Bacteriology 102: Catabolism and Oxygen Relationships

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Catabolism & O2 Relationships
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Condensed from our catabolism and oxygen relationship pages.

I.  Purposes of Catabolism:

  1. To release energy which can be used to generate ATP from ADP and phosphate.

  2. To release electrons which serve as "reducing power."

  3. Also to provide some of the "building blocks" for biosynthesis.

II.  Regarding their source of reducing power, organisms can be classified as either organotrophs or lithotrophs:

  1. ORGANOTROPHS oxidize organic compounds. As an example, the complete oxidation of a typical carbohydrate (represented by CH2O) by respiration by an organotroph can be represented as:
    CH2O + O2 --> CO2 + H2O.

  2. LITHOTROPHS oxidize inorganic compounds. Examples of electron donors that are oxidized include:
    • H2 (hydrogen gas), oxidized to H2O
    • S (sulfide), oxidized to SO42– (sulfate)
    • Fe2+ (ferrous ion), oxidized to Fe3+ (ferric ion)
    • NH4+ (ammonium), oxidized to NO2 (nitrite)
    • NO2 (nitrite), oxidized to NO3 (nitrate)

III.  Regarding their ultimate source of energy, organisms can be classified as either chemotrophs or phototrophs:

utilize chemical reactions in the generation of energy (and also reducing power). This is done by fermentation and/or respiration. In the general microbiology lab, the ability of a chemoorganotrophic organism to respire (with oxygen) and/or ferment can be determined with the "oxygen relationship test."


To make a long story short, we can use the example of a typical fermentation pathway (stepwise/sequential chain of chemical reactions) where glucose is oxidized to pyruvate (the oxidation stage of the pathway) and pyruvate is then reduced to fermentation products such as lactic acid (the reduction stage of the pathway). At a certain step in the oxidation stage where compound A loses electrons (which are picked up by co-enzyme NAD+), the electrons can be transferred to compound C in the reduction stage (thus "regenerating" the NAD+).

In the generation of ATP, the "P" (phosphate) can be "free" (inorganic) or attached to an intermediate compound in the pathway (organic). As this phosphate is transferred to ADP in the formation of ATP and does not incorporate energy associated with electron transport, the term "substrate-level phosphorylation" applies.

also oxidize chemical compounds, but the ultimate source of energy is light. "Phototrophy" is shown here as the set of light-dependant, catabolic reactions associated with photosynthesis (the other reactions of which are anabolic).


("chl" represents chlorophyll.)

Phototrophy can be OXYGENIC (evolving O2 when H2O serves as the electron donor) or ANOXYGENIC (non-O2-evolving).



While fermenters (above) tend to be organotrophs, respirers can be organotrophs or lithotrophs. For respiration, we have O2 as an external electron acceptor, and the reduction stage seen in fermentation is replaced here by continued oxidation. An organic substrate can be oxidized completely to CO2 as O2 is reduced to H2O.

ANAEROBIC RESPIRATION employs an electron acceptor other than O2 such as nitrate (NO3) which is reduced to nitrite (NO2) or N2.

IV.  An attempt to produce an abbreviated summary of catabolism based on the above follows.
Here we get down to the basics, leaving out cytochromes and other intermediates. This diagram represents what generally happens at a step in the catabolic pathway where a substrate is oxidized with (1) electrons given off which can be utilized for "reducing power" and (2) energy is released that results in the generation of ATP. For fermentation (as noted above), ATP generation is accomplished by substrate-level phosphorylation rather than with energy released at such a step in the pathway.

Note:  These pages do not (yet) address cyclic vs. non-cyclic photophosphorylation, and the following diagram does not adequately address the concept of "reducing power," the provision of electrons and ATP to anabolic activities, and the key role of NAD. Click here for clarification.

V.  Based on the above, we can characterize and classify bacteria consistently and comprehensively by applying the method(s) of energy generation of which an organism is capable:

  • aerobic respiration

  • anaerobic respiration

  • fermentation

  • anoxygenic phototrophy

  • oxygenic phototrophy

How three of these processes are associated with anaerobic growth is shown here.

VI.  Thioglycollate Medium – which we use in our Bacteriology laboratory courses – is a "standard" medium often used for the determination of oxygen relationships of bacteria.

  • One must consider the following limitations of Thioglycollate Medium:
    • The medium will support the growth of common, easily-grown chemoheterotrophic bacteria, and the pattern of growth of an inoculated organism will indicate whether it can respire (using molecular oxygen – i.e., aerobic respiration) and/or ferment. Secondarily, the oxygen relationship designations derived from the growth observations (strict aerobe, facultative anaerobe, etc.) can be helpful in comparative studies of the physiologies of these organisms.

    • Many organisms (including a lot of chemoheterotrophs) cannot grow in this medium for one reason or another.

    • No allowance is given in the medium or method for anaerobic growth (1) with alternate electron acceptors (such as nitrate) or (2) in light (such as what is seen with the anoxygenic photosynthetic bacteria). Thus, an organism which may be termed a "strict anaerobe" in the very general sense – i.e., one which cannot tolerate oxygen and can only obtain energy by reactions which do not involve O2 – would only show anaerobic growth in this test if it were capable of fermentation in this medium.

  • The results we see in Thioglycollate Medium are shown below. The accompanying table gives related information. Note that a positive catalase reaction correlates with the ability to respire (aerobic respiration) and also with sensitivity to sodium azide; azide inhibits iron-porphyrin compounds such as cytochromes and catalase – both associated with respiration. Also note that the ability to grow anaerobically in this medium goes along with the ability to ferment.

Corresponding tube no. above 1 2 3 4
Oxygen relationship designation STRICT
Aerobic respiration + +
Fermentation + + +
Oxygen tolerance + + +
Ability to grow anaerobically + + +
Catalase reaction + +
Reaction in Glucose O/F Medium
(for those able to grow well in medium)
O or – F    
Response to sodium azide in a
growth medium
aerobic conditions)
  • An organism's oxygen relationship designation can be determined by a combination of these methods if Thioglycollate Medium is not made available – i.e., (1) testing for fermentation in Glucose Fermentation Broth, (2) performing the catalase test, and (3) testing if the organism can grow in the presence of oxygen.
  • A reminder: Whether or not any organism can obtain energy by anaerobic respiration or phototrophy (and thus be able to grow anaerobically) is irrelevant to the test for oxygen relationships as performed with Thioglycollate Medium.

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John Lindquist, Department of Bacteriology

University of Wisconsin – Madison