Biological Management of Horticultural Crop Diseases Using Phyllosphere-, Rhizosphere-, and Endosphere-Derived Biocontrol Agents

A healthy plant harbors a plethora of microbes surviving as symbionts, commensals, and pathogens in its phyllosphere, rhizosphere, and endosphere, which are collectively called “plant microbiota or plant microbiome.” The microbial diversity of plant-microbe includes bacteria, fungi, oomycetes, archaea, and protists, though most of the reports on plant microbiome analysis are on bacteria and actinomycetes followed by fungi. The plant microbiome diversity is greatly influenced by edaphic factors and other environmental factors, including climate change, the presence of other pathogenic organisms and human interventions. Different studies on the microbiome analysis of diseased and healthy plants provided evidence that the plant microbiome is altered by the pathogen. Therefore, often the plant disease outbreaks are linked with some missing microorganism which ultimately results in 180the “microbial imbalance or dysbiosis.” There are several reports on the involvement of the plant microbiome in defending the plant host from biotic and abiotic stresses, priming of the plant’s innate immune system and inducing acquired resistance/tolerance in the plant host. Since the first report of biological management of plant diseases, still many workers across the world are engaged in this area of research because of the need for better and sustainable alternatives for chemical plant protection products. The next generation sequencing and bioinformatic tools and multi-omics approaches have unfurled the plant microbiome world, their ecological functions and role in plant health management and identified novel biocontrol agents (BCAs). Therefore, in the present chapter, distinct microbiome diversity on the plant’ phyllosphere, rhizosphere, and endosphere, different tools and approaches for plant microbiome analysis and their applications in plant disease management with special reference to horticultural crops along with the future prospects will be discussed.