Microorganisms &

Microbiology
Chapter 1

Introduction
o

Microbiology: the study of microorganisms

(usually too small to be seen with the unaided
eye) and their activities How small?
Scope: Study of various taxonomic groups
o
o

Bacteria: Bacteriology (includes Eubacteria) &

(Archebacteria); now Bacteria & Archae: two domains)
Viruses*: Virology
o
o

o
o
o

Also Viroids and Prions*

* acellular and usually discussed together

Algae: Phycology
Protozoa: Protozoology
Fungi: Mycology
o

Molds and Yeasts

Introduction
o

Types of study:
o Form, structure, reproduction, biochemistry,
identification, distribution and role in nature,
relationships to each other and other living
things, including both beneficial and
detrimental effects, and use as tools for
production of products [genetic engineering].
o

Practical Aspects of Microbiology: Practical aspects

recognized from the beginning and now identified by the
various practical subdisciplines within microbiology.

Few purely
applied or purely
basic as after
discovery
(knowledge) then
attempts made to
apply knowledge
to problem solving.

Subdisciplines (Some overlap):

Medical Microbiology

Medical Microbiology- one of earliest: applied emphasis

(Will cover topic extensively later in course)

Pathogenic Microbiology: host-parasite interactions

Diagnostic Microbiology: diagnosis of which microorganisms is
causative agent of infectious disease
Veterinary Microbiology: infectious diseases of animals
Related subjects:

Epidemiology: study of the occurrence, distribution and determinants of

health & disease in a population

Includes, the study of factors and mechanisms for spread of diseases through
population(s) (CDC most important): Ex. outbreak investigation of infectious and non
infectious disease.

Immunology: host resistance to disease: also an applied subdiscipline

Virology: viruses as agents of disease

Advances in Controlling
Infectious Diseases

Infectious Diseases: major causes of death over 100 years ago

Today, non microbial causes predominate

Top 3 caused by microbes

Top 7 non-microbial

Still, microbes can be a threat to survival even in developed countries.

In developing countries, microbial diseases still are a major cause of
death

Early History

Influenza: 1918-1919 (Spanish Flu):

More Americans died than were killed in WWI, WWII, Korean,

and Vietnam Wars. ( 2 million in US)
Pandemic (worldwide epidemic) spread across world:

Smallpox: one of greatest killers.

Infected 500 million people (killed 50 million) (due to antigenic shift)

10 million people killed in history.

Brought to New World by Spanish. Aztecs very susceptible.
Vaccination: No new cases since 1977 (eradicated).
Vaccination not in general use for 40 years due to eradication &
risk: 1 or 2 per million die from vaccinia virus complication.
Now a Category A Biological Warfare Agent; easily spread by
contact or aerosol spray; 30% mortality

Black plague: 1/3 pop. of Europe (25 mil) died during

one epidemic (1346-50).

Antibiotics have now controlled. Lines on ships to dock?

The Triumph of Death: Pieter Brueghel

the Elder, Flemish painter

www.artchive.com/.../B/bruegel/death.jpg.html

Emerging Diseases: Suddenly Prevalent & Include Both New

and Reemerging Diseases- Additional Threat

Legionnaires Disease: American Legion Convention in

Philadelphia in 1976
Lyme Disease
AIDS: Acquired Immune Deficiency Syndrome (HIV)
Hantavirus Pulmonary Syndrome: film on this later
Mad Cow Disease: prions
Ebola Hemorrhagic Fever
Asian Flu (1957) H2N2;Bird Flu, H5N1 (1997), Swine Flu, H1N1
(2009), e. t. c. All were pandemic and caused by antigenic shift
except Bird Flu which jumped from birds to humans! * (antigenic
reassortment in swine)
Severe Acute Respiratory Syndrome (SARS):corona virus; 50%
death rate in those over 65.
Few of the above are really new, but an increased incidence &
wider distribution (globalization) have brought them to our
attention. * see next slide

New vaccine prepared each year against major strain circulating. Vaccine
efficacy wanes with time as new surface antigens appear from mutations in
genes encoding new surface antigens. Antigenic drift
Influenza strains that originate in birds and humans can also both infect
swine. If pig infected with both, viral genomes (segments) can be mixed,
forming reassortment viruses. Can cause influenza pandemic in humans.

Viral Hemorrhagic Fever (VHF) Viruses

Subgroup of dangerous & most feared

viral pathogens & are the most lethal
infectious agents known.
Cause hemorrhagic fevers
Special Pathogens Branch of the CDC
handles these under biosafety level 4 (BSL4)

Highest level of biological containment that is

used only when working with samples that
pose a high level of risk of life-threatening
disease & no effective treatment or vaccines
exist.

VHF cause severe symptoms and show

high rate mortality.

Hantavirus only one endemic in US (1993)

4 Corners (now understand the vectors/transmission)

Ebola: endemic in parts of Africa 67% mortality

Subdisciplines: Industrial
Microbiology
Industrial Microbiology:

Old definition: study of fermentation processes (alcohol and production of

beer and wine)
New definition: conversion of raw materials into desirable end products by
selected microorganisms (large scale) & includes: (later slide on methane and
ethanol)

Primary metabolites: production of products necessary for microbial growth like

amino acids, organic acids, alcohol, certain enzymes, etc
Secondary metabolites: production of products by the microorganisms not
necessary for its growth; like antibiotics, steroids, ethanol, etc

Some products made using microorganisms as a bag of enzymes to take a

compound and convert it to a different compound.

Ex: 6 aminopenicillanic acid many different types of penicillin antibiotics

Products now made using the new genetic engineering techniques to produce
products cheaply. Ex. Human Insulin

Led to new subdiscipline: Biotechnology

Subdisciplines: Other Applied

Areas

Food and Dairy Microbiology: prevention of food spoilage: ex: cold

temperatures, canning, freeze drying, heat (pasteurization),
preservatives, radiation, etc.

Prevention of food borne disease from microbes

Not all harmful, as some dairy products depend on microbial
transformations.

Agricultural/Soil Microbiology: Examples: nitrogen fixing legumes

(bacteria in root nodules convert N2 to NH3 that plants use for
growth); bacteria in rumen of cows digest cellulose; microbial
diseases of crops and animals (mad cow disease); use of biological
pesticides, prevention of mycotoxins (peanut butter), etc
Sanitary Microbiology: water and waste, water treatment, solid
organic wastes
Aquatic Microbiology: Microbial activities in water (overlap with
Sanitary)

t
Applications
A. Methane Gas: funnel
collecting gas produced in
swamp sediments

B. Ethanol Plant: corn

Impact of Microbiology
o

Basic studies of microorganisms led to advances

in knowledge that had major impact on our lives
o
o

Early impact on medicine, food & beverages, industrial

products
But, the most important impact was the use of
microorganisms as MODEL SYSTEMS which led to
increased knowledge about cells including:
o

Genetics, metabolism: i.e. provided the model to develop an

understanding of life processes, not only in microbes, but also
in plants, animals and humans.
This knowledge impacted our ability to control infectious
diseases and through basic studies on how genes control cells,
scientists could also begin to understand how genetic diseases
or inborn errors of metabolism occurred.

Basic Science Subdisciplines

Basic Emphasis: See table 1.3 for descriptions

Microbial Systematics
Microbial Ecology: Microbial Diversity in habitats;
interactions with other living organisms
Microbial Physiology
Cytology
Bacterial Genetics: advances in this field gave rise to
the era of molecular biology and biotechnology
Molecular Biology
Biotechnology
Thus, today microbial sciences have evolved into
molecular microbiology biotechnology, genomics,
proteomics.

Focus of Microbiology Revolves

Around Two Broad Themes

Understanding Basic Life Processes

All cells have much in common: microbes good simple

models to study.

Escherichia coli was model to understand Central Dogma of

Molecular Biology

DNA RNA polypepides (protein)

Also all the biochemical metabolic pathways.

Applying Our Knowledge About Microorganisms

for the Benefit of humankind
Solving practical problems in medicine, agriculture,
and industry
Good example of this follows: 33 years ago
Related to Subdiscipline: Industrial Microbiology

Micro Hits Wall Street

o

1980: Wall Street: over 30 years ago

1000s of buyers rushed to purchase stock in a new,

obscure company that decided to go public.
Price/share increased 150% in a matter of minutes

Not an oil company locating a new reserve

Only 140 employees
No track record
Highly Speculative

Why were so many people excited about

this company?

Genentech, Inc

Genetic engineering technology

Definition: Apply gene technology or

recombinant DNA technology to development of
products:
By transferring defined genes into rapidly
growing microorganisms, it is now possible to
synthesize in an in vivo system thousands of
products useful to humanity
Ex: Vaccines - recombivax HB, human
insulin, antiviral agents - interferon,
hormones - HGH (human growth hormone)
- Somatostatin

New Field Developed: Biotechnology

Biotechnology uses genetically modified

microorganisms to synthesize products of high
commercial value.

Biotechnology uses the tools of genetic engineering.

Advantage: microbes can make a lot of gene product;

two examples:

Interferon:

100 Liters of human blood to produce 1 mg of interferon that we

now make from 1 Liter of Escherichia coli

Somatostatin:

100,000 sheep brains, make same amount with 2 L of E. coli

Bioremediation

Definition: the use of living organisms to

degrade pollutants in the environment
Examples:

Bacteria being used to degrade oil in oil spills

Bacteria degrade polychlorinated biphenyls used as
pesticides & trichloroethylene used in dry cleaning.
Uranium contamination: movement of radioactive
materials offsite via ground water from where
uranium ores have been stored. (U: long half-life)

Bacteria reduce U6+ U4+ (insoluble) limits movement

Couple oxidation of organic matter & H 2 to reduction of U6+
Organic e- donars injected into U contaminated aquafers

Cell as Fundamental Unit of Life

Cell is fundamental unit of life: Cell membrane defines compartment that makes
up the Cell (invariant structure): not closed system; semipermeable
Invariant structures (all cells have this): cell membrane, ribosomes, DNA,
RNA
Variant structures: cell wall, mitochondria, chloroplast, e. t. c.
Characteristics of microbial cellular life: Figure 1.3
Properties of All Cells:
Metabolism: all chemical reactions of the cell.
Reproduction: also, regeneration: repair and replacement
Evolution: Characteristics of cells change over time: Evolve (natural
selection acting on variations caused by mutation).
Characteristics of Some Cells
Differentiation: confusing; also used to describe how cell divisions in
multi-cellular lead to specialization of function
Communication: cells respond to chemical signals
Movement: not all do so

Properties of Cells

Cells as Coding Devices (Genetic functions)

and Machines (Catalytic Functions)

Cells can be viewed in two ways:

Chemical machines (Catalytic Functions) that

carry out chemical transformations within the
confines of a cellular structure using biological
catalysts, enzymes
Two are linked as Genetic functions code for
polypeptides that comprise the enzymes that
carry out catalytic functions (metabolism)

Coding devices (Genetic Functions), analogous to

computers, which store and process genetic
information (DNA) that is eventually passed on to
offspring during reproduction. Central Dogma

Origin of Earth

Origin of cellular life

Cyanobacteria

Began oxygenation around 3 bya

Eukayotes: 2 bya

3.8 bya (Earth 4.6 bya)

nucleated cells: include both

microbial and multicellular

Current oxygen levels not

achieved until 500-800 million
years ago.
Plants and animals: half bya
80% of Earths History was
exclusively microbial
LUCA: Last Universal
Common Ancestor

Distribution of Microbes

Marine sediments cover more than two thirds of the Earth s surface and have been
estimated to contain as much as one-third of Earths prokaryotic biomass (Whitman et
al., 1998).
Most microbes do not reside on earths surface but instead lie underground in oceanic
and terrestrial subsurface . Surface soils and waters contain only small %

Milestones in Early History

Look at Table 1.2. (13th ed.) Need to know early

history impact:

1664 Robert Hooke: molds

1684 Anton van Leeuwenhoek-1st observation of
bacteria
1798 Jenner introduces small pox vaccination
(human cow pox pustules)
1867 Lister: antisepsis preventing infections in
surgery
1864 Pasteur resolves the problem of spontaneous
generation
1881 Koch grows pure culture of anthrax
microorganism

Three Things Needed for

Microbiology to Develop as a
Science

Microscopy (1): not simple microscopes

like that of Hooke &Van Leeuwenhoek:
needed compound; also better resolution
II. Laboratory Cultivation

Sterilization and Aseptic Techniques(2)

Pasteurs work disproving spontaneous generation

Pure Culture Methods (3)

Kochs work on cause of infectious disease

First Known Description of

Microbes: 1665
a. Hookes
Microscope:
b. Mold

Leeuwenhoeks Microscope

a. Leeuwenhoeks
microscope
b. Drawings of
bacteria
c. Human blood
smear with rbcs.
Reported findings in
Letters to Royal
Society of London in
1684.

Historical Perspective
Thus, development of microbiology as a discipline awaited
advances in microscopy & laboratory cultivation of microbes

Microscopy: First to see microorganisms in any detail were

probably Van Leeuwenhoek & Huygens.

Limits of Van Leeuwenhoeks single lens (simple)

microscope lens never magnified over 300x

Typical bacterial coccus: 0.75m in diameter. We can see

these with our compound microscope because its
resolution is 0.2 m (oil immersion lens 1000x)

Leeuwenhoeks microscope was around 250x

magnification instead of 1000x of our compound in lab.
i.e. as good. 0.2 um x 4 =0.8 limit resolution.

Therefore, the typical 0.75 coccus was not resolvable.

Resolving power = diameter of smallest resolvable object =

wavelength/ 2 X NA; for 500 nm wavelength; NA=1.25 :
500/2(1.25) = 200 nm=d 0.2um

Historical Perspective

Laboratory Cultivation: aseptic and sterilization

techniques developed from the controversy over
the origin of living matter:

Spontaneous Generation: Know Pasteurs experiment

to disprove: led to sterilization by heat
Aseptic Techniques: precautionary measures taken to
prevent contamination of cultures, sterile media,
sterile instruments, etc., and/or infection of persons,
animals, plants by extraneous microorganisms.

Louis Pasteur
(1822-1895)

Saved the French beer

industry
Anthrax, rabies vaccine
Transformations of organic
matter due to microbes
Discovered anaerobic life
Disproved spontaneous
generation of
microorganisms

Historical Perspective

Laboratory Cultivation (continued): pure culture and aseptic

techniques which developed from Kochs work on the nature &
cause of communicable disease
Diseases which spread through populations were called
contagious; the unknown thing which was spread through the
population was called the contagion. After the discovery of
microorganisms, it was widely held that they were responsible.
1845 Berkeley: mold causes Irish potato blight
Semmelweis, Lister: evidence for importance of asepsis
But, not until work of Robert Koch, a physicist, was the germ
theory of disease established. Koch worked with anthrax and
developed methods for laboratory growth of microorganisms in
pure culture. *Know his postulates
Used agar as solidifying agent: draw diagram

Robert Koch
(1843-1910)

Proved bacterial
causation of anthrax
Demonstrated
biological specificity
of disease agents
Experimental
application of
Henles principles of
infection (Kochs
postulates)

Properties of Agar Diagram

Melt Agar at 100 C

0

Lower Temperature and it

remains liquid until it drops
below around 40 0 C.
When solid, and then raise
temperature from (a) (30 0
C), it remains solid until
melting at 100oC (b).
Thus, at 60 o C it can be
either a liquid or solid
depending on initial state.

Solid Media, Petri Plate, & Pure

Cultures

KOCH PLATE (c)

PETRI PLATE

COLONIES ON BLOOD AGAR

Melt Nutrient Agar 100oC

Cool to 50oC & add
Sheep rbc & mix
Pour into plate
Solidifies at room T

Agar is has ideal

properties as solidifying
agent

Agar is has ideal

Properties as solidifying
agent

Kochs Postulates

Robert Koch (19th century) provided the first

experimental evidence for the theory that
microorganisms cause disease. Through his work, he
developed criteria, now called Koch's postulates, for
proving that a specific microorganism causes a specific
disease. With these postulates as a guide, Koch and
other microbiologists discovered the causes of many
important diseases of humans and other animals.
Kochs Postulates: In developing his postulates, Koch
worked with anthrax, a spore forming bacterium that
is found mostly in cattle, but that can also infect other
animals. He experimented with mice and observed
with microscopy that the blood of diseased mice
contained high concentrations of anthrax bacteria.

Kochs Simple Experiment to Show

Anthrax was not due to a chemical toxin

Mouse Model: Took small sample of blood

from infected mouse and transferred to
uninfected mouse disease
Sample from 2nd transferred to 3rd disease
3rd 4th 5th19th 20th
Each blood sample as infectious as 1st
Toxin? Would have been diluted out
Conclusion: Not a toxin and had to be capable
of replication.

Kochs Postulates
1.

2.
3.

4.
o

The suspected pathogenic organism should be

present in all cases of the disease and absent
from healthy animals
The suspected organism should be grown in
pure culture away from the animals body
Such a culture when inoculated into susceptible
animals, should initiate the characteristic
disease symptoms
The organism should be reisolated and shown
to be the same as the original
These postulates form the basis of medical microbiology

Pure Culture Technique: Streak

in Sections: Flame Loop
Between Sections

The Growth of Microbiology in

the 20th Century
Microbiology

Characterizing agents of infectious disease

Study of immunity and its relation to disease
Search for chemotheraputic agents
Chemical activities of microorganisms
Contributed significantly to the rise of molecular
biology/biochemistry

The Growth of Microbiology in

the 20th Century

1941 - Beadle & Tatum: biochemical

mutants of the fungus Neurospora
1943 Delbruck & Luria: mutations in
bacteria
1944 Avery, McLeod, & McCarty:
bacterial transformation, DNA is the
hereditary material
Set stage for advent of molecular biology