Phytoremediation and Environmental Law: Harnessing Biomass and Microbes to Restore Soils and Advance Biofuel Innovation

Abstract

Progressing soil degradation worldwide is a complex socio-environmental threat. Implementing environmental policies and actions such as the Sustainable Development Goals, the European Green Deal, and the Renewable Energy Directive III regarding environmental protection aims to protect, conserve, and enhance the EU’s natural capital, focusing on soil protection. As assumed in the Green Deal, the European economy has to be turned into a resource-efficient and green economy with zero net emission of greenhouse gases. Since soil quality strongly influences all ecosystem elements, soil remediation is increasingly promoted as a sustainable option to enhance soil quality and, at the same time, help achieve overarching goals set out in European climate law. Biomass in phytoremediation is particularly important in regenerative agriculture, as it emphasizes improving soil quality, increasing biodiversity, and sequestering carbon. Selected plants and microbes can clean degraded agricultural areas, removing heavy metals and pesticides, thus lowering soil toxicity and improving food and feed security. Moreover, the post-phytoremediation biomass can be processed into biofuels or bioproducts, supporting the circular economy. This article summarizes the role of plants and microbial biomass in the struggle to achieve EU environmental goals, enabling the regeneration of degraded ecosystems while supporting sustainable development in agriculture.

1. Introduction

Physical, chemical, and biological soil degradation poses one of the most critical threats to all ecosystems and public health [1]. The Food and Agriculture Organization of the United Nations defined soil degradation as a ‘change in soil health status resulting in a diminished capacity of the ecosystem to provide goods and services for its beneficiaries [2]. Soil degradation results in biodiversity loss, organic matter, lower fertility and productivity, water and air pollution, salinity, and structure decline [3]. Soils with low fertility have lower abilities to sequester carbon and, in effect, emit higher CO₂ amounts, influencing climate change [4].

The problem of soil degradation worldwide increases due to human activity, intensive industry development, poorly managed agriculture, illegal waste disposal and storage, and intensive mining [5]. Due to this result, soils are increasingly contaminated with various types of pollutants such as chemicals, medicine, heavy metals (mainly lead, cadmium, mercury), polycyclic aromatic hydrocarbons (PAHs), pesticides, fertilizers and their contamination, etc. [6]. In particular, exploiting mineral resources generates waste and pollutes the soil with heavy metals, sulfates, and other toxic substances [7]. In the last few decades, there has been a deep concern about emerging contaminants (ECs) and micro- and nano-pollutants. Since 2021, 17,000 articles have been published on this aspect, emphasizing its importance and threats. The United States Environmental Protection Agency (US EPA), World Health Organization (WHO), and global environmental policy together emphasize the need for soil remediation and the removal of existing contaminants [8,9]. These actions aim to improve soil quality, protect the environment and climate, enhance food security, safeguard public health, and promote biodiversity [10,11].

This article provides a comprehensive analysis of the latest global knowledge on the role of phytoremediation in the context of legal regulations and environmental policies. The paper analyzes the mechanisms of using plant biomass and microorganisms for the remediation of degraded ecosystems and their impact on soil quality, biodiversity, carbon sequestration, and energy production. The importance of phytoremediation in achieving international environmental goals such as the Paris Agreement, the European Green Deal, and the Renewable Energy Directive III (RED III) is highlighted. Particular attention is paid to the role of biomass in regenerative agriculture and its potential for the production of biofuels and bioproducts, supporting the circular economy. The paper provides a synthetic review of current research, technologies, and challenges related to the implementation of phytoremediation on a global role in environmental and climate protection and carbon sequestration.

2. Soil Degradation: Problem Scale

Soil is the most crucial medium for crops. Essential changes in matter occur in the soil, and the circulation of matter in nature begins and ends in the soil [12]. Good-quality soil is both a determinant and guarantor of healthy, safe food [13]. Unfortunately, despite increasing knowledge about soil environmental protection and ongoing technological progress, the share of degraded soils continues to rise each year [14]. This trend is primarily the result of the irrational management of soil resources, widespread industrialization, and climate change [15]. The declining fertility of soil due to degradation is reducing the area of land suitable for agriculture, thereby intensifying global food security challenges. Therefore, soil degradation and especially soil pollution remains a major global issue [16].

Because of strong interconnections among ecosystem components, contaminated soil can lead to the contamination of groundwater, surface water, and air [17]. Substances that remain in the soil have dangerous effects on both human and animal health. Studies estimate that environmental pollution (water, soil, and air) is responsible for approximately 9 million deaths annually [18]. Such alarming data necessitate more intensive efforts to ensure a toxic-free environment. A report on the state of soils in Europe, published in 2024, revealed troubling statistics [19]. It indicated that annual soil erosion in Europe reaches 1 trillion tons, with 60–70% of soils degraded and subjected to one or more degrading factors [20]. Of these, 24% of soils are affected by water erosion, primarily in agricultural areas. Additionally, nutrient imbalances (particularly involving nitrogen) have been observed in 74% of soils. Soil degradation is also closely correlated with the decline in organic carbon content. The report notes that approximately 70 million tons of organic carbon were lost over 9 years across the EU and Great Britain. According to recent research, as much as 62% of soils in the European Union are classified as unhealthy [21]. Data from [22] indicate that, in the case of forests, 64% of soils are unhealthy, while only 36% are considered healthy (Figure 1).

Strategies for Preventing and Restoring Soil Degradation

Protecting soil, a valuable resource, requires understanding the causes and effects of soil degradation and implementing effective corrective measures [23,24]. Soil degradation refers to the loss of natural physical, chemical, biological, and ecological properties, which may result from either natural processes or human activities. Many factors contribute to soil degradation [25], including the initial condition of the soil, which largely determines its future trajectory. Other influences include the type of stress to which the soil is subjected, how the soil responds to stress factors, and the overall impact on natural resources. A quick response to soil quality regression is essential to ensure that ecosystems can continue to provide services and products [26]. Rapid action is extremely important in ensuring environmental safety and access to natural resources for future generations [27]. As part of the EU Soil Strategy for 2030, continuous monitoring of soil conditions is being carried out. The strategy’s objectives include ensuring good soil quality and promoting biodiversity. Promoting agricultural practices that protect soils, such as limiting the use of pesticides, rational use of fertilizers, and the sustainability of farming practices, also contributes to soil protection. These actions consistently aim to reduce the proportion of degraded soils and limit excessive CO₂ emissions from soils by intensifying carbon sequestration. The goals set by the EU Soil Strategy for 2030 can be achieved using biotechnological methods. The use of living organisms, such as plants and soil microflora, can help combat ongoing degradation and assist in the restoration of degraded soils [28,29].

3. Phytoremediation as a Strategy for Soil Restoration

3.1. Types and Mechanisms of Phytoremediation in Soil Decontamination

Soil decontamination can be effectively achieved using phytoremediation techniques. This method allows for soil renewal and reclamation as a standalone approach and can also complement other remediation methods [30]. It facilitates the removal, immobilization, or stabilization of contaminants, thereby mitigating soil toxicity [31]. The mechanisms governing a given phytoremediation process depend on the plant species, type of contamination, and characteristics of the soil medium [32]. The diversity of these mechanisms has led to the classification of different types of phytoremediation.

One such method is phytostabilization, which limits the mobility of contaminants but does not result in their removal from the soil. In this process, inorganic contaminants are precipitated or immobilized at the soil surface, on the root surface, or within tissues [33]. Plants used in phytostabilization typically have extensive root systems and a large rhizosphere surface area. Grasses such as fescue (Festuca sp.) and ryegrass (Lolium sp.) are common examples [34]. Phytostabilization is particularly effective for stabilizing unstable substrates in waste dumps and other post-industrial sites [35].

Another method is phytoextraction, in which plants absorb pollutants through their roots and accumulate them in above-ground parts, effectively removing them from the soil [36]. This technique is particularly useful for extracting heavy metals and radioactive substances. It requires the use of plants with high biomass yield and resistance to relatively high concentrations of pollutants, known as hyperaccumulators [37].

Phytovolatilization is a technique that uses plants to transform pollutants into vapor. It involves several chemical transformations of pollutants with the participation of the plant [38]. A characteristic plant used in this technique is Brassica juncea, known for transforming selenium into dimethyl diselenide or selenomethionine [39]. This process reduces selenium toxicity by 500–700 times [40]. Phytovolatilization can also be used to remove mercury by converting it into elemental mercury, which is less toxic [38].

Lastly, phytodegradation is used to remove organic pollutants and is mainly applied to soils contaminated with petroleum derivatives, aromatic hydrocarbons, or surfactants [41]. The degradation of organic pollutants is dependent on the plant’s ability to produce specific endogenous lytic enzymes. The activity of enzymes that break down organic compounds has also been identified in the surrounding soil medium [42]. In some cases, pollutants accumulated by plants may be decomposed and released as CO₂ and H₂O. Phytodegradation is currently a significant focus of research, especially in the context of removing emerging pollutants [43].

3.2. Limitations of Phytoremediation in Soil Remediation in Real-World Conditions

Phytoremediation, by its nature, is limited by the relatively long time required to achieve remediation effects, a restricted depth of action [44], seasonal dependence [45], and reduced effectiveness at very high contaminant concentrations [36]. The overall effectiveness of this technique is constrained by several factors that must be critically examined, especially under natural conditions. Phytoextraction is highly effective for heavy metals, but its success depends on the bioavailability of metals in the soil, which can be significantly influenced by factors such as pH, soil texture, and organic matter content [46]. Additionally, the capacity of plant biomass to absorb contaminants is limited, meaning that in heavily polluted areas, phytoextraction may not provide adequate remediation within a practical timeframe. Phytodegradation also faces challenges in degrading organic pollutants, as it relies heavily on microbial activity in the rhizosphere. This activity is influenced by soil temperature, humidity, and nutrient availability. In environments with low microbial diversity or high toxicity, the effectiveness of phytodegradation is reduced, potentially leading to incomplete contaminant breakdown [41,42]. Phytovolatilization involves the uptake of volatile pollutants by plants, which are then released into the atmosphere. Although useful for specific pollutants such as volatile organic compounds, this technique can contribute to the dispersion of contaminants into the air, potentially causing secondary pollution or air quality concerns [47]. Its effectiveness is also influenced by plant species and environmental factors such as temperature and humidity, which can vary significantly across regions. Phyto-stabilization, while effective in preventing the spread of contaminants, immobilizes them in the soil rather than removing them. This limits the potential for complete site cleanup. Moreover, the stability of immobilized contaminants can be compromised by environmental changes such as soil erosion or flooding, which may remobilize previously stabilized contaminants [48]. In addition to these technical limitations, the success of phytoremediation is also affected by environmental factors such as soil depth, climate, and the presence of competing vegetation [30]. In some cases, plant growth may be stunted by extreme weather events, or plants may fail to develop strong root systems in infertile or highly compacted soils, further diminishing their capacity to remediate pollution [49].

Beyond soil purification, phytoremediation contributes to erosion control and prevents the dispersion of pollutants into aquatic and atmospheric environments [50]. Given its versatility, phytoremediation can be integrated with other remediation methods and has low infrastructure requirements compared to chemical soil treatment as it does not necessitate the construction of complex treatment facilities. Additionally, phytoremediation offers further benefits, such as promoting biodiversity, in contrast to conventional remediation methods. It also provides an opportunity to revitalize extensively degraded areas, with the added advantage of being widely accepted by society due to its environmentally friendly and aesthetically pleasing nature [51]. A schematic presentation of the role of phytoremediation in environmental protection on both local and global scales is shown in Figure 2.

3.3. Plants in Phytoremediation

Plants employed in phytoremediation share several common characteristics, with rapid growth and substantial biomass production being among the key factors determining their suitability for such applications. High biomass output is particularly significant for effective phytoremediation, as the amount of plant organic matter directly influences the capacity of plants to remove, accumulate, and stabilize contaminants within the soil matrix [52]. This directly contributes to increased efficiency in soil remediation [38]. Plants must also demonstrate high tolerance to the specific contaminants present in a given area [53]. Another crucial determinant of plant suitability is their ability to accumulate significant concentrations of pollutants—such as heavy metals—within their tissues. This trait is especially evident in metallophytes and hyperaccumulator species, which enable the permanent removal of contaminants from the soil through biomass harvesting [54]. Additionally, a plant’s effectiveness in phytoremediation is influenced by its capacity to metabolize or degrade pollutants, thereby contributing to the detoxification and restoration of contaminated environments. Some plants can degrade organic contaminants, such as pesticides or petroleum derivatives, for example, grasses and legumes [55]. Plants with large, extensive root systems provide a greater surface area for contact between roots and pollutants enhancing the phytoremediation process in the rhizosphere [50]. This feature also allows for the purification of deeper soil layers and even groundwater [30]. Given the specificity of polluted areas, plants used in phytoremediation should have low habitat requirements, making them suitable for use in degraded and nutrient-poor regions [56]. Plants such as miscanthus and mustard have low habitat requirements, enabling them to be used for land reclamation [57]. The perfect solution seems to be using plants with a high calorific value. Collecting plant biomass after phytoremediation makes it possible to use it for energy production (for instance, poplar) [58].

The diversity of available plant species allows for the selection of the most effective plants and those best adapted for the removal of specific soil contaminants. This enables the adaptation of phytoremediation methods to particular environmental conditions and types of pollution. Phytoremediation is frequently in the reclamation of post-industrial or post-mining areas where relatively high concentrations of heavy metals are often found. Commonly used plants for heavy metal removal include poplar (Populus sp.) [59], willow (Salix sp.) [60], and mustard (Sinapis sp.) [61].

Table 1. Selected phytoremediation plants and their applications in selected pollutant removal.

Plant	Contamination	Reference
Populus sp.	Cd, Hg, Pb, and As	[59]
Salix sp.	heavy metals, petroleum substances	[60,62]
Sinapis sp.	polycyclic aromatic hydrocarbons (PAHs)	[61]
Festuca sp.	Cd, Pb, Zn, Ni, Cr, Cu	[63,64,65]
Medicago sativa L.	Cd, Pb,	[64]
Dactylis glomerate	Cd, Pb	[64]
Alyssum saxatile L.	Zn, Cd, Ni, Pb, Cr, and Cu	[65]
Poa pratensis L.	Cr, Cd	[66]
Cannabis sativa L.	Se, Co, benzo(a)pyrene, naphthalene, and chrysene	[67]
Medicago falcata L.	petroleum substance	[68]
Lolium perenne L.	polycyclic aromatic hydrocarbons (PAHs)	[69]
Miscanthus sp.	poly(ethylene terephthalate) and poly(lactic acid)	[70]
Arabidopsis sp.	2-mercaptobenzothiazole (MBT)	[71]
Salix sp., Populus sp.	per- and polyfluoroalkyl substances (PFASs)	[72]
Salix sp.	perfluoroalkyl	[73]
Medicago sativa L.	di-n-butyl	[74]
Mentha piperita	chlorpyrifos	[75]
Plantago major L., Helianthus annus L.	diazinon	[76]
Vigna radiata	estrogen	[77]
Helianthus annuus Linn.	carbofuran	[78]

presents selected phytoremediation plants along with the types of contaminants against which they are effective. It includes conventional pollutants such as heavy metals and petroleum hydrocarbons, as well as substances that have recently garnered growing interest among scientists and decision-makers—the so-called emerging contaminants. This group includes chemical compounds not yet subject to detailed legal regulation but potentially posing serious threats to human health and ecosystem function. An increasing number of studies are now focusing on the use of green technologies, including phytoremediation, to eliminate these persistent and difficult-to-remove pollutants from soil. Such developments may represent a breakthrough in the sustainable management of contaminated areas. The applicability of selected plants for the phytoremediation of specific environmental pollutants is summarized in Table 1.

3.4. Root-Zone Interactions and Soil Stabilization

The root zone is the critical environment for the processes driving phytoremediation and serves as the focal point for soil remediation mechanisms [30]. Within this zone, dynamic interactions occur between plant roots, soil microflora, and contaminants, facilitating the transformation, accumulation, or stabilization of pollutants in the soil. Plants actively respond to environmental changes by releasing root secretions [79]. Their presence makes the root zone a hot spot for dynamic changes within the plant–soil microflora–soil system. The composition of these secretions is complex and includes diffusates, exudates, and excretions. Root exudates consist of mucus, colloids, and lysates—products of root cell biometabolism [80]. By modifying the soil’s chemical, physical, and biological properties, these exudates play a key role in regulating the microecological function of the rhizosphere [81]. Their composition and quality are strictly dependent on the plant species [80]. Root exudates are pivotal in transforming toxic substances, thereby reducing soil toxicity. Furthermore, the release of various chemical compounds, such as amino acids, into the root zone creates a favorable habitat for diverse soil microorganisms—including bacteria, fungi, and protozoa—which further contribute to the remediation process [82]. These microorganisms, through the enzymes they synthesize, can degrade pollutants, directly enhancing the effectiveness of remediation. In some plants, especially hyperaccumulators, the root zone also serves as a site for contaminant accumulation [83]. Additionally, chemical secretion from plants can promote soil aggregation, facilitating pollutant immobilization and offering protection in areas susceptible to erosion. The extensive root networks developed by plants stabilize the soil and improve its permeability, looseness, ventilation, water management, and nutrient availability (for instance, altering the surface charge of absorbents) [80]. This complex network of interactions improves the living conditions for soil microflora, favoring its development and degradation activity of pollutants present in the soil. The root zone of plants can also limit the mobility of contaminants in the soil, which makes them less available to other organisms, thus limiting soil toxicity and affecting biodiversity.

3.5. Microorganisms as Allies of Plants in Phytoremediation

Microorganisms also play an important role in the phytoremediation process. Due to the complexity of plant–soil microflora interactions, microorganisms support plants at various stages of pollutant detoxification and/or accumulation [84]. Microbiota assist in both the mobilization and immobilization of contaminants. By synthesizing enzymes, they increase the bioavailability of pollutants to plants, while reducing their harmful effects [42]. The indigenous soil microflora is particularly important in the phytoremediation of contaminated soils. These microorganisms support plants in nutrient uptake, regulate plant growth, protect against pathogens, and can even collaborate with plants in the detoxification of pollutants [85]. Some microorganisms are capable of degrading organic compounds, including hazardous petroleum substances and aromatic hydrocarbons [86]. Recent studies also highlight the potential of microorganisms to remove emerging contaminants [87]. Examples of microorganisms capable of breaking down specific pollutants are provided in

Table 2. Microorganisms as a key for emerging contaminants degradation with applicability for assisted phytoremediation.

Emerging Contaminants (ECs)	Compound	Degrading Microbial Agent	Reference
Additives for food and feed	2,6-di-tert-butyl-4-methylphenol (BTH)	Komagataella phaffii (Pichia pastoris)	[89]
Endocrine-disrupting compounds (EDCs)	estrone 17β-estradiol	Sphingomonas sp.	[90]
		Sphingobacterium sp.	[91]
		Pseudomonas putida	[92]
	estrogen	Actinobacteria, Proteobacteria, Rhodococcus equi, Rhodococcus zopfii, Novosphingobium tardaugens NBRC 16725, Sphingomonas spp.	[93]
		Chaetomium sp.	[94]
	phthalate acid esters (PAEs)	Pseudomonas sp. YJB6	[95]
Pesticides	diazinon	Ochrobactrum sp., Stenotrophomonas sp., Lactobacillus brevis, Serratia marcescens, Aspergillus niger, Rhodotorula glutinis, Rhodotorula rubra	[96]
	dichlorvos	Trichoderma atroviride mutant AMT-28	[97]
		Pseudomonas stutzeri smk	[98]
		Consortium: Pseudomonas, Xanthomonas, Sphingomonas, Acidovorax, Agrobacterium Chryseobacterium	[99]
	chlorpyrifos-methyl	Pseudomonas citronellolis CF3	[100]
		Alcaligenes faecalis, Bacillus weihenstephanensis, Bacillus toyonensis, Alcaligenes sp. SCAU23, Pseudomonas sp. PB845W, Brevundimonas diminuta, uncultured bacterium clone 99	[101]
		Pseudomonas diminuta	[102]
		Pseudomonas aeruginosa RNC3	[103]
		Pseudomonas putida MAS-1	[104]
		Stenotrophomonas maltophilia RNC7	[103]
		Ochrobactrum intermedium PDB-3	[105]
	malathion	Shewanella oneidensis	[106]
		Bacillus cereus	[107]
		Aspergillus niger	[108]
	endosulfan	Pseudomonas sp., Staphylococcus sp.	[109]
	carbofuran	Pseudomonas, Flavobacterium, Achromobacterium sp., Sphingomonas sp., Arthrobacter sp., Enterobacter sp., Burkholderia PLC3, Cupriavidus sp. ISTL7, Bacillus sp.	[110]
Pharmaceuticals	diclofenac	Rhodococcus ruber IEGM 345	[111]
		Trametes trogii	[112]
	ibuprofen	Achromobacter spanius S1	[113]
		Klebsiella pneumoniae TIBU2.1, Mycolicibacterium aubagnense HPB1.1	[114]
	paracetamol	Bacillus cereus, Brevibacterium frigoritolerans, Corynebacterium nuruki, Enterococcus faecium	[115]
	carbamazepine	Gordonia polyophrenivoran	[116]
Phthalate esters	dibutyl phthalate (DnBP)	Bacillus subtilis HB-T2	[117]
		Pseudomonas aureginosa PS1	[118]
	di(2-ethylhexyl) phthalate (DEHP)	Fusarium culmorum	[119]
Plastics	polyvinyl chloride	Micrococcus sp.	[120]
		Pseudomonas citronellolis, Bacillus flexus	[121]
	poly(ethylene terephthalate)	Thermomyces lanuginosus, Thermobifida fusca, Fusarium solani	[122]
	polyurethane	Aspergillus flavus G10, Aspergillus tubingensis

. Given the capabilities of microorganisms, an integrated approach that combines their assistance with phytoremediation enables the effective reduction of pollutant toxicity. Microorganisms can convert contaminants into completely non-toxic substances and, in some cases, remove them permanently from the environment [30]. For this reason, applying microorganisms to the soil in the form of “soil vaccines” through bioaugmentation is increasingly seen as a necessary, biological, and safe alternative to synthetic soil fertilizers. Their use also reduces the need for artificial fertilizers [88]. This approach supports the Strategic Plan stemming from the European Green Deal, which includes a goal to reduce fertilizer use by 50% [9].

3.5.1. Plant-Growth-Promoting Rhizobacteria

A significant group supporting plants in phytoremediation is plant-growth-promoting rhizobacteria (PGPR). These bacteria inhabit the root zone of plants, enhance the availability of essential plant nutrients, and alleviate plant stress caused by soil contaminants [123]. Their presence significantly supports root development, and through an extensive root system, plants can more effectively absorb contaminants from the soil [124]. This is particularly important as plants can act only on the bioavailable fractions of harmful pollutants and are ineffective against nonbioavailable forms [125]. PGPR can produce organic acids (e.g., acetic acid) and chelators that increase the bioavailability of metals, including heavy metals. Compounds such as ACC deaminase (e.g., Pseudomonas koreensis S2CB45) [126], phytohormones (e.g., indole-3-acetic acid, IAA), and phosphate-solubilizing agents are all known to enhance plant growth. Moreover, the production of plant hormones by rhizobacteria contributes to pollutant accumulation in plant tissues [127]. Through the synthesis of siderophores, biosurfactants, and exopolymers, PGPR aid in the removal of metals from soil by respective metal complexes. Consequently, PGPR are widely employed in remediating heavy-metal-contaminated soils [128]. Additionally, nitrogen-fixing bacteria such as Rhizobium, Sinorhizobium, Azospirillum, Azotobacter, Bradyrhizobium, Burkholderia, Herbaspirillum significantly increase plant biomass and are especially important in agricultural soils, where biological nitrogen fixation reduces dependence on artificial fertilizers [129,130]. Furthermore, bacteria capable of degrading xenobiotic substances—including Pseudomonas aeruginosa, Burkholderia gladioli, and P. pseudoalcaligenes—are considered promising agents in phytoremediation. Other strains, such as Bacillus spp., Ciceribacter azotifigens, and Serratia marcescens, have been shown to degrade persistent pesticides effectively [131,132].

3.5.2. Arbuscular Mycorrhizal Fungi

Fungi also play a vital role in environmental purification. A notable group is arbuscular mycorrhizal fungi (AMF), which act as natural bioaccelerators by interacting with phytoremediation plants to support ecological restoration processes [133]. The glomalin produced by AMF (e.g., Glomus, Rhizophagus spp.) improves soil structure, while mycelial hyphae increase soil porosity and act as a structural scaffold, stabilizing the soil matrix. AMFs are recognized as essential agents in the remediation of heavy-metal-contaminated soils [134]. Successful removal of aromatic hydrocarbons has also been demonstrated using Salix viminalis L. supported by AMF [135]. The release of organic acids by AMF enhances pollutant degradation and uptake in contaminated soils [136]. For example, Glomus etunicatum has been shown to increase the accumulation of dichlorodiphenyltrichloroetane (DDT) in phytoremediation involving alfalfa [137]. Other observed benefits of AMF include faster biomass production in host plants, which can directly shorten the duration of remediation efforts [138]. Moreover, through interactions with soil bacteria, AMF accelerate contaminant uptake and enhance bioavailability—effects documented in soils contaminated with hydrocarbons [139].

The properties of the soil, along with the type and concentration of pollutants and the plant species used in phytoremediation, strictly determine the effect of AMF [50]. It has been observed that the chemical composition of root exudates—including flavonoid content—also influences AMF–plant interactions. These factors directly affect the efficiency of pollutant uptake by plants from the soil. For example, the use of Sorghum bicolor in phytoremediation, when supported by bioaugmentation with Claroideoglomus etunicatum (BEG168), resulted in a fourfold increase in the accumulation of molybdenum (Mo) from the soil [140]. Research by Meyer et al. [141] investigated the cultivation of fragrant vetiver (Chrysopogon zizanioides) on substrates containing mine waste and found that the application of AMF species—including Acaulospora colombiana, A. morrowiae, A. scrobiculata, and Gigaspora margarita—increased the accumulation of both heavy metals and biogenic elements (e.g., phosphorus) in the plant’s root tissues. Other studies demonstrated that the application of Glomus mosseae reduced heavy-metal-induced stress in Trifolium repens (white clover). In addition, AMF–plant mycorrhizal associations have been shown to enhance plant biomass. For instance, arbuscular mycorrhiza between Trifolium repens L. and G. mosseae and G. claroideum effectively reduced stress caused by the pathogenic fungus Pythium ultimum. This was accompanied by a reduced production of stress-related flavonoids—only two out of eight tested were produced or derived from glycosides in response to pathogen infection [142]. Further research on the same plant species found that inoculation with Funneliformis mosseae and Paraglomus occultum improved the plant’s tolerance to drought stress by enhancing proline content, soluble protein levels, flavonoid production, and nutrient uptake [143]. Interestingly AMF strains have also been shown to support plants in adapting to climate change. One study reported that a vaccine based on AMF reduced the negative impact of acidic water on Lupinus angustifolius grown on sterilized mining waste. In addition to these effects, AMF influences root metabolism. A study by Wang et al. [144] showed that inoculation of Medicago sativa Glomus mosseae increased the expression of 739 metabolites. It was indicated as a key factor in modifying the soil microbiome in this context.

3.5.3. Soil Microbial Interactions

The co-presence of PGPR and AMF induces interactions along the microflora–plant axis, which may be manifest as synergistic between the microorganisms and the host plant [145]. It has been reported that AMF and PGPR complement each other by enhancing surface absorption and facilitating the uptake of P and N [146]. Furthermore, AMF have been shown to alter root exudate composition, which, in turn, influences the microbial community in the root zone, often increasing the abundance of beneficial microorganisms. For example, the AMF Claroideoglomus tunicate not only improved the bioavailability of K, P, Ca, and Mg, but also increased the abundance of microbial genera such as Planomicrobium, Lysobacter, Saccharothrix, Agrococcus, Microbacterium, Streptomyces, and Penicillum [147]. In a cucumber monoculture, the application of arbuscular fungi with an organic substrate positively affected the root-zone microbiome and improved soil quality [148]. Mishra et al. [146] investigated the synergistic effect of AMF and PGPR on the phytoremediation of iron-contaminated soils. Three AMF genera—Glomus, Acaulospora, and Scutellospora—and four PGPR genera—Streptomyces, Azotobacter, Pseudomonas, and Paenibacillus—were examined, using Pennisetum glaucum and Sorghum bicolor as host plants. Enhanced Fe³⁺ removal was observed in samples inoculated with the AMF and PGPR consortium, showing removal efficiencies of 60.35% and 64.85% in roots and 50% and 35.55% in shoots for P. glaucum with mycorrhizal colonization at 47%. The study demonstrated that these microbial consortia significantly enhanced iron accumulation.

Colonization of the root zone by microorganisms is influenced by multiple factors, including soil hydrological conditions. Monokrousos et al. [149] suggested that AMF may exert a greater influence on the rhizosphere microbiome in dry soils than in wet soils. Their study, conducted on Festuca pratensis, Dactylis glomerata, and their mixture, involved inoculation with Rhizophagus irregularis. It was found that in wet soils, the microbial composition was more strongly influenced by the inoculum itself, while in dry soils, soil type played a larger role in shaping the microbial community. These findings suggest that the success of bioaugmentation using AMF and PGPR may vary depending on the soil’s water regime. Given the stronger microbiome impact of AMF in dry soils, bioaugmentation strategies could be particularly advantageous in arid regions or adjusted according to meteorological conditions. A relatively new approach is the use of ectomycorrhiza associated with bacteria (EMAB), which harnesses the synergy between ectomycorrhizal fungi and bacteria. Though a distinct type of mycorrhiza from AMF, EMAB has been proposed as a promising method for accelerating plant-assisted remediation. EMAB has been shown to increase ectomycorrhiza formation, promote plant growth, and enhance the accumulation of heavy metals such as Zn and Cd [150]. Additionally, bacteria have been observed to facilitate root colonization by ectomycorrhizal fungi, further improving the effectiveness of phytoextraction [151]. In summary, the synergy of plant-associated microorganisms—including PGPR, AMF, and EMAB—is a critical factor influencing the overall effectiveness of phytoremediation.

4. Role of Assisted Phytoremediation Towards Environmental Policies

4.1. Plant and Microbial Biomass Towards Achieving Sustainable Development Goals

The synergy of actions aimed at restoring natural environments is one of the key strategies for achieving the Sustainable Development Goals (SDGs)—the global objectives of the United Nations [152]. Emphasizing ecosystem services, biodiversity restoration, natural resource protection, and appropriate soil management are among the primary factors that support the achievement of the Sustainable Development Goals (SDGs) (Figure 3) [153]. Soil remediation, by reducing toxicity and increasing land suitable for agriculture, contributes directly to SDG 1: No Poverty and SDG 2: Zero Hunger [154]. Enhanced soil quality and reduced contamination levels lead to higher crop yields, greater food production, and improved food security—all essential for ensuring access to adequate, healthy food and supporting public health. Moreover, the removal of soil contaminants, including emerging pollutants, improves sanitary and hygienic conditions and positively impacts groundwater quality, supporting the achievement of SDG 6: Clean Water and Sanitation [155]. Reclaimed soils with appropriate structure, aggregation, and enzymatic activity also function as effective filters for rainwater and precipitation [156]. Soils contaminated with pesticides, heavy metals, micropollutants, pharmaceuticals, plasticizers, and other substances can serve as sources of pollution for groundwater and surface water bodies [157]. In this context, the biomass of plants and microorganisms used in assisted phytoremediation plays a vital role in preventing the migration of pollutants into other components of the ecosystem [158].

Improving soil quality can also contribute to achieving SDG 12: Responsible Consumption and Production [159]. Sustainable agricultural practices, including regenerative agriculture, help achieve this goal by reducing pressure on the soil, enhancing the efficiency of natural resource use, and promoting more balanced agricultural production [160]. In addition, the use of plant and microbial biomass in phytoremediation, alongside soil quality improvement, can play a significant role in climate protection and the achievement of SDG 13: Climate Action [161].

Increasing soil fertility—and in extreme cases, even restoring soil ecosystem services—can enhance carbon sequestration [14]. This is especially important for climate protection and the reduction in CO₂ emissions into the atmosphere. Degraded soils are major contributors to CO₂ emissions [162]. Through phytoremediation, especially when involving plant and microbial biomass, soil remediation reintroduces organic matter into poor and contaminated soil. Enhancing soil fertility parameters in this way intensifies the carbon sequestration process, supporting long-term environmental sustainability [163].

AMF can play a crucially important role in this context, particularly through the production of glomalin, which improves soil structure, stabilizes organic matter, and enhances carbon sequestration [164]. Increasing the stability of organic carbon in the soil contributes to a net reduction in CO₂ emissions, directly supporting climate protection. Furthermore, microbial-assisted phytoremediation promotes biodiversity, aligning with SDG 15: Life on Land [165]. Goal 15 emphasizes the protection of sustainable terrestrial ecosystems and the preservation of microbial biodiversity [152].

Enhancing soil quality, preventing and mitigating erosion and degradation, and removing contaminants through phytoremediation—supported by plant and microbial biomass—are key strategies for restoring degraded terrestrial ecosystems [56]. These efforts help protect biodiversity by creating new ecological habitats for soil microflora, fauna, plants, and animals. In doing so, they support the recovery of terrestrial ecosystems and their essential functions and align with the goals of the EU Biodiversity Strategy for 2030 [166]. Although many of these objectives overlap, it is important to emphasize the vital role of plant biomass and microorganisms involved in the restoration and purification of soils. Their use contributes to the creation and regeneration of productive, stable ecosystems that are more resilient to climate change, including extreme events such as droughts and floods.

4.2. Assisted Phytoremediation Towards the Green Deal

The European Green Deal (EGD) is a European directive aimed at protecting the environment and climate to achieve climate neutrality by 2050 [9]. In this context, several initiatives have been proposed, focusing primarily on reducing CO₂ emissions, limiting global warming to a maximum of +1.5 °C compared to pre-industrial levels, promoting sustainable agriculture, and protecting biodiversity [167].

Given ongoing climate change, the protection of soil resources has become especially important. Degraded soils are known to emit significantly more CO₂ into the atmosphere than healthy soils [4]. Therefore, improving soil function through phytoremediation, particularly when assisted by microorganisms, can help reduce CO₂ emissions by stabilizing and storing organic carbon in the soil [168]. Phytoremediation also supports broader nature restoration goals and contributes to creating a healthy environment for future generations—one of the EGD’s specific objectives (Figure 3) [169]. It can play a significant role in rehabilitating difficult areas such as postmining, metallurgical, or landfill sites [170]. Numerous studies have highlighted the potential of plant and microbial biomass to restore soil ecosystem services and meet several of the EGD’s key targets [171,172]. Additionally, improving soil quality contributes to increased crop yields by reducing the need for pesticide use [173]. Moreover, supporting phytoremediation with microorganisms makes microbiological vaccines act as a natural booster, protecting against biotic and abiotic stress and eliminating the use of pesticides and their contamination of soils [174]. Moreover, the plant biomass produced through phytoremediation can serve as a renewable resource for biofuels, supporting green chemistry through the production of bioethanol, biodiesel, biogas, pellets, and briquettes [175]. Biomass can also be used for electricity generation (e.g., from energy willow or giant miscanthus) [175]. Some plants, such as willow, can also serve as a raw material in paper production [45], contributing to the circular economy, another major objective of the EGD.

4.3. Plant and Microbial Biomass Towards Directive Renewable Energy Directive III

The Renewable Energy Directive III (RED III), which entered into force on 19 November 2023, is a key element of European climate policy, applying to the energy, heating, industry, and transport sectors [176]. It provides a strong legal framework that is highly significant for the energy sector and environmental protection. One of its central goals is the promotion of renewable energy, with an ambitious target of achieving a 42.5% share of renewable energy in the European Union’s overall energy consumption by 2030 [177]. RED III aims to increase the role of green energy in the economies of EU Member States, thereby supporting the implementation of the Fit For 55 package [178]. The directive focuses on transitioning energy systems toward renewable sources while also emphasizing the increased role of biofuel components.

RED III also introduces new regulations for the transport sector, mandating a minimum share of 5.5% for advanced biofuels and renewable fuels of non-biological origin (e.g., hydrogen and its derivatives) by 2030 [179]. In this context, phytoremediation can serve as a valuable source of fuel biocomponents [180]. The plant biomass collected after soil remediation may be used for energy purposes, contributing to the production of advanced biofuels, and supporting RED III targets in the transport sector (Figure 3) [181]. Biomass produced in phytoremediation can be combusted or processed in biogas installations, helping to increase the share of renewable energy sources (RESs) [181]. Using advanced technologies, this biomass can also be transformed into hydrogen or other synthetic fuels [182]. Additionally, RED III introduces sustainability criteria for biomass use, particularly aimed at forest and soil protection. In this regard, post-remediation biomass, when converted into value-added products such as biocomposites or fertilizers [175], supports the implementation of RED III objectives. Phytoremediation of degraded areas also offers a solution for growing energy crops on noncompetitive lands, avoiding conflicts with agricultural or forested areas. Focusing energy crop cultivation on degraded or marginal lands helps to limit indirect land use change, thereby preserving agriculturally productive areas for food crops and ensuring a sustainable food supply. In summary, phytoremediation—through the efficient conversion of biomass into energy or value-added products—has significant potential to contribute to Europe’s sustainable energy transformation under RED III.

4.4. Waste-Free Phytoremediation and Phycoremediation Towards a Circular Economy and RED III

The integration of phytoremediation with a zero-waste industry approach enables the recovery of valuable raw materials while simultaneously protecting the natural environment [183]. Innovative strategies combining phytoremediation and mycoremediation have been described, allowing for the effective degradation of complex contaminants and supporting the broader goal of zero-waste remediation [184]. In this context, “zero-waste” refers to designing the entire process to minimize or eliminate waste generation. Tan et al. [185] emphasize that the management of post-remediation biomass can yield significant economic value. Techniques such as pyrolysis and composting offer not only solutions to biomass disposal but also avenues for generating economic benefits [186]. Other researchers have highlighted the industrial potential of fiber plants used in phytoremediation, such as hemp and flax. Owing to their extensive root systems and ability to penetrate deep into the soil, these plants are especially useful for reclaiming contaminated soils.

Studies by Placido and Lee [187] showed that the concentrations of heavy metals in hemp fibers grown in Cd-contaminated (11 mg kg⁻¹) and Pb-contaminated (664 mg kg⁻¹) soils remained significantly below the permissible limits for textile product safety [188]. Several safe technologies have been proposed to obtain raw materials for textile production and to develop composite materials for the automotive and construction industries. Despite these applications, the primary use of phytoremediation biomass remains energy production, including the generation of biogas, bioethanol, biodiesel, and biochar. Additionally, contaminated plant biomass, once processed and purified of pollutants, can also be repurposed for sustainable building materials such as hempcrete and biocomposite panels. The proper processing of phytoremediation biomass is critical for enabling its further applications and ensuring alignment with the zero-waste approach.

Another innovative approach is phycoremediation, where algae serve as the primary agents of remediation. Their abilities in absorption, accumulation, biomineralization, and biosorption of contaminants make them highly effective in environmental purification, particularly in aquatic ecosystems. Integrating zero-waste principles into phycoremediation allows the resulting algal biomass to be used for energy production (e.g., biofuels) [189] as well as for animal feed due to its richness in proteins, vitamins, and minerals [190]. However, thorough toxicological studies must be conducted before feed application to ensure safety, especially in environments with elevated biogenic element concentrations [191]. Furthermore, biorefineries, as integrated facilities that combine multiple processes, allow for the comprehensive conversion of microalgal biomass into proteins and organic fertilizers, potentially reducing the need for chemical fertilizers [192].

Zero-waste approaches applied to the phytoremediation of heavy-metal-contaminated sites also open the door to phytomining—the recovery of metals from plant biomass. This concept supports domestic supply chains of critical minerals (e.g., Ni, Zn), offering a more environmentally sustainable alternative to traditional mining methods [193]. Although phytomining has been recognized as a promising technique for decades, its large-scale application remains limited. Nonetheless, its economic potential makes it an increasingly attractive approach [194]. Akinbile et al. [195] noted that phytomining is still not capable of fully replacing conventional metal extraction methods. However, Kumar and Singh [196] proposed an innovative direction for phytomining, utilizing leachates, sediments, and wastewater derived from e-waste processing. They suggested that implementing hydroponic baths with hyperaccumulator plants could not only improve metal recovery but also serve as a valuable complementary technique in e-waste recycling, offering a low environmental impact solution.

Zero-waste remediation enables a closed-loop system in both production and environmental protection, reducing the exploitation of natural resources and promoting a sustainable approach to environmental purification—aligned with the waste minimization principles outlined in the RED III Directive.

5. Phytoremediation in Regenerative Agriculture

It has been estimated that global agriculture is responsible for approximately 25% of annual anthropogenic greenhouse gas (GHG) emissions. Moreover, agricultural production accounts for nearly one-third of terrestrial acidification [197]. This is largely due to agriculture being the most extensive form of land use on Earth [198]. Intensive agricultural practices, driven by growing food demand, inefficient soil resource management, and excessive fertilization, significantly degrade soil quality and productivity [199]. Improving soil quality and enhancing biodiversity through the use of plants and microorganisms represents a key ecological pillar of regenerative agriculture [200]. Phytoremediation plants can be incorporated as cover crops to provide permanent vegetation cover, supporting soil structure and ecosystem resilience [201]. Soil ecosystem services and safety can also be improved through adherence to the “Farm to Fork” strategy, which aims to protect food from soil contaminants and pesticide residues.

Regenerative agriculture further integrates agroforestry practices—combining crops with trees—to improve soil quality and reduce the environmental impact of agriculture [202]. One promising approach is the use of phytoremediation plants between tree alleys in fruit orchards (e.g., apple orchards, pear orchards, etc.) [203]. This method, combined with plant biomass and microorganisms, can help remove contaminants from soil and reduce their presence in food products. Moreover, improving soil quality, increasing nutrient availability, and modifying the soil microbiome can lead to reduced reliance on fertilizers and pesticides [50]. The application of microbiological vaccines, especially those based on AMF, can further contribute to carbon sequestration in agricultural soils [204]. Thus, phytoremediation can serve as a valuable complementary technique in the implementation of regenerative agriculture.

6. Future Perspectives

6.1. Advancements in Genetic Engineering for Enhanced Phytoremediation and Soil Restoration

Despite numerous studies on microorganism–plant interactions in the phytoremediation process, a comprehensive approach that considers multi-level interactions between the entire soil microbial community and remediating plants is still lacking. A deeper understanding of these mechanisms and interactions can shed new light on ways to remove contaminants from soil and could facilitate planning an effective phytoremediation process. A thorough understanding of the mechanisms governing the relationships between the entire community of microorganisms and remediating plants may be possible thanks to molecular genetics [205]. Furthermore, detailed knowledge of substrate preferences and metabolic profiles of microorganisms will allow for more targeted and efficient implementation of assisted phytoremediation and can also form the basis for the genetic modification of plants and/or microorganisms [206]. The development of genetic engineering tools, particularly those focused on gene expression responsible for contaminant accumulation/degradation by plants, as well as genes that enhance plant resistance to abiotic stress, holds the potential to significantly improve the efficiency of soil remediation [207]. Systems based on the cooperation of genetically modified plants and/or microorganisms, or programming them for more effective uptake and degradation of pollutants, could greatly accelerate land restoration, contributing to the achievement of European environmental and climate protection goals. However, the use of GMOs is accompanied by concerns regarding societal acceptance and ethical considerations [208]. Nonetheless, genetic engineering technologies—when applied to develop modified plants and microorganisms as catch crops in regenerative agriculture—can significantly improve the quality of agricultural soils, reduce the use of artificial fertilizers and pesticides, enhance crop safety, and support the protection of biodiversity.

6.2. Integration of Phytoremediation and Nanotechnology for Soil Regeneration

A modern and promising approach to soil regeneration is the integration of phytoremediation with nanotechnology. Due to their high surface-to-volume ratio, high reactivity, and ability to interact with pollutants at the molecular level, nanoparticles can significantly enhance phytoremediation efficiency [209]. Nanotechnology is an emerging and innovative field within environmental remediation, offering novel opportunities to improve the effectiveness and precision of phytoremediation strategies. The combination of microorganism-assisted phytoremediation with the application of nanoparticles has shown promise [210]. While this concept has been tested primarily in the context of heavy metal pollution, ongoing research is expanding its application to include organic pollutants and emerging contaminants [209]. Studies indicate that nano-phytoremediation can improve plant health and reduce the effects of soil toxicity. Yasin et al. [210] reported that nanoparticles enhance soil enzymes and increase cadmium absorption. Similarly, Hussain et al. [55] found that using ZnO nanoparticles significantly increased the accumulation of Pb in the roots, stem, and leaves of Persicaria hydropiper L. Other studies have indicated a reduction in plant oxidative stress resulting from the application of nanoparticles [211]. The use of nanoparticles can effectively improve phytoremediation. Still, the optimal dose of nanoparticles should be determined beforehand because a dose that is too high can inhibit plant growth and accumulate heavy metals [55]. Nanoparticles have been shown to enhance the bioavailability of pollutants in the plant–microorganism system, thereby improving the efficiency of pollutant uptake and degradation. Additionally, they can mitigate the toxic effects of these pollutants on plants, further supporting the phytoremediation process [52]. Despite several advantages resulting from the application of nanoparticles for assisted phytoremediation, there is a lack of studies considering the fate of nanoparticles in the environment. However, due to their novelty and limited use time, the potential risks associated with using nanomaterials in this process have not yet been fully identified. Further research is needed to understand better nanotechnology’s long-term impacts on the environment and ecosystems and to develop strategies to minimize risks.

6.3. Potential Gaps in the Literature and Directions for Future Research

Although phytoremediation has been extensively studied in recent years, several gaps remain in our understanding of its full potential and limitations. While some studies emphasize the role of microorganisms in enhancing phytoremediation efficiency, there is a need for more comprehensive studies on how microbial consortia can be tailored to specific contaminants, from the droplet composition to the interactions between microorganisms. Another significant gap in the literature pertains to the long-term effects of phytoremediation on soil health and ecosystem functioning. While most studies have focused on short-term outcomes, such as contaminant removal, the long-term impact of phytoremediation on soil biodiversity, nutrient cycling, and overall soil health remains poorly understood. Therefore, studies investigating soil resilience after remediation and the risks of bioaccumulation in plant and microbial tissues should be prioritized in future research. Understanding these long-term effects is crucial for assessing the sustainability of phytoremediation as an environmental management strategy. Additionally, further investigation into the ecological consequences of prolonged phytoremediation will help guide more effective and sustainable practices. By addressing these gaps, future studies could provide valuable insights into optimizing phytoremediation for long-term soil restoration.

7. Conclusions

Plants and microorganisms form a synergistic foundation that enables comprehensive soil restoration, effective pollutant removal, and the protection of surface and groundwater. This integration enhances agricultural productivity, reduces dependence on pesticides and fertilizers, protects biodiversity, supports climate protection, and improves food safety. When properly selected, plants and microorganisms can effectively remove a wide range of soil contaminants including emerging contaminants of increasing concern. The integration of microorganism-assisted phytoremediation can significantly contribute to achieving global and European environmental goals, addressing climate change, and improving quality of life. By restoring ecosystem functions to degraded soils, this approach strengthens ecological resilience and protects against biotic and abiotic stresses. Furthermore, by supporting green infrastructure and regenerative agriculture, phytoremediation improves the carbon sequestration capacity of soil—helping to mitigate climate change and supporting the objectives of the EDG. With its strong economic, commercial, and practical potential, phytoremediation stands as a powerful tool in achieving both the SDGs and the long-term vision of regenerative agriculture.