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

Evaluation of Different Molecular Markers for Genotyping Non-Saccharomyces Wine Yeast Species

Wine quality is determined by the particular yeast strains prevailing at various stages of fermentation. Therefore, the ability to make an easy, fast, and unambiguous discrimination of yeasts at the strain level is of great importance. Here, the tandem repeat-tRNA (TRtRNA) method with the 5GAC or ISSR-MB primer sets and random amplified polymorphic DNA (RAPD) analysis with (GTG)3, R5, and RF2 oligonucleotides were tested on various non-Saccharomyces wine yeast species. The TRtRNA-PCR employing ISSR-MB showed the highest capacity in discriminating Lachancea thermotolerans and Metschnikowia pulcherrima isolates. RAPD with RF2 was the most efficient method in resolving Starmerella bacillaris isolates, although it produced few polymorphic bands. RAPD with R5 showed the highest capacity to discriminate among the Issatchenkia orientalis, Hanseniaspora guilliermondii, and Pichia anomala isolates. RAPD with either R5 or RF2 exhibited the highest ability to discriminate among the Torulaspora delbrueckii isolates. RAPD with (GTG)3 was the most discriminating method for the H. uvarum isolates. Here we concluded that both TRtRNA-PCR and RAPD-PCR offer rapid means for typing non-Saccharomyces species. However, each method performs better for a given species when paired with a particular primer set. The present results can be useful in wine research for the fast fingerprinting of non-Saccharomyces yeasts.

Occurrence of Brettanomyces bruxellensis on Grape Berries and in Related Winemaking Cellar

The spoilage yeasts belonging to the genus Dekkera (anamorph Brettanomyces) are associated with the fermentation process and can be responsible for off-flavors in wine. Brettanomyces bruxellensis is difficult to isolate from natural environments because of its low diffusion, low presence on the grape surface and low competition capacity, slow growth, and VBNC (viable but not culturable) state, even when selective media are used. In this study, to investigate the origins and occurrence of B. bruxellensis in winemaking, a total of 62 samples from grapes, winery environment, and fermenting musts were taken through direct isolation with a selective medium. B. bruxellensis was not directly detected in the grape samples but was instead widely isolated from the winery environment samples. However, using a combination of enrichment and selective media, eight of fifteen grape samples were positive for B. bruxellensis. Analysis of the genetic traits of the isolates indicated a strict relationship among the strains from the vineyard and the winery. Isolates from the vineyard and the winery were both part of the more common and dominant biotypes suggesting that the vineyard may be the contamination source of B. bruxellensis in the winery environment. For this, grapes may represent the possible primary origin source from which a flow toward the winery environment originates. On the other hand, the wide occurrence of B. bruxellensis in winery indicates that this environment can be considered as the favorable ecological niche for colonization and diffusion of these yeast.

Evaluation of fingerprinting techniques to assess genotype variation among Zygosaccharomyces strains

Molecular typing techniques are key tools in surveillance of food spoilage yeasts, in investigations on intra-species population diversity, and in tracing selected starters during fermentation. Unlike previous works on strain typing of Zygosaccharomyces spoilage species, here Zygosaccharomyces mellis and the Zygosaccharoymces rouxii complex yeasts, which include Z. rouxii, Zygosaccharomyces sapae, and a mosaic lineage (ML) of putatively hybrids, were evaluated by three typing methods for intra- and inter-species resolution. Overall these yeasts are relevant for food fermentation and spoilage, but are quite difficult to discriminate at strain and species level as they evolved by reticulation. A pool of 76 strains from different sources were typed by M13 and (GTG)₅ MSP-PCR fingerprinting and PCR-RFLP of ribosomal intergenic spacer region (IGS). We demonstrated that M13 overcame (GTG)₅ fingerprinting to group Z. sapae, Z. rouxii, Z. mellis and the ML isolates in congruent distinct clusters. Even if (GTG)₅ primer yielded a number of DNA fingerprints comparable with those obtained by M13 primer, it failed to discriminate Z. sapae, Z. mellis and Z. rouxii at species level. Clustering of IGS RFLP patterns obtained with three endonucleases produced groups congruent with species assignment and highlighted intra-species diversity similar to that observed by M13 fingerprinting. However, IGS PCR amplification failed for 14 ML and 6 Z. mellis strains under the experimental conditions tested here, indicating that this marker could be less easy to use in fast typing protocol. Finally, our results posit that the genetic diversity within Z. sapae and Z. mellis could be shaped by isolation source. The information generated in this study would facilitate the monitoring of these yeasts during food processing and storage, and provides preliminary evidences about Z. sapae and Z. mellis intra-species diversity.