Innate immunity in plants is triggered by PAMPs (pathogen-associated molecular patterns) in response to microbial infection. PAMPs are common in pathogens, non-pathogens, and saprophytes (Jeworutzki et al., 2010; Thomma et al., 2011; De Freitas and Stadnik, 2012; Vidhyasekaran, 2014). Bacterial PAMPs [e.g., certain proteins in bacterial structures and flagella, lipopolysaccharide components, muropeptides, and sugar backbone structures in peptidoglycans, the elf18 epitope in elongation factor Tu (EF-Tu), the CSP22 cold-shock protein, the Ax21 sulfated protein, rhamnolipids, superoxide dismutase (SOD), bacterial DNA, and NEP1-like proteins]; fungal PAMPs [e.g., chitooligosaccharides, ergosterol, the EIX protein, cerebrosides, and NEP1-like proteins]; and oomycete PAMPs [e.g., PEP-13, elicitins, cell wall glucans, the cell wall glycoprotein CBEL with CBD motifs, and NEP1-like proteins] are non-self-response signaling molecules recognized by plant pattern-recognition receptors (PRRs; Nicaise et al., 2009; Tsuda and Katagiri, 2010). Most PRRs are receptor-like kinase (RLK) proteins with a receptor and a signaling domain in the same molecule. In response to PAMPs, PAMP-triggered immunity (PTI) is activated (Bigeard et al., 2015), except when pathogens deliver effector proteins that interfere with PTI signaling to the host plasma membrane. In turn, plants use unique resistance (R) proteins to sense the presence of these effectors in microbes, which triggers effector-triggered immunity (ETI) (Bigeard et al., 2015).

Other intracellular signaling pathways contribute to plant immunity as well. The calcium ion, a regulator of gene expression in plants, is an intracellular second messenger involved in various defense signaling pathways in plants (Galon et al., 2010). Calcium molecules are mainly recognized by calcium sensors, which transduce calcium-mediated signals into downstream events (Hashimoto et al., 2012; Wang et al., 2012). Guanosine triphosphate (GTP)-binding proteins (G-proteins) act as molecular switches in the signal transduction system (Yalowsky et al., 2010; Zhang et al., 2012). Reactive oxygen species (ROS) and nitric oxide (NO) are highly diffusible second messengers that act in cellular signal transduction pathways. Also mitogen-activated protein kinases (MAPKs) form important signaling cascades, which act as a second line of defense in concert with PAMP. MAPKs modules are major pathways downstream of sensors/receptors that transduce extracellular stimuli into intracellular responses in plants (Hettenhausen et al., 2012). In addition to PAMP and MAPK, plant hormones such as salicylic acid (Mukherjee et al., 2010; Dempsey et al., 2011), jasmonate (Sheard et al., 2010; Bertoni, 2012), ethylene (Nambeesan et al., 2012), abscisic acid (Yazawa et al., 2012), auxin (Fu and Wang, 2011), cytokinin (Choi et al., 2011), gibberellins (Qin et al., 2013), and brassinosteroids (Vleesschauwer et al., 2012) play an important role in defense signaling against various pathogens (Vidhyasekaran, 2014). Although microbes employ various defense mechanisms to counter the pathogen attack, these mechanisms fail when pathogens reach a maximum population size.

An effective defense strategy is to block cell-signaling pathways in pathogens to arrest their growth in the host environment. The LuxI and AinS families of Acyl-HSL synthase produce AHL signals using SAM and Acyl-Acp as substrates (Gilson et al., 1995; Parsek et al., 1999). SAM analogs and the SAM biosynthesis inhibitor cycloleucine can inhibit AHL production (Hanzelka and Greenberg, 1996; Parsek et al., 1999). Mutations in AHL biosynthesis genes have direct effect on signal synthesis and biofilm formation. Mutant P. aeruginosa lasI, failing to synthesize 3OXOC12-HSL, forms a flat, unstructured biofilm in a flow cell. Likewise, many other mutants (e.g., B. cenocepacia K56-2 cepI, J2315 cepI, and cciI) are defective when grown in biofilms (Huber et al., 2001; Hentzer and Givskov, 2003; Tomlin et al., 2005; McCarthy et al., 2010; Udine et al., 2013).

Rgg-class proteins are transcriptional regulators on the cytoplasmic membrane that act as receptors for intracellular signaling peptides. They are found in low-G+C-content, Gram-positive bacteria (Firmicutes) communication mediated by peptide molecules (Chang et al., 2011). Domain architecture prediction in Rgg proteins has revealed domains similar to that of another family of regulators (RNPP: Rap, NprR, PlcR, and PrgX) that is responsible for peptide interaction (Cook and Federle, 2014). Recently, cyclosporine, a cyclic peptide compound, was found to curb the activity of Rgg peptide receptors (Parashar et al., 2015). Though they remain crucial windows into peptide-based signaling in Gram-positive bacteria, the synthesis, and processing of Rgg peptides have not been well-studied. Further attention to this field may result in the discovery of new, effective quenching molecules against these peptide receptors.

Autoinducer AI-2 is a common signaling molecule used in both intra- and interspecies communication. It is a furanosyl borate diester molecule, unique due to the presence of boron in its structure (Pereira et al., 2013). Quenching of the AI-2 molecule helps in broad-spectrum control of pathogens (Zhu and Li, 2012; Guo et al., 2013; Pereira et al., 2013), as this molecule acts as a universal language for bacterial interaction. Quenching can be accomplished either by inhibiting signal biosynthesis or by inhibiting signal detection by microbes (LaSarre and Federle, 2013). Different bacterial species sense the AI-2 molecule in different forms, so a single inhibitor cannot be used widely; however, targeting the LuxS protein—which is wholly responsible for the synthesis of AI-2—results in defective signaling and is more effective in controlling a wide range of pathogens. 5'-methylthioadenosine nucleosidase (MTAN) inhibitors play dual roles as quorum quenchers in AI-2 and AHL biosynthesis (LaSarre and Federle, 2013). Halogenated furanoes, such as brominated furanoes derived from the red alga Delisea pulchra, have a direct role in inhibiting AI-2 quorum sensing (Lennen, 2007). Increasing the concentration of in vitro-produced AI-2 has a negative impact on biofilm density (Auger et al., 2006). Several diol-containing compounds (including pyrogallol), boronic acids, and sulfones have been shown to be potent antagonists of AI-2-LuxP binding (Lowery et al., 2005, 2009; Frezza et al., 2006, 2007; Ni et al., 2008, 2009; Peng et al., 2009).

Cross-kingdom interaction leads to specific adjustments and physiological adaptations in colonized eukaryotes (Hartmann and Schikora, 2012). The process by which non-native microbes are introduced into a plant environment is termed biotization. Biotization in the rhizosphere region helps plants obtain more transition metals through siderophore production, which in turn increases plant immunity against phytopathogens. Other evidence also shows that plants with hyper-accumulation of metal have increased resistance to pathogens (Fones and Preston, 2013). In order to successfully colonize a host, microbes undergo several modifications. R. solanacearum appears to alter its membrane architecture in complex ways during adaptation to life in the xylem (Poussier et al., 2003; Brown and Allen, 2004). Thus, culturing of beneficial microbes with plant cells in in vitro conditions can be used for endophytic colonization in plants (Senthilkumar et al., 2008). In plants, endophytes have an advantage over epiphytes, in that they are protected from external growth-limiting factors such as temperature, UV radiation, and osmotic potentials.

Various quorum quenching endophytes that have been identified in plants with AHL-ase activity are presented in Table 1. The main advantage of the artificial introduction of quorum quenching bacteria into plants is that introduced bacteria will occupy most of the intercellular spaces without leaving space for later-invading pathogenic bacteria, as shown in Figure 1. Also, biotization prevents soil bacteria entering into plant tissue (Kung and Almeida, 2014). Though a few pathogenic bacteria enter into the plant system, they remain as avirulent strain due to quorum quenching activity. Virulence-expressing factors are suppressed by AHL-degrading enzymes (Figure 1). Absence of endophytes in the tissues of culture-propagated plants may be related to increased disease severity, an idea supported by Jie et al. (2009).

So far there are no universal QQ bacterai to be used for all plants. Also, biotization has been shown to be limited by the absence of AHL-based quorum sensing in Gram-positive bacteria, instead inhibition of Rgg pheromone receptors could be employed (Cook and Federle, 2014). Research has shown that there is a chance that bacteria can evolve resistance to QS-disruption-related control methods (Defoirdt et al., 2010). Hence, a deep understanding of plant-microbe interactions in both biotized and non-biotized plants should be the goal of future research. The challenges of in vitro biotization are summarized in Figure 1.

Biotization helps at various physiological and developmental stages in plants. It enhances induced biotic and abiotic stress resistance (Badosa and Montesinos, 2008; Lugtenberg and Kamilova, 2009; Senthilkumar et al., 2011). Endophytes improve plants' health mainly through siderophore production, thereby enabling biological nitrogen fixation (Ngamau et al., 2012), phosphate solubilization (Andrade et al., 2014), and effective transport of iron (Fe) and zinc (Zn) from the rhizosphere region by ZIP transporters (Krithika and Balachandar, 2016).

The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest.