, they detected signs of metabolic activity indicating that microorganisms from these depths are feeding on coal and releasing methane. The study results suggest that “microbial life is present in sediments down to around 2.5 km below the ocean floor,” says co-author Fumio Inagaki, a geomicrobiologist at the Japan Agency for Marine-Earth Science and Technology in Yokosuka.

One of the most important processes on Earth is the carbon cycle, in which carbon atoms shuttle between living things and the nonliving environment. Humans have distorted the carbon cycle by burning fossil fuels, releasing vast amounts of carbon dioxide into the atmosphere. That the microbes are eating coal and emitting methane suggests they also play “an important ecological role in [the] carbon cycle,” Inagaki says. 

To find out more about what the microbes in the cores are like, the scientists compared their gene sequences with gene sequences of microorganisms living in other habitats. The microbial groups from far below the ocean floor differed from those in shallower layers. To the researchers’ surprise, the deep-sea microbes were more similar to modern microbes that live in forest soil. Thus the types of microbes that lived in the habitat 20 million years ago had a big influence on what microbes live there now, Hinrichs says.

It is possible that the microbes the team found are the descendants of terrestrial microorganisms that adapted to life under the sea as their home sank below the surface. But it’s also possible that these microorganisms are the same cells that were alive when the habitat began to sink, meaning they are more than 20 million years old. “We don’t know exactly the turnover rate of cells” in this environment, Inagaki says.

Although some oil drillers have gone down farther, the current project is one of the deepest scientific drilling projects, if not the deepest. Marine microbiologist Andreas Teske of the University of North Carolina, Chapel Hill, describes the researchers’ efforts to obtain microbes from so far below the ocean floor as “heroic.” But Teske, who wasn’t connected to the study, cautions that the drilling technique the team used is prone to contamination, despite the researchers’ attempts to control it. Other methods that are better at excluding extraneous microbes might provide a clearer picture of what organisms live at these extreme depths, he says. “Much more will be possible with cleaner drilling techniques.”

“It’s a really valuable study” because it provides so much data about the organisms, says microbiologist Jennifer Biddle of the University of Delaware, Lewes, who also wasn’t connected to the research. You’d expect microbes from this exotic environment to be unusual, and the discovery that they are similar to familiar microorganisms is “disconcerting,” she says. “It’s like going to Pluto and seeing McDonald’s.”