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Ch 10
Classification of
Microorganisms
LEARNING OBJECTIVES
Define taxonomy, taxon, and phylogeny.
List the characteristics of the Bacteria, Archaea, and Eukarya domains.
Differentiate among eukaryotic, prokaryotic, and viral species.
Explain the scientific naming
Differentiate between culture, clone, and strain.
Compare and contrast classification and identification.
Explain the purpose of Bergey’s Manual.
Describe how staining and biochemical tests are used to identify bacteria.
Explain how serological tests and phage typing can be used to identify an unknown
bacterium.
Describe how a newly discovered microbe can be classified by ribotyping, DNA
fingerprinting, and PCR.
Describe how microorganisms can be identified by nucleic acid hybridization,
Southern blotting, DNA chips, and FISH.
Differentiate
a dichotomous key from a cladogram.
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Taxonomy and Phylogeny
Taxonmoy: science of classifying organisms with goal of
showing relationships among organisms.
 Taxonomic categories: Taxon / Taxa
 Provides universal names for organisms and a means of
identifying them.
Phylogeny (or systematics): evolutionary history of group of
organisms.
 Taxonomic hierarchy shows phylogenetic (evolutionary),
relationships among organisms.
 1969: Living organisms divided into five kingdoms.
 1978: Two types of prokaryotic cells found. Prokaryotic
relationships determined by rRNA sequencing.
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Level Above Kindom: The Three-Domain System
Carl
Woese
1978
Eubacteria (virtuosos)
Archaea (weirdoes)
Eukarya (predators and thieves)
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Classification: Species Definition
 Eukaryotic species: A group of closely related organisms
that breed among themselves
 Prokaryotic species: A population of cells with similar
characteristics (Bergey’s Manual of Systematic
Bacteriology is standard reference on bacterial
classification).
 Clone: Population of cells derived from a single cell
 Strain: Genetically different cells within a clone
 Closely related strains constitute a bacterial species.
 Viral species: Population of viruses with similar
characteristics occupying a particular ecological niche.
Viruses: not placed in a kingdom – not composed of cells
– cannot grow without a host cell.
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Scientific Nomenclature
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 typhimurium
Honors Daniel Salmon
Stupor (typh-) in mice
(muri-)
Streptococcus pyogenes
Chains of cells (strepto-)
Forms pus (pyo-)
(-myces) that
Saccharomyces cerevisiae Fungus
uses sugar (saccharo)
Makes beer
(cerevisiae)
Corkscrew-like (trypano-, Honors Oswaldo Cruz
borer; soma-, body)
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Trypanosoma cruzi
Domain Eukarya
 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
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Identification Methods
Fig 10.8
 Morphological
characteristics:
Useful for
identifying
eukaryotes
 Differential staining: Gram staining, acid-fast
staining
 Biochemical tests: Determines presence of
bacterial enzymes
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Bergey’s Manual:
Classifying and Identifying Prokaryotes
Bergey’s Manual of
Determinative Bacteriology:
Is standard reference for
laboratory identification of
bacteria.
Bergey’s Manual of
Systematic Bacteriology
Provides phylogenetic
information on bacteria and
archaea
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Morphology,
differential staining,
biochemical tests to
test for presence of
various enzymes.
Based on rRNA
sequencing
Identification Methods cont.: Serology
 Involves reactions of
microorganisms with
specific antibodies:
Combine known antiserum with unknown
bacterium
 Useful in determining the
identity of strains and
species, as well as
relationships among
organisms.
 Examples:
 Slide agglutination
 ELISA (see lab)
 Western blot (no details)
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Fig 10.10: Slide Agglutination
Identification Methods cont.: Phage Typing
Figure 10.13
Identification of
bacterial species
and strains by
determining their
susceptibility to
various phages.
More details on
bacteriophages
in Ch 13
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Identification Methods cont.: Genetics
 DNA fingerprinting:
Number and sizes of DNA
fragments (fingerprints)
produced by RE digests are
used to determine genetic
similarities.
 Ribotyping: rRNA sequencing
 Polymerase chain reaction
(PCR) can be used to amplify
a small amount of microbial
DNA in a sample. The
Fig 10.14: Electrophoresis of
presence or identification of
RE digest of plasmid DNA
an organism is indicated by
amplified DNA. (see lab)
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Identification Methods cont.:
Nucleic Acid Hybridization
Single strands of DNA or RNA, from related organisms
will hydrogen-bond to form a double-stranded molecule;
this bonding is called nucleic acid hybridization.
Examples of Applications:
• Southern blotting,
• DNA chips, and
• FISH
Figs. 10.17 and 10.18
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Fig 10.15
Putting Identification/Classification Methods Together
 Dichotomous keys are widely used for identification of
organisms. They are based on successive questions
that each have two possible answers
 Cladograms are maps that show phylogenentic
(evolutionary) relationship.
Method used to
establish cladogram
for microorganisms?
PLAY
Animation: Dichotomous Keys (The Microbiology Place)
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Microbiology in the News (p. 294): Mass Death
of Marine Mammals
Dichotomous Key