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Soil and root microbial communities play an important role in defending plants against soilborne pathogens. In particular soils, defined as suppressive soils, pathogens are present but plants show no disease symptoms. The microbiome of these soils has been compared to adjacent conducive soils in previous studies, and certain taxa have been found to be more abundant in suppressive than in conducive soils. However, there is a lack of studies comparing the microbiomes of a larger number of agricultural soils with different levels of disease resistance (eg high, low, intermediate) and not much is known about relations between bacterial and fungal members of microbial communities in response to soil disease resistance. In this study, we analysed nine representative Swiss agricultural soils planted with wheat for co-occurrence patterns in the microbial community, focussing on bacterial genera known to include biocontrol bacteria and fungal genera known to include soilborne pathogenic fungi, using 16S rRNA gene, respectively ITS amplicon sequencing. We further studied the links between the abundances of bacterial genera as well as of bacterial OTUs and soil resistance to the pathogens Pythium ultimum and Gaeumannomyces tritici. Moreover, we quantified three functional Pseudomonas traits known to be involved in suppression of fungal pathogens, ie biosynthesis genes for the antimicrobial metabolites 2, 4-diacetylphoroglucinol, phenazines and pyrrolnitrin. Network analysis revealed that keystone taxa displaying most positive or negative relations to other taxa within the microbial community were neither the most abundant fungal and …