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Bunbury-Blanchette AL, Fan L, Kernaghan G. Yeast communities of a North American hybrid wine grape differ between organic and conventional vineyards. J Appl Microbiol 2024; 135:lxae092. [PMID: 38621715 DOI: 10.1093/jambio/lxae092] [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: 12/08/2023] [Revised: 03/20/2024] [Accepted: 04/13/2024] [Indexed: 04/17/2024]
Abstract
AIMS To compare the species diversity and composition of indigenous yeast communities of hybrid grapes from conventionally and organically cultivated vineyards of an emerging cool-climate wine producing region. METHODS AND RESULTS Illumina MiSeq sequences from L'Acadie blanc grape musts were processed and filtered to characterize indigenous yeast communities in organic and conventional vineyards of the Annapolis Valley wine region in Nova Scotia, Canada. While cultivation practice was not associated with yeast diversity or species richness, there was a strong effect on yeast community composition, with conventional vineyards characterized by higher proportions of Sporidiobolales and Filobasidium magnum, and organic vineyards supporting Filobasidium species other than F. magnum and higher proportions of Symmetrospora. There was also variation in yeast community composition among individual vineyards, and from year to year. CONCLUSIONS This is the first comprehensive assessment of yeasts associated with hybrid grapes grown using different cultivation practices in a North American cool climate wine region. Communities were dominated by basidiomycete yeasts and species composition of these yeasts differed significantly between vineyards employing organic and conventional cultivation practices. The role of basidiomycete yeasts in winemaking is not well understood, but some species may influence wine characteristics.
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Affiliation(s)
- Adele L Bunbury-Blanchette
- Saint Mary's University, Faculty of Graduate Studies and Research, 923 Robie St, Atrium Building, Suite 210, Halifax, Nova Scotia B3H 1G3, Canada
| | - Lihua Fan
- Agriculture and Agri-Food Canada, Kentville Research and Development Centre, 32 Main St, Kentville, Nova Scotia B4N 1J5, Canada
| | - Gavin Kernaghan
- Mount Saint Vincent University, Department of Biology, 166 Bedford Highway, Halifax, Nova Scotia, B3M 1J9, Canada
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2
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Ohwofasa A, Dhami M, Zhang J, Tian B, Winefield C, On SLW. Influence of climatic variation on microbial communities during organic Pinot noir wine production. PLoS One 2024; 19:e0296859. [PMID: 38416719 PMCID: PMC10901304 DOI: 10.1371/journal.pone.0296859] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2023] [Accepted: 12/20/2023] [Indexed: 03/01/2024] Open
Abstract
To assess the possible impact of climatic variation on microbial community composition in organic winemaking, we employed a metabarcoding approach to scrutinize the microbiome in a commercial, organic, Pinot noir wine production system that utilizes autochthonous fermentation. We assessed microbial composition across two vintages (2018 and 2021) using biological replicates co-located at the same winery. Microbial dynamics were monitored over four important fermentation time points and correlated with contemporaneous climate data. Bacterial (RANOSIM = 0.4743, p = 0.0001) and fungal (RANOSIM = 0.4738, p = 0.0001) compositions were different in both vintages. For bacteria, Lactococcus dominated the diversity associated with the 2018 vintage, while Tatumella dominated the 2021 vintage. For fungal populations, while Saccharomyces were abundant in both vintages, key differences included Starmerella, copious in the 2018 vintage; and Metschnikowia, substantive in the 2021 vintage. Ordination plots correlated the climatic variables with microbial population differences, indicating temperature as a particularly important influence; humidity values also differed significantly between these vintages. Our data illustrates how climatic conditions may influence microbial diversity during winemaking, and further highlights the effect climate change could have on wine production.
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Affiliation(s)
- Aghogho Ohwofasa
- Department of Wine, Food and Molecular Biosciences, Lincoln University, Lincoln, New Zealand
- Centre of Foods for Future Consumers, Lincoln University, Lincoln, New Zealand
| | | | - Junwen Zhang
- Department of Wine, Food and Molecular Biosciences, Lincoln University, Lincoln, New Zealand
| | - Bin Tian
- Department of Wine, Food and Molecular Biosciences, Lincoln University, Lincoln, New Zealand
| | - Christopher Winefield
- Department of Wine, Food and Molecular Biosciences, Lincoln University, Lincoln, New Zealand
| | - Stephen L. W. On
- Department of Wine, Food and Molecular Biosciences, Lincoln University, Lincoln, New Zealand
- Centre of Foods for Future Consumers, Lincoln University, Lincoln, New Zealand
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3
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Papadopoulou E, Bekris F, Vasileiadis S, Krokida A, Rouvali T, Veskoukis AS, Liadaki K, Kouretas D, Karpouzas DG. Vineyard-mediated factors are still operative in spontaneous and commercial fermentations shaping the vinification microbial community and affecting the antioxidant and anticancer properties of wines. Food Res Int 2023; 173:113359. [PMID: 37803700 DOI: 10.1016/j.foodres.2023.113359] [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: 05/31/2023] [Revised: 07/27/2023] [Accepted: 08/03/2023] [Indexed: 10/08/2023]
Abstract
The grapevine and vinification microbiota have a strong influence on the characteristics of the produced wine. Currently we have a good understanding of the role of vineyard-associated factors, like cultivar, vintage and terroir in shaping the grapevine microbiota. Notwithstanding, their endurance along the vinification process remains unknown. Thus, the main objective of our study was to determine how these factors influence (a) microbial succession during fermentation (i.e., bacterial and fungal) and (b) the antioxidant, antimutagenic and anticancer potential of the produced wines. These were evaluated under different vinification strategies (i.e., spontaneous V1, spontaneous with preservatives V2, commercial V3), employed at near full-scale level by local wineries, for two cultivars (Roditis and Sideritis), two terroir types, and two vintages. Cultivar and vintage were strong and persistent determinants of the vinification microbiota, unlike terroir whose effect became weaker from the vineyard, and early fermentation stages, where non-Saccharomyces yeasts, filamentous fungi (i.e., Aureobasidium, Cladosporium, Lachancea, Alternaria, Aspergillus, Torulaspora) and acetic acid bacteria (AAB) (Gluconobacter, Acetobacter, Komagataeibacter) dominated, to late fermentation stages where Saccharomyces and Oenococcus become prevalent. Besides vineyard-mediated factors, the vinification process employed was the strongest determinant of the fungal community compared to the bacterial community were effects varied per cultivar. Vintage and vinification type were the strongest determinants of the antioxidant, antimutagenic and anticancer potential of the produced wines. Further analysis identified significant positive correlations between members of the vinification microbiota like the yeasts Torulaspora debrueckii and Lachancea quebecensis with the anticancer and the antioxidant properties of wines in both cultivars. These findings could be exploited towards a microbiota-modulated vinification process to produce high-quality wines with desirable properties and enhanced regional identity.
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Affiliation(s)
- Elena Papadopoulou
- University of Thessaly, Department of Biochemistry and Biotechnology, Laboratory of Plant and Environmental Biotechnology, 41500 Viopolis - Larissa, Greece
| | - Fotiοs Bekris
- University of Thessaly, Department of Biochemistry and Biotechnology, Laboratory of Plant and Environmental Biotechnology, 41500 Viopolis - Larissa, Greece
| | - Sotirios Vasileiadis
- University of Thessaly, Department of Biochemistry and Biotechnology, Laboratory of Plant and Environmental Biotechnology, 41500 Viopolis - Larissa, Greece
| | | | | | - Aristidis S Veskoukis
- University of Thessaly, Department of Nutrition and Dietetics, 42132 Trikala, Greece
| | - Kalliopi Liadaki
- University of Thessaly, Department of Biochemistry and Biotechnology, Laboratory of Plant and Environmental Biotechnology, 41500 Viopolis - Larissa, Greece
| | - Demetrios Kouretas
- University of Thessaly, Department of Biochemistry and Biotechnology, Laboratory of Animal Physiology, 41500 Viopolis - Larissa, Greece
| | - Dimitrios G Karpouzas
- University of Thessaly, Department of Biochemistry and Biotechnology, Laboratory of Plant and Environmental Biotechnology, 41500 Viopolis - Larissa, Greece.
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4
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Ohwofasa A, Dhami M, Tian B, Winefield C, On SL. Environmental influences on microbial community development during organic pinot noir wine production in outdoor and indoor fermentation conditions. Heliyon 2023; 9:e15658. [PMID: 37206017 PMCID: PMC10189187 DOI: 10.1016/j.heliyon.2023.e15658] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2023] [Revised: 04/17/2023] [Accepted: 04/19/2023] [Indexed: 05/21/2023] Open
Abstract
The role of microbial diversity in influencing the organoleptic properties of wine and other fermented products is well est ablished, and understanding microbial dynamics within fermentation processes can be critical for quality assurance and product innovation. This is especially true for winemakers using spontaneous fermentation techniques, where environmental factors may play an important role in consistency of product. Here, we use a metabarcoding approach to investigate the influence of two environmental systems used by an organic winemaker to produce wines; vineyard (outdoors) and winery (indoors) to the bacterial and fungal communities throughout the duration of a spontaneous fermentation of the same batch of Pinot Noir grapes. Bacterial (RANOSIM = 0.5814, p = 0.0001) and fungal (RANOSIM = 0.603, p = 0.0001) diversity differed significantly across the fermentation stages in both systems. Members of the Hyphomicrobium genus were found in winemaking for the first time, as a bacterial genus that can survive alcoholic fermentation. Our results also indicate that Torulaspora delbrueckii and Fructobacillus species might be sensitive to environmental systems. These results clearly reflect the substantial influence that environmental conditions exert on microbial populations at every point in the process of transforming grape juice to wine via fermentation, and offer new insights into the challenges and opportunities for wine production in an ever-changing global climate.
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Affiliation(s)
- Aghogho Ohwofasa
- Department of Wine, Food and Molecular Biosciences, Lincoln University, Lincoln 7647, New Zealand
- Centre of Foods for Future Consumers, Lincoln University, Lincoln 7647, New Zealand
| | - Manpreet Dhami
- Manaaki Whenua - Landcare Research, Lincoln, New Zealand
| | - Bin Tian
- Department of Wine, Food and Molecular Biosciences, Lincoln University, Lincoln 7647, New Zealand
| | - Christopher Winefield
- Department of Wine, Food and Molecular Biosciences, Lincoln University, Lincoln 7647, New Zealand
| | - Stephen L.W. On
- Department of Wine, Food and Molecular Biosciences, Lincoln University, Lincoln 7647, New Zealand
- Centre of Foods for Future Consumers, Lincoln University, Lincoln 7647, New Zealand
- Corresponding author. Department of Wine, Food and Molecular Biosciences, Lincoln University, Lincoln 7647, New Zealand.
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5
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Ding Y, Wei R, Wang L, Wang W, Wang H, Li H. Exploring the ecological characteristics of natural microbial communities along the continuum from grape berries to winemaking. Food Res Int 2023; 167:112718. [PMID: 37087276 DOI: 10.1016/j.foodres.2023.112718] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2022] [Revised: 03/02/2023] [Accepted: 03/14/2023] [Indexed: 03/30/2023]
Abstract
Under natural conditions, a complex and dynamic microbial ecosystem exists on the grape epidermis, which plays an important role in safeguarding grape health and facilitating the conversion of grapes into wine. However, current viticulture and vinification are flooded with excessive chemical additives and commercial ferments, leading to a reduction in microbial diversity, affecting the ecological balance of the natural microbiota and masking the wine terroir. This experiment comprehensively explored the continuous changes in the natural microbiota from the Ecolly (Vitis vinifera L.) grape epidermis to spontaneous fermentation over two years. The results suggested that microbial community structure and composition were significantly influenced by vintage and growing stage, with fungal genera being more stable than bacterial genera during the growing season. The fungal genera Alternaria, Ascochyta, Gibberella and Dissoconium and the bacterial genera Pantoea, Sediminibacterium, Ralstonia and Sphingomonas were mainly present on the grape epidermis in both years. The natural microbial diversity decreased from grape growth to spontaneous fermentation, and the fermentation environment reshapes the community structure, composition and diversity of the wine microbial consortium. These findings provide insights to promote cultivation and fermentation management strategies, advocate natural terroir attributes for grapes and wines, and promote sustainable development of the wine industry.
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6
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Bunbury-Blanchette AL, Fan L, English MM, Kernaghan G. Yeast communities before and after spontaneous fermentation of wine grapes: a case study from Nova Scotia. Can J Microbiol 2023; 69:32-43. [PMID: 36288607 DOI: 10.1139/cjm-2022-0179] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
Wine fermentations are generally completed by the domestic yeast Saccharomyces cerevisiae, but many indigenous vineyard yeasts also influence wine flavour and aroma. Despite the flourishing wine industry in Nova Scotia, there has yet to be any systematic evaluation of these yeasts in Atlantic Canada. The yeast communities of pressed L'Acadie blanc grapes sampled from an organic vineyard in the Annapolis Valley in 2018 and 2019 were characterized before and after spontaneous fermentation by both Illumina and PacBio sequencing, to address and compare potential platform biases. Chemical and sensory evaluations were also conducted. Basidiomycete yeasts, including Vishniacozyma carnescens, Filobasidium globisporum, and Curvibasidium cygneicollum, dominated pre-fermentation diversity. Species of Saccharomyces made up ∼0.04% of sequences prior to fermentation, but 85%-100% after fermentation, with some replicates dominated by S. cerevisiae and some by S. uvarum. PacBio sequencing detected high proportions of Hanseniaspora uvarum, while Illumina sequencing did not. A better understanding of Nova Scotia vineyard yeast communities will allow local wine makers to make better use of non-traditional yeasts and spontaneous fermentations to produce high-quality wines unique to the region.
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Affiliation(s)
- Adele L Bunbury-Blanchette
- Faculty of Graduate Studies and Research, Saint Mary's University, 923 Robie St, Atrium Building, Suite 210, Halifax, NS, Canada
| | - Lihua Fan
- Kentville Research and Development Centre, Agriculture and Agri-Food Canada, 32 Main St, Kentville, NS, Canada
| | - Marcia M English
- Department of Human Nutrition, St. Francis-Xavier University, 2320 Notre Dame Ave, J. Bruce Brown Hall 208, Antigonish, NS, Canada
| | - Gavin Kernaghan
- Department of Biology, Mount Saint Vincent University, 166 Bedford Highway, Halifax, NS, Canada
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7
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Yang C, Tang W, Sun J, Guo H, Sun S, Miao F, Yang G, Zhao Y, Wang Z, Sun J. Weeds in the Alfalfa Field Decrease Rhizosphere Microbial Diversity and Association Networks in the North China Plain. Front Microbiol 2022; 13:840774. [PMID: 35418969 PMCID: PMC8998637 DOI: 10.3389/fmicb.2022.840774] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2021] [Accepted: 02/07/2022] [Indexed: 11/16/2022] Open
Abstract
The competition between weeds and crops for soil nutrients is affected by soil microorganisms, which drive diverse ecological processes and are critical in maintaining the stability of agroecosystems. However, the effects of plant species identity, particularly between forage and weed, on soil microbial diversity, composition, and association are not well understood. Here, we investigate the soil physicochemical properties and bacterial/fungal communities in an agroecosystem with native alfalfa [Medicago stativa (Ms)] and five common weed species (Digitaria sanguinalis, Echinochloa crusgalli, Acalypha australis, Portulaca oleracea, and Chenopodium album) in the North China Plain. The five weeds had a lower plant carbon content than Ms. while the opposite was true for plant nitrogen and phosphorus concentrations. The Shannon diversity of bacterial and fungal communities of the five weeds were significantly lower than in Ms. Soil pH and PO43−-P were identified as the most important factors in shaping the relative abundances of bacteria (Sphingomonadaceae) and fungi (Pleosporaceae), respectively. Importantly, the weeds greatly inhibited the growth of pathogenic fungi (Nectriaceae and Pleosporaceae). Bacterial co-occurrence networks depended on specific species, indicating that Ms. harbored co-occurrence networks that were more complex than those in the bacterial communities of other weed groups. Our study examines how soil nutrients and the soil microbial community structure of five weed species changed in an Ms. field. This analysis of the microbial ecological network enhances our understanding of the influence of weeds on the soil microbiome in agroecosystems.
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Affiliation(s)
- Chao Yang
- College of Grassland Science, Grassland Agri-Husbandry Research Center, Qingdao Agricultural University, Qingdao, China
- Key Laboratory of National Forestry and Grassland Administration on Grassland Resources and Ecology in the Yellow River Delta, Qingdao, China
| | - Wei Tang
- College of Grassland Science, Grassland Agri-Husbandry Research Center, Qingdao Agricultural University, Qingdao, China
- Key Laboratory of National Forestry and Grassland Administration on Grassland Resources and Ecology in the Yellow River Delta, Qingdao, China
| | - Junqi Sun
- College of Grassland Science, Grassland Agri-Husbandry Research Center, Qingdao Agricultural University, Qingdao, China
| | - Haipeng Guo
- College of Grassland Science, Grassland Agri-Husbandry Research Center, Qingdao Agricultural University, Qingdao, China
| | - Shusheng Sun
- College of Grassland Science, Grassland Agri-Husbandry Research Center, Qingdao Agricultural University, Qingdao, China
| | - Fuhong Miao
- College of Grassland Science, Grassland Agri-Husbandry Research Center, Qingdao Agricultural University, Qingdao, China
- Key Laboratory of National Forestry and Grassland Administration on Grassland Resources and Ecology in the Yellow River Delta, Qingdao, China
| | - Guofeng Yang
- College of Grassland Science, Grassland Agri-Husbandry Research Center, Qingdao Agricultural University, Qingdao, China
- Key Laboratory of National Forestry and Grassland Administration on Grassland Resources and Ecology in the Yellow River Delta, Qingdao, China
| | - Yiran Zhao
- College of Grassland Science, Grassland Agri-Husbandry Research Center, Qingdao Agricultural University, Qingdao, China
- Key Laboratory of National Forestry and Grassland Administration on Grassland Resources and Ecology in the Yellow River Delta, Qingdao, China
| | - Zengyu Wang
- College of Grassland Science, Grassland Agri-Husbandry Research Center, Qingdao Agricultural University, Qingdao, China
- Key Laboratory of National Forestry and Grassland Administration on Grassland Resources and Ecology in the Yellow River Delta, Qingdao, China
| | - Juan Sun
- College of Grassland Science, Grassland Agri-Husbandry Research Center, Qingdao Agricultural University, Qingdao, China
- Key Laboratory of National Forestry and Grassland Administration on Grassland Resources and Ecology in the Yellow River Delta, Qingdao, China
- *Correspondence: Juan Sun,
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8
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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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9
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Reiter T, Montpetit R, Byer S, Frias I, Leon E, Viano R, Mcloughlin M, Halligan T, Hernandez D, Figueroa-Balderas R, Cantu D, Steenwerth K, Runnebaum R, Montpetit B. Transcriptomics Provides a Genetic Signature of Vineyard Site and Offers Insight into Vintage-Independent Inoculated Fermentation Outcomes. mSystems 2021; 6:e00033-21. [PMID: 33850038 PMCID: PMC8546962 DOI: 10.1128/msystems.00033-21] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2021] [Accepted: 03/16/2021] [Indexed: 01/04/2023] Open
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.
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Affiliation(s)
- Taylor Reiter
- Food Science Graduate Group, University of California Davis, Davis, California, USA
- Department of Viticulture and Enology, University of California Davis, Davis, California, USA
- Department of Population Health and Reproduction, University of California, Davis, California, USA
| | - Rachel Montpetit
- Department of Viticulture and Enology, University of California Davis, Davis, California, USA
| | - Shelby Byer
- Department of Viticulture and Enology, University of California Davis, Davis, California, USA
| | - Isadora Frias
- Department of Viticulture and Enology, University of California Davis, Davis, California, USA
| | - Esmeralda Leon
- Department of Chemical Engineering, University of California, Davis, California, USA
| | - Robert Viano
- Department of Chemical Engineering, University of California, Davis, California, USA
| | - Michael Mcloughlin
- Department of Chemical Engineering, University of California, Davis, California, USA
| | - Thomas Halligan
- Department of Chemical Engineering, University of California, Davis, California, USA
| | - Desmon Hernandez
- Department of Chemical Engineering, University of California, Davis, California, USA
| | - Rosa Figueroa-Balderas
- Department of Viticulture and Enology, University of California Davis, Davis, California, USA
| | - Dario Cantu
- Department of Viticulture and Enology, University of California Davis, Davis, California, USA
| | - Kerri Steenwerth
- Crops Pathology and Genetics Research Unit, USDA Agricultural Research Service, Davis, California, USA
| | - Ron Runnebaum
- Department of Viticulture and Enology, University of California Davis, Davis, California, USA
- Department of Chemical Engineering, University of California, Davis, California, USA
| | - Ben Montpetit
- Food Science Graduate Group, University of California Davis, Davis, California, USA
- Department of Viticulture and Enology, University of California Davis, Davis, California, USA
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10
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Griggs RG, Steenwerth KL, Mills DA, Cantu D, Bokulich NA. Sources and Assembly of Microbial Communities in Vineyards as a Functional Component of Winegrowing. Front Microbiol 2021; 12:673810. [PMID: 33927711 PMCID: PMC8076609 DOI: 10.3389/fmicb.2021.673810] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2021] [Accepted: 03/22/2021] [Indexed: 01/05/2023] Open
Abstract
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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Affiliation(s)
- Reid G Griggs
- Department of Viticulture and Enology, Robert Mondavi Institute for Wine and Food Science, University of California, Davis, Davis, CA, United States
| | - Kerri L Steenwerth
- USDA-ARS, Crops Pathology and Genetics Research Unit, Department of Land, Air and Water Resources, University of California, Davis, Davis, CA, United States
| | - David A Mills
- Department of Viticulture and Enology, Robert Mondavi Institute for Wine and Food Science, University of California, Davis, Davis, CA, United States.,Department of Food Science and Technology, Robert Mondavi Institute for Wine and Food Science, University of California, Davis, Davis, CA, United States.,Foods for Health Institute, University of California, Davis, Davis, CA, United States
| | - Dario Cantu
- Department of Viticulture and Enology, Robert Mondavi Institute for Wine and Food Science, University of California, Davis, Davis, CA, United States
| | - Nicholas A Bokulich
- Laboratory of Food Systems Biotechnology, Institute of Food, Nutrition and Health, ETH Zurich, Zurich, Switzerland
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