CHAPTER 4: MICROBIAL DIVERSITY

- ACELLULAR MICROBES

Viruses

 Complete virus particles, called virions, are very small and simple in structure.
 Viruses are extremely small. They are observed using electron microscopes.
 Viruses are not alive. To replicate, viruses must invade live host cells.
 The vast majority of viruses possess either DNA or RNA, unlike living cells, which possess both.
 They are unable to replicate (multiply) on their own; their replication is directed by the viral nucleic acid once it
has been introduced into a host cell.
 Unlike cells, they do not divide by binary fission, mitosis, or meiosis.
 They lack the genes and enzymes necessary for energy production.
 They depend on the ribosomes, enzymes, and metabolites (“building blocks”) of the host cell for protein and
nucleic acid production.
 The simplest of human viruses consists of nothing more than nucleic acid surrounded by a protein coat (the
capsid). The capsid plus the enclosed nucleic acid are referred to as the nucleocapsid.

Origin of Viruses

 Because they are not composed of cells, viruses are not considered to be living organisms. They are referred
to as acellular microbes or infectious particles.

Bacteriophages

 The viruses that infect bacteria are known as bacteriophages

 Three categories of bacteriophages, based on their shape:
1. Icosahedron bacteriophages: an almost spherical shape, with 20 triangular facets; the smallest
icosahedron phages are about 25 nm in diameter.
2. Filamentous bacteriophages: long tubes formed by capsid proteins assembled into a helical structure;
they can be up to about 900 nm lon
  Complex bacteriophages: icosahedral heads attached to helical tails; may also possess base plates and tail
fibers

Virulent bacteriophages

 Virulent bacteriophages always cause what is known as the lytic cycle, which ends with the destruction (lysis)
of the bacterial cell.
 Bacteriophages can only attach to bacteria that possess surface molecules (receptors) that can be recognized
by molecules on the phage surface.

Steps in Lytic Cycle

1. Attachment (Adsorption)
 The first step in the lytic cycle is attachment (adsorption) of the phage to the surface of the
bacterial cell.
 A protein or polysaccharide molecule on the surface of the cell that is recognized by a molecule
on the surface of the phage.

2. Penetration
 The phage injects its DNA into the bacterial cell, acting much like a hypodermic needle.
 The phage DNA “dictates” what occurs within the bacterial cell.

3. Biosynthesis
 The phage genes are expressed, resulting in the production (biosynthesis) of viral pieces.
 It is also during this step that the host cell’s enzymes (e.g., DNA polymerase and RNA
polymerase), nucleotides, amino acids, and ribosomes are used to make viral DNA and viral
proteins.

4. Assembly
 The viral pieces are assembled to produce complete viral particles (virions).
 It is during this step that viral DNA is packaged up into capsids.

5. Release
 The host cell bursts open and all of the new virions escape from the cell. Thus, the lytic cycle
ends with lysis of the host cell. Lysis is caused by an enzyme that is coded for by a phage gene

Temperate bacteriophages

 Other category of bacteriophages

 Do not immediately initiate the lytic cycle, but rather, their DNA remains integrated into the bacterial
cell chromosome, generation after generation.

Conversion and Transduction

 Two of the four major ways in which bacteria acquire new genetic information.

Animal Viruses

 Viruses that infect humans and animals are collectively referred to as animal viruses.
 Like bacteriophages, animal viruses can only attach to and invade cells bearing appropriate surface receptors.

Steps in the Multiplication of Animal Viruses

1. Attachment (adsorption)
The virus attaches to a protein or polysaccharide molecule (receptor) on the surface of a host cell

2. Penetration
The entire virus enters the host cell, in some cases because it was phagocytized by the cell

3. Uncoating
The viral nucleic acid escapes from the capsid

4. Biosynthesis
 Viral genes are expressed, resulting in the production of pieces or parts of viruses (i.e., viral DNA and viral
proteins)

5. Assembly
The viral pieces or parts are assembled to create complete virions

6. Release
The complete virions escape from the host cell by lysis or budding

Latent Virus Infections

 Herpes virus infections, such as cold sores (fever blisters), are good examples of latent virus infections.
 Latent viral infections are usually limited by the defense systems of the human body—phagocytes and
antiviral proteins called interferons that are produced by virusinfected cells
Ex. Shingles

Antiviral Agents

 Developed to interfere with virus-specific enzymes and virus production by either disrupting critical phases in
viral cycles or inhibiting the synthesis of viral DNA, RNA, or proteins.

Oncogenic Viruses

 Viruses that cause cancer are called oncogenic viruses or oncoviruse

 The first evidence that viruses cause cancers came from experiments with chickens.
Ex. Eipstein-Barr virus, Human Herpesvirus 8, Hepatitis B and C, Human Papillomavirus, T-cell lymphotrophic
Virus (HTLV-1)

Human Immunodeficiency Virus

 AIDS is caused by a single-stranded RNA virus known as human immunodeficiency virus (HIV).
 It is a member of a genus of viruses called lentiviruses, in a family of viruses called Retroviridae (retroviruses).
 HIV is able to attach to and invade cells bearing receptors that the virus recognizes. The most important of
these receptors is designated CD4, and cells possessing that receptor are called CD4 cells.

Mimivirus

 An extremely large double-stranded DNA virus, called Mimivirus, has been recovered from amebas.
 The virus was given the name Mimivirus because it “mimics” bacteria.
 Mimivirus contains several genes for sugar, lipid, and amino acid metabolism. And, unlike most DNA viruses,
Mimivirus contains some RNA molecules.

Plant Viruses

 Plant viruses are usually transmitted via insects (e.g., aphids, leaf hoppers, whiteflies); mites; nematodes
(round worms); infected seeds, cuttings, and tubers; and contaminated tools (e.g., hoes, clippers, and saws)

Viroids and Prions

 Viroids are infectious RNA molecules that cause a variety of plant diseases.

Prions
o Prions are infectious protein molecules that cause a variety of animal and human diseases.
Ex. Scrapie (sheep and goats, bovine spongiform encephalopathy; and kuru, Creutzfeldt-Jakob (C-J) disease,
Gerstmann-Sträussler-Scheinker (GSS) disease, and fatal familial insomnia.

Beware of Similar Sounding Terms

 A virion is a complete viral particle (i.e., one that has all its parts, including nucleic acid and a capsid). A viroid
is an infectious RNA molecule

THE DOMAIN BACTERIA (characteristics)

  According to Bergey’s Manual, the Domain Bacteria contains 23 phyla, 32 classes, 5 subclasses, 77 orders,
14 suborders, 182 families, 871 genera, and 5,007 species
 Organisms in this domain are broadly divided into three phenotypic categories:

(a) those that are Gram-negative and have a cell wall

(b) those that are Gram-positive and have a cell wall,
(c) those that lack a cell wall.

 A bacterium’s Gram reaction (Gram-positive or Gram-negative), basic cell shape, and morphological
arrangement of the cells are very important clues to the organism’s identification.

Cell Morphology

 The three general shapes of bacteria are round (cocci), rod-shaped (bacilli), and spiral-shaped.
 Bacteria reproduce by binary fission. The time it takes for one bacterial cell to split into two cells is referred to
as that organism’s generation time.

 Pairs of cocci are known as diplococci. Chains of cocci are known as streptococci. Clusters of cocci are
known as staphylococci.
Ex. Enterococcus spp., Neisseria spp., Staphylococcus spp., and Streptococcus spp.

Bacterial Names Sometimes Provide a Clue to Their Shape

 If “coccus” appears in the name of a bacterium, you automatically know the shape of the organism—spherical.
Ex. Enterococcus, Peptococcus, Peptostreptococcus, Staphylococcus, and Streptococcus.

 If “bacillus” appears in the name of a bacterium, you automatically know the shape of the organism—rod-
shaped or rectangular.
Ex. Actinobacillus, Bacillus, Lactobacillus, and Streptobacillus

Bacilli

 Bacilli (often referred to as rods) may be short or long, thick or thin, and pointed or with curved or blunt ends.
Ex. Enterobacteriaceae (e.g., Enterobacter, Escherichia, Klebsiella, Proteus, Salmonella, and Shigella spp.),
Pseudomonas aeruginosa, Bacillus spp., and Clostridium spp.

 Diplobacilli - They may occur singly, in pairs

 Streptobacilli - in chains, in long filaments, or branched.
 Coccobacilli - Some rods are quite short, resembling elongated cocci.
Ex. Listeria monocytogenes and Haemophilus influenza

 A bacterial species having cells of different shapes is said to be pleomorphic.

Staining Procedures

 In preparation for staining, the bacteria are smeared onto a glass microscope slide (resulting in what is known
as a “smear”), air-dried, and then “fixed.”
Two most common methods of fixation:

1. Heat fixation - is usually accomplished by passing the smear through a Bunsen burner flame
2. Methanol fixation - is accomplished by flooding the smear with absolute methanol for 30 seconds

Fixation serves 3 purposes:

1. It kills the organisms.

2. It preserves their morphology (shape).
3. It anchors the smear to the slide.

If a bacterium is blue to purple at the end of the Gram staining procedure, it is said to be Gram-positive. If, on the
other hand, it ends up being pink to red, it is said to be Gram-negative.
 Gram –Positive Gram –
Bacteria Negative
Bacteria
Color at the end of Blue-to-purple Pink-to-red
the Gram staining
procedure
Peptidoglycan in Thick layer Thin layer
cell walls
Teichoic acids and Present Absent
lipoteichoic acids
in cell walls
Lipopolysaccharide Absent Present
in cell walls

 Mycobacterium species are more often identified using a staining procedure called the acid-fast stain.
 A decolorizing agent (a mixture of acid and alcohol) is then used in an attempt to remove the red color from
the cells.
 The Gram and acid-fast staining procedures are referred to as differential staining procedures because they
enable microbiologists to differentiate one group of bacteria from another (i.e., Gram-positive bacteria from
Gram-negative bacteria, and acid-fast bacteria from non–acid-fast bacteria).

Motility

 If a bacterium is able to “swim,” it is said to be motile. Bacteria unable to swim are said to be nonmotile.
 Most spiral-shaped bacteria and about one half of the bacilli are motile by means of flagella, but cocci are
generally nonmotile
 Monotrichous, amphitrichous, lophotrichous, peritrichous - are used to describe the number and location of
flagella on bacterial cells
 Nonmotile organisms will grow only along the stab line (thus, turbidity will be seen only along the stab line),
but motile organisms will spread away from the stab line (thus, producing turbidity throughout the medium)

Colony Morphology

 A mound or pile of bacteria on a solid culture medium is known as a bacterial colony.

Atmospheric Requirements

 Obligate aerobes and microaerophiles require oxygen. Obligate aerobes require an atmosphere containing
about 20% to 21% oxygen, whereas microaerophiles require reduced oxygen concentrations (usually around
5% oxygen).
  Anaerobes - can be defined as organisms that do not require oxygen for life and reproduction
 Obligate anaerobe - is an anaerobe that can only grow in an anaerobic environment (i.e., an environment
containing no oxygen
 Aerotolerant anaerobe - does not require oxygen, grows better in the absence of oxygen, but can survive in
atmospheres containing molecular oxygen (such as air and a CO2 incubator)
 Facultative anaerobes are capable of surviving in either the presence or absence of oxygen; anywhere from
0% O2 to 20% to 21% O2
 Capnophiles (capnophilic organisms), grow better in the laboratory in the presence of increased
concentrations of CO2.

Nutritional Requirements

 All bacteria need some form of the elements carbon, hydrogen, oxygen, sulfur, phosphorus, and nitrogen for
growth. Special elements, such as potassium, calcium, iron, manganese, magnesium, cobalt, copper, zinc,
and uranium, are required by some bacteria.

Biochemical and Metabolic Activities

  To aid in the identification of certain types of bacteria in the laboratory, they are inoculated into various
substrates (e.g., carbohydrates and amino acids) to determine whether they possess the enzymes necessary
to break down those substrates

Pathogenicity

 Pathogens are able to cause disease because they possess capsules, pili, or endotoxins (biochemical
components of the cell walls of Gram-negative bacteria), or because they secrete exotoxins and exoenzymes
that damage cells and tissues

Genetic Composition

 A DNA probe is a single-stranded DNA sequence that can be used to identify an organism by hybridizing with
a unique complimentary sequence on the DNA or rRNA of that organism.

UNIQUE BACTERIA

 Rickettsias, chlamydias, and mycoplasmas are bacteria, but they do not possess all the attributes of typical
bacterial cells. Thus, they are often referred to as “unique” or “rudimentary” bacteria.
 Rickettsias and chlamydias are bacteria with a Gram negative–type cell wall.

Rickettsia

 Vitamin D deficiency
 Caused by arthropod-borne
 Diseases caused are typhus and typhuslike diseases

Closely related to rickets

Coxiella burnetii, Bartonella quintana (formerly Rochalimaea quintana), Ehrlichia spp., and Anaplasma spp. C. burnetii

Mycoplasma

 Smallest of the cellular microbes

 Because they do not possess cell walls, Mycoplasma spp. are pleomorphic
 Beware of Similar Sounding Names Do not confuse Mycoplasma with Mycobacterium. Each is a genus of
bacteria. The unique thing about Mycoplasma spp. is that they lack cell walls. The unique thing about
Mycobacterium spp. is that they are acidfast

Especially Large and Especially Small Bacteria

Thiomargarita namibiensis

 Largest of all bacteria

 A colorless, marine, sulfide-oxidizing bacterium

Beggiatoa and Thioploca

 Marine, sulfide-oxidizing bacterium

 Form filaments

Epulopiscium fishelsonii

 Isolated from the intestines of the reef surgeonfish

Nanobacteria

 Tiny bacteria
 Found in soil, minerals, ocean water, human and animal blood, human dental calculus (plaque), arterial
plaque, and even rocks (meteorites)

Photosynthetic Bacteria

 Photosynthetic bacteria are bacteria capable of converting light energy into chemical energy. Cyanobacteria
are examples of photosynthetic bacteria
THE DOMAIN ARCHAEA

 Archae means “ancient,”

 Domain Archaea contains 2 phyla, 8 classes, 12 orders, 21 families, 69 genera, and 217 species
 Many archaea are extremophiles, meaning that they live in extreme environments; e.g., environments that are
extremely hot, dry, or salty.