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Defining the core Arabidopsis thaliana root microbiome


Land plants associate with a root microbiota distinct from the complex microbial community present in surrounding soil. The microbiota colonizing the rhizosphere (immediately surrounding the root) and the endophytic compartment (within the root) contribute to plant growth, productivity, carbon sequestration and phytoremediation1,2,3. Colonization of the root occurs despite a sophisticated plant immune system4,5, suggesting finely tuned discrimination of mutualists and commensals from pathogens. Genetic principles governing the derivation of host-specific endophyte communities from soil communities are poorly understood. Here we report the pyrosequencing of the bacterial 16S ribosomal RNA gene of more than 600 Arabidopsis thaliana plants to test the hypotheses that the root rhizosphere and endophytic compartment microbiota of plants grown under controlled conditions in natural soils are sufficiently dependent on the host to remain consistent across different soil types and developmental stages, and sufficiently dependent on host genotype to vary between inbred Arabidopsis accessions. We describe different bacterial communities in two geochemically distinct bulk soils and in rhizosphere and endophytic compartments prepared from roots grown in these soils. The communities in each compartment are strongly influenced by soil type. Endophytic compartments from both soils feature overlapping, low-complexity communities that are markedly enriched in Actinobacteria and specific families from other phyla, notably Proteobacteria. Some bacteria vary quantitatively between plants of different developmental stage and genotype. Our rigorous definition of an endophytic compartment microbiome should facilitate controlled dissection of plant–microbe interactions derived from complex soil communities.

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Figure 1: Sample fraction and soil type drive the microbial composition of root-associated endophyte communities.
Figure 2: OTUs that differentiate the EC and rhizosphere from soil.
Figure 3: Dot plots of notable OTUs.
Figure 4: CARD–FISH confirmation of Actinobacteria on roots.

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We thank A. Smithlund, M. Gonek, V. Madden, H. Schmidt, M. Rott and N. Zvenigorodsky for technical assistance. We thank A. Spor, J. Pfeiffer and J. Rawls for discussions and C. Herring for research field soil. This work was supported by US NSF grant IOS-0958245 (J.L.D.), the JGI Director’s Discretionary Grand Challenge Program and the HHMI-GBMF Plant Science Program. J.L.D. is an HHMI-GBMF Plant Science Investigator. Work conducted by the US Department of Energy Joint Genome Institute is supported by the Office of Science of the US Department of Energy under contract no. DE-AC02-05CH11231. S.L.L. was supported by the National Institutes of Health, Minority Opportunities in Research division of the National Institute of General Medical Sciences grant K12GM000678.

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Authors and Affiliations



D.S.L., S.L.L. and J.L.D. designed the project, D.S.L. and S.L.L. set up the experiments and organized construction of the sequencing libraries. D.S.L., S.L.L., S.H.P. and J.G. harvested samples and prepared DNA for sequencing. A.E., V.K., T.G.d.R., S.M., P.H. and S.G.T. worked together at the JGI to perform, optimize and quality-control the sequencing. S.H.P. applied the GLMM to the data. D.S.L., S.H.P., S.Y. and R.E. created and managed the data analysis pipeline. S.Y. oversaw the data deposition. D.S.L., S.L.L., S.H.P., S.Y., J.G. and J.L.D. analysed the data and created figures. S.L.L. performed the CARD–FISH microscopy in the laboratory of T.E., at the Max-Planck-Institute for Plant Breeding in Cologne, and at UNC. R.E.L. and P.H. advised on primer design and appropriate statistical methods. D.S.L., S.L.L., S.H.P. and J.L.D. wrote the manuscript with significant input from S.Y., R.E.L., P.H. and S.G.T.

Corresponding author

Correspondence to Jeffery L. Dangl.

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Competing interests

The authors declare no competing financial interests.

Additional information

454 pyrosequencing data are deposited in the ENA Sequence Read Archive under study number ERP001384. Custom R scripts are available with documentation at and additional code is available on request.

Supplementary information

Supplementary Information

This file contains Supplementary Tables 1-2 and 4, full legends for Supplementary Tables 3 and 5 (see separate excel data files for tables) and Supplementary Figures 1-15. (PDF 4945 kb)

Supplementary Data

This zipped file contains Supplementary Database 1 (ZIP 17375 kb)

Supplementary Data

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Supplementary Data

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Supplementary Data

This file contains Supplementary Table 5 (see Supplementary Information file for full legend). (XLS 100 kb)

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Lundberg, D., Lebeis, S., Paredes, S. et al. Defining the core Arabidopsis thaliana root microbiome. Nature 488, 86–90 (2012).

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