Metagenomics reveal the effect of Bt-transgene integration on root-nodulation and associated bacterial community structure of Bt-transgenic chickpea

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. In the present investigation effect of Bt-transgene integration on nodulation and bacterial community structure of root and root-nodules of parent as well as Bt-transgenic lines (IPCa2, IPCa4, IPCT3, IPCT10, and IPCT13) were studied by metagenomics. Though the root-nodulation by native Mesorhizobium was not affected by transgene integration in all tested Bt-chickpea events, changes in bacterial species diversity and richness of root and root-nodules were observed. Bacteria belong 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. Only 11.13% reads of Mesorhizobium in DCP 92-3 were classified at species level and remaining 88.87% reads of Mesorhizobium are not classified at species level remaining 88.87% reads are unclassified at species level. Thus the present investigation revealed the existence of large diversity of Mesorhizobium in Indian Soils.