can hydrolyze the organophosphate pesticide. Illustrations include Pseudomonas diminuta MG and Flavobacterium ATCC 27551 possessing the organophosphate hydrolase enzyme [51]. Bacterial strains isolated from pesticide‐contaminated soil and these strains were tested for their degradation capability and it was found that JCp4 and FCp1 degraded 84.4 and 78.6% the chlorpyrifos pesticide respectively. Moreover, these strains also showed plant growth promoting traits, which includes phytohormone production, phosphate solubilization, and N2 fixation, etc. [49]. In Pakistan, pesticide residues were found above permissible limits in different vegetables analyzed for pesticide residues. It was found that all samples contained pesticide residues of carbofuran and chlorpyrifos and limits with concentrations ranging from 0.01–0.39 and 0.05–0.96 mg/kg, respectively were observed [81].
2.5 Strategies of Bioremediation
Bioremediation is the process of using organisms to neutralize or remove contaminants from waste. It is very important to understand that this form of waste remediation uses no toxic chemicals, although it may use an organism that can be detrimental under certain circumstances. A gory, but simple description of bioremediation is the use of maggots in wound care. Wounds that have contamination can have maggots introduced to them. The maggots then eat the contamination allowing the wound to heal correctly – a form of medical bioremediation. There are many other types that are used to control different waste contamination, which are now described.
2.5.1 Microbial Remediation
The use of microbes such as bacteria and fungi for soil rejuvenation is a form of environmental remediation. The objective of microbial remediation is to remove soil contaminants and pollutants [107]. Though the industrial use of microbes for removing contaminants goes back only three decades, microbes, aerobes, anaerobes, and facultative anaerobes have been contributing to soil improvement for billions of years. They help with N‐fixation, limiting growth of plant pathogens, and the decomposition of heavy metals, pesticides, and hydrocarbons in the soil. The microbial flora is nourished by the contaminants, degrading them for energy and reproduction. Microbial remediation can be divided into three grades:
Natural attenuation: The process takes place naturally with indigenous soil microorganisms.
Biostimulation: The natural process receives external help in the form of nutrients, moisture, and an ideal pH for the microorganisms.
Bioaugmentation: This involves the use of externally introduced microorganisms, which is the case in situations such as oil spills where the naturally occurring microbes may die out because of the intensity of the contamination [108].
Rhizofiltration: Phytofiltration is used to inhibit organic pollutants in wastewater and surface water from mixing with water streams or groundwater using plants for filtration purpose, as they can absorb or adsorb the pollutants [109]. Phytofiltration can also be: rhizofiltration in which plant roots are used; blastofiltration in which seedlings are utilized; and caulofiltration that uses excised plant shoots) [110]. Due to phytofiltration, the movement of contaminants in the soil is minimized [111]. Phytofiltration is defined as the use of plants, both terrestrial and aquatic to absorb, concentrate, and precipitate contaminants from polluted aqueous sources with low contaminant concentration in their roots. Rhizofiltration can partially treat industrial discharge, agricultural runoff, or acid mine drainage. It can be used for lead, cadmium, copper, nickel, zinc, and chromium that are primarily retained within the roots [4]. The advantages of rhizofiltration include its ability to be used in in‐situ or ex‐situ applications and species other than hyperaccumulators can also be used. Plants like sunflower, Indian mustard, tobacco, rye, spinach, and corn have been studied for their ability to remove lead from effluent, with sunflowers having the greatest ability. Indian mustard has proven to be effective in removing a wide concentration range of lead (4–500 mg/l). This technology has been tested in the field with Uranium contaminated water at concentrations of 21–874 μg/l; the treated U‐concentration reported by studies was <20 μg/l before discharge into the environment. The use of some metal accumulator aquatic plants species, both living and dead, and constructed wetlands for the removal of heavy metals from industrial wastewater has gained considerable interest [112]. Aquatic plants and microorganisms can remove metals from water through processes of biosorption and metabolism‐dependent bioaccumulation. The use of dead or dried aquatic plants, for metal removal as a simple biosorbent material has advantages in its high efficiency including minimization of the volume of chemical and/or biological sludge, no nutrient requirements, low cost, conservation, transport, handling, and metal recovery [113–116].
2.5.2 Phytovolatilization
Phytovolatization is the process in which pollutants are up taken by the plants from the soil and then converted into a volatile form and then released in the atmosphere. Phytostabilization can be used for organic pollutants and other heavy metals like Se and Hg. But, as explained earlier, phytostabilization transfers the pollutants into the atmosphere, from one medium to another, and does not remove the pollutants permanently. The pollutants in the atmosphere can also be redeposited into the soil at a later time. In phytoremediation of organics, plant metabolism contributes to the contaminant reduction by transformation breakdown, stabilization, or volatilizing contaminant compounds from soil and groundwater. Phytodegradation is the breakdown of organics, taken up by the plant to simpler molecules that are incorporated into plant tissues. Plants contain enzymes that can breakdown and convert ammunition wastes, chlorinated solvents such as trichloroethylene, and other herbicides. The enzymes are usually dehalogenases, oxygenases, and reductases. Rhizodegradation is the breakdown of organics in the soil through microbial activity of the root zone and is a much slower process than phytodegradation. Yeast, fungi, bacteria, and other microorganisms consume and digest organic substances like fuels and solvents. All phytoremediation technologies are not exclusive and may be used concurrently, but the metal extraction depends on its bioavailable fraction in soil [117, 118].
2.5.3 Phytodegradation
Phytodegradation, also known as phytotransformation, is the use of plants and microorganisms to uptake, metabolize, and degrade the organic contaminant. In this method, plant roots are used in association with microorganisms to detoxify soil contaminated with organic compounds [119]. Some plants can decontaminate soil, sludge, sediment, and ground and surface water by producing enzymes. It involves organic compounds, including herbicides, insecticides, chlorinated solvents, and inorganic contaminants [120].
2.6 Adaptive Mechanism of Bioremediation for Heavy Metals, Pesticides, and Herbicides
Plants adopt different strategies and complex mechanisms for survival under critical conditions, which are mostly caused by biotic or abiotic stresses. Plant stress occurs through damage by certain living or nonliving species. Living organisms such as viruses, bacteria, parasites, fungi, beneficial or harmful insects, and native or cultivated plants mostly initiate biotic stresses. Abiotic stresses such as, mineral toxicity, excessive watering, drought, extreme temperatures, salinity negatively impact development, growth, yield, and seed quality of plants and other crops. Differentiation between the damage caused by living or nonliving agents is a very difficult task even with the help of accurate diagnosis and close examinations. Relative oxygen species generated in the plants that accumulate in cells under environmental stress results in the oxidation of carbohydrates, proteins, lipid, chlorophyll, nucleic acids, etc. [121–123].
2.6.1 Defense System
Plant cells have evolved intricate defense systems including: (i) Plant hormones (phytohormones), such as, ethylene, jasmonic acid [JA], salicylic acid [SA], abscisic acid [ABA], and brassino‐steroids. These phytohormones are mostly required by plants for their growth and development and occasionally act as defense mechanisms. (ii) Enzymatic systems that comprise superoxide dismutase [SOD], ascorbate peroxidase [APX], catalase [CAT], glutathione reductases [GR], dehydro‐ascorbate reductases [DHAR], mono dehydro‐ascorbate