Biodegradation of Xenobiotic Compounds

Anthropogenic inorganic and organic pollutants are discrete throughout the atmosphere and in different spheres of the atmosphere, which tend to transform into another compound that may be toxic, less toxic and not toxic to flora and fauna. Xenobiotics are man-made or artificial compounds present in the ecosystem. Xenobiotics cannot be recognized by the naturally occurring microbes and therefore do not enter the common metabolic pathway. The main degrading microbes are bacteria and fungi. The selection of xenobiotics degrading bacteria and their adaptation to the xenobiotic contaminated environment is the key factor for detoxification of the environment. Xenobiotics gain entry into the ecosystem by i) pharmaceutical industry ii) chemical industry iii) bleaching and paper industry, which expels chlorinated organic compounds into the ecosystem iv) mining industry, and v) intensive agriculture (synthetic fertilizers, herbicides, and pesticides). Mostly bacillus is involved in the degradation processes, namely Actinomycetes, Pseudomonas, Nocardia, Klebsiella, Azotobacter and Flavobacterium, and fungi species such as Candida, Thielavia, Penicillium, Thermomyces and Ganoderma. Microbes possess the ability to degrade polycyclic aromatic hydrocarbons (PAHs), which are a persistent constituent of petrochemical wastes, organonitrogen compounds such as nitrotoluenes and chlorinated compounds like pentachlorophenol, polychlorinated biphenyl, and chlorinated dioxin-like compounds. A single bacterium can have the ability to degrade one or more compounds; it may also possess specialized enzymes and metabolic pathways such as chlorobiphenyls and chlorobenzenes (Singh 2017). The most common pathway involved in the degradation of polyaromatic compounds is the /i-ketoadipate pathway, which provides utilization of primary substrates which is present in both bacteria and fungi. Primary substrates are converted into protocatechuic acid catechols; finally, the end products obtained by this pathway are two aliphatic products such as succinate and acetyl-Co A (Ghosal et al. 2016).

Biodegradation of Plastics

Plastic is one of the recalcitrant compounds present in the ecosystem as it comprises of 80% of plastics found in agricultural land, landfills and water bodies (Rummel et al. 2017). Microorganisms can degrade plastics through the production of enzymes by degrading the long polymers, further these degraded polymers act as carbon and energy sources of microbes Enzymes produced by the microorganisms act on polyethylene terephthalate (PET) and polyurethane (PUR). Enzyme PETase produced by the microorganism’s hydrolyze the plastic into monomers (Danso et al. 2019). There is a wide range of plastics to be degraded; fungi, which could degrade PHB polyesters, are Fusarium, Penicillium, Cryptococcus, Aspergillus, and Rhizopus. Polyethylene adipate is biodegraded by Penicillum and Aspergillus. PLA (polylactic acid) is degraded by Tritirachium album and Penicillum roqueforti (Ghosh et al. 2013). Aspergillus niger has the ability to degrade plastics made up of polyvinyl alcohol (MogiTnitskii et al. 1987). Styrene degradation is observed in Pseudomonas, Xanthobacter, Rhodococcus and Corynebacterium (Danso et al. 2019).

Aerobic Degradation

In aerobic degradation, oxygen is supplemented to the soil to increase the vitality of the indigenous bacterial strains as it is considered to be the growth limiting factor for the bacterial strains, which could degrade hydrocarbon. By adding dissolved oxygen, biodegradation is accelerated up to 10-100 times. Dissolved oxygen, which is obtained from the natural sources, gets exhausted quickly in the presence of petroleum hydrocarbons; thus, it is untreated and oxygen depleted aquifers are slow. Low to moderate levels of contaminants can be treated. The most commonly treated compounds are BTEX, PAHs, TPH, MTBE and TBA (McGregor and Vakili 2019). In cellular respiration, oxygen gets oxidized to sugars and fats to obtain energy. Prior to this process, the glucose molecules get broken into small molecules, which enter mitochondria to take part in aerobic respiration. With the help of oxygen, the small molecules are broken down into water, C02 and energy (polimernet.com). Bacteria that are involved in degradation are various species of Pesudomonas, Rhodococcus, Mycobacterium, Burkhelderia and Alcaligens eutrophus (Srivastava and Kumar 2019).

Anaerobic Degradation

Anaerobic degradation takes place in the absence of oxygen and, more predominantly, when anaerobes are dominant over aerobes. Landfill biodegradation takes in the anaerobic condition through the digestion process. This is majorly used in the wastewater treatment of sludge as it reduces the large volume of input material. It reduces the risk of landfill gas getting emitted into the environment. It produces fertilizers and renewable energy such as methane and C02, which can be utilized for the production of biogas. Bacteria hydrolyze to produce carbohydrates to utilize them as a food source. Acetogenic bacteria are a group of bacteria that can convert proteins (amino acids) into hydrogen, ammonia, carbon dioxide, and organic acid; further, it is converted into acetic acid. Methanogens are a group of bacteria that can produce methane and C02 utilizing the products obtained from acetogenins. E. coli can take part in aerobic, anaerobic and fermentative respiration using fumarate and nitrites as electron acceptors (Sims and Kanissery 2019).


Soil pollution is a threat around the globe, which leads to human illness, soil infertility, crop productivity, biodiversity misshape and loss of natural resources. Plants are involved in cleaning up pollutants from the environment by an association with rhizospheric microbes, which is termed as phytoremediation. It is an environmentally friendly technique that provides a sustainable outcome. It can be applied to small to large contaminated sites for phytoremediation of the soil (Pandey et al. 2019). The high concentration of heavy metals was first found to be accumulated in the leaves of Viola calaminaria and Thlaspi caerulescens (Baumann 1885). Fragrant flowers that are inedible and which can tolerate stress conditions are used in phytoremediation as they do not possess a vegetative body that could affect the food chain, which belongs to the families of Lamiaceae, Geraniaceae, Poaceae, and Asteraceae. It is mostly used in industries that manufacture perfumes, cosmetics, toiletries and insect repellents (Pandey and Singh 2015). Calamagrostis epigejos, which is an aromatic wild grass of Serbia, is used in in situ phytoremediation of fly ash (Mitrovic et al. 2008); in India, Cynodon dactylon and Vetriveria zizanioides are used to phytoremediate the heavy metals (Pandey et al. 2015, Das et al. 2013). In mining, contaminated soil Cymbopogon flexuosus and Vetriveria zizanioides are used in the phytoremediation technique (Srivastava et al. 2014). V. zianioides is used in the phytoremediation of asbestos mining waste dumps (Kumar and Maiti 2015). Lavandula vera is used for phytoremediation of heavy metals like lead, cadmium and zinc (Angelova et al. 2015).

Mechanism of Phytoremediation Process

The mechanism of phytoremediation was reported in PAH, pesticides, toluene, PCB, and benzene in various ways such as the interaction of microbes in association with the rhizosphere, phytodegradation, and phytoremediation of organic pollutants in the root region (Stephenson and Black 2014). In phytoremediation, the pollutants are reduced, catabolized and converted into less toxic form. It is well illustrated by “green liver model”, which explains how the process of phytoremediation takes place with the help of enzymes at molecular level, but still it is a research subject which is used to understand the xenobiotics transformation and manipulation (Sandermann 1994). Since the last decade, phytoremediation is a hot topic and its molecular and biological mechanisms and the various strategies used in improving phytoremediation with relevance to engineering techniques are still under research. Phytoremediation is not a new technique, it is an upcoming technique.

Types of Phytoremediation

In general, phytoremediation includes six methods: phytoextraction, phytostabilization, phytodegradation, phytovolatilizationan, and rhizoremediation. It is a new technique which is very cost effective in remediating the areas which are contaminated into less toxic form. Figure 2 shows different pytoremediation that takes place in the plant.

Types of phytoremediation (Adapted from Kushwaha et al. 2015)

Figure 2 Types of phytoremediation (Adapted from Kushwaha et al. 2015).


Phytosequestration is also termed as phytostabilization. In this process, the remediation takes place in the root surface or plant exudates are formed, which get released into the root which is present closer and the contaminants get sequestered, immobilized or precipitated. Plant varieties that are tolerant of metal can be used to decrease the contaminations. This technique is suitable for the remediation of cadmium, zinc, chromium, copper, and arsenic. In extremely acidic metal contaminated soil, it has been investigated that using perennial ryegrass (folium perenne), soil heavy metals can be sequestered. The plant which is chosen for phytosequestration must possess tolerance against contaminants, high ability of root biomass and high retention root capacity. The most common species used are Juncus sps., Lavandula luisierra and Rumex induratus (Anawar et al. 2011).


Phytoextraction or immobilization is employed to remove heavy metal contamination from the soil. These biological techniques have fewer side effects than physical and chemical techniques. It is the main and most promising technique as both in situ or ex situ treatment for the removal of contaminated soils, sediments, and water. It is best suitable for the removal of hydrocarbons, heavy metals, and radionuclides. The characteristics of a plant that is chosen for phytoextraction includes the ability of high accumulation of contaminants, high biomass, and high growth rate. Also, hyperaccumulators like Thlaspi caerulescens (Brassicaceae family), Pteris vittata, Noccaea caerulescens and Arabidopsis halleri accumulate heavy metals effectively (Panesar et al. 2019). Phytoextraction is predominantly used to remove the heavy metal contaminations.

It is reported that Sedimi alfredii and Alyssum bertolonii can accumulate high levels of cadimum and nickel (Deng et al. 2007, Kramer 2010).


Plants that are involved in phytovolatilization can absorb the volatile compounds via their roots and transpire it on the metabolites produced via their leaves. Poplar trees have been shown to volatilize 90% of TCE from the roots. Heavy metals are reported to be volatilized into gas form by Arabidopsis thaliana and Brassica juncea (Ghosh and Singh 2005). The most common plants used in phytovolatilization are Salix and Popuhis.


Phytodegradation is used for the degradation of contaminants in the soil and underground water. This process doesn’t need microorganisms and it is the most advantageous aspect of this method. Plant tissue takes up the contaminants present in the soil. It gets metabolized (using enzymes) or biotransformed. It can occur in any part of the plant such as stem, root, and leaves. It is used to degrade insecticides, PCBs and herbicides. Cannas can detoxify xenobiotics (Solanki et al. 2018).


In rhizodegradation, the hydrocarbon are broken down by the microorganisms present in the root. Secondary metabolites are produced which aid in the breakdown of contaminants present in the soil. Rhizodegradation is employed to degrade TCE, TCA, PAH, BTEX, insecticides, PCB, toulene and PCP (Aybar et al. 2015). The common plants used in rhizodegradation are Typha latifolia, Medicago sativa and Moms rubra (Panesar et al. 2019).


Contaminants hold on tightly to the roots of the plants or get absorbed in the root in the rhizofiltration method. This method is effectively used to remove radionuclides present in the groundwater and wastewater contaminations. It can also be used to remove heavy metals like copper, zinc, lead, and chromium from the soil. Sunflower is reported to rhizofiltrate radioactive compounds (Panesar et al. 2019). Apart from plants, bacteria can also be used in the removal of selenium such as Stenotroph onion as maltophilia and Bacillus mycoides (Vallini et al. 2005).

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