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

Animals1,099,000 Vertebrates54,000 Fish30,000 Birds8,600 Mammals3,700 Arthropods881,000 Insects793,000 Beetles350,000 Plants328,000 Angiosperms275,000 Fungi44,000 “Protists”30,000 “Prokaryotes”3,000 Total1,504,000 Taxonomic distribution of described species

Measuring microbial diversity Culturing: traditional approach 16S ribosomal RNA –Carl Woese

Measuring microbial diversity DNA reassociation kinetics 1.Shear DNA 2.Denature 3.Cool and estimate # species via time to reassociation

“Prokaryotes”3,000 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 % of species are rare (Gans J, Wolinsky M, Dunbar J (2005) Science 309:1387–1390.)

T-RFLP 1.Extract DNA from community sample 2.Amplify 16S ribosomal DNA with fluorescently labeled primers 3.Digest product with restriction enzymes 4.Run out on automated sequencer 5.Compare fragment lengths to database of reference species 6.Repeat with various primer/enzyme combinations Measuring microbial diversity using 16S rRNA

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 August; 66(8): 3616–3620.

DNA sequencing 1.Extract community DNA 2.PCR 3.Clone to isolate individual species 4.Sequence Direct sequencing - the future? Measuring microbial diversity using 16S rRNA

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