Core Microbiome

The Plant immune system responds the same way toward both pathogenic and nonpathogenic microbes. However, response toward nonpathogenic microbes remains mild as they lack virulence factors. The ISR mechanism is well characterized in the rhizosphere and endosphere. Sphingomonas melonis fr1, a phyllosphere bacteria, suppressed disease development in Arabidopsis thaliana by inducing camalexin production [108]. Camalexin is a tryptophan-derived alkaloid that interferes with the membrane integrity of bacteria and fungi [109]. Foliar application of Bacillus amyloliquefasciens 5B6 decreased the relative abundance of cucumber mosaic virus by activating SA and ethylene signaling pathway in three years of field trials [110].

Pathogens and pests are responsible for 15–30% of crop yield losses worldwide [111]. We depend on chemical-based crop production and protection strategies using chemical fertilizers, pesticides, herbicides, and fungicides for a sufficient and steady yield. Biological chemical-free agriculture is gaining more and more support ecologically. For disease control, ecological control has been the desirable policy in which nonpathogenic microorganisms are applied to the foliar parts of the plant to affect disease suppression [112]. Microorganisms of the phyllosphere take over a large assortment of adaptation and biocontrol factors, which permit them to adopt the phyllosphere condition and discourage pathogen growth, thus assisting in plant health [113].

The genera of Pantoea and Sphingomonas have a vital contribution to wildfire disease inhibition [114]. Bacillus amyloliquefaciens as a biocontrol agent to mandarin fruit suppresses Penicillium digitatum infection by 77% [115]. Trichoderma atroviridae can be correlated with reduced infection of Botrytis cinerea in strawberries by 88% [116]. Black leaf streak disease in bananas caused by Pseudocercospora musae is restrained by Bacillus subtilis B106 up to 72% [117]. The biocontrol agent Trichoderma koningii controls up to 93% of Phytophthora cactorum pathogen that causes collar rot in apples [118]. Similarly, infection caused by Phytophthora medium in rubber trees can be controlled by using biocontrol agents, such as Alcaligenes sp . EIL-2 [119].

We studied the plant microbiome, aiming to elucidate on the new and improved tools for developing products that can enhance disease management. Our first step was to explore and discover prospective products that can invade phytopathogens and help in maintaining the overall health of plants. Plant microbiota are very useful in improving plant growth as they produce secondary metabolites that confer resistance to a wide variety of pathogens. As a whole, metabolites secreted by the plant microbiome will offer an immense contribution in opening up new opportunities to fight challenges in the environment and agriculture. Finally, the advances in metagenomics combined with NGS techniques will uncover new pools of defense metabolites by novel microbes in the rhizosphere, endosphere, and phyllosphere.

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