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: Impact of Soil, Plant-Microbe Interaction in Metal Contaminated Soils


Department of Biotechnology, CCDSD College, Sector-32-С, Chandigarh-160030, India


With the rapid progress in the field of science leading to new innovations and growing industrialization, the markets are flooded with novel products having better shelf life and quality. The production process of such compounds leads to the production of advanced effluents which when discharged into the environment leads to water, ah, and soil pollution. The degradation pathway of naturally occurring compounds is available, but these modified residues are not known to occur in the natural environment; hence their degradation pathways are not present and thus lead to accumulation of such products in the environment. Such man-made compounds are known as xenobiotic compounds. Their toxicity profile depends on many factors like the type of parent compound, degree of complexity that is alkane, alkyne, alkene, aromatics, and others. They are further categorized into persistent and recalcitrant types. The persistent compounds are one that accumulates in the environment but are degradable, although their degradation rate is slow and hence pose a toxic impact on the environment. On the other hand, those persistent compounds which do not get degraded over a long period of time and gets accumulated in the environment are known as recalcitrant compounds and are far more toxic and have an alarming impact on the environment (Thakur, 2011).

Several approaches are available for the removal of these toxic wastes depending on their nature (organic, inorganic) and their form (solid, liquid, or gaseous). Some of the commonly used techniques are physical, chemical, and biological approaches. The commonly used conventional approaches are adsorption, absorption, filtration, convection, ozonation, activated charcoal treatment, UV treatment, volatilization, chemical treatment, chlorination, air stripping, ion exchange methods, centrifugation, gravitation, oxidation ditches and rotating biological contactors (RBC). The liquid waste undergoes specific treatment steps: primary, secondary, and tertiary treatment (Peters, 2015). All the steps are crucial and lead to a drop in the BOD, COD loads at each step. But these techniques also suffer from the major drawbacks of failure to remove a certain class of modified chemical compounds. The biological approaches commonly used by the industries are divided into two categories depending on the nature of microbes: aerobic and anaerobic. The former involves activated sludge treatment, trickling filters. Tire latter type involves anaerobic reactors, an up-flow anaerobic sludge blanket reactor (UASB), and others. The above mentioned physical and chemical techniques mostly suffer from the main disadvantage of the production of chemical residues, which further contaminate the environment. Tire biological methods suffer from the poor removal rate as the microbial consortia sometimes are inhibited by the toxic effects of the chemicals (Peters, 2015).

The most promising approach nowadays is the exclusive use of specific organisms for the removal of contaminants from the environment is called biorernediation. There are many definitions available for bioremediation. The most commonly used is given by EPA, which suggests “treatment that uses naturally occurring organisms to break down hazardous substances into less toxic or nontoxic substances.” Biorernediation is a broad term and involves many techniques like compositing, co-cornpos- iting, phytoremediation, phytovolatilization, rhizorernediation, rhizofil- teration, biostimulation, bioaugmentation, bioleaching. Figure 9.1 shows the commonly used biorernediation methods. Biorernediation can also be defined as the breakdown of complex waste of plant, animal, and human origin into simpler compounds by the action of microbes (Thakur, 2011). The process of biorernediation involving natural microflora can be broadly categorized into two types: intrinsic biorernediation and biostimulation. The former involves the action of native bacteria, which utilizes the available energy sources to cany out the degradation of contaminants while the latter depends on the external energy sources to cany out the remediation process. One such smdy earned out by the US Army Corps of Engineers reported an increase in the rate of biorernediation following the techniques of windrowing and aeration in the sites contaminated with petroleum (Shah et al., 2013a). The amount of bioavailability of metal to be degraded is another important factor affecting the efficiency of Bioremediation. In the absence of regular sources of energy, microbes can efficiently utilize the alternative energy source. In one of the studies earned out by Shah et al. (2013b), the microbes successfully utilize and degrade the nitrogenous organic chemicals in the nitrogen-deficient soils. The soils with high adsorption capacity limit the bioavailability of contaminants and make them persist in the environment (Shah et al., 2013c).

Bioremediation approaches for treatment of environmental contaminants

FIGURE 9.1 Bioremediation approaches for treatment of environmental contaminants.

Microorganisms are the most studied and are the key players in bioremediation. From billions of years, they have played a key role in the cycling of nutrients across the globe by the breakdown of waste, which owes to the vast diversity of enzymes produced by them both intracellular and extracellular (Prakash et al., 2010). Apart from microbes, the other biological sources were successfully reported to cany out the removal of contaminants from the environment. One such case was the use of bone char of fish to remove cadmium and lead as a result of adsorption (Shah et al., 2013b; Shah, 2014). Microalgae were successfully employed to remove various contaminants like chromium and nitrate from tannery effluent (Gosavi et al., 2004).

The process of biomagnification poses a major threat to the health of humans and animals as it results in an increase in the concentration of the contaminant at every trophic level. The situation can be controlled by the use of phytoremediating agents. There are different types of phytoremediation, such as phytovolatilization, rhizoremediation, and phytoaccumulation, as of this phytoaccumulation was reported to be an efficient method of removal of contaminants by allowing the accumulation in harvested part of the plant including fruit, stem or flowers (Yerima et al., 2012). It is easy to extract contaminants from harvested part either by concentrating it by incineration or by other method and use it further for industrial use (Singh et al., 2012). In contrast, the native microflora, which was being exposed to petroleum hydrocarbons efficiently degraded aromatic hydrocarbons as reported by Sims (2006). The microbes showed different mechanisms for the removal of contaminants depending upon the novelty of a particular compound. The compound understudy can be directly taken by the cell and utilized or can be transformed prior to uptake. In order to design efficient bioremediation protocols, there is a need to understand the existing metabolic pathways in microbes and to further utilize the knowledge to develop novel pathways to cany out the degradation of persistent and recalcitrant class of xenobiotic compounds.

Recent advancements have also proven via the addition of matched microbe strains to the medium to enhance the resident microbe populations’ ability to break down contaminants. The elimination of a wide range of pollutants and wastes from the environment requires increasing our understanding of the relative importance of different pathways and regulatory networks to carbon flux in particular environments and for particular compounds, and they will certainly accelerate the development of bioremediation technologies and biotransformation processes (O’Loughlin et al., 2000).

Among all the pollutants, contamination of soils by various heavy metals is a crucial area of research. The persistent rate of heavy metals is reported to be quite high as compared to other pollutants. They exist in the soil in different forms such as free ions, reactive metal ions, soluble form, nonsoluble form, reactive, and noil-reactive complex forms that is carbonates, oxides, phosphates, and others (Leyval et al., 1997). Though some metals are required in trace amounts for the growth of plants, beyond a certain limit, they are known to cause negative impacts on the growth of plants and also affect the microbial diversity of that region. Some of the heavy metals like zinc, copper, nickel, iron act as cofactors for essential enzymes required for completing important metabolic pathways in plants as well as microbes. On the other hand, some metals like chromium, selenium, arsenic are highly toxic even at ppb levels and lead to the disruption of growth of plants and microbes by inhibiting the principle enzyme or competing with the crucial substrate (Panda and Chaudhary, 2005). Both natural and anthropogenic sources are responsible for the addition of heavy metals in the soil like weathering of rocks, volcanic eruptions, industrial sources, power plants, mining runoff, floods, municipal waste, refining, and burning of fossil fuels (Wang et al., 2003).

Whether microorganisms will be in destroying man-made contaminants in the subsurface depends on three factors: the type of organisms, the type of contaminant, and the geological and chemical conditions at the contaminated site. This chapter explains how these three factors influence the outcome of a subsurface bioremediation project. It also evaluates the role of plant-microbes interaction in the removal of contaminants. It reviews how microorganisms destroy contaminants, their interaction with plants and soil. The chapter will also focus on the impact of the common contaminants on plants and humans and the need for reforms in current practices of bioremediation.


The presence of heavy metals such as cadmium, chromium, lead, arsenic in an excessive amount not only affects the physical and chemical properties of soil but also poses a great threat to the plant diversity growing in that particular environment. Plants can uptake those heavy metals from soil resulting in the alteration of then cellular functioning, which can ultimately risk the human health consuming those contaminated crops. The toxic effects of some common heavy metals in the soil and plants growing in those contaminated soil are discussed below.


Chromium is a toxic metal that affects plants in many ways. Chromium is toxic in two forms Cr3+ and Cr6+. Chromium in its oxidation state of Cri~ gets easily tr ansported across the cell membrane and affects functions of the cell. Chromium gets easily reduced inside the cell and results in the generation of reactive oxygen species (ROS) such as hydroxyl radicals (OH') and damage the DNA and proteins (Stohs and Bagchi, 1995; Jaishankar et al., 2014). Plants mostly get exposed to chromium through contaminated soils receiving industrial effluents from tanneries, metallurgical industries, or pigment industries (Ghani, 2011). In addition to this, new agricultural methods are also one of the reasons for contaminating the soil and vegetation glowing in it through the release of chromium dust or residues (Duan et al., 2010). Chromium toxicity has harmful effects on plant growth and development. It causes a reduction in the growth of roots, chlorosis, and necrosis of leaves, lesser biomass (Ghani, 2011). Several studies have proven detrimental effects of chromium on plant gr owth. For example. Rout et al. (2000) reported that chromium at a concentration of 200 pM reduces seed germination by 25% in Echinochloa colona. In another study, Jain et al. (2000) reported a reduction of 32-57% with chromium at a concentration of 80 ppm in bud germination of sugarcane. Chromium toxicity also affects different enzymes in plant cells including catalase, cytochrome oxidase, amylase, protease, and many more (Nagajyoti et al., 2010; Jaishankar et al., 2014). For example, Zeid (2001) observed a reduction in seed germination is linked towards the decreased activity of amylase, which helps the supply of sugars to the developing seed.


Cadmium is a rare earth element. It exists in two oxidation states Cd+1 and Cd-2 and is highly toxic in solution form. Soils contaminated with cadmium not only have altered physical and chemical properties. Depending upon their concentration, different metals starts accumulating in the plants from where it enters the food chain and ultimately affects the humans causing severe diseases. Plants growing in cadmium contaminated soils have a great effect on their normal growth and developmental processes. Cadmium toxicity in soil cause modifications in the photosynthetic activities, metabolic processes, and also in the salt and mineral uptake processes (Tran and Popova, 2013). In soil, it occurs mostly in the oxidation state of Cd+2. Uptake of cadmium causes several changes; for example, it causes chlorosis in leaves and shortening of shoots. The harmful effect of cadmium was very w-ell smdied by Rascio et al. (2008) in rice. Treatment of rice seedlings with cadmium results in modification of the root system, showing how much cadmium is toxic to plants.

Cadmium also interferes with metabolic processes going in the plant cells by targeting the enzyme system of the cell and thus causing plant damage and sometimes results in plant death (Assche and Clijsters, 1990; Chibuike and Obiora, 2014). Cadmium metal toxicity inhibits the functioning of photosynthetic enzymes like RubisCo by modifying its structure and lowering its binding to its substrate and lowering the enzyme activity (Siedlecka et al., 1998). The concentration of these metals in soil plays a significant role in their affect against plants, animals, and humans. For example, as reported by Ahmad et al. (2012), cadmium at a concentration of 5 mg/L affects the wheat crop and results in less growth of both roots and shoots. In another study, cadmium at a concentration of 250 pM has a very toxic and rapid effect on the cellular division (Fusconi et al., 2007; Tran and Popova, 2013).


Ar senic is a common soil contaminant which, like other metals, affects the growth and development of plants growing in it. Arsenic is mostly toxic in two forms As5+ and As3+ as these are easily taken up by the plant root system (Finnegan and Chen, 2012). Arsenic is more toxic in its reduced form of As3+. Over the years, a number of toxicity studies related to arsenic with different plants have been done. Slrri et al. (2009) studied the effect of arsenic on rice seedlings and how arsenic affects the physiological and biochemical processes of the plant. It was observed that the developmental processes in the rice seedlings were greatly affected, and there was a marked decrease in root and shoot elongation, and also plant biomass was less than normal, and both the forms As3+ and As5+ accumulated in significant amount. In another study, arsenic toxicity was studied in beans.


Lead, like other heavy metals discussed before, is one of the most toxic metals present in the environment. It presence in the ecosystem can affects all life forms including plants, animals, microorganisms, and humans. It affects an organism at all the three levels, morphological, physiological, and biochemical (Poumrt et al., 2011). It is an industrially important metal and is used to manufacture batteries, home paints, pipes, and solders (Martin and Griswold, 2009). It is also produced during the combustion automobile fuel. All these sources pollute the soil in one way or the other. Plants generally uptake lead into their system from contaminated soil. Lead is mostly taken up by the roots from where it gets accumulated in the plant. It affects major metabolic processes like photosynthesis by damaging chlorophyll and lipid membrane of the cell (Jaishankar et al., 2014; Najeeb et al., 2017). It also produces ROS which have detrimental effects on cellular DNA. These ROS creates imbalance of antioxidants and free radicals in the plant cell. Lead causes decrease in the concentration of antioxidants such as glutathione which leads to a condition of oxidative stress arises in the cell and causes cellular damage (Jaishankar et al., 2014). Metals like magnesium, zinc, calcium all having an important role in completing different biochemical and metabolic processes in the plant cell, but lead replaces these metals and disturbs processes like cell signaling and enzyme activity.

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