Uncovering genetic and phenotypic diversity connections in Lachancea thermotolerans: impact on wine aromatics

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Lachancea thermotolerans is increasingly valued in winemaking for its ability to enhance acidity through lactic acid production, reduce acetic acid, and improve aroma complexity, among other beneficial traits. It has considerable strain variability offering opportunities, but necessitates thorough characterisation to select strains suited to specific oenological applications. Although high intraspecific genetic and phenotypic diversity has been reported, the relationship between the two remains unclear. This study aimed to genetically profile 20 Lachancea isolates from the SAGWRI microbial collection using microsatellite typing (and SAU-PCR where relevant) and to evaluate their phenotypic diversity in sterile Chenin blanc fermentations. The isolates were successfully differentiated into nine genetic groups. Phenotypic screening also revealed significant variability in fermentation kinetics, primary metabolites, and secondary metabolites, which generally aligned with the genetic groupings —with a few exceptions— indicating a clear genotype-phenotype link. Surprisingly, only five of the strains produced lactic acid, despite it being a metabolic marker of L. thermotolerans . Of these, two strains produced excessively high levels (∼9 g/L), significantly lowering pH. All strains yielded less ethanol and more succinic acid than Saccharomyces cerevisiae strain SafOeno™ CKS102, and several consumed over 50% of initial malic acid. Secondary metabolite profiling showed elevated levels of higher alcohols and fruity esters in some strains. Interestingly, some also produced high levels of terpenes and aldehydes, which are underexplored in L. thermotolerans , suggesting further potential to enhance aroma complexity. These findings advance understanding of L. thermotolerans strain diversity and highlight untapped potential for selecting strains with desirable traits for tailored wine production. • Clear genotype–phenotype link is established across L. thermotolerans strains. • Large phenotypic diversity is shown even within closely related genetic groups. • Though a key trait of L. thermotolerans , only 5 out of 18 strains produced lactic acid. • Malic acid consumption strongly correlated with succinic acid production in all strains. • High terpene and aldehyde levels are reported in some strains.