Regional microbial signatures positively correlate with differential wine phenotypes: evidence for a microbial aspect to terroir

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.

Trapping Entomopathogenic Fungi from Vine Terroir Soil Samples with Insect Baits for Controlling Serious Pests

Fungi are eukaryotic microorganisms with many forms and certain demands about the soil they colonize, which reveal the conditions that prevail therein. Although they can often kill pests without damaging plants or humans, they are not widely used as pesticides as they are not easy to handle and require much time before they act. Nevertheless, insects can be used as baits to trap these entomopathogenic fungi, giving information about their distribution within the terroir. The purpose of this study was to investigate the soil distribution of entomopathogenic fungi species in soil samples from two vine soil terroirs. Nine fungi were identified in total, but M. anisopliae and B. bassiana showed the greatest frequency, which was expressed by difference in adult bait mortality among species. These fungi had not been previously documented in vine terroirs.

A review on the aroma composition of Vitis vinifera L. Pinot noir wines: origins and influencing factors

Vitis vinifera L. Pinot noir still wines are some of the most popular and expensive red wines in the world. Several research articles are reported in literature concerning the impacts of viticultural and enological practices, and vineyard location, on Pinot noir still wine aroma. This review summarizes the previous and latest literature pertaining to volatile compounds including esters, higher alcohols and C₁₃-norisoprenoids, and their effect on Pinot noir wine perceived aroma. Their origin and behavior are discussed, as well as their role in regional differentiation. The first part of this review paper presents an overview of volatile compounds that are usually found in Pinot noir still wines at concentrations higher than their odor detection threshold. The second part deals with studies pertaining to human inputs that impact on Pinot noir wine aroma profile such as viticulture and winemaking interventions. The role of the vineyard site is also revised. This review concludes by considering what further opportunities are available to researchers in this field for greater control over Pinot noir wine quality outcomes.

Detection of microbiota in the vineyards of the Tokaj wine region

Tokaj is an important Central European wine-growing area with controlled planting and authorized varieties of white vines. This area has a specific microflora composition which changes based on its climate dependence, as well as during the fermentation process of wine production. Therefore, the aim of this study was, by culture examination of the samples, to detect the microbiota of soil, leaves, berries and fermentation must from two vineyards from the Slovak part of Tokaj. The highest total viable count (5.60 ±0.01 log cfu.g-1) and the highest total yeast and mould count (4.32 ±0.01 log cfu.g-1) in soil samples were recorded in vineyard Berecký. The highest total viable count in soil samples (6.71 ±0.01 log cfu.g-1) was confirmed by examination of samples originating from the vineyard of Čierna Hora. When determining the total yeast and mould count, the highest numbers were recorded in the must samples (4.15 ±0.01 log cfu.mL-1). Lactic acid bacteria were collected in samples from both vineyards, only in very low numbers. Overall, statistically significant differences (p <0.001) were detected by comparing the microbiota of the samples taken from the Berecký and Čierna Hora vineyards. The specific characterisation and identification of yeast was carried out using ITS-PCR-RFLP methods. The analysis confirmed the presence of yeasts of Saccharomyces cerevisiae, Zygosaccharomyces bailii, Zygosaccharomyces rouxii, Candida parapsilosis and Candida tenuis and their subsequent transfer to the must at varying percentages.

Geographical Origin Has a Greater Impact on Grape Berry Fungal Community than Grape Variety and Maturation State

We used barcoded sequencing to analyze the eukaryotic population in the grape berries at different ripening states in four Australian vineyards. Furthermore, we used an innovative compositional data analysis for assessing the diversity of microbiome communities. The novelty was the introduction of log-ratio balances between the detected genera. Altogether, our results suggest that fungal communities were more impacted by the geographical origin of the Australian vineyards than grape variety and harvest time. Even if the most abundant genera were Aureobasidium and Mycosphaerella, they were ubiquitous to all samples and were not discriminative. In fact, the balances and the fungal community structure seemed to be greatly affected by changes of the genera Penicillium, Colletotrichum, Aspergillus, Rhodotorula, and Botrytis. These results were not evident from the comparison of relative abundance based on OTU counts alone, remarking the importance of the balance analysis for microbiome studies.

Grapevine Phyllosphere Community Analysis in Response to Elicitor Application against Powdery Mildew

The reduction of antimicrobial treatments and mainly the application of environmentally friendly compounds, such as resistance elicitors, is an impelling challenge to undertake more sustainable agriculture. We performed this research to study the effectiveness of non-conventional compounds in reducing leaf fungal attack and to investigate whether they influence the grape phyllosphere. Pathogenicity tests were conducted on potted Vitis vinifera "Nebbiolo" and "Moscato" cultivars infected with the powdery mildew agent (Erysiphe necator) and treated with three elicitors. Differences in the foliar microbial community were then evaluated by community-level physiological profiling by using Biolog^TM EcoPlates, high throughput sequencing of the Internal Transcribed Spacer (ITS) region, and RNA sequencing for the viral community. In both cultivars, all products were effective as they significantly reduced pathogen development. EcoPlate analysis and ITS sequencing showed that the microbial communities were not influenced by the alternative compound application, confirming their specific activity as plant defense elicitors. Nevertheless, "Moscato" plants were less susceptible to the disease and presented different phyllosphere composition, resulting in a richer viral community, when compared with the "Nebbiolo" plants. The observed effect on microbial communities pointed to the existence of distinct genotype-specific defense mechanisms independently of the elicitor application.

Application of nanotechnology based-biosensors in analysis of wine compounds and control of wine quality and safety: A critical review

Nanotechnology is one of the most promising future technologies for the food industry. Some of its applications have already been introduced in analytical techniques and food packaging technologies. This review summarizes existing knowledge about the implementation of nanotechnology in wine laboratory procedures. The focus is mainly on recent advancements in the design and development of nanomaterial-based sensors for wine compounds analysis and assessing wine safety. Nanotechnological approaches could be useful in the wine production process, to simplify wine analysis methods, and to improve the quality and safety of the final product.

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.

Microbiome of vineyard soils is shaped by geography and management

BACKGROUND

Despite their importance as a reservoir of biodiversity, the factors shaping soil microbial communities and the extent by which these are impacted by cultivation are still poorly understood. Using 16S rRNA gene and ITS sequencing, we characterized the soil microbiota of vineyards and of neighboring permanent grassland soils in the Italian province of Trentino, and correlated their structure and composition to location, chemical properties of the soil, and land management.

RESULTS

Bacterial communities had a core of conserved taxa accounting for more than 60% of the reads of each sample, that was influenced both by geography and cultivation. The core fungal microbiota was much smaller and dominated by geography alone. Cultivation altered the structure and composition of the soil microbiota both for bacteria and fungi, with site-specific effects on their diversity. The diversity of bacterial and fungal communities was generally inversely correlated across locations. We identified several taxa that were impacted by the chemical properties and texture of the soil.

CONCLUSIONS

Our results highlight the different responses of bacterial and fungal communities to environmental factors and highlight the need to characterize both components of the soil microbiota to fully understand the factors that drive their variability.

Small scale fungal community differentiation in a vineyard system

Microbes influence the quality of agricultural commodities and contribute to their distinctive sensorial attributes. Increasingly studies have demonstrated not only differential geographic patterns in microbial communities and populations, but that these contribute to valuable regionally distinct agricultural product identities, the most well-known example being wine. However, little is understood about microbial geographic patterns at scales of less than 100 km. For wine, single vineyards are the smallest (and most valuable) scale at which wine is asserted to differ; however, it is unknown whether microbes play any role in agricultural produce differentiation at this scale. Here we investigate whether vineyard fungal communities and yeast populations driving the spontaneous fermentation of fruit from these same vineyards are differentiated using metagenomics and population genetics. Significant differentiation of fungal communities was revealed between four Central Otago (New Zealand) Pinot Noir vineyard sites. However, there was no vineyard demarcation between fermenting populations of S. cerevisiae. Overall, this provides evidence that vineyard microbiomes potentially contribute to vineyard specific attributes in wine. Understanding the scale at which microbial communities are differentiated, and how these communities influence food product attributes has direct economic implications for industry and could inform sustainable management practices that maintain and enhance microbial diversity.

Influence of Native Saccharomyces cerevisiae Strains from D.O. “Vinos de Madrid” in the Volatile Profile of White Wines

Yeasts during alcoholic fermentation form a vast number of volatile compounds that significantly influence wine character and quality. It is well known that the capacity to form aromatic compounds is dependent on the yeast strain. Thus, the use of native yeast strains, besides promoting biodiversity, encourages the conservation of regional sensory properties. In this work, we studied the volatile profile of Malvar wines fermented with 102 Saccharomyces cerevisiae yeast strains, isolated from vineyards and cellars belonging to the D.O. “Vinos de Madrid”. The wines elaborated with different S. cerevisiae showed a good classification by cellar of origin. Additionally, seven sensory descriptors have helped to classify the wines depending on their predominant aromatic character. Twenty-nine Saccharomyces strains, belonging to five of six cellars in the study, were characterized by producing wines with a fruity/sweet character. Floral, solvent, and herbaceous descriptors are more related to wines elaborated with Saccharomyces strains from organic cellars A, E, and F. Based on these findings, winemakers may use their best native S. cerevisiae strains, which add personality to their wine. Therefore, this study contributes to promoting the use of native Saccharomyces yeasts in winemaking.

Changes in chemical profile of Cascade hop cones according to the growing area

BACKGROUND

The growing area has a substantial effect on plants, affecting secondary metabolism. For hops, different authors have studied the effect of growing area on the chemical composition of cones with the aim of verifying and understanding the changes in hop characters. Despite the scant literature the subject receives increasing attention by brewers and hop growers. The present study aimed to characterize, using gas chromatography-mass spectrometry (GC-MS), and high-performance liquid chromatography with ultraviolet detection (HPLC-UV), cones of hop (Humulus lupulus L.) cultivar Cascade. Plant material was obtained from nine different areas of Italy and compared with Cascade samples grown in the United States, Germany and Slovenia.

RESULTS

Differences in bitter acids and xanthohumol content were observed. Nevertheless, no correlation between bitter acids and xanthohumol production, on the one hand, and rainfall, temperatures and latitude, on the other hand, were observed in our samples. The Slovenia samples were richer in molecules that confer hoppy, woody and flower notes; USA2 samples were more characterized by woody, earthy, grassy and floral aroma, quite different characters if compared to USA1, which had the lowest presence of grassy aromatic compounds. In the Italian samples, TRENTINO was the genotype most characterized by limonene presence.

CONCLUSION

The results of this study are indicative of the importance for hop users to know and characterize hops coming from different growing regions. The study pays special attention to the characterization of the differences in chemical characters of Cascade hop in Italy, where hop cultivation has developed only recently, but is in continuous expansion. © 2019 Society of Chemical Industry.

Selected Indigenous Saccharomyces cerevisiae Strains as Profitable Strategy to Preserve Typical Traits of Primitivo Wine

Wine production by inoculated fermentation with commercial Saccharomyces cerevisiae strains is an ordinary practice in modern winemaking in order to assure the final quality of wine, although this procedure results in the production of highly homogeneous wines. The use of indigenous selected starters represents a useful tool to control alcoholic grape must fermentation, safeguarding the typical sensory characteristics of wine produced from specific regions. In this study, we selected three indigenous S. cerevisiae strains among 16 indigenous strains previously isolated from the spontaneous fermentation of Primitivo grapes, which were collected from the vineyards of three different cellars. The three selected starters (one for each cellar) were tested during fermentations at pilot scale by performing in each cellar two trials: one with an indigenous starter (specific for the winery), and one with the commercial starter AWRI796 (common to all the cellars). Starter dominance ability and influence on aromatic quality of the wine were used as criteria to test the suitability of these indigenous starters to be used at the cellar scale. The results obtained in this study showed that the indigenous strains were characterized by very high dominance ability, and the aromatic quality of wine was strongly influenced both by the inoculated strain and the interaction strain/grape must.

The Biodiversity of Saccharomyces cerevisiae in Spontaneous Wine Fermentation: The Occurrence and Persistence of Winery-Strains

Saccharomyces cerevisiae populations occurring in spontaneous wine fermentations display a high polymorphism, although few strains are generally able to dominate the fermentative process. Recent studies have suggested that these indigenous S. cerevisiae strains are representative of a specific oenological ecosystem, being associated to a given wine-producing area or a single winery. In contrast, according to other ecological studies, no correlation between genotypic and phenotypic groups of the native S. cerevisiae strains and their origin was found. In this work, several S. cerevisiae strains were isolated in consecutive years from spontaneous fermentations carried out in the same wineries located in different oenological areas in Tuscany, and their persistence was assessed by molecular methods. Some predominant S. cerevisiae strains persisted in different fermentations in the same winery from one year to another and they seemed to be representative of a single winery rather than of an oenological area. Therefore, data suggested the idea of the “winery effect” or a microbial terroir at a smaller scale. The use of these typical strains as starter yeasts could provide wines with the distinctive characteristics of a particular winery or sub-zone.

Climate Changes and Food Quality: The Potential of Microbial Activities as Mitigating Strategies in the Wine Sector

Climate change threatens food systems, with huge repercussions on food security and on the safety and quality of final products. We reviewed the potential of food microbiology as a source of biotechnological solutions to design climate-smart food systems, using wine as a model productive sector. Climate change entails considerable problems for the sustainability of oenology in several geographical regions, also placing at risk the wine typicity. The main weaknesses identified are: (i) The increased undesired microbial proliferation; (ii) the improved sugars and, consequently, ethanol content; (iii) the reduced acidity and increased pH; (iv) the imbalanced perceived sensory properties (e.g., colour, flavour); and (v) the intensified safety issues (e.g., mycotoxins, biogenic amines). In this paper, we offer an overview of the potential microbial-based strategies suitable to cope with the five challenges listed above. In terms of microbial diversity, our principal focus was on microorganisms isolated from grapes/musts/wines and on microbes belonging to the main categories with a recognized positive role in oenological processes, namely Saccharomyces spp. (e.g., Saccharomyces cerevisiae), non-Saccharomyces yeasts (e.g., Metschnikowia pulcherrima, Torulaspora delbrueckii, Lachancea thermotolerans, and Starmerella bacillaris), and malolactic bacteria (e.g., Oenococcus oeni, Lactobacillus plantarum).

A Metagenomic-Based Approach for the Characterization of Bacterial Diversity Associated with Spontaneous Malolactic Fermentations in Wine

This study reports the first application of a next generation sequencing (NGS) analysis. The analysis was designed to monitor the effect of the management of microbial resources associated with alcoholic fermentation on spontaneous malolactic consortium. Together with the analysis of 16S rRNA genes from the metagenome, we monitored the principal parameters linked to MLF (e.g., malic and lactic acid concentration, pH). We encompass seven dissimilar concrete practices to manage microorganisms associated with alcoholic fermentation: Un-inoculated must (UM), pied-de-cuve (PdC), Saccharomyces cerevisiae (SC), S. cerevisiae and Torulaspora delbrueckii co-inoculated and sequentially inoculated, as well as S. cerevisiae and Metschnikowia pulcherrima co-inoculated and sequentially inoculated. Surprisingly, each experimental modes led to different taxonomic composition of the bacterial communities of the malolactic consortia, in terms of prokaryotic phyla and genera. Our findings indicated that, uncontrolled AF (UM, PdC) led to heterogeneous consortia associated with MLF (with a relevant presence of the genera Acetobacter and Gluconobacter), when compared with controlled AF (SC) (showing a clear dominance of the genus Oenococcus). Effectively, the SC trial malic acid was completely degraded in about two weeks after the end of AF, while, on the contrary, malic acid decarboxylation remained uncomplete after 7 weeks in the case of UM and PdC. In addition, for the first time, we demonstrated that both (i) the inoculation of different non-Saccharomyces (T. delbrueckii and M. pulcherrima) and, (ii) the inoculation time of the non-Saccharomyces with respect to S. cerevisiae resources (co-inoculated and sequentially inoculated) influence the composition of the connected MLF consortia, modulating MLF performance. Finally, we demonstrated the first findings of delayed and inhibited MLF when M. pulcherrima, and T. delbrueckii were inoculated, respectively. In addition, as a further control test, we also assessed the effect of the inoculation with Oenococcus oeni and Lactobacillus plantarum at the end of alcoholic fermentation, as MLF starter cultures. Our study suggests the potential interest in the application of NGS analysis, to monitor the effect of alcoholic fermentation on the spontaneous malolactic consortium, in relation to wine.

Indigenous Yeast Interactions in Dual-Starter Fermentations May Improve the Varietal Expression of Moschofilero Wine

Multi-starter wine fermentations employing non-Saccharomyces (NS) yeasts are becoming an emerging trend in winemaking. It is therefore important to determine the impacts of different NS strains in the wine phenotype and in particular the aroma outputs in different inoculation schemes and fermentation conditions. Here, two native NS yeasts, Lachancea thermotolerans LtMM7 and Hanseniaspora uvarum HuMM19, were assessed for their ability to improve the quality of Moschofilero, a Greek aromatic white wine. The NS strains were initially examined in laboratory scale fermentations in mixed inoculations with ScMM23, a native Saccharomyces cerevisiae strain. LtMM7 was selected to be further evaluated in pilot scale fermentations. Five different inoculation schemes were considered: single inoculation of ScMM23 (IS), simultaneous inoculation of ScMM23 with HuMM19 (SMH) or LtMM7 (SML), and sequential inoculation of HuMM19 (SQH) or LtMM7 (SQL) followed by ScMM23. At laboratory scale fermentations, the chemical profiles were largely affected by both the NS species and the inoculation scheme applied. The sequential inoculation using HuMM19 produced the most divergent wine phenotype. However, HuMM19 caused significant increases in acetic acid and ethyl acetate levels that impeded its use in pilot scale trials. LtMM7 significantly affected the chemical profiles of wines produced at the winery, especially in the sequential inoculation scheme. Importantly, LtMM7 significantly increased the levels of acetate esters or ethyl esters, depending on the inoculation method applied. In particular, acetate esters like isobutyl acetate, hexyl acetate, and 2-phenylethyl acetate, which all impart fruity or floral aromas, were significantly increased in SQL. On the other hand, higher levels of total ethyl esters were associated with SML. The most striking differences were observed in the levels of fruit-impair esters like ethyl decanoate, 3-methylbutyl octanoate, and isoamyl hexanoate. This is the first study to report a significant increase in the ethyl ester fraction by L. thermotolerans. Interestingly, L. thermotolerans in SQL also increased the concentrations of damascenone and geraniol, the major teprenic compound of Moschofilero, which are associated with several typical floral and fruity aromas of the variety. Present results show that L. thermotolerans may enhance the varietal character and increase the chemical complexity of Moschofilero wines.

Effect of Vine Water and Nitrogen Status, as Well as Temperature, on Some Aroma Compounds of Aged Red Bordeaux Wines

Wine aging bouquet is defined as a positive, complex evolution of aromas during bottle aging. The aim of this study was to look for the link between some of the vine status parameters and the development, during wine aging, of volatile compounds such as DMS, tabanones, and some wine aromatic heterocycles. The potential influence of air temperature was investigated as well as vine nitrogen and water status. Wines were obtained by microvinification from plots of Vitis vinifera L. cv. Merlot, Cabernet-Sauvignon, and Cabernet franc, over vintages from 1996 to 2007, and cellar-aged until 2014. Wine aging aromas were quantified using gas chromotography-mass spectrometry. The effects of the vintage and vine water and nitrogen status were greater than the varietal effects. The nine aroma compounds measured showed very high levels in the 2003 vintage. The results revealed a positive link between vine nitrogen status and dimethyl-sulfide and N, S, O-heterocycle levels measured in the aged wines. Levels of 4-[2-butylidene]-3,5,5-trimethyl-2-cyclohexen-1-one and 4-[( 3E)-1-butylidene]-3,5,5-trimethyl-2-cyclohexen-1-one (megastigmatrienones; tabanone) isomers increased when the vines were affected by a water deficit.

Yeast species isolated from Texas High Plains vineyards and dynamics during spontaneous fermentations of Tempranillo grapes

Vineyards and grape musts harbor complex locally specific microbial communities, among which yeast species can be responsible of spontaneous alcoholic fermentation. Although relying on indigenous yeast can be a risk for winemaking, local yeast diversity is associated with complexity and stronger identity of the wine produced, compared to inoculated alcoholic fermentation with commercial yeast strains. In this context, the main yeast species present on grapes, leaves and soils of Tempranillo and Cabernet Sauvignon vineyards in the hot semi-arid climate of the Texas High Plains area were investigated, as well as the presence and dynamics of yeast species during spontaneous fermentations of Tempranillo grapes from the same vineyards. Molecular characterization of yeast species was performed using culture-dependent 5.8S-ITS restriction fragment length polymorphism method and sequencing. Yeast species recovered from grapes, leaves, and soils were mainly dominated by Aureobasidium pullulans, Cryptococcus species, Filobasidium species and Naganishia species, typical members of the vineyard environment. One isolate of potential enological interest, Lachancea thermotolerans, a fermenting yeast with potential in must acidification, was recovered from the vineyard environment. However, spontaneous alcoholic fermentations revealed the presence of fermenting yeast species, including Saccharomyces cerevisiae, Lachancea thermotolerans and Hanseniaspora species. The presence of the three aforementioned species is of extreme interest for winemaking in the Texas High Plains area. Indeed, Saccharomyces cerevisiae is the model for alcoholic fermentation, Hanseniaspora species have been shown to improve palatability of wines, and Lachancea thermotolerans has become of increasing interest due to its potential to acidify musts and palatability. One of the main characteristics of grapes grown in the Texas High Plains area being the lack of acidity, focusing on these three yeast species could promote the development of locally oriented started cultures for the production of wines with a stronger local identity.

Distribution of Oenococcus oeni populations in natural habitats

Oenococcus oeni is the lactic acid bacteria species most commonly encountered in wine, where it develops after the alcoholic fermentation and achieves the malolactic fermentation that is needed to improve the quality of most wines. O. oeni is abundant in the oenological environment as well as in apple cider and kombucha, whereas it is a minor species in the natural environment. Numerous studies have shown that there is a great diversity of strains in each wine region and in each product or type of wine. Recently, genomic studies have shed new light on the species diversity, population structure, and environmental distribution. They revealed that O. oeni has unique genomic features that have contributed to its fast evolution and adaptation to the enological environment. They have also unveiled the phylogenetic diversity and genomic properties of strains that develop in different regions or different products. This review explores the distribution of O. oeni and the diversity of strains in natural habitats.

Microbiota of different wine grape berries

The wine grape berries share a complex microbial ecology including filamentous fungi, yeasts and bacteria. The microbiota reveals different physiological characteristics and depends on the grape ripening stage and the availability of nutrients with different effect on wine production. The microbiota of grape berries (n = 12) was isolated and identified in the present study. The samples were collected in September 2018. Grape berries were obtained from Vrbovo vineyard located in Slovakia. The grape berries investigated belonged to Blue Frankish, Cabernet Sauvignon, Chardonnay, Dornfelder, Feteasca regala, Green Veltliner, Irsai Oliver, Mūller Thurgau, Pálava, Pinot Blanc, Rhinriesling and Welschriesling varieties. The microorganisms were cultivated on Malt extract agar (MEA) at 25 °C for five days in aerobically for microscopic filamentous fungi and Tryptone Soya agar (TSA) at 37 °C for 24 – 48 h aerobically for bacteria and yeasts. Total bacterial counts on different wine grape berries ranged from 2.57 ±0.09 in Chardonnay to 4.39 ±0.21 log CFU.g-1 in Pálava. Microscopic filamentous fungi count ranged from 1.18 ±0.03 in Blue Frankish to 2.60 ±0.17 log CFU.g-1 in Welschriesling. MALDI-TOF MS Biotyper mass spectrometry was used for identification of microorganisms (bacteria and yeasts) and microscopic filamentous fungi with manuals. The most identified microscopic fungal species was Alternaria sp., for yeasts Issatchenkia orientalis and Leuconostoc mesenteroides subsp. mesenteroides for bacteria.

Chemical Characteristics of Sangiovese Wines from California and Italy of 2016 Vintage

Sangiovese is the most widespread Italian red cultivar and constitutes the basis of internationally known wines such as Chianti and Brunello di Montalcino. Outside of Europe, Argentina is the largest producer, followed by the United States. This study sought to define and compare 2016 vintage Sangiovese wine composition from various production regions in California and Italy. Forty-six commercial Sangiovese wines from California and Italy were analyzed for volatile profile, color, phenolic, and elemental content. This study demonstrates that it is possible to determine regional differences among wines based on these chemical profiles. However, some Californian and Italian wine had similar chemical compositions. In order to compare Californian and Italian wines, Californian wine reference models were developed using the chemical parameters from Sangiovese wines, performing a Soft Independent Modeling of Class Analogy (SIMCA). To our knowledge, this is the first time that an extensive regionality study has been attempted for Sangiovese wines.

Shared and unique features of bacterial communities in native forest and vineyard phyllosphere

Phyllosphere bacteria have received little attention despite their important roles in shaping plant performance traits. In this study, we characterize the bacterial communities on leaves of native trees inhabiting sclerophyllous forests in central Chile, one of the world's biodiversity hotspots. Additionally, we provide profiles of bacterial communities on grape leaves and berries of organic and conventional vineyards. Results of 16S rRNA gene amplicon sequence analysis showed that 45% of OTUs were shared across forest leaves, grape leaves, and grape berries. Conventional management had higher number of OTUs shared with forest leaves than organic management. In addition, grape leaves subjected to conventional management had higher alpha diversity than those with organic management, while no significant effect of agricultural management was observed in grape berries. Indicator analysis showed that Bdellovibrio, Beijerinckia, and Spirosoma were typical for forest leaves, whereas Enhydrobacter, Delftia, Proteiniclasticum, Arsenicicoccus, and Alkaliphilus were typical for the vineyard phyllosphere. Regarding agricultural managements, Beijerinckia, Sedimentibacter, Nesterenkonia, Gluconobacter, Conexibacter, and Anaeromyxobacter were typical for conventional grape leaves, whereas no genus-level indicator was found for organic vineyard leaves. These results provide new insights of the diversity patterns of the phyllosphere microbiome in native and cultivated lands and suggest that both of these microbiomes are connected and integrated systems.

Fermentation as a driver for food innovation

The following paper is reviewing the current trends in research connected to fermentation, highlighting the work carried out in the various research kitchens that have gained a new understanding of fermentation in the recent years. The reflection on the developments made both on microbiological as well on the technological level aims to create pathways within the research fields in order to foster new innovations within the food production system.

Evaluation of the ability of commercial wine yeasts to form biofilms (mats) and adhere to plastic: implications for the microbiota of the winery environment

Commercially available active dried wine yeasts are regularly used by winemakers worldwide to achieve reliable fermentations and obtain quality wine. This practice has led to increased evidence of traces of commercial wine yeast in the vineyard, winery and uninoculated musts. The mechanism(s) that enables commercial wine yeast to persist in the winery environment and the influence to native microbial communities on this persistence is poorly understood. This study has investigated the ability of commercial wine yeasts to form biofilms and adhere to plastic. The results indicate that the biofilms formed by commercial yeasts consist of cells with a combination of different lifestyles (replicative and non-replicative) and growth modes including invasive growth, bud elongation, sporulation and a mat sectoring-like phenotype. Invasive growth was greatly enhanced on grape pulp regardless of strain, while adhesion on plastic varied between strains. The findings suggest a possible mechanism that allows commercial yeast to colonise and survive in the winery environment, which may have implications for the indigenous microbiota profile as well as the population profile in uninoculated fermentations if their dissemination is not controlled.

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.

Population and oenological characteristics of non-Saccharomyces yeasts associated with grapes of Northwestern Argentina

Yeasts population associated with grapes from Northwest Argentina, a region with a significant vine-growing increase over the past years, was evaluated. Ten species of non-Saccharomyces yeasts were identified from four grape varieties (Malbec, Merlot, Syrah and Torrontes) being Hanseniaspora uvarum the dominant species. Typing of isolates revealed genetic variability within Hanseniaspora genus and also high variability was observed according to their oenological characteristics. Based on the oenological properties, the most adequate strains as starter cultures were H. uvarum HuT7, HuMe15, HuS16, H. vineae HvT-mc1 and Metschnikowia pulcherrima MpT2/MpT3. These selected yeasts exhibited moderate resistance to SO₂, reduced values of volatile acidity, null or low production of H₂S, high levels of enzymes related to aroma and did not produce killer toxins. Further studies using mixed cultures of these non-Saccharomyces strains and S. cerevisiae are needed to validate the contribution of selected indigenous yeasts on wine organoleptic characteristics.

Population genomics reveals evolution and variation of Saccharomyces cerevisiae in the human and insects gut

The quest to discover the variety of ecological niches inhabited by Saccharomyces cerevisiae has led to research in areas as diverse as wineries, oak trees and insect guts. The discovery of fungal communities in the human gastrointestinal tract suggested the host's gut as a potential reservoir for yeast adaptation. Here, we report the existence of yeast populations associated with the human gut (HG) that differ from those isolated from other human body sites. Phylogenetic analysis on 12 microsatellite loci and 1715 combined CDSs from whole-genome sequencing revealed three subclusters of HG strains with further evidence of clonal colonization within the host's gut. The presence of such subclusters was supported by other genomic features, such as copy number variation, absence/introgressions of CDSs and relative polymorphism frequency. Functional analysis of CDSs specific of the different subclusters suggested possible alterations in cell wall composition and sporulation features. The phenotypic analysis combined with immunological profiling of these strains further showed that sporulation was related with strain-specific genomic characteristics in the immune recognition pattern. We conclude that both genetic and environmental factors involved in cell wall remodelling and sporulation are the main drivers of adaptation in S. cerevisiae populations in the human gut.

From the Field to the Bottle—An Integrated Strategy for Wine Authenticity

The wine sector is one of the most economically important agro-food businesses. The wine market value is largely associated to terroir, in some cases resulting in highly expensive wines that attract fraudulent practices. The existent wine traceability system has some limitations that can be overcome with the development of new technological approaches that can tackle this problem with several means. This review aims to call attention to the problem and to present several strategies that can assure a more reliable and authentic wine system, identifying existent technologies developed for the sector, which can be incorporated into the current traceability system.

The effect of sulfur dioxide addition at crush on the fungal and bacterial communities and the sensory attributes of Pinot gris wines

Modern day winemaking often involves the addition of sulfur dioxide (SO₂) at crush to act as both an antioxidant and an antimicrobial agent. While the effects of SO₂ on microbial communities and particularly on spoilage microorganisms has been well-studied, the advent of culture-independent molecular technologies, such as Illumina sequencing, allows the subject to be re-visited in a new context. High-throughput amplicon sequencing allows for a more thorough evaluation of microbial communities, as thousands of microbial sequences per sample can be identified and even rare microorganisms can be studied. This research investigated whether the addition of different levels of SO₂ at crush (0, 20, or 40 mg/L) would affect the composition of fungal and bacterial communities, as well as the sensory attributes of the resulting wines. Samples were taken from uninoculated fermentations of Pinot gris and analyzed via high-throughput amplicon sequencing using the Illumina MiSeq platform. Yeast relative abundance and overall fungal community composition differed among the SO₂ additions. Notably, a Hanseniaspora yeast appeared in all treatments and persisted until the end of alcoholic fermentation, although its relative abundance was significantly higher in the fermentations to which low or no SO₂ had been added. Two key wine sensory attributes (citrus aroma and pome fruit flavor) differed among the SO₂ treatments. This research provides an in-depth look into the fungal and bacterial communities during alcoholic fermentation and gives a better understanding of the microbial community response to SO₂ additions during the crush period.

Evidence of the genetic diversity and clonal population structure of Oenococcus oeni strains isolated from different wine-making regions of China

Studies of the genetic diversity and population structure of Oenococcus oeni (O. oeni) strains from China are lacking compared to other countries and regions. In this study, amplified fragment length polymorphism (AFLP) and multilocus sequence typing (MLST) methods were used to investigate the genetic diversity and regional evolutionary patterns of 38 O. oeni strains isolated from different wine-making regions in China. The results indicated that AFLP was markedly more efficient than MLST for typing O. oeni strains. AFLP distinguished 37 DNA patterns compared to 7 sequence types identified using MLST, corresponding to discriminatory indices of 0.999 and 0.602, respectively. The AFLP results revealed a high level of genetic diversity among the O. oeni strains from different regions of China, since two subpopulations and an intraspecific homology higher than 60% were observed. Phylogenetic analysis of the O. oeni strains using the MLST method also identified two major phylogroups, which were differentiated into two distinct clonal complexes by minimum spanning tree analysis. Neither intragenic nor intergenic recombination verified the existence of the clonal population structure of the O. oeni strains.

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.

Quantifying the Effects of Ethanol and Temperature on the Fitness Advantage of Predominant Saccharomyces cerevisiae Strains Occurring in Spontaneous Wine Fermentations

Different Saccharomyces cerevisiae strains are simultaneously or in succession involved in spontaneous wine fermentations. In general, few strains occur at percentages higher than 50% of the total yeast isolates (predominant strains), while a variable number of other strains are present at percentages much lower (secondary strains). Since S. cerevisiae strains participating in alcoholic fermentations may differently affect the chemical and sensory qualities of resulting wines, it is of great importance to assess whether the predominant strains possess a "dominant character." Therefore, the aim of this study was to investigate whether the predominance of some S. cerevisiae strains results from a better adaptation capability (fitness advantage) to the main stress factors of oenological interest: ethanol and temperature. Predominant and secondary S. cerevisiae strains from different wineries were used to evaluate the individual effect of increasing ethanol concentrations (0-3-5 and 7% v/v) as well as the combined effects of different ethanol concentrations (0-3-5 and 7% v/v) at different temperature (25-30 and 35°C) on yeast growth. For all the assays, the lag phase period, the maximum specific growth rate (μ_max) and the maximum cell densities were estimated. In addition, the fitness advantage between the predominant and secondary strains was calculated. The findings pointed out that all the predominant strains showed significantly higher μ_max and/or lower lag phase values at all tested conditions. Hence, S. cerevisiae strains that occur at higher percentages in spontaneous alcoholic fermentations are more competitive, possibly because of their higher capability to fit the progressively changing environmental conditions in terms of ethanol concentrations and temperature.

Effects of different management regimes on microbial biodiversity in vineyard soils

An active and diverse soil biota is important for maintaining crop productivity and quality, and preservation of these traits is a major goal of sustainable farming. This study aimed at unravelling the impact of different management practices on soil fungal and bacterial biodiversity in vineyards as a model for permanent crops. Species diversity was assessed using an amplicon sequencing approach in a long-term field experiment in the Rheingau wine region of Germany where integrated, organic and biodynamic management practices had been in place for 10 years. Fungal community composition under integrated management differed significantly from organic and biodynamic management, whereas fungal species richness remained unaffected. Soil under integrated management had a significantly reduced bacterial species richness compared to organic, but community composition was similar to organically and biodynamically managed soils. Highest fungal richness was obtained under cover crop between rows in topsoil, arising from cover cropping and organic carbon supply.

Differences Between Indigenous Yeast Populations in Spontaneously Fermenting Musts From V. vinifera L. and V. labrusca L. Grapes Harvested in the Same Geographic Location

Yeast communities associated with Vitis vinifera L. ecosystems have been widely characterized. Less is known, however, about yeast communities present in grapes and fermenting musts from Vitis non-vinifera ecosystems. Moreover, there are no comparative studies concerning yeast communities in grapes from V. vinifera L. and non-vinifera Vitis species in vineyards from a shared terroir. In this work, we have used a culture-dependent strategy, phenotypic analyses, and molecular genotyping, to study the most representative yeast species present in spontaneously fermenting musts of grapes harvested from neighboring V. vinifera L. (cv. Malbec) and V. labrusca L. (cv. Isabella) vineyards. Phenotypic analyses of H₂S production, ethanol tolerance and carbon utilization, on randomly selected strains of each Hanseniaspora uvarum, Starmerella bacillaris and Saccharomyces cerevisiae strains, as well as microsatellite genotyping of S. cerevisiae isolates from each the Malbec and Isabella grape musts, suggest that V. vinifera L. and V. labrusca L. ecosystems could harbor different yeast strain populations. Thus, microbial communities in exotic Vitis species may offer opportunities to look for unique yeast strains that could not be present in conventional V. vinifera L. ecosystems.

The use of indigenous Saccharomyces cerevisiae and Starmerella bacillaris strains as a tool to create chemical complexity in local wines

The performance of two vineyard strains, Saccharomyces cerevisiae SacPK7 and Starmerella bacillaris StbPK9, was evaluated in laboratory and pilot scale fermentations of Cretan grape must under the following inoculation schemes: single inoculation of SacPK7 (IS), simultaneous inoculation of StbPK9 and SacPK7 (SM), and sequential inoculation of StbPK9 followed by SacPK7 (SQ). Un-inoculated (spontaneous) fermentations (SP) and fermentations inoculated with control S. cerevisiae strains (CS) were also conducted as reference. Star. bacillaris not only did not restrict but also slightly promoted the growth of S. cerevisiae when the two strains were co-inoculated at equal quantities. On the contrary, the SQ inoculation scheme conferred a competitive advantage to Star. bacillaris over S. cerevisiae, which maximum population was reduced, while increased levels of Star. bacillaris were recorded. The fermentation kinetics were also affected, accordingly. The completion of fermentation was faster in SM, IS and CS ferments than in SQ and SP. Ethanol accumulation had a predominant role in the early death of Star. bacillaris, since its growth was similarly arrested irrespective of the dominating yeast species, the magnitude of yeast population or the availability of energy sources. Interestingly, the inoculation scheme applied significantly affected the chemical profiles of the resulting wines. SQ produced the most divergent chemical profile in sterile must, with glycerol, acetic acid, acetaldehyde, residual glucose, malic acid, ethyl acetate and higher alcohols being the key compounds affected by the prolonged activity of StbPK9. In pilot scale ferments, the indigenous S. cerevisiae produced twice as high levels of esters and higher alcohols compared to the commercial starter. Star. bacillaris further increased the levels of ethyl esters in the respective ferments. The use of a mixed S. cerevisiae/Star. bacillaris starter culture instead of S. cerevisiae alone enhanced the chemical complexity of Cretan local wine. The magnitude of differentiation was even higher when the addition of Star. bacillaris preceded that of S. cerevisiae. The highest divergence in analytical profiles was recorded between wines produced by native strain combinations and commercial S. cerevisiae. Present results show that the use of indigenous yeast formulations provides significant diversification to local wines, in line with the microbial terroir concept and recent observations that indigenous yeast strains may confer regional characters to wines.

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.

MALDI-TOF MS Supplementary database for species identification employing the yeast diversity encountered on southern Brazil grapes

The study of grape microflora is of interest when autochthonous yeasts, which are related to typical wine characteristics, are intended to be used in winemaking. The election of matrix-assisted laser desorption-ionization time-of-flight mass spectrometry (MALDI-TOF MS) as the first method for yeast identification was based on its accuracy and rapidity compared to alternative laboratory protocols for identification. The aims of this study are to consolidate the MALDI-TOF MS Supplementary database for environmental yeasts already constructed, to expand it through the addition of standard spectra of not included yeast species, and to discuss the grape microflora encountered in Southern Brazil. A total of 358 strains, isolated from grape berries, were submitted to protein profiling employing Biotyper and Supplementary database. Molecular biology techniques were used as alternatives to identify 6.4% of strains not promptly designated by protein profiling. These strains corresponded to the species Candida californica, Zygoascus meyerae, Candida akabanensis, Candida azyma, and Hanseniaspora vineae. The MALDI-TOF MS spectra of the identified species were added to Supplementary database. The presented results strengthen the need for further expansion of the mass spectra database to broaden its microbiological application.

Co-evolution as Tool for Diversifying Flavor and Aroma Profiles of Wines

The products of microbial metabolism form an integral part of human industry and have been shaped by evolutionary processes, accidentally and deliberately, for thousands of years. In the production of wine, a great many flavor and aroma compounds are produced by yeast species and are the targets of research for commercial breeding programs. Here we demonstrate how co-evolution with multiple species can generate novel interactions through serial co-culture in grape juice. We find that after ~65 generations, co-evolved strains and strains evolved independently show significantly different growth aspects and exhibit significantly different metabolite profiles. We show significant impact of co-evolution of Candida glabrata and Pichia kudriavzevii on the production of metabolites that affect the flavor and aroma of experimental wines. While co-evolved strains do exhibit novel interactions that affect the reproductive success of interacting species, we found no evidence of cross-feeding behavior. Our findings yield promising avenues for developing commercial yeast strains by using co-evolution to diversify the metabolic output of target species without relying on genetic modification or breeding technologies. Such approaches open up exciting new possibilities for harnessing microbial co-evolution in areas of agriculture and food related research generally.

Massive Sequencing: A New Tool for the Control of Alcoholic Fermentation in Wine?

In wine industry, there is a prevalent use of starter cultures to promote a controlled and efficient alcoholic fermentation preventing the growth of spoilage microbes. However, current trends in enology aim to combine the guaranteed success of monitored process and the complexity of fermentations either by inoculating autochthonous starters or by performing spontaneously to produce distinctive wines. To understand the complex roles of microorganisms on wine fermentation, we must understand their population dynamics and their relationships with wine quality and metabolome. Current metagenomics techniques based on massive sequencing are gaining relevance to study the diversity and evolution of microbial population on every stage of the wine making process. This new tool and technique increases the throughput and sensitivity to study microbial communities. This review focuses on the current knowledge about wine alcoholic fermentation, the contribution of massive sequencing techniques and the possibility of using this tool for microbial control.

Social wasp intestines host the local phenotypic variability of Saccharomyces cerevisiae strains

Nowadays, the presence of Saccharomyces cerevisiae has been assessed in both wild and human-related environments. Social wasps have been shown to maintain and vector S. cerevisiae among different environments. The availability of strains isolated from wasp intestines represents a striking opportunity to assess whether the strains found in wasp intestines are characterized by peculiar traits. We analysed strains isolated from the intestines of social wasps and compared them with strains isolated from other sources, all collected in a restricted geographic area. We evaluated the production of volatile metabolites during grape must fermentation, the resistance to different stresses and the ability to exploit various carbon sources. Wasp strains, in addition to representing a wide range of S. cerevisiae genotypes, also represent large part of the phenotypes characterizing the sympatric set of yeast strains; their higher production of acetic acid and ethyl acetate could reflect improved ability to attract insects. Our findings suggest that the relationship between yeasts and wasps should be preserved, to safeguard not only the natural variance of this microorganism but also the interests of wine-makers, who could take advantage from the exploitation of their phenotypic variability. Copyright © 2016 John Wiley & Sons, Ltd.

Grapevine rootstocks shape underground bacterial microbiome and networking but not potential functionality

BACKGROUND

The plant compartments of Vitis vinifera, including the rhizosphere, rhizoplane, root endosphere, phyllosphere and carposphere, provide unique niches that drive specific bacterial microbiome associations. The majority of phyllosphere endophytes originate from the soil and migrate up to the aerial compartments through the root endosphere. Thus, the soil and root endosphere partially define the aerial endosphere in the leaves and berries, contributing to the terroir of the fruit. However, V. vinifera cultivars are invariably grafted onto the rootstocks of other Vitis species and hybrids. It has been hypothesized that the plant species determines the microbiome of the root endosphere and, as a consequence, the aerial endosphere. In this work, we test the first part of this hypothesis. We investigate whether different rootstocks influence the bacteria selected from the surrounding soil, affecting the bacterial diversity and potential functionality of the rhizosphere and root endosphere.

METHODS

Bacterial microbiomes from both the root tissues and the rhizosphere of Barbera cultivars, both ungrafted and grafted on four different rootstocks, cultivated in the same soil from the same vineyard, were characterized by 16S rRNA high-throughput sequencing. To assess the influence of the root genotype on the bacterial communities' recruitment in the root system, (i) the phylogenetic diversity coupled with the predicted functional profiles and (ii) the co-occurrence bacterial networks were determined. Cultivation-dependent approaches were used to reveal the plant-growth promoting (PGP) potential associated with the grafted and ungrafted root systems.

RESULTS

Richness, diversity and bacterial community networking in the root compartments were significantly influenced by the rootstocks. Complementary to a shared bacterial microbiome, different subsets of soil bacteria, including those endowed with PGP traits, were selected by the root system compartments of different rootstocks. The interaction between the root compartments and the rootstock exerted a unique selective pressure that enhanced niche differentiation, but rootstock-specific bacterial communities were still recruited with conserved PGP traits.

CONCLUSION

While the rootstock significantly influences the taxonomy, structure and network properties of the bacterial community in grapevine roots, a homeostatic effect on the distribution of the predicted and potential functional PGP traits was found.

Is microbial terroir related to geographic distance between vineyards?

While there are substantial studies suggesting that characteristics of wine are related to regional microbial community composition (microbial terroir), there has been little discussion about what factors affect variation in regional microbial community composition. In this study, we compared the microbial community composition of leaves and berries of a grape variety (Carmenere) from six different Chilean vineyards within 35 km of each other. In order to determine relationships between spatial proximity and microbial compositional dissimilarity, we sequenced amplicons of the internal transcribed spacer (ITS) region for fungi and 16S rRNA gene for bacteria. Results showed that both the fungal and the bacterial community compositions of the studied vineyards differed, but this difference was much clearer in fungi than in bacteria. In addition, while bacterial community dissimilarity was not correlated with geographic distance, the leaf and berry fungal community dissimilarities between locations increased with geographic distance. This indicates that spatial processes play an important role in structuring the biogeographic pattern of grape-associated fungal communities at local scales, which might in turn contribute to the local identity of wine.

SaccharomycesIDentifier, SID: strain-level analysis of Saccharomyces cerevisiae populations by using microsatellite meta-patterns

Saccharomyces cerevisiae is a common yeast with several applications, among which the most ancient is winemaking. Because individuals belonging to this species show a wide genetic and phenotypic variability, the possibility to identify the strains driving fermentation is pivotal when aiming at stable and palatable products. Metagenomic sequencing is increasingly used to decipher the fungal populations present in complex samples such as musts. However, it does not provide information at the strain level. Microsatellites are commonly used to describe the genotype of single strains. Here we developed a population-level microsatellite profiling approach, SID (Saccharomyces cerevisiae IDentifier), to identify the strains present in complex environmental samples. We optimized and assessed the performances of the analytical procedure on patterns generated in silico by computationally pooling Saccharomyces cerevisiae microsatellite profiles, and on samples obtained by pooling DNA of different strains, proving its ability to characterize real samples of grape wine fermentations. SID showed clear differences among S. cerevisiae populations in grape fermentation samples, identifying strains that are likely composing the populations and highlighting the impact of the inoculation of selected exogenous strains on natural strains. This tool can be successfully exploited to identify S. cerevisiae strains in any kind of complex samples.