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

2. organism grouping identification classification binomial nomenclature
organism similarity

3. identification: morphology & biochemical testing
differential staining & physiology (bacterial enzymes)
Gram negative bacillus
lactose fermenter
decarboxylates lysine
Shigella
produces hydrogen sulfide
Salmonella
lactose non-fermenter
citrate utilization
Escherichia
no citrate utilization
butanediol fermentation
Enterobacter
no butanediol fermentation
Citrobacter

4. identification: serology
Ab/Ag interaction
slide agglutination
ELISA

5. identification: blots
western (immuno-)blot
protein gel
antibody probes
seroconversion with HIV antibodies
confirmation of plasmid transformation 5

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

7. classification & identification: genetic analysis
DNA base composition
ribosomal DNA (rDNA) sequencing
DNA fingerprinting
DNA-DNA hybridization

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

9. classification: NA sequencing

10. Identification & classification: sequencing

11. identification: RFLPs

12. classification: nucleic acid hybridization

13. Method
Classification
Identification
morphology no
yes
staining
yes (Gram)
biochemical testing
serology
flow cytometry
NA hybridization
(yes)
%GC
DNA fingerprinting
rRNA/rDNA sequencing

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, 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 ___________________ Euryarchaeota
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) 18

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?