Effective Microbial Strategies to Remediate Contaminated Agricultural Soils and Conserve Functions

Abstract

The growing global emphasis on sustainable agriculture has brought increased attention to the health and productivity of soils, especially through the lens of soil microbiology. Microbial communities in soil are essential for nutrient cycling, organic matter decomposition, and maintaining overall soil health. However, agricultural practices, including synthetic fertilizers and intensive farming, have led to short time impacts in these microbial ecosystems, potentially threatening soil fertility and environmental quality. Agricultural expansion and food production generate waste and chemical inputs, such as heavy metals, pesticides, and herbicides, leading to significant environmental contamination. This scenario requires the implementation of remediation strategies that are both sustainable and energy efficient. In this context, microbiological processes present a much promising approach to mitigating the environmental impacts of soil pollution. Techniques such as bioremediation, which harness the natural metabolic capabilities of soil microorganisms, and bioaugmentation, which involves the introduction of specific microbial strains to increase degradation processes, are being explored. These approaches are vital for restoring soil health, contributing to environmental conservation and soil biodiversity, improving nutrient cycling, and promoting long-term agricultural productivity.

1. Introduction

Since the 1950s, rapid industrial and technological advancements have significantly improved living standards but have also led to increased waste and escalating environmental issues. The term “Emerging Contaminants (ECs)” has gained attention in recent years, referring to synthetic chemicals that were previously unrecognized or understudied. These contaminants have become widespread in global ecosystems, with significant increases in antibiotic consumption, pesticide contamination, and plastic pollution. ECs can accumulate in soil, negatively impacting its properties and microbial communities, and can be transmitted through the food chain, posing risks to human health. Research has found ECs in human bodily fluids and tissues, where they can harm various systems, leading to issues such as cancer and birth defects [1]. To verify the toxicity of ECs in soils, Alabi et al. (2022) assessed germ cell toxicity from crude oil-contaminated soil before and after bioremediation using murine assays [2]. Significant increases in sperm abnormalities and reductions in sperm count were noted, and histopathological changes in testes and alterations in enzyme activities were also observed. Heavy metals and total petroleum hydrocarbon (TPH) levels were linked to toxicity [3,4]. In this research, despite bioremediation reducing some contaminants, toxicity remained. Given their pervasive nature and potential health risks, there is an urgent need for effective removal or remediation strategies for ECs.

One class of ECs is electronic waste (e-waste), which poses a significant environmental threat globally, impacting both human health and ecosystem security. Traditional e-waste dismantling methods, such as acid washing, incineration, and improper disposal, have released heavy metals like cadmium (Cd) and organic pollutants such as polychlorinated biphenyls (PCBs) into the soil since the 1980s. Although natural volatilization and bioremediation have reduced these contaminants to moderate levels over the past three decades, areas around e-waste sites, such as Taizhou in Southeastern China, still show notable soil contamination. Given its cost-effectiveness and minimal environmental impact, phytoremediation is considered the most suitable method for large-scale agricultural areas to reduce pollutant concentrations [5].

Another class of contaminants is organophosphate esters (OPEs), which are widely employed as additives in various industrial and commercial products, such as furniture, toys, electronics, and construction materials. With the phasing out of polybrominated diphenyl ethers (PBDEs) due to their persistence and toxicity, OPEs have become a common substitute, resulting in increased production and environmental presence. Research on OPEs in soil and water is still emerging, mainly focusing on their occurrence, distribution, toxic effects, and health risks. While some reviews have addressed OPE degradation and removal, there is a lack of in-depth analysis of the existing degradation technologies, factors influencing degradation, and the underlying mechanisms [6].

Furthermore, rapid industrialization has led to significant cadmium (Cd) and lead (Pb) contamination in China’s soil, affecting over 13 million hectares of arable land. Cd concentrations range from 0.003 to 9.57 mg/kg, and this metal can accumulate in plants to harmful levels without impacting their growth, thereby posing severe health risks. Similarly, around 16% of Chinese land is polluted with Pb, which threatens food security due to its persistence and bioaccumulation. In a recent study, Bacillus thuringiensis HM-311 immobilized with vinegar residue biochar and hydroxyapatite was shown to effectively reduce Pb and Cd levels in contaminated soil, lowering their bioavailability and accumulation in crops while enhancing microbial diversity in the rhizosphere [7]. Ni et al. (2024) targeted pyrene remediation under lead (Pb) stress using Pseudomonas veronii and its extracellular polymeric substances (EPSs) for biofortification [8]. High-throughput sequencing revealed that the co-addition of P. veronii and EPSs increased the relative abundance of pyrene-degrading phyla, forming a symbiotic system dominated by Firmicutes and Proteobacteria. Co-occurrence network analysis indicated P. veronii’s module was positively correlated with pyrene removal. Biofortification also boosted genes related to EPS production and pyrene degradation. Lead contamination promoted Proteobacteria growth and enhanced cooperative bacterial associations. Seventeen potential functional bacteria were identified through a random forest algorithm.

Over the past 30 years and more, advances in biological processes have expanded the use of bioremediation to break down hazardous pollutants into less toxic or non-toxic substances, achieving levels below regulatory limits [9,10,11,12,13,14,15]. While ex situ bioremediation involves costs related to dredging and sediment transport, in situ bioremediation requires minimal equipment as native or designed microbial communities facilitate pollutant degradation and support ecosystem resilience. However, in situ methods are limited by the time needed to degrade polycyclic aromatic hydrocarbons (PAHs), which may take several months, and their dependence on environmental conditions and oxygen availability. Bioremediation strategies are categorized as bioaugmentation, where hydrocarbon-degrading microorganisms are introduced, or biostimulation, which involves adding nutrients to stimulate native microbial activity. Recent advances have further revealed novel applications for hydrocarbon-degrading bacteria beyond environmental remediation [16].

In view of the above, this review aims to explore the role of soil microbiology in sustainable agriculture, focusing on microbiological processes such as bioremediation and bioaugmentation as innovative solutions for restoring soil health and mitigating the environmental impacts of soil contamination. It will analyze the effectiveness of these techniques in addressing agro-waste and chemical pollution, while also discussing the scalability and potential future applications of microbial strategies for enhancing soil fertility and promoting sustainable land management practices.

2. Soil Microbiology

Agricultural productivity is the result of a complex interaction of factors that, when properly balanced, can maximize crop yields. Among these factors are climate, management practices, the physicochemical properties of the soil, and the biological interactions between plants and soil organisms [17]. From these elements, soil stands out as the central component of the agroecosystem, and maintaining its health is crucial for its fertility and the sustainability of agricultural production [18].

Healthy soils consist of a dynamic composite of organic matter, particles of varying sizes, minerals, and a diverse community soil fauna and microbiota—such as soil macro- and mesofauna, bacteria, fungi, archaea, viruses, nematodes, and protozoa [19,20]. This rich microbial biodiversity plays a critical role in nutrient cycling, organic matter decomposition, and the biological control of pathogens [21]. Additionally, soils with a well-balanced microbiota foster the development of resilient root systems, enhancing crop tolerance to environmental stresses like drought and disease, ultimately contributing to greater agricultural stability and long-term productivity [22].

Soil quality, in addition to ensuring productivity, also plays a significant role in mitigating climate change by regulating the biogeochemical cycles of carbon, nitrogen, sulfur, and phosphorus in both organic and inorganic forms [21]. These cycles maintain soil fertility and influence atmospheric composition through the absorption and release of chemical elements, particularly the biological fixation of nitrogen and carbon [23].

Soil microorganisms can exist freely or be associated with plant roots, forming a microecosystem known as the rhizosphere [24,25]. In a balanced environment, both free-living and associated microorganisms (rhizobiome) work in symbiosis with plants through a dynamic and complex process in which plant roots release compounds that serve as signals and nutrient sources for the local microbiota [26]. In return, the rhizobiome provides nutrients by recycling organic matter, biologically fixing nitrogen, producing iron-chelating compounds (siderophores), and protecting the plant from environmental stress and certain pathogenic microorganisms [24,25]. These interactions are mutually beneficial, and in agricultural systems, they promote plant growth and ensure the plants’ competitiveness and survival.

The relationship between organisms in the rhizosphere is maintained through communication based on the release of metabolites by the plant, such as plant primary metabolites, coumarins, phytohormones, volatile organic compounds, benzoxazinoids, phenols and acids, terpenoids, and flavonoids. In response, the microbial flora provides nutrients [20]. Additionally, the released metabolites attract various beneficial microorganisms, including arbuscular mycorrhizal fungi (AMFs), ectomycorrhizal fungi (ECMs), and plant growth-promoting rhizobacteria (PGPBs) [27].

AMFs are important and beneficial soil fungi that can establish symbiotic relationships with more than 80% of terrestrial plants [28]. Their nomenclature is due to the presence of arbuscules, which are structures specialized branched hyphae that facilitate nutrient exchange in the symbiosis and are located between the plasma membrane and the cell wall of plant cells. AMFs act as biofertilizers, responsible for nourishing plants, recycling nutrients, protecting plants from pathogens, and retaining water [29].

ECMs play a fundamental role in nutrient cycling in many temperate and boreal forests, particularly in the nitrogen cycle [30]. The presence of ECMs also enhances plant phosphorus and nutrient uptake by increasing the absorptive surface area. Additionally, the hyphae act as a physical barrier against pathogens, providing further protection to the plant [31].

Plant growth-promoting rhizobacteria (PGPRs) represent the main group of bacteria that colonize plant roots. These bacteria are commonly utilized in agroecosystems due to their roles in nutrient recycling, pathogen inhibition, stimulation of plant immunity, enhancement of plant growth, and production of essential metabolites. PGPR serve as the most active ingredients in biofertilizer formulation [32]. Due to their importance for agriculture, some genera of PGPRs have already reached the stage of commercial success, such as Azospirilium, Azotobacter, Bacillus Burkholderia, Pseudomonas, Rhizobium, and Serratia [33].

PGPRs are also recognized for their soil bioremediation capacity [32]. The genera Alkaligens, Pseudomonas, Rhodococcus, Sphingomonas, Xanthobacter, Agrobacterium, and Mycobacterium are capable of degrade contaminants such as hydrocarbons and pesticides under aerobic conditions [19]. The recovery of areas contaminated or degraded by industrial waste or agricultural inputs is essential for maintaining the health of the soil and the ecosystem. Table 1 presents examples of the application of microorganisms in the bioremediation of contaminants.

The agricultural sector employs intensive cultivation and land management practices to increase productivity. These agricultural practices alter the soil microbiota, whether through the use of agrochemicals, chemical fertilizers, and sewage sludge, or through mechanical soil preparation practices [43]. The use of chemical fertilizers is one method to compensate for the deficiency of macronutrients in the soil, such as nitrogen, potassium, and phosphorus, often in conjunction with agrochemicals for pest and weed control. However, the indiscriminate use of these inputs compensates for the deficiency of macronutrients and generates significant environmental impacts. These include potential accumulation in soils and water bodies, eutrophication of water resources, greenhouse gas emissions, toxic accumulation of heavy metals, and increased susceptibility to various diseases. Additionally, they pose toxic risks to non-target organisms such as bacteria, algae, fungi, insects, birds, and animals [44,45]. The practice of bioremediation plays a fundamental part in the recovery and improvement in soil quality (Figure 1).

In this context, to optimize the process, certain microbial species have been modified through natural selection and genetic engineering, to develop microorganisms capable of remediating various types of pollutants [46]. The balance between microbial communities and the use of techniques such as bioaugmentation and biostimulation, in addition to removing pollutants, enhances soil fertility, laying the foundation for more sustainable and productive agriculture [47]. For example, Anwar et al. (2023) evaluated the bioremediation of lambda-cyhalothrin (LC) in cotton-growing soils using a microbial consortium comprising Brucella intermedia Halo1, Alcaligenes faecalis CH1S, and Aquamicrobium terrae CH1T, isolated from pyrethroid-contaminated soils [48]. The CHST consortium showed a higher potential for LC degradation compared to individual strains. Optimization revealed that the most influential factors were, in a descending order of importance, pH, carbon content, LC concentration, and inoculum density. In soil with cotton, the consortium degraded 91.8% of an initial 10 mg/kg LC concentration and improved plant agronomic parameters, indicating its promise for LC remediation at contaminated sites.

3. Bioremediation

Rapid population growth has intensified agricultural production to meet rising food demands, but urbanization, industrialization, and heavy metal contamination in soils have emerged as critical threats to sustainable agriculture. Urbanization compromises soil health, which is essential for environmental stability, ecosystems, and the global economy. Industrial activities such as smelting and mining release toxic HMs into the environment, severely reducing soil quality, which negatively affects both plant health and human safety [43]. Despite various strategies to monitor and address this issue, effective solutions are still urgently needed. Bioremediation has emerged as a promising, cost-effective technology for mitigating pollution. It involves using microbial populations to degrade pollutants, either at the site of contamination (in situ) or after relocation (ex situ). Enhanced soil properties and nutrient bioavailability can improve the efficiency of bioremediation, along with controlling other process-influencing factors, as outlined in Table 2. Furthermore, genetic engineering of microorganisms holds the potential for degrading specific contaminants more effectively. Notable microbial species utilized in bioremediation include Flavobacterium, Pseudomonas, and Bacillus, among others [49].

Bioremediation has proven effective in cleaning and restoring shorelines contaminated by crude oil spills. This approach typically involves applying bioremediation treatments directly to the oil layer, using either biostimulation (adding nutrients) or bioaugmentation (introducing microbial communities with degradation capabilities). Biostimulation, often enhanced with oleophilic fertilizers, supports native microbial activity by minimizing nutrient dilution and leaching in open beach environments. Bioaugmentation is preferable when the native microorganisms capable of hydrocarbon degradation are insufficient. Autochthonous microorganisms are generally preferred over exogenous strains to avoid disrupting natural microbial diversity and to ensure competitiveness in the local environment [61].

Microbial degradation is an effective method to prevent chemical pollution in soil. Sharma et al. (2016) reports on in situ bioremediation of polyaromatic hydrocarbons (PAHs) using a microbial consortium composed of Serratia marcescens L-11, Streptomyces rochei PAH-13, and Phanerochaete chrysosporium VV-18 [62]. The consortium degraded 60–70% of PAHs in broth within 7 days under controlled conditions. Under natural conditions, with soil amendments including ammonium sulfate, paddy straw, and compost, the degradation rate increased to 56–98% within 7 days and reached 83.50–100% after 30 days. Compost-amended soil showed the fastest degradation, with respective half-lives for fluorene, anthracene, phenanthrene, and pyrene of 1.71, 4.70, 2.04, and 6.14 days. Various degradation products were identified by GC-MS, indicating the consortium’s capability for PAH oxidation and mineralization.

Heavy metal contamination of soil, primarily due to anthropogenic activities such as agriculture, industry, and mining, has become a significant global environmental issue. Heavy metals, including chromium (Cr), copper (Cu), and cadmium (Cd), pose serious risks to human health and ecosystems due to their toxic, non-biodegradable nature. Soil contamination typically involves multiple heavy metals, with complex interactions and widespread prevalence. Studies indicate that Cu, Cd, and Cr contamination is particularly common near mining areas [63]. In addition, the contamination by Cu due to Cu-based fungicides, used in conventional and in organic agriculture, also highlights the urgent need for effective remediation strategies. In this sense, Sun et al. addresses the prevalent environmental issue of combined p-Chlorophenol (4-CP) and hexavalent chromium [Cr(VI)] pollution, focusing on the limited information regarding Cr(VI) fate and its interaction with amines during dechlorination, which is influenced by pH variations [64]. The research demonstrates that Pseudomonas sp. PC effectively degrades 4-CP and converts Cr(VI) with removal efficiency following first-order reaction kinetics. In another research, two Cr(VI)-reducing bacterial strains, TJ-1 and TJ-5, were isolated from chromium-contaminated soil [65]. The 16S rRNA gene sequences revealed high similarity to Stenotrophomonas maltophilia (TJ-1) and Brucella intermedius (TJ-5). Optimal growth conditions were pH 7.0 with an initial inoculation amount of 5%. Stability tests indicated that water-soluble Cr(VI) content remained unchanged post-bioremediation. Column experiments showed total remediation efficiencies of 34.23% and 20.63% within 76 h. These findings suggest significant potential for these strains in the in situ bioremediation of chromium-contaminated sites.

Soil, essential for agriculture, is increasingly contaminated with toxic metals like lead (Pb) due to urbanization and industrialization. Lead (Pb) is a significant concern, ranking second in soil pollution in China. Pb, like cadmium, is readily absorbed by crops, negatively affecting agricultural ecosystems. It causes structural, physiological, and biochemical changes in plants, leading to growth inhibition, metabolic disorders, and reduced crop yield and quality. Pb contamination also poses serious risks to human health through food chain transfer, necessitating urgent remediation efforts to ensure food safety and agricultural sustainability [66]. In a recent research, microbially induced carbonate precipitation (MICP) was used to remediate Pb-contaminated soil and assessed its impact on soil structure [67]. Results showed a 76.34% reduction in heavy metal leaching. Soil porosity and permeability improved, with a 73.78% increase in hydraulic conductivity. Thus, MICP bioremediation effectively remedied heavy metal pollution and enhanced soil structure.

Laboratory-scale and field-scale (windrow treatment) bioremediation were compared over 6 month period in a study [68]. The contaminated soil, sourced from a coal tar distillation plant, exhibited similar degradation rates between the two systems, although the laboratory results showed less variability. After 6 months, approximately 85% of PAHs were degraded in the laboratory, while degradation in the field reached 90%. Degradation was faster for 4- and 5-ring PAHs in the field, and degradation rates followed a negative exponential trend, with 3- and 4-ring PAHs degrading 32 and 7.2 times faster than 5- and 6-ring PAHs, respectively. The initial bacterial community exhibited high diversity, with 13 strains from 9 genera, predominantly Gamma-proteobacteria, and to a lesser extent, Alpha-proteobacteria, Beta-proteobacteria, and Lactobacillales. The Gamma-proteobacteria, including Pseudomonas, Acinetobacter, Enterobacter, and Klebsiella, were bioindicators of the biodegradation of 2-, 3-, and 4-ring PAHs. Throughout the treatment, Beta-proteobacteria strains, such as Brachymonas petroleovorans and Hydrogenophaga sp., emerged after three months, once PAH concentrations had decreased to non-ecotoxic levels. These strains can be used as indicators of the endpoint of biotreatment. The study highlighted the importance of considering PAH bioavailability, in addition to chemical soil analyses, when assessing bioremediation efficiency.

Zhang et al. studied biochar as a biostimulant for the bioremediation of soil contaminated with heavy metals (HMs) in a lettuce crop, evaluating both short- and long-term effects [69]. In the long term, biochar application significantly improved soil fertility and the growth of the phylum Proteobacteria, which is highly resistant to heavy metals, while reducing the presence of Acidobacteria. These changes helped reduce the accumulation of Cd and Pb in lettuce tissues. In terms of productivity, short- and long-term applications of biochar did not substantially affect the biomass, quality, or photosynthesis of lettuce. However, even in the short term, biochar decreased the accumulation of Cd and Pb in plant tissues. Regarding soil bacterial communities, short-term reapplication of biochar did not produce significant changes, but in the long term, biochar promoted changes in the physical, chemical, and biological properties of the soil, boosting the remediation of contaminants.

Liu et al. [70] explored the bioremediation of metal-contaminated soils using microbially induced carbonate precipitation (MICP), investigating its efficacy and long-term stability, and comparing it with chemical precipitation [70]. MICP involves the application of microorganisms that, by hydrolyzing urea, raise the pH and facilitate the precipitation of calcium carbonate, which can immobilize heavy metals, reducing their bioavailability and, consequently, their environmental toxicity. The authors used Sporosarcina pasteurii to bioremediate soils contaminated with Pb, Zn, and Cd and observed a significant reduction in heavy metal leaching concentrations. When subjected to harsh environmental conditions, S. pasteurii bioremediation was superior to chemical precipitation technology in terms of long-term stability.

Furthermore, bioremediation can often be enhanced by combining it with other techniques. For example, the authors demonstrated in a study that integrating chemical oxidation with bioremediation can significantly improve the degradation of petroleum-contaminated soil [71]. In their study, an integrated biological–chemical–biological strategy was employed, utilizing both conventional microbial degradation methods and a modified Fenton process. The results indicated that this integrated strategy achieved a 68.3% removal rate, which was more effective than bioremediation (1.7 times) and chemical oxidation (2.1 times) when applied individually.

3.1. Bioaugmentation

Bioaugmentation is a remediation strategy involving the addition of specific microorganisms to contaminated sites to enhance pollutant degradation. This approach can accelerate cleanup processes compared to natural attenuation. However, challenges include the potential mortality of introduced microbes and the need for long-term establishment of adequate ecological condition to ensure their persistence and efficacy. Recent studies have demonstrated bioaugmentation effectiveness in degrading various organic residues, such as herbicides and pesticides. Microorganisms that colonize plant root systems have shown particular promise, utilizing root exudates to promote growth and improve pollutant degradation [72,73,74].

The success of bioaugmentation primarily depends on the survival capacity of the inoculated microorganisms in the contaminated environment and their interactions with the indigenous microbiota, as well as interspecies competition [53]. However, several other factors also significantly influence the effectiveness of this process, including pH, temperature, physical and chemical characteristics of the soil, concentration and type of contaminants, water and organic matter content, availability of essential nutrients, and the concentration of the applied inoculum [55]. All of these factors are essential for optimizing biodegradation and efficiently removing contaminants.

Bioaugmentation fundamentally alters microbial community structure, functional gene expression, and metabolic pathways within contaminated environments. The use of indigenous bacteria, which are strains isolated from the same environment, generally proves more stable and effective due to their pre-existing adaptability. Conversely, bioaugmentation with exogenous bacteria can lead to competition with native microorganisms for resources, potentially leading to instability or failure. Despite this, exogenous strains can still contribute to overall system improvement by optimizing the removal of target pollutants and enhancing system performance [72].

For an example of research with indigenous bacteria, Kuwaiti hypersaline soil samples contaminated with 5% weathered crude oil were bioaugmented with native halophilic hydrocarbon-degrading microorganisms. Over one year, oil degradation rates were similar across all treated and untreated soils, reducing hydrocarbon levels by 82.7% to 93%. The number of culturable oil-degrading bacteria increased significantly, while inoculant microorganisms could not be cultured. The microbial community evolved, identifying primarily Actinobacteria, Proteobacteria, and Firmicutes [75]. In another study, bioaugmentation with nondomesticated mixed microbial consortia shows promise in mitigating ammonia-induced microbial inhibition in anaerobic digestion, with methane production improvements of 5.6–11.7% and 10.3–13.5% under ammonia concentrations of 2.0 and 4.9 g-N/L, respectively. The bioaugmented culture shifted the methanogenic pathway from acetoclastic to hydrogenotrophic by regulating microbial symbiosis [76].

The efficacy of bioremediation can be augmented by incorporating biological stimulation materials. These materials, including organic carbon sources, electron donors, surfactants, and zero-valent metals (ZVI), enhance microbial degradation processes. They facilitate improved solubility of contaminants and create conducive redox conditions, thereby enabling synergistic interactions between microorganisms and the pollutants for combined degradation [77]. For example, a field-scale cleanup of petroleum-contaminated soils in Indonesia’s Minas Oil Fields used landfarming bioremediation. Sawdust mixed with manure served as a bulking agent and microbial source. Petrophilic bacteria and native microflora boosted colony-forming units and total petroleum hydrocarbons (TPH) degradation rates. After 150 days, TPH reduced from 64,799 mg/kg to 163 mg/kg, eliminating 165.79 kg of TPH from 2565 m³ of soil at a cost of USD 161/m³ [78]. Banerjee et al. (2024) [79] investigated whether pre-treatment and bioaugmentation can expedite the biodegradation of polylactic acid (PLA)-based compostable bioplastic films under thermophilic composting conditions. They also explored the use of landfill-mined soil-like fraction (LMSF) as a substitute for commercial compost. Analyzing tensile strength, hydrophobicity, morphology, and thermal profiles, the study showed that combining material pre-treatment and bioaugmentation reduced the time for 90% degradation by 27% with compost and 23% with LMSF.

Likewise, immobilized microbial technology enhances bioremediation by confining microorganisms within carrier matrices, thus providing optimal environmental conditions and ensuring high microbial density and activity. The selection of carrier materials, encompassing natural organic, inorganic, synthetic polymeric, and composite types, is pivotal. This selection must account for specific surface area, pore structure, mechanical strength, and the physiological and environmental requirements of the microorganisms [77].

Bioaugmentation is an effective and eco-friendly method for tackling hazardous pollutants, as shown in some case studies in Table 3.

Furthermore, a study explored microbial community dynamics and PIONA (paraffins, iso-paraffins, olefins, naphthenes, and aromatics) fraction changes over 60 days with exogenous Pseudomonas stutzeri M3 [84]. Effective biodegradation, particularly of paraffin (96.5% in 1% oil-contaminated soil), occurred between the 15th and 30th day. M3 supplementation altered microbial communities, enriching Balneolaceae, Halolalama, and Woeserchaeia, while delaying Alcanivorax colonization. Positive interactions between hub bacteria facilitated petroleum degradation, with significant increases in various degradation-related enzymes observed within the first 7 days.

Polycyclic aromatic hydrocarbons (PAHs) are aromatic compounds with two or more fused benzene rings. They originate from both natural processes like volcanic activities and human activities such as fossil fuel combustion. A study isolated Achromobacter xylosoxidans BP1 from PAH-contaminated soil at a coal chemical site in Northern China for PAH bioremediation. BP1 exhibited high degradation rates for phenanthrene (PHE) and benzo[a]pyrene (BaP) in liquid cultures, with 98.47% and 29.86% removal rates, respectively, after 7 days. In PAH-contaminated soil, BP1 achieved significant removal rates of 67.72% for PHE and 13.48% for BaP over 49 days. Bioaugmentation with BP1 enhanced soil dehydrogenase and catalase activities and altered the microbial community structure, notably increasing the abundance of the Proteobacteria phylum [85]. The bioremediation of PAH-contaminated soil using the bacterium Aeromonas sp. BCP-3 in slurry bioreactors was studied [86]. Optimal conditions led to the removal of 96.3% of fluoranthene and 97.2% of pyrene in 12 days. Different conditions applied to real soil resulted in the removal of 82.2% of low-molecular-weight PAHs and 51.8% of high-molecular-weight PAHs in 21 days.

Mixed bioaugmentation employing microorganisms, earthworms (vermi-remediation), and plants (phytoremediation) was successfully demonstrated at a pilot scale [82]. Total petroleum hydrocarbons (TPHs) were removed in a pilot system with Panicum maximum, comparing natural attenuation (NA treatment) with a consortium of bacteria (Bacillus sp., Pseudomonas sp., and Shigella sp.), earthworms (Pontoscolex corethrurus), and Panicum maximum grass (BIO treatment). After 112 days, the BIO treatment significantly removed more alkanes (76%), polycyclic aromatic hydrocarbons (PAHs) (68%), and TPHs (76%) compared to the NA treatment (23%, 19%, and 24%, respectively).

The preventive bioremediation of pesticide contamination was studied in an agricultural context [87]. The biodegradation of the herbicide 2,4-dichlorophenoxyacetic acid (2,4-D) was investigated in soil microcosms planted with sensitive (mustard) and insensitive (wheat) plants, using a mineralizing bacterial strain (Cupriavidus necator JMP134). The simultaneous application of a commercial 2,4-D formulation at recommended agricultural doses, along with 10⁵ cells/g dw of soil of the JMP134 strain, significantly accelerated the mineralization of the herbicide. This approach reduced its persistence in the soil by threefold, without compromising the herbicide’s effectiveness and without significantly affecting the original bacterial community.

3.2. Biostimulation

Biostimulation involves the addition of nutrients, oxygen, or other amendments to stimulate the existing microbial community’s activity to degrade pollutants, whereas bioremediation encompasses the use of microorganisms, plants, fungi, or enzymes to degrade, detoxify, or transform contaminants into less harmful forms, with biostimulation being a subset of bioremediation strategies.

The bioremediation process through biostimulation begins with the assessment of the soil, including contaminant concentration, the type of substances present, the physicochemical properties of the soil, and the native microbiota, as well as factors such as moisture and aeration [88]. Based on this evaluation, it becomes possible to identify specific nutrients or compounds lacking in the soil that are essential for enhancing the metabolic activity of native microorganisms. Alternatively, if necessary, additional microorganisms can be introduced through bioaugmentation. These interventions facilitate the degradation or transformation of contaminants into less toxic or inert forms, thereby promoting soil restoration.

The biostimulant substances are diverse and include numerous compounds such as peptides, phenolic compounds, plant hormones, saccharides, free amino acids, humic and fulvic acids, enzymes, proteins, and other organic components. These substances can be derived from natural sources, such as agro-industrial byproducts, protein hydrolysates, seaweed extracts, or microbial products [89]. Depending on the specific needs of the plant and soil conditions, these substances can be applied individually or in combination. In general, they improve plant growth by improving nutrient uptake, promoting root development, increasing resistance to abiotic stresses, stimulating the overall health of the plant–soil system, and increasing crop fertility and productivity. In addition, biostimulants can contribute to the mitigation of soil contamination. Additionally, biostimulants can support the mitigation of soil contamination when combined with bioaugmentation strategies, as demonstrated in several studies summarized in Table 4.

The strategy to improve the degradation rates of total petroleum hydrocarbons (TPHs) in contaminated soil from a machine park was optimized [91]. The study was conducted on a microcosm scale over 90 days, comparing biostimulation and bioaugmentation, with and without the addition of vermicompost. The bacterial consortium consisted of the genera Pseudomonas, Achromobacter, Cupriavidus, Comamonadaceae, and Sphingomonadaceae. Vermicompost addition significantly increased nutrient availability, such as phosphorus and potassium, and stimulated microbial activity, leading to higher TPH degradation rates. Degradation efficiencies reached approximately 32.5% and 34.4% for biostimulation and bioaugmentation, respectively. However, more resistant compounds, such as recalcitrant hydrocarbons, remained unchanged, indicating limitations in mobility and bioavailability.

In another study [92], bacteria were isolated from crude oil-contaminated agricultural fields in India. The strains Pseudomonas aeruginosa BB-BE3, Gordonia amicalis BB-DAC, Pseudomonas citronellolis BB-NA1, Rhodococcus ruber BB-VND, and Ochrobactrum anthropi BB-NM2 were applied in a consortium with NPK biostimulation to two different host plants (Azadirchta indica and Delonix regia), and their hydrocarbon degradation capabilities were assessed alongside their positive plant growth-promoting (PGP) attributes. The bacterial consortium-NPK biostimulation altered the rhizosphere microbiome, enhancing hydrocarbon degradation in crude oil-contaminated soils. After 120 days of planting, A. indica treated with bioaugmentation and NPK biostimulation exhibited hydrocarbon degradation of up to 67%, while D. regia showed 55% degradation under the same treatment.

The herbicide atrazine was bioremediated using biochar loaded with Paenarthrobacter sp. AT5 (an atrazine-degrading bacterial strain) in a system with soybean cultivated in black soil. The bacteria-loaded biochar (BBC) significantly enhanced atrazine removal rates in both unplanted and planted soil systems. Additionally, BBC application improved soybean biomass, photosynthetic pigments, and antioxidant systems, while mitigating changes in metabolic pathways induced by atrazine exposure [95].

In a recent study comparing bioaugmentation and biostimulation for microbially induced carbonate precipitation (MICP) in soil improvement, it was found that biostimulation is more environmentally friendly, cost-effective, and provides sustained mineralization. Yeast extract outperformed beef extract in both methods, though bioaugmentation with beef extract resulted in higher soil strength for the same calcium carbonate content, likely due to differences in calcium carbonate (CaCO₃) crystal precipitation patterns [96]. Mohammadi et al. (2024) also compares biostimulation and bioaugmentation methods for degrading crude oil-contaminated sediments in the Persian Gulf [97]. Six microcosms from Khark Island sediments were analyzed for marine bacteria quantity, enzyme activity, biodiversity, and crude oil degradation over 120 days. The best results were observed in the microcosm using both bioaugmentation and biostimulation, which showed the highest bacteria count (3.9 × 10⁶ CFU/g) and crude oil degradation. Predominant bacterial genera included Cellulosimicrobium, Shewanella, Alcanivorax, and Cobetia.

Combining bioaugmentation, which introduces specialized microbes, with biostimulation, which provides nutrients to enhance microbial activity, improves the efficiency of soil remediation by accelerating the degradation of various contaminants. Maluleka et al. (2024) assessed the impact of diesel spills on soil water retention and compared four bioremediation methods: natural attenuation, bioaugmentation, biostimulation, and a combination of both [98]. Higher diesel concentrations decreased soil water retention, while compost increased it. After 21 days, the Diesel Range Organics (DRO) removal efficiencies were 15.70% (natural attenuation), 23.31% (bioaugmentation), 29.65% (biostimulation), and 49.78% (combined). The combined method showed the fastest degradation rate, with complete bioremediation projected in 44 days. Machine Learning models, particularly the Artificial Neural Network, supported these results. Liu et al. (2023) explored the combined use of bioaugmentation (BA) and biostimulation (BS) to remediate oil-contaminated soil [99]. A combination of the microbial agent TY (Achromobacter and Pseudomonas) and a dehydrocoenzyme activator significantly increased crude oil degradation, achieving a 79.44% reduction in 60 days. Gas chromatography showed efficient targeting of C10–C28 oil fractions, and enzyme analysis indicated enhanced activity of coenzymes and oxygenases. Dominant microbial genera included Nocardioides, Gordonia, and Pseudomonas. The combined approach enhanced genes associated with oil degradation, making it a promising method for soil bioremediation.

Bioremediation is an effective approach for the recovery of contaminated agricultural soils, as demonstrated by [100]. The authors successfully scaled up from microcosms to mesocosms by applying a consortium of four Streptomyces sp. strains, which were biostimulated with sugarcane filter cake to remediate soil contaminated with lindane, an organochlorine pesticide. As a result, 82.6% of the lindane present in sandy soil was degraded, indicating that the combination of biostimulation and bioaugmentation is a promising strategy for restoring agricultural areas impacted by pesticide contamination.

Integrating bioaugmentation and biostimulation can offer synergistic effects, maximizing the efficiency of bioremediation. Research has demonstrated that combining these techniques can lead to significant improvements in the degradation rates of pollutants. For example, combining bioaugmentation with microbial consortia and biostimulation using nutrient amendments has shown accelerated degradation of petroleum hydrocarbons and improved soil health.

Microbial remediation technologies, while effective, encounter limitations under specific environmental conditions that can impair the survival, activity, and degradation potential of microorganisms. Temperature fluctuations also a critical role; while moderate temperatures often promote microbial growth and enzymatic degradation, excessively high or low temperatures can denature microbial proteins or slow cellular processes, thus diminishing degradation efficiency as a short time effect, given resiliency after return to better conditions. Additionally, environments with high pollutant concentrations can exert toxic effects on microbial populations. High concentrations of organic pollutants, heavy metals, or other toxic compounds can inhibit microbial growth and even induce cellular toxicity, thereby reducing biodegradation capacity. Adaptations or genetic modifications might mitigate these challenges, but such measures are not always feasible or effective across all environmental contexts. Consequently, these factors represent critical considerations in the deployment of microbial remediation strategies.

4. Future Outlooks

Rapid population growth and urbanization have exacerbated soil contamination with ECs and toxic heavy metals, posing significant threats to sustainable agriculture and human health. Despite the challenges, bioremediation has emerged as a promising, cost-effective solution for mitigating soil pollution, being the unique possibility to conserve soil functioning and soil quality. Bioaugmentation and biostimulation, as complementary strategies, enhance the degradation of various contaminants, demonstrating significant potential in field applications. Future research integrating advanced genetic engineering and microbial technologies, alongside optimized biostimulation protocols, could further improve the efficiency and resilience of bioremediation practices. As bioremediation technologies evolve, their practical implementation will be crucial for ensuring agricultural sustainability and environmental health.

Despite its advantages, bioaugmentation faces challenges related to microbial competition, environmental conditions, and scaling from laboratory to field applications. Further research is needed to fully understand the mechanisms of bioaugmentation, optimize methods, and address scalability issues to improve the effectiveness of this remediation technique. Although previous studies have investigated the effects of variables such as dosage, frequency, and strain selection on bioaugmentation efficacy, the underlying mechanisms at the microbial and metabolic levels remain inadequately addressed [72].

Furthermore, the long-term establishment of adequate ecological condition is essential in microbial remediation studies to fully assess the sustainability and stability of remediated sites. Although microbial remediation can initially reduce pollutant levels, its long-term effects on soil health, microbial diversity, and ecosystem resilience remain areas of concern. Over extended periods, it is critical to monitor shifts in microbial communities, as well as possible accumulation or transformation of pollutants into secondary, potentially toxic compounds that could adversely affect soil ecosystems.

Developing more refined biostimulation protocols that precisely tailor nutrient amendments to site-specific conditions could enhance microbial activity and pollutant degradation is necessary. Scaling up successful laboratory and pilot studies to field-scale applications requires careful consideration of environmental variables, socio-economic impacts, and long-term establishment of adequate ecological condition to ensure sustainability.

Author Contributions

Conceptualization, C.E.D.O. and B.M.S.P.; methodology, C.E.D.O. and B.M.S.P.; validation, C.E.D.O. and B.M.S.P.; investigation, C.E.D.O. and B.M.S.P.; resources, L.D.V.; data curation, L.D.V., R.M.D. and M.V.T.; writing—original draft preparation, C.E.D.O. and B.M.S.P.; writing—review and editing, C.E.D.O., B.M.S.P., L.D.V., R.M.D. and M.V.T.; supervision, R.M.D. and M.V.T. All authors have read and agreed to the published version of the manuscript.

Acknowledgments

The authors thanks URI and UFSM for their support.

Conflicts of Interest

The authors declare no conflicts of interest.

Footnotes

Disclaimer/Publisher’s Note: The statements, opinions and data contained in all publications are solely those of the individual author(s) and contributor(s) and not of MDPI and/or the editor(s). MDPI and/or the editor(s) disclaim responsibility for any injury to people or property resulting from any ideas, methods, instructions or products referred to in the content.

Figure and Tables

Figure 1. Bioremediation of soil microbiology.

Table 1

Examples of microorganisms and target contaminants removed by bioremediation.

Classification	Microorganism	Contaminant	Reference
AMF	AMFs combined with agricultural residues	Heavy metals	[34]
AMF	Acaulospora sp., Archaeospora sp., Claroideoglomus sp., Diversispora sp., Rhizophagus intraradices, Rhizophagus iranicu	Petroleum	[35]
ECM	Suillus luteus	Heavy metals	[36]
PGPR	Alcaligenes faecalis	Pesticide Chlorpyrifos	[37]
PGPR	Pseudomonas sp.	Insecticide Fipronil	[38]
PGPR	Rhodococcus pyridinivorans B403	Phenol	[39]
PGPR	Phaseolus vulgaris and Xanthobacter autotrophicus	Waste Motor Oil	[40]
PGPR	Agrobacterium rhizogenes AT13	Atrazine	[41]
PGPR	Mycobacterium N12	Polycyclic aromatic hydrocarbons (PAHs) and cadmium (Cd)	[42]

Table 2

Main factors and effects that influence bioremediation.

Factors	Effects	References
Oxygen	Oxygen is essential for the bioremediation of contaminated soils, as it regulates the activity of microorganisms that degrade pollutants. Aerobic bacteria require adequate levels of oxygen to decompose organic compounds, and the presence of 10–40% oxygen favors the efficient biodegradation of hydrocarbons. In low-oxygen conditions, common in contaminated soils, aerobic degradation is limited, affecting the effectiveness of the process, and is also influenced by the physical and chemical properties of the soil. In specific cases, anaerobic conditions are essential for the degradation of some compounds and for the dehalogenation of chlorinated molecules, such as lindane, HCB, doxine, and furane. Dechlorinated molecules may be later easily degraded under oxic conditions.	[50,51,52,53]
Moisture content	Soil moisture content has a major influence on microbial metabolism and biochemical reactions essential for bioremediation. At low moisture levels, microbial metabolism is reduced, limiting the degradation of contaminants. On the other hand, high moisture levels reduce soil aeration, reducing the availability of oxygen, which is crucial for the activity of aerobic bacteria responsible for the decomposition of organic pollutants. Longer waterlogging allows dehalogenation processes.	[51,54]
Temperature	Temperature directly affects microbial growth and the speed of chemical reactions, and each microorganism has an ideal range for development that must be considered. Therefore, evaluating thermal conditions in the field is crucial for the success of the bioremediation process. In general, increasing temperature tends to increase the solubility and absorption capacity of contaminants, facilitating their bioavailability for microorganisms and enhancing the degradation process.	[51,55,56]
pH	Soil pH influences the bioavailability of metals and contaminants, directly affecting the equilibrium of dissolution and precipitation of metal ions. At a low pH, there is a greater release of metal ions into the soil solution. This factor alters the redox balance and solubility of metals, whose different forms and valence states can increase toxicity to microorganisms and plants. In addition, pH affects the adsorption of metals and their binding to organic functional groups, such as carboxyls, hydroxyls, alcohols, and phenolics. Each microorganism has an ideal pH range for growth. Neutral to slightly alkaline pH is generally more favorable for most degrading bacteria, while extreme pHs impair bioremediation. Hydrocarbon degradation is generally more efficient at pH values between 5.2 and 7.	[50,55,57]
Soil texture	Knowing the characteristics and type of soil is important, especially in field application. The texture and particle size of the soil affect other parameters, such as the uniform distribution of nutrients, oxygen, microorganisms, moisture, and contaminants in the soil. Organic and inorganic compounds can interact and bind with contaminants, affecting their bioavailability.	[58]
Nutrient availability	During degradation, contaminants act as substrates or co-substrates, serving as sources of carbon and energy for microorganisms. Thus, nutrient accessibility is essential for microbial growth, as well as for plants and crops. For this reason, biostimulation with nutrient sources is often combined with bioaugmentation, enhancing the degradation process. Rich organic matter helps retain nutrients and water, in addition to positively influencing soil’s mechanical strength and electrical conductivity. High amounts of fresh organic matter may lead to high microbial activity and oxygen demand, oxygen deficiency, and dehalogenation processes.	[50,51,59]
Concentration and type of pollutant	The pollutant concentration must be within an appropriate range to optimize degradation. Low concentrations may not activate microorganisms’ metabolic response, limiting the production of enzymes responsible for biodegradation. On the other hand, excessively high concentrations may be toxic, inhibiting microbial activity and reducing the efficiency of the process. Therefore, initial concentration studies are essential to adjust pollutant levels and ensure effective and safe degradation, optimizing bioremediation.	[50,60]
Inoculation and biological competition	Efficient degradation of contaminants depends on the ability of microorganisms to survive in contaminated soil and metabolize pollutants into less toxic substances. To achieve this, an ideal inoculum must degrade many contaminants, survive in adverse conditions, and resist competition for nutrients. In addition, consortia between different microbial strains, combined with plants and earthworms, can increase metabolic diversity and promote degradation at multiple levels, resulting in more robust and efficient bioremediation.	[50,51]

Table 3

Case studies on the use of bioaugmentation for soil contaminant reduction.

Inoculum	Contaminant	Experimental Conditions	Removal (%)	References
Immobilized bacterial pellets (IBPs) containing Microbacterium oxydans and a controlled-release oxygen composite (CROC)	Total petroleum hydrocarbons (TPHs)	Four microcosm tests assessed the effects of IBPs and CROC on TPH removal from petroleum-contaminated site soil.	The combination of IBPs and CROC achieved the highest TPH removal rate of 70%, outperforming natural attenuation (13.2%), IBPs alone (43.0%), and CROC alone (31.9%).	[80]
Indigenous microbe, including Stenotrophomonas BaP-1	Benzo[a]pyrene (BaP)	Indigenous strains were isolated from petroleum-contaminated soil and introduced into the ryegrass rhizosphere to investigate BaP degradation.	Stenotrophomonas BaP-1 degradation efficiency was 59.46% in 14 days.	[81]
Mixed bioaugmentation (Bacillus sp., Pseudomonas sp., and Shigella sp.), vermi-remediation (Pontoscolex corethrurus), and phytoremediation (Panicum maximum)	Total petroleum hydrocarbons (TPH), alkanes, and PAHs	Pilot scale with contaminated soil forming six piles (6 m long × 2 m wide × 40 cm depth) in a system comparing natural attenuation (NA treatment) with a consortium of bacteria, earthworms, and grass (BIO treatment)	After 112 days, the BIO treatment achieved significantly higher removal rates of alkanes (76%), PAHs (68%), and TPH (76%) compared to the NA treatment, which removed 23%, 19%, and 24%, respectively.	[82]
Priestia aryabhattai MGP1	e-polymer acrylonitrile–butadiene–styrene	Old television cases were used as a carbon source to enrich soil contaminated with electronic waste (e-waste). The laboratory experiments were carried out at pH 7, with a stirring speed of 120 rpm, and a temperature of 30 °C.	Degradation of 18.88% after 60 days	[83]

Table 4

Case studies on the use of biostimulants for soil contaminant reduction.

Inoculum	Contaminant	Experimental Conditions	Removal (%)	Reference
Streptomyces sp. A2, A5, A11, and M7 biostimulated with sugarcane filter cake	Soil contaminated with the organochlorine pesticide lindane	Scaling up soil bioremediation. Three types of soils were evaluated: clayey, sandy, and silty loam. The treatments combined sugarcane bagasse with bacteria.	The removal process was significantly affected by the soil type, and the highest pesticide dissipation (82.6%) was detected in bioremediated sandy soil.	[90]
Pseudomonas, Achromobacter, Cupriavidus, Comamonadaceae, and Sphingomonadacea biostimulated with vermicompost	Soil from a machinery park contaminated with total petroleum hydrocarbons (TPHs)	The study was conducted on a microcosm scale (laboratory) over 90 days, comparing biostimulation and bioaugmentation, with and without the addition of vermicompost.	Degradation of 32.5% for biostimulation and bioaugmentation of 34.4%. However, recalcitrant hydrocarbons remained unchanged.	[91]
Bacteria isolated from crude oil-contaminated agricultural fields biostimulated with NPK	Crude oil	Field experiments were conducted in two crude oil-contaminated agricultural fields (India), where plants (Azadirchta indica and Delonix regia) were cultivated with the bacterial consortium for 120 days.	A. indica treated with bioaugmentation and NPK biostimulation exhibited hydrocarbon degradation of up to 67%, while D. regia showed 55% degradation under the same treatment.	[92]
Pseudomonas plecoglossicida (PP) assisted with biochar (BC)	2,2′,4,4′ tetrabromo diphenyl ether (DE-47) in soil contaminated with e-waste	Sandy loam soil was collected from an e-waste dismantling site. A laboratory-scale experiment was conducted for 3 months.	PP lost degradation activity to BDE-47 in 14 days with a removal of 11.8%. BC/PP showed a removal of 42.8% in 60 days. BC can prolong the survival of PP in the soil.	[93]
Pseudomonas sp. CF7b	Organophosphate pesticide Chlorpyrifos	Laboratory tests for removal of Chlorpyrifos was evaluated in the presence of sub-inhibitory concentrations (sub-MIC) of zinc oxide nanoparticles (ZnONPs).	The combination of Pseudomonas sp. CF7b and ZnONPs showed a reduction of 90.9%, Pseudomonas sp. CF7b alone showed a reduction of 81.6% and ZnONPs alone showed a reduction of 53.4%.	[94]

References

1. Hou, R.; Zhang, J.; Fu, Q.; Li, T.; Gao, S.; Wang, R.; Zhao, S.; Zhu, B. The Boom Era of Emerging Contaminants: A Review of Remediating Agricultural Soils by Biochar. Sci. Total Environ.; 2024; 931, 172899. [DOI: https://dx.doi.org/10.1016/j.scitotenv.2024.172899] [PubMed: https://www.ncbi.nlm.nih.gov/pubmed/38692328]

2. Alabi, O.A.; Olukunle, O.F.; Ojo, O.F.; Oke, J.B.; Adebo, T.C. Comparative Study of the Reproductive Toxicity and Modulation of Enzyme Activities by Crude Oil-Contaminated Soil before and after Bioremediation. Chemosphere; 2022; 299, 134352. [DOI: https://dx.doi.org/10.1016/j.chemosphere.2022.134352] [PubMed: https://www.ncbi.nlm.nih.gov/pubmed/35341768]

3. Caldelas, C.; Rezzouk, F.Z.; Aparicio Gutiérrez, N.; Diez–Fraile, M.C.; Araus Ortega, J.L. Interaction of Genotype, Water Availability, and Nitrogen Fertilization on the Mineral Content of Wheat Grain. Food Chem.; 2023; 404, 134565. [DOI: https://dx.doi.org/10.1016/j.foodchem.2022.134565] [PubMed: https://www.ncbi.nlm.nih.gov/pubmed/36444037]

4. Ouyang, Q.; Liu, N.; Fan, Z.; Li, F.; Ge, F. The Chelation Mechanism of Neonicotinoid Insecticides Influencing Cadmium Transport and Accumulation in Rice at Different Growth Stage. Sci. Total Environ.; 2024; 941, 173257. [DOI: https://dx.doi.org/10.1016/j.scitotenv.2024.173257]

5. Wang, Z.; Teng, Y.; Wang, X.; Xu, Y.; Li, R.; Hu, W.; Li, X.; Zhao, L.; Luo, Y. Removal of Cadmium and Polychlorinated Biphenyls by Clover and the Associated Microbial Community in a Long-Term Co-Contaminated Soil. Sci. Total Environ.; 2023; 871, 161983. [DOI: https://dx.doi.org/10.1016/j.scitotenv.2023.161983]

6. Zhou, X.; Wang, C.; Huang, M.; Zhang, J.; Cheng, B.; Zheng, Y.; Chen, S.; Xiang, M.; Li, Y.; Bedia, J. et al. A Review of the Present Methods Used to Remediate Soil and Water Contaminated with Organophosphate Esters and Developmental Directions. J. Hazard. Mater.; 2024; 475, 134834. [DOI: https://dx.doi.org/10.1016/j.jhazmat.2024.134834]

7. Zuo, W.; Song, B.; Shi, Y.; Zupanic, A.; Guo, S.; Huang, H.; Jiang, L.; Yu, Y. Using Bacillus Thuringiensis HM-311@hydroxyapatite@biochar Beads to Remediate Pb and Cd Contaminated Farmland Soil. Chemosphere; 2022; 307, 135797. [DOI: https://dx.doi.org/10.1016/j.chemosphere.2022.135797]

8. Ni, Z.; Gong, Z.; Song, L.; Jia, C.; Zhang, X. Adaptation Strategies and Functional Transitions of Microbial Community in Pyrene-Contaminated Soils Promoted by Lead with Pseudomonas Veronii and Its Extracellular Polymeric Substances. Chemosphere; 2024; 351, 141139. [DOI: https://dx.doi.org/10.1016/j.chemosphere.2024.141139]

9. Lu, C.W.; Lo, K.H.; Wang, S.C.; Kao, C.M.; Chen, S.C. An Innovative Permeable Reactive Bio-Barrier to Remediate Trichloroethene-Contaminated Groundwater: A Field Study. Sci. Total Environ.; 2024; 920, 170885. [DOI: https://dx.doi.org/10.1016/j.scitotenv.2024.170885]

10. Chauhan, R.; Awasthi, S.; Tiwari, P.; Upadhyay, M.K.; Srivastava, S.; Dwivedi, S.; Dhankher, O.P.; Tripathi, R.D. Biotechnological Strategies for Remediation of Arsenic-Contaminated Soils to Improve Soil Health and Sustainable Agriculture. Soil Environ. Health; 2024; 2, 100061. [DOI: https://dx.doi.org/10.1016/j.seh.2024.100061]

11. Gupta, P.K.; Nair, V.K.; Dalvi, V.; Dhali, S.; Malik, A.; Pant, K.K. Field-Scale Assessment of Soil, Water, Plant, and Soil Microbiome in and around Rania-Khan Chandpur Chromium Contaminated Site, India. J. Hazard. Mater.; 2024; 467, 133747. [DOI: https://dx.doi.org/10.1016/j.jhazmat.2024.133747] [PubMed: https://www.ncbi.nlm.nih.gov/pubmed/38350323]

12. Tang, F.; Gao, M.; Zeng, F.; Xu, Z.; Tian, G. An Old Story with New Insights into an Ignored Issue of Metabolites in Biochar-Amended Soil: Effect of Biochar on Dissipation of Carbosulfan as an Example. Sci. Total Environ.; 2021; 790, 148100. [DOI: https://dx.doi.org/10.1016/j.scitotenv.2021.148100] [PubMed: https://www.ncbi.nlm.nih.gov/pubmed/34380258]

13. Kumar, N.; Shukla, P. Microalgal Multiomics-Based Approaches in Bioremediation of Hazardous Contaminants. Environ. Res.; 2024; 247, 118135. [DOI: https://dx.doi.org/10.1016/j.envres.2024.118135] [PubMed: https://www.ncbi.nlm.nih.gov/pubmed/38218523]

14. Curiel-Alegre, S.; de la Fuente-Vivas, D.; Khan, A.H.A.; García-Tojal, J.; Velasco-Arroyo, B.; Rumbo, C.; Soja, G.; Rad, C.; Barros, R. Unveiling the Capacity of Bioaugmentation Application, in Comparison with Biochar and Rhamnolipid for TPHs Degradation in Aged Hydrocarbons Polluted Soil. Environ. Res.; 2024; 252, 118880. [DOI: https://dx.doi.org/10.1016/j.envres.2024.118880]

15. do Vale Vale, K.; Soares, D.W.F.; da Silva, A.L.B.; da Silva Abreu, F.O.M.; de Oliveira Almeida, J.L.I.; Oliveira, M.R.F.; Reck, L.; Melo, V.M.M.; Alves, D.R.; Alves, C.R. Biossurfactant Production by Isolated Bacteria from Petroleum Industry’s Effluent Targeting Bioremediation. Results Chem.; 2023; 6, 101038. [DOI: https://dx.doi.org/10.1016/j.rechem.2023.101038]

16. Tedesco, P.; Balzano, S.; Coppola, D.; Esposito, F.P.; de Pascale, D.; Denato, R. Bioremediation for the Recovery of Oil Polluted Marine Environment, Opportunities and Challenges Approaching the Blue Growth. Mar. Pollut. Bull.; 2024; 200, 116157. [DOI: https://dx.doi.org/10.1016/j.marpolbul.2024.116157]

17. Al-Shammary, A.A.G.; Al-Shihmani, L.S.S.; Fernández-Gálvez, J.; Caballero-Calvo, A. Optimizing Sustainable Agriculture: A Comprehensive Review of Agronomic Practices and Their Impacts on Soil Attributes. J. Environ. Manag.; 2024; 364, 121487. [DOI: https://dx.doi.org/10.1016/j.jenvman.2024.121487]

18. Mohapatra, D.; Rath, S.K.; Mohapatra, P.K. Soil Fungi for Bioremediation of Pesticide Toxicants: A Perspective. Geomicrobiol. J.; 2022; 39, pp. 352-372. [DOI: https://dx.doi.org/10.1080/01490451.2021.2019855]

19. Karimi, H.; Mahdavi, S.; Asgari, B.; Rajput, V.D.; Minkina, T.; Astatkie, T.; Moghiseh, E. Insights on the Bioremediation Technologies for Pesticide- Contaminated Soils. Environ. Geochem. Health; 2022; 44, pp. 1329-1354. [DOI: https://dx.doi.org/10.1007/s10653-021-01081-z]

20. Su, Y.; Wang, J.; Gao, W.; Wang, R.; Yang, W.; Zhang, H.; Huang, L.; Guo, L. Dynamic Metabolites: A Bridge between Plants and Microbes. Sci. Total Environ.; 2023; 899, 165612. [DOI: https://dx.doi.org/10.1016/j.scitotenv.2023.165612]

21. Tripathi, M.; Gaur, R. Bioactivity of Soil Microorganisms for Agriculture Development. Microbes in Land Use Change Management; Elsevier: Amsterdam, The Netherlands, 2021; pp. 197-220. [DOI: https://dx.doi.org/10.1016/B978-0-12-824448-7.00012-7]

22. dos Santos, M.S.N.; Ody, L.P.; Kerber, B.D.; Araujo, B.A.; Oro, C.E.D.; Wancura, J.H.C.; Mazutti, M.A.; Zabot, G.L.; Tres, M.V. New Frontiers of Soil Fungal Microbiome and Its Application for Biotechnology in Agriculture. World J. Microbiol. Biotechnol.; 2023; 39, 287. [DOI: https://dx.doi.org/10.1007/s11274-023-03728-8] [PubMed: https://www.ncbi.nlm.nih.gov/pubmed/37632593]

23. Hemkemeyer, M.; Schwalb, S.A.; Heinze, S.; Joergensen, R.G.; Wichern, F. Functions of Elements in Soil Microorganisms. Microbiol. Res.; 2021; 252, 126832. [DOI: https://dx.doi.org/10.1016/j.micres.2021.126832] [PubMed: https://www.ncbi.nlm.nih.gov/pubmed/34508963]

24. Custódio, V.; Gonin, M.; Stabl, G.; Bakhoum, N.; Oliveira, M.M.; Gutjahr, C.; Castrillo, G. Sculpting the Soil Microbiota. Plant J.; 2022; 109, pp. 508-522. [DOI: https://dx.doi.org/10.1111/tpj.15568] [PubMed: https://www.ncbi.nlm.nih.gov/pubmed/34743401]

25. del Carmen Orozco-Mosqueda, M.; Fadiji, A.E.; Babalola, O.O.; Glick, B.R.; Santoyo, G. Rhizobiome Engineering: Unveiling Complex Rhizosphere Interactions to Enhance Plant Growth and Health. Microbiol. Res.; 2022; 263, 127137. [DOI: https://dx.doi.org/10.1016/j.micres.2022.127137]

26. Chamkhi, I.; El Omari, N.; Balahbib, A.; El Menyiy, N.; Benali, T.; Ghoulam, C. Is The Rhizosphere a Source of Applicable Multi-Beneficial Microorganisms for Plant Enhancement?. Saudi J. Biol. Sci.; 2022; 29, pp. 1246-1259. [DOI: https://dx.doi.org/10.1016/j.sjbs.2021.09.032]

27. Nabi, M. Role of Microorganisms in Plant Nutrition and Soil Health. Sustainable Plant Nutrition; Academic Press: Cambridge, MA, USA, 2023; pp. 263-282. [DOI: https://dx.doi.org/10.1016/B978-0-443-18675-2.00016-X]

28. Xiao, L.; Lai, S.; Chen, M.; Long, X.; Fu, X.; Yang, H. Effects of Grass Cultivation on Soil Arbuscular Mycorrhizal Fungi Community in a Tangerine Orchard. Rhizosphere; 2022; 24, 100583. [DOI: https://dx.doi.org/10.1016/j.rhisph.2022.100583]

29. Alrajhi, K.; Bibi, S.; Abu-Dieyeh, M. Diversity, Distribution, and Applications of Arbuscular Mycorrhizal Fungi in the Arabian Peninsula. Saudi J. Biol. Sci.; 2024; 31, 103911. [DOI: https://dx.doi.org/10.1016/j.sjbs.2023.103911]

30. Andrew, C.; Mueller, G.M.; Avis, P.G. Do Local-Scale Context Dependencies Shape How Ectomycorrhizal Fungal Diversity Structures with Reduced or Sustained Experimental N Addition?. Pedobiologia; 2022; 90, 150791. [DOI: https://dx.doi.org/10.1016/j.pedobi.2022.150791]

31. Vasco-Palacios, A.M.; Hernandez, J.; Peñuela-Mora, M.C.; Franco-Molano, A.E.; Boekhout, T. Ectomycorrhizal Fungi Diversity in a White Sand Forest in Western Amazonia. Fungal Ecol.; 2018; 31, pp. 9-18. [DOI: https://dx.doi.org/10.1016/j.funeco.2017.10.003]

32. Khatoon, Z.; Huang, S.; Rafique, M.; Fakhar, A.; Kamran, M.A.; Santoyo, G. Unlocking the Potential of Plant Growth-Promoting Rhizobacteria on Soil Health and the Sustainability of Agricultural Systems. J. Environ. Manag.; 2020; 273, 111118. [DOI: https://dx.doi.org/10.1016/j.jenvman.2020.111118]

33. Chauhan, H.; Bagyaraj, D.J.; Selvakumar, G.; Sundaram, S.P. Novel Plant Growth Promoting Rhizobacteria—Prospects and Potential. Appl. Soil Ecol.; 2015; 95, pp. 38-53. [DOI: https://dx.doi.org/10.1016/j.apsoil.2015.05.011]

34. Farhad, M.; Noor, M.; Yasin, M.Z.; Nizamani, M.H.; Turan, V.; Iqbal, M. Interactive Suitability of Rice Stubble Biochar and Arbuscular Mycorrhizal Fungi for Improving Wastewater-Polluted Soil Health and Reducing Heavy Metals in Peas. Sustainability; 2024; 16, 634. [DOI: https://dx.doi.org/10.3390/su16020634]

35. Ryszka, P.; Zarzyka-Ryszka, M.; Anielska, T.; Choczyński, M.; Turnau, K. Arbuscular Mycorrhizal Fungi from Petroleum-Impacted Sites in the Polish Carpathians. Int. Biodeterior. Biodegrad.; 2019; 138, pp. 50-56. [DOI: https://dx.doi.org/10.1016/j.ibiod.2019.01.001]

36. Yin, S.; Zhang, X.; Xie, J.; Ye, X.; Zhang, X. Change of Microbial Communities in Heavy Metals-Contaminated Rhizosphere Soil with Ectomycorrhizal Fungi Suillus Luteus Inoculation. Appl. Soil Ecol.; 2023; 190, 105019. [DOI: https://dx.doi.org/10.1016/j.apsoil.2023.105019]

37. Yadav, U.; Kushwaha, S.; Anand, V.; Kumar, S.; Prakash, O.; Singh, P.C. Chlorpyrifos Degradation by Plant Growth-Promoting Alcaligenes Faecalis Bacteria Isolated from Oil-Contaminated Soil. Bioremediation J.; 2020; 25, pp. 80-88. [DOI: https://dx.doi.org/10.1080/10889868.2020.1837066]

38. Jaiswal, A.; Pandey, A.K.; Mishra, Y.; Dubey, S.K. Insights into the Biodegradation of Fipronil through Soil Microcosm-Omics Analyses of Pseudomonas sp. FIP_ A4. Chemosphere; 2024; 363, 142944. [DOI: https://dx.doi.org/10.1016/j.chemosphere.2024.142944]

39. Peng, F.; Liu, J.; Ping, J.; Dong, Y.; Xie, L.; Zhou, Y.; Liao, L.; Song, H. An Effective Strategy for Biodegradation of High Concentration Phenol in Soil via Biochar-Immobilized Rhodococcus Pyridinivorans B403. Environ. Sci. Pollut. Res.; 2024; 31, pp. 33752-33762. [DOI: https://dx.doi.org/10.1007/s11356-024-33386-8]

40. Martínez, B.C.S.; Benavides, L.M.; Santoyo, G.; Sánchez-Yáñez, J.M. Biorecovery of Agricultural Soil Impacted by Waste Motor Oil with Phaseolus Vulgaris and Xanthobacter Autotrophicus. Plants; 2022; 11, 1419. [DOI: https://dx.doi.org/10.3390/plants11111419]

41. Liu, Y.; Li, M.; Wu, J.; Liu, W.; Li, Y.; Zhao, F.; Tan, H. Characterization and Novel Pathway of Atrazine Catabolism by Agrobacterium Rhizogenes AT13 and Its Potential for Environmental Bioremediation. Chemosphere; 2023; 319, 137980. [DOI: https://dx.doi.org/10.1016/j.chemosphere.2023.137980]

42. Li, N.; Liu, R.; Chen, J.; Wang, J.; Hou, L.; Zhou, Y. Enhanced Phytoremediation of PAHs and Cadmium Contaminated Soils by a Mycobacterium. Sci. Total Environ.; 2021; 754, 141198. [DOI: https://dx.doi.org/10.1016/j.scitotenv.2020.141198]

43. Omotayo, A.O.; Omotayo, O.P. Potentials of Microbe-Plant Assisted Bioremediation in Reclaiming Heavy Metal Polluted Soil Environments for Sustainable Agriculture. Environ. Sustain. Indic.; 2024; 22, 100396. [DOI: https://dx.doi.org/10.1016/j.indic.2024.100396]

44. Mącik, M.; Gryta, A.; Frąc, M. Biofertilizers in Agriculture: An Overview on Concepts, Strategies and Effects on Soil Microorganisms. Adv. Agron.; 2020; 162, pp. 31-87. [DOI: https://dx.doi.org/10.1016/BS.AGRON.2020.02.001]

45. Saravanan, A.; Kumar, P.S.; Jeevanantham, S.; Anubha, M.; Jayashree, S. Degradation of Toxic Agrochemicals and Pharmaceutical Pollutants: Effective and Alternative Approaches toward Photocatalysis. Environ. Pollut.; 2022; 298, 118844. [DOI: https://dx.doi.org/10.1016/j.envpol.2022.118844] [PubMed: https://www.ncbi.nlm.nih.gov/pubmed/35032600]

46. Yaashikaa, P.R.; Kumar, P.S. Bioremediation of Hazardous Pollutants from Agricultural Soils: A Sustainable Approach for Waste Management towards Urban Sustainability. Environ. Pollut.; 2022; 312, 120031. [DOI: https://dx.doi.org/10.1016/j.envpol.2022.120031]

47. Streletskii, R.A.; Astaykina, A.A.; Belov, A.A.; Cheptsov, V.S.; Vetrova, A.A. Beneficial Soil Microorganisms and Their Role in Sustainable Agriculture. Sustainable Agricultural Practices; Academic Press: Cambridge, MA, USA, 2024; pp. 293-333. [DOI: https://dx.doi.org/10.1016/B978-0-443-19150-3.00013-8]

48. Anwar, S.; Liaqat, A.; Munir, A.; Ashraf, M.F.; Iqbal, S. Bioaugmentation of a Novel Bacterial Consortium in Cotton-Planted Soil for Degradation of Lambda-Cyhalothrin. Pedosphere; 2023; in press [DOI: https://dx.doi.org/10.1016/j.pedsph.2023.07.019]

49. Verma, S.; Kuila, A. Bioremediation of Heavy Metals by Microbial Process. Environ. Technol. Innov.; 2019; 14, 100369. [DOI: https://dx.doi.org/10.1016/j.eti.2019.100369]

50. Kebede, G.; Tafese, T.; Abda, E.M.; Kamaraj, M.; Assefa, F. Factors Influencing the Bacterial Bioremediation of Hydrocarbon Contaminants in the Soil: Mechanisms and Impacts. J. Chem.; 2021; 2021, 9823362. [DOI: https://dx.doi.org/10.1155/2021/9823362]

51. Zhang, H.; Yuan, X.; Xiong, T.; Wang, H.; Jiang, L. Bioremediation of Co-Contaminated Soil with Heavy Metals and Pesticides: Influence Factors, Mechanisms and Evaluation Methods. Chem. Eng. J.; 2020; 398, 125657. [DOI: https://dx.doi.org/10.1016/j.cej.2020.125657]

52. Kuppan, N.; Padman, M.; Mahadeva, M.; Srinivasan, S.; Devarajan, R. A Comprehensive Review of Sustainable Bioremediation Techniques: Eco Friendly Solutions for Waste and Pollution Management. Waste Manag. Bull.; 2024; 2, pp. 154-171. [DOI: https://dx.doi.org/10.1016/j.wmb.2024.07.005]

53. Cycoń, M.; Mrozik, A.; Piotrowska-Seget, Z. Bioaugmentation as a Strategy for the Remediation of Pesticide-Polluted Soil: A Review. Chemosphere; 2017; 172, pp. 52-71. [DOI: https://dx.doi.org/10.1016/j.chemosphere.2016.12.129]

54. Hamidi, Y.; Ataei, S.A.; Sarrafi, A. A Highly Efficient Method with Low Energy and Water Consumption in Biodegradation of Total Petroleum Hydrocarbons of Oily Sludge. J. Environ. Manag.; 2021; 293, 112911. [DOI: https://dx.doi.org/10.1016/j.jenvman.2021.112911]

55. Karishma, S.; Saravanan, A.; Deivayanai, V.C.; Ajithkumar, U.; Yaashikaa, P.R.; Vickram, A.S. Emerging Strategies for Enhancing Microbial Degradation of Petroleum Hydrocarbons: Prospects and Challenges. Bioresour. Technol. Rep.; 2024; 26, 101866. [DOI: https://dx.doi.org/10.1016/j.biteb.2024.101866]

56. Ayilara, M.S.; Babalola, O.O. Bioremediation of Environmental Wastes: The Role of Microorganisms. Front. Agron.; 2023; 5, 1183691. [DOI: https://dx.doi.org/10.3389/fagro.2023.1183691]

57. Rajendran, S.; Priya, T.A.K.; Khoo, K.S.; Hoang, T.K.A.; Ng, H.S.; Munawaroh, H.S.H.; Karaman, C.; Orooji, Y.; Show, P.L. A Critical Review on Various Remediation Approaches for Heavy Metal Contaminants Removal from Contaminated Soils. Chemosphere; 2022; 287, 132369. [DOI: https://dx.doi.org/10.1016/j.chemosphere.2021.132369] [PubMed: https://www.ncbi.nlm.nih.gov/pubmed/34582930]

58. Odukkathil, G.; Vasudevan, N. Toxicity and Bioremediation of Pesticides in Agricultural Soil. Rev. Environ. Sci. Biotechnol.; 2013; 12, pp. 421-444. [DOI: https://dx.doi.org/10.1007/s11157-013-9320-4]

59. Sharma, I.; Sharma, S.; Sharma, V.; Singh, A.K.; Sharma, A.; Kumar, A.; Singh, J.; Sharma, A. PGPR-Enabled Bioremediation of Pesticide and Heavy Metal-Contaminated Soil: A Review of Recent Advances and Emerging Challenges. Chemosphere; 2024; 362, 142678. [DOI: https://dx.doi.org/10.1016/j.chemosphere.2024.142678]

60. Gonçalves, C.R.; Delabona, P. da S. Strategies for Bioremediation of Pesticides: Challenges and Perspectives of the Brazilian Scenario for Global Application—A Review. Environ. Adv.; 2022; 8, 100220. [DOI: https://dx.doi.org/10.1016/j.envadv.2022.100220]

61. Stoichev, T.; Mucha, A.P.; Bernabeu, A.; Almeida, C.M.R. Buried and Surface Oil Degradation—Evaluating Bioremediation to Increase PAHs Removal through Linear Mathematical Models. Mar. Pollut. Bull.; 2023; 189, 114727. [DOI: https://dx.doi.org/10.1016/j.marpolbul.2023.114727]

62. Sharma, A.; Singh, S.B.; Sharma, R.; Chaudhary, P.; Pandey, A.K.; Ansari, R.; Vasudevan, V.; Arora, A.; Singh, S.; Saha, S. et al. Enhanced Biodegradation of PAHs by Microbial Consortium with Different Amendment and Their Fate in In-Situ Condition. J. Environ. Manag.; 2016; 181, pp. 728-736. [DOI: https://dx.doi.org/10.1016/j.jenvman.2016.08.024]

63. Nie, M.; Wu, C.; Tang, Y.; Shi, G.; Wang, X.; Hu, C.; Cao, J.; Zhao, X. Selenium and Bacillus Proteolyticus SES Synergistically Enhanced Ryegrass to Remediate Cu–Cd–Cr Contaminated Soil. Environ. Pollut.; 2023; 323, 121272. [DOI: https://dx.doi.org/10.1016/j.envpol.2023.121272]

64. Sun, S.; Wang, Y.; Li, Z.; Zhang, X.; Zhao, C.; Chen, S. Bioremediation Mechanisms of Chlorophenol-Cr(Ⅵ): The Role of Amines, Immobilization, and DEGs in Pseudomonas sp. PC. Chem. Eng. J.; 2024; 497, 154318. [DOI: https://dx.doi.org/10.1016/j.cej.2024.154318]

65. Chen, W.; Li, W.; Wang, T.; Wen, Y.; Shi, W.; Zhang, W.; Guo, B.; Yang, Y. Isolation of Functional Bacterial Strains from Chromium-Contaminated Site and Bioremediation Potentials. J. Environ. Manag.; 2022; 307, 114557. [DOI: https://dx.doi.org/10.1016/j.jenvman.2022.114557] [PubMed: https://www.ncbi.nlm.nih.gov/pubmed/35066197]

66. Wei, T.; Li, X.; Li, H.; Gao, H.; Guo, J.; Li, Y.; Ren, X.; Hua, L.; Jia, H. The Potential Effectiveness of Mixed Bacteria-Loaded Biochar/Activated Carbon to Remediate Cd, Pb Co-Contaminated Soil and Improve the Performance of Pakchoi Plants. J. Hazard. Mater.; 2022; 435, 129006. [DOI: https://dx.doi.org/10.1016/j.jhazmat.2022.129006] [PubMed: https://www.ncbi.nlm.nih.gov/pubmed/35489314]

67. Chen, M.; Li, Y.; Jiang, X.; Zhao, D.; Liu, X.; Zhou, J.; He, Z.; Zheng, C.; Pan, X. Study on Soil Physical Structure after the Bioremediation of Pb Pollution Using Microbial-Induced Carbonate Precipitation Methodology. J. Hazard. Mater.; 2021; 411, 125103. [DOI: https://dx.doi.org/10.1016/j.jhazmat.2021.125103]

68. Lors, C.; Damidot, D.; Ponge, J.F.; Périé, F. Comparison of a Bioremediation Process of PAHs in a PAH-Contaminated Soil at Field and Laboratory Scales. Environ. Pollut.; 2012; 165, pp. 11-17. [DOI: https://dx.doi.org/10.1016/j.envpol.2012.02.004]

69. Zhang, R.H.; Xie, Y.; Zhou, G.; Li, Z.; Ye, A.; Huang, X.; Xie, Y.; Shi, L.; Cao, X.; Zhang, J. et al. The Effects of Short-Term, Long-Term, and Reapplication of Biochar on the Remediation of Heavy Metal-Contaminated Soil. Ecotoxicol. Environ. Saf.; 2022; 248, 114316. [DOI: https://dx.doi.org/10.1016/j.ecoenv.2022.114316]

70. Liu, P.; Zhang, Y.; Tang, Q.; Shi, S. Bioremediation of Metal-Contaminated Soils by Microbially-Induced Carbonate Precipitation and Its Effects on Ecotoxicity and Long-Term Stability. Biochem. Eng. J.; 2021; 166, 107856. [DOI: https://dx.doi.org/10.1016/j.bej.2020.107856]

71. Zou, Y.; Hu, Y.; Li, S.; Huang, X.; Cheng, X.; Pan, W. Remediation of Crude Oil Contaminated Soil through an Integrated Biological-Chemical-Biological Strategy. Sci. Total Environ.; 2024; 919, 170756. [DOI: https://dx.doi.org/10.1016/j.scitotenv.2024.170756]

72. Ma, H.; Zhao, Y.; Yang, K.; Wang, Y.; Zhang, C.; Ji, M. Application Oriented Bioaugmentation Processes: Mechanism, Performance Improvement and Scale-Up. Bioresour. Technol.; 2022; 344, 126192. [DOI: https://dx.doi.org/10.1016/j.biortech.2021.126192]

73. Zhang, M.; Liu, X.; Zhu, W.; Hu, S.; Yan, X.; Hong, Q. Remediation of Isoproturon-Contaminated Soil by Sphingobium sp. Strain YBL2: Bioaugmentation, Detoxification and Community Structure. J. Hazard. Mater.; 2024; 476, 134968. [DOI: https://dx.doi.org/10.1016/j.jhazmat.2024.134968]

74. Chen, T.; Dong, Y.; Huang, W.; Ma, Y. Dynamics of Microbial Community and Functional Genes during Bioremediation of PAHs-Contaminated Soil by Two Biostimulants. Biochem. Eng. J.; 2024; 208, 109356. [DOI: https://dx.doi.org/10.1016/j.bej.2024.109356]

75. Lee, K.C.; Archer, S.D.J.; Kansour, M.K.; Al-Mailem, D.M. Bioremediation of Oily Hypersaline Soil via Autochthonous Bioaugmentation with Halophilic Bacteria and Archaea. Sci. Total Environ.; 2024; 922, 171279. [DOI: https://dx.doi.org/10.1016/j.scitotenv.2024.171279] [PubMed: https://www.ncbi.nlm.nih.gov/pubmed/38428597]

76. Li, C.; Lü, F.; Peng, W.; He, P.; Zhang, H. Efficacy of Bioaugmentation with Nondomesticated Mixed Microbial Consortia under Ammonia Inhibition in Anaerobic Digestion. Bioresour. Technol.; 2024; 391, 129954. [DOI: https://dx.doi.org/10.1016/j.biortech.2023.129954] [PubMed: https://www.ncbi.nlm.nih.gov/pubmed/37914055]

77. Lyu, H.; Hu, K.; Wu, Z.; Shen, B.; Tang, J. Functional Materials Contributing to the Removal of Chlorinated Hydrocarbons from Soil and Groundwater: Classification and Intrinsic Chemical-Biological Removal Mechanisms. Sci. Total Environ.; 2023; 879, 163011. [DOI: https://dx.doi.org/10.1016/j.scitotenv.2023.163011]

78. Helmy, Q.; Kardena, E. Enhancing Field-Scale Bioremediation of Weathered Petroleum Oil-Contaminated Soil with Biocompost as a Bulking Agent. Case Stud. Chem. Environ. Eng.; 2024; 9, 100735. [DOI: https://dx.doi.org/10.1016/j.cscee.2024.100735]

79. Banerjee, A.; Dhal, M.K.; Madhu, K.; Chah, C.N.; Rattan, B.; Katiyar, V.; Sekharan, S.; Sarmah, A.K. Landfill-Mined Soil-like Fraction (LMSF) Use in Biopolymer Composting: Material Pre-Treatment, Bioaugmentation and Agricultural Prospects. Environ. Pollut.; 2024; 355, 124255. [DOI: https://dx.doi.org/10.1016/j.envpol.2024.124255]

80. Zhao, S.; Li, L.L.; Wang, Y.J.; Liu, Z.W.; Yang, S.; Gao, X.; Zhang, C.Y.; Yu, A.F. Remediation of Petroleum-Contaminated Site Soil by Bioaugmentation with Immobilized Bacterial Pellets Stimulated by a Controlled-Release Oxygen Composite. Environ. Pollut.; 2024; 356, 124253. [DOI: https://dx.doi.org/10.1016/j.envpol.2024.124253]

81. Zhao, X.; Cheng, X.; Cai, X.; Wang, S.; Li, J.; Dai, Y.; Jiang, L.; Luo, C.; Zhang, G. SIP-Metagenomics Reveals Key Drivers of Rhizospheric Benzo[a]Pyrene Bioremediation via Bioaugmentation with Indigenous Soil Microbes. Environ. Pollut.; 2024; 360, 124620. [DOI: https://dx.doi.org/10.1016/j.envpol.2024.124620]

82. Martínez-Rabelo, F.; Gómez-Guzmán, L.A.; García-Segura, D.R.; Villegas-García, E.; Rodriguez-Campos, J.; Velázquez-Fernández, J.B.; Hernández-Castellanos, B.; Barois, I.; Contreras-Ramos, S.M. Hydrocarbon Bioremediation in a Pilot-Scale: A Combination of Bioaugmentation, Phytoremediation, and Vermiremediation. Environ. Technol. Innov.; 2023; 31, 103210. [DOI: https://dx.doi.org/10.1016/j.eti.2023.103210]

83. Chakraborty, M.; Sharma, B.; Ghosh, A.; Sah, D.; Rai, J.P.N. Elicitation of E-Waste (Acrylonitrile-Butadiene Styrene) Enriched Soil Bioremediation and Detoxification Using Priestia Aryabhattai MGP1. Environ. Res.; 2023; 238, 117126. [DOI: https://dx.doi.org/10.1016/j.envres.2023.117126]

84. Li, L.; Liu, Y.; Zhang, Y.; Wang, X.; Liu, H.; Liu, Q.; Chen, S.; Zhou, G. Dynamic Responses in Pseudomonas Stutzeri M3 Bioaugmentation of Crude-Oil-Contaminated Soil: Hydrocarbons, Microbial Community Structures, and Functional Genes. J. Environ. Chem. Eng.; 2024; 12, 111863. [DOI: https://dx.doi.org/10.1016/j.jece.2023.111863]

85. Zhang, B.; Xu, W.; Ma, Y.; Gao, X.; Ming, H.; Jia, J. Effects of Bioaugmentation by Isolated Achromobacter Xylosoxidans BP1 on PAHs Degradation and Microbial Community in Contaminated Soil. J. Environ. Manag.; 2023; 334, 117491. [DOI: https://dx.doi.org/10.1016/j.jenvman.2023.117491] [PubMed: https://www.ncbi.nlm.nih.gov/pubmed/36801800]

86. Bao, S.; Zhao, L.; Liu, Y.; Yang, L.; Liu, P.; Chen, C.; Mao, X. Influencing Factors of Bioaugmentation Treatment of PAH-Contaminated Soils in Slurry Bioreactors. J. Environ. Chem. Eng.; 2023; 11, 109893. [DOI: https://dx.doi.org/10.1016/j.jece.2023.109893]

87. Carles, L.; Martin-Laurent, F.; Devers, M.; Spor, A.; Rouard, N.; Beguet, J.; Besse-Hoggan, P.; Batisson, I. Potential of Preventive Bioremediation to Reduce Environmental Contamination by Pesticides in an Agricultural Context: A Case Study with the Herbicide 2,4-D. J. Hazard. Mater.; 2021; 416, 125740. [DOI: https://dx.doi.org/10.1016/j.jhazmat.2021.125740]

88. Romantschuk, M.; Lahti-Leikas, K.; Kontro, M.; Galitskaya, P.; Talvenmäki, H.; Simpanen, S.; Allen, J.A.; Sinkkonen, A. Bioremediation of Contaminated Soil and Groundwater by in Situ Biostimulation. Front. Microbiol.; 2023; 14, 1258148. [DOI: https://dx.doi.org/10.3389/fmicb.2023.1258148]

89. Dos Santos, M.S.N.; Wancura, J.H.C.; Oro, C.E.D.; Dallago, R.M.; Tres, M.V. Opportunities and Challenges of Plant Bioactive Compounds for Food and Agricultural-Related Areas. Phyton-Int. J. Exp. Bot.; 2022; 91, pp. 1105-1127. [DOI: https://dx.doi.org/10.32604/phyton.2022.020913]

90. Raimondo, E.E.; Saez, J.M.; Aparicio, J.D.; Fuentes, M.S.; Benimeli, C.S. Bioremediation of Lindane-Contaminated Soils by Combining of Bioaugmentation and Biostimulation: Effective Scaling-up from Microcosms to Mesocosms. J. Environ. Manag.; 2020; 276, 111309. [DOI: https://dx.doi.org/10.1016/j.jenvman.2020.111309]

91. Curiel-Alegre, S.; Velasco-Arroyo, B.; Rumbo, C.; Khan, A.H.A.; Tamayo-Ramos, J.A.; Rad, C.; Gallego, J.L.R.; Barros, R. Evaluation of Biostimulation, Bioaugmentation, and Organic Amendments Application on the Bioremediation of Recalcitrant Hydrocarbons of Soil. Chemosphere; 2022; 307, 135638. [DOI: https://dx.doi.org/10.1016/j.chemosphere.2022.135638]

92. Bhuyan, B.; Kotoky, R.; Pandey, P. Impacts of Rhizoremediation and Biostimulation on Soil Microbial Community, for Enhanced Degradation of Petroleum Hydrocarbons in Crude Oil-Contaminated Agricultural Soils. Environ. Sci. Pollut. Res.; 2023; 30, pp. 94649-94668. [DOI: https://dx.doi.org/10.1007/s11356-023-29033-3]

93. Qi, X.; Zhu, M.; Yuan, Y.; Dang, Z.; Yin, H. Bioremediation of PBDEs and Heavy Metals Co-Contaminated Soil in e-Waste Dismantling Sites by Pseudomonas Plecoglossicida Assisted with Biochar. J. Hazard. Mater.; 2023; 460, 132408. [DOI: https://dx.doi.org/10.1016/j.jhazmat.2023.132408]

94. Sreekanth, K.; Anjali, P.; Akshatha, B.S.; Alex, R.; Radhakrishnan, E.K. Enhanced Biodegradation of Chlorpyrifos in the Presence of Sub-Inhibitory Concentration of ZnONPs by Pseudomonas sp. CF7b. Process Saf. Environ. Prot.; 2024; 190, pp. 256-263. [DOI: https://dx.doi.org/10.1016/J.PSEP.2024.07.079]

95. Harindintwali, J.D.; Wen, X.; He, C.; Zhao, M.; Wang, J.; Dou, Q.; Xiang, L.; Fu, Y.; Alessi, D.S.; Jiang, X. et al. Synergistic Mitigation of Atrazine-Induced Oxidative Stress on Soybeans in Black Soil Using Biochar and Paenarthrobacter sp. AT5. J. Environ. Manag.; 2024; 359, 120951. [DOI: https://dx.doi.org/10.1016/j.jenvman.2024.120951] [PubMed: https://www.ncbi.nlm.nih.gov/pubmed/38669877]

96. Fan, W.; Xiao, Y.; Cao, B.; Shi, J.; Wu, H.; Shu, S. Comparison of Bioaugmentation and Biostimulation Approaches for Biocementation in Soil Column Experiments. J. Build. Eng.; 2024; 82, 108335. [DOI: https://dx.doi.org/10.1016/j.jobe.2023.108335]

97. Mohammadi, M.; Bayat, Z.; Hassanshahian, M.; Mousavi, M.; Shekarchizadeh, F. Microbial Community Response to Biostimulation and Bioaugmentation in Crude Oil-Polluted Sediments of the Persian Gulf. Environ. Res.; 2024; 249, 118197. [DOI: https://dx.doi.org/10.1016/j.envres.2024.118197]

98. Maluleka, K.; Roopchund, R.; Seedat, N.; Sillanpää, M. Developing a Predictive Machine Learning Model and a Kinetic Model for the Bioremediation of Terrestrial Diesel Spills. Results Eng.; 2024; 23, 102378. [DOI: https://dx.doi.org/10.1016/j.rineng.2024.102378]

99. Liu, Q.; Sun, S.; Chen, S.; Su, Y.; Wang, Y.; Tang, F.; Zhao, C.; Li, L. A Novel Dehydrocoenzyme Activator Combined with a Composite Microbial Agent TY for Enhanced Bioremediation of Crude Oil-Contaminated Soil. J. Environ. Manag.; 2023; 331, 117246. [DOI: https://dx.doi.org/10.1016/j.jenvman.2023.117246]

100. Raimondo, E.E.; Saez, J.M.; Aparicio, J.D.; Fuentes, M.S.; Benimeli, C.S. Coupling of Bioaugmentation and Biostimulation to Improve Lindane Removal from Different Soil Types. Chemosphere; 2020; 238, 124512. [DOI: https://dx.doi.org/10.1016/j.chemosphere.2019.124512]