Browsing by Author "Bagheri, Bahareh"

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    Co-flocculation of yeast species, a new mechanism to govern population dynamics in microbial ecosystems
    (Public Library of Science, 2015) Rossouw, D.; Bagheri, Bahareh; Setati, Mathabatha Evodia; Bauer, Florian
    Flocculation has primarily been studied as an important technological property of Saccharomyces cerevisiae yeast strains in fermentation processes such as brewing and winemaking. These studies have led to the identification of a group of closely related genes, referred to as the FLO gene family, which controls the flocculation phenotype. All naturally occurring S. cerevisiae strains assessed thus far possess at least four independent copies of structurally similar FLO genes, namely FLO1, FLO5, FLO9 and FLO10. The genes appear to differ primarily by the degree of flocculation induced by their expression. However, the reason for the existence of a large family of very similar genes, all involved in the same phenotype, has remained unclear. In natural ecosystems, and in wine production, S. cerevisiae growth together and competes with a large number of other Saccharomyces and many more non-Saccharomyces yeast species. Our data show that many strains of such wine-related non-Saccharomyces species, some of which have recently attracted significant biotechnological interest as they contribute positively to fermentation and wine character, were able to flocculate efficiently. The data also show that both flocculent and non-flocculent S. cerevisiae strains formed mixed species flocs (a process hereafter referred to as co-flocculation) with some of these non-Saccharomyces yeasts. This ability of yeast strains to impact flocculation behaviour of other species in mixed inocula has not been described previously. Further investigation into the genetic regulation of co-flocculation revealed that different FLO genes impact differently on such adhesion phenotypes, favouring adhesion with some species while excluding other species from such mixed flocs. The data therefore strongly suggest that FLO genes govern the selective association of S. cerevisiae with specific species of non-Saccharomyces yeasts, and may therefore be drivers of ecosystem organisational patterns. Our data provide, for the first time, insights into the role of the FLO gene family beyond intraspecies cellular association, and suggest a wider evolutionary role for the FLO genes. Such a role would explain the evolutionary persistence of a large multigene family of genes with apparently similar function.
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    Comparative analysis of fermentative yeasts during spontaneous fermentation of grapes from different management systems
    (Stellenbosch : Stellenbosch University, 2014-04) Bagheri, Bahareh; Setati, Mathabatha Evodia ; Stellenbosch University. Faculty of AgriSciences. Dept. of Institute for Wine Biotechnology.
    ENGLISH ABSTRACT: The microorganisms associated with grape berry surface can be influenced by numerous factors such as agronomic parameters. Hence, the focus of this study was comparison between three agronomic farming systems to evaluate their impact on yeast diversity. In addition, the dynamics of the yeast population throughout wine alcoholic fermentation were monitored. Three vineyards (conventional, biodynamic and integrated) were chosen and the experiment was carried out during the 2012 and 2013 vintages. A total of 600 yeast isolates including Saccharomyces and non-Saccharomyces were obtained from grape must and during different stages of fermentation including beginning, middle and end of alcoholic fermentation, from all three vineyards. Yeast species diversity in grape must and their population dynamics were evaluated by cultivating the yeasts in nutrient media and using “Polymerase Chain Reaction and sequence analysis of the ITS1-5.8S rRNA-ITS2 region. Eight, four and one species were detected from biodynamic, conventional and integrated must in 2012 vintage whereas, 2013 vintage displayed a higher diversity and 12, 11 and 9 different species were identified from biodynamic, conventional and integrated vineyard, respectively. Aureobasidium pullulans was the most frequent isolate in all three vineyards whereas Saccharomyces cerevisiae was below detection level in grape must and was only isolated in low frequencies in biodynamic must (3% of the total population) in both vintages. In general, the overlap of common yeast isolates (e.g. M. pulcherrima and H. uvarum) was observed in the musts obtained from different vineyards although unique minor species could be isolated and clearly demonstrated the distinction between the three vineyards. Moreover, biodynamic must displayed a higher degree of diversity in both 2012 and 2013 compared to the conventional and integrated vineyards. The beginning of all spontaneous fermentations was dominated by non-Saccharomyces yeast species (e.g. H. uvarum, C. zemplinina), as the fermentation proceeded, the population of non-Saccharomyces species were gradually decreased and strongly fermentative yeast S. cerevisiae dominated and completed the fermentations. The dynamics of S. cerevisiae strains was also evaluated during different stages of fermentation (beginning, middle and end), using interdelta PCR methods. A high diversity (10-18 strains per fermentation) and the sequential substitution of S. cerevisiae strains were observed throughout spontaneous fermentations. In addition, integrated vineyard displayed the highest S. cerevisiae strains compared to biodynamic and conventional vineyard.
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    The diversity and dynamics of indigenous yeast communities in grape must from vineyards employing different agronomic practices and their influence on wine fermentation
    (South African Society for Enology and Viticulture, 2015) Bagheri, Bahareh; Bauer, Florian; Setati, M. E.
    The current study evaluated the diversity of yeast species in Cabernet Sauvignon grape must derived from three neighbouring vineyards from a similar terroir but on which significantly different management practices are employed. The fermentation kinetics and yeast population dynamics were monitored from the beginning to the end of spontaneous fermentation. The grape musts were characterised by distinct yeast populations comprising oxidative, weakly fermentative and strongly fermentative yeasts. Different combinations of dominant non-Saccharomyces yeasts were observed in each must, with significantly different assortments of dominant species, including Starmerella bacillaris (synonym Candida zemplinina), Lachancea thermotolerans, Hanseniaspora uvarum, Candida parapsilosis and Wickerhamomyces anomalus. None of these yeast consortia appeared to affect the growth of Saccharomyces cerevisiae or inhibit the overall progress of fermentation. However, the percentage of fermentative yeasts was positively correlated with the fermentation rate. Glucose and fructose consumption rates suggested active participation of both glucophilic and fructophilic yeasts from the onset of fermentation. The data highlight two parameters, viz. initial cell concentration and yeast community composition, as important fermentation drivers and open the possibility to predict fermentation behaviour based on the initial composition of the yeast community.
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    Ecological interactions are a primary driver of population dynamics in wine yeast microbiota during fermentation
    (Nature Research (part of Springer Nature), 2020) Bagheri, Bahareh; Bauer, Florian; Cardinali, Gianluigi; Setati, Mathabatha Evodia
    Spontaneous wine fermentation is characterized by yeast population evolution, modulated by complex physical and metabolic interactions amongst various species. The contribution of any given species to the final wine character and aroma will depend on its numerical persistence during the fermentation process. Studies have primarily evaluated the effect of physical and chemical factors such as osmotic pressure, pH, temperature and nutrient availability on mono- or mixed-cultures comprising 2–3 species, but information about how interspecies ecological interactions in the wine fermentation ecosystem contribute to population dynamics remains scant. Therefore, in the current study, the effect of temperature and sulphur dioxide (SO2) on the dynamics of a multi-species yeast consortium was evaluated in three different matrices including synthetic grape juice, Chenin blanc and Grechetto bianco. The population dynamics were affected by temperature and SO2, reflecting differences in stress resistance and habitat preferences of the different species and influencing the production of most volatile aroma compounds. Evidently at 15 °C and in the absence of SO2 non-Saccharomyces species were dominant, whereas at 25 °C and when 30 mg/L SO2 was added S. cerevisiae dominated. Population growth followed similar patterns in the three matrices independently of the conditions. The data show that fermentation stresses lead to an individual response of each species, but that this response is strongly influenced by the interactions between species within the ecosystem. Thus, our data suggest that ecological interactions, and not only physico-chemical conditions, are a dominant factor in determining the contribution of individual species to the outcome of the fermentation.
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    Evaluating the effect of environmental parameters on the dynamics of the wine yeast consortium
    (Stellenbosch : Stellenbosch University, 2018-03) Bagheri, Bahareh; Setati, Mathabatha Evodia; Bauer, Florian; Stellenbosch University. Faculty of AgriSciences. Dept of Viticulture and Oenology.
    ENGLISH ABSTRACT: Wine fermentation is a complex biochemical process which is characterized by the sequential development of various weakly and strongly fermentative yeast species. Thus, in such a multispecies consortium, individual species interact with one another and with their environment. Consequently, final chemical composition of wine will be affected significantly by the contribution of individual species as well as yeast-yeast interactions present in a wine consortium. The contribution of individual strain in the wine consortium is affected by several biotic (ecological interactions, killer factors, and grape variety) as well as abiotic parameters (temperature, sulphur dioxide, oxygen and nutrient availability). However, each strain will be affected differently by the combination of these parameters. Previous studies in wine fermentations have mainly focused on mixed culture fermentations composed of two species. Thus, fundamental rules underlying the effect of these parameters in a multi-species ecosystem are not fully understood. To decipher the principles that govern the complex wine ecosystem, a simplified model consortium comprising eight species commonly encountered in South African grape microbiota was established. An Automated ribosomal intergenic spacer analysis (ARISA) method was also developed in order to monitor population dynamics of the yeast consortium. The influence of presence of Saccharomyces cerevisiae as a biotic stress was investigated on the dynamics of yeast consortium in synthetic must using plating method and ARISA. Furthermore, the yeast consortium was used as an inoculum in Chenin blanc grape must where the population dynamics were monitored by plating method. The results confirmed that a selective pressure applied by the keystone species, S. cerevisiae modified the pattern of population dynamics. Wine ecosystem was characterized by supportive and inhibitory interactions. Furthermore, in spite of the differences between the two grape matrices, a similar pattern of population dynamics was observed in both fermentations. This observation suggested broad applicability of the model consortium to study the ecological interactions in the wine fermentation. In the next step, the variation in initial cell densities of each member of the consortium was used as a tool to untangle the contribution of individual strain in the population dynamics and wine aroma. The data suggest that S. cerevisiae applied a selective pressure to suppress the growth of main competitor in the wine ecosystem. Moreover, the presence of individual non-Saccharomyces species at a higher cell density, favoured the growth of some non-Saccharomyces species while suppressing the growth of others in the yeast consortium. Lastly, the effect of temperature and sulphur addition on the dynamics of the yeast consortium was evaluated in the synthetic must and real grape must fermentations. The results demonstrated that ecological interactions are largely independent of the matrix, confirming that the constructed multispecies consortium is a robust model that can be used as a tool to predict microbial behavior from a simple ecosystem to the complex natural environment. Furthermore, the effect of temperature and sulphur dioxide on the growth of non-Saccharomyces species was species/strain dependent. The results suggest that environmental parameters modify the pattern of population dynamics. However, ecological interactions seem to drive the wine ecosystem. The current study for the first time revealed the potential of a multi-species yeast consortium in understanding the ecological interactions in wine fermentation.
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    The impact of saccharomyces cerevisiae on a wine yeast consortium in natural and inoculated fermentations
    (Frontiers Media, 2017) Bagheri, Bahareh; Bauer, Florian; Setati, Mathabatha E.
    Natural, also referred to as spontaneous wine fermentations, are carried out by the native microbiota of the grape juice, without inoculation of selected, industrially produced yeast or bacterial strains. Such fermentations are commonly initiated by non-Saccharomyces yeast species that numerically dominate the must. Community composition and numerical dominance of species vary significantly between individual musts, but Saccharomyces cerevisiae will in most cases dominate the late stages of the fermentation and complete the process. Nevertheless, non-Saccharomyces species contribute significantly, positively or negatively, to the character and quality of the final product. The contribution is species and strain dependent and will depend on each species or strain’s absolute and relative contribution to total metabolically active biomass, and will therefore, be a function of its relative fitness within the microbial ecosystem. However, the population dynamics of multispecies fermentations are not well understood. Consequently, the oenological potential of the microbiome in any given grape must, can currently not be evaluated or predicted. To better characterize the rules that govern the complex wine microbial ecosystem, a model yeast consortium comprising eight species commonly encountered in South African grape musts and an ARISA based method to monitor their dynamics were developed and validated. The dynamics of these species were evaluated in synthetic must in the presence or absence of S. cerevisiae using direct viable counts and ARISA. The data show that S. cerevisiae specifically suppresses certain species while appearing to favor the persistence of other species. Growth dynamics in Chenin blanc grape must fermentation was monitored only through viable counts. The interactions observed in the synthetic must, were upheld in the natural must fermentations, suggesting the broad applicability of the observed ecosystem dynamics. Importantly, the presence of indigenous yeast populations did not appear to affect the broad interaction patterns between the consortium species. The data show that the wine ecosystem is characterized by both mutually supportive and inhibitory species. The current study presents a first step in the development of a model to predict the oenological potential of any given wine mycobiome.
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    Investigating the effect of selected non-saccharomyces species on wine ecosystem function and major volatiles
    (Frontiers Media, 2018-11-13) Bagheri, Bahareh; Zambelli, Paolo; Vigentini, Ileana; Bauer, Florian; Setati, Mathabatha Evodia; Cao, Mingfeng
    Natural alcoholic fermentation is initiated by a diverse population of several non-Saccharomyces yeast species. However, most of the species progressively die off, leaving only a few strongly fermentative species, mainly Saccharomyces cerevisiae. The relative performance of each yeast species is dependent on its fermentation capacity, initial cell density, ecological interactions as well as tolerance to environmental factors. However, the fundamental rules underlying the working of the wine ecosystem are not fully understood. Here we use variation in cell density as a tool to evaluate the impact of individual non-Saccharomyces wine yeast species on fermentation kinetics and population dynamics of a multi-species yeast consortium in synthetic grape juice fermentation. Furthermore, the impact of individual species on aromatic properties of wine was investigated, using Gas Chromatography-Flame Ionization Detector. Fermentation kinetics was affected by the inoculation treatment. The results show that some non-Saccharomyces species support or inhibit the growth of other non-Saccharomyces species in the multi-species consortium. Overall, the fermentation inoculated with a high cell density of Starmerella bacillaris displayed the fastest fermentation kinetics while fermentation inoculated with Hanseniaspora vineae showed the slowest kinetics. The production of major volatiles was strongly affected by the treatments, and the aromatic signature could in some cases be linked to specific non-Saccharomyces species. In particular, Wickerhamomyces anomalus at high cell density contributed to elevated levels of 2-Phenylethan-1-ol whereas Starm. bacillaris at high cell density resulted in the high production of 2-methylpropanoic acid and 3-Hydroxybutanone. The data revealed possible direct and indirect influences of individual non-Saccharomyces species within a complex consortium, on wine chemical composition.