Selection of Botrytis cinerea and Saccharomyces cerevisiae strains for the improvement and valorization of Italian passito style wines

Comparative analysis of grape berry microbiota uncovers sour rot associates from a Maryland vineyard

Grape sour rot (GSR) is a disease complex involving fungi and bacteria that can cause significant yield losses of susceptible varieties. It is widely spread in the eastern U.S. and other grape-growing regions globally. Previous studies suggest that damaged fruit skin and feeding insects like Drosophila spp. are required for the disease to occur. Current control strategies for the management of sour rot are not sustainable, and research on the implications of chemical management of the disease on microbiome diversity is scarce. Our aim was to: i) investigate the effect of insecticide application and netting treatment on the microbiota of GSR-susceptible and tolerant grape varieties; and ii) identify the core microbial assemblages potentially associated with grape sour rot development in Maryland. Using a combined analysis of culture-dependent and independent data, we found that microbiota diversity of healthy grape berries did not change with netting, insecticide application, and between varieties. There was a significant difference in bacterial diversity between healthy and sour rot-affected berries. Komagataeibacter was consistently associated with infected berries followed by Acetobacter and Gluconobacter. This is the first study to report the association of Komagataeibacter with GSR-infected berries. It is thus imperative to investigate its role alongside that of other identified core microbiomes in sour rot development. Candida and Pichia were also consistent genera in infected berries. Several unidentified Candida, Pichia, and other fungal species from infected berries formed the core mycobiomes and it would be worth investigating their involvement in GSR development in Mid-Atlantic vineyards.

Specialized pollination by cecidomyiid flies and associated floral traits in Vincetoxicum sangyojarniae (Apocynaceae, Asclepiadoideae)

Specialized pollination systems frequently match a particular set of floral characteristics. Vincetoxicum spp. (Apocynaceae, Asclepiadoideae) have disk-shaped flowers with open access to rewards and reproductive organs. Flowers with these traits are usually associated with generalized pollination. However, the highly modified androecium and gynoecium that characterize asclepiads are thought to be associated with specialized pollinators. In V. sangyojarniae, we investigated floral biology, pollination, and the degree of pollinator specialization in two localities in Thailand. We examined floral traits that target legitimate pollinators. Flowers of V. sangyojarniae opened only at night, emitted floral scents containing mainly (E)-β-ocimene, 1-octen-3-ol, (E)-4,8-dimethyl-1,3,7-nonatriene (E-DMNT) and N-(3-methylbutyl)acetamide, and provided sucrose-dominated nectar openly to insect visitors. Assessment of pollinator effectiveness indicated that V. sangyojarniae is functionally specialized for pollination by cecidomyiid flies. Although various insects, particularly cockroaches, frequently visited flowers, they did not carry pollinaria. Our results suggest that V. sangyojarniae attracts its fly pollinators by emitting floral volatiles bearing olfactory notes associated with the presence of fungi or, less likely, of prey captured by predatory arthropods (food sources of its pollinators) but offers a nectar reward upon insect arrival. Hence, there is a mismatch between the advertisement and the actual reward. Our results also suggest that the size of floral parts constitutes a mechanical filter where reciprocal fit between flower and insect structures ensures that only suitable pollinators can extract the pollinaria, a prerequisite for successful pollination.

Survey of the yeast ecology of dehydrated grapes and strain selection for wine fermentation

In this study we investigated the yeast population present on partially dehydrated Nebbiolo grapes destined for 'Sforzato di Valtellina', with the aim to select indigenous starters suitable for the production of this wine. Yeasts were enumerated, isolated, and identified by molecular methods (5.8S-ITS-RFLP and D1/D2 domain sequencing). A genetic, physiological (ethanol and sulphur dioxide tolerance, potentially useful enzymatic activities, hydrogen sulphide production, adhesive properties, and killer activity) and oenological (laboratory pure micro-fermentations) characterization was also carried out. Based on relevant physiological features, seven non-Saccharomyces strains were chosen for laboratory-scale fermentations, either in pure or in mixed-culture (simultaneous and sequential inoculum) with a commercial Saccharomyces cerevisiae strain. Finally, the best couples and inoculation strategy were further tested in mixed fermentations in winery. In both laboratory and winery, microbiological and chemical analyses were conducted during fermentation. The most abundant species on grapes were Hanseniaspora uvarum (27.4 % of the isolates), followed by Metschnikowia spp. (21.0 %) and Starmerella bacillaris (12.9 %). Technological characterization highlighted several inter- and intra-species differences. The best oenological aptitude was highlighted for species Starm. bacillaris, Metschnikowia spp., Pichia kluyveri and Zygosaccharomyces bailli. The best fermentation performances in laboratory-scale fermentations were found for Starm. bacillaris and P. kluyveri, due to their ability to reduce ethanol (-0.34 % v/v) and enhance glycerol production (+0.46 g/L). This behavior was further confirmed in winery. Results of this study contribute to the knowledge of yeast communities associated with a specific environment, like those of Valtellina wine region.

Biodiversity and oenological attitude of Saccharomyces cerevisiae strains isolated in the Montalcino district: biodiversity of S. cerevisiae strains of Montalcino wines

The biodiversity of Saccharomyces cerevisiae was studied in the Montalcino area (Italy). Two wineries were involved in the study, which compared the genotypic and oenological characteristics of the S. cerevisiae strains isolated in spontaneous fermentations. After isolation yeasts were identified by 26S rRNA gene sequence analysis, and S. cerevisiae strains were characterized through interdelta sequence analysis (ISA). Oenological tests were performed in synthetic grape must by varying the magnitude of the main wine-imiting factors. The evolution of alcoholic fermentation was monitored by measuring sugar consumption and flow cytometry. The results revealed the prevalence of S. cerevisiae from the third day of fermentation and the presence of a wide range of S. cerevisiae strains having ISA profiles characteristic of each winery. From an oenological point of view, the features of such strains, in terms of resistance to wine-limiting factors, seemed to be linked to the main oenological variables applied in the production process of each winery. Extreme fermentation temperatures and copper residues are the variables that mostly depress the yeast population, in terms of fermentation rate and cell viability. Flow cytometry revealed the different impact of limiting factors on the viability of yeast by the quantification of the ratio between live/dead yeast cells of each strain, suggesting different mechanisms of inhibition, for instance stuck of cell growth or cell killing, in response to the different stress factors.

Characterization of Microbial Dynamics and Volatile Metabolome Changes During Fermentation of Chambourcin Hybrid Grapes From Two Pennsylvania Regions

Microbial diversity present on grapes in wineries, and throughout fermentation has been associated with important metabolites for final wine quality. Although microbiome-metabolome associations have been well characterized and could be used as indicators of wine quality, the impact of regionality on the microbiome and metabolome is not well known. Additionally, studies between microbiome and metabolome have been conducted on single species grape such as Vitis vinifera instead of other species and interspecific hybrids. Although the Pennsylvania wine industry is relatively young compared to California, the industry has been experiencing rapid growth over the past decade and is expected to continue to grow in the future. Pennsylvania's climate of cold winters and high levels of rainfall throughout the growing season favors cultivation of interspecific hybrid grapes such as Vitis ssp. Chambourcin, one of the most commonly grown hybrid varieties in the state. Chambourcin is a prime candidate for studying the impact of regionality on microbiome-metabolome interactions as interspecific hybrid varieties could shape the future of winemaking. Here, we identify for the first time the regional distribution of microbial communities and their interactions with volatile metabolome during fermentation (0-20 days) by integrating high throughput Illumina sequencing (16S and ITS) and headspace-solid phase microextraction-gas chromatography-mass spectrometry. Analyzing 88 samples from nine wineries in the Central and East Pennsylvania regions, we observed high microbial diversity during early stages of fermentation (1-4 days) where non-Saccharomyces yeasts such as Starmerella and Aureobasidium and non-Oenococcus bacteria, Sphingomonas, likely contribute to microbial terroir to the resulting wines. Furthermore, key differentiators between two regions in Pennsylvania, as identified by LEfSe analysis, include the fungal genera Cladosporium and Kazachstania and the bacterial genera Lactococcus and Microbacterium. Moreover, 29 volatile fermentation metabolites were discriminated significantly (variable importance in projection > 1) between the two regions as shown by Partial Least Squares-Discriminant Analysis. Finally, Spearman's correlation identified regional differences of microbial-metabolite associations throughout fermentation that could be used for targeted microbiome manipulation to improve wine quality and preserve regionality. In summary, these results demonstrate the microbial signatures during fermentation and differential microorganisms and metabolites further support impact of regionality on Chambourcin wines in Pennsylvania.

Sensorial and Volatile Analysis of Wines Made from Partially Dehydrated Grapes: An Ontario Case Study

Winemaking in cool climate viticultural areas can pose challenges due to difficulties in achieving optimal ripeness from climatic conditions that tend to vary vintage-to-vintage. To stabilize quality, the use of partially dehydrated grapes has been indicated as beneficial to the production of high-quality wine (“appassimento” style) despite climatic variation. Postharvest wine grape dehydration is a complex process that involves the concentration or formation of sugars, aromas, and flavours. One of the quality challenges facing appassimento style winemaking is elevated levels of undesirable oxidation compounds. The aim of this study was to characterize wines made from a local yeast isolate, Saccharomyces uvarum CN1, which demonstrates limited osmotolerance and may have application to this wine style, as it is a known lower producer of such compounds. Wines made with CN1 were compared to wines made with the accepted commercial standard, S. cerevisiae, EC1118. Fermentations (n = 24) were established at three target starting sugar concentrations from dehydrated Cabernet franc grapes (24.5, 26.0, and 27.5°Brix) and a control (21.5°Brix) and were assessed for volatile organic compound (VOC) composition via gas chromatography-mass spectrometry (GC-MS). Wines also underwent quantitative descriptive analysis to identify and quantify sensory attributes by a trained panel (n = 11). Results show that the wines fermented with the yeast isolate contain significant differences in the concentrations of VOCs in the wines. Sensorially, the wines differed in intensity for a number of attributes, including red fruit aroma, black fruit flavour, and length of finish both within Brix treatments and amongst yeast strains. The most important differentiating factor amongst these wines was the combination of yeast strain at the highest starting sugar concentration (27.5°Brix). These findings may assist winemakers by informing the yeast strain choice for optimizing appassimento style wine quality in cool climates.

Physico-Chemical Characteristics and Culturable Microbial Communities of Grape Berries Change Strongly during Noble Rot Development

Botrytis cinerea is a well-known pathogen of grapevine. However, under certain microclimatic conditions, Botrytis infection results in noble rot, an essential process in the production of the world-known Tokaji aszú wines in Hungary. We investigated the physico-chemical characteristics and culturable microorganisms associated with grape berries through several noble rot phases in the two main cultivars grown in Tokaj: Vitisvinifera cv. "Furmint" and "Hárslevelű". We measured physical and analytical parameters routinely tested in viticulture and analyzed the ITS rDNA sequence data of fungi isolated from the sampled berries. We observed significant differences in the physico-chemical parameters among the noble rot phases as well as sampling dates. The greatest variation in berry texture and microbial structure was observed in the initial phases, with variables converging as the noble rot progressed. By finding a bijection between the examined chemical properties and the factorial parameters (e.g., noble rot phase, collection time, cultivar), an appropriate sweet winemaking material can be designed. Fungal community differed significantly among cultivars, with higher number of species observed in Hárslevelű. Our results reveal that there is more to noble rot than only Botrytiscinerea and other microorganisms may play important roles in the aszú process.

Correlating Noble Rot Infection of Garganega Withered Grapes with Key Molecules and Odorants of Botrytized Passito Wine

Experimental passito wines with different percentages of naturally noble-rotten grapes of the Garganega variety were analyzed to evaluate key molecules and odorants related to the typical aroma and sensory profile of botrytized passito wine. Remarkable changes in the concentration of 1-octen-3-ol, 4-terpineol, benzaldehyde, N-(3-methylbutyl)acetamide, and sherry lactone 1 and 2 were observed between sound and noble-rotten wines. Wines were perceived to be different for floral, honey, figs, apricot, and caramel scents. By partial least square regression these descriptors were well correlated to samples. An important positive contribution of sherry lactones, N-(3-methylbutyl)acetamide, vanillin, benzaldehyde, and γ-butyrolactone to honey, apricot, and caramel was observed. It is conceivable that oxidative effects of Botrytis cinerea infection play an important role in the genesis of these chemical and sensory aroma markers. This study provides a predictive tool for winemakers that use natural grape withering to produce wines whose aroma profile is not standardized due to the seasonal variation of noble rot incidence.

Influence of microbial communities on the chemical and sensory features of Falanghina sweet passito wines

Natural (N) as well as starter inoculated (S, inoculated with Saccharomyces cerevisiae M3-5; CZS, Candida zemplinina T13, Zygosaccharomyces bailii NS113 and Saccharomyces cerevisiae M3-5) fermentations of Falanghina must from dehydrated grape were monitored. Culture dependent analyses and amplicon-based high-throughput sequencing targeting 18S rRNA and 16S rRNA genes were used to monitor the fungal and bacterial communities (8 sampling points during 65 days). The resulting wines were subject to both sensory evaluation and volatile organic compounds analysis. Fungal community of un-inoculated musts (N) at beginning of the fermentation was mainly represented by Aureobasidium, Cladosporium, Sclerotinia, while Candida, Debaryomyces, Hanseniaspora, Metschnikowia, Pichia, Saccharomyces and Zygosaccharomyces showed a very low occurrence. The dominance of Hanseniaspora vineae and/or Hanseniaspora uvarum was clear up to 29th days of fermentation. S. cerevisiae occurred in all the phases but become dominant only at the end of the process. The odour profiles as evaluate by Quantitative Descriptive Analysis (QDA) highlighted a significant impact of the fungal populations on the olfactory profiles of the wines. Raisins, dried fruits, Sherry and liqueur were stronger in both S and CZS, while N was mostly discriminated by solvent/chemical and floral features. Outcomes underpin the impact of microbiota on the chemical and odour traits of Falanghina passito wines.

Characterization of Saccharomyces bayanus CN1 for Fermenting Partially Dehydrated Grapes Grown in Cool Climate Winemaking Regions

This project aims to characterize and define an autochthonous yeast, Saccharomyces bayanus CN1, for wine production from partially dehydrated grapes. The yeast was identified via PCR and Basic Local Alignment Search Tool (BLAST) analysis as Saccharomyces bayanus, and then subsequently used in fermentations using partially dehydrated or control grapes. Wine grapes were dried to 28.0°Brix from the control grapes at a regular harvest of 23.0°Brix. Both the partially dehydrated and control grapes were then vinified with each of two yeast strains, S. bayanus CN1 and S. cerevisiae EC1118, which is a common yeast used for making wine from partially dehydrated grapes. Chemical analysis gas chromatography-flame ionization detector (GC-FID) and enzymatic) of wines at each starting sugar level showed that CN1 produced comparable ethanol levels to EC1118, while producing higher levels of glycerol, but lower levels of oxidative compounds (acetic acid, ethyl acetate, and acetaldehyde) compared to EC1118. Yeast choice impacted the wine hue; the degree of red pigment coloration and total red pigment concentration differed between yeasts. A sensory triangle test (n = 40) showed that wines made from different starting sugar concentrations and yeast strains both differed significantly. This newly identified S. bayanus strain appears to be well-suited for this style of wine production from partially dehydrated grapes by reducing the oxidative compounds in the wine, with potential commercial application for cool climate wine regions.

The Induction of Noble Rot (Botrytis cinerea) Infection during Postharvest Withering Changes the Metabolome of Grapevine Berries (Vitis vinifera L., cv. Garganega)

The natural or induced development of noble rot caused by the fungus Botrytis cinerea during the late stages of grapevine (Vitis vinifera L.) berry ripening is used in some traditional viticulture areas to produce high-quality wines such as Sauternes and Tokaji. In this research, we wanted to verify if by changing the environmental conditions during post-harvest withering we could induce the noble rot development on harvested berries in order to positively change the wine produced from withered Garganega berries. Therefore, we exposed the berries to postharvest withering under normal or artificially humid conditions, the latter to induce noble rot. The presence of noble rot symptoms was associated with the development of B. cinerea in the berries maintained under humid conditions. The composition of infected and non-infected berries was investigated by untargeted metabolomics using liquid chromatography/mass spectrometry. We also explored the effects of the two withering methods on the abundance of volatile organic compounds in wine by yeast-inoculated micro-fermentation followed by targeted gas chromatography/mass spectrometry. These experiments revealed significant metabolic differences between berries withered under normal and humid conditions, indicating that noble rot affects berry metabolism and composition. As well as well-known botrytization markers, we detected two novel lipids that have not been observed before in berries infected with noble rot. Unraveling the specific metabolic profile of berries infected with noble rot may help to determine the compounds responsible for the organoleptic quality traits of botrytized Garganega wines.

Whole-Metagenome-Sequencing-Based Community Profiles of Vitis vinifera L. cv. Corvina Berries Withered in Two Post-harvest Conditions

Vitis vinifera L. cv. Corvina grape forms the basis for the production of unique wines, such as Amarone, whose distinctive sensory features are strongly linked to the post-harvest grape withering process. Indeed, this process increases sugar concentration and changes must characteristics. While microorganisms involved in must fermentation have been widely investigated, few data are available on the microbiota of withered grapes. Thus, in this paper, a whole metagenome sequencing (WMS) approach was used to analyse the microbial consortium associated with Corvina berries at the end of the withering process performed in two different conditions ("traditional withering," TW or "accelerated withering," AW), and to unveil whether changes of drying parameters could have an impact on microbial diversity. Samples of healthy undamaged berries were collected and washed, to recover microorganisms from the surface and avoid contamination with grapevine genetic material. Isolated DNA was sequenced and the data obtained were analyzed with several bioinformatics methods. The eukaryotic community was mainly composed by members of the phylum Ascomycota, including Eurotiomycetes, Sordariomycetes, and Dothideomycetes. Moreover, the distribution of the genera Aspergillus and Penicillium (class Eurotiomycetes) varied between the withered berry samples. Instead, Botryotinia, Saccharomyces, and other wine technologically useful microorganisms were relatively scarce in both samples. For prokaryotes, 25 phyla were identified, nine of which were common to both conditions. Environmental bacteria belonging to the class Gammaproteobacteria were dominant and, in particular, the TW sample was characterized by members of the family Pseudomonadaceae, while members of the family Enterobacteriaceae dominated the AW sample, in addition to Sphyngobacteria and Clostridia. Finally, the binning procedure discovered 15 putative genomes which dominated the microbial community of the two samples, and included representatives of genera Erwinia, Pantoea, Pseudomonas, Clostridium, Paenibacillus, and of orders Lactobacillales and Actinomycetales. These results provide insights into the microbial consortium of Corvina withered berries and reveal relevant variations attributable to post-harvest withering conditions, underling how WMS could open novel perspectives in the knowledge and management of the withering process of Corvina, with an impact on the winemaking of important Italian wines.

Dynamic changes in microbiota and mycobiota during spontaneous 'Vino Santo Trentino' fermentation

Vino Santo is a sweet wine produced from late harvesting and pressing of Nosiola grapes in a small, well-defined geographical area in the Italian Alps. We used metagenomics to characterize the dynamics of microbial communities in the products of three wineries, resulting from spontaneous fermentation with almost the same timing and procedure. Comparing fermentation dynamics and grape microbial composition, we show a rapid increase in a small number of wine yeast species, with a parallel decrease in complexity. Despite the application of similar protocols, slight changes in the procedures led to significant differences in the microbiota in the three cases of fermentation: (i) fungal content of the must varied significantly in the different wineries, (ii) Pichia membranifaciens persisted in only one of the wineries, (iii) one fermentation was characterized by the balanced presence of Saccharomyces cerevisiae and Hanseniaspora osmophila during the later phases. We suggest the existence of a highly winery-specific 'microbial-terroir' contributing significantly to the final product rather than a regional 'terroir'. Analysis of changes in abundance during fermentation showed evident correlations between different species, suggesting that fermentation is the result of a continuum of interaction between different species and physical-chemical parameters.

Description of a taxonomically undefined Sclerotiniaceae strain from withered rotten-grapes

A necrotrophic member of the Sclerotiniaceae family (herewith named strain C10) isolated from withered rotten-grapes, is described. Interestingly, the fungus has no defined taxonomic position since it has been impossible to attribute it to an existing genus. Phylogenetic analysis of partial sequences of glyceraldehyde 3-phosphate dehydrogenase (G3PDH), heat shock protein 60 (HSP60) and DNA-directed RNA polymerase II subunit (RPB2), revealed that strain C10 is distantly related to Amphobotrys and Botrytis. This evidence clearly distinguishes this new Sclerotiniaceae member from other taxa of the family. Moreover, its morphological characteristics did not match those of Amphobotrys and Botrytis. Infectivity assays demonstrated that strain C10 could be a potential postharvest pathogen of withered grapes. This study revealed the taxonomic importance of this strain suggesting the existence of a possible new genus, a theory that requires further investigation.

Characterization and pathogenicity of Alternaria spp. strains associated with grape bunch rot during post-harvest withering

Alternaria is a fungal agent of grape bunch rot which occurs during withering, a process which produces passito style wines. Seven isolates of Alternaria spp. were characterized using morphological examination, genotypic analysis and pathogenicity. Six of these isolates produced conidiophores and conidia displaying sporulation patterns typical of the Alternaria alternata species-group. Variability in colony morphology and growth on different media was observed. Phylogenetic analysis of internal transcribed spacer (ITS) sequences clustered all isolates within a monophyletic clade, while intergenic spacer region (IGS)-RFLP profiles were congruent with those of A. alternata and Alternaria arborescens. RAPD-PCR proved helpful in discriminating between strains. To assay strain pathogenicity, grape berries were infected while undergoing withering conditions at different temperatures. Disease capacity was found to be strain dependent and varied consistently between the most and least aggressive strains. This study has provided interesting information on polymorphism within Alternaria spp. populations in withered grapes and on understanding the saprophytic role of this fungus during the post-harvest dehydrating process.