Scientists resurrect ancient life deep beneath the seafloor

July 28, 2020 5:38 PM

Biologists Revive 101.5-Million-Year-Old Microbes - "A team of biologists from Japan and the United States has successfully revived aerobic microbes found in 101.5-million-year-old sediments from the abyssal plain of the South Pacific Gyre."

Deep sea microbes dormant for 100 million years are hungry and ready to multiply - "This study shows that the subseafloor is an excellent location to explore the limits of life on Earth."

“Our main question was whether life could exist in such a nutrient-limited environment or if this was a lifeless zone,” said the paper’s lead author Yuki Morono, senior scientist at JAMSTEC. “And we wanted to know how long the microbes could sustain their life in a near-absence of food.”

With fine-tuned laboratory procedures, the scientists, led by Morono, incubated the samples to coax their microbes to grow. The results demonstrated that rather than being fossilized remains of life, the microbes in the sediment had survived, and were capable of growing and dividing.

“We knew that there was life in deep sediment near the continents where there’s a lot of buried organic matter,” said URI Graduate School of Oceanography professor and co-author of the study Steven D’Hondt. “But what we found was that life extends in the deep ocean from the seafloor all the way to the underlying rocky basement.”

Morono was initially taken aback by the results. “At first I was skeptical, but we found that up to 99.1% of the microbes in sediment deposited 101.5 million years ago were still alive and were ready to eat,” he said.

Microbes from millions of years ago - "Scientists studying sediments from the Pacific Ocean east of New Zealand have found bacteria that appear to have survived since the time of the dinosaurs. 'They're violating our sense of the [microbial] world as we know it,' says Steven D'Hondt, an oceanographer at the University of Rhode Island. And it's a finding that might be relevant to the search for life on Mars or the moons of Jupiter and Saturn."

“Basically, they’re only getting enough energy to repair their molecules as they break”, with none left over to grow and divide.

When brought into the lab and given more nutrient-rich diets, however, these bacteria prove to be not just alive, but able to revive, grow and multiply, exactly like normal bacteria.

How they can do that, D’Hondt says, is a mystery. Either the individual cells are somehow surviving for “ridiculous lengths of time” or they “are reproducing with less energy than we thought possible”. But one way or another “they are starvation artists”.

One implication is that if Mars once had life, remnants might still exist, not just as fossils or biosignatures, but as living microorganisms that could be revived and studied. “If these things can survive 100 million years, maybe they can survive a billion or three billion,” D’Hondt says.

[...]

What we don’t need to worry about, D’Hondt adds, is that digging into these old seabeds might unleash a 100-million-year-old plague here on Earth – an issue of particular relevance in the time of COVID-19.

To begin with, he says, if such a plague were possible, it would probably already have been produced by offshore drilling, which has long been stirring up similar sediments on a much larger scale. But the reality is that bacteria in the deep seabed aren’t something we need to worry about.

“Pathogens are common in harbors,” D’Hondt says, noting that these are places easily contaminated by human waste. “But they’re not common in the deep ocean or the sediment. It’s just the wrong environment for them.”

Deep sea microbes dormant for 100 million years are hungry and ready to multiply - "Before looking ahead to future research, D'Hondt took time to reflect on Morono's achievement. 'What's most exciting about this study is that it shows that there are no limits to life in the old sediment of the world's ocean', said D'Hondt. 'In the oldest sediment we've drilled, with the least amount of food, there are still living organisms, and they can wake up, grow and multiply.'"

posted by kliuless (51 comments total)

Didn't Peter Watts write a couple of books on this?
posted by notoriety public at 5:47 PM on July 28, 2020 [15 favorites]

And we all got excited when archeologists sprouted seeds stored by ancient civilizations just a few thousand years ago.

Great stuff, thanks!
posted by SaltySalticid at 5:52 PM on July 28, 2020 [1 favorite]

"What could POSSIBLY go wrong?"
posted by AsYouKnow Bob at 6:01 PM on July 28, 2020 [30 favorites]

save us microbes!
posted by Blienmeis at 6:03 PM on July 28, 2020 [3 favorites]

Alive and Hungry. Not how I prefer my slime.
posted by Jessica Savitch's Coke Spoon at 6:05 PM on July 28, 2020 [2 favorites]

Didn't Peter Watts write a couple of books on this?
posted by notoriety public

Yeah. I know how this ends.
posted by Splunge at 6:12 PM on July 28, 2020 [3 favorites]

I revived ancient R’lyeh, and all I got was this T-shirt (and a bunch of mind-eating horrors.)
posted by Guy Smiley at 6:34 PM on July 28, 2020 [9 favorites]

something something Godzilla something...
posted by tipsyBumblebee at 6:34 PM on July 28, 2020

Sure, man. Whatever gets this shit over with soonest.
posted by Ghostride The Whip at 6:54 PM on July 28, 2020 [26 favorites]

I am pleased that we got to Peter Watts with comment #1, even if it is like playing the Bleak Ecological Catastrophe version of Mornington Crescent.
posted by hototogisu at 7:01 PM on July 28, 2020 [13 favorites]

Biologists Date Microbes.
posted by dances_with_sneetches at 7:20 PM on July 28, 2020 [2 favorites]

"The abyssal plain of the South Pacific Gyre" is a georeference that could have come directly from Lovecraft.
posted by Joe in Australia at 7:28 PM on July 28, 2020 [28 favorites]

I wanna know if it gyres and gimbles in the wabe. One suspects so.
posted by Sing Or Swim at 7:31 PM on July 28, 2020 [9 favorites]

Sigh, of course they did. It's 2020.
posted by jeremias at 7:55 PM on July 28, 2020 [7 favorites]

Nice knowing you all!
posted by The Underpants Monster at 8:03 PM on July 28, 2020 [4 favorites]

This is NOT the year to play around with this.

Starve out the cultures you have in the lab now, close things up, and let everything sit for just another six months at least. THEN try.
posted by EmpressCallipygos at 8:52 PM on July 28, 2020 [9 favorites]

Dear AskMetafilter: I have "Old Ones from the Deep" on my bingo card still but I'm not sure if this counts?
posted by loquacious at 9:31 PM on July 28, 2020 [34 favorites]

if such a plague were possible, it would probably already have been produced by offshore drilling

That doesn’t make me feel good about these microbes, it just makes me worry about offshore drilling.
posted by Monochrome at 9:49 PM on July 28, 2020 [16 favorites]

Thanks for making this post. It's a kraken good read …
posted by Pinback at 9:55 PM on July 28, 2020 [6 favorites]

Lots of people daydream about a do-over of history from 2016 — 1932 — the Revolution (any) — written language — agriculture. Why not write off the Cenozoic as a bad go?
posted by clew at 10:19 PM on July 28, 2020 [2 favorites]

some said that even the trees had been a bad move, and that no-one should ever have left the oceans.
posted by Greg_Ace at 10:40 PM on July 28, 2020 [16 favorites]

> revived aerobic microbes found in 101.5-million-year-old sediments

Please can someone confirm my thinking that these microbes are not themselves 100 million years old, but have been confined for 100 million years? That is, I'm imagining they have reproduced, even if incredibly slowly - is that right?
posted by anadem at 10:52 PM on July 28, 2020

Per the quoted material above that seems to be an active subject of inquiry.
posted by vibratory manner of working at 11:20 PM on July 28, 2020

Cool. Cool cool cool
posted by potrzebie at 11:34 PM on July 28, 2020 [2 favorites]

I read it as them being millions of years old at least. This article about the Deep Carbon Observatory asks "How do subsurface microbial zombies reproduce, or live without dividing for millions to tens of millions of years?" So maybe not hundreds of millions, but possibly millions? Mindblowing that something can live on that timescale.
posted by Mister Cheese at 12:06 AM on July 29, 2020

You know, honestly it's tiring to see the same old reactionary , anti-science statements and jokes from people who didn't even bother to read, much less engage with the article. I mean it happens with every damn biology article.

I mean this is honestly a fascinating article about the limits of life, and existing in an environment we barely know anything about. There's good evidence that there's far more biomass made up of microbes in the Earth's crust than there is life in the surface. And we're seeing how they can survive and possibly reproduce in an environment where that should be impossible. I mean this is real cutting edge science.

I mean is it too much to talk about the actual science?
posted by happyroach at 12:19 AM on July 29, 2020 [30 favorites]

I agree with happyroach.

The problem for me is that it's not just the jokes. We're living through a profoundly reactionary, anti-science time, and it can be very hard to tell where your jokes are coming from.

And even if they are just jokes, bear in mind that these scientists could legitimately become political targets. There are people out there who would love to defund and delegitimize science, and scaremongering about ~ancient zombie microbes~ is right up their alley.
posted by Kutsuwamushi at 1:33 AM on July 29, 2020 [13 favorites]

Deep sea microbes dormant for 100 million years are hungry and ready to multiply

these online dating ads get weirder every day
posted by EndsOfInvention at 2:58 AM on July 29, 2020 [27 favorites]

Scientists were so preoccupied with whether or not they could, that they didn't stop to think if they should.
posted by Omon Ra at 3:46 AM on July 29, 2020

Love this part:

The new find also means that life might be even more possible than we’d previously thought in other low-productivity environments, such as subsurface oceans in the moons of Jupiter and Saturn, where the basic elements of life might be possible, but the energy to renew their food sources might be extremely limited.
posted by mediareport at 4:27 AM on July 29, 2020 [3 favorites]

Scientists were so preoccupied with whether or not they could, that they didn't stop to think if they should.
posted by Omon Ra

This is the most tired comment on any science article. YES, science should. Yes.
posted by tiny frying pan at 5:01 AM on July 29, 2020 [5 favorites]

A hundred million years, that's incredible. The Cretaceous was when most of the continents were still pretty together, and the Pacific was more than half of the planet, right? I know the Gyre is a relative dead zone now, but back then it must have been like another planet, so far from land.

I suppose it makes sense, if there's so little energy down there, for things to last so long. I've always wanted to believe that the universe is lousy with simple life, but this makes it feel like it's actually probable. That out there inside Pluto and under Europa there might be ecosystems living so slowly they seem frozen in time.
posted by lucidium at 5:16 AM on July 29, 2020 [6 favorites]

I R scientist [it's in the name innit]; been at it since the 70s. I've gone down some pretty niche ["well that's a waste of time & money"] paths, some of which have, years later, contributed something "useful". I suspect that some of the jokes about this particular project are an expression of the precautionary principle, which seems rather absent in the pieces-to-camera from the lads involved. Getting laughed at can be an important pause-button lest we lose the run of ourselves as we hack away at the frontiers of science. Too much concentrated hacking rises a dust that obscures the wider picture.

Meanwhile back at the abyss, I'm a bit skeptical about "“At first I was skeptical, but we found that up to 99.1% of the microbes in sediment deposited 101.5 million years ago were still alive and were ready to eat,” Dr. Morono said." when it has been so very difficult to culture outside of the gut many of the species that live within us (eg. Clostridium difficile). That skepticism is driven by the time-line of 68 days: WTF? why that cut-off: it's not 50 days, or 10 weeks or 2 months which you'd expect if the time was picked a priori. And what are the error bars on 101.5 million years? It's like Covid-19 antibody tests that are 100% accurate if the selling company choose the 8 people who were tested 17 days after first symptoms.
posted by BobTheScientist at 5:43 AM on July 29, 2020 [5 favorites]

This will thrill my 120 lb. neighbor, who exists on less than 1,100 calories per day and the expectation he will live healthily past 100. It's almost as if the idea is nearly infinitely on point.
posted by thecincinnatikid at 7:29 AM on July 29, 2020

Scientists were so preoccupied with whether or not they could, that they didn't stop to think if they should.
posted by Omon Ra

This is the most tired comment on any science article. YES, science should. Yes.
posted by tiny frying pan

Scientist in the biomedical field chiming in to say, no, no it's not. The urge to be uncritical about the ethics of inquiry and experimentation is huge in my field, and that *itself* is the most tired comment. Science does not need to be agnostic about its harms, but that's been a big part of the curriculum. It took me a long time to shake that off.
posted by late afternoon dreaming hotel at 7:39 AM on July 29, 2020 [12 favorites]

I'm sick of that comment being used in a joke context about totally normal science. This isn't dangerous or threatening to anyone, and it's certainly not unethical. So it's a very weird comment on science like this, and very tired.
posted by tiny frying pan at 8:02 AM on July 29, 2020 [6 favorites]

This is fine.
posted by MythMaker at 8:03 AM on July 29, 2020

Yes, it is! Interesting too!
posted by tiny frying pan at 8:04 AM on July 29, 2020 [1 favorite]

This isn't dangerous or threatening to anyone, and it's certainly not unethical.

I admit my initial comment was a joke. But I'm now asking sincerely - are we certain this isn't dangerous? The last time these microbes were at large in the environment was before mankind existed; what kind of risk mitigation or recovery is in place if the lab in question has a containment flaw?
posted by EmpressCallipygos at 8:49 AM on July 29, 2020

This isn't dangerous or threatening to anyone

I mean, that's almost certainly true, but it's still research that's looking for well-isolated microbial life. I have to admit I'd be happier if their Nature paper had a section "Precautions against potential novel pathogens" or if they clearly stated that they were operating in biosafety 2 or 3 until they had some positive reason to believe that there was nothing new and dangerous in their samples.

It could well be that they were doing something like that and it's just understood in their circles so they didn't mention it.
posted by GCU Sweet and Full of Grace at 8:50 AM on July 29, 2020

And I think these are perfectly valid concerns for a layman to be having at a time when another previously-unknown-to-us microbial entity* is causing untold havoc in the lives of peoples worldwide.

* yes I am aware that COVID-19 is a virus and that's different, but bacteria cause infections too.
posted by EmpressCallipygos at 8:51 AM on July 29, 2020 [2 favorites]

I general I don't mind a bit of pandemic gallows humour on a microbiology article, and I can understand skipping the article to look at the comments, but in this case the paragraph you're all looking for is right there in the FPP. It's even got a little [...] above it so you can tell this is a section that kliuless thought would be interesting to people skimming over the FPP looking for the juice. It makes it pretty clear that actually your scientists (or "lads"? Have we been investigating the gender distribution of this lab or what?) did stop to think whether they should. Here it is again:

What we don’t need to worry about, D’Hondt adds, is that digging into these old seabeds might unleash a 100-million-year-old plague here on Earth – an issue of particular relevance in the time of COVID-19.

To begin with, he says, if such a plague were possible, it would probably already have been produced by offshore drilling, which has long been stirring up similar sediments on a much larger scale. But the reality is that bacteria in the deep seabed aren’t something we need to worry about.

“Pathogens are common in harbors,” D’Hondt says, noting that these are places easily contaminated by human waste. “But they’re not common in the deep ocean or the sediment. It’s just the wrong environment for them.”

It seems really disrespectful to kliuless's framing of the FPP to keep commenting three steps behind on this train of thought rather than actually engaging with what's there.
posted by polytope subirb enby-of-piano-dice at 8:56 AM on July 29, 2020 [6 favorites]

And what are the error bars on 101.5 million years?

Does bring to mind an old joke where the punchline is "well, this professor came by and estimated they were about 100 million years old, and that was 1.5 million years ago."

I was curious, but in a really cursory search didn't find a definitive answer.

In Cobalt‐based age models of pelagic clay in the South Pacific Gyre (Dunlea, Murray et al. 2015):
"A final determination of uncertainty is not as simple as a standard calculation of error propagation that does not consider error covariance, since many of the uncertainties are related to each other and/or act to cancel each other."
posted by kurumi at 9:43 AM on July 29, 2020 [3 favorites]

Only speaking for myself, I saw that, but I'd be happier with something more than "Nah, that can't happen."
posted by GCU Sweet and Full of Grace at 9:58 AM on July 29, 2020 [3 favorites]

I couldn’t find it in a brief scan of the Nature article, but I would expect they would have to be practicing some contamination prevention just to make sure the zillions of bacteria/HeLa cells/whatever else didn’t get in to corrupt their sample.
It’s a lot less nifty to say “we took bits of buried ocean sediment, and then the bacteria from our hands performed uptake of carbon and nitrogen.” So, at least in that direction, they must have been preventing crossover of bacterial population.
posted by nat at 10:17 AM on July 29, 2020 [1 favorite]

black oil!
posted by bitterkitten at 12:24 PM on July 29, 2020 [4 favorites]

Whether or not they were totally dormant or merely metabolizing very slowly/intermittently, it certainly is an interesting result for the panspermia theory.
posted by chortly at 7:50 PM on July 29, 2020

I'd think they might have to divide occasionally to keep their DNA from accumulating so much damage between divisions that the division-associated repair mechanisms would be overwhelmed.

Potassium 40 seems like it might be a problem over a hundred million year period since it has a natural isotopic abundance of more than 1%, a half-life of 1.25 billion years, potassium is the most abundant cation in bacteria, and potassium ions snuggle right into the grooves of bacterial DNA and help stabilize it.

Beta decay isn't the most violent form of radioactive emission, but it's plenty good enough to mess up your DNA if it happens right next to it.
posted by jamjam at 12:12 AM on July 30, 2020 [2 favorites]

"I, for one, welcome our new microbial overlords..."
posted by AJScease at 5:56 PM on July 30, 2020 [1 favorite]

I'd think they might have to divide occasionally to keep their DNA from accumulating so much damage between divisions that the division-associated repair mechanisms would be overwhelmed.

Can DNA only be repaired by copying it?
posted by Joe in Australia at 9:56 PM on July 30, 2020

'Zombie' Microbes Redefine Life's Energy Limits - "A new model shows that the denizens of a vast, ancient biome beneath the seafloor use barely enough energy to stay alive — and broadens understanding of what life can look like."
posted by kliuless at 4:36 PM on August 12, 2020 [1 favorite]