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.

Connections between the structure of bacterial communities in suppressive soils and potato resistance to common scab (CS) are not well understood. In this study, one resistant and one susceptible cultivar were grown in a conducive and suppressive field to assess cultivar resistance × soil suppressiveness interactions. The resistant cultivar had a higher Mg content in periderm compare to susceptible cultivar, while suppressive soil had lower pH (5.3 vs 5.9), N, C, P, Ca contents but higher Fe and S compared with the conducive soil. Bacteria and actinobacteria numbers were higher in the conducive soil. Copy numbers of txtB gene (coding for a pathogenicity determinant) were similar in both soils but were higher in the conducive soil (for periderm samples) and in the susceptible cultivar (for conducive soil samples). Taxonomic microarray analysis and Illumina sequencing of 16S rRNA genes amplicon showed that bacterial community differed between resistant vs susceptible cultivar and to a lesser extend between suppressive vs conducive soil. Bacteria participating in soil suppression belonged to Pseudomonadaceae, Bradyrhizobiaceae, Acetobacteraceae and Paenibacillaceae, while resistant cultivars selected a bacterial community resembling that of the suppressive soil, which was enriched in Nitrospirae and Acidobacteria. Thus, the analysis of soil suppressiveness×cultivar resistance interactions enabled to gain new insight to CS control in the field.IMPORTANCEIt was demonstrated that potato cultivars susceptible and resistant to common scab select differing bacterial community and above that this trait is further modified in suppressive and conducive soil. Common scab severity was diminished by either resistant cultivar or suppressive soil but without additive effect between them. Out of the two factors, potato cultivar had a more significant influence on tuberosphere bacterial community composition than soil. Results highlighted the usefulness of both cultivar resistance and soil suppressiveness traits in understanding and managing disease control of crops.