title: Functional traits dominate the diversity-related selection of bacterial communities in the rhizosphere.
abstract: We studied the impact of community diversity on the selection of bacterial communities in the rhizosphere by comparing the composition and the functional traits of these communities in soil and rhizosphere. Differences in diversity were established by inoculating into sterilized soils diluted suspensions of the same soil. We used 16S ribosomal RNA amplicon sequencing to determine the taxonomical structure of the bacterial communities and a shotgun metagenomics approach to investigate the potential functional diversity of the communities. By comparing the bacterial communities in soil and rhizosphere, the selective power of the plant was observed both at the taxonomic and functional level, although the diversity indices of soil and rhizosphere samples showed a highly variable, irregular pattern. Lesser variation, that is, more homogenization, was found for both the taxonomic structure and the functional profile of the rhizosphere communities as compared to the communities of the bulk soil. Network analysis revealed stronger interactions among bacterial operational taxonomic units in the rhizosphere than in the soil. The enrichment processes in the rhizosphere selected microbes with particular functional genes related to transporters, the Embden-Meyerhof-Parnas pathway and hydrogen metabolism. This selection was not random across bacteria with these functional traits, but it was species specific. Overall, this suggests that functional traits are a key to the assembly of bacterial rhizosphere communities.
authors.affiliation: Department of Microbial Ecology, Netherlands Institute of Ecology NIOO-KNAW, Wageningen, The Netherlands.|Department of Plant Ecology and Phytochemistry, Institute of Biology Leiden, Leiden University, Leiden, The Netherlands.
authors.forename: Yan
authors.initials: Y
authors.lastname: Yan
authors.affiliation: Department of Microbial Ecology, Netherlands Institute of Ecology NIOO-KNAW, Wageningen, The Netherlands.
authors.forename: Eiko E
authors.initials: EE
authors.lastname: Kuramae
authors.affiliation: Department of Microbial Ecology, Netherlands Institute of Ecology NIOO-KNAW, Wageningen, The Netherlands.
authors.forename: Mattias
authors.initials: M
authors.lastname: de Hollander
authors.affiliation: Department of Plant Ecology and Phytochemistry, Institute of Biology Leiden, Leiden University, Leiden, The Netherlands.
authors.forename: Peter G L
authors.initials: PG
authors.lastname: Klinkhamer
authors.affiliation: Department of Microbial Ecology, Netherlands Institute of Ecology NIOO-KNAW, Wageningen, The Netherlands.|Department of Plant Ecology and Phytochemistry, Institute of Biology Leiden, Leiden University, Leiden, The Netherlands.
authors.forename: Johannes A
authors.initials: JA
authors.lastname: van Veen
mesh_terms: D001419:Bacteria / Q000145:classification / Q000235:genetics / Q000302:isolation & purification* / Q000378:metabolism; D044822:Biodiversity; D018517:Plant Roots / Q000382:microbiology; D010944:Plants / Q000382:microbiology; D012336:RNA, Ribosomal, 16S / Q000235:genetics; D058441:Rhizosphere; D012987:Soil / Q000737:chemistry; D012988:Soil Microbiology
chemical_list: D012336:RNA, Ribosomal, 16S; D012987:Soil