doi: 10.1046/j.1472-765X.2003.01314.x, Beneduce, L., Spano, G., Vernile, A., Tarantino, D., and Massa, S. (2004). Total sequences obtained for eukaryotic (ITS2 and D2) and prokaryotic (V6) microbial community for IM, SF, and EF samples. doi: 10.1300/J301v01n01_08, Keywords: grape microbiology, wine spontaneous fermentation microbiome, industrial metagenomics, Citation: Pinto C, Pinho D, Cardoso R, Custódio V, Fernandes J, Sousa S, Pinheiro M, Egas C and Gomes AC (2015) Wine fermentation microbiome: a landscape from different Portuguese wine appellations. doi: 10.1023/A:1002088931106. U.S.A. 103, 12115–12120. J. Enol. In general, and as expected, a decrease of richness was observed over the spontaneous wine fermentation for both fungi and bacteria, at the analyzed taxonomical levels (domain and phylum; Figure 1). 0000017155 00000 n Further, the fungal communities of IM samples were mainly characterized by the environmental yeasts Aureobasidium and Rhodotorula, which contributed with 64.55% for the group similarity. Appl. Principal coordinate analysis (PCO) biplot diagram of microbial community during fermentation process, based on sequence abundance of eukaryotic genus and bacterial family. In fact, the microbial community tended to be more similar and less diverse at EF. Thermal inactivation of the wine spoilage yeasts Dekkera/Brettanomyces. Regarding SF and EF samples, Enterobacteriaceae was ubiquitous to all appellations. For instance, it is considered that Dekkera/Brettanomyces, the lactic and AAB are the most important wine spoilage microorganisms (Bartowsky et al., 2003; Beneduce et al., 2004; Cocolin et al., 2004). The vineyard yeast microbiome, a mixed model microbial map. 0000011690 00000 n In this work, we tackle this using a metagenomics approach to describe the natural microbial communities, both fungal and bacterial microorganisms, associated with spontaneous wine fermentations. 48, 1034–1038. FEMS Yeast Res. The average of similarity within each group increased over the fermentation process for both fungal (IM: 39.84%; SF: 42.27%; EF: 64.19%) and bacterial community (IM: 42.64%; SF: 48.36%; EF: 46.96%). Figure S2 | Rarefaction curves at a genetic distance of 3% for each sample (IM, SF, and EF). From the IM to the wine, sequential stages of microbial development were observed, as result of fermentation activities (Fleet et al., 1984; Jolly et al., 2003). These findings open new horizons to dissect how microbiomes affect wine properties and support the need to unveil the endogenous microflora of such regions and explore its natural microbial populations in order to produce valuable wines styles. The sequence-specific portions of the used primers were: V6_F 5′-ATGCAACGCGAAGAACCT-3′ and V6_R 5′-TAGCGATTCCGACTTCA-3′ of V6 region; D2_F 5′-AAGMACTTTGRAAAGAGAG-3′ and D2_R 5′-GGTCCGTGTTTCAAGACG-3′ of D2 region; and ITS2_F 5′-GCATCGATGAAGAACGC-3′ and ITS2_R 5′-CCTCCGCTTATTGATATGC-3′ of ITS2 region. doi: 10.1111/j.1755-0238.2005.tb00031.x, Renouf, V., Claisse, O., and Lonvaud-Funel, A. 10, 619–630. Search and clustering orders of magnitude faster than BLAST. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). J. 86, 1555–1562. Lerm, E., Engelbrecht, L., and Du Toit, M. (2011). The members of rare population phyla were placed in an artificial group designed as “Others.”. Interestingly, significant differences (p < 0.05) were observed for both fungal and bacterial microbial communities at IM between wine appellations. 0000010426 00000 n (2007). 0000020374 00000 n In winemaking, there are different processes that fall under the title of "Fermentation" but might not follow the same procedure commonly associated with wine fermentation. Microbial spoilage and preservation of wine: using weapons from nature’s own arsenal - a review. 0000005472 00000 n The wine is also kept in an airlock to prevent oxidation from occurring during this process. The spontaneous wine fermentation is carried out by indigenous microbiota (Heard, 1999; Pretorius, 2000; Ciani et al., 2006; Renouf et al., 2007). The microbial communities were compared at family level for prokaryotic population and at genus level for eukaryotic population through the sequence reads analysis. The concept of terroir in viticulture. Int. Interestingly, samples which presented higher abundance of this microorganism also generally had higher abundance of AAB namely, Gluconobacter (G. oxydans). 153, 243–259. (2007). Figure S1 | Portugal map with the appellations and grape varieties chosen for study. J. Enol. The bacterial populations were found to be less dynamic than the eukaryotic populations in the later stages of fermentation process, and their geographic profiles were more similar: it was observed a clear dominance of Enterobactereaceae family at all appellations but Alentejo, where microorganisms from Halomonadaceae family were also presented with high abundance. Sci. (2010) also confirmed its prevalence at beginning, mid and final stages of MLFs in different Spanish wineries. The bacteria can be introduced to the wine via inoculation during or after alcoholic fermentation, but in many wineries the bacteria is present in the cellar so spontaneous MLF can occur. Citation: Piao H, Hawley E, Kopf S, DeScenzo R, Sealock S, Henick-Kling T and Hess M (2015) Insights into the bacterial community and its temporal succession during the fermentation of wine grapes. Yeast population dynamics in spontaneous fermentations: comparison between two different wine-producing areas over a period of three years. Environ. doi: 10.1016/S0378-1097(00)00257-3, Cocolin, L., Rantsiou, K., Iacumin, L., Zironi, R., and Comi, G. (2004). 0000008727 00000 n Molecular characterization of lactic acid populations associated with wine spoilage. doi: 10.1111/1462-2920.12456. Appl. 0000009323 00000 n (2005). The positive role of MLF is not only the conversion of malic acid to lactic acid, which removes a carbon source of … Relative abundance of the 10 most abundant eukaryotic (A) and prokaryotic (B) microorganisms through the genus and family analysis, respectively. The effect of fungicides on yeast communities associated with grape berries. Nevertheless, Alentejo had the highest abundance of Lachancea and Minho was characterized by having the richest biodiversity, which included Hanseniaspora, Lachancea, Metschnikowia, and Aureobasidium. Appl. Unveiling the microbiome and its dynamics, and understanding the ecological factors that explain such biodiversity, has been a challenge to oenology. In all samples, the dynamics of microbial populations at phylum level were very similar. 17, 1–10. Interestingly, a biogeographical correlation for both fungal and bacterial communities was identified between wine appellations at IM suggesting that each wine region contains specific and embedded microbial communities which may contribute to the uniqueness of regional wines. 0000007990 00000 n 68, 4884–4893. Species of Metschnikowia, Candida, Hanseniaspora, Pichia, Lachancea (Kluyveromyces), and Saccharomyces are often present at the initial stages of wine fermentations and form the dominant consortium (Cocolin et al., 2000; Mills et al., 2002; Fleet, 2008). doi: 10.1007/978-0-387-74520-6_6, Nisiotou, A., Rantsiou, K., Iliopoulos, V., Cocolin, L., and Nychas, G.-J. J. Regarding the bacterial community, the families of Halomonadaceae and Enterobacteriaceae contributed with 91.93% for the Alentejo appellation similarity whereas at Bairrada region, Enterobacteriaceae and Pseudomonadaceae contributed with 75.78%. doi: 10.1080/0957126060063, Vaz-Moreira, I., Egas, C., Nunes, O., and Manaia, C. (2011). The grave varieties collected were Al, Alvarinho; Ax, Alfrocheiro; B, Baga; J, Jean; L, Loureiro; P, Piriquita; T, Trincadeira; TF, Touriga Franca; TN, Touriga Nacional; and TR, Tinta Roriz (also known Aragonez). doi: 10.1111/j.1567-1364.2010.00635.x, Ciani, M., Beco, L., and Comitini, F. (2006). For both fungal (Figure 4C) and bacterial communities (Figure 4D), samples were grouped according to their similarity, where the first axis explain 21.5 and 43.4% of the total variation, respectively. 20 0000002335 00000 n Food Sci. 1, 63–77. Nisiotou et al. 0000008058 00000 n Also, the field study did not involve any endangered or protected species. Environ. Also, Saccharomyces was detected at IMs, which suggests that this community comes from grapes, reinforcing findings from Bokulich et al. Microbiol. xref The Bairrada and Estremadura appellations were also characterized by the presence of microorganisms from the Acetobacteraceae family. Mills, D., Johannsen, E., and Cocolin, L. (2002). (2009). Malolactice fermentation continues at a much slower pace than alcoholic fermentation.
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