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Shaoxing rice wine (Huangjiu) is characterized by its unique quality and flavor, however, the impact of different brewing water on the microbial community during fermentation and aromatic characteristics of Huangjiu product is less elucidated. In this study, water from Jianhu Lake and Jingling Reservoir in Shaoxing were used for brewing Huangjiu, and the purified water was used as the control. The fermentation mash at different fermentation stages was collected and sequenced to investigate the alterations of bacterial and fungal communities. Besides, the final fermented Huangjiu was analyzed for its volatile compound profiles using Gas Chromatography–Mass Spectrometry (HS-SPME/GC-MS). Water from Jingling Reservoir had higher levels of total nitrogen, chemical oxygen demand, iron and manganese ions, but lower levels of hardness and total viable counts than that from Jianhu Lake. The bacterial and fungal communities during Huangjiu fermentation were significantly different using different brewing water, as assessed by principal coordinates analysis. Besides, bacterial genera, including Enterobacter, Staphylococcus, Pantoea, Leuconostoc, Acinetobacter, Exiguobacterium, Janthinobacterium, and Limnohabitans, were significantly different. The co-occurrence network analysis identified the core genera in bacterial community, including Lactococcus, Leuconostoc, Exiguobacterium, and Pediococcus. HS-SPME/GC-MS results demonstrated 19 volatile compounds were significantly different using different brewing water. The correlation analysis further revealed the key microbial genera which are tightly associated with the alteration in aromatic characteristics using different brewing water, including 16 bacterial and 2 fungal genera. Collectively, our results demonstrated the alterations of microbial communities and aromatic profile of Huangjiu using different brewing water, and provided experimental basis for understanding the significance of brewing water in Huangjiu’s flavor.