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 ecologically and industrially relevant traits exhibit phylogenetic signal, allowing functional traits in wine yeast communities to be predicted from taxonomy. Furthermore, we demonstrate that the quantitative contributions of individual wine yeast strains to the function of complex communities followed simple quantitative rules. These regularities can be integrated to quantitatively predict the function of newly assembled consortia. Besides addressing theoretical questions in functional ecology, our results and methodologies can provide a blueprint for rationally managing microbial processes of biotechnological relevance.

Comparing the hierarchy of inter- and intra-species interactions with population dynamics of wine yeast cocultures

“…Peay et al ( 2012 ) obtained similar results for yeasts in a floral nectar flower community assembly. Our data would be in accordance with these findings since we observed significant negative interactions between species such as S. cerevisiae, T. delbrueckii or L. thermotolerans , even though Ruiz et al ( 2023 ) identified positive interactions between S. cerevisiae and L. thermotolerans or T. delbrueckii . In our study, these three species showed similar growth patterns in monocultures, except for a lower growth rate for T. delbrueckii strains (Fig.…”

“…for example (Csoma et al 2020 ). Further research is needed to confirm our findings, especially with more species to include more genera as well as species from the same genera similarly to a recent study that investigated cocultures of 60 strains of wine yeast in coculture with S. cerevisiae (Ruiz et al 2023 ). In addition, our findings are limited to only one synthetic media, whereas interactions are known to be modulated by environments (Piccardi et al 2019 , Gao et al 2021 ).…”

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

“…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).…”

“…The imposed fermentation conditions also had a minor effect on the metabolite profile of the resulting wines (Supplementary Figure S4B, Supplementary Table S4), which were mainly determined by the sample location (which includes the different metabolite composition of the initial grape musts and the dominant yeast population). This kind of studies reignite the debate about the actual possibilities of manipulating spontaneous fermentations by enological interventions, and bring consideration of whether the exclusive avenue for crafting customizable wines lies in the meticulous bottom-up design of synthetic microbial consortia (Ruiz et al, 2023). To better assess the associations between the composition and function of fermenting yeast communities we should move to a fully controlled experimental set up.…”

“…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].…”