Control of common scab disease can be reached by resistant cultivars or suppressive soils. Both mechanisms are likely to translate into particular potato microbiome profiles, but the relative importance of each is not known. Here, microbiomes of bulk and tuberosphere soil and of potato periderm were studied in one resistant and one susceptible cultivar grown in a conducive and a suppressive field. Disease severity was suppressed similarly by both means yet, the copy numbers of txtB gene (coding for a pathogenicity determinant) were similar in both soils but higher in periderms of the susceptible cultivar from conducive soil. Illumina sequencing of 16S rRNA genes for bacteria (completed by 16S rRNA microarray approach) and archaea, and of 18S rRNA genes for micro-eukarytes showed that in bacteria, the more important was the effect of cultivar and diversity decreased from resistant cultivar to bulk soil to susceptible cultivar. The major changes occurred in proportions of Actinobacteria, Chloroflexi, and Proteobacteria. In archaea and micro-eukaryotes, differences were primarily due to the suppressive and conducive soil. The effect of soil suppressiveness × cultivar resistance depended on the microbial community considered, but differed also with respect to soil and plant nutrient contents particularly in N, S and Fe.

Biology Centre of the Czech Academy of Sciences v v i Institute of Soil Biology Na Sádkách 7 370 05 České Budějovice Czech Republic

Crop Research Institute Epidemiology and Ecology of Microorganisms Drnovská 509 161 06 Prague 6 Czech Republic

Department of Microbiology Nutrition and Dietetics Faculty of Agrobiology Food and Natural Resources Czech University of Life Sciences Kamycka 129 Prague 6 Czech Republic

Faculty of Agriculture University of South Bohemia Studentská 13 370 05 České Budějovice Czech Republic

Faculty of Mathematics and Physics Department of Probability and Mathematical Statistics Charles University Sokolovská 83 186 75 Prague 8 Czech Republic

Univ Lyon Université Claude Bernard Lyon 1 CNRS INRA VetAgro Sup UMR5557 Ecologie Microbienne F 69622 Villeurbanne France

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