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Journal articles
Geometagenomics illuminates the impact of agriculture on the distribution and prevalence of plant viruses at the ecosystem scale
Pauline Bernardo
1
Tristan Charles-Dominique
2, 3
Mohamed Barakat
4, 5
Philippe Ortet
4, 5
Emmanuel Fernandez
6
Denis Filloux
1
Penelope Hartnady
Tony Rebelo
Stephen Cousins
François Mesléard
7, 8, 9
Damien Cohez
10
Nicole Yavercovski
7
Arvind Varsani
11
Gordon Harkins
Michel Peterschmitt
1
Carolyn Malmstrom
Darren Martin
Philippe Roumagnac
6
5
LEMIRE - Laboratoire d'Ecologie Microbienne de la Rhizosphère et d'Environnements Extrêmes
BIAM - Institut de Biosciences et Biotechnologies d'Aix-Marseille (ex-IBEB) : DRF/BIAM
Pauline Bernardo 1
Author
Tristan Charles-Dominique 2, 3
Author
Mohamed Barakat 4, 5
Author
Philippe Ortet 4, 5
Author
Stephen R Cousins
Author
François Mesléard 7, 8, 9
Author IdHAL : francois-mesleard
Damien Cohez 10
Author
Nicole Yavercovski 7
Author
Arvind Varsani 11
Author
Gordon W Harkins
Author
Michel Peterschmitt 1
Author
Carolyn M Malmstrom
Author
Darren P Martin
Author
Philippe Roumagnac 6
Author
1
UMR BGPI - Biologie et Génétique des Interactions Plante-Parasite (CIRAD
UMR-BGPI TA A-54/K - Campus International de Baillarguet - 34398 Montpellier Cedex 5 - France)
- Cirad - Centre de Coopération Internationale en Recherche Agronomique pour le Développement : UMR54 (Siège 42, rue Scheffer 75116 Paris - France)
- INRA - Institut National de la Recherche Agronomique : UMR0385 (France)
- Montpellier SupAgro - Centre international d'études supérieures en sciences agronomiques (2, place Pierre Viala - 34060 Montpellier Cedex 02 - France)
- Montpellier SupAgro - Institut national d’études supérieures agronomiques de Montpellier (2, place Viala 34060 Montpellier Cédex 2 - France)
2
Xishuangbanna Tropical Botanical Garden (Chinese Academy of Sciences, Center for Integrative Conservation, Community Ecology and Conservation, Menglun, Yunnan, China - China)
3
Kirstenbosch Research Centre (Private Bag X7, Claremont 7735 - South Africa)
- South African National Biodiversity Institute (South Africa)
4
BIAM - Institut de Biosciences et Biotechnologies d'Aix-Marseille (ex-IBEB) (Anciennement "Institut de Biologie Environnementale et Biotechnologie (IBEB)"
Centre CEA Cadarache
13108 Saint Paul lez Durance
- France)
- DRF (CEA) - Direction de Recherche Fondamentale (CEA) : DRF/BIAM (Direction de Recherche Fondamentale
Fundamental Research Division
CEA Saclay
91191 Gif-sur-Yvette
- France)
- CEA - Commissariat à l'énergie atomique et aux énergies alternatives (Centre de Saclay Centre de Grenoble Centre de Cadarache etc - France)
- AMU - Aix Marseille Université : UMR 7265 (Aix-Marseille Université Jardins du Pharo 58 Boulevard Charles Livon 13284 Marseille cedex 7 - France)
- CNRS - Centre National de la Recherche Scientifique : UMR 7265 (France)
5
LEMIRE - Laboratoire d'Ecologie Microbienne de la Rhizosphère et d'Environnements Extrêmes (France)
- BIAM - Institut de Biosciences et Biotechnologies d'Aix-Marseille (ex-IBEB) : DRF/BIAM (Anciennement "Institut de Biologie Environnementale et Biotechnologie (IBEB)"
Centre CEA Cadarache
13108 Saint Paul lez Durance
- France)
- DRF (CEA) - Direction de Recherche Fondamentale (CEA) : DRF/BIAM (Direction de Recherche Fondamentale
Fundamental Research Division
CEA Saclay
91191 Gif-sur-Yvette
- France)
- CEA - Commissariat à l'énergie atomique et aux énergies alternatives (Centre de Saclay Centre de Grenoble Centre de Cadarache etc - France)
- AMU - Aix Marseille Université : UMR 7265 (Aix-Marseille Université Jardins du Pharo 58 Boulevard Charles Livon 13284 Marseille cedex 7 - France)
- CNRS - Centre National de la Recherche Scientifique : UMR 7265 (France)
- DRF (CEA) - Direction de Recherche Fondamentale (CEA) : DRF/BIAM (Direction de Recherche Fondamentale
Fundamental Research Division
CEA Saclay
91191 Gif-sur-Yvette
- France)
6
Cirad - Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Siège 42, rue Scheffer 75116 Paris - France)
7
Centre de recherche de la Tour du Valat (Tour du Valat Le Sambuc - 13200 Arles - France)
8
AMU - Aix Marseille Université (Aix-Marseille Université
Jardins du Pharo
58 Boulevard Charles Livon
13284 Marseille cedex 7 - France)
9
IMBE - Institut méditerranéen de biodiversité et d'écologie marine et continentale (Aix Marseille Université, Campus Etoile, Faculté St-Jérôme case 421 Av. . escadrille Normandie-Niemen 13397 MARSEILLE CEDEX 20 - France)
- CNRS - Centre National de la Recherche Scientifique : UMR7263 (France)
- Institut de recherche pour le développement [IRD] : UMR237 : UMR7263 (France)
- AMU - Aix Marseille Université : UMR7263 (Aix-Marseille Université Jardins du Pharo 58 Boulevard Charles Livon 13284 Marseille cedex 7 - France)
- AU - Avignon Université : UMR7263 (74 rue Louis Pasteur - 84 029 Avignon cedex 1 - France)
10
Station Biologique de la Tour du Valat (Le Sambuc--13200 Arles - France)
11
Electron Microscopy Unit (Rondebosch Cape Town 7701 - South Africa)
- University of Cape Town (Private Bag X3, Rondebosch 7701, South Africa - South Africa)
Abstract : 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 km 2 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.
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https://hal-univ-avignon.archives-ouvertes.fr/hal-01790932
Contributor : François Mesleard <>
Submitted on : Monday, May 14, 2018 - 10:51:43 AM
Last modification on : Thursday, September 16, 2021 - 9:47:45 AM
Contributor : François Mesleard <>
Submitted on : Monday, May 14, 2018 - 10:51:43 AM
Last modification on : Thursday, September 16, 2021 - 9:47:45 AM
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Identifiers
- HAL Id : hal-01790932, version 1
- DOI : 10.1038/ismej.2017.155
- PRODINRA : 417631
- WOS : 000418293300014
- PUBMED : 29053145
Collections
UNIV-AVIGNON | CNRS | INRA | CEA | IMBE | UNIV-AMU | CIRAD | IRD | TOUR-DU-VALAT | OSU-INSTITUT-PYTHEAS | CEA-DRF | CEA-CAD | BIAM | MONTPELLIER-SUPAGRO | INRAE | IMBE-IRPNC | INRAEOCCITANIEMONTPELLIER
Citation
Pauline Bernardo, Tristan Charles-Dominique, Mohamed Barakat, Philippe Ortet, Emmanuel Fernandez, et al.. Geometagenomics illuminates the impact of agriculture on the distribution and prevalence of plant viruses at the ecosystem scale. ISME Journal, Nature Publishing Group, 2018, 12 (1), pp.173 - 184. ⟨10.1038/ismej.2017.155⟩. ⟨hal-01790932⟩
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