Prokaryote Taxonomy & DiversityClassification, 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 Bacteriology1st 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:

3) Morphological Characters

4) Physiological and Metabolic Characters

Very useful in identification!

1) Ecological Characters

2) Genetic Characters

Phenetic IdentificationUse of dichotomous keys for bacteria

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

Microbial Diversity Assignment