Evaluation and choice of PCR-DGGE primers in analyzing the microbial community structure of activated sludge in traditional Chinese medicine wastewater

In the study of traditional Chinese medicine wastewater, it was discussed for the effect of different sets of 16S rDNA universal primers on DGGE fingerprinting and microbial community diversity of aerobic and anaerobic activated sludge from one traditional Chinese medicine wastewater treatment. The genome DNA of activated sludge was isolated, and eleven sets of primers were used to amplify the four variable regions of 16S rDNA, the resolution of DGGE fingerprinting and community diversity was analyzed. The results indicated that community diversity with different sets of universal primers by DGGE was obviously different. Separated patterns of the V3 and V6-V8 regions were better than of V1-V3 and V3-V5. In the DGGE profiles, bands and diversity from V3 were most, bands and diversity from V3-V5 and V6-V8 were a little worse than those of V3. According to the length of targeted sequence and the resolution of DGGE fingerprinting, V6-V8 (B968F/B1401R) are recommended to be used to do the DGGE analysis. Mix I341F/I534R and B341F/B534R PCR product equally to make DGGE analysis can get more community diversity information.