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Science

Largest Bacterium Ever Discovered Has An Unexpectedly Complex Cell (science.org) 53

Posted by BeauHD from the blurring-the-lines dept.
A newly described bacterium living in the Caribbean "is visible to the naked eye, growing up to 2 centimeters -- as long as a peanut -- and 5,000 times bigger than many other microbes," writes Elizabeth Pennisi via Science.org. "What's more, this giant has a huge genome that's not free floating inside the cell as in other bacteria, but is instead encased in a membrane, an innovation characteristic of much more complex cells, like those in the human body." From the report: The bacterium was unveiled in a preprint (PDF) posted online last week and it has astounded some researchers who have reviewed its features. Aside from upending ideas about how big -- and sophisticated -- microbes can become, this bacterium "could be a missing link in the evolution of complex cells," says Kazuhiro Takemoto, a computational biologist at Kyushu Institute of Technology.

Researchers have long divided life into two groups: prokaryotes, which include bacteria and single-cell microbes called archaea, and eukaryotes, which include everything from yeast to most forms of multicellular life, including humans. Prokaryotes have free-floating DNA, whereas eukaryotes package their DNA in a nucleus. Eukaryotes also compartmentalize various cell functions into vesicles called organelles and can move molecules from one compartment to another -- something prokaryotes can't. But the newly discovered microbe blurs the line between prokaryotes and eukaryotes. [...] Furthermore, that cell includes two membrane sacs, one of which contains all the cell's DNA, [researchers] report in their 18 February preprint on bioRxiv. Volland calls that sac an organelle and that's "a big new step" that implies the two branches of life are not as different as previously thought, [Verena Carvalho, a microbiologist at the University of Massachusetts, Amherst] says. "Perhaps it's time to rethink our definition of eukaryote and prokaryote!" agrees Petra Levin, a microbiologist at Washington University in St Louis. "It's a supercool story."

The other, water-filled sac may be the reason the bacterium could grow so big. [...] The DNA-filled sac, also squished along the inner edge of this bacterium, proved extraordinary as well. When researchers at the Department of Energy Joint Genome Institute sequenced the DNA inside, they found the genome was huge, with 11 million bases harboring some 11,000 clearly distinguishable genes. Typically, bacterial genomes average about 4 million bases and about 3900 genes. By labeling the DNA with fluorescent tags, [researchers] determined the bacterium's genome was so big because there are more than 500,000 copies of the same stretches of DNA. Protein production factories called ribosomes were inside the DNA-filled sac as well, likely making the translation of a gene's code into a protein more efficient.
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Largest Bacterium Ever Discovered Has An Unexpectedly Complex Cell More

Largest Bacterium Ever Discovered Has An Unexpectedly Complex Cell

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  • 2 cm = 1 peanut? (Score:2, Insightful)

    by hazem ( 472289 )

    So how many Library of Congresses is that?

    Seriously, though, do we really need a "news for nerds" site to translate cms into "peanut lengths" in its "science" section?

    • It's 0.00000000002311 libraries of congress or 0.00000034 football fields.
    • Also do they mean the entire peanut shell, or a single seed (which are also referred to as peanuts)?

      • Also do they mean the entire peanut shell, or a single seed (which are also referred to as peanuts)?

        According to Google, the average peanut shell is 3 cm in length and the average kernel is 0.9 cm.

        So, obviously, TFA is using the geometric mean of the shell and kernel.

        • So, obviously, TFA is using the geometric mean of the shell and kernel.

          Arithmetic. If you don't know the difference, it's ok to just say average ;)

    • Re: (Score:2)

      by srussia ( 884021 )
      FTFA

      "is visible to the naked eye, growing up to 2 centimeters -- as long as a peanut -- and 5,000 times bigger than many other microbes," writes Elizabeth Pennisi via Science.org.

      I, for one, welcome our giant-peanut-appreciating overlord Elizabeth Pennisi!

    • A better size comparison should have been "growing up to 2 centimeters -- as wide as a US penny", since it's us poor US'ians that can't easily visualize metric sizes.

    • Re: (Score:1)

      by JCW01 ( 5760250 )
      At least they could have put it in a measurement we would understand: 2cm = 0.0117523 smoots.

  • a Beowulf cluster of these

  • The *filaments* are peanut-size, not the cells (Score:5, Informative)

    by washburn2 ( 9411025 ) on Friday February 25, 2022 @04:07AM (#62301917)
    From TFPreprint: Single cells are around 0.21 ± 0.05 mm (still a record-breaking size). It's the filaments that reach up to 20 mm. TFP is written so that every journalist would make the mistake, of course.
    • That's really disappointing. I had a new life goal to see, and pet, a fucking 2cm bacterium.

    • Re:The *filaments* are peanut-size, not the cells (Score:5, Interesting)

      by MilliMicro ( 6251190 ) on Friday February 25, 2022 @05:28AM (#62302029)
      Eh, the filaments don't seem to be made of discrete cells though, so it's sort of arguable. The authors claim that the genome is lacking in key genes for binary fission, so it looks like the cells extend themselves as if they were going to go through fission, fail to separate, and then just keep extending. There seems to be a vacuole which runs the whole length of the filament, and there don't appear to be any septa throughout the filament, so it does seem to be a single, long cell, even if it looks like it pinches at points. Oddly it looks like cells at the end of the filament pinch off into individual cells to go off and form their own colonies, but at a glance the authors don't seem to have tried to explain how that happens if the main filament doesn't have the genes for doing that. Some of the genes involed in the fission process which this organism is missing were named "Fts" for "Filamenting temperature-sensitive mutant", as E. coli mutants in these genes would fail to separate and would form long filaments at high temperatures. It sounds like this organism does it as a matter of routine. I've seen cells which do this under the microscope, but never to this scale (say, 10-15 um long instead of 2).

  • Huge genome? (Score:3)

    by backslashdot ( 95548 ) on Friday February 25, 2022 @04:13AM (#62301923)

    Haha, 11 million bases is only "huge" if you are a bacteria. I mean, humans have over 3 billion bases. A lungfish's genome is over 40 billion base pairs. The plant Paris Japonica DNA is almost 150 billion bases.

    • Well, there are only 3 bases in a baseball field, which is much, much larger than a 2cm bacterium, so it's pretty impressive anyway!

    • Re: (Score:2)

      by jd ( 1658 )

      A lot of plant DNA is absolutely vast, but highly repetitive. It may be that this is to protect it, using the DNA repettion as a gigantic hot standby failover system. Or there may actually be some other value in the repetition, such as being able to run an arbitrary number of copies simultaneously, so giving finer control over how much of a given protein is made. I honestly don't know on that one.

      So the big question here is whether the new sequence is 11 million significant base pairs or only 3.7 million re

  • Overlords (Score:3)

    by tonique ( 1176513 ) on Friday February 25, 2022 @04:45AM (#62301955)
    I, for one, welcome our giant bacteria overlords.

  • Not quite the largest (Score:3)

    by davmoo ( 63521 ) on Friday February 25, 2022 @05:12AM (#62301991)

    The largest bacteria in the US are concentrated in the Washington DC area.

  • "But the newly discovered microbe blurs the line between prokaryotes and eukaryotes"

    Possiblty. But then eukaryotes didn't suddenly arise spontaniously , they - presumably - evolved from prokaryotes with a few steps inbetween. So either this bacterium is a living fossil of one of those stages or convergent evolution has happened and its mimicked what happened a billion years ago. Interesting either way.

    • Re:Blurred lines (Score:4, Interesting)

      by jd ( 1658 ) <imipakNO@SPAMyahoo.com> on Friday February 25, 2022 @07:46AM (#62302277) Homepage Journal

      Well, yes. There was always going to be some fuzziness on the boundary between the two groups, but it's fascinating to see how this is working.

      For example, mitochondria live in an organelle. The question there is whether mitochondria invaded an existing organelle or whether the organelle is a remnant of whatever formed the boundary of the thing, the cell, that mitochondria were once the genetic code for.

      In other words, are empty organelles evidence of other parasites that broke into the original cell and were wholly absorbed? If so, the modern eukaryote is the amalgam of many absorbed forms of life. Reminds me a bit of the original Quatermas movie.

      In this case, if that is how organelles originate, the 11 million bases will consist of the original DNA plus code stolen from whatever lived in that region that is now filled with water. If that isn't the case, then the 11 million bases will not contain significant fossil remnants.

      My suspicion is that horizontal transfer is actually one of the most important parts of evolution, but this is an ideal test subject to determine if I'm right or completely wrong on that.

      • My suspicion is that horizontal transfer is actually one of the most important parts of evolution, but this is an ideal test subject to determine if I'm right or completely wrong on that.

        People have certainly tried to demonstrate that. I can't remember the details, but back in the early 2000s I saw reports of an analysis of various Archean genomes where they couldn't resolve a consistent descent tree for major biochemical molecules (ribosomes, that sort of thing), and the author's interpretation of this was

    • But then eukaryotes didn't suddenly arise spontaniously, they - presumably - evolved from prokaryotes with a few steps inbetween.

      You might not be 100% right there. Eukaryotes probably arose through endosymbiosis, where one archeon tried to eat a eubacterium but got indigestion and developed superpowers. It's thought to be the one, singular, craziest event in the history of the development of complex life on the whole planet, and it was the precursor to every complex life form now alive.

      I'm not saying that evolution wasn't involved at all. I am saying that eukaryotes probably didn't evolve gradually from prokaryotes; rather, two di

      • Eukaryotes probably arose through endosymbiosis,

        That is certainly a popular hypothesis - I might even say it's the leading hypothesis. It originated with the biologist Lynn Margulis in the early 1970s, and has since been strongly supported by the discovery of the independent genomes of mitochondria.

        two different prokaryotes hybridized in a once-in-a-blue-moon freak event

        Well, as Margulis said, yes, that's an explanation for mitochondria. Shortly after, it was also proposed (I'm not sure if this was Marguli

      • Re: (Score:2)

        by Briareos ( 21163 )

        But then eukaryotes didn't suddenly arise spontaniously, they - presumably - evolved from prokaryotes with a few steps inbetween.

        You might not be 100% right there. Eukaryotes probably arose through endosymbiosis, where one archeon tried to eat a eubacterium but got indigestion and developed superpowers. It's thought to be the one, singular, craziest event in the history of the development of complex life on the whole planet, and it was the precursor to every complex life form now alive.

        aka one of the biggest anime betrayals in history [youtu.be]... :)

  • Great, even bacteria are getting obese, now.

  • One tires of stories of how something is found that yet again is "upending ideas ". How many 'black swans' can there be in a century of study in a field before it's understood that lacking first principles, everything is a relatively uneducated guess. What's frightening about this is that medicine depends on biology for its insights.

    • Above there was a scientist who mentioned seeing filamentous growth in E.coli mutants, so while this discovery is very interesting and all it isn't quite turning everything on its head in a fundamental way. Its more like when someone tries a new strategy in a well established game, the rules are all the same but the meta may have changed quite a bit in ways that excite experts and aren't very relevant to others.
    • I've only read the paper, not the "news" article, so my uneducated guess is that the "news" writer wrote that, not the scientists.

      I'm not really a biologist (well, some of it is unavoidable in palaeontology; but I'm not claiming more than a casual knowledge of the field), but even I know that naked-eye visible bacteria (and even viruses) have been reported repeatedly in the past few decades.

      What's frightening about this is that medicine depends on biology for its insights.

      I've never had much respect for "d

  • *This* is much larger. https://memory-alpha.fandom.co... [fandom.com]

  • Xenophyophores also single-celled critters that are visible to the unaided eye. Although, they do have multiple nuclei in their large "cell".

    Some have speculated that the Ediacaran fauna, animal-like lifeforms before the Cambrian, are single celled. They are often labelled as "the first multicellular creatures that crawled", but nobody has proven that Ediacaran's are multicellular. Because effective predators had yet to evolve, single-celled organisms had the freedom to grow and "experiment" back then.

    • Some have speculated

      As Wiki would say, "who"?

      Sorry, but as a geologist with a significant interest in OOL (Origin(s) Of Life), I've paid quite a bit of attention to the Ediacaran - including trying to organise a field trip to Charnwood Forest to examine - well, you're familiar with the topic, you don't need me to tell you - but I've not heard anyone serious making that claim.

      but nobody has proven that Ediacaran's are multicellular.

      Your list of Cambrian and earlier fossils with preservation good enough to s

      • Re: (Score:2)

        by Tablizer ( 95088 )

        > We have lots of evidence of organisms of that vintage preserved with multiple tissues

        Example? Having different "parts" by itself doesn't make it multi-cellular. Single cells can have differentiation. Lack of clear differentiation is actually a characteristic of many Ediacarans.

        Note that we don't necessarily know if all Ediacaran's are related. For example, Kimberella and Dicksonia may be unrelated, or distantly related. Thus, Dicksonia could be single-celled by Kimberella multi.

        > and a dozen-odd ti

        • Re: (Score:1)

          by Tablizer ( 95088 )

          Correction: "Thus, Dicksonia could be single-celled but Kimberella multi, for example.

        • "Ediacaran" is a time-period, not a claim of a taxonomic category with phylogenetic implications. It's plausible that, given a million more Ediacaran fossils from a thousand more sites we'll find that they form a unified, coherent phylogenetic tree that reacts the same way if you use a brachiopod or bat as an outgroup. But it's equally plausible that they represent the stems of multiple distinct phyla today (the segmentation in Kimberella, for example is reminiscent of many phyla of vermiforms and insects).

          • Re: (Score:2)

            by Tablizer ( 95088 )

            > It's plausible that, given a million more Ediacaran fossils from a thousand more sites we'll find that they form a unified, coherent phylogenetic tree

            Plausible, yes, but it hasn't happened yet. You seem to be projecting Cambrian+ thinking into the Ediacaran. It's still a mystery. We shouldn't force classifications onto creatures we don't understand well enough. I see no reason to assume that Kimberella and Dickinsonia are related, for example. Thus, it's quite possible one is multicellular and the othe

            • > I'm not aware ANY of the Ediacaran mobile forms surviving into Cambrian. If anything, there was a roughly 20 million year gap between mobile Ediacarans and mobile Cambrians. Nobody knows why.

              A possible exception may be the "small shelly fauna" that appeared in the late Ediacaran. But these appear to be a different kind of creature than say Spriggina or Dickinsonia.

              Whether Spriggina has "differentiated parts" is controversial. Some reconstructions show a distinct "plow" for a head. But the fossils show

            • You asked :

              Example? I'm not aware ANY of the Ediacaran mobile forms surviving into Cambrian.

              Here we report typical Ediarcara-type frond- shaped fossils that occur together with an assemblage of Cambrian-type trace fossils in unequivocally Cambrian-aged sediments of the Uratanna Formation, South Australia.

              From NATURE | VOL 393 | 11 JUNE 1998 p567 [nature.com]et seq. Though I'll grant it's not simple.

              but a compelling example is the pennatulacean-like Thaumaptilon from the Middle Cambrian Burgess Shale. Despite the simi

              • Re: (Score:1)

                by Tablizer ( 95088 )

                > Motility isn't a necessary condition for being considered an animal

                Animal-ness is not something I'm making an issue of.

                My point was that we don't know if all or most of the Ediacaran (Edi) are directly related.

                Let's get back to multi-cell-ness (MC) and differentiation (Dif). To make a case that most Edi's were MC, one of two arguments are typically made: 1) Differentiation, and 2) they are early relatives of known phyla which are MC.

                #2 is still heavily debated. And even if ONE type of Edi were shown to

                • You're missing the main point that has always been the prime reason for accepting the Ediacaran fauna as being multicellular (and along with it, titanosaurs too) : the size of the things. Back at the start of this thread was the discovery of a strain of bacteria which could get up to a couple of millimetres in size - which is a lot bigger than most bacteria. But it's a lot smaller than most Ediacarans. The original Charnia was about 15cm long with a complex body structure. Very, very different to a single c

                  • Re: (Score:1)

                    by Tablizer ( 95088 )

                    > But [single cell in TFA is] a lot smaller than most Ediacarans... never been seen in modern organisms - single cells approaching a metre in size

                    Xenophyophores have been clocked in at 20cm across.

                    And current life's sizes are not a good predicter of the past. Insects several yards across used to exist. The nature of competition changes over time such that big becomes small and vice versa. Mammals, for example, got big after dino's faded. And Trilobites got smaller over time.

                    Thus, we have a lot of example

                    • Are you saying a Dickinsonia has been found with lots of and/or clear differentiation?

                      Well, yes, for years. A recent compendium (published in Geology, but you can get it from ResearchGate [researchgate.net]) describes how the structure of Dickinsonia responds to perimortem forces - it tears (fig 2, a, b, c) along the rib lines, leaving a protrusion which can be seen in the trace fossil (a mortichnus, if you like) where the body was dragged across the sediment surface before the fossil settled back to the surface (unless you b

                    • Re: (Score:1)

                      by Tablizer ( 95088 )

                      > That doesn't look to me like the response of a cell wall being opened [ripped] to expose internal structures. You'd have to have the "intracellular" structure having pretty close to the same strength as the cell's outer wall. That's not a situation I can think of a parallel for...

                      Well, okay, I don't know of any (proven) macrocellular organism that has strong intracellar structures. You have a point there.

                      But what about the each-segment-is-a-macro-cell theory (mentioned earlier)? (Okay, maybe "conjectur

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