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Wine fermentation microbiome: a landscape from different Portuguese wine appellations.

Pinto C, Pinho D, Cardoso R, Custódio V, Fernandes J, Sousa S, Pinheiro M, Egas C, Gomes AC - Front Microbiol (2015)

Bottom Line: The wine fermentation process revealed a higher impact on fungal populations when compared with bacterial communities, and the fermentation evolution clearly caused a loss of the environmental microorganisms.Furthermore, significant differences (p < 0.05) were found in the fungal populations between IM, SF, and EF, and in the bacterial population between IM and SF.Among bacterial communities, the most abundant family was Enterobacteriaceae; though families of species associated with the production of lactic acid (Lactobacillaceae, Leuconostocaceae) and acetic acid (Acetobacteriaceae) were also detected.

View Article: PubMed Central - PubMed

Affiliation: Genomics Unit, Biocant - Biotechnology Innovation Center, Cantanhede Portugal.

ABSTRACT
Grapes and wine musts harbor a complex microbiome, which plays a crucial role in wine fermentation as it impacts on wine flavour and, consequently, on its final quality and value. Unveiling the microbiome and its dynamics, and understanding the ecological factors that explain such biodiversity, has been a challenge to oenology. 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. For this, the wine microbiome, from six Portuguese wine appellations, was fully characterized as regards to three stages of fermentation - Initial Musts (IM), and Start and End of alcoholic fermentations (SF and EF, respectively). The wine fermentation process revealed a higher impact on fungal populations when compared with bacterial communities, and the fermentation evolution clearly caused a loss of the environmental microorganisms. Furthermore, significant differences (p < 0.05) were found in the fungal populations between IM, SF, and EF, and in the bacterial population between IM and SF. Fungal communities were characterized by either the presence of environmental microorganisms and phytopathogens in the IM, or yeasts associated with alcoholic fermentations in wine must samples as Saccharomyces and non-Saccharomyces yeasts (as Lachancea, Metschnikowia, Hanseniaspora, Hyphopichia, Sporothrix, Candida, and Schizosaccharomyces). Among bacterial communities, the most abundant family was Enterobacteriaceae; though families of species associated with the production of lactic acid (Lactobacillaceae, Leuconostocaceae) and acetic acid (Acetobacteriaceae) were also detected. 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.

No MeSH data available.


Related in: MedlinePlus

Biodiversity dynamics associated with V6, ITS2, and D2 region, at domain (A) and phylum level (B). The mean of Chao1 index ± SEM are represented in the graph. Significance was assessed with Friedman test and signal test. p < 0.05 was set as statistic significant level.
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Figure 1: Biodiversity dynamics associated with V6, ITS2, and D2 region, at domain (A) and phylum level (B). The mean of Chao1 index ± SEM are represented in the graph. Significance was assessed with Friedman test and signal test. p < 0.05 was set as statistic significant level.

Mentions: In order to assess the variations of microbial biodiversity, the Chao1 richness estimator was used to compare the three fermentation stages at both domain and phylum levels. 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). Considering the domain (Figure 1A), no significant differences were found for the three rDNA regions. At the phylum level, significant differences (p < 0.05) in the Basidiomycota between all stages of fermentation were observed (both for ITS2 and D2 regions), and in the Ascomycota population differences were between SF and EF, but not between IM and SF (Figure 1B). For the bacterial population, a decrease in biodiversity was observed but no significant differences were detected (V6 rDNA region). A clear relationship was observed between the microbial community biodiversity and the stage of fermentation. Interestingly, the variations of biodiversity, which were observed along the fermentation stages, revealed a higher impact on the structure of the eukaryotic population, when compared with the prokaryotic communities. Moreover, regarding the microbial biodiversity, the prokaryotic population was richer than the eukaryotic population.


Wine fermentation microbiome: a landscape from different Portuguese wine appellations.

Pinto C, Pinho D, Cardoso R, Custódio V, Fernandes J, Sousa S, Pinheiro M, Egas C, Gomes AC - Front Microbiol (2015)

Biodiversity dynamics associated with V6, ITS2, and D2 region, at domain (A) and phylum level (B). The mean of Chao1 index ± SEM are represented in the graph. Significance was assessed with Friedman test and signal test. p < 0.05 was set as statistic significant level.
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4555975&req=5

Figure 1: Biodiversity dynamics associated with V6, ITS2, and D2 region, at domain (A) and phylum level (B). The mean of Chao1 index ± SEM are represented in the graph. Significance was assessed with Friedman test and signal test. p < 0.05 was set as statistic significant level.
Mentions: In order to assess the variations of microbial biodiversity, the Chao1 richness estimator was used to compare the three fermentation stages at both domain and phylum levels. 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). Considering the domain (Figure 1A), no significant differences were found for the three rDNA regions. At the phylum level, significant differences (p < 0.05) in the Basidiomycota between all stages of fermentation were observed (both for ITS2 and D2 regions), and in the Ascomycota population differences were between SF and EF, but not between IM and SF (Figure 1B). For the bacterial population, a decrease in biodiversity was observed but no significant differences were detected (V6 rDNA region). A clear relationship was observed between the microbial community biodiversity and the stage of fermentation. Interestingly, the variations of biodiversity, which were observed along the fermentation stages, revealed a higher impact on the structure of the eukaryotic population, when compared with the prokaryotic communities. Moreover, regarding the microbial biodiversity, the prokaryotic population was richer than the eukaryotic population.

Bottom Line: The wine fermentation process revealed a higher impact on fungal populations when compared with bacterial communities, and the fermentation evolution clearly caused a loss of the environmental microorganisms.Furthermore, significant differences (p < 0.05) were found in the fungal populations between IM, SF, and EF, and in the bacterial population between IM and SF.Among bacterial communities, the most abundant family was Enterobacteriaceae; though families of species associated with the production of lactic acid (Lactobacillaceae, Leuconostocaceae) and acetic acid (Acetobacteriaceae) were also detected.

View Article: PubMed Central - PubMed

Affiliation: Genomics Unit, Biocant - Biotechnology Innovation Center, Cantanhede Portugal.

ABSTRACT
Grapes and wine musts harbor a complex microbiome, which plays a crucial role in wine fermentation as it impacts on wine flavour and, consequently, on its final quality and value. Unveiling the microbiome and its dynamics, and understanding the ecological factors that explain such biodiversity, has been a challenge to oenology. 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. For this, the wine microbiome, from six Portuguese wine appellations, was fully characterized as regards to three stages of fermentation - Initial Musts (IM), and Start and End of alcoholic fermentations (SF and EF, respectively). The wine fermentation process revealed a higher impact on fungal populations when compared with bacterial communities, and the fermentation evolution clearly caused a loss of the environmental microorganisms. Furthermore, significant differences (p < 0.05) were found in the fungal populations between IM, SF, and EF, and in the bacterial population between IM and SF. Fungal communities were characterized by either the presence of environmental microorganisms and phytopathogens in the IM, or yeasts associated with alcoholic fermentations in wine must samples as Saccharomyces and non-Saccharomyces yeasts (as Lachancea, Metschnikowia, Hanseniaspora, Hyphopichia, Sporothrix, Candida, and Schizosaccharomyces). Among bacterial communities, the most abundant family was Enterobacteriaceae; though families of species associated with the production of lactic acid (Lactobacillaceae, Leuconostocaceae) and acetic acid (Acetobacteriaceae) were also detected. 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.

No MeSH data available.


Related in: MedlinePlus