Chapter 01

Lecture Outline

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1
 Section 1.1:
The Scope of Microbiology
Learning Outcomes: Section 1.1
• List the various types of organisms.
• Identify multiple professions using
microbiology.
 The Scope of Microbiology
• 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”
 The Scope of Microbiology
• Major groups of microorganisms:
– Bacteria
– Algae
– Protozoa
– Helminths
– Fungi
– Viruses: noncellular, parasitic, protein-coated
genetic elements
 The Scope of Microbiology
• 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
• http://learn.genetics.utah.edu/content/cells/scale/
 The Scope of Microbiology
• Microbiologists study:
– Cell structure and function
– Growth and physiology
– Genetics
– Taxonomy and evolutionary history
– Interactions with living and nonliving
environment
 The Scope of Microbiology
• Microbiology includes various branches of
study:
– Medical Microbiology
– Public health Microbiology and Epidemiology
– Immunology
– Industrial Microbiology
– Agricultural Microbiology
– Environmental Microbiology
The Scope of Microbiology
The Scope of Microbiology
 Concept Check
• 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 Section 1.2
• 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
• 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.
• Bacteria, archaea, and eukaryotes arose from
this ancestor.
 The Impact of Microbes on Earth
• Eu-kary: true nucleus
– Cells with a nucleus are classified as eukaryotes
• Pro-kary: 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 distinct genetically
The Impact of Microbes on Earth
 The Impact of Microbes on Earth
• Bacteria are ubiquitous. They are
found:
– Deep in the earth’s crust
– Polar ice caps
– Oceans
– Inside the bodies of plants and animals
 The Impact of Microbes on Earth
• 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
• 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 account for
more than 70% of the earth’s photosynthesis.
Microbial Involvement in
Shaping Our Planet
 Microbial Involvement in
Shaping Our Planet
• Decomposition:
– Breakdown of dead matter and wastes
– Accomplished by bacteria and fungi
Microbial Involvement in
Shaping Our Planet
 Microbial Involvement in
Shaping Our Planet
• 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
 Concept Check
• 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 Outcomes Section 1.3
• Explain one old way and one new way that
humans manipulate organisms for their
own uses.
 Human Use of Microorganisms
• 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
Human Use of Microorganisms
• Biotechnology:
– manipulation of microorganisms to make
products in an industrial setting
• Genetic Engineering:
– manipulates the genetics of microbes, plants,
and animals for the purpose of creating new
products and genetically modified organisms
(GMOs)
Human Use of Microorganisms
• Recombinant DNA technology:
– Techniques that allow the transfer of genetic
material from one organism to another and
deliberately alter DNA
• Bioremediation:
– introduction of microbes into the environment
to restore stability or to clean up toxic
pollutants
Human Use of Microorganisms
Human Use of Microorganisms
Human Use of Microorganisms
 Concept Check
• 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 Outcomes Section 1.4
• 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
• Pathogen: any agent such as a virus,
bacterium, fungus, protozoan, or helminth
that causes disease.
– Nearly 2,000 different microbes can cause
disease
Infectious Diseases and
the Human Condition
Infectious Diseases and
the Human Condition
 Infectious Diseases and
the Human Condition
• Malaria:
– Kills between 700,000 – 1.2 million 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
 Infectious Diseases and
the Human Condition
• New (emerging) diseases as well as older
(reemerging) diseases are increasing.
– AIDS, hepatitis C and viral encephalitis
• Polio, leprosy, and parasitic worm
diseases have largely been eradicated.
 Infectious Diseases and
the Human Condition
• 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
– The Borna agent has been linked to
schizophrenia
 Infectious Diseases and
the Human Condition
• 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.
 Infectious Diseases and
the Human Condition
• 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.
 Concept Check
• True/False: All microbes cause disease.
• Why is there a difference between the top 10
causes of death in the U.S. versus
worldwide?
• Name three connections between diseases
considered to be noninfectious and a
microbe.
 Section 1.5:
The General Characteristics
of Microorganisms
 Learning Outcomes: Section 1.5
• Differentiate among bacteria, archaea, and
eukaryotic microorganisms.
• Identify a fourth type of microorganism.
• Compare and contrast the relative sizes of
microbes.
 The General Characteristics of
Microorganisms
• Bacterial and Archaeal cells:
– About 10x smaller than eukaryotic cells
– Lack organelles: small, double-membrane-
bound structures that perform specific
functions
• All bacterial and archaeal cells and some
eukaryotes are single-celled.
The General Characteristics of
Microorganisms
 The General Characteristics of
Microorganisms
• 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
 Lifestyles of Microorganisms
• The majority of microorganisms live in
habitats such as soil and water and are
either harmless or beneficial.
• Parasites:
– Harbored and nourished by the host
– Cause damage and disease in the host
 Concept Check
• 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: Section 1.6
• Make a time line of the development of
microbiology from the 1600’s to today.
• List some recent microbiological
discoveries of great impact.
• Explain what is important about the
scientific method.
 The Development of the
Microscope
• 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
 The Development of the
Microscope
• Robert Hooke:
– First observations of microbes in the 1600’s
• Antonie van Leeuwenhoek:
– Made a crude microscope to examine threads in
fabrics
– Made drawings of what he called “animalcules” in
rainwater and scraped from his teeth
The Development of the
Microscope
The Development of the
Microscope
 The Development of the
Microscope
• 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
• 1970’s: Discovery of restriction enzymes.
• 1980’s: The invention of the PCR technique.
• 1980’s and beyond: The importance of biofilms
in infectious diseases.
• 2000’s: The importance of small RNAs.
• Science is an ever-evolving collection of new
information.
Biofilms
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
• 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
 The Scientific Method
• 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
 The Scientific Method
• 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
 The Scientific Method
• 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
 The Scientific Method
• 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
 The Scientific Method
• 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.
 The Development of
Aseptic Techniques
• Robert Koch:
– 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
 The Development of
Aseptic Techniques
• 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 today
 The 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
The Development of Medical
Microbiology
 Concept Check
• Spontaneous generation was disproven by
________ with his experiment using swan-necked
flasks.
• Polymerase chain reaction (PCR) was invented in
________.
• When a hypothesis is supported by a growing
body of data and survives rigorous scrutiny, it is
known as a _______.
• Aseptic techniques were developed by ________.
 Section 1.7:
Naming, Classifying, and
Identifying Microorganisms
Learning Outcomes Section 1.7
• Differentiate between the terms
nomenclature, taxonomy, and classification.
• Create a mnemonic device for remembering
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.
 Naming, Classifying, and Identifying
Microorganisms
• Nomenclature:
– Uses an array of new, unusual, and
sometimes confusing names for organisms
– Understanding and appreciation of
microorganisms will be improved by learning
a few general rules about how they are
named
 Naming, Classifying, and Identifying
Microorganisms
• Taxonomy:
– The science of classifying living beings
– Developed by Carl von Linné in the 1700’s
– Lays down the basic rules for classification
– Establishes taxonomic categories
– Useful in categorizing 2 million or more
different kinds of organisms
 Naming, Classifying, and
Identifying Microorganisms
• Classification:
– Attempts the orderly arrangement of
organisms into taxa
• Identification:
– The process of discovering and recording the
traits of organisms so they can be recognized
and placed in a taxonomic scheme
 Assigning Specific Names
• Binomial system:
– A combination of the 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
 Assigning Specific Names
• 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 S. aureus
 Levels of Classification
• From most general to most specific:
– Domain
– Kingdom
– Phylum or Division
– Class
– Order
– Family
– Genus
– Species
Human vs. Protozoan Classification
 The Origin and Evolution of
Microorganisms
• Phylogeny:
– The taxonomic scheme that represents the
natural relatedness between groups of living
things
– Based on evolution
 Systems of Presenting a
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 in the 1870’s
 Systems of Presenting a
Universal Tree of Life
• Robert Whittaker
– Added a 5th kingdom: Fungi
– All kingdoms encompassed the two cell types:
prokaryotic and eukaryotic
– Whittaker system became the standard in the
1960’s
Systems of Presenting a
Universal Tree of Life
 Systems of Presenting a
Universal Tree of Life
• Carl Woese and George Fox:
– Studied the small subunit of the ribosome
– Proposed a separate taxonomic unit:
Archaea
– Also proposed a new taxonomic system
representing three domains: bacteria,
archaea, and eukarya
Systems of Presenting a
Universal Tree of Life
 Concept Check
• 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?