The rhizosphere – the soil compartment influenced by the root, including the root itself – is the most-active microbial habitat in soils. Indeed, the release by plant roots of a significant part of their photosynthates promotes microbial abundance and activities in the rhizosphere. This investment made by plants is paid back by microbial functions, which contribute to plant nutrition and protection against soil-borne diseases. Indeed, rhizosphere microorganisms play a major role in plant growth and health and, more generally, in soil stability and formation. Therefore, it is a major challenge to understand better multitrophic interactions occurring in the rhizosphere in order to exploit them for sustainable agriculture and bioremediation, in the context of the increasing concern of our societies over environmental and food quality issues. More specifically, there is a need for deeper understanding of the drivers of the diversity, structure and activities of the microbial communities and of the expression of corresponding functions in the rhizosphere. To achieve this comprehensive insight, inter- and intradisciplinary approaches are essential. In rhizosphere research, biological disciplines focusing on microbiology, plant physiology, plant pathology and zoology must meet soil science, functional and evolutionary ecology and modelling approaches for understanding key rhizosphere processes. Various tools and methods related to molecular biology, phylogeny, biochemistry, microscopy, etc. must be applied or specifically developed to meet the challenges of rhizosphere complexity.

In 2004, the First International RHIZOSPHERE conference took place in Munich (Germany), gathering 480 participants worldwide to celebrate the centenary of the rhizosphere concept and to launch a new series of international conferences at the interface between the above-mentioned disciplines. From 26 to 31 August 2007, the RHIZOSPHERE 2 conference at Le Corum, Palais des Congrès in Montpellier (France), excellently organized by Philippe Hinsinger and colleagues from Montpellier campus, was attended by 570 participants from 48 countries. The RHIZOSPHERE 3 conference will be held in 2011 in Perth, Western Australia (see for information).

This Rhizosphere thematic issue includes manuscripts from participants in the different sessions of this conference and other rhizosphere-related publications. The topics represent some of the most active research areas, including structural and functional community analysis, microbial signalling and interactions, plant–microorganism interactions, and symbiotic (mycorrhizas, rhizobia) and associated microorganisms. It gathers contributions dealing with either important methodological aspects or new insights into specific rhizosphere processes and microorganisms.