Isolation and Laboratory Domestication of Natural Yeast Strains

Liti, Gianni; Warringer, Jonas; Blomberg, Anders

doi:10.1101/pdb.prot089052

Cited by 18 publications

(13 citation statements)

References 19 publications

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“…Sediments were then streaked onto YPD agar plates. Single colonies were picked out and incubated in potassium acetate medium 23°C for 7-10 days 69 . Single colonies with ascus-like (four spores) structures under microscope were picked out and streaked onto YPD agar plates.…”

Section: Methodsmentioning

confidence: 99%

Deep sampling of ancestral genetic diversity reveals Saccharomyces cerevisiae pre-domestication life histories

Lee

Liu

et al. 2021

Preprint

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The ecology and genetic diversity of model yeast Saccharomyces cerevisiae prior to human domestication remain poorly understood. Taiwan is regarded as part of this yeast's geographic birthplace where the most divergent natural lineage was discovered. Here, we deep sampled the broad-leaf forests across this continental island to probe the ancestral species diversity. We found that S. cerevisiae is ubiquitously distributed at low abundance in the forests. Whole-genome sequencing of 121 isolates revealed nine distinct lineages, the highest known in any region. Three lineages are endemic to Taiwan and six lineages are widespread in Asia. Molecular dating placed the divergence of the Taiwanese and Asian lineages during the Pleistocene, when a continental shelf land bridge exposed connecting Taiwan to other major landmasses. Extensive historical and recent admixture events were detected between natural lineages. In particular, the genetic component from a lineage associated with fruits that spanned the widest geographical range was present in most admixed isolates. Collectively, Taiwanese isolates harbor genetic diversity comparable to that of the whole Asia continent, and different lineages have coexisted at a fine spatial scale even on the same tree. Patterns of variations within each lineage revealed that S. cerevisiae is highly clonal and predominantly reproduces asexually in nature. We detected prevalent purifying selection genome-wide across all natural lineages with signals of positive or directional selection independent between lineages. This study establishes that S. cerevisiae has rich natural diversity without human influences, making it a powerful model system in microbial ecology.

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Section: Methodsmentioning

confidence: 99%

Deep sampling of ancestral genetic diversity reveals Saccharomyces cerevisiae pre-domestication life histories

Lee

Liu

et al. 2021

Preprint

Self Cite

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“…An enrichment protocol with a medium consisting of 3 g yeast extract, 3 g malt extract, 5 g peptone, 10 g sucrose, 1 mg chloramphenicol, 1 mL of 1 M HCl and 76 mL ethanol per liter was successfully used for S. cerevisiae and S. paradoxus isolation from uncultivated habitats [ 19 ]. This ethanol enrichment method was then used in different field surveys of Saccharomyces species with minor modifications in carbon and nitrogen sources, and ethanol and antibiotic concentrations [ 20 , 52 , 53 ].…”

Section: Habitats Of S Cerevisiae In the Wildmentioning

confidence: 99%

The Ecology and Evolution of the Baker’s Yeast Saccharomyces cerevisiae

Bai

Han

Duan

et al. 2022

Genes

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The baker’s yeast Saccharomyces cerevisiae has become a powerful model in ecology and evolutionary biology. A global effort on field survey and population genetics and genomics of S. cerevisiae in past decades has shown that the yeast distributes ubiquitously in nature with clearly structured populations. The global genetic diversity of S. cerevisiae is mainly contributed by strains from Far East Asia, and the ancient basal lineages of the species have been found only in China, supporting an ‘out-of-China’ origin hypothesis. The wild and domesticated populations are clearly separated in phylogeny and exhibit hallmark differences in sexuality, heterozygosity, gene copy number variation (CNV), horizontal gene transfer (HGT) and introgression events, and maltose utilization ability. The domesticated strains from different niches generally form distinct lineages and harbor lineage-specific CNVs, HGTs and introgressions, which contribute to their adaptations to specific fermentation environments. However, whether the domesticated lineages originated from a single, or multiple domestication events is still hotly debated and the mechanism causing the diversification of the wild lineages remains to be illuminated. Further worldwide investigations on both wild and domesticated S. cerevisiae, especially in Africa and West Asia, will be helpful for a better understanding of the natural and domestication histories and evolution of S. cerevisiae.

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“…The advances in culture-independent metagenomic characterization of microbial communities that have enabled increasingly detailed characterization of bacterial communities (Franzosa et al 2015) do not lend themselves well to the study of yeasts; typical methods for environmental detection of bacterial microbes are less useful for eukaryotic microbes that are low-abundance community members (Pereira-Marques et al 2019). As a result, most research in yeast ecology is reliant on environmental sampling and isolation in synthetic media, either by direct plating (Boynton, Kowallik, Landermann and Stukenbrock 2019;Rose, Winston and Hieter 1990;Stefanini et al 2012) or enrichment (Knight and Goddard 2015;Liti, Warringer and Blomberg 2017;Sniegowski, Dombrowski and Fingerman 2002).…”

Section: Introductionmentioning

confidence: 99%

Substrate, temperature, and geographical patterns among nearly 2,000 natural yeast isolates

Spurley

Fisher

Langdon

et al. 2021

Preprint

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Yeasts have broad importance as industrially and clinically relevant microbes and as powerful models for fundamental research, but we are only beginning to understand the roles yeasts play in natural ecosystems. Yeast ecology is often more difficult to study compared to other, more abundant microbes, but growing collections of natural yeast isolates are beginning to shed light on fundamental ecological questions. Here we used environmental sampling and isolation to assemble a dataset of 1,962 isolates collected from throughout the contiguous United States of America (USA) and Alaska, which were then used to uncover geographic patterns, along with substrate and temperature associations among yeast taxa. We found some taxa, including the common yeasts Torulaspora delbrueckii and Saccharomyces paradoxus, to be repeatedly isolated from multiple sampled regions of the US, and we classify these as broadly distributed cosmopolitan yeasts. A number of yeast taxon - substrate associations were identified, some of which were novel and some of which support previously reported associations. Further, we found a strong effect of isolation temperature on the phyla of yeasts recovered, as well as for many species. We speculate that substrate and isolation temperature associations reflect the ecological diversity of and niche partitioning by yeast taxa.

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Isolation and Laboratory Domestication of Natural Yeast Strains

Cited by 18 publications

References 19 publications

Deep sampling of ancestral genetic diversity reveals Saccharomyces cerevisiae pre-domestication life histories

Deep sampling of ancestral genetic diversity reveals Saccharomyces cerevisiae pre-domestication life histories

The Ecology and Evolution of the Baker’s Yeast Saccharomyces cerevisiae

Substrate, temperature, and geographical patterns among nearly 2,000 natural yeast isolates

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