Exploring the virus richness and diversity in contrasted plant communities of Poaceae

Prior to the domestication of plants, it is hypothesized that plant viruses were only co-evolving with uncultivated plants growing in mixed species communities, thereby resulting 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. 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 on the virome of Poaceae communities 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. Alphaflexiviridae, 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, mycoviruses (Chrysovirus and Totivirus genera) were found in all ecosystems, in particular wheat and barley fields. Out of the 23 virus species detected in the different plots, ten of them are condidates for new virus species, revealing that virome in Poaceae-based agroecosystems remains unexplored. To confirm these results and determine the virus incidence in the different ecosystems, total RNA extraction and RT-PCR were implemented on 600 individual plants, targeting five viruses: three viruses detected in several ecosystems (Barley yellow dwarf virus, Lolium latent virus, Ryegrass mosaic virus) and two candidates for new virus species (belonging to Nepovirus and Waikavirus genera). The preliminary results are presented here.