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

General Survey of Important Microorganisms:
Prokaryotes (Bacteria & Archae) and
Eucaryotes (Protozoa and the Microscopic Fungi and Algae)

  1. Bacteria and Archae.

    1. Overview of some of the important groups:  SEE TABLE on special page.

    2. Some special notes (comments, additions, etc.) concerning the organisms on the table:

      1. Enterics, lactics, and pseudomonads – meaning of these designations plus some additional features:

        1. Enteric Bacteria (or just "enterics").  Many live in the intestinal tracts of animals – hence the name "enteric" – but there are many with close genetic ties that are free-living in the environment. (This group consists of Escherichia coli and its relatives.)

        2. Lactic Acid Bacteria (or just "lactics").  Named after the fact that lactic acid is the main end product of fermentation.

        3. Pseudomonads.  Name applied to the genus Pseudomonas and certain other genera that are much like Pseudomonas morphologically and physiologically. Most pseudomonads are free-living organisms in soil and water; they play an important role in decomposition, biodegradation, and the carbon and nitrogen cycles. They are a very diverse group of Gram-negative rods with a strictly respiratory mode of metabolism. Pseudomonas aeruginosa is the quintessential opportunistic pathogen; it is a leading cause of hospital-aquired infections and is quite resistant to a variety of antibiotics. Pseudomonad-like pathogens include Brucella (cause of brucellosis in cattle, sheep and related animals) and Bordetella (B. pertussis is cause of whooping cough in humans).

      2. What are coliforms?  These are defined as "gram-negative, facultatively anaerobic bacteria that can ferment lactose rapidly to acid and gas at 35°C." This makes them somewhat easy to detect with the use of a broth medium designed to inhibit gram-positive bacteria and also to detect (with a Durham tube) insoluble gas from lactose fermentation.(Details of detection, isolation and identification can be gone over in lab.) Among the coliforms are most strains of E. coli (the identification of which implicates fecal contamination as discussed below) and some other members of the enteric group that live in soil (lactose-fermenting strains of Enterobacter, Klebsiella and Citrobacter) whose presence in drinking water implies soil runoff and possible associated problems/hazards. Coliforms are good "indicator organisms" that abound in intestinal waste and soil; it is easier to look for these bacteria than to spend time and money looking for all of the real individual problems – i.e., specific pathogens and other hazards associated with fecal pollution and environmental contamination – in food, water and other consumable items.

      3. Escherichia coli:

        1. Habitat.  Regular inhabitant of the intestine of humans (and found in no environments that are not fecally-contaminated)

        2. Use as indicator organism.  Used by public health authorities as an indicator of fecal pollution of drinking water supplies, swimming beaches, foods, etc.

        3. Use as experimental organism.  The most studied of all organisms in biology because of its occurrence, and the ease and speed of growing the bacteria in the laboratory. It has been used in countless experiments in cell biology, physiology, and genetics.

        4. Close relationship to Shigella.  If E. coli and the four species of Shigella were to be discovered today – instead of having been studied more or less separately throughout the 20th century – they would undoubtedly be placed in one species due to the extreme similarity of their DNA. Some strains of E. coli are very Shigella-like in their capability of causing intestinal disease, and sometimes it is very difficult to identify a strain one way or the other.

        5. Pathogenicity of E. coli.  One serotype – O157:H7 – is notorious in that it keeps turning up in raw hamburger headed for fast-food restaurants. Most strains can be considered non-pathogenic unless they get into places where they are not normally found – e.g., infections of the urinary tract caused by E. coli are fairly common. Organisms such as this are termed opportunistic pathogens. (Serotypes are one way to divide up species as indicated below; this is important in defining specific kinds of Salmonella and E. coli. Strains are simply pure cultures derived from various natural sources – soil, water, food, infected patients, etc.)

      4. What is a serotype?

        1. For precise identification.  This is a way in which an organism can be identified more precisely than as a species. It could be analogous to classifying humans according to blood type. Important in epidemiology in that the finding of the same serotype among persons suffering from a certain disease – as well as in other things such as food products – can help to define the epidemic and to assist in determining the common source of the infection.

        2. O and H antigens.  An antigen is something that – when injected into a human or higher animal – causes the production of a matching antibody. Enteric bacteria and many other bacteria have antigens associated with the cell wall (O antigens) which are made up of polysaccharides. Each different antigen that has been found is given a certain number. There are also antigens associated with the flagella (H antigens) that are made up of amino acids, and each different one is given a certain letter or number.

        3. Examples.  For the following table, the O antigens are in red and the H antigens are in blue. Many serotypes of Salmonella have been given convenience names which are often written out like genus and species; for example, organisms with the antigenic formula shown below are commonly called Salmonella typhimurium. However, modern convention tends to follow this form: Salmonella enterica ser. Typhimurium. (There is more about serotypes on our Salmonella page, and the genus and species concept is briefly reviewed here.)

          genus and species example of serotype designation
          (the "antigenic formula")
          Salmonella enterica 1,4,5,12:i:1,2
          Escherichia coli O157:H7
      5. Bioterrorism concerns.

        1. Yersinia pestis.  Causes pneumonic plague and bubonic plague. Enough in an aerosol can infect many.

        2. Bacillus anthracis.  Causes anthrax. Aerosol of concentrated spores can get into lungs (causing pulmonary anthrax – usually fatal) or collect on food or objects (causing severe intestinal and skin infections). Spores can exist for considerable amount of time and can each readily germinate into a vegetative cell. Various devices to detect endospores and/or B. anthracis DNA are being worked on these days.

      6. Antibiotic-producing bacteria.

        1. Streptomyces.  One of the most common organisms in the soil and various species are responsible for most the the antibiotics in use today.

        2. Others.  Include various species of Bacillus and some other genera.


    3. Some additional notes on these organisms (from 2002 lecture notes where these items were covered at this point; most of these organisms are intended to be covered in later sections in 2003):

      1. Acetic acid bacteria.  These organisms (Acetobacter and Gluconobacter) oxidize alcohols and sugars, producing acetic acid as an end product. Important organisms in the vinegar industry.

      2. Neisseria.  Includes agents of gonorrhea (N. gonorrhoeae), and bacterial meningitis (N. meningitidis). Most species are non-pathogenic. Often the only true gram-negative coccus seen in beginning bacteriology lab courses.

      3. Chemolithotrophic organisms.

        1. General features.  Lithotrophy is a type of metabolism that involves the oxidation of inorganic compounds as sources of energy and reducing power. There are chemolithotrophs and photolithotrophs. Chemolithotrophic bacteria are typically gram-negative organisms that have great importance in the soil in that they oxidize various inorganic substrates including H2, NH4+, NO2, H2S, S, Fe2+, and CO. Most chemolithotrophs are also autotrophs, and, in some cases, they may play an important role in the primary production of organic material in nature. Chemolithotrophy is found only among prokaryotic organisms.

        2. Ecological importance.  Ecologically, the most important chemolithotrophs are the nitrifying bacteria, Nitrosomonas and Nitrobacter that together convert NH4+ to NO2, and NO2 to NO3, and the colorless sulfur bacteria such as Thiobacillus that oxidize H2S to S and S to SO42–.

      4. Staphylococcus.  This is a genus of gram-positive, facultatively-anaerobic cocci. Two species of Staphylococcus live in association with humans.

        1. Staphylococcus aureus.  May occur normally at various locales in and on the body – but in particular on the nasal membranes (nares). This species always has the potential to cause disease and so is considered a pathogen. Different strains differ in the range of diseases they can cause, including boils and pimples, wound infections, pneumonia, osteomyelitis, septicemia, food intoxication, and toxic shock syndrome. In cows it is the leading cause of mastitis.

        2. Staphylococcus epidermidis.  Lives normally on the skin and mucous membranes. Rarely a pathogen. Probably benefits its host by producing acids on the skin that retard the growth of dermatophytic fungi.

      5. Some More about the Lactic Acid Bacteria (the "lactics").  Gram-positive, nonsporeforming rods and cocci which produce lactic acid as a sole or major end product of fermentation. They are important in the food industry as fermentation organisms in the production of cheese, yogurt, buttermilk, sour cream, pickles, sauerkraut, sausage and other foods. The acid produced in these foods aids in (1) preservation, (2) taste, (3) decreased growth of pathogens and (4) solidification of the protein. They are indifferent to oxygen and will ferment under anaerobic or aerobic conditions; as they don't behave like facultative anaerobes (which respire under aerobic conditions) they are often set apart as aerotolerant anaerobes. They are often found associated with decomposing plant and animal matter. Some species are normal flora of the human body (found in the oral cavity, GI tract and vagina) and some streptococci are pathogens.

        1. The "streptococci": Streptococcus, Enterococcus and Lactococcus.  These organisms are morphologically similar in that they have the typical "streptococcus" arrangement (chains of cocci). Species now in the genera Enterococcus and Lactococcus were formerly in Streptococcus; the new genera were formed for these organisms which are not as closely-related genetically as the true Streptococcus species.

          1. S. pyogenes.  The most important species of the "Beta-hemolytic Group A streptococci" causes an array of suppurative diseases and toxinoses (diseases due to the production of a bacterial toxin), in addition to some autoimmune or allergic diseases. It is rarely found as normal flora (<5%), but it is the main streptococcal pathogen for man, most often causing tonsillitis or strep throat. It also invades the skin to cause localized infections and lesions, and produce toxins that cause scarlet fever and toxic shock. Sometimes, as a result of an acute infection, anomalous immune responses are started that lead to diseases like rheumatic fever and glomerulonephritis.

          2. S. agalactiae.  One of the major causative agents of mastitis in cows.

          3. S. pneumoniae.  The most frequent cause of bacterial pneumonia in humans. It is also a frequent cause of otitis media (infection of the middle ear) and meningitis. The bacterium colonizes the nasopharynx and from there gains access to the lung or to the eustachian tube. If the bacteria descend into the lung they can impede engulfment by alveolar macrophages if they possess a capsule which somehow prevents the engulfment process. Thus, encapsulated strains are able to invade the lung and are virulent (cause disease) and noncapsulated strains, which are readily removed by phagocytes, are nonvirulent.

          4. S. mutans.  Common oral bacterium. Produces a slimy material from sucrose (common table sugar) which becomes "plaque" on teeth. Plaque provides an anaerobic habitat for tooth decay bacteria which produce acids and enzymes to destroy the tooth enamel and underlying layers.

          5. S. thermophilus and Lactococcus.  These organisms are commonly used in the fermented milk industry. S. thermophilus has a high optimum temperature and is used along with one or two species of Lactobacillus in the production of yogurt. Lactococcus is important in the production of cheese and buttermilk.

          6. Enterococcus.  Common organism on the surfaces of plants and also in the intestinal tract. Can cause a variety of non-intestinally-related infections.

        2. Lactobacillus and Pediococcus.  High-temperature lactose-fermenting lactobacilli such as L. bulgaricus and L. acidophilus are used in the production of yogurt along with S. thermophilus (above). The fermented meat industry employs strains of either genera in the production of sausage; these organisms ferment the sugar added to the meat to produce acid.

      6. Endospore-forming bacteria.  These organisms produce a unique resting cell called an endospore. They are Gram-positive and usually rod-shaped, but there are exceptions. The two important genera are Bacillus, the species of which are aerobic and facultatively anaerobic sporeformers in the soils, and Clostridium, whose species are anaerobic sporeformers of soils, sediments and the intestinal tracts of animals. Some sporeformers are pathogens of animals, usually due to the production of powerful toxins. Some Bacillus species produce clinically-useful antibiotics; polymyxin and bacitracin are usually topical antibiotics.

        1. Bacillus anthracis.  Causes anthrax, a disease of domestic animals (cattle, sheep, etc.) which may be transmitted to humans. Very closely-related to the following two species.

        2. Bacillus cereus.  Common soil organism. Can cause two types of food poisoning. Also produces an antibiotic that inhibits growth of Phytophthera, a fungus that attacks alfalfa seedling roots causing a"damping off" disease. The bacteria, growing in association with the roots of the seedlings, can protect the plant from disease.

        3. Bacillus thuringiensis.  In association with the process of sporulation, this species form a crystalline protein inclusion called parasporal crystals. The protein crystal and the spore (actually the spore coat) are toxic to lepidopteran insects (certain moths and caterpillars) if ingested. The crystals and spores are marketed as "Bt," a natural insecticide for use on garden or crop plants.

        4. Clostridium botulinum.  Causes botulism, a form of food poisoning.

        5. Clostridium tetani.  Causes tetanus.

      7. Actinomycetes.  This is a large group of Gram-positive bacteria that usually grow by filament formation, or at least show a tendency towards branching and filament formation. Many of the organisms can form resting structures which can serve as reproductive spores, but they are not the same as endospores. Branched forms superficially resemble molds and are a striking example of convergent evolution of a prokaryote and a eukaryote together in the soil habitat. Members of this group tend to be aerobic.

        1. Mycobacterium.  M. tuberculosis and M. leprae cause tuberculosis and leprosy, respectively. Many non-pathogenic mycobacteria live in association with humans and animals.

        2. Actinomyces.  Causes "lumpy jaw" disease of cattle.

        3. Streptomyces.

          1. Importance in biodegredation.  Streptomyces has a world-wide distribution in soils. They are important in aerobic decomposition of organic compounds and have an important role in biodegradation and the carbon cycle.

          2. Geosmins.  Products of metabolism called geosmins impart a characteristic earthy odor to soils.

          3. Antibiotics.  Main producers of antibiotics in industrial settings, being the source of most tetracyclines, macrolides (e.g. erythromycin), and aminoglycosides (e.g. streptomycin, gentamicin, etc.).

      8. Corynebacterium.  Corynebacterium diphtheriae is the cause of diphtheria. Also many non-pathogenic members of genus associated with humans and animals.

      9. Photosynthetic bacteria.

        1. Cyanobacteria.  These organisms are of great ecological importance in the global carbon, oxygen and nitrogen cycles, as well as their evolutionary significance in relationship to plants. Photosynthetic cyanobacteria have chlorophyll a and conduct the same type of photosynthesis as plants and algae – oxygenic photosynthesis, so-called because it produces O2. Cyanobacteria are found in most aerobic environments where water and light are available for growth. Mainly they live in fresh water and marine habitats. The planktonic cyanobacteria fix an enormous amount of CO2 during photosynthesis, and as "primary producers" they are the basis of the food chain in marine environments. Their type of photosynthesis generates a substantial amount of oxygen present in the earth's atmosphere. Since many cyanobacteria can fix N2 under certain conditions, they are one of the most significant free-living nitrogen-fixing prokaryotes.

        2. Other photosynthetic bacteria.  These are anoxygenic (don't produce oxygen). Many are red-pigmented. Group includes Rhodospirillum – the interesting motile spiral-shaped organism seen in the lab.


  2. Protozoa.

    1. General.  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.)

    2. Nutrition.  Chemoheterotrophic – feed by ingestion of organic nutrients. Also can obtain some nutrients in solution which can get through cell membrane.

    3. 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.

    4. Associations with humans.

      1. Malaria – Plasmodium.  Infects blood stream. Spread by mosquitos. Most common serious infectious disease world-wide. "Mal-aria" is Italian for "bad air." Long associated with swamps over the past 2-3 millenia. 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. 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.

  3. The Microscopic Fungi.

    1. General facts on fungi.  Eukaryotic microorganisms that have rigid cell walls and lack chlorophyll. Chemoheterotrophic. Feed by absorption of organic nutrients.

    2. Molds.

      1. Appearance.

        1. General.  Molds grow as a cottony filament of vegetative cells that eventually form fruiting bodies with colored powdery spores. Think about a mold growing on 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.

        2. 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.)

        3. 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. Nutrition.  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.)

      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. Distribution and ecology.  Wherever enough moisture or where humid enough!

      6. Associations with humans – beneficial and harmful.

        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. 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.

        4. Disease.  There are mold-like fungi that causes superficial diseases like athlete's foot and ringworm and there are those that cause systemic diseases such as histoplasmosis and blastomycosis which colonize the respiratory tract. Systemic diseases often begin in the lung when spores are inhaled.

        5. 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.

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

    3. Yeasts.

      1. Appearance.  Generally unicellular and oval-shaped. Reproducing by budding or binary fission.

      2. Nutrition and growth.  Chemoheterotrophic as are molds and other fungi. Most common yeasts are facultatively-anaerobic organisms – i.e., they will grow with or without oxygen. In the absence of oxygen they live by fermentation. In the presence of air, they live by respiration.

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

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

      5. Associations with humans – beneficial and harmful.

        1. Useful fermentations.

          1. Overall process.  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 reproduceable 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. Bread, beer, wine and alcohol (gasohol).  (More about these when we get into food microbiology.)

        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.

        3. Spoilage.

        4. 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. The Microscopic Algae.

    1. General facts on algae.  Chlorophyll-containing eukaryotic organisms that perform plant-type (O2-producing) photosynthesis. Chlorophyll is in discrete organelles called chloroplasts. Some types of algae are microscopic and are therefore true microorganisms; some others are not and 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. Formerly Euglena used to be considered on the borderline or an overlapping area between plants and animals.

    2. Nutrition.  Photosynthetic – more specifically, photoautotrophic in the obtaining of carbon and energy for biosynthetic purposes. Classic photosynthetic equation we grew up with is this:
      CO2 + H2O ---------> CH2O (cell material) + O2

    3. 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).

    4. 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).

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

Page last modified on
3/23/03 at 5:30 PM, CST.
John Lindquist, Dept. of Bacteriology,
University of Wisconsin – Madison