1. Copyright © 2004 Pearson Education, Inc., publishing as Benjamin Cummings Taxonomy Science of Classification, Nomenclature, Identification Organisms are named and arranged into taxa Provides: universal names reference facilitates research, scholarship and communication

2. Copyright © 2004 Pearson Education, Inc., publishing as Benjamin Cummings Taxonomy Systematics or phylogeny Provides tools for clarifying evolution of organisms as well as their interrelationships All Species Inventory (2001-2025)

3. Copyright © 2004 Pearson Education, Inc., publishing as Benjamin Cummings Scientific Nomenclature Scientific binomialSource of Genus name Source of Specific epithet Kbebsiella pneumoniaeHonors Edwin KlebsThe disease Pfiesteria piscicidaHonors Lois PfiesterDisease in fish Salmonella typhimuriumHonors Daniel SalmonStupor (typh-) in mice (muri-) Streptococcus pyogenesChains of cells (strepto-)Forms pus (pyo-) Penicillium notatumTuftlike (penicill-)Spores spread in wind (nota) Trypanosoma cruziCorkscrew-like (trypano-, borer; soma-body) Honors Oswaldo Cruz

4. Copyright © 2004 Pearson Education, Inc., publishing as Benjamin Cummings History of Taxonomy 1735Carlous Linnaeus: 2 Kingdoms 1857Bacteria & fungi put in the Plant Kingdom 1866Ernst Haeckel: 3 Kingdoms 1937"Prokaryote" term introduced 1959Kingdom Fungi

5. Copyright © 2004 Pearson Education, Inc., publishing as Benjamin Cummings History of Taxonomy 1961Current definition of prokaryote introduced 1969Robert Whittaker: 5 kingdoms Plantae; Animalia; Fungi; Protista; Monera 1978Carl Woese: 3 Domains Eukarya, Bacteria and Archaea Based on variation in cellular composition Primary evidence to support comes from differences in rRNA sequences

6. Copyright © 2004 Pearson Education, Inc., publishing as Benjamin Cummings The Three-Domain System Figure 10.1

7. Copyright © 2004 Pearson Education, Inc., publishing as Benjamin Cummings Three Domains Table 10.1

8. Copyright © 2004 Pearson Education, Inc., publishing as Benjamin Cummings Nested Taxonomical Hierarchy Figure 10.5

9. Copyright © 2004 Pearson Education, Inc., publishing as Benjamin Cummings Species Definition Eukaryotic species: Prokaryotic species: Clone Strain Viral species:

10. Copyright © 2004 Pearson Education, Inc., publishing as Benjamin Cummings References for Prokaryote Identification 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 Approved Lists of Bacterial Names Lists species of known prokaryotes Based on published articles

11. Copyright © 2004 Pearson Education, Inc., publishing as Benjamin Cummings Methods of Identifying Microorganisms 1.Morphological characteristics 2.Differential and structural stains 3.Biochemical tests 4.Serology – based on antigenic nature of microbes 5.Phage typing –determines to which phages a bacteria is susceptible 6.Analysis of nucleic acids

12. Copyright © 2004 Pearson Education, Inc., publishing as Benjamin Cummings Acid fast bacilli and non-acid fast cocci Gram - bacilli and Gram + cocci Flagella stain Endospore stain

13. Copyright © 2004 Pearson Education, Inc., publishing as Benjamin Cummings Dichotomous key for biochemical tests based on enzyme activity

14. Copyright © 2004 Pearson Education, Inc., publishing as Benjamin Cummings Rapid Identification Tests Figure 10.9

15. Copyright © 2004 Pearson Education, Inc., publishing as Benjamin Cummings Microbes are antigenic Combine known antiserum + unknown bacterium Slide agglutination ELISA Western blot Figure 10.10

16. Copyright © 2004 Pearson Education, Inc., publishing as Benjamin Cummings Phage Typing Figure 10.13

17. Copyright © 2004 Pearson Education, Inc., publishing as Benjamin Cummings Analysis of nucleic acids DNA base composition DNA fingerprinting Electrophoresis of RFLPs Nucleic acid hybridization rRNA sequencing PCR