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Transgenic Bt-cotton (Gossypium hirsutum L.) GK 12 is commonly used for control of lepidopteran pests in China, but concerns exist regarding possible unintended effects on soil microbial communities. Bacterial population sizes and community structures in the rhizosphere soil under intensive cultivation of GK 12, its near-isogenic parent Simian 3 and a conventional cotton DP 5415 were analyzed during 2009 to 2011 by quantitative polymerase chain reaction (qPCR) and denaturing gradient gel electrophoresis (DGGE). Dehydrogenase, urease, and phosphatase activities were also measured. It was found that these microbial-related parameters were significantly influenced by variations due to the year and plant growth stage. There were occasional differences in bacterial population size and community structures at some growth stages, but they were not manifested throughout the growing cycle and were not considered meaningful. Generally no significant differences were found in selected enzymatic activities, and bacterial population sizes and community structures in the rhizosphere soil of GK 12 and Simian 3. Three different species or bands were unique to GK 12 and Simian 3, but they were unamplifiable. The resolvable band profile or annotatable species composition was not different between GK 12 and Simian 3. Therefore, the data of this study did not show any significant and permanent impacts of Bt-insertion in GK 12 on selected enzymatic activities, bacterial population size, and community structures in the rhizosphere soil during 3-yr tests in northern China. [ABSTRACT FROM AUTHOR]