Microbiology: A
Systems Approach,
2nd ed.
Chapter 1:
The Main Themes of Microbiology
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Chapter 1
Topics
– The Scope of Microbiology
– Impact of Microorganisms
– Human use of Microorganisms
– Infectious diseases and the human condition
– The General Characteristics of Microorganisms
– History of Microbiology
– Systematics (Taxonomy) and Evolution
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1.1 The Scope of Microbiology
• Microbiology: The study of living
things too small to be seen without
magnification
– Microorganisms or microbes -
microscopic organisms
– Commonly called “germs, bugs, viruses,
agents…” but not all terms are
accurate.
– Not all cause disease (most of them are
benign)
– Many of them are useful or even essential for3
Major Groups of Microorganisms
• Bacteria, Archaea, Algae, Protozoa,
Helminthes, and Fungi
• Viruses- non-cellular, parasitic, protein-
coated genetic elements that can infect all
living things, including other microorganisms
(most microbiologists do not consider
viruses “microorganisms” but “pathogens”)
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Branches of Microbiology
• Agricultural microbiology
• Biotechnology
• Food, dairy, and aquatic microbiology
• Genetic engineering and recombinant DNA
technology
• Immunology
• Public health microbiology and
epidemiology
• Many, many more
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Emerging Areas of Microbiology
• Emerging Pathogens
• Marine microbiology
• Geo-microbiology
• Astro- (Exo)-microbiology
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Importance of Microbiology
• First cellular organisms were bacteria
• Primary production and decomposition
as part of global biogeochemical cycles
• Human use of microorganisms
• Importance for human health
• Infectious diseases
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1.2The Impact of Microbes on Earth:
Small Organisms with a Giant Effect
• Microorganisms have a profound influence on all
aspects of the earth and its residents
• Bacterial-like organisms in the fossil record as far
back as 3.8 billion years ago (prokaryotes-
“organisms without a true nucleus”)
• ~2 billion years ago, eukaryotes (“organisms with a
true nucleus”) emerged
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Bacteria appeared approximately 3.8 billion years ago.
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Fig. 1.1 Evolutionary timeline
Ubiquity of Microorganisms
• Found nearly everywhere
• Occur in large numbers
• Live in places many other organisms cannot
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Figure 1.2
1.3 Human Use of Microorganisms
• Humans have been using
microorganisms for thousands
of years
– Baker’s and brewer’s yeast
– Cheeses & other dairy
products
– Moldy bread on
wounds
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Biotechnology & Bioremediation
• Biotechnology- when humans manipulate
(micro)organisms to make products in an industrial setting
– Genetic engineering- create new products and “genetically
modified organisms” (GMOs)
– Recombinant DNA technology- technology used to engineer
GMOs capable of synthesizing desirable proteins
(i.e. medicines, hormones, and enzymes)
• Bioremediation - activity of microbes in the environment
helping to restore stability or clean up toxic pollutants
– Oil spills
– Chemical spills
– Water and sewage treatment
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1.4 Infectious Diseases and
the Human Condition
• Pathogens - disease-causing “agents”
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The most common
infectious
diseases
worldwide.
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Figure 1.4
Worldwide Infectious Diseases
• Increasing number of emerging diseases
(SARS, AIDS, hepatitis C, viral encephalitis)
• Other diseases previously not linked to
microorganisms now are: gastric ulcers, certain
cancers, schizophrenia, multiple sclerosis,
obsessive compulsive disorder, coronary artery
disease …. and the list is growing ….
• Increasing number of drug-resistant strains of
disease-causing bacteria
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1.5 The General
Characteristics of
Microorganisms
• Cellular Organization
– “Prokaryotic” vs. “eukaryotic” cells
• Prokaryotic (bacterial and archaeal) cells are about
10 times smaller than eukaryotic cells
• Prokaryotic cells lack many cell structures such as
double membrane-bound organelles
• All prokaryotes are microorganisms, but only some
eukaryotes are
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There is a difference between the cell structure of a prokaryote
and eukaryote. Viruses are neither but are considered particles.
Fig. 1.5 Cell structure 17
There are six main types of microbes:
1.) Bacterium or Archaeon, 2.) Fungus, 3.) Alga, 4.) Virus,
5.) Protozoon (Protozoan), 6.) Helminth.
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Fig. 1.6 The six types of microorganisms
Viruses
• Are NOT independently living cellular organisms
• Much simpler than cells- basically a small
amount of DNA or RNA wrapped in protein and
sometimes by a additional lipid membrane
• Individuals are called a virus particle or virion
• Depend on the infected cell’s machinery to
multiply and disperse
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Microorganisms
vary in size -
1µm to 200 nm.
Fig. 1.7
The size of things 2
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Lifestyles of Microorganisms
• Majority of microorganisms lives a free existence called
“free-living” (in soil, water, rocks, for example) or as
“saprophytes (saprotrophs)”
• Some are parasites (mooching off goodies from living
beings, but can live freely), some of these are
opportunistic pathogens
• Fewer are obligate parasites (exo- or endo-parasitic),
some of these are pathogens
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Lifestyles of Microorganisms
What are the sources of
• Energy,
• Reductant and
• Carbon?
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1.6 The Historical
Foundations of
•
Microbiology
Key to the study of microorganisms was the development of
the microscope
• Earliest record of microbes was from the work of Robert
Hooke in the 1660s
• The most detailed observations of microbes was possible
only after Antonie van Leeuwenhoek created the single-
lens microscope, further perfected by Ernst Abbé abd Carl
Zeiss
(~late 19th century)
– Leeuwehoek is known as the father of bacteriology &
protozoology
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Microorganisms were first observed by Antonie van Leeuwenhoek,
using a primitive microscope.
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Fig. 1.9 Leeuwenhoek’s microscope
History of Microbiology
• Scientific Method
• Spores and sterilization
• Spontaneous generation
• Aseptic technique
• Germ theory
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Establishment of the Scientific Method
• Early scientists tended to explain natural phenomena
by a mixture of belief, superstition, and argument
• During the 1600s, true scientific thinking developed
• This led to the development of the scientific
method
– Formulate a hypothesis
– Most use the deductive approach to apply the scientific
method
– Experimentation, analysis, and testing ==> conclusions
– Results either support or refute the hypothesis
• Hypotheses can eventually become theories
• Theories can eventually become laws or principles
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Figure 1.10 8
The Development of Medical
Microbiology
• The Discovery of Spores and Sterilization
– Louis Pasteur- worked with infusions in the mid-
1800s
– John Tyndall- showed evidence that some
microbes have very high heat resistance and are
difficult to destroy
– Ferdinand Cohn- spores and sterilization
• The Development of Aseptic Techniques
– Physicians and scientist began to suspect that
microorganisms could cause disease
– Joseph Lister- introduced aseptic
technique 28
Spores and sterilization
• Some “microbes” in dust and air were
resistant to high heat.
• Spores were later identified.
• The term “sterile” was introduced, which
meant completely eliminating all life forms
from objects or materials.
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Spontaneous generation
Early belief that some forms of life could
arise from vital forces present in
nonliving or decomposing matter. (flies
from manure, etc)
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Louis Pasteur showed microbes caused fermentation &
spoilage, and disproved spontaneous generation.
Fig. 1.11 Louis Pasteur 32
Aseptic technique
Ignaz Semmelweis, a Hungarian
“OB/GYN” established link between
“infection” and diseases after
labor.
Joseph Lister an English Army Surgeon
first introduced the technique in order to
reduce microbes in a medical setting
and prevent wound infections.
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Germ theory of disease
Many diseases are caused by the
growth of microbes in the body and not
by sins, bad character, or poverty, etc.
• Robert Koch was the first to clearly
show the causal relationship between
bacteria as causal agents and disease
in infected animals (including humans).
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1.7 Taxonomy: Naming,
Classifying, and Identifying
Microorganisms
• Microbial nomenclature-
naming microorganisms
• Taxonomy- classifying living
things
originated over 250 years ago with the work of
Carl von Linné
• Identification- discovering, comparing
and recording the traits of organisms so
they can be named and classified
• Levels of Classification 34
Nomenclature
• Binomial (scientific) nomenclature
• Genus – Bacillus, always capitalized
• species - subtilis, lowercase
• Both italicized or underlined
– Bacillus subtilis (B. subtilis)
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Levels of Classification
• Domain
• Kingdom
• Phylum or Division
• Class
• Order
• Family
• Genus
• species
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Identification
• The process of discovering, comparing
and recording the phenetic (physical,
biochemical) and genetic traits of
organisms, thereby, placing them in a
taxonomic scheme.
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The five-kingdom system became the standard until molecular biology
techniques were used to develop the Domain system.
Fig. 1.14 Traditional
Margulis-Whittaker
system of classification
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Subdivisions or Kingdoms
• Monera
• Protista (protists)
• Fungi
• Plantae (plants)
• Animalia (animals)
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The Origin and Evolution of
Microorganisms
• Phylogeny- the degree of relatedness by descent
between groups of living things
• Based on the process of evolution- hereditary
information in living things changes gradually
through time; these changes result in structural
and functional changes through many generations
– Two preconceptions:
• All new species originate from preexisting species
• Closely related organisms have similar features because
they evolved from a common ancestor
• Phylogeny usually represented by a tree- showing
the divergent nature of evolution
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Evolution
• Classification schemes allow for a
universal tree of life “phylogenetic tree”.
• Living things change gradually over
millions of years
• Changes favoring survival are retained
& less beneficial changes are lost.
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Domains
• Domain system proposed later than the
Five-kingdom system
• Bacteria - true bacteria, peptidoglycan
• Archaea - odd “bacteria” originally believed
to only live in extreme environments
(high salt, heat, etc)
• Eukarya- have a nucleus, & organelles
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The Domain system was developed by Dr. Carl Woese.
The basis of this system is the ssu rRNA sequence
information.
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Fig. 1.15 The Woese system - universal tree of life
