Transcriptomics provides a genetic signature of vineyard site with insight into vintage-independent regional wine characteristics

Reiter, Taylor; Montpetit, Rachel; Byer, Shelby; Frias, Isadora; Leon, Esmeralda; Viano, Robert; McLoughlin, Michael; Halligan, Thomas; Hernandez, Desmond; Figueroa‐Balderas, Rosa; Steenwerth, Kerri L.; Runnebaum, Ron C.; Montpetit, Ben

doi:10.1101/2021.01.07.425830

Cited by 3 publications

(3 citation statements)

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“…Microbial communities colonizing grapevine compartments change in composition throughout the growing season in response to phenological and environmental changes (Martins et al, 2012). Grapevine microbiomes also exhibit interannual variation (probably in response to weather), but remain semistable between regions and across vintages (Bokulich et al, 2014;Cheng et al, 2020;Reiter et al, 2021). How do we account for these findings in understanding the microbial source-sink relationships between vines and the site-defined regional pool?…”

Section: Site Effects: a Combination Of Environment And Microbial Sourcesmentioning

confidence: 99%

“…The potential impacts by specific microbiota derive from interactions among vineyard site, variety, and viticultural practices (Bokulich et al, 2014(Bokulich et al, , 2016. Similarly, microorganisms exert both positive and negative effects on wine quality before, during, and following fermentation (Domizio et al, 2014(Domizio et al, , 2017Blanco-Ulate et al, 2015;Belda et al, 2017;Hall et al, 2017;Reiter et al, 2021), spurring recent interest in the use of non-Saccharomyces yeasts in winemaking (Jolly et al, 2003(Jolly et al, , 2014.…”

Section: Introductionmentioning

confidence: 99%

“…Geographic distance is often a primary factor correlated with these differences, though it is unclear if it is merely a proxy for these other drivers (Burns et al, 2015;Miura et al, 2017). For example, microbiota in musts appear to correlate with vineyard and regional level climate and weather patterns (Bokulich et al, 2014;Reiter et al, 2021;Steenwerth et al, 2021), human activity, and human transport between vineyards in the case of S. cerevisiae (Goddard et al, 2010;Gayevskiy et al, 2016). Site, encompassing the specific environmental constraints of a single place (e.g., vineyard or block), is commonly the most explanatory variable in studies of microbiome assembly in other plants, suggesting that vineyard-specific microbiomes should not come as a surprise (Knief et al, 2010;Rastogi et al, 2012;Coleman-Derr et al, 2016;Wagner et al, 2016).…”

Section: Introductionmentioning

confidence: 99%

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Sources and Assembly of Microbial Communities in Vineyards as a Functional Component of Winegrowing

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Microbiomes are integral to viticulture and winemaking – collectively termed winegrowing – where diverse fungi and bacteria can exert positive and negative effects on grape health and wine quality. Wine is a fermented natural product, and the vineyard serves as a key point of entry for quality-modulating microbiota, particularly in wine fermentations that are conducted without the addition of exogenous yeasts. Thus, the sources and persistence of wine-relevant microbiota in vineyards critically impact its quality. Site-specific variations in microbiota within and between vineyards may contribute to regional wine characteristics. This includes distinctions in microbiomes and microbiota at the strain level, which can contribute to wine flavor and aroma, supporting the role of microbes in the accepted notion of terroir as a biological phenomenon. Little is known about the factors driving microbial biodiversity within and between vineyards, or those that influence annual assembly of the fruit microbiome. Fruit is a seasonally ephemeral, yet annually recurrent product of vineyards, and as such, understanding the sources of microbiota in vineyards is critical to the assessment of whether or not microbial terroir persists with inter-annual stability, and is a key factor in regional wine character, as stable as the geographic distances between vineyards. This review examines the potential sources and vectors of microbiota within vineyards, general rules governing plant microbiome assembly, and how these factors combine to influence plant-microbe interactions relevant to winemaking.

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Section: Site Effects: a Combination Of Environment And Microbial Sourcesmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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Sources and Assembly of Microbial Communities in Vineyards as a Functional Component of Winegrowing

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Saccharomyces cerevisiaegene expression during fermentation of Pinot noir wines at industrially relevant scale

Reiter

Montpetit

Byer

et al. 2021

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During a wine fermentation, Saccharomyces cerevisiae transforms grape must through metabolic activities that generate ethanol and other compounds. Thousands of genes change expression over the course of a wine fermentation to allow S. cerevisiae to adapt to and dominate the fermentation environment. Investigations into these gene expression patterns have previously revealed genes that underlie cellular adaptation to the grape must and wine environment involving metabolic specialization and ethanol tolerance. However, the vast majority of studies detailing gene expression patterns have occurred in controlled environments that do not recapitulate the biological and chemical complexity of fermentations performed at production scale. Here, we present an analysis of the S. cerevisiae RC212 gene expression program across 40 pilot-scale fermentations (150 liters) using Pinot noir grapes from 10 California vineyards across two vintages. We observe a core gene expression program across all fermentations irrespective of vintage similar to that of laboratory fermentations, in addition to novel gene expression patterns likely related to the presence of non-Saccharomyces microorganisms and oxygen availability during fermentation. These gene expression patterns, both common and diverse, provide insight into Saccharomyces cerevisiae biology critical to fermentation outcomes at industry-relevant scales.ImportanceThis study characterized Saccharomyces cerevisiae RC212 gene expression during Pinot noir fermentation at pilot scale (150 liters) using production-relevant conditions. The reported gene expression patterns of RC212 is generally similar to that observed in laboratory fermentation conditions, but also contains gene expression signatures related to yeast-environment interactions found in a production setting (e.g., presence of non-Saccharomyces microorganisms). Key genes and pathways highlighted by this work remain under-characterized, raising the need for further research to understand the roles of these genes and their impact on industrial wine fermentation outcomes.

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Mapping global shifts inSaccharomyces cerevisiaegene expression across asynchronous time trajectories with diffusion maps

Reiter

Montpetit

Runnebaum

et al. 2021

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Grapes grown in a particular geographic region often produce wines with consistent characteristics, suggesting there are site-specific factors driving recurrent fermentation outcomes. However, our understanding of the relationship between site-specific factors, microbial metabolism, and wine fermentation outcomes are not well understood. Here, we used differences in Saccharomyces cerevisiae gene expression as a biosensor for differences among Pinot noir fermentations from 15 vineyard sites. We profiled time series gene expression patterns of primary fermentations, but fermentations proceeded at different rates, making analyzes of these data with conventional differential expression tools difficult. This led us to develop a novel approach that combines diffusion mapping with continuous differential expression analysis. Using this method, we identified vineyard specific deviations in gene expression, including changes in gene expression correlated with the activity of the non-Saccharomyces yeastHanseniaspora uvarum, as well as with initial nitrogen concentrations in grape musts. These results highlight novel relationships between site-specific variables and Saccharomyces cerevisiae gene expression that are linked to repeated wine fermentation outcomes. In addition, we demonstrate that our analysis approach can extract biologically relevant gene expression patterns in other contexts (e.g., hypoxic response of Saccharomyces cerevisiae), indicating that this approach offers a general method for investigating asynchronous time series gene expression data.

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Transcriptomics provides a genetic signature of vineyard site with insight into vintage-independent regional wine characteristics

Cited by 3 publications

References 96 publications

Sources and Assembly of Microbial Communities in Vineyards as a Functional Component of Winegrowing

Sources and Assembly of Microbial Communities in Vineyards as a Functional Component of Winegrowing

Saccharomyces cerevisiaegene expression during fermentation of Pinot noir wines at industrially relevant scale

Mapping global shifts inSaccharomyces cerevisiaegene expression across asynchronous time trajectories with diffusion maps

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