1
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Gupta G, Labrie S, Filteau M. Systematic Evaluation of Biotic and Abiotic Factors in Antifungal Microorganism Screening. Microorganisms 2024; 12:1396. [PMID: 39065164 PMCID: PMC11279232 DOI: 10.3390/microorganisms12071396] [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: 06/14/2024] [Revised: 07/05/2024] [Accepted: 07/07/2024] [Indexed: 07/28/2024] Open
Abstract
Microorganisms have significant potential to control fungal contamination in various foods. However, the identification of strains that exhibit robust antifungal activity poses challenges due to highly context-dependent responses. Therefore, to fully exploit the potential of isolates as antifungal agents, it is crucial to systematically evaluate them in a variety of biotic and abiotic contexts. Here, we present an adaptable and scalable method using a robotic platform to study the properties of 1022 isolates obtained from maple sap. We tested the antifungal activity of isolates alone or in pairs on M17 + lactose (LM17), plate count agar (PCA), and sucrose-allantoin (SALN) culture media against Kluyveromyces lactis, Candida boidinii, and Saccharomyces cerevisiae. Microorganisms exhibited less often antifungal activity on SALN and PCA than LM17, suggesting that the latter is a better screening medium. We also analyzed the results of ecological interactions between pairs. Isolates that showed consistent competitive behaviors were more likely to show antifungal activity than expected by chance. However, co-culture rarely improved antifungal activity. In fact, an interaction-mediated suppression of activity was more prevalent in our dataset. These findings highlight the importance of incorporating both biotic and abiotic factors into systematic screening designs for the bioprospection of microorganisms with environmentally robust antifungal activity.
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Affiliation(s)
- Gunjan Gupta
- Département des Sciences des Aliments, Université Laval, Quebec City, QC G1V 0A6, Canada; (G.G.); (S.L.)
- Institut sur la Nutrition et les Aliments Fonctionnels (INAF), Quebec City, QC G1V 0A6, Canada
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Quebec City, QC G1V 0A6, Canada
| | - Steve Labrie
- Département des Sciences des Aliments, Université Laval, Quebec City, QC G1V 0A6, Canada; (G.G.); (S.L.)
- Institut sur la Nutrition et les Aliments Fonctionnels (INAF), Quebec City, QC G1V 0A6, Canada
| | - Marie Filteau
- Département des Sciences des Aliments, Université Laval, Quebec City, QC G1V 0A6, Canada; (G.G.); (S.L.)
- Institut sur la Nutrition et les Aliments Fonctionnels (INAF), Quebec City, QC G1V 0A6, Canada
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Quebec City, QC G1V 0A6, Canada
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2
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Wang JJT, Steenwyk JL, Brem RB. Natural trait variation across Saccharomycotina species. FEMS Yeast Res 2024; 24:foae002. [PMID: 38218591 PMCID: PMC10833146 DOI: 10.1093/femsyr/foae002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2023] [Revised: 10/13/2023] [Accepted: 01/12/2024] [Indexed: 01/15/2024] Open
Abstract
Among molecular biologists, the group of fungi called Saccharomycotina is famous for its yeasts. These yeasts in turn are famous for what they have in common-genetic, biochemical, and cell-biological characteristics that serve as models for plants and animals. But behind the apparent homogeneity of Saccharomycotina species lie a wealth of differences. In this review, we discuss traits that vary across the Saccharomycotina subphylum. We describe cases of bright pigmentation; a zoo of cell shapes; metabolic specialties; and species with unique rules of gene regulation. We discuss the genetics of this diversity and why it matters, including insights into basic evolutionary principles with relevance across Eukarya.
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Affiliation(s)
- Johnson J -T Wang
- Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Jacob L Steenwyk
- Howard Hughes Medical Institute and Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Rachel B Brem
- Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley, CA 94720, USA
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3
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Decabooter G, Aspirault C, Filteau M, Fliss I. The Physicochemical Characterization and In Vitro Digestibility of Maple Sugar Sand and Downgraded Maple Syrups. Foods 2023; 12:3528. [PMID: 37835179 PMCID: PMC10572138 DOI: 10.3390/foods12193528] [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: 08/22/2023] [Revised: 09/15/2023] [Accepted: 09/21/2023] [Indexed: 10/15/2023] Open
Abstract
The maple syrup industry generates substandard syrups and sugar sand as by-products, which are underused. In this study, we conducted a comprehensive analysis of the physicochemical composition of these products to assess their potential for valorization. Using HPLC analysis, we measured sugar and organic acid content as well as total polyphenol content using the Folin-Ciocalteu method. Additionally, we evaluated the in vitro digestibility using the TIM-1 model. We showed that the composition of ropy and buddy downgraded syrups is comparable to that of standard maple syrup, whereas sugar sand's composition is highly variable, with carbohydrate content ranging from 5.01 mg/g to 652.89 mg/g and polyphenol content ranging from 11.30 µg/g to 120.95 µg/g. In vitro bioaccessibility reached 70% of total sugars for all by-products. Organic acid bioaccessibility from sugar sand and syrup reached 76% and 109% relative to standard maple syrup, respectively. Polyphenol bioaccessibility exceeded 100% during digestion. This can be attributed to favorable extraction conditions, the breakdown of complex polyphenol forms and the food matrix. In conclusion, our study demonstrates that sugar sand and downgraded maple syrups exhibit digestibility comparable to that of standard maple syrup. Consequently, they hold potential as a source of polyphenols, sugar or organic acids for applications such as industrial fermentation or livestock feeds.
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Affiliation(s)
- Gautier Decabooter
- Département de Science des Aliments, Faculté des Sciences de l’Agriculture et de l’Alimentation (FSAA), Université Laval, Québec City, QC G1V 0A6, Canada; (G.D.); (C.A.); (M.F.)
- Institut sur la Nutrition et les Aliments Fonctionnels (INAF), Québec City, QC G1V 0A6, Canada
| | - Claudie Aspirault
- Département de Science des Aliments, Faculté des Sciences de l’Agriculture et de l’Alimentation (FSAA), Université Laval, Québec City, QC G1V 0A6, Canada; (G.D.); (C.A.); (M.F.)
- Institut sur la Nutrition et les Aliments Fonctionnels (INAF), Québec City, QC G1V 0A6, Canada
| | - Marie Filteau
- Département de Science des Aliments, Faculté des Sciences de l’Agriculture et de l’Alimentation (FSAA), Université Laval, Québec City, QC G1V 0A6, Canada; (G.D.); (C.A.); (M.F.)
- Institut sur la Nutrition et les Aliments Fonctionnels (INAF), Québec City, QC G1V 0A6, Canada
- Institut de Biologie Intégrative et des Systèmes (IBIS), Québec City, QC G1V 0A6, Canada
| | - Ismail Fliss
- Département de Science des Aliments, Faculté des Sciences de l’Agriculture et de l’Alimentation (FSAA), Université Laval, Québec City, QC G1V 0A6, Canada; (G.D.); (C.A.); (M.F.)
- Institut sur la Nutrition et les Aliments Fonctionnels (INAF), Québec City, QC G1V 0A6, Canada
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4
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Nguyen THM, Sondhi S, Ziesel A, Paliwal S, Fiumera HL. Mitochondrial-nuclear coadaptation revealed through mtDNA replacements in Saccharomyces cerevisiae. BMC Evol Biol 2020; 20:128. [PMID: 32977769 PMCID: PMC7517635 DOI: 10.1186/s12862-020-01685-6] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2020] [Accepted: 09/07/2020] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Mitochondrial function requires numerous genetic interactions between mitochondrial- and nuclear- encoded genes. While selection for optimal mitonuclear interactions should result in coevolution between both genomes, evidence for mitonuclear coadaptation is challenging to document. Genetic models where mitonuclear interactions can be explored are needed. RESULTS We systematically exchanged mtDNAs between 15 Saccharomyces cerevisiae isolates from a variety of ecological niches to create 225 unique mitochondrial-nuclear genotypes. Analysis of phenotypic profiles confirmed that environmentally-sensitive interactions between mitochondrial and nuclear genotype contributed to growth differences. Exchanges of mtDNAs between strains of the same or different clades were just as likely to demonstrate mitonuclear epistasis although epistatic effect sizes increased with genetic distances. Strains with their original mtDNAs were more fit than strains with synthetic mitonuclear combinations when grown in media that resembled isolation habitats. CONCLUSIONS This study shows that natural variation in mitonuclear interactions contributes to fitness landscapes. Multiple examples of coadapted mitochondrial-nuclear genotypes suggest that selection for mitonuclear interactions may play a role in helping yeasts adapt to novel environments and promote coevolution.
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Affiliation(s)
- Tuc H M Nguyen
- Department of Biological Sciences, Binghamton University, Binghamton, NY, USA
| | - Sargunvir Sondhi
- Department of Biological Sciences, Binghamton University, Binghamton, NY, USA
| | - Andrew Ziesel
- Department of Biological Sciences, Binghamton University, Binghamton, NY, USA
| | - Swati Paliwal
- Department of Bioscience and Biotechnology, Banasthali Vidyapith, Rajasthan, India
| | - Heather L Fiumera
- Department of Biological Sciences, Binghamton University, Binghamton, NY, USA.
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5
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Jennifer J. P, Maria C. F. A Comprehensive Review of Maple Sap Microbiota and Its Effect on Maple Syrup Quality. FOOD REVIEWS INTERNATIONAL 2020. [DOI: 10.1080/87559129.2020.1788579] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Perry Jennifer J.
- School of Food and Agriculture, University of Maine, Orono, Maine, USA
| | - Fiore Maria C.
- School of Food and Agriculture, University of Maine, Orono, Maine, USA
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6
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Derome N, Filteau M. A continuously changing selective context on microbial communities associated with fish, from egg to fork. Evol Appl 2020; 13:1298-1319. [PMID: 32684960 PMCID: PMC7359827 DOI: 10.1111/eva.13027] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2019] [Revised: 05/13/2020] [Accepted: 05/14/2020] [Indexed: 02/06/2023] Open
Abstract
Fast increase of fish aquaculture production to meet consumer demands is accompanied by important ecological concerns such as disease outbreaks. Meanwhile, food waste is an important concern with fish products since they are highly perishable. Recent aquaculture and fish product microbiology, and more recently, microbiota research, paved the way to a highly integrated approach to understand complex relationships between host fish, product and their associated microbial communities at health/disease and preservation/spoilage frontiers. Microbial manipulation strategies are increasingly validated as promising tools either to replace or to complement traditional veterinary and preservation methods. In this review, we consider evolutionary forces driving fish microbiota assembly, in particular the changes in the selective context along the production chain. We summarize the current knowledge concerning factors governing assembly and dynamics of fish hosts and food microbial communities. Then, we discuss the current microbial community manipulation strategies from an evolutionary standpoint to provide a perspective on the potential for risks, conflict and opportunities. Finally, we conclude that to harness evolutionary forces in the development of sustainable microbiota manipulation applications in the fish industry, an integrated knowledge of the controlling abiotic and especially biotic factors is required.
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Affiliation(s)
- Nicolas Derome
- Institut de Biologie Intégrative et des Systèmes (IBIS)Université LavalQuébecQCCanada
- Département de BiologieUniversité LavalQuébecQCCanada
| | - Marie Filteau
- Département de BiologieUniversité LavalQuébecQCCanada
- Département des Sciences des alimentsInstitut sur la nutrition et les aliments fonctionnels (INAF)Université LavalQuébecQCCanada
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7
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Competition experiments in a soil microcosm reveal the impact of genetic and biotic factors on natural yeast populations. ISME JOURNAL 2020; 14:1410-1421. [PMID: 32080356 DOI: 10.1038/s41396-020-0612-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/05/2019] [Revised: 02/03/2020] [Accepted: 02/07/2020] [Indexed: 02/06/2023]
Abstract
The ability to measure microbial fitness directly in natural conditions and in interaction with other microbes is a challenge that needs to be overcome if we want to gain a better understanding of microbial fitness determinants in nature. Here we investigate the influence of the natural microbial community on the relative fitness of the North American populations SpB, SpC and SpC* of the wild yeast Saccharomyces paradoxus using DNA barcodes and a soil microcosm derived from soil associated with oak trees. We find that variation in fitness among these genetically distinct groups is influenced by the microbial community. Altering the microbial community load and diversity with an irradiation treatment significantly diminishes the magnitude of fitness differences among populations. Our findings suggest that microbial interactions could affect the evolution of yeast lineages in nature by modulating variation in fitness.
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8
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Macías LG, Morard M, Toft C, Barrio E. Comparative Genomics Between Saccharomyces kudriavzevii and S. cerevisiae Applied to Identify Mechanisms Involved in Adaptation. Front Genet 2019; 10:187. [PMID: 30930934 PMCID: PMC6425871 DOI: 10.3389/fgene.2019.00187] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2018] [Accepted: 02/21/2019] [Indexed: 12/02/2022] Open
Abstract
Yeasts belonging to the Saccharomyces genus play an important role in human-driven fermentations. The species S. cerevisiae has been widely studied because it is the dominant yeast in most fermentations and it has been widely used as a model eukaryotic organism. Recently, other species of the Saccharomyces genus are gaining interest to solve the new challenges that the fermentation industry are facing. One of these species is S. kudriavzevii, which exhibits interesting physiological properties compared to S. cerevisiae, such as a better adaptation to grow at low temperatures, a higher glycerol synthesis and lower ethanol production. The aim of this study is to understand the molecular basis behind these phenotypic differences of biotechnological interest by using a species-based comparative genomics approach. In this work, we sequenced, assembled and annotated two new genomes of S. kudriavzevii. We used a combination of different statistical methods to identify functional divergence, signatures of positive selection and acceleration of substitution rates at specific amino acid sites of proteins in S. kudriavzevii when compared to S. cerevisiae, and vice versa. We provide a list of candidate genes in which positive selection could be acting during the evolution of both S. cerevisiae and S. kudriavzevii clades. Some of them could be related to certain important differences in metabolism previously reported by other authors such us DAL3 and ARO4, involved in nitrogen assimilation and amino acid biosynthesis. In addition, three of those genes (FBA1, ZIP1, and RQC2) showed accelerated evolutionary rates in Sk branch. Finally, genes of the riboflavin biosynthesis were also among those genes with a significant higher rate of nucleotide substitution and those proteins have amino acid positions contributing to functional divergence.
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Affiliation(s)
- Laura G Macías
- Departament de Genètica, Universitat de València, Valencia, Spain.,Departamento de Biotecnología, Instituto de Agroquímica y Tecnología de Alimentos IATA, CSIC, Valencia, Spain
| | - Miguel Morard
- Departament de Genètica, Universitat de València, Valencia, Spain.,Departamento de Biotecnología, Instituto de Agroquímica y Tecnología de Alimentos IATA, CSIC, Valencia, Spain
| | - Christina Toft
- Departament de Genètica, Universitat de València, Valencia, Spain.,Departamento de Biotecnología, Instituto de Agroquímica y Tecnología de Alimentos IATA, CSIC, Valencia, Spain
| | - Eladio Barrio
- Departament de Genètica, Universitat de València, Valencia, Spain.,Departamento de Biotecnología, Instituto de Agroquímica y Tecnología de Alimentos IATA, CSIC, Valencia, Spain
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9
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Eberlein C, Hénault M, Fijarczyk A, Charron G, Bouvier M, Kohn LM, Anderson JB, Landry CR. Hybridization is a recurrent evolutionary stimulus in wild yeast speciation. Nat Commun 2019; 10:923. [PMID: 30804385 PMCID: PMC6389940 DOI: 10.1038/s41467-019-08809-7] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2018] [Accepted: 01/31/2019] [Indexed: 01/30/2023] Open
Abstract
Hybridization can result in reproductively isolated and phenotypically distinct lineages that evolve as independent hybrid species. How frequently hybridization leads to speciation remains largely unknown. Here we examine the potential recurrence of hybrid speciation in the wild yeast Saccharomyces paradoxus in North America, which comprises two endemic lineages SpB and SpC, and an incipient hybrid species, SpC*. Using whole-genome sequences from more than 300 strains, we uncover the hybrid origin of another group, SpD, that emerged from hybridization between SpC* and one of its parental species, the widespread SpB. We show that SpD has the potential to evolve as a novel hybrid species, because it displays phenotypic novelties that include an intermediate transcriptome profile, and partial reproductive isolation with its most abundant sympatric parental species, SpB. Our findings show that repetitive cycles of divergence and hybridization quickly generate diversity and reproductive isolation, providing the raw material for speciation by hybridization. Hybridization can contribute to diversity from the genomic to the species level. Here, Eberlein, Hénault et al. investigate genomic, transcriptomic and phenotypic variation among wild lineages of the yeast Saccharomyces paradoxus and suggest that an incipient species has formed by recurrent hybridization.
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Affiliation(s)
- Chris Eberlein
- PROTEO, The Quebec Network for Research on Protein Function, Engineering, and Applications, Québec, QC, G1V 0A6, Canada. .,Département de Biologie, Université Laval, Québec, QC, G1V 0A6, Canada. .,Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, 1030 Ave de la Médecine, Québec, QC, G1V 0A6, Canada. .,Centre de recherche en données massives (CRDM), Université Laval, Québec, QC, G1V 0A6, Canada.
| | - Mathieu Hénault
- PROTEO, The Quebec Network for Research on Protein Function, Engineering, and Applications, Québec, QC, G1V 0A6, Canada.,Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, 1030 Ave de la Médecine, Québec, QC, G1V 0A6, Canada.,Centre de recherche en données massives (CRDM), Université Laval, Québec, QC, G1V 0A6, Canada.,Département de Biochimie, Microbiologie et Bio-informatique, Université Laval, Québec, QC, G1V 0A6, Canada
| | - Anna Fijarczyk
- PROTEO, The Quebec Network for Research on Protein Function, Engineering, and Applications, Québec, QC, G1V 0A6, Canada.,Département de Biologie, Université Laval, Québec, QC, G1V 0A6, Canada.,Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, 1030 Ave de la Médecine, Québec, QC, G1V 0A6, Canada.,Centre de recherche en données massives (CRDM), Université Laval, Québec, QC, G1V 0A6, Canada
| | - Guillaume Charron
- PROTEO, The Quebec Network for Research on Protein Function, Engineering, and Applications, Québec, QC, G1V 0A6, Canada.,Département de Biologie, Université Laval, Québec, QC, G1V 0A6, Canada.,Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, 1030 Ave de la Médecine, Québec, QC, G1V 0A6, Canada.,Centre de recherche en données massives (CRDM), Université Laval, Québec, QC, G1V 0A6, Canada
| | - Matteo Bouvier
- PROTEO, The Quebec Network for Research on Protein Function, Engineering, and Applications, Québec, QC, G1V 0A6, Canada.,Département de Biologie, Université Laval, Québec, QC, G1V 0A6, Canada.,Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, 1030 Ave de la Médecine, Québec, QC, G1V 0A6, Canada
| | - Linda M Kohn
- Departments of Ecology and Evolutionary Biology and Cell and Systems Biology, University of Toronto Mississauga, 3359 Mississauga Rd, Mississauga, ON, L5L 1C6, Canada
| | - James B Anderson
- Departments of Ecology and Evolutionary Biology and Cell and Systems Biology, University of Toronto Mississauga, 3359 Mississauga Rd, Mississauga, ON, L5L 1C6, Canada
| | - Christian R Landry
- PROTEO, The Quebec Network for Research on Protein Function, Engineering, and Applications, Québec, QC, G1V 0A6, Canada. .,Département de Biologie, Université Laval, Québec, QC, G1V 0A6, Canada. .,Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, 1030 Ave de la Médecine, Québec, QC, G1V 0A6, Canada. .,Centre de recherche en données massives (CRDM), Université Laval, Québec, QC, G1V 0A6, Canada. .,Département de Biochimie, Microbiologie et Bio-informatique, Université Laval, Québec, QC, G1V 0A6, Canada.
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10
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Bleuven C, Dubé AK, Nguyen GQ, Gagnon‐Arsenault I, Martin H, Landry CR. A collection of barcoded natural isolates of Saccharomyces paradoxus to study microbial evolutionary ecology. Microbiologyopen 2018; 8:e00773. [PMID: 30569485 PMCID: PMC6612553 DOI: 10.1002/mbo3.773] [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] [Received: 10/26/2018] [Revised: 11/05/2018] [Accepted: 11/06/2018] [Indexed: 01/24/2023] Open
Abstract
While the use of barcoded collections of laboratory microorganisms and the development of barcode-based cell tracking are rapidly developing in genetics and genomics research, tools to track natural populations are still lacking. The yeast Saccharomyces paradoxus is an emergent microbial model in ecology and evolution. More than five allopatric and sympatric lineages have been identified and hundreds of strains have been isolated for this species, allowing to assess the impact of natural diversity on complex traits. We constructed a collection of 550 barcoded and traceable strains of S. paradoxus, including all three North American lineages SpB, SpC, and SpC*. These strains are diploid, many have their genome fully sequenced and are barcoded with a unique 20 bp sequence that allows their identification and quantification. This yeast collection is functional for competitive experiments in pools as the barcodes allow to measure each lineage's and individual strains' fitness in common conditions. We used this tool to demonstrate that in the tested conditions, there are extensive genotype-by-environment interactions for fitness among S. paradoxus strains, which reveals complex evolutionary potential in variable environments. This barcoded collection provides a valuable resource for ecological genomics studies that will allow gaining a better understanding of S. paradoxus evolution and fitness-related traits.
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Affiliation(s)
- Clara Bleuven
- Département de BiologieUniversité LavalQuébecQuébecCanada,Institut de Biologie Intégrative et des Systèmes (IBIS)Université LavalQuébecQuébecCanada,Big Data Research CenterUniversité LavalQuébecQuébecCanada,PROTEO, The Quebec Network for Research on Protein Function, Engineering, and ApplicationsQuébecQuébecCanada
| | - Alexandre K. Dubé
- Département de BiologieUniversité LavalQuébecQuébecCanada,Institut de Biologie Intégrative et des Systèmes (IBIS)Université LavalQuébecQuébecCanada,Big Data Research CenterUniversité LavalQuébecQuébecCanada,PROTEO, The Quebec Network for Research on Protein Function, Engineering, and ApplicationsQuébecQuébecCanada,Département de Biochimiede Microbiologie et de Bio‐informatique, Université LavalQuébecQuébecCanada
| | - Guillaume Q. Nguyen
- Département de BiologieUniversité LavalQuébecQuébecCanada,Institut de Biologie Intégrative et des Systèmes (IBIS)Université LavalQuébecQuébecCanada,Big Data Research CenterUniversité LavalQuébecQuébecCanada,PROTEO, The Quebec Network for Research on Protein Function, Engineering, and ApplicationsQuébecQuébecCanada,Département des Sciences des aliments, Institut sur la nutrition et les aliments fonctionnels (INAF)Université LavalQuébecQuébecCanada
| | - Isabelle Gagnon‐Arsenault
- Département de BiologieUniversité LavalQuébecQuébecCanada,Institut de Biologie Intégrative et des Systèmes (IBIS)Université LavalQuébecQuébecCanada,Big Data Research CenterUniversité LavalQuébecQuébecCanada,PROTEO, The Quebec Network for Research on Protein Function, Engineering, and ApplicationsQuébecQuébecCanada,Département de Biochimiede Microbiologie et de Bio‐informatique, Université LavalQuébecQuébecCanada
| | - Hélène Martin
- Département de BiologieUniversité LavalQuébecQuébecCanada,Institut de Biologie Intégrative et des Systèmes (IBIS)Université LavalQuébecQuébecCanada,Big Data Research CenterUniversité LavalQuébecQuébecCanada,PROTEO, The Quebec Network for Research on Protein Function, Engineering, and ApplicationsQuébecQuébecCanada,Département de Biochimiede Microbiologie et de Bio‐informatique, Université LavalQuébecQuébecCanada
| | - Christian R. Landry
- Département de BiologieUniversité LavalQuébecQuébecCanada,Institut de Biologie Intégrative et des Systèmes (IBIS)Université LavalQuébecQuébecCanada,Big Data Research CenterUniversité LavalQuébecQuébecCanada,PROTEO, The Quebec Network for Research on Protein Function, Engineering, and ApplicationsQuébecQuébecCanada,Département de Biochimiede Microbiologie et de Bio‐informatique, Université LavalQuébecQuébecCanada
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11
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Linder T. A genomic survey of nitrogen assimilation pathways in budding yeasts (sub-phylum Saccharomycotina). Yeast 2018; 36:259-273. [DOI: 10.1002/yea.3364] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2018] [Revised: 11/04/2018] [Accepted: 11/12/2018] [Indexed: 12/20/2022] Open
Affiliation(s)
- Tomas Linder
- Department of Molecular Sciences; Swedish University of Agricultural Sciences; Uppsala Sweden
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12
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N'guyen GQ, Martin N, Jain M, Lagacé L, Landry CR, Filteau M. A systems biology approach to explore the impact of maple tree dormancy release on sap variation and maple syrup quality. Sci Rep 2018; 8:14658. [PMID: 30279486 PMCID: PMC6168607 DOI: 10.1038/s41598-018-32940-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2018] [Accepted: 09/19/2018] [Indexed: 12/11/2022] Open
Abstract
Maple sap is a complex nutrient matrix collected during spring to produce maple syrup. The characteristics of sap change over the production period and its composition directly impacts syrup quality. This variability could in part be attributed to changes in tree metabolism following dormancy release, but little is known about these changes in deciduous trees. Therefore, understanding the variation in sap composition associated with dormancy release could help pinpoint the causes of some defects in maple syrup. In particular, a defect known as "buddy", is an increasing concern for the industry. This off-flavor appears around the time of bud break, hence its name. To investigate sap variation related to bud break and the buddy defect, we monitored sap variation with respect to a dormancy release index (Sbb) and syrup quality. First, we looked at variation in amino acid content during this period. We observed a shift in amino acid relative proportions associated with dormancy release and found that most of them increase rapidly near the point of bud break, correlating with changes in syrup quality. Second, we identified biological processes that respond to variation in maple sap by performing a competition assay using the barcoded Saccharomyces cerevisiae prototroph deletion collection. This untargeted approach revealed that the organic sulfur content may be responsible for the development of the buddy off-flavor, and that dormancy release is necessary for the appearance of the defect, but other factors such as microbial activity may also be contributing.
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Affiliation(s)
- Guillaume Quang N'guyen
- Département des Sciences des aliments, Institut sur la nutrition et les aliments fonctionnels (INAF), Université Laval, Québec, Québec, G1V 0A6, Canada.,Département de Biologie, Département de Biochimie, Microbiologie et Bio-informatique, PROTEO, Centre de recherche en données massives and Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, Québec, G1V 0A6, Canada
| | - Nathalie Martin
- Centre de recherche, de développement et de transfert technologique acéricole Inc., Saint-Norbert-d'Arthabaska, Québec, G0P 1B0, Canada
| | - Mani Jain
- Département de Biologie, Département de Biochimie, Microbiologie et Bio-informatique, PROTEO, Centre de recherche en données massives and Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, Québec, G1V 0A6, Canada
| | - Luc Lagacé
- Centre de recherche, de développement et de transfert technologique acéricole Inc., Saint-Norbert-d'Arthabaska, Québec, G0P 1B0, Canada
| | - Christian R Landry
- Département de Biologie, Département de Biochimie, Microbiologie et Bio-informatique, PROTEO, Centre de recherche en données massives and Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, Québec, G1V 0A6, Canada
| | - Marie Filteau
- Département des Sciences des aliments, Institut sur la nutrition et les aliments fonctionnels (INAF), Université Laval, Québec, Québec, G1V 0A6, Canada.
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Persistence of Resident and Transplanted Genotypes of the Undomesticated Yeast Saccharomyces paradoxus in Forest Soil. mSphere 2018; 3:3/3/e00211-18. [PMID: 29925673 PMCID: PMC6010622 DOI: 10.1128/msphere.00211-18] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2018] [Accepted: 05/29/2018] [Indexed: 02/06/2023] Open
Abstract
Saccharomyces yeasts are intensively studied in biological research and in their domesticated roles in brewing and baking, and yet, remarkably little is known about their mode of life in forest soils. We report here that resident genotypes of the yeast S. paradoxus are persistent on a time scale of years in their microhabitats in forest soils. We also show that resident genotypes can be replaced by transplanted yeast genotypes. The high inoculum levels in experimental transplantations rapidly decreased over time, but the transplanted genotypes persisted at low abundance. We conclude that, in forest soils, Saccharomyces yeasts exist at very low abundance and that dispersal events are rare. One might expect yeasts in soil to be highly dispersed via water or insects, forming ephemeral, genetically heterogeneous populations subject to competition and environmental stochasticity. Here, we report persistence of genotypes of the yeast Saccharomyces paradoxus in space and time. Within 1 km2 in a mixed hardwood forest on scales from centimeters to tens of meters, we detected persistence over 3 years of native genotypes, identified by single nucleotide polymorphisms (SNPs) genome-wide, of the wild yeast Saccharomyces paradoxus growing around Quercus rubra and Quercus alba. Yeasts were recovered by enrichment in ethanol-containing medium, which measures only presence or absence, not abundance. Additional transplantation experiments employed strains marked with spontaneous defects in the URA3 gene, which also confer resistance to 5-fluoroorotic acid (5FOA). Plating soil suspensions from transplant sites on 5FOA-containing medium permitted one-step quantification of yeast CFU, with no interference from other unmarked yeasts or microorganisms. After an initial steep decrease in abundance, the yeast densities fluctuated over time, increasing in association with rainfall and decreasing in association with drought. After 18 months, the transplanted yeasts remained in place on the nine sites. In vitro transplantation experiments into nonsterile soil in petri dishes showed similar patterns of persistence and response to moisture and drought. To determine whether Saccharomyces cerevisiae, not previously recovered from soils regionally, can persist in our cold climate sites, we transplanted marked S. cerevisiae alone and in mixture with S. paradoxus in the fall of 2017. Five months later, S. cerevisiae persisted to the same extent as S. paradoxus. IMPORTANCESaccharomyces yeasts are intensively studied in biological research and in their domesticated roles in brewing and baking, and yet, remarkably little is known about their mode of life in forest soils. We report here that resident genotypes of the yeast S. paradoxus are persistent on a time scale of years in their microhabitats in forest soils. We also show that resident genotypes can be replaced by transplanted yeast genotypes. The high inoculum levels in experimental transplantations rapidly decreased over time, but the transplanted genotypes persisted at low abundance. We conclude that, in forest soils, Saccharomyces yeasts exist at very low abundance and that dispersal events are rare.
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Marsit S, Leducq JB, Durand É, Marchant A, Filteau M, Landry CR. Evolutionary biology through the lens of budding yeast comparative genomics. Nat Rev Genet 2017; 18:581-598. [DOI: 10.1038/nrg.2017.49] [Citation(s) in RCA: 55] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
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15
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Yeast Population Genomics Goes Wild: The Case of Saccharomyces paradoxus. POPULATION GENOMICS: MICROORGANISMS 2017. [DOI: 10.1007/13836_2017_4] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
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