title: Root nodule symbiosis in Lotus japonicus drives the establishment of distinctive rhizosphere, root, and nodule bacterial communities.
abstract: Lotus japonicus has been used for decades as a model legume to study the establishment of binary symbiotic relationships with nitrogen-fixing rhizobia that trigger root nodule organogenesis for bacterial accommodation. Using community profiling of 16S rRNA gene amplicons, we reveal that in Lotus, distinctive nodule- and root-inhabiting communities are established by parallel, rather than consecutive, selection of bacteria from the rhizosphere and root compartments. Comparative analyses of wild-type (WT) and symbiotic mutants in Nod factor receptor5 (nfr5), Nodule inception (nin) and Lotus histidine kinase1 (lhk1) genes identified a previously unsuspected role of the nodulation pathway in the establishment of different bacterial assemblages in the root and rhizosphere. We found that the loss of nitrogen-fixing symbiosis dramatically alters community structure in the latter two compartments, affecting at least 14 bacterial orders. The differential plant growth phenotypes seen between WT and the symbiotic mutants in nonsupplemented soil were retained under nitrogen-supplemented conditions that blocked the formation of functional nodules in WT, whereas the symbiosis-impaired mutants maintain an altered community structure in the nitrogen-supplemented soil. This finding provides strong evidence that the root-associated community shift in the symbiotic mutants is a direct consequence of the disabled symbiosis pathway rather than an indirect effect resulting from abolished symbiotic nitrogen fixation. Our findings imply a role of the legume host in selecting a broad taxonomic range of root-associated bacteria that, in addition to rhizobia, likely contribute to plant growth and ecological performance.
authors.affiliation: Department of Plant Microbe Interactions, Max Planck Institute for Plant Breeding Research, 50829 Cologne, Germany.|Department of Molecular Biology and Genetics, Faculty of Science and Technology, Aarhus University, 8000 C Aarhus, Denmark.|Carbohydrate Recognition and Signaling Centre, 8000 C Aarhus, Denmark.
authors.forename: Rafal
authors.initials: R
authors.lastname: Zgadzaj
authors.affiliation: Department of Plant Microbe Interactions, Max Planck Institute for Plant Breeding Research, 50829 Cologne, Germany.|Cluster of Excellence on Plant Sciences, Heinrich Heine University Duesseldorf, 40225 Duesseldorf, Germany.|Department of Algorithmic Bioinformatics, Heinrich Heine University Duesseldorf, 40225 Duesseldorf, Germany.
authors.forename: Ruben
authors.initials: R
authors.lastname: Garrido-Oter
authors.affiliation: Department of Molecular Biology and Genetics, Faculty of Science and Technology, Aarhus University, 8000 C Aarhus, Denmark.|Carbohydrate Recognition and Signaling Centre, 8000 C Aarhus, Denmark.
authors.forename: Dorthe Bodker
authors.initials: DB
authors.lastname: Jensen
authors.affiliation: Cluster of Excellence on Plant Sciences, Heinrich Heine University Duesseldorf, 40225 Duesseldorf, Germany.|Botanical Institute, Cologne Biocenter, University of Cologne, 50674 Cologne, Germany.
authors.forename: Anna
authors.initials: A
authors.lastname: Koprivova
authors.affiliation: Department of Plant Microbe Interactions, Max Planck Institute for Plant Breeding Research, 50829 Cologne, Germany; schlef@mpipz.mpg.de radutoiu@mbg.au.dk.|Cluster of Excellence on Plant Sciences, Heinrich Heine University Duesseldorf, 40225 Duesseldorf, Germany.
authors.forename: Paul
authors.initials: P
authors.lastname: Schulze-Lefert
authors.affiliation: Department of Molecular Biology and Genetics, Faculty of Science and Technology, Aarhus University, 8000 C Aarhus, Denmark; schlef@mpipz.mpg.de radutoiu@mbg.au.dk.|Carbohydrate Recognition and Signaling Centre, 8000 C Aarhus, Denmark.
authors.forename: Simona
authors.initials: S
authors.lastname: Radutoiu
mesh_terms: D019607:Brassicaceae / Q000382:microbiology; D005308:Fertilizers; D000070116:Lotus / Q000382:microbiology*; D059013:Microbial Consortia; D009586:Nitrogen Fixation; D053204:Root Nodules, Plant / Q000382:microbiology*; D012988:Soil Microbiology; D013559:Symbiosis
chemical_list: D005308:Fertilizers
keywords: 16S; Lotus japonicus; microbiota; nitrogen fixation; symbiosis