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Background  The global area under brinjal cultivation is expected to be 1.85 million hectare with total fruit production about 32 million metric tons (MTs). Brinjal cultivars are susceptible to a variety of stresses that significantly limit productivity. The most important biotic stress is caused by the Brinjal fruit and shoot Borer (FSB) forcing farmers to deploy high doses of insecticides; a matter of serious health concern. Therefore, to control the adverse effect of insecticides on the environment including the soil, transgenic technology has emerged as the effective alternative. However, the reports, regarding the nature of interaction of transgenic crops with the native microbial community are inconsistent. The effect of a  Bt  transgenic brinjal expressing the bio-insecticidal protein (Cry1Ac) on the rhizospheric community of actinomycetes has been assessed and compared with its non-transgenic counterpart.    Results  Significant variation in the organic carbon observed between the crops (non- B t and  Bt  brinjal) may be due to changes in root exudates quality and composition mediated by genetic attributes of  Bt  transgenic brinjal. Real time quantitative PCR indicated significant differences in the actinomycetes- specific  16S rRNA  gene copy numbers between the non- Bt  (5.62-27.86)  ×  10 11  g -1  dws and  Bt  brinjal planted soil (5.62-24.04)  ×  10 11  g -1  dws. Phylogenetic analysis indicated 14 and 11, actinomycetes related groups in soil with non- Bt  and  Bt  brinjal crop, respectively.  Micrococaceaea  and  Nocardiodaceae  were the dominant groups in pre-vegetation, branching, flowering, maturation and post-harvest stage. However,  Promicromonosporaceae, Streptosporangiaceae, Mycobacteriaceae, Geodermatophilaceae, Frankiaceae, Kineosporaceae, Actisymmetaceae  and  Streptomycetaceae  were exclusively detected in a few stages in non- Bt  brinjal rhizosphere soil while  Nakamurellaceae, Corynebactericeae, Thermomonosporaceae  and  Pseudonocardiaceae  in  Bt  brinjal counterpart.    Conclusion  Field trails envisage that cultivation of  Bt  transgenic brinjal had negative effect on organic carbon which might be attributed to genetic modifications in the plant. Changes in the organic carbon also affect the actinomycetes population size and diversity associated with rhizospheric soils of both the crops. Further long-term study is required by taking account the natural cultivar apart from the  Bt  brinjal and its near-isogenic non- Bt  brinjal with particular reference to the effects induced by the  Bt  transgenic brinjal across different plant growth stages.

Changes in Actinomycetes community structure under the influence of Bttransgenic brinjal crop in a tropical agroecosystem