Download Microbiology

Chapter 10
Classification of
Microorganisms
Copyright © 2010 Pearson Education, Inc.
Lectures prepared by Christine L. Case
Q&A
 Pneumocystis
jirovecii was thought
to be a protozoan
until DNA analysis
showed it is a
fungus. Why does it
matter whether an
organism is
classified as a
protozoan or a
fungus?
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The Study of Phylogenetic
Relationships
Learning Objectives
10-1 Define taxonomy, taxon, and phylogeny.
10-2 Discuss the limitations of a two-kingdom
classification system.
10-3 Identify the contributions of Linnaeus, von
Nägeli, Chatton, Whittaker, and Woese.
10-4 Discuss the advantages of the three-domain
system.
10-5 List the characteristics of the Bacteria, Archaea,
and Eukarya domains.
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Taxonomy
 The science of classifying organisms
 Provides universal names for organisms
 Provides a reference for identifying organisms
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Systematics, or Phylogeny
 The study of the evolutionary history of organisms
 All Species Inventory (2001–2025)
 To identify all species of life on Earth
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Check Your Understanding
 Of what value is taxonomy and systematics?
10-1
 Why shouldn’t bacteria be placed in the plant
kingdom? 10-2, 10-3
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Placing Bacteria
1735 Kingdoms Plantae and Animalia
1857 Bacteria and fungi put in the Kingdom Plantae –
“Flora”
1866 Kingdom Protista proposed for bacteria,
protozoa, algae, and fungi
1937 Prokaryote introduced for cells "without a
nucleus"
1961 Prokaryote defined as cell in which nucleoplasm
is not surrounded by a nuclear membrane
1959 Kingdom Fungi
1968 Kingdom Prokaryotae proposed
1978 Two types of prokaryotic cells found
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The Three-Domain System
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Figure 10.1
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Table 10.1
A Model of the Origin of Eukaryotes
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Figure 10.2
Endosymbiotic Theory
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Figures 10.2, 10.3
Fossilized Prokaryotes
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Figure 10.4a
Fossilized Prokaryotes
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Figure 10.4b
Fossilized Prokaryotes
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Figure 10.4c
Phylogenetics
 Each species retains some characteristics of its
ancestor
 Grouping organisms according to common
properties implies that a group of organisms evolved
from a common ancestor
 Anatomy
 Fossils
 rRNA
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Check Your Understanding
 What evidence supports classifying organisms into
three domains? 10-4
 Compare Archaea and Bacteria; Bacteria and
Eukarya; and Archaea and Eukarya. 10-5
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Classification of Organisms
Learning Objectives
10-6 Explain why scientific names are used.
10-7 List the major taxa.
10-8 Differentiate culture, clone, and strain.
10-9 List the major characteristics used to
differentiate the three kingdoms of multicellular
Eukarya.
10-10 Define protist.
10-11 Differentiate eukaryotic, prokaryotic, and viral
species.
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Scientific Nomenclature
 Common names
 Vary with languages
 Vary with geography
 Binomial Nomenclature (genus + specific epithet)
 Used worldwide
 Escherichia coli
 Homo sapiens
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Scientific Names
Scientific Binomial
Source of Genus
Name
Source of
Specific Epithet
Klebsiella pneumoniae
Honors Edwin Klebs
The disease
Pfiesteria piscicida
Honors Lois Pfiester
Disease in fish
Salmonella
Honors Daniel Salmon
typhimurium
Streptococcus pyogenes Chains of cells
(strepto-)
Penicillium
Tuftlike (penicill-)
chrysogenum
Trypanosoma cruzi
Corkscrew-like
(trypano-, borer;
soma-, body)
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Stupor (typh-) in
mice (muri-)
Forms pus (pyo-)
Produces a yellow
(chryso-) pigment
Honors Oswaldo
Cruz
Taxonomic Hierarchy
Domain
Kingdom
Phylum
Class
Order
Family
Genus
Species
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The Taxonomic Hierarchy
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Figure 10.5
Check Your Understanding
 Using Escherichia coli and Entamoeba coli as examples,
explain why the genus name must always be written out for
the first use. Why is binomial nomenclature preferable to
the use of common names? 10-6
 Find the gram-positive bacteria Staphylococcus in
Appendix F. To which bacteria is this genus most closely
related: Gemella or Streptococcus? 10-7
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Classification of Prokaryotes
 Prokaryotic species: A population of cells with
similar characteristics
 Culture: Grown in laboratory media
 Clone: Population of cells derived from a single cell
 Strain: Genetically different cells within a clone
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Phylogenetic Relationships of
Prokaryotes
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Figure 10.6
Classification of Eukaryotes
 Eukaryotic species: A group of closely related
organisms that breed among themselves
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Classification of Eukaryotes
 Animalia: Multicellular; no cell walls;
chemoheterotrophic
 Plantae: Multicellular; cellulose cell walls; usually
photoautotrophic
 Fungi: Chemoheterotrophic; unicellular or
multicellular; cell walls of chitin; develop from spores
or hyphal fragments
 Protista: A catchall kingdom for eukaryotic
organisms that do not fit other kingdoms
 Grouped into clades based on rRNA
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Classification of Viruses
 Viral species: Population of viruses with similar
characteristics that occupies a particular ecological
niche
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References
International Journal of
Systematic and Evolutionary
Microbiology
Articles with evidence of
new species or classification
Bergey’s Manual of Systematic
Bacteriology
Provides phylogenetic and
identification information on
bacteria and archaea
Approved Lists of Bacterial
Names
Lists species of known
prokaryotes
Based on published articles
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Identifying Bacteria
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Applications, p. 283
Check Your Understanding
 Use the terms species, culture, clone, and strain in one
sentence to describe growing methicillin-resistant
Staphylococcus aureus (MRSA). 10-8
 Assume you discovered a new organism: it is multicellular, is
nucleated, is heterotrophic, and has cell walls. To what
kingdom does it belong? 10-9
 Write your own definition of protist. 10-10
 Why wouldn’t the definition of a viral species work for a
bacterial species? 10-11
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Classifying & Identifying
Microorganisms
Learning Objectives
10-12 Compare and contrast classification and
identification.
10-13 Explain the purpose of Bergey’s Manual.
10-14 Describe how staining and biochemical tests
are used to identify bacteria.
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Classification and Identification
 Classification: Placing organisms in groups of
related species. Lists of characteristics of known
organisms.
 Identification: Matching characteristics of an
“unknown” organism to lists of known organisms.
 Clinical lab identification
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 Identifying Klebsiella doesn’t
tell you it’s classified as
gammaproteobacteria
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Applications, p. 283
References
Bergey’s Manual of Determinative
Bacteriology
Provides identification schemes for
identifying bacteria and archaea
Morphology, differential
staining, biochemical tests
Bergey’s Manual of Systematic
Based on rRNA sequencing
Bacteriology
Provides phylogenetic information on
bacteria and archaea
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Check Your Understanding
 What is in Bergey’s Manual? 10-13
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A Clinical Microbiology Lab Report Form
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Figure 10.7
Identification Methods
 Morphological characteristics: Useful for
identifying eukaryotes
 Differential staining: Gram staining, acid-fast
staining
 Biochemical tests: Determines presence of
bacterial enzymes
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Identifying a Gram – Negative, Oxidase
– Negative Rod
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Figure 10.8
Numerical Identification
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Figure 10.9
Check Your Understanding
 Design a rapid test for a Staphylococcus aureus.
10-14
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Figure 6.10
Serology
 Combine known antiserum plus unknown bacterium
 Slide agglutination test
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Figure 10.10
ELISA





Enzyme-linked immunosorbent assay
Known antibodies
Unknown type of bacterium
Antibodies linked to enzyme
Enzyme substrate
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Figure 18.14
An ELISA Test
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Figure 10.11
The Western Blot
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Figure 10.12
Phage Typing of Salmonella enterica
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Figure 10.13
Flow Cytometry
 Uses differences in
electrical
conductivity between
species
 Fluorescence of
some species
 Cells selectively
stained with
antibody plus
fluorescent dye
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Figure 18.12
Genetics
 DNA base composition
 Guanine + cytosine
moles% (GC)
 DNA fingerprinting
 Electrophoresis of
restriction enzyme
digests
 rRNA sequencing
 Polymerase chain
reaction (PCR)
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Figure 10.14
Nucleic Acid Hybridization
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Figure 10.15
A DNA Probe Used to Identify Bacteria
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Figure 10.16
DNA Chip Technology
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Figure 10.17
DNA Chip Technology
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Figure 10.17
FISH
 Fluorescent in
situ hybridization
 Add DNA probe
for S. aureus
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Figure 10.18
Dichotomous Key
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Figure 10.8
Dichotomous Key
ANIMATION Dichotomous Keys: Overview
ANIMATION Dichotomous Keys: Sample with Flowchart
ANIMATION Dichotomous Keys: Practice
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Building a Cladogram
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Figure 10.19
Building a Cladogram
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Figure 10.19
Building a Cladogram
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Figure 10.19
Check Your Understanding
 What is tested in Western blotting and Southern
blotting? 10-15
 What is identified by phage typing? 10-16
 Why does PCR identify a microbe? 10-17
 Which techniques involve nucleic acid
hybridization?
10-18
 Is a cladogram used for identification or
classification? 10-12, 10-19
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