Endophytic Microbial Assemblage in Grapevine.
The plant vascular system has remained an under-explored niche despite its potential for hosting beneficial microbes. The aim of this work was to determine the origin of the microbial endophytes inhabiting grapevine. We focused on a single commercial vineyard in California over a two-year period and used an amplicon metagenomics approach to profile the bacterial (16S -V4) and fungal (ITS) communities of the microbiome across a continuum of six grapevine compartments; bulk soil, rhizosphere, root, cordon, cane and sap. Our data supported that roots are a bottleneck to microbial richness and that they are mostly colonized with soilborne microbes, including possible plant growth promoting bacteria recruited by the host, but also saprohytic and pathogenic fungal invaders. A core group of taxa was identified throughout the vine, however there were clear partitioning of the microbiome based on host's niche. Above and below ground plant tissues displayed distinct microbial fingerprints and were intermixed in a limited capacity mostly by way of the plant sap. We discuss how cultural practices and human contact may shape the endosphere microbiome and identify potential channels for transmission of its residents.