Chapter 2 Bacterial structure and taxonomy

Classification of all living beings, including microbes has been attempted by many over centuries (Table 2.1). Traditionally, though they were all classified into two kingdoms, plants and animals, classification was arbitrary and based on morphological and growth characteristics. With the development of novel techniques, the latter classification was expanded to include five kingdoms: monera, protista, plantae, fungi and animalia. However, the current understanding based on their genetic relatedness is that all forms of life fall into three domains: Archaea, Bacteria and Eucarya. The main differences among Archaea, Bacteria and Eucarya are listed in Table 2.2. Note that taken together, Archaea and Bacteria are also known as prokaryotes (see below).

Table 2.1 Differential characteristics of major groups of organisms

Table 2.2 Major differences among the three domains of life

Bacteria	Archaea	Eucarya
Organization of the genetic material and replication
DNA free in the cytoplasm	DNA free in the cytoplasm	DNA is contained with a membrane-bound nucleus. A nucleolus is also present
Only one chromosome	Only one chromosome	More than one chromosome. Two copies of each chromosome may be present (diploid)
DNA associated with histone-like proteins	DNA associated with histone-like proteins	DNA complexed with histone proteins
May contain extrachromosomal elements called plasmids	Plasmids may be found	Plasmids only found in yeast
Introns not found in mRNA	Introns not found in most genes	Introns found in all genes
Cell division by binary fission – asexual replication only	Reproduce asexually and spores are not found	Cells divide by mitosis
Transfer of genetic information occurs by conjugation, transduction and transformation (see Chapter 3)	Processes similar to bacterial conjugation enables exchange of genetic material	Exchange of genetic information occurs during sexual reproduction. Meiosis leads to the production of haploid cells (gametes), which can fuse
Cellular organization
Cytoplasmic membrane contains hopanoids	Membranes contain isoprenes	Cytoplasmic membrane contains sterols
Lipopolysaccharides and teichoic acids found	No lipopolysaccharides or teichoic acids found
Energy metabolism associated with the cytoplasmic membrane		Mitochondria present in most cases
Photosynthesis associated with membrane systems and vesicles in cytoplasm		Chloroplasts present in algal and plant cells
		Internal membranes, endoplasmic reticulum and Golgi apparatus present associated with protein synthesis and targeting
		Membrane vesicles such as lysosomes and peroxisomes present
		Cytoskeleton of microtubules present
Flagella consist of one protein, flagellin	Contains flagella that derive energy from proton pumps	Flagella have a complex structure with 9 + 2 microtubular arrangement
Ribosomes – 70S	Ribosomes behave more like eucarya when exposed to inhibitors	Ribosomes – 80S (mitochondrial and chloroplast ribosomes are 70S)
Peptidoglycan cell walls	Cell walls lack peptidoglycan	Polysaccharide cell walls, where present, are generally either cellulose or chitin

Viruses are not included in this classification as they are unique, acellular, metabolically inert organisms and therefore replicate only within living cells. Other differences between viruses and cellular organisms include:

• Structure. Cells possess a nucleus or, in the case of bacteria, a nucleoid with DNA. This is surrounded by the cytoplasm where energy is generated and proteins are synthesized. In viruses, the inner core of genetic material is either DNA or RNA, but they have no cytoplasm and hence depend on the host for their energy and proteins (i.e. they are metabolically inert).

• Reproduction. Bacteria reproduce by binary fission (a parent cell divides into two similar cells), but viruses disassemble, produce copies of their nucleic acid and proteins, and then reassemble to produce another generation of viruses. As viruses are metabolically inert, they must replicate within host cells. Bacteria, however, can replicate extracellularly (except rickettsiae and chlamydiae, which are bacteria that also require living cells for growth).

Eukaryotes and prokaryotes

As mentioned above, another modification of classifying cellular organisms is to divide them into prokaryotes (i.e. Archaea and Bacteria) and eukaryotes (Greek karyon: nucleus). Fungi, protozoa and humans, for instance, are eukaryotic, whereas bacteria are prokaryotic. In prokaryotes, the bacterial genome, or chromosome, is a single, circular molecule of double-stranded DNA, lacking a nuclear membrane (smaller, single or multiple circular DNA molecules called plasmids may also be present in bacteria), whereas the eukaryotic cell has a true nucleus with multiple chromosomes surrounded by a nuclear membrane.

Bacteria comprise the vast majority of human pathogens, while archaea appear rarely to cause human disease and live in extreme environments (e.g. high temperature or salt concentrations). Archaea received little attention traditionally as they cannot be easily cultured in the laboratory. Interestingly, recent studies using novel techniques such as pyrosequencing have uncovered their presence in the oral cavity. Some studies have even shown that certain species of archaea are more frequently found in subgingival plaque in periodontal disease.

Morphology

Shape and size

The shape of a bacterium is determined by its rigid cell wall. Bacteria are classified by shape into three basic groups (Fig. 2.1A and B):

Fig. 2.1 Common bacterial forms. (A) Coccus; (B) capsulated diplococci; (C, D) cocci in chains (e.g. streptococcus) and clusters (e.g. staphylococcus); (E) bacillus; (F, G) capsulated and flagellated bacillus (e.g. Escherichia coli); (H) curved bacilli (e.g. Vibrio spp.); (I) spore-bearing bacilli (e.g. Clostridium tetani); (J) spirochaete.

1. cocci (spherical)

2. bacilli (rod-shaped)

3. spirochaetes (helical).

Some bacteria with variable shapes, appearing both as coccal and bacillary forms, are called pleomorphic (pleo: many; morphic: shaped) in appearance.

The size of bacteria ranges from about 0.2 to 5 µm. The smallest bacteria approximate the size of the largest viruses (poxviruses), whereas the longest bacilli attain the same length as some yeasts and human red blood cells (7 µm).

Arrangement

Bacteria, whichever shape they may be, arrange themselves (usually according to the plane of successive cell division) as pairs (diplococci), chains (streptococci), grape-like clusters (staphylococci) or as angled pairs or palisades (corynebacteria).

Gram-staining characteristics

In clinical microbiology, bacteria can be classified into two major subgroups according to the staining characteristics of their cell walls. The stain used, called the Gram stain (first developed by a Danish physician, Christian Gram), divides the bacteria into Gram-positive (purple) and Gram-negative (pink) groups. The Gram-staining property of bacteria is useful both for their identification and in the therapy of bacterial infections because, in general, Gram-positive bacteria are more susceptible to penicillins than Gram-negative bacteria.

Flagella are whip-like filaments that act as propellers and guide the bacteria towards nutritional and other sources (Fig. 2.3). The filaments are composed of many subunits of a single protein, flagellin. Flagella may be located at one end (monotrichous, a single flagellum; lophotrichous, many flagella) or all over the outer surface (peritrichous). Many bacilli (rods) have flagella, but most cocci do not and are therefore non-motile. Spirochaetes move by using a flagellum-like structure called the axial filament, which wraps around the cell to produce an undulating motion.