Figure 1–14 The structure of a bacterium. (A) The bacterium Vibrio cholerae, showing its simple internal organization. like many other species, Vibrio has a helical appendage at one end—a flagellum—that rotates as a propeller to drive the cell forward. It can infect the human small intestine to cause cholera; the severe diarrhea that accompanies this disease kills more than 100,000 people a year. (B) An electron micrograph of a longitudinal section through the widely studied bacterium Escherichia coli (E. coli). The cell’s dnA is concentrated in the lightly stained region. Part of our normal intestinal flora, E. coli is related to Vibrio, and it has many flagella distributed over its surface that are not visible in this section. (B, courtesy of e. kellenberger.) spherical cells e.g., Streptococcus spiral cells e.g., Treponema pallidum
Figure 1–13 Shapes and sizes of some bacteria. Although most are small, as shown, measuring a few micrometers in linear dimension, there are also some giant species. An extreme example (not shown) is the cigar-shaped bacterium Epulopiscium fishelsoni, which lives in the gut of a surgeonfish and can be up to 600 μm long.
Much of this world of microscopic organisms is virtually unexplored. Traditional methods of bacteriology have given us an acquaintance with those species that can be isolated and cultured in the laboratory. But DNA sequence analysis of the populations of bacteria and archaea in samples from natural habitats—such as soil or ocean water, or even the human mouth—has opened our eyes to the fact that most species cannot be cultured by standard laboratory techniques. According to one estimate, at least 99% of prokaryotic species remain to be characterized. Detected only by their DNA, it has not yet been possible to grow the vast majority of them in laboratories.
The Tree of life has Three Primary Branches: Bacteria, Archaea, and eukaryotes
The classification of living things has traditionally depended on comparisons of their outward appearances: we can see that a fish has eyes, jaws, backbone, brain, and so on, just as we do, and that a worm does not; that a rosebush is cousin to an apple tree, but is less similar to a grass. As Darwin showed, we can readily interpret such close family resemblances in terms of evolution from common ancestors, and we can find the remains of many of these ancestors preserved in the fossil record. In this way, it has been possible to begin to draw a family tree of living organisms, showing the various lines of descent, as well as branch points in the history, where the ancestors of one group of species became different from those of another.
When the disparities between organisms become very great, however, these methods begin to fail. How do we decide whether a fungus is closer kin to a plant or to an animal? When it comes to prokaryotes, the task becomes harder still: one microscopic rod or sphere looks much like another. Microbiologists have therefore sought to classify prokaryotes in terms of their biochemistry and nutritional requirements. But this approach also has its pitfalls. Amid the bewildering variety of biochemical behaviors, it is difficult to know which differences truly reflect differences of evolutionary history.
Genome analysis has now given us a simpler, more direct, and much more powerful way to determine evolutionary relationships. The complete DNA sequence of an organism defines its nature with almost perfect precision and in exhaustive detail. Moreover, this specification is in a digital form—a string of let-ters—that can be entered straightforwardly into a computer and compared with the corresponding information for any other living thing. Because DNA is subject to random changes that accumulate over long periods of time (as we shall see shortly), the number of differences between the DNA sequences of two organisms can provide a direct, objective, quantitative indication of the evolutionary distance between them.