The effects of the transgenic chili pepper (Capsicum annuum L.) containing the viral coat protein (CP) gene and neomycin phosphotransferase (nptII) gene on the soil microbial community were investigated in a field trial using phospholipid fatty acid (PLFA) and terminal restriction fragment length polymorphism (T-RFLP) analysis. Seedlings of transgenic chili pepper, its wild-type, and a commercial variety were transplanted in the field in May and the rhizosphere soil was sampled during the flowering stage (June) and fruit ripening stage (August and September). The bulk soil was also sampled in December, one month after cultivation.

Results/Conclusions

PLFA concentrations and the diversity index of PLFAs were not significantly affected by the chili pepper line; however, sampling time had a significant effect on these factors. The diversity index of T-RFs obtained from the 16S rRNA and ITS genes also had a significant effect of sampling time. Although the chili pepper line had a significant effect on the overall diversity index of T-RFs following digestion of the ITS gene with HhaI and HinfI, Tukey’s HSD test showed that only the diversity index of the GM chili pepper and a commercial variety treatments differed. PCA analysis of PLFA and T-RFLP profiles also showed differentiation of clusters according to the sampling time.