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…

Ageing of sweet wines: oxygen evolution according to bung and barrel type

Barrel ageing is a crucial step in the wine process because it allows many changes to the wine as enrichment, colour stabilization, clarification and also a slow oxygenation. Effects of the oak barrel have to be known to prevent oxidation of the wine. The type of bung used during ageing is also a parameter to consider. Ageing sweet wines in barrel is a real challenge. These wines may need some oxygen at the beginning of ageing but they should be protected at the end of their maturation, to avoid oxidation.

The use of cation exchange resins for wine acidity adjustment: Optimization of the process and the effects on tartrate formation and oxidative stability

Acidity adjustments are key to microbial control, sensory quality and wine longevity. Acidification with cation exchange resins -in acid cycle- offers the possibility to reduce the pH by exchanging wine cations, such as potassium (K+), for hydrogen ions (H+). During the exchange process, the removal of potassium and calcium ions contributes to limiting the formation of tartrate salts, thus offering an alternative solution to conventional methods for tartrate stability. Moreover, the reduction of wine pH and the removal of metals catalyzers (e.g. iron) could positively impact the wine’s oxidative stability. Therefore, the aims of this work were (a) to optimize the ion exchange process by testing different volumes and concentrations of sulfuric acid (H2SO4) during the acid cycle, (b) evaluate the effects of the ion exchange process on the formation of tartrate salts, and (c) analyze the oxidative stability of the treated wines.

Simultaneous monitoring of dissolved CO2 and collar from Rosé sparkling wine glasses: the impact of yeast macromolecules

Champagne or sparkling wines elaborated through the same traditional method, which consists in two major yeast-fermented steps, typically hold about 10 to 12 g/L of dissolved CO2 after the second fermentation in a closed bottle. Hundreds of molecules and macromolecules originating from grape and yeast cohabit with dissolved CO2; they are essential compounds contributing to many organoleptic characteristics (effervescence, foam, aroma, taste, colour…). Indeed, the second alcoholic fermentation and the maturation on lees (which may last from 12 months up to several years) both induce various quantitative and qualitative changes in the wine through the action of yeast, as listed hereafter: development of aromas during aging on lees, release of nitrogen compounds during autolysis and release of macromolecules (polysaccharides, lipids, nucleic acids) in wine.

Prediction of the production kinetics of the main fermentative aromas in alcoholic fermentation

Fermentative aromas (especially esters and higher alcohols) highly impact the organoleptic profile of young and white wines. The production of these volatile compounds depends mainly on temperature and Yeast Available Nitrogen (YAN) content in the must. Available dynamic models predict the main reaction
(bioconversion of sugar into ethanol and CO2 production) but none of them considers the production kinetics of fermentative aroma compounds during the process of fermentation. We determined the production kinetics of the main esters and higher alcohols for different values of initial YAN content and temperature, using an innovative online monitoring Gas Chromatography device.

Impact of smoke exposure on the chemical composition of grapes

Vineyard exposure to smoke can lead to grapes and wine which exhibit objectionable smoky and ashy aromas and flavours, more commonly known as ‘smoke taint’ [1, 2]. In the last decade, significant bushfires have occurred around the world, including near wine regions in Australia, Canada, South Africa and the USA, as a consequence of the warmer, drier conditions associated with climate change. Considerable research has subsequently been undertaken to determine the chemical, sensory and physiological consequences of grapevine exposure to smoke. The sensory attributes associated with smoke-tainted wine have been linked to the presence of several smoke-derived volatile phenols, such as guaiacols, syringols and cresols [2].