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Gonzalez-Flores M, Delfino AV, Rodríguez ME, Lopes CA. Presence of Saccharomyces eubayanus in fermentative environments reveals a new adaptive scenario in Patagonia. Yeast 2023; 40:476-492. [PMID: 37594238 DOI: 10.1002/yea.3894] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2023] [Revised: 07/20/2023] [Accepted: 07/30/2023] [Indexed: 08/19/2023] Open
Abstract
Patagonia (Argentina and Chile) harbors the highest Saccharomyces eubayanus genomic diversity and its widest predominance in natural environments. In this work, S. eubayanus was isolated for the first time from a fermentative environment. This species was found dominating both a traditional apple chicha fermentation as well as feral apple trees in the Andean region of Aluminé (Argentina). S. eubayanus was the only Saccharomyces species found in the isolation substrates, although it coexisted with other non-Saccharomyces species. The absence of strong fermentative competitors of the Saccharomyces genus (like Saccharomyces uvarum or Saccharomyces cerevisiae) in the feral apples could promote the development and implantation of S. eubayanus in a spontaneous apple must fermentation. Phylogeographic analyses revealed a high intraspecific diversity in S. eubayanus, enabling the characterization of strains belonging to the genomic subpopulations PA1, PA2, and PB1 according to the sequences obtained for the intFR gene region. This result evidence that the studied sampling area represents a natural habitat for the species. Being a novel finding, studying the causes that allowed this species to prosper in a fermentative environment becomes essential. Hence, the physiological profile of the new isolates, including their ability to grow at different temperature, nitrogen, and ethanol concentrations was evaluated in comparison with a set of S. eubayanus strains previously isolated from natural environment and representing different genomic subpopulations. Greater physiological diversity was evidenced when strains isolated from both natural and fermentative environments were analyzed overall. Furthermore, no direct relationship between genomic population and physiological behavior was observed; on the opposite, strains appeared to exhibit similar behavior, primarily grouped by isolation origin.
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Affiliation(s)
- Melisa Gonzalez-Flores
- Instituto de Investigación y Desarrollo en Ingeniería de Procesos, Biotecnología y Energías Alternativas (PROBIEN, Consejo Nacional de Investigaciones Científicas y Técnicas de la República Argentina, Universidad Nacional del Comahue), Buenos Aires, Neuquén, Argentina
- Facultad de Ciencias Agrarias, Universidad Nacional del Comahue, Buenos Aires, Argentina
| | - Ana V Delfino
- Instituto de Investigación y Desarrollo en Ingeniería de Procesos, Biotecnología y Energías Alternativas (PROBIEN, Consejo Nacional de Investigaciones Científicas y Técnicas de la República Argentina, Universidad Nacional del Comahue), Buenos Aires, Neuquén, Argentina
- Facultad de Ciencias Médicas, Universidad Nacional del Comahue, Buenos Aires, Argentina
| | - María E Rodríguez
- Instituto de Investigación y Desarrollo en Ingeniería de Procesos, Biotecnología y Energías Alternativas (PROBIEN, Consejo Nacional de Investigaciones Científicas y Técnicas de la República Argentina, Universidad Nacional del Comahue), Buenos Aires, Neuquén, Argentina
- Facultad de Ciencias Médicas, Universidad Nacional del Comahue, Buenos Aires, Argentina
| | - Christian A Lopes
- Instituto de Investigación y Desarrollo en Ingeniería de Procesos, Biotecnología y Energías Alternativas (PROBIEN, Consejo Nacional de Investigaciones Científicas y Técnicas de la República Argentina, Universidad Nacional del Comahue), Buenos Aires, Neuquén, Argentina
- Facultad de Ciencias Agrarias, Universidad Nacional del Comahue, Buenos Aires, Argentina
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Peris D, Ubbelohde EJ, Kuang MC, Kominek J, Langdon QK, Adams M, Koshalek JA, Hulfachor AB, Opulente DA, Hall DJ, Hyma K, Fay JC, Leducq JB, Charron G, Landry CR, Libkind D, Gonçalves C, Gonçalves P, Sampaio JP, Wang QM, Bai FY, Wrobel RL, Hittinger CT. Macroevolutionary diversity of traits and genomes in the model yeast genus Saccharomyces. Nat Commun 2023; 14:690. [PMID: 36755033 PMCID: PMC9908912 DOI: 10.1038/s41467-023-36139-2] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2022] [Accepted: 01/17/2023] [Indexed: 02/10/2023] Open
Abstract
Species is the fundamental unit to quantify biodiversity. In recent years, the model yeast Saccharomyces cerevisiae has seen an increased number of studies related to its geographical distribution, population structure, and phenotypic diversity. However, seven additional species from the same genus have been less thoroughly studied, which has limited our understanding of the macroevolutionary events leading to the diversification of this genus over the last 20 million years. Here, we show the geographies, hosts, substrates, and phylogenetic relationships for approximately 1,800 Saccharomyces strains, covering the complete genus with unprecedented breadth and depth. We generated and analyzed complete genome sequences of 163 strains and phenotyped 128 phylogenetically diverse strains. This dataset provides insights about genetic and phenotypic diversity within and between species and populations, quantifies reticulation and incomplete lineage sorting, and demonstrates how gene flow and selection have affected traits, such as galactose metabolism. These findings elevate the genus Saccharomyces as a model to understand biodiversity and evolution in microbial eukaryotes.
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Grants
- R01 GM080669 NIGMS NIH HHS
- T32 GM007133 NIGMS NIH HHS
- We thank the University of Wisconsin Biotechnology Center DNA Sequencing Facility for providing Illumina and Sanger sequencing facilities and services; Maria Sardi, Audrey Gasch, and Ursula Bond for providing strains; Sean McIlwain for providing guidance for genome ultra-scaffolding; Yury V. Bukhman for discussing applications of the Growth Curve Analysis Tool (GCAT); Mick McGee for HPLC analysis; Raúl Ortíz-Merino for assistance during YGAP annotations; Jessica Leigh for assistance with PopART; Cecile Ané for suggestions about BUCKy utilization and phylogenetic network analyses; Samina Naseeb and Daniela Delneri for sharing preliminary multi-locus Saccharomyces jurei data; and Branden Timm, Brian Kyle, and Dan Metzger for computational assistance. Some computations were performed on Tirant III of the Spanish Supercomputing Network (‘‘Servei d’Informàtica de la Universitat de València”) under the project BCV-2021-1-0001 granted to DP, while others were performed at the Wisconsin Energy Institute and the Center for High-Throughput Computing of the University of Wisconsin-Madison. During a portion of this project, DP was a researcher funded by the European Union’s Horizon 2020 research and innovation programme Marie Sklodowska-Curie, grant agreement No. 747775, the Research Council of Norway (RCN) grant Nos. RCN 324253 and 274337, and the Generalitat Valenciana plan GenT grant No. CIDEGENT/2021/039. DP is a recipient of an Illumina Grant for Illumina Sequencing Saccharomyces strains in this study. QKL was supported by the National Science Foundation under Grant No. DGE-1256259 (Graduate Research Fellowship) and the Predoctoral Training Program in Genetics, funded by the National Institutes of Health (5T32GM007133). This material is based upon work supported in part by the Great Lakes Bioenergy Research Center, Office of Science, Office of Biological and Environmental Research under Award Numbers DE-SC0018409 and DE-FC02-07ER64494; the National Science Foundation under Grant Nos. DEB-1253634, DEB-1442148, and DEB-2110403; and the USDA National Institute of Food and Agriculture Hatch Project Number 1020204. C.T.H. is an H. I. Romnes Faculty Fellow, supported by the Office of the Vice Chancellor for Research and Graduate Education with funding from Wisconsin Alumni Research Foundation. QMW was supported by the National Natural Science Foundation of China (NSFC) under Grant Nos. 31770018 and 31961133020. CRL holds the Canada Research Chair in Cellular Systems and Synthetic Biology, and his research on wild yeast is supported by a NSERC Discovery Grant.
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Affiliation(s)
- David Peris
- Laboratory of Genetics, J. F. Crow Institute for the Study of Evolution, Wisconsin Energy Institute, Genome Center of Wisconsin, University of Wisconsin-Madison, Madison, WI, USA.
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI, USA.
- Section for Genetics and Evolutionary Biology, Department of Biosciences, University of Oslo, Oslo, Norway.
- Department of Food Biotechnology, Institute of Agrochemistry and Food Technology (IATA), CSIC, Valencia, Spain.
| | - Emily J Ubbelohde
- Laboratory of Genetics, J. F. Crow Institute for the Study of Evolution, Wisconsin Energy Institute, Genome Center of Wisconsin, University of Wisconsin-Madison, Madison, WI, USA
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI, USA
| | - Meihua Christina Kuang
- Laboratory of Genetics, J. F. Crow Institute for the Study of Evolution, Wisconsin Energy Institute, Genome Center of Wisconsin, University of Wisconsin-Madison, Madison, WI, USA
| | - Jacek Kominek
- Laboratory of Genetics, J. F. Crow Institute for the Study of Evolution, Wisconsin Energy Institute, Genome Center of Wisconsin, University of Wisconsin-Madison, Madison, WI, USA
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI, USA
| | - Quinn K Langdon
- Laboratory of Genetics, J. F. Crow Institute for the Study of Evolution, Wisconsin Energy Institute, Genome Center of Wisconsin, University of Wisconsin-Madison, Madison, WI, USA
| | - Marie Adams
- Biotechnology Center, University of Wisconsin-Madison, Madison, WI, USA
| | - Justin A Koshalek
- Biotechnology Center, University of Wisconsin-Madison, Madison, WI, USA
| | - Amanda Beth Hulfachor
- Laboratory of Genetics, J. F. Crow Institute for the Study of Evolution, Wisconsin Energy Institute, Genome Center of Wisconsin, University of Wisconsin-Madison, Madison, WI, USA
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI, USA
| | - Dana A Opulente
- Laboratory of Genetics, J. F. Crow Institute for the Study of Evolution, Wisconsin Energy Institute, Genome Center of Wisconsin, University of Wisconsin-Madison, Madison, WI, USA
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI, USA
| | | | - Katie Hyma
- Department of Biology, University of Rochester, Rochester, NY, USA
| | - Justin C Fay
- Department of Biology, University of Rochester, Rochester, NY, USA
| | - Jean-Baptiste Leducq
- Departement des Sciences Biologiques, Université de Montréal, Montreal, QC, Canada
- Département de Biologie, PROTEO, Pavillon Charles‑Eugène‑Marchand, Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Quebec City, QC, Canada
| | - Guillaume Charron
- Canada Natural Resources, Laurentian Forestry Centre, Quebec City, QC, Canada
| | - Christian R Landry
- Département de Biologie, PROTEO, Pavillon Charles‑Eugène‑Marchand, Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Quebec City, QC, Canada
| | - Diego Libkind
- Centro de Referencia en Levaduras y Tecnología Cervecera (CRELTEC), Instituto Andino Patagónico de Tecnologías Biológicas y Geoambientales (IPATEC), Consejo Nacional de Investigaciones, Científicas y Técnicas (CONICET)-Universidad Nacional del Comahue, Bariloche, Argentina
| | - Carla Gonçalves
- Laboratory of Genetics, J. F. Crow Institute for the Study of Evolution, Wisconsin Energy Institute, Genome Center of Wisconsin, University of Wisconsin-Madison, Madison, WI, USA
- Associate Laboratory i4HB - Institute for Health and Bioeconomy, NOVA School of Science and Technology, Universidade NOVA de Lisboa, Caparica, Portugal
- UCIBIO-i4HB, Departamento de Ciências da Vida, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, Caparica, Portugal
- Vanderbilt University, Department of Biological Sciences, Nashville, TN, USA
- Evolutionary Studies Initiative, Vanderbilt University, Nashville, TN, USA
| | - Paula Gonçalves
- UCIBIO-i4HB, Departamento de Ciências da Vida, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, Caparica, Portugal
| | - José Paulo Sampaio
- UCIBIO-i4HB, Departamento de Ciências da Vida, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, Caparica, Portugal
| | - Qi-Ming Wang
- Laboratory of Genetics, J. F. Crow Institute for the Study of Evolution, Wisconsin Energy Institute, Genome Center of Wisconsin, University of Wisconsin-Madison, Madison, WI, USA
- School of Life Sciences, Institute of Life Sciences and Green Development, Hebei University, Baoding, China
| | - Feng-Yan Bai
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Russel L Wrobel
- Laboratory of Genetics, J. F. Crow Institute for the Study of Evolution, Wisconsin Energy Institute, Genome Center of Wisconsin, University of Wisconsin-Madison, Madison, WI, USA
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI, USA
| | - Chris Todd Hittinger
- Laboratory of Genetics, J. F. Crow Institute for the Study of Evolution, Wisconsin Energy Institute, Genome Center of Wisconsin, University of Wisconsin-Madison, Madison, WI, USA.
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI, USA.
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Macías LG, Flores MG, Adam AC, Rodríguez ME, Querol A, Barrio E, Lopes CA, Pérez-Torrado R. Convergent adaptation of Saccharomyces uvarum to sulfite, an antimicrobial preservative widely used in human-driven fermentations. PLoS Genet 2021; 17:e1009872. [PMID: 34762651 PMCID: PMC8631656 DOI: 10.1371/journal.pgen.1009872] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2021] [Revised: 11/30/2021] [Accepted: 10/11/2021] [Indexed: 01/01/2023] Open
Abstract
Different species can find convergent solutions to adapt their genome to the same evolutionary constraints, although functional convergence promoted by chromosomal rearrangements in different species has not previously been found. In this work, we discovered that two domesticated yeast species, Saccharomyces cerevisiae, and Saccharomyces uvarum, acquired chromosomal rearrangements to convergently adapt to the presence of sulfite in fermentation environments. We found two new heterologous chromosomal translocations in fermentative strains of S. uvarum at the SSU1 locus, involved in sulfite resistance, an antimicrobial additive widely used in food production. These are convergent events that share similarities with other SSU1 locus chromosomal translocations previously described in domesticated S. cerevisiae strains. In S. uvarum, the newly described VIIXVI and XIXVI chromosomal translocations generate an overexpression of the SSU1 gene and confer increased sulfite resistance. This study highlights the relevance of chromosomal rearrangements to promote the adaptation of yeast to anthropic environments. It is known that genetically distant species can arrive to similar evolutionary solutions during the adaptation to a specific environment, a phenomena known as convergent adaptation, and this frequently occurs after point mutations, gene duplications, or species hybridizations. In this work, we discovered a new example of convergent evolution in the adaptation of two wine fermentation yeast species to the presence of sulfite, an antimicrobial additive widely used in food production. We observed that two species, Saccharomyces cerevisiae and Saccharomyces uvarum, acquired chromosomal rearrangements to convergently adapt to the presence of sulfite in fermentative environments. We describe new chromosomal translocations in S. uvarum strains that generate an overexpression of the SSU1 gene and confer increased sulfite resistance, a similar event that was already described in S. cerevisiae. Overall, this study describes a new case of convergent evolution in which the chromosomal rearrangements have a significant role in the adaptation of yeast to an environment created by humans to produce food.
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Affiliation(s)
- Laura G. Macías
- Instituto de Agroquímica y Tecnología de los Alimentos, IATA-CSIC, Paterna, Spain
- Departament de Genètica, Universitat de València, Valencia, Spain
| | - Melisa González Flores
- Instituto de Investigación y Desarrollo en Ingeniería de Procesos, Biotecnología y Energías Alternativas (PROBIEN, Consejo Nacional de Investigaciones Científicas y Técnicas de la República Argentina–Universidad Nacional del Comahue), Neuquén, Argentina
- Facultad de Ciencias Agrarias, Universidad Nacional del Comahue, Cinco Saltos, Río Negro, Argentina
| | - Ana Cristina Adam
- Instituto de Agroquímica y Tecnología de los Alimentos, IATA-CSIC, Paterna, Spain
| | - María E. Rodríguez
- Instituto de Investigación y Desarrollo en Ingeniería de Procesos, Biotecnología y Energías Alternativas (PROBIEN, Consejo Nacional de Investigaciones Científicas y Técnicas de la República Argentina–Universidad Nacional del Comahue), Neuquén, Argentina
- Facultad de Ciencias Médicas, Universidad Nacional del Comahue, Cipolletti, Río Negro, Argentina
| | - Amparo Querol
- Instituto de Agroquímica y Tecnología de los Alimentos, IATA-CSIC, Paterna, Spain
| | - Eladio Barrio
- Instituto de Agroquímica y Tecnología de los Alimentos, IATA-CSIC, Paterna, Spain
- Departament de Genètica, Universitat de València, Valencia, Spain
| | - Christian Ariel Lopes
- Instituto de Investigación y Desarrollo en Ingeniería de Procesos, Biotecnología y Energías Alternativas (PROBIEN, Consejo Nacional de Investigaciones Científicas y Técnicas de la República Argentina–Universidad Nacional del Comahue), Neuquén, Argentina
- Facultad de Ciencias Agrarias, Universidad Nacional del Comahue, Cinco Saltos, Río Negro, Argentina
| | - Roberto Pérez-Torrado
- Instituto de Agroquímica y Tecnología de los Alimentos, IATA-CSIC, Paterna, Spain
- * E-mail:
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