Distinct phylogenetic patterns and assembly processes of abundant and rare taxa in traditional grain vinegar fermentation ecosystem.

Brewing microbes play a crucial role in regulating the fermentation process and quality characteristics of Chinese traditional fermented foods, particularly grain vinegar. However, in the context of acetic acid fermentation, the phylogenetic characteristics, community assembly mechanisms, and environmental drivers of bacterial communities under complex environmental gradients remain insufficiently explored, particularly the differences between abundant and rare taxa. In this study, the acetic acid fermentation of Zhenjiang aromatic vinegar was employed as a model to systematically analyze the phylogenetic niche distribution, community assembly processes, and key environmental drivers associated with abundant and rare bacterial taxa. We found that abundant taxa exhibited broader ecological niches and lower phylogenetic clustering than rare taxa, while rare taxa displayed stronger phylogenetic signals and broader environmental response thresholds. Homogeneous selection of deterministic processes dominated the assembly of abundant taxa. In contrast, stochastic processes were the primary drivers of rare taxa assembly, as further supported by neutral theory models. pH and ethanol were identified as the key environmental factors influencing the community assembly of abundant and rare bacterial taxa, respectively. These findings provide new insights into the phylogenetic responses and community assembly mechanisms of brewing microbes adapting to environmental changes in complex fermentation ecosystems.