title: Rice root-associated bacteria: insights into community structures across 10 cultivars.
abstract: In this study, the effects of plant genotype, soil type and nutrient use efficiency on the composition of different bacterial communities associated with rice roots were investigated. Thus, total bacteria, Alpha- and Betaproteobacteria, Pseudomonas and Actinobacteria were studied using PCR, followed by denaturing gradient gel electrophoresis (PCR-DGGE). Rice genotype determined, to a large extent, the composition of the different bacterial communities across cultivars. Several cultivars belonging to Oryza sativa ssp. indica tended to select similar bacterial communities, whereas those belonging to subspecies japonica and aromatica selected ones with divergent community structures. An effect of soil type was pronounced for the Actinobacteria communities, while a small effect of 'improved' and 'traditional' plants was noted for all communities analyzed. A few dominant bands in PCR-DGGE, affiliated with Rhizobium radiobacter, Dickeya zeae, Mycobacterium bolletii and with members of the Rhizobiales, Rhodospirillaceae and Paenibacillaceae, were spread across cultivars. In contrast, a majority of bands (e.g. affiliated with Enterobacter cloacae or Burkholderia kururiensis) was only present in particular cultivars or was erratically distributed among rice replicates. These findings suggested that both bacterial adaptation and plant genotype contribute to the shaping of the dynamic bacterial communities associated with roots of rice plants.
authors.affiliation: Department of Microbial Ecology, Centre for Ecological and Evolutionary Studies, Groningen University, Groningen, The Netherlands. phardoim@gmail.com
authors.forename: Pablo Rodrigo
authors.initials: PR
authors.lastname: Hardoim
authors.forename: Fernando Dini
authors.initials: FD
authors.lastname: Andreote
authors.forename: Barbara
authors.initials: B
authors.lastname: Reinhold-Hurek
authors.forename: Angela
authors.initials: A
authors.lastname: Sessitsch
authors.forename: Leonard Simon
authors.initials: LS
authors.lastname: van Overbeek
authors.forename: Jan Dirk
authors.initials: JD
authors.lastname: van Elsas
mesh_terms: D001419:Bacteria / Q000145:classification / Q000235:genetics*; D004269:DNA, Bacterial / Q000235:genetics; D058645:Denaturing Gradient Gel Electrophoresis; D005838:Genotype; D012275:Oryza / Q000235:genetics / Q000382:microbiology*; D018517:Plant Roots / Q000235:genetics / Q000382:microbiology*; D016133:Polymerase Chain Reaction; D012336:RNA, Ribosomal, 16S / Q000235:genetics; D012987:Soil / Q000032:analysis; D012988:Soil Microbiology
chemical_list: D004269:DNA, Bacterial; D012336:RNA, Ribosomal, 16S; D012987:Soil