Let’s Learn

This module was designed and written with you in mind. It is here to help you
appreciate Biotechnology. The scope of this module permits it to be used in many
different learning situations. The language used recognizes the diverse vocabulary
level of students. The lessons are arranged to follow the standard sequence of the
course. But the order in which you read them can be changed to correspond with
the textbook you are now using.

The module covers

• Lesson 7 – Microorganisms
❖ Pathogen, Non-Pathogen and Opportunistic Pathogen
❖ Importance of Microorganisms
❖ Commonly Used Microbes
➢ Fungi
➢ Bacteria
➢ Virus

After going through this module, you are expected to:

1. define microbiology, pathogen, nonpathogen and opportunistic pathogen;
2. list several reasons why microorganisms are important; and
3. identify commonly used microbes in biotechnology.

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 Module
Lesson 7
4 Microorganisms

Germs. Likely, your mother was your first microbiology instructor. Not only did she
alert you to the fact that there were “invisible” critters in the world that could harm
you, she also taught you the fundamentals of hygiene – like handwashing (Burton,
2007).

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 Let’s Recall

What is Microbiology?

Biology is the study of living organisms (from bios, referring to living organisms,
and logy, meaning “the study of”). Micro means very small - anything so small that it
must be viewed with a microscope. Therefore, microbiology is the study of very
small living organisms – organisms called microorganisms or microbes (Burton,
2007).

The various categories of microorganisms include viruses, bacteria, archaeans,

some algae, protozoa, and some fungi. Because most scientists do not consider
viruses to be living organisms, they are often referred to as “infectious agents” or
“infectious particles”, rather than microorganisms (Burton, 2007).

Disease-causing microorganisms are technically known as pathogens. Only 3%

of known microbes are capable of causing disease (only about 3% are pathogenic).
The vast majority of known microorganisms are nonpathogens – microorganisms
that do not cause disease. Some of nonpathogens are beneficial to us and some have
no effect on us at all (Burton, 2007).

Why Study Microbiology?

Although they are very small, microorganisms play significant roles in our
lives. Listed below are a few of the many reasons to learn about microorganisms.

❖ We have, living on and in our bodies (e.g., on our skin and in our
mouths and intestinal tract), approximately 10 times as many
microorganisms as the total number of cells that make up our bodies.
Collectively, these microbes are known as our indigenous microflora
and for the most part, they are beneficial to us.
❖ Some of the organisms that colonize (inhabit) our bodies are known as
opportunistic pathogens. Although such organisms do not usually
cause us any problems, they have the potential to cause infections if
they gain access to a part of our anatomy where they do not belong.
Opportunistic pathogens can be thought of as microorganisms awaiting
the opportunity to cause disease.
❖ Microorganisms are essential for life on this planet as we know it
because microorganisms contribute more oxygen to atmosphere than
do plants.
❖ Many microorganisms are involved in the decomposition of dead
organisms and the waste products of living organisms. They are
referred to as decomposers or saprophytes. A saprophyte is an
organism that lives on dead or decaying organic matter. Saprophytes

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 aid in fertilization by returning inorganic nutrients to the soil.

❖ Many microorganisms are essential in various food and beverage

industries, whereas others are used to produce certain enzymes and
chemicals. The use of microorganisms in industry is called
biotechnology.
❖ Some bacteria and fungi produce antibiotics that are used to treat
patients with infectious diseases. An antibiotic is a substance
produced by a microorganism that is effective in killing or inhibiting the
growth of other microorganisms. The use of microbes in the antibiotic
industry is another example of biotechnology.
❖ Microbes are essential in the field of genetic engineering.

Bacteria

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); and (c) curved and spiral-shaped bacteria (sometimes referred to as
spirilla).

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 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.

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. Spiral-
shaped bacteria are referred to as spirochetes. Different species of spirochetes
vary in size, length, rigidity, and the number and amplitude of their coils.

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Fungi

Fungi are found almost everywhere on earth; some (the saprophytic fungi)
living on organic matter in water and soil, and others (the parasitic fungi) living on
and within animals and plants. Some are harmful, whereas others are beneficial.
Fungi also live on many unlikely materials, causing deterioration of leather and
plastics and spoilage of jams, pickles, and many other foods. Beneficial fungi are
important in the production of cheeses, beer, wine, and other foods, as well as certain
drugs (e.g., the immunosuppressant drug cyclosporine) and antibiotics (e.g.,
penicillin).

Although many fungi are unicellular (e.g., yeasts), others grow as filaments
called hyphae (sing., hypha), which intertwine to form a mass called a mycelium (pl.,
mycelia) or thallus; thus, they are quite different from bacteria, which are always
unicellular. Also remember that bacteria are procaryotic, whereas fungi are
eucaryotic. Some fungi have septate hyphae (meaning that the cytoplasm within the
hypha is divided into cells by cross-walls or septa), whereas others have aseptate
hyphae (the cytoplasm within the hypha is not divided into cells; no septa). Aseptate

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hyphae contain multinucleated cytoplasm (described as being coenocytic). Learning
whether the fungus possesses septate or aseptate hyphae is an important “clue”
when attempting to identify a fungus that has been isolated from a clinical specimen.

Microscopic appearance of various fungi. (A) Aspergillus fumigatus. (B)

Aspergillus flavus. (C) Penicillium sp. (D) Curvularia sp. (E) Scopulariopsis sp. (F)
Histoplasma capsulatum. (From Winn WC Jr, et al. Koneman’s Color Atlas and
Textbook of Diagnostic Microbiology, 6th ed. Philadelphia: Lippincott Williams &
Wilkins, 2006.)

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Virus

A virus is a tiny, infectious particle that can reproduce only by infecting a

host cell. Viruses "commandeer" the host cell and use its resources to make more
viruses, basically reprogramming it to become a virus factory. Because they can't
reproduce by themselves (without a host), viruses are not considered living. Nor do
viruses have cells: they're very small, much smaller than the cells of living things,
and are basically just packages of nucleic acid and protein.

Still, viruses have some important features in common with cell-based life.
For instance, they have nucleic acid genomes based on the same genetic code that's
used in your cells (and the cells of all living creatures). Also, like cell-based life,
viruses have genetic variation and can evolve. So, even though they don't meet the
definition of life, viruses seem to be in a "questionable" zone.

How are viruses different from bacteria?

Even though they can both make us sick, bacteria and viruses are very
different at the biological level. Bacteria are small and single-celled, but they are
living organisms that do not depend on a host cell to reproduce. Because of these
differences, bacterial and viral infections are treated very differently. For instance,
antibiotics are only helpful against bacteria, not viruses.

The structure of a virus

There are a lot of different viruses in the world. So, viruses vary a ton in
their sizes, shapes, and life cycles. If you're curious just how much, I recommend
playing around with the ViralZone website. Click on a few virus names at random,
and see what bizarre shapes and features you find!

Viruses do, however, have a few key features in common. These include:

➢ A protective protein
shell, or capsid
➢ A nucleic acid
genome made of
DNA or RNA, tucked
inside of the capsid
➢ A layer of membrane
called the envelope
(some but not all
viruses)

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Virus capsids

The capsid, or protein shell, of a virus is made up of many protein molecules

(not just one big, hollow one). The proteins join to make units called capsomers,
which together make up the capsid. Capsid proteins are always encoded by the virus
genome, meaning that it’s the virus (not the host cell) that provides instructions for
making them.

Capsids come in many forms, but they often take one of the following shapes
(or a variation of these shapes):

1. Icosahedral – Icosahedral capsids have twenty faces and are named after
the twenty-sided shape called an icosahedron.
2. Filamentous – Filamentous capsids are named after their linear, thin,
thread-like appearance. They may also be called rod-shaped or helical.
3. Head-tail –These capsids are kind of a hybrid between the filamentous and
icosahedral shapes. They basically consist of an icosahedral head attached
to a filamentous tail.

Virus envelopes

In addition to the capsid, some viruses also have

an external lipid membrane known as an envelope,
which surrounds the entire capsid.

Viruses with envelopes do not provide

instructions for the envelope lipids. Instead, they
"borrow" a patch from the host membranes on their way
out of the cell. Envelopes do, however, contain proteins
that are specified by the virus, which often help viral
particles bind to host cells.

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Virus genomes

All viruses have genetic material (a genome) made of nucleic acid. You, like
all other cell-based life, use DNA as your genetic material. Viruses, on the other
hand, may use either RNA or DNA, both of which are types of nucleic acid.

We often think of DNA as double-stranded and RNA as single-stranded, since

that's typically the case in our own cells. However, viruses can have all possible
combos of strandedness and nucleic acid type (double-stranded DNA, double-
stranded RNA, single-stranded DNA, or single-stranded RNA). Viral genomes also
come in various shapes, sizes, and varieties, though they are generally much smaller
than the genomes of cellular organisms.

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 Let’s Remember

➢ Microorganisms, also called microbes, include viruses, bacteria, archaeans,

certain algae, protozoa, and certain fungi.
➢ Because viruses are acellular (not composed of cells), they are often referred
to as “infectious agents” or “infectious particles” rather than microorganisms.
➢ A virus is an infectious particle that reproduces by "commandeering" a host
cell and using its machinery to make more viruses.
➢ A virus is made up of a DNA or RNA genome inside a protein shell called a
capsid. Some viruses have an external membrane envelope.
➢ Viruses are very diverse. They come in different shapes and structures, have
different kinds of genomes, and infect different hosts.
➢ Viruses reproduce by infecting their host cells and reprogramming them to
become virus-making "factories."

References
Engelkirk, P.G., and Burton, G.R.W. (2011). Burton’s Microbiology For The Health

Sciences. Retrieved from:

https://www.researchgate.net/profile/Rakesh_S_PILLAI/publication/30880

1943_Burtons-

Microbiology_for_the_Health_sciences/links/57f3549a08ae91deaa5904ba/B

urtons-Microbiology-for-the-Health-sciences.pdf

https://www.khanacademy.org/science/high-school-biology/hs-human-body-

systems/hs-the-immune-system/a/intro-to-viruses

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