Agriculture has a considerable influence on the distribution and prevalence of plant viruses in the environment. In cultivated areas, viral infections are significantly more frequent than in natural areas. This is the conclusion of a study conducted by a team of international scientists in the Camargue (France) and in the Western Cape regions (South Africa), the results of which were published in January in The ISME Journal. "The clustering and concentration of genetically similar organisms, as with crop varieties, fuel epidemics", explains Philippe Roumagnac, a researcher in plant virology at CIRAD. This study also indicates that the "natural compartment", which is still largely unexplored in terms of the biodiversity of microorganisms, contains a large number of viruses. "The areas adjacent to agricultural land could enable us to better understand the emergence of plant diseases" , he says.
Exploring the diversity of plant viruses and understanding their emergence
Although 50% of emerging plant diseases are viral, knowledge of the diversity of plant viruses is still dramatically lacking. Officially, to date, around 1 400 species of plant viruses have been characterised and taxonomically assigned. This figure is probably well below the true diversity of plant viruses, as shown by recent explorations of terrestrial and marine ecosystems. Moreover, this count is undoubtedly distorted on two levels. First, the description of viruses has been conducted almost exclusively based on a very small number of cultivated plant species and, second, most of the viruses were only characterised further to the appearance of symptoms in their hosts. "Our knowledge of the world of plant viruses therefore remains extremely partial in terms of diversity, but also in terms of distribution at the agroecosystem level" , says Denis Filloux, a researcher in plant virology at CIRAD. "This lack of knowledge is an obstacle to our understanding of the global functioning of agroecosystems, and to the definition and quantification of risk factors in the emergence of new plant viral diseases or the design of strategies to tackle these diseases" . The majority of the viruses remaining to be identified are found in areas with little human activity.
A France-South Africa collaboration within the framework of European funding
This research, initially financed by CIRAD, the Fondation pour la Recherche sur la Biodiversité (FRB - Foundation for Research on Biodiversity), the INRA metaprogramme Meta-omics and Microbial Ecosystems and the French Directorate General of Armaments, took on an international dimension thanks to European Union funding and a Marie Curie grant. The sampling and high-throughput sequencing data analysis work was achieved through a partnership with the University of Cape Town.
New viral metagenomics approaches
To achieve this result, the team of international scientists adopted a new viral metagenomics approach. "Metagenomics is a method that conducts high-throughput sequencing on all genomes of the microbes populating a given environment" , explains Philippe Roumagnac. "It enables us, for example, to access the virome, in other words all of the viral sequences contained in a host organism or in a sample containing several potential hosts." Since 2009, a new generation of metagenomics research has emerged in plant pathology, making it possible to not only analyse the overall genome of an ecosystem or organism, but also to directly link sequences of pathogenic agents to their host and/or to a geographical position. This original research in spatial metagenomics has revolutionised our view of plant virus distribution by revealing that many of the plants analysed were virus-infected.