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

Bernardo Pauline, Charles-Dominique Tristan, Barakat Mohamed, Ortet Philippe, Fernandez Emmanuel, Filloux Denis, Hartnady Penelope, Rebelo Tony A., Cousins Stephen, Mesleard François, Cohez Damien, Yaverkovski Nicole, Varsani Arvind, Harkins Gordon William, Peterschmitt Michel, Malmstrom Carolyn, Martin Darren Patrick, Roumagnac Philippe. 2018. Geometagenomics illuminates the impact of agriculture on the distribution and prevalence of plant viruses at the ecosystem scale. ISME Journal, 12 : 174-184.

Quartile : Outlier, Sujet : ECOLOGY / Quartile : Outlier, Sujet : MICROBIOLOGY

Résumé : 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.

Mots-clés Agrovoc : virus des végétaux, distribution géographique, relation hôte pathogène, génétique des populations, maladie de l'homme, transmission des maladies, agent pathogène, phylogénie, virus pathogène

Mots-clés géographiques Agrovoc : Afrique du Sud, France

Classification Agris : H20 - Maladies des plantes

Champ stratégique Cirad : Axe 4 (2014-2018) - Santé des animaux et des plantes

Auteurs et affiliations

• Bernardo Pauline, Montpellier SupAgro (FRA)
• Charles-Dominique Tristan, CAS (CHN)
• Barakat Mohamed, CNRS (FRA)
• Ortet Philippe, CNRS (FRA)
• Fernandez Emmanuel, CIRAD-BIOS-UMR BGPI (FRA)
• Filloux Denis, CIRAD-BIOS-UMR BGPI (FRA)
• Hartnady Penelope, UCT (ZAF)
• Rebelo Tony A., SANBI (ZAF)
• Cousins Stephen, SANBI (ZAF)
• Mesleard François, La Tour du Valat, Centre de recherche pour la conservation des zones humides méditerranéennes (FRA)
• Cohez Damien, La Tour du Valat, Centre de recherche pour la conservation des zones humides méditerranéennes (FRA)
• Yaverkovski Nicole, La Tour du Valat, Centre de recherche pour la conservation des zones humides méditerranéennes (FRA)
• Varsani Arvind, Arizona State University (USA)
• Harkins Gordon William, University of the Western Cape (ZAF)
• Peterschmitt Michel, CIRAD-BIOS-UMR BGPI (FRA) ORCID: 0000-0001-8709-9418
• Malmstrom Carolyn, CIRAD-BIOS-UMR BGPI (FRA)
• Martin Darren Patrick, UCT (ZAF)
• Roumagnac Philippe, CIRAD-BIOS-UMR BGPI (FRA) ORCID: 0000-0001-5002-6039 - auteur correspondant

Source : Cirad-Agritrop (https://agritrop.cirad.fr/585946/)

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