Stochastic Processes Drive the Assembly and Metabolite Profiles of Keystone Taxa during Chinese Strong-Flavor Baijiu Fermentation.

Multispecies communities participate in the fermentation of Chinese strong-flavor Baijiu (CSFB), and the metabolic activity of the dominant and keystone taxa is key to the flavor quality of the final product. However, their roles in metabolic function and assembly processes are still not fully understood. Here, we identified the variations in the metabolic profiles of dominant and keystone taxa and characterized their community assembly using 16S rRNA and internal transcribed spacer (ITS) gene amplicon and metatranscriptome sequencing. We demonstrate that CSFB fermentations with distinct metabolic profiles display distinct microbial community compositions and microbial network complexities and stabilities. We then identified the dominant taxa (Limosilactobacillus fermentum, Kazachstania africana, Saccharomyces cerevisiae, and Pichia kudriavzevii) and the keystone ecological cluster (module 0, affiliated mainly with Thermoascus aurantiacus, Weissella confusa, and Aspergillus amstelodami) that cause changes in metabolic profiles. Moreover, we highlight that the alpha diversity of keystone taxa contributes to changes in metabolic profiles, whereas dominant taxa exert their influence on metabolic profiles by virtue of their relative abundance. Additionally, our results based on the normalized stochasticity ratio (NST) index and the neutral model revealed that stochastic and deterministic processes together shaped CSFB microbial community assemblies. Stochasticity and environmental selection structure the keystone and dominant taxa differently. This study provides new insights into understanding the relationships between microbial communities and their metabolic functions. IMPORTANCE From an ecological perspective, keystone taxa in microbial networks with high connectivity have crucial roles in community assembly and function. We used CSFB fermentation as a model system to study the ecological functions of dominant and keystone taxa at the metabolic level. We show that both dominant taxa (e.g., those taxa that have the highest relative abundances) and keystone taxa (e.g., those taxa with the most cooccurrences) affected the resulting flavor profiles. Moreover, our findings established that stochastic processes were dominant in shaping the communities of keystone taxa during CSFB fermentation. This result is striking as it suggests that although the controlled conditions in the fermentor can determine the dominant taxa, the uncontrolled rare keystone taxa in the microbial community can alter the resulting flavor profiles. This important insight is vital for the development of potential manipulation strategies to improve the quality of CSFB through the regulation of keystone species.

Integrated transcriptomic and proteomic analysis of the ethanol stress response in Saccharomyces cerevisiae Sc131.

The molecular mechanism of Saccharomyces cerevisiae tolerant to ethanol stress remains to be further elucidated. In this study, a comprehensive analysis based on RNA-seq and iTRAQ LC-MS/MS was used to investigate the global mechanism of S. cerevisiae strain Sc131 in response to ethanol stress at transcriptomic and proteomic levels. Totally, 937 differentially expressed genes (DEGs) and 457 differentially expressed proteins (DEPs) were identified in Sc131 under ethanol stress. Results revealed that 4-h ethanol stress (10% v/v) can induce filamentous growth, sexual reproduction. Mitochondria and endoplasmic reticulum (ER) were proved to be two important organelles in resisting ethanol stress. Signal transduction such as G-protein coupled receptor signaling and metal ion regulation were remarkably activated at the presence of ethanol. Moreover, silent information regulator (Sir) proteins and aromatic amino acids especially tryptophan were involved in response to ethanol and might be helpful for cell survival. This study provides a global perspective on the mechanism of S. cerevisiae tolerant to ethanol stress and sheds light on the potential application of Sc131 in Chinese bayberry wine brewing. BIOLOGICAL SIGNIFICANCE: It is of great importance for S. cerevisiae to tolerate high levels of ethanol during wine fermentation. However, the molecular mechanism of S. cerevisiae tolerant to ethanol stress remains to be further elucidated at transcriptomic and proteomic levels. In present study, we employed a comprehensive analysis based on RNA-seq and iTRAQ and found several potential pathways involving in the response of Sc131 to ethanol stress. To our knowledge, this is the first integrated analysis combining transcriptomic and proteomic technologies to study the mechanism of Sc131 under ethanol stress.

Investigating the underlying mechanism of Saccharomyces cerevisiae in response to ethanol stress employing RNA-seq analysis.

Saccharomyces cerevisiae has been widely used for wine fermentation and bio-fuels production. A S. cerevisiae strain Sc131 isolated from tropical fruit shows good fermentation properties and ethanol tolerance, exhibiting significant potential in Chinese bayberry wine fermentation. In this study, RNA-sequence and RT-qPCR was used to investigate the transcriptome profile of Sc131 in response to ethanol stress. Scanning Electron Microscopy were carried out to observe surface morphology of yeast cells. Totally, 937 genes were identified differential expressed, including 587 up-regulated and 350 down-regulated genes, after 4-h ethanol stress (10% v/v). Transcriptomic analysis revealed that, most genes involved in regulating filamentous growth or pseudohyphal growth were significantly up-regulated in response to ethanol stress. The complex protein quality control machineries, Hsp90/Hsp70 and Hsp104/Hsp70/Hsp40 based chaperone system combining with ubiquitin-proteasome proteolytic pathway were both activated to recognize and degrade misfolding proteins. Genes related to biosynthesis and metabolism of two well-known stress-responsive substances trehalose and ergosterol were generally up-regulated, while genes associated with amino acids biosynthesis and metabolism processes were differentially expressed. Moreover, thiamine was also important in response to ethanol stress. This research may promote the potential applications of Sc131 in the fermentation of Chinese bayberry wine.