Ch 10 Classification of Microorganisms LEARNING OBJECTIVES Define

Ch 10 Classification of Microorganisms

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 Bergey’s 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 r. RNA 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 (Bergey’s 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 Nomenclature Source of Scientific Binomial Source of Genus Name Specific Epithet Klebsiella pneumoniae Honors Edwin Klebs The disease Pfiesteria piscicida Honors Lois Pfiester Disease in fish (typh-) in Salmonella typhimurium Honors Daniel Salmon Stupor mice (muri-) Streptococcus pyogenes Chains of cells (strepto Forms pus (pyo-) -) Saccharomyces cerevisiae Fungus (-myces) that Makes beer uses sugar (saccharo) (cerevisiae) Corkscrew-like Oswaldo Trypanosoma cruzi (trypano-, borer; soma Honors Cruz Copyright © 2006 Pearson Education, Inc. , publishing as Benjamin Cummings -, body)

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 Fig 10. 8 § Morphological characteristics: Useful for identifying eukaryotes § Differential staining: Gram staining, acid-fast staining § Biochemical tests: Determines presence of bacterial enzymes Copyright © 2006 Pearson Education, Inc. , publishing as Benjamin Cummings

Bergey’s Manual: Classifying and Identifying Prokaryotes Bergey’s Manual of Determinative Bacteriology: Is standard reference for laboratory identification of bacteria. Bergey’s Manual of Systematic Bacteriology Provides phylogenetic information on bacteria and archaea Copyright © 2006 Pearson Education, Inc. , publishing as Benjamin Cummings Morphology, differential staining, biochemical tests to test for presence of various enzymes. Based on r. RNA sequencing

Identification Methods cont. : Serology § Involves reactions of microorganisms with specific antibodies: Combine known antiserum with unknown bacterium § Useful in determining the identity of strains and species, as well as relationships among organisms. § Examples: § Slide agglutination § ELISA (see lab) § Western blot (no details) Copyright © 2006 Pearson Education, Inc. , publishing as Benjamin Cummings Fig 10. 10: Slide Agglutination

Identification Methods cont. : Phage Typing Figure 10. 13 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: r. RNA sequencing § Polymerase chain reaction (PCR) can be used to amplify a small amount of microbial DNA in a sample. The presence or identification of Fig 10. 14: Electrophoresis of an organism is indicated by RE digest of plasmid DNA amplified DNA. (see lab) Copyright © 2006 Pearson Education, Inc. , publishing as Benjamin Cummings

Identification Methods cont. : Nucleic Acid Hybridization 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. 10. 17 and 10. 18 Copyright © 2006 Pearson Education, Inc. , publishing as Benjamin Cummings Fig 10. 15

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. Method used to establish cladogram for microorganisms? PLAY Animation: Dichotomous Keys (The Microbiology Place) Copyright © 2006 Pearson Education, Inc. , publishing as Benjamin Cummings

Microbiology in the News (p. 294): Mass Death of Marine Mammals Dichotomous Key