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Oenococcus oeni is the main agent of malolactic fermentation in wine. This fermentation takes place after alcoholic fermentation, in a low nutrient medium where ethanol and other inhibitor compounds are present. In addition, some yeast-derived compounds such as mannoproteins can be stimulatory for O. oeni. The mannoprotein concentration in wine depends on the fermenting yeasts, and non-Saccharomyces in particular can increase it. As a result of the hydrolytic activity of O. oeni, these macromolecules can be degraded, and the released mannose can be taken up and used as an energy source by the bacterium. Here we look at mannoprotein consumption and the expression of four O. oeni genes related to mannose uptake (manA, manB, ptsI, and ptsH) in a wine-like medium supplemented with mannoproteins and in natural wines fermented with different yeasts. We observe a general gene upregulation in response to wine-like conditions and different consumption patterns in the studied media. O. oeni was able to consume mannoproteins in all the wines. This consumption was notably higher in natural wines, especially in T. delbrueckii and S. cerevisiae 3D wines, which presented the highest mannoprotein levels. Regardless of the general upregulation, it seems that mannoprotein degradation is more closely related to the fermenting 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.

Non-Saccharomyces yeasts have increasingly been used in vinification recently. This is particularly true of Torulaspora delbrueckii and Metschnikowia pulcherrima, which are inoculated before S. cerevisiae, to complete a sequential alcoholic fermentation. This paper aims to study the effects of these two non-Saccharomyces yeasts on malolactic fermentation (MLF) carried out by two strains of Oenococcus oeni, under cellar conditions. Oenological parameters, and volatile and phenolic compounds were analysed in wines. The wines were tasted, and the microorganisms identified. In general, non-Saccharomyces created more MLF friendly conditions, largely because of lower concentrations of SO2 and medium chain fatty acids. The most favourable results were observed in wines inoculated with T. delbrueckii, that seemed to promote the development of O. oeni and improve MLF performance.

The modification of adenosine to inosine at the first position of transfer RNA (tRNA) anticodons (I34) is widespread among bacteria and eukaryotes. In bacteria, the modification is found in tRNAArg and is catalyzed by tRNA adenosine deaminase A, a homodimeric enzyme. In eukaryotes, I34 is introduced in up to eight different tRNAs by the heterodimeric adenosine deaminase acting on tRNA. This substrate expansion significantly influenced the evolution of eukaryotic genomes in terms of codon usage and tRNA gene composition. However, the selective advantages driving this process remain unclear. Here, we have studied the evolution of I34, tRNA adenosine deaminase A, adenosine deaminase acting on tRNA, and their relevant codons in a large set of bacterial and eukaryotic species. We show that a functional expansion of I34 to tRNAs other than tRNAArg also occurred within bacteria, in a process likely initiated by the emergence of unmodified A34-containing tRNAs. In eukaryotes, we report on a large variability in the use of I34 in protists, in contrast to a more uniform presence in fungi, plans, and animals. Our data support that the eukaryotic expansion of I34-tRNAs was driven by the improvement brought by these tRNAs to the synthesis of proteins highly enriched in certain amino acids., This work was supported by the Spanish Ministry of Economy and Competitiveness (grant numbers BES2013-064551 to [A.R.-Y.], and BIO2015-64572 to [L.R.d.P.]).

The lactic acid bacterium Oenococcus oeni is the most important species involved in malolactic fermentation due to its capability to survive in presence of ethanol and in the acidic environment of wine. In order to identify novel genes involved in adaptation to wine, a new approach using genome-wide analysis based on stress-related genes was performed in strain O. oeni PSU-1, and 106 annotated stress genes were identified. The in silico analysis revealed the high similarity of all those genes through 57 O. oeni genomes; however, seven variable regions of genomic plasticity could be determined for their different presence observed among these strains. Regions 3 and 5 had the typical hallmarks of horizontal transfer, suggesting that the strategy of acquiring genes from other bacteria enhanced the fitness of O. oeni strains. Certain genes related to stress resistance were described in these regions, and similarities of putative acquired regions with other lactic acid bacteria species were found. Some genomic fragments present in all the strains were described and another new genomic island harbouring a threonine dehydrogenase was found. The association of selected sequences with adaptation to wine was assessed by screening 31 O. oeni strains using PCR of single genes, but no sequences were found to be exclusive to highly performing malolactic fermentation strains. This study provides new information about the genomic variability of O. oeni strains contributing to a further understanding of this species and the relationship of its genomic traits with the ability to adapt to stress conditions.

Oenococcus oeni, the lactic acid bacterium (LAB) mainly responsible for malolactic fermentation, has been repeatedly isolated from wines, but hardly ever from grapes. In this study, a large survey of autochthonous LAB from the Catalan wine region of Priorat was made. A total of 761 LAB isolates, 254 from Grenache and Carignan grape berries and 507 from wines, were identified and typed. Around 70% of the isolates were O. oeni, mostly from wines, but remarkably, 53 of them were isolated from grapes. A minimum spanning tree of O. oeni strains constructed from the multilocus variable number tandem repeat analysis showed considerable phylogenetic diversity. Other non-Oenococcus species were also identified and typed, Lactobacillus plantarum being predominant in grapes. Other LAB isolates were Pediococcus pentosaceus, Fructobacillus tropaeoli, L. mali, L. lindneri and L. sanfranciscensis. High-throughput sequencing (HTS) analysis was also carried out with grape samples, and Oenococcus and Lactobacillus were detected in significant quantities, which corroborates the culturing results from the same samples.

Interest in some non-Saccharomyces yeasts has increased recently, because they have been associated with an improvement in wine quality. Nevertheless, little attention has been paid to the effect that the use of these yeasts may have on malolactic fermentation (MLF). In this study, the strains Torulaspora delbrueckii Biodiva and Metschnikowia pulcherrima Flavia were evaluated by co-inoculation and sequential fermentation with S. cerevisiae QA23. A fermentation with S. cerevisiae as a single starter was also performed as a control, then MLF was performed inoculating Oenococcus oeni PSU-1 in all wines. Finally, the wines obtained after alcoholic fermentation and MLF were characterised. The results of the coinoculated fermentations were similar to those of the S. cerevisiae control fermentations. Nevertheless, significant differences were observed in sequential fermentations in terms of lower content of acetic, L-malic and succinic acids. These differences were particularly noticeable in fermentations carried out with T. delbrueckii.

The thioredoxin system protects against oxidative stress through the reversible oxidation of the thioredoxin active center dithiol to a disulphide. The genome of Oenococcus oeni PSU-1 contains three thioredoxin genes (trxA1, trxA2, trxA3), one thioredoxin reductase (trxB) and one ferredoxin reductase (fdr) which, until recently, was annotated as a second thioredoxin reductase. For the first time, the entire thioredoxin system in several O. oeni strains isolated from wine has been analysed. Comparisons at the DNA and protein levels have been undertaken between sequences from O. oeni and other genera and species, and the genera Leuconostoc and Lactobacillus were found to present the highest similarities. The gene most frequently absent from a collection of 34 strains and the sequences annotated in the NCBI database was trxA1. Moreover, phylogenetic analysis suggested that this gene was horizontally transferred from Lactobacillus to O. oeni. Strain-dependent expression profiles were determined in rich and in wine-like media. General over-expression was detected after inoculation into wine-like medium, with trxA3 being the most highly expressed gene. The increased transcriptional levels of the thioredoxin genes are indicative of the crucial role of this system in the O. oeni response to wine harsh conditions.

FIliació URV: SIInclòs a la memòria: SI Oenococcus oeni is the main species responsible for the malolactic fermentation (MLF) of wine due to its ability to survive in this environment. Some wine-related stress factors, such as ethanol and low pH, may alter the cell redox balance of O. oeni. For the first time, the ability to uptake glutathione (GSH), an almost universal tripeptide with antioxidant properties, has been associated to the improvement of stress response in O. oeni. Despite the inability of O. oeni to synthesize GSH, this bacterium can capture it from the media. The ability of 30 O. oeni strains to uptake GSH was assessed in this study. Although all of the strains tested were able to import GSH, substantial variability among them was detected. To assess the physiological function of GSH, three strains with different GSH-import capacities were selected. Significant changes in membrane fatty acids composition were observed due to GSH addition. The most relevant was the increase of cyclopropane fatty acids in cell membrane, in both the exponential and the stationary phases. Cells grown with GSH showed an improved survival against ethanol shock (14% v/v). GSH addition also increased biomass production during the adaptation to wine stress conditions (pH 4, pH 3.4 and 6% ethanol). The results suggest that GSH enrichment could improve the resistance to stress to O. oeni, which could be useful for the adaptation of MLF starter cultures.

Interest in using non-Saccharomyces yeasts in winemaking has increased in recent years due to their ability to improve wine quality. However, little information has been published regarding the possible effect on malolactic fermentation (MLF), carried out mostly by Oenococcus oeni. The aim of this paper is therefore to evaluate the effect of the most representative non-Saccharomyces species on O. oeni and wine MLF. Different strains of Torulaspora delbrueckii, Metschnikowia pulcherrima, Hanseniaspora uvarum, Hanseniaspora vineae and Starmerella bacillaris (syn. Candida zemplinina) were used in sequential alcoholic fermentation with Saccharomyces cerevisiae. The resulting wines were inoculated with four O. oeni strains. The action of non-Saccharomyces affected the final wine composition and the later role of O. oeni. Some of its strains could not perform MLF in H. uvarum wine due to high SO2 concentrations. In some cases, MLF was inhibited in wines inoculated with S. bacillaris. All the H. uvarum and H. vineae strains notably increased acetic acid concentrations, thus threatening wine quality. The best conditions for MLF were provided by some T. delbruecckii and M. pulcherrima strains, which showed increased concentrations of mannoproteins - compounds described as MLF activators -, no production of SO2, and low consumption of L-malic acid. In conclusion, non-Saccharomyces yeasts have diverse effects on O. oeni and MLF depending on the species, with T. delbrueckii and M. pulcherrima being those that showed the best compatibility with MLF development.

Fermentation processes have proceeded without microbiological control until starter cultures came up in 19th Century. However, in some processes, such as wine making a widespread use of starter cultures did not come up until the end of the 20th Century, when the cellar-friendly active dry wine yeast (ADWY) were available. However, this practice was challenged for the uniformity that brought a limited number of commercially available presentations and new tendencies in wine making have withdrawn the use of ADWY. The return to non-controlled wine fermentations may have considerable set backs especially in terms of economical losses, as these wines have much higher risks of presenting different levels of spoilage (presence of unwanted compounds that will be organoleptically detectable) that will not be acceptable for the consumer. The WILDWINE Project (EU contract 315065) proposed a system to overcome the criticism on the uniformity after use of ADWY by bringing “wild” microorganisms to the starter culture practice. The Project proposed mixed cultures as an alternative to single strain cultures that is the usual practice for starter cultures. This multi-strain and multi-species starter cultures aimed at reproducing the vineyard natural microbiota with the advantage of a selection of those strains and species that could add complexity to the final wines. The WILDWINE Project has focused the selection of this “wild” microorganism in 5 worldwide-recognised wine regions: Nemea and Crete (Greece), Piedmont (Italy), Bordeaux (France) and Priorat (Spain). The basic protocol was the same for all the regions: (i) to establish the natural biodiversity of the regions and determine the “microbial fingerprint” of the region, (ii) oenological screening of all the strains and species isolates to determine their quality for the wine making process and (iii) to use the microbial cocktails at pilot plants and in commercial cellars to determine the “microbial footprint” that the “wild” microorganisms leave on the final wines. In the Priorat region, a limited number of different strains from Saccharomyces cerevisiae were detected after sampling cellars and vineyards in two different harvests (2012 and 2013). These low number of S. cerevisiae strains is in sharp contrast with the high biodiversity observed in the same area 18 years before when a selection of strains of this species was preformed to provide a commercial “autochthonous” strain for the Priorat region. Furthermore, the main species found in the vineyards were the yeast-like fungus Aerobasidium pullulans and Hanseniaspora uvarum. A. pullulans disappeared when grapes were turned into must and then H. uvarum and Candida zemplinina were the main species. Minority species found in musts and later in wines were Metschnokowia pulcherrima and Torulaspora delbrueckii.

Trace amounts of the carcinogenic ethyl carbamate can appear in wine as a result of a reaction between ethanol and citrulline, which is produced from arginine degradation by some bacteria used in winemaking. In this study, arginine deiminase (ADI) pathway genes were evaluated in 44 Oenococcus oeni strains from wines originating from several locations in order to establish the relationship between the ability of a strain to degrade arginine and the presence of related genes. To detect the presence of arc genes of the ADI pathway in O. oeni, pairs of primers were designed to amplify arcA, arcB, arcC and arcD1 sequences. All strains contained these four genes. The same primers were used to confirm the organization of these genes in an arcABCD1 operon. Nevertheless, considerable variability in the ability to degrade arginine among these O. oeni strains was observed. Therefore, despite the presence of the arc genes in all strains, the expression patterns of individual genes must be strain dependent and influenced by the different wine conditions. Additionally, the presence of arc genes was also determined in the 57 sequenced strains of O. oeni available in GenBank, and the complete operon was found in 83 % of strains derived from wine. The other strains were found to lack the arcB, arcC and arcD genes, but all contained sequences homologous to arcA, and some of them had also ADI activity.

This work is a short review of the interactions between oenological yeasts and lactic acid bacteria (LAB), especially Oenococcus oeni, the main species carrying out the malolactic fermentation (MLF). The emphasis has been placed on non-Saccharomyces effects due to their recent increased interest in winemaking. Those interactions are variable, ranging from inhibitory, to neutral and stimulatory and are mediated by some known compounds, which will be discussed. One phenomena responsible of inhibitory interactions is the media exhaustion by yeasts, and particularly a decrease in L-malic acid by some non-Saccharomyces. Clearly ethanol is the main inhibitory compound of LAB produced by S. cerevisiae, but non-Saccharomyces can be used to decrease it. Sulfur dioxide and medium chain fatty acids (MCFAs) produced by yeasts can exhibit inhibitory effect upon LAB or even result lethal. Interestingly mixed fermentations with non-Saccharomyces present less MCFA concentration. Among organic acids derived as result of yeast metabolism, succinic acid seems to be the most related with MLF inhibition. Several protein factors produced by S. cerevisiae inhibiting O. oeni have been described, but they have not been studied in non-Saccharomyces. According to the stimulatory effects, the use of non-Saccharomyces can increase the concentration of favorable mediators such as citric acid, pyruvic acid, or other compounds derived of yeast autolysis such as peptides, glucans, or mannoproteins. The emergence of non-Saccharomyces in winemaking present a new scenario in which MLF has to take place. For this reason, new tools and approaches should be explored to better understand this new winemaking context., This work was supported by grant AGL2015-70378-R awarded by the Spanish Ministry of Economy and Competitiveness. The research leading to these results has received funding from “la Caixa” Foundation and Triptolemos Foundation. AiB was grateful to the predoctoral fellowship from the Universitat Rovira i Virgili.

International audience; The use of autochthonous strains of Oenococcus oeni for inducing malolactic fermentation (MLF) in wines is increasing because they are well adapted to the conditions of a specific area. The main aim of this work was to select O. oeni strains from Priorat (Catalonia, Spain) wines that would be able to carry out the MLF while maintaining the characteristics of the wine. Forty-five autochthonous strains were selected based on their degradation of L-malic acid, resistance to low pH and high ethanol, and the absence of biogenic amine genes. The three strains with the best characteristics were inoculated and MLF was carried out successfully with the final wines showing good characteristics. One of the inoculated O. oeni strains would be a good candidate to study as possible starter culture. It shows that autochthonous O. oeni strains, once selected, have the potential to be used as an inoculum for wines.

Filiació URV: SIInclòs a la memòria: SI Although Oenococcus oeni is the main species that is responsible for malolactic fermentation (MLF), harsh wine conditions can limit its performance. Although several mechanisms underlying the response to stress have been studied in this species, little is known regarding the cellular systems that protect against oxidative stress in other bacteria, such as glutathione (GSH). O. oeni cannot synthesize GSH but contains several genes related to its utilization. In this study, the relative expression (RE) of the seven genes involved in the GSH redox system found in O. oeni PSU-1 (gshR, gpo, three glutaredoxin-like genes and two subunits of an hypothetical transporter) has been measured. The study was performed using three strains, with each exhibiting a different GSH uptake capacity. The strains were grown in a stress-adaptation medium supplemented with 5 mM GSH and under different adaptation stress conditions (pH 4 and 6% ethanol). The RE showed that only some of these genes, including one for a possible glutaredoxin (OEOE_RS04215) and cydC for a subunit of a putative GSH transporter (OEOE_RS1995), responded to the addition of GSH. The presence of ethanol had a relevant effect on gene expression. Among the studied genes, the one for a NrdH-redoxin (OEOE_RS00645) showed a common response to ethanol in the strains, being over-expressed when grown with GSH. In most cases, the transcriptional changes were more evident for the strain with a higher capacity of GSH uptake. Malolactic performance of the three strains after pre-adaptation was evaluated in wine-like media (12% ethanol and pH 3.4). It was observed that the addition of GSH during pre-adaptation growth had a protective role in the cells exposed to low pH and ethanol, resulting in a

Table olives are one of the main fermented vegetables in the world. Olives can be processed as treated or natural. Both have to be fermented but treated green olives have to undergo an alkaline treatment before they are placed in brine to start their fermentation. It has been generally established that lactic acid bacteria (LAB) are responsible for the fermentation of treated olives. However, LAB and yeasts compete for the fermentation of natural olives. Yeasts play a minor role in some cases, contributing to the flavour and aroma of table olives and in LAB development. The main microbial genus isolated in table olives is Lactobacillus. Other genera of LAB have also been isolated but to a lesser extent. Lactobacillus plantarum and Lactobacillus pentosus are the predominant species in most fermentations. Factors influencing the correct development of fermentation and LAB, such as pH, temperature, the amount of NaCl, the polyphenol content or the availability of nutrients are also reviewed. Finally, current research topics on LAB from table olives are reviewed, such as using starters, methods of detection and identification of LAB, their production of bacteriocins, and the possibility of using table olives as probiotics.

Oenococcus oeni, the main lactic acid bacteria responsible for malolactic fermentation in wine, has to adapt to stressful conditions, such as low pH and high ethanol content. In this study, the changes in the transcriptome and the proteome of O. oeni PSU-1 during the adaptation period before MLF start have been studied. DNA microarrays were used for the transcriptomic analysis and two complementary proteomic techniques, 2-D DIGE and iTRAQ labeling were used to analyze the proteomic response. One of the most influenced functions in PSU-1 due to inoculation into wine-like medium (WLM) was translation, showing the over-expression of certain ribosomal genes and the corresponding proteins. Amino acid metabolism and transport was also altered and several peptidases were up regulated both at gene and protein level. Certain proteins involved in glutamine and glutamate metabolism showed an increased abundance revealing the key role of nitrogen uptake under stressful conditions. A strong transcriptional inhibition of carbohydrate metabolism related genes was observed. On the other hand, the transcriptional up-regulation of malate transport and citrate consumption was indicative of the use of L-malate and citrate associated to stress response and as an alternative energy source to sugar metabolism. Regarding the stress mechanisms, our results support the relevance of the thioredoxin and glutathione systems in the adaptation of O. oeni to wine related stress. Genes and proteins related to cell wall showed also significant changes indicating the relevance of the cell envelop as protective barrier to environmental stress. The differences found between transcriptomic and proteomic data suggested the relevance of post-transcriptional mechanisms and the complexity of the stress response in O. oeni adaptation. Further research should deepen into the metabolisms mostly altered due to wine conditions to elucidate the role of each mechanism in the O. oeni ability to develop MLF., This work was supported by grants AGL2009-07369ALI and AGL2012-34866ALI from the Spanish Ministry of Economy and Competitiveness. MM is grateful to the pre-doctoral fellowship from the Universitat Rovira i Virgili. JB wish to thank to the Spanish Government for his “Ayuda para la Formación Posdoctoral” research contract.

Epiphytic bacteria on grape berries play a critical role in grape health and quality, which decisively influence the winemaking process. Despite their importance, the bacteria related with grape berry surface remain understudied and most previous work has been based on culture-dependent methods, which offer a limited view of the actual diversity. Herein, we used high-throughput sequencing to investigate the bacterial diversity on the surface from two grape varieties, Grenache and Carignan, and compared them across five vineyards included within the Priorat region (Spain). We could detect up to 14 bacterial phyla with Firmicutes (37.6% Bacillales and 14% Lactobacillales), Proteobacteria (16.8% Pseudomonadales and 11.6% Enterobacteriales) and Actinobacteria (3.4% Actinomycetales) being the most abundant. Bacterial community was different at each vineyard being grape varietal, geographical situation and orientation related with changes in bacterial populations. The most abundant bacterial taxa and those driving differences between the vineyards and grape varietals were identified. This study indicates that bacterial community heterogeneities can be influenced by geographic factors like orientation.

The correct development of malolactic fermentation depends on the capacity of [i]Oenococcus oeni[/i] tosurvive under harsh wine conditions. The presence of ethanol is one of the most stressful factors affecting O. oeni performance. In this study, the effect of ethanol addition (12% vol/vol) on [i]O. oeni[/i] PSU-1 has been evaluated using a transcriptomic and proteomic approach. Transcriptomic analysis revealed that the main functional categories of the genes affected by ethanol were metabolite transport and cell wall and membrane biogenesis. It was also observed that some genes were over-expressed in response to ethanol stress (for example, the heat shock protein Hsp20 and a dipeptidase). Proteomic analysis showed that several proteins are affected by the presence of ethanol. Functions related to protein synthesis and stability are the main target of ethanol damage. In some cases the decrease in protein concentration could be due to the relocation of cytosolic proteins in the membrane, as a protective mechanism. The omic approach used to study the response of [i]O. oeni[/i] to ethanol highlights the importance of the cell membrane in the global stress response and opens the door to future studies on this issue.

The production of Arbequina naturally green olives is a traditional and spontaneous process in which lactic acid bacteria (LAB) and yeasts are present. To better control the fermentation of olives, strains of LAB and yeasts that had been isolated from brines were used in this study. A strain of Lactobacillus pentosus selected from an industrial olive fermentation was used as a starter culture for the traditional fermentation of Arbequina naturally green olives. Three more strains isolated from Arbequina olive brines were selected: one yeast, (Candida diddensiae), and two Lactobacillus (one L. plantarum and the other L. pentosus). The individual fermentation profile of all the strains and the co-inoculation profile of each one of the three with the first selected L. pentosus were studied in pilot-scale fermentations. The results showed that all the strains used as a starter, and particularly the yeast C. diddensiae, reduced the Enterobacteriaceae survival period in comparison with the spontaneous process. Only when a L. pentosus strain was inoculated were the LAB counts above 106 cfu ml−1 throughout the process. The C. diddensiae starter failed to colonize the brine until the end of the process and no LAB were detected. Results of rep-PCR using the primer GTG5 showed that both L. pentosus starters were able to colonize the brine by the end of the process but when they were co-inoculated only one strain was dominant. The L. plantarum starter failed to colonize the brine. In the control fermentation, various autochthonous strains of L. pentosus and L. plantarum were detected. The pH only reached desirable levels when a L. pentosus strain was inoculated. From the results of the sensory evaluation, panellists found significant differences between the different starters used for fermenting olives.