Strains of Bacillus thuringiensis (Bt) are commonly found in soil. The genes within Bt produce many different proteins in the soil and there are thousands of different arthropods, nematodes and microorganisms in the soil. There are books written about their potential or actual interactions, however, it should be remembered that these interactions are a natural part of the soil ecosystem.
Briefly, insecticidally active Bt proteins generally interact only with insects that have a specific pH in their digestive system and a binding site in their gut that can attach to a specific site on the Bt protein. The requirement for a specific pH and a unique binding site means that a Bt protein can have an effect on target pests or closely related insects, but at the same time have no effect on other insects or organisms. This narrow spectrum of activity also means that we would expect the Bt in genetically engineered crops to have fewer effects on insects and other microorganisms in the soil than agricultural practices such as tillage or conventional broad spectrum insecticides.
Since Bt evolved in the soil along with the other microorganism and insects, the complexities of their interactions likely have come into what might be called a balance. It is very hard to generalize, but when we have looked at organisms such as insects, nematodes, and micro-organisms in the soil, they are not harmed by the Bt proteins used in Bt products or Bt plants.