158 research outputs found

    Domesticated lineages of S. cerevisiae from fermented food environments present customized genome with selective footprints

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    Domesticated lineages of [i]S. cerevisiae[/i] from fermented food environments present customized genome with selective footprints. 2. Joint Congress on Evolutionary Biolog

    Horizontal Gene Transfer and Introgression: key mechanisms of adaptation of yeast to its ecological niches

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    Horizontal gene transfer (HGT) and introgression are increasingly recognized as a prominent source of adaptation in eukaryotes. Over the past decade, several cases of HGT from prokaryotes to the yeast Saccharomyces strains have been demonstrated. In addition, we have recently identified eukaryote-to-eukaryote gene transfers and some of them have been shown to be involved in the adaptation of the yeast S. cerevisiae to environmental conditions (1;2;3). Three large genomic regions, (A, B and C), were acquired by wine yeasts strains from more distant yeast species (1;3). The yeasts Zygosaccharomyces bailii and Torulaspora microellipsoides, species found in wine fermentations, were identified as the donors of regions B and C, respectively (1;3). We obtained evidence for the amplification of the region B (17 kb) in the genome of S. cerevisiae wine strains (4). The organization of this region differ considerably between strains and the identification of an autonomously replicating sequence functional in S. cerevisiae strongly suggest an expansion mechanism in yeast genomes involving an extrachromosomal circular DNA molecule. We also showed that region C have undergone several rearrangements and carries genes playing a key role in the adaptation of wine yeasts to the nitrogen-limited wine fermentation environment (3). The analysis of 82 S. cerevisiae strains from various ecological origins allowed identification of 33 HGT or introgression for which we have proposed potential donors using phylogenetic topology test. Among these events, we observed, the replacement of a GAL cluster in cheese strains which enables a faster switch from glucose to galactose and improves growth speed in a media containing a mix of the two hexoses such as fermented milk products. These data support the vision of customized yeast genomes associated to specific ecological niches and highlight the key role of HGT in the adaptation of fungal species to their environments.1. Novo et al. 2009, PNAS, 106: 16333-16338.2. Damon et al 2011, ISME Journal 9: 67.3. Marsit et al 2015, Mol. Biol. Evol., 32:1695‚Äď1707 4. Galeote et al 2011, PLoS One 6: e17872

    Adaptation of S. cerevisiae to fermented food environments reveals remarkable genome plasticity and the footprints of domestication

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    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

    Adaptation of Yeast to Anthropogenic Environments Using Comparative Genomics

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    Adaptation of Yeast to Anthropogenic Environments Using Comparative Genomics. 27. International Conference on Yeast Genetics and Molecular Biology (ICYGMB

    Genomic and transcriptomic analysis of Saccharomyces cerevisiae isolates with focus in succinic acid production

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    Succinic acid is a platform chemical that plays an important role as precursor for the synthesis of many valuable bio-based chemicals. Its microbial production from renewable resources has seen great developments, specially exploring the use of yeasts to overcome the limitations of using bacteria. The objective of the present work was to screen for succinate-producing isolates, using a yeast collection with different origins and characteristics. Four strains were chosen, two as promising succinic acid producers, in comparison with two low producers. Genome of these isolates was analysed, and differences were found mainly in genes SDH1, SDH3, MDH1 and the transcription factor HAP4, regarding the number of single nucleotide polymorphisms and the gene copy-number profile. Real-time PCR was used to study gene expression of 10 selected genes involved in the metabolic pathway of succinic acid production. Results show that for the non-producing strain, higher expression of genes SDH1, SDH2, ADH1, ADH3, IDH1 and HAP4 was detected, together with lower expression of ADR1 transcription factor, in comparison with the best producer strain. This is the first study showing the capacity of natural yeast isolates to produce high amounts of succinic acid, together with the understanding of the key factors associated, giving clues for strain improvement.This work was supported by the TRANSBIO project from the European Community’s Seventh Framework Programme (FP7/2007-2013, grant agreement No. 289603), by the EcoAgriFood project (NORTE-01-0145-FEDER-000009) via the North Portugal Regional Operational Programme (Norte 2020) under the Portugal 2020 Partnership Agreement, and by FCT I.P. through the strategic funding UID/BIA/04050/2013.info:eu-repo/semantics/publishedVersio

    Association between Grape Yeast Communities and the Vineyard Ecosystems

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    The grape yeast biota from several wine-producing areas, with distinct soil types and grapevine training systems, was assessed on five islands of Azores Archipelago, and differences in yeast communities composition associated with the geographic origin of the grapes were explored. Fifty-seven grape samples belonging to the Vitis vinifera grapevine cultivars Verdelho dos Acores (Verdelho), Arinto da Terceira (Arinto) and Terrantez do Pico (Terrantez) were collected in two consecutive years and 40 spontaneous fermentations were achieved. A total of 1710 yeast isolates were obtained from freshly crushed grapes and 1200 from final stage of fermentations. Twenty-eight species were identified, Hanseniaspura uvarum, Pichia terricola and Metschnikowia pulcherrima being the three most representative species isolated. Candida carpophila was encountered for the first time as an inhabitant of grape or wine-associated environments. In both sampling years, a higher proportion of H. uvarum in fresh grapes from Verdelho cultivar was observed, in comparison with Arinto cultivar. Qualitatively significant differences were found among yeast communities from several locations on five islands of the Archipelago, particularly in locations with distinctive agro-ecological compositions. Our results are in agreement with the statement that grape-associated microbial biogeography is non-randomly associated with interactions of climate, soil, cultivar, and vine training systems in vineyard ecosystems. Our observations strongly support a possible linkage between grape yeast and wine typicality, reinforcing the statement that different viti-cultural terroirs harbor distinctive yeast biota, in particular in vineyards with very distinctive environmental conditions.Joao Drumonde Neves is the recipient of a fellowship of the Azorean Government (M321/006/F/2008) and PROEMPREGO. This work was supported by the strategic programme UID/BIA/04050/2013 (POCI-01-0145-FEDER-007569) funded by national funds through the FCT I.P. and by the ERDF through the COMPETE2020 - Programa Operacional Competitividade e Internacionalizacao (POCI), and by national funds through FCT by the projects FCOMP-01-0124-008775, PTDC/AGR-ALI/103392/2008 and PTDC/AGR-ALI/121062/2010.info:eu-repo/semantics/publishedVersio

    Horizontal Gene Transfer is a key mechanism permitting adaptation of S. cerevisiae to its ecological niches

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    Horizontal Gene Transfer is a key mechanism permitting adaptation of [i]S. cerevisiae[/i] to its ecological niches. 21. Evolutionary Biology Meeting at Marseille

    Yeast biodiversity in vineyard environments is increased by human intervention

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    One hundred and five grape samples were collected during two consecutive years from 33 locations on seven oceanic islands of the Azores Archipelago. Grape samples were obtained from vineyards that were either abandoned or under regular cultivation involving common viticultural interventions, to evaluate the impact of regular human intervention on grape yeast biota diversity in vineyards. A total of 3150 yeast isolates were obtained and 23 yeast species were identified. The predominant species were Hanseniaspora uvarum, Pichia terricola, Starmerella bacillaris and Issatchenkia hanoiensis. The species Barnettozyma californica, Candida azymoides and Pichia cecembensis were reported in grapes or wine-associated environments for the first time. A higher biodiversity was found in active vineyards where regular human intervention takes place (Shannon index: 1.89 and 1.53 in the first and second years, respectively) when compared to the abandoned ones (Shannon index: 0.76 and 0.31). This finding goes against the assumptions that human intervention can destroy biodiversity and lead to homogeneity in the environment. Biodiversity indices were considerably lower in the year with the heaviest rainfall. This study is the first to report on the grape yeast communities from several abandoned vineyards that have undergone no human intervention.Joao Drumonde Neves is the recipient of a fellowship of the Azorean Government (M321/006/F/2008) and PROEMPREGO. This work was supported by the strategic programme UID/BIA/04050/2013 (POCI-01-0145-FEDER-007569) funded by national funds through the FCT I.P. and by the ERDF through the COMPETE2020 - Programa Operacional Competitividade e Internacionalizacao (POCI), and by national funds through FCT by the projects FCOMP-01-0124-008775, PTDC/AGR-ALI/103392/2008 and PTDC/AGR-ALI/121062/2010.info:eu-repo/semantics/publishedVersio

    Yeasts isolation for bio-reduction of wines volatile acidity: Combined use of differential and selective culture media

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    The main component of the volatile acidity of wines is acetic acid. The maximum acceptable limit for volatile acidity in most wines is 1.2 g/L of acetic acid due to the associated unpleasant vinegar aroma and acrid taste. Acetic acid is a by-product of alcoholic fermentation by Saccharomyces cerevisiae under winemaking conditions. However, this acid may also appear in wine due to spoilage agents, such as the acetic acid bacteria and spoilage yeasts. Winemakers have been using a refermentation process to lower the concentration of acetic acid of wines with high volatile acidity, which consists in mixing the acidic wine with freshly crushed grapes or marcs in a proportion of no more than 20-30% (v/v). Though this process implies low costs it harbors the risk of unexpected and detrimental effects on refermented wines. Thus, one challenge to find new solutions for the reduction of excessive volatile acidity is the selection of yeast from refermentation processes of acidic wines to use as starters in a controlled biological process. To this end we set up an isolation protocol with Wallerstein Laboratory Nutrient Agar (WL) to select yeast strains from refermentation processes of acidic wines carried at the winery scale. Among the isolates obtained, 135 were then randomly selected, based on the different colony color pattern and size, and tested for their ability to consume acetic acid in the presence of glucose. For this purpose we used a modified version of a Zygosaccharomyces bailii differential medium containing acetic acid and glucose. Characterization of the isolates obtained in this medium by fingerprinting with primer T3B confirmed three Saccharomyces strains and one non-Saccharomyces strain as predicted by WL and L-Lysine media. Our previous studies revealed that the yeast strains selected by this approach are adequate for the correction of acidic musts and wines with excessive levels of volatile acidity

    New integrative computational approaches unveil the Saccharomyces cerevisiae pheno-metabolomic fermentative profile and allow strain selection for winemaking

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    During must fermentation by Saccharomyces cerevisiae strains thousands of volatile aroma compounds are formed. The objective of the present work was to adapt computational approaches to analyze pheno-metabolomic diversity of a S. cerevisiae strain collection with different origins. Phenotypic and genetic characterization together with individual must fermentations were performed, and metabolites relevant to aromatic profiles were determined. Experimental results were projected onto a common coordinates system, revealing 17 statistical-relevant multi-dimensional modules, combining sets of most-correlated features of noteworthy biological importance. The present method allowed, as a breakthrough, to combine genetic, phenotypic and metabolomic data, which has not been possible so far due to difficulties in comparing different types of data. Therefore, the proposed computational approach revealed as successful to shed light into the holistic characterization of S. cerevisiae pheno-metabolome in must fermentative conditions. This will allow the identification of combined relevant features with application in selection of good winemaking strains.Ines Mendes was recipient of a fellowship from the Portuguese Science Foundation, FCT (SFRH/BD/74798/2010). This work was supported by FCT I.P. through the strategic funding UID/BIA/04050/2013, and the project PTDC/AGR-ALI/121062/2010
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