Yeast Taxonomy Research Articles

Safety assessment of dairy microorganisms: The hemiascomycetous yeasts

Hemiascomycetous yeasts constitute a class of unicellular fungi often associated with the food and drink processing industries. A number of species including Kluveromyces lactis, Debaryomyces hansenii, Yarrowia lipolytica, play a key role in the cheese-making process by providing aroma, affecting texture and/or permitting the growth of other microorgansisms. The large majority of yeast infections are due to a few opportunistic species presently classified within the genus Candida, and occur in immunocompromised patients. Recent advances in taxonomy have provided evidence for the incorrect classification of a number of yeasts and suggest that their association with the genus Candida should be reconsidered. Indeed, none of the most common pathogenic Candida species are found in cheese. Improved techniques, combined with more advanced analytical methods have brought to light several emerging pathogens, some of which are involved in cheese-making, for example D. hansenii and Y. lipolytica. Other emerging pathogens may also be found as rare occurrences in cheese. Problems in designation of these isolates are due in part to the still limited range of specific methods of identification and are exacerbated by lack of consensus concerning yeast taxonomy. These organisms cause rare infections in immunocompromised and hospitalized patients, which are generally mild and either self-limiting or easily treated. From studies with Saccharomyces cerevisiae, it seems that it is more the exposure to high doses of yeast than the identity of the species or strain that is associated with infection. As such yeasts in cheese cannot be considered to constitute a risk for healthy individuals.

Yeasts in foods and beverages: impact on product quality and safety

The role of yeasts in food and beverage production extends beyond the well-known bread, beer and wine fermentations. Molecular analytical technologies have led to a major revision of yeast taxonomy, and have facilitated the ecological study of yeasts in many other products. The mechanisms by which yeasts grow in these ecosystems and impact on product quality can now be studied at the level of gene expression. Their growth and metabolic activities are moderated by a network of strain and species interactions, including interactions with bacteria and other fungi. Some yeasts have been developed as agents for the biocontrol of food spoilage fungi, and others are being considered as novel probiotic organisms. The association of yeasts with opportunistic infections and other adverse responses in humans raises new issues in the field of food safety.

Combined application of methods to taxonomic identification of Saccharomyces strains in fermenting botrytized grape must

Although numerous physiological and molecular methods have been proposed for yeast taxonomy, the unambiguous separation of Saccharomyces sensu stricto species in natural samples is still an incompletely resolved issue. In this study the power of various methods was compared in the identification of strains isolated from fermenting botrytized grape musts. Conventional taxonomic and physiological tests and molecular methods developed for rapid identification were used. None of the methods tested was sufficiently powerful. However, the combination of electrophoretic karyotyping and the PCR-RFLP of MET2 with growth tests at 10 and 37 degrees C provided results sufficient for species identification of Saccharomyces wine strains which were not interspecific hybrids or recombinants. The proposed combination of molecular and physiological methods allows specific taxonomic identification and separation of Saccharomyces wine strains without extensive genetic and molecular analysis. The proposed combined approach can also identify hybrids and recombinants.

Symposium: "Herman Phaff: Learning from Yeast" Santiago de Compostela, Spain, 23-24 September 2003.

Thomas Gonzalez Villa , Professor of Microbiology at the University of Santiago de Compostela and former postdoctoral fellow in the laboratory of Herman J. Phaff , in conjunction with the Fundacion Ramon Areces, organized a symposium in memory of the former Professor at the University of California, Davis. The symposium, held during the 29th annual meeting of the Spanish Society for Microbiology (SEM), offered a panoramic view of Phaff's enormous contributions to the knowledge of yeast biology, taxonomy and ecology. Seminars were presented by former Phaff students and postdocs covering various aspects of yeast research originated and associated with the stay in Davis, while some Spanish yeast scientists discussed investigations indirectly inspired by Phaff. Introductory remarks were made by Thomas Villa , Carlos Hardisson , President of the Spanish Society of Microbiology, and Julio Villanueva for the Fundacion Ramon Areces. Then Arnold Demain (R.I.S.E.-Drew University, Madison, NJ) began with a moving review of Phaff's career: “ Herman Jan Phaff: professor , mentor , friend and colleague ”. Phaff left the family wine-trade in Winschoten, The Netherlands, to pursue a degree in Chemical Engineering at the Technical University of Delft under Albert Jan Kluyver. This was followed by a move to the United States and a brilliant career, first at University of California, Berkeley, and then at UC Davis. This seminar, together with that of Sally Ann Meyer (Georgia State University): “ Beer , bread and beyond ”, offered a very human picture of a great yeast scientist. Phaff was remembered as an inexhaustible worker, a stickler for details, a global scientist and a …

The 23rd International Specialized Symposium on Yeasts (ISSY 23), Budapest, Hungary, 26–29 August 2003

The 23rd ISSY was held at the Thermal Hotel Helia, Budapest, in late August 2003. Following a hot summer and prolonged drought that left the river Danube at a low level, the weather was still warm and clear. The conference ran from Tuesday 26 to Friday 29 August; delegates being advised not to arrive over the preceding weekend due to the Formula-1 Grand Prix motor race. The conference opened after lunch on Tuesday 26 August, to the unusual sound of the Adrianus Chamber Orchestra, a string trio accompanied by a mediaeval hurdy gurdy. Professor Tibor De a k welcomed delegates and recalled the occasion of the previous ISSY held in Budapest in 1977. The theme of ISSY 23 was “Interactions between Yeasts and other Organisms”. This was reflected in many papers describing interactions between yeasts and bacteria, filamentous moulds and protozoa in a variety of environments including foods. Interactions are often antagonistic, with competitive suppression of one organism by another, but also may be beneficial to both parties, such as the interactions of fermenting yeasts and low-pH bacteria. Interactions between yeasts and larger organisms were highlighted, such as with insects, or with plants, damaged fruit being a major yeast habitat, and even a possible role for birds as a yeast vector was mentioned. Perhaps the most controversial (or significant) paper of the conference was that by Cletus Kurtzman . Research using a multiplicity of gene sequences was used to construct a phylogeny of 75 ascomycete species, which fell into 14 discrete clades. Some clades neatly grouped members of existing genera, e.g. Saccharomycodes , Saccharomyces sensu stricto and Zygosaccharomyces sensu stricto . Other clades contained a complete mixture of generic names. A proposal was put forward that yeast taxonomy should be modified to reflect the new molecular data, which meant assigning …

Sympatric natural and populations have different thermal growth profiles

Saccharomyces cerevisiae and its close congener S. paradoxus are typically indistinguishable by the phenotypic criteria of classical yeast taxonomy, but they are evolutionarily distinct as indicated by hybrid spore inviability and genomic sequence divergence. Previous work has shown that these two species coexist in oak-associated microhabitats at natural woodland sites in North America. Here, we show that sympatric populations of S. cerevisiae and S. paradoxus from a single natural site are phenotypically differentiated in their growth rate responses to temperature. Our main finding is that the S. cerevisiae population exhibits a markedly higher growth rate at 37 degrees C than the S. paradoxus population; we also find possible differences in growth rate between these populations at two lower temperatures. We discuss the implications of our results for the coexistence of these yeasts in natural environments, and we suggest that thermal growth response may be an evolutionarily labile feature of these organisms that could be analyzed using genomic approaches.

Reinstatement of (Castelli) Lodder and Shifrine & Phaff, former synonyms of (Saito) Lodder

Rhodotorula aurantiaca (Saito) Lodder is an anamorphic basidiomycetous yeast species that belongs to the so-called "Erythrobasidium lineage" of the Urediniomycetes, according to molecular phylogenetic studies based on nucleotide sequence analyses of different ribosomal DNA regions. In the most recent editions of the yeast taxonomy treatises the species Rhodotorula colostri (Castelli) Lodder and Rhodotorula crocea Shifrine & Phaff were listed as synonyms of R. aurantiaca. Taxonomic heterogeneity within R. aurantiaca was demonstrated in a study based on whole-cell protein profiles and is also hinted at by the observed differences in physiological and biochemical characteristics among the different strains under that species name. We determined partial nucleotide sequences of the 26S rRNA gene (D1/D2 domains) of strains maintained in the CBS culture collection under R. aurantiaca, including the type strains of its synonyms. The results showed that R. colostri and R. crocea are clearly distinct from R. aurantiaca and from any other currently recognised basidiomycetous yeast species. Furthermore, phylogenetic analysis of the sequence data placed the former two species in separate lineages of the Microbotryomycetidae: R. colostri in the "ruineniae clade" (Sporidiobolus lineage or Sporidiobolales) and R. crocea loosely linked to Rhodotorula javanica (Microbotryum lineage).

Reflections on the classification of yeasts for different end-users in biotechnology, ecology, and medicine.

The approach to yeast identification has significantly changed in just a few decades due to the rapid increase in basic biological knowledge, increased interest in the practical applications and biodiversity of this important microbial group, and enormous technological advances. While some conventional methods can still be validly applied, many molecular techniques have been developed that allow for strain classification on all taxonomic levels. A critical evaluation of the actual scope of each identification procedure will in the end determine the most appropriate use of the many protocols now available. Nonetheless, the oldest tool of microbiology, the microscope, is still a fundamental accessory for studies involving yeast biology, biodiversity and taxonomy.

Identification of clinically relevant Trichosporon species.

A dichotomous identification key to pathogenic species of the basisiomycetous genus Trichosporon Behrend is provided. It is based on growth tests with carbon sources not traditionally used in yeast taxonomy, viz. uric acid, ethylamine, L-4-hydroxyproline, tyramine and L-phenylalanine as sources of carbon and nitrogen, and polygalacturonate, quinate, 4-ethylphenol, 2,3-dihydroxybenzoate and orcinol as sole carbon sources. Of the standard growth tests, assimilation of L-rhamnose and the maximum growth temperature proved to be useful. In addition to medically relevant species, other species able to grow at 37 degrees C were treated as well.

An overview of yeast taxonomy

An overview of yeast taxonomy

Identification of pathogenic yeasts of the imperfect genus Candida by polymerase chain reaction fingerprinting.

With the increase in the number of immunocompromised hosts, the number of fungal pathogens has increased markedly. Identification and classification, especially of yeast species and strains, is often difficult when based solely on phenotypic characteristics. Since it became clear that different fungal pathogens require specific treatment strategies, there is a need for simple, rapid and reliable methods to identify fungal isolates. Polymerase chain reaction (PCR) fingerprinting was successfully applied here to identify yeast isolates. Microsatellite [(GTG)5; (GACA)4] and minisatellite [(5'GAGGGTGGCGGTTCT 3'), derived from the core-sequence of the phage M13] specific primers were used as single primers in the PCR to amplify hypervariable interrepeat DNA sequences from over 200 European, American and Australian clinical isolates within the genus Candida. Each species, represented by its type strain, could be identified by a specific multilocus pattern, allowing for the assignment of all the isolates to the appropriate species. Intra-species variation in the multilocus profiles was about 20% compared to inter-species variation, which was up to 80%. Anamorph-teleomorph pairs could be identified by highly homologous PCR fingerprint patterns. PCR fingerprinting was more discriminatory when compared with routinely used biochemical tests (Vitek YBC and API ID 32C). PCR fingerprinting has proven to be a powerful tool for the identification of medically important yeasts. It is rapid, sensitive, reliable, highly reproducible, stable in vitro and in vivo, and applicable to large scale experiments. Potential applications include: yeast taxonomy, epidemiology, environmental surveys, and improvement of the diagnosis of mycotic diseases.

Genetic identification of biological species in theSaccharomyces sensu stricto complex

Studies on taxonomic and evolutionary genetics of theSaccharomyces sensu stricto complex are considered in light of the biological species concept. Genetic variability of some physiological properties traditionally used in yeast taxonomy is discussed. Genetic hybridization analysis and molecular karyotyping revealed six biological species in theSaccharomyces sensu stricto complex. DNA-DNA reassociation data are concordant with the data obtained by genetic analysis. A new system for naming the cultivatedSaccharomyces yeast (groups of cultivars) is proposed.

Isolation, purification, and analysis of nuclear DNA in yeast taxonomy.

The advent of molecular techniques has greatly influenced yeast taxonomy. Although it has become easier to identify an unknown organism, the use of these methods has caused a general reassessment of those tests previously considered important for the classification of yeasts.

Saccharomyces barnetti and Saccharomyces spencerorum: two new species of Saccharomyces sensu lato (van der Walt).

In the course of a study of DNA base sequence homology, 19 strains labelled as Saccharomyces exiguus, its imperfect state, Candida holmii, or C. milleri were examined. Results confirmed the separation of C. milleri as a separate species. The remaining strains can be divided into three distinct groups of genomic relatedness. The type cultures of S. exiguus and C. holmii form a cluster with 10 other strains showing variable reassociation values ranging from 100 to 40%. The remaining four strains comprise two separate species showing no nucleotide relatedness between themselves nor to either the S. exiguus complex or to C. milleri. Physiological analyses demonstrate that it is possible to separate these four taxa on the basis of a few simple tests. The two new species are described respectively as Saccharomyces barnetti honoring James Barnett in recognition of his invaluable work in the field of yeast taxonomy and Saccharomyces spencerorum in honor of J.F.T. and Dorothy M. Spencer who have made innumerable contributions to the genetics and biotechnological application of yeasts.

Changes in Lipid Composition over the Growth Cycle of Schizosaccharomyces pombe CBS 356T

Summary The lipids of Schizosaccharomyces pombe CBS 356T were extracted at different growth stages and analysed using gas chromatography (GC), column- and thin-layer chromatography (TLC). Cells of Schiz. pombe CBS 356T contained up to 11.4% (w/vv) lipids, consisting of about 79% neutral lipids (NLs), 11% glycolipids (GLs) and 11% phospholipids (PLs), during stationary growth phase. The NL probably functions as endogenous reserve material. An increased percentage of PLs in the total lipid was evident during mid exponential growth. This is probably associated with the predominance of membranes in young growing cells. A stable lipid composition was obtained in cells harvested during stationary phase highlighting the value of this phenotypic characteristic in yeast taxonomy.

Sequences of ribosomal genes and internal transcribed spacers move three plant parasitic fungi, Eremothecium ashbyi, Ashbya gossypii, and Nematospora coryli, towards Saccharomyces cerevisiae.

Phylogenetic relationships between two species from the genera Saccharomyces (S. cerevisiae, S. kluyveri) and Kluyveromyces (K. aestuarii, K. marxianus), a plant parasitic dimorphic yeast (Nematospora coryli), and two phytopathogenic filamentous fungi (Ashbbya gossypii, Eremothecium ashbyi) were investigated by comparing partial nucleotide sequences of ribosomal DNA (rDNA). The three types of sequenced regions evolve with different speed and allow the analysis at distinct taxonomic levels: conserved regions (18S rDNA, small ribosomal subunit), variable regions (25S rDNA, large ribosomal subunit), and highly variable regions ITS1 and ITS2 (internal transcribed spacers). Segments homologous to positions 619 to 1035 and 1205 to 1617 of the 18S rDNA and positions 470 to 890 and 1535 to 1984 of the 25S rDNA of S. cerevisiae were sequenced. The maximal resolving power of rDNA sequence analysis is provided by including the rapidly evolving ITS1 and ITS2 regions. In the phylogenetic sequence analysis of all regions by the genera Kluyveromyces and Saccharomyces cluster together with two filamentous pathogens on cotton, A. gossypii and E. ashby, as well as the plant pathogenic yeast N. coryli. The molecular evidence from ribosomal sequences suggests that morphology and ornamentation of ascospores, the persistence of ascus walls as well as mycelium formation should not be used as differentiating characters in yeast taxonomy, especially in family delimitation. Our sequence data support the inclusion of plant pathogenic, predominantly filamentous genera like Ashbya or Eremothecium or dimorphic genera like Nematospora with falcate ascospores within a new family of the Saccharomycetaceae. Similarly, the saprophytic genus Kluyveromyces with reniform ascospores and deliquescent ascus walls unequivocally belongs to the family of Saccharomycetaceae

Numerical taxonomic analysis of imperfect yeast species in Candida and Torulopsis shows no basis for generic separation

A numerical taxonomic analysis was performed on 79 phenotypic characters of 147 imperfect yeast species currently assigned to the genus Candida. The characters used were drawn from two monographs on yeast taxonomy. The analysis revealed 10 clusters of three or more species that were similar at the level of 75% or more, and seven clusters containing only one or two species. None of the 10 major clusters contained exclusively species that were traditionally assigned to the genus Torulopsis, while the 12 Candida species of basidiomycetous affinity fell into three clusters with only one species of ascomycetous affinity included. Statistical determination of the five most important differential characters for each cluster failed to show the property of pseudomycelium/mycelium formation as significant for any cluster. The study provides no evidence to support a distinction between taxa that were formerly divided between the genera Candida and Torulopsis and supports previous proposals that these genera should be fused.

Yeast taxonomy

Yeast taxonomy

Urease testing and yeast taxonomy.

When urease production was assayed by the hydrolysis of [14C]urea, all basidiomycetous yeasts tested, including the Cryptococcus vishniacii complex (previously reported urease negative), produced significant amounts of 14CO2. The Schizosaccharomycetaceae were the only urease-positive ascomycetous yeasts tested. Yarrowia lipolytica was urease negative. The stoichiometry of [14C]urea hydrolysis paralleled by Roberts' rapid urea hydrolysis (RUH) test indicated that causes of anomalous results in conventional urease testing include acidification and alkalinization of the test medium by products of endogenous metabolism and autolysis rather than urease activity. Anomalous results also occurred when cells were grown on media containing the chelating agent ethylenediaminetetraacetic acid (EDTA) prior to RUH. The addition of EDTA to a complex natural medium inhibited urease production in all yeasts reportedly growing at 35 degrees C (and all other yeasts tested), except Filobasidiella (Cr.) neoformans var. neoformans (NIH 12). The RUH test could differentiate at the varietal level: Fil. (Cr.) neoformans var. neoformans was about 10 times more resistant to EDTA in media used for the growth of cells prior to RUH testing than was Fil. neoformans var. bacillispora (Cr. neoformans var. gattii) (NIH 191). Urease production by Fil. neoformans var. bacillispora was specifically restored to half maximal activity by the addition of 22 microM Ni+2 (as NiCl2) to a growth medium containing 0.100 mM EDTA.

Yeast species utilizing uric acid, adenine,n-alkylamines or diamines as sole source of carbon and energy

Yeast strains utilizing uric acid, adenine, monoamines or diamines as sole source of carbon and energy were isolated from several soil samples by the enrichment culture method. The most common species was Trichosporon cutaneum. Strains of Candida catenulata, C. famata, C. parapsilosis, C. rugosa, Cryptococcus laurentii, Stephanoascus ciferrii and Tr. adeninovorans were also isolated. All strains utilizing uric acid as sole carbon source utilized some primary n-alkyl-l-amines, hydroxyamines or diamines as well. The ascomycetous yeast strains showing these characteristics all belonged to species known to assimilate hydrocarbons. Type strains of hydrocarbon-positive yeast species which were not found in the enrichment cultures generally assimilated putrescine, some type strains also butylamine or pentylamine, but none assimilated uric acid. Methanol-positive species were not isolated. Type strains of methanol-positive and of hydrocarbon-negative species did not assimilate uric acid, butylamine or putrescine. Assimilation of putrescine as sole source of carbon and energy may be a valuable diagnostic criterion in yeast taxonomy.