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

Basic Structure, Genetics, Habitats, Physiology, Nutrition and Growth of Bacteria

  1. Basic Morphology.

    1. Microscopic.

    2. Some rare exceptions.

      1. Epulopiscium.

      2. Thiomargarita.

    3. Shapes.

      1. Coccus.

      2. Bacillus.

      3. Spirillum.

    Shapes of Bacterial Cells

  2. Types of Cells.

    1. Vegetative cell.

    2. Endospore.

      1. Formation.

      2. Features.

    3. Reproductive spore.

    4. Cyst.

  3. Some Structural Components.

    1. Cell wall and cell membrane = cell envelope.

      1. Cell wall.

      2. Cell membrane.

    2. Capsule.

    3. Ribosomes.

    4. Storage granules.

    5. Flagella.

    6. Fimbriae (also called Pili).

  4. Genetic Material and Associated Activities.

    See diagrams and discussion on special handout, reproduced here.

    1. Nucleic acids – DNA and RNA.

    2. Structure of DNA.

      1. Basic unit = nucleotide – composed of:

        1. Base molecule: adenine, guanine, cytosine or thymine.

        2. Sugar molecule = deoxyribose.

        3. Phosphate.

      2. Linkage of nucleotides = strand of DNA.

    3. Replication of DNA.

    4. The genetic code.

      1. Bases in groups of three.

      2. Genes.

    5. RNA.

      1. Synthesis = transcription.

      2. Differences from DNA.

        1. Base molecule: adenine, guanine, cytosine or uracil.

        2. Sugar molecule = ribose.

    6. Protein synthesis = translation.

    7. Activities (DNA replication, transcription, translation) accomplished in any order?

  5. Genetic Differentiation and Identification of Bacteria – Base-Sequencing.

    1. Differentiating between species and establishing relationships.

    2. Identification of unknown organisms and establishing new species.

    Basis for Constructing a Phylogenetic Tree
    (Series of Diagrams from Bacteriology 102)

  6. Habitats.

  7. Unique Processes Not Found in Eukaryotes.

    1. Special types of photosynthesis.

    2. Special types of fermentation.

    3. Use of inorganic compounds as energy sources.

    4. Respiration without oxygen.

    5. Nitrogen-fixation.

    6. Degradation of complex organic substances.

  8. General Overview of Microbial Metabolism and Nutritional Requirements.

    1. Metabolism.

      A Very generalized Overview of Metabolism.

      Note: "Energy source" is better called "source of electrons." Also, the lateral lines (directed to the right) represent the transfer of energy (1) given off when electrons are released and (2) given off when ATP goes back to ADP.

    2. Nutritional requirements.

      1. Overview of major elements.

        Elements of Prime Importance and Their Sources and Functions in Bacterial Cells.

        Element % of dry weight Source Major Functions
        Carbon (C) 50 organic compounds or CO2 Essential elemental constituent of cellular material.
        Oxygen (O) 20 H2O, organic compounds, CO2, and O2 Constituent of cell material and cell water; O2 is electron acceptor in aerobic respiration.
        Nitrogen (N) 14 NH3+, NO3, organic compounds, N2 Constituent of amino acids, the bases in nucleic acids and nucleotides, coenzymes, vitamins.
        Hydrogen (H) 8 H2O, organic compounds, H2 Most numerous elemental constituent of organic compounds and cell water.
        Phosphorus (P) 3 inorganic phosphates (PO43–) Constituent of ATP and nucleic acids (the phosphate component); also phospholipids, lipopolysaccharide, teichoic acids, vitamins.
        Sulfur (S) 1 SO42–, H2S, S0, organic sulfur compounds Constituent of two amino acids (cysteine, methionine), some coenzymes, vitamins.
        Potassium (K) 1 Potassium salts Main cellular inorganic cation and cofactor for certain enzymes
        Magnesium (Mg) 0.5 Magnesium salts Inorganic cellular cation, cofactor for certain enzymatic reactions
        Calcium (Ca) 0.5 Calcium salts Inorganic cellular cation, cofactor for certain enzymes and a component of endospores
        Iron (Fe) 0.2 Iron salts Component of cytochromes and certain nonheme iron-proteins and a cofactor for some enzymatic reactions
      2. Trace elements.

      3. Growth factors.

      4. Importance of water.

  9. Sources of Energy and Reducing Power for Catabolic Reactions.

    An Attempt to Produce an Ultra-general "Universal Diagram" to Summarize Catabolism.

    1. Purposes of catabolism.

      1. Generate "reducing power."

      2. Generate energy.

      3. Provide some of the "building blocks" for anabolism.

    2. Overview of terms and reactions.

      1. Chemotrophs vs. phototrophs.

      2. Organotrophs vs. lithotrophs.

        Examples of electron donors that are oxidized include:

        • H2 (hydrogen gas), oxidized to H2O
        • S (sulfide), oxidized to SO42– (sulfate)
        • Fe2+ (ferrous ion), oxidized to Fe3+ (ferric ion)
        • NH4+ (ammonium), oxidized to NO2 (nitrite)
        • NO2 (nitrite), oxidized to NO3 (nitrate)
      3. Combining/compounding terms.

    3. Further details and applications (see figure below).

      1. Fermentation.

        1. End products.

        2. Practical applications.

      2. Respiration.

        1. Aerobic respiration.

        2. Anaerobic respiration.

      3. Oxygenic (plant) photosynthesis.

      4. Anoxygenic (bacterial) photosynthesis.


    Example: On the left side, glucose is oxidized to pyruvate. On the right side, pyruvate can be reduced to acids, alcohols and gases.


    Above shows AEROBIC RESPIRATION with the use of oxygen. ANAEROBIC RESPIRATION uses an "oxygen substitute" such as nitrate, sulfate, etc.


    ("chl" represents chlorophyll.)

    Phototrophy can be OXYGENIC (evolving O2 when H2O serves as the electron donor) or ANOXYGENIC (non-O2-evolving).

    Simplified Representations of Fermentation, Respiration and Phototrophy.

  10. Sources of Carbon.

    1. Importance of carbon.

    2. Heterotrophy vs. autotrophy.

  11. Nutritional Types of Microorganisms – Based on Carbon and Energy Sources.

    Major Nutritional Types of Microorganisms.

    Nutritional Type Carbon Source Energy Source Examples
    Photoautotrophs CO2 Light (These organisms are generally "photolithotrophic" in that electron transfer usually involves the oxidation of inorganic compounds.) Algae; cyanobacteria; some purple and green bacteria.
    Photoheterotrophs Organic compounds Light (These organisms are generally "photoorganotrophic" in that electron transfer usually involves the oxidation of organic compounds.) Some purple and green bacteria; a few algae.
    Chemoautotrophs CO2 Usually inorganic compounds (chemolithotrophy) – e.g., H2, NH4+, NO2, H2S Relatively few bacteria and many archaea.
    Chemoheterotrophs Organic compounds Usually organic compounds (chemoorganotrophy) Protozoa, fungi, most bacteria, some archaea.
  12. Physical Requirements and Restrictions.

    1. Temperature.

      1. Range (cardinal points): minimum, maximum, optimum.

        1. Psychrophiles.

        2. Psychrotrophs.

        3. Mesophiles.

        4. Thermophiles.

        5. Extreme thermophiles.

        Effect of Temperature on Growth of Bacteria.

      2. Effect on rate of cell division.

      3. Thermal death.

    2. pH (acidity and alkalinity).

      1. Range.

      2. Effect on growth rate.

      Effect of pH on Growth Rates of Different Types of Bacteria.

    3. Oxygen (O2).

      1. Classification of organisms as to use and tolerance of O2 – terms used in the most general sense.

        1. Aerobes.

        2. Anaerobes.

        3. Facultative anaerobes.

      2. Terms applied in the "oxygen relationship" laboratory test.

    Oxygen Relationships among Chemotrophic Microorganisms

    Group Aerobic
    Ability to

    (with O2)
    Ability to
    Representative Organisms
    + + Animals, plants, algae, molds, protozoa, many prokaryotes.
    + + + + Many bacteria, yeasts, some protozoa, few animal cells.
    + + + The "lactic acid bacteria." (Aerotolerant anaerobes would be included in facultative anaerobes in the more general use of these terms as listed above.)
    + + or – Many prokaryotes (e.g., Clostridium).

  13. Growth of Microorganisms.

    1. Binary fission and exponential growth.

    2. Generation time.

    3. Growth curves.

      Typical Bacterial Growth Curve.

    4. Growth relations with one another.

      1. Mutualistic associations.

        1. Normal flora.

        2. Root nodule bacteria (bacterial association with plant roots).

        3. Mycorrhiza (fungal association with plant roots – mentioned here for comparison).

      2. Parasitic associations.

      3. Commensal associations.

    5. Some obvious changes produced by microbial growth.

      1. Acid formation.

      2. Alcohol production.

      3. Gas production.

      4. Protein decomposition.

      5. Fat decomposition.

      6. Ropiness and slime.

  14. Control of Microbial Growth.

    1. Practicality.

      1. In medicine.

      2. In agriculture.

      3. In food science.

    2. Principles of prevention.

      1. Killing vs. inhibition of growth – use of cidal vs. static agents.

      2. Sterilization.

    3. Methods of control.

      1. Low temperatures (refrigeration) – lower rate of growth.

      2. High temperatures – destroy microorganisms.

        1. Simple boiling.

        2. Boiling under pressure.

        3. Mild heat (pasteurization).

        4. Heating in microwave.

        5. Dry heat (hot air oven).

        6. Incineration.

      3. Increased acidity (lower pH).

      4. Reduced water activity.

      5. Irradiation.

      6. Gas.

      7. Filtration.

      8. Chemical agents (antimicrobial agents).

        1. Antiseptics.

        2. Disinfectants.

        3. Preservatives.

        4. Antibiotics.

        5. Chemotherapeutic agents.

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
2/23/04 at 10:15 PM, CST.
John Lindquist, Dept. of Bacteriology,
University of Wisconsin – Madison