History and Overview of Microbial Ecology

I.  What is microbial ecology?

II.  How old is the microbial ecology discipline?

III.  Who were the founders of this discipline?

Microbial Evolution and Biodiversity

I.  Age of Earth (4.6 BYBP) and Microorganisms

II.  Species Concept
     A.  There is no official definition of a species in microbiology and the applicability of the 
              species concept to bacteria is refuted by some investigators.
     B.  Bacterial Species working definition 
                "a collection of isolated strains that show a high degree of overall similarity, compared to 
                 related groups of strains." 
     C.  Estimated Number of Microbial Species on Earth
     D.  It is estimated that less than 1% of all procaryotic species have been isolated, cultured and 
              described, so the number of possibly existing species is much greater than for most other 
              taxonomic groups.

III.  Importance of Biodiversity

IV.  Extent of Diversity
     A.  Early Phylogeny Attempts

     B.  Morphological Diversity
          1.  Native bacteria in Lake Superior
          2.  Major cell shapes 
          3.  Minor cell shapes
      
          Take home information - cell morphology alone is not very useful for identifying bacteria 
               or determining phylogenetic relationships

     C.  Physiological Diversity 
          1.  Heterotrophs
               a.  Aerobic
               b.  Anaerobic respiration 
                    - denitrifiers 
                    - manganese reducers
                    - iron reducers 
                    - sulfate reducers
                    - methanogens
                    - fermenters
          2.  Autotrophs
               a.  Phototrophs
                   - Aerobic
                   - Anaerobic
               b.  Chemotrophs (lithotrophs)
                   - Nitrifiers
                   - Sulfur oxidizers
                   - Iron oxidizers
                   - Manganese oxidizers
                   - Hydrogen oxidizers
                   - Methanogens
                   - Acetogens
          3.  Other Physiological Types
               a.  N2-Fixing Bacteria
               b.  Enteric Bacteria
               c.  Pseudomonads

              Take Home Information - many physiological functions are not phylogenetically 
                   conserved

     D.  Genetic Phylogeny 
          1.  Woese's Universal phylogenetic Tree
          2.  Ribosomal RNAs as molecular chronometers
          3.  Analysis of sequence alignments reveals microbial relatedness

     E.  Genetic Diversity
        Bacteria (DOMAIN)
          1.  Proteobacteria - purple bacteria (largest and most physiologically diverse kingdom; 
                  probably had a purple phototrophic ancestor)
               -  a subdivision
               -  b subdivision
               -  g subdivision
               -  d subdivision
               -  e subdivision
          2.  Gram-positive bacteria (a large kingdom)
               -  High G+C species
               -  Low G+C species
               -  Photosynthetic species
               -  Species with gram-negative like walls
          3.  Cyanobacteria (a large kingdom)
          4.  Green sulfur bacteria (photosynthetic)
          5.  Spirochetes (helical shaped bacteria; many pathogens)
          6.  Bacteriodes, flavobacteria, and their relatives
          7.  Planctomyces and their relatives (reproduce by budding and lack peptidoglycan in their 
               cells walls)
          8.  Chlamydiae (obligate intracellular parasites which cause diseases in humans and other 
                animals; only 3 species recognized)
          9.  Radiation-resistance micrococci and their relatives
        10.  Green non-sulfur bacteria and their relatives (thermophiles)
        11.  Thermotoga group (hyperthermopiles)
        12.  Aquiflex-Hydrogenobacter group (most ancient Bacteria)

        Archaea (DOMAIN)
          1.  Crenarcheota (thermophiles; aerobes and anaerobes)
                a.  Thermoplasma
                b.  Thermococcus group
                c.  Extreme thermophiles
          2.  Korarcheaota (Crenarcheota that have lost thermophily?)
          3.  Euryarcheota
               a.  Halobacteria - (aerobes)
               b.  Methanogens (extreme anaerobes)
                   - Methanococcus group
                   - Methanobacter group
                   - Methanomicrobium group

        Eucarya (DOMAIN)
          1.  Archeozoa 
               a.  Diplomonad group - Ex.:  Giardia
               b.  Microsporidia group - microsporidia
           2. Animalia
               a. Protozoans 
                    - Mastigophora (flagellates)
                    - Euglenoids (phototrophic flagellates)
                    - Sarcodina (amebas)
                    - Ciliophora (ciliates) 
                    - Sporozoa (sporozoans) - animal parasites
          3.  Slime Molds
               a. Cellular slime molds - single amebalike cells
               b. Acellular slime molds - naked masses of protoplasm of indefinite size and shape 
                    called plasmodia
          4.  Fungi 
               a. Molds (filamentous fungi)
                    - Ascomycotina (sac fungi)
                    - Deuteromycotina (fungi imperfecti)
                    - Zygomycotina (bread molds)
                b. Yeasts
                    - Ascomycotina
                    - Basidiomycotina
                c. Mushrooms (large fruiting bodies) - Basidiomycotina (club fungi, mushrooms)
                d. Oomycetes (water molds)
          5.  Plantae
               a.  Algae (terrestrial and aquatic)
                    - Chlorophyta (green algae) - unicellular to leafy
                    - Euglenophyta (euglenoids) - unicellular, flagellated
                   - Chrysophyta (golden-brown algae, diatoms) - unicellular
                   - Phaeophyta (brown algae) - filamentous to leafy
                   - Pyrrophyta (dinoflagellates) - unicellular, flagellated
                   - Rhodophyta (red algae) - unicellular and filamentous to leafy

              [Lichens (consortium of alga and fungus)]

V.  Biodiversity Resources
  A.  Bergey's Trust
     B.  Reference Collections
     C.  Databases of sequences of ribosomal RNA molecules

VI.  Designing rRNA-Based Oligonucleotide Probes
  A.  Concept
     B.  Demonstration of GDE Program
     C.  Probe Check facility on RDP Home Page (URL address in Microbiology web page links)

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