Transcriptomics Provides a Genetic Signature of Vineyard Site and Offers Insight into Vintage-Independent Inoculated Fermentation Outcomes

ABSTRACT Ribosomal DNA amplicon sequencing of grape musts has demonstrated that microorganisms occur nonrandomly and are associated with the vineyard of origin, suggesting a role for the vineyard, grape, and wine microbiome in shaping wine fermentation outcomes. Here, ribosomal DNA amplicon sequenci...

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Autores principales:	Taylor Reiter, Rachel Montpetit, Shelby Byer, Isadora Frias, Esmeralda Leon, Robert Viano, Michael Mcloughlin, Thomas Halligan, Desmon Hernandez, Rosa Figueroa-Balderas, Dario Cantu, Kerri Steenwerth, Ron Runnebaum, Ben Montpetit
Formato:	article
Lenguaje:	EN
Publicado:	American Society for Microbiology 2021
Materias:	Saccharomyces cerevisiae fermentation gene expression microbiome transcriptomics Microbiology QR1-502
Acceso en línea:	https://doaj.org/article/bc6dc848e5e24233846bd73dfa8aedd6
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spelling	oai:doaj.org-article:bc6dc848e5e24233846bd73dfa8aedd62021-12-02T18:21:19ZTranscriptomics Provides a Genetic Signature of Vineyard Site and Offers Insight into Vintage-Independent Inoculated Fermentation Outcomes10.1128/mSystems.00033-212379-5077https://doaj.org/article/bc6dc848e5e24233846bd73dfa8aedd62021-04-01T00:00:00Zhttps://journals.asm.org/doi/10.1128/mSystems.00033-21https://doaj.org/toc/2379-5077ABSTRACT Ribosomal DNA amplicon sequencing of grape musts has demonstrated that microorganisms occur nonrandomly and are associated with the vineyard of origin, suggesting a role for the vineyard, grape, and wine microbiome in shaping wine fermentation outcomes. Here, ribosomal DNA amplicon sequencing from grape musts and RNA sequencing of eukaryotic transcripts from primary fermentations inoculated with the wine yeast Saccharomyces cerevisiae RC212 were used to profile fermentations from 15 vineyards in California and Oregon across two vintages. These data demonstrate that the relative abundance of fungal organisms detected by ribosomal DNA amplicon sequencing correlated with neither transcript abundance from those same organisms within the RNA sequencing data nor gene expression of the inoculated RC212 yeast strain. These data suggest that the majority of the fungi detected in must by ribosomal DNA amplicon sequencing were not active during the primary stage of these inoculated fermentations and were not a major factor in determining RC212 gene expression. However, unique genetic signatures were detected within the ribosomal DNA amplicon and eukaryotic transcriptomic sequencing that were predictive of vineyard site and region. These signatures included S. cerevisiae gene expression patterns linked to nitrogen, sulfur, and thiamine metabolism. These genetic signatures of site offer insight into specific environmental factors to consider with respect to fermentation outcomes and vineyard site and regional wine characteristics. IMPORTANCE The wine industry generates billions of dollars of revenue annually, and economic productivity is in part associated with regional distinctiveness of wine sensory attributes. Microorganisms associated with grapes and wineries are influenced by region of origin, and given that some microorganisms play a role in fermentation, it is thought that microbes may contribute to the regional distinctiveness of wine. In this work, as in previous studies, it is demonstrated that specific bacteria and fungi are associated with individual wine regions and vineyard sites. However, this work further shows that their presence is not associated with detectable fungal gene expression during the primary fermentation or the expression of specific genes by the inoculate Saccharomyces cerevisiae strain RC212. The detected RC212 gene expression signatures associated with region and vineyard site also allowed the identification of flavor-associated metabolic processes and environmental factors that could impact primary fermentation outcomes. These data offer novel insights into the complexities and subtleties of vineyard-specific inoculated wine fermentation and starting points for future investigations into factors that contribute to regional wine distinctiveness.Taylor ReiterRachel MontpetitShelby ByerIsadora FriasEsmeralda LeonRobert VianoMichael McloughlinThomas HalliganDesmon HernandezRosa Figueroa-BalderasDario CantuKerri SteenwerthRon RunnebaumBen MontpetitAmerican Society for MicrobiologyarticleSaccharomyces cerevisiaefermentationgene expressionmicrobiometranscriptomicsMicrobiologyQR1-502ENmSystems, Vol 6, Iss 2 (2021)
institution	DOAJ
collection	DOAJ
language	EN
topic	Saccharomyces cerevisiae fermentation gene expression microbiome transcriptomics Microbiology QR1-502
spellingShingle	Saccharomyces cerevisiae fermentation gene expression microbiome transcriptomics Microbiology QR1-502 Taylor Reiter Rachel Montpetit Shelby Byer Isadora Frias Esmeralda Leon Robert Viano Michael Mcloughlin Thomas Halligan Desmon Hernandez Rosa Figueroa-Balderas Dario Cantu Kerri Steenwerth Ron Runnebaum Ben Montpetit Transcriptomics Provides a Genetic Signature of Vineyard Site and Offers Insight into Vintage-Independent Inoculated Fermentation Outcomes
description	ABSTRACT Ribosomal DNA amplicon sequencing of grape musts has demonstrated that microorganisms occur nonrandomly and are associated with the vineyard of origin, suggesting a role for the vineyard, grape, and wine microbiome in shaping wine fermentation outcomes. Here, ribosomal DNA amplicon sequencing from grape musts and RNA sequencing of eukaryotic transcripts from primary fermentations inoculated with the wine yeast Saccharomyces cerevisiae RC212 were used to profile fermentations from 15 vineyards in California and Oregon across two vintages. These data demonstrate that the relative abundance of fungal organisms detected by ribosomal DNA amplicon sequencing correlated with neither transcript abundance from those same organisms within the RNA sequencing data nor gene expression of the inoculated RC212 yeast strain. These data suggest that the majority of the fungi detected in must by ribosomal DNA amplicon sequencing were not active during the primary stage of these inoculated fermentations and were not a major factor in determining RC212 gene expression. However, unique genetic signatures were detected within the ribosomal DNA amplicon and eukaryotic transcriptomic sequencing that were predictive of vineyard site and region. These signatures included S. cerevisiae gene expression patterns linked to nitrogen, sulfur, and thiamine metabolism. These genetic signatures of site offer insight into specific environmental factors to consider with respect to fermentation outcomes and vineyard site and regional wine characteristics. IMPORTANCE The wine industry generates billions of dollars of revenue annually, and economic productivity is in part associated with regional distinctiveness of wine sensory attributes. Microorganisms associated with grapes and wineries are influenced by region of origin, and given that some microorganisms play a role in fermentation, it is thought that microbes may contribute to the regional distinctiveness of wine. In this work, as in previous studies, it is demonstrated that specific bacteria and fungi are associated with individual wine regions and vineyard sites. However, this work further shows that their presence is not associated with detectable fungal gene expression during the primary fermentation or the expression of specific genes by the inoculate Saccharomyces cerevisiae strain RC212. The detected RC212 gene expression signatures associated with region and vineyard site also allowed the identification of flavor-associated metabolic processes and environmental factors that could impact primary fermentation outcomes. These data offer novel insights into the complexities and subtleties of vineyard-specific inoculated wine fermentation and starting points for future investigations into factors that contribute to regional wine distinctiveness.
format	article
author	Taylor Reiter Rachel Montpetit Shelby Byer Isadora Frias Esmeralda Leon Robert Viano Michael Mcloughlin Thomas Halligan Desmon Hernandez Rosa Figueroa-Balderas Dario Cantu Kerri Steenwerth Ron Runnebaum Ben Montpetit
author_facet	Taylor Reiter Rachel Montpetit Shelby Byer Isadora Frias Esmeralda Leon Robert Viano Michael Mcloughlin Thomas Halligan Desmon Hernandez Rosa Figueroa-Balderas Dario Cantu Kerri Steenwerth Ron Runnebaum Ben Montpetit
author_sort	Taylor Reiter
title	Transcriptomics Provides a Genetic Signature of Vineyard Site and Offers Insight into Vintage-Independent Inoculated Fermentation Outcomes
title_short	Transcriptomics Provides a Genetic Signature of Vineyard Site and Offers Insight into Vintage-Independent Inoculated Fermentation Outcomes
title_full	Transcriptomics Provides a Genetic Signature of Vineyard Site and Offers Insight into Vintage-Independent Inoculated Fermentation Outcomes
title_fullStr	Transcriptomics Provides a Genetic Signature of Vineyard Site and Offers Insight into Vintage-Independent Inoculated Fermentation Outcomes
title_full_unstemmed	Transcriptomics Provides a Genetic Signature of Vineyard Site and Offers Insight into Vintage-Independent Inoculated Fermentation Outcomes
title_sort	transcriptomics provides a genetic signature of vineyard site and offers insight into vintage-independent inoculated fermentation outcomes
publisher	American Society for Microbiology
publishDate	2021
url	https://doaj.org/article/bc6dc848e5e24233846bd73dfa8aedd6
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Transcriptomics Provides a Genetic Signature of Vineyard Site and Offers Insight into Vintage-Independent Inoculated Fermentation Outcomes

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