The rhizosphere microbiome is structured by complex, dynamic interactions between plant genotype, soil characteristics, and environmental conditions. It plays an important role in determining plant health, nutrient cycling, and overall agroecosystem functionality (Busby et al., 2017; Massart et al., 2015). While soil is the primary reservoir of microbial inocula, its physicochemical properties such as pH, texture, organic matter content, and water-holding capacity strongly influence the baseline microbial community available for root colonization (Berg and Smalla, 2009; Berg et al., 2013). In the rhizosphere, this soil-derived pool is further filtered by plant-specific traits including root architecture, exudate composition, and immune signalling pathways. Experimental evidence demonstrates that even within identical soil types, different plant genotypes can assemble distinct microbial consortia, highlighting the host’s regulatory role in microbiome assembly (Ikeda et al., 2011; Park et al., 2023).

In addition to inherent plant–soil interactions, anthropogenic factors such as fertilization regimes, pesticides, and cropping patterns significantly shape rhizosphere microbiome structure and function. Fertilizers, particularly those applied in excess, have been linked to reduced microbial diversity and functional redundancy, potentially impairing key processes like nutrient cycling and pathogen suppression (Jacobsen and Hjelmsø, 2014). Conversely, practices such as crop rotation and organic amendments tend to promote microbial resilience, enhance beneficial taxa, and suppress soilborne pathogens (Hilton et al., 2013). These findings challenge the concept of the rhizosphere as a passive microbial habitat and instead highlight its dynamic responsiveness to agronomic management. Within the broader framework of climate-smart agriculture, the rhizosphere represents not only a site of biological activity but also a manipulable interface through which plant resilience, productivity, and sustainability can be enhanced.

The rhizosphere microbiome is a phylogenetically diverse and functionally heterogeneous assemblage of microorganisms including bacteria, fungi, archaea, protists, and viruses that collectively shape plant–soil interactions (Chukwuneme and Babalola, 2025). These groups have complementary ecological functions that influence nutrient cycling, plant defense, and stress responses.

Bacteria are the most abundant and metabolically versatile members of the rhizosphere microbiome. Dominant phyla such as Proteobacteria, Actinobacteria, Firmicutes, and Bacteroidetes contribute to key functions including nutrient cycling, siderophore production, phytohormone modulation, and pathogen suppression (Fierer, 2017; Kour et al., 2023). Bacterial community composition is highly dynamic and shaped by host genotype, soil properties, and environmental conditions, with stress factors often favoring specific functional groups, such as Proteobacteria under nitrogen limitation and Actinobacteria under drought (Negre Rodríguez et al., 2025; Sun et al., 2024). Within this context, keystone members of the rhizosphere microbiome include both functionally distinct groups and taxonomically defined but functionally versatile genera. For example, diazotrophs act as keystone functional groups through their contribution to biological nitrogen fixation (Imran et al., 2021), whereas Pseudomonas spp. represent keystone genera that influence community structure and plant performance via pathogen suppression, siderophore production, and induced systemic resistance (Mazzola, 2002; Trivedi et al., 2022).

Fungi are another major functional component of the rhizosphere microbiome. Filamentous fungi from Ascomycota and Basidiomycota contribute to organic matter decomposition, phosphorus solubilization, and pathogen suppression through mycoparasitism and secondary metabolite production (Chapelle et al., 2016; Rigobelo, 2025). Arbuscular mycorrhizal fungi (AMF; Glomeromycota) form symbiotic associations with plant roots, enhancing nutrient acquisition, water-use efficiency, and tolerance of abiotic stresses such as drought and salinity while also influencing soil structure and host immune responses (Nie et al., 2024; Wahab et al., 2023). Fungal community composition is strongly shaped by plant genotype, soil pH, and nutrient availability.

Archaea, although generally less abundant than bacteria and fungi, play important roles in rhizosphere biogeochemical cycling, particularly in ammonia oxidation and anaerobic methanogenesis (Offre et al., 2013; Prosser, 2012). These processes are especially relevant in nutrient-poor, saline, or anoxic soils, where archaeal activity complements bacterial metabolism. Protists and viruses are key regulators of rhizosphere microbial dynamics. Protists influence microbial turnover through selective bacterivory, thereby affecting nutrient mineralization and community succession (Liao et al., 2024). Bacteriophages shape bacterial populations through lytic and lysogenic interactions that regulate population dynamics and mediate horizontal gene transfer, thereby contributing to microbial adaptation and functional stability under changing environmental conditions (Chevallereau et al., 2022). Collectively, interactions among these microbial guilds underpin the ecological functioning and resilience of the rhizosphere. Table 1 summarizes the major rhizosphere microbial groups, showing representative taxa from each and their dominant functional roles.

The rhizosphere microbiome contributes to plant health through a set of interrelated functional processes that collectively influence nutrient availability, immune competence, and stress tolerance. Facilitation of nutrient acquisition is a core function, particularly under low-input or stress-prone conditions (De Faria et al., 2021). Diverse microbial taxa including Bacillus, Pseudomonas, Trichoderma, and AMF enhance the bioavailability of key nutrients such as phosphorus, potassium, and zinc through mineral solubilization, enzymatic activity, and chelation mechanisms (Ansabayeva et al., 2025; Thepbandit and Athinuwat, 2024). In parallel, diazotrophic bacteria such as Azospirillum, Burkholderia, and Rhizobium contribute to nitrogen input via biological fixation, supporting plant nutrition in resource-limited systems (Imran et al., 2021).

Beyond nutrient-related functions, rhizosphere microorganisms modulate plant physiological responses through hormonal and immune-mediated pathways. Many bacteria and fungi influence plant development by producing or regulating phytohormones, including indole-3-acetic acid (IAA), cytokinins, gibberellins, and ACC deaminase, thereby affecting root architecture and growth dynamics (Kaya, 2024; Orozco-Mosqueda et al., 2023). These microbial effects are frequently linked to improved water-use efficiency, enhanced nutrient uptake, and increased tolerance to abiotic stress. In addition, specific members of the rhizosphere microbiome can activate induced systemic resistance (ISR) by modulating jasmonic acid (JA) and ethylene (ET) signalling pathways, activating broad-spectrum defense without the growth penalties often associated with systemic acquired resistance (SAR) (Rabari et al., 2023; Zhu et al., 2022). Well-characterized ISR-inducing taxa include Pseudomonas fluorescens, Bacillus subtilis, and Trichoderma harzianum (Panpatte et al., 2016; Lee Díaz et al., 2021).

The rhizosphere microbiome also contributes to disease suppression through both direct antagonism and community-level interactions. Antagonistic microbes inhibit pathogens via competition for resources, mycoparasitism, and the production of antimicrobial metabolites such as lipopeptides, volatile organic compounds, and hydrolytic enzymes (Compant et al., 2019; Iqbal et al., 2023). Importantly, pathogen suppression often emerges from the collective activity of stable microbial consortia rather than from individual taxa. Disease-suppressive soils exemplify this principle, as they are consistently associated with enrichment of microbial groups such as Pseudomonas, Trichoderma, and Streptomyces, which constrain pathogens including Fusarium oxysporum and Rhizoctonia solani through antibiotic production and competition for iron (Table 1; De Faria et al., 2021; Mazzola, 2002). In addition to biotic interactions, rhizosphere microorganisms play a key role in mitigating abiotic stress. By enhancing antioxidant capacity, osmotic adjustment, and stress-responsive gene expression, beneficial microbes can improve plant tolerance of salinity, drought, and temperature extremes (Khan et al., 2021; Sharma et al., 2020). However, the magnitude and consistency of these benefits are strongly context-dependent, reflecting interactions between microbial composition, host genotype, and environmental conditions.

Despite its ecological adaptability, the rhizosphere microbiome is highly sensitive to environmental disturbance, with abiotic and biotic stressors often interacting to destabilize community structure and function. Abiotic stresses such as drought, salinity, pH fluctuations, and thermal extremes can reduce microbial diversity, suppress keystone taxa, and compromise microbiome-mediated processes that support plant nutrition and defense (Khan et al., 2023; Munir et al., 2022). For example, drought frequently reduces the abundance of beneficial plant-associated taxa such as Pseudomonas and Bacillus while favoring desiccation-tolerant groups like Actinobacteria (Santos-Medellín et al., 2017). Similarly, reduced soil moisture availability can limit colonization by AMF, despite its importance for plant water-use efficiency (Abdalla et al., 2023). Salinity stress further constrains microbial richness and disrupts symbiotic nutrient acquisition, particularly in non-halophilic taxa, through osmotic and ionic toxicity (Andronov et al., 2012; Munir et al., 2022).

Biotic stressors, particularly soilborne pathogens, also exert strong selective pressures on rhizosphere communities. Pathogen invasion by species such as F. oxysporum, F. solani, Ralstonia solani, and R. solani can restructure microbial networks, suppress beneficial microbes, and induce community dysbiosis (Table 1; Deng et al., 2021; Kashyap et al., 2023; Su et al., 2020). While pathogens may outcompete resident taxa through allelopathy, niche displacement, or immune manipulation, plants can partially counteract these effects through a “cry-for-help” response, releasing targeted exudates that recruit protective microbes (Berendsen et al., 2012; Rolfe et al., 2019). This response highlights the dynamic and context-dependent nature of plant–microbiome interactions under disease pressure.

Climate change exacerbates the complexity of these interactions by increasing the frequency and intensity of compound stress events such as simultaneous drought and pathogen attack. These multifactorial pressures can undermine both plant immunity and microbiome resilience, thereby reducing the rhizosphere’s buffering capacity against further disturbance (Choudhary and Senthil-Kumar, 2024). In this context, microbiome resilience reflects the capacity of the rhizosphere community to maintain or rapidly recover key structural and functional attributes following stress. Elevated CO₂ and temperature can further alter root exudation patterns by modifying plant carbon allocation and metabolic activity, reshaping microbial recruitment, and favoring stress-tolerant or opportunistic taxa over beneficial symbionts (De Faria et al., 2021; Li et al., 2021). Anthropogenic inputs including pesticides and excessive fertilizer treatment may exacerbate these effects by degrading mutualistic networks and simplifying community composition (Jacobsen and Hjelmsø, 2014). Consequently, sustaining a functionally resilient rhizosphere microbiome depends not only on microbial diversity but also on network redundancy, host compatibility, and the legacy effects of agronomic practices. The development of climate-smart adaptive agroecosystems thus requires knowledge of the thresholds at which beneficial functions collapse and the availability of strategies to restore them through inoculants, amendments, or host breeding.

The introduction of microbial BCAs into the rhizosphere to suppress phytopathogens also modulates native microbial communities via both direct and indirect mechanisms that influence community interactions and stability. These mechanisms include niche competition, secretion of antibiotics, interference with microbial signalling pathways, and metabolic cross-feeding, wherein one microbe utilizes metabolites produced by another (Table 2; Tang et al., 2025; Zhang et al., 2023). In addition to these direct microbial interactions, BCAs can influence rhizosphere community assembly through plant-mediated effects. BCA inoculation has been shown to modify the volume and composition of root exudates, for example by changing the content of sugars, organic acids, amino acids, and secondary metabolites, which in turn shape microbial recruitment and activity in the rhizosphere. Such exudate-mediated shifts can selectively promote beneficial taxa or alter competitive interactions among resident microbes, thereby indirectly contributing to microbiome restructuring and functional outcomes (Berendsen et al., 2012; Haichar et al., 2008; Rolfe et al., 2019). Through these processes, BCAs influence microbial diversity, including both alpha diversity (within-sample richness) and beta diversity (between-sample compositional differences). The magnitude and direction of these shifts depend on the host plant and soil type as well as the resident microbiota (Debode et al., 2018; Wilson and Arunachalam, 2024). Inoculation with BCAs can thus act as an ecological perturbation, triggering shifts in community structure and ecosystem function. However, such modulation is not universally beneficial. In cases of niche overlap or ecological antagonism, BCAs may competitively displace native microbial taxa crucial for nutrient cycling or stress buffering. This can potentially trigger cascading nontarget effects across the rhizosphere microbiome (Pearson and Callaway, 2003, 2005; Trabelsi and Mhamdi, 2013). Additionally, BCAs fail to persist in some settings due to poor compatibility with the indigenous microbiome or unfavorable soil conditions, reducing their long-term efficacy (Schulz et al., 2019).

The effectiveness of BCAs in shaping rhizosphere microbiomes is highly variable, particularly when comparing laboratory, greenhouse, and field settings, reflecting the interplay of abiotic, biotic, and ecological factors. Soil physicochemical traits such as pH, texture, nutrient availability, and organic matter content are key abiotic drivers that strongly influence microbial colonization and functional expression (Berg and Smalla, 2009; Trabelsi and Mhamdi, 2013). For instance, acidic soils can limit Bacillus spp. sporulation, while organic-rich soils may reduce the competitive advantage of nutrient-solubilizing strains. Beyond effects on colonization, abiotic conditions can directly regulate the expression of BCA functions including the biosynthesis and stability of antibiotics and other secondary metabolites, thereby modulating antagonistic activity independently of population size (Berg and Smalla, 2009; Raaijmakers and Mazzola, 2012). Such context-specific responses underscore the challenge of developing universally effective formulations.

Plant genotype exerts an equally strong filtering effect. Root exudate chemistry, architectural traits, and immune signalling not only shape microbial recruitment but also determine compatibility with inoculated strains. Genotype-specific filtering can facilitate or block BCA establishment depending on how introduced microbes overlap with resident microbiota niches (Philippot et al., 2013; Rawal et al., 2024). This highlights the need to consider crop genetic background in inoculant design, particularly in breeding programs that historically overlook plant–microbe interactions (Iqbal et al., 2025). Climatic variability adds another layer of complexity. Temperature extremes, soil moisture fluctuations, and seasonal cycles modulate microbial persistence and activity. For example, B. subtilis and T. harzianum have shown strong antagonism in controlled trials but exhibit inconsistent or diminished efficacy under field conditions, suggesting that environmental complexity often limits the translation of laboratory efficacy (Rigobelo et al., 2024).

Colonization and persistence are critical bottlenecks. Many inoculants fail to establish durable populations due to competitive exclusion by native microbiota, predation by protists, or suboptimal timing and delivery methods. In addition to effects on establishment, interactions with indigenous microbial communities can directly constrain or enhance BCA efficacy through interspecies metabolic interference or facilitation. For example, Stenotrophomonas maltophilia can degrade lipopeptide antibiotics produced by Bacillus spp. (e.g., iturin, fengycin, surfactin), thereby attenuating biocontrol of tomato bacterial wilt despite successful BCA colonization (Peng et al., 2025). In contrast, positive interactions with resident microbial keystone taxa can enhance BCA performance. A recent study showed that specific indigenous microbes stimulated antibiotic biosynthesis in Streptomyces, leading to improved disease suppression through metabolite-mediated induction rather than direct antagonism alone (Sun et al., 2025). These contrasting outcomes highlight that BCA efficacy is highly context-dependent rather than universally reproducible. Even when initial colonization is achieved, BCA-mediated functions such as ISR or mycoparasitism are often regulated by density-dependent microbial signalling and plant-derived cues, which may not be consistently activated across diverse soil environments (Moussa and Iasur Kruh, 2025). Moreover, traits observed during in vitro screening often fail to translate to complex rhizosphere environments, where multi-trophic interactions, fluctuating nutrient availability, and stress events shape microbial behavior. This discrepancy illustrates the limitations of current screening pipelines, which often neglect ecological compatibility and stress resilience.

Despite their potential, BCAs are not without risks. One critical concern is the displacement of native beneficial microbes, particularly in systems with already well-functioning microbial communities. The introduction of dominant inoculants can reduce microbial diversity or suppress indigenous taxa that play critical roles in nutrient cycling, pathogen suppression, and stress buffering (Pearson and Callaway, 2003; Trabelsi and Mhamdi, 2013). Such non-target effects may compromise essential ecosystem functions if introduced BCAs competitively displace resident microbes that are functionally important but not directly associated with disease suppression. These ecological trade-offs are especially evident in monospecific inoculations, which often lack the resilience and functional redundancy characteristic of native microbial consortia. Many BCAs also exhibit narrow-spectrum efficacy, performing effectively against specific pathogens under controlled conditions but showing limited broad-spectrum protection and consistency in complex field environments (Leal et al., 2024).

Beyond these general constraints, more subtle ecological risks may arise. Targeting a single pathogen can inadvertently lead to ecological release of secondary or opportunistic pathogens, thereby unpredictably altering disease complexes. Unintended effects may also result from horizontal gene transfer, interference with microbial signalling networks, or suppression of keystone taxa that support the rhizosphere’s structural stability. Repeated or high-frequency BCA applications may amplify these effects by cumulatively reshaping microbial networks and selecting for altered interaction dynamics over time. Such perturbations can compromise microbiome resilience, reduce invasion resistance, and impair ecosystem services that underpin long-term soil health. Importantly, these risks are context-dependent: BCAs may enhance resilience by restoring lost functions in degraded or simplified systems but could disrupt established microbial equilibria in biodiverse or organically managed soils. Despite these concerns, there have been few long-term evaluations of the ecological consequences of repeated BCA applications across cropping cycles and environmental conditions. Current risk assessment approaches are largely oriented toward short-term efficacy, with less emphasis on microbiome-level impacts, biosafety considerations, or cumulative ecological effects, highlighting the need for more holistic and longitudinal perspectives on the sustainability of microbial biocontrol interventions.

Climate change is reshaping the global epidemiology of fungal diseases, with increasing incidences attributed to drought, salinity, temperature extremes, and shifting precipitation patterns (Bebber et al., 2013; Singh et al., 2023). These stressors extend the geographic range of pathogens such as Fusarium spp., Verticillium spp., and Botrytis cinerea, while simultaneously enhancing their aggressiveness and survival under adverse conditions.

Plant susceptibility is aggravated under abiotic stress. Drought impairs root development, alters rhizodeposition patterns, and limits the plant’s ability to recruit beneficial microbes. These factors collectively increase plants’ vulnerability to soilborne pathogens (Preece and Peñuelas, 2016; Zahra et al., 2023). Likewise, salinity and high temperatures have been shown to downregulate key immune signalling pathways, including those regulated by SA, JA, and ET, which are essential for SAR and induced defense responses (Rossi et al., 2023). Importantly, interactions between abiotic and biotic stressors are often synergistic rather than additive. Combined stress conditions, such as drought coinciding with a pathogen challenge, can lead to greater physiological damage than either stress alone. This is partly due to compounded suppression of plant immune responses and microbiome-mediated defense mechanisms. These interactions also reduce the functional stability of rhizosphere microbial communities, which limits their capacity to buffer against pathogen invasion (Ramegowda and Senthil-Kumar, 2015; Suzuki et al., 2014).

Microbial BCAs provide two key functions under climate stress conditions: they suppress phytopathogens while simultaneously enhancing plant tolerance of abiotic stressors (Sheoran et al., 2025). These functions are mediated by stressor-specific mechanisms that operate at both the cellular and rhizosphere ecosystem levels and are linked to key climate variables including drought-induced water limitation, temperature-driven metabolic constraints, and salinity-associated osmotic stress. However, these benefits are not consistently observed across experimental scales: desirable outcomes are seen more frequently under controlled conditions than in heterogeneous field environments. Understanding and optimizing these interactions will be essential for developing climate-resilient cropping systems. Representative studies demonstrating BCA-induced microbiome and plant responses under stress conditions are summarized in Table 3.

Strawberry (Fragaria × ananassa) has emerged as a valuable model for studying interactions between microbial BCAs and rhizosphere microbiome dynamics due to its relatively short lifecycle, well-characterized microbial baseline, and high sensitivity to biotic and abiotic stresses (Debode et al., 2018; Kang et al., 2025). Its vulnerability to soilborne pathogens including B. cinerea, F. oxysporum, and Colletotrichum acutatum, combined with a microbiome that is both diverse and responsive to disturbance, provides a high-resolution framework for testing microbiome-modulating interventions (Kang et al., 2025). Inoculation with BCAs such as T. harzianum, Aureobasidium pullulans, and B. subtilis have consistently suppressed B. cinerea and C. acutatum while simultaneously enriching rhizosphere diversity and microbial network connectivity in strawberry studies (Freeman et al., 2004; Huang et al., 2023; Iqbal et al., 2021, 2023; Mannaa et al., 2023; Menéndez-Cañamares et al., 2024). These BCAs suppress pathogens via both indirect antagonistic mechanisms, including antibiosis, and direct interactions such as mycoparasitism. They also appear to facilitate beneficial shifts in core microbial taxa associated with nutrient mobilization, systemic resistance, and root colonization. Bee-vectored delivery of C. rosea and A. pullulans has demonstrated dual benefits, enhancing pre-harvest disease resistance and improving post-harvest fruit quality by extending shelf life and reducing decay incidence (Iqbal et al., 2022; Kumar et al., 2024). These strategies showcase systems-level integration of biocontrol, highlighting its potential application across plant developmental stages and the agro-supply chain. Importantly, in strawberry systems, BCA inoculation has been shown to alter the rhizosphere fungal community beyond direct pathogen suppression, including changes in community composition and associated plant defense responses (Debode et al., 2018).

Tomato (Solanum lycopersicum), muskmelon (Cucumis melo), and cucumber (Cucumis sativus) have been important systems for evaluating the dual role of microbial BCAs in disease suppression and abiotic stress mitigation. In tomato, complex microbial consortia comprising P. fluorescens, T. asperellum, B. velezensis, and B. subtilis have shown efficacy against a spectrum of soilborne pathogens, including R. solanacearum, F. oxysporum f.sp. lycopersici, and Meloidogyne spp. (root-knot nematodes) (Ali et al., 2025; Gu et al., 2023; Moussa and Iasur Kruh, 2025; Obiazikwor et al., 2025; Wan et al., 2017). These BCAs not only provided biocontrol through direct antagonism and ISR induction but also reshaped the microbial composition of the rhizosphere, shifting patterns of alpha and beta diversity. Importantly, BCA application was associated with a higher abundance of Actinobacteria and mycorrhizal fungi such as Glomus spp., which are known to contribute to enhanced phosphorus solubilization, root colonization, and pathogen exclusion (Gu et al., 2023; Wan et al., 2017).

Promising results have also been obtained in cucurbit systems, particularly muskmelon and cucumber. Applications of B. amyloliquefaciens, B. subtilis, and Pseudomonas chlororaphis reduced the incidence of F. oxysporum f. sp. radicis-cucumerinum, Podosphaera xanthii, B. cinerea, R. solani and Pythium spp., especially under drought and saline conditions in which chemical controls often fail (Mehmood et al., 2023; Ni and Punja, 2020). The BCAs also activated host stress responses including the accumulation of antioxidant enzymes (e.g., SOD, CAT, APX) and compatible solutes (e.g., proline, glycine betaine), thus contributing to osmotic adjustment and oxidative damage mitigation. These results emphasize that effective biocontrol is not limited to pathogen suppression but often coincides with improved rhizosphere functionality and resilience.

Perennial crops such as grapevine (Vitis vinifera) and banana (Musa spp.) are high-value systems that are increasingly threatened by persistent fungal pathogens and environmental stressors. In grapevines, trunk diseases caused by Phaeomoniella chlamydospora and Eutypa lata have shown significant responsiveness to treatment with T. atroviride, T. harzianum and B. subtilis, especially in Mediterranean climates characterized by thermal variability and drought stress (Di Marco et al., 2004; Gramaje et al., 2018; Kotze et al., 2011; Mesguida et al., 2023). These BCAs reduced disease severity while also inducing restructuring of both rhizosphere and endosphere microbial communities. This led to increased functional redundancy in bacterial guilds associated with xenobiotic degradation, biosynthesis of phytohormones including auxins and gibberellins, and immune modulation, suggesting enhanced ecological stability under pathogen pressure (Chen et al., 2024).

In bananas, inoculation with T. asperellum, T. reesei, and T. koningiopsis achieved partial control of F. oxysporum f. sp. cubense tropical race 4 (Foc TR4), a pathogen of global concern (Damodaran et al., 2020; Ploetz, 2015). Field studies across Asia and Latin America showed consistent suppression of disease symptoms alongside improved yield metrics. Treated plants exhibited elevated expression of PR-related genes, improved root architecture, and an increase in rhizospheric populations of plant growth-promoting bacteria (PGPB), contributing to both biotic resistance and physiological resilience (Mon et al., 2021).

Cereal staples such as rice (Oryza sativa) and maize (Zea mays) are increasingly being targeted for treatment with microbial consortia to enhance stress resilience and nutrient efficiency under climate stress (Jha et al., 2013; Tyagi et al., 2023; Zayadan et al., 2014). These consortia typically combine functionally complementary taxa like nitrogen-fixers (Azospirillum, Serratia), phosphate-solubilizers (Azotobacter, Bacillus, Enterobacter), and biocontrol fungi (Trichoderma spp.) to simultaneously address multiple agroecological constraints (Altomare et al., 1999; De Vries and Wallenstein, 2017; Hermosa et al., 2013; Kong et al., 2018; Rizvi and Khan, 2018; Woo and Pepe, 2018). Under both controlled and field environment, such inoculants have been shown to improve crop performance, particularly in low-input systems exposed to salinity or thermal extremes. Mechanistically, these benefits are linked to enhanced ion homeostasis (e.g., improved K⁺/Na⁺ ratios), modulation of antioxidant enzyme activity, and reinforcement of root–soil interactions through exopolysaccharide production and root surface colonization. In salt-affected paddy systems, inoculated rice plants exhibited reduced sodium uptake, enhanced osmolyte accumulation, and improved nutrient use efficiency, allowing biomass yields to be maintained without synthetic inputs (Marzouk et al., 2025; Sackey et al., 2025; Saleem et al., 2025). However, the performance of these consortia remains highly variable. Inoculant efficacy depends on cultivar compatibility, soil physicochemical properties, and previous land-use history, which collectively shape the recruitment, colonization, and functional integration of applied microbes. However, most studies have focused on short-term growth and yield outcomes, paying limited attention to long-term microbiome restructuring, ecological trade-offs, or economic scalability.