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).
|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|
|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:
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.
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.
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).
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).
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.
The structure of a typical bacterium is shown in Figure 2.2. Bacteria have a rigid cell wall protecting a fluid protoplast comprising a cytoplasmic membrane and a variety of other components (described below).
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.
Fimbriae and pili are fine, hair-like filaments, shorter than flagella, that extend from the cell surface. Pili, found mainly on Gram-negative organisms, are composed of subunits of a protein, pilin, and mediate the adhesion of bacteria to receptors on the human cell surface – a necessary first step in the initiation of infection. A specialized type of pilus, the sex pilus, forms the attachment between the male (donor) and the female (recipient) bacteria during conjugation, when genes ar/>