Figure 2.1 Plant–microbe interaction in rhizosphere, endosphere, and phyllosphere and biocontrol mechanism acquired by beneficial microorganism.

      2.2 Plant–Microbe Interaction in the Rhizosphere

“Rhizosphere” is derived from “rhiza” or root and “sphere” or the field of influence in ancient Greek. The rhizosphere is the soil environment surrounding plant roots, and it is a crucial underground region for plant–microbe interaction. The rhizosphere comprises 10-fold microbes more than that in the surrounding soil, and the rhizosphere microbiome may consist of fungi, bacteria, archaea, actinomycetes, and viruses [3]. Roots utilize photosynthates to produce exudates used by rhizosphere microbiota to exchange nutrients and water [4]. Root exudates also function as signaling molecules, attractants, stimulants, or repellents to rhizosphere microbes. Bioactive compounds of exudates vary with plant species that define microbial community [5]. Root secretion influences soil pH, soil structure, oxygen obtainability, and influences plant–microbe interaction. A study on secondary metabolite benzoxazinoids showed it’s defensive role in cereals, alters rhizosphere fungal and bacterial microbiota, and influences plant growth [6]. Bacteria produce protein and polysaccharides, which allow them to attach with roots as biofilm aggregates [7]. Symbiotic association evolved millions of years ago, and most living plants form a symbiotic relationship with arbuscular mycorrhizal fungi (AMF) [8]. Upon sensation of strigolactone from plant roots, AMF initiates hyphal branching to colonize roots and releases lipochito oligosaccharides, promoting plant growth by increasing root surface area [1]. Almost all soilborne fungi are necrotrophic, and they do not require the living cell to acquire nutrients.

      2.2.1 Microbial Population in the Rhizosphere

The most enriched microbiota in the rhizosphere are bacteria, which influence the plant rhizosphere significantly. Next-generation sequencing (NGS) has provided insight into microbial diversity and composition. Internal transcribed spacer (ITS), 16s rRNA sequencing of fungi and bacteria, respectively [9,10] and shotgun metagenomic sequencing [11] have unravelled root-associated microbiome. The relative abundance of taxonomic marker genes has provided more information on phyla Proteobacteria, Bacteroidetes, and Actinobacteria, which were augmented in the rhizosphere [12]. Predominant genera in the rhizosphere are Pseudomonas, Bacillus, Rhizobia, Azotobacter, Mycobacterium, Flavobacter, Cellulomonas, Agrobacterium, and Micrococcus [13]. So far, various gram-positive and aerobic spore-forming bacteria are inferior because of the low availability of oxygen [14]. For fungal communities, phyla Ascomycota, Basidiomycota followed by Zygomycota, Glomeromycota dominate in the rhizosphere of Arabidopsis thaliana. Plant-friendly microorganisms comprise nitrogen-fixing bacteria viz., Azotobacter, cyanobacteria, clostridium, plant growth-promoting rhizobacteria, fungi, and endo ectomycorrhizal fungi [13].

      2.2.2 Biocontrol Mechanism in the Rhizosphere

      To grow a healthy plant, it is necessary to examine soil niches surrounding the root area to detect pathogens and enhance advantageous microorganisms. The rhizosphere is the battlefield where phytopathogens acquire parasitic relations with the plant. Biocontrol agents have a mechanism that includes rivalry for space and nutrients, antagonistic activity, and hyperparasitism. The level of decomposition of organic matter influences microbial communities and biocontrol activities [14]. The introduction of beneficial microorganisms can also change microbial community structure in the rhizosphere.

      2.2.2.1 Competition

Some strains of Pseudomonas fluorescens act as biocontrol by competing for nutrients and root surface colonization aggressively. Pseudomonas sp. RU47 colonizes the rhizosphere with sufficient density and compete with Rhizoctonia solani and minimizes the severity of black potato scurf and lettuce bottom rot in diluvial sand, alluvial loam, and loess loam soils [15]. The competition can also be for micro-nutrients, specifically iron, associated with high-affinity chelators called siderophores secreted by microorganisms. An experiment with transgenic tobacco overexpressing ferritin showed that fluorescent Pseudomonads could survive in a less iron-containing environment and have an antagonistic activity to the pathogen [16].

      2.2.2.2 Parasitism

Parasitism as a biocontrol mechanism is mainly associated with fungal biocontrol agents. Biocontrol agents parasitize the pathogen by looping around fungal hyphae and derive nutrition from the pathogen. Some beneficial microorganism secretes hydrolytic enzymes such as chitinase and cellulase [17]. Trichoderma and Gliocladium parasitize on Rhizoctonia, Sclerotinia, Verticillium, and Gaeumannomyces and cause cell damage to the pathogen [18]. Firmicute bacteria Pasteuria penetrans also control Meloidogyne nematode, and its activity is stimulated by two beneficial rhizospheric bacteria [19].

      2.2.2.3 Antagonism

Antagonism 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