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Windholtz S, Nioi C, Coulon J, Masneuf-Pomarede I. Bioprotection by non-Saccharomyces yeasts in oenology: Evaluation of O 2 consumption and impact on acetic acid bacteria. Int J Food Microbiol 2023; 405:110338. [PMID: 37506548 DOI: 10.1016/j.ijfoodmicro.2023.110338] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2023] [Revised: 07/19/2023] [Accepted: 07/20/2023] [Indexed: 07/30/2023]
Abstract
Bioprotection by yeast addition is increasingly used in oenology as an alternative to sulfur dioxide (SO2). Recent studies have also shown that it is likely to consume dissolved O2. This ability could limit O2 for other microorganisms and the early oxidation of the grape must. However, the ability of yeasts to consume O2 in a context of bioprotection was poorly studied so far considering the high genetic diversity of non-Saccharomyces. The first aim of the present study was to perform an O2 consumption rate (OCR) screening of strains from a large multi species collection found in oenology. The results demonstrate significant inter and intra species diversity with regard to O2 consumption. In the must M. pulcherrima consumes O2 faster than Saccharomyces cerevisiae and then other studied non-Saccharomyces species. The O2 consumption was also evaluate in the context of a yeast mix used as industrial bioprotection (Metschnikowia pulcherrima and Torulaspora delbrueckii) in red must. These non-Saccharomyces yeasts were then showed to limit the growth of acetic acid bacteria, with a bioprotective effect comparable to that of the addition of sulfur dioxide. Laboratory experiment confirmed the negative impact of the non-Saccharomyces yeasts on Gluconobacter oxydans that may be related to O2 consumption. This study sheds new lights on the use of bioprotection as an alternative to SO2 and suggest the possibility to use O2 consumption measurements as a new criteria for non-Saccharomyces strain selection in a context of bioprotection application for the wine industry.
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Affiliation(s)
- Sara Windholtz
- Univ. Bordeaux, Bordeaux INP, INRAE, OENO, UMR 1366, ISVV, F-33140 Villenave d'Ornon, France; Bordeaux Sciences Agro, Bordeaux INP, INRAE, OENO, UMR 1366, ISVV, F-33170 Gradignan, France.
| | - Claudia Nioi
- Univ. Bordeaux, Bordeaux INP, INRAE, OENO, UMR 1366, ISVV, F-33140 Villenave d'Ornon, France; Bordeaux Sciences Agro, Bordeaux INP, INRAE, OENO, UMR 1366, ISVV, F-33170 Gradignan, France
| | - Joana Coulon
- BioLaffort, 11 Rue Aristide Bergès, 33270 Floirac, France
| | - Isabelle Masneuf-Pomarede
- Univ. Bordeaux, Bordeaux INP, INRAE, OENO, UMR 1366, ISVV, F-33140 Villenave d'Ornon, France; Bordeaux Sciences Agro, Bordeaux INP, INRAE, OENO, UMR 1366, ISVV, F-33170 Gradignan, France
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García-Ríos E, Guillamón JM. Genomic Adaptations of Saccharomyces Genus to Wine Niche. Microorganisms 2022; 10:microorganisms10091811. [PMID: 36144411 PMCID: PMC9500811 DOI: 10.3390/microorganisms10091811] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2022] [Revised: 09/05/2022] [Accepted: 09/08/2022] [Indexed: 11/16/2022] Open
Abstract
Wine yeast have been exposed to harsh conditions for millennia, which have led to adaptive evolutionary strategies. Thus, wine yeasts from Saccharomyces genus are considered an interesting and highly valuable model to study human-drive domestication processes. The rise of whole-genome sequencing technologies together with new long reads platforms has provided new understanding about the population structure and the evolution of wine yeasts. Population genomics studies have indicated domestication fingerprints in wine yeast, including nucleotide variations, chromosomal rearrangements, horizontal gene transfer or hybridization, among others. These genetic changes contribute to genetically and phenotypically distinct strains. This review will summarize and discuss recent research on evolutionary trajectories of wine yeasts, highlighting the domestication hallmarks identified in this group of yeast.
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Affiliation(s)
- Estéfani García-Ríos
- Department of Food Biotechnology, Instituto de Agroquímica y Tecnología de los Alimentos (CSIC), Avda. Agustín Escardino, 7, 46980 Paterna, Spain
- Department of Science, Universidad Internacional de Valencia-VIU, Pintor Sorolla 21, 46002 Valencia, Spain
- Correspondence:
| | - José Manuel Guillamón
- Department of Food Biotechnology, Instituto de Agroquímica y Tecnología de los Alimentos (CSIC), Avda. Agustín Escardino, 7, 46980 Paterna, Spain
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Windholtz S, Vinsonneau E, Farris L, Thibon C, Masneuf-Pomarède I. Yeast and Filamentous Fungi Microbial Communities in Organic Red Grape Juice: Effect of Vintage, Maturity Stage, SO 2, and Bioprotection. Front Microbiol 2022; 12:748416. [PMID: 35002998 PMCID: PMC8740202 DOI: 10.3389/fmicb.2021.748416] [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: 07/27/2021] [Accepted: 12/01/2021] [Indexed: 01/16/2023] Open
Abstract
Changes are currently being made to winemaking processes to reduce chemical inputs [particularly sulfur dioxide (SO2)] and adapt to consumer demand. In this study, yeast growth and fungal diversity were investigated in merlot during the prefermentary stages of a winemaking process without addition of SO2. Different factors were considered, in a two-year study: vintage, maturity level and bioprotection by the adding yeast as an alternative to SO2. The population of the target species was monitored by quantitative-PCR, and yeast and filamentous fungi diversity was determined by 18S rDNA metabarcoding. A gradual decrease of the α-diversity during the maceration process was highlighted. Maturity level played a significant role in yeast and fungal abundance, which was lower at advanced maturity, while vintage had a strong impact on Hanseniaspora spp. population level and abundance. The presence of SO2 altered the abundance of yeast and filamentous fungi, but not their nature. The absence of sulfiting led to an unexpected reduction in diversity compared to the presence of SO2, which might result from the occupation of the niche by certain dominant species, namely Hanseniaspora spp. Inoculation of the grape juice with non-Saccharomyces yeast resulted in a decrease in the abundance of filamentous fungi generally associated with a decline in grape must quality. Lower abundance and niche occupation by bioprotection agents were observed at the overripened stage, thus suggesting that doses applied should be reconsidered at advanced maturity. Our study confirmed the bioprotective role of Metschnikowia pulcherrima and Torulaspora delbrueckii in a context of vinification without sulfites.
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Affiliation(s)
- Sara Windholtz
- Univ. Bordeaux, INRAE, Bordeaux INP, UR OENOLOGIE, EA 4577, USC 1366, ISVV, Villenave d'Ornon, France
| | | | - Laura Farris
- Univ. Bordeaux, INRAE, Bordeaux INP, UR OENOLOGIE, EA 4577, USC 1366, ISVV, Villenave d'Ornon, France.,Bordeaux Sciences Agro, Gradignan, France
| | - Cécile Thibon
- Univ. Bordeaux, INRAE, Bordeaux INP, UR OENOLOGIE, EA 4577, USC 1366, ISVV, Villenave d'Ornon, France
| | - Isabelle Masneuf-Pomarède
- Univ. Bordeaux, INRAE, Bordeaux INP, UR OENOLOGIE, EA 4577, USC 1366, ISVV, Villenave d'Ornon, France.,Bordeaux Sciences Agro, Gradignan, France
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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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QTL mapping: an innovative method for investigating the genetic determinism of yeast-bacteria interactions in wine. Appl Microbiol Biotechnol 2021; 105:5053-5066. [PMID: 34106310 DOI: 10.1007/s00253-021-11376-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2021] [Revised: 05/11/2021] [Accepted: 05/27/2021] [Indexed: 10/21/2022]
Abstract
The two most commonly used wine microorganisms, Saccharomyces cerevisiae yeast and Oenococcus oeni bacteria, are responsible for completion of alcoholic and malolactic fermentation (MLF), respectively. For successful co-inoculation, S. cerevisiae and O. oeni must be able to complete fermentation; however, this relies on compatibility between yeast and bacterial strains. For the first time, quantitative trait loci (QTL) analysis was used to elucidate whether S. cerevisiae genetic makeup can play a role in the ability of O. oeni to complete MLF. Assessment of 67 progeny from a hybrid S. cerevisiae strain (SBxGN), co-inoculated with a single O. oeni strain, SB3, revealed a major QTL linked to MLF completion by O. oeni. This QTL encompassed a well-known translocation, XV-t-XVI, that results in increased SSU1 expression and is functionally linked with numerous phenotypes including lag phase duration and sulphite export and production. A reciprocal hemizygosity assay was performed to elucidate the effect of the gene SSU1 in the SBxGN background. Our results revealed a strong effect of SSU1 haploinsufficiency on O. oeni's ability to complete malolactic fermentation during co-inoculation and pave the way for the implementation of QTL mapping projects for deciphering the genetic bases of microbial interactions. KEY POINTS: • For the first time, QTL analysis has been used to study yeast-bacteria interactions. • A QTL encompassing a translocation, XV-t-XVI, was linked to MLF outcomes. • S. cerevisiae SSU1 haploinsufficiency positively impacted MLF by O. oeni.
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Bartel C, Roach M, Onetto C, Curtin C, Varela C, Borneman A. Adaptive evolution of sulfite tolerance in Brettanomyces bruxellensis. FEMS Yeast Res 2021; 21:6293842. [PMID: 34089329 DOI: 10.1093/femsyr/foab036] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2021] [Accepted: 06/03/2021] [Indexed: 01/06/2023] Open
Abstract
Brettanomyces bruxellensis is considered one of the most problematic microbes associated with wine production. Sulfur dioxide is commonly used to inhibit the growth of B. bruxellensis and limit the potential wine spoilage. Brettanomyces bruxellensis wine isolates can grow at higher concentrations of this preservative than isolates from other sources. Thus, it has been suggested that the use of sulfite may have selected for B. bruxellensis strains better adapted to survive in the winemaking environment. We utilized laboratory adaptive evolution to determine the potential for this to occur. Three B. bruxellensis strains, representative of known genetic variation within the species, were subjected to increasing sublethal sulfur dioxide concentrations. Individual clones isolated from evolved populations displayed enhanced sulfite tolerance, ranging from 1.6 to 2.5 times higher than the corresponding parental strains. Whole-genome sequencing of sulfite-tolerant clones derived from two of the parental strains revealed structural variations affecting 270 genes. The region containing the sulfite efflux pump encoding gene, SSU1, showed clear copy number variants in all sequenced clones. Regardless of parental strain genetic background, SSU1 copy number changes were reproducibly associated with one SSU1 haplotype. This work clearly demonstrates adaptive evolution of B. bruxellensis when exposed to sublethal sulfites and suggests that, similar to Saccharomyces cerevisiae wine yeast, the mechanism responsible involves the gene SSU1.
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Affiliation(s)
- Caroline Bartel
- The Australian Wine Research Institute, PO Box 197, Glen Osmond, Adelaide, SA 5064, Australia
| | - Michael Roach
- The Australian Wine Research Institute, PO Box 197, Glen Osmond, Adelaide, SA 5064, Australia
| | - Cristobal Onetto
- The Australian Wine Research Institute, PO Box 197, Glen Osmond, Adelaide, SA 5064, Australia
| | - Chris Curtin
- The Australian Wine Research Institute, PO Box 197, Glen Osmond, Adelaide, SA 5064, Australia
- Department of Food Science and Technology, Oregon State University, Corvallis, OR 97331, USA
| | - Cristian Varela
- The Australian Wine Research Institute, PO Box 197, Glen Osmond, Adelaide, SA 5064, Australia
- School of Agriculture, Food and Wine, Faculty of Sciences, University of Adelaide, Adelaide, SA 5005, Australia
| | - Anthony Borneman
- The Australian Wine Research Institute, PO Box 197, Glen Osmond, Adelaide, SA 5064, Australia
- School of Agriculture, Food and Wine, Faculty of Sciences, University of Adelaide, Adelaide, SA 5005, Australia
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Yeast Metabolism and Its Exploitation in Emerging Winemaking Trends: From Sulfite Tolerance to Sulfite Reduction. FERMENTATION-BASEL 2021. [DOI: 10.3390/fermentation7020057] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Sulfite is widely used as a preservative in foods and beverages for its antimicrobial and antioxidant activities, particularly in winemaking where SO2 is frequently added. Thus, sulfite resistance mechanisms have been extensively studied in the fermenting yeast Saccharomyces cerevisiae. Nevertheless, in recent years, a negative perception has developed towards sulfites in wine, because of human health and environmental concerns. Increasing consumer demand for wines with low SO2 content is pushing the winemaking sector to develop new practices in order to reduce sulfite content in wine, including the use of physical and chemical alternatives to SO2, and the exploitation of microbial resources to the same purpose. For this reason, the formation of sulfur-containing compounds by wine yeast has become a crucial point of research during the last decades. In this context, the aim of this review is to examine the main mechanisms weaponized by Saccharomyces cerevisiae for coping with sulfite, with a particular emphasis on the production of sulfite and glutathione, sulfite detoxification through membrane efflux (together with the genetic determinants thereof), and production of SO2-binding compounds.
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