Phytomicrobiomes: A Potential Approach for Sustainable Pesticide Biodegradation

Abstract

Globally, pest-induced crop losses ranging from 20% to 40% have spurred the extensive use of pesticides, presenting a double-edged sword that threatens not only human health but also our environment. Amidst various remediation techniques, bioremediation stands out as a compelling and eco-friendly solution. Recently, the phytomicrobiome has garnered increasing attention as endophytic microbes, colonizing plants from their roots, not only foster plant growth but also enhance the host plant’s resilience to adverse conditions. Given the persistent demand for high crop yields, agricultural soils often bear the burden of pesticide applications. Biodegradation, the transformation of complex pesticide compounds into simpler forms through the activation of microbial processes and plant-based enzymatic systems, emerges as a pivotal strategy for restoring soil health. Manipulating the phytomicrobiome may emerge as a viable solution for this purpose, offering a native metabolic pathway that catalyzes pollutant degradation through enzymatic reactions. This review delves into the pivotal role of phytomicrobiomes in the degradation of diverse pesticides in soil. It explores contemporary innovations and paves the way for discussions on future research directions in this promising field.

1. Introduction

In the intricate tapestry of the environment, every part of a plant plays host to a diverse array of microbes, ranging from bacteria and fungi to archaea and beyond. The soil, in particular, serves as a bustling hub for microbial communities, creating the ideal substrate for plant growth. To put this in perspective, a mere gram of soil is believed to teem with nearly 1 billion bacterial cells and 200 m of fungal hyphae [1]. These microorganisms forge a connection with plants by making the journey from soil to plant, culminating in the assembly of intricate microbial communities known as phytomicrobiomes [2,3]. Remarkably, the specific composition of these microbial cohorts can have both positive and negative ramifications for their host plants. The amalgamation of these microbial communities is aptly referred to as the phytomicrobiome [4]. The phytomicrobiome is more than just an ecological curiosity; it is a critical player in a plant’s ability to adapt to adverse conditions, such as drought, salinity, and the challenges imposed by pesticide exposure [5]. It also dons the mantle of a botanical probiotic, defending plants against pest invasions while fostering their growth. A cast of endophytic microorganisms, residing within the plant, takes center stage in developing these symbiotic relationships, exerting a pivotal influence on plant health [6]. In the grand theater of ecological interactions, understanding the dynamics between plants, their microbiota, and the surrounding environment is pivotal. This interplay, influenced by factors like soil type, temperature, climate, and human activities, is fundamental to unraveling the mysteries of the phytomicrobiome [7,8]. Moreover, the manipulation of the phytomicrobiome holds promise as a potent solution to address specific environmental challenges [9].

As the global population burgeons, so does the demand for grain production. The 21st century has witnessed a 1.4% increase in global grain production [10]. However, this growth is shadowed by a persistent problem—pest-induced damage, resulting in annual crop losses of 20–40%, with diseases and insect infestations accounting for staggering economic losses of approximately $220 billion and $70 billion, respectively [10]. Nations like China and India bear the brunt of this crisis, where tens of millions of tons of grains are lost annually to pests [11,12]. In response to these daunting losses, pesticides have been indiscriminately employed for crop protection, setting in motion a cascade of environmental consequences, including soil, water, and air pollution [13,14,15]. Amidst the environmental conundrum posed by pesticide pollution, biodegradation emerges as a potent tool for mitigating the persistence of pesticide residues in soil. Microorganisms involved in the biodegradation process produce enzymes capable of breaking down the complex organic structures of pesticides. Through mineralization, these organic compounds are transformed into inorganic forms, enriching the soil with essential nutrients [16,17,18]. The microbial world has unveiled an array of champions responsible for the degradation of various pesticides [19,20,21,22,23,24]. Furthermore, plant roots join the fray by releasing exudates, including sugars, organic acids, secondary metabolites, and complex polymers, which serve as a banquet for microbial growth in the rhizosphere [25]. Consequently, fostering microbial communities in the rhizosphere becomes a vital step in nurturing the phytomicrobiome.

The phytomicrobiome may hold the key to a sustainable future for pesticide degradation [26], offering a pathway towards climate-resilient agricultural practices that ensure the longevity of our precious soils [27]. Nonetheless, bridging the gap between fundamental and applied research remains a critical challenge in the quest to harness the potential of the phytomicrobiome for effective pesticide biodegradation. This review aims to provide a comprehensive overview of the current state of knowledge surrounding the phytomicrobiome and its application in pesticide biodegradation. Additionally, it seeks to chart a course for future research endeavors, aiming to address knowledge gaps and optimize the utilization of the phytomicrobiome.

2. Pesticides

Pesticides, chemical compounds employed to manage pest populations, encompass a spectrum of agents such as herbicides, insecticides, molluscicides, and rodenticides, to name a few [28]. Among these categories, insecticides dominate, accounting for a substantial 80% of all pesticide applications [29]. The essence of a pesticide lies in its precision—it should target pests while sparing non-target species. However, the indiscriminate use of pesticides casts a looming shadow over the environment. Recent data have cast a stark light on the environmental ramifications of pesticide usage, revealing that over 98% of insecticides and 95% of herbicides have the potential to impact non-target species in the air, water, and soil [30]. These consequences manifest in various ways. Some pesticides stubbornly persist within the soil, exerting influence on the intricate web of the soil microbiome. Others, distinguished by their mobility, percolate through the soil and may ultimately contaminate groundwater sources. Over the long term, the unbridled application of pesticides in soil correlates with diminished bacterial diversity and abundance [31]. Pesticides are not confined to the soil; their effects ripple through ecosystems. These chemical agents can infiltrate flower pollen and nectar, jeopardizing the intricate web of the flower microbiome [32]. Furthermore, the widespread use of pesticides may trigger a domino effect, resulting in a considerable reduction in biodiversity and contributing to the decline of crucial pollinator populations [33]. The environmental consequences of pesticides are profound and necessitate a comprehensive understanding, especially in the context of sustainable pesticide management.

2.1. Fate of Pesticides

The destiny of pesticides within the environment is an intricate dance dictated by the interplay of environmental conditions and the unique characteristics of each pesticide. Figure 1 offers a visual representation of the typical trajectory of pesticides in the environment. A staggering majority, nearly 80%, embarks on a downward journey, infiltrating the soil’s pores and ultimately contaminating groundwater sources [34]. This process, aptly termed leaching and percolation, is largely underpinned by soil sorption mechanisms [35]. Indeed, the persistence, movement, and accumulation of pesticides within the soil matrix are intrinsically linked to the soil’s capacity for retention and its ability to facilitate degradation processes [36]. Within the soil ecosystem, a myriad of factors come into play, exerting their influence on the migration of pesticides. Variables such as temperature, moisture levels, and the physicochemical and biological properties of the soil collectively shape the trajectory of these chemical agents. Yet, it is imperative to note that the application of pesticides, while targeting pests, carries collateral consequences for soil microbes. Pesticides have the potential to disrupt the delicate balance of microbial communities, leading to modifications in microbial diversity [35].

In the intricate soil environment, the microbial world takes center stage in the degradation of pesticides. These microscopic entities, often regarding pesticides as valuable sources of carbon (C) or nitrogen (N), engage in a biotransformation process that gives rise to diverse metabolites. These metabolites, in turn, are subject to further degradation by other members of the microbial consortium. Yet, the persistent and unchecked usage of pesticides may result in the accumulation of pesticide residues within the soil’s organic matter, particularly in the humus layer. These residues, like silent specters, await their chance to be taken up by plants, initiating a journey that leads them into the very heart of the food chain through biomagnification (see Figure 1). The implications of this complex interplay of pesticides within the natural world are far-reaching, underlining the critical need for a nuanced understanding in our pursuit of sustainable pesticide management.

2.2. Pesticide Biodegradation Processes

In our pursuit of a safer and cleaner environment, the elimination of pesticide residues is imperative. Recent investigations have explored a range of physicochemical processes, such as adsorption and percolation filters, alongside innovative techniques like photocatalysis with TiO₂ and photo-degradation, to tackle this formidable challenge [37]. However, these methods often prove to be cost-intensive, laborious, and time-consuming. The Food and Agriculture Organization of the United Nations estimates the cost of these operations to range between 3000 and 4000 USD per ton of pesticide removed [38]. Therefore, our quest for effective and sustainable pesticide degradation necessitates a shift towards eco-friendly, cost-effective, and time-efficient techniques. Pesticide biodegradation stands out as a promising solution [39]. As depicted in Figure 2, microorganisms wield a natural prowess to degrade a significant portion of pesticides through the orchestration of diverse biodegradation pathways. These pathways play a pivotal role in identifying the microorganisms capable of breaking down specific pesticides.

Table 1. Example of pesticide-degrading microorganisms isolated from different environmental components.

Name of Pesticide	Isolation Source	Microbe Used	Microbe Type	Reference
2,4-D	Pea (Pisum sativum)	Pseudomonas putida VM1450	Bacterium	[41]
Thiamethoxam	Rice (Oryza sativa)	Enterobacter cloacae TMX-6	Bacterium	[42]
2,3,4,6-tetrachlorophenol, 2,4,6-Trichloropropane	Contaminated groundwater	Herbaspirillum spp. K1	Bacterium	[43]
Imadcloprid	Coarse textured Rhizosphere soil	Pseudomonas spp. 1G	Bacterium	[44]
Acetamiprid and Imidacloprid	Tobacco plant (Nicotiana tabacum)	Acinetobacter spp. TW	Bacterium	[45]
Acetamiprid and Imidacloprid	Tobacco plant (Nicotiana tabacum)	Sphingomonas spp. TY	Bacterium	[45]
Acetamiprid	Rhizosphere Zone	Rhodotorula mucilaginosa Strain IM-2	Yeast	[46]
Acetamiprid	Pesticide factory Rhizosphere Zone	Fusarium spp. strain CS-3	Fungus	[47]
Acetamiprid	Rhizosphere Zone	Streptomyces canus CGMCC 13662	Actinomycete	[48]
Thiacloprid	Rhizosphere soil	Ensifer meliloti CGMCC7333	Bacterium	[49]
Clothianidin	Rotted wood	Phanerochaete sordida	Fungus	[50]
Nitenpyram	Rotted wood	Phanerochaete sordida YK-624	Fungus	[51]
Dinotifuran	Rotted wood	Phanerochaete sordida YK-624	Fungus	[51]
Chloropyrifos	Rhizosphere Zone	Bacillus spp.	Bacterium	[52,53]
Endosulfan	Rhizosphere Zone	Pseudomonas spp.	Bacterium	[52]
Alachlor	NITE Biological 53 Resource Center (NBRC), Japan	Aspergillus fumigates	Fungus	[54]
Diazion	Rhizosphere Zone	Pseudomonas spp.	Bacterium	[52,53]
Parathion	Rhizosphere Zone	Bacillus spp.	Bacterium	[52,53]
Malathion	Rhizosphere Zone	Rhodococcus spp.	Bacterium	[55]
Polychlorinated biphenyls (PCBs), Polycyclic aromatic hydrocarbons (PAHs)	Rhizosphere Zone	Rhodococcus spp.	Bacterium	[55]
Acibenzolar-S-methyl	Rhizosphere Zone	B. pumilus SE34	Bacterium	[56]
Atrazine	Rhizosphere Zone	Cryptococcus strain TT3	Bacterium	[57]
	Rhizosphere Zone	Pichia kudriavzevii strain Atz-EN-01	Yeast	[58]
	Wastewater	Raoultella planticola	Bacterium	[59]
bensulfuron-methyl	Rhizosphere Zone	Bacillus megaterium L1 and Brevibacterium spp. BH	Bacteria	[60]
Bispyribac sodium	Madhana ghas (Dactyloctenium aegyptium) and lamp grass (Paspalum delatatum)	Chromobacter xylosoxidans (BD1), Achromobacter pulmonis (BA2), and Ochrobactrum intermedium (BM2)	Bacterial consortium	[61]
Tebuconazole	Rhizosphere Zone	Enterobacter sakazakii and Serratia spp.	Bacteria	[62]
Diuron	Rhizosphere Zone of sugarcane crop	Stenotrophomonas acidophila TD4.7, Bacillus cereus TD4.31	Bacteria	[63]
Pyraclostrobin	Rhizosphere Zone of Orange tree	Bacillus spp. CSA-13, Bacillus aryabhattai CBMAI2223	Bacteria	[64]

provides an inventory of various phytomicrobes renowned for their pesticide-degrading abilities. Remarkably, these microorganisms can evolve to produce enzymes essential for the degradation of primary pesticide compounds, subsequently harnessing them as sources of growth [40].

Pesticide biodegradation unfolds through a symphony of enzymes, with their genetic blueprints residing on both plasmid and chromosomal DNA. Under stressful conditions, plants receive microbial signal compounds that urge them to activate defense-related genes, initiating pathways for microbial degradation [65,66]. Microbes, exhibiting an innate tendency to exploit pesticides as an energy source, embark on the journey of pesticide degradation mechanisms [67]. The pages of biodegradation history unveil pioneering bacterial strains, such as Pseudomonas putida, bearing the degradative camphor (CAM) plasmid, which boasts the capacity to orchestrate the oxidation of terrant and camphor and encode genes responsible for the degradation of 2,4-dichlorophenoxyacetic acid (2,4-D), a widely-used herbicide [68,69]. A plasmid, pJP4, isolated from Ralstonia eutropha strain JMP134, has been recognized for harboring a broad spectrum of degradation genes that enhance the breakdown of organochlorines, 2,4-D, and 3-chlorobenzoate [70]. Additionally, the genes ptrD, ptrA, ptrB, ptrC, phtAa, phtAb, phtAc, and phtAd, sourced from Arthrobacter keyseri (plasmid 12B), are instrumental in phthalate degradation [71]. Sphingobium indicum B90A chromosomes harbor genes, such as linA, linA2, linX1, linB, linC, linX2, and linX3, governing the degradation of a wide array of hydrocarbons [72].

Pesticide biodegradation entails the comprehensive transformation of organic compounds into an inorganic form, a feat achieved through the concerted efforts of microbes [73]. This process is contingent not only on the presence of microorganisms equipped with degradation enzymes but also on the surrounding environment [73]. Thanks to advanced analytical and molecular tools, we have gained unprecedented insights into the intricate pathways of pesticide degradation [74,75]. Microbial transformation, driven by an energy source, unfolds as microbes harness pesticides as both carbon (C) and nitrogen (N) sources through pesticide degradation [74]. The secretion of extracellular enzymes by numerous microbes facilitates the degradation of pesticides, with plants providing a hospitable environment for the production of pesticide-degrading enzymes. Hence, phytoremediation emerges as a favored technique to curtail pesticide pollution. Among the arsenal of enzymatic biodegraders, transferases, isomerases, hydrolases, and ligases are the most common. Pesticide metabolism typically unfolds in three phases, commencing with the conversion of the parent compound into a water-soluble, less toxic product via oxidation, reduction, or hydrolysis. The second phase yields sugars or amino acids, which are more water-soluble than the products of the first phase. Finally, the third phase sees the conversion of second-phase metabolites into non-toxic secondary conjugates, with bacteria and fungi leveraging both intra- and extracellular enzymes in the pesticide degradation process [75].

3. Phytomicrobiome and Pesticide Biodegradation

Phytomicrobiomes, encompassing various endophytic microbes that contribute to the degradation of multiple compounds, including pesticides, have emerged as a critical avenue in pesticide biodegradation processes. These microbial ecosystems permeate every part of the plant, from roots to leaves, creating a multifaceted landscape of possibilities (Figure 3). The upper portion of the phytomicrobiome constitutes the shoot, stem, leaf, seed, and flower microbiomes, collectively referred to as endo and phyllomicrobiome (Figure 3), while the root microbiome establishes critical plant–microbe interactions in the lower part.

The composition of phytomicrobiomes is far from static, shaped by the host plant species, growth stage, and the environmental conditions surrounding their growth [76]. Such distinctive properties underscore the phytomicrobiome’s relevance in pesticide degradation. Nevertheless, despite their immense potential, we still possess limited knowledge about how these microbiomes assemble in various plant parts and their specific contributions to pesticide degradation. In pesticide-driven conditions, plants employ a strategic partnership with root microbes, selectively enlisting beneficial microbes to their aid [77]. They communicate through root exudates, volatile organic compounds (VOCs), and phytohormones, facilitating the recruitment of pesticide-tolerant microbes in the root zone [78]. Figure 4 illustrates how phytomicrobiomes create niches for pesticide-degrading microbes.

Phytomicrobiomes are not isolated entities but function as intricate networks within and between species, genera, and families, regulating microbial assembly inside the plant’s body [79]. This interplay between plants and microbes shapes diverse microbiome assemblies that enable plants to thrive in the presence of applied pesticides or other stress conditions [80,81]. For example, endophytic strains like Pseudomonas spp. and Bacillus spp. enhance their functionality under stress conditions by secreting siderophores and indole acetic acid, bolstering plant growth [82] and concurrently serving as biodegraders of pesticides like 2,4-D, endosulfan, and chlorpyrifos [41,52,53]. One study focusing on shoot-tip-associated bacteria from banana cv. grand naine identified dominant bacterial families such as Pseudonocardiaceae, Nocardioidaceae, and Streptomycetaceae in shoot biomass. The microbial diversity in terms of culturable endophytes included Actinobacteria, Firmicutes, Proteobacteria, and Bacteroidetes phyla [83]. Stem microbiomes, on the other hand, typically feature phyla like Proteobacteria, Actinobacteria, Firmicutes, Ascomycota, Basidiomycota, and Bacteroidetes [84]. The application of pesticides leads to shifts in the microbial structure of the shoot and stem, opening up opportunities for exploring the pesticide biodegradation potential of these altered communities. Bacteria like Acetobacter spp. from sugarcane stems [85], Azoarcus spp. from Kallar grass shoots [86], Bacillus megaterium from maize stems [87], Burkholderia spp. from onion stems [88], Bacillus altitudinis DB26-R and Bacillus subtilis subsp. Inaquosorum B6-L from rice plants [89], and Gluconacetobacter spp. from maize stems [90] are identified as potential bacteria involved not only in promoting plant growth but also in degrading pesticides. On the other hand, successful inoculation of these degradable microbes in the rhizosphere zone poses a big challenge [91]. This is because the microorganisms are not very mobile in the soil, and hence, they always show different antagonistic/mutual relationships with other microbes, especially nematodes, creating a double critical problem when spreading the target microbes around the root zone [92]. In this context, inoculum density and inoculum methods are important to obtain desired results. Seed coating, seed priming, root colonization, foliar application, and soil drenching are the popular methods of microbial inoculation. Chai et al. (2022) observed that prolonged seed coating could efficiently boost the colonization of the endophytic bacterium C. pinensis in cereal crops [93]. On the contrary, Inoculation of Ochrobactrum spp. strain DF-1 with soil resulted in complete nitenpyram insecticide degradation in both sterile and non-sterilized soil within 14 days of incubation [94]. Similarly, soil inoculation of Tepidibacillus decaturensis strain ST1 degraded 200 mg kg⁻¹ of imidacloprid insecticides completely with a half-life of 12.95 days in non-sterile soil and 18.77 days in sterile soil [95]. Therefore, proper inoculation techniques lead to the development of higher root colonization of degradable microbes, which can provide a niche for pesticide-degrading microbes in the plant microbiome.

3.1. Shoot Microbiome

Shoot and stem microbiomes are hubs of versatile microbial communities akin to their rhizospheric counterparts, yet uniquely adapted to the host plant species, soil type, and environmental milieu in which they thrive. These microbiomes transcend their role in enhancing plant growth; they emerge as potent allies in the realm of biodegradation, venturing into the deconstruction of various foreign biochemicals, including pesticides. Highlighting the promising potential within these microbiomes, Ito et al. (2021) introduced a novel endophytic Bacillus strain isolated from cucumber stalks [96]. This remarkable bacterium swiftly dismantled 8.03 µmol/L of pentachlorophenol (PCP) within a mere 24 h, subsequently generating PCP-phosphate as a metabolite [96]. Furthermore, in the quest for bioagents capable of pesticide degradation, two exceptional endophytic bacterial strains, Acinetobacter spp. TW and Sphingomonas spp. TY, were uncovered within the annals of tobacco plant wastes [45]. Acinetobacter spp. TW, thriving at temperatures between 25 and 37 °C with a pH range of 7–8, displayed an astounding ability to entirely degrade nicotine. Simultaneously, Sphingomonas spp. TY, accustomed to conditions spanning 25–30 °C with a pH range of 6–7, demonstrated an equivalent prowess in nicotine degradation. Remarkably, these two strains unveiled their versatility in degrading neonicotinoid pesticides such as acetamiprid, imidacloprid, and thiamethoxam. Similarly, the endophytic microbial consortia can be a perfect tool for harnessing pesticide degraders. For instance, the bacterial consortia of Achromobacter xylosoxidans (BD1), Achromobacter pulmonis (BA2), and Ochrobactrum intermedium (BM2) was proven to be effective in bispyribac sodium (a common herbicide) degradation [61]. The shoot and stem microbiomes, with their unique microbial inhabitants, stand as promising reservoirs of pesticide-degrading capabilities, offering a pathway to sustainable pest management within the realm of agriculture and beyond.

3.2. Leaf Microbiome

Within the intricate realm of plant physiology, the leaf microbiome stands as a beacon of resilience against adverse weather conditions while simultaneously serving as a catalyst for plant growth and development. Dominating the tapestry of leaf microbiomes are the Actinobacteria, Firmicutes, Proteobacteria, Bacteroidetes, Leucosporidium, and Taphrina taxa, each playing a crucial role in the plant’s survival. Recent studies have unearthed species within the leaf microbiome that exhibit remarkable potential in bolstering plant defenses against stress conditions. Bacillus subtilis, discreetly tucked away in mulberry leaves, emerges as a guardian against plant wilting, providing a lifeline during challenging circumstances [97]. Meanwhile, Burkholderia phytofirmans, nurtured within the sanctuary of maize leaves, dons the mantle of drought tolerance enhancer, fortifying plants against the relentless grip of arid conditions [98]. On the other end of the spectrum, Herbaspirillum seropedicae, a silent sentinel within both maize and rice leaves, takes on the responsibility of atmospheric nitrogen fixation, elevating the nitrogen content available to the plant [99,100]. The leaf microbiome unveils another remarkable facet as a proficient degrader of toxic chemical compounds absorbed by plants from the soil. Within this enigmatic world, Enterobacter spp., found nestled in the leaf buds of hybrid poplar trees, showcases an exceptional ability to degrade trichloroethylene, offering an invaluable detoxification service to the plant [101]. Furthermore, Pseudomonas putida, a guardian of pea leaves, emerges as a potential bioagent for phytoremediation, demonstrating its prowess in the degradation of 2,4-D and the removal of this herbicide from the environment. As pesticides are introduced into this delicate ecosystem, the composition of the leaf microbial community undergoes significant shifts. The application of chiral herbicide dichlorprop to Arabidopsis thaliana plants, for instance, triggers a noteworthy increase in Proteobacteria alongside a decrease in Actinobacteria [102]. Similarly, the introduction of Penconazole fungicide induces alterations in the leaf microbiome, leading to a decline in the Enterobacteriaceae family’s abundance and an elevation in the population of Sphingobium spp. [103]. Despite these insights, the potential of the leaf microbiome in pesticide biodegradation remains largely uncharted territory, beckoning for further exploration and understanding. A journey into the intricate world of leaf microbiomes and their potential to mitigate pesticide-related challenges is a pressing frontier in the quest for sustainable and eco-friendly agricultural practices.

3.3. Seed Microbiome

Seeds, the very essence of future plant life, serve as the cornerstone of plant fitness, growth, and development. They inherit their microbial communities from diverse sources such as the environment (air, water, soil) and their parent plants. These seeds carry within them the legacy of previous generations, and the microbial torch they bear plays a pivotal role in shaping the phytomicrobiome, thereby orchestrating the future of agriculture [104,105]. Much like other parts of the plant, the seed microbiome is associated with a rich tapestry of microbial phyla, including Proteobacteria, Actinobacteria, Firmicutes, and Bacteroidetes, which are intricately woven into the fabric of the seed’s composition [106,107]. This intricate assembly is a direct reflection of the soil, environmental conditions, and the host plant species. For instance, seeds from alfalfa and Cucurbita pepo reveal the presence of Proteobacteria, Actinobacteria, and Firmicutes phyla [108,109]. The seed microbiome is not solely the domain of bacteria; it also hosts fungi, including the Ascomycota phylum [108].

Recent scientific inquiries have unveiled the seed microbiome’s profound role in controlling fundamental aspects of plant life, including germination, growth, flowering, and fruiting. Studies on wheat seed microbiota have illuminated higher microbial diversity in the seed endosperm than in the embryo [110]. This microbial consortium does not merely passively coexist with seeds; it actively releases phytohormones, enzymes, and biocontrol agents, thereby propelling the degradation of pesticides and enhancing seedling germination even under stressful conditions [111,112,113]. An intriguing avenue for pesticide degradation lies in the inoculation of microbial strains onto seeds, a promising biological approach to control and mitigate the harmful effects of pesticides. A prime example comes from the discovery of Burkholderia cepacia, a bacterium known for its prowess in degrading 2,4-D herbicide. Researchers have ingeniously coated non-sterile barley (Hordeum vulgare) seeds with this bacterium and observed its effects upon planting in non-sterile soils laced with 2,4-D. The result was a remarkable boost in microbial colonization in the roots of inoculated plants, indicating the potential for mitigating pesticide impact through seed-based strategies [114]. Further illuminating this path, sunflower seed husks were employed as hosts for Rhodococcus spp. strains, known for their proficiency in degrading hydrocarbons. This microbial alliance turned the seed husks into effective bioremediation agents against crude oil-polluted soils. The end result was a staggering 66% removal of total petroleum hydrocarbons from the soil, underscoring the promising role that seeds can play in remediating environmental contamination [115]. While recent studies have predominantly focused on the seed microbiome’s influence on plant growth, scant attention has been directed toward its role in pesticide degradation. These distinct microbial communities reside on or within seeds, poised to become the next generation of endophytic microbiomes. Exploring the depths of the seed microbiome’s potential for pesticide biodegradation is an imperative scientific quest. This journey of discovery should place particular emphasis on seedling establishment and the intricate assembly of the phytomicrobiome, opening new horizons in sustainable agriculture and environmental preservation.

3.4. Flower Microbiome

Among the myriad microbiomes that grace the botanical world, the flower microbiome has remained shrouded in relative obscurity [116,117]. Despite the lack of scientific limelight, these floral microbial communities perform a pivotal role by beckoning insects for pollination, thus wielding a substantial influence over the plant’s reproductive success. A closer look reveals Proteobacteria, Firmicutes, and Bacteroidetes as the dominant phyla that populate the enigmatic world of the flower microbiome. These microbial denizens each contribute uniquely to the intricate tapestry of this ecosystem [118]. Surprisingly, the realm of the flower microbiome remains largely uncharted territory, with a conspicuous absence of research on its structural composition, its potential contributions to pesticide degradation, or its responses to pesticide applications. This gap represents a tantalizing opportunity for advancing environmental sustainability. Noteworthy is the dynamic evolution of the flower microbiome over its lifetime, a phenomenon illuminated by this [119]. In their comprehensive study, they meticulously assessed bacterial diversity in apple flowers from their nascent bud stages to the twilight of senescence. Dissecting the flower into its constituent parts, including stigmas, stamens, receptacles, and petals, they revealed intriguing revelations. Petals emerged as havens of microbial richness and diversity, while stigmas exhibited a relatively fewer number of operational taxonomic units (OTUs). Throughout the flower’s lifecycle, Proteobacteria, Deinococcus-Thermus, Saccharibacteria, Bacteroidetes, and Firmicutes remained steadfast as dominant phyla. Notably, certain species, including Pseudomonas and Enterobacteriaceae within these phyla, showcased intriguing operational patterns that bolstered the flower’s development [119]. An uncharted realm of interplay exists between seed and flower microbiomes. Studies suggest that an augmentation of diversity within the flower microbiome cascades into heightened microbial diversity in the seed microbiome [120]. Yet, an unsettling shroud of ignorance cloaks the subject of pesticide degradation by these floral and seed-associated microbes. The flower microbiome, largely overlooked until now, awaits its moment in the spotlight. Delving into this domain holds the promise of unearthing invaluable insights into the degradation of pesticides and their interplay with these microbial enclaves. In an era marked by growing environmental concerns, this represents a compelling frontier for research, one that may hold the keys to a more sustainable coexistence between agriculture and nature.

3.5. Root Microbiome

The plant’s subterranean realm is far from desolation; in fact, the root surface fosters a vibrant ecosystem, offering fertile ground and niches that provide refuge from both biotic and abiotic stresses [121]. This sanctuary serves as the backdrop for intricate plant–microbe relationships, predominantly unfolding in the dynamic realm known as the rhizosphere (as illustrated in Figure 4). This rhizospheric stage sets the scene for nurturing the expansive phytomicrobiome [122]. Consequently, the root microbiome stands as a close ally to the upper echelons of the phytomicrobiome, conferring additional resilience to plants in the face of adverse conditions [123]. The composition of root microbiomes is a testament to their adaptability, with various soil attributes and properties, including texture, structure, and pH, as well as the identity of neighboring plant communities and the surrounding environment, intricately choreographing the assembly of these microbial communities [124,125,126,127]. Previous investigations have unearthed dominant phyla in root microbiomes, revealing a diverse cast that includes Actinobacteria, Bacteroidetes, Planctomycetes, Proteobacteria, Firmicutes, Acidobacteria, Verrucomicrobia, and Gemmatimonadetes [128,129,130,131]. It is worth noting that, alongside the beneficial microbes, pathogenic counterparts have also found their place within root microbiomes [132]. Consequently, the orchestration of root microbial communities, particularly during a plant’s formative stages, emerges as a pivotal determinant of its future well-being [133,134]. As we delve into the complex interplay between pesticides and the plant-associated microbiome, it becomes evident that the phytomicrobiome undergoes significant transformations in response to pesticide applications across various plant compartments. This intricate dance is characterized by dynamic shifts in microbial communities, orchestrating both the degradation of pesticides and the promotion of plant growth while alleviating pesticide-related stress [135]. To provide a comprehensive view of these changes, Figure 4 offers a visual representation of microbial alterations across all phytomicrobiome components. The root microbiome, endowed with remarkable diversity, emerges as a reservoir of potential pesticide degraders. Notably, organochlorine and organophosphate pesticides, ubiquitous in global agricultural practices, find functional adversaries within the root microbiome [136]. Certain microbial champions, such as Pseudomonas putida KT2440 and Pseudomonas fluorescens, isolated from the root microbiome, have demonstrated their prowess in pesticide degradation [137]. Bacteria from the genus Pseudomonas are notable contenders in this arena, harnessing pesticides as sources of carbon and nitrogen [137]. A compelling example lies in the Fusarium spp. strain CS-3, isolated from the endophytic regions of plants at an acetamiprid-producing facility. This strain showcases its ability by efficiently degrading 98% of acetamiprid, with N′-[(6-chloropyridin-3-yl) methyl]-N-methylacetamide, 2-chloro-5-hydroxymethylpyridine, and 6-chloronicotinic acid identified as prominent metabolites in this acetamiprid degradation process [47]. Intriguingly, this very Fusarium spp. finds a home in the root microbiome of the tested plant, further exemplifying the potential role of the root microbiome in pesticide degradation. Chloroacetamide, an herbicide, can be degraded by the Sphingobium strain, proliferating at the root zone in natural soil [138]. This pesticide can be transformed by microbial metabolism to produce 4,2-methyl-6-ethylaniline, which can be used by this microbe as a nutritional source [138]. Unraveling the enigma of the root microbiome has proven to be a complex endeavor. However, recent strides in sequencing technologies have ushered in a new era, providing invaluable insights into the root microbiota. What emerges from this technological advancement is a spectacle of high species diversity within the root microbiota, encompassing hitherto uncultured species. These microbial dark horses hold particular promise, beckoning researchers to delve deeper into the enigmatic world of the root microbiome. As we journey into this intricate underground ecosystem, we unlock not only the secrets of plant resilience but also potential avenues for the advancement of agriculture and environmental sustainability.

3.6. Translocation and Accumulation

The capacity of phytomicrobes to degrade pesticides is inextricably linked with the uptake and translocation of these chemical compounds within plants. The physical and chemical properties of pesticides, as well as the biological attributes of the plant, collectively influence this process. This journey begins at the plant’s roots [139], where pesticides, upon application, dissolve into soil solutions readily accessible to the plant’s root system. It is crucial to note that pesticide uptake by plant roots typically follows a passive or diffusive process, albeit with some exceptions, such as hormone-like herbicides, including phenoxy acid herbicides [140]; although, size matters—the molecular mass of a pesticide below 1000 is readily absorbed by plant roots [141]. However, pesticide uptake and translocation are significantly affected by factors like dissolved organic carbon (DOC) concentration, pH, temperature, and organic matter (OM) content of the soil. Importantly, two distinct pathways of pesticide transportation have been observed: (i) intracellular or intercellular transport and (ii) tissue transport. The choice between these pathways hinges on the size of pesticide molecules, with smaller molecules able to traverse the xylem and phloem, while larger ones are restricted from phloem transport [142]. This intricate system of pesticide uptake and translocation leaves an indelible mark on phytomicrobial diversity. For instance, a study by Karas et al. (2018) investigated the impact of various pesticides on the phytomicrobiome composition, revealing that nitrogen (N) and sulfur (S) cycling bacteria proved most sensitive to pesticide exposure [143]. Ammonia-oxidizing microorganisms exhibited a negative response to pesticide presence while denitrifying bacteria were stimulated by these chemical compounds. Remarkably, the combined application of biofertilizers and pesticides has been shown to promote phytomicrobial growth [144]. In a study of sugarcane phytomicrobiota, the combined application of pesticides and biofertilizer led to higher microbial diversity than the control, illustrating the intricate interplay between pesticide movement and fertilizer application. It is evident that phytomicrobiome diversity is shaped not only by pesticide dynamics but also by the influence of fertilizer application. The accumulation of pesticides within plant tissues opens yet another chapter in our exploration of pesticide degraders. In the case of tobacco plants, the application of N-(3,5-dichlorophenyl) succinimide, a fungicide, results in pesticide accumulation within the phyllosphere, consequently bolstering the abundance of Enterobacteriaceae relative to control conditions [145]. This Enterobacteriaceae family, a common inhabitant of plant phyllospheres in pesticide-applied settings, exhibits remarkable pesticide-degrading capabilities [146,147]. However, the identification of pesticide degraders in relation to pesticide accumulation within plants remains a fledgling field [148]. While various studies have illuminated the plant’s ability to modulate its microbiome in response to pesticide applications, creating niches for potential pesticide degraders [145,146], the mechanisms governing the abundance and roles of pesticide degraders in relation to pesticide accumulation within the plant remain veiled in mystery. To date, no comprehensive studies have explored these intricate facets of pesticide degradation. Consequently, it is paramount to initiate further research aimed at unearthing potential pesticide degraders and deciphering their roles in the context of pesticide accumulation within plant tissues. This endeavor holds the potential to unveil new dimensions of pesticide biodegradation within the intricate phytomicrobiome.

4. Omics Approaches in Pesticide Biodegradation

In our pursuit of understanding the intricacies of pesticide biodegradation, we stand on the shoulders of advancements in microbiology and biotechnology. These innovations have illuminated the role of microorganisms in the fate of pesticides, a revelation that has been significantly aided by the insights provided through omics technologies. DNA sequencing, in particular, has unveiled the mechanisms, occurrence rates, and identities of pesticide-degrading microorganisms, offering a valuable window into the microbial world.

4.1. Cell Sorting

The task of unraveling the intricate functions of various cell types within a plant is a formidable one. In a multicellular organism like a plant, each cell type contributes its specialized functions towards the collective well-being of the organism. For instance, in the roots, pericyclic cells divide to give rise to lateral root primordia, while in the leaves, mesophyll cells are dedicated to the vital process of carbon fixation during gaseous exchange with the environment. To decipher the genetic factors orchestrating these specialized functions, the process of cell sorting emerges as an indispensable tool. Cell sorting, achieved through techniques such as green fluorescent protein (GFP) tagging, fluorescence-activated cell sorting (FACS) [149], and laser-capture microdissection [150], plays a pivotal role in the omics toolkit of deciphering pesticide-degrading microorganisms. Among these methods, FACS stands out as one of the most cost-effective and efficient techniques for analyzing the omics characteristics of specific cell types. This flow cytometry-based approach offers the capability to separate cells based on morphological characteristics and the expression of multiple proteins, thereby enabling a focused exploration of the functional diversity within phytomicrobiomes. FACS operates by utilizing a fluorescent laser beam to screen and isolate target cells as they pass through the laser’s path. The collected cells are then promptly subjected to lysis for molecular extraction. Having the capability of sorting well-defined cell populations, omics technologies step into the spotlight to provide a holistic understanding of pesticide-degrading microorganisms. Transcriptomics, proteomics, metabolomics, and bioinformatics form a robust ensemble of tools for assessing the genomic characteristics of these potential microbes [151]. These omics approaches unlock the genetic information, shedding light on the complex interactions, regulatory networks, and metabolic pathways that drive pesticide degradation. As we navigate the omics technologies, we decipher the genomic blueprints of pesticide degraders, unraveling their molecular strategies for detoxifying these chemical foes. In the following sections, we will explore the insights offered by each of these omics disciplines, uncovering the genetic secrets that underpin the vital role of microorganisms in the biodegradation of pesticides. Through these revelations, we will forge new pathways towards sustainable pesticide management and environmental protection.

4.2. Transcriptomics

In the quest to understand the genetic basis underpinning pesticide biodegradation, transcriptomics emerges as a suitable tool. This omics discipline illuminates the intricate transcriptional activities of genes, unravels gene regulons, and exposes their intricate responses to various stimulants. Moreover, transcriptomics proves to be a versatile tool for mapping DNA-binding sites of genes associated with degradation, all while facilitating comparative genotyping [152]. Through the lens of transcriptomics, we gain insights into the physiology of pesticide-degrading microbial strains, revealing the ingenious optimization strategies for biodegradation. It is through transcriptomic analysis that we unearth novel, efficient pathways for dismantling these chemical adversaries. Allen et al. (2012) used microarrays to dissect the transcriptional changes occurring during paraquat exposure and the ensuing oxidative stress response in E. coli 0157:H7 [153]. Their findings showed that gene responses were significantly induced in cells in the logarithmic growth phase compared to those in the stationary phase, showcasing the dynamic nature of pesticide response mechanisms. Similarly, Dennis et al. (2003) deployed microarrays to scrutinize the expression of bacterial metabolism genes within mixed microbial communities confronted by 2,4-D [154]. Their insights reinforced the utility of microarrays as invaluable tools for the detection of bacterial gene expression in the intricate milieu of wastewater treatment and other complex ecosystems. RNA-Seq and RT-PCR methodologies took the spotlight in Huang et al.’s (2013) work with Klebsiella pneumoniae CG43, as they explored the transcriptional shifts induced by the overexpression of the yjcC gene [155]. This gene, responsible for encoding a probable phosphodiesterase activated by paraquat, held the key to understanding critical responses in pesticide-degrading pathways. Cheng et al. (2018) employed RNA sequencing to pinpoint genes controlling the biodegradation and metabolism of chlorimuron-ethyl within Rhodococcus erythropolis D310-1 [156]. Their work revealed 500 genes during the degradation process, with dominant metabolic pathways featuring “toluene degradation” and “aminobenzoate degradation”. Hence, through transcriptomics, we unravel the genetic basis that guides pesticide-degrading microorganisms, opening up avenues for innovative biodegradation strategies and environmental stewardship.

4.3. Proteomics

In complex pesticide biodegradation, proteomics stands as an important tool, unraveling the patterns, functions, and interactions of proteins [157]. This omics approach not only unravels the identity of potential enzymes and metabolic pathways linked to pesticide degradation but also uncovers the intricate protein pathways activated in response to pesticide-induced damage. Seo et al. (2003), in a pioneering proteomic study, scrutinized the degradation of methylcarbamate pesticides by Burkholderia spp. C3 [158]. Their quest explored protein expressions triggered by exposure to carbamyl compounds, with Burkholderia spp. C3 unveiling a preference for N-methylcarbamate as its exclusive carbon source. Within their proteomic approach, 60 out of 867 detected proteins played pivotal roles in pesticide metabolism, an insight that helped in understanding the protein’s involvement in biodegradation. Turning to the anaerobic realm, Schiffmann et al. (2014) used proteomic experiments to investigate the differential expression of proteins amidst the degradation of hexachlorobenzene by Dehalococcoides mccartyi CBDB1 [159]. Their meticulous efforts led to the creation of a comprehensive protein profile, unmasking the molecular mechanism that governs this intricate process. Their proteome characterization ventured to cover 70% of the 1458 annotated protein-coding sequences, offering a comprehensive glimpse into the proteins engaged in this biodegradation. Tiwari et al. (2018) unveiled the potent role of proteomics in understanding Fischerella spp.’s response to methyl parathion (MP) exposure [160]. Through proteomics, they discovered that even after 8 days of incubation with MP, the growth of Fischerella spp. remained unharmed. Instead, proteins, including antioxidative enzymes, signaling proteins, and chaperones, were invigorated, underscoring the resilience and adaptive capabilities of these microorganisms in the face of pesticide-induced stress. Proteomics is a critical player in the quest to comprehend pesticide biodegradation, unraveling the roles of proteins in this intricate ecological happening.

4.4. Metabolomics

Metabolomics, a multidimensional procedure in microbial research, delves into the qualitative and quantitative exploration of metabolite profiles, offering valuable insights into a microorganism’s biochemical activities [161]. This potent omics tool further serves as a bridge between genetic and phenotypic profiles, shedding light on the relationships governing microbial responses and behaviors [161]. The application of metabolomics plays a pivotal role in unraveling biodegradation pathways, with a specific focus on the identification of biomarkers associated with pesticides and their inherent toxicity. Furthermore, metabolomics provides a roadmap to gauge the effectiveness of microorganisms against pest populations, offering a promising route for the development of novel pesticides to counter resistant strains. In the dynamic realm of environmental metabolomics, the interactions between living organisms and their surroundings are unveiled, offering a comprehensive perspective on how microorganisms respond to environmental cues. In comparison to the proteome and transcriptome, the metabolome provides a closer link to cellular phenotypes. Thus, when deciphering the non-target community repercussions triggered by the emergence of pesticides, metabolomic approaches offer a more comprehensive understanding than their transcriptomic counterparts [162]. Metabolomics is instrumental in uncovering more efficient biodegradation pathways that hold potential for pesticide remediation. Lenert et al. (2013) embarked on a metabolomics study, exploring the production of potentially toxic chlorinated compounds resulting from the fermentation of the fungicide fenhexamid by Lactobacillus casei Shirota [163]. Their investigation revealed the formation of an O-glycosyl derivative during the fermentation process in the presence of 100 μg/mL fenhexamid. Bhat et al. (2015) turned to metabolomics to unravel the metabolic consequences of exposure to 2,4-D. Their study demonstrated that sublethal levels of 2,4-D accelerated oxidative stress, inducing notable metabolic shifts in E. coli [164]. The affected pathways spanned oxidative phosphorylation, peptidoglycan biosynthesis, the ABC transport system, and nucleotide, amino acid, and sugar metabolism. In another metabolomics-driven investigation, Chen et al. (2015) elucidated the biodegradation mechanisms of the cyhalothrin pesticide, leveraging Bacillus thuringiensis strain ZS-19 [165]. Their findings unveiled the complete degradation of cyhalothrin by the ZS-19 strain, facilitated through the cleavage of ester linkages and diaryl bonds, leading to the production of six distinct intermediate products. Metabolomics emerges as a vital tool guiding the exploration of microbial metabolic landscapes in the context of pesticide degradation. The study of pesticide biodegradation stands at the crossroads of innovative possibilities, with a plethora of publicly accessible bioinformatics databases paving the way to unravel biodegradation pathways. The strategic utilization of bioinformatics not only offers a glimpse into the microbial cellular machinery but also sheds light on the intricate metabolic roadmaps underpinning pesticide degradation [166]. The synergy between bioinformatics and omics tools propels the comprehension of the molecular biology governing pesticide-degrading microorganisms. Indeed, omics tools serve as an attractive way to decode the enigma of pesticide-degradable microbes at the molecular level. Their integrative approach not only unravels the mysteries of microbial pesticide degradation but also propels the emergence of cutting-edge technologies within this domain. As the quest for understanding the intricate world of microorganisms in their natural habitats remains a formidable challenge, the deployment of these tools is an essential endeavor. The journey into pesticide biodegradation holds the promise of unveiling new dimensions of microbial life, fostering eco-friendly pesticide management, and providing solutions for the sustainable coexistence of agriculture and the environment.

5. Future Research Scope

The advent of synthetic microbial communities (SynCom) stands as a beacon of promise in the realm of microbiome research, opening new avenues for exploration. This innovative technology entails the co-cultivation of diverse microbial taxa under controlled conditions, effectively mimicking the functional and structural attributes of a natural microbiome. The intrinsic complexity of pesticide compositions often limits the efficiency of natural pesticide degradation. In contrast, synthetic communities offer the potential for enhanced biodegradation outcomes [167]. A case in point involves Variovorax spp. WDL1, which efficiently degrades linuron by utilizing it as a source of carbon and nitrogen to support its growth. Conversely, Pseudomonas spp. WDL5 and Delftia acidovorans WDL34 produce intermediate metabolites during linuron degradation but cannot fully degrade the compound. Remarkably, when these three strains are combined to create a synthetic community, it exhibits the highest degradation efficiency due to the synergistic interactions between the strains [167]. Another instance highlights the degradation of 4-chlorosalicylate, which occurs only when Achromobacter spanius, Pseudomonas reinekei, Wautersiella falsenii, and Pseudomonas veronii strains are co-applied [168]. Given the propensity of plants to harbor a multitude of degradable microbes in pesticide-exposed environments, SynCom can be crafted by isolating endophytic pesticide-degrading microbes, thereby promoting bioremediation in pesticide-contaminated soil.

Undoubtedly, SynCom presents a promising tool for future sustainability; however, a deeper understanding of microbiome interactions among communities is essential to unlock its full potential. The dynamics of synthetic communities in association with plants remain an enigma that requires a comprehensive exploration of their role in pesticide biodegradation and bioremediation. The deployment of CRISPR-Cas9 technology, a revolutionary genomic tool, allows for targeted genetic screening, thereby elucidating the intricacies of the genotype–phenotype relationship. Through the systematic perturbation of genes on a broad scale, this technology holds promise in investigating plant–microbe interactions post-pesticide application. Such insights are invaluable for building a comprehensive database elucidating the mechanisms through which the phytomicrobiome fosters the growth of pesticide-degrading microorganisms [169]. While techniques like the super delta method can aid in data normalization during gene expression analysis, a more profound genetic-level comprehension of phytomicrobiome interactions in pesticide-treated soils is imperative to pave the way for future breakthroughs.

6. Concluding Remarks

The issue of pesticide residues in agricultural soils looms large as a substantial concern. Here, we have underscored the pivotal role of the phytomicrobiome in pesticide biodegradation, leveraging the unique ecological niches that plants provide to microorganisms within their environment. However, a more exhaustive molecular examination of diverse microbiomes is essential to unravel the intricacies of plant–microbe interactions in pesticide-treated soils. Endophytic microbes, displaying remarkable adaptability, act as ecological engineers, thriving under varying conditions. Investigating their survival mechanisms alongside host–relevant conditions represents a key avenue to construct a comprehensive database of the phytomicrobiome. While numerous studies have accentuated the significance of the microbiome in enhancing plant growth, microbial interactions and behavioral studies in the context of pesticide application and persistence remain in their infancy. Hence, the dynamic interplay between plants and microbes necessitates thorough exploration to bolster environmental sustainability. Furthermore, additional research focusing on plant physiology, genetics, and molecular adaptations in response to pesticide-induced conditions is imperative. The enigmatic mechanisms and roles of different microbiomes within the entire phytomicrobiome under pesticide-applied scenarios beg for further elucidation. To facilitate the dissemination of knowledge, the establishment of a public repository comprising a compendium of pesticide-degrading microbiomes and their functions under diverse pesticide conditions is warranted. Advanced investigations should be undertaken to unravel the intricacies of gene expression in plants at both proteomic and genomic levels, culminating in a holistic understanding of the intricate web of pesticide biodegradation. In the pursuit of a sustainable tomorrow, the revelations brought forth by this study are poised to pave the way for innovative solutions in pesticide management, contributing to the preservation of our agricultural ecosystems and environmental well-being.