1
|
Tinsley CR, Jacques N, Lucas M, Grondin C, Legras JL, Casaregola S. Molecular Genetic Analysis with Microsatellite-like Loci Reveals Specific Dairy-Associated and Environmental Populations of the Yeast Geotrichum candidum. Microorganisms 2022; 10:103. [PMID: 35056553 PMCID: PMC8780849 DOI: 10.3390/microorganisms10010103] [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: 12/01/2021] [Revised: 12/23/2021] [Accepted: 12/27/2021] [Indexed: 02/01/2023] Open
Abstract
Geotrichum candidum is an environmental yeast, also found as part of the cheese surface microbiota, where it is important in the ripening of many traditional cheeses, such as Camembert. We have previously developed a Multi Locus Sequence Typing (MLST) scheme, which differentiated five clades, of which one contained only environmental isolates, two were composed almost entirely of dairy isolates, and two others contained a mixture of dairy, environmental, and miscellaneous food isolates. In order to provide a simple method to uniquely type G. candidum strains, and in addition to permit investigation of the population structure at a fine level, we describe here a molecular analysis using a set of twelve highly discriminating microsatellite-like markers. The present study consolidates the previously suggested division between dairy and environmental strains, and in addition distinguishes a specifically European group of environmental strains. This analysis permitted the discrimination of 72 genotypes from the collection of 80 isolates, while retaining the underlying meaningful phylogenetic relation between groups of strains.
Collapse
Affiliation(s)
- Colin R. Tinsley
- Micalis Institute, INRAE, AgroParisTech, Université Paris-Saclay, 78350 Jouy-en-Josas, France; (C.R.T.); (N.J.); (M.L.); (C.G.); (S.C.)
- Unité Microbiologie et Génétique Moléculaire, Department des Sciences de la Vie et Santé, AgroParisTech, 16 Rue Claude Bernard, 75005 Paris, France
| | - Noémie Jacques
- Micalis Institute, INRAE, AgroParisTech, Université Paris-Saclay, 78350 Jouy-en-Josas, France; (C.R.T.); (N.J.); (M.L.); (C.G.); (S.C.)
| | - Marine Lucas
- Micalis Institute, INRAE, AgroParisTech, Université Paris-Saclay, 78350 Jouy-en-Josas, France; (C.R.T.); (N.J.); (M.L.); (C.G.); (S.C.)
| | - Cécile Grondin
- Micalis Institute, INRAE, AgroParisTech, Université Paris-Saclay, 78350 Jouy-en-Josas, France; (C.R.T.); (N.J.); (M.L.); (C.G.); (S.C.)
- SPO, Université de Montpellier, INRAE, Institut Agro, 34000 Montpellier, France
| | - Jean-Luc Legras
- SPO, Université de Montpellier, INRAE, Institut Agro, 34000 Montpellier, France
| | - Serge Casaregola
- Micalis Institute, INRAE, AgroParisTech, Université Paris-Saclay, 78350 Jouy-en-Josas, France; (C.R.T.); (N.J.); (M.L.); (C.G.); (S.C.)
| |
Collapse
|
2
|
Genetic, Physiological, and Industrial Aspects of the Fructophilic Non-Saccharomyces Yeast Species, Starmerella bacillaris. FERMENTATION 2021. [DOI: 10.3390/fermentation7020087] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Starmerella bacillaris (synonym Candida zemplinina) is a non-Saccharomyces yeast species, frequently found in enological ecosystems. Peculiar aspects of the genetics and metabolism of this yeast species, as well as potential industrial applications of isolated indigenous S. bacillaris strains worldwide, have recently been explored. In this review, we summarize relevant observations from studies conducted on standard laboratory and indigenous isolated S. bacillaris strains.
Collapse
|
3
|
McCarthy GC, Morgan SC, Martiniuk JT, Newman BL, McCann SE, Measday V, Durall DM. An indigenous Saccharomyces uvarum population with high genetic diversity dominates uninoculated Chardonnay fermentations at a Canadian winery. PLoS One 2021; 16:e0225615. [PMID: 33539404 PMCID: PMC7861373 DOI: 10.1371/journal.pone.0225615] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2019] [Accepted: 12/29/2020] [Indexed: 01/04/2023] Open
Abstract
Saccharomyces cerevisiae is the primary yeast species responsible for most fermentations in winemaking. However, other yeasts, including Saccharomyces uvarum, have occasionally been found conducting commercial fermentations around the world. S. uvarum is typically associated with white wine fermentations in cool-climate wine regions, and has been identified as the dominant yeast in fermentations from France, Hungary, northern Italy, and, recently, Canada. However, little is known about how the origin and genetic diversity of the Canadian S. uvarum population relates to strains from other parts of the world. In this study, a highly diverse S. uvarum population was found dominating uninoculated commercial fermentations of Chardonnay grapes sourced from two different vineyards. Most of the strains identified were found to be genetically distinct from S. uvarum strains isolated globally. Of the 106 strains of S. uvarum identified in this study, four played a dominant role in the fermentations, with some strains predominating in the fermentations from one vineyard over the other. Furthermore, two of these dominant strains were previously identified as dominant strains in uninoculated Chardonnay fermentations at the same winery two years earlier, suggesting the presence of a winery-resident population of indigenous S. uvarum. This research provides valuable insight into the diversity and persistence of non-commercial S. uvarum strains in North America, and a stepping stone for future work into the enological potential of an alternative Saccharomyces yeast species.
Collapse
Affiliation(s)
- Garrett C. McCarthy
- Department of Biology, Irfigving K. Barber School of Arts and Sciences, The University of British Columbia, Kelowna, British Columbia, Canada
| | - Sydney C. Morgan
- Department of Biology, Irfigving K. Barber School of Arts and Sciences, The University of British Columbia, Kelowna, British Columbia, Canada
| | - Jonathan T. Martiniuk
- Wine Research Centre, Faculty of Land and Food Systems, The University of British Columbia, Vancouver, British Columbia, Canada
| | - Brianne L. Newman
- Department of Biology, Irfigving K. Barber School of Arts and Sciences, The University of British Columbia, Kelowna, British Columbia, Canada
| | - Stephanie E. McCann
- Department of Biology, Irfigving K. Barber School of Arts and Sciences, The University of British Columbia, Kelowna, British Columbia, Canada
| | - Vivien Measday
- Wine Research Centre, Faculty of Land and Food Systems, The University of British Columbia, Vancouver, British Columbia, Canada
| | - Daniel M. Durall
- Department of Biology, Irfigving K. Barber School of Arts and Sciences, The University of British Columbia, Kelowna, British Columbia, Canada
| |
Collapse
|
4
|
Cheng E, Martiniuk JT, Hamilton J, McCarthy G, Castellarin SD, Measday V. Characterization of Sub-Regional Variation in Saccharomyces Populations and Grape Phenolic Composition in Pinot Noir Vineyards of a Canadian Wine Region. Front Genet 2020; 11:908. [PMID: 33110416 PMCID: PMC7489054 DOI: 10.3389/fgene.2020.00908] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2020] [Accepted: 07/22/2020] [Indexed: 01/02/2023] Open
Abstract
Wine is a product of grape juice fermentation by yeast. Terroir is a term that encompasses all environmental factors and interactions at a specific geographical site, resulting in the development of regional-specific microbial strains and grape metabolites. In this study we determine the distribution of vineyard-associated wine yeast strains and characterize the flavonoid profile of Pinot Noir grapes among 3 sub-regions in the Okanagan Valley (OV), a major wine region in British Columbia, Canada. Pinot Noir grape samples were collected from 13 vineyards among 3 sub-regions of the OV, namely Kelowna (KE), Naramata-Penticton (NP) and Oliver-Osoyoos (OO), within a week prior to the winery harvesting date in 2016 and 2017. A total of 156 spontaneous Pinot Noir fermentations were conducted and vineyard-associated Saccharomyces strains were isolated from fermentations that reached two-thirds sugar depletion. Using microsatellite genotyping, we identified 103 Saccharomyces cerevisiae strains and 9 Saccharomyces uvarum strains. We also identified Saccharomyces paradoxus in one vineyard using ITS sequencing. We developed a microsatellite database of 160 commercial S. cerevisiae strains to determine the identity of the isolated strains and we include the database herein. Commercial strains were widely distributed across the three sub-regions. Forty-two of our 103 S. cerevisiae strains were equivalent or highly similar to commercial strains whereas the remaining 61 were considered as ‘unknown’ strains. Two S. uvarum strains were previously isolated in other OV studies and none matched the S. uvarum commercial strain BMV58. S. cerevisiae population structure was driven by sub-region, although S. cerevisiae populations did not differ significantly across vintages. S. uvarum and S. paradoxus were only identified in the 2017 vintage, demonstrating dynamic wine yeast populations between vintages. We found that the flavonoid profile of Pinot Noir grapes from the same 13 vineyards was also affected by sub-regional terroir. The anthocyanin content was lower and the proportion of methoxylated anthocyanins and flavonols was higher in Pinot Noir grapes from OO, the warmer sub-region as compared to KE, the cooler sub-region. Our study demonstrates that both yeast populations and metabolites associated with the Pinot Noir variety have sub-regional variation within a viticultural area.
Collapse
Affiliation(s)
- Elaine Cheng
- Wine Research Centre, Faculty of Land and Food Systems, The University of British Columbia, Vancouver, BC, Canada
| | - Jonathan T Martiniuk
- Wine Research Centre, Faculty of Land and Food Systems, The University of British Columbia, Vancouver, BC, Canada
| | - Jonah Hamilton
- Wine Research Centre, Faculty of Land and Food Systems, The University of British Columbia, Vancouver, BC, Canada
| | - Garrett McCarthy
- Wine Research Centre, Faculty of Land and Food Systems, The University of British Columbia, Vancouver, BC, Canada.,Department of Biology, The University of British Columbia, Kelowna, BC, Canada
| | - Simone Diego Castellarin
- Wine Research Centre, Faculty of Land and Food Systems, The University of British Columbia, Vancouver, BC, Canada
| | - Vivien Measday
- Wine Research Centre, Faculty of Land and Food Systems, The University of British Columbia, Vancouver, BC, Canada
| |
Collapse
|
5
|
Non-tandem repeat polymorphisms at microsatellite loci in wine yeast species. Mol Genet Genomics 2020; 295:685-693. [DOI: 10.1007/s00438-020-01652-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2019] [Accepted: 02/07/2020] [Indexed: 10/24/2022]
|
6
|
Li P, Li T, Zhang CY, Xiao DG. Effect of ILV2 deletion and ILV3 or/and ILV5 overexpression in Saccharomyces uvarum on diacetyl and higher alcohols metabolism during wine fermentation. Eur Food Res Technol 2020. [DOI: 10.1007/s00217-019-03422-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
|
7
|
Morgan SC, McCarthy GC, Watters BS, Tantikachornkiat M, Zigg I, Cliff MA, Durall DM. Effect of sulfite addition and pied de cuve inoculation on the microbial communities and sensory profiles of Chardonnay wines: dominance of indigenous Saccharomyces uvarum at a commercial winery. FEMS Yeast Res 2019; 19:foz049. [PMID: 31344230 PMCID: PMC6666381 DOI: 10.1093/femsyr/foz049] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2019] [Accepted: 07/19/2019] [Indexed: 02/01/2023] Open
Abstract
The microbial consortium of wine fermentations is highly dependent upon winemaking decisions made at crush, including the decision to inoculate and the decision to add sulfur dioxide (SO2) to the must. To investigate this, Chardonnay grape juice was subjected to two inoculation treatments (uninoculated and pied de cuve inoculation) as well as two SO2 addition concentrations (0 and 40 mg/L). The bacterial communities, fungal communities and Saccharomyces populations were monitored throughout fermentation using culture-dependent and culture-independent techniques. After fermentation, the wines were evaluated by a panel of experts. When no SO2 was added, the wines underwent alcoholic fermentation and malolactic fermentation simultaneously. Tatumella bacteria were present in significant numbers, but only in the fermentations to which no SO2 was added, and were likely responsible for the malolactic fermentation observed in these treatments. All fermentations were dominated by a genetically diverse indigenous population of Saccharomyces uvarum, the highest diversity of S. uvarum strains to be identified to date; 150 unique strains were identified, with differences in strain composition as a result of SO2 addition. This is the first report of indigenous S. uvarum strains dominating and completing fermentations at a commercial winery in North America.
Collapse
Affiliation(s)
- Sydney C Morgan
- Department of Biology, Irving K. Barber School of Arts and Sciences, The University of British Columbia, Kelowna, British Columbia, Canada, V1V 1V7
| | - Garrett C McCarthy
- Department of Biology, Irving K. Barber School of Arts and Sciences, The University of British Columbia, Kelowna, British Columbia, Canada, V1V 1V7
| | - Brittany S Watters
- Department of Biology, Irving K. Barber School of Arts and Sciences, The University of British Columbia, Kelowna, British Columbia, Canada, V1V 1V7
| | - Mansak Tantikachornkiat
- Department of Biology, Irving K. Barber School of Arts and Sciences, The University of British Columbia, Kelowna, British Columbia, Canada, V1V 1V7
| | - Ieva Zigg
- Department of Biology, Irving K. Barber School of Arts and Sciences, The University of British Columbia, Kelowna, British Columbia, Canada, V1V 1V7
| | - Margaret A Cliff
- Summerland Research and Development Centre, Agriculture and Agri-Food Canada, Summerland, British Columbia, Canada, V0H 1Z0
| | - Daniel M Durall
- Department of Biology, Irving K. Barber School of Arts and Sciences, The University of British Columbia, Kelowna, British Columbia, Canada, V1V 1V7
| |
Collapse
|
8
|
Origone AC, Rodríguez ME, Oteiza JM, Querol A, Lopes CA. Saccharomyces cerevisiae × Saccharomyces uvarum hybrids generated under different conditions share similar winemaking features. Yeast 2018; 35:157-171. [PMID: 29131448 DOI: 10.1002/yea.3295] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2017] [Revised: 10/19/2017] [Accepted: 10/20/2017] [Indexed: 12/13/2022] Open
Abstract
Interspecific hybrids among species in the Saccharomyces genus are frequently detected in anthropic habitats and can also be obtained easily in the laboratory. This occurs because the most important genetic barriers among Saccharomyces species are post-zygotic. Depending on several factors, including the involved strains, the hybridization mechanism and stabilization conditions, hybrids that bear differential genomic constitutions, and hence phenotypic variability, can be obtained. In the present study, Saccharomyces cerevisiae × Saccharomyces uvarum hybrids were constructed using genetically and physiologically different S. uvarum parents at distinct temperatures (13 and 20°C). The effect of those variables on the main oenological features of the wines obtained with these hybrids was evaluated. Hybrids were successfully obtained in all cases. However, genetic stabilization based on successive fermentations in white wine at 13°C was significantly longer than that at 20°C. Our results demonstrated that, irrespective of the S. uvarum parent and temperature used for hybrid generation and stabilization, similar physicochemical and aromatic features were found in wines. The hybrids generated herein were characterized by low ethanol production, high glycerol synthesis and the capacity to grow at low temperature and to produce malic acid with particular aroma profiles. These features make these hybrids useful for the new winemaking industry within the climate change era frame. Copyright © 2017 John Wiley & Sons, Ltd.
Collapse
Affiliation(s)
- Andrea Cecilia Origone
- 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 1400, CP, 8300, Neuquén, Argentina
| | - María Eugenia 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 1400, CP, 8300, Neuquén, Argentina.,Facultad de Ciencias Médicas, Universidad Nacional del Comahue, (8324) Cipolletti, Río Negro, Argentina
| | - Juan Martín Oteiza
- Centro de Investigación y Asistencia Técnica a la Industria-CONICET, Argentina
| | - Amparo Querol
- Departamento de Biotecnología, Instituto de Agroquímica y Tecnología de los Alimentos, CSIC, PO Box 73, E-46100, Burjassot, 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), Buenos Aires 1400, CP, 8300, Neuquén, Argentina.,Facultad de Ciencias Agrarias, Universidad Nacional del Comahue, (8303) Cinco Saltos, Río Negro, Argentina
| |
Collapse
|
9
|
Nguyen HV, Boekhout T. Characterization of Saccharomyces uvarum (Beijerinck, 1898) and related hybrids: assessment of molecular markers that predict the parent and hybrid genomes and a proposal to name yeast hybrids. FEMS Yeast Res 2018; 17:3061370. [PMID: 28334169 DOI: 10.1093/femsyr/fox014] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2016] [Accepted: 03/01/2017] [Indexed: 11/15/2022] Open
Abstract
The use of the nuclear DNA reassociation technique has led taxonomists to consider Saccharomyces uvarum a synonym of S. bayanus. The latter, however, is not a species but a hybrid harbouring S. eubayanus (Seu) and S. uvarum (Su) subgenomes with a minor DNA contribution from S. cerevisiae (Sc). To recognize genetically pure lines of S. uvarum and putative interspecies hybrids among so-called S. bayanus strains present in public culture collections, we propose the use of four markers that were defined from the S. bayanus CBS 380T composite genome, namely SeuNTS2 (rDNA), ScMAL31, MTY1 and SuMEL1. Saccharomyces carlsbergensis CBS 1513 was found to be similar to S. bayanus except that it carries the SeuMEL1 allele. Different marker combinations revealed that among 33 strains examined only a few were similar to CBS 380T, but many pure S. uvarum lines and putative Su/Seu-related hybrids occurred. Our results demonstrated that these hybrids were erroneously considered authentic S. bayanus and therefore the varietal state 'Saccharomyces bayanus var. uvarum comb. nov. Naumov' is not valid. Our markers constitute a tool to get insights into the genomic makeup of Saccharomyces interspecies hybrids. We also make a proposal to name those hybrids that may also be applicable to other fungal hybrids.
Collapse
Affiliation(s)
- Huu-Vang Nguyen
- Micalis Institute, INRA, AgroParisTech, Université Paris-Saclay, 78350 Jouy-en-Josas, France
| | - Teun Boekhout
- CBS-KNAW Fungal Biodiversity Centre, PO Box 85167, 3508 AD Utrecht, The Netherlands.,Institute of Biodiversity and Ecosystem Dynamics (IBED), University of Amsterdam, Amsterdam, The Netherlands
| |
Collapse
|
10
|
Rating of the industrial application potential of yeast strains by molecular characterization. Eur Food Res Technol 2018. [DOI: 10.1007/s00217-018-3088-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
|
11
|
Liu X, Liu X, Zhang Z, Sang M, Sun X, He C, Xin P, Zhang H. Functional Analysis of the FZF1 Genes of Saccharomyces uvarum. Front Microbiol 2018; 9:96. [PMID: 29467731 PMCID: PMC5808186 DOI: 10.3389/fmicb.2018.00096] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2017] [Accepted: 01/16/2018] [Indexed: 11/13/2022] Open
Abstract
Being a sister species of Saccharomyces cerevisiae, Saccharomyces uvarum shows great potential regarding the future of the wine industry. The sulfite tolerance of most S. uvarum strains is poor, however. This is a major flaw that limits its utility in the wine industry. In S. cerevisiae, FZF1 plays a positive role in the transcription of SSU1, which encodes a sulfite efflux transport protein that is critical for sulfite tolerance. Although FZF1 has previously been shown to play a role in sulfite tolerance in S. uvarum, there is little information about its action mechanism. To assess the function of FZF1, two over-expression vectors that contained different FZF1 genes, and one FZF1 silencing vector, were constructed and introduced into a sulfite-tolerant S. uvarum strain using electroporation. In addition, an FZF1-deletion strain was constructed. Both of the FZF1-over-expressing strains showed an elevated tolerance to sulfite, and the FZF1-deletion strain showed the opposite effect. Repression of FZF1 transcription failed, however, presumably due to the lack of alleles of DCR1 and AGO. The qRT-PCR analysis was used to examine changes in transcription in the strains. Surprisingly, neither over-expressing strain promoted SSU1 transcription, although MET4 and HAL4 transcripts significantly increased in both sulfite-tolerance increased strains. We conclude that FZF1 plays a different role in the sulfite tolerance of S. uvarum compared to its role in S. cerevisiae.
Collapse
Affiliation(s)
- Xiaozhen Liu
- Key Laboratory for Forest Resources Conservation and Utilization in the Southwest Mountains of China, Ministry of Education, Southwest Forestry University, Kunming, China
- Key Laboratory of Biodiversity Conservation in Southwest China, State Forest Administration, Southwest Forestry University, Kunming, China
| | - Xiaoping Liu
- College of Life Science, Jinggangshan University, Ji'an, China
| | - Zhiming Zhang
- Key Laboratory of Biodiversity Conservation in Southwest China, State Forest Administration, Southwest Forestry University, Kunming, China
| | - Ming Sang
- Central Laboratory of Xiangyang No.1 Hospital, College of Basic Medical Sciences, Hubei Key Laboratory of Wudang Local Chinese Medicine Research, Hubei University of Medicine, Shiyan, China
| | - Xiaodong Sun
- Central Laboratory of Xiangyang No.1 Hospital, College of Basic Medical Sciences, Hubei Key Laboratory of Wudang Local Chinese Medicine Research, Hubei University of Medicine, Shiyan, China
| | - Chengzhong He
- Key Laboratory of Biodiversity Conservation in Southwest China, State Forest Administration, Southwest Forestry University, Kunming, China
| | - Peiyao Xin
- Key Laboratory of Biodiversity Conservation in Southwest China, State Forest Administration, Southwest Forestry University, Kunming, China
| | - Hanyao Zhang
- Key Laboratory for Forest Resources Conservation and Utilization in the Southwest Mountains of China, Ministry of Education, Southwest Forestry University, Kunming, China
| |
Collapse
|
12
|
Tittarelli F, Varela JA, Gethins L, Stanton C, Ross RP, Suzzi G, Grazia L, Tofalo R, Morrissey JP. Development and implementation of multilocus sequence typing to study the diversity of the yeast Kluyveromyces marxianus in Italian cheeses. Microb Genom 2018; 4. [PMID: 29345222 PMCID: PMC5857380 DOI: 10.1099/mgen.0.000153] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The yeast Kluyveromyces marxianus possesses advantageous traits like rapid growth, GRAS (generally regarded as safe) status and thermotolerance that make it very suitable for diverse biotechnological applications. Although physiological studies demonstrate wide phenotypic variation within the species, there is only limited information available on the genetic diversity of K. marxianus. The aim of this work was to develop a multilocus sequence typing (MLST) method for K. marxianus to improve strain classification and selection. Analysis of housekeeping genes in a number of sequenced strains led to the selection of five genes, IPP1, TFC1, GPH1, GSY2 and SGA1, with sufficient polymorphic sites to allow MLST analysis. These loci were sequenced in an additional 76 strains and used to develop the MLST. This revealed wide diversity in the species and separation of the culture collection and wild strains into multiple distinct clades. Two subsets of strains that shared sources of origin were subjected to MLST and split decomposition analysis. The latter revealed evidence of recombination, indicating that this yeast undergoes mating in the wild. A public access web-based portal was established to allow expansion of the database and application of MLST to additional K. marxianus strains. This will aid understanding of the genetic diversity of the yeast and facilitate biotechnological exploitation.
Collapse
Affiliation(s)
- Fabrizia Tittarelli
- 1Faculty of BioScience and Technology for Food, Agriculture and Environment, University of Teramo, Teramo, Italy.,2School of Microbiology, Environmental Research Institute, Centre for Synthetic Biology and Biotechnology, University College Cork, Cork T12YN60, Ireland
| | - Javier A Varela
- 2School of Microbiology, Environmental Research Institute, Centre for Synthetic Biology and Biotechnology, University College Cork, Cork T12YN60, Ireland
| | - Loughlin Gethins
- 2School of Microbiology, Environmental Research Institute, Centre for Synthetic Biology and Biotechnology, University College Cork, Cork T12YN60, Ireland
| | - Catherine Stanton
- 3Teagasc Research Centre, Moorepark, Ireland.,4School of Microbiology, APC Microbiome Institute, University College Cork, Cork, Ireland
| | - R P Ross
- 4School of Microbiology, APC Microbiome Institute, University College Cork, Cork, Ireland
| | - Giovanna Suzzi
- 1Faculty of BioScience and Technology for Food, Agriculture and Environment, University of Teramo, Teramo, Italy
| | - Luigi Grazia
- 5Department of Science and Technology for Food and Agriculture (DISTAL), Alma Mater Studiorum, University of Bologna, Bologna, Italy
| | - Rosanna Tofalo
- 1Faculty of BioScience and Technology for Food, Agriculture and Environment, University of Teramo, Teramo, Italy
| | - John P Morrissey
- 2School of Microbiology, Environmental Research Institute, Centre for Synthetic Biology and Biotechnology, University College Cork, Cork T12YN60, Ireland.,4School of Microbiology, APC Microbiome Institute, University College Cork, Cork, Ireland
| |
Collapse
|
13
|
Verspohl A, Pignedoli S, Giudici P. The inheritance of mitochondrial DNA in interspecific Saccharomyces hybrids and their properties in winemaking. Yeast 2017; 35:173-187. [PMID: 29048749 DOI: 10.1002/yea.3288] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2017] [Accepted: 10/02/2017] [Indexed: 12/22/2022] Open
Abstract
The inheritance of mitochondrial DNA (mtDNA) in yeast hybrids is heteroplasmic, turning into homoplasmic after few cell cycles. Mitotype restoration is reported to be biparental and random. This study shows that mitotype restoration follows fixed schemata. We created isogenic, interspecific Saccharomyces cerevisiae × Saccharomyces uvarum hybrids through direct mating and analysed their mating frequency and mitotype. The mating frequency increased for most crosses in staggered mating. Mitotyping revealed that breeding lines with the same parental strain of S. cerevisiae and different parental strains of S. uvarum give rise to the same mitotype. According to our results, we postulate that the inheritance of mtDNA is dominated by one parental strain and that the superior mitotype is specific to each breeding line. Technological tests showed typical hybrid heterosis. Copyright © 2017 John Wiley & Sons, Ltd.
Collapse
Affiliation(s)
- Alexandra Verspohl
- University of Modena and Reggio Emilia, Department of Life Sciences, Via Amedola 2, 42122, Reggio Emilia, Italy
| | - Samuele Pignedoli
- University of Modena and Reggio Emilia, Department of Life Sciences, Via Amedola 2, 42122, Reggio Emilia, Italy
| | - Paolo Giudici
- University of Modena and Reggio Emilia, Department of Life Sciences, Via Amedola 2, 42122, Reggio Emilia, Italy
| |
Collapse
|
14
|
Albertin W, Chernova M, Durrens P, Guichoux E, Sherman DJ, Masneuf-Pomarede I, Marullo P. Many interspecific chromosomal introgressions are highly prevalent in HolarcticSaccharomyces uvarumstrains found in human-related fermentations. Yeast 2017; 35:141-156. [DOI: 10.1002/yea.3248] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2017] [Revised: 07/26/2017] [Accepted: 07/29/2017] [Indexed: 01/12/2023] Open
Affiliation(s)
- Warren Albertin
- Université Bordeaux; ISVV, Unité de recherche OEnologie EA 4577, USC 1366 INRA, Bordeaux INP; 33140 Villenave d'Ornon France
- ENSCBP; Bordeaux INP; 33600 Pessac France
| | - Maria Chernova
- Université Bordeaux; ISVV, Unité de recherche OEnologie EA 4577, USC 1366 INRA, Bordeaux INP; 33140 Villenave d'Ornon France
| | - Pascal Durrens
- CNRS UMR 5800; Univ. Bordeaux; 33405 Talence France
- Inria Bordeaux Sud-Ouest; joint team Pleiade Inria/INRA/CNRS; 33405 Talence France
| | - Erwan Guichoux
- INRA; UMR1202 Biodiversité Gènes et Ecosystèmes, Plateforme Génomique; Cestas 33610 France
| | - David James Sherman
- CNRS UMR 5800; Univ. Bordeaux; 33405 Talence France
- Inria Bordeaux Sud-Ouest; joint team Pleiade Inria/INRA/CNRS; 33405 Talence France
| | - Isabelle Masneuf-Pomarede
- Université Bordeaux; ISVV, Unité de recherche OEnologie EA 4577, USC 1366 INRA, Bordeaux INP; 33140 Villenave d'Ornon France
- Bordeaux Sciences Agro; 33170 Gradignan France
| | - Philippe Marullo
- Université Bordeaux; ISVV, Unité de recherche OEnologie EA 4577, USC 1366 INRA, Bordeaux INP; 33140 Villenave d'Ornon France
- Biolaffort; 33100 Bordeaux France
| |
Collapse
|
15
|
Hranilovic A, Bely M, Masneuf-Pomarede I, Jiranek V, Albertin W. The evolution of Lachancea thermotolerans is driven by geographical determination, anthropisation and flux between different ecosystems. PLoS One 2017; 12:e0184652. [PMID: 28910346 PMCID: PMC5599012 DOI: 10.1371/journal.pone.0184652] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2017] [Accepted: 08/28/2017] [Indexed: 12/28/2022] Open
Abstract
The yeast Lachancea thermotolerans (formerly Kluyveromyces thermotolerans) is a species with remarkable, yet underexplored, biotechnological potential. This ubiquist occupies a range of natural and anthropic habitats covering a wide geographic span. To gain an insight into L. thermotolerans population diversity and structure, 172 isolates sourced from diverse habitats worldwide were analysed using a set of 14 microsatellite markers. The resultant clustering revealed that the evolution of L. thermotolerans has been driven by the geography and ecological niche of the isolation sources. Isolates originating from anthropic environments, in particular grapes and wine, were genetically close, thus suggesting domestication events within the species. The observed clustering was further validated by several means including, population structure analysis, F-statistics, Mantel’s test and the analysis of molecular variance (AMOVA). Phenotypic performance of isolates was tested using several growth substrates and physicochemical conditions, providing added support for the clustering. Altogether, this study sheds light on the genotypic and phenotypic diversity of L. thermotolerans, contributing to a better understanding of the population structure, ecology and evolution of this non-Saccharomyces yeast.
Collapse
Affiliation(s)
- Ana Hranilovic
- The Australian Research Council Training Centre for Innovative Wine Production, Adelaide, South Australia, Australia
- Department of Wine and Food Science, The University of Adelaide, Urbrrae, South Australia, Australia
| | - Marina Bely
- Unité de recherche Œnologie, Institut de la Science de la Vigne et du Vin, University of Bordeaux, Villenave d'Ornon, France
| | - Isabelle Masneuf-Pomarede
- Unité de recherche Œnologie, Institut de la Science de la Vigne et du Vin, University of Bordeaux, Villenave d'Ornon, France
- Bordeaux Sciences Agro, Gradignan, France
| | - Vladimir Jiranek
- The Australian Research Council Training Centre for Innovative Wine Production, Adelaide, South Australia, Australia
- Department of Wine and Food Science, The University of Adelaide, Urbrrae, South Australia, Australia
| | - Warren Albertin
- Unité de recherche Œnologie, Institut de la Science de la Vigne et du Vin, University of Bordeaux, Villenave d'Ornon, France
- ENSCBP, Bordeaux INP, Pessac, France
- * E-mail:
| |
Collapse
|
16
|
Liu XZ, Sang M, Zhang XA, Zhang TK, Zhang HY, He X, Li SX, Sun XD, Zhang ZM. Enhancing expression of SSU1 genes in Saccharomyces uvarum leads to an increase in sulfite tolerance and a transcriptome profile change. FEMS Yeast Res 2017; 17:3752510. [PMID: 28449102 DOI: 10.1093/femsyr/fox023] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2017] [Accepted: 04/21/2017] [Indexed: 01/31/2023] Open
Abstract
Saccharomyces uvarum is a good wine yeast species that may have great potential for the future. However, sulfur tolerance of most S. uvarum strains is very poor. In addition there is still little information about the SSU1 gene of S. uvarum, which encodes a putative transporter conferring sulfite tolerance. In order to analyze the function of the SSU1 gene, two expression vectors that contained different SSU1 genes were constructed and transferred into a sulfite-tolerant S. uvarum strain, A9. Then sulfite tolerance, SO2 production, and PCR, sequencing, RT-qPCR and transcriptome analyses were used to access the function of the S. uvarum SSU1 gene. Our results illustrated that enhancing expression of the SSU1 gene can promote sulfite resistance in S. uvarum, and an insertion fragment ahead of the additional SSU1 gene, as seen in some alleles, could affect the expression of other genes and the sulfite tolerance level of S. uvarum. This is the first report on enhancing the expression of the SSU1 gene of S. uvarum.
Collapse
Affiliation(s)
- X Z Liu
- Key Laboratory of Biodiversity Conservation in Southwest China, the State Forest Administration, Southwest Forestry University, Kunming, Yunnan Province, China, 650224
| | - M Sang
- Central Laboratory of Xiangyang No.1 Hospital, College of Basic Medical Sciences, Hubei Key Laboratory of Wudang Local Chinese Medicine Research, Hubei University of Medicine, Shiyan, Hubei Province, China, 442000
| | - X A Zhang
- Key Laboratory of Biodiversity Conservation in Southwest China, the State Forest Administration, Southwest Forestry University, Kunming, Yunnan Province, China, 650224
| | - T K Zhang
- Key Laboratory of Biodiversity Conservation in Southwest China, the State Forest Administration, Southwest Forestry University, Kunming, Yunnan Province, China, 650224
| | - H Y Zhang
- Key Laboratory of Biodiversity Conservation in Southwest China, the State Forest Administration, Southwest Forestry University, Kunming, Yunnan Province, China, 650224
| | - X He
- Key Laboratory of Biodiversity Conservation in Southwest China, the State Forest Administration, Southwest Forestry University, Kunming, Yunnan Province, China, 650224
| | - S X Li
- Key Laboratory of Biodiversity Conservation in Southwest China, the State Forest Administration, Southwest Forestry University, Kunming, Yunnan Province, China, 650224
| | - X D Sun
- Central Laboratory of Xiangyang No.1 Hospital, College of Basic Medical Sciences, Hubei Key Laboratory of Wudang Local Chinese Medicine Research, Hubei University of Medicine, Shiyan, Hubei Province, China, 442000
| | - Z M Zhang
- Key Laboratory of Biodiversity Conservation in Southwest China, the State Forest Administration, Southwest Forestry University, Kunming, Yunnan Province, China, 650224
| |
Collapse
|
17
|
Exploration of genetic and phenotypic diversity within Saccharomyces uvarum for driving strain improvement in winemaking. Appl Microbiol Biotechnol 2016; 101:2507-2521. [PMID: 27933455 DOI: 10.1007/s00253-016-8008-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2016] [Revised: 10/31/2016] [Accepted: 11/11/2016] [Indexed: 10/20/2022]
Abstract
The selection and genetic improvement of wine yeast is an ongoing process, since yeast strains should match new technologies in winemaking to satisfy evolving consumer preferences. A large genetic background is the necessary starting point for any genetic improvement programme. For this reason, we collected and characterized a large number of strains belonging to Saccharomyces uvarum. In particular, 70 strains were isolated from cold-stored must samples: they were identified and compared to S. uvarum strains originating from different collections, regarding fermentation profile, spore viability and stress response. The results demonstrate a large biodiversity among the new isolates, with particular emphasis to fermentation performances, genotypes and high spore viability, making the isolates suitable for further genetic improvement programmes. Furthermore, few of them are competitive with Saccharomyces cerevisiae and per se, suitable for wine fermentation, due to their resistance to stress, short lag phase and fermentation by-products.
Collapse
|