How to characterize a strain? The neglected influence of clonal heterogeneity on the phenotypes of industrialSaccharomyces

Abstract

Populations of microbes are constantly evolving heterogeneity that selection acts upon, yet heterogeneity is non-trivial to assess methodologically. The practice of isolating single cell colonies for establishing, transferring, and using a strain results in single-cell bottlenecks with a generally neglected effect on the characteristics of the strain. We used six industrial yeasts to assess the level of heterogeneity in clonal populations, especially in terms of stress tolerance. First, we uncovered the existence of genome structure variants in available sequenced genomes of clonal lineages of thes strains. Subsequent phenotyping of strains and their newly isolated subclones showed that single-cell bottlenecks during isolation can considerably influence the observable phenotype. Next, we decoupled fitness distributions on the level of individual cells from clonal interference by plating single cell colonies. We used the obtained data on colony area for statistical modeling of the heterogeneity in phenotypes. 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. Thereby 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 geno- and phenotype, and also on heterogeneity.

Adaptive response to wine selective pressures shapes the genome of a Saccharomyces interspecies hybrid

“…Hereafter, the term adapted strain will be used to refer to the pool of subclonal lineages of H14A7-etoh retrieved at this point. By definition, a strain is a genetically uniform microbial culture, and although H14A7-etoh is the result of an adaptation process, during both industrial processes and growth, populations accumulate genome variations from the initial clonal population, and as a consequence, the term adapted strain can be used [19, 27–30].…”