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Species delineation of yeasts

Final Activity Report Summary - YEAST SPECIES (Species delineation of yeasts)

Yeasts, as microscopic - predominantly single-celled organisms with nucleus and intracellular membranes, have important functions in ecology, nutrition and biotechnology, but may also be of concern as production contaminants and opportunistic pathogens (microorganisms that may cause disease when host resistance is low). A large diversity of yeast species exists and is increasingly recognised with only 164 species in 1952, but more than 1000 species in 2005, and estimated 15000 existing species. Only a small part of the existing diversity has been isolated yet. In the frame of the current project, we were able to isolate and preserve more than 700 yeast strains from under-investigated environments in Cuba and Australia. More than 600 strains from food-fermentations were made available by collaborators with industrial links or from the public culture collection Mycothéque de Université catholique de Louvain (BCCM/MUCL). Of these fermentation-related strains, 103 representative and highly characterised strains of industrial interest have been selected for the public collection.

Different yeast species share typical characteristics and can be distinguished by specific properties developed due to their evolution in differing ecological niches or geographical locations. We have found and described the new yeast species Metschnikowia cubensis, considered to be endemic to Cuba. The occurrence of this yeast in association with a specific insect species was indicated, which provides additional weight to the hypothesis that a group of yeasts in the genus Metschnikowia live in close association with specific insects.

The current, partly artificial yeast classification system is the result of problems to apply the biological species concept, based on interbreeding populations, to yeasts. Classical attributes such as morphological and physiological characters were used to group organisms based on observable traits that may have developed several times in parallel. The artificial system is gradually transformed towards a natural system based on parental patterns of ancestry and descent, called the phylogenetic species recognition. Parental pattern may be detected and visualised by analyses of the inherited genetic information of present-day organisms. The results of the current project permitted the re-classification of the yeast Debaryomyces hansenii. The species comprised the two varieties D. hansenii var. hansenii and D. hansenii var. fabryi, which were difficult to identify because of overlapping characteristics. Genome comparisons resulted in the circumscription of three different species, named D. hansenii, D. fabryi and D. subglobosus. The accompanying analyses of simple observable attributes such as growth temperatures, now allow a more exact and simplified species identification.

Knowing the parental pattern, or phylogenies, results in a better understanding of the limits of different yeast species. A broad analyse of many traits of larger numbers of organisms sharing the same parental pattern (populations) can detect traits that truly discriminate the populations and that can be used for the rapid and accurate species identification, important to control industrial production, clinical environments and assess bio-diversity. The accumulation of large strain numbers, representing different populations, has furthest progressed for the bakery and brewery yeast Saccharomyces cerevisiae during this study. The detection of populations has been realised by molecular methods in form of DNA-based fingerprint profiles and DNA sequence data; by classical methods in form of growth tests on different substrates and by a method only recently applied to microorganisms, Nuclear Magnetic Resonance (NMR) spectroscopy. The latter producing a complex overview of small molecules (metabolites) produced by the cells, data that require further analyses for their use in chemotaxonomy. Molecular analyses enabled the differentiation of brewing strains of S. cerevisiae. A correlation of molecular results and growth responses indicated the presence of subgroups within the species S. cerevisiae, which are currently under further investigation.

The major outcomes of the project are the 1) collection and identification of large numbers of yeasts, 2) detection of population-level variation to visualise natural groups, 3) comparison of their attributes, 4) establishment of predictive classifications.