Do Metabolomics and Taxonomic Barcode Markers Tell the Same Story about the Evolution of Saccharomyces sensu stricto Complex in Fermentative Environments?

Luca Roscini,Angela Conti,Vincent Robert,Debora Casagrande Pierantoni,Laura Corte,Gianluigi Cardinali

doi:10.3390/microorganisms8081242

Abstract

Yeast taxonomy was introduced based on the idea that physiological properties would help discriminate species, thus assuming a strong link between physiology and taxonomy. However, the instability of physiological characteristics within species configured them as not ideal markers for species delimitation, shading the importance of physiology and paving the way to the DNA-based taxonomy. The hypothesis of reconnecting taxonomy with specific traits from phylogenies has been successfully explored for Bacteria and Archaea, suggesting that a similar route can be traveled for yeasts. In this framework, thirteen single copy loci were used to investigate the predictability of complex Fourier Transform InfaRed spectroscopy (FTIR) and High-performance Liquid Chromatography–Mass Spectrometry (LC-MS) profiles of the four historical species of the Saccharomyces sensu stricto group, both on resting cells and under short-term ethanol stress. Our data show a significant connection between the taxonomy and physiology of these strains. Eight markers out of the thirteen tested displayed high correlation values with LC-MS profiles of cells in resting condition, confirming the low efficacy of FTIR in the identification of strains of closely related species. Conversely, most genetic markers displayed increasing trends of correlation with FTIR profiles as the ethanol concentration increased, according to their role in the cellular response to different type of stress.

Highlights

Yeast taxonomy debuted at the beginning of the 20th century with a monography based on morphology and the analysis of a few physiological traits that were eventually increased by the Dutch School to the over 70 traits suggested in the various editions of “The Yeasts—a taxonomic study” [1,2,3]
The choice of these markers was guided by the following criteria: the ITS, LSU and the concatenated ITS_LSU sequences were included as benchmark since they were used over the last 22 years as identification tool [2,7]; DAL2, FAS1 and ICL1 single copy genes were selected as genes involved in crucial metabolic pathways [35,36,37,38]; and ACT1, mtCOXII, mtSSU, RPB1, RPB2, SSU and TEF1-α sequences were selected because they are currently proposed as new generation markers for yeast taxonomy [7,39,40,41,42]
We investigated the predictability of thirteen markers towards the complex Fourier Transform InfaRed spectroscopy (FTIR) and Liquid Chromatography–Mass Spectrometry (LC-MS) metabolomic profiles of S. cerevisiae, S. paradoxus, S. bayanus and S. pastorianus reference strains

Summary

Introduction

Yeast taxonomy debuted at the beginning of the 20th century with a monography based on morphology and the analysis of a few physiological traits that were eventually increased by the Dutch School to the over 70 traits suggested in the various editions of “The Yeasts—a taxonomic study” [1,2,3]. The overwhelming amount of molecular data produced in the last quarter of a century has shaded the importance of physiology This has led to assimilate a taxon to its DNA and, to its marker DNA, to the extent that the OTU (Operational Taxonomic Unit) are transformed in the MOTU (Molecular OTU) [6]. The ability of microbial cells to withstand stress is part of the phenotypical traits used in species description with good discriminating ability both at the specific and at the subspecific level [19] Beyond this purely taxonomic application, the response of cells to the stress is of primary importance in ecology and in industrial applications. This consideration poses the question on the role of the stress response in discriminating taxa over and, more importantly, below the species level

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