Oenococcus oeni preference for peptides: qualitative and quantitative analysis of nitrogen assimilation

The use of Torulaspora delbrueckii to improve malolactic fermentation

The potential use of Torulaspora delbrueckii as a starter culture for wine alcoholic fermentation has become a subject of interest in oenological research. The use of this non-Saccharomyces yeast can modulate different wine attributes, such as aromatic substances, organic acids and phenolic compound compositions. Thus, the obtained wines are different from those fermented with Saccharomyces cerevisiae as the sole starter. Nevertheless, information about the possible effects of T. delbrueckii chemical modulation on subsequent malolactic fermentation is still not fully explained. In general, T. delbrueckii is related to a decrease in toxic compounds that negatively affect Oenococcus oeni and an increase in others that are described as stimulating compounds. In this work, we aimed to compile the changes described in studies using T. delbrueckii in wine that can have a potential effect on O. oeni and highlight those works that directly evaluated O. oeni performance in T. delbrueckii fermented wines.

Comparative study of inoculation strategies of Torulaspora delbrueckii and Saccharomyces cerevisiae on the performance of alcoholic and malolactic fermentations in an optimized synthetic grape must

Progress in oenological biotechnology now makes it possible to control alcoholic (AF) and malolactic (MLF) fermentation processes for the production of wines. Key factors in controlling these processes and enhancing wine quality include the use of selected strains of non-Saccharomyces species, Saccharomyces cerevisiae, and Oenococcus oeni, as well as the method of inoculation (co-inoculation or sequential) and the timing of inoculation. In the present work, we investigated the effects of different inoculation strategies of two Torulaspora delbrueckii (Td-V and Td-P) strains followed by S. cerevisiae. Times (two, four, and six days) and types (co-inoculation and sequential) of inoculation were evaluated on the AF of a synthetic grape must. Furthermore, this synthetic medium was optimized by adding linoleic acid and β-sitosterol to simulate the natural grape must and facilitate reproducible results in potential assays. Subsequently, the wines obtained were inoculated with two strains of Oenococcus oeni to carry out MLF. Parameters after AF were analysed to observe the impact of wine composition on the MLF performance. The results showed that the optimization of the must through the addition of linoleic acid and β-sitosterol significantly enhanced MLF performance. This suggests that these lipids can positively impact the metabolism of O. oeni, leading to improved MLF efficiency. Furthermore, we observed that a 4-day contact period with T. delbrueckii leads to the most efficient MLF process and contributed to the modification of certain AF metabolites, such as the reduction of ethanol and acetic acid, as well as an increase in available nitrogen. The combination of Td-P with Oo-VP41 for 4 or 6 days during MLF showed that it could be the optimal option in terms of efficiency. By evaluating different T. delbrueckii inoculation strategies, optimizing the synthetic medium and studying the effects on wine composition, we aimed to gain insights into the relationship between AF conditions and subsequent MLF performance. Through this study, we aim to provide valuable insights for winemakers and researchers in the field of wine production and will contribute to a better understanding of the complex interactions between these species in the fermentation process.

Oenococcus oeni allows the increase of antihypertensive and antioxidant activities in apple cider

This study aimed to investigate the impact of the malolactic fermentation (MLF) carried out by Oenococcus oeni on antihypertensive and antioxidant activities in cider. The MLF was induced using three strains of O. oeni. The modification in phenolic compounds (PCs) and nitrogen organic compounds, antioxidant, and antihypertensive activities were determined after MLF. Among the 17 PCs analyzed caffeic acid was the most abundant compound and phloretin, (-)-epicatechin, and myricetin were detected only in malolactic ciders, however, (-)-epigallocatechin was not detected after MLF. The evaluation of nitrogen organic compounds revealed a drop in total protein concentration (from 17.58 to 14.00 mg N/L) concomitantly with a significant release of peptide nitrogen (from 0.31 to a maximum value of 0.80 mg N/L) after MLF. In addition, an extracellular proteolytic activity was evidenced in all MLF supernatants. The FRAP activity increased reaching a maximum of 120.9 μmol FeSO₄/mL and the ABTS radical-scavenging activity increased until 6.8 mmol ascorbic acid/L. Moreover, the angiotensin I-converting enzyme inhibitory activity reached a maximum value of 39.8%. The MLF conducted by O. oeni in ciders enables the increase of interesting biological activities and this finding could constitute a valuable tool to add value to final product.

Simulated lees of different yeast species modify the performance of malolactic fermentation by Oenococcus oeni in wine-like medium

The use of non-Saccharomyces yeast together with S. cerevisiae in winemaking is a current trend. Apart from the organoleptic modulation of the wine, the composition of the resulting yeast lees is different and may thus impact malolactic fermentation (MLF). Yeasts of Saccharomyces cerevisiae, Torulaspora delbrueckii and Metschnikowia pulcherrima were inactivated and added to a synthetic wine. Three different strains of Oenococcus oeni were inoculated and MLF was monitored. Non-Saccharomyces lees, especially from some strains of T. delbrueckii, showed higher compatibility with some O. oeni strains, with a shorter MLF and a maintained bacterial cell viability. The supplementation of lees increased nitrogen compounds available by O. oeni. A lower mannoprotein consumption was related with longer MLF. Amino acid assimilation by O. oeni was strain specific. There may be many other compounds regulating these yeast lees-O. oeni interactions apart from the well-known mannoproteins and amino acids. This is the first study of MLF with different O. oeni strains in the presence of S. cerevisiae and non-Saccharomyces yeast lees to report a strain-specific interaction between them.

Transcriptional and Metabolic Response of Wine-Related Lactiplantibacillus plantarum to Different Conditions of Aeration and Nitrogen Availability

Lactic acid bacteria (LAB) perform the process of malolactic fermentation (MLF) in wine. Availability of oxygen and nitrogen nutrients could influence LAB growth, malolactic activity, and other metabolic pathways, impacting the subsequent wine quality. The impact of these two factors has received limited investigation within LAB, especially on a transcriptome level. The aim of this study was to evaluate metabolic changes in the strain Lactiplantibacillus plantarum IWBT B063, growing in synthetic grape juice medium (GJM) under different oxygen exposure conditions, and with low availability of nitrogen-based nutrients. Next-generation sequencing was used to analyze expression across the transcriptome (RNA-seq), in combination with conventional microbiological and chemical analysis. L. plantarum consumed the malic acid present in all the conditions evaluated, with a slight delay and impaired growth for nitrogen limitation and for anaerobiosis. Comparison of L. plantarum transcriptome during growth in GJM with and without O2 revealed differential expression of 148 functionally annotated genes, which were mostly involved in carbohydrate metabolism, genetic information processing, and signaling and cellular processes. In particular, genes with a protective role against oxidative stress and genes related to amino acid metabolism were differentially expressed. This study confirms the suitability of L. plantarum IWBT B063 to carry out MLF in different environmental conditions due to its potential adaption to the stress conditions tested and provides a better understanding of the genetic background of an industrially relevant strain.

Analytical combinations to evaluate the macromolecular composition of extracellular substances (ECS) from Lactobacillus plantarum cell culture media

Sugar-enriched media are used to produce extracellular substances (ECS) by Lactobacillus plantarum WCSF1, with a focus on growing stages and carbon source substrates. Combination of size exclusion chromatography and ATR-FTIR spectroscopy provides physicochemical patterns of bulk ECS produced along culture growing time. Secreted biopolymers present polydisperse and high molecular weight distributions, with significant amounts of carbohydrates and proteins. Results, supported by a multivariate statistical analysis, enable to differentiate the macromolecular content of bacterial ECS along the growing stages regardless of the growing media, highlighting a higher production of proteinaceous materials compared to polysaccharides. At the end of the exponential phase, common exoproteins were present in all the tested sugar-enriched media such as transglycosylases between 20 and 35 kDa, a muropeptidase at 36.9 kDa and a cell wall hydrolase. Additionally, L. plantarum WCFS1 secretes ECS with a greater diversity of proteins, when growing in the sucrose-enriched media. Graphical abstract.

The microbial challenge of winemaking: yeast-bacteria compatibility

The diversity and complexity of wine environments present challenges for predicting success of fermentation. In particular, compatibility between yeast and lactic acid bacteria is affected by chemical and physical parameters that are strain and cultivar specific. This review focuses on the impact of compound production by microbes and physical interactions between microbes that ultimately influence how yeast and bacteria may work together during fermentation. This review also highlights the importance of understanding microbial interactions for yeast-bacteria compatibility in the wine context.

Genome-Scale Reconstruction of the Metabolic Network in Oenococcus oeni to Assess Wine Malolactic Fermentation

Oenococcus oeni is the main responsible agent for malolactic fermentation in wine, an unpredictable and erratic process in winemaking. To address this, we have constructed and exhaustively curated the first genome-scale metabolic model of Oenococcus oeni, comprising 660 reactions, 536 metabolites and 454 genes. In silico experiments revealed that nutritional requirements are predicted with an accuracy of 93%, while 14 amino acids were found to be essential for the growth of this bacterial species. When the model was applied to determine the non-growth associated maintenance, results showed that O. oeni grown at 12% ethanol concentration spent 30 times more ATP to stay alive than in the absence of ethanol. Most of this ATP is employed for extruding protons outside of the cell. A positive relationship was also found between specific consumption rates of fructose, amino acids, oxygen, and malic acid and the specific production rates of erythritol, lactate, and acetate, according to the ethanol content of the medium. The metabolic model reconstructed here represents a unique tool to predict the successful completion of wine malolactic fermentation carried out either by different strains of Oenococcus oeni, as well as at any particular physico-chemical composition of wine. It will also allow the development of consortium metabolic models that could be applied to winemaking to simulate and understand the interactions between O. oeni and other microorganisms that share this ecological niche.

Wine microbiome: A dynamic world of microbial interactions

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

Impact of inhibitory peptides released by Saccharomyces cerevisiae BDX on the malolactic fermentation performed by Oenococcus oeni Vitilactic F

A previous study has shown that the malolactic fermentation (MLF) was inhibited during sequential fermentations performed with the pair Saccharomyces cerevisiae BDX/Oenococcus oeni Vitilactic F in synthetic grape juices. A yeast peptidic fraction with an apparent MW of 5-10kDa was involved in the inhibition. In the present study, the MLF was also inhibited in Cabernet Sauvignon and Syrah wines. The inhibition due to the peptidic fraction was maintained despite high phenolic contents. Kinetic studies showed that the peptidic fraction was gradually released during the alcoholic fermentation (AF). Its highest anti-MLF effect was reached when isolated from late stages of the AF stationary phase. The peptidic fraction was tested in vitro on cell-free bacterial cytosolic extracts containing the malolactic enzyme in a pH range between 3.5 and 6.7. Results showed that it was able to directly inhibit the malolactic enzyme activity with an increasing inhibitory kinetic correlated to the AF time at which it was collected.

Consensus pan-genome assembly of the specialised wine bacterium Oenococcus oeni

Background

Oenococcus oeni is a lactic acid bacterium that is specialised for growth in the ecological niche of wine, where it is noted for its ability to perform the secondary, malolactic fermentation that is often required for many types of wine. Expanding the understanding of strain-dependent genetic variations in its small and streamlined genome is important for realising its full potential in industrial fermentation processes.

Results

Whole genome comparison was performed on 191 strains of O. oeni; from this rich source of genomic information consensus pan-genome assemblies of the invariant (core) and variable (flexible) regions of this organism were established. Genetic variation in amino acid biosynthesis and sugar transport and utilisation was found to be common between strains. Furthermore, we characterised previously-unreported intra-specific genetic variations in the natural competence of this microbe.

Conclusion

By assembling a consensus pan-genome from a large number of strains, this study provides a tool for researchers to readily compare protein-coding genes across strains and infer functional relationships between genes in conserved syntenic regions. This establishes a foundation for further genetic, and thus phenotypic, research of this industrially-important species.

Electronic supplementary material

The online version of this article (doi:10.1186/s12864-016-2604-7) contains supplementary material, which is available to authorized users.

A mathematical model of the link between growth and L-malic acid consumption for five strains of Oenococcus oeni

In winemaking, after the alcoholic fermentation of red wines and some white wines, L-malic acid must be converted into L-lactic acid to reduce the acidity. This malolactic fermentation (MLF) is usually carried out by the lactic acid bacteria Oenococcus oeni. Depending on the level of process control, selected O. oeni is inoculated or the natural microbiota of the cellar is used. This study considers the link between growth and MLF for five strains of O. oeni species. The kinetics of growth and L-malic acid consumption were followed in modified MRS medium (20 °C, pH 3.5, and 10 % ethanol) in anaerobic conditions. A large variability was found among the strains for both their growth and their consumption of L-malic acid. There was no direct link between biomass productivities and consumption of L-malic acid among strains but there was a link of proportionality between the specific growth of a strain and its specific consumption of L-malic acid. Experiments with and without malic acid clearly demonstrated that malic acid consumption improved the growth of strains. This link was quantified by a mathematical model comparing the intrinsic malic acid consumption capacity of the strains.

A partial proteome reference map of the wine lactic acid bacterium Oenococcus oeni ATCC BAA-1163

Oenococcus oeni is the main lactic acid bacterium that carries out the malolactic fermentation in virtually all red wines and in some white and sparkling wines. Oenococcus oeni possesses an array of metabolic activities that can modify the taste and aromatic properties of wine. There is, therefore, industrial interest in the proteins involved in these metabolic pathways and related transport systems of this bacterium. In this work, we report the characterization of the O. oeni ATCC BAA-1163 proteome. Total and membrane protein preparations from O. oeni were standardized and analysed by two-dimensional gel electrophoresis. Using tandem mass spectrometry, we identified 224 different spots corresponding to 152 unique proteins, which have been classified by their putative function and subjected to bioinformatics analysis.

Increase in antioxidant and antihypertensive peptides from Argentinean wines by Oenococcus oeni

Cells from an exponential Oenococcus oeni m1 culture in a grape juice medium were inoculated into a synthetic wine medium (SW) supplemented with a protein and polypeptide fraction (PPF) of high molecular weight (higher than 12,400 Da) obtained from four varietals of Cafayate Argentinean wines. O. oeni maintains viability after 48 h incubation time and enables the increase in extracellular proteolytic activity and the release of low molecular weight peptides by 1.067, 0.397, 0.915 and 0.705 mg N/L in the respective SW supplemented with PPF from Cabernet Sauvignon, Malbec, Tannat and Torrontés wine varietals. After 48 h incubation time, concomitantly with peptide release, an increase in antioxidant and antihypertensive activities was detected in all studied media. The highest increase was detected in the presence of PPF from Cabernet and Tannat wine varietals. Maximum increase in antioxidant activity (366.1 μmol FeSO4/L in the case of ferric reducing antioxidant power and 8.9% in 2,2-diphenyl-1-picrylhydrazyl radical scavenging) was produced by the peptides released from PPF of Cabernet Sauvignon wine. The peptides released from PPF Tannat wine varietal caused the highest increase in antihypertensive activity (56.2% in angiotensin I-converting enzyme inhibitory activity). Oenococcus oeni m1 would provide additional benefits to wine such as an increase in bioactive peptides with multifunctional beneficial activities.

Wine features related to safety and consumer health: an integrated perspective

This review presents a global view of the current situation of the scientific knowledge about aspects of wine with possible repercussions (positive or negative) on consumer health and wine safety. The presence in wine of some potential harmful compounds such as phytosanitary products, trace metal compounds, sulfites, and some toxics of microbial origin, such as ochratoxin A, ethyl carbamate, and biogenic amines, is discussed. The different strategies and alternative methodologies that are being carried out to reduce or to avoid the presence of these substances in wines are also discussed. In recent years much work has focused on establishing the scientific explanations for the positive biological effects of some wine compounds. In this review, we also examine the latest knowledge regarding wine and health, focusing on two types of compounds that have been related to the positive effects of moderate wine consumption, such as phenolic compounds and bioactive peptides.

Role of specific components from commercial inactive dry yeast winemaking preparations on the growth of wine lactic acid bacteria

The role of specific components from inactive dry yeast preparations widely used in winemaking on the growth of three representative wine lactic acid bacteria (Oenococcus oeni, Lactobacillus hilgardii and Pediococcus pentosaceus) has been studied. A pressure liquid extraction technique using solvents of different polarity was employed to obtain extracts with different chemical composition from the inactive dry yeast preparations. Each of the extracts was assayed against the three lactic acid bacteria. Important differences in the effect of the extracts on the growth of the bacteria were observed, which depended on the solvent employed during the extraction, on the type of commercial preparations and on the lactic acid bacteria species. The extracts that exhibited the most different activity were chemically characterized in amino acids, free monosaccharides, monosaccharides from polysaccharides, fatty acids and volatile compounds. In general, specific amino acids and monosaccharides were related to a stimulating effect whereas fatty acid composition and likely some volatile compounds seemed to show an inhibitory effect on the growth of the lactic acid bacteria. These results may provide novel and useful information in trying to obtain better and more specific formulations of winemaking inactive dry yeast preparations.

Peptidases specific for proline-containing peptides and their unusual peptide-dependent regulation in Oenococcus oeni

AIMS

Growth of the lactic acid bacterium (LAB) Oenococcus oeni, which is involved in malolactic fermentation during the winemaking process, is stimulated by peptides originating from yeast. In this study, we investigated the impact of peptides on O. oeni growth, peptidase activity and the expression of genes encoding the studied peptidases.

METHODS AND RESULTS

Low levels of PepN activity and very high levels of PepI activity were observed in O. oeni, whereas levels of PepX activity were intermediate. The level of biosynthesis of these O. oeni peptidases was shown to depend on peptides present in the culture medium. These results were confirmed by transcriptional analyses of putative pep genes. The mechanism of repression by peptides did not involve a CodY-like regulator.

CONCLUSIONS

Peptides from yeast decrease the levels of enzymatic activity and relative gene expression of O. oeni peptidases. Peptidases specific for proline-containing peptides are important for O. oeni nitrogen metabolism.

SIGNIFICANCE AND IMPACT OF THE STUDY

We report here for the first time that the enzymes involved in the assimilation of proline-containing peptides by O. oeni differ from the well-described proteolytic system of milk LAB. This may reflect a specific adaptation to the wine environment.

Interaction between Oenococcus oeni and Lactobacillus hilgardii isolated from wine. Modification of available nitrogen and biogenic amine production

During the mixed culture of Lactobacillus hilgardii 5w, a common spoilage wine bacteria and Oenococcus oeni X(2)L, an amensalistic growth response of the malolactic bacteria was produced due to a competition for nitrogenous nutrients, mainly peptides. Arginine was fully consumed and peptide concentration diminished 60% with respect to both pure cultures at the end of exponential growth. Histamine release increased 34% with respect to L. hilgardii single culture. Under the poor nutritional conditions present during winemaking, L. hilgardii could increase histamine production and adversely affect malolactic fermentation conducted by O. oeni and hence the quality of the final product.

Determination of the essential nutrient requirements of wine-related bacteria from the genera Oenococcus and Lactobacillus

Wine lactic acid bacteria (LAB) are responsible for the malolactic fermentation (MLF) in wine production. Wine LAB have fastidious nutrient requirements but their auxotrophies remain little studied. The ability of specific wine nutrients to meet the nutritional requirements of wine LAB, and thus support MLF, remains unclear. This work investigated the essential growth requirements of four strains of wine LAB from the genera Oenococcus and Lactobacillus using the single omission technique with a suitable chemically defined medium. For the determination of auxotrophies, at least 3 (and up to 15) subcultures in deficient media were made, and intra- and extracellular nutrient carry over was reduced by small inoculation rates and washing cells 3 times between transfers. This careful methodology revealed more auxotrophies than those described for wine LAB in the literature. The essential bacterial nutrient requirements were found to be strain specific. 10 compounds were essential for all wine LAB tested, the carbon and phosphate source, manganese, as well as several amino acids (proline, arginine and the branched amino acids valine, leucine and isoleucine) and vitamins (nicotinic acid and pantothenic acids). Nucleotides were not essential for any of the bacteria studied. The two Oenococcus oeni strains revealed a larger number of auxotrophies (18 and 21) and had a higher degree of nutritional similarity (86%) defined as percentage of common requirements per maximum total requirements. The two Lactobacillus strains only had 11 and 14 auxotrophies and the similarity was 79%, but both were auxotroph for riboflavin, which was not needed by the O. oeni strains. Data on the common requirements may be used to further study the ability of wines or commercial nutrients to support MLF and to consider the microbiological stability of finished wines. The results indicate that absence of riboflavin in oenological nutrient preparations may allow to create a specific advantage for indigenous or inoculated O. oeni, which are generally desired for MLF.

Quantitative study of interactions between Saccharomyces cerevisiae and Oenococcus oeni strains

This study examines the interactions that occur between Saccharomyces cerevisiae and Oenococcus oeni strains during the process of winemaking. Various yeast/bacteria pairs were studied by applying a sequential fermentation strategy which simulated the natural winemaking process. First, four yeast strains were tested in the presence of one bacterial strain leading to the inhibition of the bacterial component. The extent of inhibition varied widely from one pair to another and closely depended on the specific yeast strain chosen. Inhibition was correlated to weak bacterial growth rather than a reduction in the bacterial malolactic activity. Three of the four yeast strains were then grown with another bacteria strain. Contrary to the first results, this led to the bacterial stimulation, thus highlighting the importance of the bacteria strain. The biochemical profile of the four yeast fermented media exhibited slight variations in ethanol, SO(2) and fatty acids produced as well as assimilable consumed nitrogen. These parameters were not the only factors responsible for the malolactic fermentation inhibition observed with the first bacteria strain. The stimulation of the second has not been reported before in such conditions and remains unexplained.

Oligopeptide assimilation and transport by Oenococcus oeni

AIMS

Oenococcus oeni is a slow-growing wine bacterium with a low growth yield. It thrives better on complex nitrogen sources than on free amino-acid medium. We aimed to characterize the oligopeptide use of this micro-organism.

METHODS AND RESULTS

Several peptides of two to eight amino-acid residues were able to provide essential amino acids. The disappearance of various peptides from extracellular medium was assessed with whole cells. Initial rates of utilization varied with the peptide, and free amino acids were released into the medium.

CONCLUSIONS

Oenococcus oeni was able to transport the oligopeptides with two to five amino-acid residues tested and to hydrolyse them further.

SIGNIFICANCE AND IMPACT OF THE STUDY

This study has clear implications for the relationship between wine nitrogen composition and the ability of O. oeni to cope with its environment.

Effects of yeast proteolytic activity on Oenococcus oeni and malolactic fermentation

Alcoholic fermentation of synthetic must was performed using either Saccharomyces cerevisiae or a mutant Deltapep4, which is deleted for the proteinase A gene. Fermentation with the mutant Deltapep4 resulted in 61% lower levels of free amino acids, and in 62% lower peptide concentrations at the end of alcoholic fermentation than in the control. Qualitative differences in amino acid composition were observed. Changes observed in amino acids in peptides were mainly quantitative. After alcoholic fermentation, each medium was inoculated with Oenococcus oeni. Malolactic fermentation in the medium with the Deltapep4 strain took 10 days longer than the control. This difference may have been due to a difference in the nitrogen composition of the two media. Free amino acids and amino acids in peptides were poorly consumed by O. oeni. Thus, the qualitative aspects of nitrogen composition, which depend in part on yeast metabolism, may be a determinant for the optimal growth of O. oeni in wine.