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Symbiotic nitrogen fixation (SNF) of transgenic grain legumes might be influenced either by the site of transgene integration into the host genome or due to constitutive expression of transgenes and antibiotic-resistant marker genes. The present investigation confirmed proper nodulation of five tested  Bt -chickpea events (IPCa2, IPCa4, IPCT3, IPCT10, and IPCT13) by native  Mesorhizobium  under field environment. Quantitative variations for nodulation traits among  Bt -chickpea were determined and IPCT3 was found superior for nodule number and nodule biomass. Diversity, as well as richness indices, confirmed the changes in bacterial community structure of root and root-nodules from  Bt -chickpea events IPCa2 and IPCT10. Especially, Gram-positive bacteria belonging to  Firmicutes  and  Actinobacteria  were selectively eliminated from root colonization of IPCa2. Richness indices (CHAO1 and ACE) of the root-associated bacterial community of IPCa2 was 13–14 times lesser than that of parent  cv  DCP92-3. Root nodule associated bacterial community of IPCT10 was unique with high diversity and richness, similar to the roots of non- Bt  and  Bt -chickpea. It indicated that the root nodules of IPCT10 might have lost their peculiar characteristics and recorded poor colonization of  Mesorhizobium  with a low relative abundance of 0.27. The impact of  Bt -transgene on bacterial community structure and nodulation traits should be analyzed across the years and locations to understand and stabilize symbiotic efficiency for ecosystem sustainability.

Symbiotic nitrogen fixation and endophytic bacterial community structure in Bt-transgenic chickpea (Cicer arietinum L)