**6. Future development of application**

produced by *P. stutzeri,* which caused the lysis of mycelia of *F. solani*, which causes root rot [132]. The endophytic *B. cenocepacia* 869T2 decreased the disease incidence of Fusarium wilt in treated banana plants to 3.4%, compared to 24.5% in noninoculated plants infected in a field test during a 7-month period [50]. The antibiotic Pyrrolnitrin, produced by *P. fluorescens* BL915 could prevent the damage from *Rhizoctonia solani* during the damping off of cotton

Van Peer et al. [134] described a mechanism called "Induced Systemic Resistance" in carnation plants that were systematically protected by *P. fluorescens* strain WCS417r against *F. oxysporum* f. sp. *Dianthi* and by Ardebili et al. in tomato plants, in which *P. fluorescens* CHA0 protected against *F. oxysporum f.* sp. Lycopersici acted as a bio agent that induced resistance in tomato [135]. *B. amyloliquefaciens* strain FZB42, a plant root colonizing isolate, was seen to have the ability to stimulate plant growth and suppress plant pathogens [136]. In another study, endophytes were seen to protect cucumber plants against cucumber anthracnose induced by *P. fluorescens* strain 89B-61 [137] and *Achromobacter* sp. F2feb.44. *Streptomyces* sp. Zapt10, and *Bacillus licheniformis* AE6 were exploited to induce systemic resistance in cucumber against the foliar disease of downy mildew caused by the phytopathogen *Pseudoperonospora cubensis,*

Pest management has become an issue over time because more and more pests are becoming immune to pesticides. The global pesticide market is growing at a pace of 3.6% per year and is valued around \$47 billion [139]. Development of entomopathogenic bacteria for pest management has been a new approach to handle resilient pests. Species belonging to the genera *Aschersonia*, *Agerata*, *Verticillium*, *Sphaerostilbe*, *Podonectria*, *Myriangium*, *Hirsutella*, and *Metarhizium* [140] are fungal species involved in the biological control of pests. *Bacillus thuringiensis* is the most well-known *Bacillus* species on which the efforts of the scientific community and industry have been focused [141]. *Brevibacillus laterosporus* Laubach action has

plants [133].

which enhanced yield [138].

**Figure 2.** Factors affecting plant-microbe interactions.

104 Plant Ecology - Traditional Approaches to Recent Trends

### **6.1. Techniques used to understand plant microbe interaction**

Plants have been an integral part of our diet since humans began to farm and were no longer nomads. Since then, the world has faced a continuous challenge to feed the ever-growing population. The excess use of fertilizer is causing eutrophication [147], and genetic engineering of plants is an expensive and tedious process. The role of microbes in plant-microbe interactions has been studied in detail during the past decade [148, 149]. The results of extensive studies suggest that the exploitation of beneficial microbes is a better strategy in the long run to increase crop yield, which will play an important role in disease dissemination and control [150]. Three types of plant-microbe interactions have been studied–symbiosis between plants and mycorrhizae [151], between plants and rhizobacteria [152], and pathogenesis [153]. Omics technologies such as transcriptomics, proteomics, and metabolomics coupled with bioinformatics have been extensively applied in plant abiotic stress studies [154]. The proteomics approach has been largely adopted to investigate the protein profiles in plants in response to abiotic stresses that might lead to the development of new strategies for improving stress tolerance [155]. Microbial metabolomics is another technique that has been used to study the set of metabolites present in microbial communities [156]. A rhizosphere metabolomics–driven approach was used in the study of plant-microbe interactions for the removal of polychlorinated biphenyls as demonstrated by Lee et al. [157].

Pathogens and their emergence have been a great threat to food security, agricultural practices, and the conservation of food species, and it has become a significant task to understand the emergence of new pathogens and their role [158]. In the past, plant pathosystems were best studied one gene at a time or one protein at a time; however, the genomic era marked the beginning of the in-depth study of plant-pathogen associations [159]. Commonly known pathogen genomes have been sequenced, and the analysis of these sequences has revealed the forces that have shaped pathogen evolution and has brought to light the unexpected aspects of pathogen biology [160, 161]. The genome scale reconstruction model (GSRM) is based on metabolic reconstructions on a genomic scale for the analysis and interpretation of metabolite concentrations under specific conditions [162]. GSRM has been successfully developed for many organisms including plants, bacteria, fungi, and animals [163–165].

Various techniques to study plant-microbe interactions are sequencing, chromatography, mass spectrometry, phospholipid fatty acid (PLFA), microscopy, Fourier transform infrared spectroscopy (FTIR), nuclear magnetic resonance, and real-time PCR (RT-PCR) [166]. Further advances in the postgenomic era will pave the way for a better understanding of the interactions of endophytes, plant-pathogen, and plant immunity. Genomic tools to understand major units of the host-microbiota ecology are shown in **Figure 3**.

**Figure 3.** Genomic tools to understand major units of the plant-microbe ecological system. Colored boxes indicate technique tools that can be used to characterize key factors for the corresponding unit. (modified after Kroll et al. [167]).

### **7. Conclusions**

In the face of pressure from climate change, contaminated environments, and crop pathogens, agricultural material and food production are currently at risk. Plant-associated microorganisms have important consequences for host health and performance. However, efforts to utilize beneficial microbes in the field have failed to consistently improve crops. The current understanding of interactions between plants and symbiotic microbial communities, the ecological consequences of plant-associated microorganisms and plant-microbial metabolic dynamics are limited. The advent of genomic approaches has helped a great deal in the understanding of the plant-bacterial interactions, but genomic approaches are still insufficient to clearly explain the interactions between plants and pathogens [168]. Approaches using metagenomics and amplicon sequencing coupled with other omics technologies [169] and the development of databases (PHI-based) [170], and metabolomics have enhanced our understanding of plant-bacterial interactions. Plant-microbe ecological communities are affected by plant genotype and environmental factors. The difference between genotypes causes different physiological and immune responses and leads to host-specific microbial communities. Plant root exudates (i.e., sugars, amino acids, organic acids, nucleotides, flavonoids, antimicrobial compounds, and enzymes) shape specific communities, attract plant growth-promoting colonization, and pathogen infections.

In the complex microbial community, we found that specific species could significantly affect the microbial community structure. Via a systems' framework of microbial network analysis, we could identify the "hub species" and "milestone species", which are candidate microbial assemblages for disease management. Network models of plant-associated microbiomes provide new opportunities for enhancing disease management.

### **7.1. Future perspective**

The understanding of plant-microbe and microbe-microbe interactions will provide a helpful future perspective as a modulating microbiome for minimizing disease incidence and enhancing gross plant productivity. Further, beneficial plant-associated bacteria could act as counterparts against pathogens within the microbial ecosystem, as well as stabilize the ecosystem, enhance biodiversity, avoid pathogen outbreaks, and increase plant productivity. A well-studied plant-microbe partnership in the future will also help increase crop productivity at little expense and could, in turn, lead to another "Green Revolution".
