Microbial diversity:

a super quick intro, I swear

Meade Krosby
Taxonomic distribution of described species
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
 Measuring microbial diversity
• Culturing: traditional approach
• 16S ribosomal RNA
– Carl Woese

QuickTime™ and a
TIFF (LZW) decompressor
are needed to see this picture.
 Measuring microbial diversity

• DNA reassociation kinetics

1. Shear DNA
2. Denature
3. Cool and estimate # species via time to
reassociation
Taxonomic distribution of described species
“Prokaryotes” 3,000

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