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 Source of

Name 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-)

Saccharomyces cerevisiae Fungus (-myces) that

uses sugar (saccharo)
Makes beer
(cerevisiae)

Trypanosoma cruzi Corkscrew-like (trypano-, Honors Oswaldo Cruz

borer; soma-, body)
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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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 Fig 10.8
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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 Bergey’s Manual:
Classifying and Identifying Prokaryotes

Bergey’s Manual of Morphology,

Determinative Bacteriology: differential staining,
Is standard reference for biochemical tests to
laboratory identification of test for presence of
bacteria. various enzymes.

Bergey’s Manual of
Systematic Bacteriology
Based on rRNA
Provides phylogenetic
sequencing
information on bacteria and
archaea
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 Identification Methods cont.: Serology
 Involves reactions of
microorganisms with Fig 10.10: Slide Agglutination
specific antibodies:
Combine known anti-
serum 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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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
presence or identification of Fig 10.14: Electrophoresis of
an organism is indicated by RE digest of plasmid DNA
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

Copyright © 2006 Pearson Education, Inc., publishing as Benjamin Cummings 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