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…

Modulating role of SO2 in white wine protein haze formation

Despite the extensive research performed during the last decades, the multifactorial mechanism responsible for the white wine protein haze formation is not fully characterized. Herein, a new model is proposed, which is based on the experimental identification of sulfur dioxide as a major modulating factor inducing wine protein haze upon heating. As opposed to other reducing agents, such as 2-mercaptoethanol, dithiothreitol and tris(2-carboxyethyl)phosphine hydrochloride (TCEP), the addition of SO2 to must/wine upon heating cleaves intraprotein disulfide bonds, hinders thiol-disulfide exchange during protein interactions and can lead to the formation of novel inter/intraprotein disulfide bonds. Those are eventually responsible for wine protein aggregation which follows a nucleation-growth kinetic model as shown by dynamic light scattering [1].

Comprehensive exploration of wine aroma-related compounds as promoted by alternative vinification procedures in case of Zelen (Vitis vinifera L.) grapes processing

Not only vintner’s decisions in the vineyard, but also winemaker’s choices of technology approaches in the cellar play a significant role in the final wine style and quality. Whereas traditional technologies within chosen terroir are quite well explored and thus somehow predictable, there is no proper knowledge available on possible outcomes in case of implementing novel, alternative winemaking strategies. To reveal their effects on wine aroma compounds and sensory characteristics, two alternative strategies
(cryoextraction or addition of whole grape berries during last stages of fermentation) were compared to classical Vipava valley winemaking approach as normally used for an autochthonous variety Zelen. After separate vinification and bottling, all the experimental wines were subjected to semiquantitative metabolic profiling of volatile compounds (VOCs) by means of GC/MS and were then also sensorialy evaluated by pre-trained panel.

Comparison of fortified, sfursat and passito winemaking techniques for the enhancement of the oenological potential of the black grape cultivar Moscato nero d’Acqui (Vitis vinifera L.)

One of the key factors of the economical development of viticulture and wine industry in specific limited areas is the exploitation of ancient, local grape varieties. Therefore, in recent years the growing interest to rediscover minor varieties, previously cultivated, has promoted many studies. With this regard, the focus of this study was the Vitis vinifera L. cultivar Moscato nero d’Acqui, nowadays found only in old vineyards in the Acqui zone (North-West Italy). In particular, the aims of this work were: i) to investigate secondary metabolites profile of the grapes, and ii) to evaluate the attitude to the production of special wines.

Update knowledge about the presence of condensed tannins in grapes and their contributions to astringency perception

Condensed tannin is a principle group of polyphenol compounds derived from grape, greatly contributing to the bioactivity and the sensory perception of wine. Condensed tannins present as a heterogeneous mixture in nature involving various degrees of both polymerization and galloylation. Even though multiple attempts focusing on fractionation of grape condensed tannins by solid-phase have been conducted over the past decades, few individual tannins have been purified and identified. Hence, our knowledge on grape and wine condensed tannin moleculars has to be limited at the several known monomeric, dimeric and trimeric proanthocyanidins

Field-grown Sauvignon Blanc berries react to increased exposure by controlling antioxidant homeostasis and displaying UV acclimation responses that are influenced by the level of ambient light

Leaf removal in the bunch zone is a common viticultural practice with several objectives, yet it has been difficult to conclusively link the physiological mechanism(s) and metabolic berry impact to this widely practiced treatment. We used a field-omics approach1 in a Sauvignon blanc high altitude model vineyard, showing that the early leaf removal in the bunch zone caused quantifiable and stable responses (over years) in the microclimate where the main perturbation was increased exposure. We provide an explanation for how leaf removal leads to the shifts in grape metabolites typically linked to this treatment and confirm anecdotal evidence and previous reports that leaf removal treatment at an early stage of berry development affects “quality-associated” metabolites (monoterpenes and norisoprenoids).