A Characterization of a Cool-Climate Organic Vineyard’s Microbiome

Abstract

The microbiome, an influential factor affecting plant health and growth, is attracting increasing interest with respect to wine grape production. The purpose of this study was to characterize the microbiome (fungi and bacteria) of the soil, cover crop roots, and grape (Vitis spp.) roots across rootstock and depth in a cool-climate, organic vineyard. The cover crop consisted of a fescue (Festuca sp.) grass, while grape roots were sampled from New York Muscat, a cool-climate hybrid, across three root types (ungrafted, 3309C and Riparia Gloire) at three root depths (0 to 15, 15 to 30, and 30 to 50 cm). The grape root microbiome was more specialized, with fewer observed amplicon sequence variants for both bacteria (16S) and fungi (internal transcribe spacer) than found in the cover crop and the surrounding soil. Grape roots were dominated by bacterial genera Pseudomonas, Niastella, and Rhizobium; most prominent fungal genera were Plectosphaerella, Trichosporon, and Ilyonectria. Although no correlations were found between α-diversity metrics and soil parameters, Pseudaleuria relative abundance was correlated with Mn, Fe, and Na levels. Soil depth explained a small portion of bacterial but not fungal variance and taxonomic composition. Rootstock type explained a portion of both bacterial and fungal variance and taxonomic composition, substantiating the role of host plant genetics in the development of the grape root microbiome. This is the first characterization of the grape root microbiome in a cool-climate Canadian vineyard.