Article

Microbial biogeography of wine grapes is conditioned by cultivar, vintage, and climate

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  • Constellation Brands, Inc.
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Abstract

Wine grapes present a unique biogeography model, wherein microbial biodiversity patterns across viticultural zones not only answer questions of dispersal and community maintenance, they are also an inherent component of the quality, consumer acceptance, and economic appreciation of a culturally important food product. On their journey from the vineyard to the wine bottle, grapes are transformed to wine through microbial activity, with indisputable consequences for wine quality parameters. Wine grapes harbor a wide range of microbes originating from the surrounding environment, many of which are recognized for their role in grapevine health and wine quality. However, determinants of regional wine characteristics have not been identified, but are frequently assumed to stem from viticultural or geological factors alone. This study used a high-throughput, short-amplicon sequencing approach to demonstrate that regional, site-specific, and grape-variety factors shape the fungal and bacterial consortia inhabiting wine-grape surfaces. Furthermore, these microbial assemblages are correlated to specific climatic features, suggesting a link between vineyard environmental conditions and microbial inhabitation patterns. Taken together, these factors shape the unique microbial inputs to regional wine fermentations, posing the existence of nonrandom "microbial terroir" as a determining factor in regional variation among wine grapes.

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... This concept has been defined as pseudo-scientific ("nebulous" according to Bokulich) [1], but, in recent years, new analytical techniques have revealed the actual territorial differences in even relatively close production areas. The microbiological aspect, usually underestimated when talking about terroir, has revealed all its importance thanks to the new high throughput sequencing (HTS) techniques, allowing differences between the viticultural areas in terms of microbial biodiversity to be identified, not related to chance, but typical and characteristics of those areas [1][2][3]. The microbiological characteristics that are present in the fermenting ...
... The number of used reads ranged from 41,822 to 116,524. Overall, the fungal populations at a phylum level were very similar and mainly comprised Ascomycota (62.7%) followed by Basidiomycota [3,20,21]. Phyla as Mucoromicota and Chytridiomycota had an extremely low abundance. ...
... These data confirm the findings of Alessandria et al. [24] conducted on a greater area and on a greater number of Barbera vineyards, which also includes the reference area of our study. The great environmental diffusion of A. pullulans is also recognized in the work of Barata et al. [5], in which this species is the main one on healthy grapes with a percentage ranging between 95 and 100%; the same observation was reported by Bokulich et al. [3]. ...
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In this study, the evolution of the yeast microflora present on the berry surface, during the ripening of Barbera grapes, was monitored. Sampling was performed in three vineyards located in the “Nizza” Barbera d’Asti DOC zone and different methodologies have been employed. A culture-dependent method based on the identification of strains grown on solid media by ARDRA (Amplified Ribosomal DNA Restriction Analysis) and the D1-D2 domain of ribosomal 26S DNA capillary sequencing was coupled to NGS (Next Generation Sequencing) targeting ITS (Internal Transcribed Sequence) amplicons with the Illumina MiSeq platform. By using culture-dependent techniques, the most frequently detected species was the yeast-like fungus Aureobasidium pullulans, which was dominant in the culturable fraction. Among yeasts, the presence of oligotrophic basidiomycetes such as Cryptococcus spp., Rhodotorula graminis and Sporidiobolus pararoseus was observed at the beginning of ripening. Afterward, upon approaching the harvest, a succession of oxidative or weakly fermentative copiotrophic species occurs, such as Saturnispora diversa, Issatchenkia terricola, Hanseniaspora opuntiae, Starmerella bacillaris and Hanseniaspora uvarum. The massive sequencing revealed a larger number of species, respect to the culture-dependent data. Comparing the two different approaches used in this work, it is possible to highlight some similarities since Aureobasidium, Rhodotorula and Sporobolomyces were detected by both methods. On the contrary, genera Hanseniaspora, Issatchenkia and Saturnispora were revealed by culture-dependent methods, but not by NGS, while Saccharomyces spp. were identified, with low frequency, only by NGS. The integrated application of NGS sequencing and culture-dependent techniques provides a comprehensive view of mycodiversity in the wine-growing environment, especially for yeasts with low abundance.
... Wine is unique because it is essentially a natural product, which is a result of ordered and complex biochemical transformations including the ripening of grape and the metabolism of microbes from fermentation to aging (Liu et al., 2017;Carpena et al., 2020;Echave et al., 2021). In winemaking, "microbial terroir" refers to the contribution of microorganisms in a region to the characteristics of wine, and is a process that starts in the vineyards and then develops along the different stages of fermentation (Bokulich et al., 2014;Comitini et al., 2017;Wei et al., 2022a). Thus, the microbiological aspects of wine production are influenced by the vineyard ecosystem and not simply by the winery and fermentative processes (Grangeteau et al., 2017;Liu et al., 2019). ...
... The relative abundances of the groups vary depending on the plant tissue or organ. Dominant taxa include members of the genera Pseudomonas, Sphingomonas, Frigoribacterium, Curtobacterium, Bacillus, Enterobacter, Acinetobacter, Erwinia, Citrobacter, Pantoea, and Methylobacterium (Bokulich et al., 2014;Perazzolli et al., 2014;Pinto et al., 2015;Zarraonaindia et al., 2015;Portillo et al., 2016). The fungal diversity is very similar at the phylum level, mainly composed of Ascomycetes and Basidiomycetes. ...
... Other phyla such as Zygomycota and Chytridiomycota are only present in low abundance. Frequently encountered genera of filamentous fungi include Aspergillus, Alternaria, Penicillium, Cladosporium, Lewia, Davidiella, Erysiphe, and Botrytis and the yeast-like fungus, Aureobasidium pullulans, while the yeast genera include Hanseniaspora, Issatchenkia, Pichia, Candida, Rhodotorula, Lachancea, Metschnikowia, Cryptococcus, Filobasidiella, Sporobolomyces, and Torulaspora (Bokulich et al., 2014;Pinto et al., 2014;Wang et al., 2015;Filippis et al., 2017;Liu and Howell, 2021). The grape berry surface is, nevertheless, a natural habitat of microorganisms. ...
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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.
... Previously, wine terroir was attributed to the soil and the vineyard environment, until the concept of "microbial terroir" was presented (Gilbert et al., 2014). With the development of gene sequencing technology, the microbial regional distribution pattern has been verified in several wineproducing regions worldwide (Bokulich et al., 2014;De Filippis et al., 2017;Knight et al., 2020), and further studies have proved the correlation between regional "microbial terroir" and wine style Liu et al., 2020). High-throughput sequencing (HTS) has been widely used in microbial diversity research and has been proven an effective method for studying microorganisms during fermentation Morgan et al., 2017). ...
... High-throughput sequencing (HTS) has been widely used in microbial diversity research and has been proven an effective method for studying microorganisms during fermentation Morgan et al., 2017). Compared with bacteria, fungi have a greater influence on wine style (Liu et al., 2020), and the fermentation process has a more substantial impact on the mycobiota (Pinto et al., 2015), while the fungal must consortium displays higher annual stability (Bokulich et al., 2014). ...
... Besides the frequently encountered genera Aureobasidium, Aspergillus, Alternaria, Cladosporium, Botrytis, Hanseniaspora, Rhodotorula, and Filobasidiella, which have been simultaneously detected in California, United States (Bokulich et al., 2014) and Spain , this study has discovered some pathogenic grape strains and biocontrol fungi, such as Colletotrichum, Lasiodiplodia, Metarhizium, and Filobasidium, although their proportion is not high, considering their impact on grape fruit quality (Kirchmair et al., 2004;Combrinck et al., 2011), further research is needed to determine their origin and their impact on wine quality,especially when the effect of some strains on wine aroma has been proved (Ma et al., 2021). Meanwhile, corresponds with other studies (Pinto et al., 2015; FIGURE 6 | Spearman correlation analysis of the correlation between the major fungi abundance in the Marselan must and various environmental factors. ...
Article
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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.”
... downy mildew, anthracnose, white rot, etc.) spread easily in vineyard under hot and humid conditions (Du et al., 2015;Meng et al., 2013), while other endophytes (microbes) protect their host against plant disease pathogens, abiotic stresses, and nutrient accessibility for plant development (Bamisile, Dash, Akutse, Keppanan, & Wang, 2018;Santoyo, Moreno-Hagelsieb, Orozco-Mosqueda, & Glick, 2016). These microbial community coexisting with vines is a complex and dynamic ecosystem, and affected by cultivation managements, spatiotemporal climatic variability, regional delineations and vineyard topography (Bokulich, Thorngate, Richardson, & Mills, 2014;Liu, Zhang, Chen, & Howell, 2019;Pinto et al., 2014;Van Leeuwen & Destrac-Irvine, 2017). The distribution of these microbes including fungi and bacteria varied ranging from rhizosphere (soils) and phyllosphere (e.g. ...
... berry, leaf, bark) (Compant, Mitter, Colli-Mull, Gangl, & Sessitsch, 2011;Martins et al., 2013;Pinto et al., 2014;Zarraonaindia et al., 2015), and the distinguished microbial niches of the vineyard microbiota are potentially linked to grapevine health and wine quality (Gilbert, Van, & Zarraonaindia, 2014;Martinez-Luscher et al., 2019). Early studies indicated that microbiota structure and/or distribution interacting with environmental factors described as microbial terroir shape the regional wine phenotype (Bokulich et al., 2014;Knight, Klaere, Fedrizzi, & Goddard, 2015;Knight, Karon, & Goddard, 2020). The microbiota diversity was observed to be less affected by environmental factors (vintages) within macro-regions other than the individual vineyards (Bokulich et al., 2014;Reiter, Montpetit, Byer, Frias, & Montpetit, 2021), and different grapevine compartments reserve more microbiota composition variance than geographic distance (Morrison-Whittle & Goddard, 2015). ...
... Early studies indicated that microbiota structure and/or distribution interacting with environmental factors described as microbial terroir shape the regional wine phenotype (Bokulich et al., 2014;Knight, Klaere, Fedrizzi, & Goddard, 2015;Knight, Karon, & Goddard, 2020). The microbiota diversity was observed to be less affected by environmental factors (vintages) within macro-regions other than the individual vineyards (Bokulich et al., 2014;Reiter, Montpetit, Byer, Frias, & Montpetit, 2021), and different grapevine compartments reserve more microbiota composition variance than geographic distance (Morrison-Whittle & Goddard, 2015). The reason could be the distinct microclimate/ecosystems exert selection pressure within plant compartments and vineyards by vine microclimate alteration (Chou, Vanden Heuvel, Bell, & Panke-Buisse, 2018;Martins et al., 2013;Zarraonaindia et al., 2015). ...
Article
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Rainfall particularly under continental climates with monsoonal tendency impacts the vineyard microbial niches during grapevine growth. With microbial community shifts, vine traits (grape flavor and yield) cultivated/protected under rain-shelter may ultimately be altered. Such cultivation may influence microflora dynamics via meteorological parameter variations, however this is unclear yet. Here, we used Cabernet Sauvignon, a prevalent red cultivar among wine growing regions, to evaluate the effects of the rain-shelter cultivation on the microorganism diversity. We found that average air temperature under rain-shelter conditions was 2 to 3 °C higher than the non-covered group, while air humidity the maximum reduction was 5.79% (p < 0.05). After grape setting stage, similar trends were observed on soil temperature (increased) and humidity (lowered) under the treatments (p < 0.05). UV and precipitation were less by a total of 72% and 96% of rain-shelter treatment, respectively (p < 0.05). The rain-shelter management presented lower fungal and bacterial OTUs. The fungal alpha diversity on leaves and branches under rain-shelter was lower (p < 0.05) than the control as the grape ripeness, with Ascomycota, Mycosphaerella and Cladosporium as the principal fungi. Our results revealed that the fungal microbiota patterns were differentiated by the cultivations from setting stage to the entire véraison and then tended to be similar at harvesting. Only branch fungal patterns were observed asymmetrically at all stages. Meanwhile, bacterial diversity and distribution varied on colonization locations where Proteobacteria and Actinobacteria were the primary bacteria phyla. Bacterial community structures overlapped at harvest, while the differences were observed between two cultivations at other stages, excluding grape berry. The rain-shelter cultivation reduced the abundance of Alternaria, Colletotrichum and Pseudomonas that may adversely affect grapevine health. Multivariate statistical analysis suggested that the effect of vineyard microclimate on microbiota distribution and succession were influenced by cultivation modes and grapevine developmental stages. This research provides evidence to address the dynamics of microbial ecology from vineyard to grape under rain-shelter cultivation, and its benefits as a sustainable vineyard management.
... Understanding the ecology of microbiomes in agricultural systems is particularly important because that knowledge can be used to manipulate soils towards beneficial outcomes. However, most studies on agricultural microbiomes focus on assessing biodiversity and community composition [7][8][9], rather than the assembly mechanisms that govern microbiome variation [10]. A better understanding of the mechanisms driving crop-associated microbiome assembly could be used to design new manipulation strategies based on altering both dispersal-based and selection-based processes. ...
... Knowledge of assembly processes is particularly important for viticulture and wine production, where the fermentation process and both the quality and flavour of wine strongly depend on microbial activity from the vineyard to the winery [24]. Furthermore, the soil microbiome is considered the key natural source of grape-and must-associate microbiota [25,26] and consistent biogeographic differences in soil and climate contribute to regional wine characteristics via the so-called 'microbial terroir' [8,25]. To use knowledge of assembly processes towards viticulture (or other agricultural) applications requires theoretical coherence in our understanding such that knowledge may become transferable from one system to another. ...
... In addition, regional patterns in microbial ecology can correlate with wine metabolites [28], but the main scale of variation in microbiomes appears context-dependent. The degree to which inter-vineyard variation compares to intra-vineyard variation and how spatial variation compares to temporal variation also remains unclear [8,25,27,29]. ...
Article
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Microbial communities in agricultural soils are fundamental for plant growth and in vineyard ecosystems contribute to defining regional wine quality. Managing soil microbes towards beneficial outcomes requires knowledge of how community assembly processes vary across taxonomic groups, spatial scales, and through time. However, our understanding of microbial assembly remains limited. To quantify the contributions of stochastic and deterministic processes to bacterial and fungal assembly across spatial scales and through time, we used 16 s rRNA gene and ITS sequencing in the soil of an emblematic wine-growing region of Italy. Combining null- and neutral-modelling, we found that assembly processes were consistent through time, but bacteria and fungi were governed by different processes. At the within-vineyard scale, deterministic selection and homogenising dispersal dominated bacterial assembly, while neither selection nor dispersal had clear influence over fungal assembly. At the among-vineyard scale, the influence of dispersal limitation increased for both taxonomic groups, but its contribution was much larger for fungal communities. These null-model-based inferences were supported by neutral modelling, which estimated a dispersal rate almost two orders-of-magnitude lower for fungi than bacteria. This indicates that while stochastic processes are important for fungal assembly, bacteria were more influenced by deterministic selection imposed by the biotic and/or abiotic environment. Managing microbes in vineyard soils could thus benefit from strategies that account for dispersal limitation of fungi and the importance of environmental conditions for bacteria. Our results are consistent with theoretical expectations whereby larger individual size and smaller populations can lead to higher levels of stochasticity.
... Wine terroir is a complex and somehow variable concept that posits that the taste of a wine is affected by multiple factors including the cultivar, geographical effects, such as the pedoclimate, and crop management. It has been proposed that microbial communities associated with the grape or in the cellar participate in establishing the terroir, reflecting the wine's geographical origins (Bokulich et al., 2014;Knight et al., 2015). Different terroirs are determined by distinct yeast communities. ...
... Several studies have explored the idea of a microbial signature of the terroir at the community level. Bokulich et al. (2014) using next generation sequencing reported a biogeographical signature of grape microbiota associated to region, cultivar and climatic factors across California suggesting that the different vineyards could be differentiated by their microbial communities. Several other studies have confirmed that geographical location is a major factor affecting microbial communities in vineyards (Portillo et al., 2016;Drumonde-Neves et al., 2017;Alexandre, 2020). ...
... A countless number of studies covering microorganisms associated with grape berries from Vitis vinifera ssp. vinifera cultivars have shown that the occurrence and diversity of yeast populations are determined by physiological, anthropogenic, and environmental factors [21,22], emphasizing the terroir concept of microbial components. Actually, the mycobiota is naturally shaped by vineyard location [23][24][25][26], vintage and climatic conditions [27,28], grape variety [22,29], and the ripeness and health status of the grape berries [21,30]. ...
... vinifera cultivars have shown that the occurrence and diversity of yeast populations are determined by physiological, anthropogenic, and environmental factors [21,22], emphasizing the terroir concept of microbial components. Actually, the mycobiota is naturally shaped by vineyard location [23][24][25][26], vintage and climatic conditions [27,28], grape variety [22,29], and the ripeness and health status of the grape berries [21,30]. Human activities also have a high impact on yeast diversity and distribution, such as farming system type [31,32], pest management [33,34], soil irrigation, and vineyard maintenance [35]. ...
Article
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Vitis vinifera L. ssp. sylvestris (Gmelin) Hegi is recognized as the dioecious parental generation of today’s cultivars. Climatic change and the arrival of pathogens and pests in Europe led it to be included on the International Union for Conservation of Nature (IUCN) Red List of Threatened Species in 1997. The present work focused on the study of culturable yeast occurrence and diversity of grape berries collected from wild vines. Sampling was performed in 29 locations of Azerbaijan, Georgia, Italy, Romania, and Spain. In total, 3431 yeast colonies were isolated and identified as belonging to 49 species, including Saccharomyces cerevisiae, by 26S rDNA D1/D2 domains and ITS region sequencing. Isolates of S. cerevisiae were also analyzed by SSR–PCR obtaining 185 different genotypes. Classical ecology indices were used to obtain the richness (S), the biodiversity (H’), and the dominance (D) of the species studied. This study highlights the biodiversity potential of natural environments that still represent a fascinating source of solutions to common problems in winemaking.
... Soil microbiota have also demonstrated their usefulness, both in the degradation and removal of organic pollutants (Maron et al., 2011), and by their contribution to plant growth (van der Heijden et al., 2008;Mendes et al., 2013). In vineyard contexts, soil microbiology is considered as a factor potentially contributing to wine quality by influencing its organoleptic properties (Bokulich et al., 2014;Zarraonaindia et al., 2015;Liang et al., 2019), although the role of soil microorganisms in terroir expression has not yet been fully explored. Inventorying and analysing the microbial component of soils is crucial, in order to better understand soil functioning, and to adapt management practices for long-term sustainable viticulture Burns et al., 2016;Liang et al., 2019;Karimi et al., 2020). ...
... Over the past few decades, with the development of environmental genomics and bioinformatics, substantial research has been conducted at various spatial scales and in various contexts to evaluate the complex linkages between the key factors shaping the diversity and abundance of microbial communities. At a large spatial scale, increasing evidence of differences in microbial vineyard communities from geographically distant vineyard regions supports the idea of a microbial terroir (Bokulich et al., 2014;Coller et al., 2019;Liu et al., 2019). At landscape or plot scale, soil physicochemical characteristics, such as soil organic carbon, pH, and C:N ratio (Zarraonaindia et al., 2015;Zehetner et al., 2015;Terrat et al., 2017;Liang et al., 2019), land use/land cover (LULC), and field management practices (Zehetner et al., 2015;Burns et al., 2016;Coller et al., 2019;Karimi et al., 2020;Di Giacinto et al., 2020) are identified as the most important drivers of microbial biodiversity. ...
Article
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Present-day soil physicochemical characteristics, land use/land cover (LULC), and field management practices are commonly recognised as the main drivers shaping archaeal/bacterial and fungal communities in vineyard soils. Few studies have investigated the legacy of past land uses on soil microbial biodiversity, yet anthropogenic disturbances have already been proven to affect soil characteristics over decades. In this study, we explore the possibility of long-lasting impacts of forest-to-vineyard conversion on present-day soil archaeal/bacterial and fungal communities after 15 years of vine cultivation. The selected study area is in a Burgundian vineyard (Pernand-Vergelesses, Burgundy, France), where it was possible to reconstruct the history of land cover and land use for the past 40 years. Soil samples were collected from five zones managed under similar pedo-climatic conditions but with different land-use histories (a 70-year-old vineyard, a 15-year-old vineyard converted from pine forest, a 15-year-old vineyard converted from mixed forest, a pine forest and a mixed forest). For each zone, basic physicochemical parameters (organic carbon, total nitrogen, copper, C:N ratio, and soil texture) were measured, and DNA was extracted to characterise the microbial biomass, and also the richness and taxonomic composition of archaeal/bacterial and fungal communities (16S and 18S). Our results show that changes in LULC lead to differential responses in soil microbial biomass, and in archaeal/bacterial and fungal richness and taxonomic composition. After 15 years of cultivation, the present-day microbial biomass and indigenous archaeal/bacterial communities of recent vineyard soils are shown to be partly inherited from past LULC, but no evidence was found of long-term impacts of past land use on fungal communities. Past land-use history should therefore be added to the well-established set of environmental drivers, providing valuable information to explain the spatial variability of soil microbiology, observed at intra-plot, plot, and landscape scales. Integrating the history of changes in LULC is therefore recommended to evaluate and adopt the best strategies to develop sustainable management practices.
... Thus, although industrial yeast strains represent a fundamental tool for reproducing the final quality of table wines, their massive use is not recommended for traditional wines in which peculiar traits are desired (Spano et al., 2010;Capozzi and Spano, 2011). For these reasons, indigenous yeast starters, which are supposedly well adapted to a specific grape must and reflect the biodiversity of a particular "terroir" are more and more requested by winemakers (Bokulich et al., 2014;Gilbert et al., 2014;Feghali et al., 2020). Indeed, it is hypothesized that in different vitivinicultural regions, specific yeast strains are naturally selected and that they are able to exalt the sensorial and aromatic profile of wine produced in that area. ...
... Thus, the myriad of microclimates occurring within each vineyard due to differential shading of grapes by leaves, and the aspect of each grape cluster, greatly affects the qualitative/quantitative composition of the vineyard-associated yeast microbiota. Bokulich et al. (2014) used a high-throughput short-amplicon sequencing approach to demonstrate that specific regional and grape-variety factors shape the biodiversity of fungal and bacterial consortia inhabiting wine-grape surfaces. Indeed, the microbial assemblages correlate with specific climatic features, and this suggests a link between vineyard environmental conditions and microbial residence patterns. ...
Article
This paper reports on a common experiment performed by 17 Research Units of the Italian Group of Microbiology of Vine and Wine (GMVV), which belongs to the Scientific Society SIMTREA, with the aim to validate a protocol for the characterization of wine strains of Saccharomyces cerevisiae. For this purpose, two commercial S. cerevisiae strains (EC 1118 and AWRI796) were used to carry out inter-laboratoryscale comparative fermentations using both synthetic medium and grape musts and applying the same protocol to obtain reproducible, replicable, and statistically valid results. Ethanol yield, production of acetic acid, glycerol, higher alcohols, and other volatile compounds were assessed. Moreover, the Fourier transform infrared spectroscopy was also applied to define the metabolomic fingerprint of yeast cells from each experimental trial. Data were standardized as unit of compounds or yield per gram of sugar (glucose and fructose) consumed throughout fermentation, and analyzed through parametric and non-parametric tests, and multivariate approaches (cluster analysis, two-way joining, and principal component analysis). The results of experiments carried out by using synthetic must showed that it was possible to gain comparable results from three different laboratories by using the same strains. Then, the use of the standardized protocol on different grape musts allowed pointing out the goodness and the reproducibility of the method; it showed the main traits of the two yeast strains and allowed reducing variability amongst independent batches (biological replicates) to acceptable levels. In conclusion, the findings of this collaborative study contributed to the validation of a protocol in a specific synthetic medium and in grape must and showed how data should be treated to gain reproducible and robust results, which could allow direct comparison of the experimental data obtained during the characterization of wine yeasts carried out by different research laboratories.
... To overcome this trend, in recent decades, several winemakers have carried out spontaneous fermentations exploiting indigenous yeasts coming from the vineyard or vinery equipment, with the aim to improve the analytical and aroma complexity and to give peculiar and recognizable flavors to the final wine [5,9]. Indeed, recent studies demonstrated that specific grape varieties and the climate of a specific geographical area seem to influence the yeast community [10][11][12][13][14], indicating a variation of the microbial community of grapes in the function of regional distribution [15][16][17][18][19]. Recently, the correlation between the regional microbial community and the organoleptic characteristics of wine has attracted growing attention [11,20,21]. The understanding of the mechanisms and factors that stabilize a specific epiphytic population in different grape varieties could be useful to establish a correlation with the influence of regional yeast microbiota in the analytical and aromatic characters of the final wine [11,[20][21][22]. ...
... In recent years, several investigations claimed different geographical distributions of wine microbioma [10,11]. This relationship between wine microbiota and regional areas has gained relevance in the wine industry [41]. ...
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The relation between regional yeast biota and the organoleptic characteristics of wines has attracted growing attention among winemakers. In this work, the dynamics of a native Saccharomyces cerevisiae population was investigated in an organic winery. In this regard, the occurrence and the persistence of native S. cerevisiae were evaluated in the vineyard and winery and during spontaneous fermentation of two nonconsecutive vintages. From a total of 98 strains, nine different S. cerevisiae biotypes were identified that were distributed through the whole winemaking process, and five of them persisted in both vintages. The results of the oenological characterization of the dominant biotypes (I and II) show a fermentation behavior comparable to that exhibited by three common commercial starter strains, exhibiting specific aromatic profiles. Biotype I was characterized by some fruity aroma compounds, such as isoamyl acetate and ethyl octanoate, while biotype II was differentiated by ethyl hexanoate, nerol, and β-damascenone production also in relation to the fermentation temperature. These results indicate that the specificity of these resident strains should be used as starter cultures to obtain wines with distinctive aromatic profiles.
... In relation to grapes and wine, the recent focus has been put on evidencing the existence of microbial communities dependent on biogeographical boundaries [11][12][13], encompassing the concept of terroir, associated with the highly reputed features of wine typicity and distinctiveness [14]. The inclusion of a microbial component in the terroir concept has been proposed [11,15], but not without critical limitations [16]. Nevertheless, the concept of a "microbial terroir" has gained popularity among researchers as a way of demonstrating the contribution of vineyard microbial assemblages to the valued regional wine distinctiveness [10,17,18]. ...
... The presence of WMC yeast species in must samples from wineries determined by metagenomic approaches indicates the existence of a nonrandom "microbial terroir" [15]. However, as shown in Table 6, must species were seldom coincident with vineyard samples and were entirely different from species recovered from fermented juices. ...
Article
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Winemaking involves a wide diversity of microorganisms with different roles in the process. The wine microbial consortium (WMC) includes yeasts, lactic acid bacteria and acetic acid bacteria with different implications regarding wine quality. Despite this technological importance, their origin, prevalence, and routes of dissemination from the environment into the winery have not yet been fully unraveled. Therefore, this study aimed to evaluate the WMC diversity and incidence associated with vineyard environments to understand how wine microorganisms overwinter and enter the winery during harvest. Soils, tree and vine barks, insects, vine leaves, grapes, grape musts, and winery equipment were sampled along four seasons. The isolation protocol included: (a) culture-dependent microbial recovery; (b) phenotypical screening to select fermenting yeasts, lactic acid, and acetic acid bacteria; and (c) molecular identification. The results showed that during all seasons, only 11.4% of the 1424 isolates presumably belonged to the WMC. The increase in WMC recovery along the year was mostly due to an increase in the number of sampled sources. Acetic acid bacteria (Acetobacter spp., Gluconobacter spp., Gluconoacetobacter spp.) were mostly recovered from soils during winter while spoilage lactic acid bacteria (Leuconostoc mesenteroides and Lactobacillus kunkeii) were only recovered from insects during véraison and harvest. The fermenting yeast Saccharomyces cerevisiae was only isolated from fermented juice and winery equipment. The spoilage yeast Zygosaccharomyces bailii was only recovered from fermented juice. The single species bridging both vineyard and winery environments was the yeast Hanseniaspora uvarum, isolated from insects, rot grapes and grape juice during harvest. Therefore, this species appears to be the best surrogate to study the dissemination of the WMC from vineyard into the winery. Moreover, the obtained results do not evidence the hypothesis of a perennial terroir-dependent WMC given the scarcity of their constituents in the vineyard environment along the year and the importance of insect dissemination.
... In addition, we compared the differences among the varieties using statistical methods and found that the grape variety significantly influenced the taxa in the grape microbial community. These results were consistent with the previous study [47]. ...
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Rhizosphere microflora are key determinants that contribute to plant growth and productivity, which are involved in improving the uptake of nutrients, regulation of plants’ metabolisms and activation of plants’ responses against both biotic and abiotic stresses. However, the structure and diversity of the grape rhizosphere microbiota remains poorly described. To gain a detailed understanding of the assembly of rhizosphere microbiota, we investigated the rhizosphere microbiota of nine grape varieties in northern China by high-throughput sequencing. We found that the richness and diversity of bacterial and fungal community networking in the root compartments were significantly influenced by the grape variety. The bacterial linear discriminant analysis showed that Pseudomonas and Rhizobium, which were considered as potential plant-growth-promoting bacteria, were more enriched in Pinot noir, and Nitrosospira was enriched in Gem. The fungal linear discriminant analysis showed that Fusarium was more enriched in Longan, Sporormiella was more enriched in Merlot, Gibberella and Pseudallescheria were more enriched in Gem and Mortierella was more abundant in Cabernet Sauvignon. The 16S rRNA functional prediction indicated that no significance differentiates among the grape varieties. Understanding the rhizosphere soil microbial diversity characteristics of different grape varieties could provide the basis for exploring microbial associations and maintaining the health of grapes.
... The grapevine is considered an excellent model plant system for research on fungal and bacterial microbiota. Novel high-throughput sequencing (HTS) approaches have been recently used to outline the microbiome in grapevine organs such as roots, berries and leaves in mature vines due of its importance in grape production, fruit and foliar diseases management, and the effect of endemic microorganisms on the local characteristic of a wine [5][6][7]. Culture-dependent microbial approaches have historically been used to reveal microbiota present in the grapevine endospheres [8][9][10][11]. However, culture-independent high-throughput amplicon sequencing (HTAS) techniques have recently been deployed to increase the microbiome portrait of grapevine woody organs such as the trunk and cane [12][13][14][15][16][17][18]. ...
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Rootstocks are the link between the soil and scion in grapevines, can provide tolerance to abiotic and biotic stresses, and regulate yield and grape quality. The vascular system of grapevine rootstocks in nurseries is still an underexplored niche for research, despite its potential for hosting beneficial and pathogenic microorganisms. The purpose of this study was to investigate the changes in the composition of fungal communities in 110 Richter and 41 Berlandieri rootstocks at four stages of the grapevine propagation process. Taxonomic analysis revealed that the fungal community predominantly consisted of phylum Ascomycota in all stages of the propagation process. The alphadiversity of fungal communities differed among sampling times for both rootstocks, with richness and fungal diversity in the vascular system decreasing through the propagation process. The core microbiome was composed of the genera Cadophora, Cladosporium, Penicillium and Alternaria in both rootstocks, while the pathogenic genus Neofusicoccum was identified as a persistent taxon throughout the propagation process. FUNguild analysis showed that the relative abundance of plant pathogens associated with trunk diseases increased towards the last stage in nurseries. Fungal communities in the vascular system of grapevine rootstocks differed between the different stages of the propagation process in nurseries. Numerous genera associated with potential biocontrol activity and grapevine trunk diseases were identified. Understanding the large diversity of fungi in the rootstock vascular tissue and the interactions between fungal microbiota and grapevine will help to develop sustainable strategies for grapevine protection.
... Principal coordinate analysis (β-diversity analysis) indicated that the season was the main determinant of the endophyte community structure associated with Paulownia leaves (Figure 6). These observations emphasise the key role of seasonal effects on shaping the bacterial community of endophytes, which has also been reported for elm [69], urban trees [70], and grape [71]. In these studies, endophytic colonisation increased during the rainy and warm periods, which agrees with the findings of our study. ...
Article
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The microbial structure and metabolic function of plant-associated endophytes play a key role in the ecology of various environments, including trees. Here, the structure and functional profiles of the endophytic bacterial community, associated with Paulownia elongata × fortunei, in correlation with seasonality, were evaluated using Biolog EcoPlates. Biolog EcoPlates was used to analyse the functional diversity of the microbiome. The total communities of leaf endophyte communities were investigated using 16S rRNA V5-V7 region amplicon deep sequencing via Illumina MiSeq. Community level physiological profiling (CLPP) analysis by the Biolog EcoPlate™ assay revealed that the carboxylic acids (19.67-36.18%) and amino acids (23.95-35.66%) were preferred by all by all communities, whereas amines and amides (0.38-9.46%) were least used. Seasonal differences in substrate use were also found. Based on the sequencing data, mainly phyla Proteobacteria (18.4-97.1%) and Actinobacteria (2.29-78.7%) were identified. A core microbiome could be found in leaf-associated endophytic communities in trees growing in different locations. This work demonstrates the application of Biolog EcoPlates in studies of the functional diversity of microbial communities in a niche other than soil and shows how it can be applied to the functional analyses of endomicrobiomes. This research can contribute to the popularisation of Biolog EcoPlates for the functional analysis of the endomicrobiome. This study confirms that the analysis of the structure and function of the plant endophytic microbiome plays a key role in the health control and the development of management strategies on bioenergy tree plantations.
... The NR process occurs in four phases, resulting in berries with appropriate texture and color for further processing [9,15] During infection, several changes are observed in grape berries, including water evaporation which leads to increased sugar and citric acid concentration. In addition, the cell wall is degraded, causing tissue senescence and resulting in further moisture loss and textural changes [16][17][18]. ...
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Botrytis cinerea, can lead to the formation of noble rot (NR) of grape berries under certain environmental conditions, resulting in favored metabolic and physical changes necessary for produc- ing highly regarded botrytized wines. The functional genes involved in the textural and biochemical processes are still poorly characterized. We generated and analyzed metatranscriptomic data from healthy (H) berries and from berries representing the four stages of NR from the Tokaj wine region in Hungary over three months. A weighted gene co-expression network analysis (WGCNA) was conducted to link B. cinerea functional genes to grape berry physical parameters berry hardness (BH), berry skin break force (F_sk), berry skin elasticity (E_sk), and the skin break energy (W_sk). Clustered modules showed that genes involved in carbohydrate and protein metabolism were significantly enriched in NR, highlighting their importance in the grape berry structural integrity. Carbohydrate active enzymes were particularly up-regulated at the onset of NR (during the transition from phase I to II) suggesting that the major structural changes occur early in the NR process. In addition, we identified genes expressed throughout the NR process belonging to enriched pathways that allow B. cinerea to dominate and proliferate during this state, including sulphate metabolizing genes and genes involved in the synthesis of antimicrobials.
... Researchers have proven that the rhizosphere-associated microbial population composition is also dependent on the host plant genotype (cultivar) [70]. This is termed the "rhizosphere effect", which describes that the root-associated microbiota community structure often remarkably varies not only across host plant species but also among different genotypes within a single species [55,71,72]. Jiang et al. [73] revealed that blueberry host cultivars exerted substantial effects on the root-associated bacterial diversity along with complex co-occurrence networks and that host genotype directly influenced the microbiota profiles. ...
Article
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Agriculture is a multifarious interface between plants and associated microorganisms. In contemporary agriculture, emphasis is being given to environmentally friendly approaches, particularly in developing countries, to enhance sustainability of the system with the least negative effects on produce quality and quantity. Modern agricultural practices such as extensive tillage, the use of harmful agrochemicals, mono-cropping, etc. have been found to influence soil microbial community structure and soil sustainability. On the other hand, the question of feeding the ever-growing global population while ensuring system sustainability largely remains unanswered. Agriculturally important microorganisms are envisaged to play important roles in various measures to raise a healthy and remunerative crop, including integrated nutrient management, as well as disease and pest management to cut down agrochemicals without compromising the agricultural production. These beneficial microorganisms seem to have every potential to provide an alternative opportunity to overcome the ill effects of various components of traditional agriculture being practiced by and large. Despite an increased awareness of the importance of organically produced food, farmers in developing countries still tend to apply inorganic chemical fertilizers and toxic chemical pesticides beyond the recommended doses. Nutrient uptake enhancement, biocontrol of pests and diseases using microbial inoculants may replace/reduce agrochemicals in agricultural production system. The present review aims to examine and discuss the shift in microbial population structure due to current agricultural practices and focuses on the development of a sustainable agricultural system employing the tremendous untapped potential of the microbial world.
... This has forced the wine industry to pursue winemaking alternatives, which include the agricultural management of vineyards, fermentation conditions, and more recently, the exploration of yeasts other than Saccharomyces cerevisiae, which certainly poses a significant challenge within the area [2,3]. While it is true that there is a significant number of articles that explore the use of non-Saccharomyces yeasts (NSY), it is also true that the microbiology of grapes is complex and dependent on climate and regional factors [4,5]. This means that there is a large number of species and subspecies of yeast that have not been isolated neither characterized, each with fermentation properties that might positively influence in the wine attributes. ...
Article
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The study of non-Saccharomyces yeasts in wine fermentations allows the exploration of new alternatives for the reduction of ethanol in wines. The objective of this work was to evaluate the fermentation capacity of two indigenous Candida yeasts (C. oleophila and C. boidinii) in monoculture and sequential fermentations (laboratory and microvinification scale) to produce Chilean Sauvignon Blanc wine. Fermentations were monitored by the determination of ethanol, glycerol, organic acids, and residual sugars. The results indicated that at the laboratory scale for both the monoculture and sequential fermentations it was possible to reduce the ethanol concentration on 0.77% v/v (monoculture) and 1.5% v/v (sequential) for C. oleophila and 0.50% v/v (monoculture) and 0.04% v/v (sequential) for C. boidinii compared to S. cerevisiae (12.87% v/v). Higher glycerol concentrations were produced in monoculture than sequential fermentations (C. oleophila: 9.47 g/L and C. boidinii 10.97 g/L). For microvinifications, the monoculture and sequential fermentations with C. boidinii managed to reduce ethanol content by 0.17% v/v and 0.54% v/v, respectively, over the S. cerevisiae control (13.74% v/v). In the case of C. oleophila, the reduction was only observed in sequential fermentations with 0.62% v/v. Interestingly, grapes with higher sugar concentration resulted in wines with lees ethanol concentrations. This might be associated to the use of C. oleophila (13.12% v/v) and C. boidinii (13.20% v/v) in sequential fermentations microvinification scale.
... For wine making, it is well known that good-quality grapes can be much more important than well-controlled fermentation processes. Wine grapes present a unique biogeography model, wherein microbial biodiversity simultaneously answers questions about the inherent components of the grape quality and grapevine health (Bokulich, Thorngate, Richardson, & Mills, 2014). ...
Article
To study the effects of microeukaryotic communities on development of varietal aroma of Vidal blanc grape during late harvest, metagenomics, gas chromatography–mass spectrometry, climate factors and scanning electron microscopy were jointly used to discover how freeze-thaw stress influences grape skin and shapes the microeukaryotic consortia. Most free terpenes, monoterpenes and C13-norisoprenoids developed during late harvest. Freeze-thaw cycles caused damage of the wax layer and microfissures on the cuticle of grape berries. This increased nutrients availability and supported the dominance of oxidative and fermentative ascomycetous populations. Microbial assemblages possessed certain ecosystem functions, which correlated to the development of characteristic volatile organic compounds, such as free terpenes and phenylalanine derivatives. Significantly upregulated genes of CAZy were identified as FENNEDOB12352, OJNJMGIN252777, EGHMEMAM161340, EGHMEMAM158447, KKFIDJDF144524, BEDCFLNK31943, LHALBBHN88115, BEDCFLNK41042. Zymoseptoria tritici, Kluyveromyces lactis, Yarrowia lipolytica, and Pichia kudriavzevii were selected as key factors in yeast assemblage.
... The grape microbiome is influenced by several factors like climate, region, and grape cultivar. Therefore, those factors are responsible of a nonrandom distribution of the microbial community at each terroir (Bokulich et al., 2014;Burns et al., 2016;Gilbert et al., 2014;Kioroglou et al., 2019;Morrison-Whittle et al., 2017;Pinto et al., 2014;Portillo et al., 2016;Taylor et al., 2014). ...
Article
A complex consortium of yeasts is the principal responsible of wine fermentation, being Saccharomyces cerevisiae the main driver. The use of selected yeast, beginning with Saccharomyces strains, is one of the main achievements in microbiological control in the wine industry. However, the use of single strain starters of S. cerevisiae and the limited variability of strains has increased the objections to its use due to the production of wines with a homogeneous profile. New tendencies in winemaking have emphasized the microbiological terroir and challenged the use of selected starters from different areas, including Non-Saccharomyces yeast or multi-strain starters in order to add complexity to the biochemical composition of wines. Nevertheless, these strategies also harbor their own challenges. In the present mini-review, we focus on the alternatives to current commercial yeast starters mainly based on the local multispecies starters or controlled spontaneous fermentations, considering the advantages and limitations of each strategy. Also, we present an ancestral technique based on the use of pre-fermented must (Pied-de-Cuve) because it provides certain microbial control to the alcoholic fermentation while allows the development of autochthonous microorganisms that might confer microbial typicity to the produced wines. Nevertheless, the latest strategy needs further research to establish a scientific background for the selection of the best Pied-de-Cuve development. Finally, the tendencies in winemaking should find a commitment between microbial control to guarantee alcoholic fermentation fulfillment and the production of wines reflecting microbial typicity to respond to consumer demands, without forgetting the scaling up in the cellars.
... geographical origin [20] and vintage. They also highlighted that their data demonstrate that the grape fungal community may be largely similar, but the relative abundances of fermentation-associated yeasts differ significantly between the vineyards [21,22]. ...
Article
Purpose of review The purpose of this symposium was to bring thought leaders in the microbiome from the west to Africa to share their unique experiences with African investigators in order to build the foundations for scientifically rigorous explorations into the African human and environmental microbiome that may explain why disease patterns are different in Africa where the chief killers are infectious diseases, whereas noncommunicable diseases (NCDs) are the major threat to healthcare resources in the developed world. Recent findings The application of new high throughput technologies to the investigation of the microbiome and its metabolome has revealed mechanisms whereby a traditional African high fiber diet can suppress NCDs which include colon cancer, inflammatory bowel diseases, obesity, type 2 diabetes and atherosclosis. There is concern that with migration and westernization, NCDs are becoming more common in Africa and that food security is becoming impaired by unbalanced obesogenic foods rather than inadequate food intake. Summary There is an urgent need for the formation of combined African-Western research programs to identify what is good and bad in the African diet-microbiome axis to develop strategies to prevent the incidence of NCDs rising to western levels in Africa, at the same time offering novel prevention strategies against the #1 healthcare threat in the developed world.
... Different studies analyzing the vineyard soil microbiome have been carried out, and their results mostly support the conclusions obtained by microbiome analysis of soils from other crops. Thus, it is well established that bacterial and fungal communities associated with bulk soil in vineyards depend on different biogeographical and edaphic factors [13,17,52], and also on different management regimes [17]. Thus, the fungal-community composition under integrated management is significantly different from that detected in vineyard soils under organic and biodynamic management, whereas fungal species' richness remained unaffected. ...
Article
Grapevine trunk diseases (GTDs) are one of the most devastating pathologies that threaten the survival and profitability of vineyards around the world. Progressive banning of chemical pesticides and their withdrawal from the market has increased interest in the development of effective biocontrol agents (BCAs) for GTD treatment. In recent years, considerable progress has been made regarding the characterization of the grapevine microbiome, including the aerial part microbiome (flowers, berries and leaves), the wood microbiome, the root environment and vineyard soil microbiomes. In this work, we review these advances especially in relation to the etiology and the understanding of the composition of microbial populations in plants affected by GTDs. We also discuss how the grapevine microbiome is becoming a source for the isolation and characterization of new, more promising BCAs that, in the near future, could become effective tools for controlling these pathologies.
... The role of the different species and strains of yeasts present on grapes regarding the final product is dependent on the winemaking techniques and the metabolic characteristics of the yeasts present. Species and native strains have become particularly interesting within the context of "terroir", which involves both the characteristics of cultivars, edaphoclimatic, and those associated with fermentative processes, including microorganisms, which together determine the peculiarities of a wine product (Bokulich et al., 2014;Moschetti et al., 2016;Grangeteau et al., 2017;Börlin et al., 2020). ...
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Considering the influence of natural yeasts on wine production and the organoleptic properties of the final product, the objective of the present study was to evaluate the diversity of yeasts in Cabernet-Sauvignon and Merlot (Vitis vinifera L.) grown in the highlands of the Northeast region of Rio Grande do Sul State, “Serra Gaúcha”, Brazil. Grape samples were collected from commercial vineyards between February and March in the 2017, 2018 and 2019 vintages. One hundred sixty-six isolated yeasts were classified at the species level by D1/D2 domain of 26S rRNA sequencing. A total of 31 yeast species were identified. The most prevalent species were Hanseniaspora uvarum, Issatchenkia terricola, Saturnispora diversa and Starmerella bacillaris. These same yeasts were the most frequent regardless of the year evaluated. The results indicated that there is a great diversity of yeast species in grapes cultivated in the highlands of Southern Brazil. However, the yeast communities remain similar in Cabernet-Sauvignon and Merlot grapes the analysed parameters (grape variety/vintage) are not interfering in the yeast populations found in the region highlands of Rio Grande do Sul, “Serra Gaúcha”, Brazil. This study enabled the knowledge of the yeast populations present in the region and their variations during the harvesting of wine grapes, showing that there is a majority pattern of species independent of the harvest.
... Moreover, long-term application of organic fertilizers compared to mineral fertilization induced a further increase (Treseder, 2008;Geisseler and Scow, 2014) or a slight decrease in microbial biomass with an increase in bacterial diversity (Francioli et al., 2016). Bokulich et al. (2014) proposed the term "microbial terroir" to emphasize the importance of regionallyspecific microbial communities in fermentation processes that contribute to the specific characteristics of wine (see also Gilbert et al., 2014;Burns et al., 2015;Vaudour et al., 2015;Franco et al., 2021). Microbes colonizing roots may migrate through the plant to colonize aerial tissues (Bulgarelli et al., 2013), influencing plant traits and grape quality. ...
Article
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Healthy soils form the basis of sustainable viticulture, where soil characteristics have a direct impact on wine quantity and quality. Soil not only provides water and nutrients to vines, but is also a living medium containing micro- and macroorganisms that perform many ecological functions and provide ecosystem services. These organisms are involved in many processes, from decomposing organic matter to providing minerals to vine roots. They also control diseases, pests, and weeds, in addition to improving the soil structure in terms of its capacity to retain water and nutrients. Related to decomposition processes, the carbon content of vineyard soils influences fertility, erosion and biogeochemical cycles, with significant implications for the global climate. However, common agricultural practices represent strong threats to biodiversity and associated ecosystem services provided by vineyard soils. As consumers increasingly consider environmental aspects in their purchase decisions, winegrowers have to adapt their vineyard management strategies, raising the demand for sustainable pest- and weed-control methods. This article presents a comprehensive review of the impacts of vineyard practices on the soil ecosystem, biodiversity, and biodiversity-based ecosystem services, and provides future prospects for sustainable viticulture.
... Biogeography determines the vineyard microbiome (Gobbi et al., 2022), but also the microbial populations established in the grapes' surface (Bokulich et al., 2014;Knight et al., 2015) which contribute to the flavor of wines produced in a particular region (Bokulich et al., 2016), with a special relevance of the vineyard and grape must fungal populations (Liu et al., 2020). These regional patterns exist at different spatial scales, and, at the local scale, apart from the contribution of the surrounding native ecosystems (Morrison-Whittle et al., 2018) and the role of physical forces and animal vectors (insects and birds) in yeast dispersal (Liu et al., 2019), the vineyard-winery cross connection is especially important in ...
Article
Wine fermentations are dominated by Saccharomyces yeast. However, dozens of non-Saccharomyces yeast genera can be found in grape musts and in the early and intermediate stages of wine fermentation, where they co-exist with S. cerevisiae. The diversity of non-Saccharomyces species is determinant for the sensorial attributes of the resulting wines, both directly (by producing aroma impact compounds) and indirectly (modulating the performance of Saccharomyces). Many research groups worldwide are exploring the great diversity of wine yeasts to exploit their metabolic potential to improve wine flavor or to prevent wine spoilage. In this work, we share a new dataset from a wide ITS amplicon survey of 272 wine samples, and we perform a preliminary exploration to build a catalogue of 242 fungal and yeast genera detectable in wine samples, estimating global figures of their prevalence and relative abundance patterns across wine samples. Thus, our mycobiome survey provides a broad measure of the yeast diversity potentially found in wine fermentations; we hope that the wine yeast research community finds it useful, and we also want to encourage further discussion on the advantages and limitations that meta-taxonomic studies may have in wine research and industry.
... The assessment of the structure and function of the crop microbiome is important for increasing agriculture productivity. The community structure and function of several crop microbiomes have been recognized based on high-throughput sequencing, including maize (Niu et al., 2017;Peiffer et al., 2013;, wheat (Rascovan et al., 2016), rice (Breidenbach et al., 2016;, barley (Bulgarelli et al., 2015), soybean (Rascovan et al., 2016), tomato (Kwak et al., 2018;Ottesen et al., 2013), potato (Inceoglu et al., 2011), cucumber (Ofek-Lalzar et al., 2014, citrus (Xu et al., 2018a), grapevine (Bokulich et al., 2014;Zarraonaindia et al., 2015), sugar beet (Mendes et al., 2011), sugarcane (De Souza et al., 2016), and lettuce (Cardinale et al., 2015). Collectively mentioned as the crop microbiome, all of these microorganisms contain bacteria, fungi, viruses, protozoa, and so on, are vital contributors that affect plant growth, health and crop productivity, even though mostly still a black box Sharma et al., 2020). ...
Chapter
The concentration of atmospheric carbon dioxide (CO2) has almost doubled since the preindustrial era due to global climate change and is expected to further increase if the current emission rates are not controlled. The impacts of elevated CO2 (e[CO2]) on growth, development, and yield of plant species, particularly crops, are very important concerns for the scientist. This is due to dynamic implications on global agricultural production and food security in the climate change scenario. Crops respond to the e[CO2] by stimulating the photosynthetic rate. which boosts crop yield. Higher levels of atmospheric carbon act like a carbon fertilizer for the plants and results in an increase in plant growth and productivity. Cereal crops grow larger in size and exhibit faster growth rates under e[CO2], and biomass production becomes higher. Crops have evolved strategies to enhance their physiological performance by increasing water use efficiency and reducing the transpirational water loss as well as lowering stomatal conductance under e[CO2]. C3 plants exhibit considerably higher increases in yield due to e[CO2] ranging from 20% and 35% as compared to C4 crops with only 10% to 15%. e[CO2] influences the qualitative attributes of crops, including the concentration of nutrients, which are fundamental food quality attributes having diverse implications on agricultural production, market value of crops as well as impacts on human health. Sharp declines are projected in the protein content and free amino acid of cereals under e[CO2] conditions. Under realistic field conditions experiments, free-air CO2 enrichment technology revealed significant increases in the photosynthesis activity, leaf carbohydrates, starch and sugars whereas the concentration of nitrogen per unit leaf mass has been found to decrease. The relative yield responses of grain crops under e[CO2] might increase under limiting nutrient and water conditions due to physiological adaptations. The major C3 cereals, including wheat and rice, undergo major shifts in physiological responses and C:N metabolism in response to e[CO2], However, a reduction in nutritional quality under e[CO2] appears to be a major challenge.
... The assessment of the structure and function of the crop microbiome is important for increasing agriculture productivity. The community structure and function of several crop microbiomes have been recognized based on high-throughput sequencing, including maize (Niu et al., 2017;Peiffer et al., 2013;, wheat (Rascovan et al., 2016), rice (Breidenbach et al., 2016;, barley (Bulgarelli et al., 2015), soybean (Rascovan et al., 2016), tomato (Kwak et al., 2018;Ottesen et al., 2013), potato (Inceoglu et al., 2011), cucumber (Ofek-Lalzar et al., 2014, citrus (Xu et al., 2018a), grapevine (Bokulich et al., 2014;Zarraonaindia et al., 2015), sugar beet (Mendes et al., 2011), sugarcane (De Souza et al., 2016), and lettuce (Cardinale et al., 2015). Collectively mentioned as the crop microbiome, all of these microorganisms contain bacteria, fungi, viruses, protozoa, and so on, are vital contributors that affect plant growth, health and crop productivity, even though mostly still a black box Sharma et al., 2020). ...
Chapter
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Intensified drought stress threatens plant growth and productivity, while elevated CO2 (e[CO2]) alleviates the negative impact of drought stress on plants through alteration in water use and improvement in plant growth. In the terrestrial ecosystem, crops are particularly sensitive to drought and benefit from e[CO2]. To cope with the drier and CO2-enriched climate, plants have evolved various adaptive strategies. Water-dependent crops can benefit from e[CO2] but are species-dependent and depend on the intensities and durations of drought stress. In this chapter, we summarized drought impact on crops, crop performance under e[CO2], as well as their interactions in physiological, biochemical, and molecular levels.
... Regarding yeasts, Hanseniaspora and Metschnikowia are common inhabitants of flowers and fruits. Hanseniaspora species have been encountered in alcoholization during fruit fermentation before (Bokulich et al., 2013). For instance, culture-dependent analysis of ripe grape berries has shown that Hanseniaspora is the predominant fungal genus, besides Candida, Cryptococcus, Rhodotorula, Pichia, Metschnikowia and/or Kluyveromyces (Raspor et al., 2006). ...
Article
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The fiber, vitamin, and antioxidant contents of fruits contribute to a balanced human diet. In countries such as Argentina, several tropical fruits are witnessing a high yield in the harvest season, with a resulting surplus. Fruit fermentation using autochthonous starter cultures can provide a solution for food waste. However, limited knowledge exists about the microbiota present on the surfaces of fruits and the preceding flowers. In the present exploratory study, the microbiomes associated with the surfaces of tropical fruits from Northern Argentina, such as white guava, passion fruit and papaya were investigated using a shotgun metagenomic sequencing approach. Hereto, one sample composed of 14 white guava fruits, two samples of passion fruits with each two to three fruits representing the almost ripe and ripe stage of maturity, four samples of papaya with each two to three fruits representing the unripe, almost ripe, and ripe stage of maturity were processed, as well as a sample of closed and a sample of open Japanese medlar flowers. A considerable heterogeneity was found in the composition of the fruits’ surface microbiota at the genus and species level. While bacteria dominated the microbiota of the fruits and flowers, a small number of the metagenomic sequence reads corresponded with yeasts and filamentous fungi. A minimal abundance of bacterial species critical in lactic acid and acetic acid fermentations was found. A considerable fraction of the metagenomic sequence reads from the fruits’ surface microbiomes remained unidentified, which suggested that intrinsic species are to be sequenced or discovered.
... A first microbial contamination may generate from the close contact with the soil, where manure or sewage sludge may represent a primary source of pathogenic microbes, together with irrigation water [7]. Besides pathogenic microbes, F&V usually harbor a complex microbial community that is influenced by several factors, such as the type of product and the cultivar, geographical area, agricultural practices, season and climate [8][9][10]. After harvesting, the microbiota may be affected by processing, handling and storage conditions [11][12][13]. ...
Article
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Fruits and vegetables (F&V) products are recommended for the daily diet due to their low caloric content, high amount of vitamins, minerals and fiber. Furthermore, these foods are a source of various phytochemical compounds, such as polyphenols, flavonoids and sterols, exerting antioxidant activity. Despite the benefits derived from eating raw F&V, the quality and safety of these products may represent a source of concern, since they can be quickly spoiled and have a very short shelf-life. Moreover, they may be a vehicle of pathogenic microorganisms. This study aims to evaluate the bacterial and fungal populations in F&V products (i.e., iceberg lettuces, arugula, spinaches, fennels, tomatoes and pears) by using culture-dependent microbiological analysis and high-throughput sequencing (HTS), in order to decipher the microbial populations that characterize minimally-processed F&V. Our results show that F&V harbor diverse and product-specific bacterial and fungal communities, with vegetables leaf morphology and type of edible fraction of fruits exerting the highest influence. In addition, we observed that several alterative (e.g., Pseudomonas and Aspergillus) and potentially pathogenic taxa (such as Staphylococcus and Cladosporium) are present, thus emphasizing the need for novel product-specific strategies to control the microbial composition of F&V and extend their shelf-life.
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Saccharomyces cerevisiae isolates from grapes, soil, vine bark and buds collected at seven phenological stages of an annual growth cycle, were molecular typed by Microsatellite Multiplex PCR. Subsequently 30 S. cerevisiae genotypes were selected and the effect of vineyard environmental stressors, in both sublethal upper and lower levels, on their growth parameters was evaluated. The effect of low and high temperature (7–40 °C), pH (2.5–8.0), glucose concentration (3.0–300.0 g/L), nitrogen concentration (0.008–8.0 g/L), and copper presence (24 mg/L) were modelled individually using the reparametrized Gompertz equation. Multivariate ANOVA and Generalized Procrustes Analysis were used to determine the environmental stressor's influence over the lag phase (λ) and the maximum specific growth rate (μmax). Both parameters were significantly affected by the S. cerevisiae genotype, the treatments, and the interaction between them. Despite a generalized reduction in μmax and a variable answer in λ, the 30 S. cerevisiae genotypes were able to overcome all the treatments. Extreme glucose limitation, copper presence and low temperature had the highest impact over the growth parameters. Interestingly, ten genotypes mostly distributed in the vineyard were the least affected, suggesting a greater acclimatization fitness and the possibility to persist in the changing conditions of the vine annual cycle.
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Background Shading is an important factor affecting the cultivation of American ginseng, as it influences crop quality and yield. Rhizosphere microorganisms are also crucial for normal plant growth and development. However, whether different shade types significantly change American ginseng rhizosphere microorganisms is unknown. Methods This study evaluated the rhizosphere soils of American ginseng under traditional, high flag and high arch shade sheds. High-throughput 16S rRNA gene sequencing determined the change of rhizosphere bacterial communities. Results The microbial diversity in rhizosphere soils of American ginseng significantly changed under different shading conditions. The bacteria diversity was more abundant in the high arch shade than flat and traditional shades. Different bacterial genera, including Bradyrhizobium , Rhizobium , Sphingomonas , Streptomyces and Nitrospira , showed significantly different abundances. Different shading conditions changed the microbial metabolic function in the American ginseng rhizosphere soils. The three types of shade sheds had specific enriched functional groups. The abundance of ATP-binding cassette (ABC) transporters consistently increased in the bacterial microbiota. These results help understand the influence of shading systems on the rhizosphere microecology of American ginseng, and contribute to the American ginseng cultivation.
Article
In this article, several methods of storing the harvest of the grape varieties in a natural way, including storage, vine method, storage in water-filled containers (by the method of legumes) were studied. During the experiments, discrepancy between their quality indicators, advantages and disadvantages of these methods, storage periods and conditions, as well as the amount of dry matter, the amount of nitrate, the pH environment were researched and analyzed. The pertinent results showed that the sugar content of grapes was the lowest according to the characteristics of varieties in the vine method, accounted for 16.3% and the highest in the storage method, which was 21.17 %, the amount of nitrate was not more than 60 mg/kg in the norm, which was also allowed in all methods. Noteworthy, the most acceptable method among them was the bottle method, however, the method needed to be improved in the future.
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The microbial biodiversity found in different vitivinicultural regions is an important deter- minant of wine terroir. It should be studied and preserved, although it may, in the future, be subjected to manipulation by precision agriculture and oenology. Here, we conducted a global survey of vineyards’ soil microbial communities. We analysed soil samples from 200 vine- yards on four continents to establish the basis for the development of a vineyard soil microbiome’s map, representing microbial biogeographical patterns on a global scale. This study describes vineyard microbial communities worldwide and establishes links between vineyard locations and microbial biodiversity on different scales: between continents, coun- tries, and between different regions within the same country. Climate data correlates with fungal alpha diversity but not with prokaryotes alpha diversity, while spatial distance, on a global and national scale, is the main variable explaining beta-diversity in fungal and pro- karyotes communities. Proteobacteria, Actinobacteria and Acidobacteria phyla, and Archaea genus Nitrososphaera dominate prokaryotic communities in soil samples while the overall fungal community is dominated by the genera Solicoccozyma, Mortierella and Alternaria. Finally, we used microbiome data to develop a predictive model based on random forest analyses to discriminate between microbial patterns and to predict the geographical source of the samples with reasonable precision.
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Chapter
Wine making has evolved since its origins in the Caucasus more than 8000 years ago to a modern scientific and technological discipline. Novel methodologies and practices have been implemented continuously in the elaboration of wines. The industry has been normally keen to accept those developments and incorporate them into their protocols. However, the complexity of some of the new developments, the “return” to old practices driven by some influencing wine makers or opinion makers, commercial regulations, and consumer concerns are growing limitations for the incorporation of new methodologies. This chapter is focused on new microbial methodologies that can be applied to modern winemaking to control the process microbiologically and discuss about the possible challenges of their incorporation.
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Thesis
Le concept d’holobionte considère l’unité fonctionnelle composée des plantes et de ces microorganismes. Il promeut une approche holistique à la gestion des cultures et, plus généralement, à la vision du vivant. Cependant, ce concept est sujet à débat en raison du manque de preuves expérimentales de son existence. De plus, la compréhension fine des mécanismes régissant l’assemblage des microorganismes associés aux plantes reste un des enjeux majeurs de l’écologie microbienne et de l’agriculture. Le but de cette thèse était de tester la validité du concept d’holobionte, d’étudier les facteurs qui impactent l’assemblage des communautés microbiennes de l’endosphère racinaire et d’analyser la dynamique intra- et inter-annuelle du microbiote de la vigne. Grâce à une expérimentation mise en place en association avec une pépinière viticole (greffage et plantes chimériques), nous avons pu démontrer l’existence d’un recrutement actif et déterminé de microorganismes par la plante, sous l’effet dominant du porte-greffe, ce qui nous a permis d’augmenter les preuves expérimentales à l’existence du concept d’holobionte. Dans le cadre d’une seconde partie, nous nous sommes intéressés aux dynamiques d’assemblages du microbiote de la vigne, grâce à un vaste plan d’échantillonnage mis en place au sein d’un domaine viticole. Nous avons mis en avant le rôle fondamental des facteurs environnementaux, de l’âge et du cépage dans l’assemblage du microbiote endosphérique racinaire de la vigne à petite échelle géographique et l'existence de patrons temporels intra-annuels marqués dans la structuration de ces communautés. Ces travaux fournissent un ensemble de connaissances nouvelles dans le domaine de l’écologie microbienne, soutiennent l’existence d’un terroir microbiologique et soulignent l’importance de la prise en compte de ce terroir microbien dans le cadre d’une gestion durable de la vigne.
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Global climate change has become one of the most important obstacles threaten food security, sustainable agriculture and human health. Rhizosphere microbiome can promote root nutrient absorption, regulating crop immune response, improving stress resistance of crops, and promoting crop growth and development, which is affected by climate change. In this chapter, we summarize the importance of the crop rhizosphere microbiome, highlighting the rhizosphere microbiome of crops response to abiotic and biotic factors, especially climate factors including atmospheric CO2 rising, warming, soil drought and salinity, and thus provide the current state of knowledge about the interaction of rhizosphere microbiome and crops under global climate change, and elevate the understanding of rhizosphere microbiome play role in crop productivity and sustainable agriculture to cope with future climate scenarios.
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Wine is an ancient, traditional, and widely popular alcoholic beverage fermented from grapes. Winemaking requires a succession of biotransformations that must be well managed by the winemaker. This involves not only the natural microflora but also, often, selected starters, added to the must or wine at the appropriate time. Microbial resource management has played a central role in the wine industry. There are two different fermentations in the winemaking process. The alcoholic fermentation process is mediated by the metabolic activity of common yeast, Saccharomyces cerevisiae, and the malolactic fermentation (MLF), by that of lactic acid bacteria belonging to the ancient genera-Lactobacillus, Oenococcus, Leuconostoc, and Pediococcus with a predominance of the species Oenococcus oeni. MLF is the process by which certain LAB convert l-malic acid into l-lactic acid and carbon dioxide. This fermentation is essential to produce some red wines, white wines, and sparkling base wines. The softening of the wine, by increasing its pH, is the main function of MLF, and the removal of a microbial carbon source impacts the flavor profile of the finished wines. Several species of lactic acid bacteria (LAB) can undertake MLF, of which O. oeni is one of the species most adapted to the harsh conditions of wine. MLF bacteria have the ability to transport malate into their cytoplasm via a specific malate permease, in addition to passive transport, and produce a cytoplasmic malolactic enzyme responsible for the malic acid decarboxylation. For the success of MLF, the selection of the right bacteria depends on the control of appropriate physico-chemical parameters.
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Fungal metabolic volatiles attract Drosophila suzukii which oviposits in ripening fruits, but there are few data describing the fungal microbiomes of commercial fruits susceptible to this insect pest. We tested the hypothesis that fruit type and ripening stage have a significant effect on fruit surface fungal communities using DNA metabarcoding approaches and found strong support for differences in all three fungal community biodiversity metrics analysed (numbers, types, and abundances of taxa). There was an average fivefold greater difference in fungal communities between sites with different fruit types (strawberry, cherry, raspberry, and blueberry) than across fruit developmental stages, demonstrating site and/or fruit type is the greater factor defining fungal community assemblage. The addition of a fungal internal standard (Plectosphaerella cucumerina) showed cherry had relatively static fungal populations across ripening. Raspberry had a greater prevalence of Saccharomycetales yeasts attractive to D. suzukii, including Hanseniaspora uvarum, which aligns with reports that raspberry is among the fruits with greatest susceptibility and attraction to D. suzukii. Greater knowledge of how yeast communities change during fruit maturation and between species or sites may be valuable for developing methods to manipulate fruit microbiomes for use in integrated pest management strategies to control D. suzukii.
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Vineyards are a very important perennial woody crop globally, but they are also among the most intensively managed agroecosystems. This has resulted in biologically impoverished and highly eroded vineyards. Environmentally-friendly inter-row vegetation management, particularly the use of cover crops, could contribute to avoid erosion and regenerate soil biodiversity in vineyards. In this study, we updated a global meta-analysis on the effects of inter-row extensive vegetation cover management, particularly through the use of cover crops, on ecosystem services, including supporting, regulating and provisioning services, and biodiversity in vineyards. We also analyzed the role of environmental variables (climate, including precipitation- and temperature-related bioclimatic variables and soil properties, including pH and texture) and irrigation in modulating these effects. The presence of extensive vegetation cover consistently increased biodiversity, as well as supporting ecosystem services in irrigated vineyards and regulating services in rainfed vineyards. Provisioning services, which were evaluated as grape yield, were slightly negatively affected in rainfed vineyards, but not in irrigated ones. The effects of vegetation cover on ecosystem services varied depending on the climate and edaphic characteristics of vineyards. For example, supporting ecosystem services were favored in acidic soils and were also positively related to the precipitation of the wettest quarter, whereas regulating services were particularly enhanced in alkaline soils and in locations with lower temperatures of the wettest quarter. Biodiversity was especially favored in locations with lower precipitation seasonality. Taken together, our study indicates the importance of developing strategies for the adaptive management of extensive vegetation covers tailored to the climatic and edaphic conditions of each vineyard. This adaptive management, combined with irrigation and potentially other locally-tailored adaptive strategies, could also contribute to further mitigate potential negative effects of vegetation cover on grape production while maximizing other ecosystem services such as provisioning and supporting services and biodiversity.
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Understanding the diversity and evolution of microorganisms during wine fermentation is essential for controlling its production. However, the flavors profiles associated with microbiota changes during the spontaneous fermentation have not yet been described in detail. In this study, we explored the correlations between microbial community with physicochemical properties and flavor components during the spontaneous fermentation of Cabernet Sauvignon wine. Microbial community diversity at different fermentation stages was identified using high-throughput sequencing, and physicochemical properties and volatile compounds were identified through fermentation features testing and headspace solid phase microextraction gas chromatography mass spectrometry. First, the diversity of the fungi community decreased with the fermentation process, whereas the bacteria did not change significantly until the end of the fermentation. Second, the changes of the fermentation environment had reshaped the diversity and composition of the microbial community. Finally, Aureobasidium, Cladosporium, Filobasidium, Hanseniaspora, Hannaella, Saccharomyces, Alternaria, Wickerhamomyce, Starmerella, Candida, Papiliotrema, Bradyrhizobium, Gluconobacter, Leuconostoclia, Comamonas, Acetobacter, and Massilia, were significantly correlated with changes of physicochemical properties and volatile compounds. Overall, our research results provide important insights for understanding the metabolically active microbiota, which is conducive to the expression of wine "terroir".
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Aims: The yeast community structure associated with grapes is an essential part of the wine-growing chain with a significant effect on wine quality. The aim of the present study was to evaluate the effect of the varietal factor on the yeast community assembly on grapes and during must fermentation. Methods and results: We analysed the wine yeast populations associated with four different grape varieties from the Greek national collection vineyard of Lykovryssi. The vintage effect was also considered by sampling the grapes for two consecutive years. Fourteen yeast species were recovered and genotyped to distinct subpopulations. A relatively stable yeast community structure was detected across vintages, with Hanseniaspora guilliermondii being the core species of the vineyard under study. The detected species subpopulations shared a relatively high genetic similarity with several genotypes persisting across vintages. Conclusions: It was shown that different grape cultivars were associated with distinct yeast communities, pointing to their possible implication on wine chemical diversity. Significance and impact of the study: Present findings show that the varietal factor is an important sharpener of the vineyard-associated wine yeast community, which may interfere with the organoleptic profile of the resulting wines.
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Wine is a highly complex mixture of compounds which largely define its appearance, aroma, flavour and mouth-feel properties. The compounds responsible for those attributes have been derived in turn from three major sources, viz. grapes, microbes and, when used, wood (most commonly, oak). The grape-derived compounds provide varietal distinction in addition to giving wine its basic structure. Thus, the floral monoterpenes largely define Muscat-related wines and the fruity volatile thiols define Sauvignon-related wines; the grape acids and tannins, together with alcohol, contribute the palate and mouth-feel properties. Yeast fermentation of sugars not only produces ethanol and carbon dioxide but a range of minor but sensorially important volatile metabolites which gives wine its vinous character. These volatile metabolites, which comprise esters, higher alcohols, carbonyls, volatile fatty acids and sulfur compounds, are derived from sugar and amino acid metabolism. The malolactic fermentation, when needed, not only provides deacidification, but can enhance the flavour profile. The aroma and flavour profile of wine is the result of an almost infinite number of variations in production, whether in the vineyard or the winery. In addition to the obvious, such as the grapes selected, the winemaker employs a variety of techniques and tools to produce wines with specific flavour profiles. One of these tools is the choice of microorganism to conduct fermentation. During alcoholic fermentation, the wine yeast Saccharomyces cerevisiae brings forth the major changes between grape must and wine: modifying aroma, flavour, mouth-feel, colour and chemical complexity. The wine bacterium Oenococcus oeni adds its contribution to wines that undergo malolactic fermentation. Thus flavour-active yeasts and bacterial strains can produce desirable sensory results by helping to extract compounds from the solids in grape must, by modifying grape-derived molecules and by producing flavour-active metabolites. This article reviews some of the most important flavour compounds found in wine, and their microbiological origin.
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Recent advances in molecular biotechnology have introduced an array of powerful techniques for studying the microbial ecology of beverage and food fermentations. Molecular tools such as denaturing gradient gel electrophoresis, terminal restriction fragment length polymorphism, fluorescent in situ hybridization, clone libraries, and quantitative polymerase chain reaction are sensitive methods for microbial community analysis and have several advantages over traditional, culture-based techniques. Some of these tools have far-reaching benefits, not only for fermentation research but also for rapid quality-assurance applications in the beverage fermentation industry. Additionally, the increasing accessibility of next-generation sequencing technologies, such as Illumina and 454 Life Sciences sequencing platforms, is bringing some of these powerful new tools within reach of researchers for food or fermentation analysis. This promises high-resolution studies revealing deep community structure in fermentation and processing environments, endeavors with obvious benefits to understanding and controlling mixed microbial fermentation systems and process hygiene. This review presents an overview of the current technologies available for microbial community analysis and considers their specific application for fermentation research and industrial purposes, as well as providing an outlook on the future of community profiling in beer and wine. Keywords: American coolship ale, Community Profiling, DGGE, Fermentation Lambic, Microbial Ecology, Next-generation sequencing, TRFLP
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Variable canopy densities and associated differences in sunlight distribution within the fruit zones on clusters were quantified and correlated with variable severities of powdery mildew within vineyards in the states of New York, Washington, and South Australia. Canopy density was measured with enhanced point quadrat analysis (EPQA), and the number of shading layers and the photon flux within the fruit zone of individual vines indicated that less disease developed on clusters with more exposure to sunlight. When clusters were categorized as heavily shaded (<= 10% photosynthetic photon flux), moderately exposed, or well exposed (>= 51% photosynthetic photon flux), vines with the least disease were also shown to have a significantly greater proportion of clusters in the well-exposed category relative to vines with the highest powdery mildew ratings. Consequently, these latter vines had significantly more heavily shaded clusters. The correlation remained strong and the relationship linear even with biweekly applications of either 2 kg/ha or 9 kg/ha of wettable sulfur during the growing season. Additionally, through the use of a fluorescent tracer and EPQA assessments, the deposit of spray materials on clusters was shown to be linearly related to their degree of exposure. Thus, canopy management practices designed to optimize sunlight exposure of grape clusters for fruit quality purposes should also significantly assist in the management of powdery mildew.
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GenGIS is free and open source software designed to integrate biodiversity data with a digital map and information about geography and habitat. While originally developed with microbial community analyses and phylogeography in mind, GenGIS has been applied to a wide range of datasets. A key feature of GenGIS is the ability to test geographic axes that can correspond to routes of migration or gradients that influence community similarity. Here we introduce GenGIS version 2, which extends the linear gradient tests introduced in the first version to allow comprehensive testing of all possible linear geographic axes. GenGIS v2 also includes a new plugin framework that supports the development and use of graphically driven analysis packages: initial plugins include implementations of linear regression and the Mantel test, calculations of alpha-diversity (e.g., Shannon Index) for all samples, and geographic visualizations of dissimilarity matrices. We have also implemented a recently published method for biomonitoring reference condition analysis (RCA), which compares observed species richness and diversity to predicted values to determine whether a given site has been impacted. The newest version of GenGIS supports vector data in addition to raster files. We demonstrate the new features of GenGIS by performing a full gradient analysis of an Australian kangaroo apple data set, by using plugins and embedded statistical commands to analyze human microbiome sample data, and by applying RCA to a set of samples from Atlantic Canada. GenGIS release versions, tutorials and documentation are freely available at http://kiwi.cs.dal.ca/GenGIS, and source code is available at https://github.com/beiko-lab/gengis.
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During the transformation of grapes to wine, wine fermentations are exposed to a large area of specialized equipment surfaces within wineries, which may serve as important reservoirs for two-way transfer of microbes between fermentations. However, the role of winery environments in shaping the microbiota of wine fermentations and vectoring wine spoilage organisms is poorly understood at the systems level. Microbial communities inhabiting all major equipment and surfaces in a pilot-scale winery were surveyed over the course of a single harvest to track the appearance of equipment microbiota before, during, and after grape harvest. Results demonstrate that under normal cleaning conditions winery surfaces harbor seasonally fluctuating populations of bacteria and fungi. Surface microbial communities were dependent on the production context at each site, shaped by technological practices, processing stage, and season. During harvest, grape- and fermentation-associated organisms populated most winery surfaces, acting as potential reservoirs for microbial transfer between fermentations. These surfaces harbored large populations of Saccharomyces cerevisiae and other yeasts prior to harvest, potentially serving as an important vector of these yeasts in wine fermentations. However, the majority of the surface communities before and after harvest comprised organisms with no known link to wine fermentations and a near-absence of spoilage-related organisms, suggesting that winery surfaces do not overtly vector wine spoilage microbes under normal operating conditions.
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Cheese fermentations involve the growth of complex microbial consortia, which often originate in the processing environment and drive the development of regional product qualities. However, the microbial milieus of cheesemaking facilities are largely unexplored and the true nature of the fermentation-facility relationship remains nebulous. Thus, a high-throughput sequencing approach was employed to investigate the microbial ecosystems of two artisanal cheesemaking plants, with the goal of elucidating how the processing environment influences microbial community assemblages. Results demonstrate that fermentation-associated microbes dominated most surfaces, primarily Debaryomyces and Lactococcus, indicating that establishment of these organisms on processing surfaces may play an important role in microbial transfer, beneficially directing the course of sequential fermentations. Environmental organisms detected in processing environments dominated the surface microbiota of washed-rind cheeses maturing in both facilities, demonstrating the importance of the processing environment for populating cheese microbial communities, even in inoculated cheeses. Spatial diversification within both facilities reflects the functional adaptations of microbial communities inhabiting different surfaces and the existence of facility-specific “house” microbiota, which may play a role in shaping site-specific product characteristics.
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A 16S rRNA gene database (http://greengenes.lbl.gov) addresses limitations of public repositories by providing chimera screening, standard alignment, and taxonomic classification using multiple published taxonomies. It was found that there is incongruent taxonomic nomenclature among curators even at the phylum level. Putative chimeras were identified in 3% of environmental sequences and in 0.2% of records derived from isolates. Environmental sequences were classified into 100 phylum-level lineages in the Archaea and Bacteria.
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Terroir is a highly important concept in viticulture because it relates the sensory attributes of wine to the environmental conditions in which the grapes are grown. Quality hierarchy and wine style may, to a considerable extent, be explained by terroir. However, terroir is difficult to study on a scientific basis because many factors are involved, including climate, soil, cultivar and human practices, and these factors interact. The best expression of terroir is achieved when the precocity of the grapevine variety is suited to the local climatic conditions in such a way that full ripeness is reached by the end of the growing season. For the production of high quality red wines, environmental conditions should induce moderate vine vigour, either through moderate water deficit stress or through low nitrogen supply. These conditions are most frequently met on shallow or stony soils, in moderately dry climates. Regular but not excessive vine water and nitrogen supplies are needed to produce high quality white wines. However, great terroir emerges only when socio-economic conditions are favourable to the establishment of quality-orientated wine production.
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