Where to find yeast?

Micro-organisms are everywhere. On any surface, in liquids, in the air, everywhere propagules, spores or living growing cells can be found. But how to know if what you can find at a specific location is the place the organism is actually growing?

To understand how selection affects evolution of an organism, the natural habitat of said organism needs to be known; it are the circumstances the species experience in that environment that shape its life history. For many oranisms, especially microorganisms we just don’t know, and this includes the model yeast species, Schizosaccharomyces pombe, the fission yeast we use in my lab.

As a master student, Rasha Shraim (now PhD student at SFI Centre for Research Training in
Genomics Data Sciences and School of Medicine at Trinity College Dublin, Ireland) took up the challenge of finding the natural habitats of fission yeast using publicly available meta-transcriptomic data sets. Assuming that active growth means that the cells are actively expressing their genes, we combed through a large number of raw sequences, searching for any reads that have very high similarity to one of the fission yeast species (S. octosporus, S. japonicus, S. pombe, or S. cryophilus) and deducing where the natural habitat of fission yeasts is.

graphical abstract

The results from this endeavor are now published in Yeast. After digging through some 13,000 data sets, the main conclusions are that, fission yeast can be most easily found in association with food, honey and drink – as expected, as this is where fission yeast is most easily isolated from – but can also be found in association with insects and other land arthropods. The yeast is probably quite rare, but a successful and opportunistic colonizer/contaminant of high sugar substrates. You can read more in

Shraim, Rasha, and Bart P. S. Nieuwenhuis. 2022. “The Search for Schizosaccharomyces Fission Yeasts in Environmental Metatranscriptomes.” Yeast In press. https://doi.org/10.1002/yea.3689.

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PhD position available

A three year PhD position is now available to be started soon. I recently was granted a DFG grant to hire a PhD student to work on the evolution of recombination rates. In the project we will try to study how (in)flexible the recombination landscape of fission yeast is and if strong selection can generate recombination hotspots, coldspots and super genes. This question is of relevance for the evolution of sex chromosomes, mating types, but also for example for local or divergent adaptation.

In the project we will combine experimental evolution approaches, analyses of natural variation in fission yeast and genomic analyses for variants. In collaboration with Dr. Alexander Lorenz at Aberdeen University UK, we will then perform functional analysis to further understand potential mechanisms responsible for variation in recombination rates.

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Fitness in fungi

Fitness is the relative contribution of one genotype, relative to that of another. But how does one measure and quantify this? In fungi, a variety of measures (“fitness proxies”) are used. Growth rate of the mycelium is a popular one, because it can repeatedly and consistently be measured; but does it reflect fitness? In some species under laboratory circumstances it probably does, such as in for example in Aspergillus. In the lab, the growth rate of the mycelium reflects the spore production which is linearly correlated (Gifford & Schoustra 2013). But can this be generalized? 

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New semester, New faces

Working at the Faculty of Biology at LMU means I have the pleasure of participating in the master on Evolution, Ecology and Systematics (EES). Every year a new cohort of enthusiastic students starts that originates from a wide variety of backgrounds and nationalities. The master is heavily research-focused, which means every semester the students need to perform a Individual Research Training (IRT) which is a great opportunity for me to every semester work with a group of enthusiastic and bright students! This semester I welcome three new faces and two familiar ones.

Linda Hagberg will study how in fission yeast, strains of opposite mating types that express the same pheromones and receptors are able to find each other and form successful matings.
Pilar Herrera will study reproductive isolation of a variety of natural fission yeast strains.
Mohammed Tawfeeq will be generating strains that mating-type independently have identical pheromone-receptor systems.

Franziska Brenninger and Augusto Liberti were IRT students in the previous semester and will continue for some time more. Together they applied for a Lehre@LMU Student Research Award to research the importance of pheromone production in mating competitions for mating-type switching and non-switching fission yeasts. The next few months they will perform large scale competition essays to test the role of the many copies of M-factor pheromones that naturally occur in the fission yeast genome, both during asexual and sexual reproduction.

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Pombe is a hybrid

Preprint on biorxiv.org

We just posted a preprint of our manuscript on bioRxiv. In the paper we analyzed the sequencing data from 161 different fission yeast strains and showed that these are a recent hybrids between (at least) two populations that diverged from each other about 2300 years ago, and about 20 outcrossing generations (probably sometime in the last 500 years) started to hybridize. The genomes still have large haplotype blocks from the two different populations. Long-read sequencing methods (PacBio’s SMRT and and NanoPore’s MinIon) showed some small structural variants and a few large structural variation, but these variants are present only at low frequencies and do not explain the haplotype blocks.

Tusso, Sergio, Bart P.S. Nieuwenhuis, Fritz J. Sedlazeck, John W. Davey, Daniel Jeffares, and Jochen B. W. Wolf. “Ancestral Admixture and Structural Mutation Define Global Biodiversity in Fission Yeast.” BioRxiv, September 12, 2018. https://doi.org/10.1101/415091.
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A new website

Welcome to this new website! Since I moved to the LMU university, a lot of things needed to be arranged, and this website was one of them. Finally I managed to get round to get this mostly setup.

At the moment this is still work in progress. In the future, this will be the place where you’ll be able to find more information on my group, the work we’re doing and data, protocols etc.

Many protocols can be found here too: www.pombevolution.eu/labwiki/

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