Massive Sequencing: A New Tool for the Control of Alcoholic Fermentation in Wine?

Survey of Inoculated Commercial Saccharomyces cerevisiae in Winery-Based Trials

Wine production has developed from spontaneous to controlled fermentations using commercial active dry yeasts (ADY). In this study, S. cerevisiae commercial ADY were tested, and yeast community dynamics were monitored at different fermentation stages in three winery-based trials with volumes ranging from 60 L to 250 hL. The differentiation of S. cerevisiae strains was achieved using microsatellite markers. In Experiment 1, results showed that both ADY strains revealed similar profiles, despite being described by the producer as having different properties. In Experiment 2, higher genetic diversity was detected when co-inoculation was tested, while in sequential inoculation, the initial ADY seemed to dominate throughout all fermentation. Pilot-scale red wine fermentations were performed in Experiment 3, where one single ADY strain was tested along with different oenological additives. Surprisingly, these trials showed an increase in distinct profiles towards the end of fermentation, indicating that the dominance of the ADY was lower than in the blank modality. The use of ADY is envisaged to promote a controlled and efficient alcoholic fermentation, and their purchase represents an important cost for wineries. Therefore, it is most relevant to survey commercial ADY during wine fermentation to understand if their use is effective.

Biodiversity of Oenological Lactic Acid Bacteria: Species- and Strain-Dependent Plus/Minus Effects on Wine Quality and Safety

Winemaking depends on several elaborate biochemical processes that see as protagonist either yeasts or lactic acid bacteria (LAB) of oenological interest. In particular, LAB have a fundamental role in determining the quality chemical and aromatic properties of wine. They are essential not only for malic acid conversion, but also for producing several desired by-products due to their important enzymatic activities that can release volatile aromatic compounds during malolactic fermentation (e.g., esters, carbonyl compounds, thiols, monoterpenes). In addition, LAB in oenology can act as bioprotectors and reduce the content of undesired compounds. On the other hand, LAB can affect wine consumers’ health, as they can produce harmful compounds such as biogenic amines and ethyl carbamate under certain conditions during fermentation. Several of these positive and negative properties are species- and strain-dependent characteristics. This review focuses on these aspects, summarising the current state of knowledge on LAB’s oenological diversity, and highlighting their influence on the final product’s quality and safety. All our reported information is of high interest in searching new candidate strains to design starter cultures, microbial resources for traditional/typical products, and green solutions in winemaking. Due to the continuous interest in LAB as oenological bioresources, we also underline the importance of inoculation timing. The considerable variability among LAB species/strains associated with spontaneous consortia and the continuous advances in the characterisation of new species/strains of interest for applications in the wine sector suggest that the exploitation of biodiversity belonging to this heterogeneous group of bacteria is still rising.

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.

Finding Functional Differences Between Species in a Microbial Community: Case Studies in Wine Fermentation and Kefir Culture

Microbial life usually takes place in a community where individuals interact, by competition for nutrients, cross-feeding, inhibition by end-products, but also by their spatial distribution. Lactic acid bacteria are prominent members of microbial communities responsible for food fermentations. Their niche in a community depends on their own properties as well as those of the other species. Here, we apply a computational approach, which uses only genomic and metagenomic information and functional annotation of genes, to find properties that distinguish a species from others in the community, as well as to follow individual species in a community. We analyzed isolated and sequenced strains from a kefir community, and metagenomes from wine fermentations. We demonstrate how the distinguishing properties of an organism lead to experimentally testable hypotheses concerning the niche and the interactions with other species. We observe, for example, that L. kefiranofaciens, a dominant organism in kefir, stands out among the Lactobacilli because it potentially has more amino acid auxotrophies. Using metagenomic analysis of industrial wine fermentations we investigate the role of an inoculated L. plantarum in malolactic fermentation. We observed that L. plantarum thrives better on white than on red wine fermentations and has the largest number of phosphotransferase system among the bacteria observed in the wine communities. Also, L. plantarum together with Pantoea, Erwinia, Asaia, Gluconobacter, and Komagataeibacter genera had the highest number of genes involved in biosynthesis of amino acids.

The Influence of Fungicide Treatments on Mycobiota of Grapes and Its Evolution during Fermentation Evaluated by Metagenomic and Culture-Dependent Methods

The present study evaluated the impact of organic and conventional fungicide treatments compared with untreated samples (no fungicides were used) on the grape berry yeast community of the Montepulciano variety. The yeast dynamics during the spontaneous fermentation using culture-dependent and -independent methods was also evaluated. Results showed a reduction of yeast biodiversity by conventional treatments determining a negative influence on fermenting yeasts in favor of oxidative yeasts such as Aerobasidium pullulans. Starmerella bacillaris was significantly more present in organic samples (detected by next generation sequencing (NGS)), while Hanseniaspopa uvarum was significantly less present in untreated samples (detected by the culture-dependent method). The fermenting yeasts, developed during the spontaneous fermentation, were differently present depending on the fungicide treatments used. Culture-dependent and -independent methods exhibited the same most abundant yeast species during the spontaneous fermentation but a different relative abundance. Differently, the NGS method was able to detect a greater biodiversity (lower abundant species) in comparison with the culture-dependent method. In this regard, the methodologies used gave a different picture of yeast dynamics during the fermentation process. The results indicated that the fungal treatments can influence the yeast community of grapes leading must fermentation and the final composition of wine.

The effect of sulfur dioxide addition at crush on the fungal and bacterial communities and the sensory attributes of Pinot gris wines

Modern day winemaking often involves the addition of sulfur dioxide (SO₂) at crush to act as both an antioxidant and an antimicrobial agent. While the effects of SO₂ on microbial communities and particularly on spoilage microorganisms has been well-studied, the advent of culture-independent molecular technologies, such as Illumina sequencing, allows the subject to be re-visited in a new context. High-throughput amplicon sequencing allows for a more thorough evaluation of microbial communities, as thousands of microbial sequences per sample can be identified and even rare microorganisms can be studied. This research investigated whether the addition of different levels of SO₂ at crush (0, 20, or 40 mg/L) would affect the composition of fungal and bacterial communities, as well as the sensory attributes of the resulting wines. Samples were taken from uninoculated fermentations of Pinot gris and analyzed via high-throughput amplicon sequencing using the Illumina MiSeq platform. Yeast relative abundance and overall fungal community composition differed among the SO₂ additions. Notably, a Hanseniaspora yeast appeared in all treatments and persisted until the end of alcoholic fermentation, although its relative abundance was significantly higher in the fermentations to which low or no SO₂ had been added. Two key wine sensory attributes (citrus aroma and pome fruit flavor) differed among the SO₂ treatments. This research provides an in-depth look into the fungal and bacterial communities during alcoholic fermentation and gives a better understanding of the microbial community response to SO₂ additions during the crush period.