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

SECTION 1.
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 the 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. Includes what goes on with silage (also included in food microbiology).

      3. Food 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 such can be prevented. Dairy microbiology and silage microbiology are generally treated as specialized areas; the latter is usually not conventionally considered "food microbiology" even though the overall fermentation process is much like what goes on in sauerkraut and pickles!

      4. 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.

      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. Distribution of Microorganisms and Their Associations with Humans. 

    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. Usually, they have a substantial effect on their environment.

    2. Harmful effects. 

      1. 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.

        1. Food as a medium for microorganisms. 

          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. Nutrients.  Various components of foods can be attacked by microorganisms – especially proteins, sugars and fats.

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

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

      3. Deterioration of structures, dwellings, textiles, manufactured items, 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 the 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. Biodegradation – breakdown of complex organic materials.  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.

  3. "Non-cellular Replicating Units." 

    1. Prions. 

      1. Structure and replication.  Structure of prion is almost identical to protein in certain specific neurological tissue. No genetic material. Invading prions somehow cause native proteins to change to become like them – thus a "replication" of sorts.

      2. Resistance.  Can resist being inactivated by boiling, acid (down to pH 3), UV light and formaldehyde. Having no nucleic acids, they are then not affected by nucleases (enzymes which break apart nucleic acids). Ways in which they can be inactivated include autoclaving at an advanced temperature of 132°C for at least 2 hours (usual autoclaving is done at 121°C), boiling in a detergent, treatment with alkalis (pH 10 and above) and phenol.

      3. Cause a type of amyloid disease called Transmissible Spongiform Encephalopathy (TSE).  Sponge-like holes are formed in brain tissue. TSE's are the only amyloid disease found (so far) in which infectious agents are implicated as the cause.

        SPECIAL NOTE: Amyloid diseases are characterized by normal brain proteins becoming altered such that fibers are formed. Other amyloid diseases are non-infectious and include Alzheimer's Disease, Lou Gehrig's Disease and Huntington's Disease.


      4. Some diseases. 

        1. Creutzfeldt-Jakob Disease (CJD) in humans. 

        2. Bovine Spongiform Encephalopathy (BSE) - also known as mad cow disease.  Can be transmitted to humans, causing "variant Creutzfeldt-Jakob disease" (variant CJD, vCJD).

        3. Chronic Wasting Disease (CWD) in deer and elk. 

        4. Scrapie in sheep.

        5. Kuru in humans.

        6. Feline Spongiform Encephalopathy.

        7. Transmissible Mink Encephalopathy.

    2. Viruses. 

      1. General aspects.  Are not cells at all, and therefore are not really organisms, although they are definitely microscopic. They also cause a variety of infectious diseases. The study of viruses is virology and it developed as a branch of microbiology.

      2. Structure and replication.  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.

      3. Some diseases. 

        1. Foot and mouth disease (not Hoof and Mouth Disease).  Hoof consists of non-living material which virus cannot infect. Infects cloven-hoofed animals such as cattle, sheep, pigs, goats and deer. Big epidemic in 2001 among cattle in the U.K. with over 2000 cases.

        2. Asian Bird Flu  Avian Influenza is more proper name. Can be transmitted from human to human. Major problem in Asia. Have been outbreaks in U.K. in 1992 and U.S. in the 1920s.

        3. SARS (Severe Acute Respiratory Syndrome).  First reported in Asia in early 2003; became a global outbreak later that year.

        4. West Nile Virus.  Major mosquito-borne disease with human cases in nearly all states of the U.S. Seasonal occurance in North America with flare-ups in summer that continue into fall.

        5. Monkeypox.  Small flare-up in 2003 in humans originating from pet prairie dogs.

    3. Viroids and Satellites. 

      1. Viroids  Even "lower" than viruses. Just a molecule of RNA – a single-stranded loop. Can infect potatoes and cucumbers and certain other plants.

      2. Why "satellite"?  These depend on a "helper virus" to multiply. Both the helper virus and the satellite infect a host cell. (Sometimes the helper virus may be unable to reproduce unless its satellite is present.)

      3. Satellite Virus.  If encapsulated with a protein coat, is called "satellite virus."

      4. Satellite Nucleic Acid.  If just "naked" nucleic acid, is called "satellite nucleic acid" and it can "hide" in the protein coat of its helper virus.

  4. Cellular Organisms. 

    1. Differences between prokaryotic and eukaryotic cell types. 

      1. Prokaryotic cells.  Prokaryotic means "primitive nucleus" which refers to the fact that the cell chromosome (genetic material) 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.

      2. Eukaryotic cells.  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.

      3. Summary Table & Diagrams: 

      Characteristics of prokaryotic and eukaryotic cells.

      Property Prokaryotic Eukaryotic
      general kinds of microorganisms bacteria, archae protozoa, fungi, algae, plants, animals
      nuclear membrane absent present
      number of chromosomes 1 >1
      size relatively small relatively large
      unicellular vs. multicellular basically unicellular and undifferentiated unicellular and undifferentiated, multicellular and highly differentiated, and many degrees in between
      chloroplasts and mitochondria absent present
      mitosis and meiosis absent present
      ribosomes (size) 70S 80S
      cytoplasmic streaming absent present
      membranes lack sterols and contain saturated or monounsaturated lipids contain sterols and polyunsaturated fatty acids


      Typical Procaryotic Cell


      Typical Eucaryotic Cell

    2. Bacteria – including cyanobacteria. 

      1. General aspects.  Unicellular organisms without a true nucleus (called prokaryotes), they live everywhere that life exists including in associations with animals and plants. Have variety of beneficial and harmful effects on environment. In fact, list above regarding positive and negative aspects can apply to bacteria alone – apart from other microorganisms.

      2. A few diseases of recent importance. 

        1. Anthrax – Bacillus anthracis. 

        2. Bubonic plague – Yersinia pestis. 

        3. Lyme disease – Borrelia burgdorferi. 

    3. Archaea.  A newly-recognized group of prokaryotes formerly included with the bacteria. Some 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.

    4. Protozoa. 

      1. General features and nutrition.  Non-photosynthetic, unicellular eukaryotic microorganisms that were once classified as animals. (We have some similar cells in our body – specialized body cells such as white blood cells – but we would not think of classifying them as protozoa or even microorganisms, as they are still Homo sapiens.) Feed by ingestion of organic nutrients (generally by engulfment). Also can obtain some nutrients in solution which can get through cell membrane. A few cause some important diseases.

      2. Distribution and ecology.  Wherever there is moisture. Fresh and salt water and soil. Can be free-living or parasitic. Free-living types are decomposers and live by ingesting bacteria and algae. A paramecium can ingest 5 million bacteria in a day. In the sea, they feed on algae. Protozoa (zooplankton) and algae (phytoplankton) are both eaten by higher animals including some whales.

      3. Some major diseases. 

        1. Malaria – Plasmodium – infects blood stream.  Spread by mosquitoes. Most common serious infectious disease world-wide. "Mal-aria" is Italian for "bad air." Long associated with swamps over the past 2-3 millennia. It is said that a child dies from malaria every thirty seconds.

        2. Trypanosomiasis (also known as sleeping sickness) – Trypanosoma – affects central nervous system.  Carried by the tse-tse fly.

        3. Amoebic dysentery – Entamoeba histolytica – intestinal parasite.  Found in fecally-contaminated water. Enters body by ingestion. Causes diarrhea, abdominal pain, blood in feces.

        4. Giardiasis – Giardia lamblia – intestinal parasite.  Another intestinal parasite found in fecally-contaminated water. Most commonly- identified water-borne illness in the U.S. Mild to severe intestinal disease (vomiting, explosive diarrhea, abdominal cramps, fatigue, weight loss).

        5. Cryptosporidiosis – Cryptosporidum – intestinal parasite.  Intestinal parasite. Can get into water supply and also into milk and fruit juice (such as apple juice). One water-borne outbreak involved over 400,000 people.

    5. Fungi. 

      1. General features and nutrition.  Eukaryotic microorganisms that have rigid cell walls and lack chlorophyll. Feed by absorption of organic nutrients. Absorptive nutrition means that their organic nutrients must be in solution (dissolved) to be taken up by the cells. (Generally the case also for bacteria and some protozoa.) These organisms live mainly in the soil and are responsible for the decomposition (biodegradation) of organic material. Microscopic fungi include molds and yeasts.

      2. The microscopic fungi that are called molds. 

        1. Microscopic appearance – filaments and spores.  Molds grow as a cottony mass of filamentous vegetative cells that eventually form fruiting bodies with colored powdery spores. Think about a mold growing on bread, fruit, cheese, the shower curtain, or a bale of hay; they grow the same way in all natural environments. Those growing on solid surfaces get their water from humidity. Vegetative structure: This is the cottony filamentous structure that is buried in the substrate to absorb nutrients – composed of filamentous cells called "vegetative hyphae." (Hypha=filament.) Erect filaments which bear reproductive spores are called "fertile hyphae." (Note figure below.) Fruiting bodies (asexual reproductive spores): Formed at the tips of the fertile hyphae, the spores can be released and spread in air or water to new suitable habitats.

        2. Distribution and ecology.  Simply wherever there is enough moisture or where humid enough!

        3. Conditions favoring growth.  Air, acid or neutral food, low moisture, low temperatures, high sugar. Mainly, molds grow best in dark, moist or humid environments with suitable organic matter to decompose – like your basement, bath tile, refrigerator or silo.

        4. Life cycle.  An example is shown below. Conidia (or conidiospores) are spores formed in chains. Some molds produce sporangiospores which are enclosed in sacs (sporangia).



          Asexual life cycle of a mold (Penicillium)

        5. Beneficial aspects of molds. 

          1. Antibiotics.  Most notably penicillin which is produced by Penicillium. Penicillin was the first commercially-available antibiotic. Tested for the first time on a human in 1941. Much of work on its effectiveness and potential for commercial production was done at UW-Madison in the 1940s.

          2. Cheese ripening.  For example, a species of Penicillium that is involved in making blue cheese and Camembert cheeses. The blue veins of Penicillium in the cheese produce enzymes which alter the texture and flavor as they migrate through the cheese.

          3. Other food and industrial applications.  Including soy sauce, production of gluconic acid.

          4. Biodegradation.  Rotting of corn stalks and leaves are familiar examples. In the aerobic soil habitat of the forest floor leaves disappear in a single year through the activities of fungi – makes you wonder why we rake them in the fall.

        6. Harmful aspects of molds. 

          1. Mycotoxins.  These are non-protein toxins produced by Aspergillus and other molds in that grow in feeds, nuts and grains. Mycotoxins can turn up in the tissues and milk of animals and have been shown to be carcinogenic in animals.

          2. Systemic diseases – including blastomycosis and histoplasmosis.  Colonize the respiratory tract. Systemic diseases often begin in the lung when spores are inhaled. (If not true molds, they are still mold-like fungi.)

          3. Superficial diseases – including athlete's foot and ringworm.  (Also, if not true molds, they are still mold-like fungi.)

          4. Spoilage and deterioration.  Examples: spoilage of foods and grains; deterioration of structures, clothing, etc.).

      3. The microscopic fungi that are called yeasts. 

        1. Microscopic appearance – single cells, not filamentous.  Generally unicellular and oval-shaped. Reproducing by budding or binary fission. Classic shape is large oval cell with buds forming.

        2. Distribution and ecology.  Ubiquitous: plants, humans & animals (inside & out), water, soil, etc.

        3. Conditions favoring growth.  Air, sugar, acid food, liquid, wide temperature range.

        4. Beneficial aspects of yeasts. 

          1. Useful fermentations (bread, beer, wine, industrial alcohol) – generally performed by Saccharomyces cerevisiae.  The overall process is this: The most commonly-used yeast that ferments sugars to ethanol and CO2 is Saccharomyces cerevisiae. CO2 is the desired end product of breadmakers that leavens bread, ethanol is the sought-after end product of brewers and winemakers. For a reliable and reproducible process, one needs to start off the fermentation of the raw product with a starter culture, as one cannot depend on a wild fermentation (i.e., fermentation by indigenous organisms) to do the job.

          2. Feed yeasts.  Here the yeast cells themselves are the nutrient. Such a source of "single-cell protein" is the "torula" yeast. Vitamins are also derived from yeasts.

        5. Harmful aspects of yeasts. 

          1. Food spoilage. 

          2. Disease.  There is one yeast, Candida, that associates with humans in the mouth, intestine and vagina. It grows in most moist areas. It can cause disease under some conditions. In the oral cavity, it causes thrush. It is the most common cause of vaginitis. In dogs, it causes external ear infections.

      4. Fungi that are not considered "microorganisms."  Mushrooms, rusts, smuts, etc. Some are important regarding plant disease.

    6. Algae.  

      1. General features and nutrition.  Chlorophyll-containing eukaryotic organisms that perform plant-type (O2-producing) photosynthesis. Chlorophyll is in discrete organelles called chloroplasts. Called photoautotrophic in that CO2 is source of carbon (such an organism is an autotroph) while light is source of energy (such an organism is a phototroph). Classic photosynthetic equation we grew up with is as follows: CO2 + H2O ---------> CH2O (cell material) + O2

      2. Distribution and ecology.  Often the first organisms to become established in a barren environment on land. Serve as primary producers of organic material which is used as substrate by subsequent invaders – both plant and animal – which build up more organic material. In the sea, algae make up much of the phytoplankton – free-floating photosynthetic organisms which are a major source of O2 and also a major "food source" for other sea microbes and creatures (including some whales).

      3. Microscopic algae.  (True microorganisms.)

      4. What are "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.

      5. Algae that are not considered "microorganisms."  Some can attain lengths of 45 feet or more, such as the brown algae of the sea. One type is used as the source of agar – the solidifying agent in bacteriological media.

      6. Associations with humans.  Generally considered harmless in themselves. Large numbers can be a nuisance in bodies in water when clogging machines or decomposing. Some produce toxins in the water which poison fish (e.g., "red tide"), and some produce toxins which are retained in shellfish and cause a food poisoning (toxins not destroyed by cooking).

    7. Plants. 

    8. Animals. 

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Page last modified on
3/14/05 at 3:45 PM, CST.
John Lindquist, Dept. of Bacteriology,
University of Wisconsin – Madison