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Prokaryote Taxonomy & Diversity. Classification (hierarchical grouping of taxa, based on characteristics) Nomenclature (formal naming of taxa) Identification (define characteristics that match a particular taxa). Phylogeny (study of evolutionary relationships)
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Prokaryote Taxonomy & Diversity • Classification (hierarchical grouping of taxa, based on characteristics) • Nomenclature (formal naming of taxa) • Identification (define characteristics that match a particular taxa). • Phylogeny (study of evolutionary relationships) • Bergey’s Manual of Systematic Bacteriology • 1st ed. (1984); mostly phenetic classification; 4 volumes • 2nd ed. (in prep); mostly phylogenetic classification; 5 volumes Classification, Nomenclature & Identification Phenetic Classification Molecular Phylogeny Approach
Species Concept for Prokaryotes Defined differently than Eukarya (no sexual reproduction) = genetically unique population with many stable characters distinctly different from other groups. Strains are variations within a species; characterized by minor differences in biochemical/ physiological properties (biovars), antigenic distinctions (serovars), shape (morphovars), or viral susceptibility (phage-typing).
Phenetic Characters: Very useful in identification! 1) Ecological Characters 2) Genetic Characters 4) Physiological and Metabolic Characters 3) Morphological Characters
Phenetic IdentificationUse of multi-test kits and their databases.The combination of positive results from an unknown is entered into a database of results form known bacteria. A computer model predicts the most probable match and level of certainty. Intended use is for clinical isolates.
Molecular Characters • Fatty acid profiles (FAME analysis) • Proteins • Electrophoretic Mobility • Immuno-Reactivity • A.A. Sequence Data • Nucleic Acids • Nucleotide composition (G+C content ≈ Tm) • Degree of Hybridization (>70% ≈ species) • Nucleotide Sequence Data
Phylogenetic Classification Molecular Chronometers • Phylogeny refers to grouping based on evolutionary relatedness; regardless of phenetic characters. • Phylogeny is inferred from changes in protein or rRNA sequence over time. • Attributes of an Ideal “Molecular Chronometer”: • Universally distributed. • Functionally homologous. • Ease of analysis. • Rate of sequence change commensurate with evolutionary distance measured.
Small subunit rRNA of the three domains of life. Bacteria 16SrRNA Archaea 16SrRNA Eucarya 18SrRNA