The Main Themes of Microbiology 1.

Public Health & Epidemiology:

Microbiology- specialized area of biology Monitor and control the spread of
that deals with tiny life forms that are not diseases in communities
readily observed without magnification 2. Environmental Microbiology:
(microscopic organisms) encompasses the study of
● microorganisms or microbes microorganisms and their
● ubiquitous or omnipresent ecological relationships in such
Major Groups of Microorganisms natural habitats as soil and water.
1. Bacteria: small, single-celled 3. Biotechnology and Industrial
prokaryotic organisms Microbiology: defined by any
2. Viruses: minute, noncellular process that harnesses the actions
particles that parasitize cells of living things to derive the
3. Fungi: a group of eukaryotes that desired product, ranging from beer
includes both microscopic to stem cells. Industrial Micro uses
eukaryotes (molds and yeasts) and microbes to produce and harvest
larger organisms (mushrooms) large quantities of such.
4. Protozoa: animal-like, 4. Immunology: studies the complex
single-celled eukaryotes web of protective substances and
5. Algae: simple photosynthetic reactions caused by invading
eukaryotes, ranging from microbes and other harmful
single-celled forms to large entities.
seaweeds 5. Genetic Engineering and
6. Helminths: a general term Recombinant DNA Technology:
meaning "worm", parasitic worms These interrelated fields involve
that cause a wide variety of deliberate alterations of the genetic
infectious diseases makeup of organisms to create
Common Branches of Microbiology novel microbes, plants, and
Bacteriology - the study of bacteria animals with unique behavior and
Mycology - the study of fungi physiology
Protozoology - the study of protozoans 6. Agricultural Microbiology:
Virology - the study of viruses Concerned with the relationships
Parasitology - the study of parasitism and between microbes and
parasitic organisms domesticated plants and animals.
Phycology - the study of algae (Plant specialists and Animal
Microbial specialists)
Morphology - involved in the study of the 7. Food Microbiologists: Concerned
detailed structure of microorganisms with the impact of microbes on the
Physiology - microbial function food supply, including such areas
(metabolism) at the cellular and molecular as food spoilage, food-borne
levels diseases, and production.
Taxonomy - systematics of microbes
Genetics (molecular biology) - the The Historical Foundations of
function of genetic material and Microbiology
biochemical reactions that make up a
cell's metabolism Ecology - Antonie van Leeuwenhoek
interrelationships between microbes and ● He observed rainwater from a clay
the environment pot as well as his own plaque =
Fields of Microbiology
 "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 The Scientific Method and the Search
matter. for Knowledge
FRANCISCO REDI ● 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
JOHN NEEDHAM 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
LAZARO SPALLANZANI 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
LOUIS PASTEUR
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 Physical requirement for Microbial
experienced fewer infections than growth
mothers who gave birth in the
hospital" Physical requirement Temperature
Dr. Ignaz Semmelweis ● Temperature is the most important
● "women became infected after factor that determines the rate of
examinations by physicians growth, multiplication, survival, and
coming directly from the autopsy death of all living organisms.
room." ● High temperatures damage
● Mandated handwashing microbes by denaturing enzymes,
transport carriers, and other
Joseph Lister proteins.
● Aseptic Technique // Aseptic ● Microbial membranes are
Surgery disrupted by temperature
● aimed at reducing microbes in a extremes.
medical setting ● At very low temperatures
membranes also solidify and
Louis Pasteur enzymes also do not function
● Developed vaccines for Rabies properly.
and Anthrax Minimum Temperature
● Clarified the actions of microbes in The LOWEST temperature at which
wine and beer fermentation organisms grow
● Pasteurization - heat treatment Optimum Temperature
process that destroys pathogenic The temperature at which the most rapid
microbes in food and beverages rate of multiplication occurs
Robert Koch Maximum Temperature
● Worked on and isolated The HIGHEST temperature at which
Mycobacterium tuberculosis growth occurs
● 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 Psychrophile
microorganisms in the environment ● Extremophilic organisms that are
Microbiota: can refer to all the capable of growth and
microorganisms found in an environment reproduction in cold temperatures
● Temperature range: −20°C to
MICROBIAL GROWTH +15°C.
Growth: increase in population, more ● Examples: Oscillatoria,
colonies, more mass. (not in cell size) Chlamydomonas nivalis,
Methanogenium, etc
Psychrotroph ● Most bacteria are neutrophiles,
● Cold-tolerant bacteria meaning they grow optimally at a
● Temperature range: 5°C to 30°C. pH within one or two pH units of
● Psychrotrophic fungi and bacteria the neutral pH of 7. Most familiar
are the principal cause of spoilage bacteria, like Escherichia coli,
of refrigerated food. staphylococci, and Salmonella spp.
● Examples: Pseudomonas, are neutrophiles and do not fare
Aeromonas, Bacillus, Clostridum, well in the acidic pH of the
etc. stomach. However, there are
Mesophile pathogenic strains of E. coli, S.
● Grows best in moderate Typhi, and other species of
temperature. intestinal pathogens that are much
● Temperature range: 10°C to 50°C. more resistant to stomach acid. In
● Examples: Escherichia coli, comparison, fungi thrive at slightly
Streptococcus pneumonia, etc. acidic pH values of 5.0–6.0
Thermophile Acidophile
● Heat-loving microorganisms. ● Microorganisms that grow
● Grow at 50°C or higher. Their optimally at pH less than 5.55 are
growth minimum is usually around called acidophiles. For example,
45°C and often optima between 50 the sulfur-oxidizing Sulfolobus spp.
and 80°C. These archaea survive at pH
● Examples: Thermus aquaticus, values of 2.5–3.5. Species of the
Bacillus stearothermophilus, etc. archaean genus Ferroplasma live
Hyperthermophile at pH values of 0–2.9.
● Thrives in extremely hot Lactobacillus bacteria, which are
environments an important part of the normal
● The temperature range is 65°C to microbiota of the vagina, can
130°C and above. Example: tolerate acidic environments at pH
Geogemma barossii values 3.5–6.8 and also contribute
to the acidity of the vagina (pH of
Physical requirement pH 4, except at the onset of
● Microbial growth is strongly menstruation) through their
affected by the pH of the medium. metabolic production of lactic acid
● Drastic variations in cytoplasmic Alkaliphile
pH disrupt the plasma membrane ● Microorganisms that grow best at
or inhibit the activity of enzymes pH between 8.0 and 10.5. Vibrio
and membrane transport protein 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
Neutrophile
Physical requirement Osmotic energy, which causes atoms to
Pressure lose electrons (ionize).
● Osmotic pressure is the minimum ● Ultraviolet (UV) radiation is another
pressure that needs to be applied very damaging form of radiation. It
to a solution to prevent the inward can kill microorganisms due to its
flow of water across an SPM. short wavelength (approximately
Types of solutions: from 10 to 400 nm) and high
● 1. Hypotonic energy. The most lethal UV
● 2. Isotonic radiation has a wavelength of 260
● 3. Hypertonic nm, the wavelength most
OSMOTOLERANT effectively absorbed by and
● Those microorganisms can grow at damaging to DNA.
relatively high salt concentrations.
● Examples: Aeromonasspp., Chemical requirement for Microbial
Staphylococcusspp, etc. growth
HALOPHILE
● Grow in the presence of salt at Carbon:
conc. Above 20% to 60%. ● Makes up 50% of the dry weight of
● Examples: Halobacterium the cell.
Halobium ● The structural backbone of all
organic compounds.
Physical requirement Hydrostatic ● Chemoheterotrophs: Obtain
Pressure carbon from their energy source:
● Microbes that live on land and lipids, proteins, and carbohydrates.
water surface live at 1 atm. ● Chemoautotrophs and
● Many bacteria and archaea live in Photoautotrophs: Obtain carbon
deep-sea with very high from carbon dioxide.
hydrostatic pressures. Nitrogen
● Barotolerant: increased pressure ● Makes up 14% of dry cell weight.
adversely affects them but not as ● Used to form amino acids, DNA,
much as it does nontolerant and RNA
microbes. Sources of nitrogen
● Piezophilic (barophilic): defined as ● Protein: Most bacteria
an organism that has a maximal ● Ammonium: Found in organic
growth rate at pressures greater matter
than 1 atm. ● Nitrogen gas (N2 ): Obtain N
● For instance, a piezophile directly from the atmosphere.
recovered from the Mariana trench Important nitrogen-fixing bacteria,
(depth about 10,500 m) grows only live free in soil or are associated
at pressures between about 400 to with legumes (peas, beans, alfalfa,
500 atm when incubated at 2°C. clover, etc.). Legume cultivation is
Physical requirement Radiation used to fertilize the soil naturally.
● More helpful in the control of ● Nitrates: Salts that dissociate to
growth. give NO3
● One of the most damaging is
ionizing radiation, radiation of a Sulfur
very short wavelength and high ● Used to form proteins and some
vitamins (thiamin and biotin).
Sources of sulfur: Lag phase:
● Protein: Most bacteria ● Period of little or no cell division
● Hydrogen sulfide ● Can last 1 hr or several days
● Sulfates: Salts that dissociate to ● Cells are not dormant
gives sulfate ● Undergoing a period of intense
Phosphorus metabolic activity: DNA and
● Used to form DNA, RNA, ATP, and enzyme synthesis.
phospholipids. Exponential Phase:
● Sources: Mainly inorganic ● Period of growth also knows as
phosphate salts and buffers. logarithmic increase
● Sometimes called as log phase
"Other" Elements: Potassium, ● Cellular respiration is most active
magnesium, and calcium are often during this period
required as enzyme cofactors. Calcium is ● Metabolic activity is active and is
required for cell wall synthesis in most preferable for industrial
Gram-positive bacteria. purposes
Trace Elements ● Sensitive to adverse conditions.
● Iron Stationary Phase
● Copper ● Population size begins to stabilize
● Molybdenum ● Numbers of cells produced+
● Zinc number of cells dying
● Overall cell numbers do not
Oxygen increase
● Organisms that use molecular ● Cell division begins to slow down
oxygen (O2 ), produce more Death Phase:
energy from nutrients than ● Populations size begins to
anaerobes. decrease
● Obligate Aerobes: Require ● Numbers of cells dying > number
oxygen to live. of cells produced
● Facultative Anaerobes: Can use ● Cell numbers decrease at a
oxygen, but can grow in its logarithmic rate
absence. Have a complex set of ● Cells lose their ability to divide
enzymes. ● A few cells may remain alive for a
● Obligate Anaerobes: Cannot use long period of time
oxygen and are harmed by the Generation Time: Time required for a cell
presence of toxic forms of oxygen. to divide, and its population to double.
Classification based on their oxygen ● Average for bacteria is 1-3 hours
requirements: (cont'd) ● E. coli generation time = 18-20 min
● Aerotolerant Anaerobes: Can’t 20 generations (7 hours), 1 cell
use oxygen, but tolerate its becomes 1 million cells!
presence. Can break down toxic Binary fushion: common in bacteria
forms of oxygen. Budding: not common/common in yeast
● Microaerophiles: Require oxygen, and fungi
but at low concentrations. Multiple fushion: see in plasmodium in
Sensitive to toxic forms of oxygen protozoa
. Spore production: preserve bacteria
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 ● Generation time is easily
cells. obtained from the exponential
phase of a growth curve.
Viruses: exceptionally small, don’t have
structures that normally have with a living 3. Stationary phase
cell. Coated by a protein called capsid
● Eventually population growth
either RNA or DNA forms.
decrease
Binomial System: Developed by CARL ● The growth curve becomes
VON LINNAEUS, the first word is the horizontal.
generic name (always started with a ● Rate of cell growth = rate of
capital letter) and the second word is the cell death
specific name. Names given in
4. Death phase
handwritten documents are always
underlined. In printed materials, the ● Cells are dying at an
names of organisms are given in Italics. exponential rate
● Cell death may result from
Bacteria and archaea most commonly
nutrient limitation and toxic
engage in a process known as binary
waste accumulation
fission: where a single cell splits into two
● Cells lost the ability to detoxify
equally sized cells. Other, less common
toxins, etc.
processes can include multiple fission,
budding, and the production of spores. Conjugation- is the process by which a
donor bacterium transfers a copy of a
Growth curve
plasmid to a recipient bacterium, through
1. Lag phase 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 allows a bacterial cell to acquire new
possible given their genetic genes, but it does not require cell-to-cell
potential the nature of the contact. In this process, the new genes
medium, and the condition are acquired directly from the
under which they are growing. 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 Specialized transduction- can only occur
shuttling bacteria genes from one cell to with temperate bacteriophage, since it
another, thus negating the necessity for involves the lysogenic cycle of replication.
cell-to-cell contact. There are two different The bacteriophage randomly attaches to a
types of transduction: generalized bacterial host cell, injecting viral DNA
transduction and specialized inside. The DNA integrates into the
transduction. chromosome of the host cell, forming a
prophage. At some point induction occurs,
In generalized transduction, a bacterial
where the prophage is excised from the
host cell is infected with either avirulent or
bacterial chromosome. In specialized
a temperate bacteriophage engaging in
transduction, the excision is incorrectly
the lytic cycle of replication. After the first
performed and a portion of bacterial genes
three steps of replication (absorption,
immediately adjacent to the viral genes
penetration, and synthesis), the virus
are excised too. Since this DNA is used as
enters into the assembly stage, during
the template for the synthesis stage, all
which fully formed virions are made.
copies will be a hybrid of viral and
During this stage, random pieces of
bacterial DNA, and all resulting virions will
bacterial DNA are mistakenly packaged
contain both viral and bacterial DNA.
into a phage head, resulting in the
production of a transducing particle. Once the cell is lysed, the virions are
While these particles are not capable of released to infect other bacterial host
infecting a cell in the conventional sense, cells. Each virion will attach to the host cell
they can bind to a new bacterial host cell and inject in the DNA hybrid, which could
and inject their DNA inside. If the DNA be incorporated into the host chromosome
(from the first bacterial host cell) is if a prophage is formed. At this point, the
incorporated into the recipient’s second bacterial host cell can contain its
chromosome, the genes can be own DNA, DNA from the previous
expressed. 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.