Classification of Microorganisms

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 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, DNA chips, and FISH.
Explain and apply a dichotomous key
Copyright © 2006 Pearson Education, Inc., publishing as Benjamin 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 (2001–2025)
Copyright © 2006 Pearson Education, Inc., publishing as Benjamin Cummings

The Three-Domain System
Foundation Fig 10.1
Copyright © 2006 Pearson Education, Inc., publishing as Benjamin Cummings

Level Above Kindom: The Three-Domain System
Carl
Woese
1978
Eubacteria (virtuosos)
Archaea (weirdoes)
Eukarya (predators and thieves)
Copyright © 2006 Pearson Education, Inc., publishing as Benjamin Cummings

Endosymbiotic Theory: Origin of Eukaryotes
Figs 10.2, 10.3
Copyright © 2006 Pearson Education, Inc., publishing as Benjamin Cummings
Cyanophora paradoxa: modern example of
possible evolutionary process

Scientific Nomenclature
Common names
• Vary with languages
• Vary with geography
Binomial Nomenclature (genus + specific epithet)
• Used worldwide
• Escherichia coli
• Homo sapiens
Copyright © 2006 Pearson Education, Inc., publishing as Benjamin Cummings

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
Streptococcus
pyogenes
Penicillium
chrysogenum
Trypanosoma cruzi
Honors Daniel Salmon
Chains of cells
(strepto-)
Tuftlike (penicill-)
Corkscrew-like
(trypano-, borer;
soma-, body)
Stupor (typh-) in
mice (muri-)
Forms pus (pyo-)
Produces a yellow
(chryso-) pigment
Honors Oswaldo
Cruz

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

Phylogenetic Relationships of Prokaryotes
Copyright © 2006 Pearson Education, Inc., publishing as Benjamin Cummings 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
Copyright © 2006 Pearson Education, Inc., publishing as Benjamin Cummings

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

Identifying Bacteria
Copyright © 2006 Pearson Education, Inc., publishing as Benjamin Cummings
Applications,
p. 283

Bergey’s Manual:
Classifying and Identifying Prokaryotes
Bergey’s Manual of
Determinative Bacteriology
Provides identification
schemes for identifying
bacteria and archaea
Morphology, differential
staining, biochemical
tests
Bergey’s Manual of
Systematic Bacteriology
Provides phylogenetic
information on bacteria and
archaea
Copyright © 2006 Pearson Education, Inc., publishing as Benjamin Cummings
Based on rRNA
sequencing

Clinical Lab Identification
Morphological
characteristics
Useful for identifying
eukaryotes
Differential staining
Gram staining, acidfast
staining
Biochemical tests
Determines presence
of bacterial enzymes
Numerical Rapid Identification
Copyright © 2006 Pearson Education, Inc., publishing as Benjamin Cummings

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.
Fig 10.10: Slide Agglutination
• Examples:
• Slide agglutination
• ELISA (see lab)
• Western blot (no details)
Copyright © 2006 Pearson Education, Inc., publishing as Benjamin Cummings

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

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
an organism is indicated by
Copyright amplified © 2006 Pearson Education, DNA. Inc., (see publishing as lab) Benjamin Cummings
Fig 10.14: Electrophoresis of
RE digest of plasmid DNA

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
Copyright © 2006 Pearson Education, Inc., publishing as Benjamin Cummings
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 10.18a–b

Dichotomous Key
ANIMATION Dichotomous Keys: Overview
ANIMATION Dichotomous Keys: Sample with
Flowchart
ANIMATION Dichotomous Keys: Practice