Beneficial microbes produce certain ligands like flagellin, lipopolysaccharides (LPS), exopolysaccharides, and chitin oligosaccharides (Zhang and Zhou, 2010; Zamioudis and Pieterse, 2012; Zipfel and Oldroyd, 2017; Saijo et al., 2018) that are recognized by receptor proteins of plants that transfer the signals to co-receptors. Subsequent reactions involve the phosphorylation of the downstream substrates, producing a signal cascade resulting in an oxidative burst, Ca²⁺ influx, MAP-Kinase activation, and hormone signaling activation (Bazin et al., 2020). In a wide array of eubacteria, the N-terminal part of flagellin is found to be highly conserved with 22-amino acid epitope, known as flg22 (Felix et al., 1999). The first receptor that is reported to recognize flagellin of PGPRs is the FLAGELLIN-SENSING 2 (FLS2) receptor (Trda et al., 2014). It is reported that recognition of flg22 by FLS2 initiates its heterodimerization with the co-receptors BRI1-associated kinase (BAK1) and BAK1-LIKE1 (BKK1) that phosphorylate the receptor-like cytoplasmic kinase Botrytis-induced kinase1 (BIK1), thus starting PTI signaling (Chinchilla et al., 2007; Lu et al., 2010; Segonzac and Zipfel, 2011). This was demonstrated by the experiments conducted with Arabidopsis thaliana (Lu et al., 2010).

In the case of plant symbiosis with rhizobia and AMF, the process is triggered by chitin-derived oligosaccharide signals (Zipfel and Oldroyd, 2017). In this example, acylated lipo-chitooligosaccharides known as Nod factors are produced by rhizobia that are recognized by LysM receptor-like kinases that activate common symbiotic pathways controlling both mycorrhization by AFMs and nodulation by rhizobia (Madsen et al., 2003; Gough and Cullimore, 2011; Yu et al., 2022).

PTI induced by beneficial microbes are found to be transient and relatively mild as compared to the pathogen-induced PTI that causes severe cellular damage resulting in mutually beneficial interaction with the plant. Felix et al. (1999) has reported that in the example of flg22 peptide obtained from Burkholderia phytofirmans, only small oxidative bursts sufficient enough to induce defense genes was observed. Similarly, in the case of P. fluorescens WCS417, low molecular compounds were produced that were able to suppress flagellin-triggered PTI responses in Arabidopsis roots (Millet et al., 2010). Both these examples highlight the underlying processes involved in co-evolution without the beneficial microbes getting harmed by the defense response. Furthermore, beneficial microorganisms can induce different pathways by triggering various defense responses of host plants and imparting resistance to multiple pathogens. Through such versatile ISR, Bacillus amyloliquefaciens, B. atrophaeus, B. cereus, and Pseudomonas fluorescens were demonstrated to be effective against fungal, bacterial, and viral infections. Such priming by the beneficial microbes not only induced early plant ISR events but also increased the expression of pathogenesis-related PR-genes and the activities of defense-related substances, such as phenylalanine ammonia-lyase, polyphenol oxidase, peroxidase, β-1,3 glucanase, and chitinase. The accumulation of reactive oxygen species was also reported to be enhanced (Guo et al., 2019; Wang et al., 2020).

Oxidative burst is represented by the production of a large number of reactive oxygen species (ROS), including superoxide anion (O²⁻), hydroxyl radical (OH.), and hydrogen peroxide (H₂O₂), by plants under stressed conditions (Chen et al., 1993). The induction of oxidative bursts ultimately results in an immune response toward pathogens, leading to programmed cell death and stomatal closure (Apel and Hirt, 2004). Since the accumulation of ROS also causes damage to plant tissues (Dat et al., 2000), it is required to control the production of ROS by enzymatic and non-enzymatic reactions. Enzymes like peroxidase (POX), polyphenol oxidase (PPO), superoxide dismutase (SOD), ascorbate peroxidase (APX), glutathione peroxidase (GPX), and catalase (CAT) help to control ROS production by reducing superoxide to H₂O (Yu et al., 2022). Production of ROS is reported in Bacillus cereus and Pseudomonas aeruginosa.

When a plant is attacked by a pathogen, callose, a β-1,3-glucan polymer, accumulates in the cell wall at the infection site, thickening it to restrict fungal germ tube invasion. Clay et al. (2009) explained the significance of PEN2 and PEN3 genes required for callose deposition and consequently for pathogen resistance. Sakthivel and Balachandar (2019) reported that the MAMPs released by PGPR generate ROS and increase the level of SA. High levels of SA regulate the PDLP5-dependent expression of the callose synthase gene (CALS10), triggering callose deposition by the plant.

Microbial elicitors are known to trigger ion fluxes like Ca²⁺ influx, Cl⁻ effluxes, and K⁺/H⁺ exchange. These ion influxes are important for the development of cells, immunity of the plants, and transportation of signals. Ca²⁺ ion influx is the most important ion influx, playing a significant role as a secondary messenger in diverse cellular processes and various physiological changes (Trewavas and Malho, 1998). Ca²⁺ ion influx induced by microbial elicitors not only acts as a mediator in events but, through Ca²⁺-dependent H₂O₂ production, Ca²⁺ signaling is amplified and increases Ca²⁺ ion influx from extracellular sources (Price et al., 1994; Lecourieux et al., 2002). Pretreatment with forskolin, dibutyryl cAMP, or Ca²⁺ ionophore A23187 is reported to enhance the production of ROS, thus restricting infection from Colletotrichum lindemuthianum in bean (Phaseolus vulgaris). Further, in a cross check, treatment with the Ca²⁺ channel blocker was found to decrease the oxidative burst, highlighting the role of Ca²⁺ influx in ROS production (Bindschedler et al., 2001). It is reported that, after Ca²⁺ ion influx, a Ca²⁺ ion sensor calmodulin is activated due to the binding of Ca²⁺ ions further activating protein phosphatase and Ca²⁺/calmodulin-dependent protein kinase (CDPK), membrane-bound enzymes, or transcription factors, thus regulating transcription in plants (Zhao et al., 2005; Iqbal et al., 2020). CDPK plays an important role in the defense responses of plants. Protein kinase cascades induced by Ca²⁺ spiking play a role in the production of ROS, transfers lipid signaling messengers, and amplifies the elicitor signals to downstream reactions. Ca²⁺ spiking also differentially activates transcription factors, directly regulating extensive defense gene expression (Dolmetsch et al., 1997; Yang and Poovaiah, 2002; Iqbal et al., 2020). Ca²⁺/calmodulin-binding transcription factors modulate EDS1 to regulate salicylic acid levels in plant cells (Du et al., 2009).

In the JA/ET signaling pathway, several transcription factors play a crucial role in regulating the induction of resistance. WRKY transcription factors are reported to differentially express during beneficial plant–microbe interactions (Saenz-Mata et al., 2014). The MYB family proteins that regulate plant development are also found to regulate plant–microbe interactions. MYC2, a basic helix–loop–helix (bHLH) transcription factor, is found to be involved in IR triggered by beneficial microbes (Dubos et al., 2010; Kazan and Manners, 2013). Ethylene response factor1 (ERF1) is a transcription factor that regulates the expression of pathogen response genes to prevent disease progression and is found to be functional during beneficial microbe-plant interaction. In both JA and ET signaling pathways, the expression of ERF1 is activated rapidly and synergistically (Lorenzo et al., 2003).

The induction of SA and JA/ET pathways during beneficial microbe-plant interactions is the key to activation of resistance genes to combat pathogen attack. Effective use of defense mechanisms of microbial-induced resistance depends on an accurate and context-specific regulation of gene expressions. This needs an understanding of complex circuits and regulatory networks due to interactions between genes and their products. In a study conducted by Timmermann et al. (2020), regulatory mechanisms of the induced resistance triggered by the beneficial bacterium Paraburkholderia phytofirmans PsJN was explored and a regulatory network according to gene expression and time series data was drawn. Pre-treatment of Arabidopsis thaliana with the non-pathogenic Bacillus cereus AR156 strain was found to trigger the expression of PR1, PR2, and PR5 genes and Plant Defensin 1.2 (PDF1.2) accumulation; this indicates the activation of SA and JA/ET signaling pathways (Niu et al., 2011; Niu et al., 2016a,b; Nie et al., 2017). NPR1 is reported to coordinate SA and JA signaling pathways, regulating downstream defense response genes (Cao et al., 1994; Cao et al., 1997; Pieterse et al., 1998; Spoel et al., 2003).

Secondary metabolites produced by the plants help them to adapt to various stresses under natural conditions. Interaction of these secondary metabolites with beneficial microorganisms can modulate plant growth and immune responses, thus inhibiting metabolism and/or growth of harmful microbes. For example, selective growth of PGPRs in the plant rhizosphere is controlled by root exudates enhancing biofilm formation of beneficial microbes (Zhang et al., 2014). A list of plant metabolites reported to play significant roles in beneficial microbe-plant interactions is given here (Table 1).

Secondary metabolites produced by the beneficial microbes are found to be antagonistic to the pathogen and are reported as elicitors of immune response to induce resistance in plants (Prsic and Ongena, 2020). Some significant secondary metabolites produced by beneficial microbes are listed in Table 2.

These findings demonstrate the intricate framework of secondary metabolites produced by plants to support beneficial microbes and restrict harmful ones, while also enhancing plant resistance through secondary metabolites generated by beneficial microbes, ultimately protecting the plant from pathogen attack.

Photosynthesis, respiration, and transpiration are the most important physiological activities of plants regulated by the stomata. Melotto et al. (2006) has observed that, to restrict the entry of pathogenic bacteria, the plant closes its stomatal openings, resulting in reduced gaseous exchange and thus reduced photosynthesis. Abscisic acid (ABA) produced by plants under stressed conditions is demonstrated to regulate stomatal opening. ABA mediates stomatal closure through three steps of signal transduction. In the first step, ABA binds to ABA cell receptors and interacts with PP2C, a group of type 2C protein phosphatases (Park et al., 2009; Ma et al., 2009). In the second step, this binding results in the inactivation of the inhibitory regulatory function of PP2C and the activation of SnRK2 protein kinase OST1 (Umezawa et al., 2009). In the third step, thus activated, OST1 directly binds and phosphorylates to activate the Slow Anion Channel-Associated1 (SLAC1) anion channel that mediates anion release from the guard cells. Stomatal closure then takes place (Geiger et al., 2009; Lee et al., 2009; Brandt et al., 2012). Through other routes, OST1 can catalyze hydrogen peroxide (H₂O₂) production (Sirichandra et al., 2009; Raghavendra et al., 2010) and the produced H₂O₂ modulates ABA signaling in the plasma membranes of guard cells (Pei et al., 2000) by activation of calcium channels. Lipoxygenase-encoding gene LOX1 is another signaling component that coordinates stomatal regulation. It is a JA-responsive gene that triggers stomatal defense by expressing in guard cells in response to PAMPs. This indicates that the JA signaling pathway also participates in regulating stomatal defense (Montillet et al., 2013). The triggering of ABA and JA pathways is demonstrated by PGPR B. amyloliquefaciens FZB42 by production of acetoin and 2,3-butanediol that induces the closing of stomata in response to pathogen attack (Wu et al., 2018a; Wu et al., 2018b; Xie et al., 2018). This indicates coordination of multiple signaling components to regulate microbial-mediated stomatal defense.

Beneficial fungi, such as Trichoderma spp. and AMF, are known to induce resistance to biotic stresses in plants through various mechanisms. Here, we will discuss the role of different beneficial fungi in modulating plant defense.

The beneficial root-colonizing fungi known as Arbuscular Mycorhizal Fungi (AMF) is also reported to trigger the immune response of plants to pathogen attack.

Many bacterial genera and species are reported as potential PGPRs and biocontrol agents. They will be discussed here individually.

Beneficial microbes that are applied in root zone-like PGPRs have to compete for resources and antibiotic production in their interaction with the soil microbiome (Toju et al., 2018), which affects quorum sensing and root-associated biofilm formation of PGPR (Rudrappa et al., 2008a,b). Through this, ISR is activated only when the concentration of beneficial microbes reaches 10⁵–10⁷ colony-forming units (CFU) per gram of root (Bakker et al., 2013). In addition to a successful establishment in the root zone, the induction of resistance also depends on the genetic backgrounds of the plant and microbe. For example, Pseudomonas putida strain WCS358r induces resistance in A. thaliana (Van Wees et al., 1997), Pseudomonas fluorescens WCS374r can induce resistance in radish (Rhaphanus sativus) (Leeman et al., 1995), and the P. fluorescens strain WCS417r induces resistance in both Arabidopsis and radish. Our current understanding of ISR is mostly based on model plants that may not be expressed in crop plants. Therefore, more effort is required to evaluate the strains on crop plants to explore the possibilities of their field applicability.

Similarly, herbivory is reported to induce changes in root exudate profile (Fierer and Jackson, 2006) that affect below-ground microbiota and the colonization of beneficial microbes, thus, affecting the induction of resistance (Gehring and Whitham, 2003; Rudrappa et al., 2008a,b; Yang et al., 2011; Gu et al., 2016; Malacrino et al., 2021). For instance, mycorrhizal colonization is reported to increase, decrease, or remain unaffected by herbivory (Gehring and Bennett, 2009; Barto and Rillig, 2010). Although not studied in depth, some researchers have indicated the possibilities of such alterations in the context of ISR due to insects, parasitoides (Poelman et al., 2011), and facultative endosymbionts found in sucking-type insects like Hamiltonella defensa (Su et al., 2015). On the contrary, some researchers have reported a negative effect on chewing insects and positive effect on sucking insects by feeding on the plants with ISR triggered by AMF (Hartley and Gange, 2009; Koricheva et al., 2009). Therefore, it is also required to study the effect of aerial feeding by herbivores on root exudation, the colonization of beneficial microbes, the induction of resistance, and the effect of microbial induction of resistance on herbivory.

Microbe-induced resistance is also reported to be influenced by various abiotic factors, including nutrient availability (Miransari, 2013; Oldroyd and Leyser, 2020), soil moisture levels (Auge et al., 2001; Juniper and Abbott, 2006; Ulrich et al., 2019), soil organic matter content (Schnecker et al., 2014; Del Valle et al., 2020), light quality and intensity (Nagata et al., 2015; Konvalinkova and Jansa, 2016), and soil pH (Aciego Pietri and Brookes, 2008). Hiruma et al. (2016) has described the effect of nutrient deficiency on root exudation and ultimately the interaction of plants with beneficial microbes. It is reported that, due to phosphorus (P) deficiency, plants produce strigolactones that play important roles in regulating the interaction of plants with AMF and endophytic fungi (Lopez-Raez et al., 2008; Hiruma et al., 2016). In A. thaliana, P-deficiency triggers the expression of PHR1 and PHL1, which are PSR master transcriptional regulators (Hiruma et al., 2016; Castrillo et al., 2017; Morcillo et al., 2020) and results in the induction of JA signaling but the repression of SA signaling. As reported by Khan et al. (2016), the induction of JA signaling resulted in enhanced defense against a leaf-chewing insect in A. thaliana, tomato, and tobacco but enhanced susceptibility for an oomycete pathogen and a bacteria (Castrillo et al., 2017). In a classic work from Spagnoletti et al. (2018), it is demonstrated that, due to P-deficiency, soybean plants became 2.5 times more susceptible to charcoal rot disease. However, enhanced AMF colonization resulted in a 5.0-fold induction of resistance. Due to iron (Fe) deficiency, Arabidopsis plants produce defense-related secondary metabolites—coumarins—which affect the rhizospheric microbiota (Stringlis et al., 2018). Due to nitrogen deficiency, the roots of the leguminous plant exude flavanoids to attract rhizobia and trigger their nod genes to produce Nod factors (Mbengue et al., 2020). Likewise, most nutrient deficiency is associated with triggered resistance but, in a few cases, adverse effects are also noticed. For example, due to P-deficiency, a recruited PGPR strain, B. amyloliquefaciens, induced hypersensitivity in A. thaliana by triggering its response to emit a diacetyl volatile compound that caused hypersensitivity (Morcillo et al., 2020). Here, it is noteworthy that availability of nutrients and plant defense activation is directly related. This should be explored and standardized for exploiting ISR under field conditions instead of using costly defense metabolites that are difficult to synthesize in sufficient amounts for field application (Gershenzon, 1994; Neilson et al., 2013).

ISR triggered by PGPRs is regulated by phytoharmones like JA, ET, SA, and other members of the oxylipins family (Pieterse et al., 2014; Vlot et al., 2020) and by activation of a network of signaling molecules including reactive oxygen species (ROS) (Camejo et al., 2016) and reactive nitrogen species (RNS) (Khan et al., 2019). Plants are smart enough to integrate information about their biotic and abiotic environment, resulting in cross-talk between different signaling pathways (Fujita et al., 2006; Rejeb et al., 2014). This capacity helps them to understand the challenges they are facing and to prioritize and fine-tune their responses to that (Robert-Seilaniantz et al., 2011). This means the presence of ISR potent microbes in soil is not sufficient to trigger ISR but their interplay with other biotic and abiotic factors in their environment can activate an ISR response in plants (Pozo et al., 2015) under any given situation. Therefore, it is necessary to study how responses to other biotic and abiotic factors integrates with the phytohormonal system to trigger MMIR. For example, nutrient deficiencies are found to alter the root exudation patterns, thus affecting the chemotactic responses for selective accumulation of beneficial microbes in the rhizosphere for triggering ISR (Hiruma, 2019). Therefore, it is imperative to conduct studies to understand the interplay of biotic and abiotic factors for sustainable field response of MMIR before opting for commercial application.

Regular farm practices like tillage, fertilization, and pest management greatly affect soil micro-biome and plant microbe interactions (Banerjee et al., 2019; Caradonia et al., 2019). In horticultural crops, beneficial microbes are added to growth media or substrate (that is not soil) where microbial inoculants face less competition. For field crops, microbial inoculants are added to farm soil, where they face much heterogeneous competition. Interestingly, on-farm crops are typically grown under well-fertilized conditions to achieve higher yields, which contrasts with the low-nutrient conditions that favor colonization by beneficial microbes and the induction of resistance. For instance, due to long-term phosphate fertilization, percent root colonization in maize by AMF was reported to be reduced (Wang et al., 2017) and, due to P supplementation (Gange et al., 1999) and Nitrogen supplementation (Gange and Nice, 1997), resistance to chewing-type insects was found to be reduced. Contradictory results were recorded by Vesterlund et al. (2011) when fertilization was found to improve the performance of fungal endophytes against chewing-type insects. Thus, controlled fertilization can be potentially used to selectively recruit beneficial microbes (Bakker et al., 2018; Oldroyd and Leyser, 2020). Apart from fertilization, other farm practices like tillage and crop rotation also have profound effects on microbial populations. Due to long-term organic farming, beneficial microbes become established in soil and induce resistance in subsequently grown crops (Pineda et al., 2020). Tillage can reduce the build up of insect pests in soil but also disturb the establishment of beneficial microbes and creation of disease-and pest-suppressive soils (Peters et al., 2003).