Microbial diversity: a super quick intro, I swear

1. Microbial diversity:a super quick intro, I swear Meade Krosby

2. Taxonomic distribution of described species

3. Measuring microbial diversity • Culturing: traditional approach • 16S ribosomal RNA • Carl Woese

5. Measuring microbial diversity • DNA reassociation kinetics • Shear DNA • Denature • Cool and estimate # species via time to reassociation

6. Taxonomic distribution of described species 10,000 species *Estimated by DNA reassociation kinetics (V. Torsvik, J. Goksøyr, F. L. Daae, Appl. Environ. Microbiol. 56, 782 (1990)) >1,000,000 species * A power law best describes species distribution - 99.9% of species are rare (Gans J, Wolinsky M, Dunbar J (2005) Science 309:1387–1390.)

7. Measuring microbial diversity using 16S rRNA • T-RFLP • Extract DNA from community sample • Amplify 16S ribosomal DNA with fluorescently labeled primers • Digest product with restriction enzymes • Run out on automated sequencer • Compare fragment lengths to database of reference species • Repeat with various primer/enzyme combinations

8. T-RFLP • Example of fragment profiles (using TspEl) from the Ribosomal Database Project at U Mich. • Phylotypes with the highest frequency in the database are labeled. Appl Environ Microbiol. 2000 August; 66(8): 3616–3620.

9. Measuring microbial diversity using 16S rRNA • DNA sequencing • Extract community DNA • PCR • Clone to isolate individual species • Sequence • Direct sequencing - the future?

10. Cuatro Cienegas