Soybean paste, soy sauce, preserved bean curd and lobster sauce are the four traditional fermentation foods in China. Microorganisms, especially bacterial varieties play an active role during the process of soybean paste fermentation.
The bacteria are closely related to the flavor and quality of the soybean paste. In the fermentation of traditional soybean paste, monitoring different stages of the fermentation process and the dynamics of bacteria diversity, as well as controlling the bacteria succession will provide a theoretical basis for strain selection and improvement of the process for industrial production. At present, denaturing gradient gel electrophoresis (DGGE) is widely accepted as a molecular biology tool for studying complex microbial community and behavior. In this study, we used the natural fermented soybean paste as material, extracted bacteria genomic DNA, amplified the V3 region of 16SrRNA genes by PCR, and analyzed the dynamics of bacteria community structure and the dominant population during the fermentation of soybean paste using DGGE. Our results showed that the V3 region of 16SrDNA of the complex microbial community in the fermentation of traditional soybean paste were around 230 bp, containing 19 different gel bands. Sequencing of the DGGE bands revealed the 19 microorganisms, which are Aeromonas, Weissella viridescens, Staphylococcus xylosus, Lactobacillus brevis, Aeromonas media, Staphylococcus saprophyticus, Leuconostoc lactis, Listeria grayi, Bacillus subtilis, Staphylococcus succinu, Bacillus firmus, Tetragenococcus halophilus and six unculturable bacteria. This result clearly reflects the diversity of the bacteria in the fermentation process. Through monitoring the abundance value and degree of dominance during the fermentation process, we found the growth of some initial populations and depression of other initial populations, in addition to the growth and evolution of some subpopulations. The application of PCR-DGGE method in the detection of bacteria diversity has led to valuable information. In addition, the succession of bacteria population displayed the following pattern in the fermentation process based on the Shannon-Weiner index, i.e., the variation of the bacteria population showed "low-high-low" pattern, while the dominant bacteria population showed a succession pattern from D8 (Uncultured Staphylococcus sp.,Accession Number FJ542940.1) to D18 (Uncultured bacterium,Accession Number EU873643.1) and then to D6 (Staphylococcus saprophyticus,Accession Number EU855228.1). At the initial and final stages of the fermentation process, unculturable bacteria population were dominant population, the succession speed was rapid at the initial stage of fermentation. The diversity index of the bacteria population reached peak values at 42 d and 56 d in the fermentation, which were 3.77 and 3.65, respectively. These results have provided important knowledge towards understanding the dynamic changes of bacteria populations in the soybean paste fermentation.