Summer Temperature Can Predict the Distribution of Wild Yeast Populations
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Discordant Evolution of Mitochondrial and Nuclear Yeast Genomes at Population Level
bioRxiv preprint doi: https://doi.org/10.1101/855858; this version posted November 27, 2019. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission. ARTICLE Discordant evolution of mitochondrial and nuclear yeast genomes at population level Matteo De Chiara1, Anne Friedrich2, Benjamin Barré1, Michael Breitenbach3, Joseph Schacherer2,* and Gianni Liti1,* 1Université Côte d'Azur, CNRS, INSERM, IRCAN, Nice, France 2Université de Strasbourg, CNRS, GMGM UMR 7156, F-67000 Strasbourg, France 3Universität Salzburg, Fachbereich Biowissenschaften, Salzburg, Austria *Correspondence should be addressed to GL ([email protected]) or JS ([email protected]) Abstract Mitochondria are essential organelles partially regulated by their own genomes. The mitochondrial genome maintenance and inheritance differ from nuclear genome, potentially uncoupling their evolutionary trajectories. Here, we analysed mitochondrial sequences obtained from the 1,011 Saccharomyces cerevisiae strain collection and identified pronounced differences with their nuclear genome counterparts. In contrast with most fungal species, S. cerevisiae mitochondrial genomes show higher genetic diversity compared to the nuclear genomes. Strikingly, mitochondrial genomes appear to be highly admixed, resulting in a complex interconnected phylogeny with weak grouping of isolates, whereas interspecies introgressions are very rare. Complete genome assemblies revealed that structural rearrangements are nearly absent with rare inversions detected. We tracked introns variation in COX1 and COB to infer gain and loss events throughout the species evolutionary history. Mitochondrial genome copy number is connected with the nuclear genome and linearly scale up with ploidy. We observed rare cases of naturally occurring mitochondrial DNA loss, petite, with a subset of them that do not suffer fitness growth defects. -
Saccharomyces Paradoxus Transcriptional Alterations in Cells of Distinct Phenotype and Viral Dsrna Content
microorganisms Article Saccharomyces paradoxus Transcriptional Alterations in Cells of Distinct Phenotype and Viral dsRNA Content Bazile˙ Ravoityte˙ 1,*, Juliana Lukša 1, Vyacheslav Yurchenko 2,3 , Saulius Serva 4,5 and Elena Serviene˙ 1,5,* 1 Laboratory of Genetics, Institute of Botany, Nature Research Centre, Akademijos str. 2, 08412 Vilnius, Lithuania; [email protected] 2 Life Science Research Centre, Faculty of Science, University of Ostrava, Chittussiho 10, 710 00 Ostrava, Czech Republic; [email protected] 3 Martsinovsky Institute of Medical Parasitology, Tropical and Vector Borne Diseases, Sechenov University, Malaya Pirogovskaya str. 20, 119435 Moscow, Russia 4 Department of Biochemistry and Molecular Biology, Institute of Biosciences, Vilnius University, Sauletekio˙ al. 7, 10257 Vilnius, Lithuania; [email protected] 5 Department of Chemistry and Bioengineering, Vilnius Gediminas Technical University, Sauletekio˙ al. 11, 10223 Vilnius, Lithuania * Correspondence: [email protected] (B.R.); [email protected] (E.S.) Received: 18 November 2020; Accepted: 29 November 2020; Published: 30 November 2020 Abstract: Killer yeasts are attractive antifungal agents with great potential applications in the food industry. Natural Saccharomyces paradoxus isolates provide new dsRNA-based killer systems available for investigation. The presence of viral dsRNA may alter transcriptional profile of S. paradoxus. To test this possibility, a high-throughput RNA sequencing was employed to compare the transcriptomes of S. paradoxus AML 15-66 K66 killer strains after curing them of either M-66 alone or both M-66 and L-A-66 dsRNA viruses. The S. paradoxus cells cured of viral dsRNA(s) showed respiration deficient or altered sporulation patterns. We have identified numerous changes in the transcription profile of genes including those linked to ribosomes and amino acid biosynthesis, as well as mitochondrial function. -
Interspecific Hybrids Reveal Increased Fermentation
fermentation Article Saccharomyces arboricola and Its Hybrids’ Propensity for Sake Production: Interspecific Hybrids Reveal Increased Fermentation Abilities and a Mosaic Metabolic Profile Matthew J. Winans 1,2,* , Yuki Yamamoto 1, Yuki Fujimaru 1, Yuki Kusaba 1, Jennifer E. G. Gallagher 2 and Hiroshi Kitagaki 1 1 Graduate School of Advanced Health Sciences, Saga University, 1, Honjo, Saga city, Saga 840-8502, Japan; [email protected] (Y.Y.); [email protected] (Y.F.); [email protected] (Y.K.); [email protected] (H.K.) 2 Biology Department, West Virginia University, 53 Campus Drive, Morgantown, WV 26506-6057, USA; [email protected] * Correspondence: [email protected]; Tel.: +1-(304)-483-1786; Fax: +1-(304)-293-6363 Received: 4 December 2019; Accepted: 17 January 2020; Published: 20 January 2020 Abstract: The use of interspecific hybrids during the industrial fermentation process has been well established, positioning the frontier of advancement in brewing to capitalize on the potential of Saccharomyces hybridization. Interspecific yeast hybrids used in modern monoculture inoculations benefit from a wide range of volatile metabolites that broaden the organoleptic complexity. This is the first report of sake brewing by Saccharomyces arboricola and its hybrids. S. arboricola x S. cerevisiae direct-mating generated cryotolerant interspecific hybrids which increased yields of ethanol and ethyl hexanoate compared to parental strains, important flavor attributes of fine Japanese ginjo sake rice wine. Hierarchical clustering heatmapping with principal component analysis for metabolic profiling was used in finding low levels of endogenous amino/organic acids clustered S. arboricola apart from the S. -
A Novel Bacteria-Free Method for Sour Beer Production 1 Kara Osburna
bioRxiv preprint doi: https://doi.org/10.1101/121103; this version posted March 27, 2017. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC-ND 4.0 International license. 1 Primary souring: a novel bacteria-free method for sour beer production 2 Kara Osburna, Justin Amaralb, Sara R. Metcalfa, David M. Nickensa, Cody M. Rogersa, 3 Christopher Sausena, Robert Caputoc, Justin Millerc, Hongde Lid, Jason M. Tennessend, and 4 Matthew L. Bochmana,c* 5 aMolecular and Cellular Biochemistry Department, 212 South Hawthorne Drive, Simon Hall 6 MSB1, room 405B, Indiana University, Bloomington, IN 47405, USA. 7 [email protected] 8 [email protected] 9 [email protected] 10 [email protected] 11 [email protected] 12 [email protected] 13 14 bMainiacal Brewing Company, Bangor, ME 04401, USA. 15 [email protected] 16 17 cWild Pitch Yeast, Bloomington, IN 47405, USA. 18 [email protected] 19 [email protected] 20 21 dDepartment of Biology, Indiana University, 1001 East Third Street, Bloomington, IN 47405, 22 USA. 23 [email protected] 24 [email protected] 25 26 *Corresponding author: 27 Matthew L. Bochman, Ph.D. 28 Assistant Professor 29 Molecular and Cellular Biochemistry Department 30 212 South Hawthorne Drive 31 Simon Hall MSB1, room 405B 32 Indiana University 33 [email protected] 34 812-856-2095 1 bioRxiv preprint doi: https://doi.org/10.1101/121103; this version posted March 27, 2017. -
Adaptive Evolution of Non-Saccharomyces Yeasts to Produce Wines with Low Ethanol Content Catarina Rocha
Adaptive Evolution of Non-Saccharomyces Yeasts to Produce Wines with Low Ethanol Content Catarina Rocha Abstract This work describes the implementation of adaptive evolution, a non-genetic engineering approach, applied to non- Saccharomyces yeasts to originate variants that produce reduced levels of ethanol, during alcoholic fermentation of grape must. Sub-lethal concentrations of potassium chloride and furfural were used as evolutive pressures. Both KCl and furfural impose stresses that affect the cell stability compromising the redox balance. The natural response of cell to regenerate NAD+ is increasing the production of glycerol. The original populations of two non-Saccharomyces strains, Metschnikowia pulcherrima 134|MET and Lachancea thermotolerans 483|LCH were subjected to adaptive evolution. In parallel, Saccharomyces cerevisiae 771|SAC strain was also put under adaptive evolution as a comparative evolutive line. At each 50 generations, the evolved populations were analyzed for ethanol and glycerol production and glucose and fructose consumption by enzymatic assays. The evolved populations under adaptive evolution did not show relevant differences regarding to the production of ethanol or glycerol, when compared with their originals. Additionally, ethyl methanesulfonate (EMS) was used as a mutagen to create a population of mutagenized cells. To assess the metabolome of yeasts, by identifying the metabolites present inside the cells and the ones exported to the environment, Fourier Transform Ion Cyclotron Resonance Mass Spectrometry (FTICR-MS) was applied along growth. In future, new adaptive evolution lines will be started with the EMS mutagenized cells and FTICR-MS Spectrometry will be used to compare the original yeast populations with the prospective evolved ones. Keywords: Non-Saccharomyces yeasts; Wine; Adaptive Evolution; Mutagenesis; Mass Spectrometry. -
Evaluation of the Chitin-Binding Dye Congo Red As a Selection Agent for the Isolation, Classification, and Enumeration of Ascomycete Yeasts
Archives of Microbiology (2018) 200:671–675 https://doi.org/10.1007/s00203-018-1498-y SHORT COMMUNICATION Evaluation of the chitin-binding dye Congo red as a selection agent for the isolation, classification, and enumeration of ascomycete yeasts Tomas Linder1 Received: 3 February 2018 / Revised: 19 February 2018 / Accepted: 21 February 2018 / Published online: 23 February 2018 © The Author(s) 2018. This article is an open access publication Abstract Thirty-nine strains of ascomycete yeasts representing 35 species and 33 genera were tested for their ability to grow on solid agar medium containing increasing concentrations of the chitin-binding dye Congo red. Six strains were classified as hyper- sensitive (weak or no growth at 10 mg/l Congo red), five were moderately sensitive (weak or no growth at 50 mg/l), three were moderately tolerant (weak or no growth at 100 mg/l), while the remaining 25 strains were classified as resistant (robust growth at ≥ 100 mg/l) with 20 of these strains classified as hyper-resistant (robust growth at 200 mg/l). Congo red growth phenotypes were consistent within some families but not others. The frequency of Congo red resistance among ascomycete yeasts was deemed too high for the practical use of Congo red as a selection agent for targeted isolation, but can be useful for identification and enumeration of yeasts. Keywords Antifungal · Cell wall · Phenotype · Yeast Introduction groups of yeasts. For example, chemically defined growth medium containing methanol as the sole carbon source is The development of genome sequencing over the past four commonly used to isolate species of methylotrophic yeasts decades has revolutionized yeast taxonomy and now enables (van Dijken and Harder 1974). -
Lachancea Thermotolerans Applications in Wine Technology
fermentation Review Lachancea thermotolerans Applications in Wine Technology Antonio Morata 1,* ID , Iris Loira 1 ID , Wendu Tesfaye 1, María Antonia Bañuelos 2, Carmen González 1 and José Antonio Suárez Lepe 1 1 Department of Chemistry and Food Technology, ETSIAAB, Technical University of Madrid, 28040 Madrid, Spain; [email protected] (I.L.); [email protected] (W.T.); [email protected] (C.G.); [email protected] (J.A.S.L.) 2 Department of Biotechnology-Plant Biology, ETSIAAB, Technical University of Madrid, 28040 Madrid, Spain; [email protected] * Correspondence: [email protected] Received: 20 June 2018; Accepted: 6 July 2018; Published: 11 July 2018 Abstract: Lachancea (kluyveromyces) thermotolerans is a ubiquitous yeast that can be naturally found in grapes but also in other habitats as soil, insects and plants, extensively distributed around the world. In a 3-day culture, it shows spherical to ellipsoidal morphology appearing in single, paired cells or short clusters. It is a teleomorph yeast with 1–4 spherical ascospores and it is characterized by a low production of volatile acidity that helps to control global acetic acid levels in mixed or sequential inoculations with either S. cerevisiae or other non-Saccharomyces species. It has a medium fermentative power, so it must be used in sequential or mixed inoculations with S. cerevisiae to get dry wines. It shows a high production of lactic acid able to affect strongly wine pH, sometimes decreasing wine pH by 0.5 units or more during fermentation. Most of the acidification is produced at the beginning of fermentation facilitating the effect in sequential fermentations because it is more competitive at low alcoholic degree. -
Genetic Variation and Phylogeography of the Wild Yeast Saccharomyces Paradoxus in Eurasia
UNIVERSIDADE DE LISBOA FACULDADE DE CIÊNCIAS DEPARTAMENTO DE BIOLOGIA VEGETAL Genetic variation and phylogeography of the wild yeast Saccharomyces paradoxus in Eurasia Pedro Miguel Coelho de Almeida MESTRADO EM MICROBIOLOGIA APLICADA 2011 UNIVERSIDADE DE LISBOA FACULDADE DE CIÊNCIAS DEPARTAMENTO DE BIOLOGIA VEGETAL Genetic variation and phylogeography of the wild yeast Saccharomyces paradoxus in Eurasia Dissertação orientada por Prof. Doutor José Paulo Sampaio (CREM, FCT-UNL) e Prof.ª Doutora Margarida Barata (FCUL) Pedro Miguel Coelho de Almeida MESTRADO EM MICROBIOLOGIA APLICADA 2011 Genetic variation and phylogeography of the wild yeast Saccharomyces paradoxus in Eurasia Pedro Miguel Coelho de Almeida MASTER THESIS 2011 This thesis was fully performed at CREM (Centro de Recursos Microbiológicos) research center, Department of Life Sciences of the New University of Lisbon under the direct supervision of Prof. Dr. José Paulo Sampaio. Prof. Dr. Margarida Barata was the internal designated supervisor in the scope of the Master in Applied Microbiology of the Faculty of Sciences of the University of Lisbon. Genetic variation and phylogeography of the wild yeast Saccharomyces paradoxus in Eurasia ACKNOWLEDGEMENTS I have learned much during my MSc and the first person to whom I really want to express my sincere gratitude is Prof. Dr. José Paulo Sampaio for receiving me in his laboratory, allowing me to take the research of my thesis under his supervision, and always get time when I need it. I am very thankful for the guidance and suggestions that make this thesis possible. I will always keep in mind his open-mind and the useful teachings concerning microbiology, ecology, phylogenetics, evolution … and many others… I also would like to thank Prof. -
Social Wasps Promote Social Behavior in Saccharomyces Spp
COMMENTARY Social wasps promote social behavior in Saccharomyces spp. COMMENTARY Meredith Blackwella,b,1 and Cletus P. Kurtzmanc Production of fermented beverages and bread mak- ing represents a multibillion dollar worldwide industry (1) with its origins linked to the Middle East nearly 10,000 y ago (2). Despite this long history, the cause of fermentation was not discovered until the pioneer- ing work beginning in the middle of the 19th century when Louis Pasteur demonstrated that fermentation is yeast-mediated. The long-term questions have been which yeast and where did it come from? The name selected for the wine fermentation yeast was Saccha- romyces cerevisiae, but based on phenotype, it appeared that there were related fermentative spe- cies. Early studies from DNA reassociation (3) and from gene sequencing (4) verified this premise and demon- strated that additional species of Saccharomyces were involved in fermentation, such as Saccharomyces uva- rum for lager beers. DNA sequence evidence sup- ports the use of S. cerevisiae in wine making in Egypt 5,000 y ago (5). Unresolved has been an under- standing of the natural habitat of Saccharomyces spe- cies. It has been proposed that S. cerevisiae evolved into a domesticated species found only in wineries and associated vineyards, but the discovery of Saccha- romyces species on tree bark has raised the intriguing possibility that S. cerevisiae and related species have a Fig. 1. Several studies surveyed yeasts present in the gut or on the surface of natural habitat associated with forest trees (6). More various insects. The work of Stefanini et al. -
Novel Non-Cerevisiae Saccharomyces Yeast Species Used in Beer and Alcoholic Beverage Fermentations
fermentation Review Novel Non-Cerevisiae Saccharomyces Yeast Species Used in Beer and Alcoholic Beverage Fermentations James Bruner * and Glen Fox * Food Science and Technology, University of California, Davis, CA 95616, USA * Correspondence: [email protected] (J.B.); [email protected] (G.F.) Received: 28 October 2020; Accepted: 22 November 2020; Published: 24 November 2020 Abstract: A great deal of research in the alcoholic beverage industry was done on non-Saccharomyces yeast strains in recent years. The increase in research interest could be attributed to the changing of consumer tastes and the search for new beer sensory experiences, as well as the rise in popularity of mixed-fermentation beers. The search for unique flavors and aromas, such as the higher alcohols and esters, polyfunctional thiols, lactones and furanones, and terpenoids that produce fruity and floral notes led to the use of non-cerevisiae Saccharomyces species in the fermentation process. Additionally, a desire to invoke new technologies and techniques for making alcoholic beverages also led to the use of new and novel yeast species. Among them, one of the most widely used non-cerevisiae strains is S. pastorianus, which was used in the production of lager beer for centuries. The goal of this review is to focus on some of the more distinct species, such as those species of Saccharomyces sensu stricto yeasts: S. kudriavzevii, S. paradoxus, S. mikatae, S. uvarum, and S. bayanus. In addition, this review discusses other Saccharomyces spp. that were used in alcoholic fermentation. Most importantly, the factors professional brewers might consider when selecting a strain of yeast for fermentation, are reviewed herein. -
Saccharomyces Paradoxus K66 Killer System Evidences Expanded Assortment of Helper and Satellite Viruses
viruses Article Saccharomyces paradoxus K66 Killer System Evidences Expanded Assortment of Helper and Satellite Viruses Igle˙ Vepštaite-Monstaviˇc˙ e˙ 1, Juliana Lukša 1 , Aleksandras Konovalovas 2, Dovile˙ Ežerskyte˙ 1, Ramune˙ Staneviˇciene˙ 1, Živile˙ Strazdaite-Žielien˙ e˙ 1, Saulius Serva 2,3,* and Elena Serviene˙ 1,3,* 1 Laboratory of Genetics, Institute of Botany, Nature Research Centre, LT-08412 Vilnius, Lithuania; [email protected] (I.V.-M.); [email protected] (J.L.); [email protected] (D.E.); [email protected] (R.S.); [email protected] (Ž.S.-Ž.) 2 Department of Biochemistry and Molecular Biology, Institute of Biosciences, Vilnius University, LT-10257 Vilnius, Lithuania; [email protected] 3 Department of Chemistry and Bioengineering, Vilnius Gediminas Technical University, LT-10223 Vilnius, Lithuania * Correspondence: [email protected] (S.S.); [email protected] (E.S.); Tel.: +370-52-72-9363 (S.S.); Tel.: +370-52-39-8244 (E.S.); Fax: +370-52-39-8231 (S.S.); Fax: +370-52-72-9352 (E.S.) Received: 28 August 2018; Accepted: 15 October 2018; Published: 16 October 2018 Abstract: The Saccharomycetaceae yeast family recently became recognized for expanding of the repertoire of different dsRNA-based viruses, highlighting the need for understanding of their cross-dependence. We isolated the Saccharomyces paradoxus AML-15-66 killer strain from spontaneous fermentation of serviceberries and identified helper and satellite viruses of the family Totiviridae, which are responsible for the killing phenotype. The corresponding full dsRNA genomes of viruses have been cloned and sequenced. Sequence analysis of SpV-LA-66 identified it to be most similar to S. -
Impact of Lachancea Thermotolerans Strain and Lactic Acid Concentration on Oenococcus Oeni and Malolactic Fermentation in Wine
Received: 29 March 2021 y Accepted: 7 May 2021 y Published: 17 June 2021 DOI:10.20870/oeno-one.2021.55.2.4657 Impact of Lachancea thermotolerans strain and lactic acid concentration on Oenococcus oeni and malolactic fermentation in wine Emma C. Snyder1, Vladimir Jiranek1,2,*, and Ana Hranilovic1 1 Department of Wine Science, The University of Adelaide, Urrbrae, SA, 5064, Australia 2 The Australian Research Council Training Centre for Innovative Wine Production, Urrbrae, SA, 5064, Australia *corresponding author: [email protected] Associate editor: Patrick Lucas ABSTRACT The yeast Lachancea thermotolerans can produce lactic acid during alcoholic fermentation (AF) and thereby acidify wines with insufficient acidity. However, little is known about the impact of L. thermotolerans on Oenococcus oeni, the primary lactic acid bacterium used in malolactic fermentation (MLF). This study explored the impact of sequential cultures of L. thermotolerans and Saccharomyces cerevisiae on MLF performance in white and red wines. Four L. thermotolerans strains were tested in Sauvignon blanc with sequential S. cerevisiae inoculation, compared to an S. cerevisiae control and the initially un-inoculated treatments. The L. thermotolerans wines showed large differences in acidification, and progression of MLF depended on lactic acid production, even at controlled pH. The highest and lowest lactic acid producing strains were tested further in Merlot fermentations with both co-inoculated and sequentially inoculated O. oeni. The low lactic acid producing strain enabled successful MLF, even when this failed in the S. cerevisiae treatment, with dramatically quicker malic acid depletion in O. oeni co-inoculation than in sequential inoculation. In contrast, a high lactic acid producing strain inhibited MLF irrespective of the O.