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)

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?

Phenetic Characters:

2) Morphological Characters

3) Physiological and Metabolic Characters

Very useful in identification!

1) Ecological Characters

Phenetic IdentificationUse 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.

Phenetic IdentificationUse 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.

Molecular Characters

• Fatty acid profiles (FAME analysis)

• Proteins – Electrophoretic Mobility– Immuno-Reactivity (Serotyping)– A.A. Sequence Data

• Nucleic Acids– Nucleotide composition (G+C content ≈ Tm)– Degree of Hybridization (>70% ≈ species)– Nucleotide Sequence Data

Small subunit rRNA of the three domains of life.

Bacteria 16SrRNA

Archaea 16SrRNA

Eucarya 18SrRNA

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.)

Microbial Diversity AssignmentComplete 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.