Plants endophytes: unveiling hidden agenda for bioprospecting toward sustainable agriculture

Endophytic microbes are present in nearly all of the plant species known to date but how they enter and flourish inside a host plant and display multiple benefits like plant growth promotion (PGP), biodegradation, and stress alleviation are still unexplored. Until now, the majority of the research has been conducted assuming that the host–endophyte interaction is analogous to the PGP microbes, although, studies related to the mechanisms of their infection, colonization as well as conferring important traits to the plants are limited. It would be fascinating to explore the role of these endophytic microbes in host gene expression, metabolism, and the modulation of phenotypic traits, under abiotic and biotic stress conditions. In this review, we critically focused on the following areas: (i) endophytic lifestyle and the mechanism of their entry into plant tissues, (ii) how endophytes modulate the immune system of plants and affect the genotypic and phenotypic expression of host plants under abiotic and biotic stress condition, and (iii) the role of omics and other integrated genomic approaches in unraveling complex host–endophyte signaling crosstalk. Furthermore, we discussed their role in phytoremediation of heavy metal stress and whole genomic analysis based on an understanding of different metabolic pathways these endophytes utilize to combat stress.