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Taxonomy and Phylogeny

Taxonmoy: Science of classifying organisms. Provides
universal names for organisms.
 Taxonomic categories: Taxon / Taxa
Classification Phylogeny or Systematics: Evolutionary history of group of
of organisms.

Microorganisms  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)
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The Three-Domain System Level Above Kindom: The Three-Domain System Endosymbiotic Theory: Origin of Eukaryotes
Foundation Fig 10.1
Carl Figs 10.2, 10.3
Woese

1978

Eubacteria (virtuosos)
Archaea (weirdoes) Cyanophora paradoxa: modern example of
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Scientific Nomenclature Taxonomic Hierarchy

Common names
 Vary with languages
 Vary with geography
Binomial Nomenclature (genus + specific epithet)
 Used worldwide
 Escherichia coli
 Homo sapiens

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Classification: Species Definition Phylogenetic Relationships of Prokaryotes Domain Eukarya

 Eukaryotic species: A group of closely related organisms
that breed among themselves  Animalia: Multicellular; no cell walls;
chemoheterotrophic
 Prokaryotic species: A population of cells with similar
characteristics (Bergey’s Manual of Systematic  Plantae: Multicellular; cellulose cell walls;
Bacteriology is standard reference on bacterial usually photoautotrophic
classification).
 Fungi: Chemoheterotrophic;
 Culture: Grown in laboratory media
unicellular or multicellular; cell walls of chitin;
 Clone: Population of cells derived from a single cell
 Strain: Genetically different cells within a clone develop from spores or hyphal fragments

 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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 Protista: A catchall kingdom for eukaryotic
organisms that do not fit other kingdoms
 Grouped into clades based on rRNA
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Bergey’s Manual:
Fig 10.8 Identifying Bacteria Classifying and Identifying Prokaryotes

Classification and
Bergey’s Manual of
Identification
Determinative Bacteriology Morphology, differential
Provides identification staining, biochemical
schemes for identifying tests
bacteria and archaea
Classification: Placing organisms in
groups of related species. Lists of
Bergey’s Manual of
characteristics of known organisms.
Systematic Bacteriology
Based on rRNA
Identification: Matching characteristics Provides phylogenetic
of an “unknown” to lists of known sequencing
Applications,
information on bacteria and
organisms. p. 283 archaea
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Clinical Lab Identification Serology

Morphological  Involves reactions of
microorganisms with Fig 10.10: Slide Agglutination
characteristics
specific antibodies:
Useful for identifying Numerical Rapid Identification Combine known anti-
eukaryotes serum with unknown
Differential staining bacterium
Gram staining, acid-  Useful in determining the
fast staining identity of strains and
species, as well as
Biochemical tests relationships among
Determines presence organisms.
of bacterial enzymes
 Examples:
 Slide agglutination
 ELISA (see lab)
Copyright © 2006 Pearson Education, Inc., publishing as Benjamin Cummings  Western blot (no details)
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Phage Typing Fig 10.13 Genetics Nucleic Acid Hybridization

 DNA fingerprinting:
Number and sizes of DNA Single strands of DNA or RNA, from related organisms
Identification of fragments (fingerprints) will hydrogen-bond to form a double-stranded molecule;
bacterial species produced by RE digests are this bonding is called nucleic acid hybridization.
and strains by used to determine genetic
determining their similarities.
susceptibility to
various phages.  Ribotyping: rRNA sequencing Examples of Applications:

More details on  Polymerase chain reaction • Southern blotting,

bacteriophages (PCR) can be used to amplify • DNA chips, and
a small amount of microbial
in Ch 13 • FISH
DNA in a sample. The
presence or identification of Fig 10.14: Electrophoresis of
an organism is indicated by RE digest of plasmid DNA
Copyright © 2006 Pearson Education, Inc., publishing as Benjamin Cummings amplified DNA. (see lab)
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Nucleic Acid Hybridization: DNA Chip Fluorescent In Situ Hybridization (FISH)

Fig 10.17

Add DNA or RNA

probe attached to
fluorescent dye
for S. aureus

Fig 10.18a–b