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1 Research associate, 4 Professor, Cornell Enology Group, Department of Food Science and Technology, Cornell University/New York State Agricultural Experiment Station, Geneva, NY 14456; 2 Collection curator, 5 Professor, Department of Viticulture and Enology, University of California, Davis, CA 95616; 3 Graduate student in Cornell Enology Group, now at ETS Laboratories, St. Helena, CA 94574.
Acknowledgments: We thank Dr. Jürg Gafner and his group for allowing us to use their actin primers, Dr. John Barnard, who performed the majority of the statistical analysis, the Cornell Enology group for their input in discussion, and Dr. Angela Baldo for helpful discussions and advice on computational analyses. We also thank the American Vineyard Foundation and the California Competitive Grant Program for Research in Viticulture and Enology for funding this research and the New York State Agricultural Experiment Station.
| Abstract |
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Key words: Brettanomyces bruxellensis, PCR analysis, physiology, genetic characterization
ODonnell (1993) reported the use of 26S rDNA gene primers to amplify a divergent region (D1/D2 region) demarcated by nucleotides 63-642 of the 5'-end of the large subunit of rDNA genes in Saccharomyces cerevisiae. The sequence of the region of the 26S rDNA gene was published for more than 500 yeast species and can be accessed via the Internet (Kurtzman and Robnett 1998, Altschul et al. 1990).
Little information is available about physiological and genetic differences among Brettanomyces isolates from wine. In this work, 47 strains of Brettanomyces were characterized genetically and physiological characterization was performed on 35 of these isolates. The strains of Brettanomyces selected were isolated from wines from diverse geographic regions, from different vintage years, made with different varietals. The principal aim was to determine if the genotype, as defined by DNA sequencing, was linked to physiological traits important in enology. This information might allow assignment of certain physiological characteristics to specific genetic types among isolates of Brettanomyces. A second goal was to determine whether there are patterns among isolates from certain wines or geographic regions that may allow for the differentiation of strains that produce especially objectionable off-odors from strains with less or perhaps no negative impact on wine flavor. The characterization of subgroups of Brettanomyces might allow identification of rapidly growing strains that have more potential to damage the wine as opposed to slower growing strains with little flavor impact. A final goal was to establish whether genetic analysis might be useful in predicting growth and off-flavor impact in wine, thus being a useful guide for appropriate control and sanitation practices.
| Materials and Methods |
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PCR analysis. NL-1 and NL-4, primers specific for a portion of the large subunit (LSU) of the 26S rDNA gene of ascomycetous yeast were synthesized based on sequences from a previously published method (ODonnell 1993, Kurtzman and Robnett 1998). Primers NL-1 (5'-GCATATCAATAA-GCGGAGGAAAAG-3') and NL-4 (5'-GTCCGTGTTTCAA-GACGG-3') were used in 50 µL Hot Start Taq MasterMix (Qiagen, Chatsworth, CA). Reagent concentrations were as recommended by Qiagen. The reaction was performed in a Gradient-Plus thermal cycler (Stratagene, La Jolla, CA). PCR reactions were carried out after one cycle of incubation for 15 min at 95°C. Amplification for the 26S rDNA fragment was accomplished in 40 cycles of denaturation at 95°C for 50 sec, annealing at 52°C for 50 sec, and elongation at 72°C for 2 min. A final step of 72°C for 10 min was part of the program. Amplification products were analyzed via electrophoresis at 100 V for 60 min in a 1% agarose gel stained with ethidium bromide following standard protocols (Sambrook et al. 1989). PCR products were then purified and concentrated for sequencing by using the QiaQuick PCR purification kit (Qiagen). Elution from the spin column with 30 to 50 µL of water concentrated the amplification product to the appropriate level required for sequencing following the standard methods used by the Cornell University Biotechnology Resource Center Sequencing Facility (www.brc.cornell.edu).
Automated DNA sequencing. Purified and concentrated PCR product was quantified and mixed with the same primers used for PCR. Approximately 1 µg of amplicon (10 µL) was mixed with 8 pmol of either forward or reverse primer. Sequencing reactions were carried out at the Cornell University Biotechnology Resource Center and separated on an Applied Biosystems Automated 3730 DNA Analyzer (ABI, Foster City, CA). The sequences from both strands were assembled and the result sequence analyzed with DNAStar analysis software (Lasergene, Madison, WI).
Sequence analysis. DNA consensus sequences of the portion of the large subunit (LSU) of the 26S rDNA gene were submitted to a BLAST search on the National Center for Biotechnology Information web site (http://www.ncbi.nlm.nih.gov/blast/). Multiple sequences alignment was obtained using the MegAlign DNAStar analysis software package (Lasergene) with CLUSTAL W algorithm and default settings. Phylogenetic relationships were assessed with MegAlign DNAStar. Bootstrapping values were determined by using PHYLIP (http://evolution.genetics.washington.edu/phylip.html) (values <50% were not reported).
Physiological testing. Growth tests were conducted in a minimal medium based on that used by Heresztyn (1986a) consisting of 10 g glucose, 10 g fructose, 2 g ammonium sulfate, 2 g potassium phosphate monobasic, 250 mg calcium chloride, 250 mg magnesium sulfate heptahydrate, 1 mg thiamin HCl, 30 µg biotin, 8 µg iron chloride hexahydrate, 2 µg zinc sulfate heptahydrate, and 1 µg boric acid in 1 L water. Glucose and fructose were eliminated and substituted with 1 or 2% of a given carbon source in carbon experiments. Ammonium sulfate was eliminated and substituted with 0.1% of a given nitrogen source for nitrogen experiments. Growth tests were initially done in 96-well microtiter plates with 0.25 mL of media, and growth was determined visually using a Wickerham card. A minimum of two passages on each nutrient tested was used to deplete cellular reserves. The tests were replicated at least three times and any inconsistent results were repeated in test tubes with 2 mL of medium.
Production of 4-ethylphenol (4-EP) and 4-ethylguaiacol (4-EG) was tested in wine. Grenache blanc juice was filter-sterilized to remove any indigenous Brettanomyces strains, then inoculated with Pasteur Red yeast (Red Star, Lesaffre Yeast). At 3 Brix the wine was centrifuged and filter-sterilized to remove the Saccharomyces and inoculated with ~104 cells/mL of the Brettanomyces strain to be tested. The Brettanomyces was allowed to grow for 6 weeks and then the wines were centrifuged to remove yeast before chemical analysis. ETS Laboratories (St. Helena, CA) performed the analysis of wine samples for 4-EP and 4-EG.
Statistical analysis. The data were analyzed by cluster analysis (PAST, PAlaeontological STatistics, ver.1.12; http://folk.uio.no/ohammer/past), and discriminant analysis statistical procedures (R Project for Statistical Computing; http://www.r-project.org/).
| Results |
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Characterization of physiological traits.
Growth on carbon sources.
The cultures were tested in minimal media for growth on different carbon sources (Table 2
). Most of the isolates could grow on the hexose monosaccharides glucose, fructose, galactose, and the disaccharides sucrose, maltose, cellobiose, and trehalose. Other sugars such as arabinose (pentose, monosaccharide), lactose (disaccharide), and raffinose (trisaccharide) did not support the growth of most of the isolates. The sugar alcohols adonitol (ribitol), glycerol, and mannitol also did not support the growth of most of the isolates. Few of the isolates grew on the organic acids lactate, malate, succinate, and citrate. Approximately 25% of the isolates could grow on ethanol as a sole carbon source, while less than 10% grew on soluble starch. None of these isolates was able to grow on cellulose or tartrate as sole carbon source under these conditions. None of the isolates could use the amino acids arginine or proline as a carbon source. All of the isolates required biotin and thiamin for growth.
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Physical growth conditions. All of the strains were tolerant to at least 10% ethanol when transferred into the minimal media with that percentage of alcohol. All isolates grew at pH 2.5, and 94% of them grew at pH 2.0. Slightly more than one-third of the isolates grew at 37°C and slightly less than one-third grew at 10°C. Three of the isolates could grow at both 37 and 10°C.
Production of 4-EP and 4-EG.
Almost half of the isolates produced high levels of 4-EP (>2000 µg/L) and 4-EG (>1500 µg/L) when grown in a sweet Grenache rosé wine (Table 3
). The remaining isolates were almost evenly divided between those that produced a moderate amount of 4-EP (1000 to 2000 µg/L) and 4-EG (700 to 1000 µg/L), a low amount of 4-EP and 4-EG (5 to 60 µg/L), and essentially no 4-EP or 4-EG (<4 µg/L).
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The hierarchical cluster (Single LinkageEuclidean) divided the 35 strains into three large groups (Figure 2
). One group included all strains with a production of 4-EP and 4-EG less than 100 µg/L. The other two groups were characterized by strains that produced ~1000 µg/L and by strains that produced greater than 2000 µg/L of 4-EP and 4-EG, respectively. Statistical analysis found 4-EP and 4-EG production to be the most discriminant character.
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In the 26S rDNA separation, groups a, b, c, and d were 100% correctly classified. Group e contained only one member. The first linear discriminant accounted for 63% of the variance and is as follows:
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This discriminant function primarily depends on the inability of the yeast to use ethanol, maltose, and succinic acid as the sole carbon source and on the ability to grow on soluble starch.
The second linear discriminant accounted for 31% of the intergroup difference:
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The ability of yeast to use citric acid as a carbon source has the greatest influence, followed by the ability to grow at 37°C. The predicted groups are shown in Figure 3
.
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| Discussion |
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Physiological tests also reveal subgroups of B. bruxellensis (Table 3
). By comparing sufficiently large sets of genetic fingerprints and physiological characteristics, we hope to determine whether there are distinct groups of B. bruxellensis, which have a distinct growth behavior and a distinct flavor impact on wine. Thus far, our results allow a clear differentiation of isolates and several subgroupings. With the detailed genetic typing of wine isolates, offered by sequence analysis of the 26S rDNA, we can reliably identify unknown yeast and help track the spread of contaminating individual strains of yeasts through a winery or cooperage. The ability to identify a microorganism and track it, combined with knowledge of the biological properties of the strain, allows a winemaker to devise strategies to protect the wine from uncontrolled growth and potential spoilage by Brettanomyces. In order to better estimate the growth potential and flavor impact of particular isolates, it will be necessary to define more specific genes related to the critical pathways of off-flavor production to further refine groupings of Brettanomyces.
Characterization of physiological traits. The B. bruxellensis isolates were able grow on a variety of carbon and nitrogen sources, but the growth was even more variable than previously reported (Smith 1981). The diversity of carbon utilization patterns is impressive and makes it difficult to use those patterns as a taxonomic tool. None of these isolates used cellulose alone as a carbon source, as was reported for a Brettanomyces custersianus strain (Spindler et al. 1992), but many could grow on cellobiose, which is the ß 14 linked disaccharide of glucose that makes up cellulose. Both arginine and proline served as nitrogen sources for all of the isolates. Arginine and proline can be the most abundant amino acids in grape juice (Kliewer 1967), and if other nitrogen sources are available, then they may be left behind in finished wine. However, none of the isolates tested used arginine or proline as a sole carbon source aerobically or anaerobically. Although only 25% of the isolates could use ethanol as a carbon source, this result may still concern winemakers who do not attempt to control the growth of Brettanomyces in finished dry wines. Even if no residual sugar is present, there is a population of Brettanomyces that would find it possible to grow on the ethanol in the bottle. Van der Walt and van Kerken (1958) observed that all 79 isolates of Brettanomyces that they tested from South African wines required exogenous sources of biotin and thiamin for growth. That observation was confirmed for the 35 strains examined in this study. No two isolates were exactly the same in all characteristics tested.
Production of 4-EP and 4-EG was also highly variable in the wine tested. Almost one-half of the isolates produced a large amount of both compounds while the other half produced amounts ranging from <4 µg/L to >1000 µg/ L of 4-EP and 4-EG (Table 3
). Production of 4-EP and 4-EG has been used as a method to detect the presence of Brettanomyces in wine, but it may not be useful for many strains. We also know that there are other flavor components produced by Brettanomyces that may negatively impact the character of the wine and would not be detected by simply measuring 4-EP and 4-EG. If the variability we see is true for other wines as well, then it may prove difficult to predict how Brettanomyces will ultimately affect the flavor of a wine. Further study to determine how substrates and growth conditions affect the production of flavor compounds by Brettanomyces is necessary. However, the highly variable production of ethyl phenols defined the existence of strains with differing capacities to metabolize hydroxycinnamic acid. This may help to explain those cases where the microorganism was isolated but not associated with any off-flavor.
Genetic and physiology comparison. This is the first study in which strains of Dekkera/Brettanomyces bruxellensis are analyzed and compared by genetic and physiology aspects. Our results show that some of the physiological parameters studied are related to the genetic groups established by comparing the sequence of a part the 26S rDNA gene. Specifically in 26S rDNA groupings, the production of 4-EP and 4-EG, the ability to grow at 37°C, to metabolize ethanol, maltose, succinic acid, citrate, soluble starch, and glycerol contribute to differentiation among the groups with a very good degree of separation. Moreover, our results indicate that there may be B. bruxellensis with a characteristic European genetic profile that still exists as a subgroup (group a). There may also be a subgroup that occurs in the Americas (group b) that may be indigenous to that region. Group c, which contains isolates primarily from the United States and New Zealand, seems to be intermediate to these groups both genetically and physiologically. Determining the precise evolutionary relationships among isolates from different regions would require analysis of many more isolates than were available for this study. The data also indicate that group b is particularly dangerous and difficult to control in a winery situation because of its high SO2 tolerance and high level of 4-EP and 4-EG production.
| Conclusions |
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Manuscript submitted July 2005; revised December 2005
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