The Genetics of Non-Conventional Wine Yeasts: Current Knowledge and Future Challenges
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Deep Microbial Community Profiling Along the Fermentation Process of Pulque, a Major Biocultural Resource of Mexico
bioRxiv preprint doi: https://doi.org/10.1101/718999; this version posted July 31, 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 The copyright holder for this preprint (which was not certified by peer review) is the author/funder.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. Deep microbial community profiling along the fermentation process of pulque, a major biocultural resource of Mexico. 1 1 2 Carolina Rocha-Arriaga , Annie Espinal-Centeno , Shamayim Martinez-Sanchez , Juan 1 2 1,3 Caballero-Pérez , Luis D. Alcaraz * & Alfredo Cruz-Ramirez *. 1 Molecular & Developmental Complexity Group, Unit of Advanced Genomics, LANGEBIO-CINVESTAV, Irapuato, México. 2 Laboratorio de Genómica Ambiental, Departamento de Biología Celular, Facultad de Ciencias, Universidad Nacional Autónoma de México. Cd. Universitaria, 04510 Coyoacán, Mexico City, Mexico. 3 Escuela de Agronomía, Universidad de La Salle Bajío, León, Gto, Mexico. *Corresponding authors: [email protected], [email protected] ● Our approach allowed the identification of a broader microbial diversity in Pulque ● We increased 4.4 times bacteria genera and 40 times fungal species detected in mead. ● Newly reported bacteria genera and fungal species associated to Pulque fermentation Abstract Some of the biggest non-three plants endemic to Mexico were called metl in the Nahua culture. During colonial times they were renamed with the antillan word maguey. This was changed again by Carl von Linné who called them Agave (a greco-latin voice for admirable). For several Mexican prehispanic cultures, Agave species were not only considered as crops, but also part of their biocultural resources and cosmovision. Among the major products obtained from some Agave spp since pre-hispanic times is the alcoholic beverage called pulque or octli. -
WINE YEAST: the CHALLENGE of LOW TEMPERATURE Zoel Salvadó Belart Dipòsit Legal: T.1304-2013
WINE YEAST: THE CHALLENGE OF LOW TEMPERATURE Zoel Salvadó Belart Dipòsit Legal: T.1304-2013 ADVERTIMENT. L'accés als continguts d'aquesta tesi doctoral i la seva utilització ha de respectar els drets de la persona autora. Pot ser utilitzada per a consulta o estudi personal, així com en activitats o materials d'investigació i docència en els termes establerts a l'art. 32 del Text Refós de la Llei de Propietat Intel·lectual (RDL 1/1996). Per altres utilitzacions es requereix l'autorització prèvia i expressa de la persona autora. En qualsevol cas, en la utilització dels seus continguts caldrà indicar de forma clara el nom i cognoms de la persona autora i el títol de la tesi doctoral. No s'autoritza la seva reproducció o altres formes d'explotació efectuades amb finalitats de lucre ni la seva comunicació pública des d'un lloc aliè al servei TDX. Tampoc s'autoritza la presentació del seu contingut en una finestra o marc aliè a TDX (framing). Aquesta reserva de drets afecta tant als continguts de la tesi com als seus resums i índexs. ADVERTENCIA. El acceso a los contenidos de esta tesis doctoral y su utilización debe respetar los derechos de la persona autora. Puede ser utilizada para consulta o estudio personal, así como en actividades o materiales de investigación y docencia en los términos establecidos en el art. 32 del Texto Refundido de la Ley de Propiedad Intelectual (RDL 1/1996). Para otros usos se requiere la autorización previa y expresa de la persona autora. En cualquier caso, en la utilización de sus contenidos se deberá indicar de forma clara el nombre y apellidos de la persona autora y el título de la tesis doctoral. -
Microbial and Chemical Analysis of Non-Saccharomyces Yeasts from Chambourcin Hybrid Grapes for Potential Use in Winemaking
fermentation Article Microbial and Chemical Analysis of Non-Saccharomyces Yeasts from Chambourcin Hybrid Grapes for Potential Use in Winemaking Chun Tang Feng, Xue Du and Josephine Wee * Department of Food Science, The Pennsylvania State University, Rodney A. Erickson Food Science Building, State College, PA 16803, USA; [email protected] (C.T.F.); [email protected] (X.D.) * Correspondence: [email protected]; Tel.: +1-814-863-2956 Abstract: Native microorganisms present on grapes can influence final wine quality. Chambourcin is the most abundant hybrid grape grown in Pennsylvania and is more resistant to cold temperatures and fungal diseases compared to Vitis vinifera. Here, non-Saccharomyces yeasts were isolated from spontaneously fermenting Chambourcin must from three regional vineyards. Using cultured-based methods and ITS sequencing, Hanseniaspora and Pichia spp. were the most dominant genus out of 29 fungal species identified. Five strains of Hanseniaspora uvarum, H. opuntiae, Pichia kluyveri, P. kudriavzevii, and Aureobasidium pullulans were characterized for the ability to tolerate sulfite and ethanol. Hanseniaspora opuntiae PSWCC64 and P. kudriavzevii PSWCC102 can tolerate 8–10% ethanol and were able to utilize 60–80% sugars during fermentation. Laboratory scale fermentations of candidate strain into sterile Chambourcin juice allowed for analyzing compounds associated with wine flavor. Nine nonvolatile compounds were conserved in inoculated fermentations. In contrast, Hanseniaspora strains PSWCC64 and PSWCC70 were positively correlated with 2-heptanol and ionone associated to fruity and floral odor and P. kudriazevii PSWCC102 was positively correlated with a Citation: Feng, C.T.; Du, X.; Wee, J. Microbial and Chemical Analysis of group of esters and acetals associated to fruity and herbaceous aroma. -
Influence of Nutrient Supplementation on Torulaspora Delbrueckii Wine Fermentation Aroma
fermentation Article Influence of Nutrient Supplementation on Torulaspora Delbrueckii Wine Fermentation Aroma Debora Mecca 1, Santiago Benito 2,* , Beata Beisert 1, Silvia Brezina 1, Stefanie Fritsch 1, Heike Semmler 1 and Doris Rauhut 1 1 Department of Microbiology and Biochemistry, Hochschule Geisenheim University (HGU), Von-Lade-Straße 1, 65366 Geisenheim, Germany; [email protected] (D.M.); [email protected] (B.B.); [email protected] (S.B.); [email protected] (S.F.); [email protected] (H.S.); [email protected] (D.R.) 2 Department of Food Chemistry and Technology, Polytechnic University of Madrid, Ciudad Universitaria S/N, 28040 Madrid, Spain * Correspondence: [email protected]; Tel.: +34-913363710 or +34-913363984 Received: 15 February 2020; Accepted: 19 March 2020; Published: 22 March 2020 Abstract: This study was performed with the aim of characterizing the fermentative performance of three commercial strains of Torulaspora delbrueckii and their impact on the production of volatile and non-volatile compounds. Laboratory-scale single culture fermentations were performed using a commercial white grape juice. The addition of commercial nutrient products enabled us to test the yeasts under two different nutrient conditions. The addition of nutrients promoted fermentation intensity from 9% to 20 % with significant differences (p < 0.05) among the strains tested. The strain diversity together with the nutrient availability influenced the production of volatile compounds. Keywords: Torulaspora delbrueckii; volatile compounds; nutrients 1. Introduction In the last few decades, several researchers have focused on characterizing the oenological potential of non-Saccharomyces yeasts [1–3]. Non-Saccharomyces species can contribute substantially to the quality of wines. -
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 Eubayanus, the Missing Link to Lager Beer Yeasts
MICROBE PROFILE Sampaio, Microbiology 2018;164:1069–1071 DOI 10.1099/mic.0.000677 Microbe Profile: Saccharomyces eubayanus, the missing link to lager beer yeasts Jose Paulo Sampaio* Graphical abstract Ecology and phylogeny of Saccharomyces eubayanus. (a) The ecological niche of S. eubayanus in the Southern Hemisphere – Nothofagus spp. (southern beech) and sugar-rich fructifications (stromata) of its fungal biotrophic parasite Cyttaria spp., that can attain the size of golf balls. (b) Schematic representation of the phylogenetic position of S. eubayanus within the genus Saccharomyces based on whole-genome sequences. Occurrence in natural environments (wild) or participation in different human-driven fermentations is highlighted, together with the thermotolerant or cold-tolerant nature of each species and the origins of S. pastorianus, the lager beer hybrid. Abstract Saccharomyces eubayanus was described less than 10 years ago and its discovery settled the long-lasting debate on the origins of the cold-tolerant yeast responsible for lager beer fermentation. The largest share of the genetic diversity of S. eubayanus is located in South America, and strains of this species have not yet been found in Europe. One or more hybridization events between S. eubayanus and S. cerevisiae ale beer strains gave rise to S. pastorianus, the allopolyploid yeasts responsible for lager beer production worldwide. The identification of the missing progenitor of lager yeast opened new avenues for brewing yeast research. It allowed not only the selective breeding of new lager strains, but revealed also a wild yeast with interesting brewing abilities so that a beer solely fermented by S. eubayanus is currently on the market. -
Changes in the Relative Abundance of Two Saccharomyces Species from Oak Forests to Wine Fermentations
Changes in the relative abundance of two Saccharomyces species from oak forests to wine fermentations Sofia Dashko1, 2, Ping Liu3, Helena Volk2, Lorena Butinar2, Jure Piškur1, 2, Justin C. Fay3* 1Biology, Lund University, Sweden, 2Wine Research Center, University of Nova Gorica, Slovenia, 3Genetics, Washington University, USA Submitted to Journal: Frontiers in Microbiology Specialty Section: Food Microbiology ISSN: 1664-302X Article type: Original Research Article Received on: 10 Dec 2015 Accepted on: 09 Feb 2016 Provisional PDF published on: 09 Feb 2016 Frontiers website link: www.frontiersin.org ProvisionalCitation: Dashko S, Liu P, Volk H, Butinar L, Piškur J and Fay JC(2016) Changes in the relative abundance of two Saccharomyces species from oak forests to wine fermentations. Front. Microbiol. 7:215. doi:10.3389/fmicb.2016.00215 Copyright statement: © 2016 Dashko, Liu, Volk, Butinar, Piškur and Fay. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution and reproduction in other forums is permitted, provided the original author(s) or licensor are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms. This Provisional PDF corresponds to the article as it appeared upon acceptance, after peer-review. Fully formatted PDF and full text (HTML) versions will be made available soon. Frontiers in Microbiology | www.frontiersin.org Provisional Changes in the relative abundance of two Saccharomyces species from oak forests to wine fermentations Sofia Dashko1,2, Ping Liu3, Helena Volk1, Lorena Butinar1, Jure Piškur1,2 and Justin C. -
Phylogenetic Circumscription of Saccharomyces, Kluyveromyces
FEMS Yeast Research 4 (2003) 233^245 www.fems-microbiology.org Phylogenetic circumscription of Saccharomyces, Kluyveromyces and other members of the Saccharomycetaceae, and the proposal of the new genera Lachancea, Nakaseomyces, Naumovia, Vanderwaltozyma and Zygotorulaspora Cletus P. Kurtzman à Microbial Genomics and Bioprocessing Research Unit, National Center for Agricultural Utilization Research, Agricultural Research Service, U.S. Department of Agriculture, 1815 N. University Street, Peoria, IL 61604, USA Received 22 April 2003; received in revised form 23 June 2003; accepted 25 June 2003 First published online Abstract Genera currently assigned to the Saccharomycetaceae have been defined from phenotype, but this classification does not fully correspond with species groupings determined from phylogenetic analysis of gene sequences. The multigene sequence analysis of Kurtzman and Robnett [FEMS Yeast Res. 3 (2003) 417^432] resolved the family Saccharomycetaceae into 11 well-supported clades. In the present study, the taxonomy of the Saccharomyctaceae is evaluated from the perspective of the multigene sequence analysis, which has resulted in reassignment of some species among currently accepted genera, and the proposal of the following five new genera: Lachancea, Nakaseomyces, Naumovia, Vanderwaltozyma and Zygotorulaspora. ß 2003 Federation of European Microbiological Societies. Published by Elsevier B.V. All rights reserved. Keywords: Saccharomyces; Kluyveromyces; New ascosporic yeast genera; Molecular systematics; Multigene phylogeny 1. Introduction support the maintenance of three distinct genera. Yarrow [8^10] revived the concept of three genera and separated The name Saccharomyces was proposed for bread and Torulaspora and Zygosaccharomyces from Saccharomyces, beer yeasts by Meyen in 1838 [1], but it was Reess in 1870 although species assignments were often di⁄cult. -
Saccharomyces Uvarum Yeast Isolate Consumes Acetic Acid During Fermentation of High Sugar Juice and Juice with High Starting Volatile Acidity
Received: 11 October 2019 y Accepted: 28 March 2020 y Published: 16 Avril 2020 DOI:10.20870/oeno-one.2020.54.2.2594 VINE AND WINE OPEN ACCESS JOURNAL Saccharomyces uvarum yeast isolate consumes acetic acid during fermentation of high sugar juice and juice with high starting volatile acidity Jennifer M. Kelly 1, Stephanie A. van Dyk 3, Lisa K. Dowling 2, Gary J. Pickering 2,3 , Belinda Kemp 2,3 and Debra L. Inglis 1,2,3 * 1Centre for Biotechnology, Brock University, St. Catharines, ON L2S3A1, Canada 2Cool Climate Oenology and Viticulture Institute, Brock University, St. Catharines, ON L2S3A1, Canada 3Department of Biological Sciences, Brock University, St. Catharines, ON L2S3A1, Canada *Corresponding author: [email protected] ABSTRACT Aim: A Saccharomyces uvarum isolate was assessed for its ability to metabolize acetic acid present in juice and during the fermentation of partially dehydrated grapes. The impact on other yeast metabolites was also compared using an S. uvarum isolate and an S. cerevisiae wine yeast. The upper limit of fruit concentration that allowed the S. uvarum isolate to ferment wines to < 5 g/L residual sugar was defined. Methods and results: Cabernet franc grapes were partially dehydrated to three different post-harvest sugar targets (24.5 °Brix, 26.0 °Brix, and 27.5 °Brix) along with non-dehydrated grapes (21.5 °Brix control). Musts from all treatments were vinified with either the S. uvarum isolate CN1, formerly identified as S. bayanus , or S. cerevisiae EC1118. All wines were successfully vinified to less than 5 g/L residual sugar. Fermentation kinetics between the two yeasts were similar for all wines other than 27.5 °Brix, where CN1 took three days longer. -
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. -
(Vles) in the Yeast Debaryomyces Hansenii
toxins Article New Cytoplasmic Virus-Like Elements (VLEs) in the Yeast Debaryomyces hansenii Xymena Połomska 1,* ,Cécile Neuvéglise 2, Joanna Zyzak 3, Barbara Zarowska˙ 1, Serge Casaregola 4 and Zbigniew Lazar 1 1 Department of Biotechnology and Food Microbiology, Faculty of Biotechnology and Food Science, Wrocław University of Environmental and Life Sciences (WUELS), 50-375 Wroclaw, Poland; [email protected] (B.Z.);˙ [email protected] (Z.L.) 2 SPO, INRAE, Montpellier SupAgro, Université de Montpellier, 34060 Montpellier, France; [email protected] 3 Department of Microbiology, Laboratory of Microbiome Immunobiology, Ludwik Hirszfeld Institute of Immunology and Experimental Therapy, Polish Academy of Sciences, 53-114 Wroclaw, Poland; [email protected] 4 INRAE, AgroParisTech, Micalis Institute, CIRM-Levures, Université Paris-Saclay, 78350 Jouy-en-Josas, France; [email protected] * Correspondence: [email protected]; Tel.: +48-71-3207-791 Abstract: Yeasts can have additional genetic information in the form of cytoplasmic linear dsDNA molecules called virus-like elements (VLEs). Some of them encode killer toxins. The aim of this work was to investigate the prevalence of such elements in D. hansenii killer yeast deposited in culture collections as well as in strains freshly isolated from blue cheeses. Possible benefits to the host from harboring such VLEs were analyzed. VLEs occurred frequently among fresh D. hansenii isolates (15/60 strains), as opposed to strains obtained from culture collections (0/75 strains). Eight new different systems were identified: four composed of two elements and four of three elements. Full sequences of three new VLE systems obtained by NGS revealed extremely high conservation Citation: Połomska, X.; Neuvéglise, among the largest molecules in these systems except for one ORF, probably encoding a protein C.; Zyzak, J.; Zarowska,˙ B.; resembling immunity determinant to killer toxins of VLE origin in other yeast species.