Analysis of Natural Microbial Populations

1. Traditional microbiology depends upon culturing organisms
   1. Not all organisms can be cultured
   2. "Plate count anomaly"
   3. Much of microbial diversty remains unstudied
2. Molecular approaches to microbial diversity
   1. Direct study of DNA from the environment
      1. Isolate DNA
      2. Early studies cloned DNA (or reverse transcribed rRNA).
      3. More recent studies use PCR, then clone the PCR product and screen the clone library
      4. Sequence clones
      5. Check for PCR and cloning artifacts
         1. Secondary structural analysis
      6. Perform phylogenetic analysis
   2. Find organism sequences of interest came from
      1. In situ hybridization
      2. selective cultures
   3. Long-range PCR, inverse PCR, etc.
3. Environments that have been studied
   1. Octopus Mat
   2. Marine picoplankton
   3. Protozoan symbionts
   4. Soil bacteria
   5. Obsidian Pool
4. Details on the Obsidian Pool Analyses

Barns, S.M., C.F. Delwiche, J.D. Palmer, and N.R. Pace. 1996. Perspectives on archaeal diversity, thermophily and monophyly from environmental rRNA sequences. Proc. Natl. Acad. Sci. USA 93:9188-9193.