The root microbiome influences scales from molecules to ecosystems: The unseen majority¹

Abstract

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.

Effects of Agricultural Management on Rhizosphere Microbial Structure and Function in Processing Tomato Plants

“…While linking agricultural management to large-scale outcomes such as nutrient fluxes or ecosystem services requires an analysis of bulk soil properties and processes, understanding the complex relationship between management practices and plant nutrition and productivity necessitates shifting the focus to the rhizosphere (20). Some evidence suggests that management can affect the ecosystem-level functions carried out by bulk soil microbial communities through impacts on microbial diversity (21), but the unique chemistry and microbial communities found in the rhizosphere (22) are more closely linked to plant outcomes of agricultural importance (23). Because rhizosphere soil is shaped by complex interactions between plant and bulk soil processes, the effects of agricultural management on rhizosphere communities and the functional implications are not always easy to predict.…”

Diverse Profiles of AI-1 Type Quorum Sensing Molecules in Cultivable Bacteria from the Mangrove (Kandelia obovata) Rhizosphere Environment

“…Rhizospheric bacteria are living in the direct vicinity of the roots, and root-associated bacteria play important roles in mangrove ecosystem involving nitrogen fixation (Alfaro-Espinoza and Ullrich, 2015), nutrient acquisition (Holguin et al, 2001; Berendsen et al, 2012; Prakash et al, 2015), abiotic stress tolerance (Rout and Southworth, 2013), as well as production of regulators of plant growth and development such as auxins, cytokinins, and gibberellins (Kaai et al, 2008). Additionally, the microbial communities associated with root also play an essential role in the matter cycle (for instance phosphorus, organic acids, and siderophores) and maintenance of the health of wetland ecosystem (Gomes et al, 2011; Zeng et al, 2014).…”

Functional Soil Microbiome: Belowground Solutions to an Aboveground Problem

“…Such plant habitats range from the whole organism (individual plants) to specific organs (e.g. roots, leaves, shoots, flowers, and seeds, including zones of interaction between roots and the surrounding soil, the rhizosphere; Rout and Southworth, 2013). The rhizosphere is the region of the soil being continuously influenced by plant roots through the rhizodeposition of exudates, mucilages, and sloughed cells (Uren, 2001;Bais et al, 2006;Moe, 2013).…”