Culture independent analyses and wine fermentation: an overview of achievements 10 years after first application

Wine fermentations are complex microbial ecosystems, with both yeasts and bacteria taking part in the transformation process with their metabolic activities. Traditional microbiological methods do not allow a complete understanding of the microbial ecology of complex systems. This is due mainly to the capacity of certain microorganisms to grow on microbiological media preferentially with respect to others. Moreover, with these methods, stressed or damaged cells cannot be detected on the plates. In the last 10 years new methods based on the analysis of nucleic acids (DNA and RNA) extracted directly from the sample without the need for microbial cultivation have been developed. A method often used in this type of study is the polymerase chain reaction (PCR) coupled with denaturing gradient gel electrophoresis (DGGE). This paper aims to report the most important contributions of PCR-DGGE to the study of microbiological ecology during wine fermentation.

[1]  G. Muyzer,et al.  Application of denaturing gradient gel electrophoresis (DGGE) and temperature gradient gel electrophoresis (TGGE) in microbial ecology , 2004, Antonie van Leeuwenhoek.

[2]  G. Nychas,et al.  Yeast Community Structures and Dynamics in Healthy and Botrytis-Affected Grape Must Fermentations , 2007, Applied and Environmental Microbiology.

[3]  I. Andorrà,et al.  Effect of fermentation temperature on microbial population evolution using culture-independent and dependent techniques , 2010 .

[4]  N. Pace.  A molecular view of microbial diversity and the biosphere. , 1997, Science.

[5]  L. Cocolin,et al.  Yeast biodiversity and dynamics during sweet wine production as determined by molecular methods. , 2008, FEMS yeast research.

[6]  L. Cocolin,et al.  Direct profiling of the yeast dynamics in wine fermentations. , 2000, FEMS microbiology letters.

[7]  G. de Revel,et al.  Interactions between Brettanomyces bruxellensis and other yeast species during the initial stages of winemaking , 2006, Journal of applied microbiology.

[8]  Chen Kai-hu.  Application of fluorescence in situ hybridization , 2012 .

[9]  S. Kjelleberg,et al.  rpoB-Based Microbial Community Analysis Avoids Limitations Inherent in 16S rRNA Gene Intraspecies Heterogeneity , 2000, Applied and Environmental Microbiology.

[10]  J. A. Barnett,et al.  The numbers of yeasts associated with wine grapes of Bordeaux , 1972, Archiv für Mikrobiologie.

[11]  L. Cocolin,et al.  Molecular Detection and Identification of Brettanomyces/Dekkera bruxellensis and Brettanomyces/Dekkera anomalus in Spoiled Wines , 2004, Applied and Environmental Microbiology.

[12]  J. VanderGheynst,et al.  Design and Evaluation of PCR Primers for Analysis of Bacterial Populations in Wine by Denaturing Gradient Gel Electrophoresis , 2003, Applied and Environmental Microbiology.

[13]  L. Cocolin,et al.  Yeast Diversity and Persistence in Botrytis-Affected Wine Fermentations , 2002, Applied and Environmental Microbiology.

[14]  M. Sipiczki.  Candida zemplinina sp. nov., an osmotolerant and psychrotolerant yeast that ferments sweet botrytized wines. , 2003, International journal of systematic and evolutionary microbiology.

[15]  L. Cocolin,et al.  Wine Yeast Inhibition by Sulfur Dioxide: A Comparison of Culture-Dependent and Independent Methods , 2003, American Journal of Enology and Viticulture.

[16]  Danilo Ercolini,et al.  Application of FISH technology for microbiological analysis: current state and prospects , 2006, Applied Microbiology and Biotechnology.

[17]  Danilo Ercolini,et al.  Yeast dynamics during spontaneous wine fermentation of the Catalanesca grape. , 2007, International journal of food microbiology.

[18]  G. Fleet.  Wine Microbiology and Biotechnology , 1993 .

[19]  L. Cocolin,et al.  PCR–DGGE differentiation of strains of Saccharomyces sensu stricto , 2004, Antonie van Leeuwenhoek.

[20]  L. Cocolin,et al.  Direct Identification of the Indigenous Yeasts in Commercial Wine Fermentations , 2001, American Journal of Enology and Viticulture.

[21]  Danilo Ercolini,et al.  PCR-DGGE fingerprinting: novel strategies for detection of microbes in food. , 2004, Journal of microbiological methods.

[22]  Philip Hugenholtz,et al.  Impact of Culture-Independent Studies on the Emerging Phylogenetic View of Bacterial Diversity , 1998, Journal of bacteriology.

[23]  D. Erasmus,et al.  Genome-wide expression analyses: Metabolic adaptation of Saccharomyces cerevisiae to high sugar stress. , 2003, FEMS yeast research.

[24]  I. Andorrà,et al.  Effect of oenological practices on microbial populations using culture-independent techniques. , 2008, Food microbiology.

[25]  G. Fleet,et al.  Application and evaluation of denaturing gradient gel electrophoresis to analyse the yeast ecology of wine grapes. , 2004, FEMS yeast research.

[26]  L. Cocolin,et al.  A PCR-TGGE (Temperature Gradient Gel Electrophoresis) technique to assess differentiation among enological Saccharomyces cerevisiae strains. , 2005, International journal of food microbiology.

[27]  C. Miot-Sertier,et al.  Lactic acid bacteria evolution during winemaking: use of rpoB gene as a target for PCR-DGGE analysis. , 2006, Food microbiology.