Résumé
Prior to the domestication of plants, it is hypothesized that plant viruses were co-evolving with uncultivated plants growing in mixed species communities, which probably resulted in complex interactions (antagonism, commensalism, mutualism). The development of agriculture further deeply modified natural ecosystems and land use, creating agroecosystems composed by both cultivated and uncultivated areas. It is postulated that the advent of agriculture has modified the dynamics of virus-plant interactions, which has fostered the occurrence of virus disease emergence events. At the level of natural ecosystems, the relationships between plant communities’ diversity and plant virus diversity, the distribution of plant viruses and the interactions between viruses and their uncultivated hosts, have just started to be explored. In this context, we are conducting a study in the Natural Park “Burdinale-Mehaigne” (Belgium) using high throughput sequencing technologies in order to characterize the virome of Poaceae communities, including minor species, in contrasted agricultural ecosystems (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 ecosystem (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 processed using the VANA metagenomics approach. The bioinformatic analyses 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 seed-borne. Interestingly, minor Poaceae species studied in grasslands contained a wide virus richness, sometimes greater than ecosystemic pools containing 8-11 major plant species. Moreover, some virus genera (e.g. Amalgavirus, Alphaendornavirus, Potyvirus, Sobemovirus) were found only in minor species, underlining the importance of minor plant species as virus reservoirs in wild ecosystems such as grasslands.