Sheath blight of rice caused by Rhizoctonia solani Kuhn is an important soil-borne disease throughout the rice-producing areas of the world. Twenty-nine bacterial endophytes were isolated from different plant sources and tested for their efficacy against R. solani inciting sheath blight in rice. Bacillus subtilis var. amyloliquefaciens (FZB24) caused a maximum 36% inhibition of R. solani over the control in vitro. Rice plants (cv. ADT 39) treated with FZB24, in combination with seed treatment @ 4 g kg^− 1, seedling dip @ 4 g l^− 1, soil application @ 500 g ha^− 1 and foliar application @ 500 g ha^− 1, gave the lowest severity of sheath blight (33%) with around 55% reduction over the control under glasshouse conditions. In addition, the B. subtilis (FZB24) treated rice plants showed higher induction of defence-related enzymes, peroxidase, polyphenol oxidase and phenylalanine ammonia lyase, and resulted in higher accumulation of total phenols than in the untreated control plants. The endophyte-treated rice plots had a significantly lower intensity of sheath blight than untreated control plots and also recorded a higher grain and straw yield.

Plant-microbe interactions can be either beneficial or harmful depending on the nature of the interaction. Multifaceted benefits of plant-associated microbes in crops are well documented. Specifically, the management of plant diseases using beneficial microbes is considered to be eco-friendly and the best alternative for sustainable agriculture. Diseases caused by various phytopathogens are responsible for a significant reduction in crop yield and cause substantial economic losses globally. In an ecosystem, there is always an equally daunting challenge for the establishment of disease and development of resistance by pathogens and plants, respectively. In particular, comprehending the complete view of the complex biological systems of plant-pathogen interactions, co-evolution and plant growth promotions (PGP) at both genetic and molecular levels requires novel approaches to decipher the function of genes involved in their interaction. The Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR)/Cas9 (CRISPR-associated protein 9) is a fast, emerging, precise, ecofriendly and efficient tool to address the challenges in agriculture and decipher plant-microbe interaction in crops. Nowadays, the CRISPR/Cas9 approach is receiving major attention in the field of functional genomics and crop improvement. Consequently, the present review updates the prevailing knowledge in the deployment of CRISPR/Cas9 techniques to understand plant-microbe interactions, genes edited for the development of fungal, bacterial and viral disease resistance, to elucidate the nodulation processes, plant growth promotion, and future implications in agriculture. Further, CRISPR/Cas9 would be a new tool for the management of plant diseases and increasing productivity for climate resilience farming.