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

Nature Reviews Microbiology volume 11, pages 789–799 (2013)Cite this article

Subjects

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.

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.

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Figure 1: Microorganisms in the rhizosphere.
Figure 2: The rhizosphere.
Figure 3: The composition of the bacterial community in the rhizosphere.
Figure 4: Root-induced changes in the rhizosphere.

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Acknowledgements

The authors thank A. Spor for comments on the manuscript and for his help, together with M. van der Voort, on figure 3. This work was supported by the European Commission through the Ecological Function and Biodiversity Indicators in European Soils (EcoFINDERS) project (FP7-264465). The contribution by J.M.R. was funded, in part, by the Dutch BE-Basic Program and by the Ecogenomics Innovation Center (ECOLINC) of the Netherlands Genomics Initiative.

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Authors and Affiliations

  1. Institut National de la Recherché Agronomique (INRA), UMR1347 Agroécologie, Dijon, 21065, France

    Laurent Philippot & Philippe Lemanceau

  2. The Laboratory of Phytopathology, Wageningen University, Wageningen, 6708 PB, The Netherlands

    Jos M. Raaijmakers

  3. Department of Microbial Ecology, The Netherlands Institute of Ecology (NIOO-KNAW),

    Jos M. Raaijmakers

  4. Department of Terrestrial Ecology, NIOO-KNAW, P.O. Box 50, Wageningen, 6700 AB, The Netherlands

    Wim H. van der Putten

  5. The Laboratory of Nematology, Wageningen University and Research Centre, P.O. Box 8123, Wageningen, 6700 ES, The Netherlands

    Wim H. van der Putten

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Glossary

Mycorrhizal fungi

Fungi that form a mutualistic, symbiotic association with a plant.

r-strategists

Organisms that thrive in unstable or fluctuating environments where resources are abundant, unlike K-strategists, which are more competitive in stable environments with limited resources.

Microbial seed bank

A reservoir of dormant microorganisms.

Cultivar

A variety of plant that has been selected for specific traits.

Endophytic bacteria

Bacteria that live inside plant tissue without causing negative effects.

Amensalism

An association between two different species that is detrimental to individuals of one species but not to those of the other. The secretion of chemical compounds by one species, thus damaging or killing the other species, is the most common mechanism of amensalism.

Phyllosphere

The above-ground parts of plants, mostly the leaves.

Denitrification

A microbial anaerobic respiratory pathway that consists of the sequential reduction of soluble nitrate and nitrite to the nitrogen gases NO, N2O and N2.

Nitrification

A two-step aerobic process consisting of the oxidation of ammonia to nitrite, which is carried out by the ammonia-oxidizing betaproteobacteria and thaumarchaeotes, and the subsequent conversion of nitrite to nitrate, which is carried out by nitrite-oxidizing bacteria.

Ecological engineering

The application of ecological principles for sustainable management of ecosystems, including preservation, restoration and creation, to integrate human society with its natural environment for the benefit of both.

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Philippot, L., Raaijmakers, J., Lemanceau, P. et al. Going back to the roots: the microbial ecology of the rhizosphere. Nat Rev Microbiol 11, 789–799 (2013). https://doi.org/10.1038/nrmicro3109

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