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Ch 10Classification 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 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 rRNA sequencing.
Copyright © 2006 Pearson Education, Inc., publishing as Benjamin Cummings
Level Above Kindom: The Three-Domain System
CarlWoese
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 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-)
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
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 archaea
Based on rRNA sequencing
Bergey’s 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 TypingFigure 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: 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 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
Figs. 10.17 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?
Microbiology in the News (p. 294): Mass Death of Marine Mammals
Dichotomous Key