Transcriptional Reprogramming Drives Cold Adaptation During Long-Term Starvation in Saccharomyces eubayanus

The ability of microorganisms to survive prolonged periods of nutrient scarcity is essential for their survival. Yet, the underlying adaptive mechanisms remain partly understood, especially in non-model eukaryotes. Here, we examined how the cryotolerant yeast Saccharomyces eubayanus adapts to 60 days of cold (4°C) starvation, focusing on the roles of genetic and transcriptional changes. We find that the primary engine of the long-term adaptation is a stable, reprogrammed transcriptional state, rather than the selection of point mutations. Aged isolates exhibited improved growth performance and cryotolerance, a phenotype that remained stable for ∼40 generations. This specialist adaptation involved a trade-off with tolerance to other stresses. Whole-genome sequencing revealed few fixed mutations, indicating that genetic variation did not drive the phenotype. Transcriptomic analysis revealed a significant physiological reprogramming, with cells shifting from anabolic activity to a catabolic, scavenging state driven by enhanced respiration and activation of the General Stress Response. This work highlights that a stable transcriptional state drives long-term cold adaptation, providing the foundation for the superior phenotype of aged isolates that persist through generations.