Microbial diversity:a super quick intro, I swear

Meade Krosby

Animals 1,099,000

Vertebrates 54,000

Fish 30,000

Birds 8,600

Mammals 3,700

Arthropods 881,000

Insects 793,000

Beetles 350,000

Plants 328,000

Angiosperms 275,000

Fungi 44,000

“Protists” 30,000

“Prokaryotes” 3,000

Total 1,504,000

Taxonomic distribution of described species

Measuring microbial diversity

• Culturing: traditional approach• 16S ribosomal RNA

– Carl Woese

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are needed to see this picture.

Measuring microbial diversity

• DNA reassociation kinetics1. Shear DNA2. Denature3. 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 - 99.9% of species are

rare (Gans J, Wolinsky M, Dunbar J (2005) Science 309:1387–1390.)

• T-RFLP1. Extract DNA from community sample2. Amplify 16S ribosomal DNA with fluorescently

labeled primers3. Digest product with restriction enzymes4. Run out on automated sequencer5. Compare fragment lengths to database of

reference species6. 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. 2000 August; 66(8): 3616–3620.

• DNA sequencing1. Extract community DNA2. PCR3. Clone to isolate individual species4. Sequence

• Direct sequencing - the future?

Measuring microbial diversity using 16S rRNA

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