Investigation into physical and metabolic interactions within the wine yeast ecosystem
| dc.contributor.advisor | Bauer, Florian | en_ZA |
| dc.contributor.advisor | Divol, Benoit | en_ZA |
| dc.contributor.advisor | Setati, Mathabatha Evodia | en_ZA |
| dc.contributor.author | Luyt, Natasha Alethea | en_ZA |
| dc.contributor.other | Stellenbosch University. Faculty of AgriSciences. Dept. of Viticulture and Oenology. | en_ZA |
| dc.date.accessioned | 2021-12-06T18:04:45Z | |
| dc.date.accessioned | 2022-02-22T10:18:59Z | |
| dc.date.available | 2021-12-06T18:04:45Z | |
| dc.date.issued | 2021-12 | |
| dc.description | Thesis (PhDAgric)--Stellenbosch University, 2021. | en_ZA |
| dc.description.abstract | ENGLISH ABSTRACT: The microbial community of the wine ecosystem consist of filamentous fungi, bacteria and yeast. These organisms interact and compete for space and nutrients throughout fermentation. Since yeast are the primary contributors to alcoholic fermentation, various studies have described and characterized the biotic and abiotic factors which may influence yeast-yeast interactions. Through this search for a fundamental understanding of interactions, physical and metabolic interaction have emerged as pivotal drivers of population dynamics during fermentation. Nevertheless, these interactions remain elusive and the molecular mechanisms behind them remain poorly described. This study aimed at characterizing cell-cell and metabolic interactions between Saccharomyces cerevisiae and Lachancea thermotolerans from a phenotypic and molecular viewpoint. To achieve these outcomes, synthetic grape must fermentations were performed in a compartmentalised bioreactor, followed by a transcriptomic analysis which evaluated the effect of cell-cell and metabolic contact on gene expression and finally, a qRT-PCR approach, further evaluating the expression of specific genes of interest. The data confirmed the existence of an antagonistic relationship between S. cerevisiae and L. thermotolerans, which has been previously reported. It was observed that the presence of S. cerevisiae caused cellular death in L. thermotolerans in a cell-cell and metabolic contact dependant manner and the former appears more important in S. cerevisiae’s strategy to outcompete L. thermotolerans. In turn, the data also suggest that the metabolic activity of L. thermotolerans has a negative effect on the culturability of S. cerevisiae. Analysing the transcriptomic responses as a result of cell-cell and metabolic contact revealed distinct responses in both yeasts. S. cerevisiae reacted in a targeted manner, reinforcing its cell wall through the up-regulation of genes associated with maintaining cell wall integrity and structural components of the cell wall. L. thermotolerans showed a different response, with in particular strongly up-regulated heat shock genes, some of which have previously been linked to interspecies interaction. Both yeasts avoided co-aggregation by expressing adhesion genes less when in physical contact. Genes of interest were identified and their expression was further monitored throughout different stages of fermentation and investigated as to whether these responses were generic or species-specific. In S. cerevisiae, PAU, TIR2, HSP12 and FLO gene regulation occurred in a species-specific manner when evaluated in co-fermentations. While the regulation of adhesion FLO genes occurred in a species-specific manner between two closely related non-Saccharomyces yeasts, the role of HSP genes appeared to be conserved between the two. The avoidance of co-adhesion appeared to be a generic response, both in S. cerevisiae and non-Saccharomyces yeasts. The data provide novel insights into the transcriptomic responses to cell-cell contact in S. cerevisiae and non-Saccharomyces yeasts. Furthermore, the data provides a basis for future annotation of the S. cerevisiae genome to include the role of genes in ecological interactions. | en_ZA |
| dc.description.abstract | AFRIKAANSE OPSOMMING: Die mikrobiese gemeenskap van die wyn-ekosisteem bestaan uit filamentagtige swamme, bakterieë en gis. Hierdie organismes reageer op mekaar en kompeteer vir spasie en voedingstowwe tydens fermentasie. Aangesien gis die vernaamste bydraers tot alkoholiese fermentasie is, het verskeie studies die biotiese en abiotiese faktore wat gis-gis-interaksies beïnvloed beskryf en gekarakteriseer. In die soektog na ’n fundamentele begrip in interaksies, het fisiese en metaboliese interaksies as die beslissende drywers van populasie dinamika tydens fermentasie na vore gekom. Hierdie interaksies bly nietemin ontwykend en die molekulêre meganismes wat hulle aandryf, swak beskryf. Hierdie studie het gepoog om sel-sel- en metaboliese interaksies tussen Saccharomyces cerevisiae en Lachancea thermotolerans uit ’n fenotipiese en molekulêre oogpunt te karakteriseer. Om hierdie resultate te bereik is sintetiese druiwemos-fermentasies in ’n gekompartimentaliseerde bioreaktor gedoen gevolg deur ’n transkriptomiese ontleding wat die uitwerking van sel-sel- en metaboliese kontak op geenuitdrukking evalueer en laastens, ’n qRT-PCR benadering om verder die uitdrukking van spesifieke gene van belangstelling te evalueer. Die data het die bestaan van ’n antagonistiese verhouding tussen S. cerevisiae en L. thermotolerans bevestig, wat voorheen al aangeteken is. Daar is waargeneem dat die teenwoordigheid van S. cerevisiae selsterfte in L. thermotolerans op ’n sel-sel en metaboliese kontakafhanklike manier veroorsaak het en laasgenoemde blyk belangriker in S. cerevisiae se strategie om L. thermotolerans te uitoorlê. Op sy beurt, dui die data ook op die feit dat die metaboliese aktiwiteit van L. thermotolerans ’n nadelige uitwerking het op die kultuurkwekingsvermoë van S. cerevisiae. Ontleding van die transkriptomiese reaksies as gevolg van sel-sel- en metaboliese kontak het duidelike reaksies in albei gisvorme opgelewer. S. cerevisiae het op ’n doelbewuste manier reageer en sy selwand versterk deur die opregulering van gene wat verbind word met die instandhouding van die integriteit van die selwand en die strukturele komponente van die selwand. L. thermotolerans het ’n ander reaksie getoon, met veral sterk opgereguleerde hitteskokgene, waarvan party voorheen met interspesie-interaksies verbind is. Albei giste het ko-aggregasie vermy deur kleefgene minder uit te druk wanneer dit fisies kontak maak. Gene van belangstelling is geïdentifiseer en hul uitdrukking is verder gemonitor regdeur die verskillende fases van fermentasie en ondersoek is gedoen of hul reaksies generies of spesiespesifiek was. In S. cerevisiae, het PAU, TIR2, HSP12 en FLO geenregulering op ’n spesiespesifieke manier plaasgevind toe dit in ko-fermentasies geëvalueer is. Terwyl die regulering van kleef-FLO-gene plaasgevind het in ’n spesiespesifieke manier tussen twee nie-Saccharomyces- giste wat nou met mekaar verband hou, blyk dit of die rol van HSP-gene tussen die twee behoue gebly het. Die ontwyking van mede-aanklewing vertoon as ’n generiese reaksie in S. cerevisiae en nie-Saccharomyces giste. Die data verskaf nuwe insigte in die transkriptomiese reaksies van sel- sel-kontak in S. cerevisiae en nie-Saccharomyces giste. Die data verskaf verder ook ’n grondslag vir toekomstige annotasie van die S. cerevisiae genoom om die rol van gene in ekologiese interaksies in te sluit. | 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 | 137 pages : illustrations | en_ZA |
| dc.identifier.uri | http://hdl.handle.net/10019.1/124235 | |
| dc.language.iso | en_ZA | en_ZA |
| dc.publisher | Stellenbosch : Stellenbosch University | en_ZA |
| dc.rights.holder | Stellenbosch University | en_ZA |
| dc.subject | Cell interaction | en_ZA |
| dc.subject | Yeast interaction | en_ZA |
| dc.subject | Wine fermentation | en_ZA |
| dc.subject | Saccharomyces cerevisiae | en_ZA |
| dc.subject | Lachancea thermotolerans | en_ZA |
| dc.subject | UCTD | en_ZA |
| dc.title | Investigation into physical and metabolic interactions within the wine yeast ecosystem | en_ZA |
| dc.type | Thesis | en_ZA |