As a new DNA fingerprinting technique, denaturing g radient gel electrophoresis (DGGE) was used to analyze the microbial
diversity i n different environmental samples, which has given people new ideas of studying the microbial community in soil. This technique is based on the direct extractio n of genomic DNA from soil samples, the amplification of 16S rRNA genes (V3 regi on) by using the specific primers and the separation of the PCR products by DGGE . Three strains (Escherichia coli DH 5α, Staphylococcus aureus SA 1 an d Agroba cterium tumerfaciens 13129) and seven soils sampled in different places and di ff erent depths were used in this study to evaluate the influence of GC clamp on th e result of bacterial diversity by PCR DGGE. The genomic DNA of three strains a nd the soil samples were extracted by a traditional cell lysis method and a cell lysis method based on the high NaCl (1 5mol/L) and long time high temperture (65℃ for 2 hours)respectively. Then, 16S rDNA fragments (16S rRNA gene V3 regio n) were
amplified by using two sets of specific primers F 357 GC, R 518 with a GC clamp in 5′end of the forward primer and F 357 , R 518 with out a GC clamp. The PCR products amplified by two sets primers and separated by DGGE respectively. The results showed that the 16S rDNA fragments with a GC cla mp (amplified by primers F 357 GC, R 518 ) could be clearly separated, b ut those DNA fragments without a GC clamp (amplified by primers F 357 , R 518 ) couldn't be separated well in DGGE. In conclusion, the GC clamp was av ailable for separation of PCR products of the microbial community in DGGE,and i t is more helpful for identification and classification of the microbial communi ty in environmental soil samples.