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Martins V, Teixeira A, Gerós H. A comparison of microbiota isolation methods reveals habitat preferences for fermentative yeasts and plant pathogenic fungi in the grape berry. Food Microbiol 2024; 118:104408. [PMID: 38049270 DOI: 10.1016/j.fm.2023.104408] [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: 07/31/2023] [Revised: 09/26/2023] [Accepted: 10/20/2023] [Indexed: 12/06/2023]
Abstract
The methodologies for profiling the grape berry microbiota have exponentially evolved in the past 25 years. Recently, concerns arose regarding the homogeneity in the protocols of grape harvesting, sequencing and bioinformatic analyses, but the bias introduced by the microbiota isolation method is still unexplored. This study followed a simple approach of comparing two most used methods of microbiota collection from grape berries (washing vs crushing), hypothesizing a significant impact in the outcome of the microbiota profiles analyzed by NGS metabarcoding. Experiments conducted in fruits of three cultivars of the Douro wine region showed that only 52 % of OTUs were common to both surface and juice microbiota, suggesting specific microbial niches. Thirteen fungal genera were abundantly detected in the fruit surface, including Alternaria, Aureobasidium, Cladosporium, Didymella and Bipolaris. Fermentative yeasts including Meyerozyma and Saccharomyces cerevisiae were exclusively detected in the juice, together with several Penicillium species. Distinct habitat preferences of species within the genera Alternaria, Sporobolomyces and Rhodotorula were also revealed. The study showed that the microbiota isolation method is crucial in the detection of certain plant pathogenic/saprophytic fungi and yeasts with biotechnological and oenological interest, adding novelty to the globally accepted assumption that S. cerevisiae in musts originates primarily from the cellar.
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Affiliation(s)
- Viviana Martins
- Centre of Molecular and Environmental Biology, Department of Biology, University of Minho, Campus de Gualtar, 4710-057, Braga, Portugal.
| | - António Teixeira
- Centre of Molecular and Environmental Biology, Department of Biology, University of Minho, Campus de Gualtar, 4710-057, Braga, Portugal.
| | - Hernâni Gerós
- Centre of Molecular and Environmental Biology, Department of Biology, University of Minho, Campus de Gualtar, 4710-057, Braga, Portugal.
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2
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Ohwofasa A, Dhami M, Zhang J, Tian B, Winefield C, On SLW. Influence of climatic variation on microbial communities during organic Pinot noir wine production. PLoS One 2024; 19:e0296859. [PMID: 38416719 PMCID: PMC10901304 DOI: 10.1371/journal.pone.0296859] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2023] [Accepted: 12/20/2023] [Indexed: 03/01/2024] Open
Abstract
To assess the possible impact of climatic variation on microbial community composition in organic winemaking, we employed a metabarcoding approach to scrutinize the microbiome in a commercial, organic, Pinot noir wine production system that utilizes autochthonous fermentation. We assessed microbial composition across two vintages (2018 and 2021) using biological replicates co-located at the same winery. Microbial dynamics were monitored over four important fermentation time points and correlated with contemporaneous climate data. Bacterial (RANOSIM = 0.4743, p = 0.0001) and fungal (RANOSIM = 0.4738, p = 0.0001) compositions were different in both vintages. For bacteria, Lactococcus dominated the diversity associated with the 2018 vintage, while Tatumella dominated the 2021 vintage. For fungal populations, while Saccharomyces were abundant in both vintages, key differences included Starmerella, copious in the 2018 vintage; and Metschnikowia, substantive in the 2021 vintage. Ordination plots correlated the climatic variables with microbial population differences, indicating temperature as a particularly important influence; humidity values also differed significantly between these vintages. Our data illustrates how climatic conditions may influence microbial diversity during winemaking, and further highlights the effect climate change could have on wine production.
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Affiliation(s)
- Aghogho Ohwofasa
- Department of Wine, Food and Molecular Biosciences, Lincoln University, Lincoln, New Zealand
- Centre of Foods for Future Consumers, Lincoln University, Lincoln, New Zealand
| | | | - Junwen Zhang
- Department of Wine, Food and Molecular Biosciences, Lincoln University, Lincoln, New Zealand
| | - Bin Tian
- Department of Wine, Food and Molecular Biosciences, Lincoln University, Lincoln, New Zealand
| | - Christopher Winefield
- Department of Wine, Food and Molecular Biosciences, Lincoln University, Lincoln, New Zealand
| | - Stephen L. W. On
- Department of Wine, Food and Molecular Biosciences, Lincoln University, Lincoln, New Zealand
- Centre of Foods for Future Consumers, Lincoln University, Lincoln, New Zealand
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Zhao S, Li M, Chen J, Tian J, Dai X, Kong Z. Potential Risks of Tebuconazole during Wine Fermentation at the Enantiomer Level Based on Multiomics Analysis. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2023; 71:12129-12139. [PMID: 37493492 DOI: 10.1021/acs.jafc.3c01449] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/27/2023]
Abstract
The enantioselectivity and potential risks of tebuconazole enantiomers (R-tebuconazole and S-tebuconazole) in wine fermentation were investigated in this study using Cabernet Sauvignon grapes. Tebuconazole was mainly degraded during the alcoholic fermentation stage, and no obvious transformation between R-tebuconazole and S-tebuconazole was observed. Selective degradation between these two enantiomers occurred, with R-tebuconazole degrading faster than S-tebuconazole. The residual tebuconazole inhibits glucose metabolism and the unsaturated fatty acid formation in the wine fermentation system and inhibits gene expression in the late phase of Saccharomycetales, affecting its cell wall formation. Overall, the findings highlight that R-tebuconazole exhibited a higher risk than S-tebuconazole in these processes. These insights are potentially exploitable to understand chiral pesticides at the enantiomer level using multiomics technology in food-processing systems.
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Affiliation(s)
- Shanshan Zhao
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, P. R. China
| | - Minmin Li
- Key Laboratory of Agro-Products Quality and Safety Control in Storage and Transport Process, Ministry of Agriculture and Rural Affairs/Institute of Food Science and Technology, Chinese Academy of Agricultural Sciences, Beijing 100193, P. R. China
| | - Jieyin Chen
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, P. R. China
- Western Agricultural Research Center, Chinese Academy of Agricultural Sciences, Changji 831100, China
| | - Jian Tian
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, P. R. China
| | - Xiaofeng Dai
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, P. R. China
| | - Zhiqiang Kong
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, P. R. China
- Western Agricultural Research Center, Chinese Academy of Agricultural Sciences, Changji 831100, China
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Pulcini L, Bona E, Vaudano ET, Tsolakis C, Garcia-Moruno E, Costantini A, Gamalero E. The Impact of a Commercial Biostimulant on the Grape Mycobiota of Vitis vinifera cv. Barbera. Microorganisms 2023; 11:1873. [PMID: 37630432 PMCID: PMC10457965 DOI: 10.3390/microorganisms11081873] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2023] [Revised: 07/22/2023] [Accepted: 07/23/2023] [Indexed: 08/27/2023] Open
Abstract
Reducing the use of fungicides, insecticides, and herbicides in order to limit environmental pollution and health risks for agricultural operators and consumers is one of the goals of European regulations. In fact, the European Commission developed a package of measures (the European Green Deal) to promote the sustainable use of natural resources and strengthen the resilience of European agri-food systems. As a consequence, new plant protection products, such as biostimulants, have been proposed as alternatives to agrochemicals. Their application in agroecosystems could potentially open new scenarios regarding the microbiota. In particular, the vineyard microbiota and the microbiota on the grape surface can be affected by biostimulants and lead to different wine features. The aim of this work was to assess the occurrence of a possible variation in the mycobiota due to the biostimulant application. Therefore, our attention has been focused on the yeast community of grape bunches from vines subjected to the phytostimulant BION®50WG treatment. This work was carried out in the CREA-VE experimental vineyard of Vitis vinifera cv. Barbera in Asti (Piedmont, Italy). The composition of fungal communities on grapes from three experimental conditions such as IPM (integrated pest management), IPM+BION®50WG, and IPM+water foliar nebulization was compared by a metabarcoding approach. Our results revealed the magnitude of alpha and beta diversity, and the microbial biodiversity index and specific fungal signatures were highlighted by comparing the abundance of yeast and filamentous fungi in IPM and BION®50WG treatments. No significant differences in the mycobiota of grapevines subjected to the three treatments were detected.
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Affiliation(s)
- Laura Pulcini
- Consiglio per la Ricerca e l’analisi dell’Economia Agraria—Centro di Ricerca Viticoltura ed Enologia (CREA-VE), Via P. Micca 35, 14100 Asti, Italy; (E.T.V.); (C.T.); (E.G.-M.)
- Dipartimento di Scienze e Innovazione Tecnologica (DISIT), Università del Piemonte Orientale, Viale T. Michel 11, 15121 Alessandria, Italy;
| | - Elisa Bona
- Dipartimento per lo Sviluppo Sostenibile e la Transizione Ecologica (DISSTE), Università del Piemonte Orientale, Piazza San Eusebio 5, 13100 Vercelli, Italy;
| | - Enrico Tommaso Vaudano
- Consiglio per la Ricerca e l’analisi dell’Economia Agraria—Centro di Ricerca Viticoltura ed Enologia (CREA-VE), Via P. Micca 35, 14100 Asti, Italy; (E.T.V.); (C.T.); (E.G.-M.)
| | - Christos Tsolakis
- Consiglio per la Ricerca e l’analisi dell’Economia Agraria—Centro di Ricerca Viticoltura ed Enologia (CREA-VE), Via P. Micca 35, 14100 Asti, Italy; (E.T.V.); (C.T.); (E.G.-M.)
| | - Emilia Garcia-Moruno
- Consiglio per la Ricerca e l’analisi dell’Economia Agraria—Centro di Ricerca Viticoltura ed Enologia (CREA-VE), Via P. Micca 35, 14100 Asti, Italy; (E.T.V.); (C.T.); (E.G.-M.)
| | - Antonella Costantini
- Consiglio per la Ricerca e l’analisi dell’Economia Agraria—Centro di Ricerca Viticoltura ed Enologia (CREA-VE), Via P. Micca 35, 14100 Asti, Italy; (E.T.V.); (C.T.); (E.G.-M.)
| | - Elisa Gamalero
- Dipartimento di Scienze e Innovazione Tecnologica (DISIT), Università del Piemonte Orientale, Viale T. Michel 11, 15121 Alessandria, Italy;
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Englezos V, Mota-Gutierrez J, Giacosa S, Río Segade S, Pollon M, Gambino G, Rolle L, Ferrocino I, Rantsiou K. Effect of alternative fungicides and inoculation strategy on yeast biodiversity and dynamics from the vineyard to the winery. Food Res Int 2022; 162:111935. [DOI: 10.1016/j.foodres.2022.111935] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2022] [Revised: 05/09/2022] [Accepted: 09/12/2022] [Indexed: 11/25/2022]
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Ecological Distribution and Oenological Characterization of Native Saccharomyces cerevisiae in an Organic Winery. FERMENTATION 2022. [DOI: 10.3390/fermentation8050224] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
The relation between regional yeast biota and the organoleptic characteristics of wines has attracted growing attention among winemakers. In this work, the dynamics of a native Saccharomyces cerevisiae population was investigated in an organic winery. In this regard, the occurrence and the persistence of native S. cerevisiae were evaluated in the vineyard and winery and during spontaneous fermentation of two nonconsecutive vintages. From a total of 98 strains, nine different S. cerevisiae biotypes were identified that were distributed through the whole winemaking process, and five of them persisted in both vintages. The results of the oenological characterization of the dominant biotypes (I and II) show a fermentation behavior comparable to that exhibited by three common commercial starter strains, exhibiting specific aromatic profiles. Biotype I was characterized by some fruity aroma compounds, such as isoamyl acetate and ethyl octanoate, while biotype II was differentiated by ethyl hexanoate, nerol, and β-damascenone production also in relation to the fermentation temperature. These results indicate that the specificity of these resident strains should be used as starter cultures to obtain wines with distinctive aromatic profiles.
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Windholtz S, Vinsonneau E, Farris L, Thibon C, Masneuf-Pomarède I. Yeast and Filamentous Fungi Microbial Communities in Organic Red Grape Juice: Effect of Vintage, Maturity Stage, SO 2, and Bioprotection. Front Microbiol 2022; 12:748416. [PMID: 35002998 PMCID: PMC8740202 DOI: 10.3389/fmicb.2021.748416] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2021] [Accepted: 12/01/2021] [Indexed: 01/16/2023] Open
Abstract
Changes are currently being made to winemaking processes to reduce chemical inputs [particularly sulfur dioxide (SO2)] and adapt to consumer demand. In this study, yeast growth and fungal diversity were investigated in merlot during the prefermentary stages of a winemaking process without addition of SO2. Different factors were considered, in a two-year study: vintage, maturity level and bioprotection by the adding yeast as an alternative to SO2. The population of the target species was monitored by quantitative-PCR, and yeast and filamentous fungi diversity was determined by 18S rDNA metabarcoding. A gradual decrease of the α-diversity during the maceration process was highlighted. Maturity level played a significant role in yeast and fungal abundance, which was lower at advanced maturity, while vintage had a strong impact on Hanseniaspora spp. population level and abundance. The presence of SO2 altered the abundance of yeast and filamentous fungi, but not their nature. The absence of sulfiting led to an unexpected reduction in diversity compared to the presence of SO2, which might result from the occupation of the niche by certain dominant species, namely Hanseniaspora spp. Inoculation of the grape juice with non-Saccharomyces yeast resulted in a decrease in the abundance of filamentous fungi generally associated with a decline in grape must quality. Lower abundance and niche occupation by bioprotection agents were observed at the overripened stage, thus suggesting that doses applied should be reconsidered at advanced maturity. Our study confirmed the bioprotective role of Metschnikowia pulcherrima and Torulaspora delbrueckii in a context of vinification without sulfites.
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Affiliation(s)
- Sara Windholtz
- Univ. Bordeaux, INRAE, Bordeaux INP, UR OENOLOGIE, EA 4577, USC 1366, ISVV, Villenave d'Ornon, France
| | | | - Laura Farris
- Univ. Bordeaux, INRAE, Bordeaux INP, UR OENOLOGIE, EA 4577, USC 1366, ISVV, Villenave d'Ornon, France.,Bordeaux Sciences Agro, Gradignan, France
| | - Cécile Thibon
- Univ. Bordeaux, INRAE, Bordeaux INP, UR OENOLOGIE, EA 4577, USC 1366, ISVV, Villenave d'Ornon, France
| | - Isabelle Masneuf-Pomarède
- Univ. Bordeaux, INRAE, Bordeaux INP, UR OENOLOGIE, EA 4577, USC 1366, ISVV, Villenave d'Ornon, France.,Bordeaux Sciences Agro, Gradignan, France
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8
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Martins V, Szakiel A, Pączkowski C, Teixeira A, Gerós H. The restructuring of grape berry waxes by calcium changes the surface microbiota. Food Res Int 2021; 150:110812. [PMID: 34863502 DOI: 10.1016/j.foodres.2021.110812] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2021] [Revised: 10/14/2021] [Accepted: 11/09/2021] [Indexed: 10/19/2022]
Abstract
The observation that exogenous Ca shifted the polyphenolic profile of grape berries and conferred a glossy appearance to mature fruits led us to hypothesize that the composition of grape berry waxes and thus surface microbiota are modified. In two cultivars sharing the same microclimate, the triterpenoid and steroid profile of berry cuticle was characterized by a targeted metabolomic approach, and surface microbial communities were surveyed by ITS and 16S metabarcoding. Results showed that Ca strongly decreased the levels of oleanolic acid, while steroids and neutral triterpenoids were affected in a cultivar-dependent manner. A total of 174 fungi and 192 bacteria OTUs were identified, with Dothideomycetes, Leotiomycetes, Alphaproteobacteria and Gammaproteobacteria comprising the most abundant classes. Ca decreased fungi biodiversity, favoring the growth of Basidiomycetes, and shifting fungi-bacteria relationships. Metabolite-microbiota networks revealed a tight relationship between microbial communities and triterpenoid components of fruit waxes, mainly stigmasterol, tremulone and oleanolic acid.
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Affiliation(s)
- Viviana Martins
- Centre of Molecular and Environmental Biology, Department of Biology, University of Minho, Campus de Gualtar, 4710-057 Braga, Portugal; Centre for the Research and Technology of Agro-Environmental and Biological Sciences, University of Trás-os-Montes and Alto Douro, 5001-801 Vila Real, Portugal.
| | - Anna Szakiel
- Department of Plant Biochemistry, Faculty of Biology, University of Warsaw, ul. Miecznikowa 1, 02-096 Warsaw, Poland.
| | - Cezary Pączkowski
- Department of Plant Biochemistry, Faculty of Biology, University of Warsaw, ul. Miecznikowa 1, 02-096 Warsaw, Poland.
| | - António Teixeira
- Centre of Molecular and Environmental Biology, Department of Biology, University of Minho, Campus de Gualtar, 4710-057 Braga, Portugal; Centre for the Research and Technology of Agro-Environmental and Biological Sciences, University of Trás-os-Montes and Alto Douro, 5001-801 Vila Real, Portugal.
| | - Hernâni Gerós
- Centre of Molecular and Environmental Biology, Department of Biology, University of Minho, Campus de Gualtar, 4710-057 Braga, Portugal; Centre for the Research and Technology of Agro-Environmental and Biological Sciences, University of Trás-os-Montes and Alto Douro, 5001-801 Vila Real, Portugal; Centre of Biological Engineering (CEB), Department of Biological Engineering, University of Minho, Campus de Gualtar, 4710-057 Braga, Portugal.
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Epiphytic Microbial Diversity of Vitis vinifera Fructosphere: Present Status and Potential Applications. Curr Microbiol 2021; 78:1086-1098. [PMID: 33630126 DOI: 10.1007/s00284-021-02385-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2020] [Accepted: 02/07/2021] [Indexed: 10/22/2022]
Abstract
Vineyard provides an apt environment for growth of different types of microorganisms. The microbial domain is greatly affected by changing climatic conditions, geographical region, water activity, agricultural practices, presence of different pathogens and various pests. Grapevine microbial diversity is also affected by different stages of plant growth. Epiphytic berry microflora is specifically influenced by developmental phases and plays an important role in winemaking which is studied extensively. However, very little information is available about microbial community associated with table grape berries, which are consumed as fresh fruits. Moreover, our knowledge about the important role played by these microbes is precise and their scope might be larger than what is existing in the public domain. A systematic study on effect of developmental stages of table grape berries on microbial diversity would provide new insights for exploring the applicability of these microbes in plant growth, crop protection and bioremediation. In this review, we propose an effort to relate the developmental stages of grape berry with microbial consortium present and at the same time discuss the possible applications of these microbes in plant protection and biodegradation.
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Preservation, Characterization and Exploitation of Microbial Biodiversity of Agri-Food and Environmental Interest. Microorganisms 2020; 8:microorganisms8121938. [PMID: 33297349 PMCID: PMC7762223 DOI: 10.3390/microorganisms8121938] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2020] [Accepted: 12/01/2020] [Indexed: 11/23/2022] Open
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