title: PhyloChip hybridization uncovered an enormous bacterial diversity in the rhizosphere of different potato cultivars: many common and few cultivar-dependent taxa.
abstract: The phylogenetic composition of bacterial communities in the rhizosphere of three potato cultivars grown at two distant field sites was analysed. Ribosomal gene fragments amplified from total community DNA were hybridized to PhyloChips. A total of 2432 operational taxonomic units (OTUs) were detected by the PhyloChips, of which 65% were found in the rhizosphere of all cultivars at both field sites. From all detected OTUs, 9% revealed a cultivar-dependent abundance at the one or the other field site and 4% at both sites. Differential abundance on the three cultivars was mainly observed for OTUs belonging to the Pseudomonadales, Actinomycetales and Enterobacteriales. More than 40% of OTUs belonging to Bradyrhizobiales, Sphingomonadales, Burkholderiales, Rhodocyclales, Xanthomonadales and Actinomycetales differed significantly in their abundance between the sites. A sequence analysis of six 16S rRNA gene clone libraries corresponded well with the taxonomic community structure evidenced by the PhyloChip hybridization. Most ribotypes matched OTUs detected by the PhyloChip. Those OTUs that responded to the potato cultivar at both field sites might be of interest in view of cultivar-specific effects on bacterial biocontrol strains and pathogens.
authors.affiliation: Julius Kühn-Institut, Federal Research Centre for Cultivated Plants (JKI), Institute for Epidemiology and Pathogen Diagnostics, Braunschweig, Germany.
authors.forename: Nicole
authors.initials: N
authors.lastname: Weinert
authors.forename: Yvette
authors.initials: Y
authors.lastname: Piceno
authors.forename: Guo-Chun
authors.initials: GC
authors.lastname: Ding
authors.forename: Remo
authors.initials: R
authors.lastname: Meincke
authors.forename: Holger
authors.initials: H
authors.lastname: Heuer
authors.forename: Gabriele
authors.initials: G
authors.lastname: Berg
authors.forename: Michael
authors.initials: M
authors.lastname: Schloter
authors.forename: Gary
authors.initials: G
authors.lastname: Andersen
authors.forename: Kornelia
authors.initials: K
authors.lastname: Smalla
mesh_terms: D001419:Bacteria / Q000145:classification* / Q000235:genetics* / Q000302:isolation & purification; D044822:Biodiversity; D009693:Nucleic Acid Hybridization; D020411:Oligonucleotide Array Sequence Analysis; D010802:Phylogeny; D012336:RNA, Ribosomal, 16S / Q000235:genetics; D058441:Rhizosphere; D021521:Ribotyping; D011198:Solanum tuberosum / Q000382:microbiology*
chemical_list: D012336:RNA, Ribosomal, 16S