Impact of ecosystem diversity on the Poaceae virome

This STSM was dedicated to the study of the viral diversity of different agro-ecological systems by metagenomic analyses. Indeed, 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. 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, the objective of my PhD is to study the impact of ecosystems with contrasted biodiversity (monoculture, pastures and grasslands of the Natural Park “Burdinale-Mehaigne”, Belgium) on the virome of Poaceae plant species using high throughput sequencing technologies. We developed a metagenomic approach consisting in virus particles purification, virion-associated nucleic acids (VANA) extraction and library preparation for Illumina sequencing applied on pools of 50 plant samples per ecosystem.
Bringing my data with me, I visited for one month (March 2018) the team of Professor Philippe Roumagnac (MicroQuar, UMR BGPI, CIRAD, Montpellier, France) in order to discuss the statistical approaches used to characterize viral dynamics in ecosystems and to develop knowledge in the bioinformatic tools adapted to virus detection. The bioIT analysis of my VANA samples revealed the presence of viral communities in wild and cultivated Poaceae. These viruses belong to a quite diverse set of families (e.g. Endornaviridae, Luteoviridae, Partitiviridae, Potyviridae, Reoviridae, Secoviridae), infecting a large host range within the Poaceae and transmitted by various vectors (aphids, planthoppers, mites, nematods, seeds). This STSM had a very positive impact on (1) my work by allowing me to develop my own bioIT pipeline which is still used and optimized in the framework of my ongoing analyses, and (2) my lab with whom a new collaboration was initiated with the MicroQuar team. The preliminary results obtained will be presented.