Research programmes in grapevine and wine biotechnology

Introduction

The IWBT is the only research institute in the country that is focused primarily on studying the biology of grapevine and wine microorganisms, and cooperates very closely with the wine and table grape industries of South Africa.

Approach to research

The research philosophy of the IWBT is the result of strategic decisions on how best to respond to five challenges:

• Balancing academic and industrial needs.
• Establishing know-how, knowledge and key support technologies.
• Identifying the most relevant industrial problems and how to translate them into relevant scientific questions.
• Optimising projects and train postgraduate students.
• Generating intellectual property and products.

Research portfolio

The IWBT's research theme is the understanding of the biology of wine-associated organisms, including the ecology, physiology, molecular and cellular biology of grapevine, wine yeast and wine bacteria to promote the sustainable, environmentally friendly and cost-effective production of quality grapes and wine. The Institute continually integrates the latest technologies in the biological, chemical, molecular and data analytical sciences to achieve these aims.

The specific research portfolio consists of three programmes (see Fig. 1). The first focuses on a better understanding and exploitation of wine associated microbial biodiversity, and the physiological, cellular and molecular characterisation of Saccharomyces and non-Sacharomyces yeasts, as well as the genetic improvement of wine yeast strains. A second programme is concerned with lactic acid and other bacteria, including their impact on wine, metabolic characterisation and improvement of malolactic fermentation. The third programme focuses on the physiology, cellular and molecular biology and genetic improvement of grape cultivars. These programmes are planned and executed in an integrated manner, combining research groups from the Department of Chemistry and Polymer Science, the Department of Food Science, the Department of Viticulture and Oenology and the Institute for Wine Biotechnology under the scientific theme of Metabolomics and Metrics of vine, wine and wine organisms. The focus of the research will be to provide a fully integrated and controlled research chain starting with characterised model vineyards and ending with a comprehensive chemical, sensory and quality assessment of the final product. Each of these partners offers specific postgraduate opportunities

Focus areas of research team

Grapevine molecular biology and biotechnology

Dr John Moore
Specialisation: Grapevine molecular biology and biotechnology
Focus area: Grapevine biochemistry and metabolism

His research area forms part of the Grapevine Biotechnology Programme (within the framework of the NRF supported Wine Science Research Niche Area (RNA)) of the IWBT in collaboration with Professor Melané Vivier. The goals of the programme are to improve the disease resistance, fruit quality and abiotic stress (i.e. drought) tolerance of Vitis vinifera (grapevine) cultivars utilising transgenic technology. His specific research aims are to understand the biochemical and metabolic aspects of berry development, plant pathology and abiotic stress tolerance in grapevine with a focus on the role of the cell wall. He also maintains an interest in the chemistry and biology of plant polyphenols with particular reference to their functional significance in planta as well as being key constituents of grapes and wine.

Prof Melané Vivier
Specialisation: Grapevine molecular and cellular biology
Focus area: Biotechnology product development and molecular biology of grapevine stress

Her research programme is focused on the biology of grapevine (Vitis vinifera). The genetic potential and molecular mechanisms underlying V. vinifera's reaction towards some of the biotic and abiotic stresses typically appearing in vineyards are studied. Two main themes form part of the programme: (i) Understanding and manipulating disease resistance and (ii) Metabolic engineering of grapevine towards enhanced abiotic stress resistance and improved quality parameters. The programme is supported by grapevine transformation and regeneration technologies, basic molecular biology and some systems biology technologies and an increasing list of analytical methods to evaluate grapevine and model plant tissues.

Dr Philip Young
Specialisation: Grapevine molecular biology and biotechnology
Focus area: Molecular biology of grapevine with the focus on carotenoid biosynthesis

The main focus of the grapevine biotechnology research programme is on the development of genetically improved grape cultivars with outstanding fruit quality, reduced susceptibility to diseases, pests and other stress conditions and an increased nutritive value (in the case of table grapes). The specific focus of this research is the contribution of the carotenoid biosynthetic pathway to these grape quality aspects, especially with reference to their role in flavour and aroma development and abiotic stress tolerance.

Wine biotechnology

Prof Florian Bauer
Specialisation: Wine biotechnology
Focus area:     Yeast molecular and cellular biology

My research portfolio is focused on the yeast Saccharomyces cerevisiae and investigates the molecular processes that regulate gene expression, carbon flux (ethanol yield and transfer of activated acyl-residues), aroma compound production and cellular adhesion properties. The research projects make use of all standard microbiological and molecular biology techniques, as well as genomics-, transcriptomics- and metabolomics-based approaches. Insights gained from these projects are applied to improve wine yeast strains through the use of traditional breeding, mutagenesis, directed evolution and genetic engineering

Dr Benoit Divol
Specialisation: Wine microbiology and biotechnology
Focus area: Enzymes production by wine yeasts and bacteria; microorganisms interactions with each other and with the environment

Microbial populations play an essential role in winemaking. Apart from the species responsible for completing fermentations (i.e. mainly Saccharomyces cerevisiae and Oenococcus oeni), several others occur throughout the vinification process and somehow influence the final chemical composition of the wines to various extents. Dr Divol’s research focuses on survival strategies and stress response (in particular those of spoilage microorganisms), wine ecology, population dynamics and impact of these microorganisms on the organoleptic quality of wines. Specific attention is given to key enzymes of non-Saccharomyces yeasts as well as those of lactic acid bacteria involved in various intracellular metabolisms or secreted into the wine. Antimicrobial peptides and proteins secreted by these microorganisms are also studied in order to evaluate their impact on spoilage microbes.

Prof Maret du Toit
Specialisation: Wine microbiology
Focus area:    Lactic acid bacteria, malolactic fermentation and microbial spoilage

Microorganisms form an integral part of the winemaking process and can have a positive or negative influence on wine quality. Lactic acid bacteria (LAB), especially O. oeni and L. plantarum are responsible for malolactic fermentation in wine. Apart from performing this fermentation, they can also contribute to wine aroma compounds that will improve wine quality. The focus is on the following enzymes; ß-glucosidases, esterases, citrate lyase, proteases and phenolic acid decarboxylases that are important for specific aroma compounds. LAB is also regarded as a spoilage microorganism and the focus is on bitterness, biogenic amines and volatile sulphur compounds. LAB also produce bacteriocins, which are investigated in terms of being used as an alternative to chemical preservatives. Research is currently being conducted on the omics of wine LAB, especially the metabolome produced by commercial MLF starter cultures.

Dr Evodia Setati
Specialisation: Wine Microbiology
Focus area: Microbial ecology, population dynamics and functional potential of non-Saccharomyces yeasts

Microbial diversity at different stages of wine making has been studied for many years in the quest to understand the wine ecology and the role of different microorganisms in grape must fermentation. However, none of the methods used provide comprehensive genetic information to allow for detailed analysis of the metabolic activities and interdependencies underlying the wine microbiota and the resulting impact on the organoleptic properties of wine. My research combines metagenomics, traditional microbiological analyses as well as community fingerprinting methods (e.g. T-RFLP and ARISA) to evaluate functional diversity and microbial interactions during wine making, with special focus on genes encoding antimicrobial peptides and proteins (e.g. killer toxins and cell wall lytic enzymes). Isolation and oenological characterization of non-Saccharomyces yeasts is also of special interest due to the growing interest of these yeasts as starter cultures in co-fermentation with Saccharomyces cerevisiae.

Computational Biology and Biomathematics

Dr Dan Jacobson
Specialisation:   Computational Biology
Focus area:        Omics Integration, Network Theory & Biomathematics

My group focuses on the development/application of mathematical, statistical and computational methods to biological data sets in order to yield new insights and thus transform data into knowledge.  Areas of Mathematics of interest include the use of Network Theory and Markov Clustering, Wavelet Theory, Machine Learning (e.g. Random forests, Support Vector Machines, etc.) and Linear Algebra (primarily as applied to Large Scale Multivariate Modelling and Networks).  Areas of Statistics of particular interest to this programme are the use of both frequentist (parametric and non-parametric) and Bayesian methods as well as the development of new methods in Multivariate Statistics (Chemometrics) and agglomerative methods such as Molecular Set Analysis.  These mathematical and statistical methods are applied to various Omics data sets (Genomics, Metagenomics, Phylogenomics, Transcriptomics, Proteomics, Metabolomics and Chemiomics) individually as well as in combination in an attempt to better understand evolution as well as the transcriptional, translational and chemical (kinetic) regulatory networks at play in various organisms and chemical systems.  My group also does work based on the Theory of Sampling and does the Experimental Design for many of the larger experiments undertaken within the IWBT/DVO environment.  In addition, I am actively involved in lecturing in and supervising postgraduate students from the Biomathematics programme in the Department of Mathematics as well as the African institute for Mathematical Sciences (AIMS).  My group is also involved in (and one of the campus’ largest users of) High Performance Computing (HPC) and together with colleagues from the Departments of Engineering and Information Technology oversees the central HPC environment on campus.

Analytical chemistry

Dr Helénè Nieuwoudt
Specialisation:  Biospectroscopy, bioprocess monitoring and chemical, sensory and consumer preference profiling of wine
Focus areas:      (i) Application of infrared spectroscopic techniques in viticulture, oenology and biotechnology, as well as monitoring of bioprocesses. (ii) Chemical, sensory and consumer  profiling of wine, with particular focus on the effect of winemaking techniques on wine quality.

Her research focuses on both the quantitative and qualitative profiling of grapes and wine.

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Research collaboration

The IWBT's research is conducted in collaboration with local research institutions, as well as several international laboratories.

National

• Departments of Chemistry, Food Science, Genetics, Microbiology and Viticulture and Oenology, Stellenbosch University
• Department of Biochemistry and Microbiology, Rhodes University
• Department of Cellular and Molecular Biology, University of Cape Town
• Agricultural Research Council - Infruitec/Nietvoorbij, Stellenbosch
• South African Sugar Research Institute; Distell and Elsenburg Agricultural College

International

• The Australian Wine Research Institute, Adelaide, Australia
• CSIRO Plant Industry, Australia
• Centrum Gruene Gentechnik, Germany
• Universidad de Castilla La Mancha, Ciudad Real, Spain
• Catholic University of Louvain, Belgium
• University of Bordeaux, Bordeaux, France
• Fondazione Edmund Mach, San Michele all'Adige, Italy
• Universität Roviri i Virgili, Tarragona, Spain
• Instituto de fermentaciones Industriales (CSIC), Madrid, Spain
• University of Lund, Sweden
• Matforsk, Centre for Biospectroscopy and Data Modeling, Norway
• Swiss Wine Research Institute, Wädenswil, Switzerland
• Department of Viticulture and Oenology, University of California, Davis, USA
• Complex Carbohydrate Research Center, Athens, USA
• Ryerson University, Toronto, Canada, University of Cuyo, Mendoza, Argentina
• Max Rubner Institut, Karlsruhe, Germany
• University of Udine, Italy
• Hochschule GEISENHEIM University, Germany
• Université de Bourgogne, Dijon, France

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Publications

Outputs 1995 - 2011

Outputs 2012

Scientific articles 2013

1. Joubert, D.A., de Lorenzo, G. & Vivier, M.A. (2013). Regulation of the grapevine polygalacturonase-inhibiting protein encoding gene: Expression pattern, induction profile and promoter analysis. Journal of Plant Research, 126(2), 267-281.
2. Kritzinger, E.C., Bauer, F.F. & Du Toit, W.J. (2013). Role of glutathione in winemaking: A review. Journal of Agricultural and Food Chemistry, 61(2), 269-277.
3. Moore, J.P., Nguema-Ona, E E., Vicré-Gibouin, M., Sørensen, I., Willats, W.G.T., Driouich, A. & Farrant, J.M. (2013). Arabinose-rich polymers as an evolutionary strategy to plasticize resurrection plant cell walls against desiccation. Planta, 237(3), 739-754.
4. Mtshali, P.S., Divol, B. & Du Toit, M. (2013). Evaluating Lactobacillus and Pediococcus strains for enzyme-encoding genes related to peptide and amino acid utilization in wine. Annals of Microbiology, 63(1), 233-239.
5. Smit, A.Y. & du Toit, M. (2013). Evaluating the Influence of Malolactic Fermentation Inoculation Practices and Ageing on Lees on Biogenic Amine Production in Wine. Food and Bioprocess Technology, 6(1), 198-206.
6. Nguema-Ona, E.E., Moore, J.P., Fagerström, D.A., Fangel, U.J., Willats, G.T.W., Hugo, A. & Vivier, M.A.  2013.  Overexpression of the grapevine PGIP1 in tobacco results in compositional changes in the leaf arabinoxyloglucan network in the absence of fungal infection.  BMC Plant Biology 13:46. 
7. Smit, A.Y., du Toit, W.J., Stander, M. & du Toit, M.  2013.  Evaluating the influence of maceration practices on biogenic amine formation in wine.  LWT – Food Science and Technology 53:297-307.
8. Alberts, P.,  Kidd,M., Stander, M.A., Nieuwoudt, H.H.,  Tredoux, A.G.J. & de Villiers, A. 2013.  Quantitative survey of 3-alkyl-2-methoxypyrazines and first confirmation of 3-ethyl-2-methoxypyrazine in South African Sauvignon blanc wines. South African Journal of Enology and Viticulture. 34 (1):54-67.
9. Cameron, M., Siebrits, L., du Toit, M. & Witthuhn, R.C. 2013.  PCR-based DGGE fingerprinting and identification of the microbial population in South African red grape must and wine.  Journal International des Sciences de la Vigne et du Vin 47:47-54.
10. Styger, G., Jacobson, D., Prior, B.A. & Bauer, F.F. 2013.  Genetic analysis of the metabolic pathways responsible for aroma metabolite production by Saccharomyces cerevisiae.  Applied Genetics and Molecular Biotechnology  97 (10):4429-4442.

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Patents

901996 Amylolytic Yeast Strains
907246 Biological Control Agent
907246 Wine Yeast Strains*
901903 Biological Control Agent
925949 Pectolytic Yeast Strains
93/4435 Amylolytic Cassette
96/3971 Malolactic Yeast
2005/8194 Resveratrol
2007/04132 Carnitine-synthesising

*The University of Stellenbosch has licensed Anchor Yeast to manufacture and market the VIN13 wine yeast and has received royalties on the 80 tons that have been sold over the last eleven years.