Genomic DNA fingerprinting of Oenococcus oeni strains by pulsed-field gel electrophoresis and randomly amplified polymorphic DNA-PCR

Impact of Sequential Inoculation with the Non-Saccharomyces T. delbrueckii and M. pulcherrima Combined with Saccharomyces cerevisiae Strains on Chemicals and Sensory Profile of Rosé Wines

Controlled inoculations of non-Saccharomyces yeasts are becoming increasingly used to produce high-quality wines due to their enological potential. In this study, we evaluated the impact of sequential inoculation with the commercial non-Saccharomyces yeasts (Torulaspora delbrueckii and Metschnikowia pulcherrima) in combination with Saccharomyces cerevisiae on the chemical and sensory profile of rosé wines. Sequential inoculation with T. delbrueckii produced wines with an overall reduction in esters, mainly explained by the lower concentrations of ethyl esters of medium-chain fatty acids and isoamyl acetate. The lower ester concentrations of these wines were related to a reduction in fruity descriptors. An increase was observed, however, in other minor esters such as cinnamates and ethyl esters of branched acids. Zinc, ethyl isobutyrate, and ethyl dihydrocinnamate were selected as potential markers for this fermentation strategy. Sequential inoculation with M. pulcherrima resulted in rosé wines with an enhanced ester profile, reduced acetaldehyde, and increased anthocyans and tannins. Compared to the control wines fermented with S. cerevisiae, the changes observed in these wines were far subtler, especially for the volatile profile, sensory characteristics, and color parameters, with isobutyl hexanoate and isoamyl butyrate being selected as potential markers.

Genotypic and phenotypic diversity among Lactobacillus plantarum and Lactobacillus pentosus isolated from industrial scale cucumber fermentations

The Lactobacillus plantarum and Lactobacillus pentosus genotypes existing in industrial-scale cucumber fermentations were defined using rep-PCR-(GTG)5. The ability of each genotype to ferment cucumbers under various conditions was evaluated. Rep-PCR-(GTG)5 was the technique capable of illustrating the most intraspecies discrimination compared to the sequencing of housekeeping genes (recA, dnaK, pheS and rpoA), MLST and RAPD with primers LP1, OPL5, M14 and COC. Ten genotypic clusters were defined for the 199 L. pentosus tested and three for the 17 L. plantarum clones. The ability of the 216 clones genotyped and 37 additional cucumber fermentation isolates, of the same species, to rapidly decrease the pH of cucumber juice medium under various combinations of sodium chloride (0 or 6%), initial pH (4.0 or 5.2) and temperatures (15 or 30 °C) was determined using a fractional factorial screening design. A reduced fermentation ability was observed for the L. plantarum strains as compared to L. pentosus, except for clone 3.2.8, which had a ropy phenotype and aligned to genotypic cluster A. L. pentosus strains belonging to three genotypic clusters (B, D and J) were more efficient in cucumber juice fermentation as compared to most L. plantarum strains. This research identified three genetically diverse L. pentosus strains and one L. plantarum as candidates for starter cultures for commercial cucumber fermentations.

Distribution of Oenococcus oeni populations in natural habitats

Oenococcus oeni is the lactic acid bacteria species most commonly encountered in wine, where it develops after the alcoholic fermentation and achieves the malolactic fermentation that is needed to improve the quality of most wines. O. oeni is abundant in the oenological environment as well as in apple cider and kombucha, whereas it is a minor species in the natural environment. Numerous studies have shown that there is a great diversity of strains in each wine region and in each product or type of wine. Recently, genomic studies have shed new light on the species diversity, population structure, and environmental distribution. They revealed that O. oeni has unique genomic features that have contributed to its fast evolution and adaptation to the enological environment. They have also unveiled the phylogenetic diversity and genomic properties of strains that develop in different regions or different products. This review explores the distribution of O. oeni and the diversity of strains in natural habitats.

Evidence of the genetic diversity and clonal population structure of Oenococcus oeni strains isolated from different wine-making regions of China

Studies of the genetic diversity and population structure of Oenococcus oeni (O. oeni) strains from China are lacking compared to other countries and regions. In this study, amplified fragment length polymorphism (AFLP) and multilocus sequence typing (MLST) methods were used to investigate the genetic diversity and regional evolutionary patterns of 38 O. oeni strains isolated from different wine-making regions in China. The results indicated that AFLP was markedly more efficient than MLST for typing O. oeni strains. AFLP distinguished 37 DNA patterns compared to 7 sequence types identified using MLST, corresponding to discriminatory indices of 0.999 and 0.602, respectively. The AFLP results revealed a high level of genetic diversity among the O. oeni strains from different regions of China, since two subpopulations and an intraspecific homology higher than 60% were observed. Phylogenetic analysis of the O. oeni strains using the MLST method also identified two major phylogroups, which were differentiated into two distinct clonal complexes by minimum spanning tree analysis. Neither intragenic nor intergenic recombination verified the existence of the clonal population structure of the O. oeni strains.

Lowering histamine formation in a red Ribera del Duero wine (Spain) by using an indigenous O. oeni strain as a malolactic starter

This study demonstrates for the first time that a non-commercial selected autochthonous O. oeni strain has been used to conduct malolactic fermentation (MLF) while lowering histamine formation in the same winery. Lactic acid bacteria (LAB) were isolated from 13 vats before and after spontaneous MLF at the Pago de Carraovejas winery from the Ribera del Duero region (Spain). Only O. oeni were present, typed and characterized, and both histamine producer and non-producers existed. From the non-producers, one strain was selected to become a starter according to its genetic profile, prevalence in the different wines in the winery, resistance to alcoholic degree, resistance to high polyphenolic content, inability to synthesise histamine, growth kinetics and malolactic activity. This starter was produced at semi-industrial levels to inoculate 20,000L of Tempranillo red wine. The inoculated vat showed 5-fold less histamine than the non-inoculated control vat. After 1year, the barrel-ageing histamine concentrations were 3-fold lower in the inoculated vat than in the non-inoculated vat.

Linking wine lactic acid bacteria diversity with wine aroma and flavour

In the last two decades knowledge on lactic acid bacteria (LAB) associated with wine has increased considerably. Investigations on genetic and biochemistry of species involved in malolactic fermentation, such as Oenococcus oeni and of Lactobacillus have enabled a better understand of their role in aroma modification and microbial stability of wine. In particular, the use of molecular techniques has provided evidence on the high diversity at species and strain level, thus improving the knowledge on wine LAB taxonomy and ecology. These tools demonstrated to also be useful to detect strains with potential desirable or undesirable traits for winemaking purposes. At the same time, advances on the enzymatic properties of wine LAB responsible for the development of wine aroma molecules have been undertaken. Interestingly, it has highlighted the high intraspecific variability of enzymatic activities such as glucosidase, esterase, proteases and those related to citrate metabolism within the wine LAB species. This genetic and biochemistry diversity that characterizes wine LAB populations can generate a wide spectrum of wine sensory outcomes. This review examines some of these interesting aspects as a way to elucidate the link between LAB diversity with wine aroma and flavour. In particular, the correlation between inter- and intra-species diversity and bacterial metabolic traits that affect the organoleptic properties of wines is highlighted with emphasis on the importance of enzymatic potential of bacteria for the selection of starter cultures to control MLF and to enhance wine aroma.

TdPIR minisatellite fingerprinting as a useful new tool for Torulaspora delbrueckii molecular typing

Torulaspora delbrueckii yeast strains are being increasingly applied at the industrial level, such as in the winemaking process, and so their identification and characterisation require effective, fast, accurate, reproducible and reliable approaches. Therefore, the development of typing techniques that allow discrimination at the strain level will provide an essential tool for those working with T. delbrueckii strains. Here, 28 T. delbrueckii strains from various substrates were characterised using different PCR-fingerprinting molecular methods: random amplified polymorphic DNA with polymerase chain reaction (RAPD-PCR), minisatellites SED1, AGA1, DAN4 and the newly designed T. delbrueckii (Td)PIR, and microsatellites (GAC)5 and (GTG)5. The aim was to determine and compare the efficacies, reproducibilities and discriminating powers of these molecular methods. RAPD-PCR using the M13 primers and the newly designed TdPIR3 minisatellite primer pair provided discrimination of the greatest number of T. delbrueckii strains. TdPIR3 clustered the 28 strains into 16 different groups with an efficiency of 100%, while M13 clustered the strains into 17 different groups, although with a lower efficiency of 89%. Moreover, the TdPIR3 primers showed reproducible profiles when the stringency of the PCR protocol was varied, which highlighted the great robustness of this technique. In contrast, variation of the stringency of the M13 PCR protocol resulted in modification of the amplified profiles, which suggested low reproducibility of this technique.

Multilocus sequence typing and pulsed-field gel electrophoresis analysis of Oenococcus oeni from different wine-producing regions of China

The present study established a typing method with NotI-based pulsed-field gel electrophoresis (PFGE) and stress response gene schemed multilocus sequence typing (MLST) for 55 Oenococcus oeni strains isolated from six individual regions in China and two model strains PSU-1 (CP000411) and ATCC BAA-1163 (AAUV00000000). Seven stress response genes, cfa, clpL, clpP, ctsR, mleA, mleP and omrA, were selected for MLST testing, and positive selective pressure was detected for these genes. Furthermore, both methods separated the strains into two clusters. The PFGE clusters are correlated with the region, whereas the sequence types (STs) formed by the MLST confirm the two clusters identified by PFGE. In addition, the population structure was a mixture of evolutionary pathways, and the strains exhibited both clonal and panmictic characteristics.

Implications of new research and technologies for malolactic fermentation in wine

The initial conversion of grape must to wine is an alcoholic fermentation (AF) largely carried out by one or more strains of yeast, typically Saccharomyces cerevisiae. After the AF, a secondary or malolactic fermentation (MLF) which is carried out by lactic acid bacteria (LAB) is often undertaken. The MLF involves the bioconversion of malic acid to lactic acid and carbon dioxide. The ability to metabolise L-malic acid is strain specific, and both individual Oenococcus oeni strains and other LAB strains vary in their ability to efficiently carry out MLF. Aside from impacts on acidity, LAB can also metabolise other precursors present in wine during fermentation and, therefore, alter the chemical composition of the wine resulting in an increased complexity of wine aroma and flavour. Recent research has focused on three main areas: enzymatic changes during MLF, safety of the final product and mechanisms of stress resistance. This review summarises the latest research and technological advances in the rapidly evolving study of MLF and investigates the directions that future research may take.

Selection of dominant NSLAB from a mature traditional cheese according to their technological properties and in vitro intestinal challenges

Isolates (47) of lactobacilli from 5 different productions of Melichloro cheese were examined for potential use as adjunct cultures. The sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) of whole-cell proteins classified 29 isolates as L. paraplantarum and 18 as L. paracasei subsp. paracasei. Randomly amplified polymorphic DNA-polymerase chain reaction (RAPD-PCR) analysis differentiated the L. paraplantarum and L. paracasei subsp. paracasei isolates at strain level and both, RAPD analysis and whole-cell protein profiling provided useful information about the diversity of nonstarter lactic acid bacteria (NSLAB) in the different cheese productions. The isolates were slow acidifiers and about 70% of them degraded, preferentially α(s)-casein. The amounts of amino acids accumulated in the milk increased with the incubation time. A similar enzyme profile was exhibited by strains of both species, except for α-mannosidase and α-fucosidase, which were not detected in the L. paracasei subsp. paracasei strains. All strains grew in the presence of bile at 0.3% and the majority was able to withstand pH 2.5 and pancreatin at 0.1%. Moreover, all strains reduced cholesterol in vitro, with higher removal ability recorded for strains of L. paraplantarum. A narrow spectrum of antibacterial activity was recorded for 88% of the strains. Selected isolates with appropriate technological and interesting in vitro intestinal challenges could be used as adjuncts and deserve further studies.

Genetic and phenotypic strain heterogeneity within a natural population of Oenococcus oeni from Amarone wine

AIMS

To investigate the Oenococcus oeni population occurring during spontaneous malolactic fermentation (MLF) of Amarone wine, a peculiar and hostile environment for malolactic bacteria.

METHODS AND RESULTS

Pulsed-field gel electrophoresis (PFGE) analysis showed a high level of genetic heterogeneity within the O. oeni population involved in MLF throughout an industrial vinification of Amarone wine. The 13 strains with distinct PFGE profile displayed different capability to hydrolyse esters and glycosides, as well as great variability to growth under stress parameters, such as high ethanol content (15% v/v), low pH (3·0) and temperature (15°C), and presence of SO(2). Moreover, polymorphism in the gene sacB involved in exopolysaccharide production was observed among the strains. The strains showed differences to convert l-malic acid into l-lactic acid in wine.

CONCLUSIONS

The occurrence of spontaneous MLF in stressful ecosystems such as Amarone wine is related to the heterogeneity of O. oeni community; biodiversity indexes and strain evolution analyses suggested that its success depends on its initial strain evenness.

SIGNIFICANCE AND IMPACT OF THE STUDY

Remarkable intraspecies complexity within the O. oeni natural population could explain the great versatility of this species as key of successful adaptation to harsh winemaking conditions.

Amino acids and volatile compounds in wines from Cabernet Sauvignon and Tempranillo varieties subjected to malolactic fermentation in barrels

The aim of the present paper is to compare the behaviour of industrial lactic bacteria and indigenous bacteria of the cellar when malolactic fermentation was carried out in barrels. The effects of these bacteria on the concentration of metabolised amino acids during malolactic fermentation and on the composition of volatile compounds both before and after malolactic fermentation are studied. The experiment was performed with wines of the Tempranillo and Cabernet Sauvignon varieties. An analysis has been made of the easily extractable volatile compounds of the wood and the compounds from the grapes, and the action of the yeasts during the alcoholic fermentation. Acetoin and diacetyl decreased during the malolactic fermentation in barrels and the concentrations of furfural and its derivatives were up to 100 times higher in wines not subjected to malolactic fermentation. Most of the volatile phenols increased during the malolactic fermentation in wines of the Tempranillo variety, while only guaiacol ( p < 0.05) and t-isoeugenol increased in the Cabernet Sauvignon wines. The decrease in amino acids during the malolactic fermentation depends much more on the variety than on the bacterial strain which carries out the malolactic fermentation.

Amarone: a modern wine coming from an ancient production technology

Amarone wine is a renowned dry red wine produced in Valpolicella (Verona, Northern Italy). It is made from local grapes varieties (Corvina, Rondinella, and Molinara) that are slowly dried under natural conditions during the fall into winter. After the postharvest drying, carried out for several weeks in dedicated lofts called fruttaio, the grapes are vinified: crushed, given prefermentative cold maceration, undergo alcoholic fermentation on the skins, malolactic fermentation, and finally maturation. The partially dried grapes are traditionally crushed during the second half of January to February. Because cellar conditions are unfavorable for either alcohol or malolactic fermentation, selected microbial cultures (yeasts and malolactic bacteria) are often necessary to correctly manage fermentation. The progress of both fermentation processes needs constant surveillance. During maturation conducted in vessels or wooden containers (tonneau in durmast oak), clarification and stabilization lead to improvements in quality. Product specifications require that Amarone not be bottled before the wine has been aged for 2years (Anonymous (2010). Disciplinare di produzione dei vini a denominazione di Origine Controllata e Garantita "Amarone della Valpolicella". Gazzetta Ufficiale della Repubblica Italiana. Serie generale n. 84. April 12). Amarone achieved its DOCG (Controlled and Guaranteed Denomination) status in 2010.

Development of a sequence-characterized amplified region marker-targeted quantitative PCR assay for strain-specific detection of Oenococcus oeni during wine malolactic fermentation

Control over malolactic fermentation (MLF) is a difficult goal in winemaking and needs rapid methods to monitor Oenococcus oeni malolactic starters (MLS) in a stressful environment such as wine. In this study, we describe a novel quantitative PCR (QPCR) assay enabling the detection of an O. oeni strain during MLF without culturing. O. oeni strain LB221 was used as a model to develop a strain-specific sequence-characterized amplified region (SCAR) marker derived from a discriminatory OPA20-based randomly amplified polymorphic DNA (RAPD) band. The 5' and 3' flanking regions and the copy number of the SCAR marker were characterized using inverse PCR and Southern blotting, respectively. Primer pairs targeting the SCAR sequence enabled strain-specific detection without cross amplification of other O. oeni strains or wine species of lactic acid bacteria (LAB), acetic acid bacteria (AAB), and yeasts. The SCAR-QPCR assay was linear over a range of cell concentrations (7 log units) and detected as few as 2.2 × 10(2) CFU per ml of red wine with good quantification effectiveness, as shown by the correlation of QPCR and plate counting results. Therefore, the cultivation-independent monitoring of a single O. oeni strain in wine based on a SCAR marker represents a rapid and effective strain-specific approach. This strategy can be adopted to develop easy and rapid detection techniques for monitoring the implantation of inoculated O. oeni MLS on the indigenous LAB population, reducing the risk of unsuccessful MLF.

Occurrence of biogenic amine-forming lactic acid bacteria in wine and cider

A collection of 810 lactic acid bacteria (LAB) strains isolated from wine and cider was screened for potential biogenic amine (BA) producers by combining molecular and phenotypic approaches. A newly developed multiplex PCR method allowed for the simultaneous detection of four genes involved in the production of histamine (histidine decarboxylase, hdc), tyramine (tyrosine decarboxylase, tyrdc) and putrescine (via either ornithine decarboxylase, odc, or agmatine deiminase, agdi) while TLC and HPLC analysis allowed for BA-production determination. One hundred and fifty-eight LAB strains were monitored by the molecular/phenotypic double approach and revealed a good correlation between genotypic and phenotypic data. Eighteen per cent of the tested strains were positive for at least one BA target gene with up to three detected simultaneously, in particular amongst Lactobacillus brevis and Lactobacillus hilgardii isolates for the tyrdc and agdi genes. The most frequent gene corresponded to the agdi gene detected in 112 strains (14% of all LAB strains) of 10 different LAB species. The tyrdc gene was detected in 67 strains represented by 7 different LAB species (8% overall), especially those isolated from wine. Lower levels of hdc(+) (2% of strains) and especially odc(+) (0.5% of strains) strains were observed. Interestingly, species that have never been described to carry BA-producing pathway genes were identified in this study. Furthermore, only one cadaverine-producer was detected and corresponded to Lactobacillus 30a, a collection strain not found in fermented beverages, although cadaverine is commonly detected in wines.

Characterization and technological properties of Oenococcus oeni strains from wine spontaneous malolactic fermentations: a framework for selection of new starter cultures

AIMS

To characterize the genetic and phenotypic diversity of 135 lactic acid bacteria (LAB) strains isolated from Italian wines that undergone spontaneous malolactic fermentation (MLF) and propose a multiphasic selection of new Oenococcus oeni malolactic starters.

METHODS AND RESULTS

One hundred and thirty-five LAB strains were isolated from 12 different wines. On the basis of 16S amplified ribosomal DNA restriction analysis (ARDRA) with three restriction enzymes and 16S rRNA gene sequencing, 120 O. oeni strains were identified. M13-based RAPD analysis was employed to investigate the molecular diversity of O. oeni population. Technological properties of different O. oeni genotypes were evaluated in synthetic medium at increasing selective pressure, such as low pH (3.5, 3.2 and 3.0) and high ethanol values (10, 11 and 13% v/v). Finally, the malolactic activity of one selected strain was assessed in wine by malolactic trial in winery.

CONCLUSIONS

The research explores the genomic diversity of wine bacteria in Italian wines and characterizes their malolactic metabolism, providing an efficient strategy to select O. oeni strains with desirable malolactic performances and able to survive in conditions simulating the harsh wine environment.

SIGNIFICANCE AND IMPACT OF THE STUDY

This article contributes to a better understanding of microbial diversity of O. oeni population in Italian wines and reports a framework to select new potentially O. oeni starters from Italian wines during MLF.

Miniprimer PCR assay targeting multiple genes: a new rapid and reliable tool for genotyping Pantoea stewartii subsp. stewartii

AIM

Development of a 'miniprimer' PCR assay for genotyping Pantoea stewartii subsp. stewartii, the causal agent of the Stewart's bacterial wilt on maize.

METHODS AND RESULTS

Four 10-nucleotide (10-nt) 'miniprimer' sets were designed and evaluated in the presence of Titanium Taq DNA polymerase. Under optimal reaction conditions, the miniprimer pair Uni-BacF-10/Uni-BacR-10 reproducibly generated identical banding patterns among 10 strains of P. stewartii subsp. stewartii, different patterns from strains of P. stewartii subsp. indologenes, other Panteoa species, Clavibacter michiganensis, Pectobacterium spp., Pseudomonas spp. and other bacterial species. The amplicons of Pantoea stewartii subsp. stewartii were cloned and sequenced to identify genes or DNA fragments that are targeted by the miniprimer PCR assay. Of the 14 'clone types' identified, sequences of a 1.23-kb fragment had a 99.8% similarity to part of the Pantoea stewartii zeaxanthin diglucoside biosynthetic operon (AY166713). Other dominant cloned fragments included a 411-bp amplicon that exhibited 99.8% similarity to the psaU gene (syn:ysaU; GQ249669), a type III protein-secretion system complex of P. stewartii subsp. stewartii strain DC283, and a 548-bp fragment showed 63% homology to the Asp/Glu racemase encoding gene in Erwinia tasmaniensis strain ET1/99.

CONCLUSION

The miniprimer PCR assay reported here is highly discriminatory and reproducible in genotyping Pantoea stewartii subsp. stewartii.

SIGNIFICANCE AND IMPACT OF THE STUDY

This miniprimer PCR assay could be a new reliable and rapid tool for fingerprinting the Stewart's wilt pathogen of maize.

Characterization of tetracycline-resistant Streptococcus thermophilus isolates from Italian soft cheeses

Tetracycline-resistant Streptococcus thermophilus isolates from soft cheeses harbored the genes tet(S), tet(M), and tet(L). Molecular analysis of these genes revealed their expression, localization on plasmids or Tn916-Tn1545 family transposons, and their similarity with published sequences. The study highlights the importance of an accurate safety assessment of using S. thermophilus as a starter culture.

Oenococcus oeni genome plasticity is associated with fitness

Oenococcus oeni strains are well-known for their considerable phenotypic variations in terms of tolerance to harsh wine conditions and malolactic activity. Genomic subtractive hybridization (SH) between two isolates with differing enological potentials was used to elucidate the genetic bases of this intraspecies diversity and identify novel genes involved in adaptation to wine. SH revealed 182 tester-specific fragments corresponding to 126 open reading frames (ORFs). A large proportion of the chromosome-related ORFs resembled genes involved in carbohydrate transport and metabolism, cell wall/membrane/envelope biogenesis, and replication, recombination, and repair. Six regions of genomic plasticity were identified, and their analysis suggested that both limited recombination and insertion/deletion events contributed to the vast genomic diversity observed in O. oeni. The association of selected sequences with adaptation to wine was further assessed by screening a large collection of strains using PCR. No sequences were found to be specific to highly performing (HP) strains alone. However, there was a statistically significant positive association between HP strains and the presence of eight gene sequences located on regions 2, 4, and 5. Gene expression patterns were significantly modified in HP strains, following exposure to one or more of the common stresses in wines. Regions 2 and 5 showed no traces of mobile elements and had normal GC content. In contrast, region 4 had the typical hallmarks of horizontal transfer, suggesting that the strategy of acquiring genes from other bacteria enhances the fitness of O. oeni strains.

Development of a molecular method for the typing of Brettanomyces bruxellensis (Dekkera bruxellensis) at the strain level

AIMS

In recent years, Brettanomyces/Dekkera bruxellensis has caused increasingly severe quality problems in the wine industry. A typing method at the strain level is needed for a better knowledge of the dispersion and the dynamics of these yeasts from grape to wine.

METHODS AND RESULTS

Three molecular tools, namely random-amplified polymorphic DNA, PCR fingerprinting with microsatellite oligonucleotide primers and SAU-PCR, were explored for their relevance to typing strains of Brettanomyces bruxellensis. The results indicated that discrimination of each individual strain was not possible with a single PCR typing technique. We described a typing method for B. bruxellensis based on restriction enzyme analysis and pulse field gel electrophoresis (REA-PFGE). Results showed that electrophoretic profiles were reproducible and specific for each strain under study.

CONCLUSIONS

Consequently, REA-PFGE should be considered for the discrimination of B. bruxellensis strains. This technique allowed a fine discrimination of B. bruxellensis, as strains were identified by a particular profile.

SIGNIFICANCE AND IMPACT OF THE STUDY

This study constitutes a prerequisite for accurate and appropriate investigations on the diversity of strains throughout the winemaking and ageing process. Such studies will probably give clearer and more up-to-date information on the origin of the presence of Brettanomyces in wine after vinification when they are latent spoilage agents.