1. Diversity in a modern context
   1. Various views of diversity
      1. The definition of diversity depends upon the context
   2. Extinction and the changing environment
      1. Atmospheric composition is strongly influenced by biotic factors, particularly photosynthesis
      2. Extinction is resulting in a profound loss of biological diversity
      3. Environmental change may be influencing poorly studied groups
         1. They are poorly studied, so we really don't know.
   3. DNA sequence data are being gathered at a tremendous rate
      1. Molecular studies give a different view of diversity than traditional methods
      2. Some groups previously viewed as small and unimportant turn out to be genetically diverse
      3. Measured by molecular methods, most biological diversity is microbial
2. Photosynthesis as a theme to guide the study of microbial diversity
   1. A set of organisms united by their environmental role, and by a distinctive physiology
   2. What is photosynthesis?
   3. What is the evolutionary history of photosynthesis
   4. Different kinds of photosynthesis
   5. The environmental significance of photosynthesis
3. Oxygenic photosynthesis -- the familiar kind
   1. Photosynthesis in plants
      1. Light reactions
         1. Light harvesting complexes
         2. Electron transport chain
         3. Reaction center
            1. Photosystem II
               1. Quinone
               2. Oxidizes water
            2. Photosystem I
               1. Iron-Sulfur
               2. Reduces NADP+
         4. Water as Electron Donor, generation of oxygen
         5. Production of ATP and NADPH2
      2. Dark Reactions
         1. Carbon Fixation
            1. Form I Rubisco (L8S8)
         2. Regeneration of substrates
   2. Phylogenetic distribution of oxygenic photosynthesis
      1. Cyanobacteria (period)
         1. Essentially all cyanobacteria are photosynthetic.
         2. e.g., Anabaena, Gloeobacter
      2. Cyanobacteria with other pigment systems
         1. e.g., Prochloron
      3. Plastids
   3. Pigment diversity of eukaryotes with plastids
4. Trophic diversity in prokaryotes
   1. Metabolic diversity of prokaryotes
      1. Evolutionary context - oxygenic photosynthesis is derived
   2. Prospects for reconstructing the history of evolution of metabolism
5. Anoxygenic photosynthesis
   1. Proteobacteria ("purple bacteria")
   1. anoxygenic phototrophs
   2. e.g., Rhodobacter
   3. + Quinone-type photosystem (PSII)
   4. + rubisco (either or both form I and II)
   5. Carbon fixation via Calvin cycle
   6. not all proteobacteria are phototrophic
   2. Green Sulfur Bacteria
      1. anoxygenic phototrophs
      2. e.g., Chlorobium
      3. + Fe-S type photosystem (PSI)
      4. - rubisco
      5. Carbon fixation by reverst TCA
   3. Green nonsulfur bacteria
      1. anoxygenic phototrophs
      2. e.g., Chloroflexus
      3. not related to green sulfur bacteria
      4. + Quinone-type photosystem (PSII)
      5. - rubisco; carbon fixation apparently by reverse TCA
   4. Heliobacteria
      1. photoheterotrophs
      2. e.g., Heliobacterium
      3. Gram positive
      4. Photosystem Fe-S type homodimer (PSI)
      5. - rubisco; no known carbon fixation per se

Required Reading: C&M, Chapter 3 (pp. 93-104)

Supplementary Reading: