Microbial Degradation of Soil Organic Pollutants: Mechanisms, Challenges, and Advances in Forest Ecosystem Management

Abstract

With industrialization and widespread chemical use, soil organic pollutants have become a major environmental issue. Forest ecosystems, among the most important on Earth, have unique potential for controlling and remediating soil pollution. This article explores the mechanisms of microbial community degradation of organic pollutants, their adaptability across forest ecological conditions, and the effects of environmental factors on degradation efficiency. For example, acidic pH (pH < 5.5) favors PAH degradation, near-neutral pH (6.0–7.5) enhances pharmaceutical and PPCP degradation, and alkaline conditions (pH > 7.5) facilitate petroleum hydrocarbon, VOC, and PPCP breakdown. Optimal microbial degradation occurs with humidity levels between 60% and 80%, and SOM content of 2–5%. This review analyzes advancements in microbial degradation technologies for forest ecosystem soil pollution treatment, including genetic engineering, composting, bioaugmentation, and bio-stimulation techniques, and their integration with phytoremediation. The review also addresses the challenges of real-world implementation, such as maintaining microbial diversity, managing pollutant complexity, adapting to environmental changes, and highlighting future research opportunities. The next decade will focus on synthetic biology, omics technologies, microbial-electrochemical systems, community dynamics, eco-engineering, and plant-microbe synergy to develop efficient, sustainable bioremediation strategies.

1. Introduction

Soil pollution poses a serious threat to global ecological safety and human health [1]. In forest ecosystems, human activities introduce a variety of organic pollutants into forest soil, disrupting the ecological balance [2]. In particular, industrial areas and regions with frequent human activity often exceed safety standards for pollutants in forest soil, jeopardizing the health and stability of these ecosystems. These pollutants not only impact microbial diversity and activity but may also infiltrate groundwater and enter the food chain, causing widespread harm [3,4].

Microbial degradation technology offers a promising approach to address soil pollution [5,6,7,8]. Microorganisms, with their unique metabolic capabilities, can efficiently decompose and transform harmful contaminants. This study focuses on the application of microbial degradation in forest ecosystems, exploring its potential and environmental adaptability to provide a scientific foundation for soil pollution control [9]. Bioremediation, composting, bioaugmentation, bioventing, and phytoremediation are effective soil remediation techniques, each with specific applications and limitations.

This research addresses the increasing problem of organic matter pollution in forest soils, threatening ecosystem stability and biodiversity. The scope of this study focuses on the microbial degradation of organic pollutants in forest soils, including persistent organic pollutants (POPs), petroleum hydrocarbons, pharmaceuticals, and volatile organic compounds (VOCs). It explores the mechanisms and environmental adaptability of microbial communities, the impact of soil and forest ecosystem factors on degradation efficiency, and the practical challenges and opportunities in applying microbial remediation techniques in real-world forest environments. Specifically, this study will do the following: (i) identify and analyze common organic pollutants in forest soils, such as persistent organic pollutants (POPs), petroleum hydrocarbons, pharmaceuticals, and volatile organic compounds (VOCs); (ii) examine the mechanisms and environmental adaptability of microbial communities in degrading these pollutants under various forest ecological conditions; (iii) evaluate the influence of soil properties, forest cover, and environmental factors (temperature, moisture) on microbial degradation efficiency; and (iv) address research voids related to the integration of synthetic biology, omics technologies, microbial-electrochemical systems, community dynamics, eco-engineering approaches, and plant-microbe synergy to enhance the efficiency and sustainability of microbial degradation and bioremediation strategies for soil organic pollutants.

2. Soil Organic Pollutants in Forest Ecosystems

2.1. Hazards of Organic Pollutants in Forest Soil

Forest soils are increasingly affected by various organic pollutants, each presenting unique challenges (Figure 1). Persistent organic pollutants (POPs), such as DDT and PCBs, are found in regions like the Amazon Rainforest and the Arctic [10,11], primarily due to historical pesticide use and atmospheric transport. Petroleum hydrocarbons, including PAHs and alkanes, severely impact areas such as the Canadian oil sands and the Niger Delta due to extraction and spills [12]. Pharmaceuticals and personal care products (PPCPs) contaminate river basins like the Yangtze and Danube, primarily from agricultural runoff and wastewater discharge [13]. Volatile organic compounds (VOCs), including benzene and toluene, are prominent in urban and industrial areas such as Beijing and Los Angeles [14,15], driven by vehicular and industrial emissions.

Organic pollutants in forest soils pose significant threats to environmental health and ecosystem stability. As shown in Figure 2, POPs, such as pesticides and industrial chemicals, persist in the environment, disrupting microbial communities, inhibiting plant growth, and causing bioaccumulation in wildlife, with severe human health risks in areas of intensive agriculture or industry [23,24,25]. Petroleum hydrocarbons degrade soil structure, reduce aeration, and impair microbial functions, often originating from oil spills, industrial sites, and transportation routes [26,27], while PPCPs and VOCs, introduced through wastewater discharge, improper disposal, and industrial emissions, disrupt microbial and plant health and cause endocrine disruption in wildlife (details are illustrated in Supplementary Materials Table S1). Collectively, these pollutants underscore the urgent need for effective management and remediation strategies to safeguard soil health and ecosystem stability [28].

2.2. Sources of Organic Matter Contamination in Forest Soils

Organic matter contamination in forest soils originates primarily from four sources: agricultural runoff, industrial discharges, wastewater discharge, and oil spills or leaks, as illustrated in Figure 3. Agricultural runoff is the largest contributor, accounting for 35% of total contamination, primarily due to the presence of pesticides and fertilizers [29]. Industrial discharges contribute 25%, with predominant pollutants including PCBs, dioxins, and heavy metals. Wastewater discharge accounts for 20%, introducing pharmaceuticals and personal care products as key contaminants. Finally, oil spills and leaks make up 15%, involving petroleum hydrocarbons and heavy metals.

2.3. Microbial Treatment

Microbial treatments for organic matter contamination in forest soils offer various strategies to address pollution through natural processes [37]. Bioremediation, composting, bioaugmentation, bioventing, and phytoremediation are effective soil remediation techniques, each with specific applications and limitations.

As shown in Figure 4, bioremediation is a highly versatile and cost-effective approach that utilizes microbial species, such as Pseudomonas and Phanerochaete chrysosporium, to degrade contaminants. However, its effectiveness depends on careful optimization of environmental conditions and the selection of appropriate microbial strains. Additionally, bioremediation may result in incomplete degradation products and often requires sufficient time to achieve desired outcomes [38,39,40]. Composting is an effective method for enhancing soil fertility and reducing waste volume, relying on key microorganisms such as bacteria and fungi to facilitate degradation. However, its success requires careful management to ensure complete degradation and to mitigate potential greenhouse gas emissions, such as methane, which can occur if the process is not properly controlled [41,42,43,44]. Bioaugmentation involves the introduction of specific microorganisms to enhance the degradation of particular pollutants, providing tailored solutions for targeted remediation. However, this approach may face challenges related to microbial integration into native ecosystems and compatibility with environmental conditions, highlighting the need for improved strategies to enhance microbial adaptation and minimize ecological disruption [45,46,47,48]. Bioventing is a remediation technique that enhances oxygen availability to stimulate microbial activity, making it particularly effective for treating contaminants under moderately aerobic conditions. However, it is ineffective for pollutants that degrade anaerobically and requires precise environmental control to ensure optimal performance [49,50,51,52,53]. Phytoremediation, particularly when combined with microbial assistance, utilizes plants to remove contaminants and stabilize soil, making it a cost-efficient approach for addressing surface-level contamination. However, its effectiveness relies on the careful selection of appropriate plant-microbe combinations, and it carries the potential risk of transferring pollutants into the food chain, which must be managed to ensure environmental and ecological safety [54,55,56,57,58,59].

Each method has its advantages and limitations, making the choice of treatment dependent on the specific contamination scenario and site conditions. To gain a better understanding of the mechanisms by which these methods remove organic pollutants from soil, it is essential to investigate how the microorganisms utilized in these processes degrade soil organic pollutants (Section 3).

3. Mechanism of Microbial Degradation of Soil Organic Pollutants

3.1. Complex Processes and Key Species

Microorganisms, existing in diverse populations across different soil textures and depths in forest ecosystems, play a crucial role as decomposers in the degradation of organic pollutants. Their enzymatic activity is central to this process, with enzymes acting as biological catalysts that transform complex organic pollutants into simpler, less toxic compounds [60]. Each enzyme targets specific bonds or functional groups within pollutant molecules, enabling precise and efficient breakdown [61]. The effectiveness of this degradation largely depends on the chemical nature of the pollutants, which range from petroleum hydrocarbons to synthetic chemicals such as pesticides and pharmaceuticals. Each enzyme targets a specific type of bond or functional group within the pollutant molecules (

Table 1. Types of enzymatic reactions in microbial degradation of soil organic pollutants.

Types of Enzymatic Reactions	Enzyme	Mechanism	References
Hydrolysis	Hydrolases	Hydrolysis involves the addition of water to break chemical bonds in complex organic molecules, resulting in simpler, often more polar and less toxic products.	[62,63]
Oxidation-Reduction (Redox) Reactions	Oxidases, Oxygenases, Dehydrogenases Reductases	Oxidation: Enzymes introduce oxygen into organic molecules or remove electrons, leading to the breakdown of the pollutants. Reduction: Enzymes add electrons to pollutants, often removing halogens or nitro groups, resulting in less toxic or more biodegradable compounds.	[61,64,65,66]
Dehalogenases	Dehalogenases	Dehalogenation involves the removal of halogen atoms (e.g., chlorine, bromine) from organic compounds. This process is crucial for detoxifying halogenated pollutants, which are often persistent and toxic.	[67,68]
Ring Cleavage	Dioxygenases Peroxidases	Ring cleavage involves the breaking of aromatic rings in complex pollutants, such as PAHs and phenolic compounds. This step is critical for the complete mineralization of these compounds.	[69,70]
Hydroxylation	Hydroxylases Monooxygenases	Hydroxylation introduces hydroxyl groups (-OH) into organic molecules, increasing their solubility and making them more susceptible to further degradation.	[71,72,73]

).

Certain microorganisms have evolved specialized mechanisms, including co-metabolism, to degrade specific pollutants like PAHs and chlorinated compounds. Additionally, microbial consortia, where multiple species collaborate, enhance the efficiency of degradation through synergistic interactions (Table 2). Microbial degradation of soil organic pollutants is a complex process that involves the action of various microbial species and enzymes. For instance, the degradation of PAHs is primarily carried out by Ascomycetes (e.g., Fusarium oxysporum), Basidiomycetes (e.g., Laccaria bicolor), and Actinobacteria (e.g., Streptomyces griseus) [74,75,76,77]. These microorganisms utilize oxygenases to cleave the aromatic rings in PAHs, making them more susceptible to further degradation. For PPCPs, Pseudomonas putida and Bacillus subtilis are key species involved in the oxidation and hydroxylation of complex organic compounds. Similarly, the dehydrogenases and peroxidases produced by these microbes play critical roles in the reduction and oxidation of pollutants, facilitating their breakdown [78,79,80]. The degradation of VOCs, such as benzene and toluene, is often carried out by Pseudomonas putida and Rhodococcus spp. [81], which use monooxygenases to oxidize these compounds. In the case of petroleum hydrocarbons, Alcanivorax borkumensis and Rhodococcus sp. [82,83,84] utilize specialized hydroxylases to degrade long-chain alkanes and aromatic hydrocarbons. These enzymes break down pollutants by adding oxygen atoms or removing electrons, transforming complex compounds into simpler, less toxic molecules.

Halogen-containing organic pollutants, such as polychlorinated biphenyls (PCBs), dichlorodiphenyltrichloroethane (DDT), and trichloroethylene (TCE), are persistent and toxic due to strong carbon–halogen bonds (e.g., C-Cl). Microbial degradation involves reductive dechlorination, oxidative dehalogenation, and hydrolytic processes. Dehalococcoides spp. (bacteria) and Archaeoglobus fulgidus (archaea) perform reductive dechlorination, removing chlorine atoms from PCBs and TCE under anaerobic conditions and converting them into less toxic intermediates like ethene or biphenyls, with efficiencies up to 70% in 20 days [85,86]. Pseudomonas putida and Rhodococcus spp. use oxygenases for oxidative dehalogenation of DDT, achieving 60–80% degradation in aerobic forest soils within 14 days [87]. Challenges include low bioavailability, toxicity to microbes, and slow kinetics, requiring bioaugmentation or biostimulation for enhancement [88].

Microplastics, increasingly prevalent in forest soils due to agricultural plastics and atmospheric deposition, pose a novel challenge. Microbial degradation involves bacteria (Pseudomonas spp., Rhodococcus spp.) and fungi (Aspergillus niger, Penicillium chrysogenum) that produce enzymes like hydrolases, oxidases, and esterases to break down polyethylene (PE), polypropylene (PP), and polystyrene (PS) [89,90]. Kumar et al. [91] reported that Rhodococcus ruber degrades PE by 15% over 60 days in forest soils, forming smaller fragments via oxidative cleavage. Fungi like Aspergillus niger achieve 25% PS degradation through hydrolysis, but efficiencies are low due to microplastics’ recalcitrance and limited enzyme specificity [92]. Environmental factors (e.g., pH, temperature) and microbial consortia enhance degradation, yet microplastics reduce soil microbial diversity and activity, necessitating advanced strategies like bioelectrochemical systems [93].

Table 2. Some types of organic pollutants and their microbial degradation mechanism(s).

Type of Pollutant	Microbial Species	Mechanism of Degradation	Ref.
Pesticides
DDT	Bacteria: Sphingomonas spp. Fungi: Phanerochaete chrysosporium	Reduction and Hydrolysis: Reduction of DDT to DDE, hydrolysis to DDA (dichlorodiphenyldichloroethane)	[94]
Aldrin	Bacteria: Burkholderia cepacia Fungi: Aspergillus niger	Oxidative Degradation: Oxidation of Aldrin to Dieldrin, further degradation to less toxic forms	[95]
Endrin	Bacteria: Pseudomonas putida Fungi: Trichoderma harzianum	Dechlorination: Dechlorination and hydrolysis of Endrin to less toxic products	[78]
Chlordane	Bacteria: Mycobacterium spp. Fungi: Cunninghamella echinulata	Oxidative and Hydrolytic Degradation: Oxidation of Chlordane to less toxic metabolites	[96]
Lindane	Bacteria: Rhodococcus spp. Fungi: White-rot fungi	Ring Cleavage: Ring cleavage and mineralization of Lindane to non-toxic products	[82]
Industrial Chemicals
PCBs	Bacteria: Burkholderia spp. Fungi: Phanerochaete chrysosporium	Dechlorination: Microbial dechlorination of PCBs to less chlorinated and less toxic forms	[97]
Dioxins	Bacteria: Dechloromonas spp. Fungi: Cunninghamella elegans	Reductive Dechlorination: Reduction of chlorine atoms from dioxins to less toxic forms	[98]
Furans	Bacteria: Pseudomonas spp. Fungi: Lentinus edodes	Oxidative Degradation: Oxidation of furans to less harmful products	[99]
Alkanes
n-Hexane	Bacteria: Pseudomonas putida Fungi: Phanerochaete chrysosporium	Oxidative Biodegradation: Conversion of n-Hexane to less harmful products through hydroxylation	[100]
n-Heptane	Bacteria: Mycobacterium spp. Fungi: Aspergillus niger	Hydroxylation: Oxidation of n-Heptane to heptane-1-ol, followed by further oxidation	[101]
n-Octane	Bacteria: Rhodococcus spp. Fungi: White-rot fungi	Terminal Oxidation: Terminal oxidation of n-Octane to fatty acids and further degradation	[102]
Aromatic Hydrocarbons
Benzene	Bacteria: Pseudomonas putida Fungi: Phanerochaete chrysosporium	Ring Cleavage: Conversion of benzene to catechol and further breakdown via ring cleavage	[103]
Toluene	Bacteria: Pseudomonas putida Fungi: Aspergillus niger	Monooxygenation: Oxidation of toluene to toluene-4-monooxygenase, further oxidized to benzoic acid	[79]
Ethylbenzene	Bacteria: Pseudomonas spp. Fungi: White-rot fungi	Oxidative Degradation: Oxidation of ethylbenzene to ethylbenzene-1,2-diol, then to catechol	[80]
Xylenes	Bacteria: Pseudomonas putida Fungi: Phanerochaete chrysosporium	Oxidative Degradation: Oxidation of xylenes to methylbenzoic acids and further breakdown	[104]
PAHs
Naphthalene	Bacteria: Pseudomonas putida Fungi: Phanerochaete chrysosporium	Ring Cleavage: Conversion of naphthalene to catechol and further breakdown	[74]
Anthracene	Bacteria: Mycobacterium spp. Fungi: Aspergillus niger	Ring Cleavage and Oxidation: Conversion to anthraquinone and further breakdown	[75]
Phenanthrene	Bacteria: Sphingomonas spp. Fungi: White-rot fungi	Ring Cleavage and Oxidation: Conversion to phenanthrene-2,3-diol and further breakdown	[76]
Benzo[a]pyrene	Bacteria: Mycobacterium spp. Fungi: Phanerochaete chrysosporium	Ring Cleavage and Oxidation: Conversion to less toxic metabolites	[77]
Antibiotics
Ciprofloxacin	Bacteria: Pseudomonas spp. Fungi: Aspergillus niger	Oxidative Degradation: Conversion to less toxic derivatives	[105]
Tetracycline	Bacteria: Bacillus spp. Fungi: Trichoderma harzianum	Hydrolysis and Oxidation: Hydrolysis to inactive forms and oxidative cleavage	[106]
Hormones
Estrogens	Bacteria: Comamonas testosteroni Fungi: Phanerochaete chrysosporium	Hydroxylation and Oxidation: Conversion to less active metabolites	[107]
Progesterone	Bacteria: Sphingomonas spp. Fungi: White-rot fungi	Oxidative Degradation: Conversion to less active forms through hydroxylation	[108]
Sunscreens
Oxybenzone	Bacteria: Pseudomonas putida Fungi: Aspergillus niger	Oxidative Degradation: Conversion to less toxic metabolites	[109]
Octocrylene	Bacteria: Pseudomonas spp. Fungi: Penicillium chrysogenum	Hydrolysis and Oxidation: Conversion to less harmful products through hydrolysis	[110]
Synthetic Fragrances
Phthalates	Bacteria: Burkholderia spp. Fungi: Aspergillus niger	Hydrolysis: Hydrolysis of phthalates to phthalic acid and further degradation	[111]
Musk Compounds	Bacteria: Sphingomonas spp. Fungi: White-rot fungi	Oxidative Degradation: Oxidation of musk compounds to less toxic metabolites	[112]
Solvents
Acetone	Bacteria: Pseudomonas spp. Fungi: Aspergillus niger	Oxidative Degradation: Conversion to acetic acid and further oxidation	[81]
Ethanol	Bacteria: Zymomonas mobilis Fungi: Saccharomyces cerevisiae	Fermentation: Conversion to acetaldehyde and acetic acid via fermentation	[113]
Methanol	Bacteria: Methylobacterium spp. Fungi: Aspergillus niger	Oxidative Degradation: Conversion to formaldehyde and further oxidation	[114]
Industrial Emissions
Formaldehyde	Bacteria: Methylobacterium spp. Fungi: Phanerochaete chrysosporium	Oxidative Degradation: Conversion to formic acid and further breakdown	[115]
Styrene	Bacteria: Pseudomonas putida Fungi: Aspergillus niger	Oxidative Degradation: Conversion to styrene oxide and further breakdown	[116]
Trichloroethylene	Bacteria: Dehalococcoides spp. Fungi: White-rot fungi	Reductive Dechlorination: Conversion to less toxic forms via dechlorination	[117]
BTEX
Benzene	Bacteria: Pseudomonas putida Fungi: Phanerochaete chrysosporium	Ring Cleavage: Conversion to catechol and further breakdown	[118]
Toluene	Bacteria: Pseudomonas putida Fungi: Aspergillus niger	Monooxygenation: Conversion to benzoic acid	[119]
Xylenes	Bacteria: Pseudomonas putida Fungi: Phanerochaete chrysosporium	Oxidative Degradation: Conversion to methylbenzoic acids	[119]

Table 2. Some types of organic pollutants and their microbial degradation mechanism(s).

Type of Pollutant	Microbial Species	Mechanism of Degradation	Ref.
Pesticides
DDT	Bacteria: Sphingomonas spp. Fungi: Phanerochaete chrysosporium	Reduction and Hydrolysis: Reduction of DDT to DDE, hydrolysis to DDA (dichlorodiphenyldichloroethane)	[94]
Aldrin	Bacteria: Burkholderia cepacia Fungi: Aspergillus niger	Oxidative Degradation: Oxidation of Aldrin to Dieldrin, further degradation to less toxic forms	[95]
Endrin	Bacteria: Pseudomonas putida Fungi: Trichoderma harzianum	Dechlorination: Dechlorination and hydrolysis of Endrin to less toxic products	[78]
Chlordane	Bacteria: Mycobacterium spp. Fungi: Cunninghamella echinulata	Oxidative and Hydrolytic Degradation: Oxidation of Chlordane to less toxic metabolites	[96]
Lindane	Bacteria: Rhodococcus spp. Fungi: White-rot fungi	Ring Cleavage: Ring cleavage and mineralization of Lindane to non-toxic products	[82]
Industrial Chemicals
PCBs	Bacteria: Burkholderia spp. Fungi: Phanerochaete chrysosporium	Dechlorination: Microbial dechlorination of PCBs to less chlorinated and less toxic forms	[97]
Dioxins	Bacteria: Dechloromonas spp. Fungi: Cunninghamella elegans	Reductive Dechlorination: Reduction of chlorine atoms from dioxins to less toxic forms	[98]
Furans	Bacteria: Pseudomonas spp. Fungi: Lentinus edodes	Oxidative Degradation: Oxidation of furans to less harmful products	[99]
Alkanes
n-Hexane	Bacteria: Pseudomonas putida Fungi: Phanerochaete chrysosporium	Oxidative Biodegradation: Conversion of n-Hexane to less harmful products through hydroxylation	[100]
n-Heptane	Bacteria: Mycobacterium spp. Fungi: Aspergillus niger	Hydroxylation: Oxidation of n-Heptane to heptane-1-ol, followed by further oxidation	[101]
n-Octane	Bacteria: Rhodococcus spp. Fungi: White-rot fungi	Terminal Oxidation: Terminal oxidation of n-Octane to fatty acids and further degradation	[102]
Aromatic Hydrocarbons
Benzene	Bacteria: Pseudomonas putida Fungi: Phanerochaete chrysosporium	Ring Cleavage: Conversion of benzene to catechol and further breakdown via ring cleavage	[103]
Toluene	Bacteria: Pseudomonas putida Fungi: Aspergillus niger	Monooxygenation: Oxidation of toluene to toluene-4-monooxygenase, further oxidized to benzoic acid	[79]
Ethylbenzene	Bacteria: Pseudomonas spp. Fungi: White-rot fungi	Oxidative Degradation: Oxidation of ethylbenzene to ethylbenzene-1,2-diol, then to catechol	[80]
Xylenes	Bacteria: Pseudomonas putida Fungi: Phanerochaete chrysosporium	Oxidative Degradation: Oxidation of xylenes to methylbenzoic acids and further breakdown	[104]
PAHs
Naphthalene	Bacteria: Pseudomonas putida Fungi: Phanerochaete chrysosporium	Ring Cleavage: Conversion of naphthalene to catechol and further breakdown	[74]
Anthracene	Bacteria: Mycobacterium spp. Fungi: Aspergillus niger	Ring Cleavage and Oxidation: Conversion to anthraquinone and further breakdown	[75]
Phenanthrene	Bacteria: Sphingomonas spp. Fungi: White-rot fungi	Ring Cleavage and Oxidation: Conversion to phenanthrene-2,3-diol and further breakdown	[76]
Benzo[a]pyrene	Bacteria: Mycobacterium spp. Fungi: Phanerochaete chrysosporium	Ring Cleavage and Oxidation: Conversion to less toxic metabolites	[77]
Antibiotics
Ciprofloxacin	Bacteria: Pseudomonas spp. Fungi: Aspergillus niger	Oxidative Degradation: Conversion to less toxic derivatives	[105]
Tetracycline	Bacteria: Bacillus spp. Fungi: Trichoderma harzianum	Hydrolysis and Oxidation: Hydrolysis to inactive forms and oxidative cleavage	[106]
Hormones
Estrogens	Bacteria: Comamonas testosteroni Fungi: Phanerochaete chrysosporium	Hydroxylation and Oxidation: Conversion to less active metabolites	[107]
Progesterone	Bacteria: Sphingomonas spp. Fungi: White-rot fungi	Oxidative Degradation: Conversion to less active forms through hydroxylation	[108]
Sunscreens
Oxybenzone	Bacteria: Pseudomonas putida Fungi: Aspergillus niger	Oxidative Degradation: Conversion to less toxic metabolites	[109]
Octocrylene	Bacteria: Pseudomonas spp. Fungi: Penicillium chrysogenum	Hydrolysis and Oxidation: Conversion to less harmful products through hydrolysis	[110]
Synthetic Fragrances
Phthalates	Bacteria: Burkholderia spp. Fungi: Aspergillus niger	Hydrolysis: Hydrolysis of phthalates to phthalic acid and further degradation	[111]
Musk Compounds	Bacteria: Sphingomonas spp. Fungi: White-rot fungi	Oxidative Degradation: Oxidation of musk compounds to less toxic metabolites	[112]
Solvents
Acetone	Bacteria: Pseudomonas spp. Fungi: Aspergillus niger	Oxidative Degradation: Conversion to acetic acid and further oxidation	[81]
Ethanol	Bacteria: Zymomonas mobilis Fungi: Saccharomyces cerevisiae	Fermentation: Conversion to acetaldehyde and acetic acid via fermentation	[113]
Methanol	Bacteria: Methylobacterium spp. Fungi: Aspergillus niger	Oxidative Degradation: Conversion to formaldehyde and further oxidation	[114]
Industrial Emissions
Formaldehyde	Bacteria: Methylobacterium spp. Fungi: Phanerochaete chrysosporium	Oxidative Degradation: Conversion to formic acid and further breakdown	[115]
Styrene	Bacteria: Pseudomonas putida Fungi: Aspergillus niger	Oxidative Degradation: Conversion to styrene oxide and further breakdown	[116]
Trichloroethylene	Bacteria: Dehalococcoides spp. Fungi: White-rot fungi	Reductive Dechlorination: Conversion to less toxic forms via dechlorination	[117]
BTEX
Benzene	Bacteria: Pseudomonas putida Fungi: Phanerochaete chrysosporium	Ring Cleavage: Conversion to catechol and further breakdown	[118]
Toluene	Bacteria: Pseudomonas putida Fungi: Aspergillus niger	Monooxygenation: Conversion to benzoic acid	[119]
Xylenes	Bacteria: Pseudomonas putida Fungi: Phanerochaete chrysosporium	Oxidative Degradation: Conversion to methylbenzoic acids	[119]

Microbial enzymes are essential for the biodegradation of organic pollutants in soils. Oxygenases, such as dioxygenases and monooxygenases, are involved in the breakdown of aromatic hydrocarbons and are crucial for the ring cleavage of pollutants like PAHs and aromatic hydrocarbons. Dehydrogenases play a vital role in the reduction of pollutants, facilitating the breakdown of compounds like VOCs and PPCPs [75]. These enzymes are responsible for the oxidation or reduction of pollutants, enhancing their bioavailability and subsequent microbial degradation. Peroxidases, commonly found in fungi like Phanerochaete chrysosporium, assist in the oxidative degradation of pollutants like chlorinated hydrocarbons and pesticides, breaking down the complex molecules into simpler, non-toxic compounds [119].

Future research on the microbial degradation of soil organic pollutants should focus on unraveling the molecular mechanisms underlying enzymatic pathways and microbial community interactions, particularly in response to diverse environmental conditions and complex pollutant mixtures. Emphasis should be placed on integrating multi-omics technologies, machine learning models, and advanced gene editing tools to enhance microbial efficiency and adaptability. Moreover, addressing the degradation of emerging contaminants, the formation and toxicity of secondary metabolites, and the synergistic effects of microbial consortia remains critical.

3.2. Microbial Groups and Their Roles in Soil Degradation

Microorganisms in forest ecosystems play a crucial role in degrading organic pollutants through diverse enzymatic pathways, as previously described. In addition to the key degraders like Pseudomonas, Rhodococcus, and Phanerochaete chrysosporium, soil-dwelling counterparts such as sulfate-reducing bacteria (SRB), sulfur-oxidizing bacteria (SOB), iron-reducing bacteria (IRB), and iron-oxidizing bacteria (IOB), along with their archaeal equivalents, significantly influence soil properties and pollutant degradation. These microbial groups modify soil redox potential, pH, and structure, thereby affecting the bioavailability and degradation of organic pollutants like PAHs, petroleum hydrocarbons, and chlorinated compounds.

3.2.1. SRB and Archaea

SRB, such as Desulfovibrio spp. (bacteria) and Archaeoglobus fulgidus (archaea), reduce sulfate to sulfide under anaerobic conditions, lowering redox potential (Eh < −200 mV) and creating reducing environments conducive to degrading chlorinated hydrocarbons (e.g., TCE) via reductive dechlorination. However, sulfide production can increase soil acidity (pH < 5.5), potentially inhibiting other microbial activities, as observed in waterlogged forest soils [120]. SRB also contribute to PAH degradation under sulfate-reducing conditions, albeit at lower efficiencies (e.g., 35% pyrene removal) [77].

3.2.2. SOB and Archaea

SOB, such as Thiobacillus spp. (bacteria) and Sulfolobus spp. (archaea), oxidize sulfur compounds (e.g., sulfide to sulfate) under aerobic or microaerobic conditions, increasing soil pH and redox potential (Eh > 300 mV). This enhances aerobic degradation of hydrocarbons (e.g., alkanes) by increasing oxygen availability, but excessive sulfide oxidation can lead to soil alkalinity (pH > 7.5), reducing microbial diversity and pollutant bioavailability, as reported in coniferous forest soils [121].

3.2.3. IRB and Archaea

IRB, such as Shewanella spp. (bacteria) and Methanosarcina spp. (archaea), reduce ferric iron (Fe³⁺) to ferrous iron (Fe²⁺) under anaerobic conditions, lowering redox potential and facilitating pollutant degradation (e.g., PAHs, petroleum hydrocarbons) via electron transfer. This process stabilizes soil structure but can increase acidity, impacting microbial activity, as seen in boreal forest soils [120]. IRB enhance bioelectrochemical degradation in SMFCs, improving PAH removal rates [122].

3.2.4. IOB and Archaea

IOB, such as Leptothrix spp. (bacteria) and Ferroplasma spp. (archaea), oxidize ferrous iron to ferric iron under aerobic conditions, raising redox potential and supporting oxidative degradation of pollutants like VOCs and PAHs. However, iron oxide accumulation can compact soil, reducing permeability and microbial access to pollutants, as observed in tropical rainforest soils [123].

Bacteria and archaea differ in their metabolic versatility and environmental resilience. Bacteria like Desulfovibrio and Thiobacillus are more abundant and exhibit rapid growth, dominating soil degradation under fluctuating conditions. Archaea, such as Archaeoglobus and Ferroplasma, thrive in extreme environments (e.g., low pH, high salinity), offering unique degradation pathways but with slower growth rates, making them less dominant in forest soils [123,124,125].

4. Factors Influencing Microbial Degradation Efficiency

The efficiency of microbial degradation in forest ecosystems is influenced by a myriad of factors, both environmental and biological [126,127,128,129]. Understanding these factors is crucial for enhancing the effectiveness of microbial remediation strategies.

4.1. Forest Cover Types

The type of forest cover influences the microbial degradation process through its effect on soil conditions and the microbial community structure. Different forest cover types have different levels of pH, temperature, and humidity, and the differences in vegetation and soil will lead to different types of microorganisms (

Table 3. Characteristics of different forest cover types and microorganisms in them.

Forest Type	Characteristics	Microbial Differences	Ref.
Evergreen Coniferous Forest	pH: Slightly acidic to neutral Temperature: Cool to temperate Humidity: High year-round	High fungal diversity, especially ectomycorrhizal fungi Lower bacterial diversity compared to broadleaf forests	[133,134]
Deciduous Broadleaf Forest	pH: Slightly acidic to neutral Temperature: Warm summers, cold winters Humidity: Seasonal variation, high in summer, low in winter	Diverse microbial community, especially during leaf litter decomposition Abundance of decomposer fungi and bacteria during fall	[135,136]
Mixed Forest (Coniferous and Broadleaf)	pH: Varies with soil type and tree species Temperature: Variable, depending on location Humidity: Variable, depending on location and season	Microbial diversity reflects a mix of coniferous and broadleaf forests High fungal diversity, including mycorrhizal fungi	[137,138]
Tropical Rainforest	pH: Slightly acidic Temperature: Hot and humid year-round Humidity: Very high	Extremely diverse microbial community High abundance of fungi and bacteria due to rich organic matter	[139,140]
Dry Forest/Savanna	pH: Slightly acidic to neutral Temperature: Hot during the day, cooler at night Humidity: Low to moderate, seasonal rains	Adapted to drought conditions, lower microbial diversity Fungi and bacteria tolerant to dry conditions	[141,142]
Boreal Forest	pH: Slightly acidic Temperature: Cold year-round Humidity: High, with significant snowfall	Low microbial diversity due to cold temperatures Adapted to cold conditions, including psychrophilic microorganisms	[143,144]

). Deciduous forests, for example, typically have a higher organic matter content due to leaf litter, fostering a rich microbial community capable of degrading a wide array of pollutants [130]. Coniferous forests, on the other hand, tend to have more acidic soils, which can limit microbial activity and thus degradation rates. The diversity of plant species in mixed forests can support a more diverse microbial community, potentially enhancing the degradation of a broader spectrum of pollutants [131]. The interaction between forest cover type and microbial degradation is a complex interplay of soil chemistry, microbial ecology, and pollutant characteristics, illustrating the need for ecosystem-specific approaches to bioremediation [132].

4.2. Soil Properties

Soil properties, including pH, temperature, moisture content, and organic matter content, are critical determinants of microbial degradation efficiency.

4.2.1. pH

In forest ecosystems, soil pH plays a critical role in the effectiveness of microbial remediation technologies (Figure 5). It not only directly influences the survival and activity of microorganisms but also affects the chemical forms, bioavailability, and degradation potential of pollutants [145]. The pH value of soil has a profound effect on microbial diversity and abundance.

In forest ecosystems, soil pH highly influences microbial distribution, which impacts microbial community composition and its role in organic matter degradation. In acidic soils (pH < 5.5), predominantly hosted microorganisms include Ascomycetes (e.g., Fusarium oxysporum), Basidiomycetes (e.g., Laccaria bicolor), and Acidobacteria (e.g., Acidobacterium capsulatum), which are adapted to low-pH environments but may exhibit reduced enzymatic activity [146,147]. In neutral soils (pH 6.0–7.5), a broader range of microbes thrive, including Actinobacteria like Streptomyces griseus, Firmicutes such as Bacillus subtilis, and Proteobacteria like Pseudomonas fluorescens [148]. These microbes perform highly efficient organic matter decomposition under balanced pH conditions. In alkaline soils (pH > 7.5), the dominant microbes are Alcaligenes (e.g., Alcaligenes faecalis), Nitrobacter (e.g., Nitrobacter winogradskyi), and Clostridia (e.g., Clostridium acetobutylicum), though their degradation efficiency may decline due to limited microbial diversity and nutrient availability [149,150]. The microbial degradation of soil organic pollutants—such as polycyclic aromatic hydrocarbons (PAHs), pharmaceuticals and personal care products (PPCPs), volatile organic compounds (VOCs), and petroleum hydrocarbons—is a complex process driven by these species and their specialized enzymes. For instance, Ascomycetes, Basidiomycetes, and Actinobacteria degrade PAHs using oxygenases to cleave aromatic rings, while Pseudomonas putida and Bacillus subtilis oxidize PPCPs via dehydrogenases and hydroxylases. Similarly, VOCs like benzene and toluene are broken down by Pseudomonas putida and Rhodococcus spp. using monooxygenases, and petroleum hydrocarbons are degraded by Alcanivorax borkumensis and Rhodococcus sp. through hydroxylases. These enzymes—oxygenases, dehydrogenases, and peroxidases (e.g., from fungi like Phanerochaete chrysosporium)—facilitate the oxidation, reduction, and ring cleavage of pollutants, transforming complex compounds into simpler, less toxic molecules and enhancing their bioavailability for further microbial breakdown.

Various microorganisms in forest soils exhibit specialized capabilities for degrading a range of organic pollutants (

Table 4. Degradation capabilities of various microorganisms for organic pollutants in forest soil.

Microorganism	Types of Organic Matter	Specific Organic Matter	Degradation Principle	Ref.
Acidic Soils (pH < 5.5)
Ascomycetes	PAHs Phenols	Naphthalene Phenol	Oxidative degradation via enzymes such as laccases and peroxidases.	[155]
Basidiomycetes	PAHs Pesticides	Pyrene DDT	Ligninolytic enzymes (laccases, peroxidases) oxidize aromatic compounds.	[156]
Acidobacteria	PAHs Pesticides	Fluoranthene Aldrin	Hydrolysis and oxidation of aromatic rings and side chains.	[157]
Neutral Soils (pH 6.0–7.5)
Actinobacteria	Petroleum Hydrocarbons PPCPs	Toluene Caffeine	Oxidative cleavage of aromatic rings, hydroxylation, and mineralization.	[158]
Firmicutes	Petroleum Hydrocarbons PPCPs	Benzene Diclofenac	Anaerobic degradation, hydrolysis, and fermentation of complex compounds.	[159]
Proteobacteria	Petroleum Hydrocarbons PPCPs VOCs	Xylene Estrone	Oxidative degradation, cometabolism, and mineralization of organic pollutants.	[160]
Bacteroidetes	Pharmaceuticals PPCPs	Erythromycin Bisphenol A	Hydrolytic and oxidative processes, breaking down complex organic molecules.	[161]
Alkaline Soils (pH > 7.5)
Alcaligenes	Petroleum Hydrocarbons VOCs	Octane Trichloroethylene	Oxygenase-mediated oxidation and degradation of hydrocarbons.	[162]
Nitrobacter	PPCPs Organic Nitrogen Compounds	Ammonium Nitrobenzene	Nitrification and oxidation of nitro-containing compounds.	[163]
Clostridia	Petroleum Hydrocarbons PPCPs	Butyrate, Hexachlorobenzene	Anaerobic fermentation and degradation of complex organic compounds.	[164]
Bacillus	Petroleum Hydrocarbons PPCPs VOCs	Dodecane, Paracetamol	Hydrocarbon oxidation, enzyme-mediated degradation of organic pollutants.	[165]
Arthrobacter	PAHs Petroleum Hydrocarbons	Anthracene Cyclohexane	Oxidative degradation of aromatic hydrocarbons and heterocyclic compounds.	[166]
Pseudomonas	PAHs Petroleum Hydrocarbons, PPCPs VOCs	Phenanthrene Naphthalene Atrazine Toluene	Enzyme-mediated oxidation, cometabolic degradation, and mineralization.	[158]

). Ascomycetes and Basidiomycetes are effective in breaking down polycyclic aromatic hydrocarbons (PAHs) and pesticides through oxidative processes involving enzymes such as laccases and peroxidases [151]. Actinobacteria are involved in the hydrolysis and oxidation of aromatic compounds, although their degradation rates are generally lower compared to other groups [152]. They excel in breaking down petroleum hydrocarbons and pharmaceuticals via oxidative cleavage and hydroxylation. Firmicutes perform anaerobic degradation and fermentation, effectively treating petroleum hydrocarbons and pharmaceuticals. Proteobacteria and Pseudomonas are prominent in degrading a broad spectrum of organic pollutants, including VOCs and PPCPs, through oxidative and metabolic processes [153]. Bacteroidetes and Alcaligenes are significant for their hydrolytic and oxidative degradation capabilities [152]. Nitrobacter and Clostridia contribute to the degradation of nitrogen-containing organic compounds and complex organic molecules, respectively [154]. These microorganisms employ diverse metabolic pathways to break down hazardous organic pollutants, making them essential for bioremediation in polluted forest soils. As shown in Table 4, in acidic soils (pH < 5.5), microorganisms such as Ascomycetes, Basidiomycetes, and Acidobacteria are primarily involved in the degradation of PAHs, phenols, pesticides, and other organic compounds through oxidative degradation processes using enzymes like laccases, peroxidases, and hydrolytic enzymes. In neutral soils (pH 6.0–7.5), microorganisms like Actinobacteria, Firmicutes, Proteobacteria, and Bacteroidetes play a significant role in degrading petroleum hydrocarbons, PPCPs, VOCs, and pharmaceuticals, employing oxidative cleavage, hydroxylation, fermentation, and hydrolytic processes. In alkaline soils (pH > 7.5), organisms such as Alcaligenes, Nitrobacter, Clostridia, and Bacillus help degrade petroleum hydrocarbons, PPCPs, and other organic compounds through oxygenase-mediated oxidation, nitrification, and anaerobic fermentation, while Pseudomonas and Arthrobacter engage in the oxidative degradation of aromatic hydrocarbons. The microorganisms contribute to the breakdown of complex molecules via enzyme-mediated processes, enhancing the efficiency of bioremediation in diverse soil conditions.

4.2.2. Temperature

Over the past decade, the global average temperature has shown a clear upward trend due to climate change [167]. According to National Aeronautics and Space Administration (NASA) and National Oceanic and Atmospheric Administration (NOAA) data, the global average temperature increased by approximately 0.9 °C from 2013 to 2023. This rise is consistent with long-term warming trends attributed to anthropogenic climate change. Over the last decade, temperature changes in major forest regions worldwide have generally shown an upward trend, consistent with global warming patterns (as shown in Figure 6).

Temperature significantly influences the types, diversity, and richness of microorganisms in forest soils (Figure 7) [174,175]. In cold environments (below 5 °C), psychrophiles like Psychrobacter dominate, but microbial diversity and richness are generally low due to fewer species’ adaptation to extreme cold. In moderate temperatures (15–25 °C), mesophilic microorganisms such as Bacillus and Actinobacteria thrive, leading to the highest levels of microbial diversity and richness [175,176]. However, in high-temperature environments (above 30 °C), thermophiles like Thermococcus become prevalent, with a noticeable decrease in microbial diversity and richness due to the selective pressure of heat [177]. These patterns highlight the adaptability of microbial communities to varying temperature conditions and their differing efficiencies in pollutant degradation, with mesophiles being most effective under moderate conditions, thermophiles thriving in extreme heat, and psychrophiles struggling in cold climates, emphasizing the broader implications of climate change on microbial ecosystems and their environmental functions.

Moreover, temperature affects microbial degradation processes by modulating degradation rates, enzyme activity, and microbial metabolic activity [178,179,180]. Understanding these effects is crucial for optimizing bioremediation strategies and managing soil health in varying temperature conditions.

4.2.3. Oxygen Levels

Under aerobic conditions, where oxygen is readily available, microorganisms such as Pseudomonas putida, Rhodococcus spp., and Bacillus subtilis utilize oxygen as a terminal electron acceptor in oxidative degradation pathways. Oxygen serves as a key substrate for oxygenases (e.g., monooxygenases and dioxygenases), which catalyze the cleavage of aromatic rings and oxidation of aliphatic hydrocarbons, such as petroleum hydrocarbons (e.g., alkanes, PAHs) and VOCs (e.g., benzene, toluene) [181]. These enzymes introduce oxygen atoms into pollutant molecules, increasing their solubility and susceptibility to further enzymatic breakdown, resulting in faster and more complete mineralization into carbon dioxide, water, and biomass.

Aerobic degradation is typically more efficient due to higher energy yields from oxidative phosphorylation, enabling rapid microbial growth and pollutant removal. For instance, a study by Wang et al. [122] demonstrated that Pseudomonas putida achieved a 90% degradation rate of toluene in contaminated forest soil under aerobic conditions within 7 days, leveraging oxygen-dependent monooxygenases to convert toluene into benzoic acid and subsequent intermediates. This efficiency is particularly pronounced for hydrophobic pollutants like PAHs, where oxygen enhances bioavailability by reducing adsorption to soil organic matter (SOM). In anaerobic conditions, where oxygen is absent, facultative and obligate anaerobes such as Clostridia, Desulforamulus aquiferis, and Dehalococcoides spp. rely on alternative electron acceptors (e.g., nitrate, sulfate, or ferric iron) for pollutant degradation [77]. These microorganisms employ fermentation, reductive dechlorination, and other anaerobic pathways, which are generally slower and less efficient than aerobic processes due to lower energy yields. For example, anaerobic degradation of VOCs like trichloroethylene (TCE) involves reductive dechlorination by Dehalococcoides spp., transforming TCE into less toxic ethene, but this process can take weeks to months, with efficiencies often below 50% compared to aerobic degradation [182].

The slower rate stems from the complexity of anaerobic metabolic pathways, such as the need for syntrophic interactions among microbial consortia to share electrons and degrade recalcitrant pollutants. Zhang et al. [77] reported that Desulforamulus aquiferis degraded pyrene and benzo[a]pyrene in anaerobic forest soil with a removal efficiency of only 35% over 30 days, highlighting the limitations of oxygen scarcity. However, anaerobic conditions are advantageous in waterlogged or deep soil layers where oxygen diffusion is limited, enabling the degradation of specific pollutants like chlorinated hydrocarbons and certain PAHs that resist aerobic breakdown.

4.2.4. Redox Potential

Redox potential is a critical environmental factor influencing microbial degradation of organic pollutants in forest soils, directly determining metabolic pathways and efficiency. Under high redox potential (>300 mV) aerobic conditions, microorganisms such as Pseudomonas putida and Rhodococcus spp. use oxygen as an electron acceptor, rapidly and efficiently degrading PAHs, alkanes, and VOCs via oxygenases; for instance, Johnsen et al. [183] reported removal rates of 80%, 70%, and 60% for naphthalene, phenanthrene, and pyrene, respectively, within 14 days. In low redox potential (<−200 mV) anaerobic conditions, microorganisms like Clostridia and Dehalococcoides spp. rely on nitrate, sulfate, or iron for fermentation and reductive dechlorination, degrading chlorinated hydrocarbons (e.g., tetrachloroethylene, PCE) and some PAHs, but with lower efficiency [184]. Microbes adapt to redox gradients through metabolic flexibility (e.g., facultative anaerobes switching pathways), with community synergies (e.g., Pseudomonas and Clostridia) achieving 60% phenanthrene degradation. Case studies demonstrate that manipulating redox potential via bioelectrochemical systems (e.g., SMFCs) can significantly boost degradation efficiency; for example, Wang et al. [185] increased phenanthrene degradation from 25% to 65% by adjusting potential. However, challenges such as soil heterogeneity, microbial stability, and electrode degradation limit large-scale applications. Future research should integrate omics technologies, synthetic biology, and microbial-electrochemical systems to optimize redox conditions, developing sustainable remediation strategies for polluted forest soils.

4.2.5. Humidness

Humidness in forest ecosystem has a profound influence on microbial degradation [186]. Water availability directly affects the survival, growth, and activity of microorganisms [187]. While adequate moisture enhances microbial activity, excessive water can cause soil hypoxia, impairing the metabolism of aerobic microorganisms. Conversely, insufficient moisture reduces microbial activity and slows degradation rates. Therefore, regulating and maintaining optimal soil moisture conditions is critical for optimizing microbial pollutant treatment in forest ecosystems [188].

Under optimal moisture levels (60–80% of soil moisture), microbial communities thrive, enabling efficient degradation of pollutants such as PAHs and petroleum hydrocarbons through active enzymatic processes [189]. In dry soils, microbial activity is suppressed, with drought-tolerant taxa like Actinobacteria dominating but performing less efficiently [190]. In waterlogged soils, anaerobic conditions favor facultative and obligate anaerobes like Clostridia, which can degrade VOCs, though these processes are generally slower than aerobic degradation [191]. In dry soils, microbial communities shift towards drought-resistant taxa like Firmicutes, while in moist soils, the diversity increases, incorporating phyla such as Proteobacteria, Bacteroidetes, and Acidobacteria. This enhanced diversity in moist conditions supports a more comprehensive degradation process for pollutants like petroleum hydrocarbons and VOCs [192]. However, excessive moisture can lead to the proliferation of anaerobic microorganisms, such as Methanogens, which degrade specific pollutants but at lower overall efficiencies due to oxygen limitations [193].

Moisture levels also influence pollutant bioavailability in soil. In dry conditions, hydrophobic pollutants adsorb more tightly to soil particles, reducing accessibility for microbial degradation. In contrast, optimal moisture levels increase pollutant solubility, transport, and desorption from soil particles, thereby enhancing bioavailability and microbial degradation efficiency [194]. These conditions regulate enzyme production and activity, with enzymes such as oxygenases and hydrolases functioning most effectively under moderate moisture conditions, accelerating the breakdown of organic pollutants [195]. The optimal humidity ranges for biodegradation of various pollutants are illustrated in Figure 8.

4.2.6. Soil Organic Matter

Soil organic matter (SOM) plays a crucial role in shaping microbial communities and enhancing the degradation of organic pollutants in forest soils. It acts as a nutrient reservoir, providing essential carbon and energy sources that support microbial growth and enzyme synthesis [196]. This facilitates the breakdown of complex pollutants such as pesticides and aromatic hydrocarbons by microorganisms like Pseudomonas putida, which rely on SOM for metabolic activity [197]. Additionally, SOM improves pollutant bioavailability by forming micelle-like structures with hydrophobic compounds, thereby increasing their accessibility to microbial degradation.

SOM also adsorbs pollutants, creating stable complexes that allow for slow but sustained biodegradation over time. This dual role of enhancing immediate bioavailability while enabling long-term stabilization is critical in the degradation of persistent pollutants like PCBs and PAHs by species such as Sphingomonas and Burkholderia [198,199]. Furthermore, SOM supports microbial colonization and biofilm formation, providing a protective environment that enhances microbial resilience and cooperative degradation efforts.

Beyond improving bioavailability and colonization, SOM buffers the toxicity of certain pollutants by adsorbing harmful compounds, creating conditions conducive to microbial growth [200,201]. It also promotes microbial diversity by offering a range of carbon sources, enabling different species, including bacteria, fungi, and actinomycetes, to collaborate in degrading various pollutants [202,203,204]. Overall, SOM enhances the efficiency and sustainability of bioremediation processes in forest soils (

Table 5. Effects of soil organic matter on microbial degradation of organic pollutants in forest soils.

Pollutant Group	Impact of SOM	Optimal SOM Content (%)	Degradation Rate Impact	Ref.
Pesticides	SOM increases bioavailability by adsorbing and releasing pollutants.	3–5%	Enhanced (70–85%)	[205,206,207]
Industrial Chemicals	High SOM can limit degradation by sequestering pollutants.	2–4%	Moderate (60–75%)	[205,208,209]
Alkanes	SOM aids in emulsification, enhancing microbial uptake.	1–3%	Fast (75–90%)	[210,211,212]
Aromatic Hydrocarbons	SOM enhances solubility and bioavailability.	4–6%	High (80–95%)	[213,214]
PAHs	SOM adsorbs PAHs, but microbial enzymes can release them.	3–5%	Moderate (65–85%)	[214,215,216]
Antibiotics	SOM can reduce toxicity and improve microbial tolerance.	4–6%	Moderate (60–80%)	[217,218]
Hormones	SOM enhances stability, promoting slow release.	2–4%	Moderate (65–75%)	[219,220]
Sunscreens	SOM helps in dispersing hydrophobic molecules.	3–5%	Moderate (60–75%)	[221,222,223]
Synthetic Fragrances	SOM reduces volatilization, aiding microbial degradation.	3–5%	Moderate (70–80%)	[224]
Solvents	Low SOM minimizes competition with naturally occurring compounds.	1–2%	High (80–90%)	[225,226,227,228]
Industrial Emissions	SOM can trap volatile compounds but also facilitate microbial uptake.	3–5%	Moderate (65–80%)	[229,230]
BTEX	SOM improves solubility and bioavailability.	4–6%	High (85–95%)	[231,232,233]

).

4.3. Types of Pollutant

The biodegradability of soil pollutants in forest ecosystems is heavily influenced by their chemical nature. Factors such as molecular structure, functional groups, solubility, stability, and bioavailability determine how easily microorganisms can access and degrade these compounds [234]. Understanding these relationships helps in predicting the persistence of pollutants and developing effective bioremediation strategies.

The intricate relationship between the chemical nature of pollutants and their biodegradability underscores the complexity of soil pollution management in forest ecosystems. Organic pollutants, encompassing a wide array of compounds from hydrocarbons to pesticides, present varying challenges for microbial degradation. The structure of these molecules plays a pivotal role in determining their susceptibility to breakdown processes [235]. Simple organic compounds, characterized by fewer carbon rings and a lack of complex branching, are typically more amenable to microbial attack. This is largely due to the relative ease with which microorganisms can access and metabolize these simpler structures, utilizing them as sources of carbon and energy.

In contrast, complex organic pollutants such as PAHs and chlorinated compounds, notorious for their persistence in the environment, pose significant challenges for microbial degradation [236]. The stability of PAHs, conferred by their multiple aromatic rings, and the resistance of chlorinated compounds, due to the presence of chlorine atoms, make these pollutants less readily degradable. These characteristics impede the enzymatic activity of microorganisms, often requiring specific enzymes capable of breaking these strong chemical bonds. Furthermore, the presence of functional groups, including hydroxyl and carboxyl groups, can influence the degradation process. Hydroxyl groups increase solubility through hydrogen bonding with water molecules and serve as reactive sites for oxidation and substitution reactions. Carboxyl groups, being both polar and ionizable, further enhance solubility, especially at higher pH levels where they form negatively charged carboxylate ions. These groups are also highly reactive, participating in esterification, redox processes, and interactions with other environmental components. Collectively, these functional groups influence the mobility, transformation, and potential ecological impact of pollutants in aquatic and terrestrial systems [237,238,239]. These groups may alter the solubility and reactivity of the pollutants, thereby affecting their availability to microbes and the efficiency of degradation enzymes [240].

Besides, compounds containing halogens (e.g., chlorine, bromine) or nitro groups (e.g., nitrobenzene, TNT) are generally more resistant to biodegradation [68,241,242]. The carbon-halogen bond is relatively stable, and halogenated compounds can be toxic to microorganisms. Examples include chlorinated solvents (e.g., trichloroethylene) and pesticides (e.g., DDT). The nitro group is electron-withdrawing, making the compound more stable and less reactive.

Stable compounds that resist chemical breakdown are generally more persistent in the environment and less biodegradable, such as microplastics. The effects of microplastics on soil microorganisms in forest ecosystems are reflected in many aspects, such as reducing the number and activity of microorganisms, changing the structure of microbial community, and indirectly affecting microorganisms through changing the physical and chemical properties of soil [243]. The presence of microplastics will reduce the number and activity of soil microorganisms and interfere with their normal physiological functions, which may lead to a decrease in the ability of microorganisms to decompose organic matter, which in turn affects the nutrient cycling of soil and the overall function of forest ecosystems. In addition, microplastics may also change the community structure of soil microorganisms, some microbial species sensitive to microplastics may decrease, and the microbial species tolerant to or able to use microplastics may increase [244]. Such changes in community structure not only affect soil biodiversity but also pose potential threats to the stability and functioning of forest ecosystems. In addition to their direct effects on microorganisms, microplastics may also indirectly affect microorganisms by altering the physical and chemical properties of soil. For example, microplastics may reduce soil permeability, water retention, and fertility, thereby altering the living environment and activity of microorganisms. These impacts may pose potential threats to the health and stability of forest ecosystems [245].

Water solubility also plays an important part in the process of biodegradation of organic pollutants. Hydrophilic (water-soluble) compounds are generally more accessible to microorganisms and therefore more readily biodegradable [246]. Examples include many simple alcohols and acids. Hydrophobic (water-insoluble) compounds, such as high-molecular-weight PAHs and hydrocarbons, tend to adsorb strongly to soil organic matter and are less accessible to microorganisms. This reduces their biodegradability.

The differential biodegradability of pollutants highlights the necessity for tailored remediation strategies [247]. The diverse nature of soil contaminants demands a multifaceted approach to bioremediation, one that takes into account the specific characteristics of each pollutant and the capabilities of the microbial community. Enhancing microbial diversity within the soil is crucial for this purpose, as a varied microbial population is more likely to contain species or strains capable of degrading a wider range of pollutants. Strategies such as bioaugmentation, where specific microbial degraders are introduced to the soil, and biostimulation, which involves modifying environmental conditions to favor the growth of degrading microorganisms, can be employed to enhance the degradation of challenging pollutants [248].

Future research in microbial degradation in forest ecosystems will likely focus on harnessing microbial consortia and synthetic biology for targeted pollutant removal, exploring mycorrhizal-microbial symbioses for enhanced bioremediation, and discovering novel enzymes to degrade persistent pollutants. Additionally, investigating how climate change impacts microbial communities and their degradation efficiency could provide insights for adaptive remediation strategies. Integrating omics technologies with ecological modeling will be key in predicting microbial responses to environmental stressors, paving the way for more effective, sustainable pollution management.

5. Technological Advances and Methodological Approaches

5.1. Genetic Engineering of Microorganisms

Genetic engineering stands at the forefront of enhancing microbial degradation capabilities [249]. By modifying the genetic makeup of microorganisms, scientists have been able to create strains with enhanced abilities to degrade specific pollutants, such as recalcitrant hydrocarbons and complex pesticides. This involves the introduction of genes encoding for particular enzymes that can break down pollutants into less harmful substances [250]. For instance, the engineering of bacterial strains to express enzymes capable of degrading polychlorinated biphenyls (PCBs) has shown promise in remediation efforts [251]. This approach not only increases the efficiency of degradation but also expands the range of pollutants that can be addressed through microbial processes. Practical examples of using genetically engineered microorganisms to degrade soil organic pollutants are shown in

Table 6. Practical examples of using genetically engineered microorganisms to degrade soil organic pollutants.

Pollutant Category	Microbial Species	Genetic Engineering Technology	Pollutant Name	Degradation Time	Degradation End Product	Ref.
Persistent Organic Pollutants (POPs)	Bacillus subtilis	Expression of dehalogenase genes	DDT	7 days	Non-toxic products	[252]
	Pseudomonas putida	Introduction of linA gene	Lindane	10 days	Degradation products (less toxic)	[253]
	Rhodococcus erythropolis	Engineering of dioxygenase genes	PCBs	14 days	Non-chlorinated compounds	[254]
	Mycobacterium vanbaalenii	Genetic modification for biphenyl dioxygenase	PCBs	12 days	Degradation intermediates	[255]
	Cupriavidus necator	Introduction of organophosphorus hydrolase gene	Parathion	9 days	Non-toxic products	[256]
Petroleum Hydrocarbons	Alcanivorax borkumensis	Alkane hydroxylase genes	Alkanes (crude oil)	15 days	Carbon dioxide and water	[83]
	Pseudomonas aeruginosa	Modification of n-alkane-degrading enzymes	Long-chain alkanes	8 days	Alkanes and fatty acids	[257]
	Bacillus licheniformis	PAH dioxygenase genes	PAHs	11 days	Less toxic degradation products	[258]
	Rhodococcus sp.	Enhanced catabolic pathways	Petroleum hydrocarbons	10 days	Less complex hydrocarbons	[259]
	Burkholderia cepacia	PAH-degrading plasmids	High molecular weight PAHs	12 days	Degradation intermediates	[260]
Pharmaceuticals and Personal Care Products (PPCPs)	Pseudomonas putida	Tetracycline-degrading genes	Tetracycline	6 days	Degradation products	[261]
	Escherichia coli	Esterase genes for steroid degradation	Estrone, Estradiol	7 days	Non-toxic products	[262]
	Bacillus thuringiensis	Sulfonamide-degrading enzymes	Sulfonamide antibiotics	8 days	Degradation products	[263]
	Rhizobium leguminosarum	Advanced biotransformation pathways	Various PPCPs	9 days	Less harmful products	[264]
	Acinetobacter baumannii	Synthetic estrogen-degrading pathways	Synthetic estrogens	10 days	Degradation products	[265]
Volatile Organic Compounds (VOCs)	Pseudomonas putida	Toluene-degrading operon	Toluene	5 days	Benzene and other derivatives	[266]
	Burkholderia fungorum	Xylenes-degrading pathways	Xylenes	7 days	Degradation products	[267]
	Rhodococcus sp.	VOC-degrading plasmids	Benzene, Ethylbenzene	6 days	Less harmful products	[268]
	Comamonas testosteroni	Halogenated VOC-degrading pathways	Trichloroethylene	8 days	Degradation products	[269]
	Mycobacterium smegmatis	Specialized VOC degradation pathways	Various VOCs	9 days	Degradation products	[270]

.

Genetic engineering enhances microbial degradation of soil organic pollutants by expanding catabolic pathways, improving enzyme efficiency, increasing resilience to harsh environmental conditions, enabling co-metabolic processes, and accelerating remediation time. However, potential risks include ecological disruptions, horizontal gene transfer, uncontrolled persistence of engineered microbes, and the generation of toxic byproducts. To mitigate these risks and maximize benefits, future efforts should prioritize enhancing field adaptability, systematically monitoring ecological impacts, and developing robust containment strategies for the safe and effective application of engineered microorganisms in environmental remediation.

5.2. Next-Generation Microbial Agents

Future research is poised to focus on developing next-generation microbial agents with enhanced degradation capabilities. This involves harnessing genetic engineering and synthetic biology to create microorganisms specifically tailored to degrade complex and recalcitrant pollutants under a variety of environmental conditions [271]. By integrating computational biology and machine learning algorithms, researchers can design microbial strains with optimized metabolic pathways for the efficient breakdown of pollutants, potentially revolutionizing the field of bioremediation [272].

The next generation of biological agents has shown great application potential in the degradation of soil organic matter (

Table 7. Next-generation biological agents for degrading soil organic pollutants, their target pollutants, mechanisms, and references.

Biological Agent	Target Pollutants	Mechanism	Ref.
Mixotrophic Cyanobacteria and Microalgae	Organic pollutants, hydrocarbons	Mixotrophic pathways enhance degradation efficiency and carbon sequestration	[273]
Earthworms	Pesticides and organic pollutants	Gut enzymes and microbial stimulation in processed soil	[274]
Microbial Consortia	PAHs, petroleum hydrocarbons, pharmaceuticals	Synergistic microbial interactions for efficient degradation	[275]
Photocatalytic Materials with Microbes (ICPB)	Refractory organic pollutants (e.g., VOCs)	Combines photocatalysis and biodegradation	[276]
Genetically Modified Microorganisms	PCBs, PAHs, xenobiotic organic compounds	Enhanced gene transfer for pollutant degradation pathways	[277]
Rhizosphere Microbial Synergies	Hydrophobic and persistent organic pollutants	Enhanced degradation through plant-microbe interactions in the rhizosphere	[278]

). These biologics are able to decompose organic pollutants efficiently and environmentally in soil, such as pesticide residues and petroleum hydrocarbons, by utilizing the metabolic capacity and enzyme systems of specific microorganisms. They can not only effectively reduce environmental pollution but also restore soil health and improve soil fertility and biodiversity. The development and application of a new generation of biologics has brought innovative solutions to the field of soil remediation and environmental protection, contributing to sustainable soil use and management.

Next-generation biological agents provide substantial benefits for the degradation of soil organic pollutants by enhancing efficiency, adapting to harsh conditions, targeting specific contaminants, and fostering synergistic interactions, while maintaining cost-effectiveness and sustainability. Potential risks include ecological disruptions, horizontal gene transfer, uncontrolled persistence, and the generation of toxic byproducts. To fully realize their potential and minimize risks, future efforts should prioritize optimized agent design, robust containment strategies, and comprehensive ecological risk assessments.

5.3. Nanotechnologies

The integration of nanotechnology is the integration of cutting-edge research results in nanotechnology with technologies and methods in other fields to achieve more efficient and accurate innovative applications. This interdisciplinary integration has not only promoted the development of nanomaterials and nanodevices but also brought revolutionary changes to the fields of environmental remediation, biomedicine, and energy science and technology [279,280].

Recent research on nanotechnology for microbial degradation of organic pollutants in forest ecosystems shows remarkable progress (

Table 8. Examples of nanotechnologies used to enhance microbial degradation of soil organic pollutants, target pollutants, and mechanisms.

Nanotechnology	Target Pollutants	Mechanism	Ref.
Nanobiosurfactants	Organic pollutants, pesticides, and herbicides	Enhances pollutant bioavailability for microbial degradation	[282]
Carbon Nanotubes (CNTs)	Persistent organic pollutants (POPs), heavy metals	Facilitates adsorption and transport of pollutants, improving microbial accessibility	[283]
Zero-Valent Iron Nanoparticles (nZVI)	Petroleum hydrocarbons, VOCs	Catalyzes degradation and immobilization of contaminants	[284]
Nanophytoremediation	Organic pollutants, heavy metals	Assists plant-microbe interactions to detoxify pollutants	[285]
Nanobiosorbents	Agrochemicals and organic pollutants	Enhances microbial bioremediation by adsorbing and concentrating pollutants	[282]
Green Nanomaterials (e.g., nano-chitosan)	Pesticides and industrial pollutants	Improves pollutant adsorption while minimizing toxicity to microbes	[286]
Metallic Nanoparticles	Organic dyes, antibiotics, and pesticides	Facilitates enzymatic degradation and pollutant breakdown	[287]
Modified nZVI Nanoparticles	Hydrocarbons, heavy metals	Reduced toxicity to microbes, promoting enhanced microbial activity	[283]

). The application of nanotechnology can effectively improve the efficiency and rate of microbial degradation of organic pollutants. As a catalyst or carrier, nanomaterials can enhance the enzyme activity of microorganisms and promote the biodegradation process of organic pollutants. In addition, nanotechnology can also improve the growth conditions of microorganisms, enhancing their adaptability and survival rate in polluted environments to ensure the stability and sustainability of microbial degradation processes. These research results provide a new idea and method for the bioremediation of organic pollutants in forest ecosystems and have broad applications prospects [281].

Nanotechnologies enhance microbial degradation of soil organic pollutants by increasing pollutant bioavailability, accelerating degradation rates, enhancing microbial activity, and enabling the breakdown of persistent contaminants such as PAHs and VOCs. Additionally, they integrate seamlessly with existing remediation strategies, including phytoremediation and bioaugmentation. However, potential risks include ecotoxic effects on soil microbial communities, long-term environmental persistence of nanoparticles, facilitation of horizontal gene transfer, production of secondary pollutants, and unresolved regulatory challenges. To fully leverage their benefits while minimizing risks, future efforts must focus on designing environmentally safe nanomaterials, evaluating their long-term ecological impacts, and developing comprehensive regulatory frameworks for their application in soil remediation.

5.4. Bio-Electrochemical Technologies

Bioelectrochemical technologies enhance the degradation of soil organic pollutants through the intricate coupling of microbial metabolism and electrochemical reactions [288]. The core mechanism hinges on extracellular electron transfer (EET), where electroactive microbes transfer electrons to electrodes via direct pathways (nanowires, membrane proteins) or indirect mediators (e.g., flavins) or accept electrons from electrodes, driving pollutant oxidation or reduction [289]. For instance, in anaerobic settings, electrodes substitute oxygen as electron acceptors, facilitating the breakdown of PAHs or alkanes; in aerobic conditions, electrodes supply electrons to boost oxidase activity, accelerating phenol degradation [122]. Recent soil microbial fuel cell (SMFC) breakthroughs include Mohanakrishna et al.’s 46% petroleum hydrocarbon removal with carbon electrodes, underscoring the pivotal role of electrode-surface biofilms [290]; Zhou et al.’s 2.7-fold PAH degradation increase (22.5% removal of five- and six-ring PAHs) by mixing soil with sand (2:1) to enhance mass transfer, highlighting substrate permeability’s impact on EET [291]; and Wang et al.’s 70% chlorinated hydrocarbon removal in dual-chamber SMFCs, combining electroosmosis with microbial synergy [292]. Research shows that biochar enhances electrode conductivity and microbial adhesion, while surfactants improve pollutant solubility, yet challenges persist at the electrode–soil interface, including electron transfer efficiency, microbial community stability, and electrode degradation over time. Large-scale deployment is hampered by mass transfer resistance, soil heterogeneity, and microbial dependence on electrodes. BES offers low energy consumption, sustainability, and energy recovery potential but is limited by prolonged treatment durations, efficiency variability, and engineering complexities.

Briefly, genetic engineering of microorganisms offers significant potential for improving organic matter degradation in soils by enhancing the metabolism of recalcitrant compounds like PAHs and PCBs and increasing stress tolerance. However, challenges remain due to competition with native microbes, horizontal gene transfer, and regulatory barriers. Next-generation microbial agents, such as consortia, rhizosphere-targeted microbes, and mixotrophic algae, enhance pollutant degradation through synergistic microbial-plant interactions but face difficulties in ensuring consistent performance. Nanotechnologies, including zero-valent iron nanoparticles (nZVI) and nanobiosurfactants, boost bioavailability and degradation rates, especially for persistent pollutants, but pose risks like toxicity to native microbes and high costs. Future research should focus on developing non-toxic, biodegradable nanomaterials, improving microbial survivability, and ensuring ecological containment. Combining genetic engineering, microbial consortia, and nanotechnologies could leverage their respective strengths, such as targeting specific pollutants, enhancing pollutant bioavailability, and achieving faster degradation rates. Additionally, large-scale studies in diverse environments are essential to address the gap between laboratory results and real-world applications. Effective cost management and scalability are critical to ensure practical deployment on a wider scale.

Bioremediation methods like genetic engineering, bioaugmentation, and biostimulation each offer unique benefits for degrading organic pollutants in forest soils but face distinct challenges. Genetic engineering enhances microbial efficiency by introducing genes (e.g., in Pseudomonas or Rhodococcus) to target recalcitrant pollutants like PCBs and PAHs, achieving higher degradation rates, though it risks biosafety, regulatory issues, and horizontal gene transfer. Bioaugmentation adds specialized microbes (e.g., for hydrocarbons) to boost degradation but struggles with microbial survival and integration into native communities. Biostimulation stimulates native microbes with nutrients or environmental adjustments (e.g., pH, oxygen) to enhance hydrocarbon degradation cost-effectively, yet its efficacy depends on the natural microbial capacity and precise condition control, limiting scalability.

Future research should emphasize ecological safety, regulatory clarity, and real-time monitoring tools. Minimizing unintended consequences, such as the spread of engineered genes or nanoparticle toxicity, requires comprehensive risk assessments and containment strategies. Collaboration between scientists, policymakers, and industries is crucial to develop clear guidelines for these technologies. Additionally, advancements in biosensors and analytical tools will enable real-time evaluation of remediation efficiency, safety, and ecological impacts, ensuring sustainable and effective soil restoration.

Despite the promising potential of bioremediation, several challenges remain that hinder its widespread implementation. One significant obstacle is the rivalry among microbial communities. Microbial communities in contaminated environments often compete for resources, and this competition can hinder the efficiency of pollutant degradation. For example, when introducing engineered or enhanced strains, they may struggle to outcompete native microbes, leading to reduced degradation efficiency. Additionally, there is the possibility of harmful byproduct formation during degradation. Some microorganisms may generate intermediate metabolites that are toxic or recalcitrant, complicating the bioremediation process and potentially leading to secondary pollution. Lastly, cost-effectiveness remains a major concern, particularly for large-scale applications. While genetic engineering and bioaugmentation can enhance degradation rates, the high costs associated with producing GMOs and scaling these methods in real-world environments must be addressed for bioremediation to become more widely adopted.

Future research should focus on leveraging innovative methods such as meta-genomics and synthetic biology to overcome existing bioremediation challenges. Metagenomics, for instance, allows for the comprehensive analysis of microbial communities in polluted environments without the need for cultivation. By identifying the functional genes involved in pollutant degradation, metagenomics can help uncover new microbial species and enzymes that are effective in breaking down complex pollutants, thus improving bioremediation efficiency. Additionally, synthetic biology holds great promise in designing customized microorganisms that are more efficient in degrading specific pollutants. Through gene editing techniques like CRISPR/Cas9 [293], engineered microbes can be optimized to withstand harsh environmental conditions and improve their long-term stability in the field. Moreover, synthetic biology can facilitate the production of biodegradable materials and bio-based catalysts, reducing the environmental impact and cost of large-scale remediation efforts.

Several recent studies have begun to address these challenges using innovative approaches. For example, metagenomics was used in a study by Liu et al. [294], where researchers analyzed the microbial communities in an oil-contaminated site and identified new genes responsible for hydrocarbon degradation. This discovery led to the development of novel bioremediation strategies tailored to specific pollutants. Similarly, synthetic biology has been applied in the field of heavy metal remediation, where engineered bacteria, such as Pseudomonas fluorescens, have been designed to absorb and detoxify arsenic and cadmium. In a study by Sharma et al. [295], genetically modified strains demonstrated significantly higher degradation rates than their wild counterparts, highlighting the potential of synthetic biology to address large-scale contamination issues.

6. Conclusions

Addressing soil pollution in forest ecosystems is a critical environmental challenge, and microbial degradation has emerged as a promising solution. This process leverages the natural metabolic capabilities of microorganisms to transform harmful organic pollutants into less toxic substances, thereby safeguarding ecosystem health and promoting soil functionality. The study emphasizes the importance of understanding microbial community dynamics and optimizing environmental conditions to enhance biodegradation processes. This approach aligns with sustainable forest management practices and reinforces the ecological balance necessary for long-term ecosystem stability resilience.

Advances in genetic engineering, metagenomics, and biostimulators have significantly improved the potential for microbial remediation, providing innovative tools to enhance degradation efficiency. By integrating these technologies, scientists have deepened their understanding of microbial ecology and developed novel strategies for addressing complex pollutants. However, challenges remain, including maintaining microbial diversity and adapting to pollutant complexity. Overcoming these hurdles will require interdisciplinary collaboration, combining insights from microbiology, ecology, and environmental engineering to develop robust, practical solutions. Future research must focus on refining microbial techniques and ensuring their ecological sustainability, contributing to effective and comprehensive soil pollution management.

The next decade of research on microbial degradation of soil organic pollutants is expected to focus on several innovative areas. First, synthetic biology will drive the engineering of microbial strains and consortiums with enhanced pollutant-degrading capabilities through genome modifications and optimized metabolic pathways. In parallel, omics technologies such as metagenomics and transcriptomics will allow for a deeper understanding of microbial communities and functional genes involved in pollutant degradation, leading to the discovery of novel degrading microbes. The integration of microbial-electrochemical systems will gain traction, with bio-electrochemical technologies enhancing pollutant breakdown through improved electron transfer. Research will also explore microbial community dynamics and adaptation, focusing on microbial resilience and the evolution of degradation pathways under varying environmental stressors. Moreover, eco-engineering approaches combining microbes with soil amendments will aim to improve both pollutant degradation and soil restoration. Lastly, the synergy between microbes and plants in phytoremediation will be further developed, with research focusing on microbial support for plant health in degrading complex pollutants in the rhizosphere. These advancements hold promise for creating more efficient, sustainable, and multifaceted bioremediation strategies in contaminated soils.

A pivotal development in this landscape is the rise of next-generation microbial agents, which are set to redefine bioremediation strategies. These agents—genetically engineered microorganisms tailored for heightened specificity, efficiency, and environmental adaptability—leverage cutting-edge synthetic biology tools, such as CRISPR-Cas9, and AI-driven design to optimize their pollutant-degrading capabilities. These advancements position next-generation microbial agents as superior alternatives to traditional bioremediation methods, particularly for tackling persistent pollutants like PAHs and emerging contaminants such as microplastics and PPCPs.

In terms of their proportion in future bioremediation strategies, next-generation microbial agents are expected to assume an increasingly significant role, potentially comprising 30–50% of applied approaches as the technology matures and regulatory frameworks evolve. This projection is supported by their demonstrated superiority in degradation efficiency and specificity, as evidenced by laboratory successes and preliminary field trials. Moreover, their integration with emerging technologies—such as nanotechnology and plant-microbe synergies—will further amplify their effectiveness and sustainability. However, their widespread adoption hinges on overcoming key challenges, including ecological risks, long-term stability, and cost considerations, which will require extensive field validation and risk assessments. As these barriers are addressed, next-generation microbial agents are poised to become a cornerstone of efficient, sustainable, and multifaceted bioremediation strategies, particularly in managing contaminated forest soils and addressing the complexities of modern pollutants.