Supplemental Lecture (98/03/28 update) by Stephen T. Abedon (abedon.1@osu.edu)

  1. Chapter title: Introduction to Microbiology
    1. A list of vocabulary words is found toward the end of this document
    2. "One can't overemphasize the importance of microbiology. Society benefits from microorganisms in many ways. They are necessary for the production of bread, cheese, beer, antibiotics, vaccines, vitamins, enzymes, and many other important products. Indeed, modern biotechnology rests upon a microbiological foundation. Microorganisms are indispensible components of our ecosystems. They make possible the cycles of carbon, oxygen, nitrogen, and sulfur that take place in terrestrial and aquatic ecosystems. They also are a souce of nutrients at the base of all ecological food chains and webs." (p. 3, Prescott et al., 1996)
  2. Lecture review

    3. organism:

    types:

    description:

    nutrition type:

    durable state:

    some diseases:

    algae:

    brown, red, green, diatoms, dinoflagellates, euglenoids

    photosynthetic aquatic eucaryotes, cell walls, unicellular and multicellular

    photoautotrophs

    ---

    ---

    bacteria:

    eubacteria, archaeabacteria, Gram-negative, Gram-positive, acid fast, cyanobacteria

    procaryotes, absorbers, wet conditions, animal decomposers, cell walls, unicellular

    chemoheterotrophs, photoheterotrophs, chemoautotrophs, photoautotrophs

    endospores (some)

    tetanus, botulism, gonorrhea, chlamydia, tuberculosis, etc., etc., etc.

    cyanobacteria:

    blue-green algae

    photosynthetic aquatic procaryotes, green lake scum, cell walls

    photoautotrophs

    ---

    ---

    fungi:

    yeasts (unicellular fungi), molds (filamentous fungi)

    eucaryotes, absorbers, dry conditions, plant decomposers, cell walls, ~100 human pathogens

    chemoheterotrophs

    spores

    mycoses: candida, ringworm, athlete's foot, jock itch, etc.

    helminths:

    Flatworms (platyhelminths), roundworms (nematodes)

    metazoan (multicellular animal) parasites, engulfers and absorbers

    chemoheterotrophs

    ---

    tape worm, trichinosis, hook worm, etc.

    protozoa:

    Unicellular and slime molds, flagellates, ciliates

    eucaryotes, parasites, engulfers and absorbers, wet conditions, no cell wall, ~30 human pathogens

    chemoheterotrophs

    cysts (some)

    malaria, giardiasis, amoebic dysentery, etc.

    viruses:

    Enveloped, non-enveloped

    acellular, obligate intracellular parasites

    not applicable

    virion particles, encased in durable state host

    common cold, flu, HIV, herpes, chicken pox, etc.

  3. Microbiology
    1. Study of microorganisms:
      1. The science of microbiology naturally rests upon the existence of microorganisms. Not surprisingly, the field of microbiology began simultaneously with the discovery of microorganisms.
      2. Depending upon how you would like to argue the point, microbiology as a science either did not exist, or existed in an only theoretical sense (e.g., postulated, unseen organisms) prior to the discovery of microorganisms.
    2. The reliance of the field of microbiology on such a loose definition of microorganism does not make for a terribly cohesive discipline:
      1. "The difficulty in setting the boundaries of microbiology led Roger Stanier to suggest that the field be defined not only in terms of the size of its subjects but also in terms of its techniques. A microbiologist usually first isolates a specific microorganisms from a population and then cultures it. Thus microbiology employes techniques--such as sterilization and the use of culture media--that are necesary for the successful isolation and growth of microorganisms." (p. 3, Prescott et al., 1997)
  4. Microorganism
    1. Very small organisms:
      1. Living things which individually are too small to be seen with the naked eye.
      2. Something studied using characteristic techniques including:
        1. aseptic technique
        2. pure culture technique
        3. microscopic observation of whole organisms
    2. All of the following may be considered microorganisms:
      1. bacteria (eubactera, archaebacteria)
      2. fungi (yeasts, molds)
      3. protozoa
      4. microscopic algae
      5. viruses
      6. various parasitic worms
    3. See "lecture review" (above) for an overview of these types.
  5. Environmental microbiology
    1. Basic environmental processes:
      1. The existence and functioning of microbes is absolutely crucial to environmental health.
      2. By health, I don't simply mean the cleaning up of pollution. Instead, microbes are absolutely necessary for such basic things as:
        1. making nutrients available from non-living sources
        2. providing energy to ecosystems
        3. freeing up nutrients from no longer living sources
      3. Without microorganisms we would:
        1. have no oxygen to breath
        2. nothing to eat
        3. not be able to utilize the energy in food even if we could eat it
        4. not be able move about without constantly tripping over the bodies of dead organisms
      4. In more technical terms, a sampling of what microorganisms are and do environmentally includes:
        1. microbes are producers
        2. microbes are nitrogen fixers
        3. microbes are decomposers
        4. microbes are symbionts and endosymbionts
    2. Endosymbiosis (chloroplasts and mitochondria):
      1. The first member of the above list ought to clear up at least a little of the confusion in your minds about such things as where your oxygen and food come from.
      2. Typically, if you think "macrobiologically" about where food comes from, you should think first and foremost of plants. Even if you subsist entirely on animal flesh, the animals had to have gotten their energy and nutrients from something. Ultimately that something is a plant.
      3. Or is it? In actuality, ultimately that something in many ecosystems is a microorganism such as an algae or a cyanobacterium.
      4. More generally, it turns out that inside of most cells of most plants there are little microorganisms, bacteria actually, which supply the energy gathered from sunlight to plant.
      5. Even your own cells for the most part cannot use the energy in the food you eat until bacterium found in our own cells convert that food to a usable form.
      6. In plants, these bacteria are called chloroplasts.
      7. In you, other animals, fungi, most protozoa, and in plants as well, they are called mitochondria.
      8. Together these bacteria are known as endosymbionts because they live inside other cells and are helpful to the cells in which they live.
    3. Symbiosis:
      1. Down at the roots of plants there typically are little fungi, in structures called mycorrhizae, which greatly facilitate the gathering of nutrients by the plant.
      2. Also within and among the roots of many plants are microorganisms such as bacteria which provide nitrogen and other nutrients to the plant, either directly from the atmosphere, or from the soil but in a more available form.
      3. There are many more examples of symbiotic relationships between microorganisms and larger organinisms, and in many cases the proper functioning of the larger organism depends on the proper functioning of the symbiotic microorganism.
  6. Industrial microbiology
    1. Microbes have played important roles in manufacturing products for as long as there has been history.
    2. Microorganisms are used to:
      1. ferment useful chemicals (ethanol, acetone, etc.)
      2. produce certain food stuffs (wine, cheese, yogurt, bread, half sour pickles, etc.)
      3. produce of recombinant products (recombinant insulin, human growth hormone, etc.)
      4. destroy wastes (sewage, oil spills, bioremediation)
  7. Medical microbiology
    1. Microbes both cause and prevent disease.
    2. Microbes produce antibiotics used to treat disease.
    3. The single most important achievement of modern medicine is the ability to treat or prevent microbial disease.
    4. Most of this course will consider the physiology of microbes and their role in disease.
  8. Pathogen
    1. A microorganism is considered to be a pathogen or pathogenic if it is capable of producing disease.
    2. Though only a minority of microorganisms are pathogenic, practical knowledge of microbes is necessary for their treatment so is highly relevant to medicine and related health sciences.
  9. Normal flora [normal microbiota]
    1. Not disease-causing:
      1. Normal flora are those not-typically-disease-causing microorganisms normally found in and on healthy individuals.
      2. Also known as normal microbiota.
    2. Very abundant:
      1. Normal flora are extremely abundant in terms of absolute numbers.
      2. A normal human has approximately 1013 body cells and 1014 individual normal flora!
      3. However, microorganisms also tend to be very small, bacteria especially are much smaller than are our own cells.
    3. All found externally:
      1. Normal flora are found mostly:
        1. on the skin
        2. in the eyes
        3. in the nose
        4. in the mouth
        5. in the upper throat
        6. in the lower urethra
        7. in the lower intestine
        8. especially in the large intestine
  10. Transient microbiota
    1. Normal flora that is not always present or is present for only a few days, weeks, or months before disappearing.
  11. Bacteria
    1. Procaryotes:
      1. Bacteria are simple, cellular organisms lacking a nucleus as well as other characteristics of procaryotes which distinguish them from organisms that have nucleated cells.
      2. That is, bacteria are procaryotes.

  12. Cyanobacteria [blue-green algae]

    1. Cyanobacteria, also known as blue-green algae, are photosynthetic bacteria.
    2. Not to be confused with true algae which are eucaryotes.
  13. Fungi [yeast, mold]
    1. Fungi are eucaryotic organisms including yeasts (single celled) and molds (multicelled).
    2. Defining characteristics include:
      1. cell walls, often composed of chitin
      2. obtaining of nourishment by the absorbing of extracellular digested solutions of organic material found in their environment
  14. Protozoa
    1. Unicellular engulfers:
      1. Protozoa are unicellular, eucaryotic organisms that derive nourishment from their liquid environment, often by engulfment.
  15. Algae
    1. Photosynthetic aquatic eucaryotes:
      1. Algae are eucaryotic organisms that derive nourishment from both their chemical and their physical environment (i.e., they are photosynthetic).
      2. Different types may be unicellular or multicellular.
  16. Virus
    1. Viruses are infectious agents, so small they pass through filters known to stop bacteria.
    2. Viruses are not cellular and therefore are classified as neither procaryotes nor eucaryotes.
    3. Viruses are obligate, intracellular parasites of cellular organisms.
  17. Binomial nomenclature
    1. Each "species" or organism is assigned two names corresponding the genus and "specific epithet" (i.e., species).
    2. When employing binomial nomenclature, the following conventions are employed:
      1. the genus name (e.g., Escherichia) is always capitalized
      2. the species name (e.g., coli) is never capitalized
      3. the species name is never used without the genus name (e.g., coli standing alone)
      4. the genus name may be used without the species name (e.g., Escherichia may stand alone, though no longer actually describes a species)
      5. when both genus and species name are present, the genus name always comes before the species name (e.g., "coli of Eschichia" does not work)
      6. when both genus and species name are present, the species name is always placed directly after the genus name (e.g., Escherichia coli, not coli Escherichia)
      7. genus and species are always italicized (or underlined) (e.g., Escherichia coli is a no-no)
    3. Abbreviating:
      1. The first time a binomial is used, the genus name is spelled out. There after it is abbreviated.
      2. It is a good idea to abbreviate non-ambiguously.
      3. For example, the first time you use Escherichia coli, you use both names spelled out. From then on you use E. coli instead.
      4. The species name is never abbreviated.
      5. If you are talking about another microorganism that has a genus name beginning with, in this case, E (such as Enterococcus faecalis), it may be a good idea to use a less simple genus abbreviation (such as Es. for Escherichia and En. for Enterococcus). In other words, avoid abbreviating ambiguously.
    4. Informal use:
      1. These rules ought to be followed when employing binomial nomenclature even in your speech.
      2. It is proper to refer to Escherichia coli (for example) as E. coli or even Escherichia, but it is not proper to call it coli or "E. C.
  18. Links
    1. Biology of Microorganisms
  19. Vocabulary
    1. Algae
    2. Bacteria
    3. Binomial nomenclature
    4. Blue-green algae
    5. Cyanobacteria
    6. Environmental microbiology
    7. Fungi
    8. Industrial microbiology
    9. Medical microbiology
    10. Microbiology
    11. Microorganism
    12. Normal flora
    13. Normal microbiota
    14. Pathogen
    15. Protozoa
    16. Transient microbiota
    17. Virus
  20. Practice questions
    1. What is wrong with each of the following uses of binomial nomenclature? [PEEK]
      1. Escherichia coli
      2. Bacillus subtilis
      3. B. licheniformis
      4. Human Immunodeficiency Virus
      5. Bacillus anthracis
      6. Treponema pallidum
      7. Neisseria gonorrhoeae
      8. E. coli
      9. E. faecalis (where the E. is for Enterococcus)
    2. What is a microorganism? [PEEK]
    3. What is meant by the term pathogenic?[PEEK]
    4. Which is not a characteristic of a virus? (circle only one correct answer) [PEEK]
      1. smaller than typical bacteria
      2. are procaryotes
      3. may be found in acellular state
      4. are obligate parasites of cellular organisms
      5. all of the above
      6. none of the above
    5. Yeast and molds, but not protozoa are? (single word answer)[PEEK]
    6. Distinguish (in only one way) bacteria from fungi.[PEEK]
    7. What do cyanobacteria, blue-green algae, mitochondria, and Escherichia coli all have in common?[PEEK]
    8. What characteristic profoundly distinguishes viruses from all other microorganisms? [PEEK]
    9. Name one environmental or ecological function (i.e., non-medical) of microorganisms. [PEEK]
    10. Circle or underline the four errors (or informalities) in the following paragraph: [PEEK] The coli of Escherichia are facultatively anaerobic rods. E. Coli are chemoorganotrophic bacteria normally found the lumen of the large intestine of warm-blooded animals. The type species of genus Escherichia is E. coli. A second species, Escherichia blattae, occurs as part of the normal flora of cockroaches. Together, E. coli and Es. blattae are typically non-pathogenic. A third organism, Fusobacterium nucleatum, is also often found in the gastrointestinal tract of mammals.
    11. What is a name of an organism or group of organisms which are procaryotic and photosynthesize? [PEEK]
    12. Name three industrial products ("industrial" defined broadly to include anything of commercial interest) which are either produced by microorganisms or with the aid of microorganisms. [PEEK]
    13. The three basic morphological categories under which microorganisms fall are eucaryotes, procaryotes, and ___________ (hint: I didn't say "rRNA genetic categories"). [PEEK]
    14. Microorganisms which are not pathogenic (do not cause disease) but which spend a few weeks living on your body between acquisition and departure are called __________. [PEEK]
    15. A name of a type of microorganism which is procaryotic, photosynthetic, and free living (i.e., not an endosymbiont): __________. [PEEK]
    16. Name four general areas, processes, or products an industrial microbiologist might be concerned with. [PEEK]
  21. Practice question answers
    1. See binomial nomenclaturebinomial_nomenclature for tips on how to answer these questions. The answers are:
      1. C in Coli is capitalized
      2. b in bacillus is small case
      3. nothing because the abbreviated B stands for Bacillus
      4. This is a common name so shouldn't be italicized
      5. nothing
      6. nothing
      7. gonorrhoeae shouldn't be in superscript
      8. nothing
      9. The E should be spelled because it stands for in Enterococcus rather than Escherichia, the latter but not the former already presented.
    2. An organism so small that you cannot see it with the unaided eye.
    3. disease causing. See pathogenic.
    4. ii, viruses are not procaryotes. Procaryotes are cells, viruses are not cells.
    5. Fungi
    6. bacteria but not fungi lack nuclei.
    7. They are all eubacteria as well as various aspects associated with being eubacteria.
    8. viruses are capable of an acellular existence.
    9. (i) decomposers, (ii) nitrogen fixers, (iii) denitrifiers, (iv) photosynthesizers, (v) nutrient recyclers, etc.
    10. The coli [should be found only immediately after the genera designation] of Escherichia [should be underlined or in italics] are facultatively anaerobic rods. E. Coli [the C should not be upper case] are chemoorganotrophic bacteria normally found the lumen of the large intestine of warm-blooded animals. The type species of genus Escherichia is E. coli. A second species, Escherichia blattae, occurs as part of the normal flora of cockroaches. Together, E. coli and Es. blattae [second letter of genus abbreviation is not called for] are typically non-pathogenic. A third organism, Fusobacterium nucleatum, is also often found in the gastrointestinal tract of mammals.
    11. cyanobacteria, blue-green algae
    12. everything from ethanol, to bread, to cheese, to yogurt, to recombinant insulin, etc.
    13. viruses
    14. transient microbiota
    15. cyanobacteria, blue-green algae, not chloroplast; "algae" is not sufficient.
    16. fermenting useful chemicals, producing certain food stuffs, producing recombinant products, destroying wastes; the making of ethanol, acetone, wine, cheese, yogurt, bread, half sour pickles, recombinant insulin, human growth hormone; cleaning up sewage, cleaning up oil spills, bioremediation; etc.
  22. References
    1. Black, J.G. (1996). Microbiology. Principles and Applications. Third Edition. Prentice Hall. Upper Saddle River, New Jersey. pp. 0-25.
    2. Prescott, L.M., Harley, J.P., Klein, D.A. (1996). Microbiology. Third Edition. Wm. C. Brown Pub. Dubuque, Iowa. pp. 3-16.
    3. Tortora, G.J., Funke, B.R., Case, C.L. (1995). Microbiology. An Introduction. Fifth Edition. The Benjamin/Cummings Publishing, Co., Inc., Redwood City, CA, pp. 2-22.