Insights into the bacterial community and its temporal succession during the fermentation of wine grapes

Abstract

Grapes harbor complex microbial communities. It is well known that yeasts, typically Saccharomyces cerevisiae, and bacteria, commonly the lactic acid fermenting Oenococcus oeni, work sequentially during primary and secondary wine fermentation. In addition to these main players, several microbes, often with undesirable effects on wine quality, have been found in grapes and during wine fermentation. However, still little is known about the dynamics of the microbial community during the fermentation process. In previous studies culture dependent methods were applied to detect and identify microbial organisms associated with grapes and grape products, which resulted in a picture that neglected the non-culturable fraction of the microbes. To obtain a more complete picture of how microbial communities change during grape fermentation and how different fermentation techniques might affect the microbial community composition, we employed next-generation sequencing (NGS)-a culture-independent method. A better understanding of the microbial dynamics and their effect on the final product is of great importance to help winemakers produce wine styles of consistent and high quality. In this study, we focused on the bacterial community dynamics during wine vinification by amplifying and sequencing the hypervariable V1-V3 region of the 16S rRNA gene-a phylogenetic marker gene that is ubiquitous within prokaryotes. Bacterial communities and their temporal succession was observed for communities associated with organically and conventionally produced wines. In addition, we analyzed the chemical characteristics of the grape musts during the organic and conventional fermentation process. These analyses revealed distinct bacterial population with specific temporal changes as well as different chemical profiles for the organically and conventionally produced wines. In summary these results suggest a possible correlation between the temporal succession of the bacterial population and the chemical wine profiles.

Keywords: 16S rRNA gene profile; next-generation sequencing; organic grape products; temporal succession; wine bacteria; wine fermentation.

Figure 1

Principal component analysis of 16S rRNA data from microbiomes associated with grape must during the fermentation process. 16S rRNA amplicon data was generated from PDC (O_0d and C_0d) and during organic (O_2d, O_3d, O_10d, and O_16d) and conventional (C_2d, C_6d, C_7d, and C_12d) bulk fermentation. The percentage of variation explained by the plotted principal coordinates is indicated on the axes.

Figure 2

Phylogenetic profile of microbiomes associated with grape must during the fermentation process. Phylogeny was assigned in the phylum level based on the RDP database after quality-filtered reads were clustered using 97% sequence identity cut-off.

Figure 3

Physicochemical characteristics of the organically and conventionally fermented grape musts. (A) Fermentation rate (Brix), (B) fermentation temperature, (C) grape musts pH, and (D) production of ethanol were measured on each day of fermentation.