Search

Microbe domestication has a major applied relevance but is still poorly understood from an evolutionary perspective. The yeast Torulaspora delbrueckii is gaining importance for biotechnology but little is known about its population structure, variation in gene content or possible domestication routes. Here, we show that T. delbrueckii is composed of five major clades. Among the three European clades, a lineage associated with the wild arboreal niche is sister to the two other lineages that are linked to anthropic environments, one to wine fermentations and the other to diverse sources including dairy products and bread dough (Mix‐Anthropic clade). Using 64 genomes we assembled the pangenome and the variable genome of T. delbrueckii. A comparison with Saccharomyces cerevisiae indicated that the weight of the variable genome in the pangenome of T. delbrueckii is considerably smaller. An association of gene content and ecology supported the hypothesis that the Mix‐Anthropic clade has the most specialized genome and indicated that some of the exclusive genes were implicated in galactose and maltose utilization. More detailed analyses traced the acquisition of a cluster of GAL genes in strains associated with dairy products and the expansion and functional diversification of MAL genes in strains isolated from bread dough. In contrast to S. cerevisiae, domestication in T. delbrueckii is not primarily driven by alcoholic fermentation but rather by adaptation to dairy and bread‐production niches. This study expands our views on the processes of microbe domestication and on the trajectories leading to adaptation to anthropic niches. [ABSTRACT FROM AUTHOR]

The inebriation of wild African ele phants fr om eating the ripened and rotting fruit of the marula tree is a persistent myth in Southern Africa. However, the y easts r esponsib le for alcoholic fermentation to intoxicate the elephants remain poorly documented. In this study, we consider ed Botsw ana, a countr y with the world's largest population of wild elephants, and where the marula tree is indigenous, a bundant and pr otected, to assess the occurr ence and biodiversity of yeasts with a potential to ferment and subsequently inebriate the wild elephants. We collected marula fruits from over a stretch of 800 km in Botswana and isolated 106 yeast strains representing 24 yeast species. Over 93% of these isolates, typically known to ferment simple sugars and produce ethanol comprising of high ethanol producers belonging to Sacchar om yces, Br ettanom yces, and Pichia, and intermediate ethanol producers Wickerhamom yces, Zygotorulaspora, Candida, Hanseniaspora, and Kluyver om yces. Fermentation of marula juice r ev ealed convincing fermentative and ar omatic bouquet credentials to suggest the potential to influence foraging behaviour and inebriate elephants in nature. There is insufficient evidence to refute the aforementioned myth. This work serves as the first work to war ds understanding the biodiversity marula associated yeasts to debunk the myth or appr ov e the facts. [ABSTRACT FROM AUTHOR]

Summary: The adaptation to the different biotic and abiotic factors of wine fermentation has led to the accumulation of numerous genomic hallmarks in Saccharomyces cerevisiae wine strains. IRC7, a gene encoding a cysteine‐S‐β‐lyase enzyme related volatile thiols production in wines, has two alleles: a full‐length allele (IRC7F) and a mutated one (IRC7S), harbouring a 38 bp‐deletion. Interestingly, IRC7S‐encoding a less active enzyme – appears widespread amongst wine populations. Studying the global distribution of the IRC7S allele in different yeast lineages, we confirmed its high prevalence in the Wine clade and demonstrated a minority presence in other domesticated clades (Wine‐PDM, Beer and Bread) while it is completely missing in wild clades. Here, we show that IRC7S‐homozygous (HS) strains exhibited both fitness and competitive advantages compared with IRC7F‐homozygous (HF) strains. There are some pieces of evidence of the direct contribution of the IRC7S allele to the outstanding behaviour of HS strains (i.e., improved response to oxidative stress conditions and higher tolerance to high copper levels); however, we also identified a set of sequence variants with significant co‐occurrence patterns with the IRC7S allele, which can be co‐contributing to the fitness and competitive advantages of HS strains in wine fermentations. [ABSTRACT FROM AUTHOR]

This confusion prevailed in the literature until recently and resulted in the inaccurate use of the name I S. bayanus i or I S. bayanus i variety I uvarum i to refer to I S. uvarum i (e.g. Caudy et al. [8], Cliften et al. [9], Kellis et al. [16]). That study also showed that I S. uvarum i was the sister taxon of I S. eubayanus i and, importantly, was not a synonym of I S. bayanus i , thus confirming earlier reports (e.g. Nguyen and Gaillardin [25]). Therefore, the finding of I S. eubayanus i in South America solved one mystery but created another - the Atlantic Ocean and 12 000 km separated the region where I S. eubayanus i was found from the region where, plausibly, the formation of the hybrid I S. pastorianus i took place. The genomes of I S. eubayanus i and the non-cerevisiae subgenome of I S. pastorianus i had 99.56% identity, which demonstrated that I S. eubayanus i was the elusive non-cerevisiae progenitor of lager yeasts. [Extracted from the article]

The Wickerhamiella and Starmerella genera form a clade (W/S clade) that branches close to Yarrowia lipolytica in the Saccharomycotina species tree. It comprises approximately 90 recognized species and 50 putative new species not formally described yet. The large majority of the members of the W/S clade are ecologically associated with flowers and floricolous insects. Many species exhibit unusual metabolic traits, like fructophily and the production of sophorolipids, which are glycolipids that can be used as environmentally friendly biosurfactants. Genomic data have not only firmly established the W/S clade but have also revealed a tumultuous evolution of metabolism marked by losses and gains of important metabolic pathways, among which alcoholic fermentation. Possibly the most surprising finding brought to light by comparative genomics concerned the large number of genes acquired by some species of the W/S clade from bacteria through horizontal gene transfer, many of which were shown to be functional in their new setting. This was facilitated by the genetic tractability of one species in the clade, Starmerella bombicola, which is used for the industrial production of sophorolipids. We suggest that high‐density coverage of genome sequencing in this clade, combined with the possibility to conduct molecular genetics experiments in at least one species, has the potential to set the stage for yet more exciting discoveries concerning the evolution of yeast metabolism. [ABSTRACT FROM AUTHOR]

The adaptation of the yeast Saccharomyces cerevisiae to man-made environments for the fermentation of foodstuffs and beverages illustrates the scientific, social, and economic relevance of microbe domestication. Here we address a yet unexplored aspect of S. cerevisiae domestication, that of the emergence of lineages harboring some domestication signatures but that do not fit completely in the archetype of a domesticated yeast, by studying S. cerevisiae strains associated with processed olives, namely table olives, olive brine, olive oil, and alpechin. We confirmed earlier observations that reported that the Olives population results from a hybridization between S. cerevisiae and S. paradoxus. We concluded that the olive hybrids form a monophyletic lineage and that the S. cerevisiae progenitor belonged to the wine population of this species. We propose that homoploid hybridization gave rise to a diploid hybrid genome, which subsequently underwent the loss of most of the S. paradoxus sub-genome. Such a massive loss of heterozygosity was probably driven by adaptation to the new niche. We observed that olive strains are more fit to grow and survive in olive brine than control S. cerevisiae wine strains and that they appear to be adapted to cope with the presence of NaCl in olive brine through expansion of copy number of ENA genes. We also investigated whether the S. paradoxus HXT alleles retained by the Olives population were likely to contribute to the observed superior ability of these strains to consume sugars in brine. Our experiments indicate that sugar consumption profiles in the presence of NaCl are different between members of the Olives and Wine populations and only when cells are cultivated in nutritional conditions that support adaptation of their proteome to the high salt environment, which suggests that the observed differences are due to a better overall fitness of olives strains in the presence of high NaCl concentrations. Although relic olive hybrids exhibit several characteristics of a domesticated lineage, tangible benefits to humans cannot be associated with their phenotypes. These strains can be seen as a case of adaptation without positive or negative consequences to humans, that we define as a quasi-domestication. [ABSTRACT FROM AUTHOR]

The study of microbe domestication has witnessed major advances that contribute to a better understanding of the emergence of artificially selected phenotypes and set the foundations of their rational improvement for biotechnology. Several features make Saccharomyces cerevisiae an ideal model for such a study, notably the availability of a catalogue of signatures of artificial selection and the extensive knowledge available on its biological processes. Here, we investigate with population and comparative genomics a set of strains used for cachaça fermentation, a Brazilian beverage based on the fermentation of sugar cane juice. We ask if the selective pressures posed by this fermentation have given rise to a domesticated lineage distinct from the ones already known, like wine, beer, bread, and sake yeasts. Our results show that cachaça yeasts derive from wine yeasts that have undergone an additional round of domestication, which we define as secondary domestication. As a consequence, cachaça strains combine features of wine yeasts, such as the presence of genes relevant for wine fermentation and advantageous gene inactivations, with features of beer yeasts like resistance to the effects of inhibitory compounds present in molasses. For other markers like those related to sulfite resistance and biotin metabolism our analyses revealed distributions more complex than previously reported that support the secondary domestication hypothesis. We propose a multilayered microbe domestication model encompassing not only transitions from wild to primarily domesticated populations, as in the case of wine yeasts, but also secondary domestications like those of cachaça yeasts. [ABSTRACT FROM AUTHOR]

The budding yeast Saccharomyces cerevisiae can be found in the wild and is also frequently associated with human activities. Despite recent insights into the phylogeny of this species, much is still unknown about how evolutionary processes related to anthropogenic niches have shaped the genomes and phenotypes of S. cerevisiae. To address this question, we performed population-level sequencing of 82 S. cerevisiae strains from wine, flor, rum, dairy products, bakeries, and the natural environment (oak trees). These genomic data enabled us to delineate specific genetic groups corresponding to the different ecological niches and revealed high genome content variation across the groups. Most of these strains, compared with the reference genome, possessed additional genetic elements acquired by introgression or horizontal transfer, several of which were population-specific. In addition, several genomic regions in each population showed evidence of nonneutral evolution, as shown by high differentiation, or of selective sweeps including genes with key functions in these environments (e.g. amino acid transport for wine yeast). Linking genetics to lifestyle differences and metabolite traits has enabled us to elucidate the genetic basis of several niche-specific population traits, such as growth on galactose for cheese strains. These data indicate that yeast has been subjected to various divergent selective pressures depending on its niche, requiring the development of customized genomes for better survival in these environments. These striking genome dynamics associated with local adaptation and domestication reveal the remarkable plasticity of the S. cerevisiae genome, revealing this species to be an amazing complex of specialized populations. [ABSTRACT FROM AUTHOR]

In Saccharomyces cerevisiae, the main yeast in wine fermentation, the opportunity to examine divergence at the molecular level between a domesticated lineage and its wild counterpart arose recently due to the identification of the closest relatives of wine strains, a wild population associated with Mediterranean oaks. As genomic data are available for a considerable number of representatives belonging to both groups, we used population genomics to estimate the degree and distribution of nucleotide variation between wine yeasts and their closest wild relatives. We found widespread genomewide divergence, particularly at noncoding sites, which, together with above average divergence in trans-acting DNA binding proteins, may suggest an important role for divergence at the level of transcriptional regulation. Nine outlier regions putatively under strong divergent selection were highlighted by a genomewide scan under stringent conditions. Several cases of introgressions, originating in the sibling species Saccharomyces paradoxus, were also identified in the Mediterranean oak population. FZF1 and SSU1, mostly known for conferring sulphite resistance in wine yeasts, were among the introgressed genes, although not fixed. Because the introgressions detected in our study are not found in wine strains, we hypothesize that ongoing divergent ecological selection segregates the two forms between the different niches. Together, our results provide a first insight into the extent and kind of divergence between wine yeasts and their closest wild relatives. [ABSTRACT FROM AUTHOR]

Background: Lignocellulosic biomass is a common resource across the globe, and its fermentation offers a promising option for generating renewable liquid transportation fuels. The deconstruction of lignocellulosic biomass releases sugars that can be fermented by microbes, but these processes also produce fermentation inhibitors, such as aromatic acids and aldehydes. Several research projects have investigated lignocellulosic biomass fermentation by the baker's yeast Saccharomyces cerevisiae. Most projects have taken synthetic biological approaches or have explored naturally occurring diversity in S. cerevisiae to enhance stress tolerance, xylose consumption, or ethanol production. Despite these efforts, improved strains with new properties are needed. In other industrial processes, such as wine and beer fermentation, interspecies hybrids have combined important traits from multiple species, suggesting that interspecies hybridization may also offer potential for biofuel research. Results: To investigate the efficacy of this approach for traits relevant to lignocellulosic biofuel production, we generated synthetic hybrids by crossing engineered xylose-fermenting strains of S. cerevisiae with wild strains from various Saccharomyces species. These interspecies hybrids retained important parental traits, such as xylose consumption and stress tolerance, while displaying intermediate kinetic parameters and, in some cases, heterosis (hybrid vigor). Next, we exposed them to adaptive evolution in ammonia fiber expansion-pretreated corn stover hydrolysate and recovered strains with improved fermentative traits. Genome sequencing showed that the genomes of these evolved synthetic hybrids underwent rearrangements, duplications, and deletions. To determine whether the genus Saccharomyces contains additional untapped potential, we screened a genetically diverse collection of more than 500 wild, non-engineered Saccharomyces isolates and uncovered a wide range of capabilities for traits relevant to cellulosic biofuel production. Notably, Saccharomyces mikatae strains have high innate tolerance to hydrolysate toxins, while some Saccharomyces species have a robust native capacity to consume xylose. Conclusions: This research demonstrates that hybridization is a viable method to combine industrially relevant traits from diverse yeast species and that members of the genus Saccharomyces beyond S. cerevisiae may offer advantageous genes and traits of interest to the lignocellulosic biofuel industry. [ABSTRACT FROM AUTHOR]

In fungi belonging to the phylum Basidiomycota, sexual compatibility is usually determined by two genetically unlinked MAT loci, one of which encodes one or more pheromone receptors (P/R) and pheromone precursors, and the other comprehends at least one pair of divergently transcribed genes encoding homeodomain (HD) transcription factors. Most species are heterothallic, meaning that sexual reproduction requires mating between two sexually compatible individuals harboring different alleles at both MAT loci. However, some species are known to be homothallic, one individual being capable of completing the sexual cycle without mating with a genetically distinct partner. While the molecular underpinnings of the heterothallic life cycles of several basidiomycete model species have been dissected in great detail, much less is known concerning the molecular basis for homothallism. Following the discovery in available draft genomes of the homothallic basidiomycetous yeast Phaffia rhodozyma of P/R and HD genes, we employed available genetic tools to determine their role in sexual development. Two P/R clusters, each harboring one pheromone receptor and one pheromone precursor gene were found in close vicinity of each other and were shown to form two redundant P/R pairs, each receptor being activated by the pheromone encoded by the most distal pheromone precursor gene. The HD locus is apparently genetically unlinked to the P/R locus and encodes a single pair of divergently transcribed HD1 and HD2 transcription factors, both required for normal completion of the sexual cycle. Given the genetic makeup of P. rhodozyma MAT loci, we postulate that it is a primarily homothallic organism and we propose a model for the interplay of molecular interactions required for sexual development in this species. Phaffia rhodozyma is considered one of the most promising microbial source of the carotenoid astaxanthin. Further development of this yeast as an industrial organism will benefit from new insights regarding its sexual reproduction system. [ABSTRACT FROM AUTHOR]

The natural biology of Saccharomyces cerevisiae, the best known unicellular model eukaryote, remains poorly documented and understood although recent progress has started to change this situation. Studies carried out recently in the Northern Hemisphere revealed the existence of wild populations associated with oak trees in North America, Asia, and in the Mediterranean region. However, in spite of these advances, the global distribution of natural populations of S. cerevisiae, especially in regions were oaks and other members of the Fagaceae are absent, is not well understood. Here we investigate the occurrence of S. cerevisiae in Brazil, a tropical region where oaks and other Fagaceae are absent. We report a candidate natural habitat of S. cerevisiae in South America and, using whole-genome data, we uncover new lineages that appear to have as closest relatives the wild populations found in North America and Japan. A population structure analysis revealed the penetration of the wine genotype into the wild Brazilian population, a first observation of the impact of domesticated microbe lineages on the genetic structure of wild populations. Unexpectedly, the Brazilian population shows conspicuous evidence of hybridization with an American population of Saccharomyces paradoxus. Introgressions from S. paradoxus were significantly enriched in genes encoding secondary active transmembrane transporters. We hypothesize that hybridization in tropical wild lineages may have facilitated the habitat transition accompanying the colonization of the tropical ecosystem. [ABSTRACT FROM AUTHOR]

The domestication of the wine yeast Saccharomyces cerevisiae is thought to be contemporary with the development and expansion of viticulture along the Mediterranean basin. Until now, the unavailability of wild lineages prevented the identification of the closest wild relatives of wine yeasts. Here, we enlarge the collection of natural lineages and employ whole-genome data of oak-associated wild isolates to study a balanced number of anthropic and natural S. cerevisiae strains. We identified industrial variants and new geographically delimited populations, including a novel Mediterranean oak population. This population is the closest relative of the wine lineage as shown by a weak population structure and further supported by genomewide population analyses. A coalescent model considering partial isolation with asymmetrical migration, mostly from the wild group into the Wine group, and population growth, was found to be best supported by the data. Importantly, divergence time estimates between the two populations agree with historical evidence for winemaking. We show that three horizontally transmitted regions, previously described to contain genes relevant to wine fermentation, are present in the Wine group but not in the Mediterranean oak group. This represents a major discontinuity between the two populations and is likely to denote a domestication fingerprint in wine yeasts. Taken together, these results indicate that Mediterranean oaks harbour the wild genetic stock of domesticated wine yeasts. [ABSTRACT FROM AUTHOR]

Species of Leucosporidiales are a group of psychrotolerant yeasts with biotechnological potential. In the present work, we studied the phenotypic, genetic and sexual characteristics of three species of this genus (Leucosporidium scottii, Leucosporidiella creatinivora and Le. yakutica) to clarify the evolutionary relationship among these closely related taxa. From the results obtained, it becomes clear that these yeasts can interbreed. Although genetic delimitation is possible for the three species, the extent of nucleotide substitutions and phenotypic differences observed between them are lower than that expected for species that have ended the speciation process. Our taxonomic conclusion is to maintain the three taxa until further genomic data are gathered. However, the concept of L. scottii species complex is proposed for this group of species. Finally, we transfer all Leucosporidiella and Mastigobasidium species to Leucosporidium (Leucosporidiales), and, in order to end the polyphyly condition of these taxa, we propose the new genus Pseudoleucosporidium gen. nov. and the new combination Peudoleucosporidium fasciculatum comb. nov. [ABSTRACT FROM AUTHOR]

Reticulate evolution can be a major driver of diversification into new niches, especially in disturbed habitats and at the edges of ranges. Industrial fermentation strains of yeast provide a window into these processes, but progress has been hampered by a limited understanding of the natural diversity and distribution of Saccharomyces species and populations. For example, lager beer is brewed with Saccharomyces pastorianus, an alloploid hybrid of S. cerevisiae and S. eubayanus, a species only recently discovered in Patagonia, Argentina. Here, we report that genetically diverse strains of S. eubayanus are readily isolated from Patagonia, demonstrating that the species is well established there. Analyses of multilocus sequence data strongly suggest that there are two diverse and highly differentiated Patagonian populations. The low nucleotide diversity found in the S. eubayanus moiety of hybrid European brewing strains suggests that their alleles were drawn from a small subpopulation that is closely related to one of the Patagonian populations. For the first time, we also report the rare isolation of S. eubayanus outside Patagonia, in Wisconsin, USA. In contrast to the clear population differentiation in Patagonia, the North American strains represent a recent and possibly transient admixture of the two Patagonian populations. These complex and varied reticulation events are not adequately captured by conventional phylogenetic methods and required analyses of Bayesian concordance factors and phylogenetic networks to accurately summarize and interpret. These findings show how genetically diverse eukaryotic microbes can produce rare but economically important hybrids with low genetic diversity when they migrate from their natural ecological context. [ABSTRACT FROM AUTHOR]

Microbes establish very diverse but still poorly understood associations with other microscopic or macroscopic organisms that do not follow the more conventional modes of competition or mutualism. Phaffia rhodozyma, an orange-coloured yeast that produces the biotechnologically relevant carotenoid astaxanthin, exhibits a Holarctic association with birch trees in temperate forests that contrasts with the more recent finding of a South American population associated with Nothofagus (southern beech) and with stromata of its biotrophic fungal parasite Cyttaria spp. We investigated whether the association of Phaffia with Nothofagus- Cyttaria could be expanded to Australasia, the other region of the world where Nothofagus are endemic, studied the genetic structure of populations representing the known worldwide distribution of Phaffia and analysed the evolution of the association with tree hosts. The phylogenetic analysis revealed that Phaffia diversity in Australasia is much higher than in other regions of the globe and that two endemic and markedly divergent lineages seem to represent new species. The observed genetic diversity correlates with host tree genera rather than with geography, which suggests that adaptation to the different niches is driving population structure in this yeast. The high genetic diversity and endemism in Australasia indicate that the genus evolved in this region and that the association with Nothofagus is the ancestral tree association. Estimates of the divergence times of Phaffia lineages point to splits that are much more recent than the break-up of Gondwana, supporting that long-distance dispersal rather than vicariance is responsible for observed distribution of P. rhodozyma. [ABSTRACT FROM AUTHOR]

Comparative genomics revealed in the last decade a scenario of rampant horizontal gene transfer (HGT) among prokaryotes, but for fungi a clearly dominant pattern of vertical inheritance still stands, punctuated however by an increasing number of exceptions. In the present work, we studied the phylogenetic distribution and pattern of inheritance of a fungal gene encoding a fructose transporter (FSY1) with unique substrate selectivity. 109 FSY1 homologues were identified in two sub-phyla of the Ascomycota, in a survey that included 241 available fungal genomes. At least 10 independent inter-species instances of horizontal gene transfer (HGT) involving FSY1 were identified, supported by strong phylogenetic evidence and synteny analyses. The acquisition of FSY1 through HGT was sometimes suggestive of xenolog gene displacement, but several cases of pseudoparalogy were also uncovered. Moreover, evidence was found for successive HGT events, possibly including those responsible for transmission of the gene among yeast lineages. These occurrences do not seem to be driven by functional diversification of the Fsy1 proteins because Fsy1 homologues from widely distant lineages, including at least one acquired by HGT, appear to have similar biochemical properties. In summary, retracing the evolutionary path of the FSY1 gene brought to light an unparalleled number of independent HGT events involving a single fungal gene. We propose that the turbulent evolutionary history of the gene may be linked to the unique biochemical properties of the encoded transporter, whose predictable effect on fitness may be highly variable. In general, our results support the most recent views suggesting that inter-species HGT may have contributed much more substantially to shape fungal genomes than heretofore assumed. [ABSTRACT FROM AUTHOR]

The synthesis of the UV Absorbing compounds named mycosporines (MYCs) has been detected in a few basidiomycetous yeast groups. Conspicuous accumulation of mycosporine-glutaminol-glucoside (MGG) in yeasts requires photo-induction and its photoprotective function has been postulated. The distribution of the ability to produce MYCs appeared to be related to the yeast taxonomic affiliation. In view of the potential significance of MYCs in yeast taxonomy, we here studied the distribution of this trait among dimorphic basidiomycetes of the Pucciniomycotina. Of the 94 fungal species (377 strains and 33 genera) tested, almost half were MYC-positive and MGG was the main compound produced. MGG synthesis was observed for representatives of five of seven Pucciniomycotina classes, indicating that this trait is widely distributed in this group. MGG detection proved useful for the differentiation of species of the polyphyletic genera, such as Rhodotorula and Sporobolomyces, that are phylogenetically separated. MGG quantification and UV tolerance studies in Cystobasidiomycetes supported the idea that the habitat of origin of each strains is important in the level of MGG synthesis and that MYCs have a photoprotective function in yeasts. The taxonomic value of this trait in fungal systematics is discussed. Copyright © 2011 John Wiley & Sons, Ltd. [ABSTRACT FROM AUTHOR]

The genus Saccharomyces currently includes eight species in addition to the model yeast Saccharomyces cerevisiae, most of which can be consistently isolated from tree bark and soil. We recently found sympatric pairs of Saccharomyces species, composed of one cryotolerant and one thermotolerant species in oak bark samples of various geographic origins. In order to contribute to explain the occurrence in sympatry of Saccharomyces species, we screened Saccharomyces genomic data for protein divergence that might be correlated to distinct growth temperature preferences of the species, using the dN/dS ratio as a measure of protein evolution rates and pair-wise species comparisons. In addition to proteins previously implicated in growth at suboptimal temperatures, we found that glycolytic enzymes were among the proteins exhibiting higher than expected divergence when one cryotolerant and one thermotolerant species are compared. By measuring glycolytic fluxes and glycolytic enzymatic activities in different species and at different temperatures, we subsequently show that the unusual divergence of glycolytic genes may be related to divergent evolution of the glycolytic pathway aligning its performance to the growth temperature profiles of the different species. In general, our results support the view that growth temperature preference is a trait that may have undergone divergent selection in the course of ecological speciation in Saccharomyces. [ABSTRACT FROM AUTHOR]

Mountain lakes located at a high elevation are typically exposed to high UV radiation (UVR). Little is known about the ecology and diversity of yeasts inhabiting these extreme environments. We studied yeast occurrence (with special emphasis on those producing carotenoid pigments) at five high-altitude (>1400 m a.s.l.) water bodies located in the Nahuel Huapi National Park (Bariloche, Argentina). Isolates were identified using a polyphasic approach. Production of photoprotective compounds (carotenoids and mycosporines) by yeast isolates, and UVB resistance of selected species were studied. All water samples contained viable yeast cells in variable numbers, generally ranging from 49 to 209 cells L−1. A total of 24 yeast species was found; at least four represented novel species. Carotenogenic yeasts prevailed in lakes with low water conductivity and higher transparency and chlorophyll a levels. Apparently, the ability to produce photoprotective compounds in yeasts was related to the transparency of mountain lake waters, and strains from more transparent waters developed increased UVB resistance. Our results indicate that UVR is an important environmental factor affecting the yeast community structure in aquatic habitats. [ABSTRACT FROM AUTHOR]

Abstract: Microbial deterioration is a common problem in photographic collections, and has been considered a major cause of deterioration. However, few studies have been carried out on this topic, and most of the literature concerns biodeterioration of archival documents in general, including both micro- and macroorganisms. There have been no detailed studies on the interactions between microorganisms, environment, and the composition of photographic material. This study focuses on fungal deterioration of gelatin emulsion photographs. It was part of a study of three collections in Lisbon, Portugal. The first part is quantitative research on the fungal contamination of the Horácio Novais collection, and the second involves induced contamination of experiments on gelatin emulsion photographs. At the end these data are analysed, taking into account the hypothesis that colour materials are more susceptible to fungal deterioration than are black and white ones. This hypothesis is based on the observations of professionals working with photograph collections who report that, at least in plastic base supports (negatives and slides), colour materials are frequently more contaminated than the black and white ones. An overall look at the results seems to indicate a higher susceptibility of the colour chromogenic photographic materials to fungal colonization compared to the black and white materials. However, this hypothesis could not be absolutely confirmed by this study. [Copyright &y& Elsevier]

Here we report the isolation of four Saccharomyces species (former Saccharomyces sensu stricto group) from tree bark. The employment of two temperatures (10°C in addition to the more commonly used 30°C) resulted in the isolation of S. kudriavzevii and S. uvarum, two species that grow at low temperatures, in addition to S. cerevisiae and S. paradoxus. A clear bias was found toward the bark of certain trees, particularly certain oak species. Very often, more than one Saccharomyces species was found in one locality and occasionally even in the same bark sample. Our evidence strongly suggests that (markedly) different growth temperature preferences play a fundamental role in the sympatric associations of Saccharomyces species uncovered in this survey. S. kudriavzevii was isolated at most of the sites sampled in Portugal, indicating that the geographic distribution of this species is wider than the distribution assumed thus far. However, the Portuguese S. kudriavzevii population exhibited important genetic differences compared to the type strain of the species that represents a Japanese population. In this study, S. kudriavzevii stands out as the species that copes better with low temperatures. [ABSTRACT FROM AUTHOR]

The article offers information on the heterogeneity of Rhodotorula mucilaginosa, a carotenogenic yeast from Patagonia, Argentina. Rhodotorula mucilaginosa is a yeast species with world-wide distribution in terrestrial, freshwater, and marine habitat. It also has an ability to colonize a large variety of substrate. A study was conducted to assess the phenotypic and genetic variability of Rhodotorula mucilaginosa, collected from natural and artificial environments in Argentina. The study allowed the detection of a genetically distinct group of the yeast species.

Here we report on the results of a survey of the yeast populations occurring on submerged leaves (alder, eucalyptus and oak) in a natural mountain stream, during different phases of their decomposition and through two consecutive years. Leaf litter mass loss, total yeast counts, Shannon–Weiner index ( H′), yeast community structure and physiologic abilities were analyzed to evaluate the dynamics of yeast communities during decay. Seventy-two yeast taxa were recorded, and in all litter types, species of basidiomycetous affinity predominated over ascomycetous ones. Discriminant analysis of presence/absence data (yeast species) showed significant differences both among substrate types ( P<0.0026) and with decomposition time ( P<0.0001). Carbon and nitrogen source utilization by yeast strains also varied with the substrate ( P<0.0001) and decomposition time ( P<0.0001). Further conclusions were that: (1) all litter types have in common ubiquitous yeast species, such as Cryptococcus albidus, Debaryomyces hansenii and Rhodotorula glutinis, among the common 20 yeast species; (2) only a few species were dominant, and most species were rare, being recorded once or twice throughout decomposition; and (3) the order of yeast appearance, and their substrate assimilation patterns, strongly suggest a succession phenomenon. Finally, explanations for the distribution patterns and variations in yeast communities are discussed. [ABSTRACT FROM AUTHOR]

The Iberian Pyrite Belt extends from Portugal to Spain and is one of the most important pyrite regions in the world. Its aquatic reservoirs display extreme conditions characterized by low pH and high concentrations of heavy metals. In this study, the diversity of microeukaryotes was analysed at the abandoned mines of São Domingos (Portugal) and at Rio Tinto (Spain). DNA was extracted from water samples and a set of eukaryotic universal primers directed to the small subunit rRNA genes (rDNA) was used. The amplicons were analysed by molecular cloning and temperature gradient gel electrophoresis (TGGE). In addition, a fungi-specific primer set was also used in TGGE experiments. The fungi-specific primers contributed to a substantial increase in the number of fungal taxa found due, probably, to the relative low density of fungal structures. Several microorganisms, belonging (or closely related) to the ascomycetous yeast Pichia acaciae, the basidiomycetous yeasts Cryptococcus humicola and Cystofilobasidium bisporidii, the green algae Chlamydomonas noctigama and Chlorella protothecoides var. acidicola and some uncultured microeukaryotes were present at both localities, which suggests that specific microorganisms are adapted to the peculiar conditions of the Iberian Pyrite Belt extreme environments. However, in spite of the similarities, a higher algal richness was observed at S. Domingos, whereas for R. Tinto the richness of fungi was more prominent. [ABSTRACT FROM AUTHOR]

Abstract: Temperature gradient gel electrophoresis (TGGE) was employed for the assessment of yeast diversity in the estuary of the Tagus river (Portugal). The molecular detection of yeasts was carried out directly from water samples and, in parallel, a cultivation approach by means of an enrichment step was employed. A nested PCR was employed to obtain a fungal amplicon containing the D2 domain of the 26S rRNA gene. For identification the TGGE bands were extracted, re-amplified, and sequenced. Fourteen fungal taxa were detected and all except one were yeasts. Most yeast sequences corresponded to members of the Ascomycota and only three belonged to the Basidiomycota. Five yeasts (four ascomycetes and one basidiomycete) could not be identified to the species level due to the uniqueness of their sequences. The number of species detected after enrichment was higher than the number of taxa found using the direct detection method. This suggests that some yeast populations are present in densities that are below the detection threshold of the method. With respect to the analysis of the yeast community structure, our results indicate that the dominant populations belong to Debaryomyces hansenii, Rhodotorula mucilaginosa, Cryptococcus longus, and to an uncultured basidiomycetous yeast phylogenetically close to Cr. longus. The combined analysis of direct detection and cultivation approaches indicates a similar community structure at the two sampled sites since nine species were present at both localities. [Copyright &y& Elsevier]