Mad Scientists Revive 100-Million-Year-Old MicrobesFeedzy

This is the strange saga of how scientists went to some of the deepest, darkest depths of the ocean, dug 250 feet down into the sediment, collected an ancient community of microbes, brought them back to a lab, and revived them. And you’re going to think: Why, in the already-horrible year of 2020, would they tempt fate like this? Well, it turns out that not only is everything OK, but that everything is in fact very, very excellent—at least far away from humanity in the deep-sea muck of the world’s oceans.

This story begins more than 100 million years ago in the middle of what we humans now call the Pacific Ocean. Volcanic rock had formed a hard “basement” of seafloor, as geologists call it. Over this, sediment began to accumulate. But not the kind of sediment you may expect.

Elsewhere in the world’s oceans, much of the seafloor sediment is organic matter. Dead animals, from the tiniest plankton to the biggest whales, die, sink, and form a muck that scavengers hoover up and excrete. The western coasts of the Americas are a classic example: Upwelling currents bring nutrients from the deep, which feed all kinds of organisms nearer the surface, which in turn feed bigger animals, and on up the food chain. Everything eventually dies and drifts down to the bottom, where the detritus becomes food for bottom-dwelling critters. The seas are so packed with life, they’re downright murky. (Think, for example, of California’s hyper-productive Monterey Bay.) Organic matter accumulates so fast on the seafloor, much of it gets buried under still more layers of organic matter before the scavengers can get to it.

By contrast, in the middle of the Pacific, there’s surely life, just a lot less of it. Accordingly, the water far off the coasts of Australia and New Zealand is among the clearest in the world. There’s no upwelling and much less life at the surface, so much less organic matter is sinking to the seafloor to form sediment. What little does sink is immediately hoovered up by scarce bottom-dwellers like sea cucumbers.

“It’s the least-explored large biome on Earth, because it covers 70 percent of Earth’s surface,” says the University of Rhode Island’s Steven D’Hondt, who co-led the expedition and coauthored a new paper in Nature Communications describing the findings. “And we know so little about it.”

Dropping drills up to 19,000 feet deep some 1,400 miles northeast of New Zealand, D’Hondt and his colleagues were on a mission to probe these ancient deep-sea sediments for life. Much of the seafloor could be volcanic ash blown from the land, as well as metallic bits from space. “There’s a measurable fraction of it that’s cosmic debris,” says D’Hondt. “If you trawl through the shallow clay with a magnet, you’ll pull out micrometeorites.”

Even at the surface of the sediment, where sea cucumbers roam, you’d expect to find very few microbes—relatively speaking. “At the seafloor there, you might have a million microbes per cubic centimeter,” says D’Hondt. “Whereas off of San Francisco, you might have a billion or 10 billion per cubic centimeter.” The researchers expected, then, to find fewer microbes even deeper, where organic matter is essentially nonexistent.

To capture those microbes, they drilled down through 75 meters of superfine sediment until they hit that basement of volcanic rock, then collected their samples. From previous drilling nearby, they knew they’d be grabbing 101.5-million-year-old muck—sedimentation gathers in this part of the sea at a rate of perhaps 10 centimeters every million years.

Sediment samples in hand, Yuki Morono—a geomicrobiologist at the Japan Agency for Marine-Earth Science and Technology (known as JAMSTEC) and lead author of the new paper—now had to search through the ultra-fine sediment for ultra-tiny microbes. In principle, the process should have been straightforward. Morono used a chemical that stains DNA, ferreting the microbes out of their hiding places amid multitudinous other sedimentary particles.

What he found was astonishing: 10¹¹ cells per cubic centimeter of sediment that should, in theory, be scant in terms of life. JAMSTEC’s directors were ecstatic. “They were saying that they were groundbreaking results and will rewrite the textbooks or something. And I was so worried about that,” recalls Morono. Such a high cell count in sediment almost devoid of nutrients and oxygen rang alarm bells for him. So Morono picked apart his own techniques and results and found that something was indeed awry. “Finally, within something like a half a year or so, I could prove that the results were wrong: More than 99 percent of the cells I detected by the previous technology were not cells,” he says.

A paper he had submitted to a journal was actually in peer review at the time and had to be pulled. But he decided to try again. “Based on that very bad nightmare memory, I tried to develop the technology to be sure,” Morono says.

The hangup turned out to be that DNA-staining chemical: It also stained other sedimentary particles, spherical little bits that look much like a cell. “What we found from the nightmare memory is that the microbes could be stained in greenish color as a fluorescence, whereas the organic compounds or organic particles that absorbed the DNA stain got yellowish in color with the fluorescence,” Morono says. This time, the new technique revealed that nearly all of his gaggle of microbes were ordinary bits of sediment.

But that didn’t mean microbes weren’t there—Morono just needed to figure out how to filter them. The solution was … a solution, specifically a high-density solution that biologists use to isolate cells. Morono would take a sediment sample, place it on top of the solution, and spin it all in a centrifuge. The microbes are less dense than the rest of the sediment, so they’d filter out, while higher-density inorganic particles remained in the solution.

“The final product is cultivated microbes,” Morono says. “Usually, the single microbial cells are surrounded by a bunch of yellowish material, but after purification we could get the truly green microbial cells only.”

Morono had now isolated a 100-million-year-old community of cells, mostly aerobic bacteria, or bacteria that respires oxygen, as well as single-celled organisms known as archaea. And, like any good scientist would, Morono brought them back to life by feeding them carbon and nitrogen. After a mere 68 days—an almost imperceptible sliver of time in the microbes’ geological timescale of 100 million years—certain types of microbes increased their numbers by four orders of magnitude. The researchers could actually measure how the tiny organisms gained weight as they absorbed the nutrients. “That was unbelievable,” says Morono. “Over 99 percent of the microbes could revive.”

You might tend to think of bacteria as a horde—billions upon billions of cells colonizing land, sea, air, and our own bodies. But Morono and his colleagues managed to isolate a handful of ancient cells, awaken them, and get them to form a larger community. “This approach can show what each microbial cell ‘eats’ and provides a window into a world we typically don’t see,” says ETH Zurich geobiologist Cara Magnabosco, who wasn’t involved in the work. “The ability to study bacteria and archaea as individual cells rather than a collective community will undoubtedly lead to many more discoveries about how microorganisms survive on our planet.”

Brought from their nutrient- and oxygen-poor habitat 250 feet down in the muck, itself 20,000 feet deep in the sea, the microbes had returned from a kind of hibernation—they hadn’t really been alive or dead. “It just defies our concepts, because as humans, we don’t have these observation timescales,” says Jens Kallmeyer, a geomicrobiologist at the German Research Centre for Geosciences, who was on the expedition but didn’t coauthor the new paper. “I mean, thinking about this, this is sediment that was already tens of millions of years old when the dinosaurs died out. So this is damn-old stuff.”

Fear not, though, that science may now have unleashed an ancient menace on the human species. “Human pathogens are generally not present in deep-ocean sediment, and these microbes have been trapped in their sedimentary habitat since almost 100 million years before the origin of hominids,” says D’Hondt. “So they haven’t had an opportunity to evolve alongside people or other modern animals.”

But how did the bacteria survive so long down in the muck, far away from the oxygen-providing seawater? It turns out that these deep ecosystems, where organisms have evolved to survive extreme scarcity, have an advantage over bustling seafloors where oodles of microbes are consuming the organic matter—and also oxygen while they’re at it. Here in the deep-sea wasteland, there’s much less microbial activity on the surface of the sediment, so that surplus oxygen can seep down to the ancient microbes. It’s a tiny amount, to be sure, but it’s something.

“They must be sitting there for a very long time—over geological time—just waiting for some nicer conditions. Finally, they get a chance to revive,” says geomicrobiologist Fumio Inagaki, director of JAMSTEC’s Mantle Drilling Promotion Office, who co-led the expedition and coauthored the new paper. “I think it provides some crucial information for understanding the habitability of life on Earth, of course, but also the other planets, such as Mars’ subsurface. Of course, the surface of Mars may not be an ideal place for the search for life for a habitability study, but if you go deep I think there might be a possibility to find life.”

Oh, by the way, NASA is launching its next mission to Mars as soon as Thursday, specifically to seek out life on the Red Planet. The craft will land early next year and send out its rover to collect Mars rocks. So maybe there will be a little more good (ancient microbial) news in 2021.

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