Defining the core Arabidopsis thaliana root microbiome

Rodriguez, R. J. et al. Stress tolerance in plants via habitat-adapted symbiosis. ISME J. 2, 404–416 (2008)

De Deyn, G. B., Cornelissen, J. H. C. & Bardgett, R. D. Plant functional traits and soil carbon sequestration in contrasting biomes. Ecol. Lett. 11, 516–531 (2008)

van der Lelie, D. et al. Poplar and its bacterial endophytes: coexistence and harmony. Crit. Rev. Plant Sci. 28, 346–358 (2009)

Jones, J. D. G. & Dangl, J. L. The plant immune system. Nature 444, 323–329 (2006)

Dodds, P. N. & Rathjen, J. P. Plant immunity: towards an integrated view of plant-pathogen interactions. Nature Rev. Genet. 11, 539–548 (2010)

Marschner, H., Römheld, V., Horst, W. J. & Martin, P. Root-induced changes in the rhizosphere: importance for the mineral nutrition of plants. Z. Pflanz. Boden. 149, 441–456 (1986)

Dennis, P. G., Miller, A. J. & Hirsch, P. R. Are root exudates more important than other sources of rhizodeposits in structuring rhizosphere bacterial communities? FEMS Microbiol. Ecol. 72, 313–327 (2010)

Mendes, R. et al. Deciphering the rhizosphere microbiome for disease-suppressive bacteria. Science 332, 1097–1100 (2011)

Firáková, S., Šturdíková, M. & Múčková, M. Bioactive secondary metabolites produced by microorganisms associated with plants. Biologia 62, 251–257 (2007)

Schulz, B. J. E., Boyle, C. J. C., Sieber, T. N., Schulz, B. & Boyle, C. in Microbial Root Endophytes Vol. 9, 1–13 (Springer, 2006)

Hallmann, J., Quadt-Hallmann, A., Mahaffee, W. F. & Kloepper, J. W. Bacterial endophytes in agricultural crops. Can. J. Microbiol. 43, 895–914 (1997)

Redford, A. J., Bowers, R. M., Knight, R., Linhart, Y. & Fierer, N. The ecology of the phyllosphere: geographic and phylogenetic variability in the distribution of bacteria on tree leaves. Environ. Microbiol. 12, 2885–2893 (2010)

Hardoim, P. R., van Overbeek, L. S. & Elsas, J. D. Properties of bacterial endophytes and their proposed role in plant growth. Trends Microbiol. 16, 463–471 (2008)

Inceoglu, O., Salles, J. F., van Overbeek, L. & van Elsas, J. D. Effect of plant genotype and growth stage on the β-proteobacterial community associated with different potato cultivars in two fields. Appl. Environ. Microbiol. 76, 3675–3684 (2010)

İnceoğlu, O., Al-Soud, W. A., Salles, J. F., Semenov, A. V. & van Elsas, J. D. Comparative analysis of bacterial communities in a potato field as determined by pyrosequencing. PLoS ONE 6, e23321 (2011)

Benson, A. K. et al. Individuality in gut microbiota composition is a complex polygenic trait shaped by multiple environmental and host genetic factors. Proc. Natl Acad. Sci. USA 107, 18933–18938 (2010)

Gottel, N. R. et al. Distinct microbial communities within the endosphere and rhizosphere of Populus deltoides roots across contrasting soil types. Appl. Environ. Microbiol. 77, 5934–5944 (2011)

Eickhorst, T. & Tippkötter, R. Improved detection of soil microorganisms using fluorescence in situ hybridization (FISH) and catalyzed reporter deposition (CARD-FISH). Soil Biol. Biochem. 40, 1883–1891 (2008)

Chi, F. et al. Ascending migration of endophytic rhizobia, from roots to leaves, inside rice plants and assessment of benefits to rice growth physiology. Appl. Environ. Microbiol. 71, 7271–7278 (2005)

Bulgarelli, D. et al. Structure of and assembly cues for the Arabidopsis root-inhabiting bacterial microbiota. Nature doi:10.1038/nature11336 (this issue).

Arumugam, M. et al. Enterotypes of the human gut microbiome. Nature 473, 174–180 (2011)

Spor, A., Koren, O. & Ley, R. Unravelling the effects of the environment and host genotype on the gut microbiome. Nature Rev. Microbiol. 9, 279–290 (2011)

Masclaux, C., Valadier, M., Brugière, N., Morot-Gaudry, J. & Hirel, B. Characterization of the sink/source transition in tobacco (Nicotiana tabacum L.) shoots in relation to nitrogen management and leaf senescence. Planta 211, 510–518 (2000)

Levey, S. A. W. Natural variation in the regulation of leaf senescence and relation to other traits in Arabidopsis. Plant Cell Environ. 28, 223–231 (2005)

van Elsas, J. D., Trevors, J. T. & Starodub, M. E. Bacterial conjugation between pseudomonads in the rhizosphere of wheat. FEMS Microbiol. Lett. 53, 299–306 (1988)

Engelbrektson, A. et al. Experimental factors affecting PCR-based estimates of microbial species richness and evenness. ISME J. 4, 642–647 (2010)

Lane, D. J. in Nucleic Acid Techniques in Bacterial Systematics (ed. Stackebrandt, M. G. E. ) 115–175 (Wiley, 1991)

Kunin, V. & Hugenholtz, P. PyroTagger: a fast, accurate pipeline for analysis of rRNA amplicon pyrosequence data. Open J. 1–8. (2010)

Caporaso, J. G. et al. QIIME allows analysis of high-throughput community sequencing data. Nature Methods 7, 335–336 (2010)

Sul, W. J. et al. Bacterial community comparisons by taxonomy-supervised analysis independent of sequence alignment and clustering. Proc. Natl Acad. Sci. USA 108, 14637–14642 (2011)

DeSantis, T. Z. et al. Greengenes, a chimera-checked 16S rRNA gene database and workbench compatible with ARB. Appl. Environ. Microbiol. 72, 5069–5072 (2006)

Oksanen, J. et al. Vegan: R Functions for Vegetation Ecologists . http://cc.oulu.fi/∼jarioksa/softhelp/vegan.html (2011)

Bates, D., Maechler, M. & Bolker, B. Lme4: Linear Mixed-Effects Models using S4 Classes (R package version 0.999375-42). http://CRAN.R-project.org/package=lme4 (2011)

Warnes, G. R. Gplots: Various R Programming Tools for Plotting Data . http://cran.r-project.org/web/packages/gplots/index.html (2011)

Motulsky, H. J. Prism 4 Statistics Guide: Statistical Analyses for Laboratory and Clinical Researchers (GraphPad Software, Inc., 2003)

Lozupone, C. & Knight, R. UniFrac: a new phylogenetic method for comparing microbial communities. Appl. Environ. Microbiol. 71, 8228–8235 (2005)

Eickhorst, T. & Tippkötter, R. Improved detection of soil microorganisms using fluorescence in situ hybridization (FISH) and catalyzed reporter deposition (CARD-FISH). Soil Biol. Biochem. 40, 1883–1891 (2008)

Loy, A., Maixner, F., Wagner, M. & Horn, M. probeBase–an online resource for rRNA-targeted oligonucleotide probes: new features 2007. Nucleic Acids Res. 35, D800–D804 (2007)