Distinct Domestication Trajectories in Top-Fermenting Beer Yeasts and Wine Yeasts

High Complexity and Degree of Genetic Variation in Brettanomyces bruxellensis Population

Genome-wide characterization of genetic variants of a large population of individuals within the same species is essential to have a deeper insight into its evolutionary history as well as the genotype–phenotype relationship. Population genomic surveys have been performed in multiple yeast species, including the two model organisms, Saccharomyces cerevisiae and Schizosaccharomyces pombe. In this context, we sought to characterize at the population level the Brettanomyces bruxellensis yeast species, which is a major cause of wine spoilage and can contribute to the specific flavor profile of some Belgium beers. We have completely sequenced the genome of 53 B. bruxellensis strains isolated worldwide. The annotation of the reference genome allowed us to define the gene content of this species. As previously suggested, our genomic data clearly highlighted that genetic diversity variation is related to ploidy level, which is variable in the B. bruxellensis species. Genomes are punctuated by multiple loss-of-heterozygosity regions, whereas aneuploidies as well as segmental duplications are uncommon. Interestingly, triploid genomes are more prone to gene copy number variation than diploids. Finally, the pangenome of the species was reconstructed and was found to be small with few accessory genes compared with S. cerevisiae. The pangenome is composed of 5,409 ORFs (open reading frames) among which 5,106 core ORFs and 303 ORFs that are variable within the population. All these results highlight the different trajectories of species evolution and consequently the interest of establishing population genomic surveys in more populations.

Characterization of the Fermentation and Sensory Profiles of Novel Yeast-Fermented Acid Whey Beverages

Acid whey is a by-product generated in large quantities during dairy processing, and is characterized by its low pH and high chemical oxygen demand. Due to a lack of reliable disposal pathways, acid whey currently presents a major sustainability challenge to the dairy industry. The study presented in this paper proposes a solution to this issue by transforming yogurt acid whey (YAW) into potentially palatable and marketable beverages through yeast fermentation. In this study, five prototypes were developed and fermented by Kluyveromyces marxianus, Brettanomyces bruxellensis, Brettanomyces claussenii, Saccharomyces cerevisiae (strain: Hornindal kveik), and IOC Be Fruits (IOCBF) S. cerevisiae, respectively. Their fermentation profiles were characterized by changes in density, pH, cell count, and concentrations of ethanol and organic acids. The prototypes were also evaluated on 26 sensory attributes, which were generated through a training session with 14 participants. While S. cerevisiae (IOCBF) underwent the fastest fermentation (8 days) and B. claussenii the slowest (21 days), K. marxianus and S. cerevisiae (Hornindal kveik) showed similar fermentation rates, finishing on day 20. The change in pH of the fermentate was similar for all five strains (from around 4.45 to between 4.25 and 4.31). Cell counts remained stable throughout the fermentation for all five strains (at around 6 log colony-forming units (CFU)/mL) except in the case of S. cerevisiae (Hornindal kveik), which ultimately decreased by 1.63 log CFU/mL. B. bruxellensis was the only strain unable to utilize all of the sugars in the substrate, with residual galactose remaining after fermentation. While both S. cerevisiae (IOCBF)- and B. claussenii-fermented samples were characterized by a fruity apple aroma, the former also had an aroma characteristic of lactic acid, dairy products, bakeries and yeast. A chemical odor characteristic of petroleum, gasoline or solvents, was perceived in samples fermented by B. bruxellensis and K. marxianus. An aroma of poorly aged or rancid cheese or milk also resulted from B. bruxellensis fermentation. In terms of appearance and mouthfeel, the S. cerevisiae (IOCBF)-fermented sample was rated the cloudiest, with the heaviest body. This study provides a toolkit for product development in a potential dairy-based category of fermented alcoholic beverages, which can increase revenue for the dairy industry by upcycling the common waste product YAW.

The neutral rate of whole-genome duplication varies among yeast species and their hybrids

Hybridization and polyploidization are powerful mechanisms of speciation. Hybrid speciation often coincides with whole-genome duplication (WGD) in eukaryotes. This suggests that WGD may allow hybrids to thrive by increasing fitness, restoring fertility and/or increasing access to adaptive mutations. Alternatively, it has been suggested that hybridization itself may trigger WGD. Testing these models requires quantifying the rate of WGD in hybrids without the confounding effect of natural selection. Here we show, by measuring the spontaneous rate of WGD of more than 1300 yeast crosses evolved under relaxed selection, that some genotypes or combinations of genotypes are more prone to WGD, including some hybrids between closely related species. We also find that higher WGD rate correlates with higher genomic instability and that WGD increases fertility and genetic variability. These results provide evidence that hybridization itself can promote WGD, which in turn facilitates the evolution of hybrids.

Comparative 13 C-metabolic flux analysis indicates elevation of ATP regeneration, carbon dioxide, and heat production in industrial Saccharomyces cerevisiae strains

BACKGROUND

Various industrial Saccharomyces cerevisiae strains are used for specific processes, such as sake, wine brewing and bread making. Understanding mechanisms underlying the fermentation performance of these strains would be useful for further engineering of the S. cerevisiae metabolism. However, the relationship between the fermentation performance, intra-cellular metabolic states, and other phenotypic characteristics of industrial yeasts is still unclear. In this study, ¹³ C-metabolic flux analysis of four diploid yeast strains-laboratory, sake, bread, and wine yeasts-was conducted.

RESULTS

While the Crabtree effect was observed for all strains, the metabolic flux level of glycolysis was elevated in bread and sake yeast. Furthermore, increased flux levels of the TCA cycle were commonly observed in the three industrial strains. The specific rates of CO₂ production, net ATP regeneration, and metabolic heat generation estimated from the metabolic flux distribution were two to three times greater than those of the laboratory strain. The elevation in metabolic heat generation was correlated with the tolerance to low-temperature stress.

CONCLUSION

These results indicate that the metabolic flux distribution of sake and bread yeast strains contributes to faster production of ethanol and CO₂ . It is also suggested that the generation of metabolic heat is preferable under the actual industrial fermentation conditions.

Global distribution of IRC7 alleles in Saccharomyces cerevisiae populations: a genomic and phenotypic survey within the wine clade

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 (IRC7^F ) and a mutated one (IRC7^S ), harbouring a 38 bp-deletion. Interestingly, IRC7^S -encoding a less active enzyme - appears widespread amongst wine populations. Studying the global distribution of the IRC7^S 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 IRC7^S -homozygous (HS) strains exhibited both fitness and competitive advantages compared with IRC7^F -homozygous (HF) strains. There are some pieces of evidence of the direct contribution of the IRC7^S 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 IRC7^S allele, which can be co-contributing to the fitness and competitive advantages of HS strains in wine fermentations.

The Role of Structural Variation in Adaptation and Evolution of Yeast and Other Fungi

Mutations in DNA can be limited to one or a few nucleotides, or encompass larger deletions, insertions, duplications, inversions and translocations that span long stretches of DNA or even full chromosomes. These so-called structural variations (SVs) can alter the gene copy number, modify open reading frames, change regulatory sequences or chromatin structure and thus result in major phenotypic changes. As some of the best-known examples of SV are linked to severe genetic disorders, this type of mutation has traditionally been regarded as negative and of little importance for adaptive evolution. However, the advent of genomic technologies uncovered the ubiquity of SVs even in healthy organisms. Moreover, experimental evolution studies suggest that SV is an important driver of evolution and adaptation to new environments. Here, we provide an overview of the causes and consequences of SV and their role in adaptation, with specific emphasis on fungi since these have proven to be excellent models to study SV.

How to characterize a strain? Clonal heterogeneity in industrial Saccharomyces influences both phenotypes and heterogeneity in phenotypes

Populations of microbes are constantly evolving heterogeneity that selection acts upon, yet heterogeneity is nontrivial to assess methodologically. The necessary practice of isolating single-cell colonies and thus subclone lineages for establishing, transferring, and using a strain results in single-cell bottlenecks with a generally neglected effect on the characteristics of the strain itself. Here, we present evidence that various subclone lineages for industrial yeasts sequenced for recent genomic studies show considerable differences, ranging from loss of heterozygosity to aneuploidies. Subsequently, we assessed whether phenotypic heterogeneity is also observable in industrial yeast, by individually testing subclone lineages obtained from products. Phenotyping of industrial yeast samples and their newly isolated subclones showed that single-cell bottlenecks during isolation can indeed considerably influence the observable phenotype. Next, we decoupled fitness distributions on the level of individual cells from clonal interference by plating single-cell colonies and quantifying colony area distributions. We describe and apply an approach using statistical modeling to compare the heterogeneity in phenotypes across samples and subclone lineages. One strain was further used to show how individual subclonal lineages are remarkably different not just in phenotype but also in the level of heterogeneity in phenotype. With these observations, we call attention to the fact that choosing an initial clonal lineage from an industrial yeast strain may vastly influence downstream performances and observations on karyotype, on phenotype, and also on heterogeneity.

Comparative Genomics Supports That Brazilian Bioethanol Saccharomyces cerevisiae Comprise a Unified Group of Domesticated Strains Related to Cachaça Spirit Yeasts

Ethanol production from sugarcane is a key renewable fuel industry in Brazil. Major drivers of this alcoholic fermentation are Saccharomyces cerevisiae strains that originally were contaminants to the system and yet prevail in the industrial process. Here we present newly sequenced genomes (using Illumina short-read and PacBio long-read data) of two monosporic isolates (H3 and H4) of the S. cerevisiae PE-2, a predominant bioethanol strain in Brazil. The assembled genomes of H3 and H4, together with 42 draft genomes of sugarcane-fermenting (fuel ethanol plus cachaça) strains, were compared against those of the reference S288C and diverse S. cerevisiae. All genomes of bioethanol yeasts have amplified SNO2(3)/SNZ2(3) gene clusters for vitamin B1/B6 biosynthesis, and display ubiquitous presence of a particular family of SAM-dependent methyl transferases, rare in S. cerevisiae. Widespread amplifications of quinone oxidoreductases YCR102C/YLR460C/YNL134C, and the structural or punctual variations among aquaporins and components of the iron homeostasis system, likely represent adaptations to industrial fermentation. Interesting is the pervasive presence among the bioethanol/cachaça strains of a five-gene cluster (Region B) that is a known phylogenetic signature of European wine yeasts. Combining genomes of H3, H4, and 195 yeast strains, we comprehensively assessed whole-genome phylogeny of these taxa using an alignment-free approach. The 197-genome phylogeny substantiates that bioethanol yeasts are monophyletic and closely related to the cachaça and wine strains. Our results support the hypothesis that biofuel-producing yeasts in Brazil may have been co-opted from a pool of yeasts that were pre-adapted to alcoholic fermentation of sugarcane for the distillation of cachaça spirit, which historically is a much older industry than the large-scale fuel ethanol production.

Strong effect of Penicillium roqueforti populations on volatile and metabolic compounds responsible for aromas, flavor and texture in blue cheeses

Studies of food microorganism domestication can provide important insight into adaptation mechanisms and lead to commercial applications. Penicillium roqueforti is a fungus with four genetically differentiated populations, two of which were independently domesticated for blue cheese-making, with the other two populations thriving in other environments. Most blue cheeses are made with strains from a single P. roqueforti population, whereas Roquefort cheeses are inoculated with strains from a second population. We made blue cheeses in accordance with the production specifications for Roquefort-type cheeses, inoculating each cheese with a single P. roqueforti strain, using a total of three strains from each of the four populations. We investigated differences between the cheeses made with the strains from the four P. roqueforti populations, in terms of the induced flora, the proportion of blue color, water activity and the identity and abundance of aqueous and organic metabolites as proxies for proteolysis and lipolysis as well as volatile compounds responsible for flavor and aroma. We found that the population-of-origin of the P. roqueforti strains used for inoculation had a minor impact on bacterial diversity and no effect on the abundance of the main microorganism. The cheeses produced with P. roqueforti strains from cheese populations had a higher percentage of blue area and a higher abundance of the volatile compounds typical of blue cheeses, such as methyl ketones and secondary alcohols. In particular, the Roquefort strains produced higher amounts of these aromatic compounds, partly due to more efficient proteolysis and lipolysis. The Roquefort strains also led to cheeses with a lower water availability, an important feature for preventing spoilage in blue cheeses, which is subject to controls for the sale of Roquefort cheese. The typical appearance and flavors of blue cheeses thus result from human selection on P. roqueforti, leading to the acquisition of specific features by the two cheese populations. These findings have important implications for our understanding of adaptation and domestication, and for cheese improvement.

Rapid selection response to ethanol in Saccharomyces eubayanus emulates the domestication process under brewing conditions

Although the typical genomic and phenotypic changes that characterize the evolution of organisms under the human domestication syndrome represent textbook examples of rapid evolution, the molecular processes that underpin such changes are still poorly understood. Domesticated yeasts for brewing, where short generation times and large phenotypic and genomic plasticity were attained in a few generations under selection, are prime examples. To experimentally emulate the lager yeast domestication process, we created a genetically complex (panmictic) artificial population of multiple Saccharomyces eubayanus genotypes, one of the parents of lager yeast. Then, we imposed a constant selection regime under a high ethanol concentration in 10 replicated populations during 260 generations (6 months) and compared them with propagated controls exposed solely to glucose. Propagated populations exhibited a selection differential of 60% in growth rate in ethanol, mostly explained by the proliferation of a single lineage (CL248.1) that competitively displaced all other clones. Interestingly, the outcome does not require the entire time‐course of adaptation, as four lineages monopolized the culture at generation 120. Sequencing demonstrated that de novo genetic variants were produced in all propagated lines, including SNPs, aneuploidies, INDELs and translocations. In addition, the different propagated populations showed correlated responses resembling the domestication syndrome: genomic rearrangements, faster fermentation rates, lower production of phenolic off‐flavours and lower volatile compound complexity. Expression profiling in beer wort revealed altered expression levels of genes related to methionine metabolism, flocculation, stress tolerance and diauxic shift, likely contributing to higher ethanol and fermentation stress tolerance in the evolved populations. Our study shows that experimental evolution can rebuild the brewing domestication process in ‘fast motion’ in wild yeast, and also provides a powerful tool for studying the genetics of the adaptation process in complex populations.

The International Scientific Association for Probiotics and Prebiotics (ISAPP) consensus statement on fermented foods

An expert panel was convened in September 2019 by The International Scientific Association for Probiotics and Prebiotics (ISAPP) to develop a definition for fermented foods and to describe their role in the human diet. Although these foods have been consumed for thousands of years, they are receiving increased attention among biologists, nutritionists, technologists, clinicians and consumers. Despite this interest, inconsistencies related to the use of the term 'fermented' led the panel to define fermented foods and beverages as "foods made through desired microbial growth and enzymatic conversions of food components". This definition, encompassing the many varieties of fermented foods, is intended to clarify what is (and is not) a fermented food. The distinction between fermented foods and probiotics is further clarified. The panel also addressed the current state of knowledge on the safety, risks and health benefits, including an assessment of the nutritional attributes and a mechanistic rationale for how fermented foods could improve gastrointestinal and general health. The latest advancements in our understanding of the microbial ecology and systems biology of these foods were discussed. Finally, the panel reviewed how fermented foods are regulated and discussed efforts to include them as a separate category in national dietary guidelines.

In situ Creation of the Natural Phenolic Aromas of Beer: A Pulsed Electric Field Applied to Wort-Enriched Flax Seeds

To fine tune the production of phenolic aromas in beer, a pulsed electric field (PEF) was applied to beer wort, which was enriched with flax seeds. The choice of flax seeds as a source of FA is based on its high content of ferulic precursors and their intrinsic nutritional value. PEF was applied to ground flax seeds, with and without beta glycosidase. Fermentation was carried out with Saccharomyces and non-Saccharomyces yeast strains. Moreover, 4-vinylguaiacol (4-VG), a flavor highly active derived from volatile phenol, was produced by decarboxylation of ferulic acid (FA), or its precursor and flavor-inactive (4-hydroxy-3-methoxycinnamic acid). All yeast strains could metabolize FA into 4-VG, using the pure compound in the synthetic medium or in flax seeds, with the best quantity produced by Saccharomyces cerevisiae as a precursor. The method yields 4-VG production efficiencies up to 120% (mgL⁻¹). Experimental treatment conditions were conducted with E= 1 kV/cm, total time treatment 15 min (peak time t_i = 1 μs, pause time t_p = 1 ms, Total pulses 900³). Treatment efficacy is independent of the fermentation yeast.

Never Change a Brewing Yeast? Why Not, There Are Plenty to Choose From

Fermented foods and particularly beer have accompanied the development of human civilization for thousands of years. Saccharomyces cerevisiae, the dominant yeast in the production of alcoholic beverages, probably co-evolved with human activity. Considering that alcoholic fermentations emerged worldwide, the number of strains used in beer production nowadays is surprisingly low. Thus, the genetic diversity is often limited. This is among others related to the switch from a household brewing style to a more artisan brewing regime during the sixteenth century and latterly the development of single yeast isolation techniques at the Carlsberg Research Laboratory in 1883, resulting in process optimizations in the brewing industry. However, due to fierce competition within the beer market and the increasing demand for novel beer styles, diversification is becoming increasingly important. Moreover, the emergence of craft brewing has influenced big breweries to rediscover yeast as a significant contributor to a beer's aroma profile and realize that there is still room for innovation in the fermentation process. Here, we aim at giving a brief overview on how currently used S. cerevisiae brewing yeasts emerged and comment on the rationale behind replacing them with novel strains. We will present potential sources of yeasts that have not only been used in beer brewing before, including natural sources and sources linked to human activity but also an overlooked source, such as yeast culture collections. We will briefly comment on common yeast isolation techniques and finally touch on additional challenges for the brewing industry in replacing their current brewer's yeasts.

Wild Yeast for the Future: Exploring the Use of Wild Strains for Wine and Beer Fermentation

The continuous usage of single Saccharomyces cerevisiae strains as starter cultures in fermentation led to the domestication and propagation of highly specialized strains in fermentation, resulting in the standardization of wines and beers. In this way, hundreds of commercial strains have been developed to satisfy producers’ and consumers’ demands, including beverages with high/low ethanol content, nutrient deprivation tolerance, diverse aromatic profiles, and fast fermentations. However, studies in the last 20 years have demonstrated that the genetic and phenotypic diversity in commercial S. cerevisiae strains is low. This lack of diversity limits alternative wines and beers, stressing the need to explore new genetic resources to differentiate each fermentation product. In this sense, wild strains harbor a higher than thought genetic and phenotypic diversity, representing a feasible option to generate new fermentative beverages. Numerous recent studies have identified alleles in wild strains that could favor phenotypes of interest, such as nitrogen consumption, tolerance to cold or high temperatures, and the production of metabolites, such as glycerol and aroma compounds. Here, we review the recent literature on the use of commercial and wild S. cerevisiae strains in wine and beer fermentation, providing molecular evidence of the advantages of using wild strains for the generation of improved genetic stocks for the industry according to the product style.

Exploring the potential of comparative de novo transcriptomics to classify Saccharomyces brewing yeasts

In this work the potential of comparative transcriptomics was explored of Saccharomyces (S.) cerevisiae and S. pastorianus for their discrimination. This way an alternative should be demonstrated to comparative genomics, which can be difficult as a result of their aneuoploid genomes composed of mosaics of the parental genomes. Strains were selected according to their application in beer brewing, i.e. top and bottom fermenting yeasts. Comparative transcriptomics was performed for four strains each of commercially available S. cerevisiae (top fermenting) and Saccharomyces pastorianus (bottom fermenting) brewing yeasts grown at two different temperatures to mid-exponential growth phase. A non-reference based approach was chosen in the form of alignment against a de novo assembled brewery-associated pan transcriptome to exclude bias introduced by manual selection of reference genomes. The result is an analysis workflow for self-contained comparative transcriptomics of Saccharomyces yeasts including, but not limited to, the analysis of core and accessory gene expression, functional analysis and metabolic classification. The functionality of this workflow is demonstrated along the principal differentiation of accessory transcriptomes of S. cerevisiae versus S. pastorianus strains. Hence, this work provides a concept enabling studies under different brewing conditions.

The Genome Sequence of the Jean-Talon Strain, an Archeological Beer Yeast from Québec, Reveals Traces of Adaptation to Specific Brewing Conditions

The genome sequences of archeological Saccharomyces cerevisiae isolates can reveal insights about the history of human baking, brewing and winemaking activities. A yeast strain called Jean-Talon was recently isolated from the vaults of the Intendant’s Palace of Nouvelle France on a historical site in Québec City. This site was occupied by breweries from the end of the 17^th century until the middle of the 20^th century when poisoning caused by cobalt added to the beer led to a shutdown of brewing activities. We sequenced the genome of the Jean-Talon strain and reanalyzed the genomes of hundreds of strains to determine how it relates to other domesticated and wild strains. The Jean-Talon strain is most closely related to industrial beer strains from the beer and bakery genetic groups from the United Kingdom and Belgium. It has numerous aneuploidies and Copy Number Variants (CNVs), including the main gene conferring cobalt resistance in yeast. The Jean-Talon strain has indeed higher tolerance to cobalt compared to other yeast strains, consistent with adaptation to the most recent brewing activities on the site. We conclude from this that the Jean-Talon strain most likely derives from recent brewing activities and not from the original breweries of Nouvelle France on the site.

Genomic Adaptation of Saccharomyces Species to Industrial Environments

The budding yeast has been extensively studied for its physiological performance in fermentative environments and, due to its remarkable plasticity, is used in numerous industrial applications like in brewing, baking and wine fermentations. Furthermore, thanks to its small and relatively simple eukaryotic genome, the molecular mechanisms behind its evolution and domestication are more easily explored. Considerable work has been directed into examining the industrial adaptation processes that shaped the genotypes of species and hybrids belonging to the Saccharomyces group, specifically in relation to beverage fermentation performances. A variety of genetic mechanisms are responsible for the yeast response to stress conditions, such as genome duplication, chromosomal re-arrangements, hybridization and horizontal gene transfer, and these genetic alterations are also contributing to the diversity in the Saccharomyces industrial strains. Here, we review the recent genetic and evolutionary studies exploring domestication and biodiversity of yeast strains.

Effect of the Ala234Asp replacement in mitochondrial branched-chain amino acid aminotransferase on the production of BCAAs and fusel alcohols in yeast

In the yeast Saccharomyces cerevisiae, the mitochondrial branched-chain amino acid (BCAA) aminotransferase Bat1 plays an important role in the synthesis of BCAAs (valine, leucine, and isoleucine). Our upcoming study (Large et al. bioRχiv. 10.1101/2020.06.26.166157, Large et al. 2020) will show that the heterozygous tetraploid beer yeast strain, Wyeast 1056, which natively has a variant causing one amino acid substitution of Ala234Asp in Bat1 on one of the four chromosomes, produced higher levels of BCAA-derived fusel alcohols in the brewer's wort medium than a derived strain lacking this mutation. Here, we investigated the physiological role of the A234D variant Bat1 in S. cerevisiae. Both bat1∆ and bat1^A234D cells exhibited the same phenotypes relative to the wild-type Bat1 strain-namely, a repressive growth rate in the logarithmic phase; decreases in intracellular valine and leucine content in the logarithmic and stationary growth phases, respectively; an increase in fusel alcohol content in culture medium; and a decrease in the carbon dioxide productivity. These results indicate that amino acid change from Ala to Asp at position 234 led to a functional impairment of Bat1, although homology modeling suggests that Asp234 in the variant Bat1 did not inhibit enzymatic activity directly. KEY POINTS: • Yeast cells expressing Bat1^A234D exhibited a slower growth phenotype. • The Val and Leu levels were decreased in yeast cells expressing Bat1^A234D. • The A234D substitution causes a loss-of-function in Bat1. • The A234D substitution in Bat1 increased fusel alcohol production in yeast cells.

Comparison of the Glycolytic and Alcoholic Fermentation Pathways of Hanseniaspora vineae with Saccharomyces cerevisiae Wine Yeasts

Hanseniaspora species can be isolated from grapes and grape musts, but after the initiation of spontaneous fermentation, they are displaced by Saccharomyces cerevisiae. Hanseniaspora vineae is particularly valuable since this species improves the flavour of wines and has an increased capacity to ferment relative to other apiculate yeasts. Genomic, transcriptomic, and metabolomic studies in H. vineae have enhanced our understanding of its potential utility within the wine industry. Here, we compared gene sequences of 12 glycolytic and fermentation pathway enzymes from five sequenced Hanseniaspora species and S. cerevisiae with the corresponding enzymes encoded within the two sequenced H. vineae genomes. Increased levels of protein similarity were observed for enzymes of H. vineae and S. cerevisiae, relative to the remaining Hanseniaspora species. Key differences between H. vineae and H. uvarum pyruvate kinase enzymes might explain observed differences in fermentative capacity. Further, the presence of eight putative alcohol dehydrogenases, invertase activity, and sulfite tolerance are distinctive characteristics of H. vineae, compared to other Hanseniaspora species. The definition of two clear technological groups within the Hanseniaspora genus is discussed within the slow and fast evolution concept framework previously discovered in these apiculate yeasts.

Brewing potential of the wild yeast species Saccharomyces paradoxus

Saccharomyces paradoxus is commonly isolated from environmental samples in Northern Europe and North America, but is rarely found associated with fermentation. However, as novelty has become a selling point in beer markets, interest toward non-conventional and local yeasts is increasing. Here, we report the first comprehensive investigation of the brewing potential of the species. Eight wild strains of S. paradoxus were isolated from oak trees growing naturally in Finland, screened in a series of fermentation trials and the most promising strain was selected for lager beer brewing at pilot scale (40 l). Yeasts were evaluated according to their ability to utilize wort sugars, their production of flavour-active aroma volatiles, diacetyl and organic acids, and sensorial quality of beers produced. All strains could assimilate maltose but this occurred after a considerable lag phase. Once adapted, most wild strains reached attenuation rates close to 70%. Adaptation to maltose could be maintained by re-pitching and with appropriate handling of the adapted yeast. Fermentation at 15 °C with the best performing strain was completed in 17 days. Maltose was consumed as efficiently as with a reference lager yeast, but no maltotriose use was observed. Bottled beers were evaluated by a trained sensory panel, and were generally rated as good as, or better than, reference beers. S. paradoxus beers were considered full-bodied and had a relatively clean flavour profile despite the presence of the clove-like 4-vinyl guaiacol. In conclusion, S. paradoxus exhibits a number of traits relevant to brewing, and with appropriate handling could be applied industrially.

Molecular profiling of beer wort fermentation diversity across natural Saccharomyces eubayanus isolates

The utilization of S. eubayanus has recently become a topic of interest due to the novel organoleptic properties imparted to beer. However, the utilization of S. eubayanus in brewing requires the comprehension of the mechanisms that underlie fermentative differences generated from its natural genetic variability. Here, we evaluated fermentation performance and volatile compound production in ten genetically distinct S. eubayanus strains in a brewing fermentative context. The evaluated strains showed a broad phenotypic spectrum, some of them exhibiting a high fermentation capacity and high levels of volatile esters and/or higher alcohols. Subsequently, we obtained molecular profiles by generating 'end-to-end' genome assemblies, as well as metabolome and transcriptome profiling of two Patagonian isolates exhibiting significant differences in beer aroma profiles. These strains showed clear differences in concentrations of intracellular metabolites, including amino acids, such as valine, leucine and isoleucine, likely impacting the production of 2-methylpropanol and 3-methylbutanol. These differences in the production of volatile compounds are attributed to gene expression variation, where the most profound differentiation is attributed to genes involved in assimilatory sulfate reduction, which in turn validates phenotypic differences in H2 S production. This study lays a solid foundation for future research to improve fermentation performance and select strains for new lager styles based on aroma and metabolic profiles.

Revisiting the Taxonomic Synonyms and Populations of Saccharomyces cerevisiae-Phylogeny, Phenotypes, Ecology and Domestication

Saccharomyces cerevisiae-the most emblematic and industrially relevant yeast-has a long list of taxonomical synonyms. Formerly considered as distinct species, some of the synonyms represent variants with important industrial implications, like Saccharomyces boulardii or Saccharomyces diastaticus, but with an unclear status, especially among the fermentation industry, the biotechnology community and biologists not informed on taxonomic matters. Here, we use genomics to investigate a group of 45 reference strains (type strains) of former Saccharomyces species that are currently regarded as conspecific with S. cerevisiae. We show that these variants are distributed across the phylogenetic spectrum of domesticated lineages of S. cerevisiae, with emphasis on the most relevant technological groups, but absent in wild lineages. We analyzed the phylogeny of a representative and well-balanced dataset of S. cerevisiae genomes that deepened our current ecological and biogeographic assessment of wild populations and allowed the distinction, among wild populations, of those associated with low- or high-sugar natural environments. Some wild lineages from China were merged with wild lineages from other regions in Asia and in the New World, thus giving more resolution to the current model of expansion from Asia to the rest of the world. We reassessed several key domestication markers among the different domesticated populations. In some cases, we could trace their origin to wild reservoirs, while in other cases gene inactivation associated with domestication was also found in wild populations, thus suggesting that natural adaptation to sugar-rich environments predated domestication.

Homologous Recombination: A GRAS Yeast Genome Editing Tool

The fermentation industry is known to be very conservative, relying on traditional yeast management. Yet, in the modern fast-paced world, change comes about in facets such as climate change altering the quality and quantity of harvests, changes due to government regulations e.g., the use of pesticides or SO2, the need to become more sustainable, and of course by changes in consumer preferences. As a silent companion of the fermentation industry, the wine yeast Saccharomyces cerevisiae has followed mankind through millennia, changing from a Kulturfolger, into a domesticated species for the production of bread, beer, and wine and further on into a platform strain for the production of biofuels, enzymes, flavors, or pharmaceuticals. This success story is based on the ‘awesome power of yeast genetics’. Central to this is the very efficient homologous recombination (HR) machinery of S. cerevisiae that allows highly-specific genome edits. This microsurgery tool is so reliable that yeast has put a generally recognized as safe (GRAS) label onto itself and entrusted to itself the life-changing decision of mating type-switching. Later, yeast became its own genome editor, interpreted as domestication events, to adapt to harsh fermentation conditions. In biotechnology, yeast HR has been used with tremendous success over the last 40 years. Here we discuss several types of yeast genome edits then focus on HR and its inherent potential for evolving novel wine yeast strains and styles relevant for changing markets.

An Out-of-Patagonia migration explains the worldwide diversity and distribution of Saccharomyces eubayanus lineages

Population‐level sampling and whole‐genome sequences of different individuals allow one to identify signatures of hybridization, gene flow and potential molecular mechanisms of environmental responses. Here, we report the isolation of 160 Saccharomyces eubayanus strains, the cryotolerant ancestor of lager yeast, from ten sampling sites in Patagonia along 2,000 km of Nothofagus forests. Frequency of S. eubayanus isolates was higher towards southern and colder regions, demonstrating the cryotolerant nature of the species. We sequenced the genome of 82 strains and, together with 23 available genomes, performed a comprehensive phylogenetic analysis. Our results revealed the presence of five different lineages together with dozens of admixed strains. Various analytical methods reveal evidence of gene flow and historical admixture between lineages from Patagonia and Holarctic regions, suggesting the co-occurrence of these ancestral populations. Analysis of the genetic contribution to the admixed genomes revealed a Patagonian genetic origin of the admixed strains, even for those located in the North Hemisphere. Overall, the Patagonian lineages, particularly the southern populations, showed a greater global genetic diversity compared to Holarctic and Chinese lineages, in agreement with a higher abundance in Patagonia. Thus, our results are consistent with a likely colonization of the species from peripheral glacial refugia from South Patagonia. Furthermore, fermentative capacity and maltose consumption resulted negatively correlated with latitude, indicating better fermentative performance in northern populations. Our genome analysis, together with previous reports in the sister species S. uvarum suggests that a S. eubayanus ancestor was adapted to the harsh environmental conditions of Patagonia, a region that provides the ecological conditions for the diversification of these ancestral lineages.

Lager yeast history has intrigued scientists for decades. The recent isolation of S. eubayanus, the lager yeast ancestor, represents an unprecedented opportunity to extend our knowledge on yeast phylogeography and the origins of the S. pastorianus lager hybrid. However, the genetic, phenotypic and evolutionary history of this species remains poorly known. Our work demonstrates that S. eubayanus isolates from Patagonia have the greatest genetic diversity, comprising the largest number of lineages within a single geographic region and experienced ancestral and recent admixture between lineages, likely suggesting co-occurrence in Patagonia. Importantly, some isolates exhibited significant phenotypic differences for traits such as high temperature and ethanol tolerance, together with fermentation performance, demonstrating their potential in the brewing industry for the generation of new styles of lager beers. Furthermore, our results support the idea of colonization from peripheral glacial refugia from the South, as responsible for the high genetic diversity observed in southern Chilean Patagonia. Our results allow hypothesizing a successful physiological adjustment of the species to the local conditions in Patagonia, explaining its wide distribution in the southern hemisphere.

Assessing Population Diversity of Brettanomyces Yeast Species and Identification of Strains for Brewing Applications

Brettanomyces yeasts have gained popularity in many sectors of the biotechnological industry, specifically in the field of beer production, but also in wine and ethanol production. Their unique properties enable Brettanomyces to outcompete conventional brewer’s yeast in industrially relevant traits such as production of ethanol and pleasant flavors. Recent advances in next-generation sequencing (NGS) and high-throughput screening techniques have facilitated large population studies allowing the selection of appropriate yeast strains with improved traits. In order to get a better understanding of Brettanomyces species and its potential for beer production, we sequenced the whole genome of 84 strains, which we make available to the scientific community and carried out several in vitro assays for brewing-relevant properties. The collection includes isolates from different substrates and geographical origin. Additionally, we have included two of the oldest Carlsberg Research Laboratory isolates. In this study, we reveal the phylogenetic pattern of Brettanomyces species by comparing the predicted proteomes of each strain. Furthermore, we show that the Brettanomyces collection is well described using similarity in genomic organization, and that there is a direct correlation between genomic background and phenotypic characteristics. Particularly, genomic patterns affecting flavor production, maltose assimilation, beta-glucosidase activity, and phenolic off-flavor (POF) production are reported. This knowledge yields new insights into Brettanomyces population survival strategies, artificial selection pressure, and loss of carbon assimilation traits. On a species-specific level, we have identified for the first time a POF negative Brettanomyces anomalus strain, without the main spoilage character of Brettanomyces species. This strain (CRL-90) has lost DaPAD1, making it incapable of converting ferulic acid to 4-ethylguaiacol (4-EG) and 4-ethylphenol (4-EP). This loss of function makes CRL-90 a good candidate for the production of characteristic Brettanomyces flavors in beverages, without the contaminant increase in POF. Overall, this study displays the potential of exploring Brettanomyces yeast species biodiversity to find strains with relevant properties applicable to the brewing industry.

Postglacial migration shaped the genomic diversity and global distribution of the wild ancestor of lager-brewing hybrids

The wild, cold-adapted parent of hybrid lager-brewing yeasts, Saccharomyces eubayanus, has a complex and understudied natural history. The exploration of this diversity can be used both to develop new brewing applications and to enlighten our understanding of the dynamics of yeast evolution in the wild. Here, we integrate whole genome sequence and phenotypic data of 200 S. eubayanus strains, the largest collection known to date. S. eubayanus has a multilayered population structure, consisting of two major populations that are further structured into six subpopulations. Four of these subpopulations are found exclusively in the Patagonian region of South America; one is found predominantly in Patagonia and sparsely in Oceania and North America; and one is specific to the Holarctic ecozone. Plant host associations differed between subpopulations and between S. eubayanus and its sister species, Saccharomyces uvarum. S. eubayanus is most abundant and genetically diverse in northern Patagonia, where some locations harbor more genetic diversity than is found outside of South America, suggesting that northern Patagonia east of the Andes was a glacial refugium for this species. All but one subpopulation shows isolation-by-distance, and gene flow between subpopulations is low. However, there are strong signals of ancient and recent outcrossing, including two admixed lineages, one that is sympatric with and one that is mostly isolated from its parental populations. Using our extensive biogeographical data, we build a robust model that predicts all known and a handful of additional regions of the globe that are climatically suitable for S. eubayanus, including Europe where host accessibility and competitive exclusion by other Saccharomyces species may explain its continued elusiveness. We conclude that this industrially relevant species has rich natural diversity with many factors contributing to its complex distribution and natural history.

The mysterious wild parent of hybrid-lager brewing yeasts, Saccharomyces eubayanus, has been known for less than 10 years. In this time, it has become clear that lager hybrids arose from a subpopulation that has only been isolated in Tibet and North Carolina, USA; but the global diversity of this species has been less explored. Here, we use whole genome sequencing data for 200 strains (174 newly sequenced) to investigate the genetic diversity and geographical distribution of S. eubayanus. We find that its extensive wild diversity is largely centered in northern Patagonia, which likely was a glacial refugium for this species as three of six subpopulations are endemic to this region. In contrast, S. eubayanus is rarely isolated outside of Patagonia. In North America, isolates are dominated by an invasive, near-clonal admixed lineage; the result of an outcrossing and migration event. All subpopulations are well-differentiated, with low gene flow between them. This genetic isolation of subpopulations could be due to ecological factors, such as plant host associations. With modeling, we find that many areas of the world are climatically suitable to S. eubayanus, including Europe, where it has never been isolated. We propose complex ancestries and rich ecologies underlie the global distribution and diversity of this elusive and industrially important species.

Adaptive Laboratory Evolution of Ale and Lager Yeasts for Improved Brewing Efficiency and Beer Quality

Yeasts directly impact the efficiency of brewery fermentations as well as the character of the beers produced. In recent years, there has been renewed interest in yeast selection and development inspired by the demand to utilize resources more efficiently and the need to differentiate beers in a competitive market. Reviewed here are the different, non-genetically modified (GM) approaches that have been considered, including bioprospecting, hybridization, and adaptive laboratory evolution (ALE). Particular emphasis is placed on the latter, which represents an extension of the processes that have led to the domestication of strains already used in commercial breweries. ALE can be used to accentuate the positive traits of brewing yeast as well as temper some of the traits that are less desirable from a modern brewer's perspective. This method has the added advantage of being non-GM and therefore suitable for food and beverage production.

A re-evaluation of diastatic Saccharomyces cerevisiae strains and their role in brewing

Abstract

Diastatic strains of Saccharomyces cerevisiae possess the unique ability to hydrolyze and ferment long-chain oligosaccharides like dextrin and starch. They have long been regarded as important spoilage microbes in beer, but recent studies have inspired a re-evaluation of the significance of the group. Rather than being merely wild-yeast contaminants, they are highly specialized, domesticated yeasts belonging to a major brewing yeast lineage. In fact, many diastatic strains have unknowingly been used as production strains for decades. These yeasts are used in the production of traditional beer styles, like saison, but also show potential for creation of new beers with novel chemical and physical properties. Herein, we review results of the most recent studies and provide a detailed account of the structure, regulation, and functional role of the glucoamylase-encoding STA1 gene in relation to brewing and other fermentation industries. The state of the art in detecting diastatic yeast in the brewery is also summarized. In summary, these latest results highlight that having diastatic S. cerevisiae in your brewery is not necessarily a bad thing.

Key Points

•Diastatic S. cerevisiae strains are important spoilage microbes in brewery fermentations.

•These strains belong to the ‘Beer 2’ or ‘Mosaic beer’ brewing yeast lineage.

•Diastatic strains have unknowingly been used as production strains in breweries.

•The STA1-encoded glucoamylase enables efficient maltotriose use.

Electronic supplementary material

The online version of this article (10.1007/s00253-020-10531-0) contains supplementary material, which is available to authorized users.

New genome assemblies reveal patterns of domestication and adaptation across Brettanomyces (Dekkera) species

Background

Yeasts of the genus Brettanomyces are of significant interest, both for their capacity to spoil, as well as their potential to positively contribute to different industrial fermentations. However, considerable variance exists in the depth of research and knowledgebase of the five currently known species of Brettanomyces. For instance, Brettanomyces bruxellensis has been heavily studied and many resources are available for this species, whereas Brettanomyces nanus is rarely studied and lacks a publicly available genome assembly altogether. The purpose of this study is to fill this knowledge gap and explore the genomic adaptations that have shaped the evolution of this genus.

Results

Strains for each of the five widely accepted species of Brettanomyces (Brettanomyces anomalus, B. bruxellensis, Brettanomyces custersianus, Brettanomyces naardenensis, and B. nanus) were sequenced using a combination of long- and short-read sequencing technologies. Highly contiguous assemblies were produced for each species. Structural differences between the species’ genomes were observed with gene expansions in fermentation-relevant genes (particularly in B. bruxellensis and B. nanus) identified. Numerous horizontal gene transfer (HGT) events in all Brettanomyces species’, including an HGT event that is probably responsible for allowing B. bruxellensis and B. anomalus to utilize sucrose were also observed.

Conclusions

Genomic adaptations and some evidence of domestication that have taken place in Brettanomyces are outlined. These new genome assemblies form a valuable resource for future research in Brettanomyces.

Into the wild: new yeast genomes from natural environments and new tools for their analysis

Genomic studies of yeasts from the wild have increased considerably in the past few years. This revolution has been fueled by advances in high-throughput sequencing technologies and a better understanding of yeast ecology and phylogeography, especially for biotechnologically important species. The present review aims to first introduce new bioinformatic tools available for the generation and analysis of yeast genomes. We also assess the accumulated genomic data of wild isolates of industrially relevant species, such as Saccharomyces spp., which provide unique opportunities to further investigate the domestication processes associated with the fermentation industry and opportunistic pathogenesis. The availability of genome sequences of other less conventional yeasts obtained from the wild has also increased substantially, including representatives of the phyla Ascomycota (e.g. Hanseniaspora) and Basidiomycota (e.g. Phaffia). Here, we review salient examples of both fundamental and applied research that demonstrate the importance of continuing to sequence and analyze genomes of wild yeasts.

Genome structure reveals the diversity of mating mechanisms in Saccharomyces cerevisiae x Saccharomyces kudriavzevii hybrids, and the genomic instability that promotes phenotypic diversity

Interspecific hybridization has played an important role in the evolution of eukaryotic organisms by favouring genetic interchange between divergent lineages to generate new phenotypic diversity involved in the adaptation to new environments. This way, hybridization between Saccharomyces species, involving the fusion between their metabolic capabilities, is a recurrent adaptive strategy in industrial environments. In the present study, whole-genome sequences of natural hybrids between Saccharomyces cerevisiae and Saccharomyces kudriavzevii were obtained to unveil the mechanisms involved in the origin and evolution of hybrids, as well as the ecological and geographic contexts in which spontaneous hybridization and hybrid persistence take place. Although Saccharomyces species can mate using different mechanisms, we concluded that rare-mating is the most commonly used, but other mechanisms were also observed in specific hybrids. The preponderance of rare-mating was confirmed by performing artificial hybridization experiments. The mechanism used to mate determines the genomic structure of the hybrid and its final evolutionary outcome. The evolution and adaptability of the hybrids are triggered by genomic instability, resulting in a wide diversity of genomic rearrangements. Some of these rearrangements could be adaptive under the stressful conditions of the industrial environment.

TREEasy: An automated workflow to infer gene trees, species trees, and phylogenetic networks from multilocus data

Multilocus genomic data sets can be used to infer a rich set of information about the evolutionary history of a lineage, including gene trees, species trees, and phylogenetic networks. However, user-friendly tools to run such integrated analyses are lacking, and workflows often require tedious reformatting and handling time to shepherd data through a series of individual programs. Here, we present a tool written in Python-TREEasy-that performs automated sequence alignment (with MAFFT), gene tree inference (with IQ-Tree), species inference from concatenated data (with IQ-Tree and RaxML-NG), species tree inference from gene trees (with ASTRAL, MP-EST, and STELLS2), and phylogenetic network inference (with SNaQ and PhyloNet). The tool only requires FASTA files and nine parameters as inputs. The tool can be run as command line or through a Graphical User Interface (GUI). As examples, we reproduced a recent analysis of staghorn coral evolution, and performed a new analysis on the evolution of the "WGD clade" of yeast. The latter revealed novel patterns that were not identified by previous analyses. TREEasy represents a reliable and simple tool to accelerate research in systematic biology (https://github.com/MaoYafei/TREEasy).

Independent domestication events in the blue-cheese fungus Penicillium roqueforti

Domestication provides an excellent framework for studying adaptive divergence. Using population genomics and phenotypic assays, we reconstructed the domestication history of the blue cheese mould Penicillium roqueforti. We showed that this fungus was domesticated twice independently. The population used in Roquefort originated from an old domestication event associated with weak bottlenecks and exhibited traits beneficial for pre‐industrial cheese production (slower growth in cheese and greater spore production on bread, the traditional multiplication medium). The other cheese population originated more recently from the selection of a single clonal lineage, was associated with all types of blue cheese worldwide except Roquefort, and displayed phenotypes more suited for industrial cheese production (high lipolytic activity, efficient cheese cavity colonization ability and salt tolerance). We detected genomic regions affected by recent positive selection and putative horizontal gene transfers. This study sheds light on the processes of rapid adaptation and raises questions about genetic resource conservation.

see also the Perspective by Brigida Gallone, Jan Steensels and Kevin J. Verstrepen.

Designing New Yeasts for Craft Brewing: When Natural Biodiversity Meets Biotechnology

Beer is a fermented beverage with a history as old as human civilization. Ales and lagers are by far the most common beers; however, diversification is becoming increasingly important in the brewing market and the brewers are continuously interested in improving and extending the range of products, especially in the craft brewery sector. Fermentation is one of the widest spaces for innovation in the brewing process. Besides Saccharomyces cerevisiae ale and Saccharomyces pastorianus lager strains conventionally used in macro-breweries, there is an increasing demand for novel yeast starter cultures tailored for producing beer styles with diversified aroma profiles. Recently, four genetic engineering-free approaches expanded the genetic background and the phenotypic biodiversity of brewing yeasts and allowed novel costumed-designed starter cultures to be developed: (1) the research for new performant S. cerevisiae yeasts from fermented foods alternative to beer; (2) the creation of synthetic hybrids between S. cerevisiae and Saccharomyces non-cerevisiae in order to mimic lager yeasts; (3) the exploitation of evolutionary engineering approaches; (4) the usage of non-Saccharomyces yeasts. Here, we summarized the pro and contra of these approaches and provided an overview on the most recent advances on how brewing yeast genome evolved and domestication took place. The resulting correlation maps between genotypes and relevant brewing phenotypes can assist and further improve the search for novel craft beer starter yeasts, enhancing the portfolio of diversified products offered to the final customer.

Sulfur dioxide resistance in Saccharomyces cerevisiae: beyond SSU1

Sulfite resistance is an important oenological trait for wine yeasts because this compound is used during winemaking as a microbial inhibitor and antioxidant. The molecular mechanisms by which Saccharomyces cerevisiae responds and tolerates SO2 have been mainly focused on the sulfite efflux pump encoded by SSU1. Different chromosomal rearrangements in the regulatory region of this gene have been correlated with improved sulfite tolerance. However, other molecular factors must contribute to this trait because the SSU1 gene activity does not always fit with sulfite tolerance. An interesting approach to shed light onto this issue could be found by Lage et al. (2019). These authors have combined transcriptomic and genome-wide analysis to describe how the poorly characterized transcription factor Com2 controls, directly or indirectly, the expression of more than 80% of the genes activated by SO2. Additionally, large-scale phenotyping revealed the identification of 50 Com2-targets contributing to the protection against SO2. This information is very interesting for gaining knowledge regarding this important industrial trait.

Gnathovorax cabreirai: a new early dinosaur and the origin and initial radiation of predatory dinosaurs

Predatory dinosaurs were an important ecological component of terrestrial Mesozoic ecosystems. Though theropod dinosaurs carried this role during the Jurassic and Cretaceous Periods (and probably the post-Carnian portion of the Triassic), it is difficult to depict the Carnian scenario, due to the scarcity of fossils. Until now, knowledge on the earliest predatory dinosaurs mostly relies on herrerasaurids recorded in Carnian strata of South America. Phylogenetic investigations recovered the clade in different positions within Dinosauria, whereas fewer studies challenged its monophyly. Although herrerasaurid fossils are much better recorded in present-day Argentina than in Brazil, Argentinean strata so far yielded no fairly complete skeleton representing a single individual. Here, we describe Gnathovorax cabreirai, a new herrerasaurid based on an exquisite specimen found as part of a multitaxic association form southern Brazil. The type specimen comprises a complete and well-preserved articulated skeleton, preserved in close association (side by side) with rhynchosaur and cynodont remains. Given its superb state of preservation and completeness, the new specimen sheds light into poorly understood aspects of the herrerasaurid anatomy, including endocranial soft tissues. The specimen also reinforces the monophyletic status of the group, and provides clues on the ecomorphology of the early carnivorous dinosaurs. Indeed, an ecomorphological analysis employing dental traits indicates that herrerasaurids occupy a particular area in the morphospace of faunivorous dinosaurs, which partially overlaps the area occupied by post-Carnian theropods. This indicates that herrerasaurid dinosaurs preceded the ecological role that later would be occupied by large to medium-sized theropods.

Draft Genome Analysis of Trichosporonales Species That Contribute to the Taxonomy of the Genus Trichosporon and Related Taxa

Many nomenclatural changes, including proposals of new taxa, have been carried out in fungi to adapt to the "One fungus = One name" (1F=1N) principle. In yeasts, while some changes have been made in response to 1F=1N, most have resulted from two other factors: i) an improved understanding of biological diversity due to an increase in number of known species, and ii) progress in the methods for analyzing and evaluating biological diversity. The method for constructing a backbone tree, which is a basal tree used to infer phylogeny, has also progressed from single-gene trees to multi-locus trees and further, to genome trees. This paper describes recent advances related to the contribution of genomic data to taxonomy, using the order Trichosporonales as an example.

Interspecific hybridization facilitates niche adaptation in beer yeast

Hybridization between species often leads to non-viable or infertile offspring, yet examples of evolutionarily successful interspecific hybrids have been reported in all kingdoms of life. However, many questions on the ecological circumstances and evolutionary aftermath of interspecific hybridization remain unanswered. In this study, we sequenced and phenotyped a large set of interspecific yeast hybrids isolated from brewing environments to uncover the influence of interspecific hybridization in yeast adaptation and domestication. Our analyses demonstrate that several hybrids between Saccharomyces species originated and diversified in industrial environments by combining key traits of each parental species. Furthermore, posthybridization evolution within each hybrid lineage reflects subspecialization and adaptation to specific beer styles, a process that was accompanied by extensive chimerization between subgenomes. Our results reveal how interspecific hybridization provides an important evolutionary route that allows swift adaptation to novel environments.

Fermentation innovation through complex hybridization of wild and domesticated yeasts

The most common fermented beverage, lager beer, is produced by interspecies hybrids of the brewing yeast Saccharomyces cerevisiae and its wild relative S. eubayanus. Lager-brewing yeasts are not the only example of hybrid vigour or heterosis in yeasts, but the full breadth of interspecies hybrids associated with human fermentations has received less attention. Here we present a comprehensive genomic analysis of 122 Saccharomyces hybrids and introgressed strains. These strains arose from hybridization events between two to four species. Hybrids with S. cerevisiae contributions originated from three lineages of domesticated S. cerevisiae, including the major wine-making lineage and two distinct brewing lineages. In contrast, the undomesticated parents of these interspecies hybrids were all from wild Holarctic or European lineages. Most hybrids have inherited a mitochondrial genome from a parent other than S. cerevisiae, which recent functional studies suggest could confer adaptation to colder temperatures. A subset of hybrids associated with crisp flavour profiles, including both lineages of lager-brewing yeasts, have inherited inactivated S. cerevisiae alleles of critical phenolic off-flavour genes and/or lost functional copies from the wild parent through multiple genetic mechanisms. These complex hybrids shed light on the convergent and divergent evolutionary trajectories of interspecies hybrids and their impact on innovation in lager brewing and other diverse fermentation industries.

A Hands-On Guide to Brewing and Analyzing Beer in the Laboratory

Beer would not exist without microbes. During fermentation, yeast cells convert cereal‐derived sugars into ethanol and CO₂. Yeast also produces a wide array of aroma compounds that influence beer taste and aroma. The complex interaction between all these aroma compounds results in each beer having its own distinctive palette. This article contains all protocols needed to brew beer in a standard lab environment and focuses on the use of yeast in beer brewing. More specifically, it provides protocols for yeast propagation, brewing calculations and, of course, beer brewing. At the end, we have also included protocols for analyses that can be performed on the resulting brew, with a focus on yeast‐derived aroma compounds. © 2019 The Authors.

Exploiting heterozygosity in industrial yeasts to create new and improved baker's yeasts

The main aim of the work was to utilize heterozygosity of industrial yeast strains to construct new baker's yeast strains. Commercial baker's yeast strain ALKO 743, its more ethanol tolerant descendant ALKO 554 selected initially for growth over 300 generations in increasing ethanol concentrations in a glucose medium, and ALKO 3460 from an old domestic sour dough starter were used as starting strains. Isolated meiotic segregants of the strains were characterized genetically for sporulation ability and mating type, and the ploidy was determined physically. Heterozygosity of the segregant strains was estimated by a variety of molecular characterizations and fermentation and growth assays. The results showed wide heterozygosity and that the segregants were clustered into subgroups. This clustering was used for choosing distantly or closely related partners for strain construction crosses. Intrastrain hybrids made with segregants of ALKO 743 showed 16-24% hybrid vigour or heterosis. Interstrain hybrids with segregants of ALKO 743 and ALKO 3460 showed a wide variety of characteristics but also clear heterosis of 27-31% effects as assayed by lean and sugar dough raising. Distiller's yeast ALKO 554 turned out to be a diploid genetic segregant and not just a more ethanol tolerant mutant of the tetraploid parent strain ALKO 743.

Occurrence and Importance of Yeasts in Indigenous Fermented Food and Beverages Produced in Sub-Saharan Africa

Indigenous fermented food and beverages represent a valuable cultural heritage in sub-Saharan Africa, having one of the richest selections of fermented food products in the world. In many of these indigenous spontaneously fermented food and beverages, yeasts are of significant importance. Several factors including raw materials, processing methods, hygienic conditions as well as the interactions between yeasts and other commensal microorganisms have been shown to influence yeast species diversity and successions. Both at species and strain levels, successions take place due to the continuous change in intrinsic and extrinsic growth factors. The selection pressure from the microbial stress factors leads to niche adaptation and both yeast species and strains with traits deviating from those generally acknowledged in current taxonomic keys, have been isolated from indigenous sub-Saharan African fermented food products. Yeasts are important for flavor development, impact shelf life, and nutritional value and do, in some cases, even provide host-beneficial effects. In order to sustain and upgrade these traditional fermented products, it is quite important to obtain detailed knowledge on the microorganisms involved in the fermentations, their growth requirements and interactions. While other publications have reported on the occurrence of prokaryotes in spontaneously fermented sub-Saharan food and beverages, the present review focuses on yeasts considering their current taxonomic position, relative occurrence and successions, interactions with other commensal microorganisms as well as beneficial effects and importance in human diet. Additionally, the risk of opportunistic yeasts is discussed.

Evolutionary journey and characterisation of a novel pan-gene associated with beer strains of Saccharomyces cerevisiae

The sequencing of over a thousand Saccharomyces cerevisiae genomes revealed a complex pangenome. Over one third of the discovered genes are not present in the S. cerevisiae core genome but instead are often restricted to a subset of yeast isolates and thus may be important for adaptation to specific environmental niches. We refer to these genes as "pan-genes," being part of the pangenome but not the core genome. Here, we describe the evolutionary journey and characterisation of a novel pan-gene, originally named hypothetical (HYPO) open-reading frame. Phylogenetic analysis reveals that HYPO has been predominantly retained in S. cerevisiae strains associated with brewing but has been repeatedly lost in most other fungal species during evolution. There is also evidence that HYPO was horizontally transferred at least once, from S. cerevisiae to Saccharomyces paradoxus. The phylogenetic analysis of HYPO exemplifies the complexity and intricacy of evolutionary trajectories of genes within the S. cerevisiae pangenome. To examine possible functions for Hypo, we overexpressed a HYPO-GFP fusion protein in both S. cerevisiae and Saccharomyces pastorianus. The protein localised to the plasma membrane where it accumulated initially in distinct foci. Time-lapse fluorescent imaging revealed that when cells are grown in wort, Hypo-gfp fluorescence spreads throughout the membrane during cell growth. The overexpression of Hypo-gfp in S. cerevisiae or S. pastorianus strains did not significantly alter cell growth in medium-containing glucose, maltose, maltotriose, or wort at different concentrations.

sppIDer: A Species Identification Tool to Investigate Hybrid Genomes with High-Throughput Sequencing

The genomics era has expanded our knowledge about the diversity of the living world, yet harnessing high-throughput sequencing data to investigate alternative evolutionary trajectories, such as hybridization, is still challenging. Here we present sppIDer, a pipeline for the characterization of interspecies hybrids and pure species, that illuminates the complete composition of genomes. sppIDer maps short-read sequencing data to a combination genome built from reference genomes of several species of interest and assesses the genomic contribution and relative ploidy of each parental species, producing a series of colorful graphical outputs ready for publication. As a proof-of-concept, we use the genus Saccharomyces to detect and visualize both interspecies hybrids and pure strains, even with missing parental reference genomes. Through simulation, we show that sppIDer is robust to variable reference genome qualities and performs well with low-coverage data. We further demonstrate the power of this approach in plants, animals, and other fungi. sppIDer is robust to many different inputs and provides visually intuitive insight into genome composition that enables the rapid identification of species and their interspecies hybrids. sppIDer exists as a Docker image, which is a reusable, reproducible, transparent, and simple-to-run package that automates the pipeline and installation of the required dependencies (https://github.com/GLBRC/sppIDer; last accessed September 6, 2018).

A Quasi-Domesticate Relic Hybrid Population of Saccharomyces cerevisiae × S. paradoxus Adapted to Olive Brine

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.