Bacterial dark matter

Nature Talk
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I recently came across this concept (talking to an AI, sorry) and just wondering about it. I’ve heard of mycelial networks and plants communicating with pheromones to mutual advantage, but 90%+ bacterial species influencing rhizomes are unknown? This is a potential “frontier” of human knowledge that took me by surprise as well, we barely understand soil science? the agricultural revolution was many thousand years ago, seems odd.

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Soil microbiology is certainly interesting, but its complexity and the minuscule scale make it hard to study. (Also, even defining bacterial species isn’t straightforward. You’ll see most studies using “OTUs” or “ASVs”.) You said that the agricultural revolution–I’m assuming you mean the First Agricultural Revolution, there have been a few–was a couple of millennia ago. However, bacteria were only discovered a couple centuries ago, DNA has only been seriously studied for a couple of decades, and cheap and fast DNA-sequencing has only really been available for a couple of years…

Yet, for any comprehensive survey of the diversity of soil microbiota, cheap and fast sequencing seems to be more or less required. This is because at a bacterial scale, there are only so many morphological characteristics a cell can have, and you cannot really observe it with a regular light microscope anyway. Additionally, most bacterial species cannot really be cultured in a lab (at least not easily). See: https://doi.org/10.1016/S1002-0160(21)60062-0
What doesn’t help is that many of the relevant bacterial “species” appear in low abundance, which makes it even harder to study or even find them, let alone without sequencing. See: https://doi.org/10.3389/fmicb.2017.00975

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Blockquote
What doesn’t help is that many of the relevant bacterial “species” appear in low abundance, which makes it even harder to study or even find them, let alone without sequencing.

Classification at such a granular level would possibly need to be bespoke? Taxons defined on a more behavioural or sort of ecosystem basis than species/phenotype.

Technology opening windows on these things makes sense but it just surprised me how unknown it is

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Humans have known about life since the beginning of humanity, but we only recently found out about DNA.

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