Skip to main content

Thank you for visiting nature.com. You are using a browser version with limited support for CSS. To obtain the best experience, we recommend you use a more up to date browser (or turn off compatibility mode in Internet Explorer). In the meantime, to ensure continued support, we are displaying the site without styles and JavaScript.

  • Letter
  • Published:

Revealing structure and assembly cues for Arabidopsis root-inhabiting bacterial microbiota

Nature volume 488, pages 91–95 (2012)Cite this article

Subjects

Abstract

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.

This is a preview of subscription content, access via your institution

Access options

Buy this article

  • Purchase on Springer Link
  • Instant access to full article PDF
Buy now

Prices may be subject to local taxes which are calculated during checkout

Figure 1: Taxa at high taxonomic ranks define building blocks of root-associated bacterial communities.
Figure 2: Arabidopsis assembles a distinctive root-inhabiting bacterial microbiota.
Figure 3: Arabidopsis root-inhabiting bacteria are detectable on the rhizoplane.
Figure 4: Root selectivity of soil-borne bacteria is retained in naturally grown Arabidopsis plants.

Similar content being viewed by others

Accession codes

Primary accessions

Sequence Read Archive

References

  1. Tringe, S. G. et al. Comparative metagenomics of microbial communities. Science 308, 554–557 (2005)

    Article  ADS  CAS  Google Scholar 

  2. 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)

    Article  CAS  Google Scholar 

  3. Mei, C. & Flinn, B. S. The use of beneficial microbial endophytes for plant biomass and stress tolerance improvement. Recent Pat. Biotechnol. 4, 81–95 (2010)

    Article  CAS  Google Scholar 

  4. Weyens, N., van der Lelie, D., Taghavi, S. & Vangronsveld, J. Phytoremediation: plant–endophyte partnerships take the challenge. Curr. Opin. Biotechnol. 20, 248–254 (2009)

    Article  CAS  Google Scholar 

  5. Rosenblueth, M. & Martinez-Romero, E. Bacterial endophytes and their interactions with hosts. Mol. Plant Microbe Interact. 19, 827–837 (2006)

    Article  CAS  Google Scholar 

  6. Reinhold-Hurek, B. & Hurek, T. Living inside plants: bacterial endophytes. Curr. Opin. Plant Biol. 14, 435–443 (2011)

    Article  Google Scholar 

  7. Pruesse, E. et al. SILVA: a comprehensive online resource for quality checked and aligned ribosomal RNA sequence data compatible with ARB. Nucleic Acids Res. 35, 7188–7196 (2007)

    Article  CAS  Google Scholar 

  8. Gans, J., Wolinsky, M. & Dunbar, J. Computational improvements reveal great bacterial diversity and high metal toxicity in soil. Science 309, 1387–1390 (2005)

    Article  ADS  CAS  Google Scholar 

  9. Berg, G. & Smalla, K. Plant species and soil type cooperatively shape the structure and function of microbial communities in the rhizosphere. FEMS Microbiol. Ecol. 68, 1–13 (2009)

    Article  CAS  Google Scholar 

  10. İnceoğlu, Ö., 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)

    Article  ADS  Google Scholar 

  11. Hardoim, P. R. et al. Rice root-associated bacteria: insights into community structures across 10 cultivars. FEMS Microbiol. Ecol. 77, 154–164 (2011)

    Article  CAS  Google Scholar 

  12. Lundberg, D. S. et al. Defining the core Arabidopsis thaliana root microbiome. Naturehttp://dx.doi.org/10.1038/nature11237 (this issue)

  13. Fierer, N., Bradford, M. A. & Jackson, R. B. Toward an ecological classification of soil bacteria. Ecology 88, 1354–1364 (2007)

    Article  Google Scholar 

  14. Basilio, A. et al. Patterns of antimicrobial activities from soil actinomycetes isolated under different conditions of pH and salinity. J. Appl. Microbiol. 95, 814–823 (2003)

    Article  CAS  Google Scholar 

  15. 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)

    Article  ADS  CAS  Google Scholar 

  16. Boller, T. & Felix, G. A renaissance of elicitors: perception of microbe-associated molecular patterns and danger signals by pattern-recognition receptors. Annu. Rev. Plant Biol. 60, 379–406 (2009)

    Article  CAS  Google Scholar 

  17. Chelius, M. K. & Triplett, E. W. The diversity of archaea and bacteria in association with the roots of Zea mays L. Microb. Ecol. 41, 252–263 (2001)

    Article  CAS  Google Scholar 

  18. Buchholz-Cleven, B. E. E., Rattunde, B. & Straub, K. L. Screening for genetic diversity of isolates of anaerobic Fe(II)-oxidizing bacteria using DGGE and whole-cell hybridization. Syst. Appl. Microbiol. 20, 301–309 (1997)

    Article  Google Scholar 

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

  20. Eickhorst, T. & Tippkotter, 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)

    Article  CAS  Google Scholar 

  21. Pernthaler, A., Pernthaler, J. & Amann, R. Fluorescence in situ hybridization and catalyzed reporter deposition for the identification of marine bacteria. Appl. Environ. Microbiol. 68, 3094–3101 (2002)

    Article  CAS  Google Scholar 

  22. Timmusk, S., Grantcharova, N. & Wagner, E. G. H. Paenibacillus polymyxa invades plant roots and forms biofilms. Appl. Environ. Microbiol. 71, 7292–7300 (2005)

    Article  CAS  Google Scholar 

Download references

Acknowledgements

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).

Author information

Author notes

  1. Nahal Ahmadinejad & Philipp Rauf

    Present address: 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.).,

  2. Davide Bulgarelli, Matthias Rott, Klaus Schlaeppi and Emiel Ver Loren van Themaat: These authors contributed equally to this work.

Authors and Affiliations

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

    Bruno Huettel & Richard Reinhardt

  3. Central Microscopy, Max Planck Institute for Plant Breeding Research, Cologne, 50829, 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, Bremen, 28359, Germany

    Frank Oliver Gloeckner & Rudolf Amann

  6. Soil Science, Faculty of Biology and Chemistry, University of Bremen, Bremen, 28359, Germany

    Thilo Eickhorst

Authors
  1. Davide Bulgarelli
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Matthias Rott
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Klaus Schlaeppi
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Emiel Ver Loren van Themaat
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. Nahal Ahmadinejad
    View author publications

    You can also search for this author in PubMed Google Scholar

  6. Federica Assenza
    View author publications

    You can also search for this author in PubMed Google Scholar

  7. Philipp Rauf
    View author publications

    You can also search for this author in PubMed Google Scholar

  8. Bruno Huettel
    View author publications

    You can also search for this author in PubMed Google Scholar

  9. Richard Reinhardt
    View author publications

    You can also search for this author in PubMed Google Scholar

  10. Elmon Schmelzer
    View author publications

    You can also search for this author in PubMed Google Scholar

  11. Joerg Peplies
    View author publications

    You can also search for this author in PubMed Google Scholar

  12. Frank Oliver Gloeckner
    View author publications

    You can also search for this author in PubMed Google Scholar

  13. Rudolf Amann
    View author publications

    You can also search for this author in PubMed Google Scholar

  14. Thilo Eickhorst
    View author publications

    You can also search for this author in PubMed Google Scholar

  15. Paul Schulze-Lefert
    View author publications

    You can also search for this author in PubMed Google Scholar

Contributions

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.

Corresponding author

Correspondence to Paul Schulze-Lefert.

Ethics declarations

Competing interests

The authors declare no competing financial interests.

Additional information

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

Supplementary Information

This file contains Supplementary Methods, Supplementary References, Supplementary Figures 1-19 and Supplementary Tables 1-6. (PDF 3411 kb)

Supplementary Movie 1

This zipped movie file illustrates how the roots of the soil grown plants were sampled. (ZIP 16790 kb)

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. (ZIP 8125 kb)

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. (ZIP 7144 kb)

PowerPoint slides

Rights and permissions

Reprints and permissions

About this article

Cite this article

Bulgarelli, D., Rott, M., Schlaeppi, K. et al. Revealing structure and assembly cues for Arabidopsis root-inhabiting bacterial microbiota. Nature 488, 91–95 (2012). https://doi.org/10.1038/nature11336

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1038/nature11336

This article is cited by

Comments

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.

Search

Advanced search

Quick links

Nature Briefing

Sign up for the Nature Briefing newsletter — what matters in science, free to your inbox daily.

Get the most important science stories of the day, free in your inbox. Sign up for Nature Briefing