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

Characterization and analysis of dynamic changes of microbial community associated with grape decay during storage

The rot caused by pathogens during the storage of table grapes is an important factor that affects the development of the grape industry and food safety, and it cannot be ignored. The development of innovative methods for pathogen control should be based on a comprehensive understanding of the overall microbial community changes that occur during grape storage. The study aims to investigate the relationship between the native microbiota (including beneficial, pathogenic and spoilage microorganisms) on grape surfaces and the development of disease during grape storage. In this study, the bacteria and fungi present on grape surfaces were analyzed during storage under room temperature conditions using high-throughput sequencing. During the storage of grapes at room temperature, observable diseases and a noticeable decrease in quality were observed at 8 days. Microbial community analysis showed that 4996 bacterial amplicon sequence variants (ASVs) and 488 fungal ASVs were determined. The bacterial richness exhibited an initial increase followed by a subsequent decrease. However, the diversity exhibited a distinct pattern of gradual decrease. The fungal richness and community diversity both exhibit a gradual decrease during the storage of grapes. Fungal β-diversity analysis showed that despite the absence of rot and the healthy state of grapes on the first and fourth days, the fungal β-diversity exhibited a significant difference. The analysis of changes in genera abundances suggested that Candidatus Profftella and Aspergillus exhibited dominance in the rotting grape at 16 days, which are the main pathogens that caused disease in the present study. The co-occurrence networks among the microbial showed that the Candidatus proftella genera has a positive correlation with Aspergillus niger, indicating that they work together to cause disease and promote growth in grapes. Predicting the function of bacterial communities found that the microorganisms associated with lipid metabolism at 4 days play an important role in the process of postharvest decay of grapes.

Geographical identification of Chinese wine based on chemometrics combined with mineral elements, volatile components and untargeted metabonomics

Identifying the geographic origin of a wine is of great importance, as origin fakery is commonplace in the wine industry. This study analyzed the mineral elements, volatile components, and metabolites in wine using inductively coupled plasma-mass spectrometry, headspace solid phase microextraction gas chromatography-mass spectrometry, and ultra-high-performance liquid chromatography-quadrupole-exactive orbitrap mass spectrometry. The most critical variables (5 mineral elements, 13 volatile components, and 51 metabolites) for wine origin classification were selected via principal component analysis and orthogonal partial least squares discriminant analysis. Subsequently, three algorithms-K-nearest neighbors, support vector machine, and random forest -were used to model single and fused datasets for origin identification. These results indicated that fused datasets, based on feature variables (mineral elements, volatile components, and metabolites), achieved the best performance, with predictive rates of 100% for all three algorithms. This study demonstrates the effectiveness of a multi-source data fusion strategy for authenticity identification of Chinese wine.

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.

A comparison of microbiota isolation methods reveals habitat preferences for fermentative yeasts and plant pathogenic fungi in the grape berry

The methodologies for profiling the grape berry microbiota have exponentially evolved in the past 25 years. Recently, concerns arose regarding the homogeneity in the protocols of grape harvesting, sequencing and bioinformatic analyses, but the bias introduced by the microbiota isolation method is still unexplored. This study followed a simple approach of comparing two most used methods of microbiota collection from grape berries (washing vs crushing), hypothesizing a significant impact in the outcome of the microbiota profiles analyzed by NGS metabarcoding. Experiments conducted in fruits of three cultivars of the Douro wine region showed that only 52 % of OTUs were common to both surface and juice microbiota, suggesting specific microbial niches. Thirteen fungal genera were abundantly detected in the fruit surface, including Alternaria, Aureobasidium, Cladosporium, Didymella and Bipolaris. Fermentative yeasts including Meyerozyma and Saccharomyces cerevisiae were exclusively detected in the juice, together with several Penicillium species. Distinct habitat preferences of species within the genera Alternaria, Sporobolomyces and Rhodotorula were also revealed. The study showed that the microbiota isolation method is crucial in the detection of certain plant pathogenic/saprophytic fungi and yeasts with biotechnological and oenological interest, adding novelty to the globally accepted assumption that S. cerevisiae in musts originates primarily from the cellar.

Diversity of 'Cabernet Sauvignon' Grape Epidermis and Environmental Bacteria in Wineries from Different Sub-Regions of the Eastern Foothills of Helan Mountain, Ningxia

Understanding the composition of the bacterial community on the epidermis of wine grapes and in winery environments, as well as the response of grape epidermal bacteria to climatic factors, plays a significant role in ensuring grape health and promoting grape conversion into wine. This study utilized high-throughput sequencing to explore the composition of the bacterial community on the wine grape epidermis and representative wineries of three sub-regions of the Eastern Foothills of Helan Mountain, Ningxia. The results showed that the bacterial diversity and richness in the Yongning (YN) sub-region were the highest, with Qingtongxia (QTX) having the lowest levels of grape epidermal bacteria. The bacterial diversity and richness were the highest in Yinchuan (YC) and the lowest in YN in the winery environment (p < 0.05). The composition of dominant bacteria on the grape epidermis and in winery environments of the three sub-regions was not different at the phylum and genus level, but the levels of these dominant bacteria were different among the sub-regions. There was a correlation between grape epidermal bacteria and climatic factors. Approximately 93% of the bacterial genera on the grape epidermal genera in the three sub-regions are present in the winery environment and contain all the dominant bacterial genera on the epidermis.

Floral Volatile Organic Compounds Change the Composition and Function of the Endophytic Fungal Community in the Flowers of Osmanthus fragrans

Endophytic fungi in flowers influence plant health and reproduction. However, whether floral volatile organic compounds (VOCs) affect the composition and function of the endophytic fungal community remains unclear. Here, gas chromatography-mass spectrometry (GC-MS) and high-throughput sequencing were used to explore the relationship between floral VOCs and the endophytic fungal community during different flower development stages in Osmanthus fragrans 'Rixiang Gui'. The results showed that the composition of the endophytic fungal community and floral VOCs shifted along with flowering development. The highest and lowest α diversity of the endophytic fungal community occurred in the flower fading stage and full blooming stage, respectively. The dominant fungi, including Dothideomycetes (class), Pleosporales (order), and Neocladophialophora, Alternaria, and Setophoma (genera), were enriched in the flower fading stage and decreased in the full blooming stage, demonstrating the enrichment of the Pathotroph, Saprotroph, and Pathotroph-Saprotroph functions in the flower fading stage and their depletion in the full blooming stage. However, the total VOC and terpene contents were highest in the full blooming stage and lowest in the flower fading stage, which was opposite to the α diversity of the endophytic fungal community and the dominant fungi during flowering development. Linalool, dihydro-β-ionone, and trans-linalool oxide(furan) were key factors affecting the endophytic fungal community composition. Furthermore, dihydro-β-ionone played an extremely important role in inhibiting endophytic fungi in the full blooming stage. Based on the above results, it is believed that VOCs, especially terpenes, changed the endophytic fungal community composition in the flowers of O. fragrans 'Rixiang Gui'. These findings improve the understanding of the interaction between endophytic fungi and VOCs in flowers and provide new insight into the mechanism of flower development.

Grapevine bacterial communities display compartment-specific dynamics over space and time within the Central Valley of California

BACKGROUND

Plant organs (compartments) host distinct microbiota which shift in response to variation in both development and climate. Grapevines are woody perennial crops that are clonally propagated and cultivated across vast geographic areas, and as such, their microbial communities may also reflect site-specific influences. These site-specific influences along with microbial differences across sites compose 'terroir', the environmental influence on wine produced in a given region. Commercial grapevines are typically composed of a genetically distinct root (rootstock) grafted to a shoot system (scion) which adds an additional layer of complexity via genome-to-genome interactions.

RESULTS

To understand spatial and temporal patterns of bacterial diversity in grafted grapevines, we used 16S rRNA amplicon sequencing to quantify soil and compartment microbiota (berries, leaves, and roots) for grafted grapevines in commercial vineyards across three counties in the Central Valley of California over two successive growing seasons. Community composition revealed compartment-specific dynamics. Roots assembled site-specific bacterial communities that reflected rootstock genotype and environment influences, whereas bacterial communities of leaves and berries displayed associations with time.

CONCLUSIONS

These results provide further evidence of a microbial terroir within the grapevine root systems but also reveal that the microbiota of above-ground compartments are only weakly associated with the local soil microbiome in the Central Valley of California.

Comparison of microbial communities and volatile profiles of wines made from mulberry and grape

In this study, three kinds of wines separately made from mulberry (MW), grape (GW), or mulberry/grape (MGW) were developed and their enological parameters, sensory scores, volatile components, and microbiota were investigated and compared. Contrary to the order of residual sugar and acidity of the three kinds of wines, the order of alcohol content from high to low is GW, MW, and MGW. A total of 60 volatile components (VCs), including esters (17), alcohols (12), acids (6), aldehydes (7), ketones (3), alkenes (3), amines (3), alkanes (4), pyrazines (2), benzene (1), sulfide (1), and thiazole (1), were identified by gas chromatography-ion mobility spectrometer (GC-IMS). The fingerprint of VCs and principal component analysis revealed that the volatile profiles of MGW and GW were more similar in comparison to that of MW and were significantly correlated with the mass ratio of mulberry to grape. Lactobacillus, Weissella, Pantoea, Leuconostoc, Lactococcus, Paenibacillus, Pediococcus, and Saccharomyces were identified as the main microflora at the genus level shared by the MW, MGW, and GW, suggesting that the heterolactic bacteria may contribute more to the high content of volatile acids in MW and MGW. The heatmap of core microbiota and main VCs of MW, MGW, and GW suggested the complicated and significant correlation between them. The above data implied that the volatile profiles were more closely related to the raw materials of winemaking and markedly affected by the fermentation microorganisms. This study provides references for evaluation and characterization of MGW and MW and improvement of MGW and MW winemaking process. KEY POINTS: • Fruit wine enological parameters, volatile profile, and microbiota were compared. • Sixty volatile compounds were identified by GC-IMS in three types of fruit wines. • Winemaking materials and microbiota affect volatile profiles of the fruit wines.

High Oxygen Shocking Reduces Postharvest Disease and Maintains Satisfying Quality in Fresh Goji Berries during Cold Storage by Affecting Fungi Community Composition

Fresh goji (Lycium barbarum L.) berries were treated with high-concentration (50% and 90%) oxygen shocking for 30 min and then stored at 0 ± 0.5 °C for 30 d. Decay, aerobic plate count, firmness, weight loss, total soluble solid (TSS), and titratable acidity (TA) were evaluated during storage. A total of 90% O₂ shocking more effectively reduced decay and maintained the weight loss and firmness of goji berries. Subsequently, changes in fungi communities were analyzed using high-throughput sequencing (HTS) in the 90% O₂-shocking and control groups. The results showed that 90% O₂ shocking retained the richness and diversity of fungi communities and the microbiome was related to the quality properties of the fruit. Thus, we inferred that high oxygen shocking inhibited the development of natural decay and maintained the satisfying quality of goji berries by affecting the fungi community composition, which reduced the growth of pathogenic fungi and harmful saprotrophic fungi in the genera, such as Filobasidium sp., Alternaria sp., and Cladosporium sp. We provide a new insight into the disease development and quality changes during the storage of postharvest goji berries.

Untargeted metabolomics analysis based on LC-IM-QTOF-MS for discriminating geographical origin and vintage of Chinese red wine

Identifying wine geographical origin and vintage is vital due to the abundance of fraudulent activity associated with wine mislabeling of region and vintage. In this study, an untargeted metabolomic approach based on liquid chromatography/ion mobility quadrupole time-of-flight mass spectrometry (LC-IM-QTOF-MS) was used to discriminate wine geographical origin and vintage. Wines were well discriminated according to region and vintage with orthogonal partial least squares-discriminant analysis (OPLS-DA). The differential metabolites subsequently were screened by OPLS-DA with pairwise modeling. 42 and 48 compounds in positive and negative ionization modes were screened as differential metabolitesfor the discrimination of different wine regions, and 37 and 35 compounds were screened for wine vintage. Furthermore, new OPLS-DA models were performed using these compounds, and the external verification trial showed excellent practicality with an accuracy over 84.2%. This study indicated that LC-IM-QTOF-MS-based untargeted metabolomics was a feasible tool for wine geographical origin and vintage discrimination.

Screening of cold hardiness-related indexes and establishment of a comprehensive evaluation method for grapevines (V. vinifera)

The goals of this work were to screen physiological and biochemical indexes to assess a set of V. vinifera germplasm resources, to compare evaluation methods for cold hardiness, and to establish a comprehensive method that can be used for more accurate screening for cold hardiness in V. vinifera. Four single methods were used to evaluate the cold hardiness of 20 germplasms resources and 18 physiological and biochemical indexes related to cold hardiness were determined. The LT₅₀ values determined by electrical conductivity (EL), 2,3,5-triphenyltetrazolium chloride staining (TTC), differential thermal analysis (DTA), and recovery growth (RG) methods showed extremely significant positive correlation. Bound water content (BW), proline content (Pro), total soluble sugar content (TSS), malondialdehyde content (MDA), catalase content (CAT), and ascorbic acid content (ASA) exhibited significant correlation with LT₅₀ values measured by different evaluation methods. The comprehensive cold hardiness index calculated by principal component analysis (PCA) combined with subordinate function (SF) was negatively correlated with LT₅₀ values measured by different evaluation methods. Meili and Ecolly exhibited the highest cold hardiness, indicating their potential for use as parents for cold hardiness breeding. EL, DTA, TTC, and RG methods successfully distinguished cold hardiness among different V. vinifera germplasm lines. Measurements of BW, Pro, TSS, MDA, CAT, and ASA in dormant shoots also can be used as main physiological and biochemical indexes related to cold hardiness of V. vinifera. Comprehensive evaluation by PCA combined with SF can accurately screen cold hardiness in V. vinifera. This study provides a reference and accurate identification method for the selection of cold hardiness parents and the evaluation of cold hardiness of germplasm of V. vinifera.

Study of Fungal Communities in Dry Red Wine Fermentation in Linfen Appellation, Shanxi

In this study, the fermentation mash of Cabernet Sauvignon, Cabernet Franc, and Matheran from Linfen, Shanxi Province, was sequenced using the Illumina MiSeq high-throughput sequencing platform to analyze the structural diversity of fungal communities in different samples. The results showed that a total of 10 phyla, 125 families, and 187 genera were detected in the nine samples of this study. The main fungal phyla were Ascomycota, Basidiomycota, and Mortierellomycota. The main fungal genera are Hanseniaspora, Mortierella, Sclerotinia, Aureobasidium, Saccharomyces, Aspergillus, Clavulina, Candida, etc. Hanseniaspora was the dominant genus in the pre-fermentation stage, accounting for more than 70%; Saccharomyces was the dominant genus in the middle and late fermentation stage, accounting for more than 75% in the middle fermentation stage and up to 90% in the late fermentation stage. This study provides a theoretical basis for monitoring and optimizing winemaking processes and introducing wine grape varieties in the Linfen region of Shanxi.

Bacterial Communities Related to Aroma Formation during Spontaneous Fermentation of ‘Cabernet Sauvignon’ Wine in Ningxia, China

Bacteria are an important part of wine ‘microbial terroir’ and contribute to the formation of wine flavor. Based on high-throughput sequencing and non-targeted metabonomic technology, this study first explored the bacterial composition and its effect on the aroma formation of spontaneously fermented ‘Cabernet Sauvignon’ (CS) wine in the Eastern Foot of Helan Mountain (EFHM), Ningxia. The results showed that there were significant differences in bacterial communities during fermentation of CS grapes harvested from different sub-regions of EFHM, with the earlier-established vineyard obtaining more species. The level of bacterial diversity initially decreased and then increased as the fermentation proceeded. Malolactic fermentation (MLF) was spontaneously initiated during alcohol fermentation (AF). Pantoea, Lactobacillus, Rhodococcus, Fructobacillus, and Komagataeibacter were the core bacterial genera in the fermentation mixture. Lactobacillus contributed to the synthesis of methyl and isobutyl esters and the formation of red and black fruity fragrances of wine. Fructobacillus was closely related to the synthesis of aromatic alcohols and the generation of floral flavors.

Yeast Diversity during Spontaneous Fermentations and Oenological Characterisation of Indigenous Saccharomyces cerevisiae for Potential as Wine Starter Cultures

Diversity of regional yeast can be influenced by geography, grape cultivars and the use of SO₂, but at single vineyard scale in China, the impact of these factors on yeast population, particularly Saccharomyces cerevisiae, is not well studied. Here, we characterised yeast species and dynamics during spontaneous fermentations with/without SO₂ using eight typical grape cultivars from Yuma vineyard in Ningxia wine region of China. Results show that distribution and abundance of yeast species varied by grape varieties, fermentation stage and SO₂ treatment. A number of 290 S. cerevisiae isolates were further classified into 33 genotypes by Interdelta fingerprinting. A prevailing role of grape varieties in shaping the genetic divergence of S. cerevisiae in Yuma vineyard was observed, as compared to the impacts of fermentation stage and SO₂ treatment. Pre-selected S. cerevisiae strains were subjected to vinification with Cabernet Sauvignon and Chardonnay. All strains completed fermentations but the physiochemical parameters and volatile profiles of wines were strain-specific. Some indigenous S. cerevisiae yielded more desirable aroma compounds compared to the commercial strains, among which NX16 and NX18 outcompeted others, therefore having potential for use as starters. This study provides comprehensive analysis on yeast diversity at vineyard scale in Ningxia. Information on the vinification using indigenous S. cerevisiae is of great value for improving Ningxia wine regionality.

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

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

Yeast Biodiversity in Vineyard during Grape Ripening: Comparison between Culture Dependent and NGS Analysis

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.