MICRO PARASITOLOGY
NOTES
Name: Aliah Jehann P. Madzaman Date: 05-08-2024
Teacher: Maria Lorraine Escalante Year&block: BSN1 Block B Section: BIO
100
DIVERSITY OF MICROBES
Imagine the excitement that Anton van Leeuwenhoek experienced as he gazed through
his tiny glass lenses and became the first person to see live microbes. In the years that have
followed his eloquently written late 17th to early 18th century accounts of the bacteria and
protozoa that he observed, tens of thousands of microbes have been discovered, described, and
classified. In this chapter and the next, you will be introduced to the diversity of form and
function that exists in the microbial world. As you will recall, microbiology is the study of
microbes, which are too small to be seen by the naked eye. Microbes can be divided into those
that are truly cellular (bacteria, archaea, algae, protozoa, and fungi) and those that are acellular
(viruses, viroid’s, and prions). The cellular microorganisms can be subdivided into those that
are procaryotic (bacteria and archaea) and those that are eucaryotic (algae, protozoa, and fungi).
For a variety of reasons, acellular microorganisms are not considered by most scientists to be
living organisms. Thus, rather than using the term microorganisms to describe them, viruses,
viroid’s, and prions are more correctly referred to as acellular microbes or infectious particles.
ACELLULAR MICROBES VIRUSES
Complete virus particles, called virions, are very small and simple in structure. Most viruses
range in size from 10 to 300 nm in diameter, although some— like Ebola virus—can be up to 1
m in length. The smallest virus is about the size of the large hemoglobin molecule of a red blood
cell. Scientists were unable to see viruses until electron microscopes were invented in the 1930s.
The first photographs of viruses were obtained in 1940. A negative staining procedure,
developed in 1959, revolutionized the study of viruses, making it possible to observe unstained
viruses against an electron-dense, dark background No type of organism is safe from viral
infections; viruses infect humans, animals, plants, fungi, protozoa, algae, and bacterial cells.
Viruses are extremely small. They are observed using electron microscopes.
Viruses are not alive. To replicate, viruses must invade live host cells.
Origin of Viruses
Where did viruses come from? Two main theories have been proposed to explain the origin of
viruses. One theory states that viruses existed before cells, but this seems unlikely in view of the
fact that viruses require cells for their replication. The other theory states that cells came first
and that viruses represent ancient derivatives of degenerate cells or cell fragments. The question
of whether viruses are alive depends on one’s definition of life and, thus, is not an easy question
to answer. However, most scientists agree that viruses lack most of the basic features of cells;
thus, they consider viruses to be nonliving entities.
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 (or simply,
phages). Like all viruses, they are obligate intracellular pathogens, in that they must enter a
bacterial cell to replicate. There are three categories of bacteriophages, based on their shape:
Icosahedron bacteriophages: an almost spherical shape, with 20 triangular facets; the
smallest icosahedron phages are about 25 nm in diameter.
Filamentous bacteriophages: long tubes formed by capsid proteins assembled into a
helical structure; they can be up to about 900 nm long. In addition to shape,
bacteriophages can be categorized by the type of nucleic acid that they possess; there are
single-stranded DNA phages, double-stranded DNA phages, single-stranded RNA
phages, and double stranded RNA phages. From this point, only DNA phages will be
discussed
Virulent bacteriophages always cause what is known as the lytic cycle, which ends with the
destruction (lysis) of the bacterial cell. For most phages, the whole process (from attachment to
lysis) takes less than 1 hour.
Once it enters a host cell, a virulent bacteriophage always initiates the lytic cycle, which results in the
destruction of the cell.
The first step in the lytic cycle is attachment (adsorption) of the phage to the surface of
the bacterial cell. The phage can only attach to bacterial cells that possess the appropriate
receptor—a protein or polysaccharide molecule on the surface of the cell that is recognized by a
molecule on the surface of the phage. Most bacteriophages are species- and strain-specific,
meaning that they only infect a particular species or strain of bacteria. Those that infect
Escherichia coli are called coliphages. Some bacteriophages can attach to more than one species
of bacterium.
The second step in the lytic cycle is called penetration. In this step, the phage injects its
DNA into the bacterial cell, acting much like a hypodermic needle (Fig. 4-8). From this point on,
the phage DNA “dictates” what occurs within the bacterial cell. This is sometimes described as
the phage DNA taking over the host cell’s “machinery.” The third step in the lytic cycle is called
biosynthesis. It is during this step that 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. In the fourth step of the lytic cycle, called 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.
The final step in the lytic cycle, called release, is when the host cell bursts open and all of
the new virions the virus introduces its genome into a host cell and initiates replication by
hijacking the host's cellular machinery to make new copies of the virus. Once infection is
complete, the newly replicated and assembled virus particles are released through lysis of the
host cell into the surrounding waters.
Steps in the Multiplication of Bacteriophages (Lytic Cycle)
STEP NAME OF STEP WHAT OCCURS DURING THIS STEP
1. Attachment (adsorption) The phage attaches to a protein or polysaccharide molecule
(receptor) on the surface of the bacterial cell.
2. Penetration The phage injects its DNA into the bacterial cell; the capsid remains on the
outer surface of the cell.
3. Biosynthesis Phage genes are expressed, resulting in the production of phage pieces or
parts (i.e., phage DNA and phage proteins).
4. Assembly The phage pieces or parts are assembled to create complete phages 5 Release
The complete phages escape from the bacterial cell by lysis of the cell.
Animal Viruses
Viruses that infect humans and animals are collectively referred to as animal viruses.
Some animal viruses are DNA viruses; others are RNA viruses. Animal viruses may consist
solely of nucleic acid surrounded by a protein coat (capsid), or they may be more complex. For
example, they may be enveloped or they may contain enzymes that play a role in viral
multiplication within host cells.
The first step in the multiplication of animal viruses is attachment (or adsorption) of the
virus to the cell. Like bacteriophages, animal viruses can only attach to cells bearing. Like
bacteriophages, animal viruses can only attach to and invade cells bearing appropriate surface
receptors.
The second step in the multiplication of animal viruses is penetration, but, unlike
bacteriophages, the entire virion usually enters the host cell, sometimes because the cell
phagocytizes the virus. The second step in the multiplication of animal viruses is penetration,
but, unlike bacteriophages, the entire virion usually enters the host cell, sometimes because the
cell phagocytizes the virus. This necessitates a third step that was not required for
bacteriophages—uncoating—whereby the viral nucleic acid escapes from the capsid. As with
bacteriophages, from this point on, the viral nucleic acid “dictates” what occurs within the host
cell. The fourth step is biosynthesis, whereby many viral pieces (viral nucleic acid and viral
proteins) are produced.
This step can be quite complicated, depending on what type of virus infected the cell
(i.e., whether it was a single stranded DNA virus, a double-stranded DNA virus, a single-
stranded RNA virus, or a double stranded RNA virus). Some animal viruses do not initiate
biosynthesis right away, but rather, remain latent within the host cell for variable periods.
Latent viral infections are discussed in more detail in a subsequent section.
The fifth step—assembly— involves fitting the virus pieces together to produce
complete virions. After the virus particles are assembled, they must escape from the cell—a
sixth step called release. How they escape from the cell depends on the type of virus that it is.
Some animal viruses escape by destroying the host cell, leading to cell destruction and some of
the symptoms associated with infection with that particular virus. Other viruses escape the cell
by a process known as budding.
Plant Viruses
More than 1,000 different viruses cause plant diseases, including diseases of citrus trees,
cocoa trees, rice, barley, tobacco, turnips, cauliflower, potatoes, tomatoes, and many other fruits,
vegetables, trees, and grains. These diseases result in huge economic losses, estimated to be in
excess of $70 billion per year worldwide. 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).
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 (i.e., categories
based on their physical characteristics): (a) those that are Gram-negative and have a cell wall, (b)
those that are Gram-positive and have a cell wall, and (c) those that lack a cell wall. (The terms
Gram-positive and Gram-negative are explained in a subsequent section of this chapter.) Using
computers, microbiologists have established numerical taxonomy systems that not only help to
identify bacteria by their physical characteristics, but also can help establish how closely related
these organisms are by comparing the composition of their genetic material and other cellular
characteristics. (Note: as previously mentioned, throughout this book, the term “to identify an
organism” means to learn the organism’s species name [i.e., to speciate it].)
Many characteristics of bacteria are examined to provide data for identification and
classification. These characteristics include cell shape and morphological arrangement, staining
reactions, motility, colony morphology, atmospheric requirements, nutritional requirements, biochemical
and metabolic activities, specific enzymes that the organism produces, pathogenicity (the ability to cause
disease), and genetic composition.
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
With the compound light microscope, the size, shape, and morphologic arrangement of
various bacteria are easily observed. Bacteria vary greatly in size, usually ranging from spheres
measuring about 0.2 m in diameter to 10.0-m–long spiral-shaped bacteria, to even longer
filamentous bacteria. As previously mentioned, the average coccus is about 1 m in diameter,
and the average bacillus is about 1 m wide 3 m long. Some unusually large bacteria and
unusually small bacteria have also been discovered (discussed later).
There are three basic shapes of bacteria:
(a) round or spherical bacteria—the cocci (sing., coccus)
(b) rectangular or rod-shaped bacteria—the bacilli (sing., bacillus)
(c) curved and spiral-shaped bacteria (sometimes referred to as spirilla). 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.
Cocci may be seen singly or in pairs (diplococci), chains (streptococci), clusters (staphylococci),
packets of four (tetrads), or packets of eight (octads), depending on the particular species and
the manner in which the cells divide.
Bacilli (often referred to as rods) may be short or long, thick or thin, and pointed or with curved
or blunt ends. They may occur singly, in pairs (diplobacilli), in chains (streptobacilli), in long
filaments, or branched. Some rods are quite short, resembling elongated cocci; they are called
coccobacilli. Listeria monocytogenes and Haemophilus influenzae are examples of coccobacilli.
Some bacilli stack up next to each other, side by side in a palisade arrangement, which is
characteristic of Corynebacterium diphtheriae (the cause of diphtheria) and organisms that
resemble it in appearance (called diphtheroid). Examples of medically important bacilli include
members of the family Enterobacteriaceae (e.g., Enterobacter, Escherichia, Klebsiella, Proteus,
Salmonella, and Shigella spp.), Pseudomonas aeruginosa, Bacillus spp., and Clostridium spp.
Curved and spiral-shaped bacilli are placed into a third morphologic grouping. For example,
Vibrio spp., such as V. cholerae (the cause of cholera) and V. parahaemolyticus (a cause of
diarrhea), are curved (comma shaped) bacilli. Curved bacteria usually occur singly, but some
species may form pairs. A pair of curved bacilli.
Mycobacterium
Species are more often identified using a staining procedure called the acid-fast stain. In
this procedure, carbol fuchsin (a bright red dye) is first driven into the bacterial cell using heat
(usually by flooding the smear with carbol fuchsin, and then holding a Bunsen burner flame
under the slide until steaming of the carbol fuchsin occurs). The heat is necessary because the
cell walls of mycobacteria contain waxes, which prevent the stain from penetrating the cells.
The heat softens the waxes, enabling the stain to penetrate. A decolorizing agent (a mixture of
acid and alcohol) is then used in an attempt to remove the red color from the cells. Because
mycobacteria are not decolorized by the acid–alcohol mixture (again owing to the waxes in their
cell walls), they are said to be acid-fast.
Colony Morphology
A single bacterial cell that lands on the surface of a solid culture medium cannot be seen,
but after it divides over and over again, it produces a mound or pile of bacteria, known as a
bacterial colony . A colony contains millions of organisms. The colony morphology (appearance
of the colonies) of bacteria varies from one species to another. Colony morphology includes the
size, color, overall shape, elevation, and the appearance of the edge or margin of the colony. As
is true for cell morphology and staining characteristics, colony features serve as important
“clues” in the identification of bacteria. Size of colonies is determined by the organism’s rate of
growth (generation time), and is an important characteristic of a particular bacterial species.
Colony morphology also includes the results of enzymatic activity on various types of culture
media.
Anaerobes can be defined as organisms that do not require oxygen for life and
reproduction. However, they vary in their sensitivity to oxygen. The terms obligate anaerobe,
aerotolerant anaerobe, and facultative anaerobe are used to describe the organism’s relationship
to molecular oxygen. An obligate anaerobe is an anaerobe that can only grow in an anaerobic
environment (i.e., an environment containing no oxygen) (see “Insight: Life in the Absence of
Oxygen” on the CD-ROM ).
An 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). The
concentration of oxygen that an aerotolerant anaerobe can tolerate varies from one species to
another. Facultative anaerobes are capable of surviving in either the presence or absence of
oxygen; anywhere from 0% O2 to 20% to 21% O2. Many of the bacteria routinely isolated from
clinical specimens are facultative anaerobes (e.g., members of the family Enterobacteriaceae,
most streptococci, most staphylococci). Room air contains less than 1% CO2. Some bacteria,
referred to as capnophiles (capnophilic organisms), grow better in the laboratory in the presence
of increased concentrations of CO2. Some anaerobes (e.g., Bacteroides and Fusobacterium
species) are capnophiles, as are some aerobes (e.g., certain Neisseria, Campylobacter, and
Haemophilus species). In the clinical microbiology laboratory, CO2 incubators are routinely
calibrated to contain between 5% and 10% CO2.
Obligate anaerobes, aerotolerant anaerobes, and facultative anaerobes can thrive in an
atmosphere devoid of oxygen
Pathogenicity
The characteristics that enable bacteria to cause disease are discussed in Chapter 14.
Many 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. Frequently, pathogenicity (the ability
to cause disease) is tested by injecting the organism into mice or cell cultures.
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. Because they are so small and difficult to isolate, they were formerly
thought to be viruses.
