title: Functional overlap of the Arabidopsis leaf and root microbiota.
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.
authors.affiliation: Department of Plant Microbe Interactions, Max Planck Institute for Plant Breeding Research, 50829 Cologne, Germany.
authors.forename: Yang
authors.initials: Y
authors.lastname: Bai
authors.affiliation: Institute of Microbiology, ETH Zurich, 8093 Zurich, Switzerland.
authors.forename: Daniel B
authors.initials: DB
authors.lastname: Müller
authors.affiliation: Department of Plant Microbe Interactions, Max Planck Institute for Plant Breeding Research, 50829 Cologne, Germany.
authors.forename: Girish
authors.initials: G
authors.lastname: Srinivas
authors.affiliation: Department of Plant Microbe Interactions, Max Planck Institute for Plant Breeding Research, 50829 Cologne, Germany.|Department of Algorithmic Bioinformatics, Heinrich Heine University Düsseldorf, 40225 Düsseldorf, Germany.|Cluster of Excellence on Plant Sciences (CEPLAS), Max Planck Institute for Plant Breeding Research, 50829 Cologne, Germany.
authors.forename: Ruben
authors.initials: R
authors.lastname: Garrido-Oter
authors.affiliation: Institute of Microbiology, ETH Zurich, 8093 Zurich, Switzerland.
authors.forename: Eva
authors.initials: E
authors.lastname: Potthoff
authors.affiliation: Department of Plant Microbe Interactions, Max Planck Institute for Plant Breeding Research, 50829 Cologne, Germany.
authors.forename: Matthias
authors.initials: M
authors.lastname: Rott
authors.affiliation: Department of Plant Microbe Interactions, Max Planck Institute for Plant Breeding Research, 50829 Cologne, Germany.
authors.forename: Nina
authors.initials: N
authors.lastname: Dombrowski
authors.affiliation: Computational Biology of Infection Research, Helmholtz Center for Infection Research, 38124 Braunschweig, Germany.|Max-von-Pettenkofer Institute, Ludwig Maximilian University, German Center for Infection Research (DZIF), partner site LMU Munich, 80336 Munich, Germany.|German Center for Infection Research (DZIF), partner site Hannover-Braunschweig, 38124 Braunschweig, Germany.
authors.forename: Philipp C
authors.initials: PC
authors.lastname: Münch
authors.affiliation: Department of Plant Microbe Interactions, Max Planck Institute for Plant Breeding Research, 50829 Cologne, Germany.
authors.forename: Stijn
authors.initials: S
authors.lastname: Spaepen
authors.affiliation: Institute of Microbiology, ETH Zurich, 8093 Zurich, Switzerland.
authors.forename: Mitja
authors.initials: M
authors.lastname: Remus-Emsermann
authors.affiliation: Max Planck Genome Center, Max Planck Institute for Plant Breeding Research, 50829 Cologne, Germany.
authors.forename: Bruno
authors.initials: B
authors.lastname: Hüttel
authors.affiliation: Cluster of Excellence on Plant Sciences (CEPLAS), Max Planck Institute for Plant Breeding Research, 50829 Cologne, Germany.|Computational Biology of Infection Research, Helmholtz Center for Infection Research, 38124 Braunschweig, Germany.
authors.forename: Alice C
authors.initials: AC
authors.lastname: McHardy
authors.affiliation: Institute of Microbiology, ETH Zurich, 8093 Zurich, Switzerland.
authors.forename: Julia A
authors.initials: JA
authors.lastname: Vorholt
authors.affiliation: Department of Plant Microbe Interactions, Max Planck Institute for Plant Breeding Research, 50829 Cologne, Germany.|Cluster of Excellence on Plant Sciences (CEPLAS), Max Planck Institute for Plant Breeding Research, 50829 Cologne, Germany.
authors.forename: Paul
authors.initials: P
authors.lastname: Schulze-Lefert
mesh_terms: D017360:Arabidopsis / Q000382:microbiology*; D001419:Bacteria / Q000145:classification / Q000235:genetics / Q000302:isolation & purification; D016680:Genome, Bacterial / Q000235:genetics; D005856:Germ-Free Life; D064307:Microbiota / Q000235:genetics / Q000502:physiology*; D018515:Plant Leaves / Q000382:microbiology*; D018517:Plant Roots / Q000382:microbiology*; D017422:Sequence Analysis, DNA; D012988:Soil Microbiology