Field studies show no significant effect of a Cry1Ab/Ac producing transgenic cotton on the fungal community structure in rhizosphere soil

•Fungal population size was not significantly influenced by Bt-cotton GK 12.•Fungal community structure was not significantly influenced by Bt-cotton GK 12.•Dominant fungal species composition was not different between Bt-cotton GK 12 and its parent.

Transgenic cotton GK 12 expressing insecticidal Cry1Ab/1Ac gene can effectively control the lepidopteran pests in agriculture, however it may have unintended side-effects on soil fungal communities. Therefore, the fungal community size and structure in rhizosphere soil of Bt and non-Bt cottons were analyzed by real-time polymerase chain reaction (qPCR) and denaturing gradient gel electrophoresis (DGGE) at growth stages and three annual replications in an intensive conventional cultivation system. The Cry1Ab/1Ac protein was undetectable or occasionally detectable at a low level (<0.1 ng/g soil) at seedling and senescence, and that the concentration of Cry1Ab/Ac protein in soil extracts did not increase over time or repeated cultivations. No significant differences in fungal population size and structure in rhizosphere soil were found between Bt-cotton GK 12 and its near-isogenic comparator at all growth stages, but they were different between Bt-cotton GK 12 and conventional cotton DP 5415 at some growth stages. The fungal population size and structure was significantly influenced by variation in years and plant growth stages. Sequencing results from DGGE bands showed that the dominant fungi were not different between Bt-cotton GK 12 and its near-isogenic comparator. Thus, the data of this study do not indicate any significant effect of Bt-cotton GK 12 on the fungal community size and structure in rhizosphere soil during these three continuous years.