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

Introduction to Microbiology

  1. The Scope of Microbiology.  Microbiology is both a basic and an applied biological science. Most areas of applied microbiology can be related to farming and agriculture.

    1. Definitions.

      1. Microbiology.  Microbiology is simply the study of microorganisms and their activities which impact just about everything on earth – humans, plants, animals, the geography and atmosphere.

      2. Microorganism.  Microorganisms are unicellular organisms (or at least capable of living as single cells). This is what differentiates them from multicellular organisms like plants and animals. Also, because of their one-cell size, it usually requires a microscope to see them – hence the term "microorganism."

    2. Branches of applied microbiology.  (They can overlap.)

      1. Medical and veterinary microbiology.  Deals with all aspects of infectious disease in humans and animals.

      2. Agricultural microbiology.  Deals with all aspects of farming – microbial reactions in soil, diseases of plants, etc.

      3. Microbiology of water and waste treatment.  Studying quality of water available to us and also the level of contamination of waste water such that the numbers of microorganisms can be reduced or eliminated as necessary (1) before waste water is ultimately dumped into the environment and (2) before it reaches us as drinking water.

      4. Food and dairy microbiology.  "Food" microbiology in general concerns a wide variety of products edible to humans and animals such as sausage and other meat; sauerkraut, silage, pickles and other plant products; and dairy products. Food microbiologists seek to check the magnitude of food spoilage and seek ways to prevent it. Also how to utilize microorganisms in the production of food (such as sauerkraut, yogurt and silage). Also how pathogens can be transmitted in food and ways that can be prevented.

      5. Industrial microbiology and biotechnology.  Examples: Using microorganisms to produce ethanol from grain to be used as a gasoline additive. Biotechnology can manipulate the genes of microorganisms to increase their efficiency.

  2. General Outline of Living Things and Other Replicating "Organisms."  (The latter are those on the "borderline of life" – only making new copies of themselves when in contact with higher forms of life.) We can start to put all organisms (not just microorganisms) into categories.

    1. Non-cellular.  Lack many of the structural and biochemical features that are common to all types of cells. Are these really "living"?

      1. Possess no genetic material.

        1. Prions.  Structure of prion is almost identical to protein in certain specific neurolgical tissue. Invading prions somehow causes native proteins to change to become like them – thus a "replication" of sorts. Disease caused is called "transmissible spongiform encephalopathy" in that sponge-like holes are formed in brain tissue. In humans, cause Creutzfeldt-Jakob disease (CJD). In cattle, cause bovine spongiform encephalopathy (BSE, mad cow disease) which can be transmitted to humans, causing "variant Creutzfeldt-Jakob disease" (variant CJD, vCJD). In deer and elk, cause chronic wasting disease (CWD, "mad deer disease").

        2. Any Others?

      2. Possess genetic material.

        1. Viruses.  Are not cells at all, and therefore are not really organisms, although they are definitely microscopic. Viruses are made up of nucleic acid (DNA or RNA – double-stranded or single-stranded) and protein and have some of the characteristics of life, but they only "come to life" (i.e., reproduce more of their kind) while infecting plants, animals, humans and various microorganisms including bacteria. They also cause a variety of infectious diseases. The study of viruses is virology and it developed as a branch of microbiology. (Foot and mouth disease is just one example.)

        2. Viroids.  Even "lower" than viruses. Just a molecule of RNA. Can infect potatoes and cucumbers and certain other plants.

        3. Satellites.  These depend on a "helper virus" to multiply. If encapsulated with a protein coat, is called "satellite virus." If just "naked" nucleic acid, is called "satellite nucleic acid."

    2. Cellular. (All possess genetic material.)

      1. Differences between prokaryotic and eukaryotic cell types:

        Characteristics of prokaryotic and eukaryotic cells.

        Property Eukaryotic Prokaryotic
        nuclear membrane present absent
        number of chromosomes >1 1
        size relatively large relatively small
        chloroplasts and mitochondria present absent
        mitosis and meiosis present absent
        ribosomes 80S size 70S size
        cytoplasmic streaming present absent
        membranes contain sterols and polyunsaturated fatty acids lack sterols and contain saturated or monounsaturated lipids

        Typical Procaryotic Cell

        Typical Eucaryotic Cell

      2. Prokaryotic organisms. (Basically unicellular.)  Prokaryotic means "primitive nucleus" which refers to the fact that the cell chromosome is not surrounded by a nuclear membrane. These organisms tend to be unicellular; all that a prokaryotic organism is and does is tied up in that one cell.

        1. Bacteria – including cyanobacteria.  Unicellular organisms without a true nucleus (called prokaryotes), they live everywhere that life exists including in associations with animals and plants. Most are beneficial, but some cause disease in humans, animals and plants.

        2. Archaea.  A newly-recognized group of prokaryotes formerly included with the bacteria. Some produce methane during their metabolism. Some often live in extreme environments such as high temperature, low pH or high salt concentrations. Those that produce methane (the methanogens) have relevance to farm microbiology.

      3. Eukaryotic organisms. (Increasing tendency to be multicellular.)  Eukaryotic means"true nucleus". The cell nucleus consists of chromosomes (DNA) enclosed by a nuclear membrane. Eukaryotes tend to be multicellular and differentiated except for protozoa, yeasts and many algae which are unicellular.

        1. Protozoa.  Animal-like microorganisms common in moist environments, including the intestinal tracts of animals. Generally engulf their nutrients. A few cause some important diseases.

        2. Fungi.  These organisms live mainly in the soil and are responsible for the decomposition (biodegradation) of organic material. Nutrients are absorbed. Microscopic fungi include molds and yeasts.

          • Molds.  Filamentous: Chains of cells. Often seen as hairy masses on bread and fruit. Can spoil food. Some are used in industry, making soy sauce, antibiotics, etc.

          • Yeasts.  Unicellular: classic shape is large oval cell with buds forming. Can be used for production of bread, alcoholic beverages, grain alcohol, etc.

          • Fungi which are not considered "microorganisms."  Mushrooms, rusts, smuts, etc. Microscopically can see filamentous cells and spores.

        3. Algae.  Plant-like organisms that live wherever there is light and moisture. They produce oxygen (O2) during photosynthesis.

          • Microscopic algae.  Generally unicellular.

          • Algae which are not considered "microorganisms."  Some may assume very large size (seaweed, kelp, etc.).

          • What about "blue-green algae"?  This is an old name for what are now known as cyanobacteria. Even though they have been classified with algae, their overall similarity to bacteria has been noted since the 19th century.

        4. Plants.

        5. Animals.

  3. Distribution of Microorganisms and Their Associations with Humans.  Usually, they have a substantial effect on their environment.

    1. Distribution.  Found in water, soil, air, on the surfaces of humans, plants and animals and on anything that comes into contact with water, soil, air, plants or animals. Basically, microorganisms are found everywhere on Earth where life exists, and wherever you see higher forms (plants and animals) living, you know that there are microorganisms living. Microorganisms are generally found as "mixed cultures." As a rule, microorganisms will not be found in the blood of healthy humans.

    2. Harmful effects.

      1. Agents of disease.  Microorganisms are the cause of infectious disease including anthrax, malaria, tuberculosis, tetanus, pneumonia, diarrhea, measles, colds and fever blisters.

      2. Food spoilage.  Most food spoilage, whether it is in a granary or a grocery store, is due to microbial growth. Some things to consider:

        1. Moisture.  Bacteria live in the moisture. If one dries out the food or adds a large amount of solute (salt, sugar, etc.) that gets dissolved in the water, one begins to eliminate growth of bacteria in the food and subsequent spoilage.

        2. Food as medium for bacteria.  Various components of foods can be attacked by microorganisms – especially proteins, sugars and fats.

        3. Milk.  When milk spoils due to fermenting organisms, one gets acidic milk which leads to lumpy milk (protein coagulated by the acid).

        4. Clear Liquids.  With clear liquids, one sees cloudiness when bacteria achieve a high concentration.

      3. Deterioration of structures, dwellings, textiles, manufactured products, etc.  As for food, moisture is required for microbial growth. If enough nutrients get dissolved in the moisture, then microbial growth is probable. High humidity can provide enough moisture for microbial growth (especially molds) on solid surfaces such as shower curtains.

    3. Beneficial effects.

      1. Production of essential nutrients.  Microorganisms that live in the intestinal tract produce digestive enzymes or vitamins or other nutrients useful in the nutrition of the animal.

      2. Production of O2 in atmosphere.  At least 50 percent of the O2 on Earth is produced by algae and cyanobacteria – microorganisms that possess the same photosynthetic process found in regular plants.

      3. Primary source of organic material.  At least half of the fixed (organic) carbon on Earth is produced by autotrophic microorganisms. Autotrophs (by definition) take up CO2 and convert it to organic matter; this is called primary production. (Photosynthetic organisms that produce O2 are autotrophs).

      4. Replenishment of soil nitrogen.  Many bacteria fix nitrogen, a process which removes some N2 from the atmosphere and converts it to ammonia. Thus it is a nitrogen source for these bacteria and subsequently for use by plants and animals.

      5. Degradation of complex organic materials.  This is biodegradation. It is said that there is no natural organic compound that cannot be degraded by the combined activities of microorganisms. Not just natural compounds but also a lot of man-made compounds such as TNT.

      6. Source of antibiotics and drugs.  Penicillin, tetracycline and most other antibiotics are produced by bacteria and molds that live in the soil.

      7. Manufacture of fermented foods and beverages.  Includes beer, wine, bread, yogurt, cheese, sauerkraut, silage, sausage, pickles, olives, soda crackers, tea, etc.

      8. Other biotechnological products.  Vaccines, enzymes, genes, etc.

      9. Future uses.  New fuels, foods, adhesive materials, etc.

Outline for this section.
Farm Microbiology Home Page.
CALS Farm and Industry Short Course Home Page.
Bacteriology Department Web Site.

Page last modified on
3/9/03 at 6:15 PM, CST.
John Lindquist, Dept. of Bacteriology,
University of Wisconsin – Madison