Impact of direct cell–cell contact in a three-species wine yeast consortium

Wine fermentations provide a model ecosystem for studying microbial interactions between yeast species. This includes antagonistic, neutral and synergistic interactions, in which nutrient competition, metabolic exchange, and killer toxin production were identified as factors impacting ecosystem functioning. Several studies have shown that physical contact between cells of different species also affects ecosystem functioning; however, the mechanisms by which cell-cell contact elicits such responses remains poorly understood. The molecular impact of physical contact was evaluated using membrane bioreactors to physically separate species while allowing metabolic exchange. However, bioreactor designs have been limited in such studies to evaluating two-species binary interactions. Therefore, we evaluated the impact of direct cell-cell contact on the physiology and gene expression of Saccharomyces cerevisiae within a yeast consortium including Lachancea thermotolerans and Torulaspora delbrueckii. A membrane bioreactor allowed continuous media exchange between separate fermentation vessels. Yeast growth, extracellular metabolites, and S. cerevisiae transcriptional profiles were monitored at two timepoints. Direct cell contact favored S. cerevisiae growth and resulted in significantly different amino acid profiles, while indirect (metabolic) contact favored T. delbrueckii growth at the expense of L. theromotolerans. In addition, transcriptional analysis revealed that treatment-specific gene regulation differed from responses previously reported for two-species systems of these yeasts, e.g., strong induction of HPF1, while similarities included upregulation of high-affinity hexose transporters (e.g., HXT6 and 7) and downregulation of sporulation genes. These results indicate that cell-cell contact impacts ecosystem dynamics and nutrient uptake and promotes distinct gene expression responses in S. cerevisiae within a multispecies wine consortium. KEY POINTS: • Multispecies consortium moves beyond binary yeast interaction studies. • S. cerevisiae growth and amino acid profiles differ in direct and indirect contact. • Direct contact elicits unique S. cerevisiae gene expression, e.g., HPF1 upregulation.