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The small size of prokaryotes has hindered our study of their evolutionary relationships

Until about 300 years ago, nobody had even seen an individual prokaryote. Most prokaryotes remained invisible to humans until the invention of the first simple microscope. Prokaryotes are so small, however, that even the best light microscopes don’t reveal much about them. It took advanced microscopic equipment and modern molecular techniques to open up the microbial world. (Microscopic organisms—both prokaryotes and eukaryotes—are often collectively referred to as “microbes.”)

Before DNA sequencing became practical, taxonomists based prokaryote classification on observable phenotypic characters such as shape, color, motility, nutritional requirements, and sensitivity to antibiotics. One of the characters most widely used to classify prokaryotes is the structure of their cell walls.

The cell walls of almost all bacteria contain peptidoglycan, a cross-linked polymer of amino sugars that produces a firm, protective, meshlike structure around the cell. Peptidoglycan is a substance unique to bacteria; its absence from the cell walls of archaea is a key difference between the two prokaryotic domains. Peptidoglycan is also an excellent target for combating pathogenic (disease-causing) bacteria because it has no counterpart in eukaryotic cells. Antibiotics such as penicillin and ampicillin, as well as other agents that specifically interfere with the synthesis of peptidoglycan-containing cell walls, tend to have little, if any, effect on the cells of humans and other eukaryotes.

The Gram stain is a technique that can be used to separate most types of bacteria into two distinct groups. A smear of bacterial cells on a microscope slide is soaked in a violet dye and treated with iodine; it is then washed with alcohol and counterstained with a red dye called safranin. Gram-positive bacteria retain the violet dye and appear blue to purple (Figure 25.2A). The alcohol washes the violet stain out of Gram-negative bacteria, which then pick up the safranin counterstain and appear pink to red (Figure 25.2B). For most bacteria, the effect of the Gram stain is determined by the chemical structure of the cell wall:

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A Gram-negative cell wall usually has a thin peptidoglycan layer, which is surrounded by a second, outer membrane quite distinct in chemical makeup from the cell membrane (see Figure 25.2B). Together the cell wall and the outer membrane are called the cell envelope. The space between the cell membrane and the outer membrane (known as the periplasmic space) contains proteins that are important in digesting some materials, transporting others, and detecting chemical gradients in the environment.
A Gram-positive cell wall usually has about five times as much peptidoglycan as a Gram-negative cell wall. Its thick peptidoglycan layer is a meshwork that may serve some of the same purposes as the periplasmic space of the Gram-negative cell envelope.

Figure 25.2 The Gram Stain and the Bacterial Cell Wall When treated with Gram-staining reagents, the cell walls of bacteria react in one of two ways. (A) Gram-positive bacteria have a thick peptidoglycan cell wall that retains the violet dye and appears deep blue or purple. (B) Gram-negative bacteria have a thin peptidoglycan layer that does not retain the violet dye, but picks up the counterstain and appears pink to red.

Activity 25.1 Gram Stain and Bacteria

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Shape is another phenotypic characteristic that is useful for the basic identification of bacteria. The three most common shapes are spheres, rods, and spiral forms (Figure 25.3). Many bacterial names are based on these shapes. A spherical bacterium is called a coccus (plural cocci). Cocci may live singly or may associate in two- or three-dimensional arrays such as chains, plates, blocks, or clusters of cells. A rod-shaped bacterium is called a bacillus (plural bacilli). A spiral bacterium (shaped like a corkscrew) is called a spirillum (plural spirilla). Bacilli and spirilla may be single, form chains, or gather in regular clusters. Among the other bacterial shapes are long filaments and branched filaments.

Figure 25.3 Bacterial Cell Shapes This composite, colorized micrograph shows the three most common bacterial shapes. Spherical cells are called cocci; those pictured are a species of Enterococcus from the mammalian gut. Rod-shaped cells are called bacilli; these Escherichia coli also reside in the gut. The helix-shaped spirilla are Leptospira interrogans, a human pathogen.

Less is known about the shapes of prokaryotic archaea because many of these organisms have never been seen. Many prokaryotic archaea are known only from samples of DNA from the environment. However, the species whose morphologies are known include cocci, bacilli, and even triangular and square species. Some flattened species grow on surfaces, arranged like sheets of postage stamps.