Deciphering the diversity of Vitis vinifera microbiome trough the exploration of different ecological niches

The complex microbial flora in vineyard is known to be influenced by the grape variety, the viticulture practices and the year of wine production. Commensal microbiomes are promoting productivity and health of the Vitis vinifera plant and were found to be in association with specific tissues, colonizing leaves, grapes and bark. In this study the bacterial and fungal populations of Raboso wine region, Italy, have been investigated using next-generation sequencing of 16S rRNA and internal transcribed spacer (ITS2) ribosomal sequence. The role of microbes that could impact flavour and productivity of the plant was evaluated assessing specific population of epiphytes residing on leaves, grapes and barks. Methylobacterium adhaesivum and Sphingomonas sp. were found to be dominant specifically on leaves, while grapes were mainly associated with Pseudomonas viridiflava and Erwinia sp. (>15% relative abundance). Regarding fungal community, Hypocreales sp. and an unclassified OTU belonging to Ascomycota were found to be specific taxa of bunch and bark respectively, with 5.5 and 26.4% of relative abundance; Alternaria tenuissima and Sporobolomyces genus were common to leaf and bunch environments. Bark is the richest tissue in term of biodiversity due to the fact that it is not seasonally removed from the plant. Its specific bacterial community comprises unidentified members of Micrococcaceae and Chitinophagaceae, Pedobacter and Mycoplana, generally in low abundance. Finally, interannual climate variations were explored by comparing microorganisms that colonize grapes and bark in two consecutive years and a strong decrease in bacterial diversity was found in bunch, while bark microbiota was more stable.