How to characterize a strain? Clonal heterogeneity in industrial Saccharomyces influences both phenotypes and heterogeneity in phenotypes. Issue 8 (5th May 2021)

• Record Type: Journal Article
• Authors: Rácz, Hanna Viktória; Mukhtar, Fezan; Imre, Alexandra; Rádai, Zoltán; Gombert, Andreas Károly; Rátonyi, Tamás; Nagy, János; Pócsi, István; Pfliegler, Walter P.
• Is Part Of: Yeast. Volume 38:Issue 8(2021)
• Page Start: 453
• Page End: 470
• Publication Date: 2021-05-05
• Subjects: aneuploidy -- domestication -- fermented foods and beverages -- genomic structural variation -- phenotypic variability -- Saccharomyces boulardii; Yeast -- Periodicals; Yeasts -- Periodicals; Yeasts -- genetics -- Periodicals; Electronic journals; 547
• DOI: 10.1002/yea.3562
• Languages: English
• ISSNs: 0749-503X

Abstract

Abstract: Populations of microbes are constantly evolving heterogeneity that selection acts upon, yet heterogeneity is nontrivial to assess methodologically. The necessary practice of isolating single‐cell colonies and thus subclone lineages for establishing, transferring, and using a strain results in single‐cell bottlenecks with a generally neglected effect on the characteristics of the strain itself. Here, we present evidence that various subclone lineages for industrial yeasts sequenced for recent genomic studies show considerable differences, ranging from loss of heterozygosity to aneuploidies. Subsequently, we assessed whether phenotypic heterogeneity is also observable in industrial yeast, by individually testing subclone lineages obtained from products. Phenotyping of industrial yeast samples and their newly isolated subclones showed that single‐cell bottlenecks during isolation can indeed considerably influence the observable phenotype. Next, we decoupled fitness distributions on the level of individual cells from clonal interference by plating single‐cell colonies and quantifying colony area distributions. We describe and apply an approach using statistical modeling to compare the heterogeneity in phenotypes across samples and subclone lineages. One strain was further used to show how individual subclonal lineages are remarkably different not just in phenotype but also in the level of heterogeneity in phenotype. With these observations, we call attention to the fact that choosing an initial clonal lineage from an industrial yeast strain may vastly influence downstream performances and observations on karyotype, on phenotype, and also on heterogeneity. Take Away: Industrial yeast strains are more heterogeneous than often assumed. Isolating and examining a subclone lineage alters observable genotype. Subclones may display altered phenotypes along with very variable degree of heterogeneity. Yeast products are in fact evolved, heterogeneous populations.