Soil composition and rootstock genotype drive the root associated microbial communities in young grapevines

The young plant, whose health and growth are largely influenced by microorganisms, draws its associated microbiome from the soil. In grapevine, which is often a grafted plant, the genetic dimension of the rootstock is another factor to consider in its belowground associations with microorganisms. In this greenhouse study of 5 months, the impact of the soil and the rootstock genotype on the microbial community in roots, rhizosphere and bulk soil were investigated using amplicon sequencing of the bacterial 16S rRNA gene and the fungal ITS. Vitis vinifera L. cv. Cabernet Sauvignon plants grafted on two different rootstocks, namely Riparia Gloire de Montpellier (RGM) and 1103 Paulsen (1103P) were grown in two different soils, which originated from the same vineyard partially subjected to unexplained decline (i.e., asymptomatic AS, and symptomatic S areas). The observed decline in vineyard was not related to a pathological cause or mineral disturbance, but to low growth and high mortality of the plants. Soils used for greenhouse experiment possessed similar physicochemical properties and different microbial compositions.