Oleaginous microorganisms can produce high amounts of oil (>20 % of their biomass) under suitable cultivation conditions. In this research work 200 samples were collected from soil, plant surfaces (leaves, flowers and fruits), waste oils from traditional oil milling houses and dairy products (cheese, milk and yoghurt) in Ethiopia. Three hundred and forty yeast colonies were isolated from these samples. By applying Sudan III staining tests, 18 strains were selected as possible oleaginous yeasts. The 18 strains were identified and characterized for their lipid production as a feedstock for biodiesel production in the future. They were identified using morphological and physiological methods as well as sequencing the 3'end of the small-subunit rRNA gene, the internal transcribed spacer regions (ITS; ITS 1, ITS 2 and the intervening 5.8S rRNA gene), and the D1/D2 domain of the 26S rRNA gene. The 18 yeasts were identified as Cutaneotrichosporon curvatus (syn, Cryptococcus curvatus) (PY39), Rhodotorula kratochvilovae (syn, Rhodosporidium kratochvilovae) (SY89), Rhodotorula dairenensis (SY94) and Rhodotourula mucilaginosa (SY09, SY18, SY20, PY21, PY23, PY25, SY30, PY32, SY43, PY44, SY52, PY55, PY61, SY75 and PY86). Under nitrogen-limited cultivation conditions, R. mucilaginosa PY44 produced the highest biomass (15.10 ± 0.54 g/L), while R. mucilaginosa PY32 produced the lowest biomass (10.32 ± 0.18 g/L). The highest lipid yield of 6.87 ± 0.62 g/L and lipid content of 46.51 ± 0.70 % were attained by C. curvatus (syn, C. curvatus) PY39. On the other hand, R. mucilaginosa PY61 gave the lowest lipid yield (2.06 ± 0.52 g/L) and R. mucilaginosa SY52 gave the lowest lipid content of 16.99 ± 0.85 %. The results in this research work suggest that much more oleaginous yeasts can be isolated from Ethiopian environment. On the basis of their substantial lipid production abilities, the three oleaginous yeast strains PY39, SY89 and SY18 were selected and recommended for further optimization processes.

Yeasts, which are ubiquitous in agroecosystems, are known to degrade various xenobiotics. The aim of this study was to analyze the effect of fungicides on the abundance of natural yeast communities colonizing winter wheat leaves, to evaluate the sensitivity of yeast isolates to fungicides in vivo, and to select yeasts that degrade propiconazole.

Megasatellites are a new family of long tandem repeats, recently discovered in the yeast Candida glabrata. Compared to shorter tandem repeats, such as minisatellites, megasatellite motifs range in size from 135 to more than 300 bp, and allow calculation of evolutionary distances between individual motifs. Using divergence based on nucleotide substitutions among similar motifs, we determined the smallest distance between two motifs, allowing their subsequent clustering. Motifs belonging to the same cluster are recurrently found in different megasatellites located on different chromosomes, showing transfer of genetic information between megasatellites. In comparison, evolution of the few similar tandem repeats in Saccharomyces cerevisiae FLO genes mainly involves subtelomeric homologous recombination. We estimated selective constraints acting on megasatellite motifs and their host genes, and found that motifs are under strong purifying selection. Surprisingly, motifs inserted within pseudogenes are also under purifying selection, whereas the pseudogenes themselves evolve neutrally. We propose that megasatellite motifs propagate by a combination of three different molecular mechanisms: (i) gene duplication, (ii) ectopic homologous recombination and (iii) transfer of motifs from one megasatellite to another one. These mechanisms actively cooperate to create new megasatellites, that may play an important role in the adaptation of Candida glabrata to its human host.

The use of biodegradable plastics can reduce the accumulation of environmentally persistent plastic wastes. The rate of degradation of biodegradable plastics depends on environmental conditions and is highly variable. Techniques for achieving more consistent degradation are needed. However, only a few microorganisms involved in the degradation process have been isolated so far from the environment. Here, we show that Pseudozyma spp. yeasts, which are common in the phyllosphere and are easily isolated from plant surfaces, displayed strong degradation activity on films made from poly-butylene succinate or poly-butylene succinate-co-adipate. Strains of P. antarctica isolated from leaves and husks of paddy rice displayed strong degradation activity on these films at 30°C. The type strain, P. antarctica JCM 10317, and Pseudozyma spp. strains from phyllosphere secreted a biodegradable plastic-degrading enzyme with a molecular mass of about 22 kDa. Reliable source of biodegradable plastic-degrading microorganisms are now in our hands.

Variations in gene expression have been widely explored in order to obtain an accurate overview of the changes in regulatory networks that underlie phenotypic diversity. Numerous studies have characterized differences in genomic expression between large numbers of individuals of model organisms such as Saccharomyces cerevisiae. To more broadly survey the evolution of the transcriptomic landscape across species, we measured whole-genome expression in a large collection of another yeast species: Lachancea kluyveri (formerly Saccharomyces kluyveri), using RNAseq. Interestingly, this species diverged from the S. cerevisiae lineage prior to its ancestral whole genome duplication. Moreover, L. kluyveri harbors a chromosome-scale compositional heterogeneity due to a 1-Mb ancestral introgressed region as well as a large set of unique unannotated genes. In this context, our comparative transcriptomic analysis clearly showed a link between gene evolutionary history and expression behavior. Indeed, genes that have been recently acquired or under function relaxation tend to be less transcribed show a higher intraspecific variation (plasticity) and are less involved in network (connectivity). Moreover, utilizing this approach in L. kluyveri also highlighted specific regulatory network signatures in aerobic respiration, amino-acid biosynthesis and glycosylation, presumably due to its different lifestyle. Our data set sheds an important light on the evolution of intraspecific transcriptomic variation across distant species.

Comparison [+/- 1 dilution between minimum inhibitory concentrations (MICs)] of fluconazole and flucytosine Etest MICs of 10 candidate quality control yeast isolates and 78 clinical isolates demonstrated good agreement (> or = 90%) with the reference method (National Committee for Clinical Laboratory Standards document M27-P). This study suggests that the Etest is a promising alternative method for antifungal susceptibility testing in the clinical laboratory, but that further evaluations are needed.

Since the completion of the genome sequence of Saccharomyces cerevisiae in 1996 (refs 1, 2), there has been a large increase in complete genome sequences, accompanied by great advances in our understanding of genome evolution. Although little is known about the natural and life histories of yeasts in the wild, there are an increasing number of studies looking at ecological and geographic distributions, population structure and sexual versus asexual reproduction. Less well understood at the whole genome level are the evolutionary processes acting within populations and species that lead to adaptation to different environments, phenotypic differences and reproductive isolation. Here we present one- to fourfold or more coverage of the genome sequences of over seventy isolates of the baker's yeast S. cerevisiae and its closest relative, Saccharomyces paradoxus. We examine variation in gene content, single nucleotide polymorphisms, nucleotide insertions and deletions, copy numbers and transposable elements. We find that phenotypic variation broadly correlates with global genome-wide phylogenetic relationships. S. paradoxus populations are well delineated along geographic boundaries, whereas the variation among worldwide S. cerevisiae isolates shows less differentiation and is comparable to a single S. paradoxus population. Rather than one or two domestication events leading to the extant baker's yeasts, the population structure of S. cerevisiae consists of a few well-defined, geographically isolated lineages and many different mosaics of these lineages, supporting the idea that human influence provided the opportunity for cross-breeding and production of new combinations of pre-existing variations.

Yeasts, commonly present on the surface of fruits, are of industrial interest for the production of enzymes, flavorings, and bioactive compounds, and have many other scientific uses. The Amazonian rainforest may be a good source of new species or strains of yeasts, but their presence on Amazonian fruits is unknown. The aim of this study was to identify and characterize yeasts isolated from Amazonian native fruits using molecular and phenotypic methods. In total, 81 yeast isolates were obtained from 10 fruits species. Rep-PCR showed 29 strain profiles. Using a combination of restriction-fragment length polymorphism (RFLP) of the 5.8S-ITS region and D1/D2 sequencing of the 26S rRNA gene, 16 species were identified belonging to genera Candida, Debaryomyces, Hanseniaspora, Kodamaea, Martiniozyma, and Meyerozyma. The most dominant species were Candida tropicalis, Debaryomyces hansenii, Hanseniaspora opuntiae, and Hanseniaspora thailandica. H. opuntiae and H. thailandica showed the highest number of the strain profiles. Phenotypic profiles were variable between species, and even among strains. Screening for hydrolases showed lipolytic activity in only one isolate, while proteolytic, cellulolytic and amylolytic capabilities were not detected. Yeast presence among fruits varied, with cidra (Citrus medica) and ungurahui (Oenocarpus bataua) having the highest number of species associated. This investigation broadens the understanding and possible biotechnological uses of yeast strains obtained from Amazonian native fruits. Yeasts, commonly present on the surface of fruits, are of industrial interest for the production of enzymes, flavorings, and bioactive compounds, and have many other scientific uses. The Amazonian rainforest may be a good source of new species or strains of yeasts, but their presence on Amazonian fruits is unknown. The aim of this study was to identify and characterize yeasts isolated from Amazonian native fruits using molecular and phenotypic methods. In total, 81 yeast isolates were obtained from 10 fruits species. Rep-PCR showed 29 strain profiles. Using a combination of restriction-fragment length polymorphism (RFLP) of the 5.8S-ITS region and D1/D2 sequencing of the 26S rRNA gene, 16 species were identified belonging to genera Candida, Debaryomyces, Hanseniaspora, Kodamaea, Martiniozyma, and Meyerozyma. The most dominant species were Candida tropicalis, Debaryomyces hansenii, Hanseniaspora opuntiae, and Hanseniaspora thailandica. H. opuntiae and H. thailandica showed the highest number of the strain profiles. Phenotypic profiles were variable between species, and even among strains. Screening for hydrolases showed lipolytic activity in only one isolate, while proteolytic, cellulolytic and amylolytic capabilities were not detected. Yeast presence among fruits varied, with cidra (Citrus medica) and ungurahui (Oenocarpus bataua) having the highest number of species associated. This investigation broadens the understanding and possible biotechnological uses of yeast strains obtained from Amazonian native fruits.

This work has evaluated the safety aspects of 20 yeast strains, isolated from food environments, selected in previous works due to their probiotic potential. Among the different strains, there are Saccharomyces and non-Saccharomyces yeasts. Before safety evaluation, differentiation of Saccharomyces cerevisiae strains was done by PCR amplification of inter-δ region with pairs of primers δ2-12 and δ12-21, which showed that they were all different from each other and also had different profiles to Saccharomyces boulardii (the only commercial probiotic yeast). The non-Saccharomyces ones were already known. The evaluation tests carried out were antibiotic and antifungal resistance, production of biogenic amines, deconjugation activity of bile salts, and different enzymatic activities: coagulase, deoxyribonuclease, hemolysin, proteolytic, and phospholipase. None of the studied strains demonstrated coagulase, hemolytic or DNase capacity (clear virulence factors), although all of them showed protease activity, some showed phospholipase activity, and half of the yeasts were capable of conjugating bile salts. Regarding antimicrobial compounds, all were resistant to antibiotics but showed sensitivity to the antimycotics used. Nevertheless, only one strain of Hanseniaspora osmophila was excluded for use in the food industry, due to its high production of tyramine.

It has been long thought that the stop codon in a gene is followed by another stop codon that acts as a backup if the real one is read through by a near-cognate tRNA. The existence of such 'tandem stop codons', however, remains elusive.

The telomere regulator and transcription factor Rap1 is the only telomere protein conserved in yeasts and mammals. Its functional repertoire in budding yeasts is a particularly interesting field for investigation, given the high evolutionary diversity of this group of unicellular organisms. In the methylotrophic thermotolerant species Hansenula polymorpha DL-1 the RAP1 gene is duplicated (HpRAP1A and HpRAP1B). Here, we report the functional characterization of the two paralogues from H. polymorpha DL-1. We uncover distinct (but overlapping) DNA binding preferences of HpRap1A and HpRap1B proteins. We show that only HpRap1B is able to recognize telomeric DNA directly and to protect it from excessive recombination, whereas HpRap1A is associated with subtelomere regions. Furthermore, we identify specific binding sites for both HpRap1A and HpRap1B within promoters of a large number of ribosomal protein genes (RPGs), implicating Rap1 in the control of the RP regulon in H. polymorpha. Our bioinformatic analysis suggests that RAP1 was duplicated early in the evolution of the "methylotrophs" clade, and the two genes evolved independently. Therefore, our characterization of Rap1 paralogues in H. polymorpha may be relevant to other "methylotrophs", yielding valuable insights into the evolution of budding yeasts.

Fungi have been found in every marine habitat that has been explored; however, the diversity and functions of fungi in the ocean are poorly understood. In this study, fungi were cultured from the marine environment in the vicinity of Woods Hole, MA, USA, including from plankton, sponge, and coral. Our sampling resulted in 35 unique species across 20 genera. We observed many isolates by time-lapse, differential interference contrast (DIC) microscopy and analyzed modes of growth and division. Several black yeasts displayed highly unconventional cell division cycles compared to those of traditional model yeast systems. Black yeasts have been found in habitats inhospitable to other life and are known for halotolerance, virulence, and stress resistance. We find that this group of yeasts also shows remarkable plasticity in terms of cell size control, modes of cell division, and cell polarity. Unexpected behaviors include division through a combination of fission and budding, production of multiple simultaneous buds, and cell division by sequential orthogonal septations. These marine-derived yeasts reveal alternative mechanisms for cell division cycles that seem likely to expand the repertoire of rules established from classic model system yeasts.

A Pyrosequencing assay has been used in identification of fungal species such as Candida or Aspergillus and diagnosis of pathogenic bacteria such as Helicobacter pylori but there has been no report on successful isolation and identification of Malassezia yeasts using the pyrosequencing method.

Wine reflects the specificity of a terroir, including the native microbiota. In contrast to the use of Saccharomyces cerevisiae commercial starters, a way to maintain wines' microbial terroir identities, guaranteeing at the same time the predictability and reproducibility of the wines, is the selection of autochthonous Saccharomyces and non-Saccharomyces strains towards optimal enological characteristics for the chosen area of isolation. This field has been explored but there is a lack of a compendium covering the main methods to use. Autochthonous wine yeasts from different areas of Slovakia were identified and tested, in the form of colonies grown either on nutrient agar plates or in grape must micro-fermentations, for technological and qualitative enological characteristics. Based on the combined results, Saccharomyces cerevisiae PDA W 10, Lachancea thermotolerans 5-1-1 and Metschnikowia pulcherrima 125/14 were selected as potential wine starters. This paper, as a mixture of experimental and review contributions, provides a compendium of methods used to select autochthonous wine yeasts. Thanks to the presence of images, this compendium could guide other researchers in screening their own yeast strains for wine production.

Divergence in gene regulation can play a major role in evolution. Here, we used a phylogenetic framework to measure mRNA profiles in 15 yeast species from the phylum Ascomycota and reconstruct the evolution of their modular regulatory programs along a time course of growth on glucose over 300 million years [corrected]. We found that modules have diverged proportionally to phylogenetic distance, with prominent changes in gene regulation accompanying changes in lifestyle and ploidy, especially in carbon metabolism. Paralogs have significantly contributed to regulatory divergence, typically within a very short window from their duplication. Paralogs from a whole genome duplication (WGD) event have a uniquely substantial contribution that extends over a longer span. Similar patterns occur when considering the evolution of the heat shock regulatory program measured in eight of the species, suggesting that these are general evolutionary principles. DOI:http://dx.doi.org/10.7554/eLife.00603.001.

Systemic infections caused by rare yeasts are increasing given the rise in immunocompromised or seriously ill patients. Even though globally, the clinical significance of these emerging opportunistic yeasts is increasingly being recognized, less is known about the epidemiology of rare yeasts in Latin America. This review collects, analyzes, and contributes demographic and clinical data from 495 cases of infection caused by rare yeasts in the region. Among all cases, 32 species of rare yeasts, distributed in 12 genera, have been reported in 8 Latin American countries, with Trichosporon asahii (49.5%), Rhodotorula mucilaginosa (11.1%), and Saccharomyces cerevisiae (7.8%) the most common species found. Patients were mostly male (58.3%), from neonates to 84 years of age. Statistically, surgery and antibiotic use were associated with higher rates of Trichosporon infections, while central venous catheter, leukemia, and cancer were associated with higher rates of Rhodotorula infections. From all cases, fungemia was the predominant diagnosis (50.3%). Patients were mostly treated with amphotericin B (58.7%). Crude mortality was 40.8%, with a higher risk of death from fungemia and T. asahii infections. Culture was the main diagnostic methodology. Antifungal resistance to one or more drugs was reported in various species of rare yeasts.

Nectar yeasts are common inhabitants of insect-pollinated flowers but factors determining their distribution are not well understood. We studied the influence of host identity, environmental factors related to pollution/urbanization, and the distance to a target beehive on local distribution of nectar yeasts within Robinia pseudoacacia L. and Tilia tomentosa Moench in Berlin, Germany. Nectar samples of six individuals per species were collected at seven sites in a 2 km radius from each target beehive and plated on YM-Agar to visualise the different morphotypes, which were then identified by sequencing a section of the 26S rDNA gene. Multivariate linear models were used to analyze the effects of all investigated factors on yeast occurrence per tree. Yeast distribution was mainly driven by host identity. The influence of the environmental factors (NO2, height of construction, soil sealing) strongly depended on the radius around the tree, similar to the distance of the sampled beehive. Incidence of specialist nectar-borne yeast species decreased with increasing pollution/urbanization index. Given that specialist yeast species gave way to generalist yeasts that have a reduced dependency on pollinators for between-flower dispersal, our results indicate that increased urbanization may restrict the movement of nectar-specialized yeasts, via limitations of pollinator foraging behavior.

Whereas domestication of livestock, pets, and crops is well documented, it is still unclear to what extent microbes associated with the production of food have also undergone human selection and where the plethora of industrial strains originates from. Here, we present the genomes and phenomes of 157 industrial Saccharomyces cerevisiae yeasts. Our analyses reveal that today's industrial yeasts can be divided into five sublineages that are genetically and phenotypically separated from wild strains and originate from only a few ancestors through complex patterns of domestication and local divergence. Large-scale phenotyping and genome analysis further show strong industry-specific selection for stress tolerance, sugar utilization, and flavor production, while the sexual cycle and other phenotypes related to survival in nature show decay, particularly in beer yeasts. Together, these results shed light on the origins, evolutionary history, and phenotypic diversity of industrial yeasts and provide a resource for further selection of superior strains. PAPERCLIP.

A growing body of research suggests that the mitochondrial genome (mtDNA) is important for temperature adaptation. In the yeast genus Saccharomyces, species have diverged in temperature tolerance, driving their use in high- or low-temperature fermentations. Here, we experimentally test the role of mtDNA in temperature tolerance in synthetic and industrial hybrids (Saccharomyces cerevisiae × Saccharomyces eubayanus or Saccharomyces pastorianus), which cold-brew lager beer. We find that the relative temperature tolerances of hybrids correspond to the parent donating mtDNA, allowing us to modulate lager strain temperature preferences. The strong influence of mitotype on the temperature tolerance of otherwise identical hybrid strains provides support for the mitochondrial climactic adaptation hypothesis in yeasts and demonstrates how mitotype has influenced the world's most commonly fermented beverage.

Invasive fungal diseases are a public health problem. They affect a constantly increasing number of at-risk patients, and their incidence has risen in recent years. These opportunistic infections are mainly due to Candida sp. but less common or rare yeast infections should not be underestimated. These so-called "less common" yeasts include Ascomycota of the genera Candida (excluding the five major Candida species), Magnusiomyces/Saprochaete, Malassezia, and Saccharomyces, and Basidiomycota of the genera Cryptococcus (excluding the Cryptococcus neoformans/gattii complex members), Rhodotorula, and Trichosporon. The aim of this review is to (i) inventory the less common yeasts isolated in humans, (ii) provide details regarding the specific anatomical locations where they have been detected and the clinical characteristics of the resulting infections, and (iii) provide an update on yeast taxonomy. Of the total of 239,890 fungal taxa and their associated synonyms sourced from the MycoBank and NCBI Taxonomy databases, we successfully identified 192 yeasts, including 127 Ascomycota and 65 Basidiomycota. This repertoire allows us to highlight rare yeasts and their tropism for certain anatomical sites and will provide an additional tool for diagnostic management.