Heterogeneous selection driven by pH determines the successional pattern of bacterial communities in pit mud used for...

Pit mud serves as a habitat for functional bacteria involved in Baijiu fermentation. While pH is recognized as a key driver of bacterial succession in pit mud, the underlying pattern remains insufficiently characterized. This study systematically investigated the relationship between pH and bacterial communities in pit mud by integrating dataset analysis with pH gradient experiments. The results revealed strong correlations between pH and the key bacterial families, which occurred not only across the time dimension but also in relation to spatial heterogeneity or artificial disturbance. Along the pH gradient, heterogeneous selection may govern bacterial succession. As pH increased, the appearance of Oscillospiraceae signaled the onset of bacterial succession, while the near disappearance of Lactobacillaceae indicated enhanced stability. Six representative genera were further studied, revealing distinct genomic features that changed consistently with pH. During bacterial succession, the abundance of Lactobacillus declined, which predominantly carries genes associated with lactate and acetate metabolism. In contrast, the abundance of Caproicibacterium, which possesses a complete gene cluster for reverse β-oxidation, increased. The pH gradient experiments confirmed that pH influences bacterial assembly mainly through heterogeneous selection, which appeared to be facilitated both by the lactate-utilizing ability of Caproicibacterium and the pH-mediated suppression of Lactobacillus. These findings advance the theoretical understanding of pit mud aging and contribute to the optimization of Baijiu fermentation.