Prokaryote Taxonomy & Diversity
Classification, Nomenclature & Identification
Phenetic Classification
Molecular Phylogeny Approach
• 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
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
3) Morphological
Characters
4) Physiological and
Metabolic Characters
Phenetic Identification
Use of dichotomous keys for bacteria
Phenetic Identification
Use 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”:
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–
–
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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
Microbial Diversity Assignment