Plant-microbial endophytes interactions: Scrutinizing their beneficial mechanisms from genomic explorations

The study of plant-endophyte interactions is complex and difficult to decipher. In part, this is because they are dynamic and diverse; these interactions can be mutualistic, commensalistic, symbiotic, and trophobiotic and can change over the different stages of plant development. However, revealing the complete genomes of these endophytic microorganisms (i.e., the plant endobiome) is making it possible to know more about the molecular basis for these interactions, in particular, the sequencing of complete or draft genomes of beneficial endophytic fungi and bacteria that are agriculturally relevant. Likewise, comparative genomic explorations provide new clues on the endophytic lifestyle of microbes. This work reviews the diversity of the plant microendobiome, with an emphasis on fungi and bacteria, and the beneficial interactions that have been discovered through genomic analyses. We also discuss some basic functions that would allow the differentiation of endophytic microbes from other non-endophytic associations, and how these are relevant to endophytic modus vivendi. Finally, we propose new sustainable agricultural strategies based on new knowledge of the plant endobiome and its beneficial interactions with plants, which has been revealed through genomic explorations.