Metagenomics of the rhizosphere microbiome to identify disease suppressive bacteria

Disease-suppressive soils are exceptional ecosystems in which beneficial microorganisms effectively guard plants against soil-borne pathogen infections. For most disease-suppressive soils, however, the microorganisms and mechanisms involved in disease suppression are not known. To identify such disease-suppressive microbes, PhyloChip-based metagenomics of the rhizosphere microbiome was performed and coupled with culture-dependent functional analyses to identify bacterial taxa and mechanisms involved in soil suppressiveness to the fungal root pathogen Rhizoctonia solani. The PhyloChip analyses led to the identification of more than 30,000 bacterial and archaeal taxa from soils with different levels of disease suppressiveness. The results of these analyses specifically pointed to the Proteobacteria, Firmicutes and Actinobacteria as the most dynamic groups associated with disease suppression. Although the richness of these bacterial taxa was not significantly different between suppressive and conducive soils, their relative abundance correlated well with the different levels of disease suppressiveness. Targeted isolation and functional analyses led to the identification of specific members of the ¿-Proteobacteria with in vitro and in situ activity against Rhizoctonia solani. In conclusion, this study provides new insights into rhizobacterial diversity and fundamental mechanisms underlying multi-trophic interactions in natural disease suppressive soils.