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

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.

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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.

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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).

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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.

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Correspondence to Paul Schulze-Lefert.

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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)

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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

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