Comparative analysis of phenotype and gene expression in Saccharomyces cerevisiae grown in solid versus liquid culture formats

Saccharomyces cerevisiae is a pivotal model organism in biological research. In practice, the choice between solid and liquid formats of the same culture medium is often based on convenience, with an implicit assumption that the physical format (solid vs. liquid) of the medium has minimal impact on core physiological outcomes. This study systematically tested this assumption by comparing the phenotypic and transcriptional profiles of yeast grown in identical YPD medium prepared as either agar plates or shaken liquid cultures. Yeast S288C was pre-cultured in YPD and then inoculated onto solid YPD agar plates or into liquid YPD medium, both of which were incubated in the same incubator with two-tier system at 29°C for 7 days to reach stationary phase, with liquid cultures shaken at 150 rpm. We analyzed cell viability, size, morphology, and the distribution of quiescent (Q) and non-quiescent (NQ) sub-populations. Extracellular vesicles (EVs) were isolated and characterized. Transcriptomic differences were assessed via RNA sequencing and validated by qRT-PCR for key pathways. After 7 days, total biomass and overall cell viability were similar between the two culture formats. However, cells from liquid culture exhibited larger sizes. Solid culture yielded a higher proportion and viability of Q cells, although these cells were smaller. Contrary to expectations, solid cultures produced a higher concentration of larger EVs. Transcriptomic analysis, coupled with KEGG enrichment, revealed significant differential expression, with solid cultures showing marked upregulation of genes involved in ribosome biogenesis, secondary metabolite biosynthesis, and carbon metabolism. The upregulation of genes involved in key pathways was further validated by qRT-PCR. The culture format (solid vs. liquid) profoundly influences the phenotypic and transcriptional state of S. cerevisiae, even when the chemical medium composition is identical. These differences, likely driven by variations in nutrient/oxygen gradients and mechanical environment, underscore the importance of carefully considering culture format in experimental design and interpretation, particularly in studies of stationary-phase physiology, metabolism, and extracellular vesicle biology.