Predictability of the community-function landscape in wine yeast ecosystems

Abstract

Predictively linking taxonomic composition and quantitative ecosystem functions is a major aspiration in microbial ecology, which must be resolved if we wish to engineer microbial consortia. Here, we have addressed this open question for an ecological function of major biotechnological relevance: alcoholic fermentation in wine yeast communities. By exhaustively phenotyping an extensive collection of naturally occurring wine yeast strains, we find that most enologically-relevant traits exhibit a strong phylogenetic signal, indicating that the most relevant functions in wine yeast communities can be predicted from taxonomy. Further, we demonstrate that the quantitative contributions of individual wine yeast strains to the community function followed simple quantitative rules. These regularities can be integrated to quantitatively predict the function of newly assembled consortia. Besides addressing a fundamental open question in functional ecology, our results and methodologies provide a blueprint for rationally managing microbial processes of biotechnological relevance.

Multi-omics framework to reveal the molecular determinants of fermentation performance in wine yeast populations

“…These conditions were selected because they are part of common practices in wine production [67], so it seems reasonable that winemakers have design different enological strategies that directly shape the performance of Saccharomyces, the main wine yeast. However, in a moment where spontaneous fermentations and the use of complex multi-species consortia are gaining importance in the wine industry, a deeper knowledge of the environmental preferences and metabolic traits of non- Saccharomyces species is needed [19].…”

“…To finely assess the impact of fermentation conditions in the transcriptional and metabolite patterns of wine yeasts, we replicated the fermentations using synthetic grape must (SGM), prepared as described by Ruiz et al, [19]. To obtain the greatest diversity of wild communities to further inoculate the experimental fermentations in SGM, we extracted 2 mL of fermenting grape musts at the tumultuous stage (between 23 and 45% of total sugars consumed, Supplementary Table S1 ) from each control replicate of the 18 fermentation assays performed in the natural grape musts ( Supplementary Figure S1 ).…”

Whole-genome sequencing and phenotyping reveal specific adaptations ofLachancea thermotoleransto the winemaking environment

“…In our work, we focused on L. thermotolerans, a non-Saccharomyces yeasts species, involved in winemaking, which has gained attention in recent years due to its potential as a fermentative alternative to cope with climatic conditions (Vicente et al, 2023). Through whole-genome sequencing of a large set of 145 strains, we determined the population structure of the species, deciphering the evolutionary trajectory and confirming the influence of winemaking practices on yeasts evolution and subpopulation differentiation (Freel et al, 2014;Hranilovic et al, 2017).…”

“…The yeast species L. thermotolerans, a non-Saccharomyces yeast involved in wine fermentation, has recently attracted attention for its lactic acid production during alcoholic fermentation. This characteristic is considered a valuable approach in winemaking as it provides a biological approach to deal with the effects of climate change on grape musts, such as a higher concentration of fermentable sugars and a decrease in acidity values (Hranilovic et al, 2018;Porter et al, 2019;Vicente et al, 2023;Vilela, 2018). Additionally, several L. thermotolerans enzymes have been studied due to their potential in industrial and pharmaceutical applications (Aktar et al, 2023;Fan et al, 2020;Mousavi et al, 2015;Prasad et al, 2005).…”

Design of a new model yeast consortium for ecological studies of enological fermentation

“…In addition, the range of diversity tested in this study might be limited since it varied only based on initial abundance while the number of species (and therefore species richness) was constant. For example, Ruiz et al, (2023) showed a negative effect of an increasing richness in wine yeast communities. They observed that S. cerevisiae could not finish fermentation in some communities due to the higher probability of the presence of antagonistic species.…”