Supplemental Lecture (98/04/06 update) by Stephen T. Abedon (abedon.1@osu.edu)

  1. Chapter title: Microbial Nutrition
    1. A list of vocabulary words is found toward the end of this document
    2. Nutrients may be divided into three general, often overlapping categories: Those that supply energy, those that supply carbon, and those that supply any and everything else. In this lecture we will consider nutrition from the point of view of microorganisms, though many of the principles apply to macroorganisms equally well.
  2. Nutrient
    1. "Something that nourishes or promotes growth and repairs the natural wastage of organic life." (Websters, 1986)
    2. More specifically, nutrients are elements and specific combinations of elements (chemicals) that specific organisms require for growth and repair.
  3. Nutritional pattern
    1. Organisms can be classified according to their nutritional pattern. This, minimally, is where they obtain their energy and where they obtain their carbon.
  4. Energy source
    1. This is the source of high energy electrons used to make ATP.
  5. Conversion of food to energy
    1. Conversion to ATP:
      1. To be utilized as energy, an organic compound must first be converted to ATP.
      2. This is often done by first metabolically converting the nutrient molecule to a common intermediate, very often glucose (i.e., different catabolic biochemical pathways will terminate in a common product, e.g., glucose, which, in the case of glucose, is always treated as glucose regardless of the source).
    2. Energy in bonds:
      1. Glucose as well as other foodstuff intermediates contain large amounts of energy in their molecular bonds.
      2. This energy may be converted to the high energy bonds found in ATP, by a variety of processes, by different organisms.
    3. Generally these processes by which ATP is generated are referred to as fermentation and cellular respiration.
  6. Other substrates for ATP yielding catabolism
    1. Organic, energy containing substances other then glucose include:
      1. lipids
      2. amino acids
      3. other carbohydrates
    2. Inorganic, energy containing substances include various containing or consisting of:
      1. sulfur
      2. ammonia
      3. H2
  7. Carbon source
    1. This is the source of the carbon atoms used in the organic compounds found in organisms.
  8. Phototroph
    1. An organism whose energy source is light.
  9. Chemotroph
    1. An organism whose energy sources are electron-donating compounds such as glucose.
    2. This compound(s) is not necessarily an organic compound (i.e., above).
  10. Autotroph [lithotroph]
    1. An organism whose principle carbon source is carbon dioxide.
    2. Producers:
      1. The autotrophs are what make non-CO2 carbon compounds, using CO2 as their starting compound.
      2. Because the autotrophs are what make non-CO2 carbon compounds for everything else (i.e., other organisms which eat the autotrophs), they are know ecologically as the producers.
      3. Indeed, autotrophs are "self-feeders."
  11. Heterotroph [organotroph]
    1. An organism which uses organic compounds as its principle source of carbon.
    2. Consumers:
      1. Heterotrophs feed on others.
      2. That is, Heterotrophs obtain their carbon compounds by consuming other organisms.
      3. Heterotrophs are thus consumers, decomposers, scavengers, predators, herbivors, etc.
  12. Photoautotroph
    1. An organism whose energy source is light and whose principle carbon source is carbon dioxide.
    2. Photoautotrophs include plants, alage, cyanobacteria, as well as some photosynthesizing bacteria.
  13. Photoheterotroph
    1. An organism whose energy source is light and which uses organic compounds as its principle source of carbon.
    2. These organisms are unable to convert CO2 to sugar nor produce O2.
  14. Chemoautotroph
    1. Chemical plus CO2:
      1. An organism whose energy sources are electron donating compounds and whose principle carbon source is carbon dioxide.
      2. These organisms tend to use inorganic electron donors (i.e., they eat rocks!).
      3. That is, chemoautotrophs obtain their energy from something other than light or carbon compounds.
    2. Deep-sea vent producers:
      1. Chemoautotrophs constitute the producers at the deep sea vents, i.e., the extract energy from inorganic compounds dissolved in sea water which are vented at these locations.
      2. As the producers the chemoautotrophic bacteria at deep sea vents basically constitute the first link of the deep sea vent food chain.
  15. Chemoheterotroph
    1. An organism whose energy source is electron donating compounds and which uses organic compounds as its principle source of carbon.
    2. For these organisms energy and carbon sources tend to be the same organic compounds.
    3. Humans are an example of chemoheterotrophs.
  16. Nutritional patterns of pathogens
    1. Chemoheterotrophs:
      1. Medically relevant microorganisms are almost always chemoheterotrophs.
      2. This is because pathogens tend to derive both their energy and their carbon from organic compounds obtained from their hosts, e.g., human bodies.
    2. All of the organisms on your binimials list are chemoheterotrophs.
  17. Microbial nutrient requirements
    1. Common microbial nutritional requirements include:
      1. water
      2. a carbon source
      3. an energy source
      4. nitrogen
      5. sulfur
      6. phosphorus
      7. potassium
      8. magnesium
      9. calcium
      10. oxygen*
      11. various trace elements
      12. various organic growth factors**
      13. *Not molecular oxygen but oxygen atoms incorporated into compounds other than O2.
      14. **Of all common nutrient requirements, the need for specific organic growth factors is least shared among microorganisms.
    2. Source utilization variation:
      1. Note that not all microorganisms do or are even able to assimilate all of these nutrients from the same source(s).
      2. "There are many types of laboratory prepared media available for the isolation and the cultivation of bacteria. It is important to understand that whatever growth medium is used, it must provide the necessary nutritional requirements for the organism you wish to grow." (Krueger & Kolodziej, 1986)
  18. Nitrogen
    1. Amino acids:
      1. Used in amino acids and nucleic acids.
      2. Possible organic source = amino acids.
    2. Inorganic sources:
      1. Possible inorganic sources include:
        1. NH4+ (ammonium---nitrogen in its lowest oxidation state)
        2. NO3- (nitrate---nitrogen in its highest oxidation state)
        3. atmospheric nitrogen (nitrogen fixing)
  19. Nitrogen fixation
    1. Nitrogen from air:
      1. The conversion of gaseous, elementary nitrogen (N2) into nitrogen available to cellular metabolism.
      2. Ultimately this is where all of the nitrogen found in all organisms comes from.
    2. Uncommon metabolic pathway:
      1. Only a minority of bacteria are capable of nitrogen fixation.
      2. See particularly Rhizobium spp..
  20. Sulfur
    1. Amino acids:
      1. Sulfur is found in some amino acids and in various vitamins.
      2. Possible organic source is sulfur-containing amino acids.
    2. Possible inorganic sources included SO42- (sulfate ion).
  21. Phosphorus
    1. Phosphorus is found in nucleic acids and phospholipids.
    2. The dominant inorganic source of phosphorus is phosphate ion (PO43-).
  22. Trace elements
    1. Usually present:
      1. Trace elements are often assumed to be present unless highly pure synthetic components are utilized.
      2. Even distilled water often contains adequate amounts of these element for growth.
    2. Enzyme cofactors are basically used as enzyme cofactors.
    3. Examples of cofactors include:
      1. copper
      2. iron
      3. molybdenum
      4. zinc
      5. cobalt
      6. manganese
    4. "Many microorganisms require a variety of trace elements, tiny amounts of minerals such as copper, iron, zinc, and cobalt, usually in the form of ions. Trace elements often serve as cofactors in enzymatic reactions. All organisms require some sodium and chloride, and halophiles require large amounts of these ions. Potassium, zinc, magnesium, and manganese are used to activate certain enzymes. Cobalt is required by organisms that can synthesize vitamin B12. Iron is required for the synthesis of heme-containing compounds (such as cytochromes of the electron transport system) and for certain enzymes. Although little iron is required, a shortage severly retards growth. Calcium is required by gram-positive bacteria for synthesis of cells walls and by spore-forming organisms for synthesis of spores." (p. 149, Black, 1996)
  23. Organic growth factors
    1. Strict environmental requirement:
      1. Organic growth factors are organic compounds that are products of the metabolism (particularly anabolism) of some organisms, but cannot be synthesized by all microorganisms (or all organisms, for that matter), but nevertheless are required for growth by the latter organisms.
      2. Typical organic growth factors are vitamins and amino acids.
    2. Note, under no circumstances would common carbon sources be considered organic growth factors and, in fact, it is debatable whether carbon source (no matter how obscure) and organic growth factor could ever be considered synonymous.
  24. Essential amino acids
    1. Synthesis capability:
      1. Some but not all organisms are able to synthesize all 20 amino acids directly from intermediates of carbohydrate metabolism.
      2. Escherichia coli is an example of an organism which can synthesize all 20 amino acids.
    2. Those organisms which are unable to synthesize all 20 amino acids must obtain these amino acids (or, in some cases, their anabolic intermediates) from their environment.
    3. Strict environmental requirement:
      1. These must-be-obtained amino acids are termed essential.
      2. Essential amino acids are examples of organic growth factors.
  25. Fastidious (adj.)
    1. To be fastidious means to have complex nutrient requirements.
    2. Examples of fastidious genera include:
      1. Neisseria
      2. Mycoplasma
      3. Mycobacterium
      4. etc.
    3. Note that fastidiousness has nothing to do with oxygen requirements.
  26. Auxotroph [auxotrophic mutation]
    1. Mutational deficiency:
      1. An auxotroph is a microorganism possessing a mutation in a gene that affects its ability to synthesize a crucial organic compound.
      2. In addition, the auxotroph must be recently descended (e.g., since being domesticated) from a microorganism of the same species that both lacks the mutation and is able to synthesize the organic compound in question.
    2. Auxotrophs thus a have novel requirement that a given nutrient be present in their extracellular environment for growth to occur.
  27. Vocabulary
    1. Autotroph
    2. Auxotroph
    3. Carbon source
    4. Chemoautotroph
    5. Chemoheterotroph
    6. Chemotroph
    7. Energy source
    8. Essential amino acids
    9. Fastidious
    10. Heterotroph
    11. Nitrogen
    12. Nitrogen fixation
    13. Nutrient
    14. Nutrient requirements
    15. Nutritional pattern
    16. Nutritional patterns of pathogens
    17. Organic growth factors
    18. Phosphorus
    19. Photoautotroph
    20. Photoheterotroph
    21. Phototroph
    22. Sulfur
    23. Trace elements

  28. Practice questions

    1. Amino acids are a source of (circle only one correct answer)? [PEEK]
      1. sulfur
      2. iron
      3. phosphate
      4. magnesium
      5. all of the above
      6. none of the above
    2. List six elements necessary for the growth of bacteria. [PEEK]
      1. __________
      2. __________
      3. __________
      4. __________
      5. __________
      6. __________
    3. Most medically relevant microorganisms have what nutritional classification and why (short answer)[PEEK]
    4. Are there any microorganisms whose carbon and energy sources are the same? What would you classify the nutritional pattern of such a microorganism as? Name a compound which would be a possible common carbon and energy source[PEEK]
    5. An organism that derives its energy from inorganic compounds and its carbon from CO2 has what classification of nutritional pattern? [PEEK]
    6. What might a heterotroph consume in order to obtain carbon atoms? [PEEK]
      1. other heterotrophs
      2. autotrophs
      3. reduced carbon compounds
      4. glucose
      5. all of the above
      6. none of the above
    7. What is the minimum of organic growth factors required for the growth of a fastidious microorganisms incapable of growth in a culture medium where inorganic nitrogen (e.g., NH4+, a.k.a. ammonium ion) is otherwise the sole source of nitrogen. (circle best answer) [PEEK]
      1. carbon source
      2. all amino acids
      3. trace elements
      4. essential amino acids
      5. all of the above
      6. none of the above
    8. Phosphorus atoms are not (circle correct answer) [PEEK]
      1. found in nucleic acids such as DNA
      2. trace elements
      3. a common microbial nutrient requirement
      4. components of molecules found in biological membranes
      5. all of the above
      6. none of the above
    9. What is the minimum number of types of carbon sources an organism (such as Escherichia coli) might require in order to grow? [PEEK]
    10. Cyanobacteria are photoautotrophs. Name a carbon source employed by cyanobacteria. [PEEK]
    11. __________ would typically not be an energy source of a chemoautotroph. (circle best answer) [PEEK]
      1. glucose (C6H12O6)
      2. ammonia (NH4+)
      3. hydrogen gas (H2)
      4. elemental sulfur (S0)
      5. all of the above (are not typical energy sources)
      6. none of the above (are typical energy sources)
    12. __________ most typically has an inorganic environmental source. (one word answer) [PEEK]
      1. carbon
      2. hydrogen
      3. nitrogen
      4. oxygen
      5. phosphorous
      6. all of the above
    13. __________ is a term (nutritional pattern) which could describe a hypothetical organism which receives the majority (i.e., effectively all) of its energy from light but whose organic compounds consist of carbons derived mostly from extra-organismal sources of glucose. [PEEK]
    14. Which of the following elements is not typically a macronutrient: [PEEK]
      1. phosphorus
      2. iron
      3. sulfur
      4. potassium
      5. nitrogen
      6. carbon
    15. Distinguish the meaning of the term fastidious from the meaning of the term auxotrophic (or auxotroph). [PEEK]
    16. Following long term passage on a rich bacterial medium, a strain of Escherichia coli is found to be unable to synthesize the amino acid tryptophan. Given that the strain originally could synthesize all amino acids and required no other organic growth factors, this is an example of what? [PEEK]
    17. Give an example or description of the carbon and energy sources used by the following:[PEEK]
    18. photoautotroph: ______________________
    19. photoheterotroph: ______________________
    20. chemoautotroph: ______________________
    21. chemoheterotroph: ______________________
    22. What element ("nutrient") is found in both amino acids and nucleic acids? [PEEK] acid , phosphorus, sulfur, nitrogen, manganese, or calcium
  29. Practice question answers
    1. sulfur
    2. (i) calcium, (ii). carbon, (iii) magnesium, (iv) nitrogen, (v) oxygen, (vi) phosphorus, (vii) potassium, (viii) sulfur.
    3. chemoheterotroph because these microorganisms derive both their energy and their carbon from organic molecules taken from the host.
    4. Yes, chemoheterotroph, glucose
    5. Chemoautotroph
    6. v, all of the above
    7. iv, some amino acids, specifically those which are essential.
    8. ii, trace elements
    9. 1.
    10. CO2.
    11. i, glucose.
    12. v, phosphorous.
    13. photoheterotroph.
    14. Iron
    15. A fastidious microorganism is one whose nutrient requirements include a significant number of organic growth factors. An auxotrophic microorganism (or mutant) may or may not be fastidious as compared to most microorganisms, but is more fastidious than a recent ancestor. That is, a auxotroph has, via a mutation, lost an ability to synthesize one or more organic growth factor and consequently must now obtain that (those) organic growth factor(s) from its environment, whereas its recent ancestor in question did/does not.
    16. an auxotroph, an auxotrophic mutation
    17. photoautotroph = light and carbon dioxide, photoheterotroph = light and organic molecules, chemoheterotroph = organic molecules and organic molecules, chemoautotroph = inorganic molecules and carbon dioxide
    18. iv, nitrogen
  30. References
    1. Black, J.G. (1996). Microbiology. Principles and Applications. Third Edition. Prentice Hall. Upper Saddle River, New Jersey. pp. 148-151.
    2. 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. 129-132, 145, 146, 150.