title: Defining the core Arabidopsis thaliana root microbiome.
abstract: Land plants associate with a root microbiota distinct from the complex microbial community present in surrounding soil. The microbiota colonizing the rhizosphere (immediately surrounding the root) and the endophytic compartment (within the root) contribute to plant growth, productivity, carbon sequestration and phytoremediation. Colonization of the root occurs despite a sophisticated plant immune system, suggesting finely tuned discrimination of mutualists and commensals from pathogens. Genetic principles governing the derivation of host-specific endophyte communities from soil communities are poorly understood. Here we report the pyrosequencing of the bacterial 16S ribosomal RNA gene of more than 600 Arabidopsis thaliana plants to test the hypotheses that the root rhizosphere and endophytic compartment microbiota of plants grown under controlled conditions in natural soils are sufficiently dependent on the host to remain consistent across different soil types and developmental stages, and sufficiently dependent on host genotype to vary between inbred Arabidopsis accessions. We describe different bacterial communities in two geochemically distinct bulk soils and in rhizosphere and endophytic compartments prepared from roots grown in these soils. The communities in each compartment are strongly influenced by soil type. Endophytic compartments from both soils feature overlapping, low-complexity communities that are markedly enriched in Actinobacteria and specific families from other phyla, notably Proteobacteria. Some bacteria vary quantitatively between plants of different developmental stage and genotype. Our rigorous definition of an endophytic compartment microbiome should facilitate controlled dissection of plant-microbe interactions derived from complex soil communities.
authors.affiliation: Department of Biology, University of North Carolina, Chapel Hill, North Carolina 27599, USA.|Curriculum in Genetics and Molecular Biology, University of North Carolina, Chapel Hill, North Carolina 27599, USA.
authors.forename: Derek S
authors.initials: DS
authors.lastname: Lundberg
authors.affiliation: Department of Biology, University of North Carolina, Chapel Hill, North Carolina 27599, USA.
authors.forename: Sarah L
authors.initials: SL
authors.lastname: Lebeis
authors.affiliation: Department of Biology, University of North Carolina, Chapel Hill, North Carolina 27599, USA.
authors.forename: Sur Herrera
authors.initials: SH
authors.lastname: Paredes
authors.affiliation: Department of Biology, University of North Carolina, Chapel Hill, North Carolina 27599, USA.|Curriculum in Bioinformatics and Computational Biology, University of North Carolina, Chapel Hill, North Carolina 27599, USA.
authors.forename: Scott
authors.initials: S
authors.lastname: Yourstone
authors.affiliation: Department of Biology, University of North Carolina, Chapel Hill, North Carolina 27599, USA.
authors.forename: Jase
authors.initials: J
authors.lastname: Gehring
authors.affiliation: DOE Joint Genome Institute, Walnut Creek, California 94598, USA.
authors.forename: Stephanie
authors.initials: S
authors.lastname: Malfatti
authors.affiliation: DOE Joint Genome Institute, Walnut Creek, California 94598, USA.
authors.forename: Julien
authors.initials: J
authors.lastname: Tremblay
authors.affiliation: DOE Joint Genome Institute, Walnut Creek, California 94598, USA.
authors.forename: Anna
authors.initials: A
authors.lastname: Engelbrektson
authors.affiliation: DOE Joint Genome Institute, Walnut Creek, California 94598, USA.
authors.forename: Victor
authors.initials: V
authors.lastname: Kunin
authors.affiliation: DOE Joint Genome Institute, Walnut Creek, California 94598, USA.
authors.forename: Tijana Glavina
authors.initials: TG
authors.lastname: Del Rio
authors.affiliation: Taxon Biosciences, Inc., Tiburon, California 94920, USA.
authors.forename: Robert C
authors.initials: RC
authors.lastname: Edgar
authors.affiliation: Soil Science, Faculty of Biology and Chemistry, University of Bremen, Bremen 28359, Germany.
authors.forename: Thilo
authors.initials: T
authors.lastname: Eickhorst
authors.affiliation: Department of Microbiology, Cornell University, Ithaca, New York 14853, USA.
authors.forename: Ruth E
authors.initials: RE
authors.lastname: Ley
authors.affiliation: DOE Joint Genome Institute, Walnut Creek, California 94598, USA.|Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences & Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland 4072, Australia.
authors.forename: Philip
authors.initials: P
authors.lastname: Hugenholtz
authors.affiliation: DOE Joint Genome Institute, Walnut Creek, California 94598, USA.
authors.forename: Susannah Green
authors.initials: SG
authors.lastname: Tringe
authors.affiliation: Department of Biology, University of North Carolina, Chapel Hill, North Carolina 27599, USA.|Curriculum in Genetics and Molecular Biology, University of North Carolina, Chapel Hill, North Carolina 27599, USA.|Department of Microbiology and Immunology, University of North Carolina, Chapel Hill, North Carolina 27599, USA.|Carolina Center for Genome Sciences, University of North Carolina, Chapel Hill, North Carolina 27599, USA.|Howard Hughes Medical Institute, University of North Carolina, Chapel Hill, North Carolina 27599, USA.
authors.forename: Jeffery L
authors.initials: JL
authors.lastname: Dangl
mesh_terms: D039903:Actinobacteria / Q000235:genetics / Q000302:isolation & purification; D017360:Arabidopsis / Q000145:classification / Q000254:growth & development / Q000382:microbiology*; D060026:Endophytes / Q000145:classification* / Q000235:genetics / Q000302:isolation & purification*; D005838:Genotype; D017404:In Situ Hybridization, Fluorescence; D054892:Metagenome; D018517:Plant Roots / Q000145:classification / Q000254:growth & development / Q000382:microbiology*; D020560:Proteobacteria / Q000235:genetics / Q000302:isolation & purification; D012336:RNA, Ribosomal, 16S / Q000235:genetics / Q000302:isolation & purification; D058441:Rhizosphere; D021521:Ribotyping; D017422:Sequence Analysis, DNA; D012988:Soil Microbiology; D013559:Symbiosis
chemical_list: D012336:RNA, Ribosomal, 16S