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 plantassociated 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

Colonization of non-cassava plant species by cassava whiteflies (Bemisia tabaci) in Uganda

Bemisia tabaci(Genn.) (Homoptera: Aleyrodidae) is the vector of cassava mosaic geminiviruses (CMGs), which are the main production constraint to cassava [Manihot esculenta Crantz (Euphorbiaceae)],both in Uganda and elsewhere in Africa. TwoB. tabaci genotype clusters, Ug1 and Ug2, differentiated at 8% nucleotide (nt) divergence within the mitochondrial cytochrome oxidase I (mtCOI) gene, have been shown to occur on cassava in Uganda. However, the role of alternative hosts in the ecology of cassavaB. tabaci genotypes and their possible involvement in the epidemiology of cassava mosaic disease (CMD) in Uganda remain unknown. In this study, we investigated the restriction of cassava B. tabaci genotypes to cassava and the colonization of alternative host species in select cassava-growing areas of the country in 2003 and 2004. Bemisia tabaci adults and 4th instar nymphs were collected from cassava and 11 other cultivated and uncultivated species occurring adjacent to the sampled cassava fields Phylogenetic analysis of mtCOI sequences revealed that only a single genotype cluster, Ug1, was present on both cassava and non-cassava plant species sampled in this study. The Ug1 genotypes (n = 49) shared 97–99% nt identity with the previously described cassava-associated B. tabaci populations in southern Africa, and were ∼ 8% and ∼ 13% divergent from Ug2 and the ‘Ivory Coast cassava’ genotypes in Uganda and Ivory Coast, respectively. The Ug1 genotypes occurred (as adults) on all 12 source-plant species sampled. However, based on the presence of B. tabaci 4th instar nymphs, the Ug1 genotypes (n = 13) colonized cassava and five other non-cassava plant species: Manihot glaziovii, Jatropha gossypifolia, Euphorbia heterophylla, Aspilia africana, and Abelmoschus esculentus, suggesting that cassava B. tabaci (Ug1 genotypes) are not restricted to cassava in Uganda. No Ug2-like genotypes were detected on any of the plant species sampled, including cassava, in this study. The identification of additional hosts for at least one genotype cluster, Ug1, known also to colonize cassava, and which was hitherto thought to be ‘cassava-restricted’ may have important epidemiological significance for the spread of CMGs in Uganda