Native yeast and non-yeast fungal communities of Cabernet Sauvignon berries from two Washington State vineyards, and persistence in spontaneous fermentation

Temporal Dynamics of Fungal Communities in Alkali-Treated Round Bamboo Deterioration under Natural Weathering

Microbes naturally inhabit bamboo-based materials in outdoor environments, sequentially contributing to their deterioration. Fungi play a significant role in deterioration, especially in environments with abundant water and favorable temperatures. Alkali treatment is often employed in the pretreatment of round bamboo to change its natural elastic and aesthetic behaviors. However, little research has investigated the structure and dynamics of fungal communities on alkali-treated round bamboo during natural deterioration. In this work, high-throughput sequencing and multiple characterization methods were used to disclose the fungal community succession and characteristic alterations of alkali-treated round bamboo in both roofed and unroofed habitats throughout a 13-week deterioration period. In total, 192 fungal amplicon sequence variants (ASVs) from six phyla were identified. The fungal community richness of roofed bamboo samples declined, whereas that of unroofed bamboo samples increased during deterioration. The phyla Ascomycota and Basidiomycota exhibited dominance during the entire deterioration process in two distinct environments, and the relative abundance of them combined was more than 99%. A distinct shift in fungal communities from Basidiomycota dominant in the early stage to Ascomycota dominant in the late stage was observed, which may be attributed to the increase of moisture and temperature during succession and the effect of alkali treatment. Among all environmental factors, temperature contributed most to the variation in the fungal community. The surface of round bamboo underwent continuous destruction from fungi and environmental factors. The total amount of cell wall components in bamboo epidermis in both roofed and unroofed conditions presented a descending trend. The content of hemicellulose declined sharply by 8.3% and 11.1% under roofed and unroofed environments after 9 weeks of deterioration. In addition, the contact angle was reduced throughout the deterioration process in both roofed and unroofed samples, which might be attributed to wax layer removal and lignin degradation. This study provides theoretical support for the protection of round bamboo under natural weathering.

Fungal Community Composition and Its Relationship with Volatile Compounds during Spontaneous Fermentation of Cabernet Sauvignon from Two Chinese Wine-Growing Regions

The microbial community structure associated with wine in a wine-growing region is shaped by diverse ecological factors within that region, profoundly impacting the wine flavor. In wine fermentation, fungi contribute more sensory-active biochemical compounds than bacteria. In this study, we employed amplicon sequencing to measure samples from the spontaneous fermentation process of cabernet sauvignon wines from two wine-growing regions in China to study the diversity and structural evolution of fungi during spontaneous fermentation and analyze the correlation between fungi and volatile compounds. The results showed significant differences in fungal community structure and diversity in cabernet sauvignon musts from different geographical origins, and these differences affected the flavor quality of the wines. As alcoholic fermentation progressed, Saccharomyces became the dominant fungal genus and reshaped the fungal community structure, and the diversity of the fungal community decreased. However, the fungal communities of each wine-growing region remained distinct throughout the fermentation process. Furthermore, the correlation between the fungal community and volatile compounds indicated that wine is a product of fermentation involving multiple fungal genera, and the flavor is influenced by a variety of fungi. Our study enhances the comprehension of fungal communities in Chinese wine-growing regions, explaining the regulatory role of wine-related fungal microorganisms in wine flavor.

Vineyard-mediated factors are still operative in spontaneous and commercial fermentations shaping the vinification microbial community and affecting the antioxidant and anticancer properties of wines

The grapevine and vinification microbiota have a strong influence on the characteristics of the produced wine. Currently we have a good understanding of the role of vineyard-associated factors, like cultivar, vintage and terroir in shaping the grapevine microbiota. Notwithstanding, their endurance along the vinification process remains unknown. Thus, the main objective of our study was to determine how these factors influence (a) microbial succession during fermentation (i.e., bacterial and fungal) and (b) the antioxidant, antimutagenic and anticancer potential of the produced wines. These were evaluated under different vinification strategies (i.e., spontaneous V1, spontaneous with preservatives V2, commercial V3), employed at near full-scale level by local wineries, for two cultivars (Roditis and Sideritis), two terroir types, and two vintages. Cultivar and vintage were strong and persistent determinants of the vinification microbiota, unlike terroir whose effect became weaker from the vineyard, and early fermentation stages, where non-Saccharomyces yeasts, filamentous fungi (i.e., Aureobasidium, Cladosporium, Lachancea, Alternaria, Aspergillus, Torulaspora) and acetic acid bacteria (AAB) (Gluconobacter, Acetobacter, Komagataeibacter) dominated, to late fermentation stages where Saccharomyces and Oenococcus become prevalent. Besides vineyard-mediated factors, the vinification process employed was the strongest determinant of the fungal community compared to the bacterial community were effects varied per cultivar. Vintage and vinification type were the strongest determinants of the antioxidant, antimutagenic and anticancer potential of the produced wines. Further analysis identified significant positive correlations between members of the vinification microbiota like the yeasts Torulaspora debrueckii and Lachancea quebecensis with the anticancer and the antioxidant properties of wines in both cultivars. These findings could be exploited towards a microbiota-modulated vinification process to produce high-quality wines with desirable properties and enhanced regional identity.

Genetic diversity of non-Saccharomyces yeasts associated with spontaneous fermentation of Cabernet Sauvignon wines from Ningxia, China

The organoleptic profile and quality of wine are affected by the presence of different non-Saccharomyces species and strains. Therefore, the identification and characterization of non-Saccharomyces yeasts are the first step to understand their function, and to develop a better strain selection program for winemaking. This study investigated the biodiversity of non-Saccharomyces yeasts associated with spontaneous fermentation of Cabernet Sauvignon wines from five sub-regions (Shi Zuishan, Yinchuan, Yu Quanying, Qing Tongxia and Hong Sibu) in Ningxia, China. Yeast species were identified by sequencing the 26S rRNA D1/D2 region, and strains at the subspecies level were discriminated using tandem repeat-tRNA (TRtRNA) PCR analysis. A total of 524 yeast colonies were isolated, and 19 non-Saccharomyces yeast species belonging to 10 genera were identified, including Aureobasidium pullulans, Cryptococcus albidus, Cryptococcus sp., C. flavescens, C. terrestris, C. magnus, Cystofilobasidium ferigula, Candida zemplinina, Filobasidium magnum, Filobasidium sp., F. elegans, Hanseniaspora uvarum, Metschnikowia pimensis, M. pulcherrima, Naganishia albida, Pichia kluyveri, P. kudriavzevii, Rhodotorula glutinis and R. graminis. Hanseniaspora uvarum, C. zemplinina, and M. pulcherrima were the three most dominated species, while other non-Saccharomyces species were only present in the early stage of spontaneous fermentations at different levels. Further, for the yeast discrimination at strain level, 34 profiles were obtained by amplification with primer pairs TtRNASC/5CAG, while 40 profiles were obtained with primer pairs TtRNASC/ISSR-MB. This study explored the diversity of non-Saccharomyces species in Ningxia, China, and made an important contribution of genetic resources for further strain development.

Succession of Fungal Community during Outdoor Deterioration of Round Bamboo

Bamboo's mechanical and aesthetic properties are significantly influenced by fungi. However, few studies have been conducted to investigate the structure and dynamics of fungal communities in bamboo during its natural deterioration. In this study, fungal community succession and characteristic variations of round bamboo in roofed and unroofed environments over a period of 13 weeks of deterioration were deciphered using high-throughput sequencing and multiple characterization methods. A total of 459 fungal Operational Taxonomic Units (OTUs) from eight phyla were identified. The fungal community's richness of roofed bamboo samples showed an increasing trend, whereas that of unroofed bamboo samples presented a declining trend during deterioration. Ascomycota and Basidiomycota were the dominant phyla throughout the deterioration process in two different environments: Basidiomycota was found to be an early colonizer of unroofed bamboo samples. Principal Coordinates Analysis (PCoA) analysis suggested that the deterioration time had a greater impact on fungal community variation compared to the exposure conditions. Redundancy analysis (RDA) further revealed that temperature was a major environmental factor that contributed to the variation in fungal communities. Additionally, the bamboo epidermis presented a descending total amount of cell wall components in both roofed and unroofed conditions. The correlation analysis between the fungal community and relative abundance of three major cell wall components elucidated that Cladosporium was negatively correlated with hemicellulose in roofed samples, whereas they presented a positive correlation with hemicellulose and a negative correlation with lignin in unroofed samples. Furthermore, the contact angle decreased during the deterioration process in the roofed as well as unroofed samples, which could arise from the degradation of lignin. Our findings provide novel insights into the fungal community succession on round bamboo during its natural deterioration and give useful information for round bamboo protection.

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.

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.

Diversity and Metabolic Activity of Fungi Causing Biodeterioration of Canvas Paintings

Research into the biodeteriorative potential of fungi can serve as an indicator of the condition of heritage items. Biodeterioration of canvas paintings as a result of fungal metabolic activity is understudied with respect to both the species diversity and mechanisms involved. This study brings new evidence for the physiology of fungi biodeteriorative capacity of canvas paintings. Twenty-one fungal isolates were recovered from four oil paintings (The Art Museum, Cluj-Napoca) and one gouache painting (private collection), dating from the 18th to 20th centuries. The species, identified based on the molecular markers Internal Transcribed Spacer (ITS), beta-tubulin (tub2), or translation elongation factor 1 (TEF-1), are common colonisers of canvas paintings or indoor environments (e.g., Penicillium spp., Aspergillus spp., Alternaria spp.). Fungi enzymatic profiles were investigated by means of hydrolysable substrates, included in culture media or in test strips, containing components commonly used in canvas paintings. The pigment solubilisation capacity was assessed in culture media for the primary pigments and studied in relation to the organic acid secretion. Caseinases, amylases, gelatinases, acid phosphatase, N-acetyl-β-glucosaminidase, naphthol-AS-BI-phosphohydrolase, and β-glucosidase were found to be the enzymes most likely involved in the processes of substrate colonisation and breakdown of its components. Aureobasidium genus was found to hold the strongest biodeteriorative potential, followed by Cladosporium, Penicillium, Trichoderma, and Aspergillus. Blue pigment solubilisation was detected, occurring as a result of organic acids secretion. Distinct clusters were delineated considering the metabolic activities detected, indicating that fungi specialise in utilisation of certain types of substrates. It was found that both aged and modern artworks are at risk of fungal biodeterioration, due to the enzymatic activities’ diversity and intensity, pigment solubilisation capacity or pigment secretion.

Metagenomic Assessment Unravels Fungal Microbiota Associated to Grapevine Trunk Diseases

Grapevine trunk diseases (GTDs) are among the most important problems that affect the longevity and productivity of vineyards in all the major growing regions of the world. They are slow-progression diseases caused by several wood-inhabiting fungi with similar life cycles and epidemiology. The simultaneous presence of multiple trunk pathogens in a single plant together with the inconsistent GTDs symptoms expression, their isolation in asymptomatic plants, and the absence of effective treatments make these diseases extremely complex to identify and eradicate. Aiming to gain a better knowledge of GTDs and search sustainable alternatives to limit their development, the present work studied the fungal community structure associated with GTDs symptomatic and asymptomatic grapevines, following a metagenomic approach. Two important cultivars from the Alentejo region with different levels of susceptibility to GTDs were selected, namely, ‘Alicante Bouschet’ and ‘Trincadeira’. Deep sequencing of fungal-directed ITS1 amplicon led to the detection of 258 taxa, including 10 fungi previously described as responsible for GTDs. Symptomatic plants exhibited a lower abundance of GTDs-associated fungi, although with significantly higher diversity of those pathogens. Our results demonstrated that trunk diseases symptoms are intensified by a set of multiple GTDs-associated fungi on the same plant. The composition of fungal endophytic communities was significantly different according to the symptomatology and it was not affected by the cultivar. This study opens new perspectives in the study of GTDs-associated fungi and their relation to the symptomatology in grapevines.