New report: Bacteria can remain alive for over 100 million years!

Well cut off my legs and call me Shorty (is that ableist?). A new report in the journal Nature Communications shows that some bacteria can remain dormant for over 100 million years in marine sediments—an unbelievable amount of time for an organism to remain “alive”—if you call it “alive.” I do: after all, the bacteria collected and revived by the researchers retained their ability to metabolize, take up labeled organic substances, and reproduce.  Dormancy, to me, at least, is not the same thing as “death”.

Click the screenshot to read the paper (the pdf is here and the full reference is at the bottom).

The experiment was laborious yet the results are simple. If you want to know the gory details, the paper is there for your reading.

In short, the authors sampled clay sediments of different ages from the South Pacific Gyre, and did so in a way that, they aver, precluded contamination with modern bacteria. Supporting their claim that the bacteria they found in the inside of sea-floor cores were really bacteria in situ, they argue that the clays are almost impermeable to bacteria, with very low pore size, and there are thick impermeable layer above the sampled sediments. And there were strict precautions to prevent contamination.

To see if any bacteria in the sediments were capable of biological activity including reproduction, they tested for “anabolism” (the synthesis of molecules) by incubating the bacteria with oxygen (controls lacked oxygen) as well as radioactively labeled molecules that could be taken up and made into proteins and other molecules. The added molecules included 13C6-glucose, 13C2-acetate, 13C3-pyruvate, 13C-bicarbonate, 13C-15N-amino acids mix [mixture of 20 Amino Acids], and 15N-ammonium. Another control involved killing any bacteria with formaldehyde.  The researchers could then visualize the bacteria and see, through fluorescence microscopy and radioactive visualization, if the precursor molecules had been taken up by bacteria.

Finally, the researchers could isolate bacteria at various times (the samples for activity, growth, and bacterial presence were taken at 3 weeks, 6 weeks, and 18 months) to see if the bacterial titer was increasing, i.e., they were dividing. Finally the authors isolated RNA (16S rRNA) from individual bacteria, amplified it, sequenced slow-evolving RNA, and saw what groups of living bacteria the ancient bacteria belonged to. (This assumes that we can still recognize the groups from modern sequences, but these molecules evolve very slowly).

The upshot:

1.) The aerobic bacteria (bacteria that require oxygen) were still viable, initiating metabolism and reproduction even in sediments as old as 101.5 million years. Anaerobic bacteria, which don’t require oxygen, didn’t do nearly as well, and the authors suggest that even low oxygen concentrations in the sediments over geological time simply kills anaerobic bacteria.

Here’s a figure from the paper showing photos of the bacteria, with the same bacteria then examined for uptake of added molecules. The caption is complicated, but you can see that, especially with added amino acids (and oxygen), the cells glow furiously (d and h are electron-microscope images of the same bacteria shown fluorescing in the rows).

(from paper): Cells from incubations of U1365 9H-3 with 13C-bicarbonate and 15N ammonium (a–d) and 13C,15N-Amino acid mix (e–h). (a, e) SYBR Green I-stained cells under fluorescence microscopy. b, c, f, g Ratio images of 13C/12C (b, f) and 12C15N/12C14N ratios (c, g) of the same regions imaged in a, e, demonstrating locations of 13C and 15N incorporation. Color-scale ranges of the ratios are shown as numbers appearing at top and bottom of the color bar. The background membrane region, which is identified by fluorescence images, is excluded from the ratio calculation and shown as black background. d, h. Secondary electron (NanoSIMS) images of the same regions in a, e. Bars represent 5 µm. Similar images were processed for obtaining the dataset (Supplementary Data 1) of substrate incorporations for 6986 individual cells.

2.) The bacteria divided, as measured by the increase in numbers over time in the samples.

3.)  Anaerobic bacteria were much harder to find metabolizing than aerobic bacteria. The former were effectively defunct.

4.) The lineages of bacteria identified as persisting in the sediments, judged from sequencing them and comparing the 16S rRNA to modern samples, include ActinobacteriaBacteroidetesFirmicutesAlphaproteobacteriaBetaproteobacteriaGammaproteobacteria, and Deltaproteobacteria, and cyanobacteria (“blue-green algae”). It would be interesting to compare the sequences of these early species with their modern relatives to see exactly how much and what kind of evolution has gone on.

5.) How did they survive? One thought was that they formed dormant spores, which can last a long time in bacteria. But this suggestion is ruled out because none of the bacteria identified were from spore-forming lineages. It seems the bacteria simply became dormant, surviving without any—or hardly any—detectable metabolism, and without reproduction.

This raises the question: were these things really alive for 101.5 million years? I can’t see why not, unless you think that something that becomes dormant is dead, and then, Lazarus-like, revives when the dormancy is broken. If you take the authors’ word that sufficient precautions were taken to prevent contamination with modern bacteria, then what we have here are the oldest living organisms on Earth.

h/t: Jeremy

_________________

Morono, Y., Ito, M., Hoshino, T. et al. Aerobic microbial life persists in oxic marine sediment as old as 101.5 million yearsNat Commun 11, 3626 (2020). https://doi.org/10.1038/s41467-020-17330-1

54 Comments

  1. Posted July 30, 2020 at 10:07 am | Permalink

    I look forward to Ken Ham’s response to this!

  2. Posted July 30, 2020 at 10:24 am | Permalink

    Those are some mighty durable bacteria!

  3. ThyroidPlanet
    Posted July 30, 2020 at 10:24 am | Permalink

    Amazing!

    Hasty thoughts – i.e.w/o reading the paper :

    • are phages or viruses down there with them?

    • if they dig deeper would they get even older bugs?

    • what were the control experiments to triangulate the bugs as truly not from the modern … epoch – i.e. from the materials used for the sampling, or otherwise?

    • is there a heat source near the sample site?

    • ThyroidPlanet
      Posted July 30, 2020 at 11:24 am | Permalink

      Also

      • were the experimental growths conducted at pressures near the pressure of the substrate’s environment that the bugs were taken from?

  4. GBJames
    Posted July 30, 2020 at 10:31 am | Permalink

    Wow.

  5. Posted July 30, 2020 at 10:36 am | Permalink

    I think this is profound, especially for astrobiology. These timescales can easily negotiate separate solar systems on cometary bodies.

  6. Posted July 30, 2020 at 10:38 am | Permalink

    Quite some time ago I read an article (which I can’t find now)expressing concern about the melting of permafrost as a result of climate change and some of the potential damages to be expected therefrom. In addition to soil instability causing unstable land structures leading to landslides, and the release of methane and/or carbon (Wiki: “The amount of carbon sequestered in permafrost is four times the carbon that has been released to the atmosphere due to human activities in modern time.”) from the permafrost. There also was discussion of the potential effect on humanity of ancient bacteria, etc, that has been buried in the permafrost that humanity may have lost resistance to. (Wiki: “The number of bacteria in permafrost soil varies widely, typically from 1 to 1000 million per gram of soil. Most of these bacteria and fungi…cannot be cultured in the laboratory…”) But, I don’t know if that is still considered to be so. Another article in Wiki states: “Gram positive bacteria Actinobacteria have been shown to have lived about 500,000 years in permafrost conditions of Antarctica, Canada and Siberia.”

    So, now it looks as though they may remain viable for a great deal longer and, if they these bacteria are capable of growth, we may get to see what the impact may be on humanity.

    • W.Benson
      Posted July 30, 2020 at 12:04 pm | Permalink

      I wouldn’t worry. There are probably 10’s or 100’s of kinds of “new” bacteria in every shovel of dirt dug up in a tropical rain-forest or stirred up in the mud of a mangrove swamp. These have never caused health problems. Our bodies have pretty good defense mechanisms, and pathogenic bacteria need sophisticated adapted biochemistry to overcome them. These high-salt, low temperature-adapted microbes deposited on the sea bottom most surely lack pathogenic capabilities. That is my view, anyway.

      • Posted July 30, 2020 at 9:17 pm | Permalink

        Thanks for the reassurance. It’s obvious I’m not a scientist. But given new or changed viruses, such as Covid-19, Hantavirus, Polio, HIV/AIDS, etc.; bacterial diseases such as Lyme, Tuberculosis, Typhoid, etc., one wonders what old or new disease may bite one in the tush.

        I also read about previously unknown life forms living near hydrothermal vents that no one believed could have lived there, as well as those living under Permafrost. And, plants in the desert that go dormant for years until there is rain. And seeds that don’t germinate unless there’s a fire. And, fungi, or whatever, living in the cracks of rocks. It’s all pretty amazing to me.

        By the way, I just read that the first dog known to have contracted Covid-19 in the U.S. has died.

        • Torbjörn Larsson
          Posted July 31, 2020 at 10:15 pm | Permalink

          Of the estimated 10 million operational taxonomic units – think of them as “species” – only a couple of hundreds are infectious. Typically they co-evolve with their host and rarely jump species. (Though some are, like the SARS-Cov2 ancestor, generalists on the type of receptor that humans unfortunately had. And – I guess – that dog. In UK there is a cat that got infected, IIRC.)

      • Posted July 31, 2020 at 7:12 am | Permalink

        As my biology teachers used to say: most bacteria are just there. Some do nice stuff like digest cellulose, some do stuff to annoy us (like various diseases) but most are just there, living with us, on us, in us …

  7. rickflick
    Posted July 30, 2020 at 10:39 am | Permalink

    I’d read that modern bacteria are prolific in the Earth’s crust. My first thought was, are you sure these are really that old? They are assuming, it seems, the clay layer could not be contaminated or did not, at least, have a more recent exposure. Were there fine cracks nearby that could have been a bacterial highway from the surface?
    On the other hand, I suspect if the clay is even 1/10 as old, that would show such dormancy is feasible, so why not 100,000,000 years?

    • W.Benson
      Posted July 30, 2020 at 12:41 pm | Permalink

      Molecular biology has ways to determine if the DNA of putative ancient bacteria is identical or ancestral to modern bacteria present in superficial sediment. Moreover, if the dormant bacteria of deep sediments are as old as the sediment in which they occur, it should be possible to recover descendant bacteria in successively younger sediments and produce a living phylogeny. Nature, I’m sure, would publish it.

    • Mark R.
      Posted July 30, 2020 at 1:46 pm | Permalink

      I was thinking that if they can live 100 m/y why not a billion? Who knows how long they can actually live.

  8. Steve Gerrard
    Posted July 30, 2020 at 10:43 am | Permalink

    It seems like an extraordinary claim to me, so we must ask, is the evidence extraordinary enough to support it? I have no way of judging that. What is the standard for claiming that a 100 million year old cell is still alive?

    • ThyroidPlanet
      Posted July 30, 2020 at 11:21 am | Permalink

      Organisms are known to assume a dormant state. Yeast sporulate, for example. Bacteria I’m sure without checking can go dormant. The question is if all bacteria or archea are known to assume a dormant or sporulated state.

      … actually, the data should show – somewhere in the literature- how we know in fact they were not growing down there in the clay. Perhaps they were, but just really slowly.

      Also, something should show the clay was impervious to bacterial or archaeal (?) ingress.

      • rickflick
        Posted July 30, 2020 at 12:05 pm | Permalink

        They did state that the bacteria were not of the type that form spores. Thus, simple dormancy is the hypothesis.

        • Raymond Cox
          Posted July 30, 2020 at 3:20 pm | Permalink

          Dormancy is not confined to bacteria that form endospores. This is actually a medical problem since dormant bacteria are not affected by antibiotics, and can start growing again after antibiotic treatment has finished.

  9. BobTerrace
    Posted July 30, 2020 at 10:48 am | Permalink

    Sub

  10. Simon Hayward
    Posted July 30, 2020 at 10:48 am | Permalink

    I don’t know about this example, but other proposed revivals of old bacteria (and even yeast) Have fallen short on authentication. Specifically an inability to replicate experiments between labs. There were a number of reports in the mid-90s of reviving bacteria from fossil amber but I don’t think any of them validated in the end. So put me down as skeptical for now.

  11. Ken Kukec
    Posted July 30, 2020 at 11:36 am | Permalink

    Sounds a bit like the state of “suspended animation” one encounters in high-concept movies about cryogenically preserved space-travelers or the revival of long-frozen prehistoric human ancestors.

  12. Posted July 30, 2020 at 11:38 am | Permalink

    “It would be interesting to compare the sequences of these early species with their modern relatives to see exactly how much and what kind of evolution has gone on.”

    It is astonishing that the authors did not do this basic test. The absence of this comparison is so disturbing that I think it is a reason to doubt the results and the experimenters.

    • Posted July 30, 2020 at 11:44 am | Permalink

      Such a comparison (using the right genes) would provide the best molecular clock calibration point in the whole history of biology. It would have been one of the most important results of their discovery.

      • W.Benson
        Posted July 30, 2020 at 12:50 pm | Permalink

        Why not sample bacteria in successive sediment layers and generate a living phylogeny? I assume that descendant bacterial species now live and grow in superficial sediments or the water column above it. Also, see my comment above. Interesting stuff.

    • Curtis
      Posted July 30, 2020 at 1:35 pm | Permalink

      I agree. Until this is done, I remain extremely skeptical.

    • Mike
      Posted July 30, 2020 at 2:26 pm | Permalink

      I share this skepticism: the time scale is so large that the difference in mutation accumulation should be obvious in almost any data from any part of the genomes of the “100 million year old” bacteria, even the parts that are very highly conserved like 16S. Collecting genetic data should have been very easy, especially if some of these very old bacteria can be cultured in the lab (as implied by the observations on restarting metabolism, incorporating labelled compounds, etc.). As Lou says this seems so obvious and so easy to do that absence of more data (other than 16S) seems strange.

    • Posted July 30, 2020 at 7:50 pm | Permalink

      Or date the material with radioisotopes. That is actually a standard thing to measure the isolation of a population. 14C would be flatlined to background levels, for example.

    • Torbjörn Larsson
      Posted July 31, 2020 at 10:32 pm | Permalink

      Yes.

  13. darrelle
    Posted July 30, 2020 at 11:45 am | Permalink

    This is exciting and amazing, but count me as one of the skeptical for the reasons Simon at 10 and Lou at 12, above, explained.

  14. eric
    Posted July 30, 2020 at 12:08 pm | Permalink

    Very cool.

    I was just arguing about this subject with a “I’m not religious I’m just skeptical” defender of souls/life-force on another thread. My de minimis research turned up the factoid that single-celled organisms that reproduce symmetrically can, barring predation etc., seemingly live forever. Even amongst bigger critters, freezing seems to kill things only because if you’ve got water in your cells (we do), the water to ice transition causes the cells to expand and thus burst. So if you’ve got some single-celled symmetrically-dividing organism, and it doesn’t have a lot of water in it, why not? But having said all that, empirical evidence like this is infinitely more valuable than a “theoretically, why not”.

  15. Vaal
    Posted July 30, 2020 at 1:09 pm | Permalink

    The sci-fi loving/paranoid part of my brain instantly processes this information as:

    Maybe we shouldn’t be sending probes to bring rocks home from Mars after all.

    😉

    • Mark R.
      Posted July 30, 2020 at 1:49 pm | Permalink

      My sci-fi portion of brain thought…this may lend credibility to those who espouse the theory that life started from microbes on meteorites. Don’t know how vacuum affects bacteria.

      • Torbjörn Larsson
        Posted July 31, 2020 at 10:30 pm | Permalink

        Totally different conditions though – here it was high and oxygenated pressures.

  16. Posted July 30, 2020 at 2:31 pm | Permalink

    Assuming no contamination etc (add other usual caveats here): WOW. Astonishing.

  17. bonetired
    Posted July 30, 2020 at 2:43 pm | Permalink

    I am a bit dubious as well but for another reason. All clays are naturally radioactive to some extent and I really cannot see how a dormant bacterial could not have ionising damage inflicted up over such a long period of time and still remain viable.

  18. Raymond Cox
    Posted July 30, 2020 at 4:23 pm | Permalink

    I think that the implication is the title of this post, that these are very long-lived cells, is far from proven. What they have shown is that a bacterial population trapped in impervious marine sediment for 100 million years contains bacteria which can be revived by adding nutrients.These bacteria are not particularly slow-growing with generation times of days or weeks. I do not think they have demonstrated that individual cells have remained viable for 100 million years. The original cells may have undergone multiple rounds of division and death or dormancy. The sediment is said to have a pore size so small that bacterial cells are trapped, but this would not prevent nutrient molecules diffusing in from the overlying seawater.

  19. FB
    Posted July 30, 2020 at 9:53 pm | Permalink

    The Wikipedia entry for Ancient DNA says “Even under the best preservation conditions, there is an upper boundary of 0.4–1.5 million years for a sample to contain sufficient DNA for sequencing technologies.”

    • ThyroidPlanet
      Posted July 30, 2020 at 11:07 pm | Permalink

      That number is probably for bare DNA.

      This DNA is supposedly from organisms in some dormant state, and the cellular components are – I guess, without reading – deliberately stabilizing the DNA … or DNA might be coiled more – and other things. I wonder a lower complexity like seeds or pollen what that viability is in years, and therefore also for *stabilized* DNA.

    • ThyroidPlanet
      Posted July 30, 2020 at 11:11 pm | Permalink

      Oh – “best preservation conditions”… well, that probably means of the organism – an organism that was out and about, not necessarily in a significantly different state – dormancy. Not the DNA itself.

    • ThyroidPlanet
      Posted July 30, 2020 at 11:21 pm | Permalink

      Plant seed germination record is 2000 years : https://advances.sciencemag.org/content/6/6/eaax0384

      I note this is at about one atmosphere. The bugs in this discussion here were at many times that pressure.

    • ThyroidPlanet
      Posted July 30, 2020 at 11:27 pm | Permalink

      There’s another seed that germinated after 32,000 years too : https://en.m.wikipedia.org/wiki/Oldest_viable_seed

      Reference is supposed to be in there…

    • ThyroidPlanet
      Posted July 30, 2020 at 11:44 pm | Permalink

      I just re-read the comment – it is for *sequencing*, not for biology / life itself.

      That is, the figure is saying something about sequencing technology, not necessarily life.

      … apologies for the comment storm – can’t get to sleep again.

    • sparc
      Posted July 31, 2020 at 1:41 am | Permalink

      Short stretches of broken chromosomal DNA are sufficient for sequnecing but surely not for living.

    • Torbjörn Larsson
      Posted July 31, 2020 at 10:29 pm | Permalink

      At surface conditions, I assume?

      Cold, high pressure, starving cells – who knows. I found out in an earlier search that precisely starvation conditions activate non-cell cycle gated DNA repair mechanisms in bacteria.

  20. ThyroidPlanet
    Posted July 30, 2020 at 11:37 pm | Permalink

    Some background from :

    https://en.m.wikipedia.org/wiki/List_of_longest-living_organisms

    “If the definition of lifespan does not exclude time spent in metabolically inactive states, many organisms may be said to have lifespans that are millions of years in length. Various claims have been made about reviving bacterial spores to active metabolism after millions of years of dormancy. Spores preserved in amber have been revived after 40 million years,[7] and spores from salt deposits in New Mexico have been revived after 250 million years, making these bacteria by far the longest-living organisms ever recorded.[8]”

    7. Cano, RJ; Borucki, MK (19 May 1995). “Revival and identification of bacterial spores in 25- to 40-million-year-old Dominican amber”. Science. 268 (5213): 1060–1064. Bibcode:1995Sci…268.1060C. doi:10.1126/science.7538699. PMID 7538699.

    8. ^ Vreeland, Russell H.; Rosenzweig, William D.; Powers, Dennis W. (2000-10-19). “Isolation of a 250 million-year-old halotolerant bacterium from a primary salt crystal”. Nature. 407 (6806): 897–900. doi:10.1038/35038060. ISSN 1476-4687.

    • Posted July 31, 2020 at 7:15 am | Permalink

      “metabolically inactive states”

      Sounds like here – and elsewhere the part of the discussion is over what counts as alive. Can one be resurrected? I.e., intermittently alive? If one is a human, probably not – yet, I’ve always wondered since we are a system about this … I guess that reduces to “what sort of creature are we”?

    • Torbjörn Larsson
      Posted July 31, 2020 at 10:25 pm | Permalink

      I don’t think any of those are accepted though. Too many potential confounds.

      This is also odd, which is why the primary author apparently didn’t believe that he saw at first (almost 100 % viability).

  21. sparc
    Posted July 31, 2020 at 1:38 am | Permalink

    Assuming that mutations continue to occur due to e.g. environmental background radiation some maybe smaller mutation rate should remain. Since dormancy implicates a lack of DNA repair mutations I wonder how many mutations would occur per individual bacteria cell in 100,000,000 years. Due to the circular nature of bacterial genomes every single double strand brake would make replication impossible and growth after awakening impossible. Just my 2 cents.

  22. ThyroidPlanet
    Posted July 31, 2020 at 7:12 am | Permalink

    The authors apparently did not cite the 250-million year old halophilic bacteria paper (Nature – see my other comment). Perhaps I’ll look carefully later.

    So I think the point of the 100 million year figure is that it’s a first – somehow- in a marine environment.

  23. ThyroidPlanet
    Posted July 31, 2020 at 9:29 am | Permalink

    Here’s another half-baked thought :

    How can it be ruled out that what was sampled was another symbiotic microscopic organism that associates or protected the cultured bacteria?

    For instance, a microscopic plankton, algae, or other such life form was taken in the sample, lost in the process – perhaps the cell wall breaking from the rapid loss of pressure- leaving behind the bacteria which were ultimately observed in the cultures?

  24. Torbjörn Larsson
    Posted July 31, 2020 at 10:22 pm | Permalink

    It needs to be repeated for sure.

    Among oddities – or evidence for the hypothesis – is apparently that all the bacteria were aerobs. Apparently the slow sedimentation of the nutrient poor Southern Gyre where the sediments were from allow for oxygen being trapped all through the sediments. That may or may not explain the claim that they didn’t find any spores either.

    I haven’t read the paper, so I don’t know if they really claim survival of individuals or of the population (despite the “trep” argument).


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