Grape berry bacterial microbiota: Impact of the ripening process and the farming system

Dynamic Succession of Natural Microbes during the Ecolly Grape Growth under Extremely Simplified Eco-Cultivation

The composition and continuous succession of natural microbial communities during grape growth play important roles in grape health and flavor quality as well as in characterizing the regional wine terroir. This study explored the diversity and dynamics of fruit epidermal microbes at each growth and developmental stage of Ecolly grapes under an extremely simplified eco-cultivation model, analyzed microbial interactions and associations of weather parameters to specific communities, and emphasized metabolic functional characteristics of microecology. The results indicated that the natural microbial community changed significantly during the grape growth phase. The dominant fungal genera mainly included Gibberella, Alternaria, Filobasidium, Naganishia, Ascochyta, Apiotrichum, Comoclathris, and Aureobasidium, and the dominant bacterial genera mainly contained Sediminibacterium, Ralstonia, Pantoea, Bradyrhizobium, Brevundimonas, Mesorhizobium, Planococcus, and Planomicrobium. In summary, filamentous fungi gradually shifted to basidiomycetous yeasts along with fruit ripening, with a decline in the number of Gram-negative bacteria and a relative increase in Gram-positive bacteria. The community assembly process reflects the fact that microbial ecology may be influenced by a variety of factors, but the fungal community was more stable, and the bacterial community fluctuated more from year to year, which may reflect their response to weather conditions over the years. Overall, our study helps to comprehensively profile the ecological characteristics of the grape microbial system, highlights the natural ecological viticulture concept, and promotes the sustainable development of the grape and wine industry.

Microbial dysbiosis in roots and rhizosphere of grapevines experiencing decline is associated with active metabolic functions

When grapevine decline, characterized by a premature decrease in vigor and yield and sometimes plant death, cannot be explained by pathological or physiological diseases, one may inquire whether the microbiological status of the soil is responsible. Previous studies have shown that the composition and structure of bacterial and fungal microbial communities in inter-row soil are affected in areas displaying vine decline, compared to areas with non-declining vines within the same plot. A more comprehensive analysis was conducted in one such plot. Although soil chemical parameters could not directly explain these differences, the declining vines presented lower vigor, yield, berry quality, and petiole mineral content than those in non-declining vines. The bacterial and fungal microbiome of the root endosphere, rhizosphere, and different horizons of the bulk soil were explored through enzymatic, metabolic diversity, and metabarcoding analysis in both areas. Despite the lower microbial diversity and richness in symptomatic roots and soil, higher microbial activity and enrichment of potentially both beneficial bacteria and pathogenic fungi were found in the declining area. Path modeling analysis linked the root microbial activity to berry quality, suggesting a determinant role of root microbiome in the berry mineral content. Furthermore, certain fungal and bacterial taxa were correlated with predicted metabolic pathways and metabolic processes assessed with Eco-Plates. These results unexpectedly revealed active microbial profiles in the belowground compartments associated with stressed vines, highlighting the interest of exploring the functional microbiota of plants, and more specifically roots and rhizosphere, under stressed conditions.

The Phenolic Composition, Antioxidant Activity and Microflora of Wild Elderberry in Asturias (Northern Spain): An Untapped Resource of Great Interest

The objective of this study is the characterization of the phenolic profile and antioxidant activity of elderberries (Sambucus nigra L.) from a collection of 79 wild specimens in northern Spain to assess variations in the species at the local level and evaluate its interest as a source of biocompounds. Also, a first study was carried out on the microflora present in this fruit, providing information relevant to its commercial exploitation. Moreover, the phenolic composition, antioxidant capacity and microbial composition in overripe fruits were determined, seeking a better use for this currently wasted resource. A wide variability in levels of phenolics was detected. Elderberries showed high antioxidant activity related to a high cyanidin derivative content, making them of interest to industry. Microflorae were present in very variable concentration ranges, so their levels should be monitored in those applications that require strict control. Overripe fruits are of interest as a source of anthocyanidins, since their concentration and antioxidant capacity remain after the optimal ripening period, promoting sustainability and a better use of natural resources. The database generated is of particular interest for further breeding trials based on the phenolic profile and antioxidant activity of the samples.

Fungicide sensitivity of grapevine bacteria with plant growth-promoting traits and antagonistic activity as non-target microorganisms

This study evaluates the capacity of commercial formulations of synthetic fungicides to inhibit grapevine bacterial growth when sprayed on vineyards to control diseases, such as downy mildew, powdery mildew and secondary rots. Fungicide sensitivity plate assays were carried out on bacteria isolated from vineyards that were also identified and characterized for their plant growth-promoting (PGP) traits and antifungal activity. The high taxonomic variability of bacteria screened with different chemical classes of fungicides is one new finding of this study. Seven out of 11 fungicides were able to inhibit the growth of bacteria at a concentration corresponding to the maximum dose allowed by law in spray treatments of vineyards. Bacterial sensitivity to each fungicide varied greatly. Many sensitive isolates displayed PGP traits and/or antagonistic activity. This study shows the potential impact of fungicidal treatments on grapevine bacterial microbiota. The involvement of bacteria beneficial to the growth and health of plants underlines the importance of this investigation. Our data reveal that the control of a certain disease may be possible using fungicides that have no or low impact on natural non-target microbiota. Understanding the action mechanisms of the active ingredients in these products is a priority for the development of new eco-friendly pesticides.

Epiphitic Microbiome of Alvarinho Wine Grapes from Different Geographic Regions in Portugal

Geographic location and, particularly, soil and climate exert influence on the typicality of a wine from a specific region, which is often justified by the terroir, and these factors also influence the epiphytic flora associated with the surface of the grape berries. In the present study, the microbiome associated with the surface of berries obtained from ten vineyards of the Alvarinho variety located in different geographical locations in mainland Portugal was determined and analyzed. The removal of microbial flora from the surface of the berries was carried out by washing and sonication, after which the extraction and purification of the respective DNA was carried out. High-throughput short amplicon sequencing of the fungal ITS region and the bacterial 16S region was performed, allowing for the determination of the microbial consortium associated with Alvarinho wine grapes. Analysis of α-diversity demonstrated that parcels from the Monção and Melgaço sub-region present a significantly (p < 0.05) lower fungal diversity and species richness when compared to the plots analyzed from other regions/sub-regions. The ubiquitous presence of Metschnikowia spp., a yeast with enologic potential interest in all parcels from Monção and Melgaço, was also observed.

Effect of Commercial Yeast Starter Cultures on Cabernet Sauvignon Wine Aroma Compounds and Microbiota

Commercial Saccharomyces cerevisiae plays an important role in the traditional winemaking industry. In this study, the correlation of microbial community and aroma compound in the process of alcohol fermentation of Cabernet Sauvignon by four different commercial starters was investigated. The results showed that there was no significant difference in the fermentation parameters of the four starters, but there were differences in microbial diversity among the different starters. The wine samples fermented by CEC01 had higher microbial abundance. GC-MS detected a total of 58 aromatic compounds from the fermentation process by the experimental yeasts. There were 25 compounds in the F6d variant, which was higher than in other samples. The PCA score plot showed that 796 and F15 yeast-fermented wines had similar aromatic characteristic compositions. According to partial least squares (PLS, VIP > 1.0) analysis and Spearman’s correlation analysis, 11, 8, 8 and 10 microbial genera were identified as core microorganisms in the fermentation of 796, CEC01, CECA and F15 starter, respectively. Among them, Leuconostoc, Lactobacillus, Sphingomonas and Pseudomonas played an important role in the formation of aroma compounds such as Ethyl caprylate, Ethyl caprate and Ethyl-9-decenoate. These results can help us to have a better understanding of the effects of microorganisms on wine aroma and provide a theoretical basis for improving the flavor quality of Cabernet Sauvignon wine.

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

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

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

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

The restructuring of grape berry waxes by calcium changes the surface microbiota

The observation that exogenous Ca shifted the polyphenolic profile of grape berries and conferred a glossy appearance to mature fruits led us to hypothesize that the composition of grape berry waxes and thus surface microbiota are modified. In two cultivars sharing the same microclimate, the triterpenoid and steroid profile of berry cuticle was characterized by a targeted metabolomic approach, and surface microbial communities were surveyed by ITS and 16S metabarcoding. Results showed that Ca strongly decreased the levels of oleanolic acid, while steroids and neutral triterpenoids were affected in a cultivar-dependent manner. A total of 174 fungi and 192 bacteria OTUs were identified, with Dothideomycetes, Leotiomycetes, Alphaproteobacteria and Gammaproteobacteria comprising the most abundant classes. Ca decreased fungi biodiversity, favoring the growth of Basidiomycetes, and shifting fungi-bacteria relationships. Metabolite-microbiota networks revealed a tight relationship between microbial communities and triterpenoid components of fruit waxes, mainly stigmasterol, tremulone and oleanolic acid.

Diversity and dynamics of microbial ecosystem on berry surface during the ripening of Ecolly (Vitis vinifera L.) grape in Wuhai, China

The structural and functional diversities of the microbial ecosystem on the grape surface affect the health of berries and the flavor of wines, which are also changed by many factors such as climate, weather conditions, agronomic practices, and physiological development. To understand and explore the natural characteristics of the grape surface microbial ecosystem during ripening, the species composition and dynamics of fungal and bacterial communities on the skin of Ecolly grape were determined by Illumina Novaseq platform sequencing. The results showed that 2146 fungal OTUs and 4175 bacterial OTUs were obtained, belonging to four fungal phyla and 20 bacterial phyla. The Shannon index indicated that the fungal community had the highest species diversity at the véraison stage and the bacterial community at the harvest stage. The four dominant fungal genera during grape ripening were Alternaria, Naganishia, Filobasidium, and Aureobasidium, which accounted for 82.8% of the total fungal community, and the dominant bacterial genera included Sphingomonas, Brevundimonas, Allorhizobium-Neorhizobium-Pararhizobium-Rhizobium, and Massilia, which accounted for 77.9% of the total bacterial community. The species richness and diversity in the grape microbial ecosystem changed constantly during the maturation stages, and there were strong correlations between certain core microbial genera, which may have an important impact on the function and ecological role of the community. This study provides a basis for understanding the natural characteristics of the microbial ecosystem on the grape surface during grape ripening, as well as the sustainable production concept of the microecology driving the viticulture management system.

Year, Location, and Variety Impact on Grape-Associated Mycobiota of Arkansas-Grown Wine Grapes for Wine Production

Wine grape berries (Vitis spp.) harbor a wide variety of yeasts and filamentous fungi that impact grapevine health and the winemaking process. Identification of these fungi could be important for controlling and improving wine production. The use of high-throughput sequencing (HTS) strategies has enabled identification and quantification of bacterial and fungal species in vineyards. The aims of this study were to identify mycobiota from Cabernet Sauvignon and Zinfandel (V. vinifera), Carlos and Noble muscadines (V. rotundifolia), Cynthiana (V. aestivalis), and Vignoles hybrid (cross of different Vitis spp.) grapes, and investigate the effect of grape variety, location, and year on grape fungal communities. Grape berries were collected in 2016 and 2017 from four vineyards located in Arkansas. The HTS of the Internal Transcribed Spacer 1 region was used to identify grape indigenous epiphytic and endophytic fungal communities. The predominant genera identified on the Arkansas wine grapes were Uwebraunia, Zymoseptoria, Papiliotrema, Meyerozyma, Filobasidium, and Curvibasidium. Overall, the data suggested that grape fungal community distribution and relative abundance were influenced by grape variety, year, and location, but each was influenced to a different extent. Not only were grape mycobiota influenced by year, variety, and location but also it appeared that communities from the previous year impacted microbial communities the following year. For example, an increase of the mycoparasite Ampelomyces quisqualis was noticed in 2017 on grapes that carried the causal agent of powdery mildew, Erysiphe necator, in 2016, thus, amplifying the importance of vineyard microbiota knowledge for disease management and winemaking.

Bacteria associated with wood tissues of Esca-diseased grapevines: functional diversity and synergy with Fomitiporia mediterranea to degrade wood components

Fungi are considered to cause grapevine trunk diseases such as esca that result in wood degradation. For instance, the basidiomycete Fomitiporia mediterranea (Fmed) is overabundant in white rot, a key type of wood‐necrosis associated with esca. However, many bacteria colonize the grapevine wood too, including the white rot. In this study, we hypothesized that bacteria colonizing grapevine wood interact, possibly synergistically, with Fmed and enhance the fungal ability to degrade wood. We isolated 237 bacterial strains from esca‐affected grapevine wood. Most of them belonged to the families Xanthomonadaceae and Pseudomonadaceae. Some bacterial strains that degrade grapevine‐wood components such as cellulose and hemicellulose did not inhibit Fmed growth in vitro. We proved that the fungal ability to degrade wood can be strongly influenced by bacteria inhabiting the wood. This was shown with a cellulolytic and xylanolytic strain of the Paenibacillus genus, which displays synergistic interaction with Fmed by enhancing the degradation of wood structures. Genome analysis of this Paenibacillus strain revealed several gene clusters such as those involved in the expression of carbohydrate‐active enzymes, xylose utilization and vitamin metabolism. In addition, certain other genetic characteristics of the strain allow it to thrive as an endophyte in grapevine and influence the wood degradation by Fmed. This suggests that there might exist a synergistic interaction between the fungus Fmed and the bacterial strain mentioned above, enhancing grapevine wood degradation. Further step would be to point out its occurrence in mature grapevines to promote esca disease development.

Mycobiota in the Carposphere of Sour and Sweet Cherries and Antagonistic Features of Potential Biocontrol Yeasts

Sour cherries (Prunus cerasus L.) and sweet cherries (P. avium L.) are economically important fruits with high potential in the food industry and medicine. In this study, we analyzed fungal communities associated with the carposphere of sour and sweet cherries that were freshly harvested from private plantations and purchased in a food store. Following DNA isolation, a DNA fragment of the ITS2 rRNA gene region of each sample was individually amplified and subjected to high-throughput NGS sequencing. Analysis of 168,933 high-quality reads showed the presence of 690 fungal taxa. Investigation of microbial ASVs diversity revealed plant-dependent and postharvest handling-affected fungal assemblages. Among the microorganisms inhabiting tested berries, potentially beneficial or pathogenic fungi were documented. Numerous cultivable yeasts were isolated from the surface of tested berries and characterized by their antagonistic activity. Some of the isolates, identified as Aureobasidium pullulans, Metschnikowia fructicola, and M. pulcherrima, displayed pronounced activity against potential fungal pathogens and showed attractiveness for disease control.

Sources and Assembly of Microbial Communities in Vineyards as a Functional Component of Winegrowing

Microbiomes are integral to viticulture and winemaking – collectively termed winegrowing – where diverse fungi and bacteria can exert positive and negative effects on grape health and wine quality. Wine is a fermented natural product, and the vineyard serves as a key point of entry for quality-modulating microbiota, particularly in wine fermentations that are conducted without the addition of exogenous yeasts. Thus, the sources and persistence of wine-relevant microbiota in vineyards critically impact its quality. Site-specific variations in microbiota within and between vineyards may contribute to regional wine characteristics. This includes distinctions in microbiomes and microbiota at the strain level, which can contribute to wine flavor and aroma, supporting the role of microbes in the accepted notion of terroir as a biological phenomenon. Little is known about the factors driving microbial biodiversity within and between vineyards, or those that influence annual assembly of the fruit microbiome. Fruit is a seasonally ephemeral, yet annually recurrent product of vineyards, and as such, understanding the sources of microbiota in vineyards is critical to the assessment of whether or not microbial terroir persists with inter-annual stability, and is a key factor in regional wine character, as stable as the geographic distances between vineyards. This review examines the potential sources and vectors of microbiota within vineyards, general rules governing plant microbiome assembly, and how these factors combine to influence plant-microbe interactions relevant to winemaking.

The Good, the Bad, and the Ugly: Mycotoxin Production During Postharvest Decay and Their Influence on Tritrophic Host-Pathogen-Microbe Interactions

Mycotoxins are a prevalent problem for stored fruits, grains, and vegetables. Alternariol, aflatoxin, and patulin, produced by Alternaria spp., Aspergillus spp., and Penicillium spp., are the major mycotoxins that negatively affect human and animal health and reduce fruit and produce quality. Control strategies for these toxins are varied, but one method that is increasing in interest is through host microbiome manipulation, mirroring a biocontrol approach. While the majority of mycotoxins and other secondary metabolites (SM) produced by fungi impact host–fungal interactions, there is also an interplay between the various organisms within the host microbiome. In addition to SMs, these interactions involve compounds such as signaling molecules, plant defense and growth hormones, and metabolites produced by both the plants and microbial community. Therefore, studies to understand the impact of the various toxins impacting the beneficial and harmful microorganisms that reside within the microbiome is warranted, and could lead to identification of safe analogs for antimicrobial activity to reduce fruit decay. Additionally, exploring the composition of the microbial carposphere of host plants is likely to shed light on developing a microbial consortium to maintain quality during storage and abate mycotoxin contamination.

Epiphytic Microbial Diversity of Vitis vinifera Fructosphere: Present Status and Potential Applications

Vineyard provides an apt environment for growth of different types of microorganisms. The microbial domain is greatly affected by changing climatic conditions, geographical region, water activity, agricultural practices, presence of different pathogens and various pests. Grapevine microbial diversity is also affected by different stages of plant growth. Epiphytic berry microflora is specifically influenced by developmental phases and plays an important role in winemaking which is studied extensively. However, very little information is available about microbial community associated with table grape berries, which are consumed as fresh fruits. Moreover, our knowledge about the important role played by these microbes is precise and their scope might be larger than what is existing in the public domain. A systematic study on effect of developmental stages of table grape berries on microbial diversity would provide new insights for exploring the applicability of these microbes in plant growth, crop protection and bioremediation. In this review, we propose an effort to relate the developmental stages of grape berry with microbial consortium present and at the same time discuss the possible applications of these microbes in plant protection and biodegradation.

Monitoring the microbiome for food safety and quality using deep shotgun sequencing

In this work, we hypothesized that shifts in the food microbiome can be used as an indicator of unexpected contaminants or environmental changes. To test this hypothesis, we sequenced the total RNA of 31 high protein powder (HPP) samples of poultry meal pet food ingredients. We developed a microbiome analysis pipeline employing a key eukaryotic matrix filtering step that improved microbe detection specificity to >99.96% during in silico validation. The pipeline identified 119 microbial genera per HPP sample on average with 65 genera present in all samples. The most abundant of these were Bacteroides, Clostridium, Lactococcus, Aeromonas, and Citrobacter. We also observed shifts in the microbial community corresponding to ingredient composition differences. When comparing culture-based results for Salmonella with total RNA sequencing, we found that Salmonella growth did not correlate with multiple sequence analyses. We conclude that microbiome sequencing is useful to characterize complex food microbial communities, while additional work is required for predicting specific species' viability from total RNA sequencing.

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

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

Phyllosphere bacterial assembly in citrus crop under conventional and ecological management

Divergences between agricultural management can result in different types of biological interactions between plants and microorganisms, which may affect food quality and productivity. Conventional practices are well-established in the agroindustry as very efficient and lucrative; however, the increasing demand for sustainable alternatives has turned attention towards agroecological approaches. Here we intend to explore microbial dynamics according to the agricultural management used, based on the composition and structure of these bacterial communities on the most environmentally exposed habitat, the phyllosphere. Leaf samples were collected from a Citrus crop (cultivated Orange) in Mogi-Guaçu (SP, Brazil), where either conventional or ecological management systems were properly applied in two different areas. NGS sequencing analysis and quantitative PCR allowed us to comprehend the phyllosphere behavior and µ-XRF (micro X-ray fluorescence) could provide an insight on agrochemical persistence on foliar tissues. Our results demonstrate that there is considerable variation in the phyllosphere community due to the management practices used in the citrus orchard, and it was possible to quantify most of this variation. Equally, high copper concentrations may have influenced bacterial abundance, having a relevant impact on the differences observed. Moreover, we highlight the intricate relationship microorganisms have with crop production, and presumably with crop yield as well.

Fungal Microbiota of Sea Buckthorn Berries at Two Ripening Stages and Volatile Profiling of Potential Biocontrol Yeasts

Sea buckthorn, Hippophae rhamnoides L., has considerable potential for landscape reclamation, food, medicinal, and cosmetics industries. In this study, we analyzed fungal microorganism populations associated with carposphere of sea buckthorn harvested in Lithuania. An amplicon metagenomic approach based on the ITS2 region of fungal rDNA was used to reveal the ripening-affected fungal community alterations on sea buckthorn berries. According to alpha and beta diversity analyses, depending on the ripening stage, sea buckthorn displayed significantly different fungal communities. Unripe berries were shown to be prevalent by Aureobasidium, Taphrina, and Cladosporium, while ripe berries were dominated by Aureobasidium and Metschnikowia. The selected yeast strains from unripe and mature berries were applied for volatile organic compounds identification by gas chromatography and mass spectrometry techniques. It was demonstrated that the patterns of volatiles of four yeast species tested were distinct from each other. The current study for the first time revealed the alterations of fungal microorganism communities colonizing the surface of sea buckthorn berries at different ripening stages. The novel information on specific volatile profiles of cultivable sea buckthorn-associated yeasts with a potential role in biocontrol is important for the development of the strategies for plant cultivation and disease management, as well as for the improvement of the quality and preservation of the postharvest berries. Management of the fungal microorganisms present on the surface of berries might be a powerful instrument for control of phytopathogenic and potentially antagonistic microorganisms affecting development and quality of the berries.

Identification of Yeasts with Mass Spectrometry during Wine Production

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

Epiphytic bacteria from withered grapes and their antagonistic effects on grape-rotting fungi

The bacterial community in the surface of withered grapes, which are partially dehydrated in the post-harvest period to produce Italian passito wine, has been seldom investigated. Fifty epiphytic bacterial strains isolated from withered berries were identified and characterized. Genera such as Bacillus, Brevibacillus, Curtobacterium, Micrococcus, Pseudomonas and Staphylococcus have been identified by comparative sequence and phylogenetic analyses of 16S rRNA gene sequences. Bacillus was predominant and several taxa within this genus have been recognized. All isolates were characterized by PCR fingerprinting and assayed for osmotic tolerance, motility and antifungal activity. Several Bacillus strains displayed antagonistic effects on grape-rotting fungi such as Botrytis cinerea, Penicillium expansum and Aspergillus uvarum. The other strains were weakly or non-antagonistic on these fungi. Assay on antagonistic interactions among bacteria was also carried out. Bacillus strains, which exhibit swimming and swarming motility, have the potential to colonize the grape surface and to compete with their neighbours for space and resources. The occurrence of these isolates could reduce the contamination of fungal pathogens during grape withering. Epiphytic antagonistic bacteria could potentially be of interest for fungal biocontrol in the post-harvest processing of fruit and vegetables.

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

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

Microbial Community Analyses Associated with Nine Varieties of Wine Grape Carposphere Based on High-Throughput Sequencing

Understanding the composition of microbials on the grape carposphere may provide direct guidance for the wine brewing. In this work, 16S rRNA and ITS (Internal Transcribed Spacer) fungal amplicon sequencing were performed to investigate the differences of epiphytic microbial communities inhabiting different varieties of wine grape berries. The results showed that the dominated phylum of different wine grape carpospheres were Proteobacteria, Actinomycetes, Firmicutes, Gemmatimonadete, and Bacteroidetes. The dominant bacterial genera of different wine grape varieties were Pseudomonas, Arthrobacter, Bacillus, Pantoea, Planomicrobium, Massilia, Curtobacterium, Corynebacterium, Cellulomonas, Sphingomonas, and Microvirga. The fungal communities of the grapes were dominated by Ascomycota for all nine wine varieties. The dominant fungal genera on grape carposphere were Alternaria, Cladosporium, unclassified Capnodiales, Phoma, Rhodotorula, Cryptococcus, Aureobasidium, and Epicoccum. Community structure exerts a significant impact on bacterial Bray-Curtis dissimilarity on six red grapes and also a significant bacterial impact on three white grapes. Community structure exerts a significant impact on fungal Bray-Curtis dissimilarity on six red grapes but weak or no fungal impact on three white grapes. The results revealed that grape variety plays a significant role in shaping bacterial and fungal community, varieties can be distinguished based on the abundance of several key bacterial and fungal taxa.

Vineyard Soil Microbiome Composition Related to Rotundone Concentration in Australian Cool Climate 'Peppery' Shiraz Grapes

Soil microbial communities have an integral association with plants and play an important role in shaping plant nutrition, health, crop productivity and product quality. The influence of bacteria and fungi on wine fermentation is well known. However, little is known about the role of soil microbes, other than microbial pathogens, on grape composition or their role in vintage or site (terroir) impacts on grape composition. In this study, we used an amplicon sequencing approach to investigate the potential relationships between soil microbes and inherent spatial variation in grape metabolite composition – specifically, the concentration of the ‘impact aroma compound’ rotundone in Shiraz grapes (Vitis vinifera L.) grown in a 6.1 ha vineyard in the Grampians region of Victoria, Australia. Previous work had demonstrated temporal stability in patterns of within-vineyard spatial variation in rotundone concentration, enabling identification of defined ‘zones’ of inherently ‘low’ or ‘high’ concentration of this grape metabolite. 16S rRNA and ITS region-amplicon sequencing analysis of microbial communities in the surface soils collected from these zones indicated marked differences between zones in the genetic diversity and composition of the soil bacterial and fungal microbiome. Soils in the High rotundone zone exhibited higher diversity of bacteria, but lower diversity of fungi, compared to the soils in the Low rotundone zone. In addition, the network analysis of the microbial community in the High rotundone zone soils appeared well structured, especially with respect to the bacterial community, compared to that in the Low rotundone zone soils. The key differences in the microbial community structure between the rotundone zones are obvious for taxa/groups of both bacteria and fungi, particularly for bacteria belonging to Acidobacteria-GP4 and GP7, Rhizobiales, Gaiellaceae, Alphaproteobacteria and the Nectriaceae and Tremellaceae families of fungi. Although mulching in some parts of the vineyard caused changes in bacterial and fungal composition and overall microbial catabolic diversity and activity, its effects did not mask the rotundone zone-based variation. This finding of a systematic rotundone zone-based variation in soil microbiomes suggests an opportunity to bring together understanding of microbial ecology, plant biochemistry, and viticultural management for improved management of grape metabolism, composition and wine flavor.

Diversity of epiphytic fungi on the surface of Kyoho grape berries during ripening process in summer and winter at Nanning region, Guangxi, China

The two-harvest-per-year farming system allow table grape to be harvested a year both in summer and winter in southern China. Herein, we used high-throughput sequencing to investigate the diversity of fungi on grape fruits surface during the ripening process in summer and winter at subtropical Nanning region, Guangxi, China. The results showed that 23 fungal species existed in all samples. Among them, the five most dominant species were Cladosporium ramotenellum, Pseudozyma aphidis, Gyrothrix spp., Gibberella intricans and Acremonium alternatum, with abundance from 61.62 % to 91.26 %. Analysis using the student's t-test for Shannon index indicated that components of fungal community varied significantly between the two ripening seasons. The dominant genera of core fungal community were Cladosporium, Gyrothrix, Paramycosphaerella, Acremonium, Penicillium and Tilletiopsis in the summer and Cladosporium, Pseudozyma, Gibberella, Colletotrichum, Sporobolomyces, Rhodosporidium, Alternaria and Aspergillus in the winter. Overall, fungi diversity on grape fruits surface at Nanning showed significantly differences between different ripening seasons. Our results ennrich the understanding of epiphytic communities of grape fruits in subtropics.

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

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

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

AIMS

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

METHODS AND RESULTS

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

CONCLUSIONS

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

SIGNIFICANCE AND IMPACT OF THE STUDY

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

Evaluating a preventive biological control agent applied on grapevines against Botrytis cinerea and its influence on winemaking

BACKGROUND

This research was aimed to study the influence on grape and wine quality and on the fermentation processes of the application of a preventive biological treatment against Botrytis cinerea in Tempranillo Rioja grapevines. For this purpose, a biofungicide containing Bacillus subtilis QST713 was applied twice to the vineyard.

RESULTS

Results were compared with non-treated samples from the same vineyard and with samples treated with a chemical fungicide composed of fenhexamid. Data showed that general grape quality and spontaneous alcoholic fermentation performance were not influenced by either fungicide application. The chemical fungicide had a considerable influence on the clonal diversity of Saccharomyces cerevisiae species, which led to the alcoholic fermentation. Furthermore, it caused longer malolactic fermentation than with the biological fungicide and in the control. The biofungicide made malolactic fermentation 1 day shorter because the establishment of the commercial lactic acid bacteria used as a starter culture was total. After malolactic fermentation, the wines did not show significant differences in general oenological parameters.

CONCLUSION

Preventive biofungicide treatment against B. cinerea did not negatively influence the quality of grapes and wines and the fermentation processes. Therefore, biological control of B. cinerea with B. subtilis applied on grapevines could be advisable in oenological terms. © 2018 Society of Chemical Industry.

High-throughput sequencing of microbial community diversity in soil, grapes, leaves, grape juice and wine of grapevine from China

In this study Illumina MiSeq was performed to investigate microbial diversity in soil, leaves, grape, grape juice and wine. A total of 1,043,102 fungal Internal Transcribed Spacer (ITS) reads and 2,422,188 high quality bacterial 16S rDNA sequences were used for taxonomic classification, revealed five fungal and eight bacterial phyla. At the genus level, the dominant fungi were Ascomycota, Sordariales, Tetracladium and Geomyces in soil, Aureobasidium and Pleosporaceae in grapes leaves, Aureobasidium in grape and grape juice. The dominant bacteria were Kaistobacter, Arthrobacter, Skermanella and Sphingomonas in soil, Pseudomonas, Acinetobacter and Kaistobacter in grape and grapes leaves, and Oenococcus in grape juice and wine. Principal coordinate analysis showed structural separation between the composition of fungi and bacteria in all samples. This is the first study to understand microbiome population in soil, grape, grapes leaves, grape juice and wine in Xinjiang through High-throughput Sequencing and identify microorganisms like Saccharomyces cerevisiae and Oenococcus spp. that may contribute to the quality and flavor of wine.

Impact of Chemical and Biological Fungicides Applied to Grapevine on Grape Biofilm, Must, and Wine Microbial Diversity

This study was aimed to measure the impact of the application of a bio-fungicide against Botrytis cinerea on the microbiota involved in the alcoholic fermentation (AF) of Tempranillo Rioja wines. For this purpose, a bio-fungicide composed of the biological control bacterium Bacillus subtilis QST713 was applied to the vineyard. The microbial diversity was analyzed from grape biofilm to wine. Impact on microbial diversity was measured employing indexes assessed with the software PAST 3.10 P.D. Results were compared to non-treated samples and to samples treated with a chemical fungicide mainly composed by fenhexamid. Overall, the impact of the biological-fungicide (bio-fungicide) on the microbial diversity assessed for grape biofilm and for musts was not remarkable. Neither of the tested fungicides enhanced the growth of any species or acted against the development of any microbial groups. The bio-fungicide had no significant impact on the wine microbiota whereas the chemical fungicide caused a reduction of microbial community richness and diversity. Although environmental threats might generate a detriment of the microbial species richness, in this study the tested bio-fungicide did not modify the structure of the microbial community. Indeed, some of the Bacillus applied at the grape surface, were detected at the end of the AF showing its resilience to the harsh environment of the winemaking; in contrast, its impact on wine quality during aging is yet unknown.

A survey of oenophages during wine making reveals a novel group with unusual genomic characteristics

Oenophages have so far been mostly isolated from red wines under malolactic fermentation (MLF), and correspond to temperate or ex-temperate phages of Oenococcus oeni. Their genomes are clustered into 4 integrase gene sequence groups, which are also related to the chromosomal integration site. Our aims were to survey the occurrence of oenophages in a broader and more diverse collection of samples than those previously explored. Active phages were isolated from 33 out of 166 samples, which mostly originated from must and MLF. Seventy one phage lysates were produced and 30% were assigned to a novel group with unusual genomic characteristics, called unk. All unk members produced similar RAPD and DNA restriction patterns, were negative by PCR for the signature sequences previously identified in the integrase and endolysin genes of oenophages, and lacked any BamHI restriction site in their genome. The data support that development of additional and novel signature genes for assessing oenophage diversity is now required.

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

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

Wine microbiome: A dynamic world of microbial interactions

Most fermented products are generated by a mixture of microbes. These microbial consortia perform various biological activities responsible for the nutritional, hygienic, and aromatic qualities of the product. Wine is no exception. Substantial yeast and bacterial biodiversity is observed on grapes, and in both must and wine. The diverse microorganisms present interact throughout the winemaking process. The interactions modulate the hygienic and sensorial properties of the wine. Many studies have been conducted to elucidate the nature of these interactions, with the aim of establishing better control of the two fermentations occurring during wine processing. However, wine is a very complex medium making such studies difficult. In this review, we present the current state of research on microbial interactions in wines. We consider the different kinds of interactions between different microorganisms together with the consequences of these interactions. We underline the major challenges to obtaining a better understanding of how microbes interact. Finally, strategies and methodologies that may help unravel microbe interactions in wine are suggested.

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

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