How much of the microbial world do we know about?

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This is a difficult question to answer; in fact, it cannot be realistically answered at this time within even a factor of a thousand. Some believe that bacteria may consist of a few thousands, or maybe tens of thousands, of species. This is ridiculous. There are over 350,000 described species of beetles, and even if there is only a single specific bacterial symbiont for each of these beetle species, that would imply at least 10 times more species of bacteria than these folks would believe just among these species. If you plate a typical environmental sample of onto rich media after counting cells microscopically, you typically see that less than 1 observable bacterium in a thousand grows to produce a colony (averaging about 1 in a million), and of course these are only from the most abundant species. As poorly characterized microbiologically as the world around us is, we know nothing at all about some very large microbial habitats: the subsurface world, the deep aquifer world, the hydrothermal field world, &c, &c.

Another problem is that we really don't have a very good idea of what a bacterial "species" is. This is a general problem with asexual organisms; species in plants and animals are defined in terms of breeding populations, and so this only applied to organisms that ‘breed’. The concept of a species is critical to biology; this is part of why "The Origin of Species" was so important, and most of this book was spent creating a rational description of a ‘species’ in the plant and animal worlds. (Actually, most of this is spent showing how indistinct the divisions really are between species.) A rational "concept of a bacterial species" does not yet exist. This is probably the most important open question in microbiology. 70% DNA:DNA hybridization is sometimes used as an operational definition of a species, but this is an arbitrary definition, without a theoretical underpinning. Until we have a meaningful definition of a species, how can we count them? In fact, it has ben argued that asexual organisms don’t have ‘species’, in which case some other term (and definition) might be needed.