Wild Yeast Populations Research Articles

Tremellomycetes Yeasts in Kernel Ecological Niche: Early Indicators of Enhanced Competitiveness of Endophytic and Mycoparasitic Symbionts against Wheat Pathobiota.

Tremellomycetes rDNA sequences previously detected in wheat kernels by MiSeq were not reliably assigned to a genus or clade. From comparisons of ribosomal internal transcribed spacer region (ITS) and subsequent phylogenetic analyses, the following three basidiomycetous yeasts were resolved and identified: Vishniacozyma victoriae, V. tephrensis, and an undescribed Vishniacozyma rDNA variant. The Vishniacozyma variant’s clade is evolutionarily close to, but phylogenetically distinct from, the V. carnescens clade. These three yeasts were discovered in wheat kernel samples from the Canadian prairies. Variations in relative Vishniacozyma species abundances coincided with altered wheat kernel weight, as well as host resistance to chemibiotrophic Tilletia (Common bunt—CB) and necrotrophic Fusarium (Fusarium head blight—FHB) pathogens. Wheat kernel weight was influenced by the coexistence of Vishniacozyma with endophytic plant growth-promoting and mycoparasitic biocontrol fungi that were acquired by plants. Kernels were coated with beneficial Penicillium endophyte and Sphaerodes mycoparasite, each of which had different influences on the wild yeast population. Its integral role in the kernel microbiome renders Vishniacozyma a measurable indicator of the microbiome–plant interaction. The ability of NGS technology to detect specific endophytic DNA variants and early changes in dynamics among symbionts within the kernel ecological niche enables the prediction of crop disease emergence, suggesting that advanced microbiological testing may be a potentially useful tool for both phytoprotection and more efficient wheat breeding programs.

Dynamic of Lachancea thermotolerans Population in Monoculture and Mixed Fermentations: Impact on Wine Characteristics

Lachancea thermotolerans is a non-Saccharomyces yeast appreciated for its potential of acidification due to the production of lactic acid; however, this species also synthetizes other metabolites that modulate organoleptic wine properties. The aim of this study was to evaluate the strain L. thermotolerans Lt93 to ferment ‘Treixadura’ and ‘Mencía’ musts and its impact on yeast population dynamics and wine characteristics. Fermentations using monocultures of L. thermotolerans Lt93 and S. cerevisiae strains, sequential inoculation and spontaneous process were performed. The dynamic of yeast population and wine composition were analyzed following standard methodology. L. thermotolerans Lt93 was unable to overgrow wild yeast population in ‘Treixadura’ white must; however, with ‘Mencía’ red must, Lt93 was the predominant yeast at the beginning of fermentation and remained at high frequency until the end. Lt93 Treixadura wines had slightly higher acidity and higher content of esters and acids than ScXG3 wines. Lt93 Mencía wines presented higher acidity (10.1 g/L) and 0.8% (v/v) lower ethanol content than Sc71B wines. The content of esters and fatty acids was 3.3 and 4.0 times lower, respectively, in Lt93 than in Sc71B Mencía wines. It was possible to increase wine acidity and modulate the chemical wine profile by using Lt93.

Turnover of ribosome-associated transcripts from de novo ORFs produces gene-like characteristics available for de novo gene emergence in wild yeast populations.

Little is known about the rate of emergence of de novo genes, what their initial properties are, and how they spread in populations. We examined wild yeast populations (Saccharomyces paradoxus) to characterize the diversity and turnover of intergenic ORFs over short evolutionary timescales. We find that hundreds of intergenic ORFs show translation signatures similar to canonical genes, and we experimentally confirmed the translation of many of these ORFs in laboratory conditions using a reporter assay. Compared with canonical genes, intergenic ORFs have lower translation efficiency, which could imply a lack of optimization for translation or a mechanism to reduce their production cost. Translated intergenic ORFs also tend to have sequence properties that are generally close to those of random intergenic sequences. However, some of the very recent translated intergenic ORFs, which appeared <110 kya, already show gene-like characteristics, suggesting that the raw material for functional innovations could appear over short evolutionary timescales.

Summer temperature can predict the distribution of wild yeast populations.

The wine yeast, Saccharomyces cerevisiae, is the best understood microbial eukaryote at the molecular and cellular level, yet its natural geographic distribution is unknown. Here we report the results of a field survey for S.cerevisiae,S.paradoxus and other budding yeast on oak trees in Europe. We show that yeast species differ in their geographic distributions, and investigated which ecological variables can predict the isolation rate of S.paradoxus, the most abundant species. We find a positive association between trunk girth and S.paradoxus abundance suggesting that older trees harbor more yeast. S.paradoxus isolation frequency is also associated with summer temperature, showing highest isolation rates at intermediate temperatures. Using our statistical model, we estimated a range of summer temperatures at which we expect high S.paradoxus isolation rates, and show that the geographic distribution predicted by this optimum temperature range is consistent with the worldwide distribution of sites where S.paradoxus has been isolated. Using laboratory estimates of optimal growth temperatures for S.cerevisiae relative to S.paradoxus, we also estimated an optimum range of summer temperatures for S.cerevisiae. The geographic distribution of these optimum temperatures is consistent with the locations where wild S.cerevisiae have been reported, and can explain why only human-associated S.cerevisiae strains are isolated at northernmost latitudes. Our results provide a starting point for targeted isolation of S.cerevisiae from natural habitats, which could lead to a better understanding of climate associations and natural history in this important model microbe.

The genomics of wild yeast populations sheds light on the domestication of man's best (micro) friend.

The domestication of plants, animals and microbes by humans are the longest artificial evolution experiments ever performed. The study of these long-term experiments can teach us about the genomics of adaptation through the identification of the genetic bases underlying the traits favoured by humans. In laboratory evolution, the characterization of the molecular changes that evolved specifically in some lineages is straightforward because the ancestors are readily available, for instance in the freezer. However, in the case of domesticated species, the ancestor is often missing, which leads to the necessity of going back to nature in order to infer the most likely ancestral state. Significant and relatively recent examples of this approach include wolves as the closest wild relative to domestic dogs (Axelsson etal. 2013) and teosinte as the closest relative to maize (reviewed in Hake & Ross-Ibarra 2015). In both cases, the joint analysis of domesticated lineages and their wild cousins has been key in reconstructing the molecular history of their domestication. While the identification of closest wild relatives has been done for many plants and animals, these comparisons represent challenges for micro-organisms. This has been the case for the budding yeast Saccharomyces cerevisiae, whose natural ecological niche is particularly challenging to define. For centuries, this unicellular fungus has been the cellular factory for wine, beer and bread crafting, and currently for bioethanol and drug production. While the recent development of genomics has lead to the identification of many genetic elements associated with important wine characteristics, the historical origin of some of the domesticated wine strains has remained elusive due to the lack of knowledge of their close wild relatives. In this issue of Molecular Ecology, Almeida etal. (2015) identified what is to date the closest known wild population of the wine yeast. This population is found associated with oak trees in Europe, presumably its natural host. Using population genomics analyses, Almeida and colleagues discovered that the initial divergence between natural and domesticated wine yeasts in the Mediterranean region took place around the early days of wine production. Surprisingly, genomic regions that are key to wine production today appeared not to be derived from these natural populations but from genes gained from other yeast species.

Grape Processing by High Hydrostatic Pressure: Effect on Microbial Populations, Phenol Extraction and Wine Quality

Vitis vinifera (variety Tempranillo) grapes were subjected to high hydrostatic pressure (HHP) treatments of 200, 400 and 550 MPa for 10 min, and its effect on microbial populations, phenol extraction and wine quality was examined. At ≥400 MPa, the wild yeast population was strongly reduced from 104 to <10 cfu/ml. Bacteria showed greater resistance, and a residual load remained even after the treatment at 550 MPa. The extraction of phenolic compounds from the HHP-treated grapes was improved, with higher concentrations of total phenols obtained compared to crushing alone. Anthocyanin extraction was also increased, producing wines with better colour intensity. These wines also had higher methanol and ethanol contents and returned higher aromatic quality and colour scores. The HHP treatment of grapes may assist in the use of yeast starters, increase phenol extraction from grape skins and improve wine quality.

Effect of sulfur dioxide addition in wild yeast population dynamics and polyphenolic composition during spontaneous red wine fermentation from Vitis vinifera cultivar Agiorgitiko

The aim of the present study was to assess the effect of sulfur dioxide addition in the wild yeast population dynamics as well as the polyphenolic composition during spontaneous red wine fermentation from Vitis vinifera cultivar Agiorgitiko. The grapes were crushed and fermentation took place at 21 °C without the addition of any commercial yeast, and with and without the addition of 40 mg L−1 SO2. A combination of culture-dependent and culture-independent techniques was used for wild yeast population dynamics assessment and HPLC analysis for the determination of polyphenolic compounds. Regarding the former, the effect of sulfur dioxide addition was only marginal since Saccharomyces cerevisiae strains dominated the fermentation from the first day; strains belonging to Hanseniaspora spp., Lachancea thermotolerans and Metschnikowia pulcherrima species appeared only occasionally. As far as the polyphenolic content was concerned, it was enhanced with sulfur dioxide addition; however, as time progressed, the differences were reduced, suggesting that the time the juice was in contact with the skins was of greater importance than sulfur dioxide addition.

Molecular Analysis of Genetic Variation in Prions of Saccharomyces cerevisiae

Several proteins in the yeast Saccharomyces cerevisiae act as prions, forming infectious amyloids that are transmissible to other cells during division and outcrossed mating. The parallel in‐register β‐sheet structure of yeast prions such as [PSI+] and [RNQ+] provides a template for conversion of normally unstructured prion domains into a β‐sheet with folds at sites determined by the template on the ends of the filament. Prion propagation is highly sequence specific, and polymorphisms can disrupt templating and abrogate prion transmission. To investigate intra‐species barriers for prion transmission in yeast, we sequenced prion genes of 80 wild isolates from a diverse array of geographic locations and ecological niches. Molecular population genetics was used to quantify nucleotide diversity and examine the evolutionary basis for heterogeneity of prion alleles. An array of indels, SNPs and premature stop codons were detected in wild isolates. Many novel prion haplotypes were characterized, and several variants blocked prion propagation, resulting in barriers to transmission between strains. Almost half of the wild strains analyzed were heterozygous at one or more loci, suggesting that outcrossed mating occurs quite frequently in yeast. It is possible that the observed prion sequence heterogeneity is a consequence of natural selection against prion infections in wild yeast populations.

Allopatric Divergence, Secondary Contact, and Genetic Isolation in Wild Yeast Populations

In plants and animals, new biological species clearly have arisen as a byproduct of genetic divergence in allopatry. However, our understanding of the processes that generate new microbial species remains limited [1] despite the large contribution of microbes to the world's biodiversity. A recent hypothesis claims that microbes lack biogeographical divergence because their population sizes are large and their migration rates are presumably high [2, 3]. In recapitulating the classic microbial-ecology dictum that "everything is everywhere, and the environment selects"[4, 5], this hypothesis casts doubt on whether geographic divergence promotes speciation in microbes. To date, its predictions have been tested primarily with data from eubacteria and archaebacteria [6-8]. However, this hypothesis's most important implication is in sexual eukaryotic microbes, where migration and genetic admixture are specifically predicted to inhibit allopatric divergence and speciation [9]. Here, we use nuclear-sequence data from globally distributed natural populations of the yeast Saccharomyces paradoxus to investigate the role of geography in generating diversity in sexual eukaryotic microbes. We show that these populations have undergone allopatric divergence and then secondary contact without genetic admixture. Our data thus support the occurrence of evolutionary processes necessary for allopatric speciation in sexual microbes.

Yeast species associated with the spontaneous fermentation of cider

This paper reports the influence of cider-making technology (pneumatic and traditional pressing) on the dynamics of wild yeast populations. Yeast colonies isolated from apple juice before and throughout fermentation at a cider cellar of Asturias (Spain), during two consecutive years were studied. The yeast strains were identified by restriction fragment length polymorphism analysis of the 5.8S rRNA gene and the two flanking internal transcribed sequences (ITS). The musts obtained by pneumatic pressing were dominated by non- Saccharomyces yeasts ( Hanseniaspora genus and Metschnikowia pulcherrima) whereas in the apple juices obtained by traditional pressing Saccharomyces together with non- Saccharomyces, were always present. The species Saccharomyces present were S. cerevisiae and S. bayanus. Apparently S. bayanus, was the predominant species at the beginning and the middle fermentation steps of the fermentation process, reaching a percentage of isolation between 33% and 41%, whereas S. cerevisiae took over the process in the final stages of fermentation. During the 2001 harvest, with independence of cider-making technology, the species Hanseniaspora valbyensis was always isolated at the end of fermentations.

The influence of pre‐fermentative practices on the dominance of inoculated yeast starter under industrial conditions

AbstractThe influence of pre‐fermentative practices on the growth dynamics of a ‘natural’ starter culture with specific phenotype (H2S−) concurrently with wild yeast populations was evaluated under winery conditions. Different clarification procedures and added SO2 strongly influenced species and cell numbers isolable at the pre‐fermentation stage. Independent treatments of must with sulphite addition or vacuum‐filtering clarification caused a 30‐fold reduction in viable cells. Clarification procedures, enhanced by the selective effect of SO2 addition, induced the appearance of Saccharomyces cerevisiae ‘wild’ yeasts. Correct application of the inoculum generally guarantees the dominance of fermentation by starter cultures. However, inoculated fermentations using unclarified white and red musts exhibited a consistent presence and persistence of non‐Saccharomyces and/or Saccharomyces ‘wild’ yeasts during fermentation. The extent and composition of the initial wild microflora at the start of fermentation may affect the presence and persistence of wild Saccharomyces and non‐Saccharomyces yeasts during guided fermentations under commercial conditions. The above findings confirm the results of previous works carried out at laboratory‐ or pilot‐scale level. Furthermore, they suggest a clear correlation between the modality of pre‐fermentative practices and the presence and persistence of ‘wild’ yeasts during fermentation.© 2002 Society of Chemical Industry

Winemaking with a Decanter Centrifuge

Two decanter centrifuges were purchased and operated during the 1981 and 1982 vintages. Their value as a winemaking tool was determined by a historical comparison of lees volumes produced in fermentation, and enhanced wine quality. After two years of operation benefits included increased total yield, improved fermentation control, and reduced fining costs. Yield improvements were realized by capturing as distilling material proof gallons formerly lost through a vacuum pre-coat filter. Fermentation control was improved by reducing wild yeast populations in the fermentor. Fining costs were reduced as total phenolic and iron contents were reduced by decantation. Sample wines fermented with high suspected solids were compared with their decanted counterparts for total, flavonoid, and non-flavonoid polyphenol content. All decanted juices produced dry wines with flavonoid reductions of 7% to 26%. Other analyses showed lower iron content, decreased browning capacity and higher alcohol levels in decanted samples.