Macrowine 2021
IVES 9 IVES Conference Series 9 Capture depletion of grapevine DNA: an approach to advance the study of microbial community in wine

Capture depletion of grapevine DNA: an approach to advance the study of microbial community in wine

Abstract

The use of next-generation sequencing (NGS) has helped understand microbial genetics in oenology. Current studies mainly focus on barcoded amplicon NGS but not shotgun sequencing, which is useful for functional analyses. Since the high percentage of grapevine DNA conceals the microbial DNA in must, the majority of sequencing data is wasted in bioinformatic analyses. Here we present capture depletion of grapevine whole genome DNA. By using biotinylated RNA baits made from genomic grapevine libraries, the grapevine DNA is hybridized to the baits and captured by magnetic beads while the targeted microbial DNA is left and subsequently sequenced. A pilot study was carried out to mimic degraded complex materials. Using known complex microbial samples and spiking in large portion of grapevine DNA, the hybridization and depletion took place with quantification by qPCR. Different parameters, such as hybridization hours, temperatures and bait amounts were also tested for potential effects. The aim is to provide an insight into depletion of undesired grapevine DNA and to enhance the data yield in NGS studies of microbial DNA with a more cost effective way suitable for future oenological studies.

Publication date: May 17, 2024

Issue: Macrowine 2016

Type: Poster

Authors

Sarah S.T. Mak*, Anders Hansen, Christian Carøe, Jacob Enk, Jean-Marie Rouillard, M Thomas P Gilbert

*Centre for GeoGenetics

Contact the author

Tags

IVES Conference Series | Macrowine | Macrowine 2016

Citation

Related articles…

The moment of preharvest elicitor application influence its final effect on winegrapes quality

Phenolic compounds are secondary metabolites of grapes. Plants produce a wide variety of this type of metabolites through diverse biosynthesis pathways and their production is sometimes a response to external stimuli, either environmental or biotic stresses. Some of them may act as chemical defenses against pathogens or herbivores and their synthesis is increased when the attack exists. However, it is remarkable that the synthesis of these interesting compounds can be activated even when the stimulus is not present, with the use of elicitors. These are substances that when applied exogenously trigger the biosynthetic pathways conducting to the synthesis of these defense compounds.

Attractiveness and sweetness of red wines: Synergies between American oak barrels and mannoproteins

In partnership with a Bordeaux property wanting to improve the quality of its second wine, the effects of two factors, American oak barrels and mannoproteins were studied. Their impact on the attractiveness and sweetness of wines were characterized during two successive vintages (2012 and 2013). Vinification took place with a homogeneous batch of Cabernet Sauvignon. The wine was then divided up into various groups of five barrels of French and American oak, new or reused. Analyses of volatile and non-volatile wood compounds were undertaken at four months and eight months of wood ageing, by LC-MS and GC-MS.

Correlations between N,S,O-heterocycle levels and age of Champagne base wines

Champagne regulation allows winegrowers to stock small amounts of still wines in order to compensate vintages’ quality shifts mainly due to climate variations. According to their technical requirements and house style some Champagne producers (commonly named “Champagne houses”) use these stored wines in the blend in order to introduce an element of complexity. These wines possess the particularity of being aged on fine lees in thermo-regulated stainless steel tanks. The Champagne house of Veuve Clicquot Ponsardin has several wines stored this way.

Effect of malolactic fermentation in barrels or stainless steel tanks on wine composition. Influence of the barrel toasting

Ellagitannin, anthocyanin and woody volatile composition of Cabernet Sauvignon wines aged in oak barrels for 12 months was evaluated. Depending on the container where malolactic fermentation (MLF) was carried out, two wine modalities were investigated: wines with MLF carried out in stainless steel tanks and barrel-fermented wines. Three toasting methods (medium toast, MT; medium toast with watering, MTAA; noisette) were considered for ageing of each wine modality. Sensory analyses (triangle and rating tests) were also performed. Two-way ANOVA of the raw experimental data revealed that the toasting method and the container where MLF took place, as well as the interaction between both factors, have a significant influence (p < 0.05) on ellagitannin, anthocyanin and woody volatile profiles of Cabernet Sauvignon wines.

How pressing techniques affect must composition and wine quality of Pinot blanc

This study investigates how the sensory profile of Pinot Blanc is affected from different maceration and pressing techniques. Grapes were sourced from four vineyards in the village Tramin in South Tyrol. For the experiment 200 kg of grapes from each vineyard site were hand picked the day before harvest for the commercial winery took place. Grapes were stored over night at 4°C, homogenized and processed in the experimental winery at Laimburg research centre the day after harvest. Four different pressing techniques were applied in duplicates of 100kg each.