Stuck in the Muck

"Setting aside the whole issue of cell concentrations, the amount of metabolism per cubic centimeter of [ocean] sediment is very low." -Steven D’Hondt
Credit: University of Rhode Island

Dive deep beneath the sea; dig even deeper, hundreds of meters below the sea floor, and you’ll find a hidden world of microscopic beings so numerous that they may make up a third of Earth’s total biomass – as many as a billion cells per cubic centimeter of sediment.

But according to a chemical analysis by Steven D’Hondt, Scott Rutherford and Arthur J. Spivack, they aren’t doing much. "Setting aside the whole issue of cell concentrations, the amount of metabolism per cubic centimeter of sediment is very low, in general," D’Hondt says.

D’Hondt and his colleagues, all at the University of Rhode Island, published their measurements in the March 15, 2002 issue of Science.

Counting Cells

The surprising estimates of life beneath the sediment beneath the waves come, in large part, from the laboratory of John Parkes at the University of Bristol. Researchers there use direct microscopic examination to count archaeal and bacterial cells in cores drilled into deep-sea sediments at several sites around the world.

"What they’ve done," D’Hondt says, "is count bodies. We don’t actually know for sure what fraction of those bodies is alive and what fraction is dead."

"It depends on what you call biomass," says Tommy Joe Phelps, of Oak Ridge National Laboratory. "Do you consider a dead tree biomass? If you do, then certainly they are correct. If you wanted to be conservative, you could say that what appears to be microorganisms or microbial remnants would account for ten to thirty percent of the [Earth’s total] biomass."

Because of the possibility that these cells could enter the samples by contamination during drilling, scientists doing such counts use two types of tracers. They inject both a chemical tracer and fluorescent, bacteria-sized plastic beads into the drilling fluid.

"In some ways the bead is a more realistic tracer, because it’s the size of a bacterium and has similar physical properties in some ways," D’Hondt says. "But the chemical compound is a more conservative tracer because it can go places the bacteria can’t. So if we don’t find the chemical [in the samples] then we can say ‘Well, there’s been no contamination at all.’"

Dead or Alive?

Bacteria from Pacific Ocean sediment.

To determine just how alive the organisms might be, the Rhode Island team analyzed chemical data from nearly 30 years of ocean drilling. They measured two substances, methane and sulfate, chemical indicators of differing types of microbial metabolism.

Archaeans lying in the deepest sediments release methane at a prodigious rate. "One of the points of our paper is that methane is present in sediments throughout the world ocean. There must by inference by archaea in sediments throughout the world ocean," D’Hondt says.

Bacteria in somewhat shallower sediments break down the methane seeping upward, removing sulfate from the water in the process.

But the process is not a fast one.

"Some fraction of the organisms down there is metabolizing. But we don’t know if it’s one percent or a tenth of a percent or a hundredth of a percent… or a hundred percent," D’Hondt says. "If they’re all metabolizing, then in the least active open ocean sediments, they’re doing it at a millionth of the rate of the slowest known surface bugs. Alternatively, if they’re operating at the rate of the slowest known surface bugs, only one in a million is active. There’s nothing published at this point by anyone that would really allow us to distinguish between those two extremes."

"I guess you could say that they left that unanswered," says Phelps. "I think what they’re doing is they are asking a legitimate question that the answer is pretty obvious, it’s just that it’s not proven. If you were to say that every one of those organisms that John Parkes views, is a live, viable, active microorganism, then their metabolic rate would have to be phenomenally, infinitesimally small. That doesn’t let you repair much DNA or build many proteins. In fact it doesn’t allow you to do that at all. Surely the vast majority of what we see in the deep subsurface biosphere is inactive."

Whether inactive means dead or very slowly dying remains an open question. Without the minimal activity of DNA repair, all organisms slowly accumulate so much damage that they cannot survive.

Click here for larger image. This high-magnification microscopic image shows other deep-sea sediment bacteria, this time stained with DAPI, a DNA-specific stain.
Credit: Shelly Carpenter, NOAA Ocean Explorer

D’Hondt can conceive of intermediate scenarios as well. "Let’s just imagine for the sake of discussion that only one in a thousand is actually active and that the other nine hundred and ninety nine are basically dying or dead. Then if these cells turn over once a year, and each cell survives a thousand years on average, then that’ll take us a long way toward reconciling the total cell counts with the rates that we calculated. So it’s easy to imagine populational scenarios that are not extraordinary that would take us part way there. But it’s also possible to imagine the sort of extremes that we pointed to in our paper."

What’s Next?

"We need to test the extent to which our inferences were correct and we need to document the more detailed nature of these communities," D’Hondt says. "How many microbes are truly taking part in the series of biological relationships that we’re encapsulating in a single biogeochemical equation."

Members of D’Hondt’s team and colleagues at other institutions have begun research to figure out just what percentage of subsurface microbes are active. They are also testing the assumptions they made in the March Science paper. Is sulfate a good enough indicator of overall microbial activity? Are there better indicators?

Furthermore, they hope to draw a clearer picture of just which archaeans and bacteria are present in the deep subsurface. Several groups are studying the genes found in sediment samples.

D’Hondt and an international cast of colleagues are taking the first steps toward understanding this hidden world of life beneath the sand beneath the sea.