Going back to the roots: the microbial ecology of the rhizosphere

Key Points The rhizosphere microbiome is important for plant growth, nutrition and health in agro-ecosystems, but it also directly and/or indirectly affects the composition, biomass and functioning of plant communities in natural ecosystems. The phylum Proteobacteria is the dominant bacterial phylum encountered in the rhizosphere, but fungi such as those in the phyla Ascomycota and Glomeromycota are also an integral component of the rhizosphere microbiome. Soil properties and plant species are the main drivers of the microbial community composition and structure in the rhizosphere. Multitrophic interactions in the rhizosphere, as well as their influence on above-ground communities of herbivores, carnivores, mutualists and symbionts, can be beneficial to plant growth. Integrating our knowledge from both agricultural and natural ecosystems, from single plants and multispecies plant communities, and from below-ground and above-ground multitrophic interactions holds great promise to further improve the sustainability of crop production. The rhizosphere – the interface between plant roots and soil – is an intriguingly complex and dynamic niche. Laurent Philippot and colleagues review recent progress in rhizosphere research and suggest that going back to the roots could be crucial to further improve the sustainability of crop production. The rhizosphere is the interface between plant roots and soil where interactions among a myriad of microorganisms and invertebrates affect biogeochemical cycling, plant growth and tolerance to biotic and abiotic stress. The rhizosphere is intriguingly complex and dynamic, and understanding its ecology and evolution is key to enhancing plant productivity and ecosystem functioning. Novel insights into key factors and evolutionary processes shaping the rhizosphere microbiome will greatly benefit from integrating reductionist and systems-based approaches in both agricultural and natural ecosystems. Here, we discuss recent developments in rhizosphere research in relation to assessing the contribution of the micro- and macroflora to sustainable agriculture, nature conservation, the development of bio-energy crops and the mitigation of climate change.