chapters 10 & 11
taxonomy, classification
and prokaryotic diversity
organism grouping
identification
– binomial nomenclature
classification
–
organism similarity
identification: morphology & biochemical testing
differential staining & physiology (bacterial enzymes)
Gram negative
bacillus
lactose
fermenter
lactose nonfermenter
decarboxylates
lysine
produces
hydrogen sulfide
citrate utilization
Shigella
Salmonella
Escherichia
no citrate
utilization
butanediol
fermentation
no butanediol
fermentation
Enterobacter
Citrobacter
identification: serology
• Ab/Ag interaction
– slide agglutination
– ELISA
identification: blots
western (immuno-)blot
• protein gel
• antibody probes
seroconversion with HIV antibodies
confirmation of plasmid transformation
identification: flow cytometry
laser “reads” single cells
• interspecies differences
– conductivity
– fluorescence
• Ab-stained cells
classification & identification: genetic analysis
• DNA base composition
• ribosomal DNA (rDNA) sequencing
• DNA fingerprinting
• DNA-DNA hybridization
classification: hydrogen bonds & %GC
experimentally derived
1. denature DNA
2. read abs. @ 260nm
3. abs of 1× >> 2×
from DNA/RNA sequence
classification: NA sequencing
Identification & classification: sequencing
identification: RFLPs
classification: nucleic acid hybridization
Method
Classification
Identification
morphology
no
yes
staining
yes (Gram)
yes
biochemical testing
no
yes
serology
no
yes
flow cytometry
no
yes
NA hybridization
yes
(yes)
%GC
yes
no
DNA fingerprinting
no
yes
rRNA/rDNA sequencing
yes
yes
Chapter 10 Learning Objectives
1.
Define and differentiate taxonomy, phylogeny, identification and classification.
2.
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.
3.
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.
4.
How has rDNA sequencing and the work of Carl Woese changed the way organisms are
categorized based on their similarities?
5.
How do RFLPs allow for the identification of unknown bacteria?
chapter 11:
domains Bacteria & Archaea
the prokaryotes: domains Bacteria and Archaea
Domain Archaea
Korarchaeota
• ___________________
– Pyrodictium
– Sulfolobus
Euryarchaeota
• ___________________
– Methanobacterium
• ___________________
– Halobacterium
Crenarchaeota
• ___________________
• ___________________
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)
Chapter 11 Learning Objectives
1.
What are the general characteristics shared by all prokaryotes?
2.
In general, what can be said about the habitats of Archaea?
3.
What roles do prokaryotes play in the environment? Where do
they live, what do they contribute to the biosphere?
4.
What has in situ PCR told us about microbial diversity?