Soil suppressiveness to Fusarium disease: Shifts in root-associated microbiome during reduction of root colonization by the pathogen

We studied the microbial events at the roots of cucumber seedlings following inoculation with with Fusarium oxysporum f. sp. radicis-cucumerinum (FORC) and transplanting into soil previously amended with wild rocket (Diplotaxis tenuifolia [WR]). Disease symptoms initiated in transplants in nonamended soil 6 days after inoculation and transplantation, while in WR-amended soil, first symptoms appeared only after 14 days. Real-time PCR quantification of FORC in the roots 3 days after inoculation (with no expressed symptoms) showed similar target numbers for both WR-amended and nonamended soils. Fungal and bacterial communities compositions were determined by tag-encoded 454 pyrosequencing of the nuclear ribosomal internal transcribed spacer-1 (ITS-1, for fungi) and nuclear ribosomal 16S rRNA gene fragments (for Bacteria).