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 OsiSh-2 and a pathogen 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
