OENO IVAS 2019 banner
IVES 9 IVES Conference Series 9 OENO IVAS 9 OENO IVAS 2019 9 Grape and wine microorganisms: diversity and adaptation 9 Application of high-throughput sequencing tools for characterisation of microbial communities during alcoholic fermentation

Application of high-throughput sequencing tools for characterisation of microbial communities during alcoholic fermentation

Abstract

Developments in high-throughput sequencing (HTS) technologies allow us to obtain large amounts of microbial information from wine and must samples. Thus approaches, that are aimed at characterising the microbial diversity during fermentation, can be enhanced, or possibly even replaced, with HTS-based metabarcoding. To reduce experimental biases and increase data reproducibility, we compared 3 DNA extraction methods by evaluating differences in the fungal diversity with Riesling alcoholic fermentation samples at four different vineyards. The fungal diversity profiling was done using the genetic markers ITS2 and D2 using metabarcoding. The extraction methods compared consisted of a commercial kit, a recently published protocol that includes a DNA enhancer, and a protocol based on a buffer containing common inhibitor removal reagents. All methods were able to distinguish vineyard effects on the fungal diversity, but the results differed quantitatively. 

From the results of extraction methods, we applied the chosen methods and further combined the HTS tools of metabarcoding and metagenomics, to characterise how microbial communities of those samples, and their subsequent spontaneously fermented derivatives, vary. We specifically explored microbial community variation related to vineyard level, and during alcoholic fermentation. The vineyard was shown to be strongly influencing the microbial communities. Functional analyses were additionally included to investigate the microbial interactions. An increase in non-Saccharomycetaceae fungal functions and a decrease in bacterial functions were also observed during the early fermentation stage. Overall, our results highlight the importance of standardizing DNA extraction methods when characterising fungal diversity from wine and related samples, and showcase how metagenomic functional analysis offer possibilities to improve our insights into the wine alcoholic fermentation process, including highlighting microbe interactions.

DOI:

Publication date: June 23, 2020

Issue: OENO IVAS 2019

Type: Article

Authors

Sarah Siu Tze Mak, Kimmo Sirén, Christian Carøe, Ulrich Fischer, M. Thomas P. Gilbert 

Section for Evolutionary Genomics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark 
Institute for Viticulture and Oenology, Dienstleistungszentrum Ländlicher Raum Rheinpfalz, Neustadt an der Weinstraße, Germany 

Contact the author

"> 

Keywords

Riesling, Metabarcoding, Metagenomics, DNA extraction

Tags

IVES Conference Series | OENO IVAS 2019

Citation

Related articles…

Seasonal dynamics of water and sugar compartmentalization in grape clusters under deficit irrigation

Water stress triggers functional compartmentalization in grapevines, influencing how resources are allocated to different plant organs.
Read More

Impact of canopy management on thiol precursors in white grapes: a six-year field study

The mechanisms behind thiol precursor accumulation in grapes remain incompletely understood, nor are the ways in which they can be improved by agronomic practices. A six-year field trial studied the physiological response of the Swiss white cultivar Vitis vinifera Arvine, rich in varietal thiols and precursors, to canopy management, i.e. leaf removal and canopy height.. Five treatments were set up in a randomized block design to assess the impacts of 1) pre-flowering LR (i.e. pre-flowering or full-flowering stages) and 2) compensating for the leaf area removed in the cluster zone by increasing the trimming height (i.e. 100 or 150 cm canopy height), compared with a non-defoliated control treatment.
Intensive pre-flowering LR severely reduced yield potential (–47% on average) and reduced the concentration of 3-mercaptohexanol precursors (P-3MH) in the must (–21%; p-value < 0.10).

Read More

The role of rootstock and its genetic background in plant mineral status

In this video recording of the IVES science meeting 2025, Marine Morel (EGFV, Univ. Bordeaux, Bordeaux Sciences Agro, INRAE, ISVV, Villenave-d’Ornon, France) speaks about the role of rootstock and its genetic background in plant mineral status. This presentation is based on an original article accessible for free on OENO One.

Read More

Fertilization Lysimeters provide new insights into the needs and impacts of N nutrition on table grape performance and fruit yield and quality

Table grape production requires adequate nitrogen (N) supply to sustain vine performance and obtain high yields. However, excess agricultural N fertilization is a major source of groundwater contamination and air pollution. Therefore, there is a strong need for empirically based precision N fertilization schemes in vineyards, for optimizing grape yield and quality while minimizing their environmental impact.
Our aim was to unequivocally quantify table grape N requirements, elucidate the drivers of daily N uptake, and quantify the relationship between fertigation N levels and vine growth, fruit yield, composition, and quality. For this, forty ‘Early Sweet’ (early-maturing, white) and ‘Crimson seedless’ (late-maturing, red) vines were grown in 500L drainage-lysimeters for 2 fruiting seasons, while subjected to five continuous N fertigation treatments ranging from 10 to 200 ppm.

Read More

Agroclimatic characterisation of the Portugese wine denominations of origin using a compound index

Aims: This study aims to: (1) characterize the agroclimatic conditions of the Portuguese Denominations of Origin, using a compound index that combines thermal and soil water balance conditions and a high-resolution climatic dataset (~1 km spatial resolution); (2) categorize the main grapevine varieties as a function of this compound index.

Read More