Spatiotemporal patterns of rhizosphere microbiome assembly : From ecological theory to agricultural application

Munoz-Ucros, Juana; Zwetsloot, Marie J.; Cuellar-Gempeler, Catalina; Bauerle, Taryn L.


There is urgency in optimizing agricultural production in light of climate uncertainty, human population growth and resource limitations. The rhizosphere microbiome is a promising genetic resource, yet it is poorly understood. Additionally, research into rhizosphere microbial community assembly (MCA) lacks a consistent ecological framework that incorporates the dynamics of the occurring interactions. We explore the ecological principles that guide community establishment as they pertain to the rhizosphere while reviewing relevant research and highlighting the gaps in knowledge. We propose a conceptual model for studying the rhizosphere, and argue for higher resolution characterizations of the rhizosphere, under a framework of root and microbial traits that will determine its resulting composition. For this, we borrow concepts from ecological theory to chronologically describe MCA as a function of colonization, distribution and succession under changing plant-imposed filters. We argue that there is a need to consider the temporal and spatial scale of rhizosphere processes in a manner that is relevant to its microbial components. Finally, we discuss strategies for managing the rhizosphere microbiome for agriculture and the remaining gaps in knowledge that impede their application. Synthesis and applications. We aim to initiate a comprehensive conversation on ecological processes and plant and microbial traits that affect rhizosphere assembly. Rhizosphere microbiome research is relatively new and highly multidisciplinary. The use of a shared vocabulary and ecological theory will facilitate the development and advances in this discipline.