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Classification of Organisms and Phylogenetic Relationships

Explore the importance of classifying microorganisms and the study of phylogenetic relationships. Learn about taxonomy, limitations of classification systems, contributions of key scientists, advantages of the three-domain system, and characteristics of different domains.

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Classification of Organisms and Phylogenetic Relationships

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  1. Chapter 10 Classification of Microorganisms

  2. Q&A • Pneumocystis jiroveciiwas 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. Scientific Names

  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

  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. 10-10 • 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

  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 • 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

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