Metagenomic and Metatranscriptomic Analysis of Microbial Population Dynamics on Grapes and in Musts Derived from Conventional, Organic and Biodynamic Vineyards


Project Number
IWBT MG 11-01

Project title
Metagenomic and metatranscriptomic analysis of microbial population dynamics on grapes and in musts derived from conventional, organic and biodynamic vineyards

Project leader
Setati, M E

Institution
University of Stellenbosch. Faculty of AgriSciences. Institute for Wine Biotechnology

Team members
Du Toit, M
Bauer, F F
Setati, M E
Divol, B
Jolly, N P
Volschenk, H

Project description
Organic and biodynamic agriculture are horticultural production management systems that promote and enhance biodiversity, biological cycles and soil biological activity. The primary difference between the two systems is that biodynamics uses a series of soil and plant amendments, called preparations to stimulate the soil and enhance plant health and quality of produce. Both systems have been applied in agriculture since the 1920’s albeit on a small scale. However, consumer concern about food quality, the impact of chemical fertilizers, pesticides and fungicides on the environment has encouraged the increase of organic and biodynamic farming practices worldwide. Organic and biodynamic viticulture has also been on the increase over the past ten years especially in France and the United States. In South Africa, the increase in locally produced organic and biodynamic wine is becoming more evident on supermarket shelves. Although organic and biodynamic systems are globally becoming of increased economic interest to wine producers, such practices prescribe specific management methodologies, and their impact on general vineyard health and wine quality has been the subject of some studies and debates in the industry. However, the impact of these practices on the vineyard ecosystem including microbial diversity is poorly understood, owing to the inability of classical techniques to retrieve more than 1% of species present in the environment. Metagenomics, can overcome these shortcomings and by providing detailed overview of microbial diversity in an ecosystem and have been successfully applied in a wide variety of systems including soil, marine environments, compost and the human gut. We propose to apply this relatively new technology to assess microbial diversity and evolution in vineyards, grape juice and fermenting must from vineyards managed through conventional, organic and biodynamic systems.

The objectives of this study are:
1. To evaluate the impact of conventional, organic and biodynamic farming practices on grape berry surface microbial diversity.
2. To determine the functional potential of spontaneously fermenting grape must derived from bio dynamically produced grapes.

Poster(s)
Gosh, S, Divol and Setati, M E. 2013. Using metagenomics to explore the functional potential of the wine microbiome. Poster presented at the 19th South African Society for Microbiology Congress. 24-27 November, Warmbaths, South Africa.

Presentation(s)
Andong, U, Babheri, B, Ghosh, S, Diviol, B and Bauer, F F. 2011. Structural diversity of yeast associated with grapes in biodynamical and conventionally managed vineyards. Paper presented at the 18th South African Society for Microbiology Congress. 24-27 November, Warmbaths, South Africa.

Setati, M E, Bagheri, B, Ghosh, S, Divol, B and Bauer, F F. 2013. Taxonomic and functional diversity of the grape must ecosystem. Paper presented at the 2nd International Conference on Functional Metagenomics. 2-5 June, Pretoria, South Africa.

Setati, M E, Bagheri, B and Bauer, F F. 2013. The wine microbial consortium and its evolution during spontaneous fermentation. Paper presented at the 19th South African Society for Microbiology Congress. 24-27 November, Warmbaths, South Africa.

Setati, M E. 2013. Viticulture and microbial biodiversity: The vineyard as a complex and patchy ecosystem. Paper presented at the 35th South African Society for Enology and Viticulture Conference. 13-15 November, Somerset West, South Africa.

Article
Setati, M E, Jacobson, D, Andong, U, Bauer, F F. 2012. The vineyard yeast microbiome, a mixed model microbial map, PLoS ONE, Mnth Dec v. 7 (12) (p. 8-9)
http://dx.doi.org/10.1371/journal.pone.0052609

Bagheri, B, Bauer, F F, Setati, M E. 2015. The diversity and dynamics of indigenous yeast communities in grape must from vineyards employing different agronomic practices and their influence on wine fermentation, South African Journal of Enology and Viticulture, v. 36 (2) (p. 243-251)
Article.pdf

Ghosh, S, Bagheri, B, Morgan, H H, Divol, B, Setati, M E. 2015. Assessment of wine microbial diversity using ARISA and cultivation-based methods, Annals of Microbiology, Mnth Dec v. 65 (4) (p. 1833-1840)
http://doi.org/10.1007/s13213-014-1021-x

Setati, M E, Jacobson, D, Bauer, F F. 2015. Sequence-based analysis of the Vitis vinifera L. cv Cabernet Sauvignon grape must mycobiome in three neighbouring South African vineyards, Frontiers in Microbiology, Mnth Nov v. 6 (p. 1358)
http://doi.org/10.3389/fmicb.2015.01358

FinalReport.pdf

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