Microbial community composition on grape surface controlled by geographical factors of different wine regions in Xinjiang, China

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.

Integrative metagenomics, volatilomics and chemometrics for deciphering the microbial structure and core metabolic network during Chinese rice wine (Huangjiu) fermentation in different regions

Huangjiu is a spontaneously fermented alcoholic beverage, that undergoes intricate microbial compositional changes. This study aimed to unravel the flavor and quality formation mechanisms based on the microbial metabolism of Huangjiu. Here, metagenome techniques, chemometrics analysis, and headspace solid-phase microextraction gas chromatography-mass spectrometry (HS-SPME-GC-MS) metabolomics combined with microbial metabolic network were employed to investigate the distinctions and relationship between the microbial profiles and the quality characteristics, flavor metabolites, functional metabolic patterns of Huangjiu across three regions. Significant variations (P < 0.05) were observed in metabolic rate of physicochemical parameters and biogenic amine concentration among three regions. 8 aroma compounds (phenethyl acetate, phenylethyl alcohol, isobutyl alcohol, ethyl octanoate, ethyl acetate, ethyl hexanoate, isoamyl alcohol, and diethyl succinate) out of 448 volatile compounds were identified as the regional chemical markers. 25 dominant microbial genera were observed through metagenomic analysis, and 13 species were confirmed as microbial markers in three regions. A metabolic network analysis revealed that Saccharomycetales (Saccharomyces), Lactobacillales (Lactobacillus, Weissella, and Leuconostoc), and Eurotiales (Aspergillus) were the predominant populations responsible for substrate, flavor (mainly esters and phenylethyl alcohol) metabolism, Lactobacillales and Enterobacterales were closely linked with biogenic amine. These findings provide scientific evidence for regional microbial contributions to geographical characteristics of Huangjiu, and perspectives for optimizing microbial function to promote Huangjiu quality.

Bacterial composition and physicochemical characteristics of sorghum based on environmental factors in different regions of China

The fermentation process for Jiang-flavored baijiu using sorghum as the raw material involves a variety of microorganisms. However, the specific physicochemical characteristics of sorghum and microbial composition on its surface have not been fully elucidated. We aimed to perform a comprehensive comparative analysis of the variations in physicochemical properties and surface microflora in waxy sorghum samples from three prominent production regions in China (Renhuai, Jinsha, and Duyun). Multivariate statistical assessments were conducted that incorporated local soil and climate variables. The results showed that Cyanobacteria, unclassified bacteria, Proteobacteria, Firmicutes, and Bacteroidota were the dominant bacteria in these regions. These bacteria were associated with ethyl acetate, ethyl caprylate, ethyl lactate, and butyl groups, which synergistically produce flavorful compounds. The surface bacterial communities were affected by soil total phosphorus, altitude, diurnal temperature range, monthly mean temperature, precipitation, and effective accumulated temperature. The findings of this study provide a new perspective on microorganisms related to Jiang-flavored baijiu and can help establish a reference for the stability of liquor quality.

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

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

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.

Variations of the fungal microbiome in Corydalis Rhizoma with different collection areas, processing methods, and storage conditions

Corydalis Rhizoma (CR, Yanhusuo in Chinese) has been widely used as an analgesic in herbal medicine and functional food. Cases of fungal and mycotoxin contamination in CR have been reported. In this study, the composition and diversity of fungal microbiome in CR samples from four herbal markets and two processing methods were investigated by DNA metabarcoding. Variations of the fungal microbiome in CR during cold and conventional storage were monitored. Results showed that Aspergillus was the dominant genus and saprotroph was the dominant trophic mode. Six potential toxigenic fungi, namely, Aspergillus fumigatus, Aspergillus ostianus, Aspergillus terreus, Penicillium citrinum, Penicillium oxalicum, and Trichothecium roseum, were detected. Differences in fungal composition and diversity among various groups based on collection areas and processing methods were also observed. Moreover, the relative abundance of dominant genera in CR samples stored at different temperatures was significantly different and changed with storage time. This study is the first to reveal the influence of collection areas, processing methods, and storage conditions on the fungal microbiome in CR, which was expected to provide a basis for control strategies of fungal contamination in the industrial chain of CR.

The influence of low-temperature resistant lactic acid bacteria on the enhancement of quality and the microbial community in winter Jerusalem Artichoke (Helianthus tuberosus L.) silage on the Qinghai-Tibet Plateau

Jerusalem Artichoke (Helianthus tuberosus L.), an emerging "food and fodder" economic crop on the Qinghai-Tibet Plateau. To tackle problems such as incomplete fermentation and nutrient loss occurring during the low-temperature ensilage of Jerusalem Artichokes in the plateau's winter, this study inoculated two strains of low-temperature resistant lactic acid bacteria, Lactobacillus plantarum (GN02) and Lactobacillus brevis (XN25), along with their mixed components, into Jerusalem Artichoke silage material. We investigated how low-temperature resistant lactic acid bacteria enhance the quality of low-temperature silage fermentation for Jerusalem Artichokes and clarify its mutual feedback effect with microorganisms. Results indicated that inoculating low-temperature resistant lactic acid bacteria significantly reduces the potential of hydrogen and water-soluble carbohydrates content of silage, while increasing lactic acid and acetic acid levels, reducing propionic acid, and preserving additional dry matter. Inoculating the L. plantarum group during fermentation lowers pH and propionic acid levels, increases lactic acid content, and maintains a dry matter content similar to the original material. Bacterial community diversity exhibited more pronounced changes than fungal diversity, with inoculation having a minor effect on fungal community diversity. Within the bacteria, Lactobacillus remains consistently abundant (>85%) in the inoculated L. plantarum group. At the fungal phylum and genus levels, no significant changes were observed following fermentation, and dominant fungal genera in all groups did not differ significantly from those in the raw material. L. plantarum exhibited a positive correlation with lactic acid and negative correlations with pH and propionic acid. In summary, the inoculation of L. plantarum GN02 facilitated the fermentation process, preserved an acidic silage environment, and ensured high fermentation quality; it is a suitable inoculant for low-temperature silage in the Qinghai-Tibet Plateau.

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.

Microbial diversity on grape epidermis and wine volatile aroma in spontaneous fermentation comprehensively driven by geography, subregion, and variety

On their journey from the wine grape to the resulting wine, microbiota from grape surfaces controlled by multiple factors is transferred to wine spontaneous fermentation process with indisputable consequences for wine quality parameters. The associated microbiota was regionally distinct (defined to microbial terroir) but how these microbial patterns with significantly regional distinctiveness quantitatively drive the wine regional characteristics are not definite within a complete grape ecosystem at different geographical (> 300 km), subregional (< 10 km), and varietal scales. Here, we collected 24 samples (containing two grape varieties) from four subregions of two regions in Xinjiang wine production area to investigate fungal distribution patterns and the association with wine chemical composition at different evaluation scales. Meanwhile, the relationships were established between geographical, subregional, varietal community of fungi, and wine volatile aroma using partial least squares regression (PLSR) and structural equation modeling (SEM). Results show that microbial and volatile samples present the significantly regional difference inside the complete ecosystem. Microbiota showed a stronger heterogeneity at geography scales, which drove the distributions of subregional and varietal microbiota thereby influencing the volatile composition of finished wines. Moreover, geographical microbiota seems to weaken the effects of varietal community on wine aroma compounds. Microbial communities respond to environmental changes within a completely set grape-related ecosystem at different scales, and these responses resulted in the wine regional distinctiveness based on the volatile profiles. Our findings further confirmed the important role of microbial terroir in shaping wine styles and provided the new cerebration for the terroir drivers of microbiota.

Lychee Pulp-Derived Dietary Fiber-Bound Phenolic Complex Upregulates the SCFAs-GPRs-ENS Pathway and Aquaporins in Loperamide-Induced Constipated Mice by Reshaping Gut Microbiome

This study aimed to investigate the effects of the lychee pulp-derived dietary fiber-bound phenolic complex (DF-BPC) on a murine model of loperamide-induced constipation and its molecular mechanism associated with gut microbiota modification. DF-BPC supplementation mitigated loperamide-induced dyschezia, intestinal hypomotility, and colonic impairment, as evidenced by the increased gastro-intestinal transit rate and mucus cell counts. By comparison, short-chain fatty acids (SCFAs) contents and relative abundances of associated genera (Butyricimonas, Clostridium, and Lactobacillus) were effectively upregulated following DF-BPC supplementation. Notably, DF-BPC significantly enhanced expressions of G protein-coupled receptor (GPR) 41 and 43, reaching 1.43- and 1.62-fold increase, respectively. Neurotransmitter secretions were simultaneously altered in DF-BPC-treated mice, suggesting upregulation of the SCFAs-GPRs-enteric nervous system pathway. The overexpression of aquaporins (AQP3, 8, and 9) was stimulated partly through GPRs activation. Mild inflammation associated with constipation was inhibited by suppressing LBP-TLR4-NF-κB signaling translocation. These findings suggest that DF-BPC from lychee pulp has the potential to alleviate constipation in mice through modifying the gut microbiome.

Analysis on driving factors of microbial community succession in Jiuyao of Shaoxing Huangjiu (Chinese yellow rice wine)

The microbial ecosystem of fermented food is greatly disturbed by human activities.Jiuyao is important saccharification starter for brewing huangjiu. The interaction between environmental factors and microorganisms significantly affected the microbial community structure at different stages of Jiuyao manufacturing. This study combined environmental factor analysis and high-throughput sequencing technology to comprehensively analyze the specific changes of microbial community and environmental factors in each fermentation stage of Jiuyao production and their correlation. The results showed that the activities of liquefaction enzyme, glycosylation enzyme and acid protease reached the highest value on the 8 th day (192 h) after the beginning of fermentation, and the cellulase activity reached the highest value at the end of fermentation. Pediococcus（37.5 %-58.2 %）, Weissella（9.2 %-27.0 %） and Pelomonas（0.1 %-12.1 %） were the main microbial genera in the genus bacteria, and Saccharomycopsis（37.1 %-52.0 %）, Rhizopus（12.5 %-31.0 %） and Saccharomyces（4.0 %-20.5 %） were the main microbial genera in the genus fungi. The results of correlation analysis showed that the microbial communities in Jiuyao were closely related to environmental factors. Most microbial communities were positively correlated with temperature, but negatively correlated with ambient humidity, CO2 concentration, acidity and water content of Jiuyao. In addition, the transcription levels of enzymes related to microbial glucose metabolism in Jiuyao were higher in the late stage of Jiuyao fermentation. Interestingly, these enzymes had high transcription levels in fungi such as Saccharomycopsis, Rhizopus and Saccharomyces, as well as in bacteria such as Pediococcus and Lactobacillus. This study provides a reference for revealing the succession rule of microbial community structure caused by environmental factors during the preparation of Jiuyao in Shaoxing Huangjiu.

Identification and Pathogenicity of Cladosporium, Fusarium, and Diaporthe spp. Associated with Late-Season Bunch Rots of Grape

Fungal pathogens continue to pose a significant threat to grape production. Previous studies of pathogens associated with late-season bunch rots in Mid-Atlantic vineyards had elucidated the primary causal agents of these diseases, but the significance and identity of the less commonly isolated genera was unclear. Therefore, to more fully understand the identity and pathogenicity of Cladosporium, Fusarium, and Diaporthe spp. associated with late-season bunch rots of wine grapes in the Mid-Atlantic, phylogenic analyses and pathogenicity assays were conducted. Isolates were characterized to the species level by sequencing the TEF1 and Actin, TEF1 and TUB2, and TEF1 genes for 10, 7, and 9 isolates of Cladosporium, Diaporthe, and Fusarium, respectively. Four Cladosporium, three Fusarium, and three Diaporthe species were identified, and C. allicinum, C. perangustum, C. pseudocladosporioides, F. graminearum, and D. guangxiensis had not yet been isolated from grape in North America. The pathogenicity of each species was evaluated on detached table and wine grapes, and D. eres, D. ampelina, D. guangxiensis, and F. fujikuroi were found to be the most aggressive on both table and wine grapes. Further investigations through more extensive isolate collection and of myotoxicity testing may be warranted due to the prevalence and pathogenicity of D. eres and F. fujikuroi.

Yeast communities before and after spontaneous fermentation of wine grapes: a case study from Nova Scotia

Wine fermentations are generally completed by the domestic yeast Saccharomyces cerevisiae, but many indigenous vineyard yeasts also influence wine flavour and aroma. Despite the flourishing wine industry in Nova Scotia, there has yet to be any systematic evaluation of these yeasts in Atlantic Canada. The yeast communities of pressed L'Acadie blanc grapes sampled from an organic vineyard in the Annapolis Valley in 2018 and 2019 were characterized before and after spontaneous fermentation by both Illumina and PacBio sequencing, to address and compare potential platform biases. Chemical and sensory evaluations were also conducted. Basidiomycete yeasts, including Vishniacozyma carnescens, Filobasidium globisporum, and Curvibasidium cygneicollum, dominated pre-fermentation diversity. Species of Saccharomyces made up ∼0.04% of sequences prior to fermentation, but 85%-100% after fermentation, with some replicates dominated by S. cerevisiae and some by S. uvarum. PacBio sequencing detected high proportions of Hanseniaspora uvarum, while Illumina sequencing did not. A better understanding of Nova Scotia vineyard yeast communities will allow local wine makers to make better use of non-traditional yeasts and spontaneous fermentations to produce high-quality wines unique to the region.

Analysis of Microbial Community Diversity on the Epidermis of Wine Grapes in Manasi’s Vineyard, Xinjiang

Epiphytic microbial communities significantly impact the health and quality of grape berries. This study utilized high-performance liquid chromatography and high-throughput sequencing to explore the epiphytic microbial diversity and physicochemical indicators in nine different wine grape varieties. In total, 1,056,651 high-quality bacterial 16S rDNA sequences and 1,101,314 fungal ITS reads were used for taxonomic categorization. Among the bacteria, Proteobacteria and Firmicutes were the dominant phyla, and Massilia, Pantoea, Pseudomonas, Halomonas, Corynebacterium, Bacillus, Anaerococcus, and Acinetobacter were the dominant genera. Among the fungi, Ascomycota and Basidiomycota were the dominant phyla, and Alternaria, Filobasidium, Erysiphe, Naganishia, and Aureobasidium were the dominant genera. Notably, Matheran (MSL) and Riesling (RS) exhibited the highest microbial diversity among the nine grape varieties. Moreover, pronounced differences in epiphytic microorganisms in red and white grapes suggested that the grape variety significantly influences the structure of surface microbial communities. Understanding the composition of epiphytic microorganisms on the grape skin can provide a direct guide to winemaking.

Effects of epiphytic and exogenous lactic acid bacteria on fermentation quality and microbial community compositions of paper mulberry silage

This study aimed to isolate, characterize, and identify lactic acid bacteria (LAB) strains from various sources and evaluate their effects on the nutritional quality, fermentation characteristics, and microbial compositions of paper mulberry (PM) after 60 days of ensiling. Forty-nine LAB strains were isolated from Phalaris arundinacea silage, pickle, and fresh PM leaves; three of these strains (Lactiplantibacillus plantarum, YC1; Levilactobacillus brevis, PC3; and Lactiplantibacillus plantarum, BP17) and one commercial inoculant Gaofuji (GFJ) were subsequently used. Compared with other treatments, PC3 and BP17 increased (P < 0.05) the LAB count and crude protein content and decreased (P < 0.05) the molds and coliform bacteria counts, pH, and ammonia-N content of PM silages. BP17 and PC3 increased the relative Lactiplantibacillus abundance and decreased that of Lelliottia and Cladosporium, improving PM silage quality. Therefore, PC3 and BP17 can improve the fermentation quality of PM silage and could be used as silage starter cultures.

Differences in geological conditions have reshaped the structure and diversity of microbial communities in oily soils

High-throughput sequencing was used to study the microbial community structure diversity changes in oil-contaminated soils under different spatial distances and environmental conditions. 239 Phyla, 508 Classes, 810 Orders, 1417 Families, 2048 Genera, 511 Species of microbial communities were obtained from 16 samples in three regions. The physicochemical properties of the soil, microorganisms' community structure has been changed by Petroleum hydrocarbon (PHA). Alpha diversity results showed that the soil contained high bacterial diversity, especially in Qingyang's loess soil. The bacterial abundance was in the order of loess soil > black soil > sandy soil. Beta diversity revealed that spatial distance limitation and random variation of repeated samples may be the main factors leading to soil heterogeneity and microbial community structure differences. The dominant bacteria phyla with broad petroleum hydrocarbon degradation ability such as Proteobacteria, Firmicutes, Bacteroidetes and Actinobacteria were identified. Pseudomonas, Bacillus, Nocardioides, Oceanobacillus, Sphingomonas, Alkanindiges and Streptomyces were identified as functional microbial for the PHA degradation. The microbial communities manifested the co-exclusion under different geological conditions, and played the key role in the soil PHA degradation through amino acid metabolism, energy metabolism and carbohydrate metabolism. The correlation results of amos structural equation showed that the diversity and abundance of soil microorganisms in different regions were controlled by soil PHA content and environmental factors. Altitude, annual average temperature and annual rainfall were positively correlated with microbial diversity. Annual rainfall and soil physical and chemical factors exhibited the most significant influence on it. Microbial diversity indirectly affected the PHA content in different type soil. We believe that reshape the structure and diversity of microbial communities in soil could be changed and reshaped by different geological conditions, pollutants and soil type. This study can provide helps for understanding the ecological effect of geomicrobiology formation under the driving force of geographic environment and other factors.

Bacterial community diversity and its potential contributions to the flavor components of traditional smoked horsemeat sausage in Xinjiang, China

Smoked horsemeat sausage is a famous fermented traditional food in Xinjiang, China. However, the microbial diversity and its potential contributions to the flavor components of smoked horsemeat sausage are unclear. In this study, the microbial community and flavor components of smoked horsemeat sausage from six regions of Xinjiang were measured by using amplicon sequencing and headspace solid-phase microextraction combined with gas chromatography–mass spectrometry (HS-SPME-GC–MS) technology, respectively. Relations among microbial communities, flavor components and environmental factors were subsequently predicted based on redundancy analysis (RDA) and Monte Carlo permutation tests. Although smoked horsemeat sausage samples from different regions possessed distinct microbial communities, lactic acid bacteria (LAB) were identified as the dominant consortium in smoked horsemeat sausage. Lactobacillus, Vagococcus, Lactococcus, and Carnobacterium were detected at high abundance in different sausages. The moisture content, nitrite content, and pH of the sausage might be important factors influencing the dominant bacterial community, according to the RDA. Among the dominant consortia, the eight core bacterial genera showed considerable correlations with the formation of sixteen volatile compounds in smoked horsemeat sausage based on multivariate statistical analysis. For example, the levels of Leuconostoc and Lactobacillus were positively correlated with those of 1-hexadecanol, hexyl acetate, 2-methyl-phenol, 1-pentanol, d-limonene, and 2-heptanone, and the levels of Leuconostoc, Lactobacillus, and Weissella were negatively correlated with those of 1-octanol, acetic acid, octanal, heptanal, and 1-hexanol. This study will provide a theoretical basis for understanding the microbial metabolic modes of Xinjiang smoked horsemeat sausages.

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.

Ecological Distribution and Oenological Characterization of Native Saccharomyces cerevisiae in an Organic Winery

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.

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.

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

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

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

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

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

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

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 of non-Saccharomyces yeasts of grape berry surfaces from representative Cabernet Sauvignon vineyards in Henan Province, China

Non-Saccharomyces yeasts are important players during winemaking and may come from grapes grown in vineyards. To study the diversity of non-Saccharomyces yeasts on surface grape berries, 433 strains were isolated from different Cabernet Sauvignon vineyards grown in Henan Province. Our results demonstrated that these strains were classified into 16 morphotypes according to their growth morphology on Wallerstein Laboratory agar medium, and were identified as seven species from four genera: Hanseniaspora opuntiae, Hanseniaspora vineae, Hanseniaspora uvarum, Pichia occidentalis, Pichia kluyveri, Issatchenkia terricola and Saturnispora diversa based on a series of molecular biological experiments. Hanseniaspora opuntiae was obtained from all sampling sites except Changyuan County, while Pichia kluyveri and Saturnispora diversa were only found in sites of Zhengzhou Grape Resource Garden and Minquan County, respectively. The site Minquan was home of the greatest species richness while only one single species (Hanseniaspora opuntiae) was detected at NAPA winery from Zhengzhou or at Anyang County. Finally, this study suggested that the geographic distribution and diversity of non-Saccharomyces yeast populations on Cabernet Sauvignon grape berries were likely to be determined by a combination of grape varieties and environmental factors.

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.

Succession of Fungal Communities at Different Developmental Stages of Cabernet Sauvignon Grapes From an Organic Vineyard in Xinjiang

Fungi present on grape surface considerably impact grape growth and quality. However, information of the fungal community structures and dynamics on the worldwide cash crop, the Cabernet Sauvignon grape, from the budding to ripening stages remains limited. Here, we investigated the succession of fungal communities on Cabernet Sauvignon grapes from an organic vineyard in Xinjiang, China at different developmental stages via high-throughput sequencing combined with multivariate data analysis. In total, 439 fungal amplicon sequence variants (ASVs) from six phyla were identified. The fungal communities differed over the budding to the berry stages. Moreover, Aspergillus, Malassezia, Metschnikowia, and Udeniomyces were predominant during the unripe stage, whereas Erysiphe, Cryptococcus, Vishniacozyma, and Cladosporium were dominant in the ripe stages. Notably, Vishniacozyma was the most abundant genus, conserved in all development stages. Moreover, network analysis resulted in 171 edges—96 negative and 75 positive. Moreover, fungal genera such as Vishniacozyma, Sporobolomyces, Aspergillus, Alternaria, Erysiphe, Toxicodendron, and Metschnikowia were present in the hubs serving as the main connecting nodes. Extensive mutualistic interactions potentially occur among the fungi on the grape surface. In conclusion, the current study expounded the characteristics of the Cabernet Sauvignon grape fungal community during the plant growth process, and the results provided essential insights into the potential impacts of fungal communities on grape growth and health.

Analysis of microbial community diversity of muscadine grape skins

Microorganisms in grape skins play vital roles in grapevine health, productivity, wine quality and organoleptic properties. To investigate microbial diversity of muscadine grape skins, 16S and ITS sequences of 30 samples from six muscadine (Muscadinia rotundifolia Michx.) cultivars grown in Guangxi, China, were sequenced using Illumina Novaseq platform. A total of 7,317 bacterial operational taxonomic units (OTUs) and 1,611 fungal OTUs were obtained, and clustered into 38 bacterial and 7 known fungal phyla. The dominant bacterial phyla were Proteobacteria, Firmicutes, Bacteroidetes, Planctomycetes, Actinobacteria, Verrucomicrobia, Acidobacteria, and Patescibacteria, and the dominant genera were Lelliottia, Prevotella_9, Escherichia-Shigella, Lactobacillus, Pseudomonas, Akkermansia, Faecalibacterium, Rahnella, and Acinetobacter. For fungi, the dominant phyla were Ascomycota, Basidiomycota, and Mortierellomycota, and the dominant genera were Acaromyces, Uwebraunia, Penicillium, Zygosporium, Ilyonectria, Aspergillus, Neodevriesia, Strelitziana, Mortierella, and Fusarium. Alpha diversity analysis and Kruskal-Wallis H test demonstrated that microbial diversity and composition were affected by the cultivar. The Pearson correlation analysis of species revealed complex interactions among microbes. PICRUSt2 predicted that the metabolism of carbohydrates, cofactors, vitamins, amino acids, terpenoids, polyketides, lipids and biosynthesis of other secondary metabolites were abundant. These results contribute to understanding the uniqueness of muscadine grapes and the links among microorganisms in grape skins.

Increased Organic Fertilizer and Reduced Chemical Fertilizer Increased Fungal Diversity and the Abundance of Beneficial Fungi on the Grape Berry Surface in Arid Areas

Fertilizer practices can significantly impact the fruit quality and microbial diversity of the orchards. The fungi on the surface of fruits are essential for fruit storability and safety. However, it is not clear whether fertilization affects the fungal diversity and community structure on the surface of grape berries. Here, grape quality and the fungal diversity on the surface of grapes harvested from three fertilizer treatments were analyzed shortly after grape picking (T0) and following 8 days of storage (T1). The study involved three treatments: (1) common chemical fertilizer for 2 years (CH); (2) increased organic fertilizer and reduced chemical fertilizer for 1 year (A.O); and (3) increased organic fertilizer and reduced chemical fertilizer for 2 years (B.O). The application of increased organic fertilizer and reduced chemical fertilizer increased the soluble solids content (SSC) of the grape berries and decreased the pH of the grape juice. A total of 827,947 high-quality fungal sequences were recovered and assigned to 527 operational taxonomic units. Members of the Ascomycota phylum were dominant in all samples and accounted for 94.41% of the total number of detected sequences, followed by the Basidiomycota (5.05%), and unidentified fungi (0.54%). Alpha and beta diversity analyses revealed significantly different fungal populations in the three fertilizer treatments over the two time periods. The fungal diversity and richness on the grape berry surface in the B.O and A.O treatments were higher than those in the CH treatment. Among the detected fungi, the B.O treatments were mainly Pichia, Aureobasidium, and Candida genera, while the CH treatments were Botrytis, Aspergillus, and Penicillium. Moreover, significant differences were revealed between the two assessment times (T0 and T1). The samples from the T0 timepoint had higher fungal richness and diversity than the samples from T1 timepoint. Increasing organic fertilizer usage in grape management could improve grape quality and went on to increase the fungal diversity, as well as the relative abundance (RA) of beneficial fungi on grape berry surfaces. The correlation analysis suggested that the pH of the grape juice was significantly negatively correlated with fungal diversity parameters.

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.

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

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

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.

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

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