Classification and Evolution of Bacteria

Bacteria vary greatly in their chemistry and metabolism, and it is difficult to classify them in a rational way. In higher organisms species are often defined as forms that cannot interbreed and produce fertile offspring, but such a criterion is meaningless for bacteria whose reproduction is largely asexual and which are able readily to accept “visiting genes” from other bacteria. The classification into species and genera is therefore somewhat arbitrary. A currently used scheme 20 classifies the prokaryotes into 35 groups on the basis of many characteristics including shape, staining behavior, and chemical activities. Table
1-1 also includes genus names of most of the bacteria discussed in this book.
Bacteria may have the shape of spheres or straight or curved rods. Some, such as the actinomycetes, grow in a branching filamentous form. Words used to describe bacteria often refer to these shapes: a coccus is a sphere, a bacillus a rod, and a vibrio a curved rod with a flagellum at one end. A spirillum is screwshaped. These same words are frequently used to
name particular genera or families. Other names are derived from some chemical activity of the bacterium being described. The gram stain provides an important criterion of classification that depends upon differences in the structure of the cell wall (see Chapter 20). Bacterial cells are described as gram-positive or gram-negative according to their ability to retain the basic dye crystal violet as an iodine complex. This difference distinguishes two of four large categories of bacteria. 20 Most actinomycetes, the spore-forming bacilli, and most cocci are gram-positive, while E. coli, other enterobacteria, and pseudomonads are gram-negative. A third category consists of eubacteria that lack cell walls, e.g. the mycoplasma. Comparisons of amino acid sequences of proteins and the nucleotide sequences of DNA and RNA have provided a new approach to classification of bacteria. Although the origins of life are obscure, we can easily observe that the genome changes with time through
mutation and through the enzyme-catalyzed process of genetic recombination. The latter gives rise to the deletion of some nucleotides and the insertion of others into a DNA chain. When we examine sequences of closely related species, such as E. coli and Salmonella typhimurium, we find that the sequences are very similar. However, they differ greatly from those of many other bacteria. Consider the 23S ribosomal RNA, a molecule found in the ribosomes of all bacteria. It contains ~3300 nucleotides in a single highly folded chain. The basic structure is highly conserved but between any two species of bacteria there are many nucleotide substitutions caused by mutations as well as deletions and insertions. By asking what is the minimum number of mutations that could have converted one 23S RNA into another and by assuming a more or less constant rate of mutation over millions of years it is possible to construct a phylogenetic tree such as that shown in. One conclusion from these comparisons is that the methane-producing bacteria, the methanogens, 24 are only distantly related to most other bacteria. Methanogens together with the cell wall-less Thermoplasma,
28 some salt-loving halobacteria, and some thermophilic (heat-loving) sulfur bacteria form a fourth major category. They are often regarded as a separate kingdom, the archaeobacteria, 25 which together with the kingdom of the eubacteria form the superkingdom prokaryota. Certain archaeobacteria have biochemical characteristics resembling those of eukaryotes and some biologists therefore classify them as archaea and
rank their kingdom as equal to that of the bacteria and the eukaryotes. 27,29,30,30a,30b Others disagree. 31 In Table 1-1, the archaeobacteria are found in groups 31–35. Most bacteria are very small in size but there are species large enough to be confused with eukaryotic protozoa. The record for bacteria seems to be held by Epulopiscium fishelsoni, a parasite of the surgeonfish intestinal tract. A single cell measured > 600 m by 80 m diameter, over 106 times larger in volume than a cell of E. coli. 32 The organism is a gram-positive bacterium as judged by analysis of its cloned ribosomal RNA genes.

Universal phylogenetic tree. From Wheelis et al.