Influence of host variety and community composition on the dynamics of virus infections in a North American native prairie grass.

The development high-throughput sequencing technologies offers a huge opportunity to improve virome characterization at multiple scales, from individual plants to entire ecosystems. Viral metagenomics can also contribute to better understand virus ecology in agro-ecological landscapes. This work has focused on switchgrass (Panicum virgatum L.), a North American native and perennial prairie grass which is under development as a potential bioenergy feedstock. We performed a large-scale metagenomic study to characterize the virome richness and composition in two switchgrass varieties and three other native grass species growing in artificial prairies sown a decade ago. Switchgrass virome was compared in three different diversity designs and three sites across Michigan, USA. We also monitored the dynamics of Switchgrass mosaic virus infection (Marafivirus, Tymoviridae), in the same sites and treatments over seven years. In North America, switchgrass mosaic virus (SwMV) is transmitted by leafhoppers and infects at least seven native prairie grasses.
The VANA metagenomics study performed in 1000 grass samples revealed a diversified virome with at least 18 virus species. More than two thirds of this virome were composed of unknown species, in particular from Amalgaviridae, Partitiviridae and Totiviridae families. In these 10-year-old prairies, we found a modular virus network with a specific virome infecting each grass species. Virome richness and composition were influenced by switchgrass varieties and sites, but not by the community composition. The dynamics of SwMV infection in switchgrass seemed to increase over the first several years, and then it stabilized and even tended to decrease in the later years. We observed that SwMV prevalence was also influenced by host variety, sites and diversity treatment, with higher prevalence in switchgrass planted with other grasses and forbs than in monocultures. Switchgrass genetic architecture (subpopulations, ploidy) and community composition (transmission agents, alternative hosts,…) are under investigation.