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Bioremediation - Fundamental Chemistry and Biology of Bioremediation

Fundamental Chemistry and Biology of Bioremediation



Chemistry of biodegradation

Biodegradation is an oxidation-reduction reaction involving organic compounds and facilitated by microorganisms (Sharma & Reddy, 2004). It can also be thought of as a process where an organic compound becomes smaller through chemical or biological processes (Fetter, 1993) for example a halide ion may be replaced with a hydrogen ion therefore producing a compound of lower molecular weight. Biodegradation can also be thought of as the metabolism of organic contaminants by microorganisms, i.e. microorganisms break down organic compounds to produce energy and carbon to permit growth (Sharma & Reddy, 2004). Biodegradation can occur in the presence of oxygen and is termed aerobic or without oxygen and is termed anaerobic. In aerobic biodegradation, organic compounds are oxidized by an electron acceptor, which is reduced. If the oxidation of an organic contaminant occurs with the reduction of molecular oxygen it is known as aerobic heterotrophic respiration (Sharma & Reddy, 2004). Anaerobic biodegradation processes include (Sharma & Reddy, 2004):

  • Fermentation. In fermentation, microorganisms make use of the organic contaminant (substrate) as an electron donor and an electron acceptor thus the organic compound is both oxidized and reduced (Sharma & Reddy, 2004):



  • Sulfate reduction. Sulfate reducing bacteria (SRB) use ferric iron or SO4- as an electron acceptor. The reduced products are ferrous iron and H2S. This is discussed in greater detail as part of Acid Mine Drainage (AMD).
  • Denitrifying. Bacteria use NO3- as an electron acceptor and produce NO2-, N2O and N2 as reduced products.
  • Bacteria that produce methane (methanogens) use CO2 as an electron acceptor to produce methane as an end product. Methanogens can also produce methane through the fermentation of acetic acid.

Bacteria can be classified depending on their functioning in the environment or by how they create energy (Sharma & Reddy, 2004). Classification by function has two types: 

1.Oligotrophs function in low carbon, low contaminant concentration environments.

2.Eutrophs function in high carbon, high contaminant concentration environment.


Classification by energy creation has three types:

1.Chemotrophs get energy by oxidizing organic or inorganic compounds.

2.Autotrophs create carbon within cells using small organic compounds such as CO2.

3.Heterotrophs require a carbon source to create energy.


There are 5 main requirements for successful biodegradation to occur (Sharma & Reddy, 2004):

1.Suitable microorganisms must be present. These can be native or foreign.

2.Organic contaminant to act as an energy source and a carbon source for the microorganisms.

3.For aerobic degradation, electron acceptors must be present to accept electrons produced as bacteria degrade the organic compound.

4.Nutrients required by microorganisms to thrive. These include nitrogen, phosphorous, calcium, magnesium and iron.

5.Suitable environmental conditions i.e. pH and temperature.


Biodegradation of hydrocarbons, such as alkanes, can occur under aerobic conditions. Bacteria that are able to do this include Micrococcus, Pseudomonas, Mycobacterium and Nocardia (Fetter, 1993). For example the oxidation of n-hexane is as follows (Fetter, 1993):


Branched alkanes are harder for microorganisms to biodegrade then straight chain alkanes (Fetter, 1993).

Halogenated organic compounds can be oxidized or reduced by microorganisms. An example of an oxidation reaction is α-hydroxylation, here a hydrogen atom on a carbon atom that is also bonded to a halogen is replaced by an OH- group (Fetter, 1993). An example is the α-hydroxylation of 1,1-dichloroethane to 1,1-dichloroethanol:


The halogenated oxygen can loose another hydrogen to form an aldehyde:


Reduction reactions can occur in two different processes hydrogenolysis and dihaloelimination (Fetter, 1993). In hyrdogenolysis a halide ion is replaced by a reduced species producing an alkyl radical. The alkyl radical reacts with a H+ ion and is substituted for the negatively charged halide e.g.:


Dihaloelimination occurs when halides are present on adjacent carbon atoms. The halogen removed from each carbon atom creates a double bond between the carbon atoms thus forming an alkene (Fetter, 1993). Dihaloelimination takes a halogenated alkane and produces a halogenated alkene eg. Hexachloroethane to tetrachloroethene:


The aerobic biodegradation of organic compounds, consumption of oxygen and growth of microorganisms can be described by the Michaelis-Menten functions, also known as the Monod Function (Fetter, 1993) and (Sharma & Reddy, 2004):



H – hydrocarbon concentration in the pore fluid (ML-3)

O – oxygen concentration in the pore fluid (ML-3)

Mt – total aerobic microbial concentration (ML-3)

hu – maximum hydrocarbon utilization rate per unit mass of aerobic microorganisms (T-1)

Y – microbial yield coefficient (g cells/g hydrocarbon)

Kh – hydrocarbon half saturation constant for aerobic decay (ML-3)

Ko – oxygen half saturation constant (ML-3)

kc – first order decay rate of natural organic carbon

Coc – natural organic carbon concentration (ML-3)

b – microbial decay rate (T-1)

G – ratio of oxygen to hydrocarbon consumed


Anaerobic biodegradation can be described by a different modified Monod function (Sharma & Reddy, 2004):



Ma – total anaerobic microbial concentration (ML-3)

hua – maximum hydrocarbon utilization rate per unit mass of anaerobic microorganisms (T-1)

Ka – hydrocarbon half saturation constant for anaerobic decay (ML-3)

One important note is that for a given organic substrate, the concentration of that substrate cannot be reduced below the concentration required for the survival of the microorganism. Thus there is always a minimum concentration of organic substrate, Hmin, given by (Fetter, 1993):


When a mix of hydrocarbons is present it may be possible to reduce the concentration below Hmin for a given hydrocarbon if it was the sole contaminant by utilizing other hydrocarbons to allow the microorganisms to survive.

Determination of Biodegradability

The biodegradability of a contaminant can be determined by carrying out tests to determine the Biological Oxygen Demand (BOD) and Chemical Oxygen Demand. The BOD is a measure of oxygen required by microbes to breakdown a given organic contaminant in a sample of water. The COD is an indirect measure of the amount of organic contaminant present in a sample of water. A ratio of BOD and COD gives an indication of the biodegradability of a given contaminant.


Treatment of Acid Mine Drainage

Acid Mine Drainage Chemistry

Acid mine drainage (AMD) is a common problem worldwide, an estimated 19,300 km of rivers and 72,000 ha of lakes have been damaged by AMD (Johnson & Hallberg, 2005a). Because of the association with mining and underground activity the effluent of mines is often rich in heavy metals and can contain other contaminants such as arsenic. The main source of AMD is iron pyrite (FeS2). Many metals that are mined occur naturally as metal sulfides and pyrite tends to be found in the same location as the metal ore of interest (Johnson & Hallberg, 2005a). As mining progresses and the water table is pumped down to allow advancement of tunnels and the pyrite is exposed to air and water and sets in motion a series of acid generating reactions. The processes are complicated and varied, but can be summarized as follows (Blodau, 2006):

First pyrite is oxidized releasing Fe2+ ions:



Fe2+ ions are then further oxidized to Fe3+:



The Fe3+ can then go on to oxidize more pyrite in a highly acid generating reaction:



pH is given by:



So clearly, as the number of H+ ions increase the pH will fall becoming increasingly acidic. The high acidity of drainage from mines caused by the above reactions, along with the heavy metals associated with mining pose a significant risk to the environment.


Passive Wetlands and Sulfate Reducing Bacteria

There are many possible methods that can be employed to treat AMD and each has strengths and weaknesses depending on the unique chemistry of each AMD. One popular method for the treatment of net acidic AMD is passive anaerobic wetlands that make use of sulfate reducing bacteria (SRB). A passive treatment method here is defined as a method that makes use of naturally occurring energy and decontaminating agents.

Remediation by SRB can be represented by two chemical equations described by Johnson & Hallberg, (2005a) and Doshi (2006). First sulfate reduction, here organic matter is shown as CH2O:


Then metals may precipitate out as metal sulfides, where Me represents a suitable metal:



Metals that can precipitate out this way include cadmium, copper, iron, lead, mercury, nickel, zinc and manganese. Arsenic, antimony and molybdenum can also form sulfide complexes (Doshi, 2006).

SRB that are suitable to use in anaerobic wetlands include Desulfovibrio, Desulfomicrobium, Desulfobulbus, Desulfobacter, Desulfobacterium, Desulfococcus, Desulfosarcina, Desulfomonile, Desulfonema, Desulfobotulus, and Desulfoarculus (Doshi, 2006). To optimize the efficiency of these bacteria, a balance of temperature and pH must be achieved. Anoxic conditions are also necessary, the introduction of fresh manure helps to promote bioactivity that uses up oxygen present in the water. SRB have been shown to function at pH as low as 2.5 and temperatures as low as 6°C, although optimal temperature is 20°C-40°C (Doshi, 2006).


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