Dark Microbial Matter

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  • Dark microbial matter uncultured microbes whose characteristics have never been described could be dominating nearly all the environments on the earth, scientists found.


  • • The study, published in the journal M-Systems, is the first time to estimate the population of microbes that have not yet been grown in a lab culture.
  • Researchers collected every DNA sequence deposited in public databases by researchers all over the world, totalling 1.5 million, and compared them to 26,000 DNA sequences of microbes and bacteria that have already been cultured. As many as a quarter of the microbes on earth could come from the roughly 30 phyla a taxonomic classification between kingdoms and classes of microbes that have never been cultured.


  • • Scientists have long been aware of this mass of uncultured microbes, also known by scientists as microbial dark matter. However, counting them one by one would be an impossible task and, up until now, researchers have not been able to even estimate how many of them there are.
  • The study and characterisation of uncultured microbes can be a particularly valuable tool in specific fields such as in medicine, where scientists have described cases of culture-resistant pathogens. It is also possible that these microbes can’t grow on their own in culture because they die if they are removed from their intricate relationships with each other or their particular environment. Uncultured microbes are so vastly different than cultured ones that they might be doing unusual things, like surviving on extremely low energy or growing extraordinarily slowly.
  • Since these microbes provide many ecosystem services such as helping crops grow and battling climate change solving the considerable puzzle they’ve presented us is a crucial challenge for modern microbiology.


  • Microbes comprise 60% of the earth’s biomass and they are everywhere. They are abundant in the oceans and in soil there are more microbes in a teaspoon of soil than there are humans on earth they live in deserts, on mountains in Antarctica, near boiling hydrothermal vents at the seafloor, and in the acid stomachs of mammals including us humans.
  • Life as we know it on our planet would not be possible without microbes. Much of the oxygen we breathe is produced by microbes, they are necessary to create our food such as yogurt, and cheese.
  • Also, beer and wine would not exist without their ability to ferment sugar to alcohol, and in industry microbes are used as tiny living factories, for example to produce human insulin for people with diabetes. Scientists are very curious to learn more about this microbial world, but there is one big problem. We can only study about 1% of all the microbes in our laboratory, since most of the little critters just don’t grow on artificial substrates in the lab.
  • Traditionally one would grow the microbes millions of them to get enough DNA for sequencing, because one cell has so little DNA. Since we can’t do this for the majority of microbes, they remained a mystery to us and are known as the Microbial Dark Matter (MDA).
  • The inability to culture this microbial dark matter has led to a very skewed view of the microbial world. The two largest groups of microbes (Bacteria and Archaea) have many members which are only known because we found a small piece of DNA, the 16S rRNA gene, in environmental samples. We have almost no genomic information about those microbes, so we don’t know what they are doing or what they are capable of
  • We apply a method, called single cell genomics, which omits the culturing step and allows to amplify the DNA of a single microbial cell a billion-fold, more than enough to sequence its genome.
  • The first step is to take an environmental sample and to sort individual cells into tiny droplets. This is done on a cell sorter which detects the cells by a laser and separates them into droplets by electrostatic forces, similar to how an ink-jet printer directs individual droplets of ink to print a letter on a page. Next, we break open the cell envelope, very carefully so we don’t damage the DNA.
  • • Then we add a cocktail with the enzyme phi29 which has the ability to amplify very long stretches of DNA, and after several hours we have billions of copies from the microbial genome and can start sequencing.
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