of rice Magnaporthe oryzae [58]. The study indicated that M. oryzae is dependent more on iron supplementation than OsiSh-2 for growth and follows different strategies to acquire iron. Many genes involved in siderophore synthesis and iron uptake were present in endophytes than in pathogens, and OsiSh-2 has an added advantage for capturing iron over M. oryzae [58].
2.3.2.2 Parasitism
Parasitism is another mechanism that the endophytes use to defend their plant host. Generally, it is observed when there is an interaction between bacteria and fungi or fungi and fungi. Endophytes fight the pathogens directly and produce lyase that helps in destroying the pathogen’s cell wall. For instance, out of all the endophytes isolated from poplar, the Burkholderia cepacia complex could efficiently control Cytospora chrysosperma, Phomopsis macrospora, and Fusicoccum aesculi causative agent of poplar canker. The interaction of endophytic cotton bacteria Bacillus halotolerans (Y6) hinders spore germination in vitro along with mycelial growth of Verticillium dahlia pathogen. Mousa et al. (2016) observed that the endophyte swarmed toward the root-invading pathogen and completely covered F. graminearum hyphae by forming a biofilm that acts as a physical barrier that obstructs the passage and entraps the pathogen and is eliminated then. Thus, the bacteria construct a microhabitat of their own to invade the pathogen. Furthermore, the isolated strain can increase root hair proliferation and create a barrier to block and destroy the invaders [59].
2.3.2.3 Antagonism
Endophytes and phytopathogens live in a similar niche; they release a range of bioactive compounds to suppress or impede pathogens’ average growth and activity. Production of antibiotics, metabolites with antifungal properties, and production of volatile compounds such as hydrogen cyanide (HCN) by endophytes are directed mainly toward inhibiting plant pathogens [60]. Several compounds with antimicrobial properties have been purified and identified from endophytes, including peptides, terpenoids, steroids, alkaloids, phenols, quinones, flavonoids, and polyketides [61]. When different microbial species are near each other, endophytes or the host plants obstruct the growth of invading microbes, which is evident from the secretion of bioactive metabolites [62]. Phomopsis cassia, an endophyte from Cassia spectabilis, synthesized compounds similar to cadinene sesquiterpenes and 3,11,12-trihydroxycadalene, which showed activity against fungi like Cladosporium cladsporioides and C. sphaerospermum [63]. Similarly, the antagonistic potential of five endophytic Bacillus sp. isolated from Solanum sp. was screened against Fusarium oxysporum.
It was reported that the endophyte was capable of limiting pathogen sporulation and mycelial growth by the production of extracellular metabolites such as chitinases and lipopeptide antibiotics [64]. Effective inhibition of phytopathogenic nematodes [65,66], oomycetes, and fungi [67–71] by bacterial species have been reported through the production of VOCs. Thus, VOCs have been shown to have enormous potential in biocontrol.
2.3.2.4 Induced Systemic Resistance
The ISR and SAR primes plant defense against pathogenic microbes and herbivore insects by protecting plants from future attacks. Plants exhibit resistance by several molecular defense mechanisms such as ethylene/jasmonic/salicylic acid (ET/JA/SA) signaling pathway, callose deposition, regulation of polyamines uptake, accumulation of phytoalexins, producing reactive oxygen species, and gene expression that codes for pathogenesis-related (PR) proteins [46,69]. Defense-related genes were expressed in Arabidopsis, which simultaneously activated both defense pathways triggered by Bacillus cereus AR156 [70]. This increased biomass of plants and a simultaneous reduction in pathogen density and disease severity was observed. Moreover, an up-regulation of both of the defense pathways in Arabidopsis thaliana was observed by Conn et al. [71]. Inoculation of Actinobacteria protected against infection from both fungus Fusarium oxysporum and bacteria Erwinia carotovora. However, the defense pathways primed were different for both types of pathogens. The resistance to F. oxysporum involved the SA pathway, while the jasmonic acid pathway provided resistance to E. carotovora. Thus, the bacteria used two different ways, which helped in conferring resistance to two different pathogens [71].
2.3.3 Plant Disease Management
Disease management involves strategies and methods for manipulating the antagonistic populations to hinder pathogen survival and plant growth promotion. Endophytes are environmentally benign agents and thus are ideal candidates for efficiently promoting plant growth and act as bioactive candidates against parasitic nematodes. Bogner et al. (2016) showed that Fusarium solani and F. oxysporum complexes successfully reduced penetration and subsequent galling and reproduction of root-knot nematode, which can further be used for developing disease management systems in tomato [72]. In a study on activity against nematode, endophytic bacteria that belong to Bacillus spp., Streptomyces spp., and Pseudomonas spp. suppressed phytopathogenic burrowing nematode (Meloidogyne javainica) in banana roots with 70.7% biocontrol efficiency in sterile soil compared with control [73].
Furthermore, in another study, the endophytic B. subtilis strain E1 R-j was administered to determine its inhibitory effect on the causative agent of wheat stripe rust disease Puccinia striiformis [74]. In-vitro studies revealed an 84.1% inhibition rate when 10-fold dilution of fermentation liquid was used to treat bacterial cells. At the same time, in field trials, a significant decrease in disease severity was observed compared with non-treated plots. Moreover, a seven-month trial period of endophytic Burkholderia cenocepacia 869T2 against Fusarium wilt reduced the disease incidence to 3.4% compared to 24.5% of non-inoculated plants [75]. Similarly, pre-inoculation of peanut with beneficial root endophyte curbed root rot, which was evident from a decrease in the colonization by pathogens, cell death, and disease severity [76].
After a long period of continuous cropping system, a single type of root exudate can lead to an imbalance in the microbial diversity of the soil and can cause soil deterioration. In a greenhouse experiment, exudates from root endophyte Phomopsis liquidambaris improved significantly the rhizospheric abundance of bacteria. They promoted growth in peanuts by alleviating soil sickness [77]. Adopting a rational approach for disease management for sustainable agriculture has vast potential in the future. One of the benefits of using microorganisms is their role in declining agrochemicals, making agricultural practices more viable. An extensive field trial using inoculants containing an endophytic strain of Rhizobium leguminosarum bv. Trifolii enhanced grain yield in 19 tests out of 24, thus promoting rice production capacity and curtailing the necessity of chemical N-fertilizer inputs [78]. Muscodor albus, a novel endophytic isolate, is already registered and patented by Marrone Bio Innovations as a potent mycofumigating agent. Many studies have reported its potential as a biofumigant [79,84,80].
2.4 Plant–Microbe Interaction in the Phyllosphere
“Phyllosphere” is an ancient Greek word. “Phyllo” means leaf, and “sphere” refers to the field of influence. The term “Phyllosphere” referred to the above-ground part of a plant and was coined by Last and Ruinen in the 1950s in “Analogy to the Rhizosphere” [81,82]. The phyllosphere is associated with the largest biosphere–atmosphere interphase on Earth and is dominated by aerial plant parts, such as leaves, flowers, fruits, and others. The phyllosphere microbiota interacts with host and other microbes to colonize outer plant surfaces in addition to biotic, abiotic, and anthropogenic factors. Most biomes reach the phyllosphere via soil, wind, water, or insect transmission [83]. Leaf microbiotas first interacts with the outer cuticular layer, and the leaf micro-environment determines microbial communities [84]. Stomatal opening and wounds on the leaves surface are the primary paths for microbiota entering the inner phyllosphere [85]. Leaf exudates, such as terpenes, benzenoids, methanol, sugar, amino acids, and organic acids, also shape phyllosphere microbial assembly [86].
2.4.1 Microbial Population in the Phyllosphere
Microbial