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Research

Our work is largely linked to three questions:

  • How do yeast and bacteria interact with their environment and each other in high stress environments such as seen in winemaking?
  • How can this knowledge be exploited to produce superior strains and wine process outcomes?
  • What does this knowledge tells us about the evolution and ecology of these microbes in their ‘natural’ environment.

More information on a selection of the group’s current projects is given below:

  • Yeast Functional Genomics

    Objectives

    Image on rightThis project seeks to identify the genes that are responsible for the unique properties of individual wine yeast strains and to determine how these confer their effects.

    Background

    It is widely recognised that strains of yeast can differ distinctly in terms of fermentation properties (e.g. speed, completeness, temperature optimum, etc) and production or modification of metabolites of sensory significance. In many cases the genetic basis for such differences is yet to be determined.

    Research approach

    Using high-throughput screens of yeast mutant libraries, as well as comparative genome analysis, we are identifying genetic differences between strains that relate to specific phenotypes. Further, we seek to understand the adaptive mechanisms by which yeast are able to survive in grape must and successfully complete alcoholic fermentation. This information is being used to guide further strain development and build models of how yeasts function under extreme conditions.

    Industry benefit

    The understanding behind the genetic heterogeneity and phenotypic differences exhibited by wine yeast will be exploited in future optimisation strategies to generate novel strains with desirable oenological traits. Such information also improves our understanding of the fundamentally important mechanisms by which a yeast copes with the ever-changing environments in which it finds itself.

    Project Leader Vladimir Jiranek
    Postdoctoral Investigators Jennie Gardner, Joanna Sundstrom, Michelle Walker & Tommaso Liccioli Watson
    Research Staff Jin Zhang
    PhD Student Investigators Chien-Wei ‘Max’ Huang & Josephine Jasmine Peter
    Honours Student Investigator Tom Lang

    Collaborators

    Key Publications

    Walker, ME, Nguyen, TD, Liccioli, T, Schmid, F, Kalatzis, N, Sundstrom, JF, Gardner, JM, Jiranek, V. (2014) 'Genome-wide identification of the fermentome; genes required for successful and timely completion of wine-like fermentation by Saccharomyces cerevisiae', BMC Genomics, vol. 15, no. 1, pp. 1- 17

    Project Funding

  • Directed Evolution of Yeast & Lactic Acid Bacteria

    Objectives

    Yeast & Lactic Acid BacteriaGeneration of superior yeast and lactic acid bacteria by the non-recombinant approach of directed evolution. For yeast, the aim is to create more robust strains for fermentation in high sugar and low nutrient juice. For lactic acid bacteria, the aim is to create strains better adapted to the highly inhibitory conditions of grape juice and wine.

    Background & Research Approach

    This research encompasses a broad range of microorganisms involved in the winemaking process. Our approach is to apply directed evolution (extended incubation under selective conditions) to the following organisms to improve their performance:

    Saccharomyces cerevisiae

    Pure cultures of selected strains of this relatively robust yeast are frequently inoculated by winemakers to help ensure fermentation reliability and wine quality. Nevertheless up to 10% of alcoholic fermentations are slow or prematurely arrest (‘stuck’), in part due to challenging grape must composition. Climate warming is producing shorter, drier vintages that can intensify these challenges by generating juices deficient in nutrients, high in sugar and yielding high alcohol wines. Directed evolution is being applied, targeting a number of oenological stressors including acidity, high sugar and ethanol content, in order to generate more robust strains. Additionally, other novel traits such as the metabolism of malic acid are being investigated.

    Non-Saccharomyces yeast

    When used as a single culture inoculum, such strains often fail to complete alcoholic fermentation largely due to their sensitivity to ethanol and their ability to compete with S. cerevisiae. Directed evolution is being used to generate more robust non-Saccharomyces strains so as to allow these yeasts to persist longer in fermentation and make a more significant contribution to the chemical and sensory profile of the wine.

    Lactic acid bacteria

    Lactic acid bacteria (LAB) have fastidious growth requirements and can be sensitive to the harsh conditions of winemaking (low pH, low temperature, high ethanol content and the presence of SO2). As a result they can be slow both to become established and to complete malolactic fermentation, thereby greatly extending the duration of the winemaking process. This project uses directed evolution to produce more efficient and reliable strains of LAB with higher tolerance to wine conditions.

    Industry benefit

    Superior yeast and lactic acid bacteria, generated using the non-recombinant method of directed evolution, will offer the industry greater reliability and predictability of alcoholic and malolactic fermentation. Reductions in processing times will enhance winemaking efficiency, winery throughput and reduce the risk of spoilage associate with unfinished wines being held in an unstabilised form for longer.

    Project Leader Vladimir Jiranek
    Postdoctoral Investigators Krista Sumby, Joanna Sundstrom, Michelle Walker & Tommaso Liccioli Watson
    Research Staff Alice Betteridge
    PhD Student Investigators Ana Hranilovic & Jiao Jiang

    Collaborators

    Key Publications

    McBryde, C, Gardner, JM, Lopes, MD & Jiranek, V (2006), 'Generation of novel wine yeast strains by adaptive evolution', American Journal of Enology and Viticulture, vol. 57, no. 4, pp. 423-430

    Betteridge, A, Grbin, P, Jiranek, V (2015) 'Improving Oenococcus oeni to overcome challenges of wine malolactic fermentation', Trends in Biotechnology, vol. 33, no.9, pp. 547-553

    Sumby, KM, Grbin, PR, Jiranek, V (2014) 'Implications of new research and technologies for malolactic fermentation in wine', Applied Microbiology and Biotechnology, vol. 98, no. 19, pp. 8111-8132

    Project Funding

  • Yeast Cell-Cell Communication

    Objectives

    Yeast Cell-CellThis project aims to explore the cell-cell signalling known and/or suspected to occur between microbes involved in the wine fermentation, so as to understand the impact on population and fermentation dynamics and metabolite formation.

    Background

    A yeast cell’s life is a dramatic sequence of feast and famine. Competition for nutrients can result in many cellular responses. The fate of an individual cell is not only determined by it’s own cellular machinery, but also by others in its vicinity. But how are these activities coordinated? Cell-cell communication via chemical signals is critical in this process and can result in altered growth and morphology and changes to core metabolic systems such as fermentation. A handful of signalling molecules are known, but are there others? Furthermore, do they affect fermentation dynamics or even quality of fermented products, like wine? Certainly one known signalling molecule, phenylethanol, contributes positive rose-like aromas to fermented beverages.

    Research Approach

    We have been investigating the influence of known signalling molecules on wine yeast cell growth, morphology and fermentation. Novel fermentation-specific cell-cell signalling molecules are also being identified and their impacts on yeast rigorously examined. We are defining the functional relevance of these molecules to industrial fermentation. This approach will be aided with the use of yeast mutant libraries. Where appropriate, a fermentation-specific cell-cell signalling model will be generated to provide a holistic view of the impact on wine.

    Industry benefit

    This study will provide knowledge whose application has the potential to improve industrial fermentation through new monitoring and management systems. Importantly, the findings will have relevance for how this organism interacts with its neighbours in a natural context.

    Project Leader Vladimir Jiranek
    Postdoctoral Investigators Jennie Gardner & Joanna Sundstrom
    Research Staff Jin Zhang
    PhD Student Investigators Ee Lin Tek

    Collaborators

    • Prof Steve Oliver, Department of Biochemistry & Cambridge Systems Biology Centre, University of Cambridge, UK
    • Dr Benjamin Binder, School of Mathematical Sciences, University of Adelaide

    Key Publications

    Binder, BJ, Sundstrom, JF, Gardner, JM, Jiranek, V, Oliver, SG (2015) 'Quantifying two-dimensional filamentous and invasive growth spatial patterns in yeast colonies', PLoS Computational Biology, vol. 11, no. 2, e1004070

    Project Funding

  • Brettanomyces spp. in Wine

    Objectives

    Brettanomyces logoThis project aims to gain a detailed understanding of the efficacies of current control strategies for avoidance of spoilage by the yeast Brettanomyces bruxellensis.

    Background

    It has been suggested the Brettanomyces bruxellensis are able to enter a Viable But Non Culturable (VBNC) state, allowing them to potentially survive exposure to current best practice processes in industry aimed at their control.

    Research approach

    This question is being addressed through application of rigorous cell culture methodology tied in with FACS analysis, single cell sorting, microscopy and molecular analysis.

    Industry benefit

    A better understanding of the survival methods employed by Brettanomyces bruxellensis would allow industry to more effectively:- detect, control and or ameliorate their presence in the winemaking process and reduce their destructive impact on the wine industry.

    Project Leader Paul Grbin
    Research Staff Nick van Holst

    Collaborators

    • Dr Chris Curtin, Research Manager – Biosciences, Australian Wine Research Institute

    Current Project Funding

  • Temperature Effects on Yeast

    Objectives

    Temperature graphTo understand the impact of industry-relevant temperature regimes (shifts and extremes) on yeast metabolism and fermentation outcome.

    Background & Research approach

    Fermentation temperature is a highly variable parameter that influences the rate of yeast growth, metabolism and fermentation, as well as chemical and enzymatic transformations occurring during winemaking. Consequently, efforts are usually made to control temperature or at least restrict it within an acceptable range. During the course of fermentation, yeast can be exposed to changes in temperature by as much as 30°C for periods of seconds to hours. Using a combination of lab scale fermentation modelling, flow cytometry and molecular biology techniques, we seek to elucidate the reaction of yeast to rapid, transient temperature changes, and characterise the impact on fermentation and wine quality.

    Industry benefit

    The project’s goal is to understand yeast response to dynamic temperature fluctuations during wine fermentation.  The knowledge gained has potential application in fermentation prediction models to allow for more precise control of tank temperature; a pre-requisite to fermentation reliability and consistency. In addition temperature regimes may be defined that allow better tailoring of yeast metabolite production.

    Project Leader Vladimir Jiranek
    Postdoctoral Investigators Jennie Gardner, Michelle Walker & Frank Schmid
    PhD Student Investigators Gregory Valentine

    Key Publications

    Schmid, F, Schadt, J, Jiranek, V & Block, DE (2009) 'Formation of temperature gradients in large- and small-scale red wine fermentations during cap management', Australian Journal of Grape and Wine Research, vol. 15, no. 3, pp. 249-255

    Project Funding

  • Dissecting the Complexity and Contribution of Uninoculated Fermentation

    Objectives

    The elucidation of the numbers of species present in uninoculated wine fermentations at specific time points, their relative proportions during fermentation and the impact on final wine aroma and flavour.

    Background

    Excellent winemaking outcomes and commercial success can occur for wines produced via uninoculated (indigenous) fermentations. During these, the often complex microbial populations of the grapes and winery conduct the fermentation. Much research has shown that different or more complex aroma profiles can result, but a number of key questions remain. Particularly, how and why do these populations vary from variety-to-variety and year-to-year? How are these populations interacting with each other and with the yeast or bacteria that are subsequently inoculated by the winemaker?

    Research approach

    A comprehensive analysis of uninoculated fermentations conducted at a commercial winery has been undertaken to define the nature, diversity and dynamics of yeast and lactic acid bacterial populations during inoculated and uninoculated fermentations. Sampling has occurred over 3 vintages across a number of grape varieties.  Isolates are being identified via morphology and genotyping and their impact defined through chemical and sensory analysis.

    Industry benefit

    The findings will help the winery define the extent to which the microflora and its contribution to wine composition represent a component of the unique terroir of the resulting wines. Recommendations will also be developed to help favour particular organisms over others. Ideally isolates of novel yeasts or bacteria will be identified for commercialisation by our partner yeast manufacturers.

    Project Leader Paul Grbin & Vladimir Jiranek
    PhD Student Investigators Simon Dillon, Aaron Hayes & Gang Jin

    Collaborators

    Key Publications

    Dillon, S, Jiranek, V, Grbin, P (2014) ‘Wild yeast fermentation can allow chemical and sensory differentiation in red and white wines’, Wine & Viticulture Journal, vol. 28, no. 6, pp. 23-24

    Project Funding

  • Microbiology of Winery Wastewater

    Objectives

    Winery WastewaterTo determine if efficiency and cost effectiveness of winery wastewater treatment can be improved by enhanced microbiological performance.

    Background

    While there is good knowledge of wastewater treatment in general, winery wastewater provides unique problems due to the short time that wastewater is available for treatment, the changing composition of wastewater over vintage (sugar rich to alcohol rich), and the general low organic content of wineries wastewater compared to other waste streams. Most previous work has focussed on plant design rather than the microbiology of treatment, and this is reflected in the winery wastewater resources available.

    Research approach

    The project plan starts with a microbial characterisation of winery wastewater samples supplied from multiple sites at the three keys stages of treatment (start-up, peak vintage flow, quiescent-post vintage). There will be a particular focus on filamentous organisms, because this group of microbes can impact significantly on plant operation, and on understanding how they adapt to the changing conditions in winery wastewater over the season.
    The microbiological data will be correlated with operational parameters to establish the key criteria driving treatment efficacy and cost effectiveness. If appropriate, tools to identify microbes will be developed and tested for their utility in assisting with decision making.

    Industry benefit

    The knowledge generated and tools developed in this project will allow winery operators to maximise wastewater treatment plant efficiency and reduce the likelihood of microbiologically related plant failures.

    Project Leader Paul Grbin
    Postdoctoral Investigators Kathryn Eales
    Research Staff Patrick Rea
    PhD Student Investigators Cristobal Onetto

    Collaborators

    Key Publications

    Eales, K, Carson, M, Constable, J, Kuma, A, Grbin, P (2014) Winery wastewater project refreshes understanding of treatment processes, Wine & Viticulture Journal, vol. 28, pp. 36-37

    Eales, KL, Schmid, F, Grbin, PR (2010) ‘The microbiology of winery wastewater treatment plants’, Australia and New Zealand Wine Industry Journal, vol25, pp. 22-24

    Current Project Funding

  • Fermentation Technology - 'TeeBot'

    Objectives

    Fermentation MachineryDevelop a robotic platform enabling automated sampling of large numbers of laboratory scale fermentations.

    Background

    Our research requires the screening of large numbers of yeast and lactic acid bacteria strains, to analyse their fermentation performance and associated properties (eg. metabolite production). This is particularly the case when working with yeast deletion libraries (see project ‘Yeast Functional Genomics’) or when screening individual isolates from directed evolution studies (see project ‘Directed Evolution of Yeast & Lactic Acid Bacteria’). This usually involves replicated flask fermentations (~100 mL per flask) for each strain, which are manually sampled multiple times per day, for several days to several weeks. To minimise labour and maximise research efficiency, a robotic platform capable of maintaining 96, 100 mL fermentations, was developed including the ability to automatically sample on demand.

    Research approach

    Fermentation MachineryThe Tee-Bot has been built around a Tecan Freedom EVO200, a very versatile and reliable liquid handling machine. The EVO’s work deck has been fitted with jacketed carriers, holding 96 fermentation flasks.
    Tempered water is pumped through the carriers to maintain fermentations at a desired temperature. Each flask sits on top of a stirrer for mixing and has been fitted with a custom-designed air-lock along with a silicon septum in the top, allowing the workstation’s liquid handling arm to sample the anaerobic fermentations. At user-defined intervals, aliquots are transferred directly from the flasks to purpose-built cooled microplate carriers which maintain the samples at ­10 °C until the user is ready to remove them from the workstation for subsequent analysis or storage. Setting up the Tee-Bot takes half a day to set up a 96-fermentation experiment, then the user can remotely monitor its progress via a smart phone from the office, another lab or home at any time of day.  Currently samples continue to be analysed offline. In the future, development of an automated system able to monitor a number of key metabolites (eg. sugar and alcohol), during the fermentation is desired.

    Industry benefit

    After extensive testing and method validation, the Tee-Bot become fully operational at the beginning of 2015 and has been used almost continuously, in addressing the demand users within the group. It is estimated that for each experiment (average of 2-3 weeks long) the machine saves 4 hours daily of researcher time for a total of ~100 hours. This include sampling at inconvenient times or out of office hours. Moreover, the number of flasks that researcher can effectively manage on their own it is limited to ~30, whereas the Tee-Bot allows 96 fermentations to be run simultaneously. This tripling of screening capacity with reduced effort accelerates the throughput of the group and increasing the efficiency of our research and the likelihood of identifying desirable strains for industry.

    Project Leader Vladimir Jiranek
    Postdoctoral Investigators Tommaso Liccioli Watson

    Project Funding

  • Innovative Wine Production: From Grape-Growing to Consumer

    Innovative Wine Production logo‘When less is more - achieving lower alcohol wines of improved quality’

    Objectives

    In light of climate change and perturbing stylistic preferences, the newly established ARC Training Centre for Innovative Wine Production is focusing on the development of an integrated, whole-of-production-chain approach for ethanol and flavour management in wine. The ARC TC-IWP has been formed with support from the Australian Research Council (ARC), 12 industry partners and Wine Australia.  Projects aim to elucidate the basis of sugar accumulation and concentration in grapes, achieve pre-fermentative sugar stripping and optimisation of early harvest and dealcoholisation regimes. Microbiological strategies are also being explored.  In particular, the impact of the initial juice sugar content on the diversityof Saccharomyces and non-Saccharomyces yeasts is being defined as well as the potential of selected yeasts to divert sugar away from ethanol production or to enhance flavour intensity in order to achieve lower alcohol wines of improved quality.

    Background

    Alcohol levels in wines have increased in recent decades largely due to climate change and improvements in viticultural practices and winemaking techniques. For example, from 1984 to 2008, in Australia alone, the average alcohol level in red wines has risen steadily from 12.4% to 14.4%. This trend was also driven by winemakers’ fondness for riper grapes, which make more aromatic and full-bodied wines.  However, this can have negative financial implications for winemakers, because high alcohol levels are penalised with higher taxes, which can increase the retail price. Concurrent to this trend, is a growing market interest in reduced alcohol beverages. The demand for lower alcohol wines is being driven by several factors such as the desire to be able to drive after drinking, health concerns, and wine and food pairing. Consequently, the wine industry is seeking methods to decrease the alcohol content of their wines, without significantly affecting other compounds associated with wine quality.

    Research approach

    Several approaches are being used across some 18 projects. For full details see: TC-IWP web address.  Projects being undertaken in the Wine Microbiology & Microbial Biotechnology group include the following.

    1. Exploiting communication between yeast and the grapevine
      A high-throughput, short-amplicon sequencing approach will be employed to demonstrate that ripening stage, site specific, and grape variety factors shape the fungal consortia inhabiting wine-grape surfaces.  Furthermore, the role of E3 ligases in mediating plant programmed cell death will be explored.
    2. Managing ethanol and sensory compounds by non-Saccharomyces yeasts
      This project focuses on exploring non-Saccharomyces biodiversity to select yeasts capable of diverting sugar from ethanol to other favourable or flavour-active end-products. The major objective is to define yeast strains and oenological practices leading to lower ethanol yield in high sugar must fermentations.  Use of newly-selected and improved non-Saccharomyces strains will lead to the establishment and implementation of more efficient methods for ethanol reduction, alongside reduced risk of quality loss.
    3. Impact of high sugar content on the efficiency and sensory outcomes of un-inoculated fermentations
      The project aims to uncover how wild yeast populations deal with the stressful conditions encountered during fermentation of high sugar juices. Different phenotypes will be identified together with the molecular rationale for their stress response and targets that can be used for their selection. Findings will guide selection of yeast strains with improved resistance to hyperosmotic stress and more desirable metabolic outcomes. Solutions for problematic fermentations, including recommendations for strain choice and fermentation parameters, and the ability to predict the final fermentation bouquet, will be evaluated.
    4. Selective and deliberate use of winemaking supplements to modulate sensory properties of wines
      The project will evaluate the effects of maceration enzymes, mannoproteins and tannins, added individually and in combination, on the quality of wines made from earlier harvested grapes. In addition, it will investigate the possibility of extracting phenolic compounds and polysaccharide compounds from red and white wine lees and use them as additives to potentially enhance wine quality.

    Industry benefit

    The ARC TC-IWP projects aim to improve current and/or develop new, economically feasible and environmentally viable techniques that do not generate additional capital investments and energy inputs associated with conventional methods for ethanol management. Ultimately, those projects will provide winemakers with more tools to produce good quality wines with lower alcohol content that wine consumers will enjoy.

    Project Leader Paul Grbin & Vladimir Jiranek
    Postdoctoral Investigators Shifeng Cao & Renata Ristic
    PhD Student Investigators Ana Hranilovic & Federico Tondini

    Collaborators

    Key Publications

    Bruwer, J, Jiranek, V, Halstead, L, Saliba, A (2014) 'Lower alcohol wines in the UK market: some baseline consumer behaviour metrics' British Food Journal, vol. 116, no. 7, pp. 1143-1161

    Current Project Funding

    The ARC TC-IWP links the scientific and industrial expertise, contributions and facilities of the University of Adelaide, Charles Sturt University, the Australian Wine Research Institute, CSIRO, NSW Department of Primary Industries, SA Research and Development Institute, BioInnovation SA, Treasury Wine Estates Vintners Ltd, Laffort Oenologie Australia Pty Ltd, Lowe Wines Pty Ltd, Memstar Pty Ltd, Tarac Technologies Pty Ltd and Sainsbury's Supermarkets Ltd. The centre is directed by Professor Vladimir Jiranek (UA) with the help of the TC-IWP Advisory Committee.

Wine Microbiology and Microbial Biotechnology
Address

Room 3.28, Level 3, WIC Building
WAITE CAMPUS
PMB 1, Glen Osmond SA 5064
Australia

Contact

T: +61 8 8313 0402
F: +61 8 8313 7415