Bioremediation of Contaminated Soil Using Microbes

Introduction to Bioremediation and Microbes

Bioremediation is the use of natural or deliberately introduced micro-organisms to consume and break down hazardous pollutants into less toxic compounds in order to clean an environmentally polluted site. Bioremediation is usually carried out by plants and microbes like bacteria and fungi. The contaminants may be naturally occurring compounds which are present in high concentrations like crude oil, heavy metals etc. and chemically synthesized compounds like xenobiotics.

Abundance of bacteria is represented by the soil where 1gm of soil contains up to billions of bacterial cells. Bacterial activity is of much important in the different processes of soil like −

  • Organic matter decomposition.

  • Nutrient release.

  • Atmospheric nitrogen fixation.

  • Plant pathogen inhibition or suppression of plant diseases.

  • Maintenance of soil structure.

  • Pollutant degradation.

Thus for this reason bacteria can be explored for the bioremediation of the contaminated soil.


Bioremediation of hydrocarbons may be an alternative option for waste management due to their low operating costs, easy implementation and for benefit to the environment. The high demand for hydrocarbons in soil has determined the appearance of increasing sources of contamination such as accidental spills, oil tanker accidents and generation of sludge. Hence bioremediation is a process of decontamination that uses series of biochemical reactions using a population of the micro-organisms inoculated in the contaminated soil to convert hydrocarbons into less toxic substances.

Oil Spills

The huge environmental disasters really have a viable solution. They cause environmental damage because petroleum is a toxic mix of organic compounds, heavy metals and hydrocarbons that break down to even more harmful secondary chemicals which can cause serious and acute long term effects. So certain micro-organisms like Marinobacter can break down harmful chemicals into safer non-toxic compounds.

If these left in devices, microbes in the environment would eventually break down the oil but takes a long time. Microbes limited growing in huge number by the availability of nutrients and other factors in their environment. The additional fertilizers containing like phosphorous, carbon and nitrogen allow the microbes to increase in numbers and speed up the process.

As oil spills bioremediation techniques can also be used to clean up the acidic mining damage, contaminated soils by heavy metals and plastic pollution.

Soil Bioremediation Technologies

Biological treatment technologies use micro-organisms to remediate the contaminated soil. Bioremediation transforms the hazardous contaminants to the harmless byproducts like ethane and water using the micro-organisms for biodegradation which involves mineralization and biotransformation.


Biodegradation involves the process of extracting energy from the oxidation of organic chemicals. It is a remediation technique used to decompose the contaminants by injecting the micro-organisms or nutrients into the contaminated soil or underground water.

The term biodegradation is also explained by other terms like biotransformation (modification in the structure of original compound to reduce the toxicity) and Mineralization (contaminants are used as carbon source and are completely metabolized, degradation and conversion of organic molecule to its mineral constituents like carbon dioxide).

Biodegradation is often accomplished by the synergistic relationship between the many groups of microbes and usually not one pure culture is involved in degradation. One group can carry initial step (reducing toxicity) then the other group can be involved in the later step (convert to metabolite which is easily amenable) and this process continues until all the chemicals converted to carbon dioxide. It is very rare to see one single species completely mineralize the chemicals of soil.

There are mainly two different strategies available for the soil bioremediation process.

In-situ Bioremediation

In-situ bioremediation takes place directly on the contaminated site without transporting the contaminated soil.

  • Bio-stimulation - It involves the placement of amendments (nutrients, surfactant, reducing agents like carbon rick vegetable oil, moistening, oxygen, pH control) directly on the contaminated soil in order to stimulate biodegradation by indigenous bacterial population.

  • Bioventing - This involves providing enhanced aeration by adding oxygen.

  • Bio-augmentation - It involves inoculation of selected degrading indigenous bacteria or genetically modified bacteria to the contaminant soil to speed up its degradation.

Ex-situ Bioremediation

This process involves the excavation and transfer of the contaminant soil to another site for the treatment.

  • Bioreactor – Large vessel where the contaminated soil is monitored and conditions are controlled.

  • Biopile – Soil is placed in piles then aerated and provided with nutrients.

  • Land Farming – Here the contaminated soil is spread into line beds which involves the periodical nutrient supply and mixing for the improvement of microbial activity.

Factors Affecting Bioremediation

  • Genetic potential of microbes.

  • Bioavailability of chemicals – If the chemical is absorbed into the bio layer it is not said to be bioavailable.

  • Structure of the contaminant.

  • Toxicity of contaminant.

  • Environmental factors.

    These dictates the biological rate.

    • Oxygen

    • Organic Matter

    • Nitrogen

    • Temperature

    • pH

    • Salinity

    • Water activity

All these factors decide how fast the chemical disappears from the environment.

Advantages of Bioremediation

  • Here physical and chemical methods are comparatively cheaper.

  • No additional disposable costs as most of the time compound is made less toxic by mineralizing it.

  • Generally low maintenance.

  • Treatment system does not create an eyesore.

  • Capable of impacting many source zones and decrease clean-up time at the sites.

Use of Toxicants by Microbes

Micro-organisms use the toxic soil chemicals in 3 different ways.

  • Uses as primary substrate in their metabolism as the compound itself serves as carbon source.

  • Uses as a secondary substrate when the compound itself is not in high concentrations in the environment and provides energy. It takes longer time to degrade these compounds.

  • Uses as co-metabolic substrate when there is an accidental transformation of contaminants. Here we need to add the additional carbon source for bacteria to grow on and same enzyme catalyzes the degradation.

Microbial Growth Requirements

  • Requires toxicants as carbon or energy source.

  • Provide trace elements and nitrogen and phosphorous as nutrients.

  • Environmental conditions like pH, temperature and conductivity.

  • Need to provide electron acceptor into the soil environment which includes $\mathrm{O_2, NO_{3^-}, SO_4^{2^-}}$, etc.

So when both electron acceptor and donor are present in the environment, microbes oxidize the compounds and puts electron in acceptor converting them to CO2 and water. And all the organic constituents in the contaminant becomes inorganic constituents which is done by mineralizing the compound.

Aerobic and Anaerobic Biodegradation

Most of the time bioremediation is done aerobically here the oxygen is the terminal electron acceptor where it is the limiting factor hence contaminant environment is provided with the oxygen. This process is called as aerobic biodegradation.

In anaerobic condition, anaerobic bacteria can also degrade the contaminants where we need to provide various electron acceptors like nitrate ion, sulfate ion or methanogenic or fermentation conditions. This process sis called as anaerobic biodegradation.

Anaerobic biodegradation is lot slower than that of the aerobic biodegradation as anaerobic microbes takes much time to double their number than that of aerobic bacteria. Also there are some special bacteria which are called facultative aerobes which uses oxygen and can switch to nitrate in the absence of oxygen.


Bioremediation is the most effective way to remediate the contaminated soils as an alternative for their final disposal without affecting the soil, water and air resources. This method is cost-effective environmentally friendly and publically accepted alternative approach for remediation of the contaminated soil.

Biodegradation is a remediation technique which involves break down of oil contaminants by injecting microbes or nutrients into contaminated soil. Composting is also a technology which is used to remediate soil improving the microbial activity by mixing with compost for breakdown of poorly biodegradable organics like explosives.

Updated on: 10-May-2023


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