13.1 Essential ideas

13.1.1 Microbiology: organisms in industry

  • Microorganisms are useful in industry because they are small, metabolically diverse, and they reproduce quickly.
  • Under controlled conditions, microorganisms can be grown on a range of nutrient substrates to produce many different products.

Examples of industrially useful microorganisms and their products

Metabolic pathway





(Methanobacterium sp.)

Biogas (methane)

Anaerobic respiration:

…of glucose 

…of sugars in the presence of ammonia


Multi-cellular Fungus

Aspergillus niger

Penicillum chrysogenum

Citric acid

(for food preservation and flavouring)

penicillin antibiotics

Fermenters in industry 

  • Fermenters, or bioreactors, are tanks of varying size that allow for large-scale production of metabolites of interest.
  • The conditions inside a bioreactor are controlled to optimise growth of specific microorganisms and to yield desired products.
  • The most common type of fermenter has an air supply and a stirred-tank, as shown below:

Figure 13.1.1a – A deep tank fermenter, used for the production of penicillin

  • Probes are used to monitor conditions of:
    • temperature
    • pH
    • pressure
    • aeration (oxygen concentration)
  • Computer-based probes allow technicians to monitor the vessel and take action if conditions fall outside the optimum range.

Application: Biogas production

  • Biogas production requires:
    • strictly anaerobic conditions
    • a constant temperature of about 50 °C
    • pH between 6.6 and 7.6
    • a constant supply of nutrients (manure and other organic waste).

Figure 13.1.1b – Production of biogas from organic matterFigure 13.1.1b – Production of biogas from organic matter.

Source: extension.psu.edu

  • There are three communities of microorganisms required for the production of biogas:
    • The first group of eubacteria converts solid material into liquid organic compounds.
    • The second group of eubacteria converts organic compounds into ethanoic acid, CH3COOH.
    • Finally, the methanogens convert ethanoic acid and carbon dioxide into methane. Some carbon dioxide is a by-product.


CO2 +4H2 à CH4 + 2H2

Batch and continuous culture

  • Fermentation is carried out by batch or continuous culture. Refer to the diagram below as you read about each approach.

Figure 13.1.1c – General scheme of fermentation processFigure 13.1.1c – General scheme of fermentation process

  • In batch culture:
    • Microorganisms and nutrients are added to the reaction vessel.
    • After the initial inoculation, no further nutrients or microorganisms are added.
    • Products are extracted when the concentration is high.
    • During the culture, microorganisms reproduce at variable rates, according to the sigmoid growth curve shown below:

Figure 13.1.3d – Batch culture relies on a natural growth curveFigure 13.1.3d – Batch culture relies on a natural growth curve

  • In continuousculture:
    • Nutrients and microorganisms are added continuously to the reaction vessel.
    • Products are continually extracted because high concentration is maintained throughout the process.
    • The constant availability of nutrients encourages optimum growth rates throughout the process.

Comparison of batch and continuous culture

Batch culture 

Continuous culture

  • Lower productivity
  • Lower risk of contamination
  • Less monitoring required
  • Used to produce secondary metabolites (e.g penicillin)
  • Higher productivity
  • Higher risk of contamination
  • More monitoring required
  • Used to produce primary metabolites (e.g. citric acid) and secondary metabolites

Limiting factors

  • Microorganisms in fermenters become limited by their own waste products.
  • Waste products of fermentation become important abiotic limiting factors:

Carbon dioxide

  • affects pH
  • increases gas pressure in the vessel



  • affects permeability of plasma membranes
  • is lethal at high concentrations


Metabolic pathway engineering

  • Pathway engineering optimises genetic and regulatory processes within microorganisms so that they overexpress genes that code for desired metabolites products, or so that the production of the secondary metabolites is limited.

Figure 13.1.1e – Pathway engineering results in strains of Penicillum with varying antibiotic propertiesFigure 13.1.1e – Pathway engineering results in strains of Penicillum with varying antibiotic properties

    • Metabolic pathways can be manipulated by:
      • removing factors that inhibit production of the desired product
      • maximising substrate availability for the metabolic pathway of interest
      • blocking other pathways that would divert resources from the primary pathway.

 Essential idea

The natural metabolic diversity of microorganisms can be exploited and modified to perform industrial processes.

Figure 13.1.1f – Biogas fermenterFigure 13.1.1f – Biogas fermenter
A biogas fermenter relies on many communities of bacteria.

Figure 13.1.1g – Aspergillus nigerFigure 13.1.1g – Aspergillus niger
The fungus, Aspergillus niger, is used in a continuous culture fermenter to produce citric acid.

Language tools

  • Metabolism is the entire set of life-sustaining chemical reactions that occur in an organism.
  • Fermentation refers to any anaerobic process that produces metabolites. However, some industrial 'fermentation' processes are aerobic. The term fermenter refers to the apparatus, and not the reactions taking place inside of it.
  • A primary metabolite is a product of metabolism that is required for normal growth and survival.
  • A secondary metabolite is useful but not necessary for growth and survival.

Figure 13.1.1h – Penicillum chrysogenumFigure 13.1.1h – Penicillum chrysogenum
Penicillin is a secondary metabolite produced by the fungus, Penicillum chrysogenum.

Figure 13.1.1i – Beer vatFigure 13.1.1i – Beer vat
Beer fermenters use the yeast, Saccharomyces cerevisiae, to produce alcohol in batch culture. 

Course link

  • The yeast, Saccharomyces cerevisiae, is also used to produce ethanol in bread making. 2.2.8
  • Recombinant DNA technology is covered in 13.1.2.