Scope of microbial remediation processes in Phytoremediation to combat pollution

Discussion about environmental pollution and its consequences has become a common place in the wake of frequent environmental disasters like oil spills and radiation leakage. However environmental disasters are not only caused by sudden catastrophes, but also over a long term discharge from anthropogenic activities. These include, continuous discharge of agriculture, mining and industrial effluents as direct consequence of population explosion and industrialization. As of 2016, approximately 5.73 million tons of crude oil has been accidently released into the environment during 1830 incidents in 5 decades, while 2016 alone experienced 6000 tons of crude oil spill (ITOPF, 2017). Radiation leakage either from nuclear power plants or nuclear missile tests has also been a source of life-threatening pollution, causing wide-spread and long term harm to all organisms. Most noteworthy is the Fukushima reactor meltdown which resulted in the release of 20-40 trillion Becquerel of tritium into the environment. Subsequently, it has been estimated to pose a considerable high risk to marine life near the Japanese coast in the Pacific Ocean (Reuters, 2013).


While oil spills can choke marine life and increase frequencies of ‘dead zones’ in the water column, radiation exposure can damage human tissues and DNA to cause cancer (Jernelov, 2010; Plant, Voulvoulis, & Ragnardottir, 2012; Rabotyagov, Kling, Gassman, Rabalais, & Turner, 2014).

Another class of equally dangerous pollutant is heavy metals, which is released into the environment from  anthropogenic activities like mining and primary production of alloys. Incidents like chromium discharge from tanning industries and mercury from power plants lead to their deposition in the environment. In addition to these pollutants, complex industrial chemicals like dyes and pharmaceutical by-products have added to the degradation of the environment globally.

Global mercury emissions from anthropogenic sources

The figure shows a total of mercuric emissions of 2150 tonnes in 2013-2015. The source of these emissions are majorly mercury production, gold mining, oil refining, cement production, combustion of oil, gas and coal and steel production. Majority of the emissions occurred in Asia, Sub-Sahara and South America regions, which accounted for more than 50% of the total emissions  (Source: United Nations Environment 2015).

Along with harmful health effects and impact on various organisms, the major consequence of environmental pollution is degradation of natural resources. This includes threat to clean air, water, soil for agriculture, consumption and biodiversity. For a long time, the ill effects of different pollutants on humans has been known, yet its curb or mitigation has been difficult and expensive. Consequently, rising human populations meant increasing industrialisation, such that economic and financial development has a significant negative effect on the environment (Tamazian & Rao, 2010). Mounting proof of climate change and its consequences on natural meteorological processes has added pressure on governments to address environmental pollution and draw up stricter policies for a long term mitigation.

Common microbial processes to remediate different classes of pollutants

Biological treatment systems that are used for remediation vary in the ability to treat or remove pollutants and maintain the system under changing environmental conditions (Gentile, 2004). The ability and stability of such biological treatment systems depends upon the community structure and the dynamics between them. Such biological systems are also expected to completely degrade the pollutant, thereby removing its traces and residues to stabilize the environment  (Akhtar, Chali, & Azam, 2013) .

Microbial remediation has shown significant potential in mitigating a wide range of pollutants, in a much more efficient and safe manner. Bioremediation processes can be undertaken using different types of organisms, like bacteria and archaea (microbial remediation), fungi (Phycoremediation), algae (Mycoremeidation) and plants (Phytoremediation). Of these, micro bioremediation has certain advantages over others:

    • versatility in terms of metabolising a wide range of polluting compounds,
    • ease of application and minimum disruption of contaminated site and
    • applicable under different environmental conditions.

One successful example of application of bioremediation is ‘OilZapper’. It is a patented microbial consortium capable of degrading oil and was applied during large scale cleanup of Mumbai oil spill in 2010 (Maharashtra Pollution Control Board, 2010).

As seen from the review of different processes under microbio remediation 6 types of processes show varying behaviours in  desirable size of contamination area, extent of human involvement and cost of operations. In this study, the diversity of microbes involved and their modes of action in bioremediation of specific pollutants has been studied. Overall, irrespective of cellular compounds involved, microbes achieve bioremediation through one or more processes.

Common microbial processes involved in Bioremediation

Common microbial processes involved in Bioremediation

Along with microbial remediation different pollutants were also studied simultaneously. While reviewing literature on pollutants, 6 classes were determined depending upon their chemical nature. Organic (nitrogen or phosphorous) and municipal waste is not included in the study. Microbial remediation of organic and municipal waste has been extensively studied and a myriad of technologies exists.

Global distribution of plastics post production

Global fate of plastic materials during the cycle of consumption, collection, reuse and disposal. In 2013 from a total 78.4 mn tonnes produced, apprximatly 77.5 mn tonnes was used, of which majority was collected (53 mn tonnes) while the rest was leaked or lost to the environment. Of the collected plastic, only a small fraction (20.8%) was recycled and majority was dumped into landfills (58.8%) (Source: World Economic Forum et al. 2016).

Studies on microbial remediation of polyaromatic hydrocarbons, crude oil and marine plastic  showed that release of these pollutants in the oceans on a large scale has directly influenced the microbial community. Subsequently, such interactions lead to selection or adaption of microbes capable of using xenobiotic compounds as substrates.  Heavy metals, lead, mercury, chromium, and arsenic, showed varying distribution in soil and ground water as toxic compounds. It posed a series of health hazards, because of which it was important to study the remediation process. A wide range of microbial processes can mineralise, immobilise and reduce toxic heavy metals to harmless non toxic forms. Microbes also showed remediation capabilities towards Uranium by reducing U(VI) to U(IV) through biosorption, precipitation and enzymatic degradation.

Lastly, microbial processes associated with two industrial pollutants, both of which are continuously released in large quantities into the environment; textile dyes (azo compounds) and pharmaceutical pollutants also showed unique properties.

Limitations of microbial remediation

Although microbial processes are able to use a plethora of compounds as their source of metabolism, prove to be costly in designing, implementating and maintaining. Arguably, the biggest limiting factor of microbial remediation is the highly specific inherent nature of their metabolic processes. Therefore, for favourable remediation to occur, the environmental factors have to be suitable and appropriate levels of nutrients or contaminants as a source of energy have to be present for the microbial populations to be synergistic (Vidali, 2001).

Moreover, natural bioremediation processes take a long time to effectively remove the contaminants. Introduction of appropriate foreign microbes capable of faster remediation have met with ethical and regulatory hurdles. This is justified since introducing foreign microbes can have unimaginable consequences to the immediate environment and the ecological diversity of the habitat. Moreover, microbial genetically modified organisms (GMO) can be unstable and may even evolve by exchanging genes, thereby influencing the naturally existing microbes of the site (Wozniak, McClung, Gagliardi, Segal, & Matthews, 2012). GMO have traditionally been associated with crops, which have been facing increasing regulatory hurdles in several nations. As of 2016, 28 countries allow growing GMO crops, while few like Canada, China and Japan, allow GMO cultivation only if they meet regulatory standards. However, 38 countries have banned the cultivation of GMO, although they allow import of GMO based products, crops and food (Genetic Literacy Project, 2017). The table below provides the list of countries that have banned GMO cultivation.

Algeria Ecuador Madagascar Serbia
Austria France Malta Slovenia
Azerbaijan Germany Moldova Switzerland
Belize Greece Netherlands Turkey
Bhutan Hungary Northern Ireland, Scotland, Wales Ukraine
Bosnia and Herzegovina Italy Norway Venezuela
Bulgaria Kyrgyzstan Peru Belgium (Wollonian Region only)
Croatia Latvia Poland
Cyprus Lithuania Russia
Denmark Luxembourg Saudi Arabia

Countries that have banned GMO crops (Source : Genetic Literacy Project, (2017))

In case of microbes based remediation, India is the only country that has commercialised and patented a microbe based bioremediation product known as the ‘OilZapper’.

OilZapper is developed by The Energy and Research Institute (TERI) with Oil and Natural Gas Corporation Limited (ONGC). This product is used to clean up beaches and farmlands polluted with crude oil. It is used by major oil companies in India, Kuwait and Abu Dhabi (Datta, 2010).



A change in direction from microbes to plants

Literature on microbial remediation processes that discussed their efficacies also showed several limitations in adopting it as a technology. Especially relevant is the example of oil degradation, the problems of complex chemical nature and presence of recalcitrant compounds proved a challenge for microbes to effectively break the pollutant. In case of plastics, which are also hydrocarbons, the inherent recalcitrant nature itself was found to be the main limitation for a successful degradation of the pollutant.  Furthermore, bioremediation of heavy metals, such as Lead and Arsenic, has a common limitation of inability to completely separate the non-toxic residues from the environment. But in case of industrial pollutants like textile dyes, bioremediation is slow in nature and the bioreactor effluents cannot be directly disposed off into the environment. Considering these limitations it is clear that while the microbes show high potential in remediating a wide range of pollutants, they suffer from problem of offering a stable and reliable system of remediation.

From microbes to plants in bio remediation (Source: Oregon State, 2013)

From microbes to plants in bio remediation (Source: Oregon State, 2013)

Based on the review of microbial remediation processes, it was expected that different cellular processes would be compared for an advantageous microbial system for future use. However, microbes as a remediation system were found to showcase several limitations. Considering the metabolic potential possessed by microbes, it was more desirable to combine them with a stable system, similar to the inherent system of plants. It can be achieved by genetic engineering, a technique by which the genetic information from one organism can be transferred to another (Ermak, 2015). Therefore, it is possible to express desirable metabolic or enzymatic processes found in microbes in suitable plants, depending upon the contaminant (Yadav, Arora, Kumar, & Chaudhury, 2010).

In this context, plants offer cheaper, safer and cleaner technology for remediation. Additionally, plants are also capable of cleaning up polluted air (CO2, NOx, ozone, soot particles), water (municipal, industrial and agricultural wastewater) and soil (agricultural fields, industrial and military sites) (Pilon-Smits, 2005). Plants as a system offer several advantages, owing to their dense root systems, large biomass, beneficial rhizosphere and inherent metabolic potential in degrading several organic & inorganic compounds (Pilon-Smits, 2005).  Moreover, they are also economically feasible and show widespread pollution degrading capacity. (Tangahu et al., 2011).

Scope of Phytoremediation in mitigating large scale pollutants

Phytoremediation like microbial remediation is an established technique in removing environmental contaminants using appropriate plants (Yadav et al., 2010).

Phytoremediation process (Source: Parmar and Singh, 2015)

Phytoremediation process (Source: Parmar and Singh, 2015)

These plants undertake successful removal of contaminants from soil, water and air through several processes such as:

  • Rhizofiltration: Rhizosphere filters out the pollutants from soil.
  • Rhizodegradation or Phytostimulation: Rhizosphere microbes degrade the pollutants.
  • Phytoextraction: Pollutants are accumulated into plant tissues.
  • Phytostabilization: Preventing downward leaching of pollutants or converting them to less bioavailabe forms.
  • Phytovolatilization: Post uptake of pollutants from environment, plants can convert them to volatile form.
  • Phytodegradation: Plants breakdown pollutants using tissue enzymes.

Plants have proven to be useful in remediating pollutants from the environment.

Pollutant Class Pollutants Plant
Organic Compounds (Trapp & Karlson, 2001) Polynuclear aromatic hydrocarbons (PAHs), Polychlorinated biphenyls (PCBs), explosives Poplars, Basket Willows, Balsam Poplars
Heavy Metals (Eapen & D’Souza, 2005) Cadmium, Lead, Mercury, Arsenic, Selenium Populus deltoids, Arabidopsis thaliana, Tobacco plant, Liriodendron tulipifera
Radioactive compounds (Ibrahim, Adrees, Rashid, Raza, & Abbas, 2015) Cesium, Strontium, Radon, Uranium Water hyacinth, Melilotus, Sorghum, Trifolium, Polytrichum, Festuca, Carex, Vitis, Helianthus, Pisum, Beta

Considering the potential showcased by plants to carry out remediation of common pollutants, it could be used to mitigate the limitations of microbial remediation processes. Moreover, the regulatory hurdles on microbial remediation technologies for patenting and commercialisation can be avoided. The risk in the form of ‘gene flow’ from Phytoremediating plant species to its relatives through cross-pollination in the ecosystem is low. Such gene flow is contained or mitigated by molecular mechanisms by targeting chloroplast or mitochondrial genome, male sterility and seed sterility, among others (Mackova, Dowling, & Macek, 2006).

Bridging the gap between microbial remediation and Phytoremediation

Genetic Engineering defined as the manipulation and introduction of manipulated DNA material into a cell (Gupta, 2008). It can be used to bridge the gap between microbial and plant remediation processes by combining the advantages of both the systems into a single efficient system. Based on the review and comparative analysis of genes and proteins contributing to Phytoremediation in plants the next attempt will be to accomplish:

  • Limitations of microbial remediation by exploring the potential of Phytoremediation.
  • Establish the efficiency of Phytoremediation in remediation of common pollutants.
  • Comparison between microbial and plant remediation processes with respect to their efficiencies and limitations.

Therefore, based on the findings a consensus would be reached with respect to their efficiencies and limitations on:

  1. Efficiency of remediation
  2. Limitations of both the systems

Consequently, this will shed light on how phytoremediation can change the field of environment pollution control with efficiency and overcoming limitations in combination with bioremediation to produce useful by-product.


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Chandrika Kapagunta

Chandrika Kapagunta

Research Analyst at Project Guru
Chandrika is a nature enthusiast with special love for the marine world. Her Master’s degree in Marine Biotechnology and Scuba Diving experience has made her a strong advocate of environment and marine conservation, especially through bioremediation. She believes in finding solutions of everyday human problems in nature, be it medicines, technology or philosophy. Having worked as a volunteer at The Bombay Natural History Society and as a Senior Research Fellow at Central Institute of Fisheries Education, she has had exposure to the current state of the academic research, specifically in the field of environmental biotechnology.
Chandrika Kapagunta

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