Ecology and performance of rhizosphere and endosphere microbiomes

In recent decades, endophytes have attracted significant attention for their beneficial role in plant health and fitness and have been proposed as effective alternatives to synthetic fertilizers and pesticides. As such, knowledge on nature and mechanisms underpinning plant-endophyte interactions represents an important advancement to enhance our understanding of how plants can benefit from their microbial partners. In this chapter, we review the role of the rhizosphere microbiome in the recruitment of this major subgroup of plant-associated microbes and other factors in the rhizosphere (root exudates, soil properties, and plant genotype) that, together with a range of gene expression and epigenetic mechanisms, directly regulate endophytic colonization. We conclude by highlighting emerging strategies to manipulate these associations to benefit plant health and productivity. The information and facts gathered from current plant microbiome research will greatly improve our ability to harness rhizosphere/endophytic microbiome for viable strategies to improve agricultural production.