[HN Gopher] The ocean teems with networks of interconnected bact...
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The ocean teems with networks of interconnected bacteria
Author : abe94
Score : 131 points
Date : 2025-01-27 14:24 UTC (1 days ago)
(HTM) web link (www.quantamagazine.org)
(TXT) w3m dump (www.quantamagazine.org)
| efitz wrote:
| Eywa
| asdasdsddd wrote:
| Can someone explain why there arent more multicellular bacteria?
| Terr_ wrote:
| Not yet, it seems to be an open question.
|
| See: "The Mystery of the Missing Multicellular Prokaryotes"
|
| https://www.quantamagazine.org/the-mystery-of-the-missing-mu...
| PaulHoule wrote:
| There probably are an awful lot of them. Of all the bacteria
| that exist in the world (detectable by genomic methods) only a
| tiny fraction can be isolated and grown on their own. [1][2]
|
| In many cases it might be that we just don't know how to
| provide the right environment, but part of it is that many
| bacteria only grow together with partner bacteria of other
| species [3] [4] For that matter, there are many bacteria that
| have lifestyles based around living on biofilms created by
| conspecifics. [5]
|
| [1] Like dark matter
|
| [2] https://www.worldwidejournals.com/international-journal-
| of-s...
|
| [3]
| https://ecampusontario.pressbooks.pub/microbio/chapter/10-2-...
|
| [4] https://teamaquafix.com/sulfide-reducing-
| bacteria/?form=MG0A...
|
| [5] https://en.wikipedia.org/wiki/Biofilm
| hinkley wrote:
| One of my long bets is that there are bacteria causing
| gastroenteritis that do not reproduce on growth media. I
| doubt very much that all of our problems are caused by
| chemicals.
|
| There's too many stories in modern medicine still that sound
| like, "if we can't see it, you're not sick." There's at least
| one more h pylori out there somewhere.
| baxtr wrote:
| What would Occam says about this though?
| wswope wrote:
| Occam's razor doesn't matter for shit when it comes to
| biology.
|
| The vast majority of GIs would agree with the grandparent
| post, but it even goes deeper than that. Pathogenicity of
| common bacteria is heavily mediated through HGT and
| interspecies microbial signaling - meaning that there's
| plenty we don't know about even the most studied
| organisms when they're in a dynamic environment with
| other neighbors.
|
| In other words, we know there are multiple layers of
| activity taking place that we've barely scratched the
| surface on research-wise, so we have good reason to
| believe that simpler explanations are almost certainly
| reductive and wrong.
| PaulHoule wrote:
| When results started coming out about the microbiome and
| health and there weren't any practical results (a poop
| pill that changes things) I thought it was one of those
| fads like gluten free or high-functioning autism.
|
| The results have kept coming and it's hard not to believe
| the gut-health connection now but it's still frustrating
| that it doesn't translate to any therapy.
| wswope wrote:
| Yeah, I've definitely followed that same path as the
| field has progressed - but I've come to view gut health
| as something akin to soil health.
|
| Compost does great things for plants, but you can't
| sprinkle mycorrhizal fungi or banana peels on top of
| barren earth and call it a day. Similarly, you can't
| throw probiotic bacteria or kimchi into a GI tract and
| call it a day.
|
| Instead, in both cases, you have to holistically balance
| and change inputs over time to see results, taking into
| account the unique, pre-established state of the system.
| That makes for difficult research when so much of labwork
| is about controlling and isolating variables, and IMO, is
| the biggest factor in why we're not seeing those pre-
| packaged applications yet.
| PaulHoule wrote:
| Soil health is a great example!
|
| I've been working on a monologue about reductivism vs
| reductionism and it reminds me of Doug Hofstader setting
| up a dialectic between reductionism and holism with the
| problem that you can't say holism has the same presence
| that reductionism has.
|
| But soil health really is a place where holism reigns,
| thanks for reminding me!
| throwup238 wrote:
| _> [1] Like dark matter_
|
| https://en.m.wikipedia.org/wiki/Microbial_dark_matter
|
| They're usually only observable in the rare case that they
| get randomly captured on an electron microscope slide. The
| genomic method is complicated because there's so much data
| it's hard to extract the signal and reassemble the snippets.
| There's already more data than we know what to do with.
|
| That said, recently a fellow HNer used the genomic method on
| old data and may have discovered a new class of life one step
| down from viruses:
| https://news.ycombinator.com/item?id=42547489
| wdwvt1 wrote:
| Just wanted to add some color to this good comment.
|
| In the human context we are much closer to being able to
| culture anything we want. I would estimate that we are at 75%
| coverage now -- pick a species detected genomically in the
| human gut (or skin/vagina/nose, etc.) and we are likely to be
| able to culture it or a type strain of its species 75% of the
| time. For a long time we overestimated human microbial
| diversity because of bad genomic methods and error rates with
| the early 454 and then Illumina sequencers. This error rate,
| coupled with the fact that we can't easily replicate culture
| conditions for the vast majority of earth's bacterial biomass
| (i.e. the deep lithosphere or the oceans) led to this
| persistent if somewhat untrue description of the
| unculturability of human microbes.
|
| [0] gives an estimate of 35-65% of human/mouse gut microbes
| having a culturable representative. This paper is from 2017,
| and there have been a lot of advancements since then.
|
| [1] is a good non-review paper where they got 73% of the
| genomically defined species via just a single cultivation
| medium
|
| There are others, but I finished my PhD in culturomics-
| related stuff in 2021, and haven't kept up as much as I
| should. Everything the OP cited about lithospheric, deep
| ocean, etc. still applies as far as I know. Those
| environments are just very hard to recreate with their
| pressure, temperature, and nutrient requirements.
|
| [0] https://doi.org/10.1038/s41564-023-01426-7 [1]
| https://www.nature.com/articles/nature17645
|
| Edit: typos
| roughly wrote:
| The way in which prokaryotes like bacteria and eukaryotes like
| most multicellular organisms handle their genomes is part of
| this - prokaryotes are much more promiscuous in taking up and
| emitting genetic material, which is part of how you get so many
| different variants of the same "species" of bacteria, whereas
| eukaryotes are much more protective of their genomes and rely
| more on variable gene expression (in other words, which parts
| of the genome are going to be uncovered and available to read),
| rather than changes in the genome, to determine how they behave
| and what they "do".
|
| One thing that I think is sharply underappreciated is how much
| cross-talk there is within bacterial communities as is - it's a
| normal state of affairs for a full metabolic pathway to span
| between multiple species (so, one bacterial species takes the
| starting molecule, performs a set of transformations, emits it
| into the environment, a second species takes up that derived
| material, modifies it further, re-emits it, and a third
| species, or even the first species again, takes it up and
| continues the chain). A bacteria has a cell wall, but that's a
| tool used as part of many of the bacteria's function, which
| means you really need to look at a bacteria's "zone of
| influence" inside and outside the cell wall to understand what
| it's doing.
|
| So, given the flexibility of prokaryotic genomes, I think a
| bacterial colony containing multiple species or multiple
| variants of the same species might really be the prokaryotic
| equivalent of a multicellular organism, in which case they're
| absolutely everywhere, to a degree where focusing in on a
| single species of bacteria in any given context might be as
| reductive as focusing in on a single variant of human cell
| while evaluating how humans function.
| NoMoreNicksLeft wrote:
| Reminds me of Greg Bear's _Blood Music_ and even _Vitals_.
| adolph wrote:
| Relatedly, here is an account of someone working on global ocean
| surveys of microbes.
|
| https://x.com/science_doodles/status/1879600503157592386
| mmooss wrote:
| > biologists snapping images of the cyanobacteria under a
| microscope saw a cell that had grown a long, thin tube and
| grabbed hold of its neighbor.
|
| Is there or has anyone explored a connection between this process
| and the endosymbiolsis that first created chlorplasts?
|
| Those involved captured cynanobacteria. In the OP, if I
| understand correctly, at least sometimes the cyanobacteria is
| doing the capturing.
| PaulDavisThe1st wrote:
| Isn't this one of the main technological plot lines of Star Trek:
| Discovery?
|
| Oh wait, my mistake. That's a universe teeming with networks of
| interconnected fungi.
|
| You can see how easy it would be to make the mistake though,
| right?
| block_dagger wrote:
| Related Anton video: https://youtu.be/kSGW8DmrWlU
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