Geometagenomics illuminates the impact of agriculture on the distribution and prevalence of plant viruses at the ecosystem scale.

Disease emergence events regularly result from human activities such as agriculture, which frequently brings large populations of genetically uniform hosts into contact with potential pathogens. Although viruses cause nearly 50% of emerging plant diseases, there is little systematic information about virus distribution across agro-ecological interfaces and large gaps in understanding of virus diversity in nature. Here we applied a novel landscape-scale geometagenomics approach to examine relationships between agricultural land use and distributions of plant-associated viruses in two Mediterranean-climate biodiversity hotspots (Western Cape region of South Africa and Rhône river delta region of France). In total, we analysed 1725 geo-referenced plant samples collected over two years from 4.5 × 4.5 km2 grids spanning farmlands and adjacent uncultivated vegetation. We found substantial virus prevalence (25.8-35.7%) in all ecosystems, but prevalence and identified family-level virus diversity were greatest in cultivated areas, with some virus families displaying strong agricultural associations. Our survey revealed 94 previously unknown virus species, primarily from uncultivated plants. This is the first effort to systematically evaluate plant-associated viromes across broad agro-ecological interfaces. Our findings indicate that agriculture substantially influences plant virus distributions and highlight the extent of current ignorance about the diversity and roles of viruses in nature.

High Stocking Density Controls Phillyrea Angustifolia in Mediterranean Grasslands.

Extensive grazing applied in the form of low instantaneous pressure over a long period is a widespread management practice in protected areas. However this kind of stocking method does not always achieve the expected results, in particular because it fails to limit colonization by woody plants.This is the case in the relict xero-halophytic grasslands of the northern Mediterranean coastal region, subjected to widespread colonization by the shrub Phillyrea angustifolia despite the presence of extensive grazing. In this study, we investigated, for an equal annual stocking rate, the respective impact of high stocking density applied over a short period (mob grazing) and low stocking density applied over a long period on both P. angustifolia and herbaceous cover, using an in situ experimental design run for 7 years. Only mob grazing was effective both in controlling the establishment and increasing the mortality of P. angustifolia individuals. We did not find any difference after the 7 years of experimentation between the two stocking methods with regard to the herbaceous community parameters tested: species richness, diversity, evenness, contribution of annual characteristic species. By contrast, the exclusion of domestic grazing led to a strong reduction of these values.The use of mob grazing may be well suited for meeting conservation goals such as maintaining open habitats in these grasslands.