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Harrouard J, Eberlein C, Ballestra P, Dols-Lafargue M, Masneuf-Pomarede I, Miot-Sertier C, Schacherer J, Albertin W. Brettanomyces bruxellensis: Overview of the genetic and phenotypic diversity of an anthropized yeast. Mol Ecol 2022; 32:2374-2395. [PMID: 35318747 DOI: 10.1111/mec.16439] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2021] [Revised: 03/08/2022] [Accepted: 03/16/2022] [Indexed: 12/24/2022]
Abstract
Human-associated microorganisms are ideal models to study the impact of environmental changes on species evolution and adaptation because of their small genome, short generation time, and their colonization of contrasting and ever-changing ecological niches. The yeast Brettanomyces bruxellensis is a good example of organism facing anthropogenic-driven selective pressures. It is associated with fermentation processes in which it can be considered either as a spoiler (e.g. winemaking, bioethanol production) or as a beneficial microorganism (e.g. production of specific beers, kombucha). Besides its industrial interests, noteworthy parallels and dichotomies with Saccharomyces cerevisiae propelled B. bruxellensis as a valuable complementary yeast model. In this review, we emphasize that the broad genetic and phenotypic diversity of this species is only beginning to be uncovered. Population genomic studies have revealed the co-existence of auto- and allotriploidization events with different evolutionary outcomes. The different diploid, autotriploid and allotriploid subpopulations are associated with specific fermented processes, suggesting independent adaptation events to anthropized environments. Phenotypically, B. bruxellensis is renowned for its ability to metabolize a wide variety of carbon and nitrogen sources, which may explain its ability to colonize already fermented environments showing low-nutrient contents. Several traits of interest could be related to adaptation to human activities (e.g. nitrate metabolization in bioethanol production, resistance to sulphite treatments in winemaking). However, phenotypic traits are insufficiently studied in view of the great genomic diversity of the species. Future work will have to take into account strains of varied substrates, geographical origins as well as displaying different ploidy levels to improve our understanding of an anthropized yeast's phenotypic landscape.
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Affiliation(s)
- Jules Harrouard
- UMR 1366 OENOLOGIE, Univ. Bordeaux, INRAE, Bordeaux INP, Bordeaux Sciences Agro, Institut des Sciences de la Vigne et du Vin, 33140, Villenave d'Ornon, France
| | - Chris Eberlein
- Université de Strasbourg, CNRS, GMGM, UMR 7156, Strasbourg, France
| | - Patricia Ballestra
- UMR 1366 OENOLOGIE, Univ. Bordeaux, INRAE, Bordeaux INP, Bordeaux Sciences Agro, Institut des Sciences de la Vigne et du Vin, 33140, Villenave d'Ornon, France
| | - Marguerite Dols-Lafargue
- UMR 1366 OENOLOGIE, Univ. Bordeaux, INRAE, Bordeaux INP, Bordeaux Sciences Agro, Institut des Sciences de la Vigne et du Vin, 33140, Villenave d'Ornon, France.,ENSCBP, Bordeaux INP, 33600, Pessac, France
| | - Isabelle Masneuf-Pomarede
- UMR 1366 OENOLOGIE, Univ. Bordeaux, INRAE, Bordeaux INP, Bordeaux Sciences Agro, Institut des Sciences de la Vigne et du Vin, 33140, Villenave d'Ornon, France.,BSA, 33170, Gradignan
| | - Cécile Miot-Sertier
- UMR 1366 OENOLOGIE, Univ. Bordeaux, INRAE, Bordeaux INP, Bordeaux Sciences Agro, Institut des Sciences de la Vigne et du Vin, 33140, Villenave d'Ornon, France
| | - Joseph Schacherer
- Université de Strasbourg, CNRS, GMGM, UMR 7156, Strasbourg, France.,Institut Universitaire de France (IUF), Paris, France
| | - Warren Albertin
- UMR 1366 OENOLOGIE, Univ. Bordeaux, INRAE, Bordeaux INP, Bordeaux Sciences Agro, Institut des Sciences de la Vigne et du Vin, 33140, Villenave d'Ornon, France.,ENSCBP, Bordeaux INP, 33600, Pessac, France
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Near Chromosome-Level Genome Assembly and Annotation of Rhodotorula babjevae Strains Reveals High Intraspecific Divergence. J Fungi (Basel) 2022; 8:jof8040323. [PMID: 35448555 PMCID: PMC9027234 DOI: 10.3390/jof8040323] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2021] [Revised: 03/16/2022] [Accepted: 03/19/2022] [Indexed: 02/04/2023] Open
Abstract
The genus Rhodotorula includes basidiomycetous oleaginous yeast species. Rhodotorula babjevae can produce compounds of biotechnological interest such as lipids, carotenoids, and biosurfactants from low value substrates such as lignocellulose hydrolysate. High-quality genome assemblies are needed to develop genetic tools and to understand fungal evolution and genetics. Here, we combined short- and long-read sequencing to resolve the genomes of two R. babjevae strains, CBS 7808 (type strain) and DBVPG 8058, at chromosomal level. Both genomes are 21 Mbp in size and have a GC content of 68.2%. Allele frequency analysis indicates that both strains are tetraploid. The genomes consist of a maximum of 21 chromosomes with a size of 0.4 to 2.4 Mbp. In both assemblies, the mitochondrial genome was recovered in a single contig, that shared 97% pairwise identity. Pairwise identity between most chromosomes ranges from 82 to 87%. We also found indications for strain-specific extrachromosomal endogenous DNA. A total of 7591 and 7481 protein-coding genes were annotated in CBS 7808 and DBVPG 8058, respectively. CBS 7808 accumulated a higher number of tandem duplications than DBVPG 8058. We identified large translocation events between putative chromosomes. Genome divergence values between the two strains indicate that they may belong to different species.
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Martín-Hernández GC, Müller B, Chmielarz M, Brandt C, Hölzer M, Viehweger A, Passoth V. Chromosome-level genome assembly and transcriptome-based annotation of the oleaginous yeast Rhodotorula toruloides CBS 14. Genomics 2021; 113:4022-4027. [PMID: 34648882 DOI: 10.1016/j.ygeno.2021.10.006] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2021] [Revised: 08/26/2021] [Accepted: 10/07/2021] [Indexed: 11/30/2022]
Abstract
Rhodotorula toruloides is an oleaginous yeast with high biotechnological potential. In order to understand the molecular physiology of lipid synthesis in R. toruloides and to advance metabolic engineering, a high-resolution genome is required. We constructed a genome draft of R. toruloides CBS 14, using a hybrid assembly approach, consisting of short and long reads generated by Illumina and Nanopore sequencing, respectively. The genome draft consists of 23 contigs and 3 scaffolds, with a N50 length of 1,529,952 bp, thus largely representing chromosomal organization. The total size of the genome is 20,534,857 bp and the overall GC content is 61.83%. Transcriptomic data from different growth conditions was used to aid species-specific gene annotation. We annotated 9464 genes and identified 11,691 transcripts. Furthermore, we demonstrated the presence of a potential plasmid, an extrachromosomal circular structure of about 11 kb with a copy number about three times as high as the other chromosomes.
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Affiliation(s)
| | - Bettina Müller
- Department of Molecular Sciences, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Mikołaj Chmielarz
- Department of Molecular Sciences, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Christian Brandt
- nanozoo GmbH, Leipzig, Germany; Institute for Infectious Diseases and Infection Control, Jena University Hospital, Jena, Germany
| | - Martin Hölzer
- nanozoo GmbH, Leipzig, Germany; RNA Bioinformatics and High-Throughput Analysis, Friedrich Schiller University Jena, Jena, Germany
| | - Adrian Viehweger
- nanozoo GmbH, Leipzig, Germany; Department of Medical Microbiology, University Hospital Leipzig, Germany
| | - Volkmar Passoth
- Department of Molecular Sciences, Swedish University of Agricultural Sciences, Uppsala, Sweden.
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Gounot JS, Neuvéglise C, Freel KC, Devillers H, Piškur J, Friedrich A, Schacherer J. High Complexity and Degree of Genetic Variation in Brettanomyces bruxellensis Population. Genome Biol Evol 2021; 12:795-807. [PMID: 32302403 PMCID: PMC7313668 DOI: 10.1093/gbe/evaa077] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/13/2020] [Indexed: 12/13/2022] Open
Abstract
Genome-wide characterization of genetic variants of a large population of individuals within the same species is essential to have a deeper insight into its evolutionary history as well as the genotype–phenotype relationship. Population genomic surveys have been performed in multiple yeast species, including the two model organisms, Saccharomyces cerevisiae and Schizosaccharomyces pombe. In this context, we sought to characterize at the population level the Brettanomyces bruxellensis yeast species, which is a major cause of wine spoilage and can contribute to the specific flavor profile of some Belgium beers. We have completely sequenced the genome of 53 B. bruxellensis strains isolated worldwide. The annotation of the reference genome allowed us to define the gene content of this species. As previously suggested, our genomic data clearly highlighted that genetic diversity variation is related to ploidy level, which is variable in the B. bruxellensis species. Genomes are punctuated by multiple loss-of-heterozygosity regions, whereas aneuploidies as well as segmental duplications are uncommon. Interestingly, triploid genomes are more prone to gene copy number variation than diploids. Finally, the pangenome of the species was reconstructed and was found to be small with few accessory genes compared with S. cerevisiae. The pangenome is composed of 5,409 ORFs (open reading frames) among which 5,106 core ORFs and 303 ORFs that are variable within the population. All these results highlight the different trajectories of species evolution and consequently the interest of establishing population genomic surveys in more populations.
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Affiliation(s)
| | - Cécile Neuvéglise
- Micalis Institute, INRA, AgroParisTech, Université Paris-Saclay, Jouy-en-Josas, France
| | - Kelle C Freel
- Université de Strasbourg, CNRS, GMGM UMR 7156, Strasbourg, France
| | - Hugo Devillers
- Micalis Institute, INRA, AgroParisTech, Université Paris-Saclay, Jouy-en-Josas, France
| | - Jure Piškur
- Department of Biology, Lund University, Sweden
| | - Anne Friedrich
- Université de Strasbourg, CNRS, GMGM UMR 7156, Strasbourg, France
| | - Joseph Schacherer
- Université de Strasbourg, CNRS, GMGM UMR 7156, Strasbourg, France.,Institut Universitaire de France (IUF)
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Tiukova IA, Møller-Hansen I, Belew ZM, Darbani B, Boles E, Nour-Eldin HH, Linder T, Nielsen J, Borodina I. Identification and characterisation of two high-affinity glucose transporters from the spoilage yeast Brettanomyces bruxellensis. FEMS Microbiol Lett 2020; 366:5610216. [PMID: 31665273 PMCID: PMC6847091 DOI: 10.1093/femsle/fnz222] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2019] [Accepted: 10/25/2019] [Indexed: 12/17/2022] Open
Abstract
The yeast Brettanomyces bruxellensis (syn. Dekkera bruxellensis) is an emerging and undesirable contaminant in industrial low-sugar ethanol fermentations that employ the yeast Saccharomyces cerevisiae. High-affinity glucose import in B. bruxellensis has been proposed to be the mechanism by which this yeast can outcompete S. cerevisiae. The present study describes the characterization of two B. bruxellensis genes (BHT1 and BHT3) believed to encode putative high-affinity glucose transporters. In vitro-generated transcripts of both genes as well as the S. cerevisiae HXT7 high-affinity glucose transporter were injected into Xenopus laevis oocytes and subsequent glucose uptake rates were assayed using 14C-labelled glucose. At 0.1 mM glucose, Bht1p was shown to transport glucose five times faster than Hxt7p. pH affected the rate of glucose transport by Bht1p and Bht3p, indicating an active glucose transport mechanism that involves proton symport. These results suggest a possible role for BHT1 and BHT3 in the competitive ability of B. bruxellensis.
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Affiliation(s)
- Ievgeniia A Tiukova
- Division of Systems and Synthetic Biology, Department of Biology and Biological Engineering, Chalmers University of Technology, Kemigården 4, 412 96 Gothenburg, Sweden
| | - Iben Møller-Hansen
- The Novo Nordisk Foundation for Biosustainability, Technical University of Denmark, Building 220, 2800 Kongens Lyngby, Denmark
| | - Zeinu M Belew
- Department of Plant and Environmental Sciences, DynaMo Center, Copenhagen Plant Science Center, University of Copenhagen, Thorvaldsensvej 40, 1871 Frederiksberg, Denmark
| | - Behrooz Darbani
- The Novo Nordisk Foundation for Biosustainability, Technical University of Denmark, Building 220, 2800 Kongens Lyngby, Denmark
| | - Eckhard Boles
- Institute of Molecular Biosciences, Faculty of Biological Sciences, Goethe University Frankfurt, Max-von-Laue Straße 9, 60438, Frankfurt am Main, Germany
| | - Hussam H Nour-Eldin
- Department of Plant and Environmental Sciences, DynaMo Center, Copenhagen Plant Science Center, University of Copenhagen, Thorvaldsensvej 40, 1871 Frederiksberg, Denmark
| | - Tomas Linder
- Department of Molecular Sciences, Swedish University of Agricultural Sciences, Almas allé 5, 750 07 Uppsala, Sweden
| | - Jens Nielsen
- Division of Systems and Synthetic Biology, Department of Biology and Biological Engineering, Chalmers University of Technology, Kemigården 4, 412 96 Gothenburg, Sweden
| | - Irina Borodina
- The Novo Nordisk Foundation for Biosustainability, Technical University of Denmark, Building 220, 2800 Kongens Lyngby, Denmark
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Tiukova IA, Jiang H, Dainat J, Hoeppner MP, Lantz H, Piskur J, Sandgren M, Nielsen J, Gu Z, Passoth V. Assembly and Analysis of the Genome Sequence of the Yeast Brettanomyces naardenensis CBS 7540. Microorganisms 2019; 7:microorganisms7110489. [PMID: 31717754 PMCID: PMC6921048 DOI: 10.3390/microorganisms7110489] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2019] [Revised: 10/19/2019] [Accepted: 10/23/2019] [Indexed: 01/21/2023] Open
Abstract
Brettanomyces naardenensis is a spoilage yeast with potential for biotechnological applications for production of innovative beverages with low alcohol content and high attenuation degree. Here, we present the first annotated genome of B. naardenensis CBS 7540. The genome of B. naardenensis CBS 7540 was assembled into 76 contigs, totaling 11,283,072 nucleotides. In total, 5168 protein-coding sequences were annotated. The study provides functional genome annotation, phylogenetic analysis, and discusses genetic determinants behind notable stress tolerance and biotechnological potential of B. naardenensis.
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Affiliation(s)
- Ievgeniia A. Tiukova
- Department of Biology and Biological Engineering, Systems and Synthetic Biology, Chalmers University of Technology, SE-412 96 Göteborg, Sweden;
- Department of Molecular Sciences, Swedish University of Agricultural Sciences, Box 7015, SE-75007 Uppsala, Sweden; (M.S.); (V.P.)
- Correspondence: ; Tel.: +46-31-772-3801
| | - Huifeng Jiang
- Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China;
| | - Jacques Dainat
- Department of Medical Biochemistry and Microbiology, Uppsala University, Box 582, 752 37 Uppsala, Sweden; (J.D.); (M.P.H.); (H.L.)
- National Bioinformatics Infrastructure Sweden (NBIS), 752 37 Uppsala, Sweden
| | - Marc P. Hoeppner
- Department of Medical Biochemistry and Microbiology, Uppsala University, Box 582, 752 37 Uppsala, Sweden; (J.D.); (M.P.H.); (H.L.)
- National Bioinformatics Infrastructure Sweden (NBIS), 752 37 Uppsala, Sweden
- Institute of Clinical Molecular Biology, Christian-Albrechts-University of Kiel, 24118 Kiel, Germany
| | - Henrik Lantz
- Department of Medical Biochemistry and Microbiology, Uppsala University, Box 582, 752 37 Uppsala, Sweden; (J.D.); (M.P.H.); (H.L.)
- National Bioinformatics Infrastructure Sweden (NBIS), 752 37 Uppsala, Sweden
| | - Jure Piskur
- Department of Biology, Lund University, 223 62 Lund, Sweden;
| | - Mats Sandgren
- Department of Molecular Sciences, Swedish University of Agricultural Sciences, Box 7015, SE-75007 Uppsala, Sweden; (M.S.); (V.P.)
| | - Jens Nielsen
- Department of Biology and Biological Engineering, Systems and Synthetic Biology, Chalmers University of Technology, SE-412 96 Göteborg, Sweden;
| | - Zhenglong Gu
- Division of Nutritional Sciences, Cornell University, Ithaca, NY 14853, USA;
| | - Volkmar Passoth
- Department of Molecular Sciences, Swedish University of Agricultural Sciences, Box 7015, SE-75007 Uppsala, Sweden; (M.S.); (V.P.)
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The biotechnological potential of the yeast Dekkera bruxellensis. World J Microbiol Biotechnol 2019; 35:103. [PMID: 31236799 DOI: 10.1007/s11274-019-2678-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2019] [Accepted: 06/15/2019] [Indexed: 10/26/2022]
Abstract
Dekkera bruxellensis is an industrial yeast mainly regarded as a contaminant species in fermentation processes. In winemaking, it is associated with off-flavours that cause wine spoilage, while in bioethanol production this yeast is linked to a reduction of industrial productivity by competing with Saccharomyces cerevisiae for the substrate. In spite of that, this point of view is gradually changing, mostly because D. bruxellensis is also able to produce important metabolites, such as ethanol, acetate, fusel alcohols, esters and others. This dual role is likely due to the fact that this yeast presents a set of metabolic traits that might be either industrially attractive or detrimental, depending on how they are faced and explored. Therefore, a proper industrial application for D. bruxellensis depends on the correct assembly of its central metabolic puzzle. In this sense, researchers have addressed issues regarding the physiological and genetic aspects of D. bruxellensis, which have brought to light much of our current knowledge on this yeast. In this review, we shall outline what is presently understood about the main metabolic features of D. bruxellensis and how they might be managed to improve its current or future industrial applications (except for winemaking, in which it is solely regarded as a contaminant). Moreover, we will discuss the advantages and challenges that must be overcome in order to take advantage of the full biotechnological potential of this yeast.
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