Abstract
Viral metagenomics is a powerful tool to decipher virus diversity and prevalence in agroecosystems, which may help to improve their functioning and their management. Towards this goal, we need to bring ecological concepts into virology starting by the inventory of “who is there, how many are they” to move then to question “what are they doing together”. To this aim, we established an inventory of viruses circulating between plants and insects in prototypic agroecosystems in Montpellier area. We chose two adjacent ecosystems, alfalfa fields and grassland. We sampled there plants and three invasive pest species, ie the cotton bollworm (Lepidoptera, Helicoverpa armigera), the alfalfa weevil (Curculionidae, Hypera postica) larvae and pea aphids (Hemiptera, Acyrthosiphon pisum). The viromes of about 4000 individuals, grouped in 169 samples, were obtained by viral metagenomics. We discovered 47 new arthropod and plant viral species associated with arthropod pests. We found that the composition in arthropod viruses differs completely between pest species, and plants viruses were shared by pest and plants. Finally, we analyzed the distribution of thirteen abundant viral species found in crop pests' viromes in arthropod communities using PCR approach. Arthropods were sampled, they represent twelve orders grouping about 3500 individuals. Five viruses out of the thirteen were found associated with other arthropod species, and were mainly present in predators. Our results showed that coupling viral metagenomics with PCR give insights into the viral diversity and distribution in arthropods.