CALS Farm and Industry Short Course Program: Farm Microbiology: Outlines

Soil Microbiology, Cycling of Elements and Biodegredation

  1. The Carbon Cycle.

    1. Use of CO2 as carbon source of AUTOTROPHS (by definition).

    2. Release of CO2 as an end product in respiration (and some fermentation) by CHEMOORGANOTROPHS.

    3. Methanogenesis.

    4. Methane oxidation.

    Organic compounds are used as carbon source by HETEROTROPHS (by definition). As is also the case for the Nitrogen and Sulfur Cycles (below), organic compounds are converted from one to another within plants, animals and microorganisms – also animals eating plants, microorganisms decomposing plants and animals, microorganisms undergoing fermentation, etc.

    The Carbon Cycle.

    Another View of the Carbon Cycle.

    1. Exchange between Primary Producers (Autotrophs – including Cyanobacteria) and Biodegraders (Organotrophs).

    2. Importance of Pseudomonas.

    3. Importance of Streptomyces.

    4. Methanogenesis.

    5. Methane Oxidation.

    6. The Compost Pile.

    7. The Rumen.

  2. The Oxygen Cycle.


    2. O2 production by oxygenic PHOTOTROPHS.

    The Oxygen Cycle.

    1. Exchange between Respirers and Oxygenic Phototrophs (latter includes Cyanobacteria).

    2. Association of Oxygen with Other Elements.

  3. The Nitrogen Cycle.

    1. Respiration of ammonium and nitrite by CHEMOLITHOTROPHS. This process is called nitrification.

    2. Dissimilatory nitrate reduction – a form of anaerobic respiration. This process is called denitrification when nitrate is reduced all the way to N2.

    3. Nitrogen-fixation by certain bacteria under aerobic (upper) and anaerobic (lower) conditions.

    4. Assimilatory nitrate reduction performed by plants and microorganisms.

    5. Assimilatory ammonium uptake performed by plants and microorganisms.

    6. Ammonification performed by microorganisms.

    The Nitrogen Cycle.

    Another View of the Nitrogen Cycle.

    1. Complexity.

    2. Nitrogen-Fixation.

      1. Process.

      2. Symbiotic Nitrogen-Fixing Bacteria – main example: Rhizobium.

      3. Non-Symbiotic (Free-Living) Nitrogen-Fixing Bacteria: Azotobacter, most Cyanobacteria, Klebsiella (i.e., most strains of K. pneumoniae), Bacillus & Clostridium (some species of each).

    3. Nitrification.

    4. Anaerobic Respiration of Nitrate.

      1. Process.

      2. Problem in anaerobic soil with Pseudomonas.

    5. Assimilation.

    6. Ammonification.

  4. The Sulfur Cycle.

    1. Oxidation of sulfide and sulfur by CHEMOLITHOTROPHS (by respiration) and PHOTOLITHOTROPHS.

    2. Dissimilatory sulfate reduction – a form of anaerobic respiration.

    3. Assimilatory sulfate reduction performed by plants and microorganisms.

    4. Desulfurylation performed by animals and microorganisms.

    The Sulfur Cycle.

    Another View of the Sulfur Cycle.

    1. Exchange between Lithotrophs (including the Purple and Green Sulfur Photosynthetic Bacteria) and Anaerobic Respirers.

    2. Assimilation and Desulfurylation.

  5. Overview of Elemental Cycles in a Typical Lake.

    Ecology of a Stratified Lake.

Outline: Previous Section, Next Section.
Notes for this section.
Farm Microbiology Home Page.
CALS Farm and Industry Short Course Home Page.
Bacteriology Department Web Site.

Page last modified on
3/2/04 at 10:30 PM, CST.
John Lindquist, Dept. of Bacteriology,
University of Wisconsin – Madison