The Slow-Motion Bacteria Buried Deep in the Ocean's Floor

To survive in one of the planet’s most energy-limited environments, a hardy group of microbes appears to live at a glacial pace.

A diver swims over a rocky sea floor.
Kampee Patisena / Getty

When algae die, they drift to the ocean floor, their bodies becoming one with the seabed’s muck. This algal rain falls constantly, and as layers of organic matter build up over the years, they bury the bacteria that grow on the seabed. Subsumed in the mire, many bacteria die. But some, a hardy few, survive. And when geochemists and biologists drill down into the seabed and pull up long, black cores that reflect hundreds or thousands of years of accumulation, they find the living descendants of the original bacterial internees.

How do the microbes manage to stay alive down there? Since nothing comes in or out, they must have some way of subsisting on the remains of the algae that buried their ancestors so long ago. So one answer might be that they’ve evolved to make more efficient use of the extremely scanty resources they’re entombed with.

But a recent study in PNAS suggests that something very different is true: The bacteria living meters down, under 5,000 years of dead algae, hardly seem to be evolving at all. In fact they are reproducing extremely slowly, so any adaptation, if it’s happening, would not have much chance to take effect. Although many bacteria double in number every few minutes, these researchers’ calculations suggest that in seabed bacteria, it takes on the order of hundreds of years.

Seabed bacteria are thought to be a peculiar bunch, says Kasper Kjeldsen, a biochemist at Aarhus University in Denmark. You’d have to be, to live like them: “There’s very little energy available when you have to continue eating from the same lunch box” for thousands of years, he says. “It is one of the most energy-limited environments on our planet.” But it has been difficult to study the microbes’ biology, because they will not grow in a Petri dish. Instead, researchers have had to develop techniques for inferring things about them from their DNA, which they can extract from the columns of muck. Because different depths represent known eras—the mud’s age can be pinpointed with carbon dating—it’s possible to study the bacteria’s change over time.

To that end, Kjeldsen and colleagues extracted cores from four sites in Aarhus Bay, and took samples from five different points along each core’s length. Then they sequenced the DNA of individual bacteria from each time point, and compared it with all the others’. They found that the species of bacteria that live in the depths exist on the seabed’s surface as well, though they are comparatively rare among the populations there. That reinforces the idea of a select bunch, better fit for the challenges of being buried alive, persisting after the others die.

The team also found that once the microbes were buried, their DNA did not change. “What we saw was there is a very low genetic diversity with a population across depth and time, in the sediment,” says Kjeldsen. “This tells us that the evolutionary change over time is very, very, very low.”

He continues: “It basically means that those bacteria you find at the surface of the sediment are more or less genetically identical to those that subsist under extreme energy limitation in the deep subsurface sediment. … They possess this ability already from the beginning.”

Next, the researchers monitored the bacteria’s metabolism, using radioactive isotopes. They could estimate how much time it would take, at the observed rate of converting food into energy, for the bacteria to create enough new biomass to replicate themselves. In 400-year-old sediment, the rate was about a replication per year. Deeper, in the 4,900-year-old layer, it was on the order of one per hundred years. This isn’t even the longest generation time ever calculated for bacteria; even deeper in the muck, there are others estimated to grow much more slowly, says Kjeldsen. But these numbers fit with what other groups have found at this depth.

Mutations often arise from mistakes in DNA made when cells duplicate themselves. And if there’s so little energy that replication happens only very slowly, then it makes sense that mutations would only arise very rarely—and that if any of them happened to be helpful, it would take corresponding ages for them to out-compete less-fit brethren. It’s a world moving in slow motion, encased in Jell-O—or rather, in sediment.

Still, the techniques that undergird the paper use certain assumptions, cautions Kjeldsen. For instance, he’s not sure whether the bacteria are actually making new cells, or whether they’re just using the energy to repair themselves. There could be very small genetic changes that the technique doesn’t reveal, too.

“What we don’t know,” he says, “is how much genetic change does it take to gain a competitive advantage? There’s a limit to how subtle of genetic differences we can detect with our method here.” These smaller changes might still be able to make a difference, somehow, in a microbe's ability to survive in a resource-scarce environment. “This is something we are trying to address now,” he says.