Grape microbiome as a reliable and persistent signature of field origin and environmental conditions in Cannonau wine production

PLoS One. 2017 Sep 11;12(9):e0184615. doi: 10.1371/journal.pone.0184615. eCollection 2017.

Abstract

Grape berries harbor a wide range of microbes originating from the vineyard environment, many of which are recognized for their role in the must fermentation process shaping wine quality. To better clarify the contribution of the microbiome of grape fruits during wine fermentation, we used high-throughput sequencing to identify bacterial and fungi communities associated with berries and musts of Cannonau. This is the most important cultivar-wine of Sardinia (Italy) where most vineyards are cultivated without phytochemical treatments. Results suggested that microbiomes of berries collected at four different localities share a core composition characterized by Enterobacteriales, Pseudomonadales, Bacillales, and Rhodospirillales. However, any area seems to enrich berries microbiome with peculiar microbial traits. For example, berries belonging to the biodynamic vineyards of Mamoiada were rich in Bacillales typical of manure (i.e. Lysinibacillus, Bacillus, and Sporosarcina), whereas in the Santadi locality, berries showed soil bacteria such as Pasteurellales and Bacteroidales as well as Rhodospirillales and Lactobacillales which are commonly involved in wine fermentation. In the case of fungi, the most abundant taxa were Dothioraceae, Pleosporaceae, and Saccharomycodaceae, and although the proportion of these families varied among localities, they occurred ubiquitously in all vineyards. During vinification processes performed at the same wine cellar under controlled conditions and without using any yeast starter, more than 50% of bacteria groups of berries reached musts, and each locality had its own private bacteria signature, even if Saccharomyces cerevisiae represented the most abundant fungal species. This work suggests that natural berries microbiome could be influenced by pedoclimatic and anthropologic conditions (e.g., farming management), and the fruits' microorganisms persist during the fermentation process. For these reasons, a reliable wine genotyping should include the entire holobiont (plant and all its symbionts), and bioprospecting activities on grape microbiota could lead to improved viticulture yields and wine quality.

MeSH terms

  • Agriculture
  • Bacteria / classification
  • Bacteria / genetics
  • Biodiversity
  • Cluster Analysis
  • DNA Barcoding, Taxonomic
  • Environment*
  • Fungi / classification
  • Fungi / genetics
  • Geography
  • Metagenome
  • Metagenomics / methods
  • Microbiota*
  • Vitis / microbiology*
  • Wine*

Grants and funding

This work was supported by SardegnaRicerche (www.sardegnaricerche.it) in the framework of the project AKINAS (CUP B81H11001320002). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript. FEM2-Ambiente s.r.l. provided support in the form of a salary for author Valerio Mezzasalma but did not play a role in the study design, data collection and analysis, decision to publish, or preparation of the manuscript and only provided financial support in the form of research materials. The specific roles of this author is articulated in the ‘author contributions’ section.