13.1 Essential ideas

13.1.3 Environmental protection

Biotechnology can be used in the prevention and mitigation of contamination from industrial, agricultural and municipal wastes.


  • Bioremediation is the use of microbes to treat areas of contamination.

Figure 13.1.3a – Principle of bioremediationFigure 13.1.3a – Principle of bioremediation

  • It is possible because some microorganisms are capable of metabolising common pollutants.

Named examples of microorganisms used in bioremediation

Species name



Mechanism of action

Marinobacter hydrocarbonoclasticus

Archaea, halophilic

Marine/saline environments created by oil production at sea; oil spills at sea

Degradation of benzene

Pseudomonas aeruginosa


human pathogen

Oil spill on land

Uses crude oil as a carbon source


Pseudomonas putida,




saprotropic, found in soils



  1. Oil spill on land
  2. Mercury contamination
  1. Uses crude oil as a carbon source, degrades toluene;
  2. Demethylates methyl mercury, to form methane and insoluble mercury.

Combining methods in response to pollution incidents

Figure 13.1.3b – Use of chemical dispersants for an oil spill at seaFigure 13.1.3b – Use of chemical dispersants for an oil spill at sea

Bioremediation can be combined with physical and chemical procedures to increase effectiveness of the response.

  • Oil spill at sea:
    • Chemical dispersants, made of solvents and emulsifiers, are used separate large oil slicks into small droplets of oil that can be more easily processed by microorganisms. 
    • A boom is a large floating barrier that rounds up and lifts oil off the surface of the water.
    • Oil spill on land:
      • On cultivated or mixed-use soils, dispersing the contaminated soil increases the surface area for the microorganisms’ working. Nitrogen and phosphorous fertilisers may be added to increases nutrient availability to microorganisms.
      • Physically skimming, using vacuums, or shovels to remove large deposits from beaches.

Characteristics of biofilms

  • Some species of bacteria form cooperative aggregates called biofilms.
  • The bacteria in a biofilm secrete called extracellular polysaccharide substance (ESP), which allows the cells to adhere to each other and to surfaces.

Figure 13.1.3c – Biofilm of Staphylococcus, showing ESP matrix. (source: Wikipedia)Figure 13.1.3c – Biofilm of Staphylococcus, showing ESP matrix. (Source: Wikipedia)

  • Microorganisms growing in a biofilm are highly resistant to antimicrobial agents. There may be two reasons for this:
    • ESP provides a physical barrier, preventing antimicrobials from entering the biofilm.
    • Antimicrobials interfere with bacterial cell division. Within a biofilm, the rate of cell division varies at different depths - the deepest layers having the lowest cell division rates. This means that once past the ESP barrier, antibiotics may not work on the inner-most layers of cells.

Quorum sensing

  • Many species of bacteria are able to coordinate the expression of genes so that the effect of the protein products is greater than would be possible by each individual cell.
  • The bacteria communicate with each other by emitting small diffusible chemicals that can be detected in plasma membrane receptors of the same species.

Figure 13.1.3d – Quorum sensingFigure 13.1.3d – Quorum sensing

  • When the density of a certain chemical is low, meaning the bacterial population density is low, genes are not expressed in individual cells.
  • Coordinated gene expression only occurs when a certain threshold population density (i.e. the quorum) is reached.
  • Quorum sensing is involved in the production of ESP, a necessary component of biofilms.
  • Quorum sensing and coordinate responses are two emergent properties of biofilms.

Bacteriophage for water system disinfection

  • When biofilms become established on water system pipes, they are difficult to remove and can cause life-threatening contamination.
  • Water treatment facilities have traditionally used chlorine to kill bacteria. A more recent technology is the use of bacteriophage.

Figure 13.1.3e – Viral life cycle - bacteriophageFigure 13.1.3e – Viral life cycle – bacteriophage

  • Bacteriophages are viruses that infect bacteria. There are many different types of bacteriophage, which normally only infect one type of bacteria.
  • Due to their small size, they are able to penetrate the inner layers of a biofilm and they actively destroy bacterial cells instead of preventing them from replication, like traditional antibiotics.

Quorum sensing is involved in 'group behaviours' in Vibrio fischeri. Bonnie Basseler explains in 'How bacteria talk'.

Figure 13.1.3f – Pseudomonas putrinaFigure 13.1.3f – Pseudomonas putrina
Pseudomonas putrina is used to clean up oil spills and to demethylate mercury.

Try it!

Suggest appropriate bioremediation strategies for the following situations:
i) Mercury contamination on land.
ii) Oil spill in freshwater environments

Figure 13.1.3g – DispersantFigure 13.1.3g – Dispersant
Chemical dispersant being sprayed directly over the Deepwater Horizon oil spill in 2010 (Source: Wikipedia)

Figure 13.1.3h – Oil birdFigure 13.1.3h – Oil bird

International mindedness

During oil spills, scientists from different parts of the world work together under pressure in the attempt to prevent ecological disaster. The best possible decision needs to be made as quickly as possible.

Figure 13.1.3i – Pink shower grimeFigure 13.1.3i – Pink shower grime
Biofilms form easily on damp and smooth surfaces.

Figure 13.1.3j – Vibrio cholera (source Wikipedia)Figure 13.1.3j – Vibrio cholera (Source: Wikipedia)
Vibrio cholera causes cholera. Quorum sensing enables bacteria to release toxins as group behaviour.

Did you know?

  • A genetically modified strain of Pseudomonas putrida was the first living organism ever to be patented in 1980.

Figure 13.1.3k – AnandaFigure 13.1.3k – Ananda Mohan Chakrabarty
Ananda Mohan Chakrabarty (1938) developed the P. putrida strain using plasmid transfer.