is mediated by antibiosis in which antimicrobial compounds, lytic enzymes, or effector molecules are produced by biocontrol agents toxic to pathogens. Antibiotics compounds, viz., phenazines, pyrrolnitrin, lipopeptides, hydrogen cyanide, and 2,4-diacetylphloroglucinol, produced by specific biocontrol agents are well characterized [20]. Certain Bacillus species make antifungal lipopeptide iturin A [21], antimicrobial and antiviral cyclic lipodecapeptide fengycin [22], and various biosurfactants [23]. Bacillus subtilis RB14 produces antibiotic iturin, and surfactant was found to control Rhizoctonia solani, which causes damping-off disease of tomato seedlings [24]. Several strains can also induce plant defense-related genes by biocontrol metabolites or lipopolysaccharides and flagella and can control phytopathogen [25]. Streptomyces pactum, a biocontrol agent, increases the indigenous P. koreensis GS population in ginseng rhizoplane by expressing chemotaxis and flagellar biosynthesis-related genes and antagonizes soilborne pathogens [26].
Extracellular lytic enzymes such as cellulase, protease, and chitinase produced by certain antagonistic microorganisms are common. Other lytic enzymes target phytotoxins like fusaric acid produced by Fusarium oxysporum [23]. Another mechanism acquired by Pseudomonas is the type III secretion system that targets oomycetes [27]. According to Vacheron et al. [28] plant roots preferentially shaped Pseudomonads had one to five plant-beneficial properties [28].
2.2.2.4 Induced Systemic Resistance (ISR)
In the theory of plant immune system, the initial defense system activated by plants is pathogen-associated molecular patterns (PAMP), PAMP-triggered immunity (PTI), in which pattern recognition receptors (PRRs) recognize bacterial flagella or fungal chitin. The subsequent defense after initial defense is effector-triggered immunity (ETI), in which the nucleotide binding leucine-rich repeat (NB-LRR) receptor recognizes effector molecules of a pathogen. These two lines of defense often trigger induced resistance in unexposed parts of the plant by pathogens, and the mechanism is termed “systemic acquired resistance” (SAR) [29].
Plant-microorganism are evolved to gather according to different taxa and soil types but nowadays focus has been on functional microbiota, which provides fitness to halobiont. Induced systematic resistance (ISR) is a well-studied mechanism and first described for Pseudomonas in which certain beneficial bacteria, viz., Pseudomonas, Bacillus, and Serratia strains, and nonpathogenic fungi, viz., Trichoderma, F. oxysporum, and Piriformospora isolated strains, and the symbiotic mycorrhiza species in the rhizosphere prime immune system in the unexposed parts of plants to fight against infectious agents [30]. Seed-grown maize plant exposed to Trichoderma harzianum strain T22 had minimized symptoms of anthracnose, which was explained by root colonization by Trichoderma strain-ISR [31].
2.2.3 Plant Disease Management
Every natural soil can suppress pathogens to a certain level; this phenomenon is called general disease suppression, and it depends on the total microbial biomass. Specific suppression comes into the picture when an individual or group of microorganisms causes soil to suppress disease [32]. Some soil can retain its condition by suppressing activity for a long time, while some could develop after several years of monoculture. Moreover, the establishment of disease suppression in soil was described for several diseases. In an experiment conducted on a tomato plant, a susceptible cultivar was treated with rhizosphere microbiota of resistant cultivar, which suppressed disease symptoms.
Further analysis showed that flavobacterium TRM1 could antagonize R. solanacearum and inhibited the progress of bacterial wilt in tomatoes [33]. A root disease termed as “take-all” of Triticum aestivum caused by Gaeumannomyces graminis var. tritici was suppressed through several years of monoculture in soil by disease-suppressive microorganisms. This phenomenon is called “take-all decline,” which is associated with the antagonistic activity of fluorescent Pseudomonas spp. by the antifungal compound 2,4-diacetylphloroglucinol (DAPG) [32]. Soil metagenomics study of potato plants associated with potato common scab disease revealed a positive correlation between pathogenic Streptomyces and scab severity but negative correlation with Geobacillus, Curtobacterium unclassified Geodermatophilaceae [34]. Some commercial products such as “Mycostop,” containing Streptomyces griseoviridis strain, which can suppress root rot and wilt diseases by occupying the rhizosphere are also available [35], “BlightBan A506” containing P. Fluorescens can control fire blight frost damage in fruits caused by Erwinia amylovora and “Epic Kodiak” to target Rhizoctonia solani by Bacillus subtilis [36]. A microbial consortium containing four isolates, Serratia marcescens isolate 59, Pseudomonas fluorescens 57, Rahnella aquatilis 36, and Bacillus amyloliquefaciens 63 was able to increase soil disease suppression ability against Fusarium spp. in chickpea rhizosphere, which causes wilt and root rot [37].
Various management practices in combination or isolation are being used to suppress diseases, including intercropping, organic amendments, crop rotation, and tillage management. Several years of monoculture of one variety in the same field causes replanting disease. Intercropping changes root exudates that alter the rhizospheric microbiome. An experiment with intraspecific intercropping on Radix pseudostellariae plant increased beneficial Nitrosomonadales, Nitrospirales, Pseudomonadales, and decreased pathogenic Aspergillus and Talaromyces [38]. Atractylodes lancea, a medicinal plant, suppressed Fusarium oxysporum mediated root rot disease in peanut while used as inter-crop [39] and while intercropping with aerobic rice, conquered Fusarium oxysporum mediated watermelon wilt [40]. Intercropping between maize and soybean can cause phenolic acid-mediated inhibition of Phytophthora sojae, responsible for Phytophthora blight of soybean [41]. Reduced conventional tillage practices increase organic matter, which prevents C. sativus from germinating and changes nutrient availability, which influences pathogen survival. Crop rotation changes root exudates and compounds released from crop residue decomposition, which affects the rhizosphere microbial community. Fungicide compounds released from canola residues breakdown procedure can diminish the extremity of common root rot in cereals [42]. Animal manures and organic composts also influence plant pathogens. Providing beneficial microbiota from compost to conductive soil remains the critical strategy for increasing suppression against soilborne pathogens. Five compost–peat mixtures were used to control Pythium ultimum, Rhizoctonia solani, and Sclerotinia minor – Lepidium sativum to manage dumping off diseases [43]. Combining effort with selective biological control agents, organic amendments, and suppressive disease compost can achieve natural disease control against soilborne pathogens. A positive balance is obligatory between phytopathogens and beneficial microorganisms to obtain optimal plant growth and health.
2.3 Plant–Microbe Interaction in the Endosphere
Plants develop an association with their surrounding ecosystem to thrive in their natural environment. The most common type of association is the plant–microbe association, where the indigenous microbes help plant survival in biotic and abiotic stress. The plant endosphere consists of complex microbial communities whose function ranges from mutualism to pathogenicity. These microorganisms colonize at least a part of their life inside the plant interior and are termed “endophytes” [44]. While living near plant hosts, endophytic bacteria exchange for a consistent nutrient supply exerts a beneficial effect [45]. For establishing an asymptomatic association with the host plant, the endophyte must avoid triggering the plant’s defense system, which is achieved by maintaining low cell densities. Colonization of endophytes involves competition in the plant rhizosphere for space and nutrients, which is assisted by the production of polysaccharides and motility. Once they are established in the rhizosphere and rhizoplane, they make their way in by producing adhesion molecules and ultimately gain entry into the root by an active (low levels of cell-wall degrading enzymes) or passive (through cracks in roots) process [46]. After entering the roots, they migrate to above-ground plant tissue through the plant transpiration stream. Movement through intercellular spaces requires cell-wall degrading enzymes. However,
