PhyloChip hybridisation uncovered an enormous bacterial diversity in the rhizosphere of different potato cultivars: many common and few cultivar-dependent taxa

Weinert, Nicole GND; Piceno, Yvette; Ding, Guo-Chun GND; Meincke, Remo; Heuer, Holger GND; Berg, Gabriele; Schloter, Michael; Andersen, Gary; Smalla, Kornelia GND

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 fromtotal community DNAwere hybridized to PhyloChips. A total of 2432 operational taxonomic units (OTUs) were detected by the Phylo- Chips, 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, Xanthomona- dales 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 hybridiza- tion. 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.

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Weinert, Nicole / Piceno, Yvette / Ding, Guo-Chun / et al: PhyloChip hybridisation uncovered an enormous bacterial diversity in the rhizosphere of different potato cultivars: many common and few cultivar-dependent taxa. 2011.

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