The plant root defines the interface between a multicellular eukaryote and soil, one of the richest microbial ecosystems on Earth1. Notably, soil bacteria are able to multiply inside roots as benign endophytes and modulate plant growth and development2, with implications ranging from enhanced crop productivity3 to phytoremediation4. Endophytic colonization represents an apparent paradox of plant innate immunity because plant cells can detect an array of microbe-associated molecular patterns (also known as MAMPs) to initiate immune responses to terminate microbial multiplication5. Several studies attempted to describe the structure of bacterial root endophytes6; however, different sampling protocols and low-resolution profiling methods make it difficult to infer general principles. Here we describe methodology to characterize and compare soil- and root-inhabiting bacterial communities, which reveals not only a function for metabolically active plant cells but also for inert cell-wall features in the selection of soil bacteria for host colonization. We show that the roots of Arabidopsis thaliana, grown in different natural soils under controlled environmental conditions, are preferentially colonized by Proteobacteria, Bacteroidetes and Actinobacteria, and each bacterial phylum is represented by a dominating class or family. Soil type defines the composition of root-inhabiting bacterial communities and host genotype determines their ribotype profiles to a limited extent. The identification of soil-type-specific members within the root-inhabiting assemblies supports our conclusion that these represent soil-derived root endophytes. Surprisingly, plant cell-wall features of other tested plant species seem to provide a sufficient cue for the assembly of approximately 40% of the Arabidopsis bacterial root-inhabiting microbiota, with a bias for Betaproteobacteria. Thus, this root sub-community may not be Arabidopsis-specific but saprophytic bacteria that would naturally be found on any plant root or plant debris in the tested soils. By contrast, colonization of Arabidopsis roots by members of the Actinobacteria depends on other cues from metabolically active host cells.

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We thank R. Franzen and S. Schumacher for technical assistance, S. Wulfert for providing Arabidopsis liquid cultures, H. Schmidt for sharing the CARD-FISH protocol and performing the cell counts. We thank S. Klages and K. Stüber for support with bioinformatic pipelines. We are grateful to R. Panstruga and P. Bakker for comments on the manuscript. Golm soil was shipped by J. Schwachtje and J. van Dongen. This work was supported by funds from the Max Planck Society to P.S.-L. (M.IF. A. ZUCH8048). K.S. is supported by the Swiss National Science Foundation (PBFRP3-133544).

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Author notes

    • Davide Bulgarelli
    • , Matthias Rott
    • , Klaus Schlaeppi
    •  & Emiel Ver Loren van Themaat

    These authors contributed equally to this work.

    • Nahal Ahmadinejad
    •  & Philipp Rauf

    Present addresses: INRES - Crop Bioinformatics, University of Bonn, 53115 Bonn, Germany (N.A.); Department of Developmental Immunology, Max Planck Institute of Immunobiology and Epigenetics, 79108 Freiburg, Germany (P.R.).


  1. Department of Plant Microbe Interactions, Max Planck Institute for Plant Breeding Research, 50829 Cologne, Germany

    • Davide Bulgarelli
    • , Matthias Rott
    • , Klaus Schlaeppi
    • , Emiel Ver Loren van Themaat
    • , Nahal Ahmadinejad
    • , Federica Assenza
    • , Philipp Rauf
    •  & Paul Schulze-Lefert
  2. Max Planck Genome Centre, Max Planck Institute for Plant Breeding Research, 50829 Cologne, Germany

    • Bruno Huettel
    •  & Richard Reinhardt
  3. Central Microscopy, Max Planck Institute for Plant Breeding Research, 50829 Cologne, Germany

    • Elmon Schmelzer
  4. Ribocon GmbH, 28359 Bremen, Germany

    • Joerg Peplies
    •  & Frank Oliver Gloeckner
  5. Department of Molecular Ecology, Max Planck Institute for Marine Microbiology, 28359 Bremen, Germany

    • Frank Oliver Gloeckner
    •  & Rudolf Amann
  6. Soil Science, Faculty of Biology and Chemistry, University of Bremen, 28359 Bremen, Germany

    • Thilo Eickhorst


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D.B., M.R., K.S., F.A., and E.V.L.v.T performed the experiments and analysed the data. M.R. and T.E. performed CARD-FISH experiments. E.S. generated SEM micrographs. E.V.L.v.T. coordinated computational analyses. N.A. performed the RDP classification. J.P. performed the SILVA classification. F.O.G. provided access to SILVA classification and R.A. advice on CARD-FISH, SILVA analysis. B.H. and R.R. performed pyrosequencing of amplicon libraries. D.B., M.R., K.S., P.R. and P.S.-L. designed the study. D.B., M.R., K.S., E.V.L.v.T and P.S.-L. wrote the manuscript. D.B., M.R., K.S. and E. V.L.v.T. contributed equally to this work. All authors discussed the results and commented on the manuscript.

Competing interests

The authors declare no competing financial interests.

Corresponding author

Correspondence to Paul Schulze-Lefert.

Pyrosequencing reads have been deposited in the NCBI Sequence Read Archive (SRA) database (SRA043581). The R scripts used for computational analyses are available via http://www.mpipz.mpg.de/162701/R_scripts.

Supplementary information

PDF files

  1. 1.

    Supplementary Information

    This file contains Supplementary Methods, Supplementary References, Supplementary Figures 1-19 and Supplementary Tables 1-6.

Zip files

  1. 1.

    Supplementary Movie 1

    This zipped movie file illustrates how the roots of the soil grown plants were sampled.

  2. 2.

    Supplementary Data 1

    This zipped file contains an excel file and a separate worksheet comprising the dataset description, sequencing information, the PyroTagger output file, raw and rarefied OTU count matrices, statistical analyses and identified taxa with counts at multiple taxonomic ranks assigned using SILVA and RDP databases. Worksheets indicated with the letter A contain calculation performed with the removal of reads and OTUs assigned to the phylum Chloroflexi. Worksheets indicated with the letter B contain calculation performed including reads and OTUs assigned to the phylum Chloroflexi.

  3. 3.

    Supplementary Data 2

    This zipped file contains an excel file and three separate worksheets that contain the dataset description, the PyroTagger output file, the taxonomy classification of OTUs according to SILVA database of the samples utilized for the PCR primers comparison.

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