2.1. Chemical Fertilizers

In the past, agriculture was the main human activity that had a significant influence on the soil [30]. In addition to macronutrients nitrogen (N), phosphorus (P), potassium (K), sulfur (S), calcium, and magnesium, plants require essential micronutrients for their growth and life cycle. However, certain soils may exhibit deficiencies of necessary HMs, including Co, Cu, Fe, Mn, Zn, Ni, and Molybdenum, which are crucial for healthy plant development [31], thus crops can be given these nutrients by adding them to the soil or by spraying them on the leaves. On rare instances, Cu is applied to soil as a remedy for Cu-deficient soils to address the nutritional needs of cereal crops. According to Alloway [32], Mn supplementation is also beneficial for cereal and root crops. In intensive agricultural practices, substantial quantities of fertilizers are regularly applied to provide an adequate supply of N, P, and K for crop growth. However, these fertilizer compounds may contain trace amounts of HMs such as Cd and Pb as impurities. Prolonged use of fertilizers can significantly elevate the concentrations of these metals in the soil [33]. Cd and Pb are classified as metals that lack recognized physiological functions in biological systems. The application of certain phosphatic fertilizers can inadvertently introduce Cd and other potentially hazardous metals, including F, Hg, and Pb, into the soil, as highlighted by Moolenaar and Lexmond [34].

2.2. Insecticides

In the field of horticulture and agriculture, numerous conventional pesticides that were extensively employed in the past were found to contain elevated concentrations of metals [35]. Some pesticides, including Bordeaux mixture and Cu oxychloride, are fungicidal sprays that contain Cu [36]. Historically, Pb arsenate was extensively utilized in fruit orchards as a means to combat parasitic insects. Abandoned sites that were treated with Cu, Cr, and arsenic-based formulations chromated copper arsenate to preserve timbers exhibited significantly higher soil concentrations of these elements than background levels, as highlighted by McLaughlin et al. [37]. This form of contamination can pose challenges, particularly if these sites are later repurposed for agricultural or non-agricultural activities. The application of these materials has been more geographically restricted and primarily associated with specific regions or crops, in contrast to the widespread use of fertilizers [38].

2.3. Biosolids

Land application of various biosolids, including composts and municipal sewage sludge, inadvertently results in the contamination of soil with a wide range of HMs [39]. In agriculture, it is customary to utilize animal wastes, including poultry, livestock, and pig manures, by applying them as solids or sludges to crops and pastures [40]. Although manures are generally recognized as valuable fertilizers, the use of Cu and Zn in pig and poultry industries as growth promoters and poultry health products raises concerns regarding potential soil contamination with these metals [41]. Repeated application of manures produced by animals fed diets containing elevated levels of arsenic (As), Cu, and Zn to confined land areas can Pb to substantial accumulation of these metals in the soil [42].

There is growing interest in exploring the potential of composting biosolids together with organic materials such as wood shavings, straw, or yard waste. However, if this trend continues, there is a legitimate concern regarding the potential for soil contamination by HMs. The utilization of biosolids in agricultural practices has raised substantial concerns regarding their potential to introduce toxic substances into the soil [43]. The HMs that are most frequently detected in activated sludge are Pb, Ni, Cd, Cr, Cu, and Zn. The concentrations of metal are affected by the type of industrial activity, its intensity, the procedure used to treat the biosolids, and many other factors [44]. In specific situations, metals that are deposited in soils through the application of biosolids can potentially percolate through the surface soil and contaminate groundwater [45].

2.4. Metal Mining

Metal pollutants in soil have been widely distributed as a result of metal ore mining, ore milling, and related sectors in many different nations. During mining operations, the discharge of tailings, consisting of larger and denser particles that settle at the bottom of flotation cells, directly into natural depressions, including on-site wetlands, leads to elevated concentrations of contaminants [46]. A risk to the health of people and the environment has been created by the extensive extraction and processing of Pb and Zn ore through mining and smelting operations [47]. The soil reclamation techniques utilized at these sites are often time-consuming, costly, and may not effectively enhance soil productivity. The bioavailability of HMs in the soil plays a crucial role in determining the potential environmental risks to human health [48]. The food chain and the availability of contaminants are present in the soil for oral absorption and assimilation [47]. Other materials are produced by numerous industries, including fabric, bronzing, petrochemical products from unintentional oil spills or use of crude oil ingredients, herbicides, and pharmacological amenities, and they have a very varying composition [49]. Despite some being dumped on land, very few are useful for forestry or agriculture. Moreover, some substances are rarely, or never, utilized for land application due to their potential hazard, such as the presence of HMs (such as Cr, Pb, and Zn) or toxic organic compounds. In addition, certain substances exhibit inadequate soil conditioning properties or possess minimal nutritional value for plant growth [40].

2.5. Sewage Water

It has been a regular practice for 400 years in various regions of the world to apply municipal, industrial, and associated wastes and effluents to land [50]. An estimated 20 million acres of cultivable land globally are reported to utilize wastewater for irrigation purposes. Studies indicate that in numerous Asian and African towns, wastewater irrigation-based agriculture provides 50% of total of the city’s supply of vegetables [51]. Farmers are typically more concerned with increasing their yields and earnings than they are with the advantages or risks to the environment. Although the metal concentrations in industrial wastewaters are typically low, prolonged irrigation of land with such waters can eventually result in the accumulation of HMs in the soil.

4.1. Physical Techniques

4.2. Chemical Remediation

It describes a particular technique for removing pollutants that makes use of chemical reagents, processes, and principles. Common methods for remediating contaminated soil include solidification/stabilization, soil washing, and soil flushing [70]. Solidification technology is often employed to reduce the mobility of heavy-metal pollutants by mixing contaminated soils with chemicals or materials. Stabilization involves implementing chemical reactions to reduce the mobility of pollutants, while solidification entails physically encapsulating the impurities within a solid matrix consisting of cement, asphalt, or thermoplastic binders [72]. Chemical bondings as well as encapsulation are the two basic interactions that can immobilize HMs in the glass matrix. Nitrification is a process of solidification and stabilization that requires thermal energy (1400–2000°C). It can be accomplished by combining polluted soil with glass-forming intermediates, heating the compounds until they become liquid, and then cooling the liquid to produce an amorphous relatively homogenous glass [73]. Chemical bondings as well as encapsulation are the two basic interactions that can immobilize HMs in the glass matrix [74]. Soil washing and soil flushing are highly effective techniques for remediation purposes aimed at eliminating pollutants from the soil. Various agents, such as water [75], organic acids [76], chelating agents [77], surfactants [78], saponin [79], and low-molecular-weight organic acids [80], have been identified as successful washing agents, ensuring optimal removal of HMs. Among these, EDTA has proven to be the most efficient chelating agent for extracting HMs from contaminated soils [81]. EDTA offers advantages such as minimal impact on soil microorganisms and enzyme activity, low biodegradability, enhanced metal extraction efficiency, accessibility to appropriate recycling methods, and availability for use in the remediation process [82].

4.3. Biological Techniques

4.3.3. Bioremediation

Bioremediation is the process of converting environmental pollutants into less harmful forms by using living organisms, primarily microbes. Methodology used in bioremediation is mostly based on biodegradation. It refers to the complete conversion of harmful or naturally occurring organic contaminants into substances that are safe for human, animal, plant, and marine life [93]. The biodegradation of a wide range of organic compounds has been explained by a variety of mechanisms and pathways; for instance, it can occur both with and without oxygen. Bioremediation is an effective method that aims to mitigate the presence of toxic compounds, including HMs, by converting them into less harmful substances. This technique contributes to the removal of potentially hazardous materials from contaminated environments, as well as the degradation of organic substances, leading to the complete mineralization of organic matter into components such as carbon dioxide, water, and nitrogen gas [94]. The application of bioremediation can be carried out using in situ or ex situ approaches, both of which are suitable for treating soil contamination [Figure 3]. There are several in -situ methods, including bioattenuation, biostimulation, biosparging, and bioventing. To encourage the growth of native or introduced microorganisms, bioventing entails adding oxygen to the soil. Biostimulation entails the provision of particular nutrients and ideal environmental conditions at the site to promote the growth of local microorganisms [95]. A contaminated site can be passively remedied through bioattenuation, which is applicable for both disintegrating and recalcitrant chemicals and necessitates ongoing monitoring. Biosparging is the process of supplying air under compression underneath the water table to raise the oxygen concentration and speed up microbial activity [96]. Over the past two decades, significant advancements have been achieved in bioremediation techniques with the primary goal of restoring polluted areas in an environmentally friendly and cost-effective manner [97].

Figure 3: Factors affecting bioremediation. [Click here to view]

6.1. As Remediation

Arsenic is difficult to remove from the environment since it is soluble. Arsenic is remedied physically and chemically by an oxidation process that changes As³⁺ into As⁵⁺. It can happen with air oxygen, which normally happens very slowly, or with chemical oxidants like ozone, chlorine, or hydrogen peroxide. This approach costs a lot of money and results in undesirable externalities [110]. The enzyme As oxidase, primarily located within the protoplasm of bacteria capable of oxidizing As, plays a significant role in As metabolism, converts the poisonous As³⁺ into its less toxic version, As⁵⁺, as a result of microorganisms using Arsenic as a source of energy in their metabolic processes [111]. Numerous researches undertaken over the years have revealed that Bacillus spp. can absorb Arsenic, making it one of the most significant bacteria for minimizing As contamination [Liao et al., 2011]. Arsenic removal conducted by Bacillus spp. such as B. cereus, Bacillus aryabhattai [112], and Bacillus megaterium [113]. Anaerobic respiration of As⁵⁺ is also done by B. cereus [114]. Oxidative phosphorylation is essential for all living things, and this is unavoidable. Since As⁵⁺ and phosphate are structurally identical, it may act as an inhibitor of oxidative phosphorylation [115]. The pathways known as Pit and Pst, commonly utilized for phosphate uptake, serve as the means through which As⁵⁺ enters the biological system of organisms [116]. Adenosine triphosphate production is inhibited and phosphorylation metabolic pathways are hampered [117]. When it internalizes, it attaches to the respiratory enzymes right away using their sulfur residue [118]. In Bacillus species, the Ars operon uses genes such as arsA, arsB, arsC, arsD, and arsR to bioremediate As. ArsA and ArsB are ATPases, ArsC converts As³⁺ to As⁵⁺, ArsD is a metallochaperone, and ArsR is a repressive inhibitor [119,120]. Normally, As³⁺ is carried out of the cell by ArsB after being converted from As⁵⁺ that enters the cell by ArsC [121].

6.2. Zn Remediation

The capacity of Bacillus spp. effectively eliminate Zn from polluted environments has been emphasized in various bioremediation trials. Bacillus species can either evolve resistance mechanisms or acquire resistance using plasmids to control this ability [Christofi and Ivshina, 2002]. The Zur family controls Zn absorption in B. subtilis, allowing Zn ions to be transported using two transporter proteins. When there is oxidative stress, the Zn ion absorption pathway in B. subtilis termed ZosA (P-type ATPase) is expressed [122]. In the bacterium B. subtilis, a CPx-type ATPase extrusion pump called CadA plays a crucial role in facilitating the excretion of Zn from highly concentrated solutions. Furthermore, it has also been revealed in latest studies that certain Bacillus species, including Bacillus altitudinis, B. subtilis, B. cereus, Bacillus jeotgali, and B. licheniformis remove Zn from the environment [123-125].

6.3. Ni and Cd Remediation

Although there are various ways to remove Ni from solid matrices, the best ones are those that can do it before the Ni enters the environment. Throughout the years, various physicochemical techniques have been employed to eliminate Ni from aqueous media [126]. Regardless of the techniques previously employed, recent advancements have introduced more cost-effective and efficient methods for Ni removal. Among these methods, adsorption techniques, particularly utilizing biomass such as sugarcane, corn cobs, citrus peels, and barks, have gained prominence [127]. The more effective way to remove Ni ions from media that has been contaminated with Ni is through bioremediation employing gram-positive bacteria like Bacillus spp. Extensive studies [128,129] have shown the consumption and removal of nano particles from polluted sites like soils, sewage, and streams. It has also often been reported that Bacillus thuringiensis may absorb and eliminate Ni from polluted surroundings [130]. In a latest study, B. megaterium was obtained from soils that had been contaminated with Ni, and it was able to absorb more than 500 mg of Ni there, despite the presence of more than 3000 mg/L of Ni salt there earlier [131]. Bacterial resistance mechanisms, which ultimately make it easier for metal ions to enter and exit the cell, are necessary for the elimination of Ni by bacteria. It has long been known that members of the CDF family, which includes Ni, facilitate the efflux of several metal ions [132]. The cation diffusing transporter CzcD in B. subtilis is considered to prevent the cell from excessive Ni^2+, Cu+, Zn2+, and Co2+ concentrations. Under favorable conditions, metal ions in association with citrate can be absorbed by B. subtilis through the metaldicitrate absorption system known as CitM, thereby potentially increasing their toxicity [133]. Since B. licheniformis eliminated more than 98% of Cd²⁺, it is a highly efficient adsorbent for the effective removal of Cd²⁺ ions [134]. There are other reports that Bacillus safensis and Bacillus catenulatus are capable of eradicating Cd²⁺ [135,136].

6.4. Pb Remediation

There have been reports of Pb- resistant capability of Bacillus spp. in the past. Bacillus speciesexploit the pbr operon and active transport as possible defenses against the harmful effects of Pb [137,138]. It is immobilized by microorganisms through biosorption, adsorption, chelation, extrinsic sedimentation, complexation, and adsorption. Several methods incorporate phosphate, carboxyl, carbonyl, sulfhydryl, and hydroxyl groups in bacterial cell walls, which give the cell wall a negative charge. When Pb binds to any of these, an insoluble material is produced. The capacity of organic macromolecules such as proteins, polypeptides, and polysaccharides to sequester Pb using electrostatic forces including covalent bonds, ionic bonds, and Van der Waal’s forces make adsorption through the cell wall a viable alternative route [139]. By altering the DNA, proteins, and lipids and even substituting the necessary ions inside the enzymes, Pb interacts with bacterial metabolism, structure, and biological activities [140]. To protect themselves from Pb toxicity, microbes exhibit interfacial deposition, ostracization, volatilization, biomethylation, cellular binding, intrinsic sequestration, and increased siderophore synthesis. Bacillus spp. especially B. cereus use one or more of these techniques, similar to other Gram-positive bacteria, to remove Pb from polluted sites [141].

6.5. Cu Remediation

Similar to several other HMs, copper is considered to play a key role in the physiology of B. subtilis, although quantities over typical ranges can be hazardous to the cells. B. cereus, B. thuringiensis, Bacillus sphaericus, and B. licheniformis species are known to participate in the removal of Cu from environments when its concentrations exceed the permissible levels [142-145]. The transport of Cu in the cytosol of B. licheniformis is facilitated by CueR, a protein that is similar to CueR found in other bacterial species [146]. B. subtilis CueR controls the copZA operon, which encodes a P-type ATPase for Cu extrusion, a constituent of the vital category that exports metal from the cell, along with a Cu facilitator. CopB is in charge of Cu extrusion and decontamination in the latter, whereas CopZ is essential as a Cu chaperone in the former, transporting Cu to CopA, which helps to Cu absorption [147]. B. subtilis has shown that YcnJ is associated with the Cu absorption function of the copZA operon. According to their model, this protein works in collaboration with specific Cop proteins to facilitate the transport of Cu both within and outside of the cell [148].

6.6. Cr Remediation

The innate resistance of microbes in Cr-contaminated habitats allows them to avoid metal stress by metal absorption, efflux, or detoxifying by lowering metal ion immobilization [149]. The enzyme-mediated biotransformation of Cr⁶⁺ by bacteria out of its hazardous to non-hazardous state (Cr³⁺) is thought to be one of the most effective and affordable ways to remove Cr from polluted site and wastewater. The enzymatic reduction of chromate in both Gram-positive and Gram-negative bacteria is regulated by an enzyme known as ChrR, also known as chromate reductase. This enzyme is predominantly found in Cr-resistant bacteria and is not commonly associated with plasmids [150]. The membrane-bound component and the cytosolic component, respectively, can mediate this reduction both aerobically and anaerobically. Furthermore, the reduction of chromate ions in Bacillus spp. is mediated by an aerobic mechanism, in which electrons are moved from the hexavalent to the trivalent state of Cr. An unstable intermediate is produced during this transition (Cr⁵⁺), which is controlled by NADH/NADPH [151]. Numerous studies Nguema et al. [152] and Joshi et al. [153] indicated that B. licheniformis removed 95% and 69.4% of Cr. Over 81% of the Cr was eliminated by B. cereus. The effectiveness of other Bacillus species in reducing Cr contamination has also been reported [154].

6.7. Hg Remediation

According to several studies conducted over the years, the several species of Bacillus contribute to the bioremediation of Hg in a positive way. Hg has a hazardous impact on biological systems due to its high toxicity. Bacteria are armed with a variety of methods to protect their survival when exposed to high levels of harmful Hg. Hg resistance genes and operons, such as the Mer operon, have been identified in both gram-positive and gram-negative bacteria [155]. A limited range Mer operon and a broad range operon are the two different forms of Hg resistance genes found in bacteria. Inside the cell, Hg is forced to undergo reversible detoxification from its hazardous to non-hazardous form, yet diffusion aids in Hg’s exit from the body. Once the metal ions have left the cell, different bacterial species may once more subject them to oxidation [156]. Numerous bacteria have been used to study the phenomena, where the activation of this phenomenon by the activator protein MerR results in the target identification of Hg. The mercuric reductase and lyase enzymes, which are inherited by the MerA and MerB genes, assist the elimination of inorganic Hg²⁺ and organic Hg [157]. In addition, the various other forms of Hg might regulate its transit and bioaccumulation, which might lead to Hg toxicity in environments and ecosystems close to Hg mines or emission sites [158]. Metallothioneins play a significant role in the bioremediation of Hg by accumulating Hg ions in an inactive state and facilitating their transformation through enzymatic processes. Gram-positive and Gram-negative bacteria both share the Mer operon. Although the pathway of Hg resistance in Gram-negative bacteria is better understood compared to Gram-positive bacteria, significant progress has been made in unraveling the mechanisms of Hg resistance in both bacterial groups [159]. Moreover, it was reported that soil-isolated Bacillus spp. possessed Hg-resistant genes, which aided in the removal and subsequent bioremediation of Hg [160]. To enhance the biosorption and exudation of Hg from contaminated sites, genetic modification was performed on B. cereus by introducing a mer operon derived from another Bacillus species, B. thuringiensis. This modification aimed to confer Hg resistance to B. cereus and improve its capacity for Hg removal [161].

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