Experimental evolution: its principles and applications in developing stress-tolerant yeasts

Signatures of selection in Mulinia lateralis underpinning its rapid adaptation to laboratory conditions

The dwarf surf clam, Mulinia lateralis, is considered as a model species for bivalves because of its rapid growth and short generation time. Recently, successful breeding of this species for multiple generations in our laboratory revealed its acquisition of adaptive advantages during artificial breeding. In this study, 310 individuals from five different generations were genotyped with 22,196 single nucleotide polymorphisms (SNPs) with the aim of uncovering the genetic basis of their adaptation to laboratory conditions. Results revealed that M. lateralis consistently maintained high genetic diversity across generations, characterized by high observed heterozygosity (H o: 0.2733-0.2934) and low levels of inbreeding (F is: -0.0244-0.0261). Population analysis indicated low levels of genetic differentiation among generations of M. lateralis during artificial breeding (F st <0.05). In total, 316 genomic regions exhibited divergent selection, with 168 regions under positive selection. Furthermore, 227 candidate genes were identified in the positive selection regions, which have functions including growth, stress resistance, and reproduction. Notably, certain selection signatures with significantly higher F st value were detected in genes associated with male reproduction, such as GAL3ST1, IFT88, and TSSK2, which were significantly upregulated during artificial breeding. This suggests a potential role of sperm-associated genes in the rapid evolutionary response of M. lateralis to selection in laboratory conditions. Overall, our findings highlight the phenotypic and genetic changes, as well as selection signatures, in M. lateralis during artificial breeding. This contributes to understanding their adaptation to laboratory conditions and underscores the potential for using this species to explore the adaptive evolution of bivalves.

Food yeasts: occurrence, functions, and stress tolerance in the brewing of fermented foods

With the rapid development of systems biology technology, there is a deeper understanding of the molecular biological mechanisms and physiological characteristics of microorganisms. Yeasts are widely used in the food industry with their excellent fermentation performances. While due to the complex environments of food production, yeasts have to suffer from various stress factors. Thus, elucidating the stress mechanisms of food yeasts and proposing potential strategies to improve tolerance have been widely concerned. This review summarized the recent signs of progress in the variety, functions, and stress tolerance of food yeasts. Firstly, the main food yeasts occurred in fermented foods, and the taxonomy levels are demonstrated. Then, the main functions of yeasts including aroma enhancer, safety performance enhancer, and fermentation period reducer are discussed. Finally, the stress response mechanisms of yeasts and the strategies to improve the stress tolerance of cells are reviewed. Based on sorting out these related recent researches systematically, we hope that this review can provide help and approaches to further exert the functions of food yeasts and improve food production efficiency.

Dung beetle-associated yeasts display multiple stress tolerance: a desirable trait of potential industrial strains

BACKGROUND

Stress-tolerant yeasts are highly desirable for cost-effective bioprocessing. Several strategies have been documented to develop robust yeasts, such as genetic and metabolic engineering, artificial selection, and natural selection strategies, among others. However, the significant drawbacks of such techniques have motivated the exploration of naturally occurring stress-tolerant yeasts. We previously explored the biodiversity of non-conventional dung beetle-associated yeasts from extremophilic and pristine environments in Botswana (Nwaefuna AE et.al., Yeast, 2023). Here, we assessed their tolerance to industrially relevant stressors individually, such as elevated concentrations of osmolytes, organic acids, ethanol, and oxidizing agents, as well as elevated temperatures.

RESULTS

Our findings suggest that these dung beetle-associated yeasts tolerate various stresses comparable to those of the robust bioethanol yeast strain, Saccharomyces cerevisiae (Ethanol Red™). Fifty-six percent of the yeast isolates were tolerant of temperatures up to 42 °C, 12.4% of them could tolerate ethanol concentrations up to 9% (v/v), 43.2% of them were tolerant to formic acid concentrations up to 20 mM, 22.7% were tolerant to acetic acid concentrations up to 45 mM, 34.0% of them could tolerate hydrogen peroxide up to 7 mM, and 44.3% of the yeasts could tolerate osmotic stress up to 1.5 M.

CONCLUSION

The ability to tolerate multiple stresses is a desirable trait in the selection of novel production strains for diverse biotechnological applications, such as bioethanol production. Our study shows that the exploration of natural diversity in the search for stress-tolerant yeasts is an appealing approach for the development of robust yeasts.

Contributions of Adaptive Laboratory Evolution towards the Enhancement of the Biotechnological Potential of Non-Conventional Yeast Species

Changes in biological properties over several generations, induced by controlling short-term evolutionary processes in the laboratory through selective pressure, and whole-genome re-sequencing, help determine the genetic basis of microorganism's adaptive laboratory evolution (ALE). Due to the versatility of this technique and the imminent urgency for alternatives to petroleum-based strategies, ALE has been actively conducted for several yeasts, primarily using the conventional species Saccharomyces cerevisiae, but also non-conventional yeasts. As a hot topic at the moment since genetically modified organisms are a debatable subject and a global consensus on their employment has not yet been attained, a panoply of new studies employing ALE approaches have emerged and many different applications have been exploited in this context. In the present review, we gathered, for the first time, relevant studies showing the ALE of non-conventional yeast species towards their biotechnological improvement, cataloging them according to the aim of the study, and comparing them considering the species used, the outcome of the experiment, and the employed methodology. This review sheds light on the applicability of ALE as a powerful tool to enhance species features and improve their performance in biotechnology, with emphasis on the non-conventional yeast species, as an alternative or in combination with genome editing approaches.

Long-Term Adaptation to Galactose as a Sole Carbon Source Selects for Mutations Outside the Canonical GAL Pathway

Galactose is a secondary fermentable sugar that requires specific regulatory and structural genes for its assimilation, which are under catabolite repression by glucose. When glucose is absent, the catabolic repression is attenuated, and the structural GAL genes are fully activated. In Saccharomyces cerevisiae, the GAL pathway is under selection in environments where galactose is present. However, it is unclear the adaptive strategies in response to long-term propagation in galactose as a sole carbon source in laboratory evolution experiments. Here, we performed a 4,000-generation evolution experiment using 48 diploid Saccharomyces cerevisiae populations to study adaptation in galactose. We show that fitness gains were greater in the galactose-evolved population than in identically evolved populations with glucose as a sole carbon source. Whole-genome sequencing of 96 evolved clones revealed recurrent de novo single nucleotide mutations in candidate targets of selection, copy number variations, and ploidy changes. We find that most mutations that improve fitness in galactose lie outside of the canonical GAL pathway. Reconstruction of specific evolved alleles in candidate target of selection, SEC23 and IRA1, showed a significant increase in fitness in galactose compared to glucose. In addition, most of our evolved populations (28/46; 61%) fixed aneuploidies on Chromosome VIII, suggesting a parallel adaptive amplification. Finally, we show greater loss of extrachromosomal elements in our glucose-evolved lineages compared with previous glucose evolution. Broadly, these data further our understanding of the evolutionary pressures that drive adaptation to less-preferred carbon sources.

Adaptive Laboratory Evolution of Yeasts for Aroma Compound Production

Aroma compounds are important in the food and beverage industry, as they contribute to the quality of fermented products. Yeasts produce several aroma compounds during fermentation. In recent decades, production of many aroma compounds by yeasts obtained through adaptive laboratory evolution has become prevalent, due to consumer demand for yeast strains in the industry. This review presents general aspects of yeast, aroma production and adaptive laboratory evolution and focuses on the recent advances of yeast strains obtained by adaptive laboratory evolution to enhance the production of aroma compounds.

Looking into the world's largest elephant population in search of ligninolytic microorganisms for biorefineries: a mini-review

Gastrointestinal tracts (GIT) of herbivores are lignin-rich environments with the potential to find ligninolytic microorganisms. The occurrence of the microorganisms in herbivore GIT is a well-documented mutualistic relationship where the former benefits from the provision of nutrients and the latter benefits from the microorganism-assisted digestion of their recalcitrant lignin diets. Elephants are one of the largest herbivores that rely on the microbial anaerobic fermentation of their bulky recalcitrant low-quality forage lignocellulosic diet given their inability to break down major components of plant cells. Tapping the potential of these mutualistic associations in the biggest population of elephants in the whole world found in Botswana is attractive in the valorisation of the bulky recalcitrant lignin waste stream generated from the pulp and paper, biofuel, and agro-industries. Despite the massive potential as a feedstock for industrial fermentations, few microorganisms have been commercialised. This review focuses on the potential of microbiota from the gastrointestinal tract and excreta of the worlds' largest population of elephants of Botswana as a potential source of extremophilic ligninolytic microorganisms. The review further discusses the recalcitrance of lignin, achievements, limitations, and challenges with its biological depolymerisation. Methods of isolation of microorganisms from elephant dung and their improvement as industrial strains are further highlighted.

Evolutionary engineering to improve Wickerhamomyces subpelliculosus and Kazachstania gamospora for baking

The conventional baker's yeast, Saccharomyces cerevisiae, is the indispensable baking yeast of all times. Its monopoly coupled to its major drawbacks, such as streamlined carbon substrate utilisation base and a poor ability to withstand a number of baking associated stresses, prompt the need to search for alternative yeasts to leaven bread in the era of increasingly complex consumer lifestyles. Our previous work identified the inefficient baking attributes of Wickerhamomyces subpelliculosus and Kazachstania gamospora as well as preliminarily observations of improving the fermentative capacity of these potential alternative baker's yeasts using evolutionary engineering. Here we report on the characterisation and improvement in baking traits in five out of six independently evolved lines incubated for longer time and passaged for at least 60 passages relative to their parental strains as well as the conventional baker's yeast. In addition, the evolved clones produced bread with a higher loaf volume when compared to bread baked with either the ancestral strain or the control conventional baker's yeast. Remarkably, our approach improved the yeasts' ability to withstand baking associated stresses, a key baking trait exhibited poorly in both the conventional baker's yeast and their ancestral strains. W. subpelliculosus evolved the best characteristics attractive for alternative baker's yeasts as compared to the evolved K. gamospora strains. These results demonstrate the robustness of evolutionary engineering in development of alternative baker's yeasts.

Non-Conventional Yeasts as Alternatives in Modern Baking for Improved Performance and Aroma Enhancement

Saccharomyces cerevisiae remains the baker’s yeast of choice in the baking industry. However, its ability to ferment cereal flour sugars and accumulate CO2 as a principal role of yeast in baking is not as unique as previously thought decades ago. The widely conserved fermentative lifestyle among the Saccharomycotina has increased our interest in the search for non-conventional yeast strains to either augment conventional baker’s yeast or develop robust strains to cater for the now diverse consumer-driven markets. A decade of research on alternative baker’s yeasts has shown that non-conventional yeasts are increasingly becoming important due to their wide carbon fermentation ranges, their novel aromatic flavour generation, and their robust stress tolerance. This review presents the credentials of non-conventional yeasts as attractive yeasts for modern baking. The evolution of the fermentative trait and tolerance to baking-associated stresses as two important attributes of baker’s yeast are discussed besides their contribution to aroma enhancement. The review further discusses the approaches to obtain new strains suitable for baking applications.

Forest Saccharomyces paradoxus are robust to seasonal biotic and abiotic changes

Microorganisms are famous for adapting quickly to new environments. However, most evidence for rapid microbial adaptation comes from laboratory experiments or domesticated environments, and it is unclear how rates of adaptation scale from human-influenced environments to the great diversity of wild microorganisms. We examined potential monthly-scale selective pressures in the model forest yeast Saccharomyces paradoxus. Contrary to expectations of seasonal adaptation, the S. paradoxus population was stable over four seasons in the face of abiotic and biotic environmental changes. While the S. paradoxus population was diverse, including 41 unique genotypes among 192 sampled isolates, there was no correlation between S. paradoxus genotypes and seasonal environments. Consistent with observations from other S. paradoxus populations, the forest population was highly clonal and inbred. This lack of recombination, paired with population stability, implies that selection is not acting on the forest S. paradoxus population on a seasonal timescale. Saccharomyces paradoxus may instead have evolved generalism or phenotypic plasticity with regard to seasonal environmental changes long ago. Similarly, while the forest population included diversity among phenotypes related to intraspecific interference competition, there was no evidence for active coevolution among these phenotypes. At least ten percent of the forest S. paradoxus individuals produced "killer toxins," which kill sensitive Saccharomyces cells, but the presence of a toxin-producing isolate did not predict resistance to the toxin among nearby isolates. How forest yeasts acclimate to changing environments remains an open question, and future studies should investigate the physiological responses that allow microbial cells to cope with environmental fluctuations in their native habitats.

An assessment of serial co-cultivation approach for generating novel Zymomonas mobilis strains

Objective

The alphaproteobacterium Zymomonas mobilis is an efficient ethanol producer, and Z. mobilis-based biorefinery shows great potential for biofuel production. Serial co-cultivation is an emerging approach that promotes inter-species interactions which can improve or rewire the metabolic features in industrially useful microorganisms by inducing frequent mutations. We applied this method to assess if it improves or rewires the desirable physiological features of Z. mobilis, especially ethanol production.

Results

We performed serial co-culture of Z. mobilis with the baker’s yeast, Saccharomyces cerevisiae. We observed filamentation of Z. mobilis cells in the co-culture, indicating that the Z. mobilis cells were exposed to stress due to the presence of a competitor. After 50 times of serial transfers, we characterized the generated Z. mobilis strains, showing that long term co-culture did not drive significant changes in either the growth or profile of excreted metabolites in the generated strains. In line with this, whole genome sequencing of the generated Z. mobilis strains revealed only minor genetic variations from the parental strain. 50 generations of Z. mobilis monoculture did not induce morphological changes or any significant genetic variations. The result indicates that the method needs to be carefully optimized for Z. mobilis strain improvement.

Evolution of mutualistic behaviour between Chlorella sorokiniana and Saccharomyces cerevisiae within a synthetic environment

Yeast and microalgae are microorganisms with widely diverging physiological and biotechnological properties. Accordingly, their fields of applications diverge: yeasts are primarily applied in processes related to fermentation, while microalgae are used for the production of high-value metabolites and green technologies such as carbon capture. Heterotrophic-autotrophic systems and synthetic ecology approaches have been proposed as tools to achieve stable combinations of such evolutionarily unrelated species. We describe an entirely novel synthetic ecology-based approach to evolve co-operative behaviour between winery wastewater isolates of the yeast Saccharomyces cerevisiae and microalga Chlorella sorokiniana. The data show that biomass production and mutualistic growth improved when co-evolved yeast and microalgae strains were paired together. Combinations of co-evolved strains displayed a range of phenotypes, including differences in amino acid profiles. Taken together, the results demonstrate that biotic selection pressures can lead to improved mutualistic growth phenotypes over relatively short time periods.