chapters 10 & 11 taxonomy, classification and prokaryotic diversity

organism grouping identification classification binomial nomenclature organism similarity

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

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 5

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 denature DNA read abs. @ 260nm 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) biochemical testing serology flow cytometry NA hybridization (yes) %GC DNA fingerprinting rRNA/rDNA sequencing

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?

chapter 11: domains Bacteria & Archaea

the prokaryotes: domains Bacteria and Archaea

Domain Archaea Korarchaeota ___________________ Euryarchaeota 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) 18

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?