Pesticides are industrially synthesized chemical compounds, which are broadly applied to agricultural crops to protect them from pests (Zhou et al., 2025). A range of pesticides, for example, organochlorines, organophosphates, carbamates, pyrethroids etc. are frequently used to manage or lessen pest load in agricultural systems (Lin et al., 2020; Zhan et al., 2020). Pesticides are in use in agriculture since several years, and the earliest pesticide to be synthesized was dichloro-diphenyl-trichloroethane (DDT). After twenty years of its invention, its use was prohibited in agricultural ecosystems (Egbuna and Sawicka, 2020). Ever since then, numerous other pesticides have been introduced in the market globally, majority of them claiming to be harmless. The application of pesticides has increased dramatically to ensure adequate food for an ever-expanding population (Aryal and Aryal, 2023). India, where the greater part of the population is reliant on agriculture, has experienced a considerable increase in pesticide consumption over time (Kashyap et al., 2024). In 2023, the gross amount of pesticides employed in the farming sector globally was around 3.728 million tonnes, with an average application to crops around 2.40 kg/ha (FAOSTAT, 2023). Out of 3.728 million tonnes of total pesticides used, herbicides constituted approximately 2.009, insecticides 0.759, fungicides and bactericides 0.778, rodenticides 0.017 and other pesticides 0.114 million tonnes (FAOSTAT, 2023). Brazil, United States, Indonesia, Argentina, China, Australia, Vietnam, Russia Federation, Canada and France are the top 10 countries in agricultural consumption of pesticides worldwide (Sasu, 2025). There are certain pesticides whose products have either deteriorated, been banned, or were procured in excess, and hence they are no longer in use (called obsolete pesticides). The total quantity of such pesticides in developing countries is around 400,000–500,000 tonnes. For example, use of DDT is banned worldwide under the Stockholm Convention but in India, its restricted use for public health programs (e.g., malaria control) is allowed up to 10,000 metric tonnes yearly under stringent governmental administration. Similarly, a study reported that approximately 146,000 tonnes of pesticides were banned in European Union but they were being used in United States in 2016 (Donley, 2019). In 2024, nearly 122,000 tonnes of banned pesticides were permitted for export from the European Union, including 1, 3-dichloropropene: over 20,000 tonnes, Glufosinate: almost 20,000 tonnes and Mancozeb: more than 8,500 tonnes (Fleck, 2025).

Nearly ≤5% of the total used pesticides inhibits the targeted pest organisms, whereas left over >95% of these pesticides do not reach the designated pests. Subsequently, the remains of the pesticides are accumulated in the adjacent environments, get mixed with water and soil and contaminate them (Sarker et al., 2021). Pesticide remains have damaging impacts on diverse life forms and ecosystems (Yadav and Devi, 2017) because of their persistent and bio-magnification properties. Pesticides frequently pollute water, soil and air, leading to long-lasting damage to environment and a major threat to human health (Rani et al., 2021; Mukherjee et al., 2024), even in minute traces. Approximately 2.2 million people, generally from developing countries, are at larger risk from pesticide exposure (Kaur et al., 2019). According to World Health Organization (WHO), pesticides are accountable for roughly three million people suffering from poisoning and 2,00,000 deaths yearly (López-Benítez et al., 2024). Furthermore, rigorous use of pesticides has caused surface and groundwater pollution (Dhankhar and Kumar, 2023), ensuing from agricultural runoff, with their subsequent percolation into the soil (Sharma et al., 2019a), as well as contaminating the marine ecosystem. Pesticides are also harmful for the plants (Dreistadt, 2016) and get distributed via food webs (Kumar et al., 2021a). Several regulations/guidelines have been recommended to evaluate human health risks and environmental effects emanating from the use of extremely lethal and persistent pesticides, to restrain their market value, and to ensure proper control of their residues. International organizations, for instance, World Health Organization (WHO), Food and Agriculture Organization (FAO) and Environmental Protection Agency (EPA) have established legal guidelines for pesticide regulation (Naidenko, 2020). In spite of these regulatory attempts, pesticide pollution remains a universal challenge, especially for developing nations, where pesticide use is continuously rising without proper regulation (Zikankuba et al., 2019). Therefore, developing potent and sustainable means for pesticide degradation is important for mitigation of their harmful impacts and protection of natural resources.

Various methods of remediation have been developed, which are largely based on the type and class of pollutants (Karimi et al., 2022; Mahalle et al., 2025). Pesticides present in the soil can be degraded by several ways; the conventional methods include physical, chemical, and physio-chemical degradation, which mostly result in secondary pollution (Karimi et al., 2022). Bioremediation is a broadly recognized, environment-friendly, and sustainable method of depolluting a contaminated environment (Bokade et al., 2021). Microorganisms have great resilience, biochemical flexibility, functional diversity, and employ diverse kinds of metabolisms to degrade pesticides, which they use as source of nitrogen, carbon, phosphorus and energy (Kumar et al., 2021b; Rodríguez et al., 2020). In general, microbes metabolize pesticides in two ways, (1) complete breakdown of the compounds or (2) mineralization of pesticides, in which majority of the by-products are fit for release into the environment (Dar et al., 2022). Additionally, biodegradation of pesticides is less costly than traditional approaches, which makes it economically feasible, and the by-products released are almost harmless to the environment (Carles et al., 2021; Dar et al., 2022). According to the US Environmental Protection Agency (USEPA), bioremediation is a useful and eco-friendly approach for restoring polluted environments and boosting sustainable development (Kour et al., 2022). Diverse microorganisms have an inherent capability to degrade pesticides, including bacteria (Bacillus, Pseudomonas, Arthrobacter, Acinetobacter, Serratia), actinomycetes (Streptomyces), archaea (Sulfolobus, Methanobacterium), fungi (Aspergillus, Penicillium, Trichoderma), and algae (Chlorella, Chlamydomonas) (Guerrero Ramírez et al., 2023; Aparici-Carratalá et al., 2023; Dinakarkumar et al., 2024; Akmukhanova et al., 2025). Nevertheless, the slow efficiency of these microbes, coupled with a complex and unstable natural environment, may influence the viability and efficiency of microbe-mediated degradation of pesticides. Therefore, there is a dire need to create genetically engineered microorganisms (GEMs) to increase the production of genes and their products with an aim to enhance their pesticide degradation potential.

Several reviews highlighting the potential use of microorganisms in pesticide degradation are available in the literature. However, a review on the genetic manipulation of microbes to increase their pesticide degradation capability in agricultural soil ecosystems has not been performed. Such a review would aid in identifying the potential of microbial engineering technology and examine the existing information, thereby assisting in the development of effective remediation approaches for agricultural soils. This review aimed to gather and analyze scientific research conducted on the use of genetic engineering for producing GEMs, along with the advantages of using microbial consortia as an alternative to conventional technologies for the degradation of pesticides in agricultural soils. The examination of the collected literature facilitated exploring whether the use of GEMs is financially feasible to improve the efficiency of pesticide degradation. This review provides a holistic perspective on the impacts of pesticides on growth and metabolism of crop plants, conventional approaches employed for microbe-mediated degradation of pesticides, how genetic manipulation in microbes can be efficiently utilized in pesticide bioremediation, benefits of using microbial consortia for pesticide degradation, advantages of microbial engineering for environment and economic benefits, thereby identifying new research opportunities and establishing novel practical applications. To achieve the aim, a comprehensive meta-analysis of relevant literature was conducted. We focused on microbiome engineering, microbial pesticides, rhizosphere and patents related to microbial pesticides and their biodegradation properties. The primary databases used for searching literature included Web of Science, PubMed, Scopus, and others. This approach enabled a structured evaluation of existing knowledge, while also highlighting opportunities for future research and innovation.

Pesticides can deliver agronomic benefits when used in appropriate amounts. Seed treatments suppress early seed- and soil-borne pests and pathogens, improve seedling emergence and establishment, and grain yield in winter wheat under real field conditions (Turkington et al., 2016). Strobilurin fungicides have also been shown to improve nitrogen use efficiency and support yield and protein targets in durum wheat grown under rainfed Mediterranean conditions, consistent with better maintenance of green area and delayed senescence reported for this fungicide class (Carucci et al., 2020). The defence activator acibenzolar-S-methyl (ASM) primes systemic acquired resistance and can reduce disease severity and spray intensity, an effect confirmed in Arabidopsis and reviewed across crops (Ito et al., 2024). Herbicide safeners have been reported to assist crops in tolerating herbicides by inducing detoxification pathways such as glutathione S-transferases (GSTs), UDP-glycosyltransferases (UGTs), and ABC transporters, thereby reducing crop injury (Dimaano and Iwakami, 2021; Deng, 2022). However, pesticide residues in harvested commodities introduce a food-safety dimension. Although processing steps, such as washing, peeling, and thermal treatment, cause reduction in residues (Kim et al., 2017; García-Vara et al., 2022), still they may be present in alarming levels. Current European surveillance indicated that 3.9% of 87,863 samples exceeded maximum residue limits in 2021 and 3.7% of 110,829 samples in 2022 (EFSA et al., 2023, 2024).

Despite their positive role, pesticides can have negative effects on plant growth and metabolism when applied incorrectly or in excessive amounts (Alengebawy et al., 2021) (Table 1; Figure 1). Studies have documented reduced biomass, altered phenology and architecture, visible injury such as chlorosis and necrosis, and hormonal disruptions affecting auxins, cytokinins, gibberellins, ethylene, and abscisic acid in response to excess pesticide applications (Sharma et al., 2019b; Mukherjee et al., 2022; Guedes et al., 2023; Virk et al., 2024). Mechanistically, many pesticides impair photosynthetic machinery, reduce pigment pools, and trigger oxidative stress that damages membranes and disrupts carbon and nitrogen metabolism (Zhang et al., 2019; Hasanuzzaman et al., 2020; Hatamleh et al., 2022; Traxler et al., 2023). Experimental work demonstrates that chlorophyll fluorescence (PSII) and chlorophyll content can decline after neonicotinoid exposure in crops and seedlings, resulting in associated yield penalties, as observed in long-term studies in chickpea and lettuce (Liu et al., 2021; Shahid et al., 2021). These physiological changes are consistent with earlier canopy senescence and reduced photosynthetic capacity under stress (Hasanuzzaman et al., 2020). Organophosphates exemplify redox-driven phytotoxicity. In rice, sub-chronic chlorpyrifos exposure perturbed physiology and induced oxidative stress (Mu et al., 2022). In maize also, chlorpyrifos caused toxicity, however, soil amendments such as biochar and compost mitigated pigment loss, membrane damage, and oxidative markers (Aziz et al., 2021). These effects lead to yield loses through smaller or prematurely senescing canopies and impaired photochemistry that lower radiation-use efficiency. Beyond direct plant effects, pesticides also reshape soil biology. Studies have reported reductions in microbial biomass and shifts in community structure, as well as suppression of soil enzymes, including dehydrogenases, β-glucosidases, and phosphatases, which regulate nutrient cycling and rhizosphere signalling (Walder et al., 2022; Hou et al., 2011; Ghosh et al., 2023; Daunoras et al., 2024). Table 2 summarizes some studies demonstrating the effects of various pesticides on different plants. Thus, while pesticides play a role in crop protection, their adverse impacts on plant growth and metabolism necessitate careful management and adoption of sustainable practices.

The widespread use of chemical pesticides has led to significant adverse impacts on the environment, prompting the use of various physico-chemical and microbial techniques to eliminate pesticide contamination. However, compared to physico-chemical methods, microbial approaches have proven to be more robust and effective due to their efficiency and eco-friendly nature. From a microbiological perspective, many researchers have focused on axenic cultures for studying microbial pesticide degradation (Qian et al., 2019). Various gene expression pathways, metabolic pathways, and functional proteins have been identified in culturable microbes, which play a pivotal role in pesticide degradation. However, studies suggest that combined microbial applications exhibit a higher level of bioremediation efficiency compared to monoculture approaches (Lee et al., 2018; Qian et al., 2019; Bhatt et al., 2021; Zhang and Zhang, 2022). Traditional metabolic engineering using pure cultures provides essential insights into microbial pathways and their key metabolic products (Lopes et al., 2022). The absence of genes and enzymes in silent metabolic pathways, along with stringent culture requirements, significantly limits yield and productivity of metabolic products (Bhatia et al., 2018). Various commercially available pure-cultured microbes have been used on a large scale as bio-decontaminating and soil- conditioning agents. However, literature suggests that approximately 99% of environmentally friendly microbes cannot be cultivated in laboratories using traditional techniques (Egelkamp et al., 2019).

Researchers have suggested that microbial consortia from diverse environments holds strong potential for degrading toxic chemical pesticides compared to single microbes (Qian et al., 2019). Previously, microbiologists have employed various genetic engineering approaches to upregulate biomolecules; however, these efforts have only achieved limited success for commercialization in large-scale remediation (Rebello et al., 2021). One major limitation of using a single microbial strain for pesticide toxicity reduction is its metabolic burden. Due to limited resources, a single strain is often unable to perform multiple tasks simultaneously. Pesticide-induced toxicity causes cellular stress, prompting the host cell to consume increased amounts of energy in the form of NADH (nicotinamide adenine dinucleotide) and ATP (adenosine triphosphate) (He et al., 2017; Vermelho et al., 2024). Pesticide-degrading microbial strains synthesize these energy-rich molecules through universal metabolic pathways (He et al., 2017). The combined effects of metabolic burden and cellular stress lead to a significant decline in microbial biosynthesis, a phenomenon known as metabolic cliff (Vermelho et al., 2024). To address the limitations of single microbial strains, microbiologists have developed an alternative approach known as microbial consortium strategy (Nunes et al., 2024). In terms of metabolic pathways, single eukaryotic strain often perform better due to compartmentalization within the eukaryotic cell, which plays a crucial role in mitigating the effects of the metabolic cliff. In microbial consortia, various strains coordinate through a division of labour, with each member assigned a distinct metabolic role. Some members are responsible for pesticide bioremediation, while others play a pivotal role in regulating the production of biochemical compounds within the cells (Ram et al., 2022; Nunes et al., 2024). Therefore, microbial consortia offer the most effective solution for pesticide degradation and managing metabolic load in contaminated environment (Li et al., 2022).

Various studies have demonstrated that microbial consortia can rapidly degrade pesticides in a better way compared to single microorganism (Roell et al., 2019) (Table 3). Mixed microbial strains have been shown to perform complex tasks more effectively than individual strains (Nunes et al., 2024). In pesticide degradation, these consortia enhance efficiency by sharing metabolic responsibilities through interconnected degradation pathways. Each strain within the consortium can independently carry out specific steps in the degradation process—tasks that may be too complex for a single strain to handle alone. In natural environments, microbial consortia exhibit greater resilience to environmental fluctuations compared to individual strains. They also tend to resist invasion by foreign microbial species more effectively (Harcombe et al., 2018). A crucial factor in the functionality of these consortia is intercellular communication, which defines the role of each strain during degradation. The primary mechanism for such coordination is quorum sensing (QS), wherein bacterial cells produce and respond to signalling molecules, primarily lactones that serve as diffusible signals. It has been reported that inoculation with a microbial consortium in different soil samples enhanced plant growth and pollutant remediation by approximately 48 and 80%, respectively, whereas inoculation with a single microbial strain resulted in only about 29 and 48% improvement in plant growth and pollutant remediation, respectively (Liu et al., 2023). As per the high rate of environmental remediation processes is concerned, microbial consortia is commonly used than the single strain. The microbial consortia have been reported to exhibit a higher degradation capacity for toxic compounds in soil and sewage compared to single microbial strain applications. Reports also suggest that consortia-treated soil significantly enhances the growth and vigor of various shrubs and trees, while consortia-treated sewage water can be safely utilized for irrigating non-edible commercial crops (Biswas et al., 2021). Microbial consortia possess a superior ability to degrade complex compounds such as starch and cellulose, which cannot be efficiently broken down by a single strain. Within the consortium, different microbial strains work synergistically—some degrade these complex polymers into simpler sugars, which then serve as carbon sources for other microorganisms in the group (Wang S. et al., 2019; Tondro et al., 2020).

Książek-Trela et al. (2025) reported a high degradation rate of herbicide diflufenican (DFF) (approximately 70.1%) when a single strain, Streptomyces atratus (strain ROA017-D1), was inoculated in a liquid medium. However, in the same medium, supplementation of a synthetic bacterial consortium consisting of four strains—Pseudomonas sp. 10Kp8 (A1), Pseudomonas chlororaphis subsp. aureofaciens strain B19 (A2), Pseudomonas baetica strain JZY4-9 (C1), and Streptomyces atratus strain ROA017 (D1)—resulted in a higher degradation rate of DFF, reaching about 74.4%. Furthermore, the application of strain D1 alone in soil medium achieved approximately 79% degradation of DFF, whereas the consortium of four strains exhibited the highest degradation efficiency, reaching around 82.2%. The researchers explained that consortium-based biodegradation of DFF proceeded through three sequential steps: (a) Step I (Initiation Phase) was mediated by Pseudomonas sp. 10Kp8 (A1) and Pseudomonas chlororaphis subsp. aureofaciens B19 (A2). These metabolically versatile strains employed monooxygenases, dioxygenases, and amidases to initiate DFF transformation through aromatic ring hydroxylation and amide bond cleavage, generating less toxic, more polar intermediates that were accessible to downstream degraders; (b) In Step II (Defluorination and Intermediate Transformation), Pseudomonas baetica strain JZY4-9 (C1) further metabolized these intermediates. This strain facilitated reductive or co-metabolic defluorination and additional ring-cleavage reactions, converting fluorinated pyridine derivatives into simpler, low-molecular-weight organic acids and preventing the accumulation of persistent metabolites; (c) The final phase, Step III (Mineralization), was carried out by Streptomyces atratus strain ROA017 (D1). This actinomycete produced extracellular oxidative and hydrolytic enzymes, including laccases and peroxidases, which enabled complete breakdown of residual aromatic structures and mineralization into CO₂, H₂O, NH₄⁺, and simple organic acids (Książek-Trela et al., 2025). Overall, the enhanced degradation of DFF by this four-member consortium resulted from sequential and complementary metabolic interactions, wherein Pseudomonas strains initiated transformation, P. baetica detoxified fluorinated intermediates, and S. atratus completed mineralization. This cooperative mechanism underscores the ecological and biotechnological potential of microbial consortia for bioremediation of persistent fluorinated herbicides.

Communication within the consortium often occurs through biofilm formation, enabling efficient cell-to-cell signalling—an essential feature for the development of synthetic microbial consortia. This intercellular communication system is modular and engineerable, offering a foundation for the rational design of synthetic consortia. However, consortia are not always beneficial; in some cases, they may produce inhibitory compounds that are toxic to the member strains, impeding their growth and functionality. Therefore, careful design and selection of strains is critical for developing effective and stable microbial consortia for pesticide degradation.

Advancements in recent technologies for the degradation of pesticides have led to the clean-up of various habitats due to the sheer limitations in conventional procedures. Microbes play pivotal roles in growth and development of plants, animals and other microbes (Góngora-Echeverría et al., 2020; Bhatt et al., 2021; Ali et al., 2022; Gul et al., 2023; Tyagi et al., 2024). Hence, using and manipulating the genetic information of microbes plays a pivotal role in mitigating the eco-toxicity mediated by pesticides, which in turn leads to various diseases in humans. Recent approaches have focussed on the production of genetically engineered microorganisms (GEMs) to increase the production of genes and their products with an aim to degrade a specific type of pesticide (Rafeeq et al., 2023) (Figure 3). The alteration of microbial strains for the breakdown of the pollutants is believed to be an effective solution for the ineffective decomposition of pollutants by traditional approaches (Mishra et al., 2020; Peng et al., 2020).

Pesticides such as organophosphates (OP) and organochlorines (OC) are persistent hazards that have significant negative impacts on human health and also destabilize the environmental homeostasis. For instance, the OPs act as potent neurotoxins by inhibiting the enzyme acetylcholine esterase (Singh and Verma, 2024). Additionally, the Hexachlorocyclohexane (HCH) is reported to accumulate and severely impair the functioning of kidneys, nervous system and liver (Yadav and Kumar, 2024). A wide range of research supports the existence of genes critical for catabolizing OPs from various habitats (Table 4). The bacterial enzymes are the major players in detoxifying pesticides effectively and at low costs. For example, ethyl parathion degrading enzyme (mpd) encoded by Plesiomonas sp. strain genome is able to hydrolyse a wide range of thion and oxon OPs (Khan et al., 2025; Mahmoud A. M. et al., 2025; Mahmoud G. A. E. et al., 2025). Methyl parathion hydrolase (MPH) enzyme targets the central phosphorus atom of organophosphates and break phosphoester bond in specific P-O or P-S aryl bond (Dong et al., 2005). Upon binding to OPs, such as ethyl parathion or methyl parathion, the phosphate group is removed by using a water molecule in active site through nucleophilic attack. This leads to hydrolytic cleavage of P–O bond (the aryl ester bond) leading to the formation of less toxic by products such as, 4-Nitrophenol (p-nitrophenol) and diethyl thiophosphate from ethyl parathion or dimethyl thiophosphate from methyl parathion (Mahmoud A. M. et al., 2025; Mahmoud G. A. E. et al., 2025). Additionally, the mpd produced by bacteria can use pesticides as their nutritive source. Researchers have engineered Sphingomonas sp. with gene encoding mpd (methyl parathion hydrolase) derived from Pseudomonas putida to degrade OP and carbamate pesticides in a wide range of habitats (Xu et al., 2020). Similarly, the gene pytH encoding a non-specific carboxylase esterase was cloned from Sphingobium sp. strain JZ-1 to degrade wide variety of pyrethroids (Xu et al., 2020). This enzyme with a molecular weight of 31kDA, belonging to alpha/beta-hydrolase (ABH) fold superfamily, consists of catalytic triad of Ser78, His230, and Asp202 in its active side (Xu et al., 2020). Further, the hydrophobic pocket in pytH enzyme which is large and deep consisting of 29 amino acid residues, allows this enzyme to accommodate complex and bulky pesticides such as bifenthrin and permethrins for degradation (Xu et al., 2020). The His230 residue in catalytic pocket of pytH deprotonates hydroxyl group of Ser78, which in turn performs nucleophilic attack on carbonyl carbon of the pyrethroid’s ester bond (Xu et al., 2020). The resulting tetrahedral transition state is further stabilized by “oxyanion hole,” consisting of nitrogen atoms as backbone. Later mechanism leads to the release of alcohol moity (3-phenoxybenzyl alcohol) from pesticide, whereas the acid moity remains covalently attached to the enzyme. Further, the deprotonated His230 becomes hydroxide ion, which in turn attacks the acyl-enzyme intermediate to create a second tetrahedral intermediate. Subsequently, the intermediate collapses and releases the acid moity to restore the native state of pytH enzyme (Xu et al., 2020). The pytH enzyme has wide range of effectiveness against various pyrethroids such as, deltamethrin, permethrin and cypermethrin. In addition, pytH does not show specificities to chiral isomers, evolving it as a robust tool for complete detoxification of pesticides (Zhan et al., 2020).

Genes coding for carbofuran hydrolase (mcd) and carbaryl hydrolase (cehA) were also cloned from Achromobacter sp. strain WM111 and Rhizobium sp. strain AC100, respectively, for pesticide degradation (Zhu et al., 2018). Previously, researchers identified oxon and thion organophosphates (OPs) degrading enzymes encoded by Plesiomonas sp. strain. Also the OCs degrading gene linA coding enzyme γ-hexachlorocyclohexane dehydrochlorinase from Sphingomonas paucimobilis UT26 has been reported to catalyse the γ-hexachlorocyclohexane (γ-HCH) to 1,2,4-trichloro benzene (1,2,4-TCB) via γ-1,3,4,5,6-pentachlorocyclo hexene (γ-PCCH) (Deng et al., 2024). The construction of a recombinant E. coli strain overexpressing the enzyme methyl parathion hydrolase (MPH) was able to efficiently degrade methyl parathion (Xu et al., 2022). Yang et al. (2012) constructed the genetically engineered E. coli strain expressing both MPH and LinA aimed to degrade the OPs and OCs with ease and efficiency. The genetically modified E. coli constructed to express fusion protein of Enhanced Green Fluorescent Protein (EGFP) and an Organophosphate Hydrolase (OPH), exhibited strong hydrolase activity to degrade the organophosphorus pesticide in the environment (Lourthuraj et al., 2022). In conclusion, nature has endowed us with huge number of microbiomes that could be manipulated to eradicate the toxic metabolites from the environment. These GEMs can play pivotal role in decreasing the concentration of pesticides in food webs.

Organochlorine pesticides (OCPs) are also persistent pollutants that have drawn much attention due to their toxic and persistent biological effects (Liu et al., 2025; de Souza Pomacena et al., 2025; Wang et al., 2024). Among all the existing organochlorine pesticides, the aldrin, α-, β-, and γ-hexachlorocyclohexane (HCH), 1,1,1-trichloro-2,2-bis(4-chlorophenyl) ethane (DDT), chlordecone, chlordane, dieldrin, endrin, heptachlor, hexachlorobenzene (HCB), mirex, pentachlorobenzene, and toxaphene are the most dominantly affecting the living systems (Tzanetou and Karasali, 2022). These OCPs have been proven to be hormone disruptors in humans. Several studies have been carried out to devise strategies for degrading the OCPs in environment. Further, a large number of genes have been reported to degrade a wide range of OCPs (Table 4). For instance, the gene linA coding for dehydrochlorinase derived from Pseudomonas paucimobilis UT26 was cloned into Escherichia coli to mediate the degradation of γ-HCH to 1,3,5, or 1,2,4-trichlorobenzene via tetrachorohexadiene (TCDN) and γ-pentachlorocyclohexane (γ-PCCH) (Yusuf et al., 2023: Deng et al., 2024). LinA (member of NTF2-like superfamily) mediates its enzymatic activity through stereochemical arrangement of its substrates. This enzyme requires 1, 2-trans-diaxial arrangement coordinated between hydrogen and chlorine atoms on the cyclohexane ring (Trantı́rek et al., 2001). The active site of LinA consists of catalytic dyad formed by Asp25 and His73, whereas His73 acts as a catalytic base for the removal of protons from the pesticide substrate (Manna et al., 2015). During this E2 elimination mechanism, the chloride ion is removed from the opposite rings to form carbon–carbon double bond. The LinA catalyses the initial dehydrochlorination of γ-hexachlorocyclohexane (γ-HCH) to form γ-pentachlorocyclohexene (γ-PCCH). Consequently, three axial chlorine substituents in γ-HCH, two distinct 1,2-diaxial H–Cl pairs are available for elimination to aid catalysis. Further, the LinA exhibits stringent stereochemical control by selectively targeting one of these pairs, resulting in the formation of a single, well-defined enantiomer of γ-PCCH. In a subsequent reaction, LinA catalyses a second dehydrochlorination, and removes an additional HCl moiety from γ-PCCH to produce 1,3,4,6-tetrachloro-1,4-cyclohexadiene (1,4-TCDN). The outcome of this step is to increase the degree of unsaturation of the cyclohexane ring through incorporation of a second double bond. The resulting metabolite, 1,2,4-trichlorobenzene (1,2,4-TCB), is converted to less toxic chlorinated catechols (like 3,4,6-trichlorocatechol) by enzymes chlorobenzene dioxygenase/monooxygenase, which introduces hydroxyl groups to 1,2,4-TCB ring. Subsequently, the dihydrodiol dehydrogenase rearomatizes the dihydrodiol intermediate. The later product is further degraded by chlorocatechol-1,2-dioxygenase (TcbC) to catechol ring (Brahushi et al., 2017).

Previous studies revealed that genes LinA1 and LinA2 encoding two variants of hexachlorocyclohexane dehydrochlorinase are responsible for degradation of lindane (Heeb et al., 2021; Deng et al., 2024). In another study, Cupriavidus necator JMP134 was reported to degrade 2,4-D by stepwise conversion from 2,4-dichlorophenol (2,4-DCP) by 2,4-D dioxygenase encoded by TfdA gene, and 2,4-DCP was further degraded to β-ketoadipate by 2,4-DCP hydroxylase encoded by TfdB, chlorocatechol dioxygenase encoded by TfdC, chloromuconate cycloisomerase encoded by TfdD, dienelactone hydrolase encoded by TfdE, and chloromaleylacetate reductase encoded by TfdF gene. The end-product β-Ketoadipate was shuttled to tricarboxylic acid (TCA) cycle for further metabolism (Pettinato et al., 2022). The hydrolases encoded by atzABCDEF, located on 108-kb IncP-1 β plasmid pADP-1 of Pseudomonas sp. strain ADP was reported to degrade the atrazine in six steps (Medić and Karadžić, 2022). Different groups of researchers have engineered Pseudomonas putida KT2440 to mineralize pesticides such as 1,2-dichloroethane (DCA), 1,2,3-trichloropropane (TCP), γ-hexachlorocyclohexane (γ-HCH), p-nitrophenol (PNP) and methyl parathion (MP) (Gong et al., 2016; Zhao et al., 2021; Huo et al., 2022, 2023). Wang et al. (2024) produced a novel E. coli strain BL-3164 by reconstructing pET-3164 plasmid containing a complete set of genes responsible for degradation of 2, 4-D. Recently, Xiong et al. (2025) engineered Halomonas cupida for efficient mineralization of 2,4-D in highly saline waste waters. These studies clearly indicate the repository of genes from natural sources that could be exploited to regulate the levels of pesticides in natural habitats.

The heterologous expression of carboxylesterase B1 (CarE B1) gene, derived from mosquito Culex pipiens quinquefasciatus was employed to degrade pesticides such as, pyrethroids and organochlorines (Li Q. et al., 2020). The CarE B1 enzyme catalyses the hydrolysis of ester bonds found in pesticides. For instance, the cleavage of ester linkages in organophosphates and carbamates neutralizes their neurotoxic potential. Similarly, CarE B1 enzyme breaks pyrethroids and organochlorines into less toxic polar metabolites. The neurotoxic organophosphates such as, chlorpyrifos, parathion can be degraded by employing GEMs such as Escherichia coli and Pseudomonas putida overexpressing opd gene derived from Flavobacterium or Pseudomonas. The opd genes targeted to periplasm or cell surface of GEMs encodes organophosphorus hydrolase (OPH) which cleaves phosphotriester bond in pesticides for detoxification (Li Q. et al., 2020). GEMs, such as, Bacillus subtilis have been genetically modified to express gat gene encoding glyphosate N-acetyltransferase and gox encoding glyphosate oxidoreductase. The glyphosate N-acetyltransferase catalyses the transfer of acetyl groups to pesticides making them less toxic to plant and animal systems. Similarly, the gox gene product glyphosate oxidoreductase cleaves C-N bonds in pesticides to produce glyoxylate and aminomethylphosphonic acid (AMPA).

The pyrethriods and carbamamte pesticides are degraded by GEMs Bacillus megaterium and Pichia pastoris (yeast) overexpressing mpd derived from insects. The mpd enzyme hydrolyzes the ester linkage resulting in reduction of half life of pesticides such as, cypermethrin and fenpropathrin (Tutika and Himabindu, 2025). Overall, the construction of GEMs plays a pivotal role in clearing pesticides from the environment. The emerging techniques, such as antioxidant systems, use of microbial consortia and genome editing techniques such as CRIPSR/Cas systems, could be utilized to engineer the microbial genomes to mitigate the ecotoxicity induced by pesticides in a wide range of habitats (Barooah and Hazarika, 2022).

Pesticide contamination in soil is a significant environmental and agricultural challenge, leading to long-term ecological damage, reduced soil fertility, and risks to human and animal health (Zhou et al., 2025). Traditional methods for pesticide remediation, such as soil excavation, chemical treatments, or thermal desorption, are often expensive, inefficient, and environmentally disruptive (Liu M. et al., 2024). In contrast, microbial engineering offers a promising, sustainable, and cost-effective solution for cleaning pesticide residues in soil (Pant et al., 2021). Microbial engineering involves modifying microorganisms, often bacteria, actinomycetes, and fungi, through genetic or synthetic biological techniques to enhance their natural capacity to degrade toxic compounds. One of its primary advantages is the targeted degradation of persistent organic pollutants (POPs) such as organophosphates, carbamates, and chlorinated pesticides. Engineered microbes can break down these compounds into harmless substances, significantly reducing environmental toxicity (Kumar et al., 2025; Sadiq et al., 2025). Liu et al. (2016) developed a genetically modified strain of Pseudomonas putida capable of degrading chlorpyrifos, a widely used organophosphate pesticide. The engineered strain showed very good degradation efficiency, outperforming native microbial populations. Similarly, recently, Bacillus subtilis strains engineered to express organophosphorus hydrolase (OPH) have shown enhanced capability to detoxify various pesticides (Bahrulolum and Ahmadian, 2025). Li Q. et al. (2020) constructed a genetically engineered bacterium having the ability to degrade pesticides like organochloride, organophosphorus, carbamates, and pyrethoid insecticides. Another advantage of microbial engineering is its role in restoring soil health and biodiversity. Unlike harsh physical or chemical remediation techniques, bioengineered microbes can detoxify pollutants while maintaining or even improving soil structure and microbial diversity. This helps preserve beneficial soil functions, including nutrient cycling and plant-microbe interactions, which are essential for sustainable agriculture (Rebello et al., 2021; Karnwal et al., 2025). Engineered microbes can also be designed for enhanced survival and activity in harsh soil conditions, such as extreme pH or temperature, where natural strains may fail. Through synthetic biology, traits such as stress resistance, biofilm formation, or root colonization can be introduced to improve microbial persistence and effectiveness in contaminated fields (Sudheer et al., 2020; Misu et al., 2025). Additionally, microbial engineering enables precision biodegradation, where specific enzymes are optimized or overexpressed to target particular pesticide molecules. This selective degradation reduces the risk of non-specific microbial activity that might otherwise affect non-target compounds or disrupts soil ecosystems (Bittencourt et al., 2023; Qattan, 2025).

The economic viability of using engineered microbes is another key advantage. Compared to mechanical or chemical methods, microbial solutions are relatively low-cost, scalable, and require minimal labour or infrastructure. Once established, these microbes can continue to function over extended periods, providing long-term soil decontamination (Wend et al., 2024; Luan et al., 2025). In agriculture, engineered microbes are revolutionizing crop production. For instance, genetically modified rhizobacteria can enhance nitrogen fixation in non-leguminous crops like wheat and maize. This innovation reduces the dependency on synthetic nitrogen fertilizers, which are both costly and damaging to environment (Mayung, 2024). According to Kumar S. et al. (2022), deploying engineered Azospirillum strains in Indian wheat fields reduced fertilizer usage by up to 40%, saving farmers an estimated $75 per hectare. Similarly, engineered phosphate-solubilizing bacteria are improving nutrient availability, cutting back on the use of expensive phosphate fertilizers (Guo et al., 2023). Another economic advantage lies in pest and disease control. Engineered microbes such as Bacillus thuringiensis (Bt) and other biocontrol agents can be tailored for targeted pathogen suppression, reducing the need for chemical pesticides. This not only lowers input costs but also boosts crop quality and export potential. A study by Abbey et al. (2021) demonstrated that using a microbial bio-fungicide in blueberry farming resulted in a 20% yield increase and a significant reduction in fungicide expenditures.

Despite these benefits, regulatory hurdles, biosafety concerns, and public perception of GEMs remain a big challenge. However, new developments in bio-containment strategies, such as genetic kill-switches or dependency on synthetic nutrients, are helping to address these issues and improve environmental safety (Lea-Smith et al., 2025). Finally, it can be concluded that microbial engineering offers a highly effective and environment friendly approach for cleaning pesticide-contaminated soils. Its ability to degrade persistent pesticides, restore soil quality, and offer long-term, cost-effective remediation makes it a vital tool in the movement toward sustainable agriculture and environmental health.

Recent advances in microbial biotechnology and genetic engineering offer transformative opportunities for sustainable pesticide remediation in agricultural soils. Several innovations emerging from this field can be translated into patentable technologies and scalable applications.

Microorganisms cause breakdown of the pesticide residues in soil, are inexpensive, environment friendly and do not cause secondary pollution. But their slow rate of pesticide degradation may affect the practicability and efficiency. Research on microbe-assisted degradation of pesticides has been largely conducted. Many pesticide-degrading microbial strains have been identified; however, the practical application of microbial bioremediation is restricted. The key challenges involving microbial degradation of pesticides include the development of highly efficient pesticide-degrading GEMs, cultivation of microbial consortia and the quantitative research on pesticide biodegradation models. Recently, with the development of genetic engineering and molecular biology, on one hand, scientists have started shifting to the construction of efficient engineered bacteria through gene recombination techniques; on the other hand, they have altered the enzyme-producing gene to construct vectors that could express the attributes of degrading pesticides. The future prospects of bioremediation of pesticides are highly promising with the integration of advanced technologies such as synthetic biology, genetic engineering, and artificial intelligence. These innovations are enabling the development of genetically modified microorganisms and plants with enhanced capabilities to degrade persistent pesticide residues more efficiently and selectively. Enzyme engineering and nanotechnology are further improving the stability and delivery of biocatalysts in contaminated environments. Additionally, AI-driven monitoring systems and biosensors are being employed to track bioremediation progress in real-time, optimizing treatment strategies. These advancements not only enhance the efficiency and scalability of bioremediation processes but also support sustainable agricultural practices and environmental restoration.