Microbial biochemistry

Bioinformational trends in grape and wine biotechnology

The creative destruction caused by the coronavirus pandemic is yielding immense opportunity for collaborative innovation networks. The confluence of biosciences, information sciences, and the engineering of biology, is unveiling promising bioinformational futures for a vibrant and sustainable bioeconomy. Bioinformational engineering, underpinned by DNA reading, writing, and editing technologies, has become a beacon of opportunity in a world paralysed by uncertainty. This article draws on lessons from the current pandemic and previous agricultural blights, and explores bioinformational research directions aimed at future-proofing the grape and wine industry against biological shocks from global blights and climate change.

Lemon juice and apple juice used as source of citrate and malate, respectively, enhance the formation of buttery aroma compounds and/or organic acids during Type 2 and Type 3 sourdough productions performed with Companilactobacillus crustorum LMG 23699

Extra ingredients are often used in traditional sourdough production recipes by artisan bakeries. These ingredients may be the source of microorganisms or stimulate the growth and/or the metabolic activities of the microorganisms added to or naturally present in the flour-water mixture. The present study examined the influence of the addition of lemon juice or apple juice as source of citrate or malate, respectively, on the growth and activity of the citrate- and malate-positive Companilactobacillus crustorum LMG 23699 strain (formerly known as Lactobacillus crustorum LMG 23699), used to initiate firm (dough yield of 200) wheat sourdough productions, and on the flavour of the baked goods produced. Three fermentation strategies were applied, namely one-step long fermentation sourdough production processes with the addition of juice at the start (Type 2) and backslopped fermentations with the addition of juice either only at the start of the sourdough productions or at the start of the sourdough productions and at the beginning of each subsequent refreshment step during the whole backslopping process (both Type 3). It turned out that the starter culture strain used prevailed during all sourdough productions performed. Yeasts were particularly present in Type 3 sourdough productions, although lemon juice retarded their growth. Due to high yeast activity, high concentrations of ethanol and glycerol were produced toward the end of the sourdough productions. Addition of lemon juice stimulated the production of lactic acid, acetic acid, and the buttery flavour compounds acetoin and diacetyl, because of citrate conversion, during the Type 2 and Type 3 sourdough productions. In Type 3 sourdough productions, these compounds were found in higher concentrations only when lemon juice was added at each backslopping step. Alternatively, the addition of apple juice led to high concentrations of lactic acid because of malolactic fermentation in both Type 2 and Type 3 sourdough productions. Moreover, the addition of apple juice increased the initial concentrations of the carbohydrates (fructose, glucose, and sucrose) and sugar alcohols (mannitol and sorbitol), which were exhausted upon backslopping or accumulated in the sourdough matrix, respectively. Baked goods produced using sourdoughs obtained from the Type 2 and Type 3 sourdough productions with the addition of juice at each backslopping step were significantly different in flavour from doughs supplemented with the respective juices and lactic acid and/or Type 3 sourdough productions with the addition of juice only at the start.

Evaluation of five commercial non-Saccharomyces yeasts in fermentation of soy (tofu) whey into an alcoholic beverage

Soy (tofu) whey is a nutritious liquid substrate that is often discarded by tofu manufacturers. Recent research has shown that tofu whey can be converted into a soy alcoholic beverage using Saccharomyces yeasts. In this study, five commercially available non-Saccharomyces yeasts (Torulaspora delbrueckii; Lachancea thermotolerans; Metschnikowia pulcherrima; Pichia kluyveri and Williopsis saturnus) were evaluated in tofu whey fermentation and each of the yeasts showed different growth kinetics and fermentation performance. T. delbrueckii and L. thermotolerans consumed the supplemented sucrose and produced 6-7% (v/v) ethanol, while M. pulcherrima, P. kluyveri and W. saturnus only utilized the endogenous fructose and glucose, producing trace levels of ethanol. Besides, different yeasts showed different β-glucosidase activities with 22-97% reduction in isoflavone glucosides; T. delbrueckii, L. thermotolerans and W. saturnus also decreased the level of GABA in tofu whey. Endogenous volatile compounds (mainly short-chain aldehydes) in tofu whey were reduced to trace levels, but different volatile compounds were produced by different yeasts at varying levels that can contribute to the different aroma profiles of the beverages. Therefore, selection of appropriate non-Saccharomyces yeasts can serve as a new strategy to valorize tofu whey and alter the aroma profile of the beverage.

Metabolism of SO₂ binding compounds by Oenococcus oeni during and after malolactic fermentation in white wine

Sulfur dioxide SO₂ is the key additive for the preservation of wines. Carbonyl and keto compounds in wine can bind to SO₂ and decrease its efficacy, resulting in higher total SO₂ requirements. Increased consumer demand for low sulfite and organic wines pose production challenges if SO₂ binders have not been properly managed during vinification. Malolactic fermentation (MLF) has been known to reduce bound SO₂ levels but detailed time course studies are not available. In this work, the kinetics of major SO₂ binding compounds and malic acid were followed during MLF in wine with 12 commercially available strains of Oenococcus oeni. Pyruvic acid, acetaldehyde and α-ketoglutaric acid were degraded to various degrees by O. oeni, but galacturonic acid was not. At the time of malic acid depletion, percent degradation of pyruvate, α-ketoglutaric acid and acetaldehyde was 49%, 14% and 30%, respectively. During MLF, the decrease in average bound SO₂ levels, as calculated from carbonyl metabolism, was 22%. The largest reduction in wine carbonyl content occurred in the week after completion of MLF and was 53% (107 mg/L to 34 mg/L) calculated as bound SO₂. Prolonged activity of bacteria in the wines (up to 3 weeks post malic acid depletion) resulted only in reduced additional reductions in bound SO₂ levels. The results suggest that microbiological wine stabilization one week after malic acid depletion is an effective strategy for maximum removal of SO₂ binders while reducing the risk of possible post-ML spoilage by O. oeni leading to the production acetic acid and biogenic amines.

Characterization of fermentative behaviors of lactic acid bacteria in grape wines through 1H NMR- and GC-based metabolic profiling

The effects of five commercial Oenococcus oeni strains (MCW, Enoferm alpha, Wyeast, Vinibacti111, and Vinibacti222) on fermentative behaviors, and variations of metabolites in Meoru ( Vitis coigneties ) wines during malolactic fermentation (MLF) were investigated by metabolomic analysis of (1)H NMR and GC data sets. In the development of MLF with various O. oeni strains, the fastest conversions of malic acid to lactic acid occurred in wines fermented with Enoferm alpha and Vinibacti111 strains. Seventeen primary metabolites and 65 secondary metabolites of volatile compounds in the wines were identified by (1)H NMR spectroscopy and GC-MS, respectively. In pattern recognition models of principal component analysis (PCA) and orthogonal projection to latent structures discriminant analysis (OPLS-DA), significant differentiations between wines with O. oeni strains were identified by the secondary metabolites rather than by the primary metabolites, showing the effects of O. oeni strains only on the secondary metabolites. Twelve volatile compounds, 2-phenylethanol, isoamyl alcohol, 2-butanol, ethyl octanoate, ethyl hexanoate, hexadecanoic acid, diethyl succinate, butyl butyrate, octanoic acid, 9-hexadecanoic acid, isobutyric acid, and 2-ethyl-1-hexanol, contributed to the differentiation of wines according to O. oeni strain, including spontaneous MLF. This study demonstrates that O. oeni strains affect the secondary metabolites, which are easily identified through multivariate statistical analysis of GC-MS data set.

Changes in the concentration of yeast-derived volatile compounds of red wine during malolactic fermentation with four commercial starter cultures of Oenococcus oeni

The effects of malolactic fermentation (MLF) on the concentration of volatile compounds released by yeasts during the production of red wine were investigated by inoculation with four commercial starters of Oenococcus oeni. Volatile compounds in wine at the end of MLF were extracted, analyzed by GC-MS and GC, and compared with those extracted form a noninoculated reference sample. Several esters known to play a role in the aroma profile of red wine, such as C4-C8 ethyl fatty acid esters and 3-methylbutyl acetate, were found to increase with MLF, and their final concentration was dependent on the bacterial starter employed for the induction of MLF. The overall increase of ethyl fatty acid esters was generally larger than the one observed for acetate esters. Ethyl lactate, 3-hydroxybutanoate, 2-phenylethanol, methionol, and gamma-butyrolactone were also increased by bacterial metabolism. The impact of MLF on other volatiles or red wine, including several higher alcohols, fatty acids, and nitrogen compounds, was generally negligible.

Cloning and expression of the malolactic gene of Pediococcus damnosus NCFB1832 in Saccharomyces cerevisiae

Wine production is characterized by a primary alcoholic fermentation, conducted by Saccharomyces cerevisiae, followed by a secondary malolactic fermentation (MLF). Although most lactic acid bacteria (LAB) have the ability to metabolize L-malate, only a few species survive the high ethanol and SO2 levels in wine. Wines produced in colder viticultural regions have a lower pH than wines produced in warmer regions. The decarboxylation of L-malate in these wines leads to an increase in pH, more organoleptic complexity and microbiological stability. MLF is, however, difficult to control and problems often occur during filtering of such wines. Pediococcus spp. are known to occur in high pH wines and have strong malolactic activity. However, some pediococci synthesize exocellular polysaccharides, which may lead to abnormal viscosity in wine. In this study, the malolactic gene from Pediococcus damnosus NCFB1832 (mleD) was cloned into S. cerevisiae and co-expressed with the malate permease gene (mae1) of Schizosaccharomyces pombe. Expression of the mleD gene was compared to the expression of two other malolactic genes, mleS from Lactococcus lactis MG1363 and mleA from Oenococcus oeni Lal1. The genetically modified strain of S. cerevisiae decreased the level of L-malate in grape must to less than 0.3 gl(-1) within 3 days. This is the first expression of a malolactic gene from Pediococcus in S. cerevisiae.

Potential application of a glucose-transport-deficient mutant of Schizosaccharomyces pombe for removing gluconic acid from grape must

Musts from rotten grapes typically contain high levels of gluconic acid, which can raise severe problems in winemaking processes. In this work, the ability of the glucose-transport-deficient mutant YGS-5 of Schizosaccharomyces pombe to completely or partly remove gluconic acid from a synthetic glucose-containing medium and the potential use of this yeast strain for the same purpose in musts and wines were examined. Surprisingly, the S. pombe YGS-5 strain successfully removed 93% of the initial gluconic acid (2.5 gL(-1)) and 80% of the initial malic acid (1.0 gL(-1)) within 30 h after inoculation. Also, the yeast strain produced no volatile compounds other than those obtained in fermentations conducted with the wine yeast Saccharomyces cerevisiae. S. pombe YGS-5 could thus be used to remove gluconic acid present in musts from rotten grapes. On the basis of these results, various ways of using S. pombe YGS-5 to treat musts containing gluconic acid in order to solve the problems due to the high gluconic acid concentrations in botrytized grape must are proposed.

Differential malic acid degradation by selected strains of Saccharomyces during alcoholic fermentation

To produce a high-quality wine, it is important to obtain a fine balance between the various chemical constituents, especially between the sugar and acid content. The latter is more difficult to achieve in wines that have high acidity due to excess malic acid, since wine yeast in general cannot effectively degrade malic acid during alcoholic fermentation. An indigenous Saccharomyces paradoxus strain RO88 was able to degrade 38% of the malic acid in Chardonnay must and produced a wine of good quality. In comparison, Schizosaccharomyces pombe strain F effectively removed 90% of the malic acid, but did not produce a good-quality wine. Although commercially promoted as a malic-acid-degrading wine yeast strain, only 18% of the malic acid was degraded by Saccharomyces cerevisiae Lalvin strain 71B. Preliminary studies on the transcriptional regulation of the malic enzyme gene from three Saccharomyces strains, i.e. S. paradoxus RO88, S. cerevisiae 71B and Saccharomyces bayanus EC1118, were undertaken to elucidate the differences in their ability to degrade malic acid. Expression of the malic enzyme gene from S. paradoxus RO88 and S. cerevisiae 71B increased towards the end of fermentation once glucose was depleted, whereas no increase in transcription was observed for S. bayanus EC1118 which was also unable to effectively degrade malic acid.

Ser3p (Yer081wp) and Ser33p (Yil074cp) are phosphoglycerate dehydrogenases in Saccharomyces cerevisiae

Two genes YER081W and YIL074C, renamed SER3 and SER33, respectively, which encode phosphoglycerate dehydrogenases in Saccharomyces cerevisiae were identified. These dehydrogenases catalyze the first reaction of serine and glycine biosynthesis from the glycolytic metabolite 3-phosphoglycerate. Unlike either single mutant, the ser3Delta ser33Delta double mutant lacks detectable phosphoglycerate dehydrogenase activity and is auxotrophic for serine or glycine for growth on glucose media. However, the requirement for the SER-dependent "phosphoglycerate pathway" is conditional since the "glyoxylate" route of serine/glycine biosynthesis is glucose-repressed. Thus, in cells grown on ethanol both expression and activity of all SER-encoded proteins are low, including the remaining enzymes of the phosphoglycerate pathway, Ser1p and Ser2p. Moreover the available nitrogen source regulates the expression of SER genes. However, for only SER33, and not SER3, expression was regulated in relation to the available nitrogen source in a coordinated fashion with SER1 and SER2. Based on these mRNA data together with data on enzyme activities, Ser33p is likely to be the main isoenzyme of the phosphoglycerate pathway during growth on glucose. Moreover, since phosphoglycerate dehydrogenase activity requires NAD(+) as cofactor, deletion of SER3 and SER33 markedly affected redox metabolism as shown by substrate and product analysis.

Distribution of 14C-labelled carbon from glucose and glutamate during anaerobic growth of Saccharomyces cerevisiae

The distribution of carbon from glucose and glutamate was studied using anaerobically grown Saccharomyces cerevisiae. The yeast was grown on glucose (20 g l-1) as the carbon/energy source and glutamic acid (3.5 g l-1) as additional carbon and sole nitrogen source. The products formed were identified using labelled [U-14C]glucose or [U-14C]glutamic acid. A seldom-reported metabolite in S. cerevisiae, 2-hydroxyglutarate, was found in significant amounts. It is suggested that 2-hydroxyglutarate is formed from the reduction of 2-oxoglutarate in a reaction catalysed by a dehydrogenase. Succinate, 2-oxoglutarate and 2-hydroxyglutarate were found to be derived exclusively from glutamate. Based on radioactivity measurements, 55%, 17% and 14% of the labelled glutamate was converted to 2-oxoglutarate, succinate and 2-hydroxyglutarate, respectively, and 55%, 9% and 3% of the labelled glucose was converted to ethanol, glycerol and pyruvate, respectively. No labelled glucose was converted to 2-oxoglutarate, succinate or 2-hydroxyglutarate. Furthermore, very little of the evolved CO2 was derived from glutamate. Separation of the amino acids from biomass by paper chromatography revealed that the glutamate family of amino acids (glutamic acid, glutamine, proline, arginine and lysine) originated almost exclusively from the carbon skeleton of glutamic acid. It can be concluded that the carbon flow follows two separate paths, and that the only major reactions utilized in the tricarboxylic acid (TCA) cycle are those reactions involved in the conversion of 2-oxoglutarate to succinate.

Effects of ethanol and other alkanols on transport of acetic acid in Saccharomyces cerevisiae

In glucose-grown cells of Saccharomyces cerevisiae IGC 4072, acetic acid enters only by simple diffusion of the undissociated acid. In these cells, ethanol and other alkanols enhanced the passive influx of labelled acetic acid. The influx of the acid followed first-order kinetics with a rate constant that increased exponentially with the alcohol concentration, and an exponential enhancement constant for each alkanol was estimated. The intracellular concentration of labelled acetic acid was also enhanced by alkanols, and the effect increased exponentially with alcohol concentration. Acetic acid is transported across the plasma membrane of acetic acid-, lactic acid-, and ethanol-grown cells by acetate-proton symports. We found that in these cells ethanol and butanol inhibited the transport of labelled acetic acid in a noncompetitive way; the maximum transport velocity decreased with alcohol concentration, while the affinity of the system for acetate was not significantly affected by the alcohol. Semilog plots of Vmax versus alcohol concentration yielded straight lines with negative slopes from which estimates of the inhibition constant for each alkanol could be obtained. The intracellular concentration of labelled acid was significantly reduced in the presence of ethanol or butanol, and the effect increased with the alcohol concentration. We postulate that the absence of an operational carrier for acetate in glucose-grown cells of S. cerevisiae, combined with the relatively high permeability of the plasma membrane for the undissociated acid and the inability of the organism to metabolize acetic acid, could be one of the reasons why this species exhibits low tolerance to acidic environments containing ethanol.

Energy conservation in malolactic fermentation by Lactobacillus plantarum and Lactobacillus sake

A comparably poor growth medium containing 0.1% yeast extract as sole non-defined constituent was developed which allowed good reproducible growth of lactic acid bacteria. Of seven different strains of lactic acid bacteria tested, only Lactobacillus plantarum and Lactobacillus sake were found to catalyze stoichiometric conversion of L-malate to L-lactate and CO2 concomitant with growth. The specific growth yield of malate fermentation to lactate at pH 5.0 was 2.0 g and 3.7 g per mol with L. plantarum and L. sake, respectively. Growth in batch cultures depended linearly on the malate concentration provided. Malate was decarboxylated nearly exclusively by the cytoplasmically localized malo-lactic enzyme. No other C4-dicarboxylic acid-decarboxylating enzyme activity could be detected at significant activity in cell-free extracts. In pH-controlled continuous cultures, L. plantarum grew well with glucose as substrate, but not with malate. Addition of lactate to continuous cultures metabolizing glucose or malate decreased cell yields significantly. These results indicate that malo-lactic fermentation by these bacteria can be coupled with energy conservation, and that membrane energetization and ATP synthesis through this metabolic activity are due to malate uptake and/or lactate excretion rather than to an ion-translocating decarboxylase enzyme.

Spoilage yeasts

Yeasts are best known for their beneficial contributions to society, and the literature abounds with discussions of their role in the fermentation of alcoholic beverages, bread, and other products. Yeasts also cause spoilage, but, with a few exceptions, this unwanted activity often goes unrecognized and underestimated as a major problem in the food and beverage industries. In some cases, there is only a fine line between what is perceived as either a spoilage or beneficial activity. This review examines the occurrence and growth of yeasts in foods and beverages with respect to their spoilage activities, the biochemistry of this spoilage, and technologies for the enumeration and identification of spoilage yeasts.

Transport of malic acid and other dicarboxylic acids in the yeast Hansenula anomala

DL-Malic acid-grown cells of the yeast Hansenula anomala formed a saturable transport system that mediated accumulative transport of L-malic acid with the following kinetic parameters at pH 5.0: Vmax, 0.20 nmol.s-1.mg (dry weight)-1; Km, 0.076 mM L-malate. Uptake of malic acid was accompanied by proton disappearance from the external medium with rates that followed Michaelis-Menten kinetics as a function of malic acid concentration. Fumaric acid, alpha-ketoglutaric acid, oxaloacetic acid, D-malic acid, and L-malic acid were competitive inhibitors of succinic acid transport, and all induced proton movements that followed Michaelis-Menten kinetics, suggesting that all of these dicarboxylates used the same transport system. Maleic acid, malonic acid, oxalic acid, and L-(+)-tartaric acid, as well as other Krebs cycle acids such as citric and isocitric acids, were not accepted by the malate transport system. Km measurements as a function of pH suggested that the anionic forms of the acids were transported by an accumulative dicarboxylate proton symporter. The accumulation ratio at pH 5.0 was about 40. The malate system was inducible and was subject to glucose repression. Undissociated succinic acid entered the cells slowly by simple diffusion. The permeability of the cells by undissociated acid increased with pH, with the diffusion constant increasing 100-fold between pH 3.0 and 6.0.

Evaluation of Malolactic Bacteria Isolated from Oregon Wines

Oregon is a cool wine-producing region where grapes characteristically contain high concentrations of organic acids. To reduce the natural acidity and increase the microbiological stability and flavor complexity of the wine, malolactic fermentation is encouraged. In this study, strains of Leuconostoc oenos indigenous to Oregon wines were evaluated for their suitability to conduct malolactic fermentation in Oregon wines. Tests determined the malolactic activity of the Oregon isolates in comparison with commercial strains ML-34, PSU-1, MLT-kli, and ens 44-40 under various temperature and pH conditions. Sensitivities to sulfur dioxide, ethanol, and fumaric acid also were determined. Two Oregon strains, Er-1a and Ey-2d, were selected for commercial winemaking tests because they had greater malolactic activity under conditions of low pH (3.0) and low temperature (15 and 8°C), respectively.

Malate transport in Schizosaccharomyces pombe

The transport of malate was studied in a Schizosaccharomyces pombe wild-type strain and in mutant strains unable to utilize malic acid. Two groups of such mutants, i.e., malic enzyme-deficient and malate transport-defective mutants, were differentiated by a 14C-labeled L-malate transport assay and by starch gel electrophoresis followed by activity staining for malic enzyme (malate dehydrogenase [oxaloacetate decarboxylating] [NAD+]; 1.1.1.38) and malate dehydrogenase (1.1.1.37). Transport of malate in S. pombe was constitutive and strongly inhibited by inhibitors of oxidative phosphorylation and of the formulation of proton gradients. Transport was a saturable function of the malate concentration. The apparent Km and Vmax values for transport by the parent were 3.7 mM and 40 nmol/min per mg of protein, respectively, while those of the malic enzyme-deficient mutant were 5.7 mM and 33 nmol/min per mg of protein, respectively. Malate transport was pH and temperature dependent. The specificity of transport was studied with various substrates, including mono- and dicarboxylic acids, and the possibility of a common transport system for dicarboxylic acids is discussed.