Comparative metagenomics of disease suppressive soils

SPE IPM EcolDurNatural control of soil-borne plant pathogens in disease suppressive soils has been documented for decades in various agricultural systems. Contrary to what is observed in disease conducive soils, suppression is characterized by a low disease incidence in spite of the presence of a susceptible plant host and a virulent pathogen. This phenomenon has been shown in many cases to be biologically-based, however our understanding of the microorganisms, microbial interactions and mechanisms underlying disease suppressiveness of soils is limited. Analysis of 16S rDNA amplicon libraries from a soil suppressive to Fusarium oxysporum f. sp. lini on flax revealed structural shifts among rhizosphere bacterial communities in suppressive soil in the absence and in the presence of the pathogen, as well as for a disease conducive soil. Comparisons of suppressive and conducive soils identified 25 differentially represented bacterial families, out of the 166 that could be identified among all treatments. Ten families were found at higher relative abundance in the conducive soils (such as Flavobacteriaceae, Phyllobacteraceae, or Hyphomicrobiaceae) and 15 were present at higher abundance in the suppressive soil (e.g Cytophagaceae, Comamonadaceae, Oxalobacteriaceae or Sphingobacteriaceae). Furthermore, the Sphingobacteriaceae family also showed a significant increase in the suppressive soil in the presence of the pathogen (vs the non-inoculated S soil). Interestingly, members of this group, such as some Sphingobacterium or Pedobacter isolates were previously described as antifungal agents. Corresponding metagenome libraries were generated from the Fusarium wilt suppressive soil and from soils suppressive to Rhizoctonia solani to i) gain further insight into the functional genes present in these communities, ii) identify the taxa and functional genes that correlate with the level of disease control in each system, and iii) determine if a core disease suppressive rhizosphere microbiome exists. Up-to-date results of the individual and cross-comparative analyses will be presented