Microbial Evolution and Taxonomy

Question 1

Phenetic Classification

Answer 1

Grouped according to similar phenotypic characteristics

• Use as many attributes as possible
• Of practical use in identification – Clinical diagnostics

Question 2

Phylogenetic Classification

Answer 2

Classification according to evolutionary relationships between organisms

Question 3

The API Strip

Answer 3

• Cupules contain dried reagents
• Inoculated with bacterial suspension
• Incubated at 37°C
• Colour changes indicate metabolic properties
• Profile can be used to give identification

Question 4

Molecular clocks

Answer 4

Nucleotide changes accumulate in proportion to time • Changes are random • Changes are usually neutral – Don’t affect structure or function of encoded proteins

Properties of a suitable gene • Present in all the organisms to be compared • Has the same function in all the organisms to be compared • Conserved – Will have stable regions that are constant – Will also have variable regions • Long enough – Has sufficient information

Question 5

16S rRNA is used as a molecular clock:

Answer 5

• Present in all the organisms to be compared – All living things have ribosomes
• Has the same function – The function of 16S rRNA is essential
• Conserved – Has stable regions – Has variable regions
• Long – ~1500 nucleotides

Question 6

16S rRNA sequence analysis

Answer 6

The gene for the 16S rRNA is sequenced

1. The 16S rRNA gene is amplified by PCR
2. The sequence is determined
3. The sequence is compared with known sequences

– Compare sequence with known sequences in the data base for identification

– Calculate “relatedness” for classification and phylogeny

Question 7

Species concept for Prokaryotes

Answer 7

• A group of strains sharing a high degree of similarity in several independent traits – Phenotypic and genetic
• A group of strains cluster closely phylogenetically and are distinct from other groups of strains – DNA sequences of multiple genes – 97% or greater 16S rRNA gene sequence identity

Question 8

Universal Phylogenetic Tree

Answer 8

• Ribosomal RNA is found in all living things • Based on SSU rRNA sequences • Small subunit (SSU) rRNA – Bacteria and Archaea: 30S subunit, 16S rRNA – Eukaryotes: 40S subunit, 18S rRNA • Confirmed by sequencing other genes

Question 9

Key features distinguishing Bacteria and Archaea from Eukarya

Answer 9