1. Classification of Microorganisms
Chapter 10
Classification of Microorganisms

2. Q&A
Pneumocystis jirovecii was thought to be a protozoan until DNA analysis showed it is a fungus. Why does it matter whether an organism is classified as a protozoan or a fungus?

3. The Study of Phylogenetic Relationships
10-1 Define taxonomy, taxon, and phylogeny.
10-2 Discuss the limitations of a two-kingdom classification system.
10-3 Identify the contributions of Linnaeus, von Nägeli, Chatton, Whittaker, and Woese.
10-4 Discuss the advantages of the three-domain system.
10-5 List the characteristics of the Bacteria, Archaea, and Eukarya domains.

4. Taxonomy The science of classifying organisms
Provides universal names for organisms
Provides a reference for identifying organisms

5. Systematics, or Phylogeny
The study of the evolutionary history of organisms
All Species Inventory (2001–2025)
To identify all species of life on Earth

6. Of what value is taxonomy and systematics? 10-1
Why shouldn’t bacteria be placed in the plant kingdom? 10-2, 10-3

7. Placing Bacteria 1735 Kingdoms Plantae and Animalia
1857 Bacteria and fungi put in the Kingdom Plantae –“Flora”
1866 Kingdom Protista proposed for bacteria, protozoa, algae, and fungi
1937 Prokaryote introduced for cells "without a nucleus"
1961 Prokaryote defined as cell in which nucleoplasm is not surrounded by a nuclear membrane
1959 Kingdom Fungi
1968 Kingdom Prokaryotae proposed
1978 Two types of prokaryotic cells found

8. The Three-Domain System
Figure 10.1

9. Table 10.1

10. A Model of the Origin of Eukaryotes
Figure 10.2

11. Endosymbiotic Theory
Figures 10.2, 10.3

12. Fossilized Prokaryotes
Figure 10.4a

13. Fossilized Prokaryotes
Figure 10.4b

14. Fossilized Prokaryotes
Figure 10.4c

15. Phylogenetics
Each species retains some characteristics of its ancestor
Grouping organisms according to common properties implies that a group of organisms evolved from a common ancestor
Anatomy
Fossils
rRNA

16. What evidence supports classifying organisms into three domains? 10-4
Compare Archaea and Bacteria; Bacteria and Eukarya; and Archaea and Eukarya. 10-5

17. Classification of Organisms
10-6 Explain why scientific names are used.
10-7 List the major taxa.
10-8 Differentiate culture, clone, and strain.
10-9 List the major characteristics used to differentiate the three kingdoms of multicellular Eukarya.
10-10 Define protist.
10-11 Differentiate eukaryotic, prokaryotic, and viral species.

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

19. 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

20. Taxonomic Hierarchy Domain Kingdom Phylum Class Order Family Genus
Species

21. The Taxonomic Hierarchy
Figure 10.5

22. Using Escherichia coli and Entamoeba coli as examples, explain why the genus name must always be written out for the first use. Why is binomial nomenclature preferable to the use of common names? 10-6
Find the gram-positive bacteria Staphylococcus in Appendix F. To which bacteria is this genus most closely related: Gemella or Streptococcus? 10-7

23. Classification of Prokaryotes
Prokaryotic species: A population of cells with similar characteristics
Culture: Grown in laboratory media
Clone: Population of cells derived from a single cell
Strain: Genetically different cells within a clone

24. Phylogenetic Relationships of Prokaryotes
Figure 10.6

25. Classification of Eukaryotes
Eukaryotic species: A group of closely related organisms that breed among themselves

26. Classification of Eukaryotes
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

27. Classification of Viruses
Viral species: Population of viruses with similar characteristics that occupies a particular ecological niche

28. References
International Journal of Systematic and Evolutionary Microbiology
Articles with evidence of new species or classification
Bergey’s Manual of Systematic Bacteriology
Provides phylogenetic and identification information on bacteria and archaea
Approved Lists of Bacterial Names
Lists species of known prokaryotes
Based on published articles

29. Identifying Bacteria
Applications, p. 283

30. Use the terms species, culture, clone, and strain in one sentence to describe growing methicillin-resistant Staphylococcus aureus (MRSA). 10-8
Assume you discovered a new organism: it is multicellular, is nucleated, is heterotrophic, and has cell walls. To what kingdom does it belong? 10-9
Write your own definition of protist
Why wouldn’t the definition of a viral species work for a bacterial species? 10-11

31. Classifying & Identifying Microorganisms
10-12 Compare and contrast classification and identification.
10-13 Explain the purpose of Bergey’s Manual.
10-14 Describe how staining and biochemical tests are used to identify bacteria.

32. Classification and Identification
Classification: Placing organisms in groups of related species. Lists of characteristics of known organisms.
Identification: Matching characteristics of an “unknown” organism to lists of known organisms.
Clinical lab identification

33. Identifying Klebsiella doesn’t tell you it’s classified as gammaproteobacteria
Applications, p. 283

34. References 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

35. What is in Bergey’s Manual? 10-13

36. A Clinical Microbiology Lab Report Form
Figure 10.7

37. Identification Methods
Morphological characteristics: Useful for identifying eukaryotes
Differential staining: Gram staining, acid-fast staining
Biochemical tests: Determines presence of bacterial enzymes

38. Identifying a Gram – Negative, Oxidase – Negative Rod
Figure 10.8

39. Numerical Identification
Figure 10.9

40. Design a rapid test for a Staphylococcus aureus. 10-14
Figure 6.10

41. Serology Combine known antiserum plus unknown bacterium
Slide agglutination test
Figure 10.10

42. ELISA Enzyme-linked immunosorbent assay Known antibodies
Unknown type of bacterium
Antibodies linked to enzyme
Enzyme substrate
Figure 18.14

43. An ELISA Test
Figure 10.11

44. The Western Blot
Figure 10.12

45. Phage Typing of Salmonella enterica
Figure 10.13

46. Flow Cytometry
Uses differences in electrical conductivity between species
Fluorescence of some species
Cells selectively stained with antibody plus fluorescent dye
Figure 18.12

47. Genetics DNA base composition DNA fingerprinting rRNA sequencing
Guanine + cytosine moles% (GC)
DNA fingerprinting
Electrophoresis of restriction enzyme digests
rRNA sequencing
Polymerase chain reaction (PCR)
Figure 10.14

48. Nucleic Acid Hybridization
Figure 10.15

49. A DNA Probe Used to Identify Bacteria
Figure 10.16

50. DNA Chip Technology
Figure 10.17

51. DNA Chip Technology
Figure 10.17

52. FISH Fluorescent in situ hybridization Add DNA probe for S. aureus
Figure 10.18

53. Dichotomous Key
Figure 10.8

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

55. Building a Cladogram
Figure 10.19

56. Building a Cladogram
Figure 10.19

57. Building a Cladogram
Figure 10.19

58. What is tested in Western blotting and Southern blotting? 10-15
What is identified by phage typing? 10-16
Why does PCR identify a microbe? 10-17
Which techniques involve nucleic acid hybridization?
Is a cladogram used for identification or classification? 10-12, 10-19