Microbial dark matter

Microbial dark matter is that pervasive yet practically invisible infrastructure of life on the planet, which can have profound influences on the most significant environmental processes from plant growth and health, to nutrient cycles in terrestrial and marine environments, the global carbon cycle, and possibly even climate processes.

Microbial dark matter comprises the vast majority of microbial organisms that biologists are unable to culture in a lab due to a lack of knowledge or ability to supply the required growth conditions. Most microbial species are “dark matter.”

The potential theoretical importance of such “known unknowns” and even “unknown unknowns” of the microbial world (e.g., unknown genes, genomes, functions, organisms, processes, and communities associated with uncultured microbes and viruses), that were often popularized under the catch-phrase “microbial dark matter,” should not be underestimated. Many scientists find the metaphor misleading or inaccurate because the “microbial dark matter” does not correspond to the dark matter studied by astronomers and physicists. This latter represents a hypothetical, still unobserved, although widely accepted, kind of matter, which does not interact with light but interacts through gravity.

Taking the mass of this unseen astronomic dark matter into account would explain the incorrect predictions of the movement of galaxies by classic astronomy theories. This astronomic dark matter is thus unquestionably different from the microbial dark matter. However, other microbiologists have endorsed the analogy (Rinke et al. 2013; Lobb et al. 2015; Lok 2015; Saw et al. 2015; Bruno et al. 2017; Krishnamurthy and Wang 2017; Lewis 2017), since the sentence nonetheless conveniently stresses that, to some extent, newly discovered microbes can harbor different biology from those that had been cultured.

First, it is a convenient shorthand for the idea that unknown microbial life may be playing an important and even dominant role in ecosystem processes. Second, it has some editorial and educational virtues, as it effectively helps to raise the interest for microbiology studies beyond the field of microbiology (in which none would conflate astronomic and microbial dark matter), surely enhancing the general interest for the unexplored diversity of microbes and their genes.


  1. Impact of single-cell genomics and metagenomics on the emerging view of extremophile “microbial dark matter.” https://link.springer.com/article/10.1007/s00792-014-0664-7
  2. Phylogenetically Novel Uncultured Microbial Cells Dominate Earth Microbiomes. https://msystems.asm.org/content/3/5/e00055-18
  3. Microbial Dark Matter Investigations: How Microbial Studies Transform Biological Knowledge and Empirically Sketch a Logic of Scientific Discovery. https://doi.org/10.1093/gbe/evy031
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