The book discusses the complex interactions between plants and their associated microbial communities. It also elucidates the ways in which these microbiomes are connected with the plant system, and how they affect plant health. The different chapters describe how microbiomes affect plants with regard to immunity, disease conditions, stress management and productivity. In addition, the book describes how an additional plant genome functions as a whole organ system of the host, and how it presents both challenges and opportunities for the plant system. Moreover, the book includes a dedicated section on using omics tools to understand these interactions, and on exploiting them to their full potential.