Ch 10

Classification
of
Microorganisms

Student Learning Outcomes

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 Bergeys 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, DNA chips, and FISH.
Explain
and
apply
a Inc.,
dichotomous
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Pearson
Education,
publishing as Benjamin key
Cummings

Taxonomy and Phylogeny

Taxonmoy: Science of classifying organisms. Provides
universal names for organisms.
Taxonomic categories: Taxon / Taxa
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.
All Species Inventory (20012025)
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The Three-Domain System

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Foundation Fig 10.1

Level Above Kindom: The Three-Domain System

Carl
Woese
1978

Eubacteria (virtuosos)
Archaea (weirdoes)
Eukarya (predators and thieves)

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Endosymbiotic Theory: Origin of Eukaryotes

Figs 10.2, 10.3

Cyanophora paradoxa: modern example of

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Cummings evolutionary process
possible

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
typhimurium

Honors Daniel
Salmon

Stupor (typh-) in
mice (muri-)

Streptococcus
pyogenes

Chains of cells
(strepto-)

Forms pus (pyo-)

Penicillium
chrysogenum

Tuftlike (penicill-)

Produces a
yellow (chryso-)
pigment

Trypanosoma

Corkscrew-like
(trypano-, borer;

Honors Oswaldo

Classification: Species Definition

Eukaryotic species: A group of closely related organisms
that breed among themselves
Prokaryotic species: A population of cells with similar
characteristics (Bergeys Manual of Systematic
Bacteriology is standard reference on bacterial
classification).
Culture: Grown in laboratory 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 occupying a particular ecological niche.
Viruses: not placed in kingdom nor domain not
composed of cells cannot grow without a host cell.
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Phylogenetic Relationships of Prokaryotes

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Fig. 10.6

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 kingdom for eukaryotic
organisms that do not fit other kingdoms
Grouped into clades based on rRNA
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Fig 10.8

Classification and
Identification

Classification: Placing organisms in

groups of related species. Lists of
characteristics of known organisms.
Identification: Matching characteristics
of an unknown to lists of known
organisms.
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Identifying Bacteria

Applications,
p. 283
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Bergeys Manual:
Classifying and Identifying Prokaryotes
Bergeys Manual of
Determinative
Bacteriology
Provides identification
schemes for identifying
bacteria and archaea

Morphology,
differential staining,
biochemical tests

Bergeys Manual of
Systematic
Bacteriology
Provides phylogenetic
information on bacteria
and archaea

Based on rRNA
sequencing

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Clinical Lab Identification

Morphological
characteristics
Useful for identifying
eukaryotes

Numerical Rapid Identification

Differential staining
Gram staining, acidfast staining
Biochemical tests
Determines
presence of bacterial
enzymes
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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

Phage Typing

Fig 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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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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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

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Fig 10.15

Nucleic Acid Hybridization: DNA Chip

Fig 10.17

Fluorescent In Situ Hybridization (FISH)

Add DNA or RNA

probe attached to
fluorescent dye
for S. aureus

Fig 10.18ab

Dichotomous Key
ANIMATION Dichotomous Keys: Overview

ANIMATION Dichotomous Keys: Sample with

Flowchart
ANIMATION Dichotomous Keys: Practice