1. Ch 10
Classification of Microorganisms

2. 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.

3. 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.

4. Level Above Kindom: The Three-Domain System
Carl
Woese
1978
Eubacteria (virtuosos)
Archaea (weirdoes)
Eukarya (predators and thieves)

5. 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.

6. 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-)
Saccharomyces cerevisiae
Fungus (-myces) that uses sugar (saccharo)
Makes beer (cerevisiae)
Trypanosoma cruzi
Corkscrew-like (trypano-, borer; soma-, body)
Honors Oswaldo Cruz

7. 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

8. Identification Methods
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

9. Bergey’s Manual: Classifying and Identifying Prokaryotes
Bergey’s Manual of Determinative Bacteriology:
Is standard reference for laboratory identification of bacteria.
Morphology, differential staining, biochemical tests to test for presence of various enzymes.
Bergey’s Manual of Systematic Bacteriology
Provides phylogenetic information on bacteria and archaea
Based on rRNA sequencing

10. Identification Methods cont.: Serology
Involves reactions of microorganisms with specific antibodies: Combine known anti-serum 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)

11. 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

12. 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 an organism is indicated by amplified DNA. (see lab)
Fig 10.14: Electrophoresis of RE digest of plasmid DNA

13. 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 and 10.18
Fig 10.15

14. 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)

15. Microbiology in the News (p. 294): Mass Death of Marine Mammals
Dichotomous Key
The End