In contemporary agriculture, PGPRs have drawn a lot of interest because of their capacity to stimulate plant development to contribute as a substitute to synthetic fertility compounds. Besides promoting growth of plant, several rhizopspheric bacterial communities are appreciated to encourage defence mechanism in plants during their collaboration with the host plant. Similar to an animal’s innate immune system, plants have a broad-spectrum, nonspecific immune system that helps them defend against a wide range of phytopathogens. Studies on the adaptive immune system are very scarce. Few recent reports have recommended adaptive immune responses in plants and the presence of immunological reminiscence. The new insights on the employment of tools allied with omics and enlisted techniques in functional sectors, like transcriptomics, metaproteomics, metabolomics, etc., have helped a lot to understand the data sets recovered as an important output to understand the plant microbiome. How several annotation tools in association with the omics approach, preceded by several advanced molecular tool-mediated applications, analyse the plant–microbe metabolite affected interaction study, which has been facilitated in this chapter we have also discussed the basics of plant defence system, function of PGPR inducing plant defence, how plant–PGPR interactions can be exploited to immunize plants before planting, and recent studies on adaptive immunity in plant body.