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, migration through the xylem element occurs through perforated plates [47].
2.3.1 Microbial Population in the Endosphere
Numerous studies have already characterized endophytes from a plethora of plant hosts and different plant compartments above and below the ground. Endophytes are present ubiquitously in most of the plant, either actively or latently colonizing the plant tissue. Generally, the plant endosphere is enriched with members of Proteobacteria [48] and to a lesser amount with Actinobacteria, Firmicutes, and Bacteroidetes [49]. Other classes that are less commonly found include Acidobacteria, Chloroflexi, Verrucomicrobia, and Planctomycetes [48]. Endophytic genera of bacteria commonly found to belong to Microbacterium, Burkholderia, Micrococcus, Bacillus, Pseudomonas, and Pantoea, where Bacillus and Pseudomonas spp. dominate [50]. Fungal endophytes commonly found belong to Ascomycota, and a few belong to Basidiomycota, Zygomycota, and Oomycota. Common genera that are reported are Trichoderma, Fusarium, and Aureobasidium [51]. However, the dominance of the phyla varies depending on the plant host species.
2.3.2 Biocontrol Mechanism in the Endosphere
Endophytes produce various substances that directly help enhance the growth of the host plant and discourage phytopathogens and plant pests’ survival. These metabolites could be antibiotics, siderophores, hydrolytic enzymes, volatile organic compounds (VOCs), and toxins [52]. Antimicrobial activity has been reported for endophytic Pseudomonas putida (PpBP25) in black pepper with aggressive action against plant pathogen Phytophthora capsici and Radopholus similis [52]. The most common genera with antagonistic activity against phytopathogens include Bacillus, Enterobacter, Actinobacteria, Pseudomonas, Serratia, and Paenibacillus [53,54].
2.3.2.1 Competition
There is a race between endophytes and phytopathogens to prevent host tissue colonization [55]. They colonize either systemically or locally and act by inhabiting locations available for the pathogens and lurking for nutrients that are available for the proper functioning of the plant [56]. There are not many reports on how nutrient management/uptake by beneficial microbiomes is related. Still, some reports confirm the crosstalk between Fe-deficient/nutrient starvation and resistance elicited by microorganisms. For instance, Herbaspirillum seropedicae Z67, a nitrogen-fixing endophyte, is dependent on iron for its vital cellular processes and produces serobactins (siderophores) to fulfill its iron requirement [57]. Some studies have provided valuable insights into the iron competition between endophyte Streptomyces sporocinereus