Sciences pour L’Œnologie

Summary The rhizosphere differs from the bulk soil in a range of biochemical, chemical and physical processes that occur as a consequence of root growth, water and nutrient uptake, respiration and rhizodeposition. These processes also affect microbial ecology and plant physiology to a considerable extent. This review concentrates on two features of this unique environment: rhizosphere geometry and heterogeneity in both space and time. Although it is often depicted as a soil cylinder of a given radius around the root, drawing a boundary between the rhizosphere and bulk soil is an impossible task because rhizosphere processes result in gradients of different sizes. For instance, because of diffusional constraints, root uptake can result in a depletion zone extending <1 mm for phosphate to several centimetres for nitrate, while respiration may affect the bulk of the soil. Rhizosphere processes are responsible for spatial and temporal heterogeneities in the soil, although these are sometimes difficult to distinguish from intrinsic soil heterogeneity. A further complexity is that these processes are regulated by plants, microbial communities and soil constituents, and their many interactions. Novel in situ techniques and modelling will help in providing a holistic view of rhizosphere functioning, which is a prerequisite for its management and manipulation.

The authors propose a new classification for the genus Leishmania Ross, 1903 based both on the use of intrinsic and extrinsic characters and on Linnean and Adansonian methods. The type of vertebrate host makes it possible to recognize the genus group: Leishmania designates Kinetoplastida parasites of mammals. Neighbouring forms which parasite reptiles are now grouped in the genus Sauroleishmania Ranque, 1973. Characteristics of the intravectorial cycle (supra- and peri-pyloric) are used to define the subgenus group (Leishmania, Viannia Lainson and Shaw, 1987). The classification uses biochemical, particularly enzymatic, characters. Elementary taxonomic units are made up of all the strains having the same isoenzyme profile, i.e. the zymodeme. The grouping of the zymodemes is usually performed through automatic techniques which lead to bush-like trees (dendrograms) showing either simple affinities between units (phenograms) or their phyletic relationships (cladograms). The branches recognized as being stable are individualized as "zymodeme complexes". They bear the name of either the previously defined species taxa or that of a specially created one. Two examples of taxonomic constructions, phenetic and cladistic, are presented. Finally, a general classification of the genus is proposed.

Grape phenolics are structurally diverse, from simple molecules to oligomers and polymers that are usually designated “tannins,” referring to their ability to interact with proteins. Anthocyanin pigments and tannins are particularly important for red wine quality. Their extraction depends on their location in the berry and their solubility. All phenolic compounds are unstable and undergo numerous enzymatic and chemical reactions. Color and taste changes during red wine aging have been ascribed to anthocyanin-tannin reactions. The structures and properties of tannins and pigmented tannins from these reactions are often misunderstood. Current research on wine phenolic composition is reviewed, with emphasis on the following issues: (1) reactions of tannins yield both larger polymers and smaller species; (2) anthocyanin reactions can generate colorless species as well as polymeric and small various pigments; (3) some polymeric pigments undergo sulfite bleaching while some low molecular weight pigments do not; (4) polymers are both soluble and astringent, so the astringency loss during aging may involve cleavage rather than polymerization; and (5) sensory properties of anthocyanins and tannins are modulated by interactions with other wine components.

Abstract A range of structurally defined apple and grape proanthocyanidins was isolated in sufficient amount to carry out a formal sensory descriptive analysis study. Purified proanthocyanidin fractions differed in chain length, degree of galloylation and epigallocatechin content. Astringency attributes of the preparations in a model wine medium were rated while the fractions were held in the mouth and after expectoration. The degree of polymerization appeared to be the variable that discriminated among the fractions to the greatest extent. It affected both the overall astringency and the different individual astringency attributes, with increased ‘drying’, ‘chalky’, ‘adhesive’ and ‘pucker’ characters correlating with increasing chain length. A rougher sensation with increased ‘coarseness’, ‘drying’ and ‘chalkiness’ correlated with an increased degree of galloylation of the fractions. The presence of epigallocatechin units in the proanthocyanidin tended to lower the ‘coarse’ perception. Copyright © 2003 Society of Chemical Industry

Saccharomyces cerevisiae has been used for millennia in winemaking, but little is known about the selective forces acting on the wine yeast genome. We sequenced the complete genome of the diploid commercial wine yeast EC1118, resulting in an assembly of 31 scaffolds covering 97% of the S288c reference genome. The wine yeast differed strikingly from the other S. cerevisiae isolates in possessing 3 unique large regions, 2 of which were subtelomeric, the other being inserted within an EC1118 chromosome. These regions encompass 34 genes involved in key wine fermentation functions. Phylogeny and synteny analyses showed that 1 of these regions originated from a species closely related to the Saccharomyces genus, whereas the 2 other regions were of non-Saccharomyces origin. We identified Zygosaccharomyces bailii, a major contaminant of wine fermentations, as the donor species for 1 of these 2 regions. Although natural hybridization between Saccharomyces strains has been described, this report provides evidence that gene transfer may occur between Saccharomyces and non-Saccharomyces species. We show that the regions identified are frequent and differentially distributed among S. cerevisiae clades, being found almost exclusively in wine strains, suggesting acquisition through recent transfer events. Overall, these data show that the wine yeast genome is subject to constant remodeling through the contribution of exogenous genes. Our results suggest that these processes are favored by ecologic proximity and are involved in the molecular adaptation of wine yeasts to conditions of high sugar, low nitrogen, and high ethanol concentrations.

• Specific leaf area (leaf area to dry mass ratio), leaf dry matter content (leaf dry mass to saturated fresh mass ratio) and leaf nitrogen concentration (LNC) have been proposed as indicators of plant resource use in data bases of plant functional traits. • We tested whether species ranking based on these traits was repeatable by studying spatio-temporal variations in specific leaf area and leaf dry matter content of water-saturated leaves (SLASAT and LDMCSAT), as well as in LNC, for 57 herbaceous and woody species (or subsets thereof) growing under the Mediterranean climate of southern France. • Interseason and intersite variations were more pronounced than interannual variations, but species ranking for a given trait remained mostly consistent in space and time. Classifications based on LDMCSAT were generally more repeatable across years and sites, whereas those based on SLASAT were more stable over seasons. LNC usually gave the least repeatable classifications. • Species rankings were not completely similar for the three traits. Discussion of reproducibility, ease of trait measurement, as well as trait–function relationships led us to propose that measurements of the leaf traits, SLASAT and/or LDMCSAT, were the most suitable in large screening programmes.

DNA microarrays were used to investigate the expression profile of yeast genes in response to ethanol. Up to 3.1% of the genes encoded in the yeast genome were up-regulated by at least a factor of three after 30 min ethanol stress (7% v/v). Concomitantly, 3.2% of the genes were down-regulated by a factor of three. Of the genes up-regulated in response to ethanol 49.4% belong to the environmental stress response and 14.2% belong to the stress gene family. Our data show that in addition to the previously identified ethanol-induced genes, a very large number of genes involved in ionic homeostasis, heat protection, trehalose synthesis and antioxidant defence also respond to ethanol stress. It appears that a large number of the up-regulated genes are involved in energy metabolism. Thus, 'management' of the energy pool (especially ATP) seems to constitute an ethanol stress response and to involve different mechanisms.

The development of functional-structural plant models requires an increasing amount of computer modelling. All these models are developed by different teams in various contexts and with different goals. Efficient and flexible computational frameworks are required to augment the interaction between these models, their reusability, and the possibility to compare them on identical datasets. In this paper, we present an open-source platform, OpenAlea, that provides a user-friendly environment for modellers, and advanced deployment methods. OpenAlea allows researchers to build models using a visual programming interface and provides a set of tools and models dedicated to plant modelling. Models and algorithms are embedded in OpenAlea 'components' with well defined input and output interfaces that can be easily interconnected to form more complex models and define more macroscopic components. The system architecture is based on the use of a general purpose, high-level, object-oriented script language, Python, widely used in other scientific areas. We present a brief rationale that underlies the architectural design of this system and we illustrate the use of the platform to assemble several heterogeneous model components and to rapidly prototype a complex modelling scenario.

Because of the vast range of functions that phenylpropanoids possess, their synthesis requires precise spatiotemporal coordination throughout plant development and in response to the environment. The accumulation of these secondary metabolites is transcriptionally controlled by positive and negative regulators from the MYB and basic helix-loop-helix protein families. We characterized four grapevine (Vitis vinifera) R2R3-MYB proteins from the C2 repressor motif clade, all of which harbor the ethylene response factor-associated amphiphilic repression domain but differ in the presence of an additional TLLLFR repression motif found in the strong flavonoid repressor Arabidopsis (Arabidopsis thaliana) AtMYBL2. Constitutive expression of VvMYB4a and VvMYB4b in petunia (Petunia hybrida) repressed general phenylpropanoid biosynthetic genes and selectively reduced the amount of small-weight phenolic compounds. Conversely, transgenic petunia lines expressing VvMYBC2-L1 and VvMYBC2-L3 showed a severe reduction in petal anthocyanins and seed proanthocyanidins together with a higher pH of crude petal extracts. The distinct function of these regulators was further confirmed by transient expression in tobacco (Nicotiana benthamiana) leaves and grapevine plantlets. Finally, VvMYBC2-L3 was ectopically expressed in grapevine hairy roots, showing a reduction in proanthocyanidin content together with the down-regulation of structural and regulatory genes of the flavonoid pathway as revealed by a transcriptomic analysis. The physiological role of these repressors was inferred by combining the results of the functional analyses and their expression patterns in grapevine during development and in response to ultraviolet B radiation. Our results indicate that VvMYB4a and VvMYB4b may play a key role in negatively regulating the synthesis of small-weight phenolic compounds, whereas VvMYBC2-L1 and VvMYBC2-L3 may additionally fine tune flavonoid levels, balancing the inductive effects of transcriptional activators.

The transcriptome of a wine yeast was monitored throughout an alcoholic fermentation under conditions mimicking an enological environment. Major changes in gene expression occurred during fermentation, affecting more than 2000 genes, as the yeast adapted to changing nutritional, environmental and physiological conditions. The genes of many pathways are regulated in a highly coordinated manner, and genes involved in the key metabolic pathways of fermentation are strongly expressed. We showed that, during fermentation of a synthetic medium mimicking a natural must in which growth arrest was caused by nitrogen exhaustion, entry into the stationary phase triggered major transcriptional reprogramming. Many TOR target genes involved in nitrogen utilization or other functions are induced at this stage, suggesting that this signalling pathway plays a critical role in changes in gene expression in response to nitrogen depletion. Entry into stationary phase is a key physiological event and is followed by a general stress response. The superimposition of multiple stresses, including starvation and ethanol stress, gives rise to a unique stress response, involving hundreds of genes encoding proteins involved in various cellular processes, many of unknown function.

Accumulation of anthocyanins in the exocarp of red grapevine (Vitis vinifera) cultivars is one of several events that characterize the onset of grape berry ripening (véraison). Despite our thorough understanding of anthocyanin biosynthesis and regulation, little is known about the molecular aspects of their transport. The participation of ATP binding cassette (ABC) proteins in vacuolar anthocyanin transport has long been a matter of debate. Here, we present biochemical evidence that an ABC protein, ABCC1, localizes to the tonoplast and is involved in the transport of glucosylated anthocyanidins. ABCC1 is expressed in the exocarp throughout berry development and ripening, with a significant increase at véraison (i.e., the onset of ripening). Transport experiments using microsomes isolated from ABCC1-expressing yeast cells showed that ABCC1 transports malvidin 3-O-glucoside. The transport strictly depends on the presence of GSH, which is cotransported with the anthocyanins and is sensitive to inhibitors of ABC proteins. By exposing anthocyanin-producing grapevine root cultures to buthionine sulphoximine, which reduced GSH levels, a decrease in anthocyanin concentration is observed. In conclusion, we provide evidence that ABCC1 acts as an anthocyanin transporter that depends on GSH without the formation of an anthocyanin-GSH conjugate.

The reactivity of polyphenols is due to the position of the hydroxyl groups on their aromatic nuclei. Ortho-hydroxyl groups promote oxidation while meta-hydroxyl groups induce electrophilic aromatic substitution. Both hydroxylation patterns are encountered in flavonoid structures, on the B and A rings, respectively. In addition to oxidation and electrophilic aromatic substitution, flavonoids undergo nucleophilic addition on the central C ring when it is positively charged. Reactions of the A and C rings are pH-dependent. The A ring of flavonoids undergoes a polycondensation reaction mediated by an aldehyde. The products are anthocyanin and flavanol polymers and copolymers constituted of both. Flavanol polymers are not stable and rearrange into vinyl flavanols and xanthylium pigments. Vinyl flavanols can react with the positively charged C ring of anthocyanins, yielding pyranoanthocyanins, which can also be formed from components that have a reactive double bond, such as carbonyl and ethylene bonds. The positively charged C ring primarily undergoes direct reactions. Since the positive charge on the C ring of anthocyanins and flavanols is pH-dependent, their dehydration and interflavan bond cleavage reactions are also pHdependent. This leads to flavanol-anthocyanin (F-A + ) adducts at lower pH values and anthocyanin-flavanol (A + -F) adducts above pH 3.8. Temperature seems to favor formation of the latter.

Rats were fed a grape seed extract (GSE) containing (+)-catechin, (-)-epicatechin and dimers, trimers, tetramers and polymeric procyanidins. Liver, kidney, brain and gastrointestinal (GI) tract together with plasma, urine and faeces were collected over a 24 h period and their flavan-3-ol content was analysed by HPLC with tandem mass spectrometry and diode array detection. Small amounts of the GSE flavan-3-ols moved out of the stomach and into the duodenum/jejunum, and to a greater extent the ileum 1 h after ingestion, and into the caecum after 2 h with relatively small amounts being detected in the colon after 3 h. The GI tract contained the parent GSE flavan-3-ols and procyanidins with only trace amounts of metabolites and there were no indications that proanthocyanidins were depolymerised in the GI tract releasing monomeric flavan-3-ols. Plasma contained exclusively catechin glucuronides and methylated glucuronide metabolites which were also detected in the liver and kidneys. These metabolites were also present in urine together with sulphated metabolites and low amounts of the procyanidin dimers B1, B2, B3 and B4 as well as the trimer C2 and an unknown GSE trimer. The amounts of (+)-catechin and (-)-epicatechin metabolites excreted in urine relative to the quantity of the monomers ingested were 27 and 36 %, respectively, after 24 h. This is similar to the levels of urinary excretion reported to occur by other investigators after feeding (-)-epicatechin to rats and provides further, albeit indirect, evidence that the procyanidin oligomers in the GSE were not depolymerised to monomers to any extent after ingestion. No convincing analytical data were obtained for the presence of flavan-3-ol metabolites in the brain.

In cells, anthocyanin pigments are synthesized at the cytoplasmic surface of the endoplasmic reticulum, and are then transported and finally accumulated inside the vacuole. In Vitis vinifera (grapevine), two kinds of molecular actors are putatively associated with the vacuolar sequestration of anthocyanins: a glutathione-S-transferase (GST) and two MATE-type transporters, named anthoMATEs. However, the sequence of events by which anthocyanins are imported into the vacuole remains unclear. We used MYBA1 transformed hairy roots as a grapevine model tissue producing anthocyanins, and took advantage of the unique autofluorescence of anthocyanins to study their cellular trafficking. In these tissues, anthocyanins were not only visible in the largest vacuoles, but were also present at higher concentrations in several vesicles of different sizes. In the cell, small vesicles actively moved alongside the tonoplast, suggesting a vesicular trafficking to the vacuole. Subcellular localization assays revealed that anthoMATE transporters were closely related with these small vesicles, whereas GST was localized in the cytoplasm around the nucleus, suggesting an association with the endoplasmic reticulum. Furthermore, cells in hairy roots expressing anthoMATE antisense did not display small vesicles filled with anthocyanins, whereas in hairy roots expressing GST antisense, anthocyanins were accumulated in vesicles but not in the vacuole. This suggests that in grapevine, anthoMATE transporters and GST are involved in different anthocyanin transport mechanisms.

Saccharomyces cerevisiae is one of the most important model organisms and has been a valuable asset to human civilization. However, despite its extensive use in the last 9,000 y, the existence of a seasonal cycle outside human-made environments has not yet been described. We demonstrate the role of social wasps as vector and natural reservoir of S. cerevisiae during all seasons. We provide experimental evidence that queens of social wasps overwintering as adults (Vespa crabro and Polistes spp.) can harbor yeast cells from autumn to spring and transmit them to their progeny. This result is mirrored by field surveys of the genetic variability of natural strains of yeast. Microsatellites and sequences of a selected set of loci able to recapitulate the yeast strain's evolutionary history were used to compare 17 environmental wasp isolates with a collection of strains from grapes from the same region and more than 230 strains representing worldwide yeast variation. The wasp isolates fall into subclusters representing the overall ecological and industrial yeast diversity of their geographic origin. Our findings indicate that wasps are a key environmental niche for the evolution of natural S. cerevisiae populations, the dispersion of yeast cells in the environment, and the maintenance of their diversity. The close relatedness of several wasp isolates with grape and wine isolates reflects the crucial role of human activities on yeast population structure, through clonal expansion and selection of specific strains during the biotransformation of fermented foods, followed by dispersal mediated by insects and other animals.

Yeasts of the Saccharomyces sensu stricto species complex are able to convert sugar into ethanol and CO(2) via fermentation. They have been used for thousands years by mankind for fermenting food and beverages. In the Neolithic times, fermentations were probably initiated by naturally occurring yeasts, and it is unknown when humans started to consciously add selected yeast to make beer, wine or bread. Interestingly, such human activities gave rise to the creation of new species in the Saccharomyces sensu stricto complex by interspecies hybridization or polyploidization. Within the S. cerevisiae species, they have led to the differentiation of genetically distinct groups according to the food process origin. Although the evolutionary history of wine yeast populations has been well described, the histories of other domesticated yeasts need further investigation.

The treatment of grape berries ( Vitis vinifera L. cv. Cabernet Sauvignon) with the ethylene‐releasing compound, 2‐chloroethylphosphonic acid (2‐CEPA), at veraison is a method known to enhance grape skin colour. We observed that it produced a 6‐fold increase, up to 30 pmol g −1 FW, of the cluster internal ethylene compared to untreated controls within the 24 h following treatment. This ethylene upsurge was associated with increased levels of chalcone synthase ( CHS ) and flavanone 3‐hydroxylase ( F3H ) transcripts, which persisted over the following 20 days. Transcript levels of leucoanthocyanidin dioxygenase ( LDOX ) and UDP glucose‐flavonoid 3‐ O ‐glucosyl transferase ( UFGT ) were similarly enhanced by 2‐CEPA, although to a lesser extent. The effect on UFGT was confirmed at the protein level by an immunoblot analysis. The transcript accumulation of dihydroflavonol 4‐reductase ( DFR ) was unaffected by 2‐CEPA treatment. Examination of the levels of CHS , F3H and UFGT mRNAs in berries during bunch exposure to ethylene, revealed elevated levels of each transcript within the first 6 h of treatment when compared to nonethylene‐treated controls. HPLC analyses of berry skin extracts showed that levels of each of the anthocyanins analysed (delphinidin, cyanidin, petunidin, peonidin and malvidin) increased over the 10 days following the ethylene burst, and decreased thereafter. However, anthocyanin levels at harvest were still higher in ethylene treated grapes than in controls. This data is the first evidence that ethylene triggers gene expression related to anthocyanin synthesis in grapes, and in addition, our results also confirm the existence of other regulatory modes in the anthocyanin biosynthetic pathway.

Quantitative and qualitative modifications of tannins and anthocyanins in grape skin were investigated at different dates of harvest, from berries sorted on the basis of their density. Free anthocyanins accumulated until 170 g/L of sugars in pulp before undergoing a slight decrease. Changes in anthocyanin composition were observed with increasing sugar levels in the pulp that reflected structural differences between classes of anthocyanins. The proportion of methoxylated anthocyanins continued to increase in the skin as sugar accumulated while the proportion of coumaroylated anthocyanins initially increased (up to 200 g/L of sugars in the pulp) and then rapidly decreased. In comparison, no major quantitative nor qualitative change was observed for tannins, except for a slight increase of the mean degree of polymerization. Whatever the physiological stage of the pulp, the extraction yield of skin phenolics into hydroalcoholic solution for 5 h was lower than 77% for anthocyanins and 38% for proanthocyanidins. For both classes of compounds, no clear evolution in these extraction yields could be observed as sugars accumulated in pulp (from 162.6 to 275.0 g/L). Nevertheless, some structural features within each family of compounds significantly influenced extractability, for example, a lower extraction yield for coumaroylated anthocyanins and for tannins with a high degree of polymerization. Finally, no direct relationship could be found in extraction media between the amounts of all red pigments (measured in acidic conditions) and the color intensity at 520 nm (measured in wine-like model solutions).

In order to more precisely describe the kinetics of alcoholic fermentation and to show its considerable variability according to the musts, a study using an automatic device for monitoring fermentation was carried out; 45 musts were tested under isothermal standard conditions. The on-line measurement of the fermentation rate appeared to be particularly worthwhile because: <i>(1)</i> its maximum value, obtained early during the fermentation process, was well correlated with the fermentability of the musts; and <i>(2)</i> the trend of the rate curve was independent of temperature and was characteristic of the pair must-yeast strain.

BACKGROUND: Fruit composition at harvest is strongly dependent on the temperature during the grapevine developmental cycle. This raises serious concerns regarding the sustainability of viticulture and the socio-economic repercussions of global warming for many regions where the most heat-tolerant varieties are already cultivated. Despite recent progress, the direct and indirect effects of temperature on fruit development are far from being understood. Experimental limitations such as fluctuating environmental conditions, intra-cluster heterogeneity and the annual reproductive cycle introduce unquantifiable biases for gene expression and physiological studies with grapevine. In the present study, DRCF grapevine mutants (microvine) were grown under several temperature regimes in duly-controlled environmental conditions. A singly berry selection increased the accuracy of fruit phenotyping and subsequent gene expression analyses. The physiological and transcriptomic responses of five key stages sampled simultaneously at day and nighttime were studied by RNA-seq analysis. RESULTS: A total of 674 millions reads were sequenced from all experiments. Analysis of differential expression yielded in a total of 10 788 transcripts modulated by temperature. An acceleration of green berry development under higher temperature was correlated with the induction of several candidate genes linked to cell expansion. High temperatures impaired tannin synthesis and degree of galloylation at the transcriptomic levels. The timing of malate breakdown was delayed to mid-ripening in transgressively cool conditions, revealing unsuspected plasticity of berry primary metabolism. Specific ATPases and malate transporters displayed development and temperature-dependent expression patterns, besides less marked but significant regulation of other genes in the malate pathway. CONCLUSION: The present study represents, to our knowledge the first abiotic stress study performed on a fleshy fruits model using RNA-seq for transcriptomic analysis. It confirms that a careful stage selection and a rigorous control of environmental conditions are needed to address the long-term plasticity of berry development with respect to temperature. Original results revealed temperature-dependent regulation of key metabolic processes in the elaboration of berry composition. Malate breakdown no longer appears as an integral part of the veraison program, but as possibly triggered by an imbalance in cytoplasmic sugar, when efficient vacuolar storage is set on with ripening, in usual temperature conditions. Furthermore, variations in heat shock responsive genes that will be very valuable for further research on temperature adaptation of plants have been evidenced.