Deciphering phenotypic and genomic features in Saccharomyces cerevisiae strains with high dominance potential and formic acid resistance.

Lignocellulosic biomass is one of the most promising substrates for the production of bioethanol. However, the fermentation of this feedstock is still nonprofitable. In fact, lignocellulosic substrates require a pretreatment step, which releases inhibitors detrimental to the growth of S. cerevisiae and, thus, to the fermentation itself. Nowadays, in sugarcane-to-ethanol industrial plants, there is usually a rapid succession of yeast strains, and the dominant one(s) can overcome the starter. Therefore, both dominant potential and inhibitor tolerance are crucial traits for the selection of superior yeast strains. In this study, thanks to a hybrid approach combinings biotechnology and bioinformatics, a wide collection of S. cerevisiae strains composed of laboratory, industrial and oenological strains was investigated using a comparative genomic analysis. A cluster of 20 strains was then selected on the basis of their promising robustness and tested for their ability to survive when mixed together. During the selection process, different stresses typical of lignocellulosic ethanol production were applied, including i) low readily assimilable nitrogen (RAN) (30 mg/L); ii) high concentrations of acetic acid (3 g/L); iii) formic acid (1.0 and 1.2 g/L). Few strains showed outstanding fitness and were selected for genomic insights. Gene copy numbers and SNPs were analyzed in order to prioritize variants and better assess their linkage with phenotypes. A novel cluster of variants impacting key genes involved in formic acid and yeast dominance was found and deeply investigated. These findings can support the development of superior S. cerevisiae strains for lignocellulosic bioethanol production.