Automated screening in environmental arrays allows analysis of quantitative phenotypic profiles in Saccharomyces cerevisiae

Quantifying massively parallel microbial growth with spatially mediated interactions

Quantitative understanding of microbial growth is an essential prerequisite for successful control of pathogens as well as various biotechnology applications. Even though the growth of cell populations has been extensively studied, microbial growth remains poorly characterised at the spatial level. Indeed, even isogenic populations growing at different locations on solid growth medium typically show significant location-dependent variability in growth. Here we show that this variability can be attributed to the initial physiological states of the populations, the interplay between populations interacting with their local environment and the diffusion of nutrients and energy sources coupling the environments. We further show how the causes of this variability change throughout the growth of a population. We use a dual approach, first applying machine learning regression models to discover that location dominates growth variability at specific times, and, in parallel, developing explicit population growth models to describe this spatial effect. In particular, treating nutrient and energy source concentration as a latent variable allows us to develop a mechanistic resource consumer model that captures growth variability across the shared environment. As a consequence, we are able to determine intrinsic growth parameters for each local population, removing confounders common to location-dependent variability in growth. Importantly, our explicit low-parametric model for the environment paves the way for massively parallel experimentation with configurable spatial niches for testing specific eco-evolutionary hypotheses.

'Small volume-big problem': culturing Yarrowia lipolytica in high-throughput micro-formats

With the current progress in the 'design' and 'build' stages of the 'design-build-test-learn' cycle, many synthetic biology projects become 'test-limited'. Advances in the parallelization of microbes cultivations are of great aid, however, for many species down-scaling leaves a metabolic footprint. Yarrowia lipolytica is one such demanding yeast species, for which scaling-down inevitably leads to perturbations in phenotype development. Strictly aerobic metabolism, propensity for filamentation and adhesion to hydrophobic surfaces, spontaneous flocculation, and high acidification of media are just several characteristics that make the transfer of the micro-scale protocols developed for the other microbial species very challenging in this case. It is well recognized that without additional 'personalized' optimization, either MTP-based or single-cell-based protocols are useless for accurate studies of Y. lipolytica phenotypes. This review summarizes the progress in the scaling-down and parallelization of Y. lipolytica cultures, highlighting the challenges that occur most frequently and strategies for their overcoming. The problem of Y. lipolytica cultures down-scaling is illustrated by calculating the costs of micro-cultivations, and determining the unintentionally introduced, thus uncontrolled, variables. The key research into culturing Y. lipolytica in various MTP formats and micro- and pico-bioreactors is discussed. Own recently developed and carefully pre-optimized high-throughput cultivation protocol is presented, alongside the details from the optimization stage. We hope that this work will serve as a practical guide for those working with Y. lipolytica high-throughput screens.

Wild Patagonian yeast improve the evolutionary potential of novel interspecific hybrid strains for lager brewing

Lager yeasts are limited to a few strains worldwide, imposing restrictions on flavour and aroma diversity and hindering our understanding of the complex evolutionary mechanisms during yeast domestication. The recent finding of diverse S. eubayanus lineages from Patagonia offers potential for generating new lager yeasts with different flavour profiles. Here, we leverage the natural genetic diversity of S. eubayanus and expand the lager yeast repertoire by including three distinct Patagonian S. eubayanus lineages. We used experimental evolution and selection on desirable traits to enhance the fermentation profiles of novel S. cerevisiae x S. eubayanus hybrids. Our analyses reveal an intricate interplay of pre-existing diversity, selection on species-specific mitochondria, de-novo mutations, and gene copy variations in sugar metabolism genes, resulting in high ethanol production and unique aroma profiles. Hybrids with S. eubayanus mitochondria exhibited greater evolutionary potential and superior fitness post-evolution, analogous to commercial lager hybrids. Using genome-wide screens of the parental subgenomes, we identified genetic changes in IRA2, IMA1, and MALX genes that influence maltose metabolism, and increase glycolytic flux and sugar consumption in the evolved hybrids. Functional validation and transcriptome analyses confirmed increased maltose-related gene expression, influencing greater maltotriose consumption in evolved hybrids. This study demonstrates the potential for generating industrially viable lager yeast hybrids from wild Patagonian strains. Our hybridization, evolution, and mitochondrial selection approach produced hybrids with high fermentation capacity and expands lager beer brewing options.

An endogenous DNA virus in an amphibian-killing fungus associated with pathogen genotype and virulence

The global panzootic lineage (GPL) of the pathogenic fungus Batrachochytrium dendrobatidis (Bd) has caused severe amphibian population declines, yet the drivers underlying the high frequency of GPL in regions of amphibian decline are unclear. Using publicly available Bd genome sequences, we identified multiple non-GPL Bd isolates that contain a circular Rep-encoding single-stranded (CRESS)-like DNA virus, which we named Bd DNA virus 1 (BdDV-1). We further sequenced and constructed genome assemblies with long read sequences to find that the virus is integrated into the nuclear genome in some strains. Attempts to cure virus-positive isolates were unsuccessful; however, phenotypic differences between naturally virus-positive and virus-negative Bd isolates suggested that BdDV-1 decreases the growth of its host in vitro but increases the virulence of its host in vivo. BdDV-1 is the first-described CRESS DNA mycovirus of zoosporic true fungi, with a distribution inversely associated with the emergence of the panzootic lineage.

Sourdough Yeast Strains Exhibit Thermal Tolerance, High Fermentative Performance, and a Distinctive Aromatic Profile in Beer Wort

The increasing popularity of home brewing and the fast evolution of craft beer companies have fuelled the interest in novel yeasts as the main actors diversifying the beer portfolio. Here, we have characterized the thermal tolerance and brewing-related features of two sourdough (SD) isolates of Saccharomyces cerevisiae, SDy01 and SDy02, at different temperatures, 20 and 37 °C, comparing them with commercial brew strains, AaB and kNB. The SD strains exhibited tolerance to the main brewing-related stress conditions and increased growth rates and lower lag phases than the reference beer strains at both temperatures. Consistent with this, SDy01 and SDy02 displayed higher fermentative activity in terms of sugar rate depletion and the release of metabolic by-products. Moreover, SDy01 and SDy02 brewing at 20 °C increased their total amount of volatile compounds (VOCs), in particular, their esters and carboxyl compounds, as compared to the reference AaB strain. In contrast, fermentation at 37 °C resulted in a drastic reduction in the number of VOCs in wort fermented with SD yeast, especially in its level of esters. In conclusion, our results stress the high fermentative performance of SD strains in beer wort and their ability to provide a complex and specific aromatic profile at a wide range of temperatures.

Real-time monitoring of mycelial growth in liquid culture using hyphal dispersion mutant of Aspergillus fumigatus

Hyphal pellet formation by Aspergillus species in liquid cultures is one of the main obstacles to high-throughput anti-Aspergillus reagent screening. We previously constructed a hyphal dispersion mutant of Aspergillus fumigatus by disrupting the genes encoding the primary cell wall α-1,3-glucan synthase Ags1 and putative galactosaminogalactan synthase Gtb3 (Δags1Δgtb3). Mycelial growth of the mutant in liquid cultures monitored by optical density was reproducible, and the dose-response of hyphal growth to antifungal agents has been quantified by optical density. However, Δags1Δgtb3 still forms hyphal pellets in some rich growth media. Here, we constructed a disruptant lacking all three α-1,3-glucan synthases and galactosaminogalactan synthase (Δags1Δags2Δags3Δgtb3), and confirmed that its hyphae were dispersed in all the media tested. We established an automatic method to monitor hyphal growth of the mutant in a 24-well plate shaken with a real-time plate reader. Dose-dependent growth suppression and unique growth responses to antifungal agents (voriconazole, amphotericin B, and micafungin) were clearly observed. A 96-well plate was also found to be useful for the evaluation of mycelial growth by optical density. Our method is potentially applicable to high-throughput screening for anti-Aspergillus agents.

Identification and biotechnological characterisation of yeast microbiota involved in spontaneous fermented wholegrain sourdoughs

BACKGROUND

New strategies in the cereal-based industry has brought about the elaboration of new sourdoughs with better microbial stability and safety as well as nutritional value such as those based on wholegrain flours. This has led to an increasing interest in the selection of adapted yeasts for using them as new starters. Therefore, this study aimed to isolate, identify, and characterise diverse yeast strains from wholegrain spontaneous sourdoughs.

RESULTS

Three wholegrain sourdoughs (wheat, rye, and oat) were fermented and monitored for 96 h. Minimum pH values ranged from 3.1 to 3.5 while maximum yeast counts were reached at 72 h. A total of 76 yeast isolates were identified by polymerase chain reaction random amplification of polymorphic DNA (PCR-RAPD) and catalogued in six different species by sequencing the internal transcribed spacer (ITS) region. The major species were Candida glabrata, Saccharomyces cerevisiae, Kazachstania unispora, and Wickerhamomyces anomalus. The studied kinetic parameters of the growth curves (λ, G, ODmax , and μmax ) and the fermentation capacity allowed to ascertain that 12 and 5 strains, respectively, were better than baker's yeast control. The fibre assimilation ability (cellulose, xylose, and β-glucan) was observed in the 27% of the strains and only four strains showed phytase activity.

CONCLUSIONS

The yeast population in the three wholegrain sourdoughs were variable along the fermentation time. Genetic identification showed that strains and species presented a different trend for each sourdough although common species were determined (e.g., W. anomalus). Candida glabrata (4T1) and Saccharomyces cerevisiae (3A6) showed, respectively, better kinetics and impedance results than the positive control, while W. anomalus (C4) was notorious in fibre assimilation and phytase degradation. © 2023 The Authors. Journal of The Science of Food and Agriculture published by John Wiley & Sons Ltd on behalf of Society of Chemical Industry.

Nunchaku: optimally partitioning data into piece-wise contiguous segments

MOTIVATION

When analyzing 1D time series, scientists are often interested in identifying regions where one variable depends linearly on the other. Typically, they use an ad hoc and therefore often subjective method to do so.

RESULTS

Here, we develop a statistically rigorous, Bayesian approach to infer the optimal partitioning of a dataset not only into contiguous piece-wise linear segments, but also into contiguous segments described by linear combinations of arbitrary basis functions. We therefore present a general solution to the problem of identifying discontinuous change points. Focusing on microbial growth, we use the algorithm to find the range of optical density where this density is linearly proportional to the number of cells and to automatically find the regions of exponential growth for both Escherichia coli and Saccharomyces cerevisiae. For budding yeast, we consequently are able to infer the Monod constant for growth on fructose. Our algorithm lends itself to automation and high throughput studies, increases reproducibility, and should facilitate data analyses for a broad range of scientists.

AVAILABILITY AND IMPLEMENTATION

The corresponding Python package, entitled Nunchaku, is available at PyPI: https://pypi.org/project/nunchaku.

Dissecting aneuploidy phenotypes by constructing Sc2.0 chromosome VII and SCRaMbLEing synthetic disomic yeast

Aneuploidy compromises genomic stability, often leading to embryo inviability, and is frequently associated with tumorigenesis and aging. Different aneuploid chromosome stoichiometries lead to distinct transcriptomic and phenotypic changes, making it helpful to study aneuploidy in tightly controlled genetic backgrounds. By deploying the engineered SCRaMbLE (synthetic chromosome rearrangement and modification by loxP-mediated evolution) system to the newly synthesized megabase Sc2.0 chromosome VII (synVII), we constructed a synthetic disomic yeast and screened hundreds of SCRaMbLEd derivatives with diverse chromosomal rearrangements. Phenotypic characterization and multi-omics analysis revealed that fitness defects associated with aneuploidy could be restored by (1) removing most of the chromosome content or (2) modifying specific regions in the duplicated chromosome. These findings indicate that both chromosome copy number and specific chromosomal regions contribute to the aneuploidy-related phenotypes, and the synthetic chromosome resource opens new paradigms in studying aneuploidy.

Single nucleotide polymorphisms associated with wine fermentation and adaptation to nitrogen limitation in wild and domesticated yeast strains

For more than 20 years, Saccharomyces cerevisiae has served as a model organism for genetic studies and molecular biology, as well as a platform for biotechnology (e.g., wine production). One of the important ecological niches of this yeast that has been extensively studied is wine fermentation, a complex microbiological process in which S. cerevisiae faces various stresses such as limited availability of nitrogen. Nitrogen deficiencies in grape juice impair fermentation rate and yeast biomass production, leading to sluggish or stuck fermentations, resulting in considerable economic losses for the wine industry. In the present work, we took advantage of the "1002 Yeast Genomes Project" population, the most complete catalogue of the genetic variation in the species and a powerful resource for genotype-phenotype correlations, to study the adaptation to nitrogen limitation in wild and domesticated yeast strains in the context of wine fermentation. We found that wild and domesticated yeast strains have different adaptations to nitrogen limitation, corroborating their different evolutionary trajectories. Using a combination of state-of-the-art bioinformatic (GWAS) and molecular biology (CRISPR-Cas9) methodologies, we validated that PNP1, RRT5 and PDR12 are implicated in wine fermentation, where RRT5 and PDR12 are also involved in yeast adaptation to nitrogen limitation. In addition, we validated SNPs in these genes leading to differences in fermentative capacities and adaptation to nitrogen limitation. Altogether, the mapped genetic variants have potential applications for the genetic improvement of industrial yeast strains.

Spatiotemporal Dynamics of Single-stranded DNA Intermediates in Escherichia coli

Single-stranded DNA gaps form within the E. coli chromosome during replication, repair and recombination. However, information about the extent of ssDNA creation in the genome is limited. To complement a recent whole-genome sequencing study revealing ssDNA gap genomic distribution, size, and frequency, we used fluorescence microscopy to monitor the spatiotemporal dynamics of single-stranded DNA within live E. coli cells. The ssDNA was marked by a functional fluorescent protein fusion of the SSB protein that replaces the wild type SSB. During log-phase growth the SSB fusion produces a mixture of punctate foci and diffuse fluorescence spread throughout the cytosol. Many foci are clustered. Fluorescent markers of DNA polymerase III frequently co-localize with SSB foci, often localizing to the outer edge of the large SSB features. Novel SSB-enriched features form and resolve regularly during normal growth. UV irradiation induces a rapid increase in SSB foci intensity and produces large features composed of multiple partially overlapping foci. The results provide a critical baseline for further exploration of ssDNA generation during DNA metabolism. Alterations in the patterns seen in a mutant lacking RecB function tentatively suggest associations of particular SSB features with the repair of double strand breaks and post-replication gaps.

A high-throughput yeast approach to characterize aquaporin permeabilities: Profiling the Arabidopsis PIP aquaporin sub-family

INTRODUCTION

Engineering membrane transporters to achieve desired functionality is reliant on availability of experimental data informing structure-function relationships and intelligent design. Plant aquaporin (AQP) isoforms are capable of transporting diverse substrates such as signaling molecules, nutrients, metalloids, and gases, as well as water. AQPs can act as multifunctional channels and their transport function is reliant on many factors, with few studies having assessed transport function of specific isoforms for multiple substrates.

METHODS

High-throughput yeast assays were developed to screen for transport function of plant AQPs, providing a platform for fast data generation and cataloguing of substrate transport profiles. We applied our high-throughput growth-based yeast assays to screen all 13 Arabidopsis PIPs (AtPIPs) for transport of water and several neutral solutes: hydrogen peroxide (H2O2), boric acid (BA), and urea. Sodium (Na+) transport was assessed using elemental analysis techniques.

RESULTS

All AtPIPs facilitated water and H2O2 transport, although their growth phenotypes varied, and none were candidates for urea transport. For BA and Na+ transport, AtPIP2;2 and AtPIP2;7 were the top candidates, with yeast expressing these isoforms having the most pronounced toxicity response to BA exposure and accumulating the highest amounts of Na+. Linking putative AtPIP isoform substrate transport profiles with phylogenetics and gene expression data, enabled us to align possible substrate preferences with known and hypothesized biological roles of AtPIPs.

DISCUSSION

This testing framework enables efficient cataloguing of putative transport functionality of diverse AQPs at a scale that can help accelerate our understanding of AQP biology through big data approaches (e.g. association studies). The principles of the individual assays could be further adapted to test additional substrates. Data generated from this framework could inform future testing of AQP physiological roles, and address knowledge gaps in structure-function relationships to improve engineering efforts.

Automation of yeast spot assays using an affordable liquid handling robot

The spot assay of the budding yeast Saccharomyces cerevisiae is an experimental method that is used to evaluate the effect of genotypes, medium conditions, and environmental stresses on cell growth and survival. Automation of the spot assay experiments from preparing a dilution series to spotting to observing spots continuously has been implemented based on large laboratory automation devices and robots, especially for high-throughput functional screening assays. However, there has yet to be an affordable solution for the automated spot assays suited to researchers in average laboratories and with high customizability for end-users. To make reproducible spot assay experiments widely available, we have automated the plate-based yeast spot assay of budding yeast using Opentrons OT-2 (OT-2), an affordable liquid-handling robot, and a flatbed scanner. We prepared a 3D-printed mount for the Petri dish to allow for precise placement of the Petri dish inside the OT-2. To account for the uneven height of the agar plates, which were made by human hands, we devised a method to adjust the z-position of the pipette tips based on the weight of each agar plate. During the incubation of the agar plates, a flatbed scanner was used to automatically take images of the agar plates over time, allowing researchers to quantify and compare the cell density within the spots at optimal time points a posteriori. Furthermore, the accuracy of the newly developed automated spot assay was verified by performing spot assays with human experimenters and the OT-2 and quantifying the yeast-grown area of the spots. This study will contribute to the introduction of automated spot assays and the automated acquisition of growth processes in conventional laboratories that are not adapted for high-throughput laboratory automation.

Adaptation of the yeast gene knockout collection is near-perfectly predicted by fitness and diminishing return epistasis

Adaptive evolution of clonally dividing cells and microbes is the ultimate cause of cancer and infectious diseases. The possibility of constraining the adaptation of cell populations, by inhibiting proteins enhancing the evolvability, has therefore attracted interest. However, our current understanding of how genes influence adaptation kinetics is limited, partly because accurately measuring adaptation for many cell populations is challenging. We used a high-throughput adaptive laboratory evolution platform to track the adaptation of >18,000 cell populations corresponding to single-gene deletion strains in the haploid yeast deletion collection. We report that the preadaptation fitness of gene knockouts near-perfectly (R2= 0.91) predicts their adaptation to arsenic, leaving at the most a marginal role for dedicated evolvability gene functions. We tracked the adaptation of another >23,000 gene knockout populations to a diverse range of selection pressures and generalized the almost perfect (R2=0.72-0.98) capacity of preadaptation fitness to predict adaptation. We also reconstructed mutations in FPS1, ASK10, and ARR3, which together account for almost all arsenic adaptation in wild-type cells, in gene deletions covering a broad fitness range and show that the predictability of arsenic adaptation can be understood as a by global epistasis, where excluding arsenic is more beneficial to arsenic unfit cells. The paucity of genes with a meaningful evolvability effect on adaptation diminishes the prospects of developing adjuvant drugs aiming to slow antimicrobial and chemotherapy resistance.

The role of the Aspergillus nidulans high mobility group B protein HmbA, the orthologue of Saccharomyces cerevisiae Nhp6p

The mammalian HMGB1 is a high-mobility-group B protein, which is both an architectural and functional element of chromatin. Nhp6p, the extensively studied fungal homologue of HMGB1 in Saccharomyces cerevisiae has pleiotropic physiological functions. Despite the existence of Nhp6p orthologues in filamentous ascomycetes, little is known about their physiological roles besides their contribution to sexual development. Here we study the function of HmbA, the Aspergillus nidulans orthologue of Nhp6p. We show that HmbA influences the utilization of various carbon- and nitrogen sources, stress tolerance, secondary metabolism, hyphae elongation and maintenance of polarized growth. Additionally, by conducting heterologous expression studies, we demonstrate that HmbA and Nhp6p are partially interchangeable. HmbA restores SNR6 transcription and fitness of nhp6AΔBΔ mutant and reverses its heat sensitivity. Nhp6Ap complements several phenotypes of hmbAΔ, including ascospore formation, utilization of various carbon- and nitrogen-sources, radial growth rate, hypha elongation by polarized growth. However, Nhp6Ap does not complement sterigmatocystin production in a hmbAΔ strain. Finally, we also show that HmbA is necessary for the normal expression of the endochitinase chiA, a cell wall re-modeller that is pivotal for the normal mode of maintenance of polar growth.

Using colony size to measure fitness in Saccharomyces cerevisiae

Competitive fitness assays in liquid culture have been a mainstay for characterizing experimental evolution of microbial populations. Growth of microbial strains has also been extensively characterized by colony size and could serve as a useful alternative if translated to per generation measurements of relative fitness. To examine fitness based on colony size, we established a relationship between cell number and colony size for strains of Saccharomyces cerevisiae robotically pinned onto solid agar plates in a high-density format. This was used to measure growth rates and estimate relative fitness differences between evolved strains and their ancestors. After controlling for edge effects through both normalization and agar-trimming, we found that colony size is a sensitive measure of fitness, capable of detecting 1% differences. While fitnesses determined from liquid and solid mediums were not equivalent, our results demonstrate that colony size provides a sensitive means of measuring fitness that is particularly well suited to measurements across many environments.

Gene loss and compensatory evolution promotes the emergence of morphological novelties in budding yeast

Deleterious mutations are generally considered to be irrelevant for morphological evolution. However, they could be compensated by conditionally beneficial mutations, thereby providing access to new adaptive paths. Here we use high-dimensional phenotyping of laboratory-evolved budding yeast lineages to demonstrate that new cellular morphologies emerge exceptionally rapidly as a by-product of gene loss and subsequent compensatory evolution. Unexpectedly, the capacities for invasive growth, multicellular aggregation and biofilm formation also spontaneously evolve in response to gene loss. These multicellular phenotypes can be achieved by diverse mutational routes and without reactivating the canonical regulatory pathways. These ecologically and clinically relevant traits originate as pleiotropic side effects of compensatory evolution and have no obvious utility in the laboratory environment. The extent of morphological diversity in the evolved lineages is comparable to that of natural yeast isolates with diverse genetic backgrounds and lifestyles. Finally, we show that both the initial gene loss and subsequent compensatory mutations contribute to new morphologies, with their synergistic effects underlying specific morphological changes. We conclude that compensatory evolution is a previously unrecognized source of morphological diversity and phenotypic novelties.

Analysing and meta-analysing time-series data of microbial growth and gene expression from plate readers

Responding to change is a fundamental property of life, making time-series data invaluable in biology. For microbes, plate readers are a popular, convenient means to measure growth and also gene expression using fluorescent reporters. Nevertheless, the difficulties of analysing the resulting data can be a bottleneck, particularly when combining measurements from different wells and plates. Here we present omniplate, a Python module that corrects and normalises plate-reader data, estimates growth rates and fluorescence per cell as functions of time, calculates errors, exports in different formats, and enables meta-analysis of multiple plates. The software corrects for autofluorescence, the optical density’s non-linear dependence on the number of cells, and the effects of the media. We use omniplate to measure the Monod relationship for the growth of budding yeast in raffinose, showing that raffinose is a convenient carbon source for controlling growth rates. Using fluorescent tagging, we study yeast’s glucose transport. Our results are consistent with the regulation of the hexose transporter (HXT) genes being approximately bipartite: the medium and high affinity transporters are predominately regulated by both the high affinity glucose sensor Snf3 and the kinase complex SNF1 via the repressors Mth1, Mig1, and Mig2; the low affinity transporters are predominately regulated by the low affinity sensor Rgt2 via the co-repressor Std1. We thus demonstrate that omniplate is a powerful tool for exploiting the advantages offered by time-series data in revealing biological regulation.

Time series of growth and of gene expression via fluorescent reporters are rich ways to characterise the behaviours of cells. With plate readers, it is straightforward to measure 96 independent time series in a single experiment, with readings taken every 10 minutes and each time series lasting tens of hours. Analysing such data can become challenging, particularly if multiple plate-reader experiments are required to characterise a phenomenon, which then should be analysed simultaneously. Taking advantage of existing packages in Python, we have written code that automates this analysis but yet still allows users to develop custom routines. Our omniplate software corrects both measurements of optical density to become linear in the number of cells and measurements of fluorescence for autofluorescence. It estimates growth rates and fluorescence per cell as continuous functions of time and enables tens of plate-reader experiments to be analysed together. Data can be exported in text files in a format immediately suitable for public repositories. Plate readers are a convenient way to study cells; omniplate provides an equally convenient yet powerful way to analyse the resulting data.

Highly diverged lineages of Saccharomyces paradoxus in temperate to subtropical climate zones in China

The wild yeast Saccharomyces paradoxus has become a new model in ecology and evolutionary biology. Different lineages of S. paradoxus have been recognized across the world, but the distribution and genetic diversity of the species remain unknown in China, where the origin of its sibling species S. cerevisiae lies. In this study, we investigated the ecological and geographic distribution of S. paradoxus through an extensive field survey in China and performed population genomic analysis on a set of S. paradoxus strains, including 27 strains, representing different geographic and ecological origins within China, and 59 strains representing all the known lineages of the species recognized in the other regions of the world so far. We found two distinct lineages of S. paradoxus in China. The majority of the Chinese strains studied belong to the Far East lineage, and six strains belong to a novel highly diverged lineage. The distribution of these two lineages overlaps ecologically and geographically in temperate to subtropical climate zones in China. With the addition of the new China lineage, the Eurasian population of S. paradoxus exhibits higher genetic diversity than the American population. We observed more possible lineage-specific introgression events from the Eurasian lineages than from the American lineages. Our results expand the knowledge on ecology, genetic diversity, biogeography, and evolution of S. paradoxus.

High Prevalence of Antibiotic-Resistant Escherichia coli Isolates from Retail Poultry Products in Spain

The prevalence of Escherichia coli was analysed in poultry products from different Spanish retailers and determined its antibiotic resistance capability by phenotypic (ampicillin, amoxicillin, chloramphenicol, gentamicin, imipenem, cefotaxime, tetracycline, ciprofloxacin, trimethoprim, and colistin) and genotypic assays. A total of 30 samples (hindquarters or livers) were collected from supermarkets and butchers. Enterobacteriaceae counts ranged between 3.2 and 6.5 log colony-forming units (CFU)/g, and the highest values were found in livers and in samples from supermarkets. E. coli was detected in 83% of the samples tested, and the highest prevalence was observed in livers (100%) and supermarkets (91%). Regarding the antibiotic sensitivity test, 100% of the E. coli showed resistance to at least one antibiotic. The highest resistance rates were detected for colistin (87%) and gentamicin (79%), while only two antibiotics (chloramphenicol and cefotaxime) showed a resistance lower than 10%. Furthermore, the resistance genes of tetracycline and beta-lactams were analysed by multiplex PCR, revealing that tet(A) and blaTEM were the majority genes, respectively.

Study of potential probiotic and biotechnological properties of non-Saccharomyces yeasts from fruit Brazilian ecosystems

Yeast isolates from flowers and fruits from a Brazilian forest were studied. The yeasts were identified at species and strain level by PCR-RFLP and PCR-RAPD, respectively. The 46 isolated yeasts were classified into 11 different species belonging to the genera Candida, Diutina, Hanseniaspora, Meyerozyma, Pichia, Rhodotorula, and Torulaspora. A total of 20 different strains were found. In order to ascertain the probiotic potential, the resistance to gastrointestinal conditions, autoaggregation, and hydrophobicity assays were studied, along with the capacity to form biofilm. The results indicate that, although most of the strains presented better results than Saccharomyces boulardii (the only strain recognized as a probiotic yeast), four strains were the most promising, namely, Rhodotorula mucilaginosa 32, Meyerozyma caribbica 35, and Diutina rugosa 12 and 45, according to the Duncan test. Several biotechnological properties were evaluated. D. rugosa inhibited Dekkera bruxellensis. The assimilation or fermentation of seven sugars was tested, and only five of the yeasts did not show a capacity to assimilate any of the sugars under aerobic conditions. However, all strains were able to ferment at least one of the sugars under anaerobic conditions. As far as enzyme production is concerned, positive results were only found for the enzymes' amylase, pectinase, and protease. D. rugosa 42 and Hanseniaspora opuntiae 18, followed of Pichia kluyveri 26, showed high values for the production of melatonin. In conclusion, the results of this study show that several non-Saccharomyces present probiotic characteristics, and these have good potential for industrial applications in the food or biotechnology industries.

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.

Characterization of Cold-Tolerant Saccharomyces cerevisiae Cheongdo Using Phenotype Microarray

The cold-tolerant yeast Saccharomyces cerevisiae is industrially useful for lager fermentation, high-quality wine, and frozen dough production. S. cerevisiae Cheongdo is a recent isolate from frozen peach samples which has a good fermentation performance at low temperatures and desirable flavor profiles. Here, phenotype microarray was used to investigate industrial potentials of S. cerevisiae Cheongdo using 192 carbon sources. Compared to commercial wine yeast S. cerevisiae EC1118, Cheongdo showed significantly different growth rates on 34 substrates. The principal component analysis of the results highlighted that the better growth of Cheongdo on galactose than on EC1118 was the most significant difference between the two strains. The intact GAL4 gene and the galactose fermentation performance at a low temperatures suggested that S. cerevisiae Cheongdo is a promising host for industrial fermentation rich in galactose, such as lactose and agarose.

Potential probiotic and food protection role of wild yeasts isolated from pistachio fruits (Pistacia vera)

BACKGROUND

The biotechnological potential of yeasts from nuts such as pistachio, not only for health applications but also for industry use, has been scarcely studied. Interest in the probiotic capability of yeasts has increased in the past years as well as their utilization as food or feed preservatives. Their capabilities as biocontrol against problematic (spoilage or toxigenic) microorganisms or as antioxidants have been revalued. As a result, both abilities would be desirable to develop a new potential probiotic microorganism which could be added to food or feed to improve their properties.

RESULTS

Molecular techniques allowed the identification of a total of seven different species and 15 strains. A screening of the probiotic potential of these strains was carried out. It was found that 65% of the strains resisted the gastrointestinal conditions as well as presented a generation time of < 22 h. Additionally, some strains showed better kinetic parameters than Saccharomyces boulardii (positive control). Complementary tests were done to determine their auto-aggregation capacity, cell surface hydrophobicity, behaviour in a sequential simulated digestion, biofilm formation capability and carbon source assimilation. Finally, 67% and 13% of the studied yeasts showed biocontrol and antioxidant activities, respectively.

CONCLUSIONS

Diutina rugosa 14 followed by Diutina rugosa 8 were the best wild yeast from Pistacia vera as potential probiotic and in carbon source utilization. However, Hanseniaspora guilliermondii 6 and Aureobasidium proteae 5 could be used to improve food or feed product preservation because of their notable biocontrol and antioxidant capabilities. © 2020 Society of Chemical Industry.

Improved redox homeostasis owing to the up-regulation of one-carbon metabolism and related pathways is crucial for yeast heterosis at high temperature

Heterosis or hybrid vigor is a common phenomenon in plants and animals; however, the molecular mechanisms underlying heterosis remain elusive, despite extensive studies on the phenomenon for more than a century. Here we constructed a large collection of F1 hybrids of Saccharomyces cerevisiae by spore-to-spore mating between homozygous wild strains of the species with different genetic distances and compared growth performance of the F1 hybrids with their parents. We found that heterosis was prevalent in the F1 hybrids at 40°C. A hump-shaped relationship between heterosis and parental genetic distance was observed. We then analyzed transcriptomes of selected heterotic and depressed F1 hybrids and their parents growing at 40°C and found that genes associated with one-carbon metabolism and related pathways were generally up-regulated in the heterotic F1 hybrids, leading to improved cellular redox homeostasis at high temperature. Consistently, genes related with DNA repair, stress responses, and ion homeostasis were generally down-regulated in the heterotic F1 hybrids. Furthermore, genes associated with protein quality control systems were also generally down-regulated in the heterotic F1 hybrids, suggesting a lower level of protein turnover and thus higher energy use efficiency in these strains. In contrast, the depressed F1 hybrids, which were limited in number and mostly shared a common aneuploid parental strain, showed a largely opposite gene expression pattern to the heterotic F1 hybrids. We provide new insights into molecular mechanisms underlying heterosis and thermotolerance of yeast and new clues for a better understanding of the molecular basis of heterosis in plants and animals.

Rhodotorula glutinis T13 as a potential source of microbial lipids for biodiesel generation

Single cell oils (SCO) are a promising source of oils that could be exploited in different industrial areas. SCO for biodiesel production circumvents the controversy food vs. fuel, does not require large land areas for culture, and is independent of climate and seasonal variations, among other advantages in comparison to vegetable oils. In this study, a red yeast isolated from a mountain water source, identified as Rhodotorula glutinis T13, showed high potential for lipid production (40% w/w) with suitable growth parameters, yields, and fatty acids profile. Yeast lipids showed a high content of unsaturated fatty acids (56.44%; C18:1, C18:2), and the fuel properties (cetane number, iodine value, density, kinematic viscosity, etc.) of yeast oil analysed were in good agreement with international biodiesel standards. The results show that R. glutinis T13 can be used in the future as a promising microorganism for the commercial production of biodiesel.

Phenotypic and genomic differences among S. cerevisiae strains in nitrogen requirements during wine fermentations

Nitrogen requirements by S. cerevisiae during wine fermentation are highly strain-dependent. Different approaches were applied to explore the nitrogen requirements of 28 wine yeast strains. Based on the growth and fermentation behaviour displayed at different nitrogen concentrations, high and low nitrogen-demanding strains were selected and further verified by competition fermentation. Biomass production with increasing nitrogen concentrations in the exponential fermentation phase was analysed by chemostat cultures. Low nitrogen-demanding (LND) strains produced a larger amount of biomass in nitrogen-limited synthetic grape musts, whereas high nitrogen-demanding (HND) strains achieved a bigger biomass yield when the YAN concentration was above 100 mg/L. Constant rate fermentation was carried out with both strains to determine the amount of nitrogen required to maintain the highest fermentation rate. Large differences appeared in the analysis of the genomes of low and high-nitrogen demanding strains showed for heterozygosity and the amino acid substitutions between orthologous proteins, with nitrogen recycling system genes showing the widest amino acid divergences. The CRISPR/Cas9-mediated genome modification method was used to validate the involvement of GCN1 in the yeast strain nitrogen needs. However, the allele swapping of gene GCN1 from low nitrogen-demanding strains to high nitrogen-demanding strains did not significantly influence the fermentation rate.

Growth Inhibition by Amino Acids in Saccharomyces cerevisiae

Amino acids are essential metabolites but can also be toxic when present at high levels intracellularly. Substrate-induced downregulation of amino acid transporters in Saccharomyces cerevisiae is thought to be a mechanism to avoid this toxicity. It has been shown that unregulated uptake by the general amino acid permease Gap1 causes cells to become sensitive to amino acids. Here, we show that overexpression of eight other amino acid transporters (Agp1, Bap2, Can1, Dip5, Gnp1, Lyp1, Put4, or Tat2) also induces a growth defect when specific single amino acids are present at concentrations of 0.5-5 mM. We can now state that all proteinogenic amino acids, as well as the important metabolite ornithine, are growth inhibitory to S. cerevisiae when transported into the cell at high enough levels. Measurements of initial transport rates and cytosolic pH show that toxicity is due to amino acid accumulation and not to the influx of co-transported protons. The amino acid sensitivity phenotype is a useful tool that reports on the in vivo activity of transporters and has allowed us to identify new transporter-specific substrates.

Rational design of balanced dual-targeting antibiotics with limited resistance

Antibiotics that inhibit multiple bacterial targets offer a promising therapeutic strategy against resistance evolution, but developing such antibiotics is challenging. Here we demonstrate that a rational design of balanced multitargeting antibiotics is feasible by using a medicinal chemistry workflow. The resultant lead compounds, ULD1 and ULD2, belonging to a novel chemical class, almost equipotently inhibit bacterial DNA gyrase and topoisomerase IV complexes and interact with multiple evolutionary conserved amino acids in the ATP-binding pockets of their target proteins. ULD1 and ULD2 are excellently potent against a broad range of gram-positive bacteria. Notably, the efficacy of these compounds was tested against a broad panel of multidrug-resistant Staphylococcus aureus clinical strains. Antibiotics with clinical relevance against staphylococcal infections fail to inhibit a significant fraction of these isolates, whereas both ULD1 and ULD2 inhibit all of them (minimum inhibitory concentration [MIC] ≤1 μg/mL). Resistance mutations against these compounds are rare, have limited impact on compound susceptibility, and substantially reduce bacterial growth. Based on their efficacy and lack of toxicity demonstrated in murine infection models, these compounds could translate into new therapies against multidrug-resistant bacterial infections.

GTR1 Affects Nitrogen Consumption and TORC1 Activity in Saccharomyces cerevisiae Under Fermentation Conditions

The TORC1 pathway coordinates cell growth in response to nitrogen availability present in the medium, regulating genes related to nitrogen transport and metabolism. Therefore, the adaptation of Saccharomyces cerevisiae to changes in nitrogen availability implies variations in the activity of this signaling pathway. In this sense, variations in nitrogen detection and signaling pathway are one of the main causes of differences in nitrogen assimilation during alcoholic fermentation. Previously, we demonstrated that allelic variants in the GTR1 gene underlying differences in ammonium and amino acids consumption between Wine/European (WE) and West African (WA) strains impact the expression of nitrogen transporters. The GTR1 gene encodes a GTPase that participates in the EGO complex responsible for TORC1 activation in response to amino acids availability. In this work, we assessed the role of the GTR1 gene on nitrogen consumption under fermentation conditions, using a high sugar concentration medium with nitrogen limitation and in the context of the WE and WA genetic backgrounds. The gtr1Δ mutant presented a reduced TORC1 activity and increased expression levels of nitrogen transporters, which in turn favored ammonium consumption, but decreased amino acid assimilation. Furthermore, to identify the SNPs responsible for differences in nitrogen consumption during alcoholic fermentation, we studied the polymorphisms present in the GTR1 gene. We carried out swapping experiments for the promoter and coding regions of GTR1 between the WE and WA strains. We observed that polymorphisms in the coding region of the WA GTR1 gene are relevant for TORC1 activity. Altogether, our results highlight the role of the GTR1 gene on nitrogen consumption in S. cerevisiae under fermentation conditions.

Transcriptional Activity and Protein Levels of Horizontally Acquired Genes in Yeast Reveal Hallmarks of Adaptation to Fermentative Environments

In the past decade, the sequencing of large cohorts of Saccharomyces cerevisiae strains has revealed a landscape of genomic regions acquired by Horizontal Gene Transfer (HGT). The genes acquired by HGT play important roles in yeast adaptation to the fermentation process, improving nitrogen and carbon source utilization. However, the functional characterization of these genes at the molecular level has been poorly attended. In this work, we carried out a systematic analysis of the promoter activity and protein level of 30 genes contained in three horizontally acquired regions commonly known as regions A, B, and C. In three strains (one for each region), we used the luciferase reporter gene and the mCherry fluorescent protein to quantify the transcriptional and translational activity of these genes, respectively. We assayed the strains generated in four different culture conditions; all showed low levels of transcriptional and translational activity across these environments. However, we observed an increase in protein levels under low nitrogen culture conditions, suggesting a possible role of the horizontally acquired genes in the adaptation to nitrogen-limited environments. Furthermore, since the strains carrying the luciferase reporter gene are null mutants for the horizontally acquired genes, we assayed growth parameters (latency time, growth rate, and efficiency) and the fermentation kinetics in this set of deletion strains. The results showed that single deletion of 20 horizontally acquired genes modified the growth parameters, whereas the deletion of five of them altered the maximal CO₂ production rate (Vmax). Interestingly, we observed a correlation between growth parameters and Vmax for an ORF within region A, encoding an ortholog to a thiamine (vitamin B1) transporter whose deletion decreased the growth rate, growth efficiency, and CO₂ production. Altogether, our results provided molecular and phenotypic evidence highlighting the importance of horizontally acquired genes in yeast adaptation to fermentative environments.

Discovery and identification of medium-chain fatty acid responsive promoters in Saccharomyces cerevisiae

Medium-chain fatty acids (MCFAs) and their derivatives are important chemicals that can be used in lubricants, detergents, and cosmetics. MCFAs can be produced in several microbes, although production is not high. Dynamic regulation by synthetic biology is a good method of improving production of chemicals that avoids toxic intermediates, but chemical-responsive promoters are required. Several MCFA sensors or promoters have been reported in Saccharomyces cerevisiae. In this study, by using transcriptomic analysis of S. cerevisiae exposed to fatty acids with 6-, 12-, and 16-carbon chains, we identified 58 candidate genes that may be responsive to MCFAs. Using a fluorescence-based screening method, we identified MCFA-responsive promoters, four that upregulated gene expression, and three that downregulated gene expression. Dose-response analysis revealed that some of the promoters were sensitive to fatty acid concentrations as low as 0.02-0.06 mM. The MCFA-responsive promoters reported in this study could be used in dynamic regulation of fatty acids and fatty acid-derived products in S. cerevisiae.

Interactively AUDIT Your Growth Curves with a Suite of R Packages

Bottlenecks often occur during data analysis when studying microbial growth in liquid culture at large scale. A researcher can collect thousands of growth curves, repeated measures of a microbial liquid culture, at once in multiple micro titer plates by purpose-built robotic instruments. However, it can be difficult and time-consuming to inspect and analyze these data. This is especially true for researchers without programming experience. To enable this researcher, we created and describe an interactive application: Automated Usher for Data Inspection and Tidying (AUDIT). It allows the user to analyze growth curve data generated from one or more runs each with one or more micro titer plates alongside their experimental design. AUDIT covers input, pre-processing, summarizing, visual exploration and output. Compared to previously available tools AUDIT handles more data, provides live previews and is built from individually re-usable pieces distributed as R packages.

Evaluation of Saccharomyces cerevisiae Wine Yeast Competitive Fitness in Enologically Relevant Environments by Barcode Sequencing

When a wine yeast is inoculated into grape juice the potential variation in juice composition that confronts it is huge. Assessing the performance characteristics of the many commercially available wine yeasts in the many possible grape juice compositions is a daunting task. To this end we have developed a barcoded Saccharomyces cerevisiae wine yeast collection to facilitate the task of performance assessment that will contribute to a broader understanding of genotype-phenotype relations. Barcode sequencing of mixed populations is used to monitor strain abundance in different grape juices and grape juice-like environments. Choice of DNA extraction method is shown to affect strain-specific barcode count in this highly related set of S. cerevisiae strains; however, the analytical approach is shown to be robust toward strain dependent variation in DNA extraction efficiency. Of the 38 unique compositional variables assessed, resistance to copper and SO₂ are found to be dominant discriminatory factors in wine yeast performance. Finally, a comparison of competitive fitness profile with performance in single inoculum fermentations reveal strain dependent correspondence of yeast performance using these two different approaches.

Improving Chromosome Synthesis with a Semiquantitative Phenotypic Assay and Refined Assembly Strategy

Recent advances in DNA synthesis technology have made it possible to rewrite the entire genome of an organism. The major hurdles in this process are efficiently identifying and fixing the defect-inducing sequences (or "bugs") during rewriting. Here, we describe a high-throughput, semiquantitative phenotype assay for evaluating the fitness of synthetic yeast and identifying potential bugs. Growth curves were measured under a carefully chosen set of testing conditions. Statistical analysis revealed strains with subtle defects relative to the wild type, which were targeted for debugging. The effectiveness of the assay was demonstrated by phenotypic profiling of all intermediate synthetic strains of the synthetic yeast chromosome XII. Subsequently, the assay was applied during the process of constructing another synthetic chromosome. Furthermore, we designed an efficient chromosome assembly strategy that integrates iterative megachunk construction with CRISPR/Cas9-mediated assembly of synthetic segments. Together, the semiquantitative assay and refined assembly strategy could greatly facilitate synthetic genomics projects by improving efficiency during both debugging and construction.

Adaptation by Loss of Heterozygosity in Saccharomyces cerevisiae Clones Under Divergent Selection

Loss of heterozygosity (LOH) is observed during vegetative growth and reproduction of diploid genotypes through mitotic crossovers, aneuploidy caused by nondisjunction, and gene conversion. We aimed to test the role that LOH plays during adaptation of two highly heterozygous Saccharomyces cerevisiae genotypes to multiple environments over a short time span in the laboratory. We hypothesized that adaptation would be observed through parallel LOH events across replicate populations. Using genome resequencing of 70 clones, we found that LOH was widespread with 5.2 LOH events per clone after ∼500 generations. The most common mode of LOH was gene conversion (51%) followed by crossing over consistent with either break-induced replication or double Holliday junction resolution. There was no evidence that LOH involved nondisjunction of whole chromosomes. We observed parallel LOH in both an environment-specific and environment-independent manner. LOH largely involved recombining existing variation between the parental genotypes, but also was observed after de novo, presumably beneficial, mutations occurred in the presence of canavanine, a toxic analog of arginine. One highly parallel LOH event involved the ENA salt efflux pump locus on chromosome IV, which showed repeated LOH to the allele from the European parent, an allele originally derived by introgression from S. paradoxus Using CRISPR-engineered LOH we showed that the fitness advantage provided by this single LOH event was 27%. Overall, we found extensive evidence that LOH could be adaptive and is likely to be a greater source of initial variation than de novo mutation for rapid evolution of diploid genotypes.

The fission yeast FHIT homolog affects checkpoint control of proliferation and is regulated by mitochondrial electron transport

Genetic analysis has strongly implicated human FHIT (Fragile Histidine Triad) as a tumor suppressor gene, being mutated in a large proportion of early‐stage cancers. The functions of the FHIT protein have, however, remained elusive. Here, we investigated aph1⁺, the fission yeast homolog of FHIT, for functions related to checkpoint control and oxidative metabolism. In sublethal concentrations of DNA damaging agents, aph1Δ mutants grew with a substantially shorter lag phase. In aph1Δ mutants carrying a hypomorphic allele of cds1 (the fission yeast homolog of Chk2), in addition, increased chromosome fragmentation and missegregation were found. We also found that under hypoxia or impaired electron transport function, the Aph1 protein level was strongly depressed. Previously, FHIT has been linked to regulation of the human 9‐1‐1 checkpoint complex constituted by Hus1, Rad1, and Rad9. In Schizosaccharomyces pombe, the levels of all three 9‐1‐1 proteins are all downregulated by hypoxia in similarity with Aph1. Moreover, deletion of the aph1⁺ gene reduced the Rad1 protein level, indicating a direct relationship between these two proteins. We conclude that the fission yeast FHIT homolog has a role in modulating DNA damage checkpoint function, possibly through an effect on the 9‐1‐1 complex, and that this effect may be critical under conditions of limiting oxidative metabolism and reoxygenation.

Rapid decline of bacterial drug-resistance in an antibiotic-free environment through phenotypic reversion

Antibiotic resistance typically induces a fitness cost that shapes the fate of antibiotic-resistant bacterial populations. However, the cost of resistance can be mitigated by compensatory mutations elsewhere in the genome, and therefore the loss of resistance may proceed too slowly to be of practical importance. We present our study on the efficacy and phenotypic impact of compensatory evolution in Escherichia coli strains carrying multiple resistance mutations. We have demonstrated that drug-resistance frequently declines within 480 generations during exposure to an antibiotic-free environment. The extent of resistance loss was found to be generally antibiotic-specific, driven by mutations that reduce both resistance level and fitness costs of antibiotic-resistance mutations. We conclude that phenotypic reversion to the antibiotic-sensitive state can be mediated by the acquisition of additional mutations, while maintaining the original resistance mutations. Our study indicates that restricting antimicrobial usage could be a useful policy, but for certain antibiotics only.

Nitrogen sources preferences of non-Saccharomyces yeasts to sustain growth and fermentation under winemaking conditions

Wine-related non-Saccharomyces yeasts are becoming more widely used in oenological practice for their ability to confer wine a more complex satisfying aroma, but their metabolism remains unknown. Our study explored the nitrogen utilisation profile of three popular non-Saccharomyces species, Torulaspora delbrueckii, Metschnikowia pulcherrima and Metschnikowia fructicola. The nitrogen source preferences to support growth and fermentation as well as the uptake order of different nitrogen sources during wine fermentation were investigated. While T. delbrueckii and S. cerevisiae strains shared the same nitrogen source preferences, Metschnikowia sp. Displayed a lower capacity to efficiently use the preferred nitrogen compounds, but were able to assimilate a wider range of amino acids. During alcoholic fermentation, the non-Saccharomyces strains consumed different nitrogen sources in a similar order as S. cerevisiae, but not as quickly. Furthermore, when all the nitrogen sources were supplied in the same amount, their assimilation order was similarly affected for both S. cerevisiae and non-Saccharomyces strains. Under this condition, the rate of nitrogen source consumption of non-Saccharomyces strains and S. cerevisiae was comparable. Overall, this study expands our understanding about the preferences and consumption rates of individual nitrogen sources by the investigated non-Saccharomyces yeasts in a wine environment. This knowledge provides useful information for a more efficient exploitation of non-Saccharomyces strains that improves the management of the wine fermentation.

Limited Evolutionary Conservation of the Phenotypic Effects of Antibiotic Resistance Mutations

Multidrug-resistant clinical isolates are common in certain pathogens, but rare in others. This pattern may be due to the fact that mutations shaping resistance have species-specific effects. To investigate this issue, we transferred a range of resistance-conferring mutations and a full resistance gene into Escherichia coli and closely related bacteria. We found that resistance mutations in one bacterial species frequently provide no resistance, in fact even yielding drug hypersensitivity in close relatives. In depth analysis of a key gene involved in aminoglycoside resistance (trkH) indicated that preexisting mutations in other genes-intergenic epistasis-underlie such extreme differences in mutational effects between species. Finally, reconstruction of adaptive landscapes under multiple antibiotic stresses revealed that mutations frequently provide multidrug resistance or elevated drug susceptibility (i.e., collateral sensitivity) only with certain combinations of other resistance mutations. We conclude that resistance and collateral sensitivity are contingent upon the genetic makeup of the bacterial population, and such contingency could shape the long-term fate of resistant bacteria. These results underlie the importance of species-specific treatment strategies.

Genetic variants of TORC1 signaling pathway affect nitrogen consumption in Saccharomyces cerevisiae during alcoholic fermentation

In the alcoholic fermentation process, Saccharomyces cerevisiae strains present differences in their nitrogen consumption profiles, these phenotypic outcomes have complex genetic and molecular architectures. In this sense, variations in nitrogen signaling pathways regulated by TORC1 represent one of the main sources of phenotypic diversity in nitrogen consumption. This emphasizes the possible roles that allelic variants from the TORC1 pathway have in the nitrogen consumption differences observed in yeast during the alcoholic fermentation. Here, we studied the allelic diversity in the TORC1 pathway across four yeast strains and determined how these polymorphisms directly impact nitrogen consumption during alcoholic fermentation. Using a reciprocal hemizygosity approach combined with phenotyping under fermentative conditions, we found that allelic variants of GTR1, TOR2, SIT4, SAP185, EAP1, NPR1 and SCH9 underlie differences in the ammonium and amino acids consumption phenotypes. Among these, GTR1 alleles from the Wine/European and West African genetic backgrounds showed the greatest effects on ammonium and amino acid consumption, respectively. Furthermore, we identified allelic variants of SAP185, TOR2, SCH9 and NPR1 from an oak isolate that increased the amino acid consumption preference over ammonium; representing putative candidates coming from a non-domesticated strain that could be used for genetic improvement programs. In conclusion, our results demonstrated that a large number of allelic variants within the TORC1 pathway significantly impacts on regulatory mechanisms of nitrogen assimilation during alcoholic fermentation.

Saccharomyces cerevisiae and Hanseniaspora osmophila strains as yeast active cultures for potential probiotic applications

This work allowed the evaluation of the gastrointestinal resistance of five yeasts (Saccharomyces and non-Saccharomyces) in order to assess some biotechnological characteristics linked to the potential probiotics, using a dynamic gastrointestinal simulator (simgi®). The best results obtained were for strains Saccharomyces cerevisiae 3 and Hanseniaspora osmophila 1056. Having optimised the method, the yeasts were subsequently lyophilised, and the one that showed the least loss of viability, S. cerevisiae 3, was used in a freeze-dried form to obtain a new functional food. On the other hand, some characteristics of the product were compared with those of probiotic supplements and other commercial probiotic foods. The obtained functional product showed better parameters than the rest of the samples containing yeasts which, together with the great acceptance shown after the consumer tests, means that it can be presented as a possible commercial functional product.

Reverse Evolution of a Classic Gene Network in Yeast Offers a Competitive Advantage

Glucose repression is a central regulatory system in yeast that ensures the utilization of carbon sources in a highly economical manner. The galactose (GAL) metabolism network is stringently regulated by glucose repression in yeast and has been a classic system for studying gene regulation. We show here that a Saccharomyces cerevisiae (S. cerevisiae) lineage in spontaneously fermented milk has swapped all its structural GAL genes (GAL2 and the GAL7-10-1 cluster) with early diverged versions through introgression. The rewired GAL network has abolished glucose repression and conversed from a strictly inducible to a constitutive system through polygenic changes in the regulatory components of the network, including a thymine (T) to cytosine (C) and a guanine (G) to adenine (A) transition in the upstream repressing sequence (URS) sites of GAL1 and GAL4, respectively, which impair Mig1p-mediated repression, loss of function of the repressor Gal80p through a T146I substitution in the protein, and subsequent futility of GAL3. Furthermore, the milk lineage of S. cerevisiae has achieved galactose-utilization rate elevation and galactose-over-glucose preference switch through the duplication of the introgressed GAL2 and the loss of function of the main glucose transporter genes HXT6 and HXT7. In addition, we demonstrate that GAL2 requires GAL7 or GAL10 for its expression, and Gal2p likely requires Gal1p for its transportation function in the milk lineage of S. cerevisiae. We show a clear case of reverse evolution of a classic gene network for ecological adaptation and provide new insights into the regulatory model of the canonical GAL network.

Fermentative behaviour and competition capacity of cryotolerant Saccharomyces species in different nitrogen conditions

The selection of yeasts with low nitrogen requirement is a current need in winemaking. In this work, we analysed nitrogen requirements of strains belonging to the cryotolerant species S. uvarum, S. eubayanus and S. kudriavzevii, in order to evaluate their potential for conducting the fermentation of low nitrogen content grape musts. Our result demonstrated that S. eubayanus is the species less influenced by the increasing nitrogen concentrations in both growth and fermentation conditions. Strains showing the best behaviours, S. eubayanus NPCC 1285 and S. uvarum NPCC 1317, were selected to be tested in mixed cultures with S. cerevisiae T73 at different temperatures (12 °C, 20 °C and 28 °C) in synthetic grape must with different nitrogen concentrations (60, 140 and 300 mg/L YAN). The cryotolerant strains dominated the fermentations carried out at 12 °C while S. cerevisiae prevailed at 28 °C independently from the nitrogen concentration. At intermediate temperature, 20 °C, S. eubayanus mono and mixed cultures showed the best fermentative behaviour especially with low and intermediate nitrogen concentration. In summary, cryotolerant Saccharomyces species, particularly S. eubayanus, could be interesting tools to avoid fermentations stucks caused by low nitrogen content in grape musts.

The Crabtree Effect Shapes the Saccharomyces cerevisiae Lag Phase during the Switch between Different Carbon Sources

When faced with environmental changes, microbes often enter a temporary growth arrest during which they reprogram the expression of specific genes to adapt to the new conditions. A prime example of such a lag phase occurs when microbes need to switch from glucose to other, less-preferred carbon sources. Despite its industrial relevance, the genetic network that determines the duration of the lag phase has not been studied in much detail. Here, we performed a genome-wide Bar-Seq screen to identify genetic determinants of the Saccharomyces cerevisiae glucose-to-galactose lag phase. The results show that genes involved in respiration, and specifically those encoding complexes III and IV of the electron transport chain, are needed for efficient growth resumption after the lag phase. Anaerobic growth experiments confirmed the importance of respiratory energy conversion in determining the lag phase duration. Moreover, overexpression of the central regulator of respiration, HAP4, leads to significantly shorter lag phases. Together, these results suggest that the glucose-induced repression of respiration, known as the Crabtree effect, is a major determinant of microbial fitness in fluctuating carbon environments.IMPORTANCE The lag phase is arguably one of the prime characteristics of microbial growth. Longer lag phases result in lower competitive fitness in variable environments, and the duration of the lag phase is also important in many industrial processes where long lag phases lead to sluggish, less efficient fermentations. Despite the immense importance of the lag phase, surprisingly little is known about the exact molecular processes that determine its duration. Our study uses the molecular toolbox of S. cerevisiae combined with detailed growth experiments to reveal how the transition from fermentative to respirative metabolism is a key bottleneck for cells to overcome the lag phase. Together, our findings not only yield insight into the key molecular processes and genes that influence lag duration but also open routes to increase the efficiency of industrial fermentations and offer an experimental framework to study other types of lag behavior.

Transition between fermentation and respiration determines history-dependent behavior in fluctuating carbon sources

Cells constantly adapt to environmental fluctuations. These physiological changes require time and therefore cause a lag phase during which the cells do not function optimally. Interestingly, past exposure to an environmental condition can shorten the time needed to adapt when the condition re-occurs, even in daughter cells that never directly encountered the initial condition. Here, we use the molecular toolbox of Saccharomyces cerevisiae to systematically unravel the molecular mechanism underlying such history-dependent behavior in transitions between glucose and maltose. In contrast to previous hypotheses, the behavior does not depend on persistence of proteins involved in metabolism of a specific sugar. Instead, presence of glucose induces a gradual decline in the cells' ability to activate respiration, which is needed to metabolize alternative carbon sources. These results reveal how trans-generational transitions in central carbon metabolism generate history-dependent behavior in yeast, and provide a mechanistic framework for similar phenomena in other cell types.