Wine microbiology is driven by vineyard and winery anthropogenic factors

Microbial Diversity Associated with the Cabernet Sauvignon Carposphere (Fruit Surface) from Eight Vineyards in Henan Province, China

The microbial diversity on the carposphere (berry) surface of the grape cultivar Cabernet Sauvignon grown in eight different locations/vineyards of Henan Province was determined by high-throughput sequencing of the bacterial 16S rRNA gene and fungal 18S rRNA gene. The structure of bacterial and fungal communities varied according to the sampling sites, but with some common phyla. Proteobacteria and Ascomycota were dominant/common phyla for bacteria and fungi, respectively. A total of 27 and 20 bacterial and fungal families, respectively, and 39 and 20 bacterial and fungal genera, respectively, with statistically significant differences, were found among different sampling sites. The difference for metabolic pathways of bacteria among the sampling sites existed. In addition, various abundances of enzymes from different sites might indicate that different function patterns exist in microbiota from different sites. The results revealed that locations of grape vineyards might play a significant role in shaping the microbiome, as well as the fact that vineyards can be distinguished based on the abundance of several key bacterial and fungal taxa. Overall, these findings extend our understanding of the similarities and differences in microbial community and their metabolic function on Cabernet Sauvignon grape surfaces from different geographic locations.

Diversity of fungal communities on Cabernet and Aglianico grapes from vineyards located in Southern Italy

Grape-associated microbial community is influenced by a combination of viticultural, climatic, pedological and anthropological factors, collectively known as terroir. Therefore, grapes of the same cultivar grown in different areas can be appreciated for their distinctive biogeographic characteristics. In our previous study, we showed that the phenotypic response of Aglianico and Cabernet grapevines from Molise and Sicily regions is significantly influenced by the prevailing pedoclimatic conditions, particularly soil physical properties. However, the scale at which microbial communities differ could be important in clarifying the concept of terroir, including whether it is linked to the grape variety present in a particular vineyard. To explore this further, in the research presented here, a comparative study on the fungal communities inhabiting the berry surfaces of Cabernet and Aglianico cultivars was conducted on different vineyards located in Southern Italy (Molise, Sicily and Campania regions, the first two of which had been involved in our previous study) by using high-throughput sequencing (HTS) and multivariate data analysis. The descriptive approach through relative abundance analysis showed the most abundant phyla (Ascomycota, Basidiomycota, and Chytridiomycota), families (Cladosporiaceae, Saccotheciaceae, Pleosporaceae, Saccharomycodaceae, Sporidiobolaceae, Didymellaceae, Filobasidiaceae, Bulleribasidiaceae, and Saccharomycetaceae) and genera (Cladosporium, Aureobasidium, Alternaria, Stemphylium and Filobasidium) detected on grape berries. The multivariate data analysis performed by using different packages (phyloseq, Vegan, mixOmics, microbiomeMarker and ggplot2) highlighted that the variable "vineyard location" significantly affect the fungal community, while the variable "grape variety" has no significant effect. Thus, some taxa are found to be part of specific vineyard ecosystems rather than specific grape varieties, giving additional information on the microbial contribution to wine quality, thanks to the presence of fermentative yeasts or, conversely, to the involvement in negative or detrimental roles, due to the presence of grape-deriving fungi implied in the spoilage of wine or in grapevine pathogenesis. In this connection, the main functions of core taxa fungi, whose role in the vineyard environment is still poorly understood, are also described.

Alcoholic and non-alcoholic rosé wines made with Saccharomyces cerevisiae var. boulardii probiotic yeast

The production of alcoholic and non-alcoholic rosé wines using Saccharomyces cerevisiae var. boulardii probiotic yeast is described in this study for the first time. Before and after fermentation and distillation, the volatile acidity, lactic, and malic acid levels were evaluated for S. cerevisiae var. boulardii. These contents were compared to those obtained with a standard S. cerevisiae EC-1118 yeast. We measured the levels of gluconic acid and free amino nitrogen in the musts. After fermentation and distillation, yeast viability was assessed as a function of time (0, 15 days, 3 months, and 6 months), both at ambient temperature (25 ± 0.5 °C) and refrigerator temperature (4 ± 0.5 °C). The outcomes revealed that the rosé wine made with S. cerevisiae var. boulardii had the same values and preliminary sensory characteristics as other commercial wines made with S. cerevisiae EC-1118. The S. cerevisiae var. boulardii yeast successfully survived the high alcohol level produced during fermentation and vacuum distillation. The study also revealed that this unique rosé wine retains its probiotic viability for at least 6 months when stored at room temperature or in the refrigerator, making it a suitable candidate for large-scale production where long storage intervals are required by both producers and consumers.

Diversity and Dynamics of Epidermal Microbes During Grape Development of Cabernet Sauvignon (Vitis vinifera L.) in the Ecological Viticulture Model in Wuhai, China

Grapevine-related microorganisms affect the health and yield of grapes, the metabolic pathways of the fermentation process, and the regional characteristics of wine. However, the diversity of epidermal microorganisms during the development of berries under the ecological viticulture model has not been described in detail. In this study, high-throughput amplicon sequencing technology was used to perform ITS and 16S sequencing of Cabernet Sauvignon epidermal microbes at different developmental stages in the Wuhai region to investigate the succession of epidermal microbes and their response to developmental stages and vineyard weather. The results showed that the diversity of fungi and bacteria decreased during development. Epidermal microorganisms recruited members according to their developmental stages, but retained the core taxa, such as the fungi genera Alternaria, Jattaea, and Jattaea and the bacteria genera Brevundimonas, Sphingomonas, Acinetobacter, and Pseudomonas. In addition, the microbial diversity was associated with specific meteorological parameters, implying that there was a connection between the environmental conditions of the vineyard and the microbial distribution pattern such as the fungus genus Filobasidium was positively correlated with relative humidity and negatively correlated with average high temperature, average low temperature, and average ground temperature; the bacterium genus Lactobacillus was positively correlated with sunlight time, and negatively correlated with relative humidity. In conclusion, this study can help vineyard managers understand the microbial consortia associated with particular diseases, and also the dynamics of infection processes in order to take preventive actions, especially at the most critical moments.

A Metagenetic Insight into Microbial Diversity of Spontaneously Fermented Polish Red Wines and an Analysis of Selected Physicochemical Properties

Due to changes in climatic conditions in Poland interest in viticulture and wine production has considerably boosted. One of the worldwide trends in winemaking is use of indigenous strains of yeast and lactic acid bacteria (LAB). The aim of the study was to analyse the microbial diversity of Polish red wines and their key properties and combine them for better understanding of the processes responsible for creating the sensory attributes. Metagenetic analysis was used to characterise the bacterial and yeast diversity of wines produced by spontaneous fermentation of grapes of the Regent variety, which came from three vineyards: “Dom Bliskowice” (DB), “Małe Dobre” (MD), and “Winnica Janowiec” (WJ). Among bacteria, Tatumella ptyseos was the most abundant species in DB and WJ wines and Leuconostoc pseudomesenteroides was the most abundant in MD wine. Among yeasts, Saccharomyces cerevisiae was found in DB and WJ wines, Saccharomyces cariocanus in MD wine, and Hanseniaspora uvarum in all samples studied. Studied wines had statistically significantly different antioxidant capacities and distinct glucose, fructose, and lactic acid concentrations. The presence of acetic and lactic acid bacteria was positively related to the concentrations of acetic and lactic acid, respectively, while the lack of malic acid was indicative of malolactic fermentation. This knowledge may be useful in the development of unique local starter cultures for the production of wines with specific characteristics.

The Biogeography of Fungal Communities Across Different Chinese Wine-Producing Regions Associated With Environmental Factors and Spontaneous Fermentation Performance

Chinese Marselan grapes are believed to possess the potential to become a characteristic regional variety, whose quality is internationally recognized. The fermentation-related mycobiota from six climatically diverse Marselan-producing regions in China were analyzed via high-throughput sequencing (HTS), while the influence of environmental factors was evaluated as well. The results implied that the phyla Ascomycota and genus Aureobasidium dominated the fungal communities in 166 Marselan must and fermented samples. Significant differences were detected in the fungal microbiota from the regions, as well as the wineries, while these discrepancies decreased as the fermentation progressed. Moreover, the discrepancy in fungal communities between the wineries exceeded the variation involving the regions. Geoclimatic elements (Gc) and physicochemical indexes (Pi) exerted a significant effect on the fungal must consortium, explaining 58.17% of the taxonomic information. Furthermore, a correlation was proposed between the spontaneous fermentation performance and their association with fungal taxonomic composition. In addition to depicting a fundamental landscape of fungal biogeography patterns across Chinese main wine-producing regions, we firstly proposed the correlation between the must polyphenol content and fungal microbiota, which may provide a new strategy for harnessing autochthonous “microbial terroir.”

Community succession of the grape epidermis microbes of cabernet sauvignon (Vitis vinifera L.) from different regions in China during fruit development

Grape surface microorganisms play a vital role in grape health and yield, wine quality, and regional wine characteristics. To investigate the succession of fungal and bacterial communities of the grape epidermis and the effects of development stages, vineyard location, and macroclimatic conditions on the diversity of epidermal microorganisms, 16S and ITS sequences of 36 samples from three different regions and four development stages were sequenced using the Illumina Novaseq platform. The Shannon index showed that the α-diversity of fungi and bacteria decreased during development. An analysis of variance showed that microbial diversity was influenced by development stage and vineyard location, and the development stage had a greater impact on the microbial diversity than the vineyard location. Grapes recruited microbes according to their developmental stages, but retain the core microbiome. Based on network analysis, this study found a significant correlation between epidermal microbial communities and macroclimatic conditions. In conclusion, the study described in detail the complex community dynamics of grape epidermal microorganisms during berry development. The result will help improve vineyard management techniques, rationally utilize the ecological functions of the vineyard, and reduce the application of chemical fungicides or pesticides to keep the vines healthy, produce high-quality grapes, and highlight the regional characteristics of the wine.

Towards a Better Understanding of the Potential Benefits of Seaweed Based Biostimulants in Vitis vinifera L. Cultivars

Globally, 7.4 million hectares of arable land is planted with grapevine with a farm gate value of $68.3 billion. The production of grapes faces growing pressure associated with challenges such as climate change, diminishing resources as well as the overuse of chemical fertilizers and synthetic pesticides, which have an impact on sustainability. Consequently, viticulture has over the years embraced and implemented various practices such integrated pest management, organic and biodynamic farming to curb the high chemical inputs typically used in conventional farming. Biostimulants and biofertilizers are considered environmentally friendly and cost-effective alternatives to synthetic fertilizers and plant growth regulators. Seaweed is of particular interest because of its availability globally. It was reported that brown seaweed (Ascophyllum spp.) improves plant growth and agricultural productivity, hormonal signalling, and an improved secondary plant metabolism. It also provides an alternative to soil supplementation, avoiding some of the negative effects of fertilizers through the leaching of nutrients into groundwater sources. This review aims to provide a summary of the use of seaweed extracts in grape production and their influence on grapevine physiology and stress adaptation mechanisms.

Yeast and Filamentous Fungi Microbial Communities in Organic Red Grape Juice: Effect of Vintage, Maturity Stage, SO2, and Bioprotection

Changes are currently being made to winemaking processes to reduce chemical inputs [particularly sulfur dioxide (SO₂)] and adapt to consumer demand. In this study, yeast growth and fungal diversity were investigated in merlot during the prefermentary stages of a winemaking process without addition of SO₂. Different factors were considered, in a two-year study: vintage, maturity level and bioprotection by the adding yeast as an alternative to SO₂. The population of the target species was monitored by quantitative-PCR, and yeast and filamentous fungi diversity was determined by 18S rDNA metabarcoding. A gradual decrease of the α-diversity during the maceration process was highlighted. Maturity level played a significant role in yeast and fungal abundance, which was lower at advanced maturity, while vintage had a strong impact on Hanseniaspora spp. population level and abundance. The presence of SO₂ altered the abundance of yeast and filamentous fungi, but not their nature. The absence of sulfiting led to an unexpected reduction in diversity compared to the presence of SO₂, which might result from the occupation of the niche by certain dominant species, namely Hanseniaspora spp. Inoculation of the grape juice with non-Saccharomyces yeast resulted in a decrease in the abundance of filamentous fungi generally associated with a decline in grape must quality. Lower abundance and niche occupation by bioprotection agents were observed at the overripened stage, thus suggesting that doses applied should be reconsidered at advanced maturity. Our study confirmed the bioprotective role of Metschnikowia pulcherrima and Torulaspora delbrueckii in a context of vinification without sulfites.

A fundamental landscape of fungal biogeographical patterns across the main Chinese wine-producing regions and the dominating shaping factors

The microbial terroir plays an indispensable role in the formation of regional wine characteristics. A fundamental landscape of the fungal biogeographical patterns across Chinese wine-producing regions was obtained by characterizing the fungal communities in spontaneous fermentation. After confirming the established national microbial terroir, the fungal heterogeneity was evaluated at different geographical levels. The result showed that the variation between the wineries was more evident than at a regional level. Moreover, the microbial comparability from various regions with similar climates or wineries within the same regions was revealed. Further discriminant analysis determined the specific fungal biomarkers in different regions, while the associated reverse identification model displayed reliable accuracy (>70%). Correlation analysis illustrated the primary role of the geoclimatic factors (>41%) in shaping the fungal geographical patterns, and the relationship between the microbiome and spontaneous fermentation performance. In addition to expanding the knowledge regarding wine microbes, these findings provided a new benchmark for harnessing the microbial terroir to enhance regional wine expression.

Metataxonomic Analysis of Grape Microbiota During Wine Fermentation Reveals the Distinction of Cyprus Regional terroirs

Wine production in Cyprus has strong cultural ties with the island's tradition, influencing local and foreign consumers' preferences and contributing significantly to Cyprus' economy. A key contributor to wine quality and sensorial characteristics development is the microbiota that colonizes grapes and performs alcoholic fermentation. Still, the microbial patterns of wines produced in different geographic regions (terroir) in Cyprus remain unknown. The present study investigated the microbial diversity of five terroirs in Cyprus, two from the PGI Lemesos region [Kyperounta (PDO Pitsilia) and Koilani (PDO Krasochoria)], and three from the PGI Pafos region [Kathikas (PDO Laona Akamas), Panayia, and Statos (PDO Panayia)], of two grape varieties, Xynisteri and Maratheftiko, using high-throughput amplicon sequencing. Through a longitudinal analysis, we examined the evolution of the bacterial and fungal diversity during spontaneous alcoholic fermentation. Both varieties were characterized by a progressive reduction in their fungal alpha diversity (Shannon index) throughout the process of fermentation. Additionally, the study revealed a distinct separation among different terroirs in total fungal community composition (beta-diversity) for the variety Xynisteri. Also, Kyperounta terroir had a distinct total fungal beta-diversity from the other terroirs for Maratheftiko. Similarly, a significant distinction was demonstrated in total bacterial diversity between the PGI Lemesos region and the PGI Pafos terroirs for grape juice of the variety Xynisteri. Pre-fermentation, the fungal diversity for Xynisteri and Maratheftiko was dominated by the genera Hanseniaspora, Aureobasidium, Erysiphe, Aspergillus, Stemphylium, Penicillium, Alternaria, Cladosporium, and Mycosphaerella. During and post-fermentation, the species Hanseniaspora nectarophila, Saccharomyces cerevisiae, Hanseniaspora guilliermondii, and Aureobasidium pullulans, became the predominant in most must samples. Regarding the bacterial diversity, Lactobacillus and Streptococcus were the predominant genera for both grape varieties in all stages of fermentation. During fermentation, an increase was observed in the relative abundance of some bacteria, such as Acetobacter, Gluconobacter, and Oenococcus oeni. Finally, the study revealed microbial biomarkers with statistically significant higher relative representation, associated with each geographic region and each grape variety, during the different stages of fermentation. The present study's findings provide an additional linkage between the grape microbial community and the wine terroir.

Spatio-Temporal Analysis of Satellite Imagery (NDVI) to Identify Terroir and Vineyard Yeast Differences according to Appellation of Origin (AOP) and Biogeographic Origin

Terroir is one of the core concepts associated with wine and presumes that the land from which the grapes are grown, the plant habitat, imparts a unique quality that is specific to that growing site. Additionally, numerous factors can influence yeast diversity, and terroir is among the most relevant. Therefore, it can be interesting to use Remote Sensing tools that help identify and give helpful information about the terroir and key characteristics that define the AOP (Appellation of Origin). In this study, the NDVI (Normalized Difference Vegetation Index) calculated from Landsat 8 imagery was used to perform a spatio-temporal analysis during 2013, 2014, and 2015 of several vineyards belonging to four different AOP in Galicia (Spain). This work shows that it is possible to use Remote Sensing for AOP delimitation. Results suggest: (i) satellite imagery can establish differences in terroir, (ii) the higher the NDVI, the higher the yeast species richness, (iii) the relationship between NDVI, terroir, and yeasts shows a stable trend over the years (Pearson’s r = 0.3894, p = 0.0119).

Inoculation with Mycorrhizal Fungi and Irrigation Management Shape the Bacterial and Fungal Communities and Networks in Vineyard Soils

Vineyard-living microbiota affect grapevine health and adaptation to changing environments and determine the biological quality of soils that strongly influence wine quality. However, their abundance and interactions may be affected by vineyard management. The present study was conducted to assess whether the vineyard soil microbiome was altered by the use of biostimulants (arbuscular mycorrhizal fungi (AMF) inoculation vs. non-inoculated) and/or irrigation management (fully irrigated vs. half irrigated). Bacterial and fungal communities in vineyard soils were shaped by both time course and soil management (i.e., the use of biostimulants and irrigation). Regarding alpha diversity, fungal communities were more responsive to treatments, whereas changes in beta diversity were mainly recorded in the bacterial communities. Edaphic factors rarely influence bacterial and fungal communities. Microbial network analyses suggested that the bacterial associations were weaker than the fungal ones under half irrigation and that the inoculation with AMF led to the increase in positive associations between vineyard-soil-living microbes. Altogether, the results highlight the need for more studies on the effect of management practices, especially the addition of AMF on cropping systems, to fully understand the factors that drive their variability, strengthen beneficial microbial networks, and achieve better soil quality, which will improve crop performance.

Tasting the terroir of wine yeast innovation

Wine is an archetypal traditional fermented beverage with strong territorial and socio-cultural connotations. Its 7000 year history is patterned by a tradition of innovation. Every value-adding innovation − whether in the vineyard, winery, supply chain or marketplace − that led to the invention of a new tradition spurred progress and created a brighter future from past developments. In a way, wine traditions can be defined as remembered innovations from the distant past − inherited knowledge and wisdom that withstood the test of time. Therefore, it should not be assumed a priori that tradition and innovation are polar opposites. The relations between the forces driven by the anchors of tradition and the wings of innovation do not necessarily involve displacement, conflict or exclusiveness. Innovation can strengthen wine tradition, and the reinvention of a tradition-bound practice, approach or concept can foster innovation. In cases where a paradigm-shifting innovation disrupts a tradition, the process of such an innovation transitioning into a radically new tradition can become protracted while proponents of divergent opinions duke it out. Sometimes these conflicting opinions are based on fact, and sometimes not. The imperfections of such a debate between the ‘ancients’ and the ‘moderns’ can, from time to time, obscure the line between myth and reality. Therefore, finding the right balance between traditions worth keeping and innovations worth implementing can be complex. The intent here is to harness the creative tension between science fiction and science fact when innovation's first-principles challenge the status quo by re-examining the foundational principles about a core traditional concept, such as terroir. Poignant questions are raised about the importance of the terroir (biogeography) of yeasts and the value of the microbiome of grapes to wine quality. This article imagines a metaphorical terroir free from cognitive biases where diverse perspectives can converge to uncork the effervescent power of territorial yeast populations as well as ‘nomadic’ yeast starter cultures. At the same time, this paper also engages in mental time-travel. A future scenario is imagined, explored, tested and debated where terroir-less yeast avatars are equipped with designer genomes to safely and consistently produce, individually or in combination with region-specific wild yeasts and or other starter cultures, high-quality wine according to the preferences of consumers in a range of markets. The purpose of this review is to look beyond the horizon and to synthesize a link between what we know now and what could be. This article informs readers where to look without suggesting what they must see as a way forward. In the context of one of the world's oldest fermentation industries − steeped in a rich history of tradition and innovation − the mantra here is: respect the past, lead the present and secure the future of wine.

The ecology of wine fermentation: a model for the study of complex microbial ecosystems

The general interest in microbial ecology has skyrocketed over the past decade, driven by technical advances and by the rapidly increasing appreciation of the fundamental services that these ecosystems provide. In biotechnology, ecosystems have many more functionalities than single species, and, if properly understood and harnessed, will be able to deliver better outcomes for almost all imaginable applications. However, the complexity of microbial ecosystems and of the interactions between species has limited their applicability. In research, next generation sequencing allows accurate mapping of the microbiomes that characterise ecosystems of biotechnological and/or medical relevance. But the gap between mapping and understanding, to be filled by "functional microbiomics", requires the collection and integration of many different layers of complex data sets, from molecular multi-omics to spatial imaging technologies to online ecosystem monitoring tools. Holistically, studying the complexity of most microbial ecosystems, consisting of hundreds of species in specific spatial arrangements, is beyond our current technical capabilities, and simpler model systems with fewer species and reduced spatial complexity are required to establish the fundamental rules of ecosystem functioning. One such ecosystem, the ecosystem responsible for natural alcoholic fermentation, can provide an excellent tool to study evolutionarily relevant interactions between multiple species within a relatively easily controlled environment. This review will critically evaluate the approaches that are currently implemented to dissect the cellular and molecular networks that govern this ecosystem. KEY POINTS: • Evolutionarily isolated fermentation ecosystem can be used as an ecological model. • Experimental toolbox is gearing towards mechanistic understanding of this ecosystem. • Integration of multidisciplinary datasets is key to predictive understanding.

Unexpected high production of biohydrogen from the endogenous fermentation of grape must deposits

The aim of this work was to assess the performances of wine byproduct biomass for hydrogen production by dark fermentation. Grape must deposits from two grape varieties (Pinot Gris and Chardonnay) were considered, either with external microbial inoculum or without. We show that grape must residues contain endogenous microflora, well adapted to their environment, which can degrade sugars (initially contained in the biomass) to hydrogen without any nutrient addition. Indeed, hydrogen production during endogenous fermentation is as efficient as with an external heat-treated inoculum (2.5 ± 0.4 L_H2.L^-1_reactor and 1.61 ± 0.41 mol_H2.mol^-1_{consumed hexose}, respectively) with a lower energy cost. Hydrogen-producing bacteria were selected from the endogenous microflora during semi-batch bioreactor operation, as shown by T-RFLP profiles and 16S rRNA sequencing, with Clostridium spp. (butyricum, beijerinckii, diolis, roseum) identified as the major phylotype. Such hydrogen production efficiency opens new perspectives for innovating in the valorization of winery by-products.

High-Throughput Sequencing Approach to Analyze the Effect of Aging Time and Barrel Usage on the Microbial Community Composition of Red Wines

Wine aged in barrels or bottles is susceptible to alteration by microorganisms that affect the final product quality. However, our knowledge of the microbiota during aging and the factors modulating the microbial communities is still quite limited. The present work uses high-throughput sequencing (HTS) techniques to deal with the meta-taxonomic characterization of microbial consortia present in red wines along 12 months aging. The wines obtained from two different grape varieties were aged at two different cellars and compared based on time of wine aging in the barrels, previous usage of the barrels, and differences between wine aging in oak barrels or glass bottles. The aging in barrels did not significantly affect the microbial diversity but changed the structure and composition of fungal and bacterial populations. The main microorganisms driving these changes were the bacterial genera Acetobacter, Oenococcus, Lactobacillus, Gluconobacter, Lactococcus, and Komagataeibacter and the fungal genera Malassezia, Hanseniaspora, and Torulaspora. Our results showed that the oak barrels increased effect on the microbial diversity in comparison with the glass bottles, in which the microbial community was very similar to that of the wine introduced in the barrels at the beginning of the aging. Furthermore, wine in the bottles harbored higher proportion of Lactobacillus but lower proportion of Acetobacter. Finally, it seems that 1 year of previous usage of the barrels was not enough to induce significant changes in the diversity or composition of microbiota through aging compared with new barrels. This is the first meta-taxonomic study on microbial communities during wine aging and shows that the microorganism composition of barrel-aged wines was similar at both cellars. These results hint at the possibility of a common and stable microbiota after aging in the absence of exogenous alterations. Further corroborations on the current outcome would be valuable for the comparison and detection of microbial alterations during aging that could potentially prevent economic losses in the wine industry.

Discovering the indigenous microbial communities associated with the natural fermentation of sap from the cider gum Eucalyptus gunnii

Over the course of human history and in most societies, fermented beverages have had a unique economic and cultural importance. Before the arrival of the first Europeans in Australia, Aboriginal people reportedly produced several fermented drinks including mangaitch from flowering cones of Banksia and way-a-linah from Eucalyptus tree sap. In the case of more familiar fermented beverages, numerous microorganisms, including fungi, yeast and bacteria, present on the surface of fruits and grains are responsible for the conversion of the sugars in these materials into ethanol. Here we describe native microbial communities associated with the spontaneous fermentation of sap from the cider gum Eucalyptus gunnii, a Eucalyptus tree native to the remote Central Plateau of Tasmania. Amplicon-based phylotyping showed numerous microbial species in cider gum samples, with fungal species differing greatly to those associated with winemaking. Phylotyping also revealed several fungal sequences which do not match known fungal genomes suggesting novel yeast species. These findings highlight the vast microbial diversity associated with the Australian Eucalyptus gunnii and the native alcoholic beverage way-a-linah.

Biodiversity of yeasts isolated during spontaneous fermentation of cool climate grape musts

Biodiversity of native yeasts, especially in winemaking, has hidden potential. In order to use the value of non-Saccharomyces strains in wine production and to minimise the possibility of its deterioration, it is necessary to thoroughly study the yeast cultures present on grape fruits and in grape must, as well as their metabolic properties. The aim of the study was to characterise the yeast microbiota found during spontaneous fermentation of grape musts obtained from grape varieties ‘Rondo’, ‘Regent’ and ‘Johanniter’. Grapes from two vineyards (Srebrna Góra and Zadora) located in southern Poland were used for the research. Succession of subsequent groups of yeasts was observed during the process. Metschnikowia pulcherrima yeasts were identified both at the beginning and the end of the process. Hanseniaspora uvarum, Wickerhamomyces onychis and Torulaspora delbrueckii strains were also identified during the fermentation. Torulaspora delbrueckii and Wickerhamomyces onychis strains were identified only in grape musts obtained from grapes of the Zadora vineyard. These strains may be characteristic of this vineyard and shape the identity of wines formed in it. Our research has provided specific knowledge on the biodiversity of yeast cultures on grapes and during their spontaneous fermentation. The research results presented indicate the possibility of using native strains for fermentation of grape musts, allowing to obtain a product with favourable chemical composition and sensory profile.

Wine Yeast Terroir: Separating the Wheat from the Chaff-for an Open Debate

Wine terroir is characterized by a specific taste and style influenced by the cultivar of the fermented grapes, geographical factors such as the vineyard, mesoclimate, topoclimate, and microclimate, soil geology and pedology, and the agronomic approach used. These characteristics together define the concept of "terroir". Thus, regional distinctive flavors in wine have been the subject of many studies aimed at better understanding the link between the wine and the vineyard. Indeed, the identification of key environmental elements involved in the regional variation of grape and wine quality characteristics is a critical feature for improving wine production in terms of consumer preference and economic appreciation. Many studies have demonstrated the role of abiotic factors in grape composition and consequently in wine style. Biotic factors are also involved such as grape microbial communities. However, the occurrence and effects of region-specific microbiota in defining wine characteristics are more controversial issues. Indeed, several studies using high throughput sequencing technologies have made it possible to describe microbial communities and revealed a link between grape must and soil microbial communities, and the geography of the territory. Based on these observations, the concept of "microbial terroir" emerged. However, this concept has been subject to contradictory studies. The aim of this opinion article is to take a step back and examine in perspective the concept of microbial terroir, by comparing numerous data from different studies and providing arguments in favor of or against this concept to stimulate discussion and point out that experimental research is still needed to study the contribution of this assembly of microorganisms to the final product and to support or refute the concept.

Effect of Co-Inoculation of Candida zemplinina, Saccharomyces cerevisiae and Lactobacillus plantarum for the Industrial Production of Negroamaro Wine in Apulia (Southern Italy)

The employment of multi-species starter cultures has growing importance in modern winemaking for improving the complexity and wine attributes. The assessment of compatibility for selected species/strains at the industrial-scale is crucial to assure the quality and the safety associated with fermentations. An aspect particularly relevant when the species belong to non-Saccharomyces, Saccharomyces spp. and malolactic bacteria, three categories with different biological characteristics and oenological significance. To the best of our knowledge, the present report is the first study regarding the utilization of a combined starter culture composed of three strains of non-Saccharomyces, Saccharomyces cerevisiae and Lactobacillus plantarum for production of wine at the industrial scale. More in-depth, this work investigated the oenological potential of the autochthonous characterized strains from the Apulian region (Southern Italy), Candida zemplinina (syn. Starmerella bacillaris) 35NC1, S. cerevisiae (NP103), and L. plantarum (LP44), in co-inoculation following a complete scale-up scheme. Microbial dynamics, fermentative profiles and production of volatile secondary compounds were assessed in lab-scale micro-vinification tests and then the performances of the mixed starter formulation were further evaluated by pilot-scale wine production. The above results were finally validated by performing an industrial-scale vinification on 100HL of Negroamaro cultivar grape must. The multi-starter formulation was able to rule the different stages of the fermentation processes effectively, and the different microbial combinations enhanced the organoleptic wine features to different extents. The findings indicated that the simultaneous inoculation of the three species affect the quality and quantity of several volatile compounds, confirming that the complexity of the wine can reflect the complexity of the starter cultures. Moreover, the results underlined that the same mixed culture could differently influence wine quality when tested at the lab-, pilot- and industrial-scale. Finally, we highlighted the significance of employment non-Saccharomyces and L. plantarum, together with S. cerevisiae, autochthonous strains in the design of custom-made starter culture formulation for typical regional wine production with pronounced unique quality.

New Insights into the Oenological Significance of Candida zemplinina: Impact of Selected Autochthonous Strains on the Volatile Profile of Apulian Wines

In this investigation, we explored the oenological significance of Candida zemplinina (syn. Starmerella bacillaris) isolates from Apulian grape musts. Moreover, we provide the first evidence of the impact of different C. zemplinina strains on the wine aromatic properties tested as monocultures. We described the diversity of C. zemplinina strains isolated from grapes and the variability of 'volatile' phenotypes associated with this intraspecific variability. Thirty-three isolates were characterized at strain level by PCR-based approach and, among these, 16 strains were identified and then tested by microfermentation tests carried out in grape must. Analyzed strains were low producers of acetic acid and hydrogen sulphide, not able to decarboxylate a panel of representative amino acids, whereas they showed fructophilic character and significant glycerol production. Volatile profiles of produced wines were investigated by gas chromatography-mass spectrometry. The Odor Activity Values of all molecules were calculated and 12 compounds showed values above their odor thresholds. Two selected strains (35NC1 and 15PR1) could be considered as possible starter cultures since they were able to positively affect the sensory properties of obtained wine. This report firstly supplies evidence on the strain-specific impact of different C. zemplinina strains on the final aroma of produced wines.

Discovering the bacteriome of Vitis vinifera cv. Pinot Noir in a conventionally managed vineyard

The structure of the bacteriome associated with grapevine roots can affect plant development, health and grape quality. We previously investigated the bacterial biodiversity of the Vitis vinifera cv. Pinot Noir rhizosphere in a vineyard subjected to integrated pest management. The aim of this work is to characterize the bacteriome of V. vinifera cv. Pinot Noir in a conventionally managed vineyard using a metabarcoding approach. Comparisons between the microbial community structure in bulk soil and rhizosphere (variable space) were performed and shifts of bacteriome according to two sampling times (variable time) were characterized. Bacterial biodiversity was higher at the second than at the first sampling and did not differ according to the variable space. Actinobacteria was the dominant class, with Gaiella as the most represented genus in all the samples. Among Proteobacteria, the most represented classes were Alpha, Beta and Gamma-Proteobacteria, with higher abundance at the second than at the first sampling time. Bradyrhizobium was the most frequent genus among Alpha-Proteobacteria, while Burkholderia was the predominant Beta-Proteobacteria. Among Firmicutes, the frequency of Staphylococcus was higher than 60% in bulk soil and rhizosphere. Finally, the sampling time can be considered as one of the drivers responsible for the bacteriome variations assessed.

Identification of Yeasts with Mass Spectrometry during Wine Production

The aim of the present study was to identify yeasts in grape, new wine “federweisser” and unfiltered wine samples. A total amount of 30 grapes, 30 new wine samples and 30 wine samples (15 white and 15 red) were collected from August until September, 2018, from a local Slovak winemaker, including Green Veltliner (3), Mūller Thurgau (3), Palava (3), Rhein Riesling (3), Sauvignon Blanc (3), Alibernet (3), André (3), Blue Frankish (3), Cabernet Sauvignon (3), and Dornfelder (3) grapes; federweisser and unfiltered wine samples were also used in our study. Wort agar (WA), yeast extract peptone dextrose agar (YPDA), malt extract agar (MEA) and Sabouraud dextrose agar (SDA) were used for microbiological testing of yeasts. MALDI-TOF Mass Spectrometry (Microflex LT/SH) (Bruker Daltonics, Germany) was used for the identification of yeasts. A total of 1668 isolates were identified with mass spectrometry. The most isolated species from the grapes was Hanseniaspora uvarum, and from federweisser and the wine—Saccharomyces cerevisiae.

Impact of Chemical and Alternative Fungicides Applied to Grapevine cv Nebbiolo on Microbial Ecology and Chemical-Physical Grape Characteristics at Harvest

Viticulture is a cropping system in which treatment against fungal diseases (in particular powdery and downy mildews) can be extremely frequent. Accordingly, a reduction in antimicrobial treatments and the application of environmentally-friendly compounds are becoming increasingly important for a more sustainable viticulture. In addition to their effect against pathogens, the impact of these products on the quality of the grapes is very important for the oenological industries, but unfortunately at present few data are available. We evaluated the effect of the application of biocontrol products and resistance inducers in the vineyard on the mechanical properties, microbial ecology, technological and phenolic maturity of Vitis vinifera "Nebbiolo" grapes at harvest. The yield and vigor of vines were not influenced by the treatments, nor were the production of primary and secondary metabolites. However, the active ingredients influenced the mechanical properties of the skin (hardness and thickness). A significant hardening of the skin was detected when laminarin and chito-oligosaccharides were used, and sulfur induced a thickening of the skin with potential consequences for wine quality. Furthermore, the yeast community present on grape berries was influenced by the treatments. The abundance of Aureobasidium pullulans, the dominant species on the grape berry, changed in response to the compounds used. In addition, Alternaria sp. was reduced in some treatments with a potentially positive effect on the quality and the safety of the grapes. This study provides an overview of the effect of biocontrol products and resistance inducers on microbial ecology and "Nebbiolo" grape quality, contributing to the establishment of more sustainable and effective defense strategies in viticulture.

Fungal Diversity of Deteriorated Sparkling Wine and Cork Stoppers in Catalonia, Spain

Filamentous fungi are rarely reported as responsible for spoiling wine. Cork taint was detected in sparkling wine; therefore, we investigated fungal contamination as a possible cause of organoleptic alteration. Spoiled wine was filtered and membranes were plated onto potato dextrose agar (PDA). The cork stoppers used for sealing bottles were cut and also plated onto PDA. Fungal strains were phenotypically characterized and molecularly identified by sequencing of a fragment of the 28S nrRNA gene (LSU) and (occasionally) by other additional molecular markers. Twenty-seven strains were isolated and sixteen species were identified, all of them belonging to the phylum Ascomycota. The fungi isolated from wine were three species of Aspergillus section Nidulantes, a species of Penicillium section Exicaulis and Beauveria bassiana. Candida patagonica was isolated from both sort of samples, and the fungi isolated from cork stoppers were Altenaria alternata and Cladosporium cladosporioides. Surprisingly, most of the taxa recovered from the cork stoppers and/or wine were new to the science: a new genus (Dactylodendron) and seven new species belonging to the genera Cladophialophora, Dactylodendron, Kirschsteiniothelia, Rasamsonia, and Talaromyces. Future studies could let us know if these fungi would be able to produce compounds responsible for cork taint.

From the Vineyard to the Winery: How Microbial Ecology Drives Regional Distinctiveness of Wine

Wine production is a complex process from the vineyard to the winery. On this journey, microbes play a decisive role. From the environment where the vines grow, encompassing soil, topography, weather and climate through to management practices in vineyards, the microbes present can potentially change the composition of wine. Introduction of grapes into the winery and the start of winemaking processes modify microbial communities further. Recent advances in next-generation sequencing (NGS) technology have progressed our understanding of microbial communities associated with grapes and fermentations. We now have a finer appreciation of microbial diversity across wine producing regions to begin to understand how diversity can contribute to wine quality and style characteristics. In this review, we highlight literature surrounding wine-related microorganisms and how these affect factors interact with and shape microbial communities and contribute to wine quality. By discussing the geography, climate and soil of environments and viticulture and winemaking practices, we claim microbial biogeography as a new perspective to impact wine quality and regionality. Depending on geospatial scales, habitats, and taxa, the microbial community respond to local conditions. We discuss the effect of a changing climate on local conditions and how this may alter microbial diversity and thus wine style. With increasing understanding of microbial diversity and their effects on wine fermentation, wine production can be optimised with enhancing the expression of regional characteristics by understanding and managing the microbes present.

Genetic and Phenotypic Characterisation of a Saccharomyces cerevisiae Population of 'Merwah' White Wine

The study of yeast biodiversity represents an important step in the preservation of the local heritage, and this work in particular has an innovative character since no further studies have investigated 'Merwah', one of the main grape varieties used in winemaking in Lebanon. To gain deeper knowledge of the genetic diversity and population structure of native Saccharomyces cerevisiae wine strains, 202 isolates were collected during spontaneous alcoholic fermentation of eight must/wine samples of cultivar 'Merwah', over two consecutive years (2016, 2017) in a traditional winery in Mount Lebanon (1400 m a.s.l.). The isolates were identified as S. cerevisiae on the basis of their morphology and preliminary sequence analysis of their internal transcribed spacer (ITS) PCR. They were then characterised at the strain level by interdelta PCR and genotyped using multiplex PCR reactions of 12 microsatellite markers. High genetic diversity was observed for the studied population. To select potential yeast starter strains from this population, micro-fermentations were carried out for 22 S. cerevisiae strains that were selected as representative of the 'Merwah' wine yeast population in order to determine their technological and oenological properties. Three indigenous yeast strains might represent candidates for pilot-scale fermentation in the winery, based on relevant features such as high fermentation vigour, low production of volatile acidity and H₂S and low residual sugar content at the end of alcoholic fermentation.

Live yeast in juvenile diet induces species-specific effects on Drosophila adult behaviour and fitness

The presence and the amount of specific yeasts in the diet of saprophagous insects such as Drosophila can affect their development and fitness. However, the impact of different yeast species in the juvenile diet has rarely been investigated. Here, we measured the behavioural and fitness effects of three live yeasts (Saccharomyces cerevisiae = SC; Hanseniaspora uvarum = HU; Metschnikowia pulcherrima = MP) added to the diet of Drosophila melanogaster larvae. Beside these live yeast species naturally found in natural Drosophila populations or in their food sources, we tested the inactivated "drySC" yeast widely used in Drosophila research laboratories. All flies were transferred to drySC medium immediately after adult emergence, and several life traits and behaviours were measured. These four yeast diets had different effects on pre-imaginal development: HU-rich diet tended to shorten the "egg-to-pupa" period of development while MP-rich diet induced higher larval lethality compared to other diets. Pre- and postzygotic reproduction-related characters (copulatory ability, fecundity, cuticular pheromones) varied according to juvenile diet and sex. Juvenile diet also changed adult food choice preference and longevity. These results indicate that specific yeast species present in natural food sources and ingested by larvae can affect their adult characters crucial for fitness.

Quantitative and qualitative composition of yeast microbiota in spontaneously fermented grape musts obtained from cool climate grape varieties 'Rondo' and 'Regent'

The aim of the study was to characterise, quantitatively and qualitatively, the yeast microbiota found during spontaneous fermentation of grape musts obtained from the red grape varieties 'Rondo' and 'Regent'. For the research, grapes originating from two vineyards (Srebrna Góra and Spotkaniówka) located in southern Poland were used. Musts of the studied grape varieties provided a favourable environment for the growth of microorganisms. Musts obtained from fruits from the Spotkaniówka vineyard were characterised by a higher overall number of yeasts. A maximum number of cells were recorded from the fourth to the ninth day of the process, in all of the analysed musts. The growing season of 2013 proved to be the least favourable for the growth of microorganisms on grapes, which resulted in their smaller number in the batches during spontaneous fermentation. During the process, succession of different groups of yeasts was observed. It was initiated by Hanseniaspora uvarum and Candida railenensis strains, which, with the progress of spontaneous fermentation, were replaced by Saccharomyces cerevisiae strains. Metschnikowia pulcherrima and Pichia membranifaciens yeasts were identified at both the beginning and the end of the process. During fermentation, Zygoascus meyerae, Kluyveromyces lactis and Nakazawaea ishiwadae strains were also identified.

Diversity of Saccharomyces cerevisiae yeasts associated to spontaneous and inoculated fermenting grapes from Spanish vineyards

The use of commercial yeast strains is a common practice in winemaking leading to a predictable quality in wine production, avoiding stuck or sluggish fermentations. However, the use of commercial yeasts leads to a consequent reduction in autochthonous microbial diversity. In this study, 1047 isolates from three Spanish appellations of origin were checked for fingerprinting on interdelta polymorphisms and the strain composition and diversity analysed using an extensible open-source platform for processing and analysis of an in-house polymorphism database developed for this study. Ancient vineyards managed with organic practices showed intermediate to low levels of strains diversity indicating the existence of stable populations of Saccharomyces cerevisiae strains. A drastic reduction in the number of different S. cerevisiae strains was observed in vineyards with cellars using a selected autochthonous S. cerevisiae strain for winemaking. Contrary, the use of allochthonous commercial strains in wineries did not seem to affect the native S. cerevisiae strain composition and diversity. SIGNIFICANCE AND IMPACT OF THE STUDY: The aim of this study was to compare different viticulture and oenological practices to determine their influence on the composition and diversity of Saccharomyces cerevisiae strains in wine fermentations. The study shows that the use of autochthonous strains of S. cerevisiae as starters for wine fermentation could have an important incidence on S. cerevisiae strains diversity in surrounding vineyards. The use of autochthonous strains of S. cerevisiae reduced the detected number of S. cerevisiae strains, a fact that was not observed when allochthonous commercial strains were used. Furthermore, vineyards managed with organic practices showed intermediate to low levels of S. cerevisiae strain diversity, whereas conventional practices showed higher levels.

Bark and Grape Microbiome of Vitis vinifera: Influence of Geographic Patterns and Agronomic Management on Bacterial Diversity

In recent years, the concept of “microbial terroir” has been introduced in the frame of the more renowned notion of “vitivinicultural terroir,’ since several studies demonstrated that wine characteristics are related to regional microbial community compositions. Most of the existing research focused on grape berries microbiota, since it can directly impact wine quality. In this work we studied, for the first time through next-generation sequencing, the epiphytic bacterial community of vine bark and its relationships with grape microbiota. The study was carried out in two Italian wine appellations (situated in different regions) to explore the impact of biogeography, and the influence of two agronomical practices (biodynamic and conventional) was evaluated as well. Overall, our results show that grapevine bark harbors a rich epiphytic microbiota and displays a higher microbial biodiversity than grape berry. Moreover, this study suggests that geographic and anthropogenic factors impact both bark and grape bacteriomes, but to a different extent. The evidence of a “microbial terroir” seems to be even more marked in bark than in berries, possibly due to its permanence over time and to its physical proximity with soil. The importance of vine trunk bark, as potential source of inoculum for grapes and as interesting bacterial diversity habitat, is evidenced. This opens new fields of investigation, not only for researchers that aim at describing this little-known habitat within the vineyard, but also for stakeholders from the wine industry that want to understand the roles of microorganisms on the entire winemaking process, from vineyard to cellar.

Grape berry surface bacterial microbiome: impact from the varieties and clones in the same vineyard from central China

AIMS

Bacterial microbiome on grape berry surface may play an important role in grape quality and health. This study aims to investigate the impact of grape varieties and clones on grape berry surface bacterial microbiome from the same vineyard.

METHODS AND RESULTS

High-throughput sequencing strategy was used to investigate the bacterial diversity and abundance on the grape surfaces of 12 clones belonging to six varieties grown in the same vineyard of Zhengzhou Fruit Research Institute in Henan Province. In total, 45 bacterial phyla and 933 genera were detected from all samples. Cyanobacteria, Proteobacteria and Firmicutes were the most abundant and prevalent phyla, while Bacteroidetes, Chloroflexi, Acidobacteria and Planctomycetes were grape clone specific phyla. The nonrank genus from phylum Cyanobacteria occupied 30-81% of grape clones from Italian Riesling (GRX), Cabernet Franc (PLZ), Pinot Blanc (BBN) and Riesling (LSL). Interestingly, Bacillus, Pseudomonas and Lactococcus were the only three prevalent genera found on all the clones. Furthermore, the predicted functional activities of grape surface bacterial communities varied according to the clones.

CONCLUSIONS

The present study revealed that in addition to the grape varieties, the variations in grape clone background may also affect the bacterial microbiome on grape surfaces which may ultimately determine their functional activities.

SIGNIFICANCE AND IMPACT OF THE STUDY

This research provides an important information for grape planting and wine fermentation that not only the grape varieties need to be paid attention but also grape clones from the specific variety need to be concerned.

Spoilage yeasts: What are the sources of contamination of foods and beverages?

Foods and beverages are nutrient-rich ecosystems in which most microorganisms are able to grow. Moreover, several factors, such as physicochemical characteristics, storage temperature, culinary practices, and application of technologies for storage, also define the microbial population of foods and beverages. The yeast population has been well-characterised in fresh and processed fruit and vegetables, dairy products, dry-cured meat products, and beverages, among others. Some species are agents of alteration in different foods and beverages. Since the most comprehensive studies of spoilage yeasts have been performed in the winemaking process, hence, these studies form the thread of the discussion in this review. The natural yeast populations in raw ingredients and environmental contamination in the manufacturing facilities are the main modes by which food contamination occurs. After contamination, yeasts play a significant role in food and beverage spoilage, particularly in the alteration of fermented foods. Several mechanisms contribute to spoilage by yeasts, such as the production of lytic enzymes (lipases, proteases, and cellulases) and gas, utilisation of organic acids, discolouration, and off-flavours. This review addresses the role of yeasts in foods and beverages degradation by considering the modes of contamination and colonisation by yeasts, the yeast population diversity, mechanisms involved, and the analytical techniques for their identification, primarily molecular methods.

Vineyard under-vine floor management alters soil microbial composition, while the fruit microbiome shows no corresponding shifts

The microbiome of a vineyard may play a critical role in fruit development, and consequently, may impact quality properties of grape and wine. Vineyard management approaches that have directly manipulated the microbiome of grape clusters have been studied, but little is known about how vineyard management practices that impact the soil microbial pool can influence this dynamic. We examined three under-vine soil management practices: 1) herbicide application, 2) soil cultivation (vegetation removal), and 3) natural vegetation (no vegetation removal) in a Riesling vineyard in New York over a three-year period. The microbiomes associated with soil and grapes were profiled using high-throughput sequencing of the bacterial 16 S rRNA gene and fungal ITS regions. Our results showed that soil bacterial composition under natural vegetation differs from that seen in glyphosate-maintained bare soil. Soil fungal composition under the natural vegetation treatment was distinct from other treatments. Although our study revealed soil microbiome shifts based on under-vine management, there were no corresponding changes in fruit-associated microbial composition. These results suggested that other vineyard management practices or environmental factors are more influential in shaping the grape-associated microbiome.

Metagenomic Approaches to Investigate the Contribution of the Vineyard Environment to the Quality of Wine Fermentation: Potentials and Difficulties

The winemaking is a complex process that begins in the vineyard and ends at consumption moment. Recent reports have shown the relevance of microbial populations in the definition of the regional organoleptic and sensory characteristics of a wine. Metagenomic approaches, allowing the exhaustive identification of microorganisms present in complex samples, have recently played a fundamental role in the dissection of the contribution of the vineyard environment to wine fermentation. Systematic approaches have explored the impact of agronomical techniques, vineyard topologies, and climatic changes on bacterial and fungal populations found in the vineyard and in fermentations, also trying to predict or extrapolate the effects on the sensorial characteristics of the resulting wine. This review is aimed at highlighting the major technical and experimental challenges in dissecting the contribution of the vineyard and native environments microbiota to the wine fermentation process, and how metagenomic approaches can help in understanding microbial fluxes and selections across the environments and specimens related to wine fermentation.

Geographical and Cultivar Features Differentiate Grape Microbiota in Northern Italy and Spain Vineyards

Recent studies have highlighted the role of the grapevine microbiome in addressing a wide panel of features, ranging from the signature of field origin to wine quality. Although the influence of cultivar and vineyard environmental conditions in shaping the grape microbiome have already been ascertained, several aspects related to this topic, deserve to be further investigated. In this study, we selected three international diffused grapevine cultivars (Cabernet Sauvignon, Syrah, and Sauvignon Blanc) at three germplasm collections characterized by different climatic conditions [Northern Italy (NI), Italian Alps (AI), and Northern Spain (NS)]. The soil and grape microbiome was characterized by 16s rRNA High Throughput Sequencing (HTS), and the obtained results showed that all grape samples shared some bacterial taxa, regardless of sampling locality (e.g., Bacillus, Methylobacterium, Sphingomonas, and other genera belonging to Alphaproteobacteria, Gammaproteobacteria, and Actinobacteria). However, some Operational Taxonomic Units (OTUs) could act as geographical signatures and in some cases as cultivar fingerprint. Concerning the origin of the grape microbiome, our study confirms that vineyard soil represents a primary reservoir for grape associated bacteria with almost 60% of genera shared between the soil and grape. At each locality, grapevine cultivars shared a core of bacterial genera belonging to the vineyard soil, as well as from other local biodiversity elements such as arthropods inhabiting or foraging in the vineyard. Finally, a machine learning analysis showed that it was possible to predict the geographical origin and cultivar of grape starting from its microbiome composition with a high accuracy (9 cases out of 12 tested samples). Overall, these findings open new perspectives for the development of more comprehensive and integrated research activities to test which environmental variables have an effective role in shaping the microbiome composition and dynamics of cultivated species over time and space.

Starter cultures as biocontrol strategy to prevent Brettanomyces bruxellensis proliferation in wine

Brettanomyces bruxellensis is a common and significant wine spoilage microorganism. B. bruxellensis strains generally detain the molecular basis to produce compounds that are detrimental for the organoleptic quality of the wine, including some classes of volatile phenols that derive from the sequential bioconversion of specific hydroxycinnamic acids such as ferulate and p-coumarate. Although B. bruxellensis can be detected at any stage of the winemaking process, it is typically isolated at the end of the alcoholic fermentation (AF), before the staring of the spontaneous malolactic fermentation (MLF) or during barrel aging. For this reason, the endemic diffusion of B. bruxellensis leads to consistent economic losses in the wine industry. Considering the interest in reducing sulfur dioxide use during winemaking, in recent years, biological alternatives, such as the use of tailored selected yeast and bacterial strains inoculated to promote AF and MLF, are actively sought as biocontrol agents to avoid the “Bretta” character in wines. Here, we review the importance of dedicated characterization and selection of starter cultures for AF and MLF in wine, in order to reduce or prevent both growth of B. bruxellensis and its production of volatile phenols in the matrix.

The Grapevine and Wine Microbiome: Insights from High-Throughput Amplicon Sequencing

From the time when microbial activity in wine fermentation was first demonstrated, the microbial ecology of the vineyard, grape, and wine has been extensively investigated using culture-based methods. However, the last 2 decades have been characterized by an important change in the approaches used for microbial examination, due to the introduction of DNA-based community fingerprinting methods such as DGGE, SSCP, T-RFLP, and ARISA. These approaches allowed for the exploration of microbial community structures without the need to cultivate, and have been extensively applied to decipher the microbial populations associated with the grapevine as well as the microbial dynamics throughout grape berry ripening and wine fermentation. These techniques are well-established for the rapid more sensitive profiling of microbial communities; however, they often do not provide direct taxonomic information and possess limited ability to detect the presence of rare taxa and taxa with low abundance. Consequently, the past 5 years have seen an upsurge in the application of high-throughput sequencing methods for the in-depth assessment of the grapevine and wine microbiome. Although a relatively new approach in wine sciences, these methods reveal a considerably greater diversity than previously reported, and identified several species that had not yet been reported. The aim of the current review is to highlight the contribution of high-throughput next generation sequencing and metagenomics approaches to vineyard microbial ecology especially unraveling the influence of vineyard management practices on microbial diversity.

From Vineyard Soil to Wine Fermentation: Microbiome Approximations to Explain the "terroir" Concept

Wine originally emerged as a serendipitous mix of chemistry and biology, where microorganisms played a decisive role. From these ancient fermentations to the current monitored industrial processes, winegrowers and winemakers have been continuously changing their practices according to scientific knowledge and advances. A new enology direction is emerging and aiming to blend the complexity of spontaneous fermentations with industrial safety of monitored fermentations. In this context, wines with distinctive autochthonous peculiarities have a great acceptance among consumers, causing important economic returns. The concept of terroir, far from being a rural term, conceals a wide range of analytical parameters that are the basis of the knowledge-based enology trend. In this sense, the biological aspect of soils has been underestimated for years, when actually it contains a great microbial diversity. This soil-associated microbiota has been described as determinant, not only for the chemistry and nutritional properties of soils, but also for health, yield, and quality of the grapevine. Additionally, recent works describe the soil microbiome as the reservoir of the grapevine associated microbiota, and as a contributor to the final sensory properties of wines. To understand the crucial roles of microorganisms on the entire wine making process, we must understand their ecological niches, population dynamics, and relationships between ‘microbiome- vine health’ and ‘microbiome-wine metabolome.’ These are critical steps for designing precision enology practices. For that purpose, current metagenomic techniques are expanding from laboratories, to the food industry. This review focuses on the current knowledge about vine and wine microbiomes, with emphasis on their biological roles and the technical basis of next-generation sequencing pipelines. An overview of molecular and informatics tools is included and new directions are proposed, highlighting the importance of –omics technologies in wine research and industry.

Isolation and Identification of the Indigenous Yeast Population during Spontaneous Fermentation of Isabella (Vitis labrusca L.) Grape Must

Grape must harbors a complex community of yeast species responsible for spontaneous alcoholic fermentation. Although there are detailed studies on the microbiota of Vitis vinifera L. grapes, less is known about the diversity and behavior of yeast communities present on fermenting grape must from other species of Vitis. In this work, we used a culture-dependent method to study the identity and dynamics of the indigenous yeast population present during the spontaneous fermentation of Isabella (Vitis labrusca L.) grape must. Alcoholic fermentation was conducted using standard enological practices, and the associated non-Saccharomyces and S. cerevisiae yeast community was analyzed using selective growth media and 5.8-ITS DNA sequencing. Candida californica, Candida hellenica, Starmerella bacillaris (synonym Candida zemplinina), Hanseniaspora uvarum, and Hanseniaspora vineae were the main non-Saccharomyces species identified on Isabella fermenting must. Issatchenkia hanoiensis, a yeast species rarely found on Vitis vinifera L. grapes, was also recognized on Isabella grape must. Candida azymoides, Candida californica and Pichia cecembensis, identified in this work on Isabella fermenting must, have not previously been found on Vitis vinifera L. grape must. Interestingly, C. azymoides, I. hanoiensis and P. cecembensis have recently been isolated from the surface of Vitis labrusca L. grapes from vineyards in the Azores archipelago, suggesting that specific Vitis-yeast species associations are formed independently of geographic origin. We suggest that C. azymoides, C. californica, and P. cecembensis are yeast species preferentially associated with Vitis labrusca L. grapes. Specific biological interactions between grapevines and yeast species may underlie the assembly of differential Vitis-microbial communities.

The quest for lower alcoholic wines

Wine industry is engaged in finding technological ways to decrease alcohol concentration in wines without spoiling their organoleptic properties. Such challenge requires, among other strategies, modification of the yeast strains carrying out the fermentation. In this issue of Microb. Biotechnol., Goold and colleagues have reviewed one of the most straightforward yeast modification, altering its metabolism to produce glycerol instead of alcohol.

Wine microbiology is driven by vineyard and winery anthropogenic factors

The effects of different anthropic activities (vineyard: phytosanitary protection; winery: pressing and sulfiting) on the fungal populations of grape berries were studied. The global diversity of fungal populations (moulds and yeasts) was performed by pyrosequencing. The anthropic activities studied modified fungal diversity. Thus, a decrease in biodiversity was measured for three successive vintages for the grapes of the plot cultivated with Organic protection compared to plots treated with Conventional and Ecophyto protections. The fungal populations were then considerably modified by the pressing‐clarification step. The addition of sulfur dioxide also modified population dynamics and favoured the domination of the species Saccharomyces cerevisiae during fermentation. The non‐targeted chemical analysis of musts and wines by FT‐ICR‐MS showed that the wines could be discriminated at the end of alcoholic fermentation as a function of adding SO₂ or not, but also and above all as a function of phytosanitary protection, regardless of whether these fermentations took place in the presence of SO₂ or not. Thus, the existence of signatures in wines of chemical diversity and microbiology linked to vineyard protection has been highlighted.