The Main Themes of Microbiology

Chapter 01
The Main Themes of

Microbiology
Lecture Outline
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• Section 1.1:
The Scope of
Microbiology
Learning Outcomes
• List the various types of microorganisms.
• Identify multiple professions using microbiology.
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• The Scope of Microbiology (1)
Microbiology: the specialized area of biology that deals with

organisms too small to be seen with the naked eye
• Microorganisms or microbes
• Germs, viruses, or agents
• “Bugs”
Major groups of microorganisms:

• Bacteria
• Algae
• Protozoa
• Helminths
• Fungi
• Viruses: noncellular, parasitic, protein-coated genetic
elements that cause harm to host cells
Microbes are easy and difficult to study

• Reproduce rapidly, large populations can be grown in the
laboratory
• Can’t be seen directly, must be analyzed through indirect
methods in addition to using microscopes
Microbiologists study:
• Cell structure and function
• Growth and physiology
• Genetics
• Taxonomy and evolutionary history
• Interactions with living and nonliving environment
• Branches of Microbiology (1)
Medical Microbiology
• Deals with microbes that cause
diseases in humans and animals
Public Health Microbiology and
Epidemiology
• Monitor and control the spread of
diseases in communities
• USPHS, CDC, WHO
• Branches of
Immunology
Microbiology • Complex web of protective
(2) substances and cells produced in
response to infection
• Includes vaccination, blood testing,
and allergy
• Role of the immune system in
cancer and autoimmune diseases
Industrial Microbiology
• Safeguards our food and water
• Biotechnology
• Microbes used to create amino
acids, beer, drugs, enzymes, and
vitamins
• Branches of
Microbiology (3)
Agricultural Microbiology
• Relationships between microbes and
domesticated plants and animals
• Plant specialists, animal specialists
Environmental Microbiology
• Study the effect of microbes on the
earth’s diverse habitats
• Aquatic, soil, and geomicrobiology,
and astrobiology
• Concept Check (1)
• What types of organisms are considered microbes?

• What types of cells can viruses infect?
• List and describe three branches of microbiology.
• Section 1.2:
The Impact of Microbes on Earth:
Small Organisms with a Giant
Effect
Learning Outcomes
• Describe the role and impact of microbes on the earth.
• Explain the theory of evolution and why it is called a theory.
• The Impact of Microbes on Earth
(1)
• Microbes have shaped the development of the
earth’s habitats and the evolution of other life forms
for billions of years
• Single-celled organisms arose 3.5 billion years ago
and were the only living inhabitants until ~2.9 billion
years ago
• Bacteria, archaea, and eukaryotes arose from the
last universal common ancestor (LUCA)
• The Impact of Microbes on Earth (2)
Eukary: true nucleus

• Cells with a nucleus are classified as eukaryotes
Prokary: pre nucleus

• Bacteria and archaea do not have a nucleus and have been
traditionally classified as prokaryotes
• This classification is no longer used because bacteria and
archaea are so distant genetically
• Evolutionary Time Line
Jump to long description
Bacteria are ubiquitous. They are found:

• deep in the earth’s crust
• polar ice caps
• oceans
• inside the bodies of plants and animals
Evolution: the accumulation of changes that occur in

organisms as they adapt to their environments
Theory of Evolution:
• Documented every day in all corners of the planet
• An observable phenomenon testable by science
• A label for a well-studied and well-established natural
phenomenon
• Microbial Involvement in
Shaping Our Planet (1)
Microbes are deeply involved in the flow of energy and
food through the earth’s ecosystems
• Bacteria: anoxygenic photosynthesis
• The production of oxygen by microbes allowed species
diversification
• Photosynthetic microorganisms (bacteria and algae) account
for more than 70% of the earth’s photosynthesis, contributing
the majority of the oxygen to the atmosphere
• Examples of Microbial
Habitats: Pond with Algae
(a) © Jerome Wexler/Science Source

Decomposition:
• Breakdown of dead matter
and wastes
• Accomplished by bacteria
and fungi
(b) © Michel & Christine Denis-Huot/Science Source
Microbes are the main forces that drive the structure

and content of soil, water, and atmosphere
• Gas production by microbes
• Microbes living within the earth’s crust
• Bacteria and fungi living in complex associations with plants
and animals
• Describe the difference between a prokaryote and

a eukaryote.
• Describe the basic tenets of the Theory of
Evolution.
• True/False: Microscopic organisms produce more
oxygen than plants.
• True/False: More than 50% of the microbes on the
planet live below the earth’s crust.
• Section 1.3:
Human Use of
Microbes
Learning Outcome
• Explain one old way and one new way that humans
manipulate organisms for their own uses.
• Human Use of Microorganisms (1)
Humans have been using microorganisms for thousands

of years to improve life and even shape civilizations
• Yeast for production of bread, wine, and beer
• Other fungi used for cheese production
• Moldy bread used in Egypt to treat wounds
Biotechnology:
• Manipulation of microorganisms
to make products in an industrial
setting
Genetic Engineering: (a) NREL/US Department of Energy/Dennis Schroeder
• Manipulates the genetics of

microbes, plants, and animals for
the purpose of creating new
products and genetically
modified organisms (GMOs)
(b) © Bloomberg via Getty Images
Recombinant DNA
technology:
• Techniques that allow the
transfer of genetic material
from one organism to another
and deliberately alter DNA
Bioremediation:
• Introduction of microbes (c) © Accent Alaska.com/Alamy
into the environment to
restore stability or to clean
up toxic pollutants
• Name three products produced by genetically

modified organisms that benefit humans.
• Describe one method in which microbes are used
for bioremediation.
• Section 1.4:
Infectious Diseases and the Human Condition
Learning Outcome
• Summarize the relative burden of human disease caused by
microbes, emphasizing the differences between developed
countries and developing countries.
• Infectious Diseases and
the Human Condition
(1)
Pathogen: any agent such as a virus, bacterium, fungus,
protozoan, or helminth that causes disease
• Nearly 2000 different microbes can cause disease
• Top Causes of Death—All Diseases
United States No. of Deaths Worldwide No. of Deaths
1. Heart disease 611,105 1. Heart disease 7.3 million
2. Cancer 584,881 2. Stroke 6.7 million
3.Chronic lower respiratory 149,205 3.Lower-respiratory infections 3.1 million

diseases (influenza and pneumonia)*
4. Accidents (unintentional 130,557 4.Chronic obstructive 3.1 million
injuries) pulmonary disease
5.Stroke (cerebrovascular 128,978 5.Trachea, bronchus, lung 1.6 million
diseases) cancers
6. Alzheimer’s disease 84,767 6. HIV/AIDS 1.5 million
7. Diabetes 75,578 7. Diarrheal diseases 1.5 million
8. Influenza and pneumonia 56,979 8. Diabetes 1.5 million
9.Nephritis, nephrotic 47,112 9. Road injury 1.3 million

syndrome, and nephrosis
10. Intentional self-harm (suicide) 41,149 10. Hypertensive heart disease 1.1 million
Diseases most clearly caused by microorganisms: influenza, pneumonia, HIV/AIDS, and diarrheal diseases
• Causes of Death in the United
States and the World

the Human Condition (2)
Malaria:
• Kills between 440,000 and 700,000 people every year
• Transmitted by mosquitoes
• Prevention of infection is through the use of bed nets, which
although inexpensive, are too expensive for poor families
the Human Condition
(3)
New (emerging) diseases as well as older (reemerging)
diseases are increasing
• Ebola, AIDS, hepatitis C, and viral encephalitis
Polio, leprosy, and parasitic worm diseases have largely

been eradicated
the Human Condition (4)
Certain diseases once considered noninfectious are
now found to be caused by microbes:
• Gastric ulcers caused by Helicobacter pylori
• Link between certain cancers and bacteria and viruses
• Cocksackie virus has been associated with diabetes and
schizophrenia
• Multiple sclerosis, OCD, coronary artery disease, obesity
linked to chronic microbial infections
the Human Condition
(5)
First Golden Age of Microbiology: “obvious” diseases
were characterized and cures or preventions were
devised
Today, we are discovering the subtler side of
microorganisms and the quiet, slow, destructive
diseases they cause
• Female infertility caused by Chlamydia infection
• Liver cancer (hepatitis viruses) and cervical cancer (human
papillomavirus)
• Infectious Diseases
and the Human
Condition (6)
An increasing number of patients with weakened
immune systems are subject to infections by common
microbes not pathologic to healthy people
Drug-resistant microbes also contribute to the increase
in infectious disease
• True/False: All microbes cause disease.

• Why is there a difference between the top 10 causes
of death in the United States versus worldwide?
• Name three connections between diseases
considered to be noninfectious and a microbe.
• Section 1.5:
The General
Characteristics of
Microorganisms
Learning Outcomes
• Differentiate among bacteria, archaea, and eukaryotic
microorganisms.
• Identify a fourth type of microorganism.
• Compare and contrast the relative sizes of the different
microbes.
• General Characteristics of Microorganisms (1)
Bacterial and Archaeal cells:

• About 10x smaller than eukaryotic cells
• Lack organelles: small, double-membrane-bound structures
that perform specific functions
The majority of microorganisms are single-celled (all

bacterial and archaeal and some eukaryotes)
• Cell Structure
• General Characteristics of Microorganisms (2)
Helminths (worms) are not microorganisms but are

included in the study of infectious disease:
• They are transmitted similarly to bacterial diseases
• The human body responds to them in the same way as it
responds to bacterial diseases
• Five Types of Microorganisms
Top Left) CDC; (Middle Left) CDC/Dr. Lucille K. Georg; (Bottom Left) © Nancy Nehring/E+/Getty Images RF; (Bottom Center) CDC/Janice Carr; (Bottom Right) CDC
• Lifestyles of Microorganisms
Majority of microorganisms:
• Live in habitats such as soil and water
• Are relatively harmless and often beneficial
• Derive food and other factors from the nonliving environment
Parasites:
• Harbored and nourished by the host
• Cause damage and disease in the host
• In terms of size, how are eukaryotes different from

bacteria and archaea?
• Give three examples of eukaryotic organelles.
• Why are helminths (worms) considered in the study
of microbiology?
• Section 1.6:
The Historical Foundations
of Microbiology
Learning Outcomes
• Make a time line of the development of microbiology from
the 1600s to today.
• List some recent microbiological discoveries of great impact.
• Explain what is important about the scientific method.
• Early Ideas About Disease Transmission
Certain foods spoiled, became inedible, or caused

illness
Black plague and smallpox caused by some kind of

transmissible matter
Belief in spontaneous generation
• Pasteur Disproved Spontaneous Generation
© Steve Gschmeissner/Science Source

• Development of the Microscope (1)
Robert Hooke:
• First observations of microbes in the
1600s
Antonie van Leeuwenhoek:
• Made a crude microscope to examine (a) © Biophoto Associates/Science Source; (b) CDC/Dr. Lucille K. Georg
threads in fabrics
• Made drawings of what he called
“animalcules” in rainwater and
scraped from his teeth
© Tetra Images/Alamy RF
• Biofilms
© Steve Gschmeissner/Science Source
• Development of the Microscope (2)
Modern microscopes:
• More refined lenses, a condenser, finer focusing devices, and
built in light sources
• Student microscopes are not greatly different in structure and
function than early microscopes
• The Century of Biology
1970s: Discovery of restriction enzymes

1980s: The invention of the PCR technique
2000s: The importance of small RNAs
2010s: The role of the human microbiome
Science is an ever-evolving collection of new
information
• Polymerase Chain Reaction
© Adam Gault/age fotostock RF
• Establishment of the Scientific Method
Scientific method:
• General approach taken by scientists to explain a natural
phenomenon
Hypothesis:
• A tentative explanation to account for what has been
observed or measured
• Deductive and Inductive Reasoning (1)
Deductive Reasoning:
• Using general principles to explain specific observations
Inductive Reasoning:
• The process of discovering general principles by careful
examination of specific cases
• Making observations through experimentation
• A discovery process that leads to the creation of a general
principle
• Deductive and Inductive Reasoning (2)
© Tom Grill/Corbis RF Jump to long description

• The Scientific Method (1)
A lengthy process of experimentation, analysis, and

testing
• Eventually leads to conclusions that either support or refute
the hypothesis
• If experiments do not uphold the hypothesis, the hypothesis
or some parts of it are rejected
• The hypothesis is discarded or modified to fit the results of
the experiment
If experimentation supports the hypothesis, it is not

immediately accepted as fact
• The hypothesis must be tested and retested
• The results of the experiment must be published and
repeated by other investigators
Theory:
• A collection of statements, propositions, or concepts that
explains or accounts for a natural event
• The entire body of ideas that expresses or explains many
aspects of a phenomenon
• A viable declaration that has stood the test of time and has
yet to be disproved by serious scientific endeavors
Science and its hypotheses and theories must progress

with technology
• Advances in instrumentation allow new, more detailed views
of living phenomena
• Old theories may be reexamined and altered and new ones
proposed
• Characteristics of Effective Scientists
Curiosity
Open-mindedness
Skepticism
Creativity
Cooperation
Readiness to revise their views of natural processes as
new discoveries are made
• The Development of
Medical Microbiology
Early experiments showed that microbes are
everywhere:
• Air and dust are full of them
• The entire surface of the earth and its waters, and all objects
are inhabited by them
• The Discovery of Spores
and Sterilization
John Tyndall:
• Found that microbes in the dust and air have high heat
resistance
Ferdinand Cohn:
• Discovered and described bacterial endospores
• Sterile: completely free of all life forms including endospores
and virus particles
• Development of
Aseptic Techniques
Robert Koch: (1)
• Linked a specific microorganism with a specific disease
Dr. Oliver Wendell Holmes and Dr. Ignaz Semmelweis:

• Showed that women became infected in the maternity ward
after examinations by physicians who had been working in the
autopsy rooms
• Development of
Aseptic Techniques (2)
Joseph Lister:
• First to utilize hand washing
and misting operating
rooms with antiseptic
chemicals
• Techniques became the
foundation for modern
microbial control still in use © Bettmann/Corbis
today
• Discovery of Pathogens and the
Germ Theory of Disease
Pasteur:
• Invented pasteurization
• Showed that human diseases could arise from infection
Robert Koch:
• Established a series of proofs that verified the germ theory of
disease
1. Spontaneous generation was disproven by

with his experiment using swan-necked
flasks.
2. Polymerase chain reaction (PCR) was invented in
3. When a hypothesis is supported by a growing body

of data and survives rigorous scrutiny, it is known as
a
4. Aseptic techniques were developed by
• Section 1.7:
Naming, Classifying, and Identifying
Microorganisms
Learning Outcomes
• Differentiate among the terms nomenclature, taxonomy, and
classification.
• Create a mnemonic device for remembering the taxonomic
categories.
• Correctly write the binomial name for a microorganism.
• Draw a diagram of the three major domains.
• Explain the difference between traditional and molecular
approaches to taxonomy.
• Nomenclature: Assigning Specific Names
Nomenclature:
• The assignment of scientific names to the various taxonomic
categories and individual organisms
• Understanding and appreciation of microorganisms will be
improved by learning a few general rules about how they are
named
• Binomial System of Nomenclature
Binomial system:
• A combination of the generic (genus) and species name
• The genus name is always capitalized and the species name
begins with a lower case letter
• Both names should be italicized when in print or underlined
when written by hand
Abbreviations:
• The genus name can be abbreviated to save space or if the
genus name has already been stated
• Example: Staphylococcus aureus can be abbreviated as S.
aureus
• Classification: Constructing Taxonomy
Classification:
• Attempts the orderly arrangement of organisms into a
hierarchy of taxa (categories)
Identification:
• The process of discovering and recording the traits of
organisms so they can be recognized or named and placed
in a taxonomic scheme
• Levels of Classification
From most general to most specific:

• Domain
• Kingdom
• Phylum or Division
• Class
• Order
• Family
• Genus
• Species
• Origin and Evolution
of Microorganisms (1)
Taxonomy:
• The science of classifying biological species
• Developed by Carl von Linné in the 1700s
• Lays down the basic rules for classification
• Establishes taxonomic categories
• Used to organize all of the forms of modern and extinct life
• Sample Taxonomy
DOMAIN: Eukarya (all eukaryotic organisms)
Eukaryotic, heterotrophic, Kingdom: Animalia Kingdom: Protozoan Includes

and mostly multicellular protozoa and
algae
Possess notochord, dorsal Phylum: Chordata Phylum: Ciliatea Only protozoa

nerve cord, pharyngeal with cilia
slits (if only in embryo)
Possess hair, Class: Mammalia Class: Hymenostomea Single cells with

mammary glands regular rows of
cilia; rapid
swimmers
Digital dexterity, Order: Primates Order: Hymenostomatida Elongated oval

large cerebral cells with cilia in
cortex, slow the oral cavity
reproductive rate,
long life span
Large brain, no tail, Family: Hominoidea Family: Parameciidae Cells rotate

long upper limbs while swimming
and have oral
grooves
Genus: Homo Genus: Paramecium

Erect posture, large cranium, Pointed, cigar-shaped cells with
opposable thumbs macronuclei and micronuclei
Species: sapiens Species: caudatum
Humans Cells cylindrical,
long, and pointed
at one end
• Origin and Evolution
of Microorganisms
Phylogeny:
(2)
• The taxonomic scheme that
represents the natural
relatedness between groups
of living things
• Based on evolution
• Universal Tree of Life
Charles Darwin and Ernst Haeckel:

• Two kingdoms: Plants and Animals
• Based on morphological characteristics
• Third and fourth kingdoms named by Haeckel: Protista and
Monera
Robert Whittaker
• Added a fifth kingdom: Fungi
• All kingdoms encompassed the two cell types: prokaryotic and
eukaryotic
• Whittaker system became the standard
• Tree of Life: A phylogenetic System

• How are the names of bacteria assigned and

abbreviated?
• What are the eight taxonomic categories?
• What are the five kingdoms of the Whittaker system
of classification?
• What are the three domains of the Woese-Fox
system of classification?
Appendix of Image Long Descriptions
Evolutionary Time Line Long Description
Bar graph showing that the first cells appeared 3.5 billion years ago and that eukaryotes, archaea, and
bacteria arose 2.9 billion years ago from LUCA. Insects, reptiles, mammals, and humans appeared much later.
Jump back to slide containing original image

Causes of Death in the United States
and the World Long Description
Noncommunicable diseases are much more frequent than communicable diseases in both the United States
(>400 deaths per 100,000) and the world (~525 deaths per 100,000). The United States experiences relatively
few communicable diseases (<50 deaths per 100,000) compared to the number of communicable diseases
worldwide (~180). Injuries are more prominent than communicable diseases in the US and only slightly
higher worldwide than in the US (both less than 100 deaths per 100,000).

Pasteur Disproved Spontaneous
Combustion Long Description
Pasteur filled flasks with broth and fashioned their openings into long, swan-neck-shaped tubes. The broth in
the flasks was still open to the air but curved so that gravity would deposit any contaminants in the neck of
the flask. He boiled the flasks to sterilize the broth and incubated them to encourage the growth of microbes.
As long as the neck of the flask was intact, no microbes grew. If the swan-necked flask was broken off so that
dust could fall into the container, microbes grew and the broth became cloudy.

Deductive and Inductive Reasoning (2)
Long Description
Deductive reasoning: Knowing that opening attachments from unknown senders can introduce viruses or
other bad things to your computer, you choose the specific action of not opening the attachment. Inductive
reasoning: You have performed the specific action of clicking on unknown attachments three different times
and each time your computer crashed. This leads you to conclude that opening unknown attachments can be
damaging to your computer.

Tree of Life: A phylogenetic System Long
Description
A system for representing the origins of cell lines and major taxonomic groups. There are three distinct cell
lines placed in superkingdoms called domains. The first primitive cells, were ancestors of both lines of
“prokaryotes” (Domains Bacteria and Archaea), and the Archaea emerged from the same cell line as
eukaryotes (Domain Eukarya).

The Main Themes of Microbiology

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Chapter 01

The Main Themes of

Microbiology: the specialized area of biology that deals with

Major groups of microorganisms:

Microbes are easy and difficult to study

• What types of organisms are considered microbes?

Eukary: true nucleus

Prokary: pre nucleus

Jump to long description

Bacteria are ubiquitous. They are found:

Evolution: the accumulation of changes that occur in

(a) © Jerome Wexler/Science Source

(b) © Michel & Christine Denis-Huot/Science Source

Microbes are the main forces that drive the structure

• Describe the difference between a prokaryote and

Humans have been using microorganisms for thousands

• Manipulates the genetics of

(b) © Bloomberg via Getty Images

• Name three products produced by genetically

3.Chronic lower respiratory 149,205 3.Lower-respiratory infections 3.1 million

9.Nephritis, nephrotic 47,112 9. Road injury 1.3 million

Jump to long description

Polio, leprosy, and parasitic worm diseases have largely

• True/False: All microbes cause disease.

Bacterial and Archaeal cells:

The majority of microorganisms are single-celled (all

Helminths (worms) are not microorganisms but are

• In terms of size, how are eukaryotes different from

Certain foods spoiled, became inedible, or caused

Black plague and smallpox caused by some kind of

Belief in spontaneous generation

Jump to long description

© Steve Gschmeissner/Science Source

© Steve Gschmeissner/Science Source

1970s: Discovery of restriction enzymes

© Adam Gault/age fotostock RF

© Tom Grill/Corbis RF Jump to long description

A lengthy process of experimentation, analysis, and

If experimentation supports the hypothesis, it is not

Science and its hypotheses and theories must progress

Dr. Oliver Wendell Holmes and Dr. Ignaz Semmelweis:

1. Spontaneous generation was disproven by

3. When a hypothesis is supported by a growing body

From most general to most specific:

Eukaryotic, heterotrophic, Kingdom: Animalia Kingdom: Protozoan Includes

Possess notochord, dorsal Phylum: Chordata Phylum: Ciliatea Only protozoa

Possess hair, Class: Mammalia Class: Hymenostomea Single cells with

Digital dexterity, Order: Primates Order: Hymenostomatida Elongated oval

Large brain, no tail, Family: Hominoidea Family: Parameciidae Cells rotate

Genus: Homo Genus: Paramecium

Charles Darwin and Ernst Haeckel:

Jump to long description

• How are the names of bacteria assigned and

Jump back to slide containing original image

Jump back to slide containing original image

Jump back to slide containing original image

Jump back to slide containing original image

Jump back to slide containing original image

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