Screening of Brazilian Isolated Yeasts Reveals Multiple Potential Chassis for Industrial Biotechnology.

Abstract

The future of sustainable industrial biotechnology relies on microbial hosts that can thrive where conventional strains fail. Although Saccharomyces cerevisiae remains the dominant industrial yeast, its metabolic constraints and stress sensitivity highlight the need for alternative microbial chassis. Environmental selection shapes microbial phenotypes, and ecologically diverse isolates represent an underexplored reservoir of industrially relevant traits. Here, we established the Brazilian Yeast Collection (BRYC), comprising 79 isolates spanning 18 genera and 28 named species collected across Brazilian biomes, and systematically characterized their phenotypic diversity under 19 industrially relevant conditions-including carbon sources, biomass-derived inhibitors, elevated temperatures, and high ethanol concentrations-as well as performance on biomass feedstock for industrial bioenergy applications. Across 19 conditions, an industrial S. cerevisiae control ranked first in only one (14% ethanol) despite the panel including strains selected or engineered for low pH tolerance, aldehyde tolerance, xylose utilization, and industrial fermentation performance. 68% of BRYC isolates also exceeded the industrial controls in growth rate robustness. Twenty isolates ranked in the top 10 across three or more conditions, with Wickerhamomyces anomalus (BRYC03 and BRYC30), Pichia kudriavzevii (BRYC98), and Sungouiella flosculorum (BRYC21) emerging as the most versatile performers. Stress-tolerance profiles predicted performance on complex industrial substrates, supporting condition-relevant phenotyping as a framework for rational strain selection. These rankings were, however, substantially format-dependent, with low concordance between liquid and solid cultivation across most conditions (median top-10 overlap = 0.20), underscoring the importance of matching cultivation format to target industrial processes. These findings expand the portfolio of stress-resilient, metabolically versatile yeasts and provide a foundation for their development as next-generation industrial fermenters.