It was reports, in some cases, it would affect soil bacteria. See 2015 article below:
Article Belowground environmental effects of transgenic crops: A soi...
"Plants modified to express phytopathogen/phytoparasite resistance, or traits beneficial to food industries and consumers, differentially affected soil microorganisms depending on transformation events."
There are number of reports both in favor of GMO and others questioning the GMO. I mean mixed response is there. As far as the "Transgenic DNA" is concerned, it has also been reported in the non-GMO crops also which is generally called natural transgenic.