Plant-associated microbes, referred to as plant microbiomes, are an integral
part of the plant system. The multifaceted role of plant microbiota in combating both
abiotic and biotic stresses is well documented in different crop species. However,
understanding the co-evolution of plant growth- promoting microbes (PGPM) and PGP
traits at genetic and molecular levels requires robust molecular tools to unravel the
functional gene orthologues involved in plant-microbe interaction. The advent of
Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR)/Cas9 (CRISPRassociated protein 9) is of paramount importance in deciphering the plant-microbe
interaction and addressing the challenges of unraveling endophytic microbes and their
benefits thereof. Our knowledge of plant microbiome composition, signaling cues,
secondary metabolites, microbial volatiles, and other driving factors in plant
microbiome has been enlightened. In recent years, scientists have focused more on
below-ground dialogue in recruiting efficient microbiome/engineered rhizosphere.
More recently, base editing techniques using endo-nucleolytic ally deactivated dCas9
protein and sgRNAs (CRISPR interference or CRISPRi) have emerged as a useful
approach to study the gene functions and have potential merits in exploring plantmicrobe interactions and the signaling cues involved. A systemic understanding of the
signaling events and the respective metabolic pathways will enable the application of genome editing tools to enhance the capacity of microbes to produce more targeted
metabolites that will enhance microbial colonization.
Further, it will be exciting to employ CRISPR technologies for editing plant-microbe
interactions to discover novel metabolic pathways and their modulation for plant
immunity and fitness against abiotic as well as biotic stresses. Such metabolites possess
tremendous scope in tailoring newer smart nano-based bio-formulations, besides
formulating beneficial microbiomes or cocktails, which is the best alternative for
climate resilient farming. The present review sheds light upon the deployment of
CRISPR/Cas techniques to comprehend plant-microbe interactions, microbe-mediated
abiotic and biotic stress resistance, genes edited for the development of fungal,
bacterial, and viral disease resistance, nodulation process, PGP activity, CRISPR
interference-based gene repression in the PGPM, metabolic pathway editing and their
future implications in sustainable agriculture.
Keywords: CRISPR/Cas, Genome editing, Plant-microbe interaction, Sustainable agriculture.
