2.1: The Bacteria - An Introduction

Bacteria evolved some 600 million years ago, and were probably responsible for the production of the earth's atmosphere (cyanobacteria). Bacteria were discovered in the 17^th century after the development of the microscope.

• Single cell organism
• Widely dispersed in the environment
• Invisible to naked eye, but discernible by their actions - milk sours, wounds become septic, meat putrefies, etc.
• Prokaryotic type cells (other organisms are eukaryotic type cells)

Major differences between prokaryotic and eukaryotic cells

Prokaryotic cells	Eukaryotic cells
No nuclear membrane: chromosome(s) in direct contact with cytoplasm	Chromosomes are enclosed in a double layered nuclear membrane
Simple chromosome structure	Complex chromosome structure; DNA associated with histone proteins
Cell division does not involve meiosis	Cell division involves mitosis and meiosis
If present, cell walls contain peptidoglycan, no cellulose or chitin	If present, cell walls contain cellulose or chitin, never peptidoglycan
No mitochondria or chloroplasts	Mitochondria usually present, chloroplasts in photosynthetic cells
Cells contain ribosomes of only one size	Cells contains two types of ribosomes, one in cytoplasm, and smaller type in mitochondria
Flagella, if present, have a simple structure	Flagella, if present, have complex structure

Note: bacteria are microorganisms, but not all microorganisms are bacteria. Algae, fungi, lichens, protozoa, viruses and subviral agents are all microorganisms (with most of these being eukaryotic type cells

Bacterial activities

Pathogenic (disease causing) bacteria:

• Cholera (vomiting, profuse diarrhea)
• Botulism (muscle paralysis)
• Tetanus (uncontrollable contractions of skeletal muscle)
• Staphylococcal food poisoning (vomiting, diarrhea)
• Shiga toxin (verotoxin) (classic dysentery)
• Typhoid (septicemia: bacteria in blood, destruction of host tissue)
• Oroya fever (Bartonella bacilliformis - destroys red blood cells)
• Endotoxic shock (lipopolysaccharide cell wall component causes release of host inflammatory agents leading to shock and death)
• Reactive arthritis (response in some people to Salmonella infection)

Most bacteria do no harm to humans, and can be quite useful:

• Antibiotic production
• Enzyme additives for detergents
• Insecticides
• Production of biodegradable plastics
• "Biomining" - leaching of metals from low grade ores
• Uses in food industry
  • Butter
  • Cheese
  • Yogurt
  • Vinegar
  • Cocoa
  • Coffee
• Soil fertility

Classifying and Naming of bacteria

Differences between bacteria can include

• shape
• size
• structure
• chemical activities
• required nutrients
• form of energy required
• required environment
• reaction to certain dyes

Family, genus, species, strain

Bacteria in the same Family, in general would have:

• similar structure
• use the same form of energy
• react similarly to certain dyes

Bacteria in the same Family may be divided into different Genera based on differences in

• chemical activities
• nutrient requirements
• conditions for growth
• shape and size (to some extent)

Strains of bacteria are bacteria of the same species, but with some subtle difference (maybe a single mutational difference)

Latin binomial name

• Name of the genus, capitalized.
• Followed by name of species, lower case
• Italicized. Sometimes the genus name is abbreviated to a single letter (with a period)

Escherichia coli E. coli

• Strain name follows, usually in parentheses. In the vernacular, the strain name is commonly used to identify the bacteria

E. coli (JM101) E. coli (CJ236) "Can I borrow some JM101?"

Some Characteristics of Bacteria

Shape

• Rounded or spherical cells - cocci (singular: coccus)
• Elongated or rod-shaped cells - bacilli (singular: bacillus)
• Rigid spirals - spirilla (singular: spirillum)
• Flexible spirals - spirochetes (singular: spirochete)

Note

There is a genus of bacteria called Bacillus. Some bacillus shaped bacteria belong to the genus Bacillus, some do not.

Size

• Bacteria are usually measured in micrometers (1x10^-6 m)
• The smallest bacteria are about 0.2 micrometers (Chlamydia)
• The largest bacteria are about 600 micrometers (Epulopiscium fishelsoni. - inhabits the gut of a fish)
• "Average" bacteria are 1-10 micrometers (note: limit of resolution of the light microscope is about 0.2 micrometers)

A "generalized" bacterium:

Figure 2.1.1: General bacterium diagram

• The cell's DNA is extensively folded to form a body called the nucleoid
• The cytoplasm fills the interior of the cells, and bathes the nucleoid
• Storage granules contain a reserve of nutrients - typically polymeric forms of b-hydroxybutyrate and phosphate. Poly-b-hydroxybutyrate is the basis of a biodegradable plastic (Biopol)

Figure 2.1.2: Poly-b-hydroxybutyrate

• The nucleoid, ribosomes, cytoplasm and storage granules are bounded by a membranous sac, the cytoplasmic membrane (cell membrane, or plasma membrane)
• The outermost layer is a tough cell wall. Together, the plasma membrane and cell wall are called the cell envelope
• The region between the plasma membrane and the cell wall is called the periplasmic space
• The flagellum is used for motility

Cytoplasmic membrane

• lipid bilayer, 7-8 nm thick, with protein molecules partly or completely embedded
• The inner and outer layers are hydrophilic, while the interior of the bilayer is hydrophobic
• In E. coli the main lipid is phosphatidylethanolamine; minor lipid components include phosphatidylglycerol and diphosphatidylglycerol

Figure 2.1.3: Phospholipid bilayer

The cytoplasmic membrane proteins include:

• enzymes involved in the synthesis of the cell wall peptidoglycan
• transport proteins (translocated ions and molecules across the cytoplasmic membrane
• proteins of energy converting systems (ATPases and electron transport chains)
• "sensory" proteins, which detect changes in cell's external environment

The cytoplasmic membrane is not freely permeable to most molecules

• some small uncharged molecules (O₂, CO₂, NH₃, H₂O) can freely pass through
• charged ions typically cannot pass across the membrane, and must be transported (with the expenditure of energy)

If the cell wall is removed, what remains of the cell is called the protoplast

• can survive (in a test tube) and carry out most normal cell processes
• quite sensitive to osmotic shock - if placed in pure water it will swell (as water enters the cell to balance the osmotic force) and rupture (osmotic lysis)
• In an intact cell the cell wall prevents the protoplast from swelling and undergoing osmotic lysis
• The cell wall also determines the shape of the bacteria - all protplasts are spherical, regardless of the shape of the intact bacteria

The Cell Wall

Among the Eubacteria (Kingdom of all bacteria excluding the archebacteria, which are typically halophiles and thermophiles) there are only two major types of cell wall

• They can be identified by their reaction to certain dyes (characterized by Christian Gram in 1880's):

Figure 2.1.4: Gram positive and Gram negative bacteria

Gram positive type cell wall

• relatively thick (30-100 nm)
• 40-80% of the wall is made of a tough complex polymer called peptidoglycan (linear heteropolysaccharide chains cross-linked by short peptides)

Figure 2.1.5: Gram positive cell wall

• The cell wall of a gram-positive cell is a multi-layed network which appears to be continually growing by the addition of new peptidoglycan at the inner face, with concommitant loss at the outer surface

Gram-negative type cell wall (e.g. E. coli)

• thinner than gram-positive type cell wall (only 20-30 nm thick)
• has distinctly layered appearance
• inner region consists of a monolayer of peptidoglycan
• outer layer of cell wall is essentially a protein containing lipid bilayer
  • inward facing lipids are phospholipids
  • outward facing lipids are macromolecules called lipopolysaccharides

Figure 2.1.6: Gram negative cell wall

• half the mass of the outer membrane consists of proteins
  • the Braun protein, which is covalently linked to the peptidoglycan layer
  • transport proteins
  • porins - molecules which span the outer membrane to create a 'pore' through the membrane. These pores allow certain molecules and ions to pass through the outer membrane (e.g. ompC, ompF proteins)
• adjacent outer lipopolysaccharides are held together by electrostatic interactions with divalent metal ions (Ca²⁺, Mg²⁺)
  • the addition of chelating agents (e.g. EDTA) can disrupt these interactions and weaken the outer membrane
• lysozyme (produced by phage lambda, for example) can cleave the saccharide links in the inner peptidoglycan layer

How to lyse a gram-negative bacteria (e.g. E. coli):

1. Add a chelating agent of divalent metals (e.g. EDTA) to disrupt outer membrane lipopolysaccharides
2. Add lysozyme to break up peptidoglycan layer
3. cell wall is now structurally weakened and cannot protect the protoplast from osmotic shock
4. osmotically shock the cell to disrupt protoplast and release cytoplasmic contents (i.e. high osmotic shock using sucrose solution; low osmotic shock using pure water),
5. or use mechanical shear/cavitation (French Press, Menton Gaulin press)

Human microflora: some of the bacteria commonly associated with the human body

Location	Genus
Colon	Bacteroides, Clostridium, Escherichia, Proteus
Ear	Corynebacterium, Mycobacterium, Staphylococcus
Mouth	Actinomyces, Bacteriodes, Streptococcus
Nasal passages	Corynebacterium, Staphylococcus
Nasopharynx	Streptococcus, Haemophilus (e.g. H. influenzae)
Skin	Propionibacterium, Staphylococcus, Others (personal hygiene, environment)
Urethra	Acinetobacter, Escherichia, Staphylococcus
Vagina (adult, pre-menopausal)	Acinetobacter, Corynebacterium, Lactobacillus, Staphylococcus