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Sequence-based Analysis of the Vitis vinifera L. cv Cabernet Sauvignon Grape Must Mycobiome in Three South African Vineyards Employing Distinct Agronomic Systems.

Setati ME, Jacobson D, Bauer FF - Front Microbiol (2015)

Bottom Line: Data generated in vineyards have furthermore highlighted significant regional differences in vineyard biodiversity, hinting at the possibility that such differences might be responsible for regional differences in wine style and character, a hypothesis referred to as "microbial terroir." The current study further contributes to this body of work by comparing the mycobiome associated with South African (SA) Cabernet Sauvignon grapes in three neighboring vineyards that employ different agronomic approaches, and comparing the outcome with similar data sets from Californian vineyards.The Biodynamic vineyard was found to harbor a more diverse fungal community (H = 2.6) than the conventional (H = 2.1) and integrated (H = 1.8) vineyards.Comparison of metagenomic datasets from the three SA vineyards and previously published data from Californian vineyards revealed only 25% of the fungi in the SA dataset was also present in the Californian dataset, with greater variation evident amongst ubiquitous epiphytic fungi.

View Article: PubMed Central - PubMed

Affiliation: Institute for Wine Biotechnology, Stellenbosch University Stellenbosch, South Africa.

ABSTRACT
Recent microbiomic research of agricultural habitats has highlighted tremendous microbial biodiversity associated with such ecosystems. Data generated in vineyards have furthermore highlighted significant regional differences in vineyard biodiversity, hinting at the possibility that such differences might be responsible for regional differences in wine style and character, a hypothesis referred to as "microbial terroir." The current study further contributes to this body of work by comparing the mycobiome associated with South African (SA) Cabernet Sauvignon grapes in three neighboring vineyards that employ different agronomic approaches, and comparing the outcome with similar data sets from Californian vineyards. The aim of this study was to fully characterize the mycobiomes associated with the grapes from these vineyards. The data revealed approximately 10 times more fungal diversity than what is typically retrieved from culture-based studies. The Biodynamic vineyard was found to harbor a more diverse fungal community (H = 2.6) than the conventional (H = 2.1) and integrated (H = 1.8) vineyards. The data show that ascomycota are the most abundant phylum in the three vineyards, with Aureobasidium pullulans and its close relative Kabatiella microsticta being the most dominant fungi. This is the first report to reveal a high incidence of K. microsticta in the grape/wine ecosystem. Different common wine yeast species, such as Metschnikowia pulcherrima and Starmerella bacillaris dominated the mycobiome in the three vineyards. The data show that the filamentous fungi are the most abundant community in grape must although they are not regarded as relevant during wine fermentation. Comparison of metagenomic datasets from the three SA vineyards and previously published data from Californian vineyards revealed only 25% of the fungi in the SA dataset was also present in the Californian dataset, with greater variation evident amongst ubiquitous epiphytic fungi.

No MeSH data available.


Rarefaction analysis of community richness estimates based on sequences that passed Phred quality score of 30.
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Figure 1: Rarefaction analysis of community richness estimates based on sequences that passed Phred quality score of 30.

Mentions: We previously assessed the grape berry associated diversity in the three vineyards and demonstrated using Automated Ribosomal Intergenic Spacer analysis (ARISA) that the fungal community structure was distinct (Setati et al., 2012). In addition, data derived from culture dependent microbiological analysis suggested that the BD vineyard had a more diverse fungal community than the CONV and integrated (IPW) vineyard (Setati et al., 2012). In the current study, Illumina paired end sequencing was used to explore the fungal biota (mycobiome) of the different vineyard samples. ITS1-5.8S rDNA-ITS2 libraries were generated from genomic DNA extracted from freshly crushed grape must samples prepared from composite samples. Chemical analysis of the musts shows differences in the ripeness level of the grapes (Supplementary Table S1). For the sequence data, quality filtering removed 29% of the reads from the BD and CONV libraries while only 24% was removed from the IPW library (Supplementary Table S2). The Streptophyta (data not included in further analysis) only accounted for less than 1% of the total sequence data in the three libraries. Unassigned sequences accounted for 295, 777, and 153 reads of the total reads in the BD, CONV, and IPW libraries, respectively. Our data revealed good correlation between taxonomic assignments from the forward reads (mainly containing partial ITS1-5.8S sequences) and the data sets containing all reads (i.e., joined ITS1-5.8S-ITS2) and single reads (partial ITS1-5.8S and ITS2-5.8S), while the reverse reads (containing partial ITS2-5.8S sequences) from the BD and IPW showed poor correlation with the forward and joined reads (Supplementary Table S3). Based on this, we chose to use the dataset containing both joined and single reads. Therefore, for yeast species with short ITS-5.8S rRNA regions the taxonomic assignment was based on the full ITS1-5.8S rRNA-ITS2 gene while for other yeasts only the partial gene would have been used. Rarefaction curves showed that the sampling depth and sequencing coverage were good for all three samples, especially for the CONV sample which had clearly reached a plateau (Figure 1). Diversity analysis revealed that the BD library comprised a more diverse mycobiome with low dominance (H′ = 2.6; D = 0.11) followed by the CONV (H′ = 2.1; D = 0.21), while the IPW had the lowest diversity and highest dominance (H′ = 1.77; D = 0.3). ANOVA analysis performed on the presence/absence transformed data showed that the community in the three vineyards was significantly different (p = 0.025).


Sequence-based Analysis of the Vitis vinifera L. cv Cabernet Sauvignon Grape Must Mycobiome in Three South African Vineyards Employing Distinct Agronomic Systems.

Setati ME, Jacobson D, Bauer FF - Front Microbiol (2015)

Rarefaction analysis of community richness estimates based on sequences that passed Phred quality score of 30.
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4663253&req=5

Figure 1: Rarefaction analysis of community richness estimates based on sequences that passed Phred quality score of 30.
Mentions: We previously assessed the grape berry associated diversity in the three vineyards and demonstrated using Automated Ribosomal Intergenic Spacer analysis (ARISA) that the fungal community structure was distinct (Setati et al., 2012). In addition, data derived from culture dependent microbiological analysis suggested that the BD vineyard had a more diverse fungal community than the CONV and integrated (IPW) vineyard (Setati et al., 2012). In the current study, Illumina paired end sequencing was used to explore the fungal biota (mycobiome) of the different vineyard samples. ITS1-5.8S rDNA-ITS2 libraries were generated from genomic DNA extracted from freshly crushed grape must samples prepared from composite samples. Chemical analysis of the musts shows differences in the ripeness level of the grapes (Supplementary Table S1). For the sequence data, quality filtering removed 29% of the reads from the BD and CONV libraries while only 24% was removed from the IPW library (Supplementary Table S2). The Streptophyta (data not included in further analysis) only accounted for less than 1% of the total sequence data in the three libraries. Unassigned sequences accounted for 295, 777, and 153 reads of the total reads in the BD, CONV, and IPW libraries, respectively. Our data revealed good correlation between taxonomic assignments from the forward reads (mainly containing partial ITS1-5.8S sequences) and the data sets containing all reads (i.e., joined ITS1-5.8S-ITS2) and single reads (partial ITS1-5.8S and ITS2-5.8S), while the reverse reads (containing partial ITS2-5.8S sequences) from the BD and IPW showed poor correlation with the forward and joined reads (Supplementary Table S3). Based on this, we chose to use the dataset containing both joined and single reads. Therefore, for yeast species with short ITS-5.8S rRNA regions the taxonomic assignment was based on the full ITS1-5.8S rRNA-ITS2 gene while for other yeasts only the partial gene would have been used. Rarefaction curves showed that the sampling depth and sequencing coverage were good for all three samples, especially for the CONV sample which had clearly reached a plateau (Figure 1). Diversity analysis revealed that the BD library comprised a more diverse mycobiome with low dominance (H′ = 2.6; D = 0.11) followed by the CONV (H′ = 2.1; D = 0.21), while the IPW had the lowest diversity and highest dominance (H′ = 1.77; D = 0.3). ANOVA analysis performed on the presence/absence transformed data showed that the community in the three vineyards was significantly different (p = 0.025).

Bottom Line: Data generated in vineyards have furthermore highlighted significant regional differences in vineyard biodiversity, hinting at the possibility that such differences might be responsible for regional differences in wine style and character, a hypothesis referred to as "microbial terroir." The current study further contributes to this body of work by comparing the mycobiome associated with South African (SA) Cabernet Sauvignon grapes in three neighboring vineyards that employ different agronomic approaches, and comparing the outcome with similar data sets from Californian vineyards.The Biodynamic vineyard was found to harbor a more diverse fungal community (H = 2.6) than the conventional (H = 2.1) and integrated (H = 1.8) vineyards.Comparison of metagenomic datasets from the three SA vineyards and previously published data from Californian vineyards revealed only 25% of the fungi in the SA dataset was also present in the Californian dataset, with greater variation evident amongst ubiquitous epiphytic fungi.

View Article: PubMed Central - PubMed

Affiliation: Institute for Wine Biotechnology, Stellenbosch University Stellenbosch, South Africa.

ABSTRACT
Recent microbiomic research of agricultural habitats has highlighted tremendous microbial biodiversity associated with such ecosystems. Data generated in vineyards have furthermore highlighted significant regional differences in vineyard biodiversity, hinting at the possibility that such differences might be responsible for regional differences in wine style and character, a hypothesis referred to as "microbial terroir." The current study further contributes to this body of work by comparing the mycobiome associated with South African (SA) Cabernet Sauvignon grapes in three neighboring vineyards that employ different agronomic approaches, and comparing the outcome with similar data sets from Californian vineyards. The aim of this study was to fully characterize the mycobiomes associated with the grapes from these vineyards. The data revealed approximately 10 times more fungal diversity than what is typically retrieved from culture-based studies. The Biodynamic vineyard was found to harbor a more diverse fungal community (H = 2.6) than the conventional (H = 2.1) and integrated (H = 1.8) vineyards. The data show that ascomycota are the most abundant phylum in the three vineyards, with Aureobasidium pullulans and its close relative Kabatiella microsticta being the most dominant fungi. This is the first report to reveal a high incidence of K. microsticta in the grape/wine ecosystem. Different common wine yeast species, such as Metschnikowia pulcherrima and Starmerella bacillaris dominated the mycobiome in the three vineyards. The data show that the filamentous fungi are the most abundant community in grape must although they are not regarded as relevant during wine fermentation. Comparison of metagenomic datasets from the three SA vineyards and previously published data from Californian vineyards revealed only 25% of the fungi in the SA dataset was also present in the Californian dataset, with greater variation evident amongst ubiquitous epiphytic fungi.

No MeSH data available.