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Ch 10 Classification of Microorganisms
Copyright © 2006 Pearson Education, Inc., publishing as Benjamin Cummings LEARNING OBJECTIVES Define taxonomy, taxon, and phylogeny. List the characteristics of the Bacteria, Archaea, and Eukarya domains. Differentiate among eukaryotic, prokaryotic, and viral species. Explain the scientific naming Differentiate between culture, clone, and strain. Compare and contrast classification and identification. Explain the purpose of Bergeys Manual. Describe how staining and biochemical tests are used to identify bacteria. Explain how serological tests and phage typing can be used to identify an unknown bacterium. Describe how a newly discovered microbe can be classified by ribotyping, DNA fingerprinting, and PCR. Describe how microorganisms can be identified by nucleic acid hybridization, Southern blotting, DNA chips, and FISH. Differentiate a dichotomous key from a cladogram.
Copyright © 2006 Pearson Education, Inc., publishing as Benjamin Cummings Taxonomy and Phylogeny Taxonmoy: science of classifying organisms with goal of showing relationships among organisms. Taxonomic categories: Taxon / Taxa Provides universal names for organisms and a means of identifying them. Phylogeny (or 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.
Copyright © 2006 Pearson Education, Inc., publishing as Benjamin Cummings Level Above Kindom: The Three-Domain System Carl Woese 1978 Eubacteria (virtuosos) Archaea (weirdoes) Eukarya (predators and thieves)
Copyright © 2006 Pearson Education, Inc., publishing as Benjamin Cummings Classification: Species Definition Eukaryotic species: A group of closely related organisms that breed among themselves Prokaryotic species: A population of cells with similar characteristics (Bergeys Manual of Systematic Bacteriology is standard reference on bacterial classification). Clone: Population of cells derived from a single cell Strain: Genetically different cells within a clone Closely related strains constitute a bacterial species. Viral species: Population of viruses with similar characteristics occupying a particular ecological niche. Viruses: not placed in a kingdom – not composed of cells – cannot grow without a host cell.
Copyright © 2006 Pearson Education, Inc., publishing as Benjamin Cummings Scientific Binomial Source of Genus Name Source of Specific Epithet Klebsiella pneumoniaeHonors Edwin KlebsThe disease Pfiesteria piscicidaHonors Lois PfiesterDisease in fish Salmonella typhimuriumHonors Daniel Salmon Stupor (typh-) in mice (muri-) Streptococcus pyogenesChains of cells (strepto-)Forms pus (pyo-) Saccharomyces cerevisiae Fungus (-myces) that uses sugar (saccharo) Makes beer (cerevisiae) Trypanosoma cruzi Corkscrew-like (trypano-, borer; soma-, body) Honors Oswaldo Cruz Scientific Nomenclature
Copyright © 2006 Pearson Education, Inc., publishing as Benjamin Cummings Domain 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 for eukaryotic organisms that do not fit other kingdoms
Copyright © 2006 Pearson Education, Inc., publishing as Benjamin Cummings Identification Methods Morphological characteristics: Useful for identifying eukaryotes Differential staining: Gram staining, acid-fast staining Biochemical tests: Determines presence of bacterial enzymes Fig 10.8
Copyright © 2006 Pearson Education, Inc., publishing as Benjamin Cummings Bergeys Manual of Determinative Bacteriology: Is standard reference for laboratory identification of bacteria. Morphology, differential staining, biochemical tests to test for presence of various enzymes. Bergeys Manual of Systematic Bacteriology Provides phylogenetic information on bacteria and archaea Based on rRNA sequencing Bergeys Manual: Classifying and Identifying Prokaryotes
Copyright © 2006 Pearson Education, Inc., publishing as Benjamin Cummings Identification Methods cont.: Serology 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 organisms. Fig 10.10: Slide Agglutination Examples: Slide agglutination ELISA (see lab) Western blot (no details)
Copyright © 2006 Pearson Education, Inc., publishing as Benjamin Cummings Identification Methods cont.: Phage Typing Figure Identification of bacterial species and strains by determining their susceptibility to various phages. More details on bacteriophages in Ch 13
Copyright © 2006 Pearson Education, Inc., publishing as Benjamin Cummings Identification Methods cont.: Genetics DNA fingerprinting: Number and sizes of DNA fragments (fingerprints) produced by RE digests are used to determine genetic similarities. 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 10.14: Electrophoresis of RE digest of plasmid DNA
Copyright © 2006 Pearson Education, Inc., publishing as Benjamin Cummings Identification Methods cont.: Nucleic Acid Hybridization Fig Single strands of DNA or RNA, from related organisms will hydrogen-bond to form a double-stranded molecule; this bonding is called nucleic acid hybridization. Examples of Applications: Southern blotting, DNA chips, and FISH Figs and 10.18
Copyright © 2006 Pearson Education, Inc., publishing as Benjamin Cummings Putting Identification/Classification Methods Together Dichotomous keys are widely used for identification of organisms. They are based on successive questions that each have two possible answers Cladograms are maps that show phylogenentic (evolutionary) relationship. PLAY Animation: Dichotomous Keys (The Microbiology Place) Method used to establish cladogram for microorganisms?
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