Metagenomic-based impact study of transgenic grapevine rootstock on its associated virome and soil microbiome

Authors: HILY, JEAN-MICHEL - Université De Strasbourg: Accueil; DEMANECHE, SANDRINE - University Of Lyon; POULICARD, NILS - Centro De Cooperation Internationale En Recherche Agronomique Pour Le Development (CIRAD); TANNIERES, MÉLANIE - European Biological Control Laboratory (EBCL); DJENNANE, SAMIA - Université De Strasbourg: Accueil; BEUVE, MONIQUE - Université De Strasbourg: Accueil; VIGNE, EMMANUELLE - Université De Strasbourg: Accueil; DEMANGEAT, GERARD - Université De Strasbourg: Accueil; KOMAR, VERONIQUE - Université De Strasbourg: Accueil; GERTZ, CLAUDE - Université De Strasbourg: Accueil

Submitted to: Plant Biotechnology Journal
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 5/20/2017
Publication Date: 5/25/2017
Citation: Hily, J., Demaneche, S., Poulicard, N., Tannieres, M., Djennane, S., Beuve, M., Vigne, E., Demangeat, G., Komar, V., Gertz, C. 2017. Metagenomic-based impact study of transgenic grapevine rootstock on its associated virome and soil microbiome. Plant Biotechnology Journal. doi:10.1111/pbi.12761.

Interpretive Summary: Some genes are known to be horizontally transferred between species by various mechanisms such as by infection by viruses or bacteria. This raises the question of whether new genes placed in genetically modified (GM) plants can move into plant viruses or soil bacteria under natural field conditions. We studied a gene (F13-cp) that was transferred into grapevine rootstocks to protect them from grapevine fanleaf virus (GFLV). This virus is normally transmitted by the dagger nematode, which lives in the soil. We analyzed soil bacteria associated with transgenic or control plants six years after exposure to GFLV and the nematode using traditional microbiology culture methods and by molecular genetic methods, including state-of-the-art high-throughput sequencing technology, to determine if they had acquired the F13-cp gene. The gene was not detected in soil bacteria, or in the scion grapevine tissue. Furthermore, no differences in the composition of soil bacterial communities were detected. Our study strongly suggests that genetically modified grapevine rootstock does not favor the development of recombinant viruses or endophytes of biosafety concern nor does it disturb the composition of non-targeted soil bacterial communities.

Technical Abstract: For some crops, the only possible approach to gain a specific trait requires genome modification. The development of virus-resistant transgenic plants based on the pathogen-derived resistance strategy has been a success story for over three decades. However, potential risks associated with the technology, such as horizontal gene transfer (HGT) of any part of the transgene to an existing gene pool, have been raised. Here, we report no evidence of any undesirable impacts of genetically modified (GM) grapevine rootstock on its biotic environment. Using state-of-the-art metagenomics, we analyzed two compartments in depth, the targeted Grapevine fanleaf virus (GFLV) populations and non-targeted root-associated microbiota. Our results reveal no statistically significant differences in the genetic diversity of bacteria that can be linked to the GM trait. In addition, no novel virus or bacteria recombinants of biosafety concern can be associated with transgenic grapevine rootstocks cultivated in commercial vineyard soil under greenhouse conditions for over 6 years.