Roots and leaves of healthy plants host taxonomically structured bacterial assemblies, and members of these communities contribute to plant growth and health. We established Arabidopsis leaf- and root-derived microbiota culture collections representing the majority of bacterial species that are reproducibly detectable by culture-independent community sequencing. We found an extensive taxonomic overlap between the leaf and root microbiota. Genome drafts of 400 isolates revealed a large overlap of genome-encoded functional capabilities between leaf- and root-derived bacteria with few significant differences at the level of individual functional categories. Using defined bacterial communities and a gnotobiotic Arabidopsis plant system we show that the isolates form assemblies resembling natural microbiota on their cognate host organs, but are also capable of ectopic leaf or root colonization. While this raises the possibility of reciprocal relocation between root and leaf microbiota members, genome information and recolonization experiments also provide evidence for microbiota specialization to their respective niche.

Access optionsAccess options

Rent or Buy article

Get time limited or full article access on ReadCube.


All prices are NET prices.


Primary accessions

European Nucleotide Archive

Data deposits

Sequencing reads (454 16S rRNA, MiSeq 16S rRNA and WGS HiSeq reads) have been deposited in the European Nucleotide Archive (ENA) under accession numbers PRJEB11545, PRJEB11583 and PRJEB11584, and genome assemblies and annotations corresponding to the leaf, root and soil culture collections have been deposited in the BioProject database under accession numbers PRJNA297956, PRJNA297942 and PRJNA298127. Isolates have been deposited at the Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures (https://www.dsmz.de/).


  1. 1.

    & The Hologenome Concept: Human, Animal and Plant Microbiota (Springer, 2013)

  2. 2.

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

  3. 3.

    , & The rhizosphere microbiome and plant health. Trends Plant Sci. 17, 478–486 (2012)

  4. 4.

    et al. Cultivating healthy growth and nutrition through the gut microbiota. Cell 161, 36–48 (2015)

  5. 5.

    et al. Community proteogenomics reveals insights into the physiology of phyllosphere bacteria. Proc. Natl Acad. Sci. USA 106, 16428–16433 (2009)

  6. 6.

    et al. Revealing structure and assembly cues for Arabidopsis root-inhabiting bacterial microbiota. Nature 488, 91–95 (2012)

  7. 7.

    et al. Defining the core Arabidopsis thaliana root microbiome. Nature 488, 86–90 (2012)

  8. 8.

    Microbial life in the phyllosphere. Nature Rev. Microbiol. 10, 828–840 (2012)

  9. 9.

    , & Bacterial communities associated with the leaves and the roots of Arabidopsis thaliana. PLoS One 8, e56329 (2013)

  10. 10.

    , & Microbial genome-enabled insights into plant-microorganism interactions. Nature Rev. Genet. 15, 797–813 (2014)

  11. 11.

    et al. Genome-wide association study of Arabidopsis thaliana leaf microbial community. Nat. Commun. 5, 5320 (2014)

  12. 12.

    , , , & Quantitative divergence of the bacterial root microbiota in Arabidopsis thaliana relatives. Proc. Natl Acad. Sci. USA 111, 585–592 (2014)

  13. 13.

    et al. Structure, variation, and assembly of the root-associated microbiomes of rice. Proc. Natl Acad. Sci. USA 112, E911–E920 (2015)

  14. 14.

    et al. Microbiota and host nutrition across plant and animal kingdoms. Cell Host Microbe 17, 603–616 (2015)

  15. 15.

    et al. Structure and function of the bacterial root microbiota in wild and domesticated barley. Cell Host Microbe 17, 392–403 (2015)

  16. 16.

    et al. Salicylic acid modulates colonization of the root microbiome by specific bacterial taxa. Science 349, 860–864 (2015)

  17. 17.

    , , , & Ecological succession and stochastic variation in the assembly of Arabidopsis thaliana phyllosphere communities. MBio 5, e00682–e13 (2014)

  18. 18.

    et al. The soil microbiome influences grapevine-associated microbiota. MBio 6, e02527–14 (2015)

  19. 19.

    , , & Culturing a plant microbiome community at the cross-Rhodes. New Phytol. 196, 341–344 (2012)

  20. 20.

    et al. Extensive personal human gut microbiota culture collections characterized and manipulated in gnotobiotic mice. Proc. Natl Acad. Sci. USA 108, 6252–6257 (2011)

  21. 21.

    , & Molecular communication in the rhizosphere. Plant Soil 321, 279–303 (2009)

  22. 22.

    , , , & The role of root exudates in rhizosphere interactions with plants and other organisms. Annu. Rev. Plant Biol. 57, 233–266 (2006)

  23. 23.

    , , , & Adaptation of Rhizobium leguminosarum to pea, alfalfa and sugar beet rhizospheres investigated by comparative transcriptomics. Genome Biol. 12, R106 (2011)

  24. 24.

    UPARSE: highly accurate OTU sequences from microbial amplicon reads. Nature Methods 10, 996–998 (2013)

  25. 25.

    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)

  26. 26.

    & The diversity of Archaea and Bacteria in association with the roots of Zea mays L. Microb. Ecol. 41, 252–263 (2001)

  27. 27.

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

  28. 28.

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

  29. 29.

    et al. PyNAST: a flexible tool for aligning sequences to a template alignment. Bioinformatics 26, 266–267 (2010)

  30. 30.

    , & Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics 30, 2114–2120 (2014)

  31. 31.

    , , & An integrated pipeline for de novo assembly of microbial genomes. PLoS One 7, e42304 (2012)

  32. 32.

    et al. De novo assembly of human genomes with massively parallel short read sequencing. Genome Res. 20, 265–272 (2010)

  33. 33.

    , , , & Improved microbial gene identification with GLIMMER. Nucleic Acids Res. 27, 4636–4641 (1999)

  34. 34.

    Prokka: rapid prokaryotic genome annotation. Bioinformatics 30, 2068–2069 (2014)

  35. 35.

    et al. The subsystems approach to genome annotation and its use in the project to annotate 1000 genomes. Nucleic Acids Res. 33, 5691–5702 (2005)

  36. 36.

    & KEGG: Kyoto encyclopedia of genes and genomes. Nucleic Acids Res. 28, 27–30 (2000)

  37. 37.

    et al. Data, information, knowledge and principle: back to metabolism in KEGG. Nucleic Acids Res. 42, D199–D205 (2014)

  38. 38.

    Accelerated profile HMM searches. PLOS Comput. Biol. 7, e1002195 (2011)

  39. 39.

    & A simple, fast, and accurate method of phylogenomic inference. Genome Biol. 9, R151 (2008)

  40. 40.

    et al. Fast, scalable generation of high-quality protein multiple sequence alignments using Clustal Omega. Mol. Syst. Biol. 7, 539–539 (2011)

  41. 41.

    , & FastTree 2 – approximately maximum-likelihood trees for large alignments. PLoS One 5, e9490 (2010)

  42. 42.

    , & Taxator-tk: precise taxonomic assignment of metagenomes by fast approximation of evolutionary neighborhoods. Bioinformatics 31, 817–824 (2015)

  43. 43.

    , & Prokaryotes: the unseen majority. Proc. Natl Acad. Sci. USA 95, 6578–6583 (1998)

  44. 44.

    , , & A synthetic community approach reveals plant genotypes affecting the phyllosphere microbiota. PLoS Genet. 10, e1004283 (2014)

Download references


We thank D. Lundberg, S. Lebeis, S. Herrera-Paredes, S. Biswas and J. Dangl for sharing the calcined clay utilization protocol before publication; M. Kisielow of the ETH Zurich Flow Cytometry Core Facility for help with bacterial cell sorting as well as M. Baltisberger, D. Jolic and D. Weigel for their help in finding natural Arabidopsis populations; E. Kemen and M. Agler for sharing the Illumina Mi-Seq protocol for profiling of defined communities before publication and A. Sczyrba for his advice with the genome assembly. This work was supported by funds to P.S.-L. from the Max Planck Society, a European Research Council advanced grant (ROOTMICROBIOTA), the ‘Cluster of Excellence on Plant Sciences’ program funded by the Deutsche Forschungsgemeinschaft, the German Center for Infection Research (DZIF), by funds to J.A.V. from ETH Zurich (ETH Research Grant ETH-41 14-2), a grant from the Swiss National Research Foundation (310030B_152835), and a European Research Council advanced grant (PhyMo).

Author information

Author notes

    • Yang Bai
    • , Daniel B. Müller
    • , Girish Srinivas
    • , Ruben Garrido-Oter
    • , Julia A. Vorholt
    •  & Paul Schulze-Lefert

    These authors contributed equally to this work.


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

    • Yang Bai
    • , Girish Srinivas
    • , Ruben Garrido-Oter
    • , Matthias Rott
    • , Nina Dombrowski
    • , Stijn Spaepen
    •  & Paul Schulze-Lefert
  2. Institute of Microbiology, ETH Zurich, 8093 Zurich, Switzerland

    • Daniel B. Müller
    • , Eva Potthoff
    • , Mitja Remus-Emsermann
    •  & Julia A. Vorholt
  3. Department of Algorithmic Bioinformatics, Heinrich Heine University Düsseldorf, 40225 Düsseldorf, Germany

    • Ruben Garrido-Oter
  4. Cluster of Excellence on Plant Sciences (CEPLAS), Max Planck Institute for Plant Breeding Research, 50829 Cologne, Germany

    • Ruben Garrido-Oter
    • , Alice C. McHardy
    •  & Paul Schulze-Lefert
  5. Computational Biology of Infection Research, Helmholtz Center for Infection Research, 38124 Braunschweig, Germany

    • Philipp C. Münch
    •  & Alice C. McHardy
  6. Max-von-Pettenkofer Institute, Ludwig Maximilian University, German Center for Infection Research (DZIF), partner site LMU Munich, 80336 Munich, Germany

    • Philipp C. Münch
  7. German Center for Infection Research (DZIF), partner site Hannover-Braunschweig, 38124 Braunschweig, Germany

    • Philipp C. Münch
  8. Max Planck Genome Center, Max Planck Institute for Plant Breeding Research, 50829 Cologne, Germany

    • Bruno Hüttel


  1. Search for Yang Bai in:

  2. Search for Daniel B. Müller in:

  3. Search for Girish Srinivas in:

  4. Search for Ruben Garrido-Oter in:

  5. Search for Eva Potthoff in:

  6. Search for Matthias Rott in:

  7. Search for Nina Dombrowski in:

  8. Search for Philipp C. Münch in:

  9. Search for Stijn Spaepen in:

  10. Search for Mitja Remus-Emsermann in:

  11. Search for Bruno Hüttel in:

  12. Search for Alice C. McHardy in:

  13. Search for Julia A. Vorholt in:

  14. Search for Paul Schulze-Lefert in:


J.A.V. and P.S.-L. initiated, coordinated and supervised the project. Y.B., M.R., N.D. and S.S. isolated root and soil bacteria strains. Y.B. collected root material and performed culture-independent community profiling. D.B.M., E.P. and M.R.-E. collected environmental leaf material, D.B.M. and E.P. isolated leaf strains and performed culture-independent community profiling. G.S. and R.G.-O. analysed culture-independent 16S rRNA amplicon sequencing data. Y.B., D.B.M. isolated DNA and prepared samples for genome sequencing. R.G.-O., P.C.M, B.H. and A.C.M. organized the genome sequencing data. R.G.-O. assembled and annotated draft genomes and performed comparative genome analyses. Y.B. and D.B.M. performed recolonization experiments; G.S. and R.G.-O. analysed the recolonization data. Y.B., D.B.M., R.G.-O., J.A.V. and P.S.-L. wrote the manuscript.

Competing interests

The authors declare no competing financial interests.

Corresponding authors

Correspondence to Julia A. Vorholt or Paul Schulze-Lefert.

Extended data

Supplementary information

PDF files

  1. 1.

    Supplementary Figures

    This file contains Supplementary Figures 1-9.

Zip files

  1. 1.

    Supplementary Data

    This zipped folder contains Supplementary Data files 1-7 and a Supplementary Data guide.

About this article

Publication history







By submitting a comment you agree to abide by our Terms and Community Guidelines. If you find something abusive or that does not comply with our terms or guidelines please flag it as inappropriate.