E. CHAPELLE - Metagenomics of the rhizosphere microbiome under fungal attack: unravelling bacterial taxa and functions involved in natural disease suppression in soils

Abstract

In natural disease suppressive soils, susceptible plants are protected against fungal infection in spite of the presence of a virulent pathogen. Disease suppressiveness is, in many cases, microbial in origin and develops in the field after several years of disease outbreak. Hence, interactions between the plant, the fungal pathogen and the rhizosphere microbiome appear to be required for shaping and activating a plant-protective microbial assemblage. To get insight into the active taxa and molecular mechanisms involved in pathogen control, we conducted a comparative metatranscriptomic analyses on the rhizosphere of plants grown in in the suppressive soil in the presence (Sr) or absence (S) of the fungal pathogen. Analyses of the rRNA derived-reads showed that bacterial families belonging to the β- and α-Proteobacteria, Actinomycetales and Sphingobacteria were significantly over-represented in the Sr treatment. On the other hand, a global analysis of the mRNA derived reads binned to the aforementioned dynamic families showed that their expression of genes linked to stress perception and response (ppGpp metabolism, oxidative stress response) was relatively higher than in the non-challenged bacterial community (S treatment). We hypothesized that this stress could be triggered directly or indirectly by the release of some fungal metabolites and could lead to the expression of fungal control activities. We are now experimentally testing some candidate compounds for their ability to trigger the establishment of the disease suppressive microbiome in a conducive soil. Such findings would hopefully help us to develop new tools for a sustainable management of plant diseases in agricultural fields.

See Chapelle et al., The ISME Journal, 2015. (doi: 10.1038/ismej.2015.82)

Lien sur page personnelle

https://www.researchgate.net/profile/Emilie_Chapelle

Contact

Benjamin Gourion (LIPM) >>>