Résumé
Prior to plant domestication, it is hypothesized that plant viruses were co-evolving with uncultivated plants growing in mixed species communities, thereby resulting in complex interactions (antagonism, commensalism, mutualism). Development of agriculture further deeply modified natural ecosystems, land use and dynamics of virus-plant interactions, which has fostered occurrence of virus disease emergence events. In this context, we are conducting a study in the Natural Park “Burdinale-Mehaigne” (Belgium) using high throughput sequencing technologies in order to examine the impact of plant species diversity on the virome (e.g. the genomes of viral community) of Poaceae in contrasted plant communities (cereal monocultures, grazed pastures and natural grasslands). We adapted a virion-associated nucleic acids (VANA) metagenomics protocol to sequence at high throughput pools of 50 plant samples per plant community (50 samples reflecting plant species composition) and per plant species. Over two years, about 4,300 Poaceae plants (corresponding to 24 species) were sampled and bioinformatic analyses revealed presence of diverse viral communities in wild and cultivated Poaceae, even though they did not present any symptoms. These viruses belong to diverse families (e.g. Alphaflexiviridae, Luteoviridae, Partitiviridae, Totiviridae), infecting a large range of hosts within Poaceae and transmitted by different vectors (insects, mites, nematods) or seed-borne. More than 30 virus species were detected in the different plots and at least half of them are candidates for new virus species, revealing that virome in Poaceae-based agroecosystems and its impact on the dynamic of plant communities remain largely unexplored.