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

Bulgarelli, D., Rott, M., Schlaeppi, K., van Themaat, E. V. L., Ahmadinejad, N., Assenza, F., et al. (2012). Revealing structure and assembly cues for Arabidopsis root-inhabiting bacterial microbiota. Nature, 488(7409), 91-95.

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 Creators:
Bulgarelli, D., Author
Rott, M., Author
Schlaeppi, K., Author
van Themaat, E. V. L., Author
Ahmadinejad, N., Author
Assenza, F., Author
Rauf, P., Author
Huettel, B., Author
Reinhardt, R.1, Author           
Schmelzer, E., Author
Peplies, J.2, Author           
Gloeckner, F. O.2, Author           
Amann, R.3, Author           
Eickhorst, T., Author
Schulze-Lefert, P., Author
Affiliations:
1Department of Microbiology, Max Planck Institute for Marine Microbiology, Max Planck Society, ou_2481695              
2Microbial Genomics Group, Department of Molecular Ecology, Max Planck Institute for Marine Microbiology, Max Planck Society, ou_2481697              
3Department of Molecular Ecology, Max Planck Institute for Marine Microbiology, Max Planck Society, ou_2481696              

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 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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Language(s): eng - English
 Dates: 2012-08-02
 Publication Status: Issued
 Pages: 5
 Publishing info: -
 Table of Contents: -
 Rev. Type: Peer
 Identifiers: eDoc: 634641
ISI: 000307010700039
 Degree: -

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Title: Nature
  Abbreviation : Nature
Source Genre: Journal
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Publ. Info: London : Nature Publishing Group
Pages: - Volume / Issue: 488 (7409) Sequence Number: - Start / End Page: 91 - 95 Identifier: ISSN: 0028-0836
CoNE: https://pure.mpg.de/cone/journals/resource/954925427238