The Tree of Life 2 - Prokaryotes

1. Prokaryotes
   1. Major groups of prokaryotes
   2. Carl Woese and the SSU rRNA model
   3. The advantages (and disadvantages) of a natural classification
   4. This classification differs from the "traditional" metabolic approach
   5. Because this is a new classification, some major groups are very poorly understood
2. Archaea
   1. Archaea remain poorly understood, and many new species have recently been discovered
   2. Crenarchaeota
      1. Many are extreme thermophiles
   3. Euryarchaeota
      1. Many are methanogens or extreme halophiles
   4. Other
   5. Phototrophy in the Archaea
      1. Some halophiles use bacteriorhodopsin to create a proton gradient that is used to generate ATP
      2. They are capable of a form of photoheterotrophy, but this process is probably not related to bacterial photosynthesis involving electron transport chains
      3. Rubisco (similar to form II) has been identified in the complete genome sequences of Methanococcus (a methanogen) and Archaeoglobus (an extreme thermophile in the Euryarchaeota), but rubisco carbon fixation is not thought to be coupled to photosynthesis in any archaea.
3. Bacteria - Major groups in the Woese system
   1. Thermotogales
      1. Thermophilic - often extreme thermophiles
   2. Deinococci
      1. Radiation resistant bacteria
      2. Deinococcus radiodurans can withstand huge doses of radiation (>> 5000 Gy; 5 Gy lethal to humans)
         1. First isolated from radiation sterilized meat
         2. Also found in nuclear reactor fuel storage sites, etc.
      3. Probably not originally an adaptation to life in nuclear reactor cores, but rather to desiccation and UV radiation.
         1. Survival is based on an elaborate DNA repair mechanism that assembles the genome from multiple copies
            1. Parenthetical comment: nature came up with random fragment assembly of genomes before humans
         2. recA is essential to DNA repair; this gene is also involved in sex in eukaryotes
   3. Green nonsulfur bacteria
   1. Small group, includes both photosynthetic and nonphotosynthetic taxa
   2. Many are thermophilic
   4. Cyanobacteria ("blue-green algae")
   1. All are Photosynthetic
   5. Proteobacteria ("purple bacteria")
      1. A large and important group, very diverse physiologies
      2. Many are photosynthetic
      3. Subdivided into subgroups designated by greek letters - alpha, beta, gamma, delta, epsilon.
         1. Phototrophs are found in alpha, beta, and gamma subgroups
   6. Gram Positive bacteria ("Firmicutes")
      1. Photosynthesis known only in Heliobacteria (photoheterotrophy)
      2. The gram stain is a key diagnostic tool in traditional determinative microbiology. Gram positives are probably a monophyletic group, while gram negatives definitely are not - they are everything except for gram positive bacteria.
   7. Green Sulfur bacteria
      1. Most (all?) are photosynthetic
   8. Bacteroides/Flavobacterium group
      1. not photosynthetic
      2. Two subgroups, rather dissimilar from each other
         1. Obligate anaerobes, fermentative
         2. Aerobic gliding bacteria
   9. Spirochaetes
      1. not photosynthetic
      2. Distinctive structure
      3. Widespread, some are pathogenic
   10. Chlamydiae
       1. not photosynthetic
       2. Intracelular parasites
       3. Proteinaceous cell wall
   11. Planctomyces group
       1. not photosynthetic
       2. Obligate aerobes
       3. Proteinaceous cell wall
4. The relationship between Bacteria, Archaea, and Eukaryotes
   1. Current hypotheses are based on limited data, and may be mistaken
   2. Archaea and Eukarya are probably more closely related than either is to bacteria

Required Reading:

Supplemental Reading:

Balows, A., H.G. Trüper, M. Dworkin, W. Harder, and H.-H. Schleifer. 1992. The Prokaryotes. Springer-Verlag, NY. This is an encyclopedic three volume set with descriptions of each major prokaryotic group. It is on reserve in the Chemistry Library.

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.

Brock, T.D., and M.T. Madigan. 1997. Biology of Microorganisms, 8th ed. Prentice Hall, NJ

Olsen, G.J., C.R. Woese, and R. Overbeek. 1994. The winds of (evolutionary) change: breathing new life into microbiology. J. Bacteriol. 176:1-6.

Van de Peer, Y., J.-M. Neefs, P. De Rijk, P. De Vos, and R. De Wachter. 1994. About the order of divergence of the major bacterial taxa during evolution. System. Appl. Microbiol. 17:32-38.

Woese, C.R. 1994. There must be a prokaryotes somewhere: microbiology's search for itself. Microbiol. Rev. 58:1-9.