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…

Evaluating South African Chenin blanc wine styles using an LC-MS screening method

Sorting Chenin blanc is one of the most important white wine cultivars in South Africa. It has received a lot of attention and accolades in the past years and more research than ever is dedicated to this versatile cultivar. According to the Chenin blanc association of South Africa, there are three recognized dry wine styles, Fresh and Fruity (FF), Rich and Ripe Unwooded
(RRU), and Rich and Ripe Wooded (RRW). They are traditionally established with the aid of expert sensory evaluation, but the cost and the (subjective) human factor are aspects to be taken into account. A more objective and possibly robust way of assessing and attributing these styles can be the use of chemical analysis.

Wood from barrique: release of phenolic compounds and permeability to oxygen

Chemical and sensory changes occurring in red wine during ageing in oak barrique are due to the slow and gradual entrance of oxygen along with a release of ellagic tannin from the wood. Though oxygen can enter the cask through the bunghole, it is not clear the role of permeation through the wood staves as well as the amount of oxygen entering by permeation. The distribution of the released ellagic tannins in the wine ageing is also unknown. The oxygen passing through the bunghole may have a different wine ageing effect compared to the oxygen permeating through the wooden staves owing to the uneven ellagic tannin concentration throughout the wine.

Influence of methyl jasmonate foliar application to vineyard on grape volatile composition over three consecutive vintages

An alternative to improve grape quality is the application to the vineyard of elicitors. Although these compounds were first used to increase resistance of plants against pathogens, it has been found that they are also able to induce mechanisms involved in the synthesis of phenolic compounds and some amino acids. However, researches about the influence of elicitors on grape volatile composition are scarcely. Therefore, the aim of this work was to study the influence of methyl jasmonate (MeJ) foliar application on grape aroma composition over three consecutive vintages. MeJ was applied to Tempranillo grapevines at a concentration of 10 mM in 2013, 2014, and 2015 years. Control plants were sprayed with water.

Measurements of the oxygen dissolved in white wines elaborated in barrels without to open the bung of the barrels

Bases on oxoluminescence, we have developed an innovative device for measuring dissolved oxygen in wines in barrels without opening the bung. This system is directly inserted into the wood during the barrel elaboration and can be positioned at different locations of the barrel (the head, the hull …). During two successive vintages we have used this device notably to follow the oxygen dissolved of whites wines elaborated in barrels. This allowed us initially to monitor the oxygen levels of the harvest to bottling the whole elaboration process in barrels of white wines without using techniques of measurement suitable to modify the real values in wines (opening the bung to plunge an oximeter).

Fractionation of copper and iron in wine: Assessment of potential macromolecule and sulfur binding agents

Copper and iron are known to substantially impact wine stability through oxidative, reductive or colloidal phenomena. However, the binding of metal ions to different wine components under wine conditions, and the impact of this binding on the ability of the metal ions to induce spoilage processes, is not well understood. This study surveyed a range of red and white wines for an understanding of the variability of broad metal categories within the wines. The techniques utilized included an electrochemical constant current stripping potentiometry technique (ccSP), and solid phase extraction (SPE) fractionation of wine with subsequent analysis of the metal content of each fraction by inductively coupled plasma – optical emission spectroscopy (ICP-OES).