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…

Evidence for terroir effect associated with botrytisation relatively to compounds implicated in typical aromas of noble rot sweet wines

Recent studies have demonstrated the role of certain lactones, particularly 2-nonen-4-olide, and volatile thiols (3-sulfanylhexan-1-ol) in the over ripped aromas of noble rot sweet wines (Stamatopoulos et al. 2014ab). These compounds are partly formed during the maturation and under the activity of B. cinerea on grapes. This research was carried out in the vineyard of Sauternes with aim to better understand their genesis depending on the grape over-ripening on two different soil types during 3 vintages. Thus, the study was conducted, with the Sémillon grape, during vintages 2012, 2014 & 2015, at 4 stages of over-maturation of the grapes (healthy, pourri plein, pourri roti, pourri roti + 15 days) considering two vineyard plots with different soil characteristics (calcosol & peyrosol) planted with the 315 Sémillon clone and grafted on 101-14 rootstock respectively in 1981 and 1980 and cultivated with the same vineyard management. Volatile lactones were assayed by liquid-liquid extraction followed by GC/MS analysis and the precursors of 3-sulfanylhexanol by an adaptation of the method by Capone et al. 2010 (SPE-
UPLC/FTMS).

Quantification of the production of hydrogen peroxide H2O2 during wine oxidation

Chemical studies aiming at assessing how a wine reacts towards oxidation usually focus on the characterization of wine constituents, such as polyphenols, or oxidation products. As an alternative, the key oxidation intermediate hydrogen peroxide H2O2 has never been quantified, although it plays a pivotal role in wine oxidation. H2O2 is obtained from molecular oxygen as the result of a first cascade of oxidation reactions involving metal ions and polyphenols. The produced H2O2 then reacts in a second cascade of oxidation to produce reactive hydroxyl radicals that can attack almost any chemical substrate in wine.

Testing the effectiveness of Cell-Wall material from grape pomace as fining agent for red wines

Lately several works highlighted the capacity of grape cell-wall material (CWM) to interact with proanthocyanidins (PA), indicating its potential use as fining agent for red wines.1–4 However, those studies were performed by using purified PAs and very high doses of CWM (almost ten-fold higher than those used in wine industry for other commercial fining agents). The present study focuses on the applicability of CWM from Cabernet sauvignon pomace as fining agent for red wines under real winery conditions. Grapes of cultivar Cabernet sauvignon were harvested at three different maturity levels
(unripe, mature, and overripe) and used for red winemaking. The pomace of such vinifications were used as source of CWM, and applied into red wines at two different concentrations: 0.2 g/L and 2.5 g/L.

DNA and type of grain: which factor does better explain sensory differences of sessile and pedunculate oaks?

Sessile oak and pedunculate oak have shown several differences of interest for enological purposes. Tannic and aromatic composition among sessile oak or pedonculate oak has been well studied. Sessile oak is generally more aromatic than pedunculated, while the later is more tannic. This scientific point of view is rarely applied to classify oak in cooperages. Most coopers use the type of grain to distinguish wide and thin grain.

Use of glutathione under different grape processing and winemaking conditions and its impact on the formation of sulfide off-flavors, colour, and sensory characteristics of Riesling, Sauvignon blanc, and Chardonnay

The use of glutathione (GSH) in winemaking has been legitimated recently, according to OIV resolutions OENO 445-2015 and OENO 446-2015 a maximum dose of 20 mg/L is now allowed to use in must and wine. Several studies have proven the benefits of GSH, predominantly in Sauvignon blanc. Thus, oxidative coloration of must and wine is limited, aroma compounds such as volatile thiols are preserved, and the development of ageing flavors such as sotolon and 2-aminoacetophenone is impeded. The protective effect may be explained by the high affinity of GSH to bind o-quinones which are formed during phenolic oxidation and which are known to initiate browning and other oxidative changes. Some researchers have proposed the hydroxycinnamic acid to GSH ratio (HGR) as an indicator of oxidation susceptibility of must and could show that lower ratios yielded lighter musts.