The grapevine FanLeaf (FL) corresponds to an infectious decline (nepovirus) which appears in patches within the plots. This disease leads to a progressive degeneration of grapevine plants which ultimately leads to the death. At present, about 60% of the French vineyard would be affected, of which 30% in an important way. Sixteen nepoviruses are responsible for grapevine degeneration or decline. Nevertheless, the Grapevine FanLeaf Virus (GFLV) is the main responsible agent. It is specifically transmitted from plant to plant by a soil-borne ectoparasitic nematode, Xiphinema index. The nematodes, by successively biting two neighboring plants whose roots are close, inoculate the virus from the diseased grapevine plant to the healthy one. In spring ,new growth is languishing in infected plants. It is frequent to observe on branches a flattening (fasciation) or a shortening of the internodes, a "zigzag" growth, a division of the branch in "witches' broom". The repercussions on leaves are expressed by venation disorders, deformations and reticulated or diffuse variegations of the foliage. In a vineyard plot located in Champaign (France), rhizospheric soil, fine roots, rootstock, internodes and leaves were sampled on many symptomanic and asymptomatic grapevine plants. Meta-genomics and -transcriptomics approaches were developed to follow (i) the species distribution, (ii) the genes and (iii) the expressed genes of fungi, bacteria and virus in a continuum from the soil to the leaves. In this context, our results reveal major modifications of the grapevine holobiont during the decline Our data suggest different communities of microbes and virus among plant tissues and between symptomatic and asymptomatic plants. In addition, expressed genes of virus as well as microbes are different between symptomatic and asymtomatic plants. For the time, our results bring some informations about the influence of the microbiota and virome in the grapevine holobiont disease.