The Main Themes of Microbiology
Public Health & Epidemiology:
Microbiology- specialized area of biology
that deals with tiny life forms that are not
readily observed without magnification
(microscopic organisms)
● microorganisms or microbes
● ubiquitous or omnipresent
Major Groups of Microorganisms
1. Bacteria: small, single-celled
prokaryotic organisms
2. Viruses: minute, noncellular
particles that parasitize cells
3. Fungi: a group of eukaryotes that
includes both microscopic
eukaryotes (molds and yeasts) and
larger organisms (mushrooms)
4. Protozoa: animal-like,
single-celled eukaryotes
5. Algae: simple photosynthetic
eukaryotes, ranging from
single-celled forms to large
seaweeds
6. Helminths: a general term
meaning "worm", parasitic worms
that cause a wide variety of
infectious diseases
Common Branches of Microbiology
Bacteriology - the study of bacteria
Mycology - the study of fungi
Protozoology - the study of protozoans
Virology - the study of viruses
Parasitology - the study of parasitism and
parasitic organisms
Phycology - the study of algae
Microbial
Morphology - involved in the study of the
detailed structure of microorganisms
Physiology - microbial function
(metabolism) at the cellular and molecular
levels
Taxonomy - systematics of microbes
Genetics (molecular biology) - the
function of genetic material and
biochemical reactions that make up a
cell's metabolism Ecology -
interrelationships between microbes and
the environment
Fields of Microbiology
1.
Monitor and control the spread of
diseases in communities
2. Environmental Microbiology:
encompasses the study of
microorganisms and their
ecological relationships in such
natural habitats as soil and water.
3. Biotechnology and Industrial
Microbiology: defined by any
process that harnesses the actions
of living things to derive the
desired product, ranging from beer
to stem cells. Industrial Micro uses
microbes to produce and harvest
large quantities of such.
4. Immunology: studies the complex
web of protective substances and
reactions caused by invading
microbes and other harmful
entities.
5. Genetic Engineering and
Recombinant DNA Technology:
These interrelated fields involve
deliberate alterations of the genetic
makeup of organisms to create
novel microbes, plants, and
animals with unique behavior and
physiology
6. Agricultural Microbiology:
Concerned with the relationships
between microbes and
domesticated plants and animals.
(Plant specialists and Animal
specialists)
7. Food Microbiologists: Concerned
with the impact of microbes on the
food supply, including such areas
as food spoilage, food-borne
diseases, and production.
The Historical Foundations of
Microbiology
Antonie van Leeuwenhoek
● He observed rainwater from a clay
pot as well as his own plaque =
 "many very little living animalcules,
very prettily a-moving."
● Animalcules - Bacteria and
Protozoa
● Regarded as the Father of
Microbiology (Bacteriology &
Protozoology)
The Development of the Microscope
Spontaneous Generation: The idea that
certain living things arose from vital forces
present in nonliving or decomposing
matter.
FRANCISCO REDI
JOHN NEEDHAM
LAZARO SPALLANZANI
LOUIS PASTEUR
The Scientific Method and the Search
for Knowledge
● Deductive Reasoning Approach -
general observations to develop an
explanation
● Hypothesis - Early explanation
● Inductive Reasoning Approach -
specific observations to develop a
general explanation
● Theory - a collection of statements,
propositions, or concepts that
explains or accounts for a natural
event.
● Law (Principle) - next level of
confidence
Edward Jenner
● Modeled the Scientific Method, first
to use scientific thought to
construct a rigorous experiment
model to inoculate people against
disease. (First viable method to
control smallpox.)
● Father of Immunology
John Tyndall
● provided initial evidence that some
microbes have very high heat
resistance and that particularly
vigorous treatment is required to
destroy them.
Ferdinand Cohn
● discovery of heat-resistant
bacterial endospores which
explained why heat would
sometimes fail to completely
eliminate all microorganisms.
● Beginning of the word "Sterile"
Dr. Oliver Wendell Holmes Sr
 ● "mothers who gave birth at home
experienced fewer infections than
mothers who gave birth in the
hospital"
Dr. Ignaz Semmelweis
● "women became infected after
examinations by physicians
coming directly from the autopsy
room."
● Mandated handwashing
Joseph Lister
● Aseptic Technique // Aseptic
Surgery
● aimed at reducing microbes in a
medical setting
Louis Pasteur
● Developed vaccines for Rabies
and Anthrax
● Clarified the actions of microbes in
wine and beer fermentation
● Pasteurization - heat treatment
process that destroys pathogenic
microbes in food and beverages
Robert Koch
● Worked on and isolated
Mycobacterium tuberculosis
● Bacterial Isolation
● Established Koch's Postulates
Germ Theory of Disease: States that
microorganisms known as pathogens or
germs can lead to disease
Koch's Postulates: A series of proofs
that verified the germ theory and could
establish whether an organism was
pathogenic and which disease it caused.
The Microbiome: Microbiome: refers to
the collection of genomes from all the
microorganisms in the environment
Microbiota: can refer to all the
microorganisms found in an environment
MICROBIAL GROWTH
Growth: increase in population, more
colonies, more mass. (not in cell size)
Physical requirement for Microbial
growth
Physical requirement Temperature
● Temperature is the most important
factor that determines the rate of
growth, multiplication, survival, and
death of all living organisms.
● High temperatures damage
microbes by denaturing enzymes,
transport carriers, and other
proteins.
● Microbial membranes are
disrupted by temperature
extremes.
● At very low temperatures
membranes also solidify and
enzymes also do not function
properly.
Minimum Temperature
The LOWEST temperature at which
organisms grow
Optimum Temperature
The temperature at which the most rapid
rate of multiplication occurs
Maximum Temperature
The HIGHEST temperature at which
growth occurs
Psychrophile
● Extremophilic organisms that are
capable of growth and
reproduction in cold temperatures
● Temperature range: −20°C to
+15°C.
● Examples: Oscillatoria,
Chlamydomonas nivalis,
Methanogenium, etc
Psychrotroph
● Cold-tolerant bacteria
● Temperature range: 5°C to 30°C.
● Psychrotrophic fungi and bacteria
are the principal cause of spoilage
of refrigerated food.
● Examples: Pseudomonas,
Aeromonas, Bacillus, Clostridum,
etc.
Mesophile
● Grows best in moderate
temperature.
● Temperature range: 10°C to 50°C.
● Examples: Escherichia coli,
Streptococcus pneumonia, etc.
Thermophile
● Heat-loving microorganisms.
● Grow at 50°C or higher. Their
growth minimum is usually around
45°C and often optima between 50
and 80°C.
● Examples: Thermus aquaticus,
Bacillus stearothermophilus, etc.
Hyperthermophile
● Thrives in extremely hot
environments
● The temperature range is 65°C to
130°C and above. Example:
Geogemma barossii
Physical requirement pH
● Microbial growth is strongly
affected by the pH of the medium.
● Drastic variations in cytoplasmic
pH disrupt the plasma membrane
or inhibit the activity of enzymes
and membrane transport protein
Neutrophile
● Most bacteria are neutrophiles,
meaning they grow optimally at a
pH within one or two pH units of
the neutral pH of 7. Most familiar
bacteria, like Escherichia coli,
staphylococci, and Salmonella spp.
are neutrophiles and do not fare
well in the acidic pH of the
stomach. However, there are
pathogenic strains of E. coli, S.
Typhi, and other species of
intestinal pathogens that are much
more resistant to stomach acid. In
comparison, fungi thrive at slightly
acidic pH values of 5.0–6.0
Acidophile
● Microorganisms that grow
optimally at pH less than 5.55 are
called acidophiles. For example,
the sulfur-oxidizing Sulfolobus spp.
These archaea survive at pH
values of 2.5–3.5. Species of the
archaean genus Ferroplasma live
at pH values of 0–2.9.
Lactobacillus bacteria, which are
an important part of the normal
microbiota of the vagina, can
tolerate acidic environments at pH
values 3.5–6.8 and also contribute
to the acidity of the vagina (pH of
4, except at the onset of
menstruation) through their
metabolic production of lactic acid
Alkaliphile
● Microorganisms that grow best at
pH between 8.0 and 10.5. Vibrio
cholera, the pathogenic agent of
cholera, grows best at the slightly
basic pH of 8.0; it can survive pH
values of 11.0 but is inactivated by
the acid of the stomach. When it
comes to survival at high pH, the
bright pink archaean
Natronobacterium, found in the
soda lakes of the African Rift
Valley, may hold the record at a pH
of 10.5
Physical requirement Osmotic
Pressure
● Osmotic pressure is the minimum
pressure that needs to be applied
to a solution to prevent the inward
flow of water across an SPM.
Types of solutions:
● 1. Hypotonic
● 2. Isotonic
● 3. Hypertonic
OSMOTOLERANT
● Those microorganisms can grow at
relatively high salt concentrations.
● Examples: Aeromonasspp.,
Staphylococcusspp, etc.
HALOPHILE
● Grow in the presence of salt at
conc. Above 20% to 60%.
● Examples: Halobacterium
Halobium
Physical requirement Hydrostatic
Pressure
● Microbes that live on land and
water surface live at 1 atm.
● Many bacteria and archaea live in
deep-sea with very high
hydrostatic pressures.
● Barotolerant: increased pressure
adversely affects them but not as
much as it does nontolerant
microbes.
● Piezophilic (barophilic): defined as
an organism that has a maximal
growth rate at pressures greater
than 1 atm.
● For instance, a piezophile
recovered from the Mariana trench
(depth about 10,500 m) grows only
at pressures between about 400 to
500 atm when incubated at 2°C.
Physical requirement Radiation
● More helpful in the control of
growth.
● One of the most damaging is
ionizing radiation, radiation of a
very short wavelength and high
energy, which causes atoms to
lose electrons (ionize).
● Ultraviolet (UV) radiation is another
very damaging form of radiation. It
can kill microorganisms due to its
short wavelength (approximately
from 10 to 400 nm) and high
energy. The most lethal UV
radiation has a wavelength of 260
nm, the wavelength most
effectively absorbed by and
damaging to DNA.
Chemical requirement for Microbial
growth
Carbon:
● Makes up 50% of the dry weight of
the cell.
● The structural backbone of all
organic compounds.
● Chemoheterotrophs: Obtain
carbon from their energy source:
lipids, proteins, and carbohydrates.
● Chemoautotrophs and
Photoautotrophs: Obtain carbon
from carbon dioxide.
Nitrogen
● Makes up 14% of dry cell weight.
● Used to form amino acids, DNA,
and RNA
Sources of nitrogen
● Protein: Most bacteria
● Ammonium: Found in organic
matter
● Nitrogen gas (N2 ): Obtain N
directly from the atmosphere.
Important nitrogen-fixing bacteria,
live free in soil or are associated
with legumes (peas, beans, alfalfa,
clover, etc.). Legume cultivation is
used to fertilize the soil naturally.
● Nitrates: Salts that dissociate to
give NO3
Sulfur
● Used to form proteins and some
vitamins (thiamin and biotin).
Sources of sulfur:
● Protein: Most bacteria
● Hydrogen sulfide
● Sulfates: Salts that dissociate to
gives sulfate
Phosphorus
● Used to form DNA, RNA, ATP, and
phospholipids.
● Sources: Mainly inorganic
phosphate salts and buffers.
"Other" Elements: Potassium,
magnesium, and calcium are often
required as enzyme cofactors. Calcium is
required for cell wall synthesis in
Gram-positive bacteria.
Trace Elements
● Iron
● Copper
● Molybdenum
● Zinc
Oxygen
● Organisms that use molecular
oxygen (O2 ), produce more
energy from nutrients than
anaerobes.
● Obligate Aerobes: Require
oxygen to live.
● Facultative Anaerobes: Can use
oxygen, but can grow in its
absence. Have a complex set of
enzymes.
● Obligate Anaerobes: Cannot use
oxygen and are harmed by the
presence of toxic forms of oxygen.
Classification based on their oxygen
requirements: (cont'd)
● Aerotolerant Anaerobes: Can’t
use oxygen, but tolerate its
presence. Can break down toxic
forms of oxygen.
● Microaerophiles: Require oxygen,
but at low concentrations.
Sensitive to toxic forms of oxygen
. Spore production: preserve bacteria
Lag phase:
● Period of little or no cell division
● Can last 1 hr or several days
● Cells are not dormant
● Undergoing a period of intense
metabolic activity: DNA and
enzyme synthesis.
Exponential Phase:
● Period of growth also knows as
logarithmic increase
● Sometimes called as log phase
● Cellular respiration is most active
during this period
● Metabolic activity is active and is
most preferable for industrial
purposes
● Sensitive to adverse conditions.
Stationary Phase
● Population size begins to stabilize
● Numbers of cells produced+
number of cells dying
● Overall cell numbers do not
increase
● Cell division begins to slow down
Death Phase:
● Populations size begins to
decrease
● Numbers of cells dying > number
of cells produced
● Cell numbers decrease at a
logarithmic rate
● Cells lose their ability to divide
● A few cells may remain alive for a
long period of time
Generation Time: Time required for a cell
to divide, and its population to double.
● Average for bacteria is 1-3 hours
● E. coli generation time = 18-20 min
20 generations (7 hours), 1 cell
becomes 1 million cells!
Binary fushion: common in bacteria
Budding: not common/common in yeast
and fungi
Multiple fushion: see in plasmodium in
protozoa
Bacteria - are essential to human life and ● Nucleoid: a nucleus-like
life on planet Earth. Although they are region of the cell where genetic
notorious for their role in causing human material is kept
diseases, there are beneficial species that ● Plasmid: a small molecule of
are essential to good health. DNA that can reproduce
Antoni van Leeuwenhoek became the independently
first to study bacteria under the
microscope. During the nineteenth Eukaryotes are organisms made up of
century, the French scientist Louis Pasteur cells that possess a membrane-bound
and the German physician Robert Koch nucleus (that holds DNA in the form of
demonstrated the role of bacteria as chromosomes) as well as
pathogens (causing disease). membrane-bound organelles. Eukaryotic
● The discovery that some bacteria organisms may be multicellular or
produced compounds lethal to single-celled organisms. All animals are
other bacteria led to the eukaryotes. Other eukaryotes include
development of antibiotics, which plants, fungi, and protists.
revolutionized the field of
medicine.
Prokaryotes are organisms made up of
cells that lack a cell nucleus or any
membrane-encased organelles. This
means the genetic material DNA.
Scientists have divided the prokaryotes
into two groups, the Bacteria, and the
Archaea.
● Bacteria- including E Coli,
Salmonella, and Listeria, are found
in foods and can cause disease;1
other is actually helpful to human
digestion and other functions.
● Archaea- Archaea were
discovered to be a unique life form
that is capable of living indefinitely
in extreme environments such as
hydrothermal vents or arctic ice.
Bacteria- are prokaryotes, lacking
A typical prokaryotic cell might contain the
well-defined nuclei and membrane-bound
following parts:
organelles, and with chromosomes
● Cell wall: the membrane composed of a single closed DNA circle.
surrounding and protecting the
cell Common pili or fimbriae are often
● Cytoplasm: all of the material involved in adherence (attachment) of
inside a cell except the nucleus bacterial cells to surfaces in nature. In
● Flagella and pili: medical situations, they are major
protein-based filaments found determinants of bacterial virulence
on the outside of some because they allow pathogens to attach to
prokaryotic cells (colonize) tissues and, sometimes, to
resist attack by phagocytic white blood
cells.
Viruses: exceptionally small, don’t have
structures that normally have with a living
cell. Coated by a protein called capsid
either RNA or DNA forms.
Binomial System: Developed by CARL
VON LINNAEUS, the first word is the
generic name (always started with a
capital letter) and the second word is the
specific name. Names given in
handwritten documents are always
underlined. In printed materials, the
names of organisms are given in Italics.
Bacteria and archaea most commonly
engage in a process known as binary
fission: where a single cell splits into two
equally sized cells. Other, less common
processes can include multiple fission,
budding, and the production of spores.
Growth curve
1. Lag phase
● Generation time is easily
obtained from the exponential
phase of a growth curve.
3. Stationary phase
● Eventually population growth
decrease
● The growth curve becomes
horizontal.
● Rate of cell growth = rate of
cell death
4. Death phase
● Cells are dying at an
exponential rate
● Cell death may result from
nutrient limitation and toxic
waste accumulation
● Cells lost the ability to detoxify
toxins, etc.
Conjugation- is the process by which a
donor bacterium transfers a copy of a
plasmid to a recipient bacterium, through
a pilus

● The period of apparent

inactivity is which the cells are
adapting to a new environment
and preparing for reproductive
growth.
● Associated with physiological
adaptation.
● Cells are synthesizing new
components.
● Cells increase in size but do
not divide.

2. Log (exponential) phase

● The period in which organisms The process of transformation- also

are growing at the maximal
possible given their genetic
potential the nature of the
medium, and the condition
under which they are growing.
allows a bacterial cell to acquire new
genes, but it does not require cell-to-cell
contact. In this process, the new genes
are acquired directly from the
environment. Typically the process
requires a donor cell that at some point
lysed and released naked DNA to the
environment.
Transduction- the use of a virus, a
bacteriophage, to act as a conduit for
shuttling bacteria genes from one cell to
another, thus negating the necessity for
cell-to-cell contact. There are two different
types of transduction: generalized
transduction and specialized
transduction.
In generalized transduction, a bacterial
host cell is infected with either avirulent or
a temperate bacteriophage engaging in
the lytic cycle of replication. After the first
three steps of replication (absorption,
penetration, and synthesis), the virus
enters into the assembly stage, during
which fully formed virions are made.
During this stage, random pieces of
bacterial DNA are mistakenly packaged
into a phage head, resulting in the
production of a transducing particle.
While these particles are not capable of
infecting a cell in the conventional sense,
they can bind to a new bacterial host cell
and inject their DNA inside. If the DNA
(from the first bacterial host cell) is
incorporated into the recipient’s
chromosome, the genes can be
expressed.
Specialized transduction- can only occur
with temperate bacteriophage, since it
involves the lysogenic cycle of replication.
The bacteriophage randomly attaches to a
bacterial host cell, injecting viral DNA
inside. The DNA integrates into the
chromosome of the host cell, forming a
prophage. At some point induction occurs,
where the prophage is excised from the
bacterial chromosome. In specialized
transduction, the excision is incorrectly
performed and a portion of bacterial genes
immediately adjacent to the viral genes
are excised too. Since this DNA is used as
the template for the synthesis stage, all
copies will be a hybrid of viral and
bacterial DNA, and all resulting virions will
contain both viral and bacterial DNA.
Once the cell is lysed, the virions are
released to infect other bacterial host
cells. Each virion will attach to the host cell
and inject in the DNA hybrid, which could
be incorporated into the host chromosome
if a prophage is formed. At this point, the
second bacterial host cell can contain its
own DNA, DNA from the previous
bacterial host cell, and viral DNA.
 transposable elements or “jumping
genes.” While these can play a very big
role in the activation and inactivation of
bacterial genes, the best explanation
derives from the work of Barbara
McClintock in corn, who won the Nobel
Prize for her research in 1983. She
demonstrated that transposable elements
can be responsible for the activation or
inactivation of genes within an organism.

Transposable elements are relatively

simple in structure, designed to move from
one location to another within a DNA
molecule by a process known as
transposition. All transposable elements
code for the enzyme transposase, the
enzyme responsible for allowing
transposition to occur, and have short
inverted repeats (IRs) at each end.