5

Origins of Life and Earth Prehistory

43

currently estimated as 10 Superscript 710⁷ (metazoa), 2.5 times 10 Superscript 52.5 × 10⁵ (plantae), 2 times 10 Superscript 52 × 10⁵ (protozoa), and

5 times 10 Superscript 45 × 10⁴ (fungi).

Problem. Estimate the fraction of all possible DNA sequences that are represented

in extant species.

The Problem of Bacterial Identification

Darwin’s notion of species was “a term arbitrarily given for the sake of convenience

to a set of individuals closely resembling each other” (cf. the slightly more formal

notion of quasispecies in sequence space: a cluster of genomes). Since bacteria pre-

dominantly proliferate asexually and can acquire new genetic material rather readily

(“lateral” or “horizontal” gene transfer), the criterion of reproductive isolation that

is rather helpful for defining species in metazoans is of little use. The first systematic

attempt to classify bacteria dates from 1872, when Ferdinand Cohn proposed a system

based on their morphology. The shape of individual bacteria can be easily seen in a

(high-power) optical microscope, and colonies growing on agar plates (for example)

often have characteristic morphologies themselves. Such a scheme can be readily

extended to include features such as pathogenicity and characteristic biochemistry,

and even characteristic habitat. The range of useful attributes depends essentially

on what measuring tools are available. Thus, for example, a classification based on

the compressibility of the bacterium placed between two parallel plates might also

be a useful one. Gram’s stain, which distinguishes between different characteristic

polysaccharides coating the bacterium, is well known. This is a dichotomous classi-

fication, and a hierarchy of dichotomies should lead unerringly to the identification

of a species (provided it is already known). All this knowledge has been captured

in the well-known Bergey’s Manual. Bacteria whose attributes did not match those

already known would be granted the status of a new species.

The advent of molecular biology provided further vastification of the range of use-

ful attributes. In particular, the nucleic acid sequence of the so-called 16S ribosomal

RNA (rRNA), part of the smaller subunit of the ribosome, was used by Carl Woese as

a new way of classifying bacteria and, together with an assumption about the rate of

mutations, could be used to construct a comprehensive phylogeny of bacteria. Bac-

teria seem to vary greatly in their genotypic (and phenotypic) stability, however, and

any classification based on the assumption of relative stability has some limitations. ²

2 See Coenye and Vandamme (2004) and Hanage et al. (2006) for some discussion of the matter;

Trüper (1999) has written an interesting article on prokaryotic nomenclature.