Abstract
The rhizosphere is a living physical space that is constantly evolving and is characterized by a complex interplay between beneficial microbes, pathogens, and plants, mediated by molecular and ecological interactions. These three-way relationships constitute a rhizosphere “triangular warfare system,” which controls plant health, nutrient uptake, disease resistance, and plant resilience. This review provides a mechanistic overview of the molecular, metabolic and ecological processes underlying these tripartite interactions. We discuss how plants integrate pattern-triggered immunity (PTI), effector-triggered immunity (ETI), microbiome exudation, and hormone signaling to select beneficial microbes to exclude pathogen entry. Beneficial microbes deploy volatile organic compounds, induction of systemic resistance (ISR), secretion systems, phytotoxins, siderophores, lytic enzymes, and microbiome-disrupting strategies to enhance plant fitness, whereas pathogens use virulence effectors, lytic enzymes, secretion systems, phytotoxins, siderophores, and microbiome-disrupting strategies to overcome host defenses and restructure rhizosphere communities. Recent advances in multi-omics have revealed the intricate signaling networks, metabolic interactions, and microbial competition shaping these relationships under various environmental conditions. We further explore emerging opportunities in microbiome engineering, synthetic microbial consortia and disease-suppressive soil management for sustainable crop protection. This review synthesizes existing mechanistic knowledge and introduces the concept of ‘rhizosphere triangular warfare’ as a stepping stone toward the next generation of microbiome-based agriculture and precision rhizosphere engineering under environmental changes.
Graphical Abstract
Highlights
Introduces a mechanistic framework for rhizosphere triangular warfare.
Integrates plant immunity, beneficial microbes, and pathogen strategies.
Discusses root exudate-mediated microbiome assembly and disease suppression.
Develops multi-omics for decoding rhizosphere signaling networks.
Explores precision microbiome engineering for sustainable crop protection.
1 Introduction
One of the most fertile microhabitats on earth is the rhizosphere, a zone surrounding plant roots where chemical signaling, metabolic activity and microbial diversity are at a peak (Jamil et al., 2022; Philippot et al., 2013). In this dynamic setting, plants, beneficial microbes, and pathogens continuously interact at the molecular and ecological levels, which help to control plant growth, nutrient uptake, immunity, and disease development (; Upadhyay, 2026a). These dynamic three-way interaction between plants, beneficial microbes, and pathogenic microorganisms inside the rhizosphere is intertwined, forming a “rhizosphere triangular warfare”; cooperation and competition determine plant health, soil fertility, and ecosystem sustainability (Li et al., 2021).
Plants actively attract beneficial microbes by releasing exudates containing root metabolites such as sugars, amino acids, organic acids, phenolics, flavonoids and secondary metabolites that act as nutrient sources and signaling molecules influencing the microbial community of the rhizosphere (Hemelda and Noutoshi, 2025; Wankhade et al., 2025). Meanwhile, plants utilize pattern-triggered immunity (PTI) and effector-triggered immunity (ETI) to detect microbial signals and to control pathogen invasion (Nguyen et al., 2021). They can increase the acquisition of nutrients, lead to the production of antimicrobial metabolites, siderophores, lytic enzymes, volatile organic compounds (VOCs), and quorum-quenching molecules, and induce systemic resistance (ISR), thus fortifying plant defense and resilience (Timofeeva et al., 2023; Vacheron et al., 2013; Yu et al., 2019, Yu et al., 2022).
In contrast, pathogens use secretion systems (Type I-VI), virulence effectors, phytotoxins, cell wall-degrading enzymes, and molecular mimicry to inhibit plant immunity, alter host metabolism and disrupt beneficial microbial colonization (Matte et al., 2024; Ramachandran et al., 2021; Zhang et al., 2022). They also have the capacity to alter the exudation of roots and the existing microbial communities, creating an environment that is conducive to infection (Jin et al., 2024). At the same time, the interactions between beneficial and pathogenic microorganisms on the ecological niche and/or on the limiting resource is influenced by their ability to form biofilm, produce antimicrobial metabolites, use siderophores, and by chemical communication, while additional environmental factors like soil type, pH, moisture, nutrient availability, and abiotic stress can impact the outcome of these interactions (; Gu et al., 2020).
The advent of multi-omics technologies such as metagenomics, metatranscriptomics, proteomics, metabolomics, spatial imaging, and single-cell analyses has revolutionized knowledge of rhizosphere ecology and its dynamic feedback between plants, microbial communities and environmental conditions (; ). These strategies show that the rhizosphere is a complex network of life, in which plants can select beneficial partners, pathogens develop counterstrategies, and microbial communities as a whole suppress or promote disease (Li et al., 2021). This information unlocks new possibilities for microbiome engineering, synthetic microbial consortia, targeted biocontrol, and disease-suppressive soils to enhance sustainable and climate-resilient agriculture (Moretti et al., 2024; Pandey and Saharan, 2025).
While several reviews have covered immunity in plants, disease-suppressive microbiomes, or plant-microbe interaction in isolation, there is little integration of plants with beneficial microbes and pathogens that underpins the mechanistic response (Gupta et al., 2021; Mashabela et al., 2022). This review addresses the following points: (i) summarizing the molecular mechanisms responsible for plant-beneficial microbe-pathogen interactions, (ii) describing the role of plant immunity, root exudates, root microbe competition and metabolite-mediated signaling in shaping the rhizosphere, (iii) outlining recent advances in multi-omics technologies, (iv) discussing opportunities for microbiome engineering and synthetic microbial consortia, and (v) pinpointing future research priorities for sustainable crop protection by using the plant and soil microbiome.
2 The battle in the rhizosphere as a dynamic interaction
The rhizosphere is a dynamic environment that hosts a complex mix of physical, chemical, and ecological interactions among plants, beneficial microbes, and pathogens, all of which influence plant health and disease outcomes (Ling et al., 2022). The microbial recruitment, colonization and activity in this narrow soil zone are controlled by root exudates such as sugars, amino acids, organic acids, phenolics, flavonoids and signaling molecules (; Upadhyay et al., 2026). These exudates provide nutrients and chemical signals, which in turn can favor or prevent the proliferation of chemical signal favors or prevents the proliferation of beneficial microbes or pathogens and influence the assembly of the rhizosphere microbiome (Philippot et al., 2013; Upadhyay, 2026a, Upadhyay, 2026b). The rhizosphere is therefore the first line of defense in which plants actively select antagonistic fungi and plant growth-promoting rhizobacteria (PGPR) to strengthen their defense against invading pathogens (Vives-Peris et al., 2020).
Plants dynamically adjust their root exudation in response to pathogen attack to attract beneficial microbes that can produce antibiotics, siderophores, volatile organic compounds (VOCs), lytic enzymes and other bioactive metabolites that inhibit pathogen establishment. This adaptive reaction is called the “cry-for-help” strategy, which helps to promote disease suppression through enrichment of protective microbial communities (Liu et al., 2024). Similarly, plants facing aboveground herbivores benefit from recruitment of beneficial microbes that suppress herbivore damage and enhance the fitness of the plants, via an indirect defense system (Dicke and Baldwin, 2010).
On the other hand, pathogens alter the rhizosphere by exuding virulence effectors, phytotoxins, hydrolytic enzymes, and signaling molecules that weaken the plant’s defense mechanism, change the composition of root exudates, and disrupt the beneficial microbes (Upadhyay, 2026b; Yang et al., 2024). In addition, many pathogens alter the availability of carbon and iron to improve their competitive ability and to disrupt microbial quorum sensing (Rovenich et al., 2014). This means that ecological niche, nutrient and iron competition, as well as production of antimicrobial metabolites and disruption of signaling pathways, play a major role in the establishment of pathogens and/or disease suppression (; Du et al., 2025).
Soil physicochemical properties like pH, moisture, temperature, organic matter and agricultural management practices play a crucial role in determining the outcome of this ecological competition (). Recent developments in multi-omics technologies such as metagenomics, metatranscriptomics, metabolomics and imaging have made the rhizosphere a more complex biochemical network with coordinated signaling, metabolic exchange and microbial interactions (Rajguru et al., 2024). The comprehension of these mechanisms opens up the doors for microbiome engineering, developing synthetic microbial consortia, and targeted biocontrol strategies to improve disease suppression and sustainable agriculture (Dubey et al., 2025; Sahoo et al., 2025).
2.1 Physical and chemical landscape of the rhizosphere
The rhizosphere is a dynamic microenvironment influenced by root architecture, soil physicochemical properties and root-microbe interaction (Fadiji et al., 2025). The physical and chemical properties control microbial recruitment, nutrient availability and may influence the outcome of interactions between plant and beneficial microbes and pathogens (Pantigoso et al., 2022). The integrated physical and chemical landscape of the rhizosphere and its effect on plant-microbe interaction is shown in Figure 1. While soil moisture, pH, temperature, gaseous exchange, and redox conditions affect microbial activity and nutrient transformations, root exudates play a role as central regulators, affecting microbial recruitment, nutrient availability and metabolic communication. All these physicochemical drivers contribute to shaping microbial community assembly, competition, and biochemical signals, which ultimately affect nutrient uptake, plant immunity, disease suppression, and the overall functionality of the rhizosphere.
Figure 1
2.1.1 Physical structure of the rhizosphere
2.1.1.1 Soil aggregation and microstructure
At all times, plant roots change the soil architecture by creating aggregates, binding soil particles and modifying the pore network (Hamza et al., 2025). The polysaccharide-rich mucilage secreted by the roots promotes soil cohesion, water retention, and formation of microhabitats (Li et al., 2024). These aggregates create microsites with different moisture, oxygen and organic carbon levels and thus create a greater diversity of niches for microbes (Khabir et al., 2023).
2.1.1.2 Water and oxygen gradients
The root water uptake and respiration generate strong moisture gradients and oxygen gradients, which strongly affect the distribution of microorganisms (Tan et al., 2021). The rhizoplane is dominated by aerobic microorganisms, and oxygen-limited microsites by anaerobic and microaerophilic microorganisms (). Water depletion zones can also control nutrient diffusion and the mobility of chemicals in the rhizosphere (York et al., 2016).
2.1.1.3 Root surface topography
Root hairs, border cells and exudate coatings generate unique micro-habitats that help microbial attachment and colonization (Omelyanchuk et al., 2024). The rhizoplane is therefore typically more microbiologically active than the bulk soil due to a higher availability of attachment sites and hot spots of nutrients.
2.1.2 Chemical properties of the rhizosphere
2.1.2.1 Root exudates and nutrient hot spots
Sugars, amino acids, organic acids, phenolics, fatty acids, and signaling molecules are among the key chemical components of the rhizosphere, called root exudates, that dictate the rhizosphere processes (Sibanyoni et al., 2026). These compounds act as carbon sources and as signals to attract desirable microorganisms, to control the composition of microorganisms and to affect the activity of pathogens (Feng et al., 2025). They can be very dynamic and can change depending on the nutrient status of the soil, the plant growth stage, and environmental stress (de Haas et al., 2025).
2.1.2.2 pH modification
Rhizosphere pH changes are actively done by plants through the process of extrusion of protons and the release of organic acids (Kanwar et al., 2025). Rhizosphere acidification may facilitate the uptake of nutrients like phosphorus and also affect the structure of microbial communities (Lurthy et al., 2021). In contrast, nitrate uptake tends to cause alkalinization, and consequently, nitrate-induced chemical gradients can occur at a distance of only a few millimeters from the root surface (Wang and Tang, 2018).
2.1.2.3 Nutrient gradients (N, P, Fe, K, micronutrients)
Zones of nutrient deficiency and sufficiency develop around the root, influencing microbial activity and plant-microbe interactions (York et al., 2016). In addition to iron, gradients of nitrogen, phosphorus and other nutrients affect microbial competition, survival mechanisms and production of specialized metabolites, favoring microorganisms that have the ability to produce siderophores, which are involved in disease suppression (Gu et al., 2020).
2.1.2.4 The study of redox potential and ion dynamics
The root metabolism, microbial respiration and soil water content (Husson, 2013) influence rhizosphere redox potential. These will affect the bioavailability of the nutrients, especially the Fe²+/Fe³+ ratio, as well as the activity of beneficial microbes that participate in nitrogen fixation and biological control (Molnár et al., 2023).
2.1.3 Explored interactions between physical and chemical factors
The rhizosphere is a unified physicochemical system, where physical and chemical properties work together to regulate the assembly of microbial communities and the functioning of the ecosystem as a whole, and not separately (; Upadhyay, 2026b). To enhance nutrient-use efficiency and develop strategies for sustainable agriculture based on the microbiome, understanding these interactions is crucial (Griffin et al., 2024). Root mucilage, for instance, regulates water distribution and nutrient diffusion; soil aggregation affects oxygen supply and microbial metabolism; root-induced pH gradients affect enzyme activity, carbon turnover and nutrient transformations (Oburger et al., 2022). These factors collectively influence resource availability, niche differentiation of microorganisms, and signaling networks which regulate interactions between plant beneficial microbes and pathogens (Philippot et al., 2013). Soils are therefore strongly affected by soil structure, moisture, oxygen, pH and gradients of nutrients, which all have an impact on microbial colonization, metabolic activity, plant performance, and disease suppression (Hinsinger et al., 2009; Philippot et al., 2013).
2.1.3.1 Nutrient acquisition
The chemical and physical environment around the rhizosphere can affect the transformation, movement, and bioavailability of nutrients (Liu et al., 2022). Beneficial microbes improve nutrient acquisition by biological nitrogen fixation, phosphate solubilization, mobilization of iron and mineral weathering, while pathogens adversely affect nutrient acquisition by damaging root tissue and other nutrient fluxes (Richardson et al., 2009; Timofeeva et al., 2023). Microbiological recruitment, nutrient cycling and competitive interactions in the rhizosphere are additionally regulated by root-induced changes in pH and exudate composition (Feng et al., 2024; Philippot et al., 2013).
2.1.3.2 Photosynthetic efficiency
The effects of rhizosphere processes on photosynthetic performance are indirect through control of nutrient availability and plant stress responses. Beneficial microbes stimulate the biosynthesis of chlorophyll, increase the stability of PSII, increase the uptake of nutrients, and regulate the hormones and metabolism in the plant to reduce oxidative stress (Olanrewaju et al., 2017). In contrast, pathogen infection causes a reduction in photosynthetic efficiency through the activation of reactive oxygen species (ROS), vascular dysfunction and stomatal impairment (). Thus, water and nutrient availability (regulated by the rhizosphere) directly impact carbon assimilation and plant productivity (Vurukonda et al., 2016).
2.1.3.3 Carbon allocation
Carbon allocation is related to ecological processes in the rhizosphere and metabolism of plants. A significant portion of the photosynthetically fixed carbon is also released as root exudates that can be used to guide the assembly of the microbial community and to selectively attract beneficial microbes (Sasse et al., 2018). The balance of carbon partitioning for growth, defense, and rhizosphere investment is continually shifted by microbial colonization, pathogen attack, and availability of nutrients. Carbon reallocated to defense pathways is lost from other processes, including belowground carbon allocation, which is accompanied by an increase in nutrient uptake and stress tolerance by beneficial microbes ().
2.1.3.4 Root system architecture
The root architecture is the result of the interactions between physicochemical conditions and microbial signaling. Beneficial microbes induce phytohormone production, volatile compounds and/or signaling molecules that promote root elongation, lateral root emergence and root hair extension, which enhance resource acquisition and soil exploration (Lugtenberg and Kamilova, 2009; Vacheron et al., 2013; Upadhyay, 2026c). On the other hand, pathogens have a negative effect on root growth due to direct damage to tissues and interference with hormones, microbial habitat changes and rhizosphere interaction changes (; Pieterse et al., 2014).
2.1.3.5 Water-use efficiency
The water-use efficiency is a result of the interaction and coordination between soil, roots, and microorganisms. Microbial extracellular polymers, mucilage, pore connectivity and soil aggregation control water retention and make it available to the rhizosphere (; ; Vurukonda et al., 2016). Beneficial microbes enhance soil aggregation by producing exopolysaccharides, improve root hydraulic conductivity, osmotic adjustment and signaling in response to water stress (; Kumar et al., 2024; Timmusk et al., 2014; Vurukonda et al., 2016). Pathogenic microorganisms, on the other hand, cause damage to the vascular tissues, leading to a decrease in the uptake of water and an increase in drought susceptibility. Therefore, the combined action of physicochemical and biological processes in the rhizosphere is essential for efficient water use (Philippot et al., 2013; Vurukonda et al., 2016).
Together, the physical and chemical characteristics of the rhizosphere control resource availability, the metabolism of microorganisms, communication between microorganisms and plants, and competition between microorganisms and pathogens, and thus influence plant-beneficial microbe-pathogen interactions (; Philippot et al., 2013; Zhuang et al., 2024). These integrated processes govern microbiome assembly, plant health, disease suppression and crop resilience in the face of fluctuating environmental conditions, and lay the foundation for microbiome-based sustainable agriculture (Dubey et al., 2025; Trivedi et al., 2020).
3 Plant strategies in triangular warfare
Plants use a range of integrated defense mechanisms, including complex hormonal crosstalk (e.g. salicylic acid, jasmonic acid and ethylene), which fine-tunes defensive signaling networks, as well as sophisticated innate immune responses including PTI and ETI and root-mediated recruitment and modulation of beneficial microbes that collectively shape plant resistance and resilience against pathogens while balancing growth and stress responses (Pandey et al., 2025). Plants use various interconnected strategies such as selective root exudation, immune priming, rhizosphere chemical modulation and recruitment of beneficial microbes to build a resilient rhizosphere microbiome that is resistant to invasion by pathogens and to maintain a healthy plant state (Figure 2).
Figure 2
3.1 Plant innate immunity
Plant innate immunity (de Wit, 2007) is the natural defense mechanism in which plants recognize and react to the invasion of pathogens, including bacteria, fungi, viruses, nematodes and insect herbivores. Unlike animals that possess an adaptive immune system, plants are unable to rely on adaptive immune processes for defense, and therefore are dependent on innate immune processes (Spoel and Dong, 2012). Pattern-triggered immunity (PTI), which is triggered by cell-surface pattern recognition receptors (PRRs), and ETI, which is mediated by intracellular nucleotide-binding leucine-rich repeat (NLR) proteins that identify pathogen effectors, make up this multilayered surveillance system (Nabi et al., 2024). To check pathogen growth and spread, these immune layers act synergically to trigger downstream signaling pathways that involve influx of calcium, ROS, mitogen-activated protein kinase (MAPK) cascades, phytohormones and defensive gene expression (Dodds et al., 2024).
3.1.1 Pattern triggered immunity
The first level of innate immunity in plants, called PTI, is activated by the recognition of conserved microbial entities called pathogen- or microbe-associated molecular patterns (PAMPs/MAMPs) (Li et al., 2016). Plant cells have PRRs on the surface that recognize these molecular patterns, such as bacterial flagellin, fungal chitin, elongation factor Tu (EF-Tu), and lipopolysaccharides (Trdá et al., 2015). Once the PAMPs are recognized by PRRs like FLS2, EFR and CERK1, a signaling pathway is activated (Macho and Zipfel, 2014). This cascade leads to a swift influx of calcium (Ca2+) into the cell, formation of reactive oxygen species (ROS), activation of mitogen-activated protein kinase (MAPK) pathways, and a wide transcriptomic reprogramming (Köster et al., 2022). The early responses lead to outputs of defense mechanisms, which collectively reduce the ability of the pathogen to colonize the plant, such as production of antimicrobial compounds, induction of pathogenesis-related (PR) genes, and reinforcement of the cell wall (callose deposition) (Wu et al., 2014a). In connection with its ability to provide broad-spectrum and long-lasting resistance and its role as an important defense barrier that pathogens need to breach through effector secretion, PTI is tied to ETI (Yu et al., 2024).
3.1.2 Effector-triggered immunity
The second layer of plant innate immunity is called effector-triggered immunity (ETI), and it works as a powerful intracellular defense mechanism to support PTI, the first layer (Nguyen et al., 2021). ETI is activated by the detection of pathogen-derived effector proteins by the intracellular receptors that contain nucleotide-binding leucine-rich repeats (NLRs), with the pathogens providing the effector proteins to suppress PTI and facilitate infection. Unlike PTI, which provides general defense against pathogens, ETI is characterized by highly specific defense responses, such as transcriptional reprogramming, production of reactive oxygen species (ROS), influx of calcium and activation of mitogen-activated protein kinase (MAPK) cascades, and these responses are generally strong and often persistent (Nguyen et al., 2021). One of the characteristics of ETI is hypersensitive response (HR), also known as localized programmed cell death at the infection site, due to which pathogen growth is restricted (Wu et al., 2014b). Additionally, ETI increases defense pathways that may have been inhibited by pathogens and effectors and fortifies systemic acquired resistance (SAR) (Ding et al., 2022). Recent studies have demonstrated that the two are not completely independent, with both having downstream-signaling components in common and PTI and ETI amplifying each other’s responses (Yuan et al., 2021). ETI allows plants to develop a comprehensive multi-layer defense system that provides an effective barrier to pathogen penetration without adversely affecting other stress factors and growth (Islam et al., 2024).
3.1.3 Hormonal crosstalk in defense during rhizosphere triangular warfare
The rhizosphere harbors a complex environment of beneficial microbes, pathogens and plant roots, with their interactions being dynamic and competitive (). Such interactions between phytohormones constitute an important regulatory node in this tripartite warfare scenario, enabling plants to reduce fitness costs whilst interpreting multiple microbial signals and initiating appropriate defense strategies (Pieterse et al., 2012). Plant hormones do not act alone, but rather in concert to affect trade-offs in growth stress, recruitment of microbes, and activation of immunity (Pieterse et al., 2012).
3.1.3.1 Core defense hormones: salicylic acid, jasmonic acid, and ethylene
The main regulator of resistance to biotrophic and hemibiotrophic diseases, such as several bacteria and fungi that infect roots, is salicylic acid (SA) (Denancé et al., 2013). The SAR is built up, and pathogenesis-related (PR) genes are transcriptionally activated when SA accumulates, resulting in sustained plant defense (Zheng and Xinnian, 2013). The stimulation of “good” microorganisms associated with disease suppression by SA signaling also indirectly impacts the composition of the microbial community because of changes in rhizosphere exudation patterns (Lebeis et al., 2015). In addition to its extensive role in abiotic stress tolerance, salicylic acid (SA), also known as salicylate, is ubiquitous in terrestrial plants and has lately gained recognition for its role in defense mechanisms and plant responses to pathogen stressors (). The pathogen-specific, interconnected, and overlapping crucial role of SA in plant defense and immunity has been reported in several studies thus far (Ullah et al., 2023). According to Ullah et al. (2023), salicylic acid is principally in charge of triggering defense reactions against biotrophic and hemibiotrophic infections.
The ethylene (ET) and jasmonic acid (JA) pathways are mostly triggered by herbivorous insects and necrotrophic diseases (Pieterse et al., 2012). JA and ET induce the expression of defense genes that encode antimicrobial peptides, secondary metabolites and enzymes that strengthen the cell wall (Van der Does et al., 2013). Of particular note, many beneficial rhizosphere microbes can induce a primed state of defense (ISR) through the JA/ET pathway, which allows for rapid and strong responses when attacked by pathogens without activation of a basal defense (van Loon et al., 1998). To defend plants against infections, SA and JA phytohormones work both antagonistically and cooperatively in a complex web of signaling pathways ().
3.1.3.2 Hormonal antagonism and synergy in rhizosphere
The antagonistic interaction between the SA and JA pathways, which enables plants to adapt defenses to the lifestyle of pathogens, is a characteristic of hormonal crosstalk (Pieterse et al., 2012). By triggering JA signaling to inhibit SA-mediated defenses or vice versa, numerous soil-borne pathogens try to control this antagonistic relationship (Zhang et al., 2025). By adjusting hormone signaling, helpful bacteria resist this tactic and guarantee efficient defense activation without jeopardizing beneficial plant-microbe relationships (Zhu et al., 2022). Furthermore, there are synergistic interactions between JA and ET, such interactions being effective in controlling root-associated defensive responses and ISR (Shoresh et al., 2005). When no pathogen is a threat, this hormonal control ensures that defense is activated in a time- and space-limited fashion, this way preventing unnecessary energy loss (Vos et al., 2015).
3.2 Integrated signaling network governing rhizosphere triangular warfare
Plants use an integrated signaling network to identify and discriminate beneficial rhizosphere microbes from invading pathogens and initiate appropriate defense responses (Pieterse et al., 2014). The first line of defense is PTI, which is activated by the recognition of conserved microbial molecules by pattern recognition receptors (PRRs) (Zipfel, 2014). PTI triggers rapid Ca²+ influx, production and accumulation of reactive oxygen species (ROS), activation of mitogen-activated protein kinase (MAPK) cascades and activation of WRKY transcription factors, which results in the induction of defense-related genes. Pathogens use effector proteins to enter host cells and block immune signaling as a strategy to overcome PTI (; Xiangzong and Shuqun, 2013). The intracellular nucleotide-binding leucine-rich repeat (NLR) receptors detect these effectors and trigger ETI, which is a more powerful and persistent defense with enhanced ROS accumulation, MAPK signaling and localized immune responses (Jones and Dangl, 2006).
These immune pathways are further interconnected by hormonal signaling and help mediate pathogen resistance while maintaining healthy interactions with microorganisms. Nonexpresser of pathogenesis-related genes 1 (NPR1) is the central regulator of SA-mediated signaling and systemic acquired resistance (SAR) (Zheng and Xinnian, 2013; Pieterse et al., 2012; Wasternack and Song, 2017), while MYC2 coordinates jasmonic acid (JA)-dependent signaling associated with ISR (Pieterse et al., 2012; Wasternack and Song, 2017). Further, ethylene-responsive transcription factor EIN3 interacts with JA signaling to boost defense responses without compromising rhizosphere interactions. When combined, these interconnected signaling pathways coordinate microbial recognition, immune activation and hormonal control, allowing plants to control pathogens while maintaining the rhizosphere beneficial microbial flora (; Pieterse et al., 2014) (Figure 3).
Figure 3
4 Molecular mechanisms leading to triangular interactions (plant-beneficial microbe–pathogen)
The rhizosphere is a constantly changing molecular interface in which plants, beneficial microbes, and pathogens interact in complex ways, with their interconnected signaling processes playing a key role in plant health, plant microbiome assembly and disease outcome (Yang et al., 2024). For plants to distinguish between beneficial microbes and pathogens, they have innate immune system mechanisms that involve pattern recognition receptors (PRRs) triggering PTI and intracellular nucleotide-binding leucine-rich repeat (NLR) receptors detecting pathogen effectors to initiate ETI (Nabi et al., 2024). Salicylic acid (SA), JA, and ET signaling further regulate this immune specificity by coordinating defense responses and ensuring beneficial microbial association (Yang et al., 2015). In parallel, plants influence rhizosphere microbiome structure by their dynamic exudation of primary and secondary metabolites that serve as nutrient sources and signaling molecules to attract beneficial microbes, especially under stress (Wankhade et al., 2025). Beneficial microbes subsequently boost the plant’s fitness by synthesizing antimicrobial metabolites, volatile organic compounds, siderophores, phytohormones and immune-modulating compounds that reduce pathogen virulence and lead to systemic resistance (ISR) at low fitness costs (Pieterse et al., 2014). In addition to these plant-mediated processes, there is a synergistic molecular network in the rhizosphere, involving direct microbial competition through antibiosis, nutrient sequestration, and niche exclusion that helps maintain rhizosphere homeostasis and reduce the development of diseases (Jamil et al., 2022) (Table 1).
Table 1
| Mechanism | Description | Role in tripartite interaction (plant-beneficial microbe-pathogen) | References |
|---|---|---|---|
| Root exudate signaling | Plants release root exudates (e.g., amino acids, sugars, organic acids) that act as chemical signals in the rhizosphere. | Attracts beneficial microbes (PGPR/PGPF) and can shape microbial community composition; it also influences pathogen behavior. | Yang et al., 2024 |
| Microbial chemotaxis and attachment | Beneficial microbes detect root exudates via chemoreceptors and migrate toward roots; attach using adhesins and exopolysaccharides. | Enables beneficial microbes to colonize niches and compete with pathogens for space and resources. | Yang et al., 2024 |
| Pattern-triggered immunity (PTI) | Plant PRRs (Pattern recognition receptors) recognize microbial patterns (PAMPs/MAMPs) to trigger basal immune signaling. | First line of plant defense; can be activated by pathogens and also modulated by beneficial microbes to “prime” defenses. | Yang et al., 2024 |
| Effector-triggered immunity (ETI) | Pathogen effectors are recognized by plant R-proteins, leading to robust immune responses. | Pathogens use effectors to suppress defenses, while beneficial microbes can indirectly enhance host alertness. | Liu et al., 2025 |
| Induced systemic resistance (ISR) | Beneficial microbes (PGPR/PGPF) trigger systemic defense via JA and ET signaling pathways. | Enhances plant resistance against pathogens without direct pathogen exposure, critical in tripartite defense. | Yu et al., 2022 |
| Quorum sensing (QS) | Microbial communication via diffusible signals (e.g., AHLs) affects gene regulation, biofilm formation, and virulence. | Beneficial microbes use QS for root colonization/biofilms; pathogens use QS to coordinate infection. Competitive QS outcomes shape interactions. | Farrar et al., 2014 |
| Secondary metabolites/VOCs | Beneficial microbes release volatile organic compounds (VOCs) and secondary metabolites (e.g., siderophores) that influence plant signaling and microbial competition. | VOCs can induce ISR and suppress pathogen growth, enhancing plant resilience. | Jain et al., 2024 |
| Hormonal crosstalk modulation | Interactions involve phytohormones (auxins, cytokinins, SA, JA, ET), which are produced/modified by microorganisms and perceived by plants. | Beneficial microbes manipulate hormonal balance to stimulate growth/defense; pathogens manipulate hormones to suppress immunity. | Liu et al., 2025 |
| Biofilm formation and competition for niches | Beneficial microbes form biofilms on roots that block pathogen colonization and provide physical/chemical defense. | Biofilms enhance survival/colonization of beneficial microbes, reducing pathogen establishment. | Farrar et al., 2014 |
| Metabolome reshaping and chemical dialogues | Complex chemical exchanges (metabolites/signals) define recruitment, suppression, and activation of defense and growth pathways. | Metabolomic profiling reveals how tripartite signals influence plant defense prioritization. | Sibanyoni et al., 2026 |
Molecular mechanisms driving plant-beneficial microbe-pathogen interactions.
AHLs, N-Acyl homoserine lactones; PGPR, Plant Growth Promoting Rhizobacteria; PGPF, Plant Growth Promoting Fungi; PAMPs, Pathogen-Associated Molecular Patterns; MAMPs, Microbe-Associated Molecular Patterns; SA, Salicylic Acid.
4.1 Secretion systems
The microbial secretion systems play an important role in plant-beneficial microbe-pathogen interactions through virulence regulation, microbial competition, and host colonization (Trivedi et al., 2020; Upadhyay, 2026d). A few of these, including the Type III (T3SS), Type IV (T4SS) and Type VI (T6SS) secretion systems, are critical in determining rhizosphere ecology (Green and Mecsas, 2016).
The T3SS is mainly associated with Gram-negative phytopathogens, which secrete effector proteins directly into plant cells, resulting in a suppression of PTI and promoting the infection process (Galán and Waksman, 2018). Plants do have specific intracellular immune receptors, however, that detect effectors and trigger ETI, thereby preventing pathogens from colonizing the plant ().
The T4SS is active in pathogenic and mutualistic microorganisms, and is responsible for the delivery of proteins or nucleic acids into either plant cells or microbial cells. Pathogenic bacteria use T4SS to increase their virulence, but positive microorganisms use it to facilitate horizontal gene transfer, biofilm formation and stable association with plant roots, thus promoting long-term plant-microbe relations ().
The T6SS is mainly responsible for intermicrobial competition by injecting antibacterial effectors into the cells of the neighboring microorganisms, thereby eliminating competitors and increasing the ecological fitness of the T6SS producer (Russell et al., 2014). Rhizobacteria are often able to use T6SS for pathogen protection, thereby creating disease-suppressive microbial communities around plant roots.
In addition to their function in pathogenicity, secretion systems are also important in beneficial plant-microbe communication. The plant growth-promoting rhizosphere bacteria produce protein effectors and/or signaling molecules that regulate plant immunity, activate ISR, improve nutrient uptake, and colonize the roots without causing disease (Trivedi et al., 2020). Together, T3SS, T4SS and T6SS act as multi-functional molecular platforms that communicate microbial interaction, immune modulation and rhizosphere communication, which in turn dictate the stability of the microbiome and the resilience of the ecosystem ().
4.2 Multi-omics perspectives
The recent developments of multi-omics technologies have revolutionized our understanding of plant-beneficial microbe–pathogen interactions, facilitating a system-wide analysis of the processes occurring in the rhizosphere (Kumar et al., 2023; Upadhyay et al., 2026). Genomics and metagenomics provide insights into the diversity of microorganisms and functional genes linked to nutrient uptake, secondary metabolite synthesis, and pathogen resistance (). Transcriptomics studies the changes in plant and microbial gene expression that occur in response to their changing environments; during beneficial and pathogenic interactions, it provides information on how plants respond to microbial colonization, as well as microbial strategies for colonization (Roy and Solomon Maina, 2024). In addition to transcriptomics, proteomics is used to detect secreted effectors, enzymes and signaling proteins that regulate immune responses and competition with microorganisms, while metabolomics is used to decipher the chemistry of dialogue between roots, microorganisms and microbial metabolites in the form of signaling molecules (Mhlongo et al., 2018; Sahoo et al., 2025; Secomandi et al., 2025). A combination of these complementary omics approaches can help in reconstructing the rhizosphere triangle regulatory network between plant immunity, microbial activity, and environmental cues, thereby delivering a comprehensive understanding of rhizosphere triangle interactions and microbiome-based approaches for sustainable crop protection (Roy and Solomon Maina, 2024; Kumar et al., 2023).
4.3 Metagenomics for community profiling
By providing culture-independent characterization of the rhizosphere microbiomes, metagenomics has emerged as a key strategy for investigating microbe-pathogen interactions in plant–beneficial contexts (Fadiji et al., 2021). The Amplicon sequencing method of 16S rRNA and ITS regions can generate high-resolution taxonomic profiles that can explain the relationship between the genotype of plants and developmental stage on the one hand and the microbial community composition on the other, depending on the environmental conditions (Quiza et al., 2023). Shotgun metagenomics, on the other hand, reveals functional genes involved in nutrient cycling, secondary metabolite biosynthesis, quorum sensing, antibiotic production, and virulence, thereby giving a better understanding of the microbial ecological functions (). Comparative metagenomic analysis also shows that disease suppression can be achieved by increased functional abundance of microbial guilds and that microbial signatures linked with pathogen exclusion and beneficial microbial recruitment can be identified (Tracanna et al., 2021; Xiao et al., 2024). Therefore, metagenomics provides a strong platform for the understanding of the assembly of the microbiome and its role in rhizosphere health and disease suppression (Rajguru et al., 2024).
4.4 Transcriptomics for changes in gene expression of plants and microorganisms
Transcriptomics offers dynamic insights into gene expression changes associated with the interactions between plants and beneficial microbes and pathogens as they colonize, compete and infect the host plant (; Nobori et al., 2022). The coordinated regulation of PTI, ETI, hormone signaling and secondary metabolism in response to beneficial microbes and pathogens (Wang et al., 2020) has been discovered by plant transcriptome analyses. In general, beneficial microbes create a transcriptionally “primed” state that results in a rapid response to defense activation with low fitness costs (Pieterse et al., 2014). On the other hand, pathogen transcriptomes indicate virulence-related pathways, while microbial transcriptomes reveal genes related to root colonization, production of antimicrobial metabolites and communication with the host (Du et al., 2022). Moreover, the plant and microbial dual RNA sequencing enables the simultaneous profiling of both plant and microbial transcripts, which is unprecedented and provides novel insights into cross-kingdom signaling and coordinated regulatory networks that dictate disease resistance and rhizosphere function (Jain et al., 2024; Zhang et al., 2019).
4.5 Metabolomics for root exudate and metabolite mapping
Metabolomics is used to characterize metabolites excreted from plant roots and related microorganisms and to gain a comprehensive insight into the chemical interactions of plant-beneficial microbes and pathogens (Sibanyoni et al., 2026). The ability to control which sugars, amino acids, organic acids, phenolics, flavonoids and specialized metabolites are excreted from plant roots is strongly dynamic and changes throughout microbial colonization and pathogen attack, as revealed by the metabolomics of root exudates (Ku et al., 2025). These metabolites serve as a source of nutrients and potent signaling molecules that attract beneficial bacteria, inhibit pathogenic bacteria and regulate microbial behavior (Feng et al., 2024). Furthermore, the “cry for help” hypothesis was supported by metabolomics data, in which metabolites produced during stress selectively increase the abundance of protective microbial taxa and increase antagonistic activities (Rizaludin et al., 2021). Meanwhile, microbial metabolomics can discover antibiotics, siderophores, volatile organic compounds (VOCs) and quorum-sensing molecules that mediate microbial competition and immune-priming. Metabolomics integration with metagenomics and transcriptomics consequently allows the correlation of metabolic signatures with functional genes and pathways, thus offering a systems-level view of rhizosphere communication and disease suppression (Mmotla et al., 2025; Go et al., 2024; Sibanyoni et al., 2026).
Multiple metabolites produced in the rhizosphere by the roots have key roles in regulating the assembly of the rhizosphere microbiome. Coumarins, such as scopoletin and fraxetin, selectively promote the growth of beneficial microbes and mobilize iron, as well as inhibit soil-borne pathogens (Voges et al., 2019). Flavonoids and strigolactones can promote beneficial interactions between plant growth-promoting bacteria and arbuscular mycorrhizal fungi (Hassan and Mathesius, 2012), while benzoxazinoids can restructure the microbial communities and suppress pathogens (Hu et al., 2018). Similarly, organic acids like citrate and malate promote nutrient-solubilizing microorganisms and enhance nutrient availability, including P and Fe (Jacoby et al., 2017) (Figure 4).
Figure 4
These metabolites are secreted by specialized transporters at the level of the membrane, which tightly regulate their secretion. Altogether, these sugar efflux (SWEET) transporters, coumarin export (MATE) transporters, antimicrobial and signaling compound export (ABC) transporters and malate export (ALMT) transporters help regulate the recruitment of microorganisms and mobilization of nutrients (; Kang et al., 2011; Voges et al., 2019). In the presence of pathogens, plants redirect the activity of transporters and exudation of metabolites to strengthen defense-related molecules and to limit molecules that are beneficial for pathogen growth, driving plants to keep rhizosphere homeostasis and favoring beneficial microbial communities (Devanna et al., 2021; ).
4.6 Signaling molecules
The complexity of the interactions between the plant, beneficial microbes and pathogens in the rhizosphere is managed by chemical signaling (). The collective regulation of microbial communication, competition and plant defense involves antimicrobial metabolites, volatile organic compounds (VOCs) and quorum-sensing (QS) molecules (Jamil et al., 2022). In response to microbial population density, QS molecules such as N-acyl homoserine lactones and autoinducing peptides act as regulators for biofilm formation, colonization of roots, production of antibiotics, and virulence (Nachiyar et al., 2025). Pathogens use QS to increase virulence, which can be sensed or modulated by plants to reduce pathogen fitness, but beneficial microbes can use QS to enhance ecological fitness and disease suppression (Zheng et al., 2025).
The beneficial microbial VOCs are long-distance signaling molecules that promote plant growth, trigger immune reactions, and suppress the growth of pathogens without physical contact (Rani et al., 2023; Raza et al., 2021). They may also impact phytohormone signaling and inhibit pathogen sporulation and mycelial growth, while pathogen VOCs can alter plant metabolic activities to promote infection (; Surovy et al., 2023). Furthermore, at sub-inhibitory levels, antimicrobial metabolites such as antibiotics, lipopeptides, phenazines, and siderophores act as signal molecules to control microbial interactions, immune priming, and gene expression, which provides an antagonistic effect on microorganisms (Shao et al., 2024). These QS molecules, VOCs, and antimicrobial metabolites interact with each other to form an integrated chemical communication network, regulating plant immunity, microbial cooperation, and pathogen inhibition in rhizosphere triangular interactions (Jamil et al., 2022; Sibanyoni et al., 2026).
4.7 Medications such as lipopeptides and Signal Transduction Pathways
Lipopeptides are multifunctional microbial metabolite that directly inhibits microbial growth and act as an activator of plant defense signaling, hence, they are central regulators of plant-beneficial microbe-pathogen interactions (Ding et al., 2025). Surfactins, fengycins, iturins and viscosins are cyclic lipopeptides produced mainly by Bacillus and Pseudomonas species that disrupt the membrane of pathogens, inhibit spore germination, and suppress biofilm formation (). In addition to these antimicrobial actions, they are microbe-associated molecular patterns (MAMPs) which trigger PTI (; Farace et al., 2015; Hudson et al., 2024).
Lipopeptides that are recognized by plasma membrane receptors trigger rapid influx of Ca2+, production of reactive oxygen species (ROS) and MAPK signaling, resulting in the activation of defense genes that are involved in cell wall reinforcement, synthesis of pathogenesis-related proteins and production of secondary metabolites (Escocard de Azevedo Manhães et al., 2021; Ma et al., 2024). Lipopeptide signaling also interacts with JA and ET signaling pathways to reinforce induced resistance (Jourdan et al., 2009). Furthermore, lipopeptides modulate quorum sensing, biofilms, and microbial competition, resulting in improved pathogen inhibition and rhizosphere stability (Zhao et al., 2026). As such, lipopeptides are antimicrobial molecules and immune system activators that connect microbial antagonism and plant immune activation and are important players in rhizosphere triangular warfare (). Additionally, recent research has demonstrated that lipopeptides produced from Bacillus can enhance systemic resistance against bacterial and fungal infections by activating JA/ET-associated defense signaling (Yang et al., 2023). All these metabolites create a chemically integrated communication network which regulates beneficial microbial recruitment and pathogen suppression in the rhizosphere (Figure 4).
5 Application of rhizosphere triangular warfare in plant protection
Rhizosphere triangular warfare offers a mechanism to create sustainable plant protection strategies that combine plant immunity, beneficial microbes, and pathogen ecology ().
Prescribed in this framework, however, is not only the use of chemical pesticides, but the use of naturally occurring biological interactions to increase disease suppression, crop robustness and rhizosphere stability.
Beneficial microbes such as Bacillus spp., Pseudomonas spp., Trichoderma spp. and Streptomyces spp. suppress pathogens by different mechanisms, including antibiosis, lipopeptides, bacteriocins and volatile organic compounds (VOCs), iron chelating (siderophore), niche exclusion and enzymatic degradation of pathogen cell walls, which limit pathogen establishment and virulence (Zhou et al., 2021).
These microorganisms trigger ISR, including JA- and ET-mediated pathways, to provide plants with more efficient and timely defense responses at little fitness cost (Yu et al., 2022).
Plants also support these interactions by changing their exudation patterns, such as the secretion of sugars, organic acids, flavonoids, and coumarins, to specifically attract protective microbes and thus build a disease-suppressive rhizosphere microbiome (Du et al., 2025).
Mechanistic understanding of these interactions has helped the development of microbial biocontrol agents, synthetic microbial consortia and microbiome-based soil management for increased functional stability and long-term disease suppression (Niu et al., 2020).
The development of multi-omics, metabolomics and microbiome engineering has enabled the identification of keystone taxa, functional genes, and metabolic traits that dictate microbiome performance across a range of environmental conditions (Go et al., 2024).
Real-world conditions expose plants and their associated microbiomes to a wide range of environmental elements, such as soil properties, climate, and seasonal variations, in contrast to laboratory-controlled trials (Singh et al., 2020).
These factors affect the functionality and composition of microbial communities, making it more difficult to forecast and control plant-microbiome interactions consistently in various agricultural contexts (; French et al., 2021).
The discoveries open avenues for precision control of rhizosphere microbial communities, which can contribute to the development of environmentally friendly alternatives to chemical pesticides and promote sustainable and climate-resistant farming practices (Rezaee Danesh, 2025) (Table 2).
Moving forward, future plant protection strategies are anticipated to combine the principles of microbiome engineering, synthetic ecology and precision agriculture to create rhizosphere communities that ensure the productivity of the crop in the face of the growing biotic and abiotic pressures.
The rhizosphere triangular warfare concept is not only a conceptual approach to the interaction between plants, microorganisms and pathogens, but also a foundation for next-generation crop protection with the microbiome.
Table 2
| Application | Mechanistic basis | Role of beneficial microbes | References |
|---|---|---|---|
| Biological Disease Control in Crops | Antagonism, competition, and induced systemic resistance (ISR). | Beneficial microbes inhibit pathogens via antimicrobial compounds, niche competition, and induction of plant defenses. | ; Singh et al., 2021 |
| Induced Systemic Resistance (ISR) | Jasmonic acid (JA)/ethylene (ET) signaling, primed defense. | Plant growth-promoting rhizobacteria (PGPR)/plant growth-promoting fungi (PGPF) (e.g., Pseudomonas, Trichoderma) prime the plant immune system for broad-spectrum resistance without pathogen contact. | Pieterse et al., 2014 |
| Microbiome Engineering for Crop Health | Root exudate recruitment, community assembly. | Manipulating rhizosphere communities to enrich protective microorganisms and suppress pathogens. | Li et al., 2021 |
| Biofertilizer Development | Nutrient mobilization and growth-defense trade-off. | Beneficial microbes enhance nutrient uptake (Indole-3-acetic acid, 1-aminocyclopropane- carboxylate deaminase, siderophores) while aiding disease suppression. | ; Singh et al., 2022a, Singh et al., 2022b, Singh et al., 2022c |
| Integrated Pest Management (IPM) | Multiple suppression mechanisms. | Beneficial microbes incorporated into IPM reduce chemical pesticide dependency and enhance sustainable control. | |
| Stress Resilience Enhancement | Synergistic immune and physiological regulation. | Microorganisms help plants resist both biotic and abiotic stress by modulating immunity and stress responses. | Palkina et al., 2025 |
| Post-Harvest Disease Mitigation | Surface colonization and induced defenses. | Microbial sprays reduce spoilage and pathogen growth on harvested produce. | Dehbi et al., 2023 |
| Commercial Bioprotectants/Biopesticides | Microbial inoculants as products. | Beneficial strains developed into commercial products to protect crops sustainably. | Dehbi et al., 2023 |
| Crop Quality and Yield Improvement | Growth promotion and disease suppression combined. | Improved yield and quality through PGPR/PGPF modulation of growth and immunity. |
Applications of rhizosphere triangular warfare (plant-beneficial microbe-pathogen interactions).
6 Future prospects
Mechanistic understanding and future advancements in rhizosphere triangular warfare will depend on the integration of emerging technologies with mechanistic understanding for the precision manipulation of plant-beneficial microbe-pathogen interaction (Trivedi et al., 2020). The combination of these three factors-artificial intelligence (AI), machine learning (ML), and multi-omics data-promises to enhance the prediction of microbial changes and disease outbreaks, as well as the positive functions of beneficial microbes, thereby enabling more effective data-driven microbiome engineering and precision crop management (Pace et al., 2025). Similarly, there are new opportunities to develop rhizosphere designer microbial consortia through genome engineering, the use of synthetic biology, nanotechnology-enabled delivery systems, and real-time rhizosphere biosensors that can manipulate rhizosphere processes to optimize root exudation and improve plant immunity (; Ragland et al., 2024; Rodríguez-Leal et al., 2017; Webster et al., 2024).
Meanwhile, the recent development of spatial transcriptomics, spatial metabolomics, and single-cell RNA sequencing will allow us to dissect the spatiotemporal organization of microbial communities and to uncover cell-specific signaling networks controlling rhizosphere interactions in a changing environment (Li et al., 2025). These practices, in conjunction with the development of beneficial microbes that are resistant to climatic conditions, will enhance the crop’s ability to resist several biotic and abiotic stresses (Gahlot, 2026).
Although considerable progress has been made in understanding the rhizosphere, the transfer of laboratory findings to the field is plagued by several problems, as rhizosphere interactions are highly dependent on plant genotype, soil heterogeneity, environmental variations, and the complexity of the microbial community. Predictive modelling, long-term field validation, and incorporating the multi-omics data with ecological and agronomic data are therefore recommended for future studies to further increase the stability and reproducibility of microbiome-based interventions. All these advances together will speed up precision microbiome engineering and will lay the groundwork for sustainable crop protection and climate-smart agriculture (Rezaee Danesh et al., 2025; Trivedi et al., 2020).
7 Conclusion
The rhizosphere is a highly dynamic biological interface that is characterized by molecular and ecological interactions between plants, beneficial microbes and pathogens, which constantly influence the health of plants, plant disease resistance and ecosystem functioning. This review shows that rhizosphere triangular warfare is not driven by independent plant or microbial processes but by four elements of coordinated immune signaling, recruitment of the plant-associated microbiome by rhizosphere exudates, microbial competition, and pathogen counterstrategies. Virulence effectors and immune-suppressive mechanisms of pathogens cause changes to rhizosphere communities and overcome host defense, while beneficial microbes ISR, produce antimicrobial metabolites and mobilize nutrients for plant fitness. This results in the balance of these antagonistic forces dictating microbiome assembly, disease suppression and crop resilience.
The new opportunities unlocked by multi-omics, spatial biology and microbiome engineering are revolutionizing the way these interactions are understood, and new microbial consortia are designed which are functionally stable and contain keystone microorganisms. A combination of these mechanistic insights with predictive modelling, synthetic biology, and precision will help to pave the way for next-generation microbiome-assisted crop protection strategies. The idea of rhizosphere triangular warfare offers a single framework for the interactions between plants, microorganisms and pathogens, and lays the groundwork for sustainable and climate-smart farming through precision rhizosphere engineering.
Statements
Author contributions
PS: Conceptualization, Writing – original draft, Writing – review & editing. RS: Conceptualization, Writing – original draft, Writing – review & editing. D-JG: Visualization, Writing – review & editing. MS: Writing – review & editing. B-QZ: Writing – review & editing. X-PS: Writing – review & editing. SU: Writing – review & editing. Y-RL: Funding acquisition, Supervision, Writing – review & editing.
Funding
The author(s) declared that financial support was received for this work and/or its publication. Central Government-funded Local Science and Technology Development Projects (GK-ZY23055011); Fund of Guangxi Academy of Agricultural Sciences (2026YT042).
Conflict of interest
The remaining author(s) declared that this work was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest.
The author(s) PS, RS, D-JG, MS and X-PS declared that they were an editorial board member of Frontiers, at the time of submission. This had no impact on the peer review process and the final decision.
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References
1
Abdul RahmanN. S. N.Abdul HamidN. W.NadarajahK. (2021). Effects of abiotic stress on soil microbiome. Int. J. Mol. Sci.22, 9036. doi: 10.3390/ijms22169036
2
AdedayoA. A.OlorunkosebiM. T. (2025). Coevolution dynamics of beneficial and pathogenic microbes in plant-microbe interactions. Biology14, 1505. doi: 10.3390/biology14111505
3
AkinolaS. A.AyangbenroA. S.BabalolaO. O. (2021). The diverse functional genes of maize rhizosphere microbiota assessed using shotgun metagenomics. J. Sci. Food Agric.101, 3193–3201. doi: 10.1002/jsfa.10948
4
AliJ.MukarramM.OjoJ.DawamN.RiyazuddinR.GhramhH. A.et al. (2024). Harnessing phytohormones: Advancing plant growth and defense strategies for sustainable agriculture. Physiol. Plant176, e14307. doi: 10.1111/ppl.14307
5
AliS.AkhtarM. S.SirajM.ZamanW. (2024a). Molecular communication of microbial plant biostimulants in the rhizosphere under abiotic stress conditions. Int. J. Mol. Sci.25, 12424. doi: 10.3390/ijms25221242439596488
6
AliS.TyagiA.MirZ. A. (2024b). Plant immunity: At the crossroads of pathogen perception and defense response. Plants13, 1434. doi: 10.3390/plants13111434
7
AnC.SunC.LiN.HuangB.JiangJ.ShenY.et al. (2022). Nanomaterials and nanotechnology for the delivery of agrochemicals: Strategies towards sustainable agriculture. J. Nanobiotechnol.20, 11. doi: 10.1186/s12951-021-01214-7
8
AssenaM. W.PfannstielJ.RascheF. (2024). Inhibitory activity of bacterial lipopeptides against Fusarium oxysporum f.sp. Strigae. BMC Microbiol.24, 227. doi: 10.1186/s12866-024-03386-2
9
BaetzU.MartinoiaE. (2014). Root exudates: The hidden part of plant defense. Trends Plant Sci.19, 90–98. doi: 10.1016/j.tplants.2013.11.006
10
BalleuxG.HöfteM.Arguelles-AriasA.DeleuM.OngenaM. (2025). Bacillus lipopeptides as key players in rhizosphere chemical ecology. Trends Microbiol.33, 80–95. doi: 10.1016/j.tim.2024.08.001
11
BatistaA. M.PessoaT. N.PuttiF. F.AndreoteF. D.LibardiP. L. (2024). Root influences rhizosphere hydraulic properties through soil organic carbon and microbial activity. Plants (Basel Switzerland)13, 1981. doi: 10.3390/plants13141981
12
BerendsenR. L.PieterseC. M.BakkerP. A. (2012). The rhizosphere microbiome and plant health. Trends Plant Sci.17, 478–486. doi: 10.1016/j.tplants.2012.04.001
13
BergG. (2009). Plant-microbe interactions promoting plant growth and health: Perspectives for controlled use of microorganisms in agriculture. Appl. Microbiol. Biotechnol.84, 11–18. doi: 10.1007/s00253-009-2092-7
14
BergerS.SinhaA. K.RoitschT. (2007). Plant physiology meets phytopathology: Plant primary metabolism and plant-pathogen interactions. J. Exp. Bot.58, 4019–4026. doi: 10.1093/jxb/erm298
15
BerrutoC. A.DemirerG. S. (2024). Engineering agricultural soil microbiomes and predicting plant phenotypes. Trends Microbiol.32, 858–873. doi: 10.1016/j.tim.2024.02.003
16
BhattacharyyaA.MavrodiO.BhowmikN.WellerD.ThomashowL.MavrodiD. (2023). Bacterial biofilms as an essential component of rhizosphere plant-microbe interactions. Methods Microbiol.53, 3–48. doi: 10.1016/bs.mim.2023.05.006
17
BhimaniP.MahavarP.RajguruB.BhattV. D.NathaniN. M.ShriM.et al. (2024). Unveiling the green dialogue: Advancements in omics technologies for deciphering plant–microbe interactions in soil. Discover Plants1, 4. doi: 10.1007/s44372-024-00004-3
18
BigeardJ.ColcombetJ.HirtH. (2015). Signaling mechanisms in pattern-triggered immunity (PTI). Mol. Plant8, 521–539. doi: 10.1016/j.molp.2014.12.022
19
BroekgaardenC.CaarlsL.VosI. A.PieterseC. M.Van WeesS. C. (2015). Ethylene: Traffic controller on hormonal crossroads to defense. Plant Physiol.169, 2371–2379. doi: 10.1104/pp.15.01020
20
CarvalhaisL. C.DennisP. G.TysonG. W.SchenkP. M. (2012). Application of metatranscriptomics to soil environments. J. Microbiol. Methods91, 246–251. doi: 10.1016/j.mimet.2012.08.011
21
ChaparroJ. M.BadriD. V.VivancoJ. M. (2014). Rhizosphere microbiome assemblage is affected by plant development. ISME J.8, 790–803. doi: 10.1038/ismej.2013.196
22
ChenL. Q.HouB. H.LalondeS.TakanagaH.HartungM. L.QuX. Q.et al. (2010). Sugar transporters for intercellular exchange and nutrition of pathogens. Nature468, 527–532. doi: 10.1038/nature09606
23
ChepsergonJ.MolelekiL. N. (2023). Rhizosphere bacterial interactions and impact on plant health. Curr. Opin. Microbiol.73, 102297. doi: 10.1016/j.mib.2023.102297
24
ChhanaU. (2025). Plant pathogens under biological control using beneficial microbes: Mechanisms and applications. J. Microbial Biochem. Technol.17, 641.
25
ChukwunemeC. F.AyangbenroA. S.BabalolaO. O. (2021). Metagenomic analyses of plant growth-promoting and carbon-cycling genes in maize rhizosphere soils with distinct land-use and management histories. Genes12, 1431. doi: 10.3390/genes12091431
26
CordovezV.MommerL.MoisanK.Lucas-BarbosaD.PierikR.MummR.et al. (2017). Plant phenotypic and transcriptional changes induced by volatiles from the fungal root pathogen Rhizoctonia solani. Front. Plant Sci.8, 1262. doi: 10.3389/fpls.2017.01262
27
CostaT. R. D.PatkowskiJ. B.MacéK.ChristieP. J.WaksmanG. (2024). Structural and functional diversity of type IV secretion systems. Nat. Rev. Microbiol.22, 170–185. doi: 10.1038/s41579-023-00974-3
28
CostaO. Y. A.RaaijmakersJ. M.KuramaeE. E. (2018). Microbial extracellular polymeric substances: Ecological function and impact on soil aggregation. Frontier Microbiol.9, 1636. doi: 10.3389/fmicb.2018.01636
29
CuiH.TsudaK.ParkerJ. E. (2015). Effector-triggered immunity: From pathogen perception to robust defense. Annu. Rev. Plant Biol.66, 487–511. doi: 10.1146/annurev-arplant-050213-040012
30
da Silva LimaL.OlivaresF. L.Rodrigues de OliveiraR.Raquel Garcia VegaM.Oliveira AguiarN. (2014). Root exudate profiling of maize seedlings inoculated with Herbaspirillum seropedicae and humic acids. Chem. Biol. Technol. Agric.1, 23. doi: 10.1186/s40538-014-0023-z
31
de HaasB.DhoogheE.GeelenD. (2025). Root exudates in soilless culture conditions. Plants14, 479. doi: 10.3390/plants14030479
32
DehbiI.AchemrkO.EzzouggariR.El JarroudiM.MokriniF.LegrifiI.et al. (2023). Beneficial microorganisms as bioprotectants against foliar diseases of cereals: A review. Plants12, 4162. doi: 10.3390/plants12244162
33
DenancéN.Sánchez-ValletA.GoffnerD.MolinaA. (2013). Disease resistance or growth: The role of plant hormones in balancing immune responses and fitness costs. Front. Plant Sci.4, 155. doi: 10.3389/fpls.2013.00155
34
DevannaB. N.JaswalR.SinghP. K.KapoorR.JainP.KumarG.et al. (2021). Role of transporters in plant disease resistance. Physiol. Plant171, 849–867. doi: 10.1111/ppl.13377
35
de WitP. J. (2007). How plants recognize pathogens and defend themselves. Cell. Mol. Life Sci.64, 2726–2732. doi: 10.1007/s00018-007-7284-7
36
DickeM.BaldwinI. T. (2010). The evolutionary context for herbivore-induced plant volatiles: Beyond the “cry for help. Trends Plant Sci.15, 167–175. doi: 10.1016/j.tplants.2009.12.002
37
DingN.DongH.OngenaM. (2025). Bacterial cyclic lipopeptides as triggers of plant immunity and systemic resistance against pathogens. Plants (Basel Switzerland)14, 2644. doi: 10.3390/plants14172644
38
DingL. N.LiY. T.WuY. Z.LiT.GengR.CaoJ.et al. (2022). Plant disease resistance-related signaling pathways: Recent progress and future prospects. Int. J. Mol. Sci.23, 16200. doi: 10.3390/ijms232416200
39
DoddsP. N.ChenJ.OutramM. A. (2024). Pathogen perception and signaling in plant immunity. Plant Cell36, 1465–1481. doi: 10.1093/plcell/koae020
40
DuY.HanX.TsudaK. (2025). Microbiome-mediated plant disease resistance: Recent advances and future directions. J. Gen. Plant Pathol.91, 1–17. doi: 10.1007/s10327-024-01204-1
41
DuH.YangJ.ChenB.ZhangX.XuX.WenC.et al. (2022). Dual RNA-seq reveals the global transcriptome dynamics of Ralstonia solanacearum and pepper (Capsicum annuum) hypocotyls during bacterial wilt pathogenesis. Phytopathology112, 630–642. doi: 10.1094/PHYTO-01-21-0032-R
42
DubeyA.MallaM. A.VimalS. R.KumarA.PrasadS. M.KhanM. L.et al. (2025). Plant-microbiome engineering: Synergistic microbial partners for crop health and sustainability. Plant Growth Regul. 105, 1825–1839. doi: 10.1007/s10725-025-01385-5
43
Escocard de Azevedo ManhãesA. M.Ortiz-MoreaF. A.HeP.ShanL. (2021). Plant plasma membrane-resident receptors: Surveillance for infections and coordination for growth and development. J. Integr. Plant Biol.63, 79–101. doi: 10.1111/jipb.13051
44
FadijiA. E.AdenijiA.LanrewajuA. A.BabalolaO. O. (2025). Dynamics of soil microbiome and allelochemical interactions: An overview of current knowledge and prospects. Ann. Microbiol.75, 21. doi: 10.1186/s13213-025-01812-y
45
FadijiA. E.KanuJ. O.BabalolaO. O. (2021). Metagenomic profiling of rhizosphere microbial community structure and diversity associated with maize plant as affected by cropping systems. Int. Microbiology: Off. J. Spanish Soc. For. Microbiol.24, 325–335. doi: 10.1007/s10123-021-00169-x
46
FaraceG.FernandezO.JacquensL.CoutteF.KrierF.JacquesP.et al. (2015). Cyclic lipopeptides from Bacillus subtilis activate distinct patterns of defense responses in grapevine. Mol. Plant Pathol.16, 177–187. doi: 10.1111/mpp.12170
47
FarrarK.BryantD.Cope-SelbyN. (2014). Understanding and engineering beneficial plant-microbe interactions: Plant growth promotion in energy crops. Plant Biotechnol. J.12, 1193–1206. doi: 10.1111/pbi.12279
48
FengY.KangY.WangZ.DuC.TanJ.ZhaoX.et al. (2025). Ralstonia solanacearum infection induces tobacco root to secrete chemoattractants to recruit antagonistic bacteria and defensive compounds to inhibit pathogen. Pest. Manage. Sci.81, 1817–1828. doi: 10.1002/ps.8581
49
FengZ.LiangQ.YaoQ.BaiY.ZhuH. (2024). The role of the rhizobiome recruited by root exudates in plant disease resistance: Current status and future directions. Environ. Microbiome19, 91. doi: 10.1186/s40793-024-00638-6
50
FrenchE.KaplanI.Iyer-PascuzziA.NakatsuC. H.EndersL. (2021). Emerging strategies for precision microbiome management in diverse agroecosystems. Nat. Plants7, 256–267. doi: 10.1038/s41477-020-00830-9
51
GahlotK. D. (2026). Microbial strategies for drought stress mitigation- a sustainable frontier in plant resilience. Front. Plant Sci.16, 1740879. doi: 10.3389/fpls.2025.1740879
52
GalánJ. E.WaksmanG. (2018). Protein-injection machines in bacteria. Cell.172, 1306–1318. doi: 10.1016/j.cell.2018.01.034
53
GoD.YeonG. H.ParkS. J.LeeY.KohH. G.KooH.et al. (2024). Integration of metabolomics and other omics: from microbes to microbiome. Appl. Microbiol. Biotechnol.108, 538. doi: 10.1007/s00253-024-13384-z
54
GreenE. R.MecsasJ. (2016). Bacterial secretion systems: an overview. Microbiol. Spectr.4, 10.1128/microbiolspec.VMBF–0012-2015. doi: 10.1128/microbiolspec.VMBF-0012-2015
55
GriffinC.OzM. T.DemirerG. S. (2024). Engineering plant-microbe communication for plant nutrient use efficiency. Curr. Opin. Biotechnol.88, 103150. doi: 10.1016/j.copbio.2024.103150
56
GuS.WeiZ.ShaoZ.FrimanV. P.CaoK.YangT.et al. (2020). Competition for iron drives phytopathogen control by natural rhizosphere microbiomes. Nat. Microbiol.5, 1002–1010. doi: 10.1038/s41564-020-0719-8
57
GuptaR.AnandG.GaurR.YadavD. (2021). Plant-microbiome interactions for sustainable agriculture: a review. Physiol. Mol. Biol. Plants: An. Int. J. Funct. Plant Biol.27, 165–179. doi: 10.1007/s12298-021-00927-1
58
HamzaA.KarčauskienėD.MockevičienėI.RepšienėR.TahirM. A.ManzoorM. Z.et al. (2025). Soil aggregate dynamics and stability: natural and anthropogenic drivers. Agric. 15(23), 2500. doi: 10.3390/agriculture15232500
59
HassanS.MathesiusU. (2012). The role of flavonoids in root-rhizosphere signalling: opportunities and challenges for improving plant-microbe interactions. J. Exp. Bot.63, 3429–3444. doi: 10.1093/jxb/err430
60
HemeldaN. M.NoutoshiY. (2025). Root-exuded sugars as drivers of rhizosphere microbiome assembly. Plant Biotechnol. (Tokyo Japan)42, 215–227. doi: 10.5511/plantbiotechnology.25.0214a
61
HinsingerP.BengoughA. G.VetterleinD.YoungI. M. (2009). Rhizosphere: biophysics, biogeochemistry and ecological relevance. Plant Soil321, 117–152. doi: 10.1007/s11104-008-9885-9
62
HuL.RobertC. A. M.CadotS.ZhangX.YeM.LiB.et al. (2018). Root exudate metabolites drive plant-soil feedbacks on growth and defense by shaping the rhizosphere microbiota. Nat. Communication9, 2738. doi: 10.1038/s41467-018-05122-7
63
HudsonA.MullensA.HindS.JamannT.Balint-KurtiP. (2024). Natural variation in the pattern-triggered immunity response in plants: investigations, implications and applications. Mol. Plant Pathol.25, e13445. doi: 10.1111/mpp.13445
64
HussonO. (2013). Redox potential (Eh) and pH as drivers of soil/plant/microorganism systems: a transdisciplinary overview pointing to integrative opportunities for agronomy. Plant Soil362, 389–417. doi: 10.1007/s11104-012-1429-7
65
IslamF.KhanM. S. S.ChenH.ChenJ. (2024). Utilizing effector-triggered immunity (ETI) as a robust priming agent to protect plants from pathogens. Stress Biol.4, 51. doi: 10.1007/s44154-024-00204-7
66
JacobyR.PeukertM.SuccurroA.KoprivovaA.KoprivaS. (2017). The role of soil microorganisms in plant mineral nutrition-current knowledge and future directions. Frontier Plant Sci.8, 1617. doi: 10.3389/fpls.2017.01617
67
JainA.SarsaiyaS.SinghR.GongQ.WuQ.ShiJ. (2024). Omics approaches in understanding the benefits of plant-microbe interactions. Front. Microbiol.15, 1391059. doi: 10.3389/fmicb.2024.1391059
68
JamilF.MukhtarH.FouillaudM.DufosséL. (2022). Rhizosphere signaling: insights into plant-rhizomicrobiome interactions for sustainable agronomy. Microorganisms10, 899. doi: 10.3390/microorganisms10050899
69
JinX.JiaH.RanL.WuF.LiuJ.SchlaeppiK.et al. (2024). Fusaric acid mediates the assembly of disease-suppressive rhizosphere microbiota via induced shifts in plant root exudates. Nat. Communication15, 5125. doi: 10.1038/s41467-024-49218-9
70
JonesJ.DanglJ. (2006). The plant immune system. Nature444, 323–329. doi: 10.1038/nature05286
71
JourdanE.HenryG.DubyF.DommesJ.BarthélemyJ. P.ThonartP.et al. (2009). Insights into the defense-related events occurring in plant cells following perception of surfactin-type lipopeptide from Bacillus subtilis. Mol. Plant-Microbe Interactions: MPMI22, 456–468. doi: 10.1094/MPMI-22-4-0456
72
KangJ.ParkJ.ChoiH.BurlaB.KretzschmarT.LeeY.et al. (2011). Plant ABC transporters. Arabidopsis Book9, e0153. doi: 10.1199/tab.0153
73
KanwarP.AltmeischS.BauerP. (2025). Quantitative tools for analyzing rhizosphere pH dynamics: localized and integrated approaches. Biol. Methods Protoc.10, bpaf026. doi: 10.1093/biomethods/bpaf026
74
KhabirM. I. U.ToppsD.JhumurJ. F.AdesemoyeA.BrownJ.NewmanA.et al. (2023). Linking rhizosphere soil aggregates with belowground and aboveground plant traits. Ecologies4, 74–87. doi: 10.3390/ecologies4010007
75
KösterP.DeFalcoT. A.ZipfelC. (2022). Ca2+ signals in plant immunity. EMBO J.41, EMBJ2022110741. doi: 10.15252/embj.2022110741
76
KuY. S.ChengS. S.LukC. Y.LeungH. S.ChanT. Y.LamH. M.et al. (2025). Deciphering metabolite signalling between plant roots and soil pathogens to design resistance. BMC Plant Bioliogy25, 308. doi: 10.1186/s12870-025-06321-3
77
KumarA.NarojuS. P.KumariN.ArseyS.KumarD.GubreD. F.et al. (2024). The role of drought response genes and plant growth promoting bacteria on plant growth promotion under sustainable agriculture: a review. Microbiol. Res.286, 127827. doi: 10.1016/j.micres.2024.127827
78
KumarU.RajS.SreenikethanamA.MaddheshiyaR.KumariS.HanS.et al. (2023). Multi-omics approaches in plant-microbe interactions hold enormous promise for sustainable agriculture. Agron.13(7), 1804. doi: 10.3390/agronomy13071804
79
LebeisS. L.ParedesS. H.LundbergD. S.BreakfieldN.GehringJ.McDonaldM.et al. (2015). Plant microbiome. Salicylic acid modulates colonization of the root microbiome by specific bacterial taxa. Sci. (New York N.Y.)349, 860–864. doi: 10.1126/science.aaa8764
80
LiY.HongY.ChenY.ZhuN.JiangS.YaoZ.et al. (2024). Rhizosheath formation and its role in plant adaptation to abiotic stress. Agronomy14, 2368. doi: 10.3390/agronomy14102368
81
LiB.MengX.ShanL.HeP. (2016). Transcriptional regulation of pattern-triggered immunity in plants. Cell. Host Microbe19, 641–650. doi: 10.1016/j.chom.2016.04.011
82
LiJ.WangC.LiangW.LiuS. (2021). Rhizosphere microbiome: the emerging barrier in plant-pathogen interactions. Front. Microbiol.12, 772420. doi: 10.3389/fmicb.2021.772420
83
LiR.WangF.WangJ. (2025). Spatial metabolomics and its application in plant research. Int. J. Mol. Sci.26, 3043. doi: 10.3390/ijms26073043
84
LingN.WangT.KuzyakovY. (2022). Rhizosphere bacteriome structure and functions. Nat. Commun.13, 836. doi: 10.1038/s41467-022-28448-9
85
LiuS.HeF.KuzyakovY.XiaoH.HoangD. T. T.PuS.et al. (2022). Nutrients in the rhizosphere: a meta-analysis of content, availability, and influencing factors. Sci. Total Environ.826, 153908. doi: 10.1016/j.scitotenv.2022.153908
86
LiuY.ZhangH.WangJ.GaoW.SunX.XiongQ.et al. (2024). Non-pathogenic Pseudomonas syringae derivatives and its metabolites trigger the plant “cry for help” response to assemble disease suppressing and growth promoting rhizomicrobiome. Nat. Communication15, 1907. doi: 10.1038/s41467-024-46254-3
87
LiuY.ShiA.ChenY.XuZ.LiuY.YaoY.et al. (2025). Beneficial microorganisms: Regulating growth and defense for plant welfare. Plant Biotechnol. J, 23, 986–998. doi: 10.1111/pbi.14554
88
LugtenbergB.KamilovaF. (2009). Plant-growth-promoting rhizobacteria. Annu. Rev. Microbiol.63, 541–556. doi: 10.1146/annurev.micro.62.081307.162918
89
LurthyT.PivatoB.LemanceauP.MazurierS. (2021). Importance of the rhizosphere microbiota in iron biofortification of plants. Front. Plant Sci.12, 744445. doi: 10.3389/fpls.2021.744445
90
MaN.SunP.LiZ. Y.ZhangF. J.WangX. F.YouC. X.et al. (2024). Plant disease resistance outputs regulated by AP2/ERF transcription factor family. Stress Biol.4, 2. doi: 10.1007/s44154-023-00140-y
91
MachoA. P.ZipfelC. (2014). Plant PRRs and the activation of innate immune signaling. Mol. Cell54, 263–272. doi: 10.1016/j.molcel.2014.03.028
92
MashabelaM. D.PiaterL. A.DuberyI. A.TugizimanaF.MhlongoM. I. (2022). Rhizosphere tripartite interactions and PGPR-mediated metabolic reprogramming towards ISR and plant priming: a metabolomics review. Biology11, 346. doi: 10.3390/biology11030346
93
MatteL. M.GenalA. V.LandoltE. F.DankaE. S. (2024). T6SS in plant pathogens: unique mechanisms in complex hosts. Infect. Immun.92, e0050023. doi: 10.1128/iai.00500-23
94
MhlongoM. I.PiaterL. A.MadalaN. E.LabuschagneN.DuberyI. A. (2018). The chemistry of plant-microbe interactions in the rhizosphere and the potential for metabolomics to reveal signaling related to defense priming and induced systemic resistance. Front. Plant Sci.9, 112. doi: 10.3389/fpls.2018.00112
95
MmotlaK.AllieF.MafunaT.MashabelaM. D.MhlongoM. I. (2025). Metabolomic profiling of VOC-driven interactions between Priestia megaterium and Bacillus licheniformis in a simulated rhizosphere using split petri dishes. Arch. Microbiol.207, 224. doi: 10.1007/s00203-025-04426-9
96
MolnárZ.SolomonW.MutumL.JandaT. (2023). Understanding the mechanisms of Fe deficiency in the rhizosphere to promote plant resilience. Plants12, 1945. doi: 10.3390/plants12101945
97
MorettiL. G.CrusciolC. A. C.LeiteM. F. A.MomessoL.BossolaniJ. W.CostaO. Y. A.et al. (2024). Diverse bacterial consortia: key drivers of rhizosoil fertility modulating microbiome functions, plant physiology, nutrition, and soybean grain yield. Environ. Microbiome19, 50. doi: 10.1186/s40793-024-00595-0
98
NabiZ.ManzoorS.NabiS. U.WaniT. A.GulzarH.FarooqM.et al. (2024). Pattern-triggered immunity and effector-triggered immunity: crosstalk and cooperation of PRR and NLR-mediated plant defense pathways during host-pathogen interactions. Physiol. Mol. Biol. Plants: An. Int. J. Funct. Plant Biol.30, 587–604. doi: 10.1007/s12298-024-01452-7
99
NachiyarC. V.SunkarS.NelloreJ.RenugadeviK.NamasivayamS. K. R.BavanilathaM.et al. (2025). Microbial disease resistance mechanisms with special reference to quorum sensing and quorum quenching: a review. Discover Biotechnol.2, 9. doi: 10.1007/s44340-025-00017-y
100
NguyenQ. M.IswantoA. B. B.SonG. H.KimS. H. (2021). Recent advances in effector-triggered immunity in plants: new pieces in the puzzle create a different paradigm. Int. J. Mol. Sci.22, 4709. doi: 10.3390/ijms22094709
101
NiuB.WangW.YuanZ.SederoffR. R.SederoffH.ChiangV. L.et al. (2020). Microbial interactions within multiple-strain biological control agents impact soil-borne plant disease. Front. Microbiol.11, 585404. doi: 10.3389/fmicb.2020.585404
102
NoboriT.CaoY.EntilaF.DahmsE.TsudaY.Garrido-OterR.et al. (2022). Dissecting the cotranscriptome landscape of plants and their microbiota. EMBO Rep.23, EMBR202255380. doi: 10.15252/embr.202255380
103
OburgerE.SchmidtH.StaudingerC. (2022). Harnessing belowground processes for sustainable intensification of agricultural systems. Plant Soil478, 177–209. doi: 10.1007/s11104-022-05508-z
104
OlanrewajuO. S.GlickB. R.BabalolaO. O. (2017). Mechanisms of action of plant growth promoting bacteria. World J. Microbiol. Biotechnol.33, 197. doi: 10.1007/s11274-017-2364-9
105
OmelyanchukN. A.CherenkoV. A.ZemlyanskayaE. V. (2024). Root cap border cells as regulators of rhizosphere microbiota. Vavilovskii Zhurnal Genetiki i Selektsii28, 918–926. doi: 10.18699/vjgb-24-99
106
PaceR.Schiano Di ColaV.MontiM. M.AffinitoA.CuomoS.LoretoF.et al. (2025). Artificial intelligence in soil microbiome analysis: a potential application in predicting and enhancing soil health- a review. Discover Appl. Sci.7, 85. doi: 10.1007/s42452-024-06381-4
107
PalkinaK. A.ChoobV. V.YampolskyI. V.MishinA. S.BalakirevaA. V. (2025). Pros and cons of interactions between crops and beneficial microbes. Agriculture15, 2526. doi: 10.3390/agriculture15242526
108
PandeyE.KumariR.FaizanS.et al. (2025). Linking the interaction of salicylates and jasmonates for stress resilience in plants. Stress Biol.5, 64. doi: 10.1007/s44154-025-00250-9
109
PandeyE.KumariR.FaizanS.PandeyS (2025). Soil microbiomes: a promising strategy for boosting crop yield and advancing sustainable agriculture. Discover Agric.3, 54. doi: 10.1007/s44279-025-00208-5
110
PantigosoH. A.NewbergerD.VivancoJ. M. (2022). The rhizosphere microbiome: plant-microbial interactions for resource acquisition. J. Appl. Microbiol.133, 2864–2876. doi: 10.1111/jam.15686
111
PhilippotL.RaaijmakersJ. M.LemanceauP.van der PuttenW. H. (2013). Going back to the roots: the microbial ecology of the rhizosphere. Nat. Rev. Microbiol.11, 789–799. doi: 10.1038/nrmicro3109
112
PieterseC. M. J.Van der DoesD.ZamioudisC.Leon-ReyesA.Van WeesS. C. M. (2012). Hormonal modulation of plant immunity. Annu. Rev. Cell. Dev. Biol.28, 489–521. doi: 10.1146/annurev-cellbio-092910-154055
113
PieterseC. M. J.ZamioudisC.BerendsenR. L.WellerD. M.Van WeesS. C. M.BakkerP. A. H. M. (2014). Induced systemic resistance by beneficial microbes. Annu. Rev. Phytopathol.52, 347–375. doi: 10.1146/annurev-phyto-082712-102340
114
QuizaL.TremblayJ.PagéA. P.GreerC. W.PozniakC. J.LiR.et al. (2023). The effect of wheat genotype on the microbiome is more evident in roots and varies through time. ISME Commun.3, 32. doi: 10.1038/s43705-023-00238-4
115
RaglandC. J.ShihK. Y.DinnenyJ. R. (2024). Choreographing root architecture and rhizosphere interactions through synthetic biology. Nat. Communication15, 1370. doi: 10.1038/s41467-024-45272-5
116
RajguruB.ShriM.BhattV. D. (2024). Exploring microbial diversity in the rhizosphere: a comprehensive review of metagenomic approaches and their applications. 3 Biotech.14, 224. doi: 10.1007/s13205-024-04065-9
117
RamachandranP.JB. J.Maupin-FurlowJ. A.UthandiS. (2021). Bacterial effectors mimicking ubiquitin-proteasome pathway tweak plant immunity. Microbiol. Res.250, 126810. doi: 10.1016/j.micres.2021.126810
118
RaniA.RanaA.DhakaR. K.SinghA. P.ChaharM.SinghS.et al. (2023). Bacterial volatile organic compounds as biopesticides, growth promoters and plant-defense elicitors: current understanding and future scope. Biotechnol. Adv.63, 108078. doi: 10.1016/j.bioteChadv.2022.108078
119
RazaW.WeiZ.JoussetA.ShenQ.FrimanV. P. (2021). Extended plant metarhizobiome: understanding volatile organic compound signaling in plant-microbe metapopulation networks. mSystems6, e0084921. doi: 10.1128/mSystems.00849-21
120
Rezaee DaneshY. (2025). Harnessing beneficial microbes and sensor technologies for sustainable smart agriculture. Sensors (Basel Switzerland)25, 6631. doi: 10.3390/s25216631
121
Rezaee DaneshY.MuletJ. M.PorcelR. (2025). Bridging microbial biocontrol and phytochemical biopesticides: synergistic approaches for sustainable crop protection. Plants (Basel Switzerland)14, 3453. doi: 10.3390/plants14223453
122
RichardsonA. E.BareaJ. M.McNeillA. M.Prigent-CombaretC. (2009). Acquisition of phosphorus and nitrogen in the rhizosphere and plant growth promotion by microorganisms. Plant Soil321, 305–339. doi: 10.1007/s11104-009-9895-2
123
RizaludinM. S.StopnisekN.RaaijmakersJ. M.GarbevaP. (2021). The chemistry of stress: understanding the ‘cry for help’ of plant roots. Metabolites11, 357. doi: 10.3390/metabo11060357
124
Rodríguez-LealD.LemmonZ. H.ManJ.BartlettM. E.LippmanZ. B. (2017). Engineering quantitative trait variation for crop improvement by genome editing. Cell.171, 470–480.e8. doi: 10.1016/j.cell.2017.08.030
125
RovenichH.BoshovenJ. C.ThommaB. P. (2014). Filamentous pathogen effector functions: of pathogens, hosts and microbiomes. Curr. Opin. Plant Biol.20, 96–103. doi: 10.1016/j.pbi.2014.05.001
126
RoyN. K.Solomon Maina (2024). Unraveling plant–microbe interactions: can integrated omics approaches offer concrete answers? J. Exp. Bot.75, 1289–1313. doi: 10.1093/jxb/erad448
127
RussellA.PetersonS.MougousJ. (2014). Type VI secretion system effectors: poisons with a purpose. Nat. Rev. Microbiol.12, 137–148. doi: 10.1038/nrmicro3185
128
SahooA.YadavG.MehtaT.et al. (2025). Omics-driven insights into plant growth-promoting microorganisms for sustainable agriculture. Discover Sustainability6, 659. doi: 10.1007/s43621-025-01582-2
129
SasseJ.MartinoiaE.NorthenT. (2018). Feed your friends: do plant exudates shape the root microbiome? Trends Plant Sci.23, 25–41. doi: 10.1016/j.tplants.2017.09.003
130
SecomandiE.De GregorioM. A.Garcia-PerezP.VaccariF.PuglisiE.LuciniL. (2025). Waterlogging alone and combined with other abiotic stresses provides unique metabolic signatures at the plant-rhizosphere interface: a multi-omics perspective on root metabolome, root exudation and rhizomicrobiome. Plant Physiol. Biochemistry: PPB221, 109646. doi: 10.1016/j.plaphy.2025.109646
131
ShaoZ.GuS.ZhangX.XueJ.YanT.GuoS.et al. (2024). Siderophore interactions drive the ability of Pseudomonas spp. consortia to protect tomato against Ralstonia solanacearum. Hortic. Res.11, uhae186. doi: 10.1093/hr/uhae186
132
ShoreshM.YedidiaI.ChetI. (2005). Involvement of jasmonic acid/ethylene signaling pathway in the systemic resistance induced in cucumber by Trichoderma asperellum T203. Phytopathology95, 76–84. doi: 10.1094/PHYTO-95-0076
133
SibanyoniN. R.MmotlaK.MashabelaM. D.PiaterL. A.KerchevP.MhlongoM. I.et al. (2026). Chemical dialogues in the rhizosphere: metabolomics perspectives on plant defense and microbial interactions. Plant Soil518, 577–603. doi: 10.1007/s11104-025-08010-4
134
SinghP.ChauhanP. K.UpadhyayS. K.SinghR. K.DwivediP.WangJ.et al. (2022a). Mechanistic insights and potential use of siderophore-producing microbes in the rhizosphere for mitigation of stress in plants grown in degraded land. Front. Microbiol.13, 898979. doi: 10.3389/fmicb.2022.898979
135
SinghA.KumarM.VermaS.ChoudharyP.ChakdarH. (2020). “ Plant microbiome: trends and prospects for sustainable agriculture,” in Plant Microbe Symbiosis. Eds. VarmaA.TripathiS.PrasadR. ( Springer, Cham, Switzerland), 129–151.
136
SinghP.SinghR. K.GuoD.-J.SharmaA.SinghR. N.LiD.-P.et al. (2021). Whole genome analysis of sugarcane root-associated endophyte Pseudomonas aeruginosa B18-A plant growth-promoting bacterium with antagonistic potential against Sporisorium scitamineum. Front. Microbiol.12, 628376. doi: 10.3389/fmicb.2021.628376
137
SinghR. K.SinghP.SharmaA.GuoD.-J.UpadhyayS. K.SongQ.-Q.et al. (2022c). Unraveling nitrogen-fixing potential of endophytic diazotrophs of different Saccharum species for sustainable sugarcane growth. Int. J. Mol. Sci.23, 6242. doi: 10.3390/ijms23116242
138
SinghP.SinghR. K.ZhouY.WangJ.JiangY.ShenN.et al. (2022b). Unlocking the strength of plant growth-promoting Pseudomonas in improving crop productivity in normal and challenging environments: a review. J. Plant Interact.17, 220–238. doi: 10.1080/17429145.2022.2029963
139
SpoelS.DongX. (2012). How do plants achieve immunity? Defense without specialized immune cells. Nat. Rev. Immunol.12, 89–100. doi: 10.1038/nri3141
140
SurovyM. Z.RahmanS.RostásM.IslamT.von TiedemannA. (2023). Suppressive effects of volatile compounds from Bacillus spp. on Magnaporthe oryzae Triticum (MoT) pathotype, causal agent of wheat blast. Microorganisms11, 1291. doi: 10.3390/microorganisms11051291
141
TanB.LiY.LiuT.TanX.HeY.YouX.et al. (2021). Response of plant rhizosphere microenvironment to water management in soil- and substrate-based controlled environment agriculture (CEA) systems: a review. Front. Plant Sci.12, 691651. doi: 10.3389/fpls.2021.691651
142
TimmuskS.Abd El-DaimI. A.CopoloviciL.TanilasT.KännasteA.BehersL.et al. (2014). Drought-tolerance of wheat improved by rhizosphere bacteria from harsh environments: enhanced biomass production and reduced emissions of stress volatiles. PloS One9, e96086. doi: 10.1371/journal.pone.0096086
143
TimofeevaA. M.GalyamovaM. R.SedykhS. E. (2023). Plant growth-promoting soil bacteria: nitrogen fixation, phosphate solubilization, siderophore production, and other biological activities. Plants (Basel Switzerland)12, 4074. doi: 10.3390/plants12244074
144
TracannaV.OssowickiA.PetrusM. L. C.OverduinS.TerlouwB. R.LundG.et al. (2021). Dissecting disease-suppressive rhizosphere microbiomes by functional amplicon sequencing and 10× metagenomics. mSystems6, e0111620. doi: 10.1128/mSystems.01116-20
145
TrdáL.BoutrotF.ClaverieJ.BruléD.DoreyS.PoinssotB. (2015). Perception of pathogenic or beneficial bacteria and their evasion of host immunity: pattern recognition receptors in the frontline. Front. Plant Sci.6, 219. doi: 10.3389/fpls.2015.00219
146
TrivediP.LeachJ. E.TringeS. G.SaT.SinghB. K. (2020). Plant–microbiome interactions: from community assembly to plant health. Nat. Rev. Microbiol.18, 607–621. doi: 10.1038/s41579-020-0412-1
147
UllahC.ChenY. H.OrtegaM. A.TsaiC. J. (2023). The diversity of salicylic acid biosynthesis and defense signaling in plants: Knowledge gaps and future opportunities. Curr. Opin. Plant Biol.72, 102349. doi: 10.1016/j.pbi.2023.102349
148
UpadhyayS. K. (2026a). Holobiont plasticity under abiotic stress: A systems biology perspective on plant-bacteria-fungi interactions. Physiol. Plant178, e70971. doi: 10.1111/ppl.70971
149
UpadhyayS. K. (2026b). Phytohormone-microbial nexus targeting next-generation strategy for fruit growth and postharvest resilience. Plant Sci.367, 113098. doi: 10.1016/j.plantsci.2026.113098
150
UpadhyayS. K. (2026c). Strigolactones targeting plant–microbe dialogues from roots to soil: Unlocking pathways for sustainable agriculture. Physiol. Plant178, e70787. doi: 10.1111/ppl.70787
151
UpadhyayS. K. (2026d). Transporter promiscuity and redox-driven metal partitioning in plant responses to chemically analogous metals. Plant Cell Rep.45, 201. doi: 10.1007/s00299-026-03876-9
152
UpadhyayS. K.LiuS.PandeyD. K.JainD.DwivediP. (2026). Multitrophic rhizosphere-phyllosphere signaling networks regulating plant physiological adaptation and stress resilience. Plant Physiol. Biochem.237, 111531. doi: 10.1016/j.plaphy.2026.111531
153
VacheronJ.DesbrossesG.BouffaudM.-L.TouraineB.Moënne-LoccozY.MullerD.et al. (2013). Plant growth-promoting rhizobacteria and root system functioning. Frontier Plant Sci.4, 356. doi: 10.3389/fpls.2013.00356
154
Van der DoesD.Leon-ReyesA.KoornneefA.Van VerkM. C.RodenburgN.PauwelsL.et al. (2013). Salicylic acid suppresses jasmonic acid signaling downstream of SCFCOI1-JAZ by targeting GCC promoter motifs via transcription factor ORA59. Plant Cell25, 744–761. doi: 10.1105/tpc.112.108548
155
van LoonL. C.BakkerP. A. H. M.PieterseC. M. J. (1998). Systemic resistance induced by rhizosphere bacteria. Annu. Rev. Phytopathol.36, 453–483. doi: 10.1146/annurev.phyto.36.1.453
156
Vives-PerisV.de OllasC.Gómez-CadenasA.Pérez-ClementeR. M. (2020). Root exudates: from plant to rhizosphere and beyond. Plant Cell Rep.39, 3–17. doi: 10.1007/s00299-019-02447-5
157
VogesM. J. E. E. E.BaiY.Schulze-LefertP.SattelyE. S. (2019). Plant-derived coumarins shape the composition of an Arabidopsis synthetic root microbiome. PNAS116, 12558–12565. doi: 10.1073/pnas.1820691116
158
VosI. A.MoritzL.PieterseC. M.Van WeesS. C. (2015). Impact of hormonal crosstalk on plant resistance and fitness under multi-attacker conditions. Front. Plant Sci.6, 639. doi: 10.3389/fpls.2015.00639
159
VurukondaS. S.VardharajulaS.ShrivastavaM.SkZA. (2016). Enhancement of drought stress tolerance in crops by plant growth promoting rhizobacteria. Microbiol. Res.184, 13–24. doi: 10.1016/j.micres.2015.12.003
160
WangX.LiN.LiW.GaoX.ChaM.QinL.et al. (2020). Advances in transcriptomics in the response to stress in plants. Global Med. Genet.7, 30–34. doi: 10.1055/s-0040-1714414
161
WangX.TangC. (2018). The role of rhizosphere pH in regulating the rhizosphere priming effect and implications for the availability of soil-derived nitrogen to plants. Ann. Bot.121, 143–151. doi: 10.1093/aob/mcx138
162
WankhadeA.WilkinsonE.BrittD. W.KaundalA. (2025). A review of plant–microbe interactions in the rhizosphere and the role of root exudates in microbiome engineering. Appl. Sci.15, 7127. doi: 10.3390/app15137127
163
WasternackC.SongS. (2017). Jasmonates: biosynthesis, metabolism, and signaling by proteins activating and repressing transcription. J. Exp. Bot.68, 1303–1321. doi: 10.1093/jxb/erw443
164
WebsterC. F.KimW. J.RegueraG.FriesenM. L.BeyenalH. (2024). Review: Can bioelectrochemical sensors be used to monitor soil microbiome activity and fertility? Curr. Opin. Biotechnol.90, 103222. doi: 10.1016/j.copbio.2024.103222
165
WuL.ChenH.CurtisC.FuZ. Q. (2014a). Go in for the kill: How plants deploy effector-triggered immunity to combat pathogens. [Corrected. Virulence5, 710–721. doi: 10.4161/viru.29755
166
WuS.ShanL.HeP. (2014b). Microbial signature-triggered plant defense responses and early signaling mechanisms. Plant Science: An. Int. J. Exp. Plant Biol.228, 118–126. doi: 10.1016/j.plantsci.2014.03.001
167
XiangzongM.ShuqunZ. (2013). MAPK cascades in plant disease resistance signaling. Annu. Rev. Phytopathol.51, 245–266. doi: 10.1146/annurev-phyto-082712-102314
168
XiaoY.ZhangS.LiH.TengK.WuS.LiuY.et al. (2024). Metagenomic insights into the response of soil microbial communities to pathogenic Ralstonia solanacearum. Front. Plant Sci.15, 1325141. doi: 10.3389/fpls.2024.1325141
169
YangY. X.AhammedG. J.WuC.FanS. Y.ZhouY. H. (2015). Crosstalk among jasmonate, salicylate and ethylene signaling pathways in plant disease and immune responses. Curr. Protein Pept. Sci.16, 450–461. doi: 10.2174/1389203716666150330141638
170
YangL.QianX.ZhaoZ.WangY.DingG.XingX. (2024). Mechanisms of rhizosphere plant-microbe interactions: molecular insights into microbial colonization. Front. Plant Sci.15, 1491495. doi: 10.3389/fpls.2024.1491495
171
YangQ.ZhangH.YouJ.YangJ.ZhangQ.ZhaoJ.et al. (2023). Transcriptome and metabolome analyses reveal that Bacillus subtilis BS-Z15 lipopeptides mycosubtilin homologue mediates plant defense responses. Front. Plant Sci.13, 1088220. doi: 10.3389/fpls.2022.1088220
172
YorkL. M.CarminatiA.MooneyS. J.RitzK.BennettM. J. (2016). The holistic rhizosphere: integrating zones, processes, and semantics in the soil influenced by roots. J. Exp. Bot.67, 3629–3643. doi: 10.1093/jxb/erw108
173
YuY.GuiY.LiZ.JiangC.GuoJ.NiuD. (2022). Induced systemic resistance for improving plant immunity by beneficial microbes. Plants (Basel Switzerland)11, 386. doi: 10.3390/plants11030386
174
YuX. Q.NiuH. Q.LiuC.WangH. L.YinW.XiaX. (2024). PTI-ETI synergistic signal mechanisms in plant immunity. Plant Biotechnol. J.22, 2113–2128. doi: 10.1111/pbi.14332
175
YuK.PieterseC. M. J.BakkerP. A. H. M.BerendsenR. L. (2019). Beneficial microbes going underground of root immunity. Plant Cell Environ.42, 2860–2870. doi: 10.1111/pce.13632
176
YuanM.NgouB. P. M.DingP.XinX. F. (2021). PTI-ETI crosstalk: an integrative view of plant immunity. Curr. Opin. Plant Biol.62, 102030. doi: 10.1016/j.pbi.2021.102030
177
ZhangW.CorwinJ. A.CopelandD. H.FeusierJ.EshbaughR.CookD. E.et al. (2019). Plant-necrotroph co-transcriptome networks illuminate a metabolic battlefield. eLife8, e44279. doi: 10.7554/eLife.44279
178
ZhangP.JacksonE.LiX.ZhangY. (2025). Salicylic acid and jasmonic acid in plant immunity. Hortic. Res.12, uhaf082. doi: 10.1093/hr/uhaf082
179
ZhangS.LiC.SiJ.HanZ.ChenD. (2022). Action mechanisms of effectors in plant-pathogen interaction. Int. J. Mol. Sci.23, 6758. doi: 10.3390/ijms23126758
180
ZhaoN.FanX.SheasM. N.YuT.YanF. (2026). Broad-spectrum antibacterial action of lipopeptides derived from Bacillus smithii by targeting quorum sensing. Probiotics Antimicrob. Proteins18, 4581–4597. doi: 10.1007/s12602-025-10762-5
181
ZhengX.LiuJ.WangX. (2025). Quorum signaling molecules: Interactions between plants and associated pathogens. Int. J. Mol. Sci.26, 5235. doi: 10.3390/ijms26115235
182
ZhengQ. F.XinnianD. (2013). Systemic acquired resistance: Turning local infection into global defense. Annu. Rev. Plant Biol.64, 839–863. doi: 10.1146/annurev-arplant-042811-105606
183
ZhouL.SongC.LiZ.KuipersO. P. (2021). Antimicrobial activity screening of rhizosphere soil bacteria from tomato and genome-based analysis of their antimicrobial biosynthetic potential. BMC Genomics22, 29. doi: 10.1186/s12864-020-07346-8
184
ZhuL.HuangJ.LuX.ZhouC. (2022). Development of plant systemic resistance by beneficial rhizobacteria: Recognition, initiation, elicitation and regulation. Front. Plant Sci.13, 952397. doi: 10.3389/fpls.2022.952397
185
ZhuangY.WangH.TanF.WuB.LiuL.QinH.et al. (2024). Rhizosphere metabolic cross-talk from plant-soil-microbe tapping into agricultural sustainability: Current advance and perspectives. Plant Physiol. Biochemistry: PPB210, 108619. doi: 10.1016/j.plaphy.2024.108619
186
ZipfelC. (2014). Plant pattern-recognition receptors. Trends Immunol.35, 345–351. doi: 10.1016/j.it.2014.05.004
Summary
Keywords
effector-triggered immunity, induced systemic resistance (ISR), pattern-triggered immunity (PTI), plant-microbe-pathogen interactions, rhizosphere triangular warfare
Citation
Singh P, Singh RK, Guo D-J, Singh MP, Zhang B-Q, Song X-P, Upadhyay SK and Li Y-R (2026) Rhizosphere triangular warfare: mechanistic insights for plant- beneficial microbe- pathogen interactions. Front. Plant Sci. 17:1942866. doi: 10.3389/fpls.2026.1942866
Received
20 July 2026
Revised
26 August 2026
Accepted
07 September 2026
Published
30 September 2026
Volume
17 - 2026
Edited by
Udai B. Singh, National Bureau of Agriculturally Important Microorganisms (ICAR), India
Reviewed by
Satyendra Pratap Singh, Agricultural Research Organization (ARO), Israel
Manish Kumar, Amity University, India
Deepti Malviya, National Bureau of Agriculturally Important Microorganisms (ICAR), India
Updates
Copyright
© 2026 Singh, Singh, Guo, Singh, Zhang, Song, Upadhyay and Li.
This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.
*Correspondence: Rajesh Kumar Singh, rajeshsingh999@gmail.com; Yang-Rui Li, liyr@gxaas.net
Disclaimer
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