What can viral metagenomics bring to our understanding of the diversity and ecology of plant viruses in agro ecological landscapes ?

High throughput sequencing (HTS) gave access for the first time to the viral metagenome or virome, by allowing to characterize, without a priori, all or nearly all viruses in a given sample. This broad-spectrum capability of HTS is raising a growing interest to study the diversity and ecology of plant viruses, in particular the richness and composition of viral communities at the agro-ecosystem scale, as well as the virus circulation among host reservoirs and the discovery of new and emerging viruses.
Recent viromics studies revealed diversified and largely unknown phytoviromes in natural ecosystems, with high rates of co-infection and the abundance of so-called persistent (or cryptic) viruses representing more than half of the viruses identified in wild plants. The influence of plant traits (e.g., lifespan, height, occurrence) on the virome richness, and the relationships between host-pathogen richness in cultivated and non-cultivated plant communities were also unravelled. In particular, the richness and diversity of plant communities appeared as influencing the richness and composition of phytoviromes, especially the distribution of persistent and acute viruses. Other results demonstrated the stability of virome richness over time but the large viral intraspecific variability within and among plant communities. Thus, HTS technologies have highlighted and will continue to serve the exploration of the complex network of viral communities in nature for the times to come...