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Microbial biodegradation methods

Microbial degradation techniques are broadly classified into two categories based on whether the degradation is carried out in situ or ex situ.

In situ microbial degradation

In Latin, in situ means “in the origin place”. In this technique, the polluted substances are treated at the site of pollution. Compared to ex situ techniques, it is less costly since no excavation and transport of contaminants is required. But these techniques are a highly time-consuming and seasonal variation of microbes in the soil also affects the degradation processes. If the native microbes lack biodegradation ability, then genetically engineered microbes are introduced at the site of contamination to enhance the degradation process. There are different types of in situ degr adation processes.

a) Bioventing

In this technique, the flow of oxygen is supplied to the unsaturated zones in the soil through controlled airflow stimulation to enhance the biodegradation process. In this technique, the biodegradation is enhanced by adding nutrients and moisture to the soil. The success of

Table 2. Enzymes involved m pesticide degradation.




Klebsiella sp. Alcaligenes sp. Staphylococcus sp. Pseudomonas sp.


Organochlorine compounds

Flavobacterium Pseudomonas sp.

Agrobacterium radiobacter Alteromonas sp.

Plesiomonas sp.


Pseudaminobacter Ochrobactrum


B. diminuta

Flavobacterium sp.


Aspergillus sp.

Penicillium sp.

Organophosphoms hydrolase (OPH) Organophosphoms acid anhydrolase (OPAA)


Aspergillus enzyme (A-OPH) Penicillium enzyme (P-OPH)

Organophosphoms compounds

Achromobacter sp.







Carbofuran hydrolase

Carbamate compounds

Setratia Pseudomonas Aspergillus niger

Carboxyl esterase Pliosphotnesterase Pyretliroid hydrolase


Adapted from Parte et al. 2017.

bioventing based bioremediation techniques relies upon the uniform distribution of air in the unsaturated zone.

b) Bioslurping

Bioshupiug involves vacuum enhanced pumping, soil vapour extraction, and bioventing by the indirect provision of oxygen simulating the enhanced biodegradation of pesticides. This technique is used to remediate soils contaminated with volatile and semi-volatile organic compounds.

c) Biosparging

Biospargiug is very similar to bioventing with a difference that in this technique air is injected into a saturated zone causing upward movement of the volatile organic compounds to the unsaturated zone promoting biodegradation. Biosparging increases the contact between soil and groundwater. This technique is commonly used in aquifers contaminated with hydrocarbons.

d) Phytoremediation

This technique involves plant interaction in the contaminated sites resulting in the degradation of pesticides. Plant promoting rhizobacteria play a major role in phytoremediation techniques since it enhances biomass production.

e) Permeable reactive barriers

This is used for decontaminating groundwater contaminated with different pollutants. In this technique, a permanent or semi-permanent reactive barrier made up of zero-valent non is used in the way of polluted groundwater. The polluted water is trapped and undergoes several reactions to give clean water.

J) Intrinsic bioremediation or natural attenuation

It is the passive remediation of contaminated sites without any human intervention. In this, both aerobic and anaerobic microbial degr adation causes the removal of contaminants from the site. This technique is less expensive compared to other in-situ techniques.

Ex situ microbial degradation

In this technique, the pollutants are excavated from their sites and transported to other sites for treatment. These involve aerobic techniques. It is a costly process compared to in situ degradation processes. Based on the nature of contaminants, ex situ microbial degradation systems are broadly classified into two classes: (1) sluiiy phase microbial degradation and (2) solid-phase microbial degradation. In slimy phase degradation, contaminated soil is mixed with water to form a slurry and is treated in bioreactors or contained ponds or lagoons. In solid-phase degradation techniques, polluted soils are excavated and placed in piles for treatment. The soils are sprayed with water to maintain the moisture. There are different techniques under which ex situ microbial degradation takes place.

a) Biopile

In this technique, bioremediatiou is done by the above-ground piling of excavated contaminated soil, followed by nutrient addition and aeration to increase the microbial degradation of contaminants. This technique involves different components such as aeration, irrigation, nutrients and leachate collection systems, and a treatment bed.

b) Windrows

In this technique, a periodic turning of the polluted soil is done to enhance bioremediation by microbes. The periodic turning along with the addition of water increases aeration, uniform distribution of contaminants, and the rate of microbial degradation.

c) Bioreactor

In bioreactors, the polluted soil is fed and due to different biological reactions, contaminants are converted to specific products. In this, the different parameters such as pH. temperature, substrate, etc. can be controlled. But this technique is costly and labour intensive.

d) Land fanning

This is the simplest form of bioremediation technique. This technique requires less equipment and the process is cost-effective. This technique can be in situ or ex situ based on the site of treatment. If the contaminated soil is excavated and treated on-site, it is called in situ otherwise it is ex situ. If the contaminants are present at a depth of less than 1 m, then it can be treated without excavation. Excavation needs to be done if the contaminants are present at a depth of more than 1.7 m. This technique is very simple to design and implement and efficient in treating a large volume of contaminated soil.

One of the advantages of ex situ treatment is that extensive initial assessment of the polluted site is not required which reduces the labour and cost. These techniques are generally faster, easy to control, and can be used to treat several contaminants (Azubuike et al. 2016).

Microbial degradation can take place under the aerobic and anaerobic conditions depending upon the availability of oxygen.

Aerobic and Anaerobic microbial degradation

In aerobic degradation, the microbes utilise the atmospheric oxygen for its metabolic activities to mineralize pesticides. Different electron-withdrawing substituents such as chloro, nitro groups restrict the use of oxygenase enzyme by aerobic microbes to initiate the electrophilic attack on aromatic molecules. The microbes catalyse the hydrolysis reactions through co-metabolism. In some pesticides, anaerobic degradation works better than the aerobic degradation processes.

In anaerobic degradation, microbes utilize the organic compounds present in soil as substrate for its energy needs. In this type of degradation, nucleophilic attack initiates the degr adation of aromatic compounds. Unlike in aerobic degradation, the substituents such as chloro, nitro groups favour the attack of anaerobic microbes on aromatic compounds. The electron donating groups hinder the anaerobic transformation of aromatic compounds. The common degradation reactions in the anaerobic degradation of pesticides include: (a) replacement of hydrogen atoms with hydroxyl groups, (b) oxidation of S to S02 which is a common reaction resulting in the formation of epoxides, (c) addition/rernoval of methyl groups, (d) dechlorination, (e) migration of chlorine groups, (f) conversion of the nitro group to an amino group (nitrate reduction), etc. Generally, the halogenated compounds are easily degraded under anaerobic conditions.

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