Quantitative PCR: An appropriate tool to detect viable but not culturable Brettanomyces bruxellensis in wine

Quantitative PCR as a tool has been used to detect Brettanomyces bruxellensis directly from wine samples. Accurate and timely detection of this yeast is important to prevent unwanted spoilage of wines and beverages. The aim of this study was to distinguish differences between DNA and mRNA as template for the detection of this yeast. The study was also used to determine if it is possible to accurately detect cells in the viable but not culturable (VBNC) state of B. bruxellensis by qPCR. Several methods including traditional plating, epifluorescence counts and qPCR were used to amplify DNA and mRNA. It was observed that mRNA was a better template for the detection in terms of standard curve analysis and qPCR efficiencies. Various primers previously published were tested for their specificity, qPCR efficiency and accuracy of enumeration. A single primer set was selected which amplified a region of the actin-encoding gene. The detection limit for this assay was 10 cells mL− 1. B. bruxellensis could also be quantified in naturally contaminated wines with this assay. The mRNA gave a better indication of the viability of the cells which compared favourably to fluorescent microscopy and traditional cell counts. The ability of the assay to accurately estimate the number of cells in the VBNC state was also demonstrated.

► Primer pairs were tested for the enumeration of Brettanomyces bruxellensis.
► Genomic DNA and mRNA were tested as PCR template.
► Actin primers using mRNA gave the best results.
► The use of mRNA allowed the detection of cells in a viable but non-culturable state.
► This was demonstrated in synthetic wine medium and confirmed in real wine.