Plants are teeming with microbial organisms including those that colonize internal tissues as well as those that adhere to external surfaces. In the rhizosphere, the plant-associated microbiome is intricately involved in plant health and serves as a reservoir of additional genes that plants can access when needed. Microbiome regulation of plant trait expression affects plant performance, which in turn influences various ecosystem functions, such as primary productivity and soil health. Understanding these plant- and microbe-driven interactions requires a study of the nature and effects of the plant microbiome. Conceptualizing the microbiome requires a synthesis of microbial ecology, physiology, and bioinformatics, integrated with insight into host biology and ecology. Microbiome structure and function analyses are recognized as essential components to understand the genetic and functional capacity of the host (previously assigned solely to the host) and include vital aspects of metabolism and physiology. Here, as a special section, we present a set of papers that address the complex interactions between plants and root microbiomes in the rhizosphere. This unseen majority spans scales; with its microorganisms numerically dominant in terrestrial ecosystems, the root microbiome is also involved in plant genetics through integral roles in plant trait expression that can effect community composition and ecosystem functions, such as soil health.
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