Introduction to Microbiology Branches

Introduction

What is Microbiology?
• the study of microscopic organisms
(microorganisms), such as bacteria,
viruses, archaea, fungi and protozoa
• Microorganisms are minute living things
that cannot be seen with the unaided eye.
• Revolves around two interconnected PURE MICROBIOLOGY
themes: • Microbial taxonomy - a means by which
a) understanding the nature and microorganisms can be grouped/classified
functioning of the microbial world together.
b) applying our understanding of the • Bacteriology - study of bacteria
microbial world for the benefit of • Phycology/algology - the study of algae
humankind and the Earth. • Mycology - study of fungi
MICROORGANISMS ARE EVERYWHERE! • Protozoology - study of protozoa
• Parasitology - study of parasites
• Virology - study of viruses
• Immunology - study immune response of
humans to microorganisms.
• Microbial Metabolism - the means by
which a microbe obtains the energy and
nutrients (e.g. carbon) it needs to live and
reproduce.
• Microbial Genetics - the study of how
genes are organized and regulated in
microbes in relation to their cellular
functions.
Major Themes • Microbial Ecology - the relationship
between microorganisms and their
environment.

APPLIED MICROBIOLOGY
Medical Microbiology - the study of the
pathogenic microbes and the role of
microbes in human illness.
Pharmaceutical microbiology - the study of
microorganisms that are related to the
production of antibiotics, enzymes,
vitamins, vaccines, and other
Domains of Organisms pharmaceutical products
Industrial microbiology - the exploitation of
microbes for use in industrial processes.
Microbial biotechnology - the
manipulation of microorganisms at the
genetic and molecular level to generate THE DISCOVERY OF MICROORGANISMS
useful products. •Robert Hooke - illustrated in his book,
Food microbiology - the study of Micrographia (1665), the fruiting
microorganisms causing food spoilage and structures of molds among many other
foodborne illness. Using microorganisms to things
produce foods • stated that life’s smallest structural units
Agricultural microbiology - the study of were cells
agriculturally relevant microorganisms •first known description of microorganisms
Water microbiology (or aquatic
microbiology) - the study of those • Anton van Leeuwenhoek – the first
microorganisms that are found in water. person to see bacteria/microorganism
Aeromicrobiology (or air microbiology) -
the study of airborne microorganisms. SPONTANEOUS GENERATION
Environmental microbiology - the study of THEORY/ABIOGENESIS
the function and diversity of microbes in
their natural environments.

Importance

THE IMPACT OF MICROORGANISMS ON

HUMANS
1) Microorganisms and Diseases
2) Microorganisms, Agriculture and Human Aristotle: “Microorganisms arise
Nutrition spontaneously from non-
3) Microorganisms and Food, Energy and living/decomposing matter.”
the Environment
CHALLENGING THE SPONTANEOUS
THE APPLICATION OF MICROORGANISMS GENERATION THEORY
IN OUR DAILY LIVES 1. Francesco Redi
•Agriculture/Aquaculture 2. Louis Joblot
•Food processing 3. John Needham
•Biogeochemical cycles 4. Lazzaro Spallanzani
•Pest management •Decomposition
•Waste management 1. Francesco Redi
•Pollution Prevention and Mitigation Flies are necessary to produce flies: they do
not arise spontaneously from rotting meat.
Historical Context Redi's experiment simply but effectively
Early Observations in Microbiology demonstrates that life is necessary to
produce life. Redi expressed this in his
famous dictum as "Omne vivum ex vivo“
("All life comes from life").
2. Louis Joblot DISPROVING THE SPONTANEOUS
Divided boiled hay into two containers: GENERATION THEORY
1 – open (developed microorganisms) Louis Pasteur
2 – uncovered - countered Spontaneous Generation by
constructing a swan-necked flask (1864)
- predicted that microorganisms in
putrefying materials were descendants of
cells that entered from the air or cells that
had been on the decaying materials to
begin with.
3. John Needham - if food were rendered sterile and then
• Tried to prove spontaneous generation protected from further contamination, it
• A broth was boiled in the belief that it should not putrefy.
would kill all the microorganisms. He - used heat to kill contaminating
sealed the broth and left it for a few days. microorganisms.
He observed that the broth had become
cloudy and that it has microscopic John Tyndall
organisms in it. - built elaborate boxes to eliminate dust
• In reality, the broth was not boiled - demonstrated that dust carries
vigorously so as to kill all the microorganisms
microorganisms. - finally laid abiogenesis to rest
His experiments were later challenged and - discovered that there are 2 types of
repeated by Lazzaro Spallanzani. Using a bacteria:
slightly different protocol (with a longer a) heat-resistant (endospores)
boiling time), Spallanzani did not have any b) heat-sensitive (vegetative)
microbes grow in his sealed flasks, - demonstrated that the alternate process
contradicting Needham's findings. of heating & cooling (5x) can kill
endospores
- STERILIZATION/ TYNDALLIZATION

4. Lazzaro Spallanzani
- microorganisms could be killed by boiling
- This proved to Lazzaro that microbes do
not form out of nowhere. If microbes
formed out of nowhere then all flasks
would have microbes.
- critics of Spallanzani said he killed the life
force that was required for spontaneous
generation.
This experiment paved the way for
research later done by Louis Pasteur.
GERM THEORY OF DISEASE – showed that the pébrine disease of
• It states that microorganisms known as silkworms was caused by a protozoan
pathogens or "germs" can lead to disease. parasite
These small organisms, too small to see – developed other vaccines including those
without magnification, invade humans, for chicken cholera, anthrax, and rabies
other animals, and other living hosts. Their – “Father of bacteriology and immunology”
growth and reproduction within their hosts
can cause disease. Smallpox
• "Germ" may refer to not just a bacterium • Killed more than 300 million people
but to any type of microorganism or even worldwide in the 20th century alone, and
non-living pathogens that can cause most of the native inhabitants of the
disease. Americas.
• Pasteur postulated the germ theory of • Smallpox (also known by the Latin names
disease but his experiments to prove it Variola or Variola vera) is a contagious
were unsuccessful. disease unique to humans.
• Robert Koch provided the proof by • Smallpox is caused by either of two virus
cultivating the bacteria that cause anthrax variants named Variola major and Variola
apart from any other type of organism. minor.
• Koch then injected pure cultures of • The deadlier form, V. major, has a
anthrax bacteria into mice and showed that mortality rate of 30–35%, while V. minor
they invariably caused anthrax. causes a milder form of disease called
• These experiments proved the germ alastrim and kills ~1% of its victims.
theory of disease. The procedures used by • In 1980, the World Health Assembly
Koch came to be known as Koch’s announced that the world was free of
postulates. smallpox.
Long-term side-effects for survivors include
GERM THEORY OF DISEASE: KOCH’S the characteristic skin scars. Occasional
POSTULATES side effects include blindness due to
1. The microorganism must be found in all corneal ulcerations and infertility in male
cases of the disease. survivors.
2. It must be isolated from the host and
grown in pure culture. Edward Jenner
3. It must reproduce the original disease • Developed the first vaccine and used a
when introduced into a susceptible host. vaccination procedure to protect
4. It must be found present in the individuals from smallpox.
experimental host so infected. • As part of his practice, Jenner performed
variolation on his patients. In this rural
ROLE OF MICROORGANISMS IN DISEASE
setting he learned that dairymaids and
Oliver Holmes (1773 - 1843)
other individuals who contracted cowpox,
– showed that sepsis could be transmitted
a minor infection marked by a few pustules,
by hands of medical student and may cause
would not later contract smallpox
disease
• Jenner also observed that he could not
– demonstrated that the Great Potato
successfully inoculate such persons with
Blight of Ireland was caused by a fungus.
smallpox. Noting this connection, Jenner
concluded that cowpox not only protected
Louis Pasteur (1822 - 1895)
against smallpox but could also be
transmitted from one person to another as Hans Christian Gram (1853-1935)
a deliberate mechanism of protection. • Staining method that demonstrate
Dr. Edward Jenner performing his first bacteria and distinguish between Gram
vaccination against smallpox on James positive and Gram negative bacteria.
Phipps, May 14, 1796, oil on canvas by Angelina Fanny Hesse (1850-1934)
Ernest Board. • developed the use of agar to grow
microorganisms.
• She was the wife of Walter Hesse who
worked in Koch’s laboratory
• Advantages of agar- It was not attacked
by most bacteria.
• Agar is better than gelatin because of its
higher melting point (96°c) and solidifying
(40–45°c) points.

Why develop culture media?

– To enable the isolation of pure cultures
(only one type of organism)
• Especially important during Koch’s period
HISTORY OF PANDEMICS • Gelatin not useful as solidifying agent
(melts at >28 ºC and some bacteria
hydrolyze it with enzymes)
• Fannie Hesse, the wife of one of Koch’s
assistants, proposed using agar
– Not digested by most bacteria
– Melts at 100 ºC
– Used today - ~2% in solid media

Joseph Lister (1827 - 1912)

- developed a system of surgery designed
to prevent microorganisms from entering
wounds – phenol (Carbolic Acid) sprayed in
air around surgical incision in 1867
OTHER IMPORTANT DISCOVERIES (Antiseptic Surgery).
Walter Hesse ( 1846-1911) – Decreased number of post-operative
• Used Agar as a solidifying agent to harden infections in patients
media. – his published findings (1867) transformed
• Agar is extracted from seaweeds red the practice of surgery.
algae.
• He also worked with Robert Koch. ALEXANDER FLEMING
Julius Richard Petri (1852-1921) • In 1928 Fleming observed that the
• Used agar dish to provide a large area to growth of the bacterium Staphyloccus
grow. aureus was inhibited in the areas
• He was one of Robert Koch’s assistants. surrounding the colony of a mold that had
Raymond Sabouraud ( 1890-1910) contaminated a Petri plate.
Develop culture media to study yeast and
molds.
• The mold was identified as Penicillium their rates of reproduction. In order to
notatum, and its active compound was study this array of organisms, researchers
named penicillin (the first antibiotic). needed a way to systematically organize
them.
Discovery of Penicillin
• classification, nomenclature and
• 1928: Alexander Fleming discovered the identification of living organisms
first antibiotic. • Classification is the practice of organizing
• He observed that Penicillium fungus organisms into different groups based on
made an antibiotic, penicillin, that killed S. their shared characteristics.
aureus. • An international code governs the
• 1940s: Penicillin was tested clinically and naming of organisms by genus and species.
mass produced and was available towards In 1735, Carolus Linnaeus published
the end of World War II Systema Naturae, in which he proposed the
Linnaean taxonomy.
Louis Pasteur
– demonstrated that alcoholic
fermentations were the result of microbial
activity
– that some organisms could decrease
alcohol yield and sour the product, and
that some fermentations were aerobic and
some anaerobic;
– he also developed the process of
pasteurization to preserve wine during
storage.

Ruska (1938) – First Electron Microscope Classification of Microorganisms: The

• The electron microscope is capable of Phylogenetic Tree of Life
magnifying biological specimens up to one
million times.
• To study detail structures of viruses.

Microbial Diversity & Taxonomy

TAXONOMY
Microorganisms vary in all sorts of ways,
including their size, their appearance, and
Naming Microorganisms - have relatively rigid cell walls Molds:
Binomial nomenclature multicellular; grow as branching filaments
• two-word naming system for identifying - interlace to form mycelium Yeasts:
organisms by genus and specific epithet unicellular; reproduce asexually (budding)
• genus = capitalized; specific epithet name or sexually (spores).
= not capitalized
• Both names are italicized (typewritten) or 4. Protozoa
underlined (handwritten). - unicellular, eukaryotic
• Examples: a. Homo sapiens (H. sapiens) - non-photosynthetic
b. Fasciola hepatica (F. hepatica) c. - free-living or parasitic
Escherichia coli (E. coli) - reproduce sexually or asexually

Major Groups 5. Algae

- unicellular or multicellular
Major Groups of Microorganisms: - eukaryotic
1. Bacteria - photosynthetic
2. Archaea - prominent in bodies of water
3. Fungi
4. Protozoa 6. Viruses
5. Algae - acellular, obligate parasites
6. Viruses - none can grow in an inanimate nutrient
o Cellular medium
o Acellular
Anatomy
1. Bacteria
- unicellular
- prokaryotic (do not have organelles or a
true nucleus)
- less complex than eukaryotic cells - main
groups of bacteria are:
a. Gram-positive
b. Gram-negative

2. Archaea Cell Types

- unicellular 1) PROKARYOTIC CELLS
- prokaryotic – have no nucleus
- similar to bacteria but have different – have simpler structures
characteristics – found in organisms of the domains
- live in extreme habitat e.g., hydrothermal Bacteria & Archaea
vents, hot springs, highly acidic habitats, 2) EUKARYOTIC CELLS
environments with low to no oxygen or – contain nucleus
with high salt content. - membrane-bound structures
– more complex structures (protists, fungi,
3. Fungi plants & animals)
- multicellular or unicellular
- eukaryotic 1) Prokaryotic cells
- non-photosynthetic
a. Plasma Membrane: the “bag” that holds
all of the intracellular material and
regulates the movement of materials into
and out of the cell.
b. Cytoplasm: gel-like fluid inside the
plasma membrane where all of the cellular
organelles suspended within.
c. Cytoskeletal Proteins: provides structural
support to the cell and plays a role in cell
division.
d. Ribosomes: tiny protein-making
machines that carry out the genetic
instructions of the cell.
e. Nucleoid: region that contains the
genome—the main genetic material (DNA)
of the cell and typically have a single,
circular chromosome.
f. Plasmids: confers antibiotic resistance,
virulence (the ability to cause disease) and
conjugation (a bacterium’s ability to share
its plasmids with other bacteria).
g. Glycocalyx: layer outside of the cell wall
present in some bacteria.
- Slime layers help bacteria stick to things
and protect them from drying out
- Capsules allow bacteria to stick to things,
but have the added benefit of helping
encapsulated bacteria hide from the host's
immune system.
h. Flagella: These are long whip-like
extensions for movement.

2) Eukaryotic cells (Animal Cell)

In animal cells but not in plant cells:
1. Lysosomes
2. Centrosomes with centrioles
3. Flagella (but present in some plant
sperm)
In plant cells but not in animal cells:
1. Chloroplasts
2. Central vacuole
3. Cell wall
4. Plasmodesmata