Classification of Microorganisms

1 Ch 10 Classification of MicroorganismsCopyright 2006 Pearson Education, Inc., publishing as Benjamin CummingsStudent Learning OutcomesDefine taxonomy, taxon, and the characteristics of the Bacteria, Archaea, and among eukaryotic, prokaryotic, and viral the scientific namingDifferentiate between culture, clone, and and contrast Classification and the purpose of Bergey how staining and biochemical tests are used to identify how serological tests and phage typing can be used to identify an unknown how a newly discovered microbe can be classified by ribotyping, DNA fingerprinting, and how Microorganisms can be identified by nucleic acid hybridization, DNA chips, and and apply a dichotomous key Copyright 2006 Pearson Education, Inc.

2 , publishing as Benjamin CummingsTaxonomy and Phylogeny Taxonmoy: Science of classifying organisms. Provides universal names for organisms. Taxonomic categories: Taxon / TaxaPhylogenyor Systematics: Evolutionary history of group of organisms. Taxonomic hierarchy shows phylogenetic (evolutionary), relationships among organisms. 1969: Living organisms divided into five kingdoms. 1978: Two types of prokaryotic cells found. Prokaryotic relationships determined by rRNA sequencing. All Species Inventory (2001 2025)Copyright 2006 Pearson Education, Inc., publishing as Benjamin CummingsThe Three-Domain SystemFoundation Fig 2006 Pearson Education, Inc., publishing as Benjamin CummingsLevel Above Kindom: The Three-Domain SystemCarlWoese1978 Eubacteria (virtuosos)Archaea (weirdoes)Eukarya (predators and thieves)Copyright 2006 Pearson Education, Inc.

3 , publishing as Benjamin CummingsEndosymbiotic Theory: Origin of EukaryotesCyanophora paradoxa:modern example of possible evolutionary processFigs , 2006 Pearson Education, Inc., publishing as Benjamin CummingsScientific NomenclatureCommon names Vary with languages Vary with geographyBinomial Nomenclature (genus + specific epithet) Used worldwide Escherichia coli Homo sapiensScientific NamesScientific BinomialSource of Genus NameSource of Specific EpithetKlebsiella pneumoniaeHonors Edwin KlebsThe diseasePfiesteriapiscicidaHonors Lois PfiesterDisease in fishSalmonella typhimuriumHonors Daniel SalmonStupor (typh-) in mice (muri-)Streptococcus pyogenesChains of cells (strepto-)Forms pus (pyo-)PenicilliumchrysogenumTuftlike (penicill-)Produces a yellow (chryso-) pigmentTrypanosomacruziCorkscrew-like (trypano-, borer; soma-, body)Honors OswaldoCruzCopyright 2006 Pearson Education, Inc.

4 , publishing as Benjamin CummingsClassification: Species Definition Eukaryotic species: A group of closely related organisms that breed among themselves Prokaryotic species: A population of cells with similar characteristics (Bergey s Manual of systematic Bacteriologyis standard reference on bacterial Classification ). Culture: Grown in laboratory media Clone: Population of cells derived from a single cell Strain: Genetically different cells within a clone Viral species: Population of viruses with similar characteristics occupying a particular ecological niche. Viruses: not placed in kingdom nor domain not composed of cells cannot grow without a host 2006 Pearson Education, Inc., publishing as Benjamin CummingsFig. Relationships of ProkaryotesCopyright 2006 Pearson Education, Inc.

5 , publishing as Benjamin CummingsDomain Eukarya Animalia: Multicellular; no cell walls; chemoheterotrophic Plantae: Multicellular; cellulose cell walls; usually photoautotrophic Fungi: Chemoheterotrophic; unicellular or multicellular; cell walls of chitin; develop from spores or hyphal fragments Protista: A catchall kingdom for eukaryotic organisms that do not fit other kingdoms Grouped into cladesbased on rRNAC opyright 2006 Pearson Education, Inc., publishing as Benjamin CummingsClassification: Placing organisms in groups of related species. Lists of characteristics of known : Matching characteristics of an unknown to lists of known organisms. Fig and IdentificationCopyright 2006 Pearson Education, Inc., publishing as Benjamin CummingsApplications, p.

6 283 Identifying BacteriaCopyright 2006 Pearson Education, Inc., publishing as Benjamin CummingsBergey s Manual:Classifying and Identifying ProkaryotesBergey sManual of Determinative BacteriologyProvides identificationschemes for identifying bacteria and archaeaMorphology, differential staining, biochemical testsBergey s Manual of systematic BacteriologyProvides phylogeneticinformation on bacteria and archaeaBased on rRNAsequencingCopyright 2006 Pearson Education, Inc., publishing as Benjamin CummingsClinical Lab IdentificationMorphological characteristicsUseful for identifying eukaryotesDifferential stainingGram staining, acid-fast stainingBiochemical testsDetermines presence of bacterial enzymesNumerical Rapid IdentificationCopyright 2006 Pearson Education, Inc.

7 , publishing as Benjamin CummingsSerology Involves reactions of Microorganisms with specific antibodies: Combine known anti-serum with unknown bacterium Useful in determining the identity of strains and species, as well as relationships among :Slide Agglutination Examples: Slide agglutination ELISA (see lab) Western blot (no details)Copyright 2006 Pearson Education, Inc., publishing as Benjamin CummingsPhage TypingFig of bacterial species and strains by determining their susceptibility to various details on bacteriophages in Ch 13 Copyright 2006 Pearson Education, Inc., publishing as Benjamin CummingsGenetics DNA fingerprinting:Number and sizes of DNA fragments (fingerprints) produced by RE digests are used to determine genetic similarities.

8 Ribotyping: rRNA sequencing Polymerase chain reaction (PCR) can be used to amplify a small amount of microbial DNA in a sample. The presence or identification of an organism is indicated by amplified DNA. (see lab)Fig : Electrophoresis of RE digest of plasmid DNA Copyright 2006 Pearson Education, Inc., publishing as Benjamin CummingsNucleic Acid HybridizationFig strands of DNA or RNA, from related organisms will hydrogen-bond to form a double-stranded molecule; this bonding is called nucleic acid of Applications: Southern blotting, DNA chips, and FISH Nucleic Acid Hybridization: DNA ChipFig In Situ Hybridization (FISH)Fig bAdd DNA or RNA probe attached to fluorescent dyefor S. aureusDichotomous KeyANIMATION Dichotomous Keys: PracticeANIMATION Dichotomous Keys: Sample with FlowchartANIMATION Dichotomous Keys: Overview