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

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.

Diploid genome assembly of Kluyveromyces marxianus NRRL Y-50883 (SLP1)

“…An NJ phylogenetic tree was generated with CLC Sequence Viewer 8.0 to establish taxonomic distance using the K. marxianus SLP1 fatty acid synthase subunit beta ( FAS1 ) gene. The FAS1 gene is present during different stress responses, considered a wide-range fermentative yeasts taxonomic marker ( Roscini et al 2020 ) and was proven to be essential in the adaptive evolution of K. marxianus .…”

Tightening the requirements for species diagnoses would help integrate DNA-based descriptions in taxonomic practice

“…Among the major recent changes in modern taxonomic practice is the increasing reliance on data harvested by means of modern technological advances, first and foremost DNA sequencing and bioimaging [ 8 ], but also other approaches such as metabolomics [ 9 , 10 ] and near-infrared spectrometry [ 11 ]. In order to better understand the challenges that the nomenclatural accommodation of such new sources of data might pose, we first examine existing areas of controversy and disagreement in how newly proposed species have been diagnosed or described.…”

Editorial for Special Issue “Yeast in Winemaking”

“…Many efforts have been done to identify yeast involved in the wine profile. While DNA based tools allowed precise yeast taxonomy, it has recently been proved the existence of a strong link between physiology and taxonomy suggesting that many loci could be particularly interesting as “double usage” markers for taxonomy and general metabolic evolution or ethanol stress [ 1 ]. Besides Saccharomyces cerevisiae , from many years now, it has been shown that the so-called ‘non-Saccharomyces’ encompasses different yeast species that contribute positively to wine quality thanks to their flavor contribution.…”