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The Degradation of Organic and Inorganic Pollutants

Chapter · July 2021

DOI: 10.1201/9781003131427-11


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4 authors:

Mahdieh Houshani Sarieh Tarigholizadeh

University of Tabriz University of Tabriz


Vishnu D. Rajput Hanuman Singh Jatav

Southern Federal University Sri Karan Narendra Agriculture University, Jobner Jaipur


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11 The Degradation
of Organic and
Inorganic Pollutants
Mahdieh Houshani, Sarieh Tarigholizadeh,
Vishnu D. Rajput and Hanuman Singh Jatav

11.1 Introduction�������������������������������������������������������������������������������������������������� 134
11.2 Sources of Soil Pollutants���������������������������������������������������������������������������� 134
11.2.1 Industrial Activities�������������������������������������������������������������������������� 135 Mining and Smelting��������������������������������������������������������� 135
11.2.2 Waste and Sewage Disposal������������������������������������������������������������� 136
11.2.3 Military Activities����������������������������������������������������������������������������� 136
11.2.4 Intensive Agricultural Activities������������������������������������������������������� 136
11.2.5 Road and Transport Infrastructures�������������������������������������������������� 137
11.3 Phytoremediation Processes������������������������������������������������������������������������� 137
11.4 Organic Pollutants���������������������������������������������������������������������������������������� 140
11.4.1 Uptake, Translocation, and Accumulation of Organic Pollutants���� 140
11.4.2 Degradation of Organic Pollutants��������������������������������������������������� 141 Microbial Degradation������������������������������������������������������ 141  Polycyclic Aromatic Hydrocarbons
(PAHs)����������������������������������������������������������� 142  Aliphatic Hydrocarbons�������������������������������� 142 Pesticides������������������������������������������������������� 144 Phytodegradation��������������������������������������������������������������� 144
11.5 Inorganic Pollutants�������������������������������������������������������������������������������������� 145
11.5.1 Uptake and Sequestration of Inorganic Pollutants��������������������������� 145
11.5.2 Plant Response to Inorganic Pollutants�������������������������������������������� 146 Phytostabilization�������������������������������������������������������������� 146 Phytoextraction����������������������������������������������������������������� 146 Phytovolatization��������������������������������������������������������������� 148
11.6 Future Prospects������������������������������������������������������������������������������������������� 148
11.7 Conclusion���������������������������������������������������������������������������������������������������� 148

134 Basic Concepts in Environmental Biotechnology

The industrial and urban wastes produced by anthropogenic activities are one of
the critical environmental concerns. Different organic and inorganic pollutants are
severely polluting the world’s soil and water resources, causing deterioration of both
soil and food quality. These include polycyclic aromatic hydrocarbons (PAHs), pes-
ticides, polychlorinated biphenyls (PCBs), explosives, metals, metalloids, and radio-
nuclides. These pollutants are mutagens and carcinogens, which are present almost
everywhere in the environment. Great attention is owed to them due to their pres-
ence in high concentrations, persistence in the environment, and long-­term toxic-
ity. Human and wildlife exposure to such persistent and toxic compounds occurs
because of bioaccumulation in plants, which subsequently transfers to the natural
and agricultural food chain.
Various physical and chemical approaches have been employed for the elimina-
tion of these pollutants from the environment. However, these techniques are mainly
expensive, are energy consuming, and may create toxic products which contrib-
ute to secondary pollution in the environment. The use of biological approaches
for removing toxic pollutants has received increasing attention because of their
economic viability. Accordingly, developing new remediation technologies can be
environmentally compatible and inexpensive compared to dangerous and expensive
engineering-­based remediation technologies. Bioremediation uses living organisms
to improve and treat contaminated sites. The bioremediation agents include bacteria,
fungi, and higher plants with the capability of decamping pollutants with the help of
a natural biological activity.
However, as an alternative approach, phytoremediation has emerged as the most
desirable technology for the elimination of environmental pollutants. This approach
employs plants to degrade and eliminate organic and inorganic contaminants from
polluted soil, water, and sediment. Plant-­based methods are based on multiple pro-
cesses such as metabolism, volatilization, and sequestration, followed by harvest.
The compounds/enzymes produced by plants facilitate the breakdown of pollutants
and activate microbial biodegradation in the rhizosphere. Phytoremediation uses
resistant and hyperaccumulator plants to degrade, transform, translocate, extract,
and detoxify organic and inorganic pollutants present in the soil. This approach has
been successfully implemented in the bioremediation of various pollutants including
PAHs, radionuclides, metals/metalloids, pesticides, and PCBs.
However, there is a profound gap of knowledge about the degradation, detoxifica-
tion, and elimination of pollutants by higher plants. Accordingly, this study aims to
discuss their uptake mechanisms and recent progress in the understanding of deg-
radation, detoxification, and removal of organic and inorganic pollutants by plants.
It is essential to understand the primary sources of contaminants and their possible
concentration in soils (Table 11.1).


There are two main sources of soil pollutants: natural and anthropogenic. Natural
events leading to the accumulation of pollutants into the environment can be volcanic
The Degradation of Pollutants 135

eruptions, geographical alterations, forest fires, earthquakes, soil degradation, air

pollution, and changes in rainfall patterns. Over centuries, anthropogenic activities
(intentional or accidental) have been causing widespread pollution in soils along
with natural processes. The primary intentional anthropogenic sources of soil pol-
lution are fossil fuel combustion, industries, fertilizer and pesticide application, land
application of sewage sludge, disposal of wastes, irrigation with untreated wastewa-
ter, smelting, mining, sport shooting, application of agrochemicals and sewage, and
military training. Leaching or spills from landfills, nuclear explosions, and flooding
by rivers or seas are examples of accidental emission of pollutants into the eco-
system. Soil pollution can also contribute to air pollution via emission of volatile
compounds into the atmosphere and water contamination via leaching chemicals
into groundwater or reaching to lakes, seas, and oceans. Some of the main human-­
caused reasons for soil pollution, including industrial, agricultural, and municipal
are discussed next.

11.2.1 Industrial Activities
Industrial activities release pollutants into the environment in forms of gas, liquid,
or solid. The most important gaseous pollutants, such as carbon dioxide (CO2), car-
bon monoxide (CO), sulphur dioxide (SO2), and nitrogen dioxide (NO2), released
into the atmosphere can readily enter into soils via wet or dry deposition of par-
ticles or washing out by acid rain. Direct discharge and incorrect chemical storage
of some chemicals (such as fly ash, sawdust, plastics, and sludge) and garbage
(e.g. wood, glass, and metals) can contaminate or cause physicochemical changes
in soils, rivers, lakes, and oceans. Industrial wastes can be categorized into sev-
eral groups, including mining wastes, smelting, chemical wastes, and solid wastes.
These activities cause diffusion of organic pollutants (such as PAHs) and toxic
heavy metals (HMs) into the soil. Mining and Smelting

Mining operations (including metal smelting) is one of the major sources of toxic
elements. In every stage of mining activity, vast amounts of chemicals, including
HMs (e.g. Cu, Pb, Zn, etc.), can be released into the environment. Many documented
examples can be found for heavily contaminated soils associated with mining activi-
ties around the world. Though mining operations are limited to smaller areas, the
consequences of its related activities (smelting operations, tailings, etc.) have major
impacts on the environment. Extraction, the processing of mineral ores, and the
blowing of tailing particles (a waste product and a large part of ore known as tail-
ings) as well as acid mine drainage are the most harmful activities. These can cover
the topsoil layer of lands in and around the area and spoil natural resources. Tailings
usually contain different undesired substances. They can contain a mixture of water,
any residual chemicals applied in processing stages such as cyanide, xanthates, and
other flotation agents, surfactants and sulfuric acid, and finely ground ore. Tailings
may also contain HMs (As, Hg, Cu, Pb, Cd, Se, Zn, and Ni) that can create environ-
mental concerns as well as sulphides due to the natural composition of the ore. The
136 Basic Concepts in Environmental Biotechnology

mining of gold creates severe environmental pollution due to the emission of very
lethal substances such as Hg, As, and cyanide.

11.2.2 Waste and Sewage Disposal

Together with mining activities, waste disposal is one of the oldest sources of con-
tamination. The problem associated with sewage disposal has become a major con-
cern, and the overall waste generation will rise drastically to 3.40 billion metric tons
per year by 2050. The most common ways to manage waste are incineration and
landfilling/open dumping. Both processes release many toxic chemical substances,
such as HMs (Hg, Pb, Cd, Cr, etc.), PAHs, polybrominated biphenyls (PBBs), poly-
brominated diphenyl ethers (PBDEs), and PCBs. The landfill leachates contaminate
soil and underground water. The ash fallout from incineration can change the qual-
ity of groundwater and subsequently the food chain. Nowadays, the fastest-­growing
category of solid waste is known as electronic waste (e-­waste), which contains valu-
able elements, such as Cu and Au. However, inappropriately recycled e-­wastes can
become a source of the aforementioned hazardous substances. Other approaches
for waste and sludge disposal include establishments for recycling of lead batteries,
application of untreated sewage sludge in soil amendments, dumping and incinera-
tion of biodegradable and non-­biodegradable domestic and urban wastes.

11.2.3 Military Activities
Conflicts and related military activities are ever-­present forces which can over-
whelmingly impact and alter the nature of adjacent soils as well as water resources.
This type of pollution source differs remarkably from other types, such as waste
depositories, industrial activities, and so on owing to the intensity of activities.
These activities include direct armed conflict, military training and related produc-
tion of chemical and metals contamination, rocket launching, blasting and armament
destruction, projectile and mortar fire impact, and nuclear warfare, which commonly
use hazardous substances, for example trace or radioactive elements for weapons.
Previously, conflicts were limited to local areas, resulting in pollution of small mag-
nitude. However, since the 20th century, modern conflicts utilize non-­degradable
weapons of mass destruction, and the chemicals remain in the area for centuries
after the end of the war. For instance, the devastating world wars not only caused
destruction, death, and significant detrimental effects at the time of their incidence
but also threatened the environment around the world with such leftovers as mines
and unexploded ordnance (UXO). There are few studies on these type of pollutants,
most likely due to restrictions imposed by governments related to security reasons.

11.2.4 Intensive Agricultural Activities

Intensive agriculture is a major cause of local and diffuse contamination, which
releases massive amounts of pesticides and excessive chemical fertilizers. Despite
their potential benefit for agriculture, it has been demonstrated that using exces-
sive agrochemicals can alter the physical-­chemical character of agricultural soils
The Degradation of Pollutants 137

and make them infertile. Compounds such as PAHs and Pb, As, and Hg accumu-
late permanently in soils and subsequently influence the metabolism of plants. They
also influence the productivity of soil as well as the native microflora and hence
human health too. Another source for agricultural pollutants can be accidental spills
of hydrocarbons used as fuels for machines and improper management of livestock
production, which can result in the disposition of urine and faeces, leading to soil

11.2.5 Road and Transport Infrastructures

The major sources of soil pollution associated with transport include combustion
processes, the wearing of vehicles (engine, tires, brakes), road surface degradation,
and the leaking of oil and coolants. The chemicals involved in road maintenance
(de-­icing salts) disseminate pollutants, as do splashes generated by traffic during
rainfall events, which also spreads specific polluting substances such as HMs, PAHs,
and mineral oil into the environment. Moreover, all other sorts of organic and inor-
ganic materials which fall from vehicles or originate from car accidents can also
contaminate soils. The soil contamination that originated from these activities is
higher in urban than in rural areas. Mainly, Pb and PAHs originate from combustion
processes. It seems that most of the heavy metals have mixed origins. However, Zn
and Cu are reported to have mainly come from tire dust and the corrosion of radia-
tors and brakes, respectively. Cu and Mn are used in automotive engines and piping.
Also, Cr and Ni are derived from the combustion of lubricating oils and also are used
in chrome plating. Surprisingly, the soil pollution caused by transportation activities
has received little attention in comparison with other types of activities.

In recent years, the increase of pollutants in the environment has attracted a great deal
of attention. The elimination of pollutants from a contaminated environment through
biological resources seems to be an outstanding alternative. Phytoremediation or
plant-­assisted bioremediation means the use of plants to remove toxic inorganic and
organic environmental pollutants presented in a solid and liquid substrate. Generally,
phytoremediation of pollutants by a plant includes uptake, translocation, transfor-
mation, compartmentalization, and sometimes mineralization. Various mechanisms
such as rhizoremediation, phytoextraction, phytostabilization, phytovolatilization,
and phytodegradation are employed by plants to remove or degrade soil pollutants
(Figure 11.1). Such mechanisms are used for the effective elimination of wastes such
as phenolic compounds, metals, azo dyes, colourants, and various other organic and
inorganic pollutants.
Organic pollutants are chiefly degraded by two mechanisms: phytodegradation
or phytotransformation and rhizoremediation, whereas the degradation of inorganic
pollutants is based on phytoextraction and phytostabilization. The approach known
as rhizodegradatio/phytostimulation defines enhanced microbial degradation of con-
taminants in the root zone due to the exudates secreted by plant roots. The pollutant,
in some cases, is immobilized in the root zone, which is known as phytostabilization.

TABLE 11.1 
Concentrations of Organic and Inorganic Pollutants in Soil from Cities around the World
Pollutants Source(s) Location(s) Concentration References
Organic PAHs Agriculture; diffuse pollution; China (Hong Kong) 30–170 Aichner et al., 2007; Banger et al.,
industrial and traffic/vehicle China (Shanghai) 83–7220 2010; Baumard et al., 1998; Kumar
emissions USA (Miami, Florida) 251–2364 & Kothiyal, 2011; Morillo et al.,
Spain (Seville) 89.5–4004 2008; Trapido, 1999; Vane et al.,
France (Arcachon Bay) 32–4120 2014; Wang et al., 2013; Zhang
UK (Greater London) 67,000 et al., 2006
India (Jalandhar, Punjab) 4040–16,380
Nepal (Kathmandu) 184–10,279
PCBs Burning of old appliances; France (Seine River basin) 0.09–150 Aichner et al., 2007; Martinez et al.,
electrical products; urban Nigeria (Lagos) 3.6–23.6 2012; Motelay-­Massei et al., 2004;
water runoff; industrial/ China (Beijing) 11 Rose et al., 2013; Wu et al., 2011;
commercial activities, spills, Nepal (Kathmandu) 0.4–447 Vane et al., 2014
and disposal UK (Greater London) 123
USA (Cedar Rapids, Iowa) 56–160
Pesticides (e.g. Agriculture China (Tianjin) (DDT) 628–2841 Gong et al., 2002; Kannan et al.,
DDT, HCN, China (Tianjin) (HCN) 387–4689 2003; Babu et al., 2003
AMPA) USA (Southern California) (DDT) 0.11–45
USA (Southern California) (HCN) 0.1–0.54
India (DDT) 122–638
India (HCN) 13–238
Dioxin-­like PCBs Industrial activity Brazil (Belo Horizonte-­MG) 0.04–0.93 Pussente et al., 2017
Basic Concepts in Environmental Biotechnology
Inorganic Zn Wastewater China (Beijing) 157 Abdu et al., 2011; Khan et al., 2008
(e.g. West Africa (Kano, Bobo-­Dioulasso 167
some and Sikasso)
HMs) Pb Digested sludge; industrial China (Tianjin & Beijing) 41.5–49 Khan et al., 2008; Meng et al., 2016;
effluents; fertilizer and sewage USA 140–5210 Qishlaqi et al., 2008; Sterrett et al.,
sludge; wastewater Iran (Shiraz suburban) 412 1996; Wong, 1985
India (Gujarat) 46
China (Hong Kong) 33
Cu Digested sludge; pig manure China (Beijing) 33 Akoto et al., 2015; Khan et al., 2008;
compost; wastewater China (Hong Kong) 52–105 Wong, 1985
Ghana (Kumasi) 7.4
The Degradation of Pollutants

Cd Fertilizer and sewage sludge, USA 3–10 Abedi-­Koupai et al., 2015; Baker
wastewater Iran (Isfahan) 6 et al., 1979; Sterrett et al., 1996;
India (Gujarat) 19.3 Tiwari et al., 2011
140 Basic Concepts in Environmental Biotechnology

Phytoextraction means to accumulate pollutants in harvestable plant tissues, espe-

cially shoot tissues, and this approach is notably utilized for inorganic pollutants.
In some cases, plants can degrade pollutants inside their tissues, and this method
is called phytodegradation and is mostly suitable for organic pollutants since inor-
ganic pollutants can only be moved and not degraded. Plants can also volatilize some
pollutants, and the process is known as phytovolatilization. This method is used to
volatilize organic compounds and specific metal such as Hg, As, and Se.
The mechanisms of phytoremediation are dependent on the type of pollutants, bio-
availability, soil structures, plant species, and their tolerance to pollutants. The deg-
radation of organic pollutants depends on many factors, such as their distribution and
transformation. These factors, in turn, are governed by physical and chemical charac-
teristics of the compound, such as water solubility, molecular weight, and octanol-­water
partition coefficient (Kow). The degradation process is also governed by environmen-
tal circumstances such as temperature, pH, organic matter, and soil moisture.

Most of the organic pollutants are xenobiotic and hence are not present naturally in
the environment. Most of them are toxic even at low concentrations and may also bear
a carcinogenic character. They are released into the environment through accidental
discharge (using fuels, solvents), industrial activities (e.g. chemical, petrochemical),
agriculture (e.g. pesticides), and military operations (e.g. explosives, chemical weap-
ons). Moreover, polluted sites often contain a mixture of both organic and inorganic
pollutants. Further, there are various types of organic pollutants: solvents (e.g. tri-
chloroethylene), explosives (e.g. trinitrotoluene (TNT) and cyclotrimethylene trinit-
ramine), PAHs, petroleum products including benzene, toluene, ethylbenzene, and
xylene (BTEX), PCBs, and pesticides (e.g. atrazine, chlorpyrifos, 2,4-­D).

11.4.1 Uptake, Translocation, and Accumulation of

Organic Pollutants
Some of these pollutants, like chlorinated solvents and polycyclic aromatic hydrocar-
bons (PAHs), can be absorbed from the soil through plant roots and transpired from
the shoot. The plants can take up organic pollutants from the environment through
four mechanisms. These mechanisms include passive or active uptake through the
root system, gaseous and particulate deposition to aboveground shoots, and direct
contact between soil and plants’ aerial parts. The mechanisms are influenced by
the chemical and physical properties of pollutants such as their lipophilicity, water
solubility, and vapour pressure; environmental conditions such as temperature and
content of organic compounds; and the plant species and structure. Additionally,
some plants have more capacity for uptake of some unique pollutants because of
particular root exudates which actively mobilize them from the soil and make these
compounds available for absorption and translocation.
The organic pollutants are taken up by plants simultaneously via different path-
ways. A pollutant may enter the plants from polluted soil to the roots and may be
translocated by the xylem. Organic pollutants may also enter the vegetation from the
The Degradation of Pollutants 141

atmosphere as gas or by particle deposition onto the waxy cuticle of the leaves or by
uptake through the stomata and may be translocated by phloem. The low-­molecular-­
weight pollutants enter the leaves through stomata, while high-­molecular-­weight pol-
lutants enter leaves more often through the cuticle. Thus, the mechanism of uptake of
high-­molecular-­weight compounds is based on adsorption on the cuticle leaf surface.
Accordingly, leaves adsorb substances more selectively than roots do because of the
easier mechanism of the entrance. The uptake via roots is determined by surface and
the ratio of lipid components in roots. The lipid components in roots enable easier
absorption of lipophilic pollutants. The plants with a high content of lipid compo-
nents have high accumulation capacity for organic compounds such as PAHs. Higher
accumulation of organic pollutants by plants was proved by comparing species with
a large surface area of leaves to plants with a lower surface area. For example, vege-
tables like spinach and lettuce have higher potential for absorption and accumulation
of organic pollutants because of the broad surface area of their leaves. It seems that
organic pollutants can accumulate on the trichomes and then gradually diffuse to the
base of the cell and spread into the adjacent cells of the trichome basement; finally,
the trichome collapses. This fact that trichomes act as entering points for the organic
pollutants or that they import organic pollutants coming from other cell types and
tissues is still unclear. Trichomes of Brassica juncea accumulated cadmium and
Arabidopsis thaliana trichomes contained a high glutathione concentration suggest-
ing that trichomes may function as an efficient site of xenobiotic conjugation. Hence,
trichome-­specific engineering with organic pollutants degrading enzymes may be
one strategy for future phytoremediation strategies.

11.4.2 Degradation of Organic Pollutants Microbial Degradation
Biodegradation has been recognized as an effective approach for the remediation
of organic pollutants in which microorganisms and their diverse metabolites break
down toxic pollutants in different environments. In most cases, microbes transform
organic pollutants to other soluble organic compounds or mineralize them into inor-
ganic end products to use these pollutants as carbon and energy sources. The degra-
dation of organic contaminants in microorganisms like fungi and bacteria have been
vastly studied. The presence of various catabolic genes coding enzymes contributes
to different potential activities in microorganisms. Besides, microorganisms have
other adaptation strategies; for example, they can apply the efflux pumps to reduce
the concentration of toxic pollutants within the cell and to generate biosurfactants.
All these strategies and metabolic potentials make microorganisms a purification
tool for the bioremediation of contaminants in the environment.
The physicochemical interactions of microbes with pollutants lead to the structural
modification or degradation of the target pollutants. During an oxidation-­reduction
(redox) reaction, which involves the transfer of electrons between two compounds,
the organic pollutants are oxidized by loss of electrons (electron donor), while the
lost electron(s) is gained by other compounds (electron acceptor) that is reduced in
this process. Microbes can also rebuild different strategies that enable them to clean
up the environment and are generally classified into two types: aerobic and anaerobic
142 Basic Concepts in Environmental Biotechnology

processes. Aerobic processes occur in the presence of oxygen, where O2 acts as the
terminal electron acceptor. In the aerobic process, microorganisms use oxygen to
oxidize the pollutants to CO2 and biomass. Also, in this process, O2 availability
promotes the rate and efficiency of replication of aerobic microbes. The anaerobic
process occurs in the absence of O2, sub-­categorizing into anaerobic respiration,
fermentation, and methane fermentation. In this process, other oxidized inorganic or
organic molecules replace O2 as the terminal electron acceptor.
The microbial degradation of organic pollutants under aerobic and anaerobic condi-
tions occurs through denitrification, methanogenesis, and sulphidogenesis. The initial
enzymatic reaction in aerobic biodegradation is oxidation catalyzed by oxygenases
(monooxygenases and dioxygenases) and peroxidases. A number of bacteria such as
Pseudomonas, Bacillus, Rhodococcus, and Mycobacterium are recognized to break-
down PAHs via metabolic enzymes such as methane and ammonia monooxygenases.  Polycyclic Aromatic Hydrocarbons (PAHs)

Biodegradation of PAHs as organic pollutants has been frequently studied. It was
determined that a phthalic acid and its derivatives are produced through the PAHs’
degradation by white-­rot fungi and bacteria, which are reduced to CO2 and polar
metabolites. In bacteria, initiation reaction of PAHs degradation is via attack on the
aromatic rings via dioxygenase leading to the formation of cis-­dihydrodiole, which
consequently is dehydrogenated to form pyrocatechol. Pyrocatechol is the primary
intermediate of this cleavage. Such intermediates were also observed in fungal deg-
radation processes. For example, wood-­rot fungi are capable of releasing extracel-
lular enzymes which degrade lignin in wood. But despite that, these enzymes are not
only specific for lignin degradation but can also transform organic pollutants such as
PAHs to quinone intermediates. In this process, some wood-­rot fungi may then split
the rings and finally degrade the compounds to CO2 and water; however, for other
fungi, it appears that the quinones are dead-­end products. Moreover, fungi can also
oxidize PAHs by the cytochrome P-­450 enzyme system to form phenols and trans-­
dihydrodiols, which can conjugate and be eliminated from the microorganisms.  Aliphatic Hydrocarbons

Aliphatic compounds are also called linear alkanes, and the decomposition time
of linear hydrocarbon compounds in the environment is shorter than that of aro-
matic compounds. Aliphatic hydrocarbons, as prevalent soil pollutants, define as
open-­chain methane derivatives which are both non-­aromatic and non-­cyclic organic
compounds. These pollutants are carcinogenic at high concentrations and bring
notable hazard to biological receptors due to the formation of toxic and carcinogenic
metabolites during their biodegradation. These compounds can be subdivided into
three structurally different groups, including alkanes (saturated hydrocarbons with
single bonds), alkenes (unsaturated hydrocarbons with double bonds), and alkynes
(unsaturated hydrocarbons with triple bonds). Alkanes as aliphatic hydrocarbons are
one of the most significant percentages of petroleum-­related contaminants being eas-
ily destroyed, especially those that have shorter chains and lower hydrophobicity.
However, their degradation potential is decreased with an increase in the number
of carbon chain-­length due to decreasing in their solubility in an aqueous medium.
The Degradation of Pollutants 143

The fastest and the most complete breakdown of most organic pollutants occurs in
aerobic conditions because of the metabolic benefits of having the O2 availability as an
electron acceptor. Aerobic bacteria like Pseudomonas, Alcaligenes, Sphingomonas,
Rhodococcus, and Mycobacterium degrade both alkanes and polyaromatic com-
pounds. The main process of aerobic degradation of aliphatic hydrocarbons is via
the addition of one or two oxygen atoms to the hydrocarbon molecule. This process
is catalyzed either by oxygenases or by cytochrome P450. The activated molecule
is then changed into an alkanol, which is then oxidized to the related aldehyde and
finally converted into fatty acid. The fatty acid is bonded to CoA, forming an acyl-­
CoA and processed by oxidation to produce acetyl-­CoA. Therefore, the ultimate
product of the oxidation of aliphatic hydrocarbons is acetyl-­CoA being catabolized
in the Krebs cycle and completely oxidizing the substrate into CO2 and H2O. In
contrast to aliphatic hydrocarbons, the oxidation of aromatic hydrocarbons produces
phenolic intermediates. Their further degradations are via central pathways cata-
lyzed by intradiol or extradiol dioxygenases leading to the formation of simpler com-
pounds, which are then inserted into the Krebs cycle and utilized (Figure 11.1).

FIGURE 11.1  Degradation of aliphatic and aromatic hydrocarbons by aerobic bacteria.

(Source: Rohrbacher and St-­A rnaud, 2016)
144 Basic Concepts in Environmental Biotechnology Pesticides
Pesticides as organic chemical pollutants are purposely intended to control the insect
population and decrease losses of agricultural products resulting in agricultural
yield enhancement. Recently, powerful and remedial technologies have appeared
to degrade or remove pesticides by using native or genetically modified organisms.
There are many reports of various organisms such as bacteria, algae, yeasts, fungi,
and plants which are specified in terms of their genome and enzymes applying for
bioremediation of soil and water.
Pesticides could be degraded by different methods in the soil, such as physical
degradation, chemical degradation, physical-­
­ chemical degradation, and micro-
bial degradation. The latter one has been used more frequently in recent years because
the applied pesticides are mostly microbial nutrients, which are finally degraded into
small molecules like CO2 and H2O in microbial degradation processes. Through the
enzymatic reactions, the pesticide compound firstly enters into a microorganism’s
body in a certain way. Then they are completely degraded or broken down into less
toxic compounds by a series of physiological and biochemical reactions under the
action of various enzymes.
Both plants and microorganisms have metabolic pathways that can degrade most
of the pesticide compounds released in the environment. However, the long-­term
persistence of some pesticides, such as organochlorine compounds, limits the abil-
ity of microbes and plants to degrade them due to their hydrophobic nature, which
prohibits their uptake and translocation.
To degrade most of the pesticide compounds, microbial transformation in the soil
must play an essential role in making them more available for uptake and degrada-
tion by plants. Thus, various chlorinated pesticides can be broken down better in
a vegetated soil than in a non-­vegetated soil. A higher microbial population con-
tributes to a faster rate of degradation of lindane, atrazine, metolachlor, trifluralin,
butachlor, and aldicarb in the rhizospheric soil of some herbicide-­tolerant plants in
comparison with bare soil.
Some of the researchers have also indicated the role of endophytes in facilitat-
ing the phytoremediation of various pesticides. The decrease in phytotoxicity and
an increase in phytoremediation of 2,4-­dichlorophenolxyacetic acid (2,4-­D) resulted
from the colonization of the roots of phytoremedial plant with some endophytes. The
removal potential of 2,4-­D and the pea plants’ biomass were enhanced after success-
ful colonization of its roots with a poplar tree endophyte, Pseudomonas putida, hav-
ing the ability for breaking this compound. Accordingly, it might be proposed that a
plant-­endophyte partnership could be employed as the main mechanism not only to
increase the phytoremediation of pesticide-­contaminated soils but also to decrease
the concentrations of toxic herbicide residues in crop plants. Phytodegradation
The transformation of organic pollutants is a specific species process which may be
restricted in the given plant only to a particular tissue or organ or even in one particu-
lar developmental stage. The degradation processes of pollutants can be carried out
in three phases: transformation, conjugation, and elimination reactions. In the first
The Degradation of Pollutants 145

stage, the reactions are oxidation, reduction, and hydrolysis. These reactions may
modify compounds which enable them to convert into more polar and water-­soluble
forms through enzymes like cytochrome P450 and carboxylesterases. It is assumed
that these processes are localized inside mitochondria or the endoplasmic reticulum.
These reactions may modify compounds so that they can conjugate with amines,
acids, and alcohols in the second phase of detoxification. The second stage of pollut-
ant degradation is the biotransformation phase, including specific conjugation pro-
cesses with saccharide, glutathione, or amino acids, sulphatizing, and methylation.
These processes may be marked as a group of synthetic metabolic reactions when
a xenobiotic reacts with either endogenous compound. The reactions are catalyzed
by relatively few specific enzymes such as glycosyl transferases and glutathione
S-­transferases, transferring them into the different parts of the cell, such as into the
vacuole or cell wall.
The third stage of biotransformation is detoxification, in which the organic pol-
lutants are essentially removed from metabolic tissues. This process is also defined
as sequestration/compartmentalization, where conjugates are isolated by catabolic
and anabolic mechanisms in plants. Created conjugates are transferred from the
cytoplasm to the vacuole by trans-­membrane ATP-­dependent transporters (ABC-­
transporters) for accumulation. Alternatively, they can be additionally processed by
hydrolytic reactions within the vacuole and then re-­exported into the cytoplasm for
more metabolisms.
Plants can also accumulate soluble conjugates in the vacuole and non-­soluble
conjugates in the cell wall for further metabolism. The organic pollutants such
as aromatic compounds with hydroxyl, carboxyl, amino, or sulfhydryl groups are
deposited into lignin or to other cell wall components such as protein, hemicellulose,
and cellulose. A study on organic pollutants has shown that in maize, phenanthrene
can be metabolized into more polar products, and in another study anthracene and
its derived-­compounds are bound to cell wall components such as pectin, lignin,
hemicellulose, and cellulose.

Inorganic pollutants are naturally present in the earth’s crust and atmosphere. They
are also contributed by human activities such as industry, mining, motorized traffic,
agriculture, and military actions promoting their release and concentration in the
environment leading to toxicity. These pollutants comprise metals or metalloids such
as, Cd, Cu, Hg, Mn, Se, and Zn, radionuclides such as Cs, P, and U, and plant fertil-
izers such as nitrate and phosphate. The inorganic pollutant mainly constitutes heavy
metals, making them more persistent than organic contaminants are. Although they
cannot be broken down, they can be modified by reduction or oxidation. They can
also migrate into different plant parts and be accumulated and volatilized.

11.5.1 Uptake and Sequestration of Inorganic Pollutants

The uptake of inorganic pollutants such as HMs consists of ion uptake from the soil
and into the root cells. The metal must mobilize into the soil solution for uptake and
146 Basic Concepts in Environmental Biotechnology

accumulation by plants. Siderophores, including mugineic acids and avenic acids,

are set free by some plant species (grass species) to increase the bioavailability of
HMs for root uptake. The transportation and accumulation of HMs are carried out by
different compounds such as organic acids (OAs) within tissues and other compart-
ments. OAs (citrate, malate, and oxalate) also perform a substitutive role of excluding
metals from plants. For example, Al absorb is prevented by the exudation of OAs,
making the OAs-­Al complex in wheat. Similarly, Cu uptake in Populus tremula root
is prevented by the exudation of formate, malate, and oxalate, while Zn absorption is
prevented through the exudation of formate.
After uptake from the root, HMs enter into the cytosol by transporter protein,
mainly ZRT-­IRT-­like proteins (ZIP) family members. Into the cytosol, HMs pro-
vokes phytochelatin synthase (PCS) as an enzyme by which the reaction of phy-
tochelatin (PC) production through glutathione is catalyzed. HMS phytochelatin
complexes (HM-­PC) (low-­molecular-­weight complexes) move to the vacuole through
ABC-­transporters. This complex collects within the vacuole, and as more HMs are
added, they convert into a high-­molecular-­weight (HMW) complex. HMS is also
transferred into the vacuole through cation/proton exchanger (CAX) transporters
exchanging the HMs directly with protons, metal tolerance proteins (MTP) as HMs-­
proton exchanger transporters, and natural resistance associated macrophage pro-
teins (NRAMPs). These transporter proteins are established into the tonoplast and
mediate the pathway of metal ions for compartmentation or remobilization.
Further, metallothioneins (MT) are low-­ molecular-­weight, cysteine-­ rich, and
metal-­binding proteins applying for HMs remediation through intracellular transfer-
ence or sequestration. These chelators join to the metals and make a complex moving
into vacuole like Zn transporting within the vacuole by MTP (Figure 11.2).

11.5.2 Plant Response to Inorganic Pollutants

Plants present various mechanisms for removing metals indicating the rate of metal
uptake by the plants. In general, phytoremediation approaches for inorganic pol-
lutants are phytostabilization (immobilization), phytoextraction (rhizofiltration), and
phytovolatilization. Phytostabilization
Phytostabilization, also named as phytosequestration or phytodeposition, is an
approach dealing with stabilizing or moving pollutants in the soil near the root to
forbid the movement of heavy metals to either groundwater or food. In recent years,
two kinds of grass—Agrostis species and Festuca species—were applied in the phy-
tostabilization of soil polluted with Cu, Zn, and Pb. Thus, phytostabilization is con-
sidered as a distinct approach to restrict migrations of HMs and to inactivate toxins. Phytoextraction
Phytoextraction, also named as phytoaccumulation, is used to absorb pollutants from
soil and water through roots and transferring the pollutants to the shoot and leaves.
Hyperaccumulator plants are generally small and slow growing. But they are able to
The Degradation of Pollutants

FIGURE 11.2  Metabolism of organic and inorganic pollutants in plants cells. (Sources: Modified from Yang and Chu, 2011; Yadav et al.,
2015; Chandra et al., 2017)
148 Basic Concepts in Environmental Biotechnology

take up HMs 50–500 times more than non-­hyperaccumulator plants can without any
negative influence on their growth and development. Accordingly, they can accumu-
late and detoxify exceptionally high levels of metal ions like Ni, Co, Pb, Zn, Mn, Cd,
and more in their shoots.
Recently, nearly 450 plant species of 45 families have been determined to be
hyperaccumulators. These hyperaccumulators mostly consist of Brassicaceae,
Asteraceae, Fabaceae, Lamiaceae, Poaceae, Euphorbiaceae, Caryophyllaceae, and
Violaceae. Phytovolatization
Phytovolatilization means using plants to absorb pollutants from the soil and trans-
forming them into volatile form and releasing them into the atmosphere. This
approach is used for organic and inorganic pollutants such as Hg, Se, and As from
soil. For example, Se changes into volatile methyl selenate form and is released into
the atmosphere.

Although the application of biotechnology to establish effective, low-­cost, and clean
bioremediation technologies is much promised, several challenges have remained.
Most phytoremediation experiments are carried out on a labscale and in a hydro-
ponic environment, while the soil environment is quite different, and there are many
metals in insoluble forms that are poorly accessible. Extending laboratory results
to the real environment is one of the key research activities that can exploit the
real potential of plants in the elimination of organic and inorganic pollutants. The
efficiency and capability of many plants in the degradation of pollutants are still
unknown, and the production of transgenic plants by genetic engineering is one pos-
sible future role of plants in the purification of the environment. Therefore, illustrat-
ing how genes are involved in the pathway of pollutant decomposition and detecting
suitable genes for phytoremediation can provide other cases of future perspectives.

Phytoremediation is an innovative and safe technique for the management of pol-
luted soil with organic and inorganic pollutants; it is inexpensive and solar energy
driven, and naturally clean technology is useful for removing a wide range of envi-
ronmental pollutions. There are various mechanisms in which plants are applied to
remove or remediate polluted sites. To remove pollutants, plants can break down
organic contaminants and stabilize inorganic pollutants through acting as filters
or traps. Using only one remediation mechanism cannot always guarantee the suc-
cess of phytoremediation. Thus, a combination of mechanisms, including uptake,
transformation, stabilization, and rhizosphere degradation, may be required to break
down pollutants.

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