Microbial Communities Surviving Over 100 Million Years Found Under the Sea

How exactly the sun-loving cyanobacteria among them survived for millions of years in pitch-black sediment is a mystery, even if it is the toughest microbe on Earth

Ruth Schuster
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A surface bloom of cyanobacteria
A surface bloom of cyanobacteriaCredit: Pseudopanax
Ruth Schuster

Microbial communities that have survived inside the seabed for over 100 million years have been discovered beneath the South Pacific Gyre current, a team of scientists from Japan and Rhode Island reported in Nature on Tuesday.

And we feel special if we hang on for 100 years. So much for us.

Yes, these microbial communities inside the seabed sediment are still alive from the time when dinosaurs ruled the land.

In the abyssal plain beneath the South Pacific Gyre whence the cores were extracted (in 2010), productivity is the lowest in the world. The sediment is extremely poor in nutrients and oxygen, and the microbial life is extremely sparse relative to other seabed environments. But it is there, report lead author Prof. Yuki Morono, of the Japan Agency for Earth-Marine Science and Technology, and colleagues.

The team is confident these are not “migrating” microbes, because the clayey layers above the microorganisms are impermeable to cells, though oxygen molecules can and do slowly diffuse from the water into the sediment. “The microbes found in that sediment should have been isolated from the time of their burial,” Morono tells Haaretz – from 4.4 million years in some sites to 101.5 million years.

Who are these microbes? Most turned out to be aerobic bacteria, and astonishingly, mostly non-sporulating ones at that. Some bacteria form metabolically dormant spores when life frowns upon them. These can’t. (Identification was done by DNA analysis and other means.)

But perhaps the strangest discovery is that some of the microorganisms under the ocean floor are cyanobacteria, aka blue-green algae, which should live by photosynthesis – i.e., harvesting sunlight for energy. But these cyanos have been living alone in the dark for eons.

Live long and prosper

Prof. Yuki Morono and team in the shipboard refrigerator working on sediment samples
Prof. Yuki Morono and team in the shipboard refrigerator working on sediment samplesCredit: IODP JRSO

Saying that microbes lived for 100 million years – that doesn’t refer to individual microorganisms but to the community, right?

Well. In conversation with Haaretz, Morono points out that bacteria proliferate by division. They split. One becomes two, which are clones of the original one, and so on down the eons, unto 101.5 million years. And in the individual sense, bacteria trapped in rocks, sediment and the like metabolize excruciatingly slowly.

“In my concept – since they should divide very few times during the entrapment, I think we may be able to say they’re the same or similar ones,” he says. An individual cell can theoretically survive on and on if it has enough energy to metabolize even minimally and repair damage done to its DNA and its cellular mechanisms, he explains.

To survive, microbes needs to metabolize a certain amount of carbon relative to their own size. To divide, they need even more.

Sediment sample
Sediment sampleCredit: JAMSTEC

The sediment beneath the South Pacific Gyre seabed is peculiarly poor in organic compounds. Based on criteria pertaining to their cousins on the surface, our microscopic friends in the sediment don’t have enough nutrients to survive, let alone divide, Morono says. So it’s quite the mystery how they’ve survived for 4 to 101.5 million years in intensely hostile conditions: immense pressure, freezing cold, with hardly a nice chemical to eat and barely any oxygen.

Cold feet

In 2010, Morono was sitting in a refrigerator on a ship, absolutely freezing despite layers of jackets, trousers and socks. He and the team were taking clay plugs from the seabed cores and incubating them.

Normally, microbiologists incubate bacteria in petri dishes full of nice agar – an algae-based substrate into which a yummy nutrient is added, like sugar, blood or whatever. The happy bacteria divide and form colonies.

But extracting the microbes from their spartan primordial environment and moving them to luxury petri dishes would shock them. So the scientists left them inside the cores where they had lived for 4.3 million to 101.5 million years (different sites had different ages), under low oxygen conditions as they were used to, and dripped nutrient substrate onto the core samples, in a fridge kept at 8 degrees Celsius (46 degrees Fahrenheit).

The substrate (food) the bacteria were given was labeled with isotopes of carbon and nitrogen, so they could tell when the bacteria were active and “eating”. And lo, eat they did.

The microbes went to town. They made merry and proliferated – though the older the sample, the slower they reacted. The microbes in the 4.3-million-year-old sediment proliferated several-fold times faster than the guys in the 101.5-million-year-old clay. We don’t know why.

All in all, the scientists were surprised at the rapid reaction given the extreme ages of the sediments. “The youngest specimen was still over 4 million years old,” Morono says. Perhaps the older bacteria needed more time to rev their engines.

Now, any self-disrespecting B-movie knows how humans can survive millennia in outer space to reach their new home in another galaxy: hibernation.

Bacteria aren’t bears. They don’t hibernate as such, but some species sporulate: under harsh conditions, they desiccate and become effectively metabolically dormant. They revive when the conditions improve.

Compared with the needs of surface bacteria, the energy available in the subsea floor environment is below the minimum required energy, Morono says. So were they alive but “hibernating” all those years?

Yet more cyanobacterial blooms on the surface
Yet more cyanobacterial blooms on the surfaceCredit: Kleber Renan de Souza Santos

The rub is that most of the subsea sediment bacteria aren’t the hibernating type, it turns out.

So if they’re revivable into frisky germs millennia after their interment, they have apparently been metabolizing, albeit extremely slowly, all this time. “If they were [like the] surface microbes, they would be dead,” Morono spells out. “But they’re not. They could survive for a period of 100 million years, somehow. We’re not sure how.”

How to survive for 100 million years

Even in the oldest sediment, 101.5 million years old, only a small fraction of the micro-beasts were sporulating types. The sporulators were related to Paenibacillus – another hardy type that can live with or without oxygen.

Very few anaerobic bacteria were identified. The team posits that long-term exposure to the oxygen dissolved in the sediment, over eons, killed off even the sporulating forms of anaerobic bacteria.

What they did find included Actinobacteria, a common germ in soil and water; different types of Proteobacteria – also a common type today. Alphaproteobacteria really are primordial: scientists think the mitochondria organelles in the cells of just about every living creature stemmed from them. The scientists also identified a thermophilic (heat-loving) archaea in 13.5-million-year-old clay.

Obviously these subsea microbes cannot be 100 percent identical to the surface-zone microbes, or they’d be dead.

“I envision an evolutionary concept study for the subsea microbes. They may be slowly evolved species, much slower than surface counterpart microbes because they’re slower,” Morono says. The next stage is to compare their genomes to see where they differ, which could shed light on their mysterious survivability for over 100 million years. In the dark.

And there were all those cyanobacteria, which, speaking of primordial, some think was the first form of life on the planet. The predominant cyano was Chroococcidiopsis. Chuck Norris, you are a child compared with this insanely tough microbe, which can survive in the most extreme conditions: high salt, aridity, high temperatures and high radiation.

Chroococcidiopsis, the toughest guy on Earth
Chroococcidiopsis, the toughest guy on EarthCredit: T. Darienko/CC BY-SA 4.

Amazingly, somehow the cyanobacteria evidently also survive in pitch-black.

Asked how that could be, Morono answers frankly: "We have actually no idea.” It is, however, the great and mighty Chroococcidiopsis, “which is known to be pretty much the toughest guy on Earth.”

Even so, to live without breathing for millions of years is quite the feat. They presumably survive by a mechanism other than photosynthesis – so that rules out the cyanobacteria as the potential source of the bit of oxygen that is down there, Morono points out.

Surface-dwelling Chroococcidiopsis has the nasty propensity of poisoning water supplies by its toxic emissions, by the way.

So what do we have? Microbes older than dinosaurs, mostly aerobic non-sporulating bacteria and, mysteriously, cyanobacteria too, which survived in nutrient-poor seabed sediment for millions of years. We may be destroying our planet for larger beings, but it seems life finds a way.