Exploring multispecies interactions between wine-associated yeasts
| dc.contributor.advisor | Bauer, Florian | en_ZA |
| dc.contributor.advisor | Rossouw, Debra | en_ZA |
| dc.contributor.advisor | Blassoples-Naidoo, Rene | en_ZA |
| dc.contributor.author | Conacher, Cleo Gertrud | en_ZA |
| dc.contributor.other | Stellenbosch University. Faculty of AgriSciences. Institute for Wine Biotechnology. | en_ZA |
| dc.date.accessioned | 2022-02-23T06:55:10Z | |
| dc.date.available | 2022-02-23T06:55:10Z | |
| dc.date.issued | 2021-12 | |
| dc.description | Thesis (PhDAgric)--Stellenbosch University, 2021. | en_ZA |
| dc.description.abstract | ENGLISH ABSTRACT: The fermentation of grape must to wine is catalysed by a diverse microbial community. Yeast are primary drivers of the associated alcoholic fermentation process and have therefore garnered considerable research interest. The diversity of yeast species present during wine fermentation influences the chemical composition and related sensory properties of wine as a result of the metabolic functioning of particular yeast species in response to abiotic and biotic factors. The latter is a relatively new research field, given that microbiological science has a significant monoculture bias, and as such, there is much still to be understood about the role and mechanisms of biotic stress in wine yeast ecosystems. Moreover, while the wine yeast ecosystem was the model used in this study, there are several other yeast ecosystems of biotechnological importance, including in biofuels production, bioremediation and other food and beverage industries, that would benefit from insight into these biotic stress mechanisms. The current basis of our understanding of the molecular mechanisms of yeast interactions in the wine ecosystem is based on two-species pairings, which keeps the system interaction network uncomplicated. However, there are many more role-players in natural ecosystems, and they do not interact in a linear fashion. At the micro- and macroscopic level, the importance of these often overlooked higher-order interactions has been highlighted in other ecosystems. There is very little information on higher-order interactions in the yeast ecology field, and this must be remedied for predictive understanding of these systems. Here, we sought to address the current status quo in multispecies yeast research, by aiming to develop new tools to investigate the mechanistic basis of interaction in systems comprised of more than two species. Furthermore, the study aimed to generate a greater depth of understanding of these systems, by investigating transcriptional responses of Saccharomyces cerevisiae to co-culture in mixed-species cultures of increasing complexity. Firstly, these aims were achieved by developing a fluorescence-based multi-colour flow cytometric method for tracking of a consortium consisting of wine-associated yeast species. This involved optimizing the genetic modification of the selected environmentally isolated yeast species, followed by extensive validation to confirm the representativeness of the system as well as development of the flow cytometric protocol. This was followed by addressing the pertinent issue of reproducibility in multispecies cultures, and showing the role of the physiological state of pre-cultures in determining their growth performance in three-species and four-species consortia. Finally, to contribute to our understanding of the molecular mechanisms of interaction in non-linear yeast systems, we showed that Saccharomyces cerevisiae expresses a combination of known pair-wise as well as unique genes when grown in a three-species system. By using interactive network visualizations of the generated transcriptomic data, we were able to functionally characterize the cellular responses in more detail than has been done before in similar studies. | en_ZA |
| dc.description.abstract | AFRIKAANSE OPSOMMING: Die fermentasie van druiwemos tot wyn word deur 'n diverse mikrobiese gemeenskap gekataliseer. Gis is die primêre drywers van die gepaardgaande alkoholiese fermentasie proses en het dus 'n aansienlike hoeveelheid navorsing belangstelling ontlok. Die diversiteit van gis spesies teenwoordig tydens wyn fermentasie beïnvloed die chemiese samestelling en verwante sensoriese eienskappe van wyn. Hierdie gebeur as gevolg van die metaboliese funksionering van bepaalde gis spesies in reaksie op abiotiese en biotiese faktore. Die invloed van biotiese faktore is 'n relatiewe nuwe navorsing veld, gegewe dat mikrobiologiese wetenskap 'n beduidende monokultuur vooroordeel het, en dus is daar nog baie om te verstaan oor die rol en meganismes van biotiese stres in wyngis-ekosisteme. Boonop, terwyl die wyngis- ekosisteem die model was wat in hierdie studie gebruik is, is daar 'n aantal ander gis-ekosisteme van biotegnologiese belang, insluitend in biobrandstof produksie, bioremediëring en ander voedsel- en drank bedrywe, wat baat sal vind by insig in hierdie biotiese stres meganismes. Die huidige basis van ons begrip van die molekulêre meganismes van gis-interaksies in die wyn-ekosisteem is gebaseer op twee- spesie parings, wat die stelsel interaksie netwerk ongekompliseerd hou. In natuurlike ekosisteme is daar egter baie meer rolspelers, en hulle werk nie op 'n lineêre wyse met mekaar nie. In ander ekosisteme, op die mikro- en makroskopiese vlak, is die belangrikheid van hierdie hoër-orde interaksies al reeds uitgelig. Daar is egter vergelykend baie min inligting oor hoër-orde interaksies in die gis ekologie veld, en moet dus reggestel word om ‘n voorspellende begrip te hê van hierdie stelsels. Hier het ons gepoog om die huidige status quo in multi-spesie gis navorsing te opdateer, deur nuwe metodes te ontwikkel vir die ondersoek van die meganistiese basis van gis-gis interaksies in sintetiese- ekosisteme wat uit meer as twee spesies bestaan. Verder was die studie daarop gemik om 'n beter begrip van hierdie sisteme te genereer, deur om na die transkripsie reaksie van Saccharomyces cerevisiae op mede-kultuur in gemengde-spesie kulture van toenemende kompleksiteit te ondersoek. Hierdie doelwitte is bereik deur eerstens 'n fluoressensie-gebaseerde multi-kleur vloeisitometriese metode te ontwikkel vir die monitering van 'n konsortium wat uit wyn-geassosieerde gis spesies bestaan. Hierdie het die optimalisering van die genetiese modifikasie van die geselekteerde omgewings- geïsoleerde gis spesies behels, gevolg deur uitgebreide validering om die verteenwoordigendheid van die gis in die sisteem te bevestig asook die ontwikkeling van die vloeisitometriese protokol. Dit was gevolg deur die tersaaklike kwessie van reproduseerbaarheid in multi-spesie kulture aan te spreek, en die rol van die fisiologiese toestand van voor-kulture in die bepaling van hul groei prestasie in drie- spesie en vier-spesie konsortia. Ten slotte, om by te dra tot die begrip van die molekulêre meganismes van interaksie in nie-lineêre gis stelsels, het ons getoon dat Saccharomyces cerevisiae 'n kombinasie van bekende paar gewyse sowel as heeltemal unieke gene uitdruk wanneer dit in 'n drie-spesie sisteem gekweek word. Deur interaktiewe netwerk visualisering van die gegenereerde transkriptomiese data, was ons in staat om die sellulêre reaksie in meer detail funksioneel te karakteriseer as wat voorheen in soortgelyke studies gedoen is. Hierdie studie dra by tot die kennisbasis oor multi-spesie interaksies in mikrobiese ekosisteme deur metodologieë te verbeter om hierdie stelsels meer doeltreffend te bestudeer en potensiële meganismes van interaksie voor te stel wat gis konsortia beheer. | af_ZA |
| dc.description.sponsorship | National Research Foundation (NRF) | en_ZA |
| dc.description.version | Doctoral | en_ZA |
| dc.embargo.terms | 2022-06-06 | |
| dc.format.extent | xii, 125 pages : illustrations | en_ZA |
| dc.identifier.uri | http://hdl.handle.net/10019.1/124300 | |
| dc.language.iso | en_ZA | en_ZA |
| dc.publisher | Stellenbosch : Stellenbosch University | en_ZA |
| dc.rights.holder | Stellenbosch University | en_ZA |
| dc.subject | Wine and wine making | en_ZA |
| dc.subject | Saccharomyces cerevisiae -- Biotechnology | en_ZA |
| dc.subject | Wine-associated yeast species | en_ZA |
| dc.subject | Yeast ecology | en_ZA |
| dc.subject | Yeast interaction | en_ZA |
| dc.title | Exploring multispecies interactions between wine-associated yeasts | en_ZA |
| dc.type | Thesis | en_ZA |