1. Classification of Microorganisms
Chapter 10
Classification of Microorganisms

2. Taxonomy Learning objectives: Define taxonomy, taxon, and phylogeny
Discuss the limitations of a 2-kingdom classification system.
Taxonomy
Taxonomy
The science of classifying organisms
Provides universal names for organisms
Provides a reference for identifying organisms
Goal of showing relationships among organisms
Taxon
Taxonomic categories to show similarities among organisms

3. Taxonomy Systematics or phylogeny
The study of the evolutionary history of organisms and their relationships
All Species Inventory ( )
To identify all species of life on Earth
Two-kingdom system not based upon natural classification based upon ancestral relationships (e.g., DNA sequencing places fungi closer to animals than plants)

4. Taxonomy History 1735 Plant and Animal Kingdoms
1857 Bacteria & fungi put in the Plant Kingdom
1866 Kingdom Protista proposed for bacteria, protozoa, algae, & fungi
1937 "Prokaryote" introduced for cells "without a nucleus"
1961 Prokaryote defined as cells in which nucleoplasm is not surrounded by a nuclear membrane
1959 Kingdom Fungi
1968 Kingdom Prokaryotae proposed
1969 Organisms divided into five kingdoms
1978 Two types of prokaryotic cells found

5. The Three-Domain System
Learning objectives:
List characteristics of 3-domain system
A domain can be divided into kingdoms
Classified by cell type, cell wall, rRNA, membrane lipid structure, tRNA, sensitivity to antibiotics
Table 10.1

6. The Three-Domain System
Peptidoglycan Unusual cell walls
3-domain recognizes 3 types of cells. Eukarya includes Kingdoms Fungi, Plantae, and Animalia, plus certain protists
Figure 10.1

7. Phylogenetic Hierarchy
Organisms grouped into taxa by phylogenetic relationships
Some eukaryotic relationships obtained from fossil records
Prokaryotic relationships determined by rRNA sequencing
Table 10.2

8. Endosymbiotic Theory
Mutualistic symbiosis between eukaryotic host and bacterium – possible precursor to reproductive capability as a unit
Similarities in rRNA sequences supporting endosymbiotic theory
Figure 10.2
Figure 10.3

9. Source of Specific epithet
Learning objectives:
Explain why scientific names are used.
Scientific Names
Scientific binomial
Source of Genus name
Source of Specific epithet
Kbebsiella 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 notatum
Tuftlike (penicill-)
Spores spread in wind (nota)
Trypanosoma cruzi
Corkscrew-like (trypano-, borer; soma-body)
Honors Oswaldo Cruz
Binomials (Genus Species) used by scientists worldwide which enables them to share knowledge efficiently and accurately

10. Prefer Phylum/ Division Cheese Class Over Order Fried Family
Learning objectives: List the major taxa.
Differentiate between culture, clone, and strain.
Taxonomic Hierarchy
Similar species are grouped into a genus; similar genera are grouped into a family, etc.
Kids Kingdom
Prefer Phylum/ Division
Cheese Class
Over Order
Fried Family
Green Genus
Spinach Species
Figure 10.5

11. Species Definition Eukaryotic species:
A group of closely related organisms that breed among themselves
Prokaryotic species:
A population of cells with similar characteristics
Culture: bacteria grown at a give time in 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 that occupies a particular ecological niche

12. Domain Eukarya
Learning objectives: List the major characteristics used to differentiate the three kingdoms of multicellular Eukarya.
Define protist.
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; currently being assigned to kingdoms
Viruses not placed in a kingdom (must have host)

13. Prokaryotes
Phylogenetic relationships of prokaryotes (Kingdom – Phylum)
Figure 10.6

14. References Learning objectives:
Compare/contrast classification and identification
Explain purpose of Bergey’s Manual
• Bergey’s Manual of Determinative Bacteriology (for lab identification)
Provides identification schemes for identifying bacteria and archaea
Morphology, differential staining, biochemical tests, cell wall composition, oxygen requirements (treatment)
• Bergey’s Manual of Systematic Bacteriology
Provides phylogenetic information on bacteria and archaea
Based on rRNA sequencing
• Approved Lists of Bacterial Names
Lists species of known prokaryotes
Based on published articles

15. Learning objectives:
Describe how staining and biochemical tests are used to identify bacteria

16. Methods to Classify and Identify Microbes
Morphological characteristics (aided by staining)
Presence of certain enzymes
Serological tests (antigen – antibody response)
Phage typing (susceptibility of bacteria to phages)
Fatty acid profiles
Flow cytometry
Percentage of G-C pairs in nucleic acid
Number and sizes of DNA fragments (fingerprints) produced by restriction enzymes
Sequence of bases in rRNA
Polymerase chain reaction (PCR) to detect DNA

17. Identification Methods
Using metabolic characteristics to identify selected genera of enteric (intestinal) bacteria
Morphological characteristics: Useful for identifying eukaryotes
Differential staining: Gram staining, acid-fast staining
Biochemical tests: Determines presence of bacterial enzymes
Figure 10.8

18. Morphology and differential staining important to proper treatment for microbial diseases

19. Numerical Identification
Rapid identification tools for groups of medically important bacteria (e.g., enterics) are designed to perform several biochemical tests simultaneously.
The value for each positive test is circled and compared to a computerized listing.
In this case a confirma-tory test is advised.
Figure 10.9

20. Serology Combine known antiserum + unknown bacterium
Learning objectives:
Differentiate Western blotting from Southern blotting.
Explain how serological tests and phage typing can be used to identify an unknown bacterium.
Combine known antiserum + unknown bacterium
Slide agglutination
ELISA (enzyme-linked immunosorbent assay)
Western blot
Left grainy appearance is positive for agglutination – bacteria was mixed with antibodies produced in response to same strain
Figure 10.10

21. Western Blot
Proteins separated by electrophoresis can be detected by their reactions with antibodies
Figure 10.12

22. Phage Typing Determining which phages a bacterium is susceptible to:
The tested strain was grown over entire plate; known phages are placed in different squares; plaques (areas of lysis) appear dark indicating sensitivity to a specific phage
Figure 10.13

23. Flow Cytometry Uses
Used to identify bacteria in a sample without culturing the bacteria
Differences in electrical conductivity between species
Fluorescence of some species
Cells selectively stained with antibody + fluorescent dye
Figure 18.11

24. Genetics DNA base composition Guanine + cytosine moles% (GC)
Learning objectives:
Describe how newly discovered microbe can be classified by: DNA base composition, rRNA sequencing, DNA fingerprinting, PCR, and nucleic acid hybridization
Plasmids from 7 different bacteria digested with same restriction enzyme: none of these bacteria happen to be identical (source of hospital-acquired infections).
DNA base composition
Guanine + cytosine moles% (GC)
DNA fingerprinting
Electrophoresis of restriction enzyme digests
rRNA sequencing
Polymerase Chain Reaction (PCR)
Figure 10.14

25. Nucleic Acid Hybridization
Greater degree of hybridization (pairing of two strands of DNA, each from a different microbe) indicates greater similarity
Figure 10.15

26. Nucleic Acid Hybridization: DNA probe
Figure 10.16

27. Nucleic Acid Hybridization: DNA chip
Figure 10.17

28. Dichotomous Key Learning objectives:
Differentiate a dichotomous key from a cladogram.
Dichotomous key: successive questions with two possible answers.

29. Cladogram
Cladogram:
Maps showing evolutionary relationships among organisms.
Figure

30. Cladogram
Figure

31. Figure 10.5