Functional overlap of the Arabidopsis leaf and root microbiota

Yang Bai, Daniel B. Müller, Girish Srinivas, Ruben Garrido-Oter, Eva Potthoff, Matthias Rott, Nina Dombrowski, Philipp C. Münch, Stijn Spaepen, Mitja Remus-Emsermann, Bruno Hüttel, Alice C. McHardy, Julia A. Vorholt () and Paul Schulze-Lefert ()
Additional contact information
Yang Bai: Max Planck Institute for Plant Breeding Research
Daniel B. Müller: Institute of Microbiology, ETH Zurich
Girish Srinivas: Max Planck Institute for Plant Breeding Research
Ruben Garrido-Oter: Max Planck Institute for Plant Breeding Research
Eva Potthoff: Institute of Microbiology, ETH Zurich
Matthias Rott: Max Planck Institute for Plant Breeding Research
Nina Dombrowski: Max Planck Institute for Plant Breeding Research
Philipp C. Münch: Computational Biology of Infection Research, Helmholtz Center for Infection Research
Stijn Spaepen: Max Planck Institute for Plant Breeding Research
Mitja Remus-Emsermann: Institute of Microbiology, ETH Zurich
Bruno Hüttel: Max Planck Genome Center, Max Planck Institute for Plant Breeding Research
Alice C. McHardy: Cluster of Excellence on Plant Sciences (CEPLAS), Max Planck Institute for Plant Breeding Research
Julia A. Vorholt: Institute of Microbiology, ETH Zurich
Paul Schulze-Lefert: Max Planck Institute for Plant Breeding Research

Nature, 2015, vol. 528, issue 7582, 364-369

Abstract: Abstract 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.

Date: 2015
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DOI: 10.1038/nature16192

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