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.