RNA-seq-based transcriptomic comparison of Saccharomyces cerevisiae during spontaneous and inoculated fermentations of organic and conventional grapes

Abstract

Viticulture practices influence yeast genetics and phenotypes during wine fermentation by affecting grape quality and yeast microflora attached to grape berries, but the influence is limited understood yet. The aim of this study was to evaluate the impact of organic viticulture on wine quality and yeast transcriptome-wide response, and their associated mechanisms. This work compared the yeast transcriptional response during the spontaneous and inoculated fermentation of grapes from organic and conventional agriculture systems, through genome-wide analysis of gene expression, by Illumina Hiseq sequencing platforms. Transcriptome profiling showed that 991 and 96 differentially expressed genes (DEGs) were detected in spontaneous and inoculated fermentations, respectively, indicating that organic viticulture was more likely to affect yeast transcriptome by influencing yeast microflora rather than grape/juice quality. Several pathways of Saccharomyces cerevisiae had more up-regulated DEGs than down-regulated ones in organic samples and in spontaneous fermentation group, including central carbon metabolism, translation, transport and catabolism, and energy metabolism. Besides, viticulture practices and fermentation modes had specific effects on wine quality. This study could enhance the understanding of yeast transcription changes during the fermentation of different grapes and with different strains, as well as elucidate the effect of viticulture practice on yeast transcriptome and wine quality.