Advancing Phytoremediation: A Review of Soil Amendments for Heavy Metal Contamination Management

Abstract

Heavy metal (HM) contamination poses a major threat to environmental health, agriculture and human well-being, requiring effective and sustainable remediation strategies. Phytoremediation, an eco-friendly and cost-effective approach, is widely used for the remediation of HM-contaminated soils. Although phytoremediation holds considerable potential in the extraction, stabilisation and degradation of HMs, its effectiveness is often constrained by limited metal bioavailability, plant stress under toxic conditions and slow metal uptake rates. To address these limitations, this review examines the integration of various soil amendments—the application of biochar, compost, plant exudates, microbial agents and chelating agents—to enhance phytoremediation efficiency. This review critically evaluates empirical evidence on the effectiveness, scalability, economic feasibility and environmental impact of these amendments. By synthesising recent studies, this review advances the understanding of amendment-assisted phytoremediation as a viable solution for treating HM-contaminated soils. In addition, this review identifies practical applications, discusses limitations and explores the potential synergies of these amendments to optimise phytoremediation strategies, ultimately contributing to more effective and sustainable environmental cleanup efforts.

1. Introduction

Contamination by heavy metals (HMs) and metalloids in soils poses severe environmental and health risks because of their toxicity, persistence and bioaccumulation in ecosystems. HMs such as Cd, Pb, Ni and Cr and metalloids, particularly As, are substantial threats to both ecological and human health. Unlike most HMs and metalloids, which are typically cationic, As exists in anionic forms. Despite this difference, As remains a potent pollutant owing to its ability to disrupt cellular function, often at considerably low exposure levels [1]. The contamination of soil by HMs primarily stems from anthropogenic activities such as industrial processes, mining, wastewater irrigation and fertiliser and pesticide use. This contamination is further exacerbated by natural processes such as mineral weathering and volcanic activity, which contribute smaller amounts of metals to soil compared to the contribution of human activities [2]. This widespread contamination not only affects soil productivity and food security but also contributes to environmental degradation and reduced resilience to climate change. Conventional soil remediation techniques, including physical, chemical and thermal techniques, are highly effective; however, they are often associated with high costs, energy consumption and secondary contamination risks [3]. Consequently, these techniques are unsuitable for large-scale or long-term application, particularly in resource-constrained settings. Phytoremediation is an emerging, sustainable, plant-based remediation technique that exploits the natural ability of plants to accumulate, stabilise or transform soil contaminants. It is environmentally friendly and socially acceptable and preserves the integrity of soil ecosystems offering an eco-conscious alternative with potential climate co-benefits [4].

Phytoremediation encompasses a variety of biological processes, including phytoextraction, phytostabilisation, rhizodegradation, rhizofiltration, phytovolatilisation and phytodegradation. These mechanisms differ in their function—some accumulate contaminants into aboveground biomass, while others immobilise or detoxify pollutants within the root zone. Among them, phytostabilisation is especially relevant for preventing the mobility and leaching of metal ions and complexes in soil [5,6,7]. Phytostabilisation involves using plants to reduce the mobility and bioavailability of metal ions and metal–organic complexes. This process includes root sequestration, adsorption to soil particles and precipitation, effectively preventing leaching into groundwater or bioaccumulation in the food chain. Suitable plant species develop extensive root systems and release compounds that alter the rhizosphere chemistry to immobilise contaminants [5,6]. The overall success of these processes is influenced by a complex interplay of biological, chemical and environmental factors, such as contaminant concentration, soil pH and texture, organic matter content, plant genotype and rhizospheric microbial activity. To enhance the effectiveness of phytoremediation and overcome these limitations, various strategies and techniques have been developed. These include leveraging beneficial microbial interactions (Microbial-Mediated Phytoremediation), where symbiotic microbes such as rhizobacteria and mycorrhizal fungi enhance metal solubility and plant stress tolerance; applying chemical agents to alter contaminant mobility and uptake (Chemical-Mediated Phytoremediation); incorporating organic materials such as compost or biochar to improve soil health and contaminant availability (Organic Amendment-Assisted Phytoremediation); and utilising naturally tolerant or genetically engineered plant species to improve uptake and detoxification capacities (Plant-Based or Genetically Enhanced Phytoremediation) [8].

Integrating soil amendments with phytoremediation has been a widely studied strategy for enhancing phytoremediation efficiency. Amendments such as biochar, compost, microbial agents, plant exudates and chelating agents improve phytoremediation efficiency by modifying soil properties, increasing nutrient availability and enhancing contaminant bioavailability [9,10]. Research indicates that biochar reduces metal toxicity to plants while maintaining metal bioavailability for uptake and improves soil structure and nutrient retention [11]. Compost, derived from organic waste, supports microbial diversity and nutrient cycling, both of which are crucial for sustained plant growth [12]. Several microbial agents, such as plant growth-promoting bacteria (PGPB) and mycorrhizal fungi, help plants resist metal stress by facilitating metal uptake or stimulating plant metal tolerance mechanisms. In addition, plant exudates—particularly root exudates—can alter soil pH and redox potential, increasing metal availability for plant absorption while fostering beneficial microbial interactions [8].

Several studies have examined the role of soil amendments in enhancing phytoremediation, as shown in Figure 1. According to Mahar et al. [10], various soil amendments can enhance the phytoextraction of HMs by enhancing their mechanisms and effectiveness. Gavrilescu et al. [8] explored strategies to enhance phytoremediation by optimising plant–microbe interactions and improving soil conditions. Lenoir et al. [13] reported that arbuscular mycorrhizal fungi (AMF) support the phytoremediation of contaminated soils, particularly when persistent organic pollutants are present in such soils. In addition, Wang et al. [4] discussed the environmental, social and economic implications of using green materials and remediation technologies.

This review advances current research by synthesising published studies on the effects of various soil amendments on phytoremediation. This review aims to compile empirical evidence demonstrating that amendments such as biochar, compost, microbial inoculants and plant exudates enhance contaminant uptake and support plant health in HM-contaminated soils. In addition, it evaluates the effectiveness, limitations and economic feasibility of these strategies. By emphasising field studies and real-world applications, this review positions phytoremediation as a viable, sustainable and climate-conscious solution for HM-contaminated soils. Its low-energy, nature-based approach aligns with global goals for ecological restoration and carbon footprint reduction.

2. Materials and Methods

2.1. Data Collection and Methodology

In this study, we conducted a bibliometric analysis to examine research trends in phytoremediation and soil amendments for HM contamination. Initially, searches were conducted using both the Web of Science (WOS) and Scopus databases. After comparing the results, we chose to proceed with Scopus. The search included the keywords ‘phytoremediation’, ‘soil amendments’ and ‘heavy metals’ within the title, abstract and keyword sections of the analysed articles. Covering the period from 2014 to 2024, the search yielded approximately 285 articles, of which approximately 170 relevant articles were selected for systematic analysis. The analysis was performed using VOSviewer version 1.6.20. to visualise collaborative networks, keyword co-occurrence and research trends over time.

2.2. Research Trends over Time

Publication and citation numbers in this field have progressively increased over the past decade. Initial phytoremediation studies (2014–2016) resulted in publications focused on fundamental mechanisms, while later studies (2017–2024) resulted in a sharp increase in the number of publications that highlighted applied research and advanced soil amendments. This rapid increase in the number of publications reflects the increasing interest in sustainable, environmentally friendly remediation technologies for HM pollution.

The trends in publication and citation counts (cumulative citations received by publications from each year from 2014 to 2024) are shown in Figure 2. The bar chart represents the citation count, and the line graph depicts the annual publication output. Publication trends are an indicator of research interest in this field (phytoremediation). Between 2014 and 2016, research output remained low. However, a sharp increase between 2017 and 2024 indicates a growing interest in this field. Steeper slopes in the publishing trend indicate periods of heightened research activity, reflecting increased awareness and the significance of studies published during those years.

2.3. Leading Countries in Research Output

Table 1. Leading countries in phytoremediation and soil amendment research.

Country	Documents	Citations	Total Link Strength
China	73	5585	28
Pakistan	14	2536	16
United States	23	2680	15
Australia	11	2435	11
Poland	14	464	9
Spain	16	822	9
France	12	522	7
India	25	1877	4
Italy	9	406	4
Iran	8	156	3

presents the top 10 countries based on publication count and total citations. China leads the field with 73 publications and 5585 citations, followed by the United States, Pakistan and Australia. The total link strength highlights strong international collaboration, particularly between China, the United States and Pakistan.

2.4. Keyword Co-Occurrence Analysis

A keyword co-occurrence analysis was conducted to identify emerging research themes and key focus areas in phytoremediation and soil amendments for HM-contaminated soils. Figure 3 shows the network of frequently co-occurring keywords, providing insights into major research directions.

The primary research themes identified include the following:

• Phytoremediation mechanisms such as phytoextraction, phytostabilisation and bioaccumulation.
• HM contaminants such as Cd, Pb, As and Cr.
• Soil amendment strategies using biochar, immobilisation agents and organic amendments as commonly studied solutions.
• Bioremediation approaches focusing on microbial interactions, mycorrhizal fungi and bioavailability reduction.
• Environmental impact considerations, including soil pollution, remediation effectiveness and sustainability.

The most frequently occurring keywords are summarised in

Table 2. Most frequently occurring keywords in phytoremediation and soil amendment research.

Keyword	Frequency
Heavy metals	120
Phytoremediation	98
Soil amendments	85
Biochar	72
Immobilisation	65
Cadmium	60
Soil remediation	58
Bioremediation	54

, highlighting key research trends in phytoremediation and soil amendments. The data presented in Table 2 indicate a growing focus on innovative soil amendment and plant-based remediation techniques.

2.5. Document Co-Citation Analysis

A co-citation analysis was conducted to identify the most influential studies on phytoremediation and soil amendments. This analysis highlights key studies that have shaped the field.

Table 3. Most cited documents in phytoremediation and soil amendment research.

Document	Citations
Ali et al. [14]	3137
Bolan et al. [15]	1748
Sarwar et al. [16]	1131
Mahar et al. [10]	996
Koptsik [17]	165
Chirakkara et al. [18]	129
Gascó et al. [19]	101
Mosa et al. [20]	96

lists the most cited documents in this domain.

The data presented in Table 3 indicate that extensive studies on biochar applications, microbial-assisted remediation and immobilisation have considerably influenced the field. These foundational studies continue to influence research and applications in soil remediation. The bibliometric analysis further revealed a growing research interest in phytoremediation and soil amendments for HM-contaminated soils. China leads in research output, followed by the United States and Pakistan, all of which exhibit strong international collaboration. Keywords that dominate research include biochar, immobilisation and microbial-assisted phytoremediation. Future research should prioritise field-scale implementation and the integration of machine learning for predictive modelling to enhance phytoremediation strategies.

3. Amendments Used in Phytoremediation

3.1. Biochar

3.1.1. Properties and Mechanisms of Biochar in Phytoremediation

Biochar is gaining widespread attention owing to its efficiency in numerous applications. Furthermore, its beneficial properties have captured scientific interest, leading to the creation of multidisciplinary areas in science and engineering [21]. Biochar is a fine-grained, carbon-rich porous material produced via the pyrolysis or carbonisation of various feedstocks such as plant residues, sludge and organic manure under oxygen-limited conditions [22]. As a soil amendment, biochar enhances soil quality and serves as a long-term carbon sequestration agent, reducing atmospheric CO₂ levels. The physicochemical properties of biochar are considerably influenced by the type of feedstock and specific pyrolysis conditions used in its production [23,24]. Slow pyrolysis yields biochar with consistent and homogenous properties, whereas fast pyrolysis produces biochar with a more diverse chemical composition [25].

Because of its unique physicochemical properties, such as alkaline pH, large specific surface area (SSA) and strong HM immobilisation capacity, biochar plays a crucial role in soil improvement and HM remediation [26]. Its large surface area drastically enhances HM absorption by increasing the number of active sites and optimising the pore structure, thereby improving the chemical interactions and stability. Biochar facilitates the formation of metal–biochar complexes via cation-exchange with metals such as Na⁺, K⁺, Ca²⁺ and Mg²⁺ as well as via physical adsorption [27,28]. Its alkaline nature, particularly at high pyrolysis temperatures or when derived from specific feedstock, can increase soil pH, leading to the precipitation of HMs as insoluble compounds. This process reduces the mobility and bioavailability of HMs in contaminated soil [29]. The pH of biochar is considerably affected by the pyrolysis temperature. Higher temperatures generally produce more alkaline biochar. For example, biochar generated at 700 °C typically has a higher pH than that produced at 400 °C, regardless of the feedstock type or residence time [30,31]. Figure 4 shows the overall impact of biochar on soil properties and phytoremediation.

Research on the use of biochar in phytoremediation has considerably increased over the past decade. A WOS database search using keywords such as ‘phytoremediation’, ‘biochar’ and ‘heavy metals’ identified over 400 relevant publications. China leads this research area, followed by India and Pakistan. Studies indicate that the effectiveness of biochar in phytoremediation depends on the feedstock type, preparation process and application dosage, all of which determine its physical, chemical and biological properties.

Biochar is primarily derived from forestry biomass, crop residues and organic solid waste. Common feedstocks include straw, seed husk, wood chips, bark, pericarp, animal waste and sludge. The characteristics of plant and organic solid waste biomass differ considerably. Plant biomass has a low ash content, high calorific value, high bulk density and small void fraction, whereas organic solid waste has a high ash content, low calorific value, low bulk density and large void fraction [32]. Feedstock selection is crucial because manure-based biochar generally contains high nutrient levels, making it beneficial for phytoremediation. Additionally, biochars with a high ash content (such as those obtained from certain manures) exhibit a greater cation-exchange capacity (CEC), which helps to enhance the properties of biochar-added soils [33,34]. The CEC of biochars can be enhanced by increasing the negative charge density of soil. This enhancement is primarily attributable to the negative surface charge and charge density of biochar as well as to the contribution of oxygen-containing functional groups that form on the surface of a material owing to oxidation that further increase its negative charge density [35].

The pyrolysis temperature and production methods are crucial in determining the structural and chemical properties of biochar. Increasing the pyrolysis temperature drastically alters nutrient availability [36,37]. In particular, with increasing pyrolysis temperature, the C, P, K, Ca and ash contents, pH and SSA increase, whereas the N, H and O contents decrease. The trend has also been observed in studies conducted by Lehmann and Joseph [38] and Weber and Quicker [39]. Biochar plays a vital role in the phytoremediation of HMs by regulating their mobility and bioavailability through multiple mechanisms, including metal immobilisation, enhanced metal uptake and microbe–metal interaction.

Biochar immobilises HMs by reducing their bioavailability in soil through surface adsorption, cation-exchange and precipitation. Functional groups such as hydroxyl (–OH), carboxyl (–COOH) and phenolic moieties actively bind with HMs, preventing their leaching [28]. In addition, biochar increases soil CEC, facilitating the exchange of toxic metals with less toxic cations such as Ca²⁺, Mg²⁺ and K⁺ [34]. Its alkaline nature increases soil pH, leading to the precipitation of HMs as insoluble, stable hydroxides, which further limits their mobility and toxicity [30].

However, under certain conditions, biochar can enhance metal mobility, thereby improving phytoremediation efficiency. It releases dissolved organic carbon (DOC) and humic-like metal-binding compounds, increasing metal bioavailability for plant uptake [40]. Additionally, biochar affects redox-sensitive metals such as As, Cr and Fe, altering their speciation. For example, biochar with electron-donating functional groups can reduce Cr(VI) to the less toxic and more stable Cr(III) [29]. Engineered biochars, e.g., Fe-modified and Mn-doped biochars, selectively increase the mobility of metals, facilitating their uptake by hyperaccumulator plants [35].

Biochar also affects soil microbial communities, further enhancing phytoremediation. It provides a favourable habitat for beneficial microorganisms, such as plant growth-promoting rhizobacteria (PGPR) and mycorrhizal fungi, both of which facilitate metal uptake and improve plant tolerance to metal-induced stress [41]. Additionally, biochar modulates microbial enzyme activity, promoting metal detoxification and organic pollutant degradation and thereby contributing to increased plant biomass yield [42]. By adsorbing toxic metal ions, biochar mitigates HM stress on plant roots, facilitating plant establishment and growth [43].

Table 4. Selected studies on biochar-assisted phytoremediation of metal- and metalloid-contaminated soils.

Feedstock and Pyrolysis Degree	HMs	Plant Species	Key Observations and Effects	References
Bamboo, rice straw (>500 °C)	Cd, Cu, Pb and Zn	Sedum plumbizincicola	Increased the aboveground biomass of Sedum plumbizincicola while reducing the solubility and accumulation of Cd, Cu, Pb and Zn.	Lu et al. [44]
Corn straw (≥500 °C)	Pb	Populus deltoides (male and female)	Biochar enhanced total biomass by 29% in females and 26% in males under Pb stress. Without biochar, biomass was reduced by 11% in females and 3% in males. Enhanced antioxidative response in males. Improved soil microbial diversity and stability.	Su et al. [45]
Coconut shells (800 °C)	Cd, Pb and Zn	Salix smithiana Willd.	Increased phytoextraction efficiency. High biochar application (5, 10 and 15% w/w) reduced metal phytotoxicity in soil solution, improved biomass growth in Salix smithiana and enhanced HM uptake by plants in the amendment treatments.	Pračke et al. [46]
Pine needle (500 °C)	Cd	Bidens pilosa L.	Biochar amendment enhanced Cd accumulation in roots and shoots, promoting dry weight and root elongation.	Manori et al. [47]
Bamboo biochar (600 °C)	Cd and Zn	Salix psammophila	Stimulated Cu, Cd and Zn accumulation in plant tissues. The 3% bamboo biochar (BBC-3%) treatment significantly improved Cd and Zn uptake. Bamboo biochar amendment improved the transfer and bioconcentration factor values of Cd, Zn and Cu compared with the control.	Li et al. [48]
Cornstalk biochar (500 °C)	Cd	Beta vulgaris var. cicla L.	Increased Cd concentrations in leaves (36%) and roots (52%). Root dry weight increased by 267% and Cd accumulation increased by 206%.	Gu et al. [49]
Wood-derived biochar	Cd and Zn	Noccaea caerulescens	Improved seed germination and plant survival. Increased root surface density. The hyperaccumulating plants removed approximately 40% of the initial Cd contamination from the soil.	Rees et al. [50]
Coconut shell biochar	Cd and Zn	Salix × smithiana (willow)	Reduced Cd and Zn leachate concentrations by 99% in all biochar treatments. Biochar significantly increased biomass production.	Břendová et al. [51]
Oak wood (400 °C)	Pb	Lactuca sativa	Biochar reduced Pb bioavailability by 75.8% and bioaccessibility by 12.5% in soil. Increased seed germination by 360% and root length by 189% compared to unamended soil. Improved soil quality and supported plant growth.	Ahmad et al. [52]
Pruning residues in orchards (550 °C), fir tree pellets (350–400 °C) and manure pellets mixed with fir tree pellets	Cd and Pb	Anthyllis vulneraria subsp. polyphylla, Noccaea rotundifolium subsp. cepaeifolium and Poa alpina subsp. alpina	Different biochars influenced pH, EC, CEC and metal bioavailability. Manure pellets and pruning residue biochar reduced Cd and Pb in plant shoots. Manure pellet biochar at a 1.5% dose increased biomass production. Biochar effects vary with feedstock and soil characteristics.	Fellet et al. [53]

presents the key studies on the biochar-assisted phytoremediation of metal- and metalloid-contaminated soils.

3.1.2. Biochar in Combination with Other Amendments

Despite growing interest in combining biochar with other soil amendments to improve soil quality and support plant growth, research on the co-application of biochar within the environmental system remains limited. This gap is particularly evident in the phytoremediation of HMs. A bibliometric analysis indicates that research on the integration of biochar with bacteria for HM remediation has recently gained momentum, with a considerable increase in the number of annual publications from 2019 to 2024.

A recent study investigated the use of rice straw–derived biochar for remediation of HM-contaminated soils, specifically targeting Cd and Pb, by stimulating the beneficial fungus Aspergillus spp. [54]. The findings revealed that biochar considerably altered the composition of soil fungal communities, particularly enriching the Aspergillus genus, which was found to correlate with improved soil remediation. The researchers further isolated a specific Aspergillus strain (strain F8) that enhanced plant growth and facilitated the immobilisation of Cd and Pb. These results indicate that biochar contributes to HM remediation by modifying the soil microbiome and promoting the growth of beneficial fungi [54]. Another study highlighted the role of biochar as a soil in HM-contaminated soil remediation when used in combination with beneficial microorganisms (BMs) and plants [55]. Wu et al. [56] reported that biochar substantially enhances the effectiveness of bioremediation for HM-contaminated soils by improving plant resistance to HM stress and increasing BM colonisation. Additionally, they demonstrated that biochar stabilises HMs in soil through various mechanisms such as ion-exchange, electrostatic adsorption, redox reactions and complex precipitation. This stabilisation reduces the bioavailability of HMs, thereby minimising their toxicity.

Multiple studies have shown that the combined application of fertilisers and biochar yields superior results compared to the use of fertilisers alone, increasing crop production, plant nutrient concentration and soil fertility [57,58]. Additionally, studies have demonstrated that biochar can be effectively integrated with other amendments such as compost, lime and nanoparticles to enhance phytoremediation outcomes [59]. For example, a study revealed that combining neem tree wood biochar with ethylenediaminetetraacetic acid (EDTA) substantially enhanced Pb uptake in Brassica juncea compared with either treatment alone. This finding indicates that biochar can improve the efficiency of chelating agents in mobilising HMs for plant absorption [60]. Furthermore, multiple studies have demonstrated that the combined application of iron sulphate and biochar effectively stabilises As and reduces its bioavailability in contaminated soils through adsorption or surface precipitation. This combination improves soil fertility and promotes plant growth and survival [61,62,63].

Several studies have evaluated the effectiveness of combining biochar with compost for the phytoremediation of HM-contaminated soils [64,65]. For example, a previous study assessed the ability of Bromus tomentellus to remediate Cr- and Zn-contaminated soils using a mixture of biochar and urban waste compost. The results indicated that this combination substantially enhanced HM uptake by seedlings [66]. Similarly, Forján et al. [67] showed that a treatment combining Juncea L. with compost and biochar was the most effective in reducing Zn, Pb, Ni and Cu concentrations in polluted soils.

3.1.3. Limitations, Potential Risks and Critical Assessment of Biochar Applications in Phytoremediation Studies

Biochar is gaining considerable attention for its ability to improve soil quality and immobilise pollutants [68]. However, its application presents potential risks that require critical evaluation to ensure effectiveness and environmental safety. One of the primary challenges in using biochar for phytoremediation is its variable effectiveness, which is influenced by its physicochemical properties. These properties depend on the feedstock type and production conditions [21]. For example, biochars derived from different biomass sources exhibit varying HM adsorption capacities and different effects on soil structure. This variability complicates the development of standard guidelines for biochar applications at different contaminated sites. The diverse physicochemical properties of biochar indicate that its effectiveness in soil remediation can be inconsistent. Therefore, carefully selecting biochar types that are specifically suited to the target soil conditions and contaminants is crucial [69]. Although biochar improves soil properties, its long-term effects on soil health are not completely understood. Interactions between biochar and soil microorganisms can enhance nutrient cycling; however, the precise nature of these interactions and their implications for soil health and pollutant degradation require further investigation. Understanding the long-term influence of biochar on microbial diversity and function is crucial for accurately predicting its effectiveness in remediation efforts [70,71].

Another area of uncertainty is the role of biochar in nutrient cycling. Although biochar enhances nutrient retention and availability, its effect on soil enzyme activity and microbial processes is not yet fully understood. For example, the effects of biochar on soil enzymes such as urease and phosphatase vary, necessitating further research to determine its long-term influence on nutrient dynamics [72].

The literature increasingly acknowledges the environmental risks associated with biochar use, including in phytoremediation. Biochar may contain toxic elements such as Cd, Cu and Pb, particularly when derived from contaminated sources such as industrial waste or sewage sludge. If not properly managed, these contaminants pose substantial environmental risks. Certain surface characteristics of biochar, such as organic functional groups and inorganic components, can trigger chemical reactions that generate harmful compounds, potentially releasing HMs and other pollutants into the environment and degrading soil and water quality [73]. In addition, biochar has a strong capacity to adsorb agrochemicals, such as herbicides and pesticides, which can accumulate in soil and act as secondary pollutants. Its physicochemical properties, including porosity, pH, redox potential, moisture and CEC, considerably influence the soil microenvironment. Changes in these properties can affect contaminant bioavailability, potentially leading to unintended consequences such as the mobilisation of toxic metals [68].

A major challenge in biochar research is its heavy reliance on laboratory studies, which often fail to address the complexities of real-world conditions, such as soil variability, climate change and interactions with existing vegetation. These limitations underscore a critical gap in the field of biochar science. There exists an urgent need for long-term field studies to validate laboratory findings and develop evidence-based applications suitable for diverse environmental settings [74]. Field research enables the examination of the combined effects of biochar and other soil amendments and agricultural practices, enabling the exploration of their synergistic interactions. Understanding the interactions between biochar and fertilisers, cover crops and soil management strategies can optimise its effectiveness and promote sustainable solutions for improving soil health [75,76]. These investigations are essential for assessing the long-term efficacy of biochar, optimising its application, evaluating potential environmental risks and ensuring its safe and effective use in agriculture and environmental management [77].

3.2. Compost and Vermicompost

Compost is produced through the aerobic biological decomposition of organic matter (e.g., animal wastes (such as cattle dung and animal droppings), sewage sludge, green wastes, municipal solid wastes and food wastes) by microorganisms, including bacteria and fungi. This process produces humus-rich products that improve soil properties. Vermicompost is produced through a similar process; however, the organic matter is decomposed by both microorganisms and various earthworm species, such as red wigglers and white worms, producing nutrient-rich materials for soil fertilisation [78].

Compost and vermicompost are effective organic amendments for enhancing phytoremediation efficiency by improving soil health and structure, stimulating microbial activity, supplying plant growth-promoting hormones, contributing organic matter and facilitating the uptake of HMs and pollutants by plants [68]. These benefits enhance plant resilience and support sustainable agricultural practices (

Table 5. Summary of the roles of compost and vermicompost in phytoremediation.

Aspect	Compost	Vermicompost
Nutrient Content	Low levels of macro- and micro-nutrients and primarily enhance soil fertility through organic matter.	High concentrations of macro- and micro-nutrients (N, P, K, Ca, Mg and Zn) are due to earthworm processing [81,82].
Soil Structure Improvement	Enhances soil aeration, moisture retention and overall structure [83].	Improves porosity, aeration and water-holding capacity and reduces bulk density [82].
Microbial Activity	Increases microbial diversity and activity in the soil [83].	Significantly enhances microbial populations and improves nutrient cycling [84].
Heavy Metal Stabilisation	Reduces the bioavailability of HMs through immobilisation [83].	Enhances the phytostabilisation potential and effectively adsorbs HMs.
Promotion of Plant Growth	Supports plant growth by improving nutrient availability and soil conditions [83].	Promotes root development and overall plant vigour owing to enriched nutrients and growth hormones.
Contaminant Degradation	Facilitates organic pollutant degradation through enhanced microbial activity [83].	Stimulates microbial bioremediation for effective pollutant breakdown [84].
Application Rate	Typically requires higher application rates for effectiveness.	More effective at lower application rates owing to higher nutrient availability [84].
Production Time	Longer production time (several months).	Shorter production time (few weeks to months).

). Because of its high organic matter content, vermicompost increases the soil CEC more effectively than raw manure or compost. Its large surface area further supports the phytoremediation process. Additionally, vermicomposting is faster than conventional composting, although its efficiency varies depending on factors such as the waste type, processing method and environmental conditions. Despite these advantages, the use of compost and vermicompost as soil amendments in phytoremediation has certain limitations. The effectiveness of compost and vermicompost depends on the type and concentration of the contaminants, soil conditions and plant species used. Table 5 summarises the distinct roles of compost and vermicompost in phytoremediation [79,80].

Compost enhances the accumulation of HMs such as Zn, Cu, Pb and Cr, thereby supporting the phytoextraction process [85]. In addition, compost improves soil organic carbon and increases plant yield, both of which are crucial for enhancing phytoremediation [61]. Because of its rich organic matter, vermicompost is effective in adsorbing heavy metals (Cd, Ni and Cr) in tropical acidic soils [86]. The relatively high CEC of vermicompost enhances nutrient retention and promotes plant growth, further contributing to the remediation process.

3.2.1. Challenges and Limitations

Although compost and vermicompost offer benefits for phytoremediation, they also present certain challenges. One major issue is the variability in the effectiveness of compost and vermicompost, which depends on the soil type, contaminant composition and organic amendment properties. For example, nutrients or pollutant levels in compost can fluctuate depending on the feedstock used, potentially influencing soil remediation outcomes [87]. Similarly, different feedstocks used in vermicomposting can affect the metal adsorption capacity and soil improvement effectiveness. Another issue is the risk of contamination because compost and vermicompost derived from polluted wastes may contain pesticides, HMs or pathogens. Although composting eliminates pathogens, some survive and pass into the soil, posing risks to soil health and plant growth. Therefore, the appropriate selection and treatment of source materials are essential to ensure high-quality soil amendments based on compost and vermicompost for use in phytoremediation [88].

Furthermore, compost and vermicompost can reduce the bioavailability of HMs but do not always increase plant uptake, which is a key factor in phytoextraction. For example, compost immobilises metals in soil, thereby decreasing their availability for plant absorption [86], which can be beneficial for metal stabilisation but less effective in phytoremediation strategies that aim to extract metals from contaminated sites. Numerous studies have demonstrated the positive effects of compost and vermicompost on phytoremediation. Shrestha et al. [89] investigated the amendment of HM-contaminated soils containing Cd, Co, Ni, Pb and Zn with compost, vermicompost and coconut coir. These organic amendments considerably enhanced the phytoremediation potential of contaminated soils. Liu et al. [87] reported that tropical cattle manure vermicomposts effectively reduced the levels of extractable Cd, Ni and Cr in acidic soils in China.

In addition to facilitating metal removal, compost can modify the physical and chemical properties of soils contaminated with multiple HMs. For example, Zhou et al. [90] reported that the application of red mud and compost to tropical contaminated soils effectively decreased the Cu, Pb, Zn and Cd concentrations while increasing the microbial biomass and soil pH. These findings indicate that mixing compost with other amendments may better enhance the effectiveness of remediation than using compost alone.

3.2.2. Future Directions and Research Gaps

Although considerable progress has been made, further research is needed to understand the long-term effects of compost and vermicompost on soil health and contaminant behaviour. Because of the limited experimental data, additional studies are required to optimise their application across diverse soil types and environmental conditions. In particular, improving phytoremediation efficiency requires investigating the combination effects between compost, vermicompost and other amendments such as biochar, red mud or microbial inoculants [91]. Furthermore, investigating the mechanisms by which compost and vermicompost influence HM bioavailability and plant uptake is essential. A fundamental understanding of these mechanisms will provide guidance for developing phytoremediation strategies tailored to specific contaminants and soil conditions while promoting the sustainable use of compost and vermicompost.

3.3. Plant Exudates and Extracts

Plant exudates and extracts can enhance phytoremediation by influencing microbial activity, soil chemistry and plant growth. Although these organic constituents are derived from plants, they are not soil amendments in the conventional sense but function as adjunctive agents that improve the efficiency of phytoremediation. This section presents their roles, mechanisms and limitations, particularly in relation to sustainable remediation practices in conjunction with conventional amendments. Furthermore, the challenges and limitations associated with using exudates and extracts—whether individually or in combination—must be critically assessed to determine their viability as green alternatives to conventional chemical amendments [92,93].

3.3.1. Root Exudates in Phytoremediation

Root exudates comprise a diverse group of compounds, such as phenolic acids, organic acids, sugars and amino acids, that are released from plant roots. These metabolites facilitate interactions between plants, soil and microorganisms, influencing nutrient availability, pollutant behaviour and microbial communities in the rhizosphere [94]. Notably, root exudates enhance the phytoextraction of HMs such as Cd and Pb by increasing their bioavailability, thereby improving plant uptake and accumulation [95].

However, the impact of the aforementioned amendments on phytoremediation varies considerably. Root exudate composition is species-specific and is influenced by environmental factors, such as the soil type, contamination levels and plant stress [96]. For example, certain root exudates, such as citric acid, enhance the solubility of HMs, promoting their uptake by plants [97]. Moreover, plant exudates can suppress microbe activity or limit contaminant bioavailability. Stressed plants, such as Elymus angustus, may release exudates that suppress hydrocarbon mineralisation [98], which may add complexity to the interactions between exudates, soil and microbes.

Furthermore, root exudates do not always directly affect pollutant mobility. Their effect depends on their chemical properties, with some exudates enhancing contaminant mobility while others inhibit it. For example, carboxylic acids are associated with increased contaminant mobilisation, whereas certain phenolic compounds exhibit the opposite effect. This variability highlights the importance of selecting appropriate plant species and understanding the specific exudates that enhance or hinder phytoremediation processes under given conditions.

3.3.2. Plant Extracts as Phytoremediation Enhancers

Plant extracts derived from various plant parts contain various bioactive compounds such as alkaloids, flavonoids and terpenoids, which enhance phytoremediation through multiple mechanisms. For example, extracts from Phyllanthus emblica and Citrus reticulata have been shown to promote the accumulation of HMs such as Cd and Pb in Solanum nigrum, considerably improving phytoextraction efficiency without reducing plant biomass [99].

Studies have shown that plant extracts can function as chelating agents, improving the solubility and bioavailability of HMs in the soil. They also promote plant growth and stress tolerance, which are crucial for maintaining plant health during phytoremediation. By supplying macro- and micro-nutrients, amino acids and hormone-like growth stimulants, plant extracts improve yields and soil vitality [100]. Additionally, bioactive compounds in plants possess natural antimicrobial properties, which reduce pathogen populations in contaminated soils and thereby foster a healthier rhizosphere [101].

Despite the aforementioned advantages of plant extracts, their use in phytoremediation encounters some challenges. The bioactivity of plant extracts depends on factors such as the extraction method, plant parts used and the concentration of active compounds. Overly concentrated extracts can be phytotoxic, inhibiting plant growth and microbial activity, while excessively diluted extracts may fail to considerably enhance metal uptake [102]. Additionally, for large-scale applications, the ecological sustainability of sourcing plant materials for producing extracts remains a concern.

3.3.3. Challenges and Future Direction in Using Exudates and Extracts

Although root exudates and plant extracts offer promising, eco-friendly strategies for enhancing phytoremediation, their effectiveness varies across different environments, posing a substantial challenge. This variability underscores the need for further research on the composition and functional role of exudates in plant stress responses under various contamination scenarios. In addition, the wide-scale use of plant extracts may be unsustainable if the extraction is resource-intensive or involves cultivation in ecologically sensitive areas. Furthermore, the long-term effects of introducing concentrated bioactive compounds into soils are unclear, with potential consequences such as shifts in microbial community composition or the accumulation of soil-derived secondary metabolites.

To address the aforementioned limitations, future research should focus on standardising protocols for the application of plant extracts and exudates in phytoremediation. This includes selecting plant species that consistently release bioactive compounds that enhance pollutant absorption and degradation. Additionally, the effectiveness of these amendments could be improved by integrating them with other natural soil amendments. Another promising avenue is the genetic or metabolic engineering of plants to optimise exudate production for enhancing phytoremediation performance. Such advancements could enable plants to release specific exudates that target particular contaminants, making phytoremediation more effective and selective.

3.4. Microbial Agents

Excessive HM contamination in soil inhibits plant growth and development, reduces contaminant breakdown and limits metal uptake, ultimately decreasing the effectiveness of phytoremediation [103]. For successful phytoremediation, plants must grow quickly, attain high biomass and absorb significant amounts of HMs through their roots [104]. Microbial agents, particularly PGPR, endophytic bacteria and AMF, play crucial roles in enhancing phytoremediation through multiple mechanisms. These microbes act as growth stimulators, pollutant degraders, nutrient and metal mobilisers and biofilm formers, improving plant resilience and metal uptake [105,106,107].

To address soil and water contamination, biostimulation and bioaugmentation are key strategies that leverage microbial activity. Biostimulation enhances the activity of native microorganisms by supplying nutrients and electron donors, thereby accelerating pollutant degradation. Bioaugmentation introduces specialised or genetically modified microbes that degrade specific pollutants. In some cases, biostimulation can further support bioaugmentation. Both approaches provide effective and sustainable solutions for environmental restoration, enabling tailored remediation strategies [108,109].

3.4.1. Plant Growth-Promoting Bacteria (PGPR)

PGPR are among the most widely used microorganisms in phytoremediation and have recently gained attention for their ability to promote plant growth. Beyond this role, PGPR actively support phytoremediation by improving plant performance and facilitating HM uptake through modifications in metal bioavailability in the rhizosphere. PGPR-mediated mechanisms, including sorption, mineralisation and transformation, play crucial roles in metal uptake by plants [110]. In HM phytoremediation, PGPR function through both direct and indirect mechanisms. Directly, they produce essential compounds such as exopolysaccharide (EPS); siderophore; phytohormones such as auxins, cytokinins and gibberellins; organic acids; and enzymes. These compounds interact with HMs in the rhizosphere, influencing oxidation–reduction reactions, acidification and metal bioavailability, ultimately enhancing uptake by plants. PGPR can also regulate gene expressions related to metal transport, tolerance and chelation in plants, while their role in atmospheric nitrogen fixation further supports phytoremediation. Indirectly, PGPR create a favourable environment for plant growth by producing antibiotics that suppress plant pathogens, thereby improving plant health and inducing systemic resistance. Through these diverse mechanisms, PGPR influence HM bioavailability and accumulation in the rhizosphere, optimising the soil for effective phytoremediation [111,112]. Table 6 shows recent examples of PGPR-assisted phytoremediation of metal-contaminated soil. Despite these advantages of PGPR, their application in phytoremediation has certain limitations:

• Limited effectiveness at high metal concentrations: The effectiveness of PGPR may decrease in soils with high HM levels probably owing to toxic effects, restricting their application to moderately contaminated environments.
• Extended remediation time: PGPR-based remediation is slower than physical and chemical remediation and often requires years to achieve significant results.
• Complex interaction dependencies: PGPR activity is influenced by environmental conditions, the availability of supplementary nutrients and pollutants and interactions with existing microbial populations. These dependencies introduce challenges in terms of precision and practical management.

Table 6. Recent examples of the phytoremediation of metal-contaminated soil assisted by plant growth-promoting rhizobacteria (PGPR).

Host Plant	PGPR Strain	Origin	Key Beneficial Properties	Observed Effects on Plant Growth and Soil Quality	Reference
Helianthus annuus	Trichoderma harzianum, Azotobacter chroococcum and Bacillus subtilis	Cd-contaminated soil	Reduces Cd bioavailability, enhances antioxidant activity and improves nutrient uptake (indole-3-acetic acid (IAA) and siderophores).	Increased biomass, reduced oxidative damage, enhanced metabolite and enzyme activity and reduced Cd levels.	Abeed et al. [113]
Sorghum bicolour	Bacillus thuringiensis SE1C2 + biochar (5%)	Cd- and Zn-contaminated soil	Enhance PGPB colonisation and improve stress tolerance (siderophores, IAA).	Increased shoot/root growth, chlorophyll content and antioxidant activity and reduced Cd and Zn uptake.	Anbuganesan et al. [114]
Brassica juncea	Consortium-BC8 (Klebsiella variicola and Pseudomonas otitidis)	Ni- and Pb-contaminated soil from mines and dumpsites.	Forms a biofilm on roots and enhances metal solubility and uptake (IAA, siderophores and phytoextraction enhancement).	Increased vegetative growth, Ni phytoextraction (TF 1.58) and Pb phytostabilisation.	Sharma and Saraf [115]
Brassica juncea	Bacillus sp. Kz5 and Enterobacter sp. Kz15	Isolated from the rhizospheres of plants grown in copper mine soils	Enhances Cd uptake and improves root morphology and soil health (IAA, siderophores and phytoextraction enhancement).	Increased biomass, Cd concentration, root morphology, photosynthetic activity and rhizosphere soil properties.	Zhang et al. [116]
Lolium multiflorum	Pseudomonas aeruginosa	Isolated from Cu–Cd co-contaminated soil	IAA and siderophores	Increased growth, Cu and Cd uptake and shoot translocation. Biomass increased by 43.1% (T7 vs. T1) and approximately 89% or Cu and Cd were removed.	Shi et al. [117]
Triticum aestivum	Bacillus cereus	-	Enhance antioxidant enzymes (superoxide dismutase (SOD), glutathione S-transferase (GST) and ascorbate peroxidase (APX)) and reduce reactive oxygen species (ROS) and HM bioavailability (IAA and siderophores).	Improved growth rate, photosynthetic efficiency and stress tolerance.	Direk et al. [118]
Helianthus annuus	Brucella intermedium (E1) and Bacillus velezensis (EW8)	Ni–Cd battery waste-contaminated soil	Enhanced antioxidant enzyme activity (IAA and siderophores).	Increased metal accumulation, improved soil quality index and enhanced plant growth.	Kriti et al. [119]

Table 6. Recent examples of the phytoremediation of metal-contaminated soil assisted by plant growth-promoting rhizobacteria (PGPR).

Host Plant	PGPR Strain	Origin	Key Beneficial Properties	Observed Effects on Plant Growth and Soil Quality	Reference
Helianthus annuus	Trichoderma harzianum, Azotobacter chroococcum and Bacillus subtilis	Cd-contaminated soil	Reduces Cd bioavailability, enhances antioxidant activity and improves nutrient uptake (indole-3-acetic acid (IAA) and siderophores).	Increased biomass, reduced oxidative damage, enhanced metabolite and enzyme activity and reduced Cd levels.	Abeed et al. [113]
Sorghum bicolour	Bacillus thuringiensis SE1C2 + biochar (5%)	Cd- and Zn-contaminated soil	Enhance PGPB colonisation and improve stress tolerance (siderophores, IAA).	Increased shoot/root growth, chlorophyll content and antioxidant activity and reduced Cd and Zn uptake.	Anbuganesan et al. [114]
Brassica juncea	Consortium-BC8 (Klebsiella variicola and Pseudomonas otitidis)	Ni- and Pb-contaminated soil from mines and dumpsites.	Forms a biofilm on roots and enhances metal solubility and uptake (IAA, siderophores and phytoextraction enhancement).	Increased vegetative growth, Ni phytoextraction (TF 1.58) and Pb phytostabilisation.	Sharma and Saraf [115]
Brassica juncea	Bacillus sp. Kz5 and Enterobacter sp. Kz15	Isolated from the rhizospheres of plants grown in copper mine soils	Enhances Cd uptake and improves root morphology and soil health (IAA, siderophores and phytoextraction enhancement).	Increased biomass, Cd concentration, root morphology, photosynthetic activity and rhizosphere soil properties.	Zhang et al. [116]
Lolium multiflorum	Pseudomonas aeruginosa	Isolated from Cu–Cd co-contaminated soil	IAA and siderophores	Increased growth, Cu and Cd uptake and shoot translocation. Biomass increased by 43.1% (T7 vs. T1) and approximately 89% or Cu and Cd were removed.	Shi et al. [117]
Triticum aestivum	Bacillus cereus	-	Enhance antioxidant enzymes (superoxide dismutase (SOD), glutathione S-transferase (GST) and ascorbate peroxidase (APX)) and reduce reactive oxygen species (ROS) and HM bioavailability (IAA and siderophores).	Improved growth rate, photosynthetic efficiency and stress tolerance.	Direk et al. [118]
Helianthus annuus	Brucella intermedium (E1) and Bacillus velezensis (EW8)	Ni–Cd battery waste-contaminated soil	Enhanced antioxidant enzyme activity (IAA and siderophores).	Increased metal accumulation, improved soil quality index and enhanced plant growth.	Kriti et al. [119]

3.4.2. Endophytic Bacteria

Endophytic bacteria are microorganisms that live within plant tissues without causing harm or disease to the host [120]. Their role in plant microbiomes is well documented [121], with significant applications in plant disease control [122]. Beyond these functions, endophytes enhance nutrient uptake, stress resistance and phytoremediation. Understanding these complex phenomena deepens our knowledge of plant–microbe relationships, facilitating resilient agriculture and ecosystem restoration. The beneficial effects of endophytic bacteria on host plants are similar to those of PGPR. Similar to PGPR, endophytes stimulate plant growth either directly or indirectly. Their role in enhancing the phytoremediation efficiency of HM is shown in Figure 5.

Endophytes play an important role in phytoremediation by influencing plant growth, reducing phytotoxicity and enhancing plant adaptation to environmental stress. In addition to producing phytohormones, enzymes, organic acids and biosurfactants, endophytes secrete EPS that facilitate metal bioaccumulation and nutrient uptake in plant tissues. EPS, which primarily comprise polysaccharides, nucleic acids, proteins and lipids, considerably contribute to metal complexation, thereby reducing metal bioavailability. Several studies [123,124] have shown that endophytic bacteria isolated from metal-hyperaccumulating plants exhibit remarkable resistance to high metal concentrations, likely due to adaptation to metal-enriched environments. These plants often harbour diverse metal-resistant endophytes that enhance plant growth in highly polluted soils. Bacterial endophytes demonstrate greater efficiency than soil-inoculated bacteria because of their direct involvement in bioaugmentation [125]. Table 7 presents the case studies demonstrating the use of endophytic bacteria in the phytoremediation of HM-contaminated sites.

Challenges Associated with Endophytes:

• Survival in contaminated soils: Endophytes may struggle to survive or establish in heavily contaminated soils, particularly in the absence of suitable host plants.
• Host compatibility: Not all bacterial endophytes that colonise one plant species or cultivar are able to colonise others, leading to host specificity and limiting their broad applicability in phytoremediation.

3.4.3. Arbuscular Mycorrhizal Fungi (AMF)

AMF are widely recognised for their substantial contributions to plant growth and phytoremediation (Table 7). Their cost-effectiveness and environmentally friendly nature make them an ideal choice for sustainable remediation strategies. Notably, AMF form a symbiotic relationship with their host plants, colonising the roots of more than 80% of cultivated vascular plants [126,127]. These fungi establish close intracellular interactions with host roots, playing a crucial role in natural ecosystems by relying on the host for nutrients while simultaneously enhancing soil conditions and plant resilience in challenging environments. AMF improve soil structure and promote plant health by facilitating nutrient and water uptake in exchange for the carbohydrates needed for their own growth [128]. Additionally, they enhance soil properties, serve as natural filters against environmental pollutants and immobilise HMs in plant roots [129].

Table 7. Case studies demonstrating the use of endophytic bacteria in the phytoremediation of heavy metal-contaminated sites.

Bacterial Strains	Plant Species	Heavy Metals	Type of Soil	Significance and Impact	References
Kocuria sp. (LC2, LC3 and LC5), Enterobacter sp. (LC1, LC4 and LC6) and Kosakonia sp. (LC7)	Solanum nigrum	As	Soil with high As concentrations	Enhanced plant growth in Solanum nigrum. Increased bioaccumulation and root-to-shoot transport of As.	Mukherjee et al. [130]
Micrococcus yunnanensis SMJ12, Vibrio sagamiensis SMJ18 and Salinicola peritrichatus SMJ30	Spartina maritima	As, Cu and Zn	HM-contaminated soil	Endophytic bacteria exhibited resistance to multiple HMs and metalloids. Displayed plant growth-promoting properties.	Mesa et al. [131]
Bacillus sp. SLS18	Solanum nigrum L.	Cd	Mine tailing soil	Isolation of 30 Cd-tolerant bacterial endophytes from the roots, stems and leaves of Solanum nigrum L.	Luo et al. [132]
Paenibacillus sp. RM	Tridax procumbens	Cu, Zn, Pb and As	-	Highly resistant to Cu, Zn, Pb and As. Produced growth-promoting substances that enhanced metal tolerance and bioremediation potential.	Govarthanan et al. [133]
Enterobacter sp. (strain SVUB4)	Eichhornia crassipes	Cd and Zn	-	Exhibited several plant growth-promoting traits. Demonstrated the ability to grow in the presence of Cd and Zn.	El-Deeb et al. [134]
Pseudomonas sp. Lk9	Solanum nigrum L.	Cd, Zn and Cu	-	Inoculation with Pseudomonas sp. Lk9 led to improved Fe and P mineral availability in soil, enhanced soil HM availability, increased Solanum. nigrum shoot dry biomass and greater total accumulation of HMs.	Chen et al. [135]

Table 7. Case studies demonstrating the use of endophytic bacteria in the phytoremediation of heavy metal-contaminated sites.

Bacterial Strains	Plant Species	Heavy Metals	Type of Soil	Significance and Impact	References
Kocuria sp. (LC2, LC3 and LC5), Enterobacter sp. (LC1, LC4 and LC6) and Kosakonia sp. (LC7)	Solanum nigrum	As	Soil with high As concentrations	Enhanced plant growth in Solanum nigrum. Increased bioaccumulation and root-to-shoot transport of As.	Mukherjee et al. [130]
Micrococcus yunnanensis SMJ12, Vibrio sagamiensis SMJ18 and Salinicola peritrichatus SMJ30	Spartina maritima	As, Cu and Zn	HM-contaminated soil	Endophytic bacteria exhibited resistance to multiple HMs and metalloids. Displayed plant growth-promoting properties.	Mesa et al. [131]
Bacillus sp. SLS18	Solanum nigrum L.	Cd	Mine tailing soil	Isolation of 30 Cd-tolerant bacterial endophytes from the roots, stems and leaves of Solanum nigrum L.	Luo et al. [132]
Paenibacillus sp. RM	Tridax procumbens	Cu, Zn, Pb and As	-	Highly resistant to Cu, Zn, Pb and As. Produced growth-promoting substances that enhanced metal tolerance and bioremediation potential.	Govarthanan et al. [133]
Enterobacter sp. (strain SVUB4)	Eichhornia crassipes	Cd and Zn	-	Exhibited several plant growth-promoting traits. Demonstrated the ability to grow in the presence of Cd and Zn.	El-Deeb et al. [134]
Pseudomonas sp. Lk9	Solanum nigrum L.	Cd, Zn and Cu	-	Inoculation with Pseudomonas sp. Lk9 led to improved Fe and P mineral availability in soil, enhanced soil HM availability, increased Solanum. nigrum shoot dry biomass and greater total accumulation of HMs.	Chen et al. [135]

AMF enhance the phytoremediation of HMs. AMF directly secrete glomalin, a glycoprotein that binds with HMs and reduces their bioavailability. Their intricate fungal structures also facilitate HM accumulation, restricting metal translocation in plants. They can also adsorb HMs on their surfaces, immobilising them in soil and preventing their uptake. Indirectly, AMF stimulate plant growth and activate enzymatic and nonenzymatic defence systems. They produce enzymes such as superoxide dismutase (SOD), catalase and peroxidase [136]. AMF also synthesise stress-tolerance metabolites that enhance nutrient uptake and improve plant tolerance to HM toxicity [137]. Furthermore, they contribute to soil health by increasing microbial abundance and diversity, thereby enhancing nutrient cycling.

The efficiency of AMF in phytoremediation is influenced by several factors, including the concentration and type of HMs in soils, soil acidity levels and the presence of other mycotrophic plants in soils contaminated with HMs. Despite these challenges, AMF represent one of the best strategies for enhancing HM phytoremediation. Numerous studies have demonstrated that AMF mitigate HM toxicity through direct and indirect mechanisms.

Table 8. Role of arbuscular mycorrhizal fungi (AMF) in the phytoremediation of HM-contaminated soil.

Mycorrhizal Species	Host Plant	Heavy Metals	Significance and Impact	References
Glomus monosporum, Glomus clarum and Gigaspora nigra	Trigonella sp.	Cd	AMF improved Trigonella plant growth, chlorophyll content and protein levels in Trigonella under Cd stress. Reduced Cd translocation and oxidative damage while enhancing antioxidant activity.	Abdelhameed and Metwally [138]
Funneliformis mosseae and Diversispora spurcum (AMF)	Bermudagrass (Cynodon dactylon (L.) Pers.)	Pb, Zn and Cd	Diversispora spurcum significantly enhanced bermudagrass growth and HM uptake. AMF increased soil pH and nutrient levels (P and S) while reducing the availability of Pb and Zn in soil. Decreased Pb translocation in shoots improves bermudagrass suitability for mine wasteland restoration.	Zhan et al. [139]
Rhizophagus irregularis (AMF)	Common Reed (Phragmites australis)	Cu	AMF inoculation promoted plant growth and improved physiological activity in Phragmites australis under Cu stress.	Wu et al. [129]
Glomus mosseae and Glomus intraradices (AMF)	Rosemary (Rosmarinus officinalis)	Cu, Zn, Mn, Cd, Pb and Fe	AMF facilitated plant survival in metal-contaminated soil by enhancing nutrient uptake, reducing metal toxicity and facilitating metal absorption.	Abbaslou et al. [140]
Funneliformis geosporum (AMF)	Wheat (Triticum aestivum L. cv. Gemmeza-10)	Zn	Inoculation with F. geosporum significantly reduced Zn accumulation and inhibited its translocation to wheat shoots and grains.	Abu-Elsaoud et al. [141]
Glomus versiforme and Rhizophagus intraradices (AMF)	Lonicera japonica	Cd	AMF reduced Cd levels in the shoots and roots of Lonicera japonica, increased P acquisition and enhanced antioxidant activity (catalase (CAT), ascorbate peroxidase (APX) and glutathione reductase (GR)), leading to improved plant growth and Cd tolerance and making the plant safer for use in Cd-contaminated soils.	Jiang et al. [142]

presents recent case studies illustrating the role of AMF in reducing HM toxicity and improving plant resilience.

Challenges and Future Directions for AMF:

• Need for field testing: Most AMF studies are conducted under laboratory conditions, and research on their effectiveness in real-world contaminated soils is limited.
• Limited understanding of nutrient pathways: The mechanisms through which AMF acquire nutrients under HM stress, particularly during long-distance metal transport in host plants, remain poorly understood.
• Synergies with other microbes: AMF frequently interact with bacteria in the rhizosphere; however, the full potential of these interactions, such as AMF–PGPR combinations, for enhancing phytoremediation requires further investigation.

Environmental Risks and Potential Impacts:

• Pathogen proliferation: Some microbial amendments, particularly non-native strains, may exhibit pathogenic traits that pose risks to plant, animal or human health. Ensuring microbial safety is essential.
• Nutrient runoff: The addition of nutrients to enhance microbial activity can lead to nutrient leaching, potentially causing eutrophication in nearby water bodies.
• Horizontal gene transfer: The exchange of genetic material between introduced microbes and native soil organisms can lead to unintended ecological consequences, particularly when genetically engineered microbes are involved.

Potential Synergies and Interactions:

• Microbe–microbe interactions: Microbial agents such as PGPR and AMF can interact synergistically to enhance phytoremediation. For example, PGPR may facilitate AMF colonisation, improve metal uptake and increase plant tolerance to HMs.
• Organic and microbial amendment: Combining organic and microbial amendments can enhance phytoremediation. For example, humic substances improve soil conditions, creating a favourable environment for microbial activity that mobilises metals for plant uptake.
• Plant–microbe synergies: Different types of microbes (PGPR, endophytes and AMF) provide complementary benefits at different plant interaction sites, from root-associated processes to internal plant functions, thereby strengthening plant health, increasing plant stress tolerance and enhancing HM accumulation.

3.5. Chelating Agents

The use of chelating agents is a promising strategy for considerably enhancing phytoremediation, particularly in metal-contaminated soils. Chelation, a term derived from the concept of ‘binding’, refers to the process in which ions and molecules form strong complexes with metal ions. In recent decades, this method has been widely applied in various fields. Chelator compounds form stable complexes with metal ions, increasing metal bioavailability and thereby facilitating plant uptake and translocation. However, concerns regarding the environmental impact, biodegradability and toxicity of chelating agents must be evaluated to determine their suitability for phytoremediation. This section discusses commonly used chelators, their mechanisms of action, advantages, limitations and environmental considerations.

3.5.1. Synthetic Chelators: Ethylenediaminetetraacetic Acid (EDTA) and, Diethylenetriaminepentaacetic Acid (DTPA)

EDTA (ethylenediaminetetraacetic acid) is a synthetic chelator that is widely recognised for its ability to enhance metal solubility and plant uptake. Its strong chelating capacity for Pb, Zn, Cd, Cu and Ni improves metal availability in plants. Hosseinniaee et al. [143] reported that EDTA considerably increases the bioconcentration factor of metals such as Pb, Cd and Zn in various plant species. In addition, EDTA application can induce oxidative stress in plants, triggering increased antioxidant enzyme activity, which helps to mitigate HM toxicity. Further research has indicated the effectiveness of EDTA in promoting Cd and Zn uptake in different plants [144]. Moreover, EDTA has been shown to improve plant growth under HM stress and facilitate the remediation of various HMs, making it a versatile solution for phytoremediation [145].

However, the persistence and nonbiodegradability of EDTA pose significant environmental concerns because it remains in soil and leaches into groundwater, increasing soil toxicity. Studies have shown that EDTA treatment enhances Pb and Cd uptake in Pelargonium hortorum and Pelargonium zonale, while high EDTA concentrations reduce biomass, indicating potential phytotoxicity [146]. Kamal et al. [147] reported that high EDTA levels negatively affect plant growth and biomass.

Another effective chelator is DTPA (diethylenetriaminepentaacetic acid), which has shown promising results in the phytoextraction of heavy metals, particularly chromium (Cr) and nickel (Ni) [148]. By increasing the solubility and bioavailability of metals such as lead, thallium, Cr and Ni, DTPA facilitates their uptake by plants, thereby improving remediation outcomes. However, like EDTA, the use of DTPA requires careful management due to the risk of metal mobilisation and leaching into surrounding environments [91].

3.5.2. Biodegradable Chelators: Nitrilotriacetic Acid (NTA) and Ethylenediamine-N,N′-Disuccinic Acid (EDDS)

Biodegradable chelators such as NTA and EDDS are more environmentally friendly alternatives to EDTA. Although considerably less well studied, NTA can enhance metal uptake while exhibiting low soil persistence. Hart et al. [149] demonstrated that NTA combined with APG (alkyl polyglucoside) enhanced Pb phytoextraction in Panicum virgatum. Similarly, Freitas and Nascimento [150] reported that NTA increased Pb uptake in maize, with considerably lower metal leaching risks compared with EDTA.

EDDS has demonstrated effective metal mobilisation with a minimal environmental risk, making it a promising option for enhancing Pb uptake without substantial leaching. In the case of Pb-contaminated soil, EDDS improved metal extraction and reduced phytotoxicity [151]. Additional studies have shown that EDDS enhances Zn accumulation in Medicago sativa and biodegrades within weeks, minimising long-term soil contamination risks [152]. These findings highlight NTA and EDDS as viable alternatives to EDTA for applications requiring eco-friendly chelators.

Comparative studies on EDDS and other biodegradable chelators, such as NTA, have shown that both enhance metal mobilisation; however, EDDS is more effective in facilitating plant uptake while posing fewer environmental risks than EDTA [153]. Therefore, EDDS is a more promising alternative to sustainable phytoremediation practices.

3.5.3. Natural Chelators: Organic Acids

Low-molecular-weight organic acids, such as citric, oxalic, malic and tartaric acids, are natural chelating agents that enhance metal solubility and reduce metal toxicity. Citric acid improves metal mobility and supports plant growth. De Araújo and Do Nascimento [154] reported that the application of citric acid improved Pb mobility, thereby reducing soil toxicity. Furthermore, research on Cucurbita pepo and Raphanus sativus revealed that citric acid enhances Cd and Ni mobilisation, highlighting its potential for the remediation of multiple HMs [155].

Oxalic acid can enhance metal mobilisation, especially for Pb. Fomina et al. [156] reported that the application of oxalic acid considerably increases metal solubility, thereby improving metal availability for plant uptake. Further studies have revealed that oxalic acid considerably increases Pb and Tl extraction by 86% and 43% (compared with the control group without chelating), respectively, highlighting its effectiveness in complex metal remediation strategies [91].

3.5.4. Combination Approaches, Synergies and Future Directions

Combining chelating agents with other soil amendments has yielded synergistic phytoremediation effects. For example, the combined application of citric acid and AMF improved V uptake in Medicago sativa, highlighting the role of AMF in improving metal tolerance [157]. Similarly, the co-application of citric acid and EDTA enhanced Cu uptake in jute, demonstrating the improved efficiency of mixed chelator treatments for metal extraction [158]. Another study demonstrated that the combined application of citric acid and tea saponin improved Pb bioavailability. Research on Salvia virgata revealed that combining citric acid with tea saponin improved Pb bioavailability, leading to increased metal accumulation without excessive leaching [159].

Despite advancements, the use of chelating agents in phytoremediation poses challenges, including metal leaching, soil toxicity and harm to nontarget organisms. Although EDTA enhances metal uptake by plants, the risk of groundwater contamination and soil degradation limits its practicality. Field testing of the chelator performance under real-world conditions is essential to optimise the balance between metal uptake efficiency and environmental safety. Additionally, understanding the synergies and interactions between different chelators and soil amendments is crucial for identifying effective and environmentally sustainable soil amendment strategies.

4. Economic Feasibility of Implementing Soil Amendments in Phytoremediation Projects

The economic feasibility of using soil amendments in phytoremediation requires a thorough assessment of their cost, scalability and suitability for specific contaminants and environmental conditions. Although some amendments are inexpensive, others pose significant economical and practical constraints, potentially limiting their widespread adoption.

To evaluate the economic feasibility, a baseline price of USD 75,375.2/per hectare for a two-year phytoremediation project was used, as reported in a previous study [160]. This cost estimate accounts for both capital and operational expenditures and provides a basis for comparing additional costs associated with soil amendments.

Biochar has been extensively studied in phytoremediation, particularly for its role in stabilising HMs and improving soil structure. The application rate of biochar ranges typically ranges from 10 to 20 tonnes per hectare, with an estimated cost of approximately USD 400 per metric tonnes, resulting in an additional cost of USD 4000–USD 8000 per hectare for a phytoremediation project. For example, Narayanan and Ma [34] highlighted the potential of biochar to immobilise contaminants, which is beneficial for phytostabilisation. Given the baseline project cost, the inclusion of biochar increases expenses by 5–10%, a cost that may be justified if it enhances remediation efficiency and potentially shortens the project duration [161].

Compost application rates typically range from 5 to 10 tonnes per hectare, with costs ranging from USD 30 to USD 70 per tonne (averaging at USD 50 per tonne) translating into an additional cost of USD 250 to USD 500 per hectare. The United States Environmental Protection Agency highlighted the benefits of compost in improving soil health, which can enhance plant growth and remediation effectiveness. Additionally, a practical guide from the appropriate technology transfer for rural areas recommends application rates of approximately 12.35–24.7 tonnes per hectare. Given the total project cost, the low additional cost of compost makes it an economically viable amendment, particularly if it reduces reliance on other inputs [162,163].

Microbial agents, including plant growth-promoting bacteria and fungi, play crucial roles in enhancing the efficiency of phytoremediation. The cost of microbial inoculants varies based on strain selection, production methods and site conditions. Large-scale production requires specialised facilities and monitoring to maintain microbial viability, but their overall cost is low, often comparable to or lower than that of chemical fertilisers. For example, many researchers have highlighted that using microbial agents is cost-effective and affords improved yields compared with the use of chemical alternatives. Additionally, Santos et al. [164] pointed out their role in sustainable agriculture, suggesting that their small application rates result in minimal additional costs for phytoremediation projects. Given their ability to enhance plant resilience and contaminant degradation, microbial agents are an economically viable alternative that adds negligible cost to the overall remediation efforts.

Chelating agents, such as EDTA, are widely used in phytoremediation to enhance HM uptake by plants. Although EDTA is a common reagent, biodegradable alternatives are also being explored. Application rates typically range from 1 to 5 g/m² (10–50 kg per hectare). At a cost of USD 1–5 per kg, the additional expense is estimated between USD 10 and USD 250 per hectare. However, higher application rates, such as 2190 kg/ha at 5 mmol/kg of soil (for the top 10 cm), could increase costs to USD 2190—USD 10,950 per hectare, depending on the mixing depth and application methods. A review conducted by You et al. [165] highlights the effectiveness of chelators, indicating that costs are manageable at low application rates, contributing only a small fraction to overall project expenses.

Biochar increases the total project costs by 5–10%, compost incurs a cost increase of less than 1%, microbial proliferation incurs negligible costs, plant exudates do not incur additional expenses and chelating agents when applied at low rates incur less than a 0.5% increase in cost. The economic feasibility of these amendments depends on their ability to improve the remediation efficiency, either by reducing the treatment duration or increasing the overall effectiveness of the treatment.

Table 9. Comparative analysis of soil amendments for phytoremediation.

Amendment	Cost Considerations/Hectare	Effectiveness	Scalability	Environmental Impact
Biochar	Varies between USD 4000 and USD 8000 depending on feedstock and processing	High	Medium	Positive (carbon sequestration)
Compost	USD 250–USD 500 when locally sourced	Moderate	High	Positive (waste reduction)
Microbial Agents	Costs vary with production and monitoring activities	High	Low–Medium	Positive (biodegradable)
Chelating Agents	USD 2190–USD 10,950 with environmental risks	Very High	Low	Negative (metal leaching risk)
Plant Extracts	Included in project costs	Moderate	Low	Positive (biodegradable)

shows a comparative analysis of the aforementioned amendments considering their cost, effectiveness, scalability and environmental impact, providing insights into their suitability for large-scale phytoremediation applications.

Critical Evaluation and Feasibility of Large-Scale Use

Assessing the economic feasibility of amendments for large-scale phytoremediation is crucial. Sustainable, cost-effective options such as biochar, compost and plant-based substances are particularly viable when sourced from local waste materials. However, their effectiveness is limited to low-to-moderate contamination levels, making them less suitable for highly polluted sites. In contrast, synthetic chelators and specialised microbial agents offer superior remediation outcomes but with considerably higher costs, environmental risks and management requirements. Given the large-scale feasibility, an integrated approach that combines multiple amendments could be a cost-effective solution. For example, biochar and compost can improve soil structure and nutrient levels, while low-cost chelating agents or plant extracts enhance metal uptake, creating a balance between cost and effectiveness. However, the coordination of such strategies and their adaptation to different contamination profiles and environmental conditions require careful evaluation.

5. Molecular and Genetic Basis of Phytoremediation

Amendments—whether organic, inorganic or synthetic—primarily act on the external environment by improving soil properties and enhancing metal bioavailability, thereby increasing phytoremediation efficiency. However, to fully harness the potential of this approach, it is essential to understand the internal genetic and molecular mechanisms that control plant responses to environmental contaminants. To understand the internal biological machinery governing plant responses, the transport and detoxification of contaminants is important to fully exploit plant-based remediation. A complex network supports metal uptake plus tolerance mechanisms. This network involves transporters, detoxification pathways and regulatory elements according to recent advances in molecular biology and plant genetics. In the end, these intrinsic factors determine just how a plant is able to respond to soil amendments and to environmental stressors at both the cellular and systemic levels.

Central to phytoremediation, highly conserved gene families regulate metal uptake, translocation and sequestration via encoding transporter proteins. The ZIP (ZRT/IRT-like Protein) family constituents convey important trace elements such as zinc and iron. These proteins also transport non-necessary and noxious metals like cadmium [166]. NRAMP (Natural Resistance-Associated Macrophage Protein) transporters likewise ease the translocation of divalent cations across cellular membranes. This migration includes manganese and iron, elements whose homeostasis is often disrupted under high metal stress. Heavy metal ATPases, also known as HMAs, plus ABC ATP-binding cassette transporters additionally strengthen intracellular detoxification via helping the movement of surplus metal ions toward vacuoles and across membranes for the minimisation of cytosolic toxicity [167,168]. Hyperaccumulator species evolve these systems particularly well, and they always manifest many transporters. Heightened metal tolerance and accumulation stems from their regulatory alterations [169].

Chelation coupled with compartmentalisation principally accomplishes the detoxification of heavy metals within plant cells. Phytochelatins and metallothioneins function as two ligand classes to mediate this process. Phytochelatins curtail metal bioavailability inside the cytosol via the formation of metal–chelate complexes sequestered into vacuoles, and phytochelatin synthase (PCS) enzymatically engenders them from glutathione [170,171]. Metallothioneins represent diminutive proteins with a large cysteine content that fulfil supporting functions. They firmly attach metal ions by means of thiol groups, thereby furnishing metal buffering and redox homeostasis [172,173]. Since this represents a highly preserved and strong mechanism within the hytoremediation capacity, active control over the genes coding these ligands matters to plant survival when facing metal stress.

Importantly, complex regulatory networks oversee detoxification with transport systems. Transcription factors such as WRKY, MYB, bZIP and NAC function as central hubs, since they integrate environmental cues for controlling the expression of metal transporters, antioxidant enzymes and chelator biosynthetic genes [174,175]. Plants possess the capacity to swiftly regulate detoxification routes using these TFs. These TFs react in response to mutable stress states. Endocrine communication systems orchestrate ontogenetic malleability together with responses to adversity. These networks are mediated in parallel by abscisic acid (ABA), ethylene, and jasmonic acid (JA). ABA acts via improved osmotic regulation and governs stomatal activity, while JA and ethylene alter root structure and distribute biomass—thus affecting pollutant interactions [176]. Concurrently, these transduction pathways equilibrate defence activation and growth sustenance, an important compromise among ecological pressures.

Genetic engineering has become a pivotal tool in phytoremediation research, allowing the enhancement of intrinsic plant capacities for metal uptake, tolerance and detoxification. Metal assimilation, resilience and accretion have been efficiently augmented within diverse plant species via the transgenic upregulation of genes like AtHMA4, BjMT2 and GSH1 (glutathione synthetase) [177]. In instances where microbial genes like merA and merB are introduced within plants, they ease revolutionary detoxification routes like the enzymatic diminution of ionic mercury toward its gaseous manifestation, which can then be emitted safely toward the atmosphere [178]. In recent times, CRISPR-Cas9-based genome editing accurately modulates endogenous phytoremediation-related genes, which averts issues with transgene expression, and this opens access to fine-tuned, trait-specific plant development [179].

Concerning omics-based strategies like transcriptomics, proteomics and metabolomics, these are easing the progress of the systems biology viewpoint of plant responses to contaminants coupled with genetic engineering. These tools have pinpointed many stress-inducible genes and enzymatic pathways, in addition to secondary metabolites. These genes, pathways and metabolites contribute to metal detoxification and cellular repair [177,180]. Integrated omics data inform rational design toward phytoremediation strategies through predictive modelling coupled with synthetic biology and also reveal key regulatory nodes. Fabricated regulatory pathways exhibiting a dynamic response to pollutants’ presence are consequently established. This frontier of synthetic biology, guided by omics-informed insights, holds immense promise for developing highly efficient, context-specific phytoremediation systems tailored to diverse environmental conditions.

6. Conclusions

Phytoremediation efficiency has been improved through the use of various amendments, including the application of biochar, compost, microbial agents and plant exudates, which offer a sustainable approach to addressing HM contamination in soils. Despite persistent challenges such as limited metal bioavailability, plant stress and slow uptake rates, integrating these amendments can substantially enhance the efficiency of phytoremediation. Empirical evidence highlights the role of these amendments in optimising contaminant removal, minimising environmental impact and improving soil management. Natural amendments are generally preferred over synthetic alternatives because of their lower environmental risks. The selection and application of amendments should be tailored to specific pollutants and site conditions, with biochar and organic amendments being the most widely used because of their ecological benefits and broad applicability.

Future research should focus on refining these methodologies in real-world scenarios and translating successful laboratory findings into field applications. Investigating innovative combinations of organic and microbial amendments could further enhance efficiency and sustainability.

An interdisciplinary approach that integrates ecological, biochemical and technological perspectives is essential for advancing the field of phytoremediation and supporting environmental restoration. Further studies and field applications are necessary to fully realise the scalability and economic feasibility of phytoremediation.