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100-Million-Year-Old Seafloor Sediment Bacteria Have Been Resuscitated



In 2010, Japanese scientists from the Integrated Ocean Drilling Program’s Expedition 329 sailed into the South Pacific Gyre with a giant drill and a big question.

The gyre is a marine desert more barren than all but the aridest places on Earth. Ocean currents swirl around it, but within the gyre, the water stills and life struggles because few nutrients enter. Near the center is both the Oceanic Pole of Inaccessibility (made famous by H.P. Lovecraft as the home of the be-tentacled Cthulhu) and the South Pacific garbage patch. At times the closest people are astronauts passing above on the International Space Station.

The sea here is so miserly that it takes one million years for a meter of marine “snow”—corpses, poo and dust—to accumulate on the bottom. The tale of all that time can total as little as 10 centimeters. It is the least productive patch of water on the planet.

Through nearly 6,000 meters of this seawater the IODP team lowered a drill. The strawlike bit plunged into pelagic clay and calcareous nanofossil ooze at three sites on the bottom.

By the time the cores of sediment were raised to the surface, the tubes contained up to 100 million years of Earth history. What the team wanted to know was how long and in what state microbes trapped in this milieu could survive in an almost-completely raided oceanic refrigerator. They were in for a surprise.

Their results, published in Nature Communications in July, revealed that the sediments contained bacterial cells, which they expected (not many, though: just 100 to 3,000 per cubic centimeter). But when given food, most of them quickly revived, which the scientists did not expect.

The microbes got straight to work doing what bacteria do, and within 68 days of incubation had increased their numbers up to 10,000-fold. They doubled about every five days (E. coli bacteria in the lab double in around 20 minutes). Their progeny contained specially labeled isotopes of carbon and nitrogen that made the scientists sure that the microbes were eating what they had been offered.

It’s worth pausing to consider the meaning of these results. In this experiment, cells awoke and multiplied that settled to the bottom when pterosaurs and plesiosaurs drifted overhead. Four geologic periods had ground by, but these microbes, protected from radiation and cosmic rays by a thick coat of ocean and sediment, quietly persisted. And now, when offered a bite, they awoke and carried on as if nothing unusual had happened.

In a sense, it hadn’t. If you think it feels like 100 million years since the pandemic began, think about the conditions (and entertainment options) of these poor microbes. It was a really long 100 million years down there. The toll of all that time was not zero, though. The oldest cells multiplied about half as fast as their spryer brethren that had “only” been there a few million years.

Consider now that 70 percent of Earth’s surface is covered by marine sediment, whose microbial residents represent somewhere between a tenth and a half of all microbial biomass on Earth. There’s a whole lot of senior citizen microbes down there.

Somewhat surprisingly, the majority of the cells were, like us, forms that breathe oxygen. In fact, the sediment they were pulled from is full of oxygen. Clearly, lack of “air” is not the problem for the life in gyre sediments. It’s the lack of food.

Contributing to the problem is the density of the sediment, which approaches something like flourless chocolate cake: the pore size is an estimated 0.02 micrometers. Given that a typical bacterium is a few micrometers across, you can see the problems inherent to migrating in search of food, or even hoping some blunders into you. Once you end up in South Pacific Gyre seafloor sediment, you are trapped—unless rescued by an ocean drilling program.

More surprises lay in store when the scientists checked the identities of the cells by probing their DNA; there was a lack of spore-forming bacteria. Some bacteria make resistant structures called endospores that are fortified and metabolically inactive, seemingly formed to allow bacteria to endure harsh conditions. Yet these bacteria were relatively absent. Spores were not how these superannuated bacteria had survived.

Even more surprising, discovered in one sample was a thriving population of light-harvesting bacteria called Chroococcidiopsis,cyanobacteria with a reputation for survival so formidable that they are being considered for terraforming Mars. (In addition to being able to live under translucent rocks in dry, cold, salty and radiation-drenched places, they have the unusual ability to capitalize on red light, possibly a result of their preferred dim conditions). How these photosynthetic microbes managed to reproduce in the dark after 13 million years beneath the seafloor remains a mystery.

Putting it all together—the tight quarters, the lack of spores and the rapid reanimation—these scientists think it’s likely that the majority of the bacteria in this impoverished sediment have been alive but idling these 100 million years.

A few years ago, I wrote about bacteria that may have been resurrected from coal from the Paleozoic. Now we have reports of bacteria from the Cretaceous seafloor sediment waking apparently nonplussed. Back then I speculated that under certain highly constrained but possibly abundant conditions, bacteria may be effectively immortal. Now it seems even more likely we may be sitting atop a planet that’s full of living fossils that are literally that—both fossils and alive.

The dinosaur people (and to be fair, who among us aren’t dinosaur people?) have their museums filled with bones and teeth and tracks. The plant people have their petrified forests and fossil fronds. But the microbe people have something even better: our dinosaurs aren’t dead.

This is an opinion and analysis article.



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