Distinct co-occurrence patterns and driving forces of abundant and rare bacterial communities in the multispecies solid-state fermentation process of cereal vinegar

Multispecies solid-state fermentation is a traditional processing technique for the traditional Chinese food, such as cereal vinegar, Baijiu, etc. Generally, few abundant and many rare microbes were involved in such processes, and the necessity and roles of the latter are less studied. Here the co-occurrence patterns of abundant and rare bacterial community and abiotic factors influencing their community assembly were investigated in acetic acid fermentation following starter inoculation, using Zhenjiang aromatic vinegar as a model system. Abundant taxa that contribute to the function of accumulating acid exhibited a ubiquitous distribution while the distribution of rare taxa along the fermentation process unraveled. The species composition of the rare taxa significantly altered, but abundant taxa were maintained after inoculation. Moreover, the diversity of rare taxa changed more significantly than that of abundant taxa. Both abundant and rare sub-communities, which were contributed more with species turnover than species richness, were demonstrated to be driven by pH, acetic acid, ammonium nitrogen, and ethanol. Stochastic processes regulated the assembly of both sub-communities, but more prominent on rare sub-communities. Co-occurrence network was more governed by rare sub-communities, and the co-variations between microbial communities were predominantly positive, implying that rare taxa played more important role in the fermentation stability and network robustness. Furthermore, seven network connectors were identified, and three of them belonged to rare taxa. These microbes of different modules were enriched at particular phases of fermentation. These results demonstrate the ecological significance of rare bacteria and provide new insights into understanding the abiotic factors influence microbial structure in traditional fermented foods.