Chapter 8 Classification PDF

Taxonomy is the science of classifying & naming organisms  Learning Objectives Learning Objectives 10-1 Define taxonomy, taxon, and phylogeny. 10-2 Discuss the limitations of a two-kingdom classification system....

Taxonomy is the science of classifying & naming organisms  Learning Objectives Learning Objectives 10-1 Define taxonomy, taxon, and phylogeny. 10-2 Discuss the limitations of a two-kingdom classification system. 10-3 Identify the contributions of Linnaeus, Whittaker, and Woese. 10-4 Discuss the advantages of the three-domain system. 10-5 List the characteristics of the Bacteria, Archaea, and Eukarya domains. 10-6 Explain why scientific names are used. 10-7 List the major taxa. 10-8 Differentiate culture, clone, and strain. 10-9 List the major characteristics used to differentiate the three kingdoms of multicellular Eukarya. 10-10 Define protist. 10-11 Differentiate eukaryotic, prokaryotic, and viral species. 10-12 Compare and contrast classification and identification. 10-13 Explain the purpose of Bergey’s Manual. 10-14 Describe how staining and biochemical tests are used to identify bacteria. 10-15 Differentiate Western blotting from Southern blotting. 10-16 Explain how serological tests and phage typing can be used to identify an unknown bacterium. 10-17 Describe how a newly discovered microbe can be classified by DNA base composition, DNA fingerprinting, and PCR. 10-18 Describe how microorganisms can be identified by nucleic acid hybridization, Southern blotting, DNA chips, ribotyping, and FISH. 10-19 Differentiate a dichotomous key from a cladogram. — Taxonomy is the science of classifying organisms — Shows degree of similarity among organisms — Systematics, or phylogeny, is the study of the evolutionary history of organisms Classification of Organisms Carlos Linnaeus — I. Binomial Nomenclature: In Italic or underlined & Latin 1. Genus name (noun) 2. Species epithet (adjective) Examples: — Escherichia coli — Vibrio cholerae — Staphylococcus epiderrmidis — Saccharomyces cerevisiae  Carlos Linnaeus II. The Taxonomic Hierarchy A series of subdivisions developed by Linnaeus to classify plants and animals Eukaryotic species: a group of closely related organisms that breed among themselves 1. Species 2. Genus 3. Family 4. Order 5. Class 6. Phylum 7. kingdom Carlos Linnaeus — Species: a group of organisms that interbreed to produce viable off springs. — Strain: is a group of bacterial cells (microorganisms) all derived from a single Parent (cell). — Linnaeus divided all organisms into only two kingdoms: 1. Plantae: Algae, ferns & flowering plants (Photosynthesis) 2. Animalia : Insects and animals (vertebrates). They obtain nutrients through mouth  Classification of Organisms — Whittaker’s five-kingdom taxonomic based on phylogenetic hierarchy (added 3 more kingdoms)-(no viruses) — Phylogenetic hierarchy is the ways in which organisms are grouped should reflect their evolution from common ancestors. Prokaryotic species: a population of cells with similar characteristics — Protista: a catchall kingdom for a variety of organisms; autotrophic and heterotrophic (unicellular). — Fungi: chemoheterotrophic; unicellular or multicellular; cell walls of chitin; develop from spores or hyphal fragments Carl Woese (1928-) — The Three Domains Three domain system based on ribosomal (rRNA) nucleotide sequences. 1. Eukarya 2. Bacteria 3. Archaea — Methanogens — Extreme halophiles — Hyperthermophiles  Methods of Classifying Bergey’s Manual Contains information used for the identification of prokaryotes. — Types of information microbiologists commonly use to distinguish among microorganisms: 1. Physical Characteristic 2. Biochemical Tests 3. Serological Tests 4. Nucleic Acid Analysis Physical Characteristic — Morphology, size and arrangement of cells. — Gram positive or negative — Acid fast — Wall-less — Oxygen requirement — Optimal pH — Growth temperature — Endospore — Motility (Flagella)  Methods of Classifying Biochemical tests — Biochemical tests are based on enzymatic activities & their ability to utilize or produce certain chemicals. Ex: The ability to ferment carbohydrate, utilize amino acid or starch. They ability to produce H2o or acids as an end products. — We use selective and differential media for these tests. — Numerical identification or rapid identification methods (picture next slide) Figure 10. 9 One type of Rapid Identification Method for Bacteria: EnteroPluri Test From BD Diagnostics One tube containing media for 15 biochemical tests is inoculated with an unknown enteric bacterium. After incubation, the tube is observed for results. Phenylalanine Arabinose Ornithine Adonitol Glucose Lactose Sorbitol Dulcitol Urease Citrate Lysine Indole V–P Gas H2 S The value for each positive test is circled, and the numbers from each group of tests are added to give the code number. Comparing the resultant code number with a Code Number Microorganism Atypical Test Results computerized listing shows that the organism in the tube is Citrobacter freundii. 62352 Citrobacter freundii Citrate 62353 Citrobacter freundii None The Use of Metabolic Characteristics to Identify Selected Genera of Enteric Bacteria Serology The science that studies serum and immune responses in serum — Microorganisms are antigenic—they stimulate the body to form antibodies in the serum — In an antiserum, a solution of antibodies is tested against an unknown bacterium — Antibody: Immune system proteins that bind very specifically to target antigen. — Specificity (between Ag &Ab) Methods of Classifying Serological tests 1. Slide agglutination test is based on Ag- Ab interaction (involves the clumping of antigen & antibody). 2. ELISA: enzyme linked immunosorbent assay-is labeled antibody test 3. Western blotting: Identifies antibodies in a patient's serum; confirms HIV infection, and Lyme disease ELISA (enzyme linked immunosorbent assay) is labeled antibody test Figure 10.11 - Overview  Nucleic Acid analysis 1. DNA base composition — G+ C ratio — Guanine + cytosine % — GC + AT = 100% — Two organisms that are closely related have similar amounts of various bases — Online databases (NCBI Genome Database) 2. DNA fingerprinting — Electrophoresis of restriction enzyme digests of an organism's DNA — Comparing fragments from different organisms provides information on genetic similarities and differences  3. PCR: Use PCR to amplify DNA of an unknown microorganism that cannot be cultured.  Dichotomous Keys Is a guide that directs the user through a step-by-step process to identify a microbe Animation: Dichotomous Keys: Overview Animation: Dichotomous Keys: Sample with Flowchart Animation: Dichotomous Keys: Practice In class activities Construct a Dichotomous key diagram with the following species of bacteria using gram stain and morphology. First make a table. 1. Escherichia coli (gram negative rod), 2. Bacillus megaterium (gram positive rod), 3. Micrococcus luteus (Gram positive cocci)].. Because learning changes everything. ® www.mheducation.com