The natural ecology of Saccharomyces yeasts

There are some organisms on Earth that have an especially close relationship with humankind, and one of them is Saccharomyces cerevisiae. This species, which is also known as the baker´s or brewer´s yeast, has been used for thousands of years, and almost all around the world, for the production of alcoholic beverages and bread. Today, we owe even more to this organism than wine, as it became one of the best studied model organisms in biology and is widely used in different scientific disciplines like Cell Biology, Biochemistry, Genetics and Molecular Biology. But surprisingly little is known about its natural ecology. The habitat of wild, undomesticated Saccharomyces yeasts cannot be reliably defined and contrary hypotheses exist. There is some evidence that the yeast is adapted to live in sugar rich environments like fruits, but on the other hand there is also indication that wild Saccharomyces yeasts are associated with oak trees, especially their bark. In both environments, yeast is only found in a small proportion of samples and most studies additionally suffer from different biases making it impossible to conclude which, if either, environment is truly the natural habitat of the yeast. In this thesis the natural ecology of Saccharomyces spp. was studied, with an emphasis on the natural environment. The oak bark environment was analyzed by characterizing the associated microbial community using culturing and pyrosequencing methods. S. paradoxus, the wild and undomesticated relative of S. cerevisiae, could indeed grow on nutrients present in oak bark but is only a rare member of the microbial community. Studying the influence of co-isolated oak bark microorganisms on S. paradoxus’ growth and survival in natural oak bark medium revealed a wide range of effects strongly dependent on temperature. Further experimental analysis of the interactions between the yeast and two of the bacteria gave insights into the diversity and complexity of natural microbial interactions. While one Pseudomonas spp. killed the yeast, another bacterium; Mucilaginibacter spp. promoted its growth. Saccharomyces’ metabolic specialty of fermenting under aerobic conditions (Crabtree effect) is taken as evidence that the yeast is adapted to sugary fruit environments. To test this, a Crabtree positive (“fermenter”) and its isogenic Crabtree negative mutant strain (“respirer”) were competed in laboratory media and grape juice, confirming that the Crabtree effect provides a benefit under resource competition in lab medium. Unexpectedly, this benefit was absent in the more natural grape juice, although adding natural microbial competitors restored the benefit of fermentation over respiration, perhaps by interference competition. Finally, the yeast / oak association could be confirmed by an intense sampling study, but Saccharomyces was found to be much more abundant in oak leaf litter than on bark. Oak leaf litter provides a stable habitat over the year from which yeast can be easily isolated and studied. This is a useful discovery for the ecology and evolutionary history of Saccharomyces yeasts, with great promise for future studies

A systematic forest survey showing an association of Saccharomyces paradoxus with oak leaf litter.

Although we understand the genetics of the laboratory model yeast Saccharomyces cerevisiae very well, we know little about the natural ecology and environment that shaped its genome. Most isolates of Saccharomyces paradoxus, the wild relative of S. cerevisiae, come from oak trees, but it is not known whether this is because oak is their primary habitat. We surveyed leaf litter in a forest in Northern Germany and found a strong correlation between isolation success of wild Saccharomyces and the proximity of the nearest oak. We compared the four most common tree genera and found Saccharomyces most frequently in oak litter. Interestingly, we show that Saccharomyces is much more abundant in oak leaf litter than on oak bark, suggesting that it grows in litter or soil rather than on the surfaces of oaks themselves. The distribution and abundance of Saccharomyces over the course of a year shows that oak leaf litter provides a stable habitat for the yeast, although there was significant tree-to-tree variation. Taken together, our results suggest that leaf litter rather than tree surfaces provide the better habitat for wild Saccharomyces, with oak being the preferred tree genus. 99.5% of all strains (633/636) isolated were S. paradoxus

Facial imitation improves emotion recognition in adults with different levels of sub-clinical autistic traits

We used computer-based automatic expression analysis to investigate the impact of imitation on facial emotion recognition with a baseline-intervention-retest design. The participants: 55 young adults with varying degrees of autistic traits, completed an emotion recognition task with images of faces displaying one of six basic emotional expressions. This task was then repeated with instructions to imitate the expressions. During the experiment, a camera captured the participants’ faces for an automatic evaluation of their imitation performance. The instruction to imitate enhanced imitation performance as well as emotion recognition. Of relevance, emotion recognition improvements in the imitation block were larger in people with higher levels of autistic traits, whereas imitation enhancements were independent of autistic traits. The finding that an imitation instruction improves emotion recognition, and that imitation is a positive within-participant predictor of recognition accuracy in the imitation block supports the idea of a link between motor expression and perception in the processing of emotions, which might be mediated by the mirror neuron system. However, because there was no evidence that people with higher autistic traits differ in their imitative behavior per se, their disproportional emotion recognition benefits could have arisen from indirect effects of imitation instructions

Measuring microbial fitness in a field reciprocal transplant experiment

Microbial fitness is easy to measure in the laboratory, but difficult to measure in the field. Laboratory fitness assays make use of controlled conditions and genetically modified organisms, neither of which are available in the field. Among other applications, fitness assays can help researchers detect adaptation to different habitats or locations. We designed a competitive fitness assay to detect adaptation of Saccharomyces paradoxus isolates to the habitat they were isolated from (oak or larch leaf litter). The assay accurately measures relative fitness by tracking genotype frequency changes in the field using digital droplet PCR (DDPCR). We expected locally adapted S. paradoxus strains to increase in frequency over time when growing on the leaf litter type from which they were isolated. The DDPCR assay successfully detected fitness differences among S. paradoxus strains, but did not find a tendency for strains to be adapted to the habitat they were isolated from. Instead, we found that the natural alleles of the hexose transport gene we used to distinguish S. paradoxus strains had significant effects on fitness. The origin of a strain also affected its fitness: strains isolated from oak litter were generally fitter than strains from larch litter. Our results suggest that dispersal limitation and genetic drift shape S. paradoxus populations in the forest more than local selection does, although further research is needed to confirm this. Tracking genotype frequency changes using DDPCR is a practical and accurate microbial fitness assay for natural environments

Quantifying the efficiency and biases of forest Saccharomyces sampling strategies

Saccharomyces yeasts are emerging as model organisms for ecology and evolution, and researchers need environmental Saccharomyces isolates to test ecological and evolutionary hypotheses. However, methods for isolating Saccharomyces from nature have not been standardized, and isolation methods may influence the genotypes and phenotypes of studied strains. We compared the effectiveness and potential biases of an established enrichment culturing method against a newly developed direct plating method for isolating forest floor Saccharomyces spp. In a European forest, enrichment culturing was both less successful at isolating Saccharomyces paradoxus per sample collected and less labour intensive per isolated S. paradoxus colony than direct isolation. The two methods sampled similar S. paradoxus diversity: The number of unique genotypes sampled (i.e., genotypic diversity) per S. paradoxus isolate and average growth rates of S. paradoxus isolates did not differ between the two methods, and growth rate variances (i.e., phenotypic diversity) only differed in one of three tested environments. However, enrichment culturing did detect rare Saccharomyces cerevisiae in the forest habitat and also found two S. paradoxus isolates with outlier phenotypes. Our results validate the historically common method of using enrichment culturing to isolate representative collections of environmental Saccharomyces. We recommend that researchers choose a Saccharomyces sampling method based on resources available for sampling and isolate screening. Researchers interested in discovering new Saccharomyces phenotypes or rare Saccharomyces species from natural environments may also have more success using enrichment culturing. We include step-by-step sampling protocols in the supplemental materials

Strong selection and high mutation supply characterize experimental Chlorovirus evolution

Characterizing how viruses evolve expands our understanding of the underlying fundamental processes, such as mutation, selection and drift. One group of viruses whose evolution has not yet been extensively studied is the Phycodnaviridae, a globally abundant family of aquatic large double-stranded (ds)DNA (dsDNA) viruses. Here we studied the evolutionary change of Paramecium bursaria chlorella virus 1 during experimental coevolution with its algal host. We used pooled genome sequencing of six independently evolved populations to characterize genomic change over five time points. Across six experimental replicates involving either strong or weak demographic fluctuations, we found single nucleotide polymorphisms (SNPs) at sixty-seven sites. The occurrence of genetic variants was highly repeatable, with just two of the SNPs found in only a single experimental replicate. Three genes A122/123R, A140/145R and A540L showed an excess of variable sites, providing new information about potential targets of selection during Chlorella–Chlorovirus coevolution. Our data indicated that the studied populations were not mutation-limited and experienced strong positive selection. Our investigation highlighted relevant processes governing the evolution of aquatic large dsDNA viruses, which ultimately contributes to a better understanding of the functioning of natural aquatic ecosystems

Der Beitrag des Zinsbuchs zum Gesamtergebnis einer Sparkasse

Insbesondere für Sparkassen und andere, relativ kleine regional operie-rende Kreditinstitute stellt der Zinsüberschuss die bei weitem wichtigste Ertragsquelle dar. Dieser bildet sich zum einen durch die am Markt erzielbare Zinsmarge sowie die Bereitschaft zur Fristentransformation, d.h. die Ausnutzung der zumeist positiven Differenz zwischen lang-fristigen Kredit- und kurzfristigen Einlagenzinssätzen. Weitgehend unklar und damit auch Gegenstand der Diskussion ist die faktische Gewichtung dieser beiden Komponenten. Insbeson-dere bei untypisch verlaufenden Zinsstrukturkurven und vor allem bei negativen Zinsniveaus stellt die Fristentransformation eine Strategie dar, die mit erheblichen Ertragsririsiken einher geht. Unsere Analyse versucht, den (historischen) quantitaiven Einfluß der Fristentransformation auf das Betriebsergebnis der Sparkassen abzuschätzen und für die nähere Zukunft zu prognostizieren. Unsere Resultate lassen erwarten, dass die bis dato positiven Ertragswirkungen der Fristentransformation deutlich zurückgehen werde