Post on 13-Dec-2015
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Student Learning Outcomes
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, DNA chips, and FISH.
Explain and apply a dichotomous key
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Taxonomy and Phylogeny
Taxonomy: Science of classifying organisms. Provides universal names for organisms.
Taxonomic categories: Taxon / Taxa
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.
All Species Inventory (2001–2025)
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The Three-Domain SystemFoundation Fig 10.1
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Level Above Kindom: The Three-Domain System
CarlWoese
1978
Eubacteria (virtuosos)Archaea (weirdoes)
Eukarya (predators and thieves)
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Endosymbiotic Theory: Origin of Eukaryotes
Cyanophora paradoxa: modern example of possible evolutionary process
Figs 10.2, 10.3
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Scientific Nomenclature
Common names
Vary with languages
Vary with geography
Binomial Nomenclature (genus + specific epithet)
Used worldwide
Escherichia coli
Homo sapiens
Scientific Names
Scientific Binomial Source of Genus Name
Source of Specific Epithet
Klebsiella pneumoniae Honors Edwin Klebs The disease
Pfiesteria piscicida Honors Lois Pfiester Disease in fish
Salmonella typhimurium Honors Daniel Salmon Stupor (typh-) in
mice (muri-)Streptococcus pyogenes
Chains of cells (strepto-) Forms pus (pyo-)
Penicillium chrysogenum Tuftlike (penicill-) Produces a yellow
(chryso-) pigment
Trypanosoma cruziCorkscrew-like (trypano-, borer; soma-, body)
Honors Oswaldo Cruz
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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). 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 cell.
Copyright © 2006 Pearson Education, Inc., publishing as Benjamin Cummings Fig. 10.6
Phylogenetic Relationships of Prokaryotes
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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 kingdom for eukaryotic organisms that do not fit other kingdoms
Grouped into clades based on rRNA
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Classification: Placing organisms in groups of related species. Lists of characteristics of known organisms.
Identification: Matching characteristics of an “unknown” to lists of known organisms.
Fig 10.8
Classification and Identification
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Applications, p. 283
Identifying Bacteria
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Bergey’s Manual:Classifying and Identifying Prokaryotes
Bergey’s Manual of Determinative BacteriologyProvides identification schemes for identifying bacteria and archaea
Morphology, differential staining, biochemical tests
Bergey’s Manual of Systematic BacteriologyProvides phylogenetic information on bacteria and archaea
Based on rRNA sequencing
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Clinical Lab Identification
Morphological characteristics Useful for identifying eukaryotes
Differential staining Gram staining, acid-fast staining
Biochemical tests Determines presence of bacterial enzymes
Numerical Rapid Identification
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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)
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Phage Typing Fig 10.13
Identification of bacterial species and strains by determining their susceptibility to various phages.
More details on bacteriophages in Ch 13
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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
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Nucleic Acid Hybridization
Fig 10.15
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
Fluorescent In Situ Hybridization (FISH)
Fig 10.18a–b
Add DNA or RNA probe attached to fluorescent dyefor S. aureus