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