title: Revealing structure and assembly cues for Arabidopsis root-inhabiting bacterial microbiota.
abstract: The plant root defines the interface between a multicellular eukaryote and soil, one of the richest microbial ecosystems on Earth. Notably, soil bacteria are able to multiply inside roots as benign endophytes and modulate plant growth and development, with implications ranging from enhanced crop productivity to phytoremediation. 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 multiplication. Several studies attempted to describe the structure of bacterial root endophytes; 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.
authors.affiliation: Department of Plant Microbe Interactions, Max Planck Institute for Plant Breeding Research, 50829 Cologne, Germany.
authors.forename: Davide
authors.initials: D
authors.lastname: Bulgarelli
authors.forename: Matthias
authors.initials: M
authors.lastname: Rott
authors.forename: Klaus
authors.initials: K
authors.lastname: Schlaeppi
authors.forename: Emiel
authors.initials: E
authors.lastname: Ver Loren van Themaat
authors.forename: Nahal
authors.initials: N
authors.lastname: Ahmadinejad
authors.forename: Federica
authors.initials: F
authors.lastname: Assenza
authors.forename: Philipp
authors.initials: P
authors.lastname: Rauf
authors.forename: Bruno
authors.initials: B
authors.lastname: Huettel
authors.forename: Richard
authors.initials: R
authors.lastname: Reinhardt
authors.forename: Elmon
authors.initials: E
authors.lastname: Schmelzer
authors.forename: Joerg
authors.initials: J
authors.lastname: Peplies
authors.forename: Frank Oliver
authors.initials: FO
authors.lastname: Gloeckner
authors.forename: Rudolf
authors.initials: R
authors.lastname: Amann
authors.forename: Thilo
authors.initials: T
authors.lastname: Eickhorst
authors.forename: Paul
authors.initials: P
authors.lastname: Schulze-Lefert
mesh_terms: D039903:Actinobacteria / Q000302:isolation & purification; D017360:Arabidopsis / Q000145:classification / Q000382:microbiology*; D001419:Bacteria / Q000145:classification / Q000235:genetics / Q000302:isolation & purification* / Q000648:ultrastructure; D041963:Bacteroidetes / Q000302:isolation & purification; D044822:Biodiversity; D002473:Cell Wall / Q000378:metabolism / Q000382:microbiology; D017753:Ecosystem; D060026:Endophytes / Q000145:classification / Q000235:genetics / Q000254:growth & development / Q000302:isolation & purification; D058507:Host Specificity; D017404:In Situ Hybridization, Fluorescence; D054892:Metagenome; D059828:Plant Cells / Q000382:microbiology; D018517:Plant Roots / Q000382:microbiology*; D020560:Proteobacteria / Q000302:isolation & purification; D012336:RNA, Ribosomal, 16S / Q000235:genetics; D058441:Rhizosphere; D021521:Ribotyping; D012987:Soil / Q000032:analysis / Q000737:chemistry; D012988:Soil Microbiology
chemical_list: D012336:RNA, Ribosomal, 16S; D012987:Soil