1. Ch 10
Classification
of Microorganisms

2. 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

3. Taxonomy and Phylogeny
Taxonomy: 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)
Experts estimate that there are around 100 million species in the world. What percentage of these flora and fauna have we named in the 250 years since Carl Linnaeus devised a classification system to complete Adam's task? Remarkably, only 2 or 3 percent. So two blue-sky thinkers in San Francisco - Kevin Kelly and Stewart Brand - recently came up with a solution to this problem: the All-Species Inventory. The goal is to identify and name every living thing, all in a single human generation.
This effort will be organized by the newly created All-Species Foundation, which has already raised $1 million for the project. What the moon shot did for technology, the All-Species Inventory hopes to do for ecology.

4. The Three-Domain System
Foundation Fig 10.1

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

6. Endosymbiotic Theory: Origin of Eukaryotes
Figs 10.2, 10.3
Cyanophora paradoxa: modern example of possible evolutionary process

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

8. Source of Specific Epithet
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 cruzi
Corkscrew-like (trypano-, borer; soma-, body)
Honors Oswaldo Cruz

9. 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.

10. Phylogenetic Relationships of Prokaryotes
Fig. 10.6

11. 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

12. Classification and Identification
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.

13. Identifying Bacteria
Applications, p. 283

14. 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
Based on rRNA sequencing

16. Clinical Lab Identification
Morphological characteristics Useful for identifying eukaryotes Differential staining Gram staining, acid- fast staining Biochemical tests Determines presence of bacterial enzymes
Numerical Rapid Identification

17. 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)

18. 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

19. 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

20. 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
Fig 10.15

21. Nucleic Acid Hybridization: DNA Chip
Fig 10.17

22. Fluorescent In Situ Hybridization (FISH)
Add DNA or RNA probe attached to fluorescent dye
for S. aureus
Fig 10.18a–b

23. Dichotomous Key The End ANIMATION Dichotomous Keys: Overview
ANIMATION Dichotomous Keys: Sample with Flowchart
ANIMATION Dichotomous Keys: Practice
The End