Résumé
Before the domestication of plants, it is hypothesized that plant viruses were co-evolving with wild plants growing in mixed species communities, thereby resulting in complex interactions (antagonism, commensalism, mutualism). The development of agriculture deeply modified ecosystems, which is postulated to have altered the dynamics of virus-plant pathosystems and accelerated the rate of virus evolution and emergence. 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 species diversity (in terms of richness and density) on the virome of Poaceae communities in contrasted agricultural ecosystems (cereal monocultures, grazed pastures and natural grasslands).We developed a metagenomic approach consisting in virus particles purification, virion-associated nucleic acids (VANA) extraction and library preparation for Illumina sequencing and applied it on pools of 50 plant samples per ecosystem (50 samples reflecting plant species composition) or plant species (50 individual plants). Over two years, 4096 Poaceae plants were thus sampled and the bioinformatic analysis revealed the 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. Endornaviridae, Luteoviridae, Partitiviridae, Potyviridae, Reoviridae, Secoviridae), infecting a large range of hosts within the Poaceae and transmitted by different vectors (aphids, planthoppers, mites, nematods) or seeds-bornes. Virus richness was compared between ecosystems: limited viral diversity (e.g. Hordeum vulgare endornavirus, Brome mosaic virus) were detected in barley and wheat fields, whereas a larger diversity was found in less anthropic ecosystems. Lolium latent virus (Alphaflexiviridae) and Ryegrass mosaic virus (Potyviridae) were strongly present in grazed pastures, particularly in Lolium perenne L. Several tentative new virus species belonging to the Nepovirus genus and the Partitiviridae family were found in natural grasslands.