Abstract
The plant individual is a holobiont as it hosts diverse microbial assemblages in and on vegetative, reproductive or disseminative organs. All plant compartments - roots, stems, leaves, flowers, fruits and seeds - have been shown to host microorganisms that can influence positively or negatively the plants performance. Some of these microorganisms thrive as endophytes inside plant tissues. Identifying the environmental sources of these microorganisms and the route they take to colonize plant tissues, visualizing their niches within their hosts and understanding how they make intimate associations with plants are of crucial importance in developing biocontrol and biofertilization approaches, both in organic and integrated protection systems. This chapter considers that the plant individual is part of a complex network of biotic interactions influenced by the environment in the phytobiome and provides a comprehensive review on the development of the interactions between plants and beneficial bacterial endophytes.