Abstract
<title>Abstract</title> <p> <bold>Background</bold> Soil-borne fungal pathogens are major yield-limiting factors in crop production. Current measures to control these pathogens are limited or environmentally unfriendly. Disease-suppressive soils are exceptional ecosystems where soil-borne fungal pathogens cause little disease due to the specific antagonistic activities of root-associated microbes. In the field, disease suppressiveness against fungal root pathogens is typically observed after successive cultivation of a susceptible host and a severe disease outbreak. To date, however, the successional changes in root microbiome composition and functions during the transition of a soil from a conducive to a disease suppressive state, a process referred to as rebiosis, are largely unknown. <bold>Results</bold> We show that suppressiveness against damping-off disease of sugar beet seedlings, caused by the fungal pathogen <italic>Rhizoctonia solani</italic> , can be induced in controlled greenhouse assays by successive cultivation and repeated root infections of the susceptible host plant. Successional community profiling and metatranscriptome analyses revealed relatively small changes in rhizobacterial microbiome composition during rebiosis, whereas significant temporal changes were observed in the expression of specific functional genes. Various genes differentially expressed during rebiosis were assigned to the genus <italic>Fluviicola</italic> , with several transcripts mapping to pirin family proteins. <bold>Conclusions</bold> Our results indicate that the transition of a <italic>R. solani</italic> conducive soil to a disease-suppressive state is not associated with major compositional changes in the rhizobacterial microbiome, but with strain-level specific changes in gene expression of only few bacterial genera. These results are instrumental for designing microbiome-based strategies to mitigate crop losses caused by fungal root pathogens. </p>