Ch 10 Classification of Microorganisms

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

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) Experts estimate that there are around 100 million species in the world. What percentage of these flora and fauna have we named in the 250 years since Carl Linnaeus devised a classification system to complete Adam's task? Remarkably, only 2 or 3 percent. So two blue-sky thinkers in San Francisco - Kevin Kelly and Stewart Brand - recently came up with a solution to this problem: the All-Species Inventory. The goal is to identify and name every living thing, all in a single human generation. This effort will be organized by the newly created All-Species Foundation, which has already raised $1 million for the project. What the moon shot did for technology, the All-Species Inventory hopes to do for ecology.

The Three-Domain System Foundation Fig 10.1

Level Above Kindom: The Three-Domain System Carl Woese 1978 Eubacteria (virtuosos) Archaea (weirdoes) Eukarya (predators and thieves)

Endosymbiotic Theory: Origin of Eukaryotes Figs 10.2, 10.3 Cyanophora paradoxa: modern example of possible evolutionary process

Scientific Nomenclature Common names Vary with languages Vary with geography Binomial Nomenclature (genus + specific epithet) Used worldwide Escherichia coli Homo sapiens

Source of Specific Epithet 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 cruzi Corkscrew-like (trypano-, borer; soma-, body) Honors Oswaldo Cruz

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.

Phylogenetic Relationships of Prokaryotes Fig. 10.6

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

Classification and Identification Fig 10.8 Classification and Identification 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.

Identifying Bacteria Applications, p. 283

Bergey’s Manual: Classifying and Identifying Prokaryotes Bergey’s Manual of Determinative Bacteriology Provides identification schemes for identifying bacteria and archaea Morphology, differential staining, biochemical tests Bergey’s Manual of Systematic Bacteriology Provides phylogenetic information on bacteria and archaea Based on rRNA sequencing

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

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)

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

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

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 Fig 10.15

Nucleic Acid Hybridization: DNA Chip Fig 10.17

Fluorescent In Situ Hybridization (FISH) Add DNA or RNA probe attached to fluorescent dye for S. aureus Fig 10.18a–b

Dichotomous Key The End ANIMATION Dichotomous Keys: Overview ANIMATION Dichotomous Keys: Sample with Flowchart ANIMATION Dichotomous Keys: Practice The End