chapters 10 & 11 taxonomy, phylogenetics and prokaryotic diversity

1. chapters 10 & 11 taxonomy, phylogenetics and prokaryotic diversity

2. organism grouping identification • binomial nomenclature classification & phylogenetics • organism similarity

3. 16S rDNA sequence analysis & phylogeny

4. identification: biochemical testing differential staining & physiology (bacterial enzymes)

5. identification: serology • Ab/Ag interaction • slide agglutination • ELISA

6. western (immuno-)blot protein gel antibody probes identification: blots • Southern blot • DNA gel • DNA probes seroconversion with HIV antibodies confirmation of plasmid transformation

7. identification: flow cytometry laser “reads” single cells • interspecies differences • conductivity • fluorescence • Ab-stained cells

8. classification, phylogeny & identification: genetic analysis • DNA base composition • ribosomal DNA (rDNA) sequencing • DNA fingerprinting • DNA-DNA hybridization

9. classification: hydrogen bonds & %GC experimentally derived • denature DNA • read abs. @ 260nm • abs of 1× >> 2× from DNA/RNA sequence

10. classification & phylogeny: sequencing

11. identification, classification & phylogeny: sequencing

12. identification: RFLPs

13. phylogeny: nucleic acid hybridization

14. Chapter 10 Learning Objectives • Define and differentiate taxonomy, phylogeny, identification and classification. • Categorize each of the following in terms of the classification and identification of bacteria: morphology, differential staining, biochemical testing, western blot, Southern blot, serology, ELISA, flow cytometry, DNA fingerprinting, %GC analysis, rDNA (rRNA) sequencing, DNA-DNA hybridization. Know why each does or doesn’t work for classification and/or identification. • If given the percent similarities for a group of organisms and a blank phylogenetic tree, be able to place the 4 organisms appropriately onto the tree. • How has rDNA sequencing and the work of Carl Woese changed the way organisms are categorized based on their similarities? • How do RFLPs allow for the identification of unknown bacteria?

15. chapter 11: domains Bacteria & Archaea

16. the prokaryotes: domains Bacteria and Archaea

17. Domain Archaea Korarchaeota • ___________________ • Pyrodictium • Sulfolobus Euryarchaeota • ___________________ • Methanobacterium • ___________________ • Halobacterium Crenarchaeota • ___________________ • ___________________

18. microbial diversity habitat variety ___________________ ___________________ ___________________ ___________________ ___________________ _________________________________________________________ metabolize highly unique substances integral to many ___________________ cycles nutrient “fixing” into organic molecules in situ PCR >billions of bacteria/gm of soil 30-50% of aquatic plankton are Archaea 5000 non-eukaryotic formally described (cf. 1/2 million insects)

19. Chapter 11 Learning Objectives • What are the general characteristics shared by all prokaryotes? • In general, what can be said about the habitats of Archaea? • What roles do prokaryotes play in the environment? Where do they live, what do they contribute to the biosphere? • What has in situ PCR told us about microbial diversity?