The importance of the microbiome of the plant holobiont

Summary Plants can no longer be considered as standalone entities and a more holistic perception is needed. Indeed, plants harbor a wide diversity of microorganisms both inside and outside their tissues, in the endosphere and ectosphere, respectively. These microorganisms, which mostly belong to Bacteria and Fungi, are involved in major functions such as plant nutrition and plant resistance to biotic and abiotic stresses. Hence, the microbiota impact plant growth and survival, two key components of fitness. Plant fitness is therefore a consequence of the plant per se and its microbiota, which collectively form a holobiont. Complementary to the reductionist perception of evolutionary pressures acting on plant or symbiotic compartments, the plant holobiont concept requires a novel perception of evolution. The interlinkages between the plant holobiont components are explored here in the light of current ecological and evolutionary theories. Microbiome complexity and the rules of microbiotic community assemblage are not yet fully understood. It is suggested that the plant can modulate its microbiota to dynamically adjust to its environment. To better understand the level of plant dependence on the microbiotic components, the core microbiota need to be determined at different hierarchical scales of ecology while pan‐microbiome analyses would improve characterization of the functions displayed.ContentsSummary 1196 I. Introduction 1196 II. Plants as holobionts 1197 III. Recruitment of the plant microbiota: what are the driving factors? 1198 IV. The plant holobiont: an existing core plant microbiota? 1200 V. The plant and its microbiome: what controls what? 1201 VI. Concluding remarks and prospects 1204Acknowledgements 1204References 1204