Résumé
Over the past three years we have developed a geometagenomics approach which, because of the sampling design it applies and the depth of sampling it involves, enables the quantitative ecosystem?scale evaluation of spatial variations in, amongst other things, viral demographics, host distributions, and viral gene-flow. The approach is particularly well suited to analysing how viruses respond to ecosystem perturbations. As with the ecogenomics approach of Marilyn Roossink et al. (2009), the geometagenomics approach can precisely link individual sequence reads from bulked mixed sequencing reactions to information on abiotic and biotic conditions of the samples from which the sequences were obtained, the plant hosts from which samples were collected and the spatial arrangement of the samples. However, unlike with the ecogenomics experimental design, where sampling locations are randomly distributed within a reference ecosystem, in a geometagenomics experimental design sampling locations are systematically placed within a predefined grid; the location of which is placed according to available geographic information systems data. This a priori choice of the sampling points allows the identification of reference ecosystems that should be appropriate for determining, for example, the impacts of agriculture on viral demographics and evolution within natural endangered ecosystems or the transmission rates of viruses between wild and cultivated plants. Our study was conducted in 2010 and 2012 in the Cape Floristic Region, which includes wild areas, including renosterveld shrubland and strandveld shrubland besides wide fertile plains under introduced crops such as barley, wheat and wine. Besides determining the spatial and temporal host distributions of various groups of both known and previously unknown virus species, we compare the virus species richness of the various wild and cultivated sampling locations. Amongst a large number of newly discovered virus species (including many apparently novel single stranded DNA viruses) was one belonging to a new Geminivirus genus that we have tentatively named, Capulavirus. (Résumé d'auteur)