1. Taxonomy of Cellular Life Taxonomy: classification (hierarchical grouping based on characteristics); nomenclature (naming); identification (define characteristics that match taxa). Phylogeny: study of evolutionary relationships. Comparison of rRNA base sequences is most common. Know domains: (Tables 10.1 & 10.2)

2. Classification: Taxa Hierarchy Eukaryote (e.g. Humans) Domain: Eukarya Kingdom: Animalia Phylum: Chordata Class: Mammalia Order: Primata Family: Hominidae Group: Homo Species: sapiens Prokaryote (e.g. E. coli) Domain: Bacteria (no kingdom) Phylum: Proteobacteria Class: γ-proteobacteria Order: Enterobacteriales Family: Enterobacteriaceae Genus: Escherichia Species: coli Binomial nomenclature: Genus species (italic or underlined) Just like varieties of apples, or races of people, there are strains of a prokaryote species (e.g. the harmless Escherichia coli K12 versus the deadly pathogenic E. coli O157:H7). Why so?

3. Phenetic Characters: 2) Morphological Characters 3) Physiological and Metabolic Characters Very useful in identification! 1) Ecological Characters

4. Phenetic Identification Use of dichotomous keys for bacteria Manually run individual analyses of phenotype (staining, metabolic tests, etc…) needed in the key. Sequentially progress through the key until you reach an end point. The example here stops at the genus level.

5. Phenetic Identification Use of multi-test kits and their databases. This is the EnteroTube II test for members of the Enterobacteriaceae Different media are used to determine specific metabolic capabilities (e.g. lactose fermentation or citrate use) Numerical code is interpreted from an established database. Often there are different kits for different groups; mostly restricted to medically important bacteria.

6. Molecular Characters Fatty acid profiles (FAME analysis) Proteins – Electrophoretic Mobility – Immuno-Reactivity (Serotyping) – A.A. Sequence Data Nucleic Acids – Nucleotide composition (G+C content ≈ T m ) – Degree of Hybridization (>70% ≈ species) – Nucleotide Sequence Data

7. Small subunit rRNA of the three domains of life. Bacteria 16SrRNA Archaea 16SrRNA Eucarya 18SrRNA

8. 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 (get enough information quickly). –Sequence changes reflects a measurement of evolutionary distance between organisms. Similarity between organisms’ sequences are used to create a graphical representation, called a cladogram or phylogenetic tree. (See example Fig 10.17.)

10. Microbial Diversity Assignment Complete by Exam #3 on April 9th, 2003, for participation marks (2% final grade). You may work in groups of three or fewer. (1% Extra Credit if completed by Friday, March 21st, 2003.) Total Extra Credit Ops: 4% STSS; 2% Ch 7; 1% M.D.A. (Ch 11 & 12) = 7% (about two grade intervals). Know these 13 prokaryote groups, including five classes of Proteobacteria, and selected fungi, algae, protozoa and helminths.