1. Taxonomy II: Applied systems

2. Modern Classification Systems Robert Whittaker (1969) Five Kingdom System –Monera –Protista –Fungi –Plantae –Animalia

3. Modern Classification Systems Carl Woese Three domain system »Archea »Eubacteria » Eukarya

4. Fig. 14-2 stromatolites

5. Fig. 14-9

6. Archaea may be closer to Eukarya than Eubacteria.

7. Phenotypes

8. Replica plating (lederberg) All colonies grow Mutants do not grow Press plate onto velveteen Velveteen with imprint of all colonies Complete medium Incubate All colonies grow Mutants do not grow Minimal medium Transfer imprint of colonies to fresh media Master plate; growth on complete medium Velveteen; sterilized Plastic hoop Wooden block Testing phenotypes

9. Complementation via recombination DNA from Trp + cells Agar lacking tryptophan Trp – cellsNo growthTrp – cellsRecombinants form colonies Agar lacking tryptophan “Trp auxotroph”

10. 16s RNA map

11. Basic Local Alignment Search Tool BLAST Number of sequence of matches After alignment Before alignment Species 1 Species 2 Species 1 Species 2 9 15 Nonidentities Gaps More distant = more differences

12. Making a phylogenetic tree

13. node 1 node 2 node 3 node 4

14. Hybridization analysiis Hybridization experiment: Same genus, but different species Organisms to be compared: Genomic DNA Heat to denature Mix DNA from two organisms—unlabeled DNA is added in excess: DNA preparation Genomic DNA Results and interpretation: Same species Different genera 100%< 25% 100 75 50 25 0 Same strain (control) 1 and 2 are likely different genera Percent hybridization Unhybridized Organism 2 DNA Hybridized DNA Shear and label ( ) Hybridized DNA Shear DNA Organism 1 Organism 2

15. Fig. 14-21 Genomic DNA–DNA hybridization (%) 16S rRNA gene sequence similarity (%) 0 20 40 60 70 80 100 100 98 96 94 92 90 88

16. GC content Thermophiles have higher GC content, why?

17. B. Applied Taxonomic Systems

18. 3. Bacterial taxonomy Bergey's Manual Criteria for identification and classification

19. 3a. Bacterial taxonomy - Bergey's Manual Criteria for identification and classification Morphology –Cell Shape & Arrangement –Cell Size –Staining Reactions

20. 3b. Bacterial taxonomy - Bergey's Manual Criteria for identification and classification Chemical –Chemical Composition »Teichoic acid »LPS

21. 3c. Bacterial taxonomy - Bergey's Manual Criteria for identification and classification Cultural –Nutritional Requirements –Living Host Requirement –Physical Conditions »Temperature, Light, Gas

22. 3d. Bacterial taxonomy - Bergey's Manual Criteria for identification and classification Metabolic –Energy Yielding Processes - Fermentation –Energy Utilizing Processes - Nutrient transport –Motility –Enzymes

23. 3e. Bacterial taxonomy - Bergey's Manual Criteria for identification and classification Antigens –Stimulate the immune system -antigens Genetics –G-C ratio –Plasmids

24. 3f. Bacterial taxonomy - Bergey's Manual Criteria for identification and classification Pathogenic –Cause disease –Host - plant, animal Ecological least reliable –Habitat

25. C. Nomenclature

26. 1a. Nomenclature Sample First Words »Latin Root Bacillus - Small Rod »Greek Root Clostridium - small spindle Corynebacterium - club bacterium »Personal Names Erwinia

27. 1b. Nomenclature Sample Second Words –Albus - White –Aureus - Gold –Lutea - Yellow –Meningitis - inflammation of meninges

28. 2. Nomenclature Writing technical names –First word - always capitalized & in italics –Second word - never capitalized & in italics Bacillus subtilis B. subtilis