1
|
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.
Collapse
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.
| |
Collapse
|
2
|
Balmaseda A, Lorentzen M, Dutilh L, Bauduin R, Guichard H, Ollivier S, Miot-Sertier C, Lucas PM. Alcoholic fermentation drives the selection of Oenococcus oeni strains in wine but not in cider. Int J Food Microbiol 2023; 400:110276. [PMID: 37270987 DOI: 10.1016/j.ijfoodmicro.2023.110276] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2023] [Revised: 05/10/2023] [Accepted: 05/28/2023] [Indexed: 06/06/2023]
Abstract
Oenococcus oeni is the predominant lactic acid bacteria species in wine and cider, where it performs the malolactic fermentation (MLF). The O. oeni strains analyzed to date form four major genetic lineages named phylogroups A, B, C and D. Most of the strains isolated from wine, cider, or kombucha belong to phylogroups A, B + C, and D, respectively, although B and C strains were also detected in wine. This study was performed to better understand the distribution of the phylogroups in wine and cider. Their population dynamics were determined by qPCR all through wine and cider productions, and the behavior of the strains was analyzed in synthetic wines and ciders. Phylogroups A, B and C were all represented in grape must and throughout the alcoholic fermentation, but on the transition to MLF, only phylogroup A remained at high levels in all wine productions. In the case of cider, phylogroups A, B and C were detected in stable levels during the process. When they were tested in synthetic wine and cider, all phylogroups performed MLF, but with different survival rates depending on the ethanol content. In this sense, ethanol and fermentation kinetics are the main agent that drives the selection of phylogroup A strains in wine, while B and C strains dominates in cider containing less ethanol.
Collapse
Affiliation(s)
- Aitor Balmaseda
- Univ. Bordeaux, INRAE, Bordeaux INP, UMR 1366, OENO, ISVV, F-33140 Villenave d'Ornon, France; Bordeaux Sciences Agro, F-33170 Gradignan, France; Universitat Rovira i Virgili, Departament de Bioquímica i Biotecnologia, Facultat d'Enologia, Grup de Biotecnologia Enològica, C/Marcel·líDomingo 1, 43007 Tarragona, Catalonia, Spain.
| | - Marc Lorentzen
- Univ. Bordeaux, INRAE, Bordeaux INP, UMR 1366, OENO, ISVV, F-33140 Villenave d'Ornon, France; Bordeaux Sciences Agro, F-33170 Gradignan, France
| | - Lucie Dutilh
- Univ. Bordeaux, INRAE, Bordeaux INP, UMR 1366, OENO, ISVV, F-33140 Villenave d'Ornon, France; Bordeaux Sciences Agro, F-33170 Gradignan, France
| | - Rémi Bauduin
- Institut Français des Produits Cidricoles (IFPC), Domaine de la Motte, Le Rheu 35653, France
| | - Hugues Guichard
- Institut Français des Produits Cidricoles (IFPC), Domaine de la Motte, Le Rheu 35653, France
| | - Séverine Ollivier
- Institut Français des Produits Cidricoles (IFPC), Domaine de la Motte, Le Rheu 35653, France
| | - Cécile Miot-Sertier
- Univ. Bordeaux, INRAE, Bordeaux INP, UMR 1366, OENO, ISVV, F-33140 Villenave d'Ornon, France; Bordeaux Sciences Agro, F-33170 Gradignan, France
| | - Patrick M Lucas
- Univ. Bordeaux, INRAE, Bordeaux INP, UMR 1366, OENO, ISVV, F-33140 Villenave d'Ornon, France; Bordeaux Sciences Agro, F-33170 Gradignan, France
| |
Collapse
|
3
|
Ma Y, Chen X, Khan MZ, Xiao J, Cao Z. A Combination of Novel Microecological Agents and Molasses Role in Digestibility and Fermentation of Rice Straw by Facilitating the Ruminal Microbial Colonization. Front Microbiol 2022; 13:948049. [PMID: 35910602 PMCID: PMC9329086 DOI: 10.3389/fmicb.2022.948049] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2022] [Accepted: 06/17/2022] [Indexed: 11/13/2022] Open
Abstract
In this study, we evaluated the effect of microecological agents (MA) combined with molasses (M) on the biodegradation of rice straw in the rumen. Rice straw was pretreated in laboratory polyethylene 25 × 35 cm sterile bags with no additive control (Con), MA, and MA + M for 7, 15, 30, and 45 days, and then the efficacy of MA + M pretreatment was evaluated both in vitro and in vivo. The scanning electron microscopy, X-ray diffraction analysis, and Fourier-transform infrared spectroscopy results showed that the MA or MA + M pretreatment altered the physical and chemical structure of rice straw. Meanwhile, the ruminal microbial attachment on the surface of rice straw was significantly increased after MA+M pretreatment. Furthermore, MA + M not only promoted rice straw fermentation in vitro but also improved digestibility by specifically inducing rumen colonization of Prevotellaceae_UCG-001, Butyrivibrio, and Succinimonas. Altogether, we concluded that microecological agents and molasses could be the best choices as a biological pretreatment for rice straw to enhance its nutritive value as a ruminant's feed.
Collapse
Affiliation(s)
- Yulin Ma
- State Key Laboratory of Animal Nutrition, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Xu Chen
- State Key Laboratory of Animal Nutrition, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Muhammad Zahoor Khan
- State Key Laboratory of Animal Nutrition, College of Animal Science and Technology, China Agricultural University, Beijing, China
- Faculty of Veterinary and Animal Sciences, Department of Animal Sciences, University of Agriculture, Dera Ismail Khan, Pakistan
| | - Jianxin Xiao
- State Key Laboratory of Animal Nutrition, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Zhijun Cao
- State Key Laboratory of Animal Nutrition, College of Animal Science and Technology, China Agricultural University, Beijing, China
- *Correspondence: Zhijun Cao
| |
Collapse
|
4
|
Rivas GA, Valdés La Hens D, Delfederico L, Olguin N, Bravo-Ferrada BM, Tymczyszyn EE, Semorile L, Brizuela NS. Molecular tools for the analysis of the microbiota involved in malolactic fermentation: from microbial diversity to selection of lactic acid bacteria of enological interest. World J Microbiol Biotechnol 2022; 38:19. [PMID: 34989896 DOI: 10.1007/s11274-021-03205-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2021] [Accepted: 12/08/2021] [Indexed: 01/19/2023]
Abstract
Winemaking is a complex process involving two successive fermentations: alcoholic fermentation, by yeasts, and malolactic fermentation (MLF), by lactic acid bacteria (LAB). During MLF, LAB can contribute positively to wine flavor through decarboxylation of malic acid with acidity reduction and other numerous enzymatic reactions. However, some microorganisms can have a negative impact on the quality of the wine through processes such as biogenic amine production. For these reasons, monitoring the bacterial community profiles during MLF can predict and control the quality of the final product. In addition, the selection of LAB from a wine-producing area is necessary for the formulation of native malolactic starter cultures well adapted to local winemaking practices and able to enhance the regional wine typicality. In this sense, molecular biology techniques are fundamental tools to decipher the native microbiome involved in MLF and to select bacterial strains with potential to function as starter cultures, given their enological and technological characteristics. In this context, this work reviews the different molecular tools (both culture-dependent and -independent) that can be applied to the study of MLF, either in bacterial isolates or in the microbial community of wine, and of its dynamics during the process.
Collapse
Affiliation(s)
- Gabriel Alejandro Rivas
- Departamento de Ciencia y Tecnología, Instituto de Microbiología Básica y Aplicada (IMBA), Laboratorio de Microbiología Molecular, Universidad Nacional de Quilmes, Roque Sáenz Peña 352, Bernal, B1876BXD, Buenos Aires, Argentina
| | - Danay Valdés La Hens
- Departamento de Ciencia y Tecnología, Instituto de Microbiología Básica y Aplicada (IMBA), Laboratorio de Microbiología Molecular, Universidad Nacional de Quilmes, Roque Sáenz Peña 352, Bernal, B1876BXD, Buenos Aires, Argentina
| | - Lucrecia Delfederico
- Departamento de Ciencia y Tecnología, Instituto de Microbiología Básica y Aplicada (IMBA), Laboratorio de Microbiología Molecular, Universidad Nacional de Quilmes, Roque Sáenz Peña 352, Bernal, B1876BXD, Buenos Aires, Argentina
| | - Nair Olguin
- Departamento de Ciencia y Tecnología, Instituto de Microbiología Básica y Aplicada (IMBA), Laboratorio de Microbiología Molecular, Universidad Nacional de Quilmes, Roque Sáenz Peña 352, Bernal, B1876BXD, Buenos Aires, Argentina
| | - Bárbara Mercedes Bravo-Ferrada
- Departamento de Ciencia y Tecnología, Instituto de Microbiología Básica y Aplicada (IMBA), Laboratorio de Microbiología Molecular, Universidad Nacional de Quilmes, Roque Sáenz Peña 352, Bernal, B1876BXD, Buenos Aires, Argentina
| | - Emma Elizabeth Tymczyszyn
- Departamento de Ciencia y Tecnología, Instituto de Microbiología Básica y Aplicada (IMBA), Laboratorio de Microbiología Molecular, Universidad Nacional de Quilmes, Roque Sáenz Peña 352, Bernal, B1876BXD, Buenos Aires, Argentina
| | - Liliana Semorile
- Departamento de Ciencia y Tecnología, Instituto de Microbiología Básica y Aplicada (IMBA), Laboratorio de Microbiología Molecular, Universidad Nacional de Quilmes, Roque Sáenz Peña 352, Bernal, B1876BXD, Buenos Aires, Argentina
| | - Natalia Soledad Brizuela
- Departamento de Ciencia y Tecnología, Instituto de Microbiología Básica y Aplicada (IMBA), Laboratorio de Microbiología Molecular, Universidad Nacional de Quilmes, Roque Sáenz Peña 352, Bernal, B1876BXD, Buenos Aires, Argentina.
| |
Collapse
|
5
|
Microbial diversity of the soil, rhizosphere and wine from an emerging wine-producing region of Argentina. Lebensm Wiss Technol 2022. [DOI: 10.1016/j.lwt.2021.112429] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
|
6
|
Liu J, Liu M, Ye P, He C, Liu Y, Zhang S, Huang J, Zhou J, Zhou R, Cai L. Characterisation of the metabolite profile and microbial community of repeated batch and coculture-fermented greengage wine. Process Biochem 2021. [DOI: 10.1016/j.procbio.2021.06.016] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
|
7
|
Kamilari E, Mina M, Karallis C, Tsaltas D. Metataxonomic Analysis of Grape Microbiota During Wine Fermentation Reveals the Distinction of Cyprus Regional terroirs. Front Microbiol 2021; 12:726483. [PMID: 34630353 PMCID: PMC8494061 DOI: 10.3389/fmicb.2021.726483] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2021] [Accepted: 08/23/2021] [Indexed: 12/25/2022] Open
Abstract
Wine production in Cyprus has strong cultural ties with the island's tradition, influencing local and foreign consumers' preferences and contributing significantly to Cyprus' economy. A key contributor to wine quality and sensorial characteristics development is the microbiota that colonizes grapes and performs alcoholic fermentation. Still, the microbial patterns of wines produced in different geographic regions (terroir) in Cyprus remain unknown. The present study investigated the microbial diversity of five terroirs in Cyprus, two from the PGI Lemesos region [Kyperounta (PDO Pitsilia) and Koilani (PDO Krasochoria)], and three from the PGI Pafos region [Kathikas (PDO Laona Akamas), Panayia, and Statos (PDO Panayia)], of two grape varieties, Xynisteri and Maratheftiko, using high-throughput amplicon sequencing. Through a longitudinal analysis, we examined the evolution of the bacterial and fungal diversity during spontaneous alcoholic fermentation. Both varieties were characterized by a progressive reduction in their fungal alpha diversity (Shannon index) throughout the process of fermentation. Additionally, the study revealed a distinct separation among different terroirs in total fungal community composition (beta-diversity) for the variety Xynisteri. Also, Kyperounta terroir had a distinct total fungal beta-diversity from the other terroirs for Maratheftiko. Similarly, a significant distinction was demonstrated in total bacterial diversity between the PGI Lemesos region and the PGI Pafos terroirs for grape juice of the variety Xynisteri. Pre-fermentation, the fungal diversity for Xynisteri and Maratheftiko was dominated by the genera Hanseniaspora, Aureobasidium, Erysiphe, Aspergillus, Stemphylium, Penicillium, Alternaria, Cladosporium, and Mycosphaerella. During and post-fermentation, the species Hanseniaspora nectarophila, Saccharomyces cerevisiae, Hanseniaspora guilliermondii, and Aureobasidium pullulans, became the predominant in most must samples. Regarding the bacterial diversity, Lactobacillus and Streptococcus were the predominant genera for both grape varieties in all stages of fermentation. During fermentation, an increase was observed in the relative abundance of some bacteria, such as Acetobacter, Gluconobacter, and Oenococcus oeni. Finally, the study revealed microbial biomarkers with statistically significant higher relative representation, associated with each geographic region and each grape variety, during the different stages of fermentation. The present study's findings provide an additional linkage between the grape microbial community and the wine terroir.
Collapse
Affiliation(s)
- Eleni Kamilari
- Department of Agricultural Sciences, Biotechnology, and Food Science, Cyprus University of Technology, Lemesos, Cyprus
| | - Minas Mina
- Department of Agricultural Sciences, Biotechnology, and Food Science, Cyprus University of Technology, Lemesos, Cyprus
- Kyperounda Winery, P. Photiades Group, Nicosia, Cyprus
| | | | - Dimitrios Tsaltas
- Department of Agricultural Sciences, Biotechnology, and Food Science, Cyprus University of Technology, Lemesos, Cyprus
| |
Collapse
|
8
|
Li H, James A, Shen X, Wang Y. Roles of microbiota in the formation of botrytized grapes and wines. CYTA - JOURNAL OF FOOD 2021. [DOI: 10.1080/19476337.2021.1958925] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Affiliation(s)
- Hua Li
- Beijing Advanced Innovation Center For Food Nutrition And Human Health, Beijing Technology & Business University (BTBU), Beijing, P.R. China
| | - Armachius James
- Beijing Advanced Innovation Center For Food Nutrition And Human Health, Beijing Technology & Business University (BTBU), Beijing, P.R. China
| | - Xuemei Shen
- Beijing Advanced Innovation Center For Food Nutrition And Human Health, Beijing Technology & Business University (BTBU), Beijing, P.R. China
| | - Yousheng Wang
- Beijing Advanced Innovation Center For Food Nutrition And Human Health, Beijing Technology & Business University (BTBU), Beijing, P.R. China
| |
Collapse
|
9
|
Qiu X, Yu L, Wang W, Yan R, Zhang Z, Yang H, Zhu D, Zhu B. Comparative Evaluation of Microbiota Dynamics and Metabolites Correlation Between Spontaneous and Inoculated Fermentations of Nanfeng Tangerine Wine. Front Microbiol 2021; 12:649978. [PMID: 34046021 PMCID: PMC8144288 DOI: 10.3389/fmicb.2021.649978] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2021] [Accepted: 03/31/2021] [Indexed: 01/16/2023] Open
Abstract
Understanding the evolution of microorganisms and metabolites during wine fermentation is essential for controlling its production. The structural composition and functional capacity of the core microbiota determine the quality and quantity of fruit wine. Nanfeng tangerine wine fermentation involves a complex of various microorganisms and a wide variety of metabolites. However, the microbial succession and functional shift of the core microbiota in this product fermentation remain unclear. Therefore, high-throughput sequencing (HTS) and headspace-gas chromatography-mass spectrometry (HS/GC-MS) were employed to reveal the core functional microbiota for the production of volatile flavors during spontaneous fermentation (SF) and inoculated fermentation (IF) with Saccharomyces cerevisiae of Nanfeng tangerine wine. A total of 13 bacterial and 8 fungal genera were identified as the core microbiota; Lactobacillus and Acetobacter were the dominant bacteria in SF and IF, respectively. The main fungal genera in SF and IF were Hanseniaspora, Pichia, and Saccharomyces with a clear succession. In addition, the potential correlations analysis between microbiota succession and volatile flavor dynamics revealed that Lactobacillus, Acetobacter, Hanseniaspora, and Saccharomyces were the major contributors to the production of the volatile flavor of Nanfeng tangerine wine. The results of the present study provide insight into the effects of the core functional microbiota in Nanfeng tangerine wine and can be used to develop effective strategies for improving the quality of fruit wines.
Collapse
Affiliation(s)
- Xiangyu Qiu
- Key Laboratory of Protection and Utilization of Subtropic Plant Resources of Jiangxi Province, College of Life Sciences, Jiangxi Normal University, Nanchang, China
| | - Linlin Yu
- Key Laboratory of Protection and Utilization of Subtropic Plant Resources of Jiangxi Province, College of Life Sciences, Jiangxi Normal University, Nanchang, China
| | - Weiying Wang
- Key Laboratory of Protection and Utilization of Subtropic Plant Resources of Jiangxi Province, College of Life Sciences, Jiangxi Normal University, Nanchang, China
| | - Riming Yan
- Key Laboratory of Protection and Utilization of Subtropic Plant Resources of Jiangxi Province, College of Life Sciences, Jiangxi Normal University, Nanchang, China
| | - Zhibin Zhang
- Key Laboratory of Protection and Utilization of Subtropic Plant Resources of Jiangxi Province, College of Life Sciences, Jiangxi Normal University, Nanchang, China
| | - Huilin Yang
- Key Laboratory of Protection and Utilization of Subtropic Plant Resources of Jiangxi Province, College of Life Sciences, Jiangxi Normal University, Nanchang, China
| | - Du Zhu
- Key Laboratory of Protection and Utilization of Subtropic Plant Resources of Jiangxi Province, College of Life Sciences, Jiangxi Normal University, Nanchang, China.,Key Laboratory of Bioprocess Engineering of Jiangxi Province, College of Life Sciences, Jiangxi Science and Technology Normal University, Nanchang, China
| | - Bo Zhu
- College of Life Sciences, Gannan Normal University, Ganzhou, China
| |
Collapse
|
10
|
Kioroglou D, Mas A, Portillo MC. High-Throughput Sequencing Approach to Analyze the Effect of Aging Time and Barrel Usage on the Microbial Community Composition of Red Wines. Front Microbiol 2020; 11:562560. [PMID: 33013793 PMCID: PMC7509142 DOI: 10.3389/fmicb.2020.562560] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2020] [Accepted: 08/13/2020] [Indexed: 11/25/2022] Open
Abstract
Wine aged in barrels or bottles is susceptible to alteration by microorganisms that affect the final product quality. However, our knowledge of the microbiota during aging and the factors modulating the microbial communities is still quite limited. The present work uses high-throughput sequencing (HTS) techniques to deal with the meta-taxonomic characterization of microbial consortia present in red wines along 12 months aging. The wines obtained from two different grape varieties were aged at two different cellars and compared based on time of wine aging in the barrels, previous usage of the barrels, and differences between wine aging in oak barrels or glass bottles. The aging in barrels did not significantly affect the microbial diversity but changed the structure and composition of fungal and bacterial populations. The main microorganisms driving these changes were the bacterial genera Acetobacter, Oenococcus, Lactobacillus, Gluconobacter, Lactococcus, and Komagataeibacter and the fungal genera Malassezia, Hanseniaspora, and Torulaspora. Our results showed that the oak barrels increased effect on the microbial diversity in comparison with the glass bottles, in which the microbial community was very similar to that of the wine introduced in the barrels at the beginning of the aging. Furthermore, wine in the bottles harbored higher proportion of Lactobacillus but lower proportion of Acetobacter. Finally, it seems that 1 year of previous usage of the barrels was not enough to induce significant changes in the diversity or composition of microbiota through aging compared with new barrels. This is the first meta-taxonomic study on microbial communities during wine aging and shows that the microorganism composition of barrel-aged wines was similar at both cellars. These results hint at the possibility of a common and stable microbiota after aging in the absence of exogenous alterations. Further corroborations on the current outcome would be valuable for the comparison and detection of microbial alterations during aging that could potentially prevent economic losses in the wine industry.
Collapse
Affiliation(s)
- Dimitrios Kioroglou
- Department Bioquímica i Biotecnologia, Facultat d'Enologia, Universitat Rovira i Virgili, Tarragona, Spain
| | - Albert Mas
- Department Bioquímica i Biotecnologia, Facultat d'Enologia, Universitat Rovira i Virgili, Tarragona, Spain
| | - Maria C Portillo
- Department Bioquímica i Biotecnologia, Facultat d'Enologia, Universitat Rovira i Virgili, Tarragona, Spain
| |
Collapse
|
11
|
Böhmer M, Smoľak D, Ženišová K, Čaplová Z, Pangallo D, Puškárová A, Bučková M, Cabicarová T, Budiš J, Šoltýs K, Rusňáková D, Kuchta T, Szemes T. Comparison of microbial diversity during two different wine fermentation processes. FEMS Microbiol Lett 2020; 367:5902846. [PMID: 32897314 DOI: 10.1093/femsle/fnaa150] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2020] [Accepted: 09/03/2020] [Indexed: 02/06/2023] Open
Abstract
Wine production is a complex procedure in which an important role is played by many microorganisms, particularly yeasts and bacteria. In modern wineries, alcoholic fermentation is usually carried out by adding microbial starter cultures of Saccharomyces cerevisiae strains for precisely controlled production. Nowadays, in the Slovak Republic, autochthonous vinification is getting more popular. The present article deals with the comparison of two vinification approaches, namely spontaneous fermentation and fermentation controlled by a standard commercial S. cerevisiae starter, from the point of view of microbiota dynamics and the chemical characteristics of the wines produced. The dynamics of microbial populations were determined during the fermentation process by a 16S and 28S rRNA next-generation sequencing approach. A profile of the volatile compounds during these fermentation processes was identified by solid-phase microextraction (SPME) coupled to gas chromatography-mass spectrometry (GC-MS). In summary, the microbial diversity in the m1 phase (initial must) was higher, despite the presence of the starter culture. In the m3 phase (young wine), the microbiome profiles of both batches were very similar. It seems that the crucial phase in order to study the relationship of the microbiome and the resulting product should be based on the m2 phase (fermented must), where the differences between the autochthonous and inoculated batches were more evident.
Collapse
Affiliation(s)
- Miroslav Böhmer
- Department of Molecular Biology, Faculty of Natural Sciences, Comenius University in Bratislava, Ilkovičova 6, 842 15 Bratislava, Slovakia.,Science park, Comenius University in Bratislava, Ilkovičova 8, 841 04 Bratislava, Slovakia
| | - Dávid Smoľak
- Department of Molecular Biology, Faculty of Natural Sciences, Comenius University in Bratislava, Ilkovičova 6, 842 15 Bratislava, Slovakia.,Geneton Ltd., 841 04 Bratislava, Slovakia
| | - Katarína Ženišová
- Department of Microbiology, Molecular Biology and Biotechnology, Food Research Institute, National Agricultural and Food Centre, Priemyselná 4, 824 75 Bratislava, Slovakia
| | - Zuzana Čaplová
- Department of Microbiology, Molecular Biology and Biotechnology, Food Research Institute, National Agricultural and Food Centre, Priemyselná 4, 824 75 Bratislava, Slovakia
| | - Domenico Pangallo
- Institute of Molecular Biology, Slovak Academy of Sciences, Dúbravská cesta 21, 845 51 Bratislava, Slovakia
| | - Andrea Puškárová
- Institute of Molecular Biology, Slovak Academy of Sciences, Dúbravská cesta 21, 845 51 Bratislava, Slovakia
| | - Mária Bučková
- Institute of Molecular Biology, Slovak Academy of Sciences, Dúbravská cesta 21, 845 51 Bratislava, Slovakia
| | - Tereza Cabicarová
- Institute of Molecular Biology, Slovak Academy of Sciences, Dúbravská cesta 21, 845 51 Bratislava, Slovakia
| | - Jaroslav Budiš
- Science park, Comenius University in Bratislava, Ilkovičova 8, 841 04 Bratislava, Slovakia.,Geneton Ltd., 841 04 Bratislava, Slovakia.,Slovak Centre of Scientific and Technical Information, Lamačská cesta 8/A, 811 04 Bratislava, Slovakia
| | - Katarína Šoltýs
- Department of Molecular Biology, Faculty of Natural Sciences, Comenius University in Bratislava, Ilkovičova 6, 842 15 Bratislava, Slovakia.,Science park, Comenius University in Bratislava, Ilkovičova 8, 841 04 Bratislava, Slovakia
| | - Diana Rusňáková
- Department of Molecular Biology, Faculty of Natural Sciences, Comenius University in Bratislava, Ilkovičova 6, 842 15 Bratislava, Slovakia.,Geneton Ltd., 841 04 Bratislava, Slovakia
| | - Tomáš Kuchta
- Department of Microbiology, Molecular Biology and Biotechnology, Food Research Institute, National Agricultural and Food Centre, Priemyselná 4, 824 75 Bratislava, Slovakia
| | - Tomáš Szemes
- Department of Molecular Biology, Faculty of Natural Sciences, Comenius University in Bratislava, Ilkovičova 6, 842 15 Bratislava, Slovakia.,Science park, Comenius University in Bratislava, Ilkovičova 8, 841 04 Bratislava, Slovakia.,Geneton Ltd., 841 04 Bratislava, Slovakia
| |
Collapse
|
12
|
Bubeck AM, Preiss L, Jung A, Dörner E, Podlesny D, Kulis M, Maddox C, Arze C, Zörb C, Merkt N, Fricke WF. Bacterial microbiota diversity and composition in red and white wines correlate with plant-derived DNA contributions and botrytis infection. Sci Rep 2020; 10:13828. [PMID: 32796896 PMCID: PMC7427798 DOI: 10.1038/s41598-020-70535-8] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2020] [Accepted: 07/27/2020] [Indexed: 12/18/2022] Open
Abstract
Wine is a globally produced, marketed and consumed alcoholic beverage, which is valued for its aromatic and qualitative complexity and variation. These properties are partially attributable to the bacterial involvement in the fermentation process. However, the organizational principles and dynamic changes of the bacterial wine microbiota remain poorly understood, especially in the context of red and white wine variations and environmental stress factors. Here, we determined relative and absolute bacterial microbiota compositions from six distinct cultivars during the first week of fermentation by quantitative and qualitative 16S rRNA gene amplification and amplicon sequencing. All wines harboured complex and variable bacterial communities, with Tatumella as the most abundant genus across all batches, but red wines were characterized by higher bacterial diversity and increased relative and absolute abundance of lactic and acetic acid bacteria (LAB/AAB) and bacterial taxa of predicted environmental origin. Microbial diversity was positively correlated with plant-derived DNA concentrations in the wine and Botrytis cinerea infection before harvest. Our findings suggest that exogenous factors, such as procedural differences between red and white wine production and environmental stress on grape integrity, can increase bacterial diversity and specific bacterial taxa in wine, with potential consequences for wine quality and aroma.
Collapse
Affiliation(s)
- Alena M Bubeck
- Department of Microbiome Research and Applied Bioinformatics, Institute of Nutritional Sciences, University of Hohenheim, Stuttgart, Germany
| | - Lena Preiss
- Department of Microbiome Research and Applied Bioinformatics, Institute of Nutritional Sciences, University of Hohenheim, Stuttgart, Germany
| | - Anna Jung
- Department of Microbiome Research and Applied Bioinformatics, Institute of Nutritional Sciences, University of Hohenheim, Stuttgart, Germany
| | - Elisabeth Dörner
- Department of Microbiome Research and Applied Bioinformatics, Institute of Nutritional Sciences, University of Hohenheim, Stuttgart, Germany
| | - Daniel Podlesny
- Department of Microbiome Research and Applied Bioinformatics, Institute of Nutritional Sciences, University of Hohenheim, Stuttgart, Germany
| | - Marija Kulis
- Department of Microbiome Research and Applied Bioinformatics, Institute of Nutritional Sciences, University of Hohenheim, Stuttgart, Germany
| | - Cynthia Maddox
- Department of Microbiome Research and Applied Bioinformatics, Institute of Nutritional Sciences, University of Hohenheim, Stuttgart, Germany.,Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, USA.,Personal Genome Diagnostics, Baltimore, MD, USA
| | - Cesar Arze
- Department of Microbiome Research and Applied Bioinformatics, Institute of Nutritional Sciences, University of Hohenheim, Stuttgart, Germany.,Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, USA.,Ring Therapeutics, Cambridge, MA, USA
| | - Christian Zörb
- Department of Plant Quality and Viticulture, Institute of Crop Science, University of Hohenheim, Stuttgart, Germany
| | - Nikolaus Merkt
- Department of Plant Quality and Viticulture, Institute of Crop Science, University of Hohenheim, Stuttgart, Germany
| | - W Florian Fricke
- Department of Microbiome Research and Applied Bioinformatics, Institute of Nutritional Sciences, University of Hohenheim, Stuttgart, Germany. .,Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, USA.
| |
Collapse
|
13
|
Bartle L, Sumby K, Sundstrom J, Jiranek V. The microbial challenge of winemaking: yeast-bacteria compatibility. FEMS Yeast Res 2020; 19:5513997. [PMID: 31187141 DOI: 10.1093/femsyr/foz040] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2019] [Accepted: 06/10/2019] [Indexed: 12/25/2022] Open
Abstract
The diversity and complexity of wine environments present challenges for predicting success of fermentation. In particular, compatibility between yeast and lactic acid bacteria is affected by chemical and physical parameters that are strain and cultivar specific. This review focuses on the impact of compound production by microbes and physical interactions between microbes that ultimately influence how yeast and bacteria may work together during fermentation. This review also highlights the importance of understanding microbial interactions for yeast-bacteria compatibility in the wine context.
Collapse
Affiliation(s)
- Louise Bartle
- Department of Wine and Food Science, University of Adelaide, Adelaide, SA 5064, Australia
| | - Krista Sumby
- Department of Wine and Food Science, University of Adelaide, Adelaide, SA 5064, Australia.,Australian Research Council Training Centre for Innovative Wine Production, PMB1, Glen Osmond, SA, 5064, Australia
| | - Joanna Sundstrom
- Department of Wine and Food Science, University of Adelaide, Adelaide, SA 5064, Australia.,Australian Research Council Training Centre for Innovative Wine Production, PMB1, Glen Osmond, SA, 5064, Australia
| | - Vladimir Jiranek
- Department of Wine and Food Science, University of Adelaide, Adelaide, SA 5064, Australia.,Australian Research Council Training Centre for Innovative Wine Production, PMB1, Glen Osmond, SA, 5064, Australia
| |
Collapse
|
14
|
Shen Y, Nie J, Kuang L, Zhang J, Li H. DNA sequencing, genomes and genetic markers of microbes on fruits and vegetables. Microb Biotechnol 2020; 14:323-362. [PMID: 32207561 PMCID: PMC7936329 DOI: 10.1111/1751-7915.13560] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2020] [Revised: 03/01/2020] [Accepted: 03/02/2020] [Indexed: 12/20/2022] Open
Abstract
The development of DNA sequencing technology has provided an effective method for studying foodborne and phytopathogenic microorganisms on fruits and vegetables (F & V). DNA sequencing has successfully proceeded through three generations, including the tens of operating platforms. These advances have significantly promoted microbial whole‐genome sequencing (WGS) and DNA polymorphism research. Based on genomic and regional polymorphisms, genetic markers have been widely obtained. These molecular markers are used as targets for PCR or chip analyses to detect microbes at the genetic level. Furthermore, metagenomic analyses conducted by sequencing the hypervariable regions of ribosomal DNA (rDNA) have revealed comprehensive microbial communities in various studies on F & V. This review highlights the basic principles of three generations of DNA sequencing, and summarizes the WGS studies of and available DNA markers for major bacterial foodborne pathogens and phytopathogenic fungi found on F & V. In addition, rDNA sequencing‐based bacterial and fungal metagenomics are summarized under three topics. These findings deepen the understanding of DNA sequencing and its application in studies of foodborne and phytopathogenic microbes and shed light on strategies for the monitoring of F & V microbes and quality control.
Collapse
Affiliation(s)
- Youming Shen
- Institute of Pomology, Chinese Academy of Agricultural Sciences/Laboratory of Quality & Safety Risk Assessment for Fruit (Xingcheng), Ministry of Agriculture and Rural Affairs/Quality Inspection and Test Center for Fruit and Nursery Stocks (Xingcheng), Ministry of Agriculture and Rural Affairs, Xingcheng, 125100, China
| | - Jiyun Nie
- Institute of Pomology, Chinese Academy of Agricultural Sciences/Laboratory of Quality & Safety Risk Assessment for Fruit (Xingcheng), Ministry of Agriculture and Rural Affairs/Quality Inspection and Test Center for Fruit and Nursery Stocks (Xingcheng), Ministry of Agriculture and Rural Affairs, Xingcheng, 125100, China.,College of Horticulture, Qingdao Agricultural University, Qingdao, 266109, China
| | - Lixue Kuang
- Institute of Pomology, Chinese Academy of Agricultural Sciences/Laboratory of Quality & Safety Risk Assessment for Fruit (Xingcheng), Ministry of Agriculture and Rural Affairs/Quality Inspection and Test Center for Fruit and Nursery Stocks (Xingcheng), Ministry of Agriculture and Rural Affairs, Xingcheng, 125100, China
| | - Jianyi Zhang
- Institute of Pomology, Chinese Academy of Agricultural Sciences/Laboratory of Quality & Safety Risk Assessment for Fruit (Xingcheng), Ministry of Agriculture and Rural Affairs/Quality Inspection and Test Center for Fruit and Nursery Stocks (Xingcheng), Ministry of Agriculture and Rural Affairs, Xingcheng, 125100, China
| | - Haifei Li
- Institute of Pomology, Chinese Academy of Agricultural Sciences/Laboratory of Quality & Safety Risk Assessment for Fruit (Xingcheng), Ministry of Agriculture and Rural Affairs/Quality Inspection and Test Center for Fruit and Nursery Stocks (Xingcheng), Ministry of Agriculture and Rural Affairs, Xingcheng, 125100, China
| |
Collapse
|
15
|
Rantsiou K, Giacosa S, Pugliese M, Englezos V, Ferrocino I, Río Segade S, Monchiero M, Gribaudo I, Gambino G, Gullino ML, Rolle L. Impact of Chemical and Alternative Fungicides Applied to Grapevine cv Nebbiolo on Microbial Ecology and Chemical-Physical Grape Characteristics at Harvest. FRONTIERS IN PLANT SCIENCE 2020; 11:700. [PMID: 32547588 PMCID: PMC7272676 DOI: 10.3389/fpls.2020.00700] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/22/2019] [Accepted: 05/04/2020] [Indexed: 05/07/2023]
Abstract
Viticulture is a cropping system in which treatment against fungal diseases (in particular powdery and downy mildews) can be extremely frequent. Accordingly, a reduction in antimicrobial treatments and the application of environmentally-friendly compounds are becoming increasingly important for a more sustainable viticulture. In addition to their effect against pathogens, the impact of these products on the quality of the grapes is very important for the oenological industries, but unfortunately at present few data are available. We evaluated the effect of the application of biocontrol products and resistance inducers in the vineyard on the mechanical properties, microbial ecology, technological and phenolic maturity of Vitis vinifera "Nebbiolo" grapes at harvest. The yield and vigor of vines were not influenced by the treatments, nor were the production of primary and secondary metabolites. However, the active ingredients influenced the mechanical properties of the skin (hardness and thickness). A significant hardening of the skin was detected when laminarin and chito-oligosaccharides were used, and sulfur induced a thickening of the skin with potential consequences for wine quality. Furthermore, the yeast community present on grape berries was influenced by the treatments. The abundance of Aureobasidium pullulans, the dominant species on the grape berry, changed in response to the compounds used. In addition, Alternaria sp. was reduced in some treatments with a potentially positive effect on the quality and the safety of the grapes. This study provides an overview of the effect of biocontrol products and resistance inducers on microbial ecology and "Nebbiolo" grape quality, contributing to the establishment of more sustainable and effective defense strategies in viticulture.
Collapse
Affiliation(s)
- Kalliopi Rantsiou
- Department of Agricultural, Forest and Food Sciences, University of Turin, Grugliasco, Italy
| | - Simone Giacosa
- Department of Agricultural, Forest and Food Sciences, University of Turin, Grugliasco, Italy
| | - Massimo Pugliese
- Department of Agricultural, Forest and Food Sciences, University of Turin, Grugliasco, Italy
- Agroinnova-Centre of Competence for the Innovation in the Agro-Environmental Sector, University of Turin, Grugliasco, Italy
| | - Vasileios Englezos
- Department of Agricultural, Forest and Food Sciences, University of Turin, Grugliasco, Italy
| | - Ilario Ferrocino
- Department of Agricultural, Forest and Food Sciences, University of Turin, Grugliasco, Italy
| | - Susana Río Segade
- Department of Agricultural, Forest and Food Sciences, University of Turin, Grugliasco, Italy
| | | | - Ivana Gribaudo
- Institute for Sustainable Plant Protection, National Research Council (IPSP-CNR), Turin, Italy
| | - Giorgio Gambino
- Institute for Sustainable Plant Protection, National Research Council (IPSP-CNR), Turin, Italy
- *Correspondence: Giorgio Gambino,
| | - Maria Lodovica Gullino
- Department of Agricultural, Forest and Food Sciences, University of Turin, Grugliasco, Italy
- Agroinnova-Centre of Competence for the Innovation in the Agro-Environmental Sector, University of Turin, Grugliasco, Italy
| | - Luca Rolle
- Department of Agricultural, Forest and Food Sciences, University of Turin, Grugliasco, Italy
| |
Collapse
|
16
|
Yang H, Yang L, Zhang J, Li H, Tu Z, Wang X. Exploring functional core bacteria in fermentation of a traditional Chinese food, Aspergillus-type douchi. PLoS One 2019; 14:e0226965. [PMID: 31887171 PMCID: PMC6936781 DOI: 10.1371/journal.pone.0226965] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2019] [Accepted: 12/09/2019] [Indexed: 12/03/2022] Open
Abstract
Douchi is a type of traditional Chinese flavoring food that has been used for thousands of years and is produced by multispecies solid-state fermentation. However, the correlation between the flavor, the microbiota, and the functional core microbiota in Aspergillus-type douchi fermentation remains unclear. In this study, Illumina MiSeq sequencing and chromatography were used to investigate the bacterial community and flavor components in Aspergillus-type douchi fermentation. The dominant phyla were Firmicutes, Proteobacteria, and Actinobacteria, and the dominant genera were Weissella, Bacillus, Anaerosalibacter, Lactobacillus, Staphylococcus, and Enterococcus. A total of 58 flavor components were detected during fermentation, including two alcohols, 14 esters, five pyrazines, three alkanes, four aldehydes, three phenols, six acids, and five other compounds. Bidirectional orthogonal partial least square modeling showed that Corynebacterium_1, Lactococcus, Atopostipes, Peptostreptococcus, norank_o__AKYG1722, Truepera, Gulosibacter, norank_f__Actinomycetaceae, and unclassified_f__Rhodobacteraceae are the functional core microbiota responsible for the formation of the flavor components during douchi fermentation. This is the first study to investigate the functional core microbiota in douchi fermentation using Illumina MiSeq sequencing and chromatographic techniques. Our findings extend our understanding of the relationships between flavor, the microbiota, and the functional core microbiota during Aspergillus-type douchi fermentation.
Collapse
Affiliation(s)
- Huilin Yang
- Key Lab of Protection and Utilization of Subtropic Plant Resources of Jiangxi Province, Jiangxi Normal University, Nanchang, China
| | - Lin Yang
- Key Lab of Protection and Utilization of Subtropic Plant Resources of Jiangxi Province, Jiangxi Normal University, Nanchang, China
| | - Ju Zhang
- Key Lab of Protection and Utilization of Subtropic Plant Resources of Jiangxi Province, Jiangxi Normal University, Nanchang, China
| | - Hao Li
- Key Lab of Protection and Utilization of Subtropic Plant Resources of Jiangxi Province, Jiangxi Normal University, Nanchang, China
| | - Zongcai Tu
- Key Lab of Protection and Utilization of Subtropic Plant Resources of Jiangxi Province, Jiangxi Normal University, Nanchang, China
| | - Xiaolan Wang
- Key Lab of Protection and Utilization of Subtropic Plant Resources of Jiangxi Province, Jiangxi Normal University, Nanchang, China
- * E-mail:
| |
Collapse
|
17
|
Berbegal C, Borruso L, Fragasso M, Tufariello M, Russo P, Brusetti L, Spano G, Capozzi V. A Metagenomic-Based Approach for the Characterization of Bacterial Diversity Associated with Spontaneous Malolactic Fermentations in Wine. Int J Mol Sci 2019; 20:ijms20163980. [PMID: 31443334 PMCID: PMC6721008 DOI: 10.3390/ijms20163980] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2019] [Revised: 08/13/2019] [Accepted: 08/13/2019] [Indexed: 01/13/2023] Open
Abstract
This study reports the first application of a next generation sequencing (NGS) analysis. The analysis was designed to monitor the effect of the management of microbial resources associated with alcoholic fermentation on spontaneous malolactic consortium. Together with the analysis of 16S rRNA genes from the metagenome, we monitored the principal parameters linked to MLF (e.g., malic and lactic acid concentration, pH). We encompass seven dissimilar concrete practices to manage microorganisms associated with alcoholic fermentation: Un-inoculated must (UM), pied-de-cuve (PdC), Saccharomyces cerevisiae (SC), S. cerevisiae and Torulaspora delbrueckii co-inoculated and sequentially inoculated, as well as S. cerevisiae and Metschnikowia pulcherrima co-inoculated and sequentially inoculated. Surprisingly, each experimental modes led to different taxonomic composition of the bacterial communities of the malolactic consortia, in terms of prokaryotic phyla and genera. Our findings indicated that, uncontrolled AF (UM, PdC) led to heterogeneous consortia associated with MLF (with a relevant presence of the genera Acetobacter and Gluconobacter), when compared with controlled AF (SC) (showing a clear dominance of the genus Oenococcus). Effectively, the SC trial malic acid was completely degraded in about two weeks after the end of AF, while, on the contrary, malic acid decarboxylation remained uncomplete after 7 weeks in the case of UM and PdC. In addition, for the first time, we demonstrated that both (i) the inoculation of different non-Saccharomyces (T. delbrueckii and M. pulcherrima) and, (ii) the inoculation time of the non-Saccharomyces with respect to S. cerevisiae resources (co-inoculated and sequentially inoculated) influence the composition of the connected MLF consortia, modulating MLF performance. Finally, we demonstrated the first findings of delayed and inhibited MLF when M. pulcherrima, and T. delbrueckii were inoculated, respectively. In addition, as a further control test, we also assessed the effect of the inoculation with Oenococcus oeni and Lactobacillus plantarum at the end of alcoholic fermentation, as MLF starter cultures. Our study suggests the potential interest in the application of NGS analysis, to monitor the effect of alcoholic fermentation on the spontaneous malolactic consortium, in relation to wine.
Collapse
Affiliation(s)
- Carmen Berbegal
- Department of Agriculture, Food and Environment Sciences, University of Foggia, Via Napoli 25, 71122 Foggia, Italy
- EnolabERI BioTecMed, Universitat de València, 46100 Valencia, Spain
| | - Luigimaria Borruso
- Faculty of Science and Technology, Free University of Bozen-Bolzano, 39100 Bozen-Bolzano, Italy
| | - Mariagiovanna Fragasso
- Department of Agriculture, Food and Environment Sciences, University of Foggia, Via Napoli 25, 71122 Foggia, Italy
| | - Maria Tufariello
- Istituto di Scienze delle Produzioni Alimentari, Consiglio Nazionale delle Ricerche, Unità Operativa di Supporto di Lecce, 73100 Lecce, Italy
| | - Pasquale Russo
- Department of Agriculture, Food and Environment Sciences, University of Foggia, Via Napoli 25, 71122 Foggia, Italy
| | - Lorenzo Brusetti
- Faculty of Science and Technology, Free University of Bozen-Bolzano, 39100 Bozen-Bolzano, Italy
| | - Giuseppe Spano
- Department of Agriculture, Food and Environment Sciences, University of Foggia, Via Napoli 25, 71122 Foggia, Italy
| | - Vittorio Capozzi
- Department of Agriculture, Food and Environment Sciences, University of Foggia, Via Napoli 25, 71122 Foggia, Italy.
| |
Collapse
|
18
|
Chemical and Bacterial Components in Sake and Sake Production Process. Curr Microbiol 2019; 77:632-637. [DOI: 10.1007/s00284-019-01718-4] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2019] [Accepted: 06/11/2019] [Indexed: 01/25/2023]
|
19
|
The Influence of Fungicide Treatments on Mycobiota of Grapes and Its Evolution during Fermentation Evaluated by Metagenomic and Culture-Dependent Methods. Microorganisms 2019; 7:microorganisms7050114. [PMID: 31035521 PMCID: PMC6560393 DOI: 10.3390/microorganisms7050114] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2019] [Revised: 04/20/2019] [Accepted: 04/24/2019] [Indexed: 11/17/2022] Open
Abstract
The present study evaluated the impact of organic and conventional fungicide treatments compared with untreated samples (no fungicides were used) on the grape berry yeast community of the Montepulciano variety. The yeast dynamics during the spontaneous fermentation using culture-dependent and -independent methods was also evaluated. Results showed a reduction of yeast biodiversity by conventional treatments determining a negative influence on fermenting yeasts in favor of oxidative yeasts such as Aerobasidium pullulans. Starmerella bacillaris was significantly more present in organic samples (detected by next generation sequencing (NGS)), while Hanseniaspopa uvarum was significantly less present in untreated samples (detected by the culture-dependent method). The fermenting yeasts, developed during the spontaneous fermentation, were differently present depending on the fungicide treatments used. Culture-dependent and -independent methods exhibited the same most abundant yeast species during the spontaneous fermentation but a different relative abundance. Differently, the NGS method was able to detect a greater biodiversity (lower abundant species) in comparison with the culture-dependent method. In this regard, the methodologies used gave a different picture of yeast dynamics during the fermentation process. The results indicated that the fungal treatments can influence the yeast community of grapes leading must fermentation and the final composition of wine.
Collapse
|
20
|
Sirén K, Mak SST, Melkonian C, Carøe C, Swiegers JH, Molenaar D, Fischer U, Gilbert MTP. Taxonomic and Functional Characterization of the Microbial Community During Spontaneous in vitro Fermentation of Riesling Must. Front Microbiol 2019; 10:697. [PMID: 31024486 PMCID: PMC6465770 DOI: 10.3389/fmicb.2019.00697] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2019] [Accepted: 03/19/2019] [Indexed: 12/11/2022] Open
Abstract
Although there is an extensive tradition of research into the microbes that underlie the winemaking process, much remains to be learnt. We combined the high-throughput sequencing (HTS) tools of metabarcoding and metagenomics, to characterize how microbial communities of Riesling musts sampled at four different vineyards, and their subsequent spontaneously fermented derivatives, vary. We specifically explored community variation relating to three points: (i) how microbial communities vary by vineyard; (ii) how community biodiversity changes during alcoholic fermentation; and (iii) how microbial community varies between musts that successfully complete alcoholic fermentation and those that become 'stuck' in the process. Our metabarcoding data showed a general influence of microbial composition at the vineyard level. Two of the vineyards (4 and 5) had strikingly a change in the differential abundance of Metschnikowia. We therefore additionally performed shotgun metagenomic sequencing on a subset of the samples to provide preliminary insights into the potential relevance of this observation, and used the data to both investigate functional potential and reconstruct draft genomes (bins). At these two vineyards, we also observed an increase in non-Saccharomycetaceae fungal functions, and a decrease in bacterial functions during the early fermentation stage. The binning results yielded 11 coherent bins, with both vineyards sharing the yeast bins Hanseniaspora and Saccharomyces. Read recruitment and functional analysis of this data revealed that during fermentation, a high abundance of Metschnikowia might serve as a biocontrol agent against bacteria, via a putative iron depletion pathway, and this in turn could help Saccharomyces dominate the fermentation. During alcoholic fermentation, we observed a general decrease in biodiversity in both the metabarcoding and metagenomic data. Unexpected Micrococcus behavior was observed in vineyard 4 according to metagenomic analyses based on reference-based read mapping. Analysis of open reading frames using these data showed an increase of functions assigned to class Actinobacteria in the end of fermentation. Therefore, we hypothesize that bacteria might sit-and-wait until Saccharomyces activity slows down. Complementary approaches to annotation instead of relying a single database provide more coherent information true species. Lastly, our metabarcoding data enabled us to identify a relationship between stuck fermentations and Starmerella abundance. Given that robust chemical analysis indicated that although the stuck samples contained residual glucose, all fructose had been consumed, we hypothesize that this was because fructophilic Starmerella, rather than Saccharomyces, dominated these fermentations. Overall, our results showcase the different ways in which metagenomic analyses can improve our understanding of the wine alcoholic fermentation process.
Collapse
Affiliation(s)
- Kimmo Sirén
- Institute for Viticulture and Oenology, Dienstleistungszentrum Ländlicher Raum Rheinpfalz, Neustadt an der Weinstraße, Germany
- Department of Chemistry, University of Kaiserslautern, Kaiserslautern, Germany
| | - Sarah Siu Tze Mak
- Section for Evolutionary Genomics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
| | - Chrats Melkonian
- Systems Bioinformatics, Faculty of Science, Vrije Universiteit Amsterdam, Amsterdam, Netherlands
| | - Christian Carøe
- Section for Evolutionary Genomics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
| | | | - Douwe Molenaar
- Systems Bioinformatics, Faculty of Science, Vrije Universiteit Amsterdam, Amsterdam, Netherlands
| | - Ulrich Fischer
- Institute for Viticulture and Oenology, Dienstleistungszentrum Ländlicher Raum Rheinpfalz, Neustadt an der Weinstraße, Germany
| | - M. Thomas P. Gilbert
- Section for Evolutionary Genomics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
- University Museum, Norwegian University of Science and Technology, Trondheim, Norway
| |
Collapse
|
21
|
Measures to improve wine malolactic fermentation. Appl Microbiol Biotechnol 2019; 103:2033-2051. [DOI: 10.1007/s00253-018-09608-8] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2018] [Accepted: 12/27/2018] [Indexed: 01/06/2023]
|
22
|
Castañeda LE, Miura T, Sánchez R, Barbosa O. Effects of agricultural management on phyllosphere fungal diversity in vineyards and the association with adjacent native forests. PeerJ 2018; 6:e5715. [PMID: 30397540 PMCID: PMC6211267 DOI: 10.7717/peerj.5715] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2018] [Accepted: 09/10/2018] [Indexed: 12/18/2022] Open
Abstract
Agriculture is one of the main drivers of land conversion, and agriculture practices can impact on microbial diversity. Here we characterized the phyllosphere fungal diversity associated with Carménère grapevines under conventional and organic agricultural management. We also explored the fungal diversity present in the adjacent sclerophyllous forests to explore the potential role of native forest on vineyard phyllosphere. After conducting D2 and ITS2 amplicon sequencing, we found that fungal diversity indices did not change between conventional and organic vineyards, but community structure was sensitive to the agricultural management. On the other hand, we found a high proportion of shared fungal OTUs between vineyards and native forests. In addition, both habitats had similar levels of fungal diversity despite forest samples were derived from multiple plant species. In contrast, the community structure was different in both habitats. Interestingly, the native forest had more unidentified species and unique OTUs than vineyards. Forest dominant species were Aureobasidium pullulans and Endoconidioma populi, whereas Davidiella tassiana, Didymella sp., and Alternaria eichhorniae were more abundant in vineyards. Overall, this study argues that a better understanding of the relationship native forests and agroecosystems is needed for maintaining and enhancing ecosystem services provided by natural ecosystems. Finally, knowledge of microbial communities living in the Chilean Mediterranean biome is needed for appropriate conservation management of these biomes and their classification as biodiversity hotspots.
Collapse
Affiliation(s)
- Luis E. Castañeda
- Programa de Genética Humana, Instituto de Ciencias Biomédicas, Facultad de Medicina, Universidad de Chile, Santiago, Chile
- Instituto de Ciencias Ambientales y Evolutivas, Facultad de Ciencias, Universidad Austral de Chile, Valdivia, Chile
| | - Toshiko Miura
- Research Institute of Environment, Agriculture and Fisheries, Osaka Prefecture, Japan
- Instituto de Ecología y Biodiversidad, Santiago, Chile
| | - Roland Sánchez
- Instituto de Ciencias Ambientales y Evolutivas, Facultad de Ciencias, Universidad Austral de Chile, Valdivia, Chile
- Instituto de Ecología y Biodiversidad, Santiago, Chile
| | - Olga Barbosa
- Instituto de Ciencias Ambientales y Evolutivas, Facultad de Ciencias, Universidad Austral de Chile, Valdivia, Chile
- Instituto de Ecología y Biodiversidad, Santiago, Chile
| |
Collapse
|
23
|
Breniaux M, Dutilh L, Petrel M, Gontier E, Campbell-Sills H, Deleris-Bou M, Krieger S, Teissedre PL, Jourdes M, Reguant C, Lucas P. Adaptation of two groups of Oenococcus oeni strains to red and white wines: the role of acidity and phenolic compounds. J Appl Microbiol 2018; 125:1117-1127. [PMID: 29904988 DOI: 10.1111/jam.13946] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2017] [Revised: 04/17/2018] [Accepted: 06/01/2018] [Indexed: 11/28/2022]
Abstract
AIMS Oenococcus oeni is the lactic acid bacteria species which is the most adapted to wine. Recently, two groups of strains that form two genetic lineages were described in red and white Burgundy wines. The aim of this study was to analyse the phenotypes of these strains in order to determine how they have adapted specifically to either red or white wine. METHODS AND RESULTS Four strains from each group were tested in grape must and in wines to evaluate their tolerance to pH and to phenolic compound content. White wine strains proved to be the most tolerant to low pH, both in grape must and in wine, whereas they were inhibited by the presence of grape tannins in wine. Red wine strains were more sensitive to acidity, but very resistant to phenolic compounds. CONCLUSIONS The results suggest that pH and phenolic compounds drive strain selection at several stages of wine production. SIGNIFICANCE AND IMPACT OF THE STUDY Although it is well known that O. oeni is well adapted to wine, this study shows that strains of some genetic lineages within this species have evolved to adapt better than others to specific types of wines.
Collapse
Affiliation(s)
- M Breniaux
- Unité de recherche Œnologie, Univ. Bordeaux, Villenave d'Ornon Cedex, France
| | - L Dutilh
- Unité de recherche Œnologie, Univ. Bordeaux, Villenave d'Ornon Cedex, France
| | - M Petrel
- Univ. Bordeaux, Bordeaux Imaging Center, Bordeaux, France
| | - E Gontier
- Univ. Bordeaux, Bordeaux Imaging Center, Bordeaux, France
| | - H Campbell-Sills
- Unité de recherche Œnologie, Univ. Bordeaux, Villenave d'Ornon Cedex, France.,LALLEMAND SAS, Blagnac, France
| | | | | | - P-L Teissedre
- Unité de recherche Œnologie, Univ. Bordeaux, Villenave d'Ornon Cedex, France
| | - M Jourdes
- Unité de recherche Œnologie, Univ. Bordeaux, Villenave d'Ornon Cedex, France
| | - C Reguant
- Department of Biochemistry and Biotechnology, University Rovira i Virgili, Tarragona, Catalonia, Spain
| | - P Lucas
- Unité de recherche Œnologie, Univ. Bordeaux, Villenave d'Ornon Cedex, France
| |
Collapse
|
24
|
Zaller JG, Cantelmo C, Santos GD, Muther S, Gruber E, Pallua P, Mandl K, Friedrich B, Hofstetter I, Schmuckenschlager B, Faber F. Herbicides in vineyards reduce grapevine root mycorrhization and alter soil microorganisms and the nutrient composition in grapevine roots, leaves, xylem sap and grape juice. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2018; 25:23215-23226. [PMID: 29862481 PMCID: PMC6096560 DOI: 10.1007/s11356-018-2422-3] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/23/2018] [Accepted: 05/25/2018] [Indexed: 04/12/2023]
Abstract
Herbicides are increasingly applied in vineyards worldwide. However, not much is known on potential side effects on soil organisms or on the nutrition of grapevines (Vitis vinifera). In an experimental vineyard in Austria, we examined the impacts of three within-row herbicide treatments (active ingredients: flazasulfuron, glufosinate, glyphosate) and mechanical weeding on grapevine root mycorrhization; soil microorganisms; earthworms; and nutrient concentration in grapevine roots, leaves, xylem sap and grape juice. The three herbicides reduced grapevine root mycorrhization on average by 53% compared to mechanical weeding. Soil microorganisms (total colony-forming units, CFU) were significantly affected by herbicides with highest CFUs under glufosinate and lowest under glyphosate. Earthworms (surface casting activity, density, biomass, reproduction) or litter decomposition in soil were unaffected by herbicides. Herbicides altered nutrient composition in grapevine roots, leaves, grape juice and xylem sap that was collected 11 months after herbicide application. Xylem sap under herbicide treatments also contained on average 70% more bacteria than under mechanical weeding; however, due to high variability, this was not statistically significant. We conclude that interdisciplinary approaches should receive more attention when assessing ecological effects of herbicides in vineyard ecosystems.
Collapse
Affiliation(s)
- Johann G Zaller
- Institute of Zoology, University of Natural Resources and Life Sciences Vienna (BOKU), Gregor Mendel Straße 33, A-1180, Vienna, Austria.
| | - Clemens Cantelmo
- Institute of Zoology, University of Natural Resources and Life Sciences Vienna (BOKU), Gregor Mendel Straße 33, A-1180, Vienna, Austria
| | - Gabriel Dos Santos
- Institute of Zoology, University of Natural Resources and Life Sciences Vienna (BOKU), Gregor Mendel Straße 33, A-1180, Vienna, Austria
| | - Sandrina Muther
- Institute of Zoology, University of Natural Resources and Life Sciences Vienna (BOKU), Gregor Mendel Straße 33, A-1180, Vienna, Austria
| | - Edith Gruber
- Institute of Zoology, University of Natural Resources and Life Sciences Vienna (BOKU), Gregor Mendel Straße 33, A-1180, Vienna, Austria
| | - Paul Pallua
- Institute of Zoology, University of Natural Resources and Life Sciences Vienna (BOKU), Gregor Mendel Straße 33, A-1180, Vienna, Austria
| | - Karin Mandl
- Federal College and Reseach Center of Viticulture and Pomology, Wiener Straße 74, A-3400, Klosterneuburg, Austria
| | - Barbara Friedrich
- Federal College and Reseach Center of Viticulture and Pomology, Wiener Straße 74, A-3400, Klosterneuburg, Austria
| | - Ingrid Hofstetter
- Federal College and Reseach Center of Viticulture and Pomology, Wiener Straße 74, A-3400, Klosterneuburg, Austria
| | - Bernhard Schmuckenschlager
- Federal College and Reseach Center of Viticulture and Pomology, Wiener Straße 74, A-3400, Klosterneuburg, Austria
| | - Florian Faber
- Federal College and Reseach Center of Viticulture and Pomology, Wiener Straße 74, A-3400, Klosterneuburg, Austria
| |
Collapse
|
25
|
Stefanini I, Cavalieri D. Metagenomic Approaches to Investigate the Contribution of the Vineyard Environment to the Quality of Wine Fermentation: Potentials and Difficulties. Front Microbiol 2018; 9:991. [PMID: 29867889 PMCID: PMC5964215 DOI: 10.3389/fmicb.2018.00991] [Citation(s) in RCA: 59] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2017] [Accepted: 04/27/2018] [Indexed: 01/08/2023] Open
Abstract
The winemaking is a complex process that begins in the vineyard and ends at consumption moment. Recent reports have shown the relevance of microbial populations in the definition of the regional organoleptic and sensory characteristics of a wine. Metagenomic approaches, allowing the exhaustive identification of microorganisms present in complex samples, have recently played a fundamental role in the dissection of the contribution of the vineyard environment to wine fermentation. Systematic approaches have explored the impact of agronomical techniques, vineyard topologies, and climatic changes on bacterial and fungal populations found in the vineyard and in fermentations, also trying to predict or extrapolate the effects on the sensorial characteristics of the resulting wine. This review is aimed at highlighting the major technical and experimental challenges in dissecting the contribution of the vineyard and native environments microbiota to the wine fermentation process, and how metagenomic approaches can help in understanding microbial fluxes and selections across the environments and specimens related to wine fermentation.
Collapse
Affiliation(s)
- Irene Stefanini
- Division of Biomedical Sciences, University of Warwick, Coventry, United Kingdom
| | | |
Collapse
|
26
|
Mezzasalma V, Sandionigi A, Guzzetti L, Galimberti A, Grando MS, Tardaguila J, Labra M. Geographical and Cultivar Features Differentiate Grape Microbiota in Northern Italy and Spain Vineyards. Front Microbiol 2018; 9:946. [PMID: 29867854 PMCID: PMC5962658 DOI: 10.3389/fmicb.2018.00946] [Citation(s) in RCA: 56] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2018] [Accepted: 04/23/2018] [Indexed: 12/17/2022] Open
Abstract
Recent studies have highlighted the role of the grapevine microbiome in addressing a wide panel of features, ranging from the signature of field origin to wine quality. Although the influence of cultivar and vineyard environmental conditions in shaping the grape microbiome have already been ascertained, several aspects related to this topic, deserve to be further investigated. In this study, we selected three international diffused grapevine cultivars (Cabernet Sauvignon, Syrah, and Sauvignon Blanc) at three germplasm collections characterized by different climatic conditions [Northern Italy (NI), Italian Alps (AI), and Northern Spain (NS)]. The soil and grape microbiome was characterized by 16s rRNA High Throughput Sequencing (HTS), and the obtained results showed that all grape samples shared some bacterial taxa, regardless of sampling locality (e.g., Bacillus, Methylobacterium, Sphingomonas, and other genera belonging to Alphaproteobacteria, Gammaproteobacteria, and Actinobacteria). However, some Operational Taxonomic Units (OTUs) could act as geographical signatures and in some cases as cultivar fingerprint. Concerning the origin of the grape microbiome, our study confirms that vineyard soil represents a primary reservoir for grape associated bacteria with almost 60% of genera shared between the soil and grape. At each locality, grapevine cultivars shared a core of bacterial genera belonging to the vineyard soil, as well as from other local biodiversity elements such as arthropods inhabiting or foraging in the vineyard. Finally, a machine learning analysis showed that it was possible to predict the geographical origin and cultivar of grape starting from its microbiome composition with a high accuracy (9 cases out of 12 tested samples). Overall, these findings open new perspectives for the development of more comprehensive and integrated research activities to test which environmental variables have an effective role in shaping the microbiome composition and dynamics of cultivated species over time and space.
Collapse
Affiliation(s)
- Valerio Mezzasalma
- Zooplantlab, Department of Biotechnology and Biosciences, University of Milano-Bicocca, Milan, Italy
| | - Anna Sandionigi
- Zooplantlab, Department of Biotechnology and Biosciences, University of Milano-Bicocca, Milan, Italy
| | - Lorenzo Guzzetti
- Zooplantlab, Department of Biotechnology and Biosciences, University of Milano-Bicocca, Milan, Italy
| | - Andrea Galimberti
- Zooplantlab, Department of Biotechnology and Biosciences, University of Milano-Bicocca, Milan, Italy.,BEST4FOOD, University of Milano-Bicocca, Milan, Italy
| | - Maria S Grando
- Research and Innovation Centre, Fondazione Edmund Mach, San Michele all'Adige, Italy.,Center Agriculture Food Environment (C3A), University of Trento, San Michele all'Adige, Italy
| | - Javier Tardaguila
- Instituto de Ciencias de la Vid y del Vino, University of La Rioja, CSIC, Rioja Regional Government, Logroño, Spain
| | - Massimo Labra
- Zooplantlab, Department of Biotechnology and Biosciences, University of Milano-Bicocca, Milan, Italy.,BEST4FOOD, University of Milano-Bicocca, Milan, Italy
| |
Collapse
|
27
|
High-throughput sequencing of microbial community diversity in soil, grapes, leaves, grape juice and wine of grapevine from China. PLoS One 2018; 13:e0193097. [PMID: 29565999 PMCID: PMC5863948 DOI: 10.1371/journal.pone.0193097] [Citation(s) in RCA: 56] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2017] [Accepted: 02/04/2018] [Indexed: 11/20/2022] Open
Abstract
In this study Illumina MiSeq was performed to investigate microbial diversity in soil, leaves, grape, grape juice and wine. A total of 1,043,102 fungal Internal Transcribed Spacer (ITS) reads and 2,422,188 high quality bacterial 16S rDNA sequences were used for taxonomic classification, revealed five fungal and eight bacterial phyla. At the genus level, the dominant fungi were Ascomycota, Sordariales, Tetracladium and Geomyces in soil, Aureobasidium and Pleosporaceae in grapes leaves, Aureobasidium in grape and grape juice. The dominant bacteria were Kaistobacter, Arthrobacter, Skermanella and Sphingomonas in soil, Pseudomonas, Acinetobacter and Kaistobacter in grape and grapes leaves, and Oenococcus in grape juice and wine. Principal coordinate analysis showed structural separation between the composition of fungi and bacteria in all samples. This is the first study to understand microbiome population in soil, grape, grapes leaves, grape juice and wine in Xinjiang through High-throughput Sequencing and identify microorganisms like Saccharomyces cerevisiae and Oenococcus spp. that may contribute to the quality and flavor of wine.
Collapse
|
28
|
Miura T, Sánchez R, Castañeda LE, Godoy K, Barbosa O. Is microbial terroir related to geographic distance between vineyards? ENVIRONMENTAL MICROBIOLOGY REPORTS 2017; 9:742-749. [PMID: 28892290 DOI: 10.1111/1758-2229.12589] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/17/2017] [Accepted: 08/28/2017] [Indexed: 05/20/2023]
Abstract
While there are substantial studies suggesting that characteristics of wine are related to regional microbial community composition (microbial terroir), there has been little discussion about what factors affect variation in regional microbial community composition. In this study, we compared the microbial community composition of leaves and berries of a grape variety (Carmenere) from six different Chilean vineyards within 35 km of each other. In order to determine relationships between spatial proximity and microbial compositional dissimilarity, we sequenced amplicons of the internal transcribed spacer (ITS) region for fungi and 16S rRNA gene for bacteria. Results showed that both the fungal and the bacterial community compositions of the studied vineyards differed, but this difference was much clearer in fungi than in bacteria. In addition, while bacterial community dissimilarity was not correlated with geographic distance, the leaf and berry fungal community dissimilarities between locations increased with geographic distance. This indicates that spatial processes play an important role in structuring the biogeographic pattern of grape-associated fungal communities at local scales, which might in turn contribute to the local identity of wine.
Collapse
Affiliation(s)
- Toshiko Miura
- Instituto de Ciencias Ambientales y Evolutivas, Facultad de Ciencias, Universidad Austral de Chile, Valdivia, Chile
- Instituto de Ecología & Biodiversidad (IEB-Chile), Casilla 653, Santiago, Chile
| | - Roland Sánchez
- Instituto de Ciencias Ambientales y Evolutivas, Facultad de Ciencias, Universidad Austral de Chile, Valdivia, Chile
- Instituto de Ecología & Biodiversidad (IEB-Chile), Casilla 653, Santiago, Chile
| | - Luis E Castañeda
- Instituto de Ciencias Ambientales y Evolutivas, Facultad de Ciencias, Universidad Austral de Chile, Valdivia, Chile
- Millennium Nucleus Center in Molecular Ecology and Evolutionary Applications in the Agroecosystems, Universidad de Talca, Talca, Chile
| | - Karina Godoy
- Instituto de Ciencias Ambientales y Evolutivas, Facultad de Ciencias, Universidad Austral de Chile, Valdivia, Chile
- Instituto de Ecología & Biodiversidad (IEB-Chile), Casilla 653, Santiago, Chile
| | - Olga Barbosa
- Instituto de Ciencias Ambientales y Evolutivas, Facultad de Ciencias, Universidad Austral de Chile, Valdivia, Chile
- Instituto de Ecología & Biodiversidad (IEB-Chile), Casilla 653, Santiago, Chile
| |
Collapse
|
29
|
Li Q, Kang J, Ma Z, Li X, Liu L, Hu X. Microbial succession and metabolite changes during traditional serofluid dish fermentation. Lebensm Wiss Technol 2017. [DOI: 10.1016/j.lwt.2017.06.051] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
|
30
|
Xie X, Wang J, Guan L, Liu J. Effect of changing forage on the dynamic variation in rumen fermentation in sheep. Anim Sci J 2017; 89:122-131. [DOI: 10.1111/asj.12915] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2017] [Accepted: 07/20/2017] [Indexed: 11/27/2022]
Affiliation(s)
- Xiao Xie
- Institute of Dairy Science College of Animal Sciences Zhejiang University Hangzhou China
| | - Jia‐kun Wang
- Institute of Dairy Science College of Animal Sciences Zhejiang University Hangzhou China
| | - Leluo Guan
- Institute of Dairy Science College of Animal Sciences Zhejiang University Hangzhou China
- Department of Agricultural Food and Nutritional Science University of Alberta Edmonton AB Canada
| | - Jian‐Xin Liu
- Institute of Dairy Science College of Animal Sciences Zhejiang University Hangzhou China
| |
Collapse
|
31
|
He GQ, Liu TJ, Sadiq FA, Gu JS, Zhang GH. Insights into the microbial diversity and community dynamics of Chinese traditional fermented foods from using high-throughput sequencing approaches. J Zhejiang Univ Sci B 2017; 18:289-302. [PMID: 28378567 DOI: 10.1631/jzus.b1600148] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Chinese traditional fermented foods have a very long history dating back thousands of years and have become an indispensable part of Chinese dietary culture. A plethora of research has been conducted to unravel the composition and dynamics of microbial consortia associated with Chinese traditional fermented foods using culture-dependent as well as culture-independent methods, like different high-throughput sequencing (HTS) techniques. These HTS techniques enable us to understand the relationship between a food product and its microbes to a greater extent than ever before. Considering the importance of Chinese traditional fermented products, the objective of this paper is to review the diversity and dynamics of microbiota in Chinese traditional fermented foods revealed by HTS approaches.
Collapse
Affiliation(s)
- Guo-Qing He
- College of Biosystems Engineering and Food Science, Zhejiang University, Hangzhou 310058, China.,Zhejiang Provincial Key Laboratory of Food Microbiology, Zhejiang University, Hangzhou 310058, China
| | - Tong-Jie Liu
- College of Biosystems Engineering and Food Science, Zhejiang University, Hangzhou 310058, China.,Zhejiang Provincial Key Laboratory of Food Microbiology, Zhejiang University, Hangzhou 310058, China
| | - Faizan A Sadiq
- College of Biosystems Engineering and Food Science, Zhejiang University, Hangzhou 310058, China.,Zhejiang Provincial Key Laboratory of Food Microbiology, Zhejiang University, Hangzhou 310058, China
| | - Jing-Si Gu
- College of Biosystems Engineering and Food Science, Zhejiang University, Hangzhou 310058, China.,Zhejiang Provincial Key Laboratory of Food Microbiology, Zhejiang University, Hangzhou 310058, China
| | - Guo-Hua Zhang
- College of Biosystems Engineering and Food Science, Zhejiang University, Hangzhou 310058, China.,Zhejiang Provincial Key Laboratory of Food Microbiology, Zhejiang University, Hangzhou 310058, China
| |
Collapse
|
32
|
Philippe C, Jaomanjaka F, Claisse O, Laforgue R, Maupeu J, Petrel M, Le Marrec C. A survey of oenophages during wine making reveals a novel group with unusual genomic characteristics. Int J Food Microbiol 2017. [PMID: 28651079 DOI: 10.1016/j.ijfoodmicro.2017.06.014] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
Oenophages have so far been mostly isolated from red wines under malolactic fermentation (MLF), and correspond to temperate or ex-temperate phages of Oenococcus oeni. Their genomes are clustered into 4 integrase gene sequence groups, which are also related to the chromosomal integration site. Our aims were to survey the occurrence of oenophages in a broader and more diverse collection of samples than those previously explored. Active phages were isolated from 33 out of 166 samples, which mostly originated from must and MLF. Seventy one phage lysates were produced and 30% were assigned to a novel group with unusual genomic characteristics, called unk. All unk members produced similar RAPD and DNA restriction patterns, were negative by PCR for the signature sequences previously identified in the integrase and endolysin genes of oenophages, and lacked any BamHI restriction site in their genome. The data support that development of additional and novel signature genes for assessing oenophage diversity is now required.
Collapse
Affiliation(s)
- Cécile Philippe
- Univ. Bordeaux, ISVV, EA 4577, Unité de recherche Oenologie, F-33882 Villenave d'Ornon, France
| | - Fety Jaomanjaka
- Univ. Bordeaux, ISVV, EA 4577, Unité de recherche Oenologie, F-33882 Villenave d'Ornon, France; Institut Polytechnique de Bordeaux, ISVV, EA 4577 Oenologie, F-33140 Villenave d'Ornon, France
| | - Olivier Claisse
- Univ. Bordeaux, ISVV, EA 4577, Unité de recherche Oenologie, F-33882 Villenave d'Ornon, France; INRA, ISVV, USC 1366 Oenologie, F-33882 Villenave d'Ornon, France
| | - Rémi Laforgue
- Univ. Bordeaux, ISVV, EA 4577, Unité de recherche Oenologie, F-33882 Villenave d'Ornon, France; MICROFLORA, ISVV, EA 4577 Oenologie, F-33140 Villenave d'Ornon, France
| | - Julie Maupeu
- Univ. Bordeaux, ISVV, EA 4577, Unité de recherche Oenologie, F-33882 Villenave d'Ornon, France; MICROFLORA, ISVV, EA 4577 Oenologie, F-33140 Villenave d'Ornon, France
| | - Melina Petrel
- Univ. Bordeaux, Bordeaux Imaging Center, UMS 3420 CNRS-US4 INSERM, Bordeaux, France
| | - Claire Le Marrec
- Univ. Bordeaux, ISVV, EA 4577, Unité de recherche Oenologie, F-33882 Villenave d'Ornon, France; Institut Polytechnique de Bordeaux, ISVV, EA 4577 Oenologie, F-33140 Villenave d'Ornon, France.
| |
Collapse
|
33
|
Morgan HH, du Toit M, Setati ME. The Grapevine and Wine Microbiome: Insights from High-Throughput Amplicon Sequencing. Front Microbiol 2017; 8:820. [PMID: 28553266 PMCID: PMC5425579 DOI: 10.3389/fmicb.2017.00820] [Citation(s) in RCA: 81] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2016] [Accepted: 04/21/2017] [Indexed: 12/21/2022] Open
Abstract
From the time when microbial activity in wine fermentation was first demonstrated, the microbial ecology of the vineyard, grape, and wine has been extensively investigated using culture-based methods. However, the last 2 decades have been characterized by an important change in the approaches used for microbial examination, due to the introduction of DNA-based community fingerprinting methods such as DGGE, SSCP, T-RFLP, and ARISA. These approaches allowed for the exploration of microbial community structures without the need to cultivate, and have been extensively applied to decipher the microbial populations associated with the grapevine as well as the microbial dynamics throughout grape berry ripening and wine fermentation. These techniques are well-established for the rapid more sensitive profiling of microbial communities; however, they often do not provide direct taxonomic information and possess limited ability to detect the presence of rare taxa and taxa with low abundance. Consequently, the past 5 years have seen an upsurge in the application of high-throughput sequencing methods for the in-depth assessment of the grapevine and wine microbiome. Although a relatively new approach in wine sciences, these methods reveal a considerably greater diversity than previously reported, and identified several species that had not yet been reported. The aim of the current review is to highlight the contribution of high-throughput next generation sequencing and metagenomics approaches to vineyard microbial ecology especially unraveling the influence of vineyard management practices on microbial diversity.
Collapse
Affiliation(s)
- Horatio H Morgan
- Department of Viticulture and Oenology, Institute for Wine Biotechnology, Stellenbosch UniversityStellenbosch, South Africa
| | - Maret du Toit
- Department of Viticulture and Oenology, Institute for Wine Biotechnology, Stellenbosch UniversityStellenbosch, South Africa
| | - Mathabatha E Setati
- Department of Viticulture and Oenology, Institute for Wine Biotechnology, Stellenbosch UniversityStellenbosch, South Africa
| |
Collapse
|
34
|
Belda I, Zarraonaindia I, Perisin M, Palacios A, Acedo A. From Vineyard Soil to Wine Fermentation: Microbiome Approximations to Explain the " terroir" Concept. Front Microbiol 2017; 8:821. [PMID: 28533770 PMCID: PMC5420814 DOI: 10.3389/fmicb.2017.00821] [Citation(s) in RCA: 90] [Impact Index Per Article: 12.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2016] [Accepted: 04/21/2017] [Indexed: 11/13/2022] Open
Abstract
Wine originally emerged as a serendipitous mix of chemistry and biology, where microorganisms played a decisive role. From these ancient fermentations to the current monitored industrial processes, winegrowers and winemakers have been continuously changing their practices according to scientific knowledge and advances. A new enology direction is emerging and aiming to blend the complexity of spontaneous fermentations with industrial safety of monitored fermentations. In this context, wines with distinctive autochthonous peculiarities have a great acceptance among consumers, causing important economic returns. The concept of terroir, far from being a rural term, conceals a wide range of analytical parameters that are the basis of the knowledge-based enology trend. In this sense, the biological aspect of soils has been underestimated for years, when actually it contains a great microbial diversity. This soil-associated microbiota has been described as determinant, not only for the chemistry and nutritional properties of soils, but also for health, yield, and quality of the grapevine. Additionally, recent works describe the soil microbiome as the reservoir of the grapevine associated microbiota, and as a contributor to the final sensory properties of wines. To understand the crucial roles of microorganisms on the entire wine making process, we must understand their ecological niches, population dynamics, and relationships between ‘microbiome- vine health’ and ‘microbiome-wine metabolome.’ These are critical steps for designing precision enology practices. For that purpose, current metagenomic techniques are expanding from laboratories, to the food industry. This review focuses on the current knowledge about vine and wine microbiomes, with emphasis on their biological roles and the technical basis of next-generation sequencing pipelines. An overview of molecular and informatics tools is included and new directions are proposed, highlighting the importance of –omics technologies in wine research and industry.
Collapse
Affiliation(s)
- Ignacio Belda
- Biome Makers Inc., San FranciscoCA, USA.,Department of Microbiology, Biology Faculty, Complutense University of MadridMadrid, Spain
| | - Iratxe Zarraonaindia
- Department of Genetics, Physical Anthropology and Animal Physiology, University of the Basque CountryLeioa, Spain.,IKERBASQUE - Basque Foundation for ScienceBilbao, Spain
| | | | - Antonio Palacios
- Biome Makers Inc., San FranciscoCA, USA.,Laboratorios Excell IbericaLogroño, Spain
| | | |
Collapse
|
35
|
Cappello MS, Zapparoli G, Logrieco A, Bartowsky EJ. Linking wine lactic acid bacteria diversity with wine aroma and flavour. Int J Food Microbiol 2016; 243:16-27. [PMID: 27940412 DOI: 10.1016/j.ijfoodmicro.2016.11.025] [Citation(s) in RCA: 116] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2016] [Revised: 11/09/2016] [Accepted: 11/27/2016] [Indexed: 10/20/2022]
Abstract
In the last two decades knowledge on lactic acid bacteria (LAB) associated with wine has increased considerably. Investigations on genetic and biochemistry of species involved in malolactic fermentation, such as Oenococcus oeni and of Lactobacillus have enabled a better understand of their role in aroma modification and microbial stability of wine. In particular, the use of molecular techniques has provided evidence on the high diversity at species and strain level, thus improving the knowledge on wine LAB taxonomy and ecology. These tools demonstrated to also be useful to detect strains with potential desirable or undesirable traits for winemaking purposes. At the same time, advances on the enzymatic properties of wine LAB responsible for the development of wine aroma molecules have been undertaken. Interestingly, it has highlighted the high intraspecific variability of enzymatic activities such as glucosidase, esterase, proteases and those related to citrate metabolism within the wine LAB species. This genetic and biochemistry diversity that characterizes wine LAB populations can generate a wide spectrum of wine sensory outcomes. This review examines some of these interesting aspects as a way to elucidate the link between LAB diversity with wine aroma and flavour. In particular, the correlation between inter- and intra-species diversity and bacterial metabolic traits that affect the organoleptic properties of wines is highlighted with emphasis on the importance of enzymatic potential of bacteria for the selection of starter cultures to control MLF and to enhance wine aroma.
Collapse
Affiliation(s)
- Maria Stella Cappello
- CNR, Institute of Science of Food Production (ISPA), Prov.le Lecce-Monteroni, 73100 Lecce, Italy.
| | - Giacomo Zapparoli
- Department of Biotechnology, University of Verona, Strada le Grazie 15, 37134 Verona, Italy.
| | - Antonio Logrieco
- CNR, Institute of Science of Food Production, Via G. Amendola, 122/0, 70126 Bari, Italy
| | - Eveline J Bartowsky
- The Australian Wine Research Institute, PO Box 197, Glen Osmond, SA 5064, Australia
| |
Collapse
|
36
|
Liu J, Zhang M, Xue C, Zhu W, Mao S. Characterization and comparison of the temporal dynamics of ruminal bacterial microbiota colonizing rice straw and alfalfa hay within ruminants. J Dairy Sci 2016; 99:9668-9681. [PMID: 27692708 DOI: 10.3168/jds.2016-11398] [Citation(s) in RCA: 82] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2016] [Accepted: 08/13/2016] [Indexed: 12/24/2022]
Abstract
Three ruminally cannulated Holstein cows were used to characterize the dynamics of bacterial colonization of rice straw and alfalfa hay and to assess the differences in the composition and inferred gene function of the colonized microbiota between these 2 forages. Nonincubated (0h) rice straw and alfalfa hay samples and residues in nylon bags incubated for 0.5, 2, 6, 16, and 48h were analyzed for dry matter and were used for DNA extraction and MiSeq (Illumina Inc., San Diego, CA) sequencing of the 16S rRNA gene. The microbial communities that colonized the air-dried and nonincubated (0h) rice straw and alfalfa hay were both dominated by members of the Proteobacteria (contributing toward 70.47% of the 16S RNA reads generated). In situ incubation of the 2 forages revealed major shifts in the community composition: Proteobacteria were replaced within 30min by members belonging to the Bacteroidetes and Firmicutes, contributing toward 51.9 and 36.6% of the 16S rRNA reads generated, respectively. A second significant shift was observed after 6h of rumen incubation, when members of the Spirochaetes and Fibrobacteria phyla became abundant in the forage-adherent community. During the first 30min of rumen incubation, ~20.7 and 36.1% of the rice straw and alfalfa hay, respectively, were degraded, whereas little biomass degradation occurred between 30min and 2h after the rice straw or alfalfa hay was placed in the rumen. Significant differences were noted in attached bacterial community structure between the 2 forage groups, and the abundances of dominant genera Anaeroplasma, Butyrivibrio, Fibrobacter, and Prevotella were affected by the forage types. Real-time PCR results showed that the 16S rRNA copies of total bacteria attached to these 2 forages were affected by the forage types and incubation time, and higher numbers of attached bacterial 16S rRNA were observed in the alfalfa hay samples than in the rice straw from 0.5 to 16h of incubation. The metagenomes predicted by phylogenetic investigation of communities by reconstruction of unobserved states (PICRUSt) revealed that the forage types significantly affected 21 metabolic pathways identified in the Kyoto Encyclopedia of Genes and Genomes, and 33 were significantly changed over time. Collectively, our results reveal a difference in the dynamics of bacterial colonization and the inferred gene function of microbiota associated with rice straw and alfalfa hay within the rumen. These findings are of great importance for the targeted improvement of forage nutrient use efficiency in ruminants.
Collapse
Affiliation(s)
- Junhua Liu
- Jiangsu Key Laboratory of Gastrointestinal Nutrition and Animal Health, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing 210095, China
| | - Mengling Zhang
- Jiangsu Key Laboratory of Gastrointestinal Nutrition and Animal Health, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing 210095, China
| | - Chunxu Xue
- Jiangsu Key Laboratory of Gastrointestinal Nutrition and Animal Health, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing 210095, China
| | - Weiyun Zhu
- Jiangsu Key Laboratory of Gastrointestinal Nutrition and Animal Health, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing 210095, China
| | - Shengyong Mao
- Jiangsu Key Laboratory of Gastrointestinal Nutrition and Animal Health, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing 210095, China.
| |
Collapse
|
37
|
Salvetti E, Campanaro S, Campedelli I, Fracchetti F, Gobbi A, Tornielli GB, Torriani S, Felis GE. Whole-Metagenome-Sequencing-Based Community Profiles of Vitis vinifera L. cv. Corvina Berries Withered in Two Post-harvest Conditions. Front Microbiol 2016; 7:937. [PMID: 27445999 PMCID: PMC4917526 DOI: 10.3389/fmicb.2016.00937] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2016] [Accepted: 05/31/2016] [Indexed: 12/20/2022] Open
Abstract
Vitis vinifera L. cv. Corvina grape forms the basis for the production of unique wines, such as Amarone, whose distinctive sensory features are strongly linked to the post-harvest grape withering process. Indeed, this process increases sugar concentration and changes must characteristics. While microorganisms involved in must fermentation have been widely investigated, few data are available on the microbiota of withered grapes. Thus, in this paper, a whole metagenome sequencing (WMS) approach was used to analyse the microbial consortium associated with Corvina berries at the end of the withering process performed in two different conditions ("traditional withering," TW or "accelerated withering," AW), and to unveil whether changes of drying parameters could have an impact on microbial diversity. Samples of healthy undamaged berries were collected and washed, to recover microorganisms from the surface and avoid contamination with grapevine genetic material. Isolated DNA was sequenced and the data obtained were analyzed with several bioinformatics methods. The eukaryotic community was mainly composed by members of the phylum Ascomycota, including Eurotiomycetes, Sordariomycetes, and Dothideomycetes. Moreover, the distribution of the genera Aspergillus and Penicillium (class Eurotiomycetes) varied between the withered berry samples. Instead, Botryotinia, Saccharomyces, and other wine technologically useful microorganisms were relatively scarce in both samples. For prokaryotes, 25 phyla were identified, nine of which were common to both conditions. Environmental bacteria belonging to the class Gammaproteobacteria were dominant and, in particular, the TW sample was characterized by members of the family Pseudomonadaceae, while members of the family Enterobacteriaceae dominated the AW sample, in addition to Sphyngobacteria and Clostridia. Finally, the binning procedure discovered 15 putative genomes which dominated the microbial community of the two samples, and included representatives of genera Erwinia, Pantoea, Pseudomonas, Clostridium, Paenibacillus, and of orders Lactobacillales and Actinomycetales. These results provide insights into the microbial consortium of Corvina withered berries and reveal relevant variations attributable to post-harvest withering conditions, underling how WMS could open novel perspectives in the knowledge and management of the withering process of Corvina, with an impact on the winemaking of important Italian wines.
Collapse
Affiliation(s)
- Elisa Salvetti
- Department of Biotechnology, University of VeronaVerona, Italy
| | | | | | | | - Alex Gobbi
- Department of Biotechnology, University of VeronaVerona, Italy
| | | | - Sandra Torriani
- Department of Biotechnology, University of VeronaVerona, Italy
| | | |
Collapse
|
38
|
Marzano M, Fosso B, Manzari C, Grieco F, Intranuovo M, Cozzi G, Mulè G, Scioscia G, Valiente G, Tullo A, Sbisà E, Pesole G, Santamaria M. Complexity and Dynamics of the Winemaking Bacterial Communities in Berries, Musts, and Wines from Apulian Grape Cultivars through Time and Space. PLoS One 2016; 11:e0157383. [PMID: 27299312 PMCID: PMC4907434 DOI: 10.1371/journal.pone.0157383] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2016] [Accepted: 05/27/2016] [Indexed: 11/19/2022] Open
Abstract
Currently, there is very little information available regarding the microbiome associated with the wine production chain. Here, we used an amplicon sequencing approach based on high-throughput sequencing (HTS) to obtain a comprehensive assessment of the bacterial community associated with the production of three Apulian red wines, from grape to final product. The relationships among grape variety, the microbial community, and fermentation was investigated. Moreover, the winery microbiota was evaluated compared to the autochthonous species in vineyards that persist until the end of the winemaking process. The analysis highlighted the remarkable dynamics within the microbial communities during fermentation. A common microbial core shared among the examined wine varieties was observed, and the unique taxonomic signature of each wine appellation was revealed. New species belonging to the genus Halomonas were also reported. This study demonstrates the potential of this metagenomic approach, supported by optimized protocols, for identifying the biodiversity of the wine supply chain. The developed experimental pipeline offers new prospects for other research fields in which a comprehensive view of microbial community complexity and dynamics is desirable.
Collapse
Affiliation(s)
| | - Bruno Fosso
- Institute of Biomembranes and Bioenergetics, CNR, Bari, Italy
| | | | - Francesco Grieco
- Institute of Sciences of Food Production, CNR, Operative Unit of Lecce, Lecce (Le), Italy
| | - Marianna Intranuovo
- Department of Biosciences, Biotechnology and Biopharmaceutics, University of Bari “A. Moro” Bari, Italy
| | - Giuseppe Cozzi
- Institute of Sciences of Food Production, CNR, Bari, Italy
| | | | | | - Gabriel Valiente
- Algorithms, Bioinformatics, Complexity and Formal Methods Research Group, Polytechnic University of Catalonia, Barcelona, Spain
| | | | | | - Graziano Pesole
- Institute of Biomembranes and Bioenergetics, CNR, Bari, Italy
- Department of Biosciences, Biotechnology and Biopharmaceutics, University of Bari “A. Moro” Bari, Italy
- * E-mail: (MS); (GP)
| | - Monica Santamaria
- Institute of Biomembranes and Bioenergetics, CNR, Bari, Italy
- * E-mail: (MS); (GP)
| |
Collapse
|
39
|
Associations among Wine Grape Microbiome, Metabolome, and Fermentation Behavior Suggest Microbial Contribution to Regional Wine Characteristics. mBio 2016; 7:mBio.00631-16. [PMID: 27302757 PMCID: PMC4959672 DOI: 10.1128/mbio.00631-16] [Citation(s) in RCA: 220] [Impact Index Per Article: 27.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
Regionally distinct wine characteristics (terroir) are an important aspect of wine production and consumer appreciation. Microbial activity is an integral part of wine production, and grape and wine microbiota present regionally defined patterns associated with vineyard and climatic conditions, but the degree to which these microbial patterns associate with the chemical composition of wine is unclear. Through a longitudinal survey of over 200 commercial wine fermentations, we demonstrate that both grape microbiota and wine metabolite profiles distinguish viticultural area designations and individual vineyards within Napa and Sonoma Counties, California. Associations among wine microbiota and fermentation characteristics suggest new links between microbiota, fermentation performance, and wine properties. The bacterial and fungal consortia of wine fermentations, composed from vineyard and winery sources, correlate with the chemical composition of the finished wines and predict metabolite abundances in finished wines using machine learning models. The use of postharvest microbiota as an early predictor of wine chemical composition is unprecedented and potentially poses a new paradigm for quality control of agricultural products. These findings add further evidence that microbial activity is associated with wine terroir. Wine production is a multi-billion-dollar global industry for which microbial control and wine chemical composition are crucial aspects of quality. Terroir is an important feature of consumer appreciation and wine culture, but the many factors that contribute to terroir are nebulous. We show that grape and wine microbiota exhibit regional patterns that correlate with wine chemical composition, suggesting that the grape microbiome may influence terroir. In addition to enriching our understanding of how growing region and wine properties interact, this may provide further economic incentive for agricultural and enological practices that maintain regional microbial biodiversity.
Collapse
|