Inventory and monitoring of wine microbial consortia

The evolution of the wine microbial ecosystem is generally restricted to Saccharomyces cerevisiae and Oenococcus oeni, which are the two main agents in the transformation of grape must into wine by acting during alcoholic and malolactic fermentation, respectively. But others species like the yeast Brettanomyces bruxellensis and certain ropy strains of Pediococcus parvulus can spoil the wine. The aim of this study was to address the composition of the system more precisely, identifying other components. The advantages of the polymerase chain reaction-denaturing gradient gel electrophoresis (PCR-DGGE) approach to wine microbial ecology studies are illustrated by bacteria and yeast species identification and their monitoring at each stage of wine production. After direct DNA extraction, PCR-DGGE was used to make the most exhaustive possible inventory of bacteria and yeast species found in a wine environment. Phylogenetic neighbor-joining trees were built to illustrate microbial diversity. PCR-DGGE was also combined with population enumeration in selective media to monitor microbial changes at all stages of production. Moreover, enrichment media helped to detect the appearance of spoilage species. The genetic diversity of the wine microbial community and its dynamics during winemaking were also described. Most importantly, our study provides a better understanding of the complexity and diversity of the wine microbial consortium at all stages of the winemaking process: on grape berries, in must during fermentation, and in wine during aging. On grapes, 52 different yeast species and 40 bacteria could be identified. The diversity was dramatically reduced during winemaking then during aging. Yeast and lactic acid bacteria were also isolated from very old vintages. B. bruxellensis and O. oeni were the most frequent.     

Lactic acid bacteria associated with wine grapes from several Australian vineyards

AIMS: The detection and isolation of lactic acid bacteria by enrichment methods from wine grapes cultivated in vineyards located in New South Wales, Australia. METHODS AND RESULTS: Enrichment cultures in de Man, Rogosa and Sharpe (MRS) broth, MRS + ethanol (5%), MRS broth supplemented with 15% (v/v) tomato juice (MRST), pH 5.5 and 3.5 and autoenrichment in grape juice homogenate were used to detect lactic acid bacteria on wine grapes. Bacteria were isolated from enrichment cultures by plating onto MRS and MRST agar and identified by 16S rDNA sequence analysis and phenotypical methods. A molecular method, PCR-denaturing gradient gel electrophoresis (DGGE) was also used to examine the bacteria that developed in enrichment cultures. Species of Lactobacillus, Enterococcus, Lactococcus and Weissella were detected in enrichments by plating and PCR-DGGE. Other bacteria (Sporolactobacillus, Asaia, Bacillus ssp.) were also found in some enrichment cultures. The principal malolactic bacterium, Oenococcus oeni, was not isolated. CONCLUSIONS: The incidence and populations of lactic acid bacteria on wine grapes were very low. Damaged grape berries showed a greater presence of these bacteria than undamaged berries. The diversity of bacterial species isolated from the grapes was greater than those previously reported and represented both lactic acid bacteria and nonlactic acid bacteria. Some of these bacteria (i.e. Lactobacillus lindneri, Lactobacillus kunkeei) could be detrimental to wine production. Oenococcus oeni was not found on grapes, but its recovery could be obscured by overgrowth from other species. SIGNIFICANCE AND IMPACT OF THE STUDY: Lactic acid bacteria are significant in wine production because they conduct the malolactic fermentation and cause stuck or sluggish alcoholic fermentation and wine spoilage. This study investigates wine grapes as a potential source of these bacteria.     

Monitoring of Saccharomyces and Hanseniaspora populations during alcoholic fermentation by real-time quantitative PCR

Real-time, or quantitative, PCR (QPCR) was developed for the rapid quantification of two of the most important yeast groups in alcoholic fermentation (Saccharomyces spp. and Hanseniaspora spp.). Specific primers were designed from the region spanning the internal transcribed spacer 2 (ITS2) and the 5.8S rRNA gene. To confirm the specificity of these primers, they were tested with different yeast species, acetic acid bacteria and lactic acid bacteria. The designed primers only amplified for the intended group of species and none of the PCR assays was positive for any other wine microorganisms. This technique was performed on reference yeast strains from pure cultures and validated with both artificially contaminated wines and real wine fermentation samples. To determine the effectiveness of the technique, the QPCR results were compared with those obtained by plating. The design of new primers for other important wine yeast species will enable to monitor yeast diversity during industrial wine fermentation and to detect the main spoilage yeasts in wine.     

Spoilage of bottled red wine by acetic acid bacteria

AIMS: To determine the bacterial species associated with an outbreak of spoilage in commercially bottled red wine where the bottles had been stored in an upright vertical compared with horizontal position. METHODS AND RESULTS: Bottled wines comprising Cabernet Sauvignon, Pinot Noir, Shiraz, Merlot and blended red varieties were examined for visible spoilage. Analysis of visibly affected and non-affected wines revealed a spectrum of aroma and flavour defects, ranging from loss of fruity aroma, staleness, oxidized character to overt volatile acidity. Only acetic acid bacteria, and not yeast or lactic acid bacteria, could be isolated from both spoiled and unspoiled wines and were found to grow only on Wallerstein Nutrient (WL) medium supplemented with 10% red wine or 1-2% ethanol. Analysis of the 16S rRNA region and RAPD-PCR analysis showed the isolates to be a closely related group of Acetobacter pasteurianus, but this group was differentiated from the group comprising beer, vinegar and cider strains. CONCLUSIONS: A. pasteurianus was the species considered responsible for the spoilage but the isolates obtained had atypical properties for this species. In particular, they failed to grow on WL nutrient medium without ethanol or wine supplementation. Storage of the bottles of wine containing A. pasteurianus in an upright vertical position specifically induced growth and spoilage in a proportion of the bottles under conditions that were inhibitory for horizontally stored bottles. We hypothesize that the upright position created a heterogeneous environment that allowed the growth of bacteria in only those bottles sealed with cork closures that had upper limit for the natural permeability to oxygen. Such a heterogeneous environment would not exist in horizontally stored bottles as the larger volume of wine adjacent to the cork would strongly compete with the bacteria for the oxygen as it diffuses through the cork closure. SIGNIFICANCE AND IMPACT OF THE STUDY: A low level of bacteria (acetic acid bacteria) in wine can proliferate and cause wine spoilage in bottles stored in an upright vertical as opposed to an horizontal position under conditions that would normally limit bacterial development.     

Dynamics of lactic acid bacteria populations in Rioja wines by PCR-DGGE, comparison with culture-dependent methods

Lactic acid bacteria populations of red wine samples from industrial fermentations, including two different vinification methods were studied. For this investigation, polymerase chain reaction–denaturing gradient gel electrophoresis (PCR-DGGE) analysis was employed to supplement previous results that were obtained by culture-dependent methods. PCR-DGGE was aimed to study two targeted genes, 16S ribosomal DNA (rDNA) and rpoB, and the results were useful to evaluate the microbial populations in wine samples. Moreover, an improvement of a detection limit determined so far for DGGE analysis was obtained with the method described in this study, what made possible to identify lactic acid bacteria populations below 10¹ colony-forming unit/mL. The species Oenococcus oeni was the most frequently detected bacterium, but identifications close to species Oenococcus kitaharae and Lactococcus lactis that are not often found in wine were firstly identified in samples of this research. PCR-DGGE allowed to detect 9 out of 11 lactic acid bacteria species identified in this study (nine by PCR-16S rDNA/DGGE and four by PCR-rpoB/DGGE), while five species were detected using the modified de Man, Rogosa and Sharpe agar. Therefore, the two methods were demonstrated to be complementary. This finding suggests that analysis of the lactic acid bacteria population structure in wine should be carried out using both culture-dependent and culture-independent techniques with more than one primer pair.     

Occurrence of Lactic Acid Bacteria During the Different Stages of Vinification and Conservation of Wines

We showed that the growth of lactic acid bacteria during alcoholic fermentation depends on the composition of the must. We illustrated how the addition of sulfur dioxide to the must before fermentation and the temperature of storage both affect the growth of these bacteria in the wine. Whereas species of Lactobacillus and Leuconostoc mesenteroides were isolated from grapes and must, Leuconostoc oenos was the only species isolated after alcoholic fermentation. This organism was responsible for the malolactic fermentation. Isolates of this species varied in their ability to ferment pentoses and hexoses. The survival of Leuconostoc oenos in wines after malolactic fermentation depended on wine pH, alcohol concentration, SO₂ concentration, and temperature of storage.     

Which lactic acid bacteria are responsible for histamine production in wine?

AIMS: To quantify the ability of 136 lactic acid bacteria (LAB), isolated from wine, to produce histamine and to identify the bacteria responsible for histamine production in wine. METHODS AND RESULTS: A qualitative method based on pH changes in a plate assay was used to detect wine strains capable of producing high levels of histamine. Two quantitative, highly sensitive methods were used, an enzymatic method and HPLC, to quantify the histamine produced by LAB. Finally, an improved PCR test was carried out to detect the presence of histidine decarboxylase gene in these bacteria. The species exhibiting the highest frequency of histamine production is Oenococcus oeni. However, the concentration of histamine produced by this species is lower than that produced by strains belonging to species of Lactobacillus and Pediococcus. A correlation of 100% between presence of histidine decarboxylase gene and histamine production was observed. Wines containing histamine were analysed to isolate and characterize the LAB responsible for spoilage. CONCLUSIONS: Oenococcus was able to synthesize low concentrations of histamine in wines, while Pediococcus parvulus and Lactobacillus hilgardii have been detected as spoilage, high histamine-producing bacteria in wines. SIGNIFICANCE AND IMPACT OF THE STUDY: Information regarding histamine-producing LAB isolated from wines can contribute to prevent histamine formation during winemaking and storage.     

Antibacterial activity of wine phenolic compounds and oenological extracts against potential respiratory pathogens

Aims: To investigate the effect of seven wine phenolic compounds and six oenological phenolic extracts on the growth of pathogenic bacteria associated with respiratory diseases (Pseudomonas aeruginosa, Staphylococcus aureus, Moraxella catarrhalis, Enterococcus faecalis, Streptococcus sp Group F, Streptococcus agalactiae and Streptococcus pneumoniae). Methods and Results: Antimicrobial activity was determined using a microdilution method and quantified as IC₅₀. Mor. catarrhalis was the most susceptible specie to phenolic compounds and extracts. Gallic acid and ethyl gallate were the compounds that showed the greatest antimicrobial activity. Regarding phenolic extracts, GSE (grape seed extract) and GSE‐O (oligomeric‐rich fraction from GSE) were the ones that displayed the strongest antimicrobial effects. Conclusions: Results highlight the antimicrobial properties of wine phenolic compounds and oenological extracts against potential respiratory pathogens. The antimicrobial activity of wine phenolic compounds was influenced by the type of phenolic compounds. Gram‐negative bacteria were more susceptible than Gram‐positive bacteria to the action of phenolic compounds and extracts; however, the effect was species‐dependent. Significance and Impact of Study: The ability to inhibit the growth of respiratory pathogenic bacteria as shown by several wine phenolic compounds and oenological extracts warrants further investigations to explore the use of grape and wine preparations in oral hygiene.     

Evolution of Acetic Acid Bacteria During Fermentation and Storage of Wine

Acetic acid bacteria were present at all stages of wine making, from the mature grape through vinification to conservation. A succession of Gluconobacter oxydans, Acetobacter pasteurianus, and Acetobacter aceti during the course of these stages was noted. Low levels of A. aceti remained in the wine; they exhibited rapid proliferation on short exposure of the wine to air and caused significant increases in the concentration of acetic acid. Higher temperature of wine storage and higher wine pH favored the development and metabolism of these species.     

Design and Evaluation of PCR Primers for Analysis of Bacterial Populations in Wine by Denaturing Gradient Gel Electrophoresis

Denaturing gradient gel electrophoresis (DGGE) of PCR-amplified ribosomal DNA (rDNA) is routinely used to compare levels of diversity of microbial communities and to monitor population dynamics. While using PCR-DGGE to examine the bacteria in wine fermentations, we noted that several commonly used PCR primers for amplifying bacterial 16S rDNA also coamplified yeast, fungal, or plant DNA present in samples. Unfortunately, amplification of nonbacterial DNA can result in a masking of bacterial populations in DGGE profiles. To surmount this problem, we developed two new primer sets for specific amplification of bacterial 16S rDNA in wine fermentation samples without amplification of eukaryotic DNA. One primer set, termed WLAB1 and WLAB2, amplified lactic acid bacteria, while another, termed WBAC1 and WBAC2, amplified both lactic acid bacterial and acetic acid bacterial populations found in wine. Primer specificity and efficacy were examined with DNA isolated from numerous bacterial, yeast, and fungal species commonly found in wine and must samples. Importantly, both primer sets effectively distinguished bacterial species in wine containing mixtures of yeast and bacteria.     

Design and evaluation of PCR primers for analysis of bacterial populations in wine by denaturing gradient gel electrophoresis

Denaturing gradient gel electrophoresis (DGGE) of PCR-amplified ribosomal DNA (rDNA) is routinely used to compare levels of diversity of microbial communities and to monitor population dynamics. While using PCR-DGGE to examine the bacteria in wine fermentations, we noted that several commonly used PCR primers for amplifying bacterial 16S rDNA also coamplified yeast, fungal, or plant DNA present in samples. Unfortunately, amplification of nonbacterial DNA can result in a masking of bacterial populations in DGGE profiles. To surmount this problem, we developed two new primer sets for specific amplification of bacterial 16S rDNA in wine fermentation samples without amplification of eukaryotic DNA. One primer set, termed WLAB1 and WLAB2, amplified lactic acid bacteria, while another, termed WBAC1 and WBAC2, amplified both lactic acid bacterial and acetic acid bacterial populations found in wine. Primer specificity and efficacy were examined with DNA isolated from numerous bacterial, yeast, and fungal species commonly found in wine and must samples. Importantly, both primer sets effectively distinguished bacterial species in wine containing mixtures of yeast and bacteria.     

Studies on the Bacteria Found during the Process of Wine Making

Malic acid-decomposing bacteria were isolated from wine and their morphological and cytochemical properties were investigated. The results showed that the bacteria isolated were classified into three groups, Lactobacillus plantarum and two unknown bacteria belonging to a certain Lactobacillus species. One of the unknown bacteria fermented arabinose and ribose much faster than hexose. The other strain of the unknown bacteria required a certain factor(s) derived from tomato juice for its growth, and the best growth of the bacteria occurred on ribose containing medium supplied with the tomato juice factor(s).     

Lactic Acid Bacteria and Yeasts as Means of Decreasing Wine Acidity

Two hundred monocultures of lactic acid bacteria and 30 associations of yeasts and lactic acid bacteria have been studied. A stable association was developed which was capable of decreasing wine acidity. The association contained two species of bacteria, Leuconostoc oenosand Pediococcus pentosaceus, and the yeast Saccharomyces cerevisiae. The physiology of the microorganisms was studied, and their effects on the chemical composition of wines were determined.     

Characterization of the lytic activity of bacteriophages of Leuconostoc oenos isolated from wine

Two phage species (sl. ls and lco23) of Leuconostoc oenos , isolated in Switzerland and in Australia, were compared for their ability to inhibit growth of L. oenos in wine. The effect of pH, ethanol, SO₂, temperature and time of infection on phage activity was evaluated in synthetic media and in wine. The phages differed in their response to pH in that the activity of phage sl.ls was highest at low pH (3.5), while that of phage lco23 was highest at a high pH (5.5). The phages were not inhibited by low temperature (15°C) or by 50 mg/l SO_2. Both phages were inhibited by ethanol at a concentration greater than 5% (v/v). In a white and a red wine tested, the red wine partially inhibited and the white wine completely inhibited phage activity. When phage infection at pH 3.5 occurred during the exponential phase of growth, the bacteria outgrew the phage. Phage-resistant mutants developed between 3 and 35 d after phage infection, depending on pH and temperature. Recommendations for the use of starter cultures of L. oenos in the wine industry are given.     

Bacterial spoilage of wine and approaches to minimize it

Bacteria are part of the natural microbial ecosystem of wine and play an important role in winemaking by reducing wine acidity and contributing to aroma and flavour. Conversely, they can cause numerous unwelcome wine spoilage problems, which reduce wine quality and value. Lactic acid bacteria, especially Oenococcus oeni, contribute positively to wine sensory characters, but other species, such as Lactobacillus sp. and Pediococcus sp can produce undesirable volatile compounds. Consequences of bacterial wine spoilage include mousy taint, bitterness, geranium notes, volatile acidity, oily and slimy-texture, and overt buttery characters. Management of wine spoilage bacteria can be as simple as manipulating wine acidity or adding sulfur dioxide. However, to control the more recalcitrant bacteria, several other technologies can be explored including pulsed electric fields, ultrahigh pressure, ultrasound or UV irradiation, and natural products, including bacteriocins and lysozyme.     

Timing of malolactic fermentation inoculation in Shiraz grape must and wine: influence on chemical composition

Malolactic fermentation (MLF) is an integral step in red winemaking, which in addition to deacidifying wine can also influence the composition of volatile fermentation-derived compounds with concomitant affects on wine sensory properties. Long-established winemaking protocols for MLF induction generally involve inoculation of bacteria starter cultures post alcoholic fermentation, however, more recently there has been a trend to introduce bacteria earlier in the fermentation process. For the first time, this study shows the impact of bacterial inoculation on wine quality parameters that define red wine, including wine colour and phenolics, and volatile fermentation-derived compounds. This study investigates the effects of inoculating Shiraz grape must with malolactic bacteria at various stages of alcoholic fermentation [beginning of alcoholic fermentation (co-inoculation, with yeast), mid-alcoholic fermentation, at pressing and post alcoholic fermentation] on the kinetics of MLF and wine chemical composition. Co-inoculation greatly reduced the overall fermentation time by up to 6 weeks, the rate of alcoholic fermentation was not affected by the presence of bacteria and the fermentation-derived wine volatiles profile was distinct from wines produced where bacteria were inoculated late or post alcoholic fermentation. An overall slight decrease in wine colour density observed following MLF was not influenced by the MLF inoculation regime. However, there were differences in anthocyanin and pigmented polymer composition, with co-inoculation exhibiting the most distinct profile. Differences in yeast and bacteria metabolism at various stages in fermentation are proposed as the drivers for differences in volatile chemical composition. This study demonstrates, with an in-depth analysis, that co-inoculation of yeast and bacteria in wine fermentation results in shorter total vinification time and produces sound wines, thus providing the opportunity to stabilise wines more rapidly than traditional inoculation regimes permit and thereby reducing potential for microbial spoilage.     

Growth of yeasts, lactic and acetic acid bacteria in palm wine during tapping and fermentation from felled oil palm (Elaeis guineensis) in Ghana

AIM: To investigate the microbiological and biochemical changes which occur in palm wine during the tapping of felled oil palm trees. METHODS AND RESUlts: Microbiological and biochemical contents of palm wine were determined during the tapping of felled oil palm trees for 5 weeks and also during the storage. Saccharomyces cerevisiae dominated the yeast biota and was the only species isolated in the mature samples. Lactobacillus plantarum and Leuconostoc mesenteroides were the dominated lactic acid bacteria, whilst acetic acid bacteria were isolated only after the third day when levels of alcohol had become substantial. The pH, lactic and acetic acid concentrations during the tapping were among 3.5-4.0%, 0.1-0.3% and 0.2-0.4% respectively, whilst the alcohol contents of samples collected within the day were between 1.4% and 2.82%; palm wine which had accumulated over night, 3.24% to 4.75%; and palm wine held for 24 h, over 7.0%. CONCLUSION: Accumulation of alcohol in palm wine occurs in three stages during the tapping and marketing with the concurrent lactic and acetic acid fermentation taking place as well. SIGNIFICANCE AND IMPACT OF THE STUDY: Yeasts, lactic and acetic acid bacteria are all important in the fermentation of palm wine and influence the composition of the product.     

Expression analysis of putative arcA, arcB and arcC genes partially cloned from Lactobacillus plantarum isolated from wine

AIMS: The aim of this paper was to study if homofermentative strains (Lacobacillus plantarum) capable of malolactic fermentation in wine can degrade arginine via the ADI pathway. METHODS AND RESULTS: Homofermentative lactic acid bacteria (LAB) isolated from a typical red wine were investigated for their ability to produce citrulline. Citrulline was formed suggesting that the arginine metabolism takes place via the arginine deiminase (ADI) pathway and not via the arginase/urease pathway. Ammonia was also detected with Nessler's reagent, and all the strains examined were able to produce ammonia. Identification of homofermentative LAB was performed using 16S ribosomal sequence analysis. The strains were further classified as belonging to L. plantarum species. Furthermore, the genes encoding for the three pathway enzymes (ADI, ornithine transcarbamylase, carbamate kinase) were partially cloned and gene expression was performed at two different pH values (3.6 and 4.5). CONCLUSIONS: The results suggest that citrulline production in wine, could be performed by homofermentative LAB. SIGNIFICANCE AND IMPACT OF THE STUDY: Homofermentative malolactic bacteria (L. plantarum) may degrade arginine through the ADI pathway.     

Identification of lactic acid bacteria isolated from Portuguese wines and musts by SDS-PAGE

Thirty-two strains were isolated from spoiled port wines, from musts and from various styles of young, Northeastern Portuguese red table wines that had undergone spontaneous malolactic fermentation. Comparison of their SDS-PAGE whole-cell protein patterns with an SDS-PAGE database of lactic acid bacteria indicated that the isolates were members of the species Leuconostoc oenos or Lactobacillus paracasei subsp. paracasei. The latter were found in low acidity table wines and in port wine. The isolation of Lactobacillus paracasei strains from wines indicates the importance of using known strains for wine deacidification because spontaneous malolactic fermentation of table wines can occur from an indigenous flora, adapted to the particular composition of the wine.