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TORTORA • FUNKE
• CASE
Microbiology
AN INTRODUCTION
EIGHTH EDITION
B.E Pruitt & Jane J. Stein
Chapter 10
Classification of Microorganisms
PowerPoint® Lecture Slide Presentation prepared by Christine L. Case
Copyright © 2004 Pearson Education, Inc., publishing as Benjamin Cummings
Learning objectives:
Define taxonomy, taxon, and phylogeny
Discuss the limitations of a 2-kingdom classification system.
Taxonomy
• Taxonomy
• The science of classifying organisms
• Provides universal names for organisms
• Provides a reference for identifying organisms
• Goal of showing relationships among organisms
• Taxon
• Taxonomic categories to show similarities
among organisms
Copyright © 2004 Pearson Education, Inc., publishing as Benjamin Cummings
Taxonomy
• Systematics or phylogeny
• The study of the evolutionary history of
organisms and their relationships
• All Species Inventory (2001-2025)
• To identify all species of life on Earth
• Two-kingdom system not based upon natural
classification based upon ancestral
relationships (e.g., DNA sequencing places
fungi closer to animals than plants)
Copyright © 2004 Pearson Education, Inc., publishing as Benjamin Cummings
Taxonomy History
• 1735
Plant and Animal Kingdoms
• 1857
Bacteria & fungi put in the Plant Kingdom
• 1866
Kingdom Protista proposed for bacteria,
protozoa, algae, & fungi
• 1937
"Prokaryote" introduced for cells "without a
nucleus"
• 1961
Prokaryote defined as cells in which
nucleoplasm is not surrounded by a nuclear
membrane
• 1959
Kingdom Fungi
• 1968
Kingdom Prokaryotae proposed
• 1969
Organisms divided into five kingdoms
• 1978
Two types of prokaryotic cells found
Copyright © 2004 Pearson Education, Inc., publishing as Benjamin Cummings
Learning objectives:
List characteristics
of 3-domain system
The Three-Domain System
A domain can be divided into kingdoms
Classified by cell type,
cell wall, rRNA,
membrane lipid
structure, tRNA,
sensitivity to antibiotics
Copyright © 2004 Pearson Education, Inc., publishing as Benjamin Cummings
Table 10.1
The Three-Domain System
Peptidoglycan
Unusual cell walls
3-domain recognizes 3
types of cells. Eukarya
includes Kingdoms
Fungi, Plantae, and
Animalia, plus certain
protists
Copyright © 2004 Pearson Education, Inc., publishing as Benjamin Cummings
Figure 10.1
Phylogenetic Hierarchy
•Organisms grouped into taxa by phylogenetic relationships
•Some eukaryotic relationships obtained from fossil records
•Prokaryotic relationships determined by rRNA sequencing
Copyright © 2004 Pearson Education, Inc., publishing as Benjamin Cummings
Table 10.2
Endosymbiotic Theory
Similarities in rRNA
sequences supporting
endosymbiotic theory
Figure 10.2
Copyright © 2004 Pearson Education, Inc., publishing as Benjamin Cummings
Mutualistic symbiosis
between eukaryotic host
and bacterium – possible
precursor to reproductive
capability as a unit Figure 10.3
Learning objectives:
Scientific Names
Explain why
scientific names are
used.
Kbebsiella pneumoniae
Honors Edwin Klebs
Source of
Specific epithet
The disease
Pfiesteria piscicida
Honors Lois Pfiester
Disease in fish
Salmonella typhimurium
Honors Daniel Salmon
Stupor (typh-) in mice
(muri-)
Streptococcus pyogenes
Chains of cells (strepto-)
Forms pus (pyo-)
Penicillium notatum
Tuftlike (penicill-)
Spores spread in wind
(nota)
Trypanosoma cruzi
Corkscrew-like (trypano-, Honors Oswaldo Cruz
borer; soma-body)
Scientific binomial
Source of Genus name
Binomials (Genus Species) used by scientists worldwide which
enables them to share knowledge efficiently and accurately
Copyright © 2004 Pearson Education, Inc., publishing as Benjamin Cummings
Learning objectives: List the major taxa.
Taxonomic Hierarchy
Differentiate between culture, clone, and strain.
• Similar species are
grouped into a
genus; similar
genera are grouped
into a family, etc.
• Kids
Kingdom
• Prefer
Phylum/
Division
• Cheese
Class
• Over
Order
• Fried
Family
• Green
Genus
• Spinach Species
Copyright © 2004 Pearson Education, Inc., publishing as Benjamin Cummings
Figure 10.5
Species Definition
• Eukaryotic species:
• A group of closely related organisms that breed
among themselves
• Prokaryotic species:
• A population of cells with similar characteristics
• Culture: bacteria grown at a give time in media
• Clone: Population of cells derived from a single cell
• Strain: Genetically different cells within a clone
• Viral species:
• Population of viruses with similar characteristics that
occupies a particular ecological niche
Copyright © 2004 Pearson Education, Inc., publishing as Benjamin Cummings
Domain Eukarya
Learning objectives: List the major characteristics used to
differentiate the three kingdoms of multicellular Eukarya.
Define protist.
• 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 for eukaryotic organisms that do not
fit other kingdoms; currently being assigned to
kingdoms
• Viruses not placed in a kingdom (must have host)
Copyright © 2004 Pearson Education, Inc., publishing as Benjamin Cummings
Prokaryotes
Phylogenetic
relationships of
prokaryotes (Kingdom –
Phylum)
Copyright © 2004 Pearson Education, Inc., publishing as Benjamin Cummings
Figure 10.6
References
Learning objectives:
Compare/contrast classification and identification
Explain purpose of Bergey’s Manual
•• Bergey’s Manual of Determinative
Bacteriology (for lab identification)
•Provides identification schemes for
identifying bacteria and archaea
•Morphology, differential
staining, biochemical tests, cell
wall composition, oxygen
requirements (treatment)
•• Bergey’s Manual of Systematic
Bacteriology
•Provides phylogenetic information
on bacteria and archaea
•Based on rRNA sequencing
•• Approved Lists of Bacterial Names
•Lists species of known prokaryotes
•Based on published articles
Copyright © 2004 Pearson Education, Inc., publishing as Benjamin Cummings
Learning objectives:
Describe how staining and
biochemical tests are used to
identify bacteria
Copyright © 2004 Pearson Education, Inc., publishing as Benjamin Cummings
Methods to Classify and Identify Microbes
• Morphological characteristics (aided by staining)
• Presence of certain enzymes
• Serological tests (antigen – antibody response)
• Phage typing (susceptibility of bacteria to phages)
• Fatty acid profiles
• Flow cytometry
• Percentage of G-C pairs in nucleic acid
• Number and sizes of DNA fragments (fingerprints)
produced by restriction enzymes
• Sequence of bases in rRNA
• Polymerase chain reaction (PCR) to detect DNA
Copyright © 2004 Pearson Education, Inc., publishing as Benjamin Cummings
Identification Methods
• Morphological
characteristics:
Useful for
identifying
eukaryotes
Using metabolic characteristics to
identify selected genera of enteric
(intestinal) bacteria
• Differential
staining: Gram
staining, acid-fast
staining
• Biochemical
tests: Determines
presence of
bacterial
enzymes
Copyright © 2004 Pearson Education, Inc., publishing as Benjamin Cummings
Figure 10.8
Morphology and
differential staining
important to proper
treatment for microbial
diseases
Copyright © 2004 Pearson Education, Inc., publishing as Benjamin Cummings
Numerical Identification
Rapid identification tools
for groups of medically
important bacteria (e.g.,
enterics) are designed to
perform several
biochemical tests
simultaneously.
The value for each
positive test is circled
and compared to a
computerized listing.
In this case a confirmatory test is advised.
Copyright © 2004 Pearson Education, Inc., publishing as Benjamin Cummings
Figure 10.9
Serology
Learning objectives:
Differentiate Western blotting from Southern blotting.
Explain how serological tests and phage typing can be used
to identify an unknown bacterium.
• Combine known
antiserum +
unknown
bacterium
Left grainy appearance is positive for agglutination –
bacteria was mixed with antibodies produced in
response to same strain
• Slide
agglutination
• ELISA (enzymelinked
immunosorbent
assay)
• Western blot
Copyright © 2004 Pearson Education, Inc., publishing as Benjamin Cummings
Figure 10.10
Western Blot
Proteins separated by electrophoresis
can be detected by their reactions with
antibodies
Copyright © 2004 Pearson Education, Inc., publishing as Benjamin Cummings
Figure 10.12
Phage Typing
Determining which
phages a bacterium is
susceptible to:
The tested strain was
grown over entire plate;
known phages are
placed in different
squares; plaques (areas
of lysis) appear dark
indicating sensitivity to a
specific phage
Copyright © 2004 Pearson Education, Inc., publishing as Benjamin Cummings
Figure 10.13
Flow Cytometry Uses
• Used to identify
bacteria in a sample
without culturing the
bacteria
• Differences in electrical
conductivity between
species
• Fluorescence of some
species
• Cells selectively stained
with antibody +
fluorescent dye
Copyright © 2004 Pearson Education, Inc., publishing as Benjamin Cummings
Figure 18.11
Genetics
Learning objectives:
Describe how newly discovered microbe can be classified by:
DNA base composition, rRNA sequencing, DNA fingerprinting,
PCR, and nucleic acid hybridization
• DNA base composition
• Guanine + cytosine
moles% (GC)
Plasmids from 7 different bacteria digested
with same restriction enzyme: none of these
bacteria happen to be identical (source of
hospital-acquired infections).
• DNA fingerprinting
• Electrophoresis of
restriction enzyme
digests
• rRNA sequencing
• Polymerase Chain
Reaction (PCR)
Copyright © 2004 Pearson Education, Inc., publishing as Benjamin Cummings
Figure 10.14
Nucleic Acid Hybridization
Greater degree of hybridization (pairing of two strands of DNA, each
from a different microbe) indicates greater similarity
Copyright © 2004 Pearson Education, Inc., publishing as Benjamin Cummings
Figure 10.15
Nucleic Acid Hybridization: DNA probe
Copyright © 2004 Pearson Education, Inc., publishing as Benjamin Cummings
Figure 10.16
Nucleic Acid Hybridization: DNA chip
Copyright © 2004 Pearson Education, Inc., publishing as Benjamin Cummings
Figure 10.17
Dichotomous Key
Learning objectives:
Differentiate a
dichotomous key
from a cladogram.
Dichotomous key:
successive questions
with two possible
answers.
Copyright © 2004 Pearson Education, Inc., publishing as Benjamin Cummings
Cladogram
Cladogram:
Maps showing evolutionary relationships among
organisms.
Copyright © 2004 Pearson Education, Inc., publishing as Benjamin Cummings
Figure 10.18.1
Cladogram
Copyright © 2004 Pearson Education, Inc., publishing as Benjamin Cummings
Figure 10.18.2
Copyright © 2004 Pearson Education, Inc., publishing as Benjamin Cummings
Figure 10.5