The rhizosphere, the narrow zone of soil that surrounds and is influenced by plant roots, is home to an over- whelming number of microorganisms and invertebrates and is considered to be one of the most dynamic interfaces on Earth. Organisms that are present in the rhizosphere microbiota can have profound effects on the growth, nutrition and health of plants in agro-ecosystems 1–3 . Rhizosphere microbiotas can also directly and/or indirectly affect the composition and biomass of plant communities in natural ecosystems 4,5 . Numerous organ- isms contribute to these processes, leading to countless interactions between plants, antagonists and mutualistic symbionts, both below ground and above ground 6–9 . Many of the current insights into interactions and processes in the rhizosphere have emerged from studies on agricultural or horticultural crop plants and model species such as Arabidopsis thaliana and Medicago truncatula. However, considerable progress is also being made in understanding the microbial ecology of the rhizosphere of non-cultivated plant species in natu- ral ecosystems 10 and how microorganisms influence resource allocation, biodiversity and above-ground interactions with herbivores and their natural ene- mies 11 . To better understand the players and processes that operate in the rhizosphere, a variety of molecular techniques, such as metagenomics and stable-isotope probing, have been applied over the past decade 2,12–14 . At the plant community level, substantial progress has been made in studying intermingled root systems from differ- ent plant species 15,16 . Such studies on natural ecosystems are complementing and extending our current knowl- edge of the rhizosphere, as they resolve how multitrophic interactions may have co-evolved in the rhizospheres of plants grown in their native habitats as compared to in the rhizospheres of agricultural or exotic plant species introduced into new habitats 17 . Recent studies have further shown that, in non-culti- vated ecosystems, plant community diversity and the genotypes of individual plants can influence the com- position of their associated communities both above ground and below ground 18–21 . This might also explain why some plant species promote the decomposition of their own litter rather than that of other plant species or genotypes: it grants a ‘home-field advantage’ (REF. 22). Although the effects of decomposition and mineraliza- tion might seem to be less relevant in agricultural pro- duction systems, where mineral fertilizers can provide the majority of nutrient inputs, knowledge of the inter- linkages between decomposers and soil-borne symbi- onts, and between antagonists and phytopathogens, in the rhizospheres of non-cultivated ecosystems might become more relevant when conventional agriculture becomes less dependent on external inputs of nutrients, biocides and fossil fuels. The rhizosphere microbiota can also be examined in relation to other ecological phenomena, such as natural succession. For example, in primary dune succession, one of the pioneer plant spe- cies, Ammophila arenaria (marram grass), is protected against plant parasitic nematodes by complex bottom-up and top-down interactions in the rhizosphere 23 . These Going back to the roots: the microbial ecology of the rhizosphere Laurent Philippot 1 , Jos M. Raaijmakers 2,3 , Philippe Lemanceau 1 and Wim H. van der Putten 4,5 Abstract | 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. 1 Institut National de la Recherché Agronomique (INRA), UMR1347 Agroécologie, 21065, Dijon, France. 2 The Laboratory of Phytopathology, Wageningen University, 6708 PB Wageningen, The Netherlands. 3 Department of Microbial Ecology, The Netherlands Institute of Ecology (NIOO-KNAW). 4 Department of Terrestrial Ecology, NIOO-KNAW, P.O. Box 50, 6700 AB Wageningen, The Netherlands. 5 The Laboratory of Nematology, Wageningen University and Research Centre, P.O. Box 8123, 6700 ES Wageningen, The Netherlands. Correspondence to L.P.  e-mail: laurent.philippot@ dijon.inra.fr doi:10.1038/nrmicro3109 Published online 23 September 2013 REVIEWS NATURE REVIEWS | MICROBIOLOGY VOLUME 11 | NOVEMBER 2013 | 789 FOCUS ON plaNt–mICRObE INtERaCtIONS © 2013 Macmillan Publishers Limited. All rights reserved