Credit: Image by G J Whitby from Pixabay 

 Article Writer-   Sudipta Biswas, Int. MSc., School of Biological Sciences, NISER, Odisha(India)

As our life’s comforts are rising exponentially day by day, the waste that we create is increasing too. According to a 2018 survey, the world produces nearly 3.5 million tonnes of plastic and solid waste per day on average [1]. Multiply it with 365, and that is the huge amount of solid waste per year. The number is quite significant. However, it has been observed that these figures are only increasing [2]. There are various ways to manage these wastes; some are non-eco-friendly options like open burning, dumping it into the sea and land, or just discharging into the sewers [3]. Plus, there are many eco-friendly alternatives, too, like sanitary landfills and composting [4]. But these methods don’t stop the misery here as they are not entirely effective in dealing with this massive amount of wastes produced. Hence, eventually, these pollutants start to contaminate the environment heavily. The soil, water, the air becomes equally polluted by our actions. And that’s where bioremediation becomes the hope with which a cleaner and better environment can be created. Bioremediation is how microbes are used to treat pollutants from the environment and change them into non or less toxic substances [5]. The process is one of the most sustainable and economical options to do the work. It is done by altering the polluted/contaminated environments to support microbes’ growth, which helps clean the place by using the pollutants as their food source, leading to its eventual degradation [6]. Hence, advancing research in this sector will be quite beneficial and many research bodies are working in this field

How does it work?

Microbes used in the bioremediation for degrading the pollutants are called as bioremediators [7]. There are complex sets of procedures that are followed for it. However, for ease, it can be divided into the following steps [8]:

1.Examination of the polluted environment (i.e., Soil, River, Groundwater, etc.) and the microbes from the spot. Mostly, the local microbes are used as bioremediators.


 2.Treatability studies of the microbes: The microbes, after being isolated, are then sent for several tests to check their performance for degrading the pollutants.


 3.The suitable cultures are then put back into the place where pollutants are present. Some bioremediation systems are also built for the procedure.


 4.The bacteria’s performance is monitored, and some additives(called amendments) are added into the polluted environment to enhance the conditions needed for the survival of the microbes. Sometimes external microbial cultures are also added for this process, it’s called bioaugmentation [9].

The microbes’ growth depends on various factors like temperature, pH, oxygen concentration, nutrients, and water from the environment. Microbes can grow efficiently when the optimum conditions are present [10].

The reaction that takes place usually during the bioremediation process is the redox reaction. In redox reactions, a chemical species donates an electron to another species that can accept the electron. The former is called the electron donor; it becomes oxidized, and the next one is known as the electron acceptor, which becomes reduced [11]. Common electron acceptors in bioremediation include nitrate, oxygen, manganese (III and IV), chromium(IV), iron (III), carbon dioxide, and some pollutants like explosives, chlorinated solvents, oxidized metals, and some radionuclides. Simultaneously, the electron donors include organic materials like sugars, fats, alcohol, fuel hydrocarbons, and a variety of other reduced organic pollutants [12]. These reactions drive the microbes’ metabolism, allowing them to degrade the contaminants in a less toxic form for the environment. Under redox reaction, there are different types of processes like aerobic reduction, anaerobic reduction, denitrification, fermentation, manganese reduction(IV), etc. that are employed [12].

Types of bioremediation:

 In-situ Bioremediation: It is the process where the polluted sites are treated by using endogenous or exogenous microbes. It means that the decontamination process occurs in the same place where the contamination has taken place [13]. Typical locations treated by this method are marine oil spills, groundwater/aquifers, polluted soils, and others. The microbe’s cultures are inoculated in these places using nutrients and/or fertilizers. It is mostly used for the degradation of hydrocarbon molecules, chlorinated compounds, and aromatics [12]. The most notable occasions are those of the Deepwater Horizon oil spill in 2010 and the Exxon Valdez oil spill in 1989.

Ex-situ Bioremediation: Here, the contaminated materials are removed or taken away from the polluted site and processed in other places like bioreactors. The microbes are implanted into the pollutants after that is transferred to a specific location. In bioreactors, the process can be monitored, and the conditions can be controlled [14]. The factors like temperature, pH, mixing rate, and nutrient levels can be monitored to suit the microbes growing there. In-situ methods are the one which is cost-effective for most of the time as they don’t need the transportation of the pollutants from one place to other. But sometimes, it takes a tremendous amount of time for the degradation of the contaminants there as the reactions are not controlled. Here, the ex-situ reactions are useful, because if the degradation takes a massive amount of time, then there is a chance that the pollutants may spread to larger areas and come in contact with the nearby wildlife [15]. The ex-situ reactions make degradation occur quickly and efficiently.

Some important uses of bioremediation:

Bioremediation of contaminated Aquifer: Aquifers are porous and sedimented rock bodies, which is saturated with groundwater. They are present deep inside the soil; however, the ones near the surface are used to get water for various irrigation and other uses [16]. These aquifers’ contamination occurs by products like oils, organic and inorganic waste, chemicals, biological forms of bacteriological/microbial wastes, and others. When these materials seep under the ground by various human activities(like agriculture), the contamination happens [17].

In-situ bioremediation is the method that is used to treat such kind of cases. The aerobic bacteria are used as the primary organisms that start the biological reduction process. Aerobic remediation is the most effective treatment in reducing the contaminant levels of aliphatic and/or aromatic petroleum hydrocarbons like gasoline and diesel [18]. Also, the aerobic bacteria residing in the aquifer (i.e., between the subsurface and air-water interface) are attracted to the rich carbon-containing contaminants. These aggregation of microbes and contaminants form biofilms. Such a formation of biofilm is used as an indicator for localizing the aquifer’s area where the pollution started. Hence the bioremediation efforts can be targeted towards that source [18]. The factors needed for a smooth microbial degradation are pH(6-9 is the ideal) of the aquifer, nutrients for the microbes, and oxygen availability in that environment. Therefore, air sparging is used to pump oxygen into the contaminated aquifer to stimulate degradation.


Bioremediation of the Marine oil spills: An oil spill is generally regarded as the release of petroleum-based hydrocarbons into the marine environment. However, some oil spills have happened on land; the main spotlight goes to marine issues. They occur due to the release of petroleum-based products from the sites of offshore platforms, drilling rigs, tankers, etc [19]. It takes a significant toll on marine life and other organisms present near the place of the accident, and usually, a lot of time, it is needed to be cleaned immediately [15]. Physical clean-up for these types of contaminants is quite tricky. However, the microbes like Alcanivorax bacteria, Methylocellasilvestris, or Fusobacteria species have shown more significant potential via biodegradation [19]. These species of microbes can degrade the oils and clean the water bodies. The microbes are grown by adding the inoculum and then fertilizer for their growth in the contaminated areas. Along with this, additives are too added to supplement the work.


Bioremediation of contaminated soils: Soils also become polluted by human activities like agriculture, industrial waste disposal, improper disposal of solid waste, etc. Both the in-situ and ex-situ methods can do the decontamination of soil [20]. The in-situ method is used for the sandy soils and larger areas [8]. However, sometimes some oxygen donating or excepting species are also added into the soil. Contaminants are heavy metals, and harmful chemicals like fertilizers are the main culprits. However, the heavy metals can’t be biodegraded; only the mobility of these metals can be reduced on the surface by using bioremediation. The mobility of certain heavy metals like chromium and uranium varies depending on their oxidation state; here, the microbes come in handy by reducing them to their lesser mobile forms [21].


Technologies related to bioremediation:

  • Phytoremediation: The process of planting trees, plants, or shrubs whose roots go deep into the soil and help absorb the contaminants from there. Example: Cottonwood trees absorbing mercury from the ground [22].

  • Biostimulation: Here, the environment is modified by adding some nutrients and other substances that stimulate the growth of indigenous microbes present for bioremediation [23].
  • Vermicomposting: The process of using different varieties of worms like an earthworm, white worm to help the decomposition of food waste, and other things. The mixture made from this decomposition is called the vermicompost; it can be used as a nutrient-rich fertilizer [24].
  • Rhizofiltration: It’s a type of phytoremediation where the cultivated plant’s roots can decontaminate the polluted groundwater [25].
  •  Bioleaching: The process of extraction of metals from ores by using microbes. It has been done by appointing several ferrous and sulfur-oxidizing microbes, specifically bacteria [26].

Advances in bioremediation:

  • Genetic engineering for designing microbes: The bioremediation industry is now shifting to genetic engineering to create certain genetically modified microbes explicitly needed for this job. There are two main types of genes which are either targeted for mutations or inserted into the microbe’s genomes for this purpose. Half of them are the genes required for protein synthesis that help degrade the pollutants. The other half has the reporter genes whose proteins are used to detect the amount of contamination in a particular environment [12]. Example: Most of the plants/trees used in phytoremediation are genetically modified like modified sunflower (Helianthus annuus) for absorbing arsenic.
  • Extremophiles: Recently, the extremophiles are used for the bioremediation process. They are regarded as micro-factories that provide us with a house full of genetic and metabolic metabolism that helps them withstand under highly extreme environments [27]. One such condition is the increase in heavy metal concentrations. Microbes like the one in phylum Firmicutes can withstand such high metal concentrations and reduce such metals to decrease their mobility upon the surface.

  • Acidophilic bacteria for metal recovery: The acidic mine drainage(AMD) is the outflow of acidic water from any coal/metal mines. It is regarded as a pollutant and a source of metals. Hence, recently the treatment of AMD has been started by using bioreactors having acidophilic bacteria. These microbes can both recover the metal oxides from the water and decontaminate it [28]. As the metal sources are dwindling on the Earth’s surface, the use of such acidophilic bacteria to recover metals should be encouraged. Hence this process opens up a new avenue for the usage of bioremediation.
  • Nanobioremediation: It’s a new field that uses both the nanoparticles and microbes to decontaminate the polluted environments. There are various ways by which nanoparticles can be included in the process. They are often attached to metal-reducing enzymes in the microbes. This is used to increase the longevity and stability of the enzymes [29]. Sometimes, these nanoparticles are also incorporated in other ways. 

Comparing the pros and cons:

Bioremediation has its advantages like it is less expensive, needs less site destruction, and also a minimal human interruption is required for it [8]. Similarly, it can be regarded as one of the most eco-friendly options to decontaminate. However, with every advantage, there are disadvantages too. In many situations, the microbes cannot degrade the pollutants because many pollutants are not biodegradable [12]. Sometimes, the product formed after the degradation is more toxic than the reactant pollutant. For example, under aerobic reactions of the microbes, the chemical trichloroethylene(TCE) can turn to dichloroethylene and vinyl chloride, which are categorized as carcinogens [30]. Now, another round of bioremediation will be required to turn these chemicals to less toxic ones. It should also be taken into deliberation that biological processes are precise. It only happens under certain circumstances, and many additives might be needed to match its requirement [10]. This factor might cause an issue too.

However, even if it has some disadvantages in its bag, we still look up to bioremediation to clean up all the polluted grounds. This process has shown very positive results in decontaminating materials, and by using naturally occurring microbes, we tend to save the environment too. Hence, there’s a lot of scope on it, and hopefully, with future advances, we will be able to use this process in a newer and more innovative way.




30.Maymó-Gatell, Xavier; Chien, Yueh-tyng; Gossett, James M.; Zinder, Stephen H. (1997-06-06). “Isolation of a Bacterium That Reductively Dechlorinates Tetrachloroethene to Ethene”. Science. 276 (5318): 1568–1571.