2 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 namingDifferentiate 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.
3 Taxonomy and Phylogeny Taxonmoy: science of classifying organisms with goal of showing relationships among organisms.Taxonomic categories: Taxon / TaxaProvides 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.
4 Level Above Kindom: The Three-Domain System CarlWoese1978Eubacteria (virtuosos)Archaea (weirdoes)Eukarya (predators and thieves)
5 Classification: Species Definition Eukaryotic species: A group of closely related organisms that breed among themselvesProkaryotic 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 cellStrain: Genetically different cells within a cloneClosely 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.
6 Scientific Nomenclature Scientific BinomialSource of Genus NameSource of Specific EpithetKlebsiella pneumoniaeHonors Edwin KlebsThe diseasePfiesteria piscicidaHonors Lois PfiesterDisease in fishSalmonella typhimuriumHonors Daniel SalmonStupor (typh-) in mice (muri-)Streptococcus pyogenesChains of cells (strepto-)Forms pus (pyo-)Saccharomyces cerevisiaeFungus (-myces) that uses sugar (saccharo)Makes beer (cerevisiae)Trypanosoma cruziCorkscrew-like (trypano-, borer; soma-, body)Honors Oswaldo Cruz
7 Domain EukaryaAnimalia: Multicellular; no cell walls; chemoheterotrophicPlantae: Multicellular; cellulose cell walls; usually photoautotrophicFungi: Chemoheterotrophic; unicellular or multicellular; cell walls of chitin; develop from spores or hyphal fragmentsProtista: A catchall for eukaryotic organisms that do not fit other kingdoms
9 Bergey’s Manual: Classifying and Identifying Prokaryotes Bergey’s Manual of Determinative Bacteriology:Is standard reference for laboratory identification of bacteria.Morphology, differential staining, biochemical tests to test for presence of various enzymes.Bergey’s Manual of Systematic BacteriologyProvides phylogenetic information on bacteria and archaeaBased on rRNA sequencing
10 Identification Methods cont.: Serology Involves reactions of microorganisms with specific antibodies: Combine known anti-serum with unknown bacteriumUseful in determining the identity of strains and species, as well as relationships among organisms.Fig 10.10: Slide AgglutinationExamples:Slide agglutinationELISA (see lab)Western blot (no details)
11 Identification Methods cont.: Phage Typing Figure 10.13Identification of bacterial species and strains by determining their susceptibility to various phages.More details on bacteriophages in Ch 13
12 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 sequencingPolymerase 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
13 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, andFISHFigs and 10.18Fig 10.15
14 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 answersCladograms are maps that show phylogenentic (evolutionary) relationship.Method used to establish cladogram for microorganisms?PLAYAnimation: Dichotomous Keys (The Microbiology Place)
15 Microbiology in the News (p. 294): Mass Death of Marine Mammals Dichotomous KeyThe End