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chapters 10 & 11 taxonomy, classification and prokaryotic diversity

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organism grouping identification binomial nomenclature classification organism similarity

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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

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Ab/Ag interaction slide agglutination ELISA identification: serology

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western (immuno-)blot protein gel antibody probes identification: blots seroconversion with HIV antibodiesconfirmation of plasmid transformation

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laser reads single cells interspecies differences conductivity fluorescence Ab-stained cells identification: flow cytometry

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

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classification: hydrogen bonds & %GC experimentally derived 1.denature DNA 2.read abs. @ 260nm 3.abs of 1 >> 2 from DNA/RNA sequence

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classification: NA sequencing

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Identification & classification: sequencing

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identification: RFLPs

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classification: nucleic acid hybridization

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MethodClassificationIdentification morphologynoyes stainingyes (Gram)yes biochemical testingnoyes serologynoyes flow cytometrynoyes NA hybridizationyes(yes) %GCyesno DNA fingerprintingnoyes rRNA/rDNA sequencingyes

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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 doesnt 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?

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chapter 11: domains Bacteria & Archaea

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the prokaryotes: domains Bacteria and Archaea

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Korarchaeota ___________________ Pyrodictium Sulfolobus Euryarchaeota ___________________ Methanobacterium ___________________ Halobacterium Crenarchaeota ___________________ Domain Archaea

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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)

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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?