Evidences of inhibited arbuscular mycorrhizal fungal development and colonization in multiple lines of Bt cotton

•Bt cotton inhibited spore germination and pre-symbiotic hyphal differentiation.•Appressorium number decreased on Bt roots.•Root colonization intensity and arbuscule abundance decreased within Bt roots.•More collapsed arbuscules were observed in Bt roots.•Interference of signal perception or Bt toxin toxicity directly impact on AM fungi.