The purpose of the document is to summarize the methods and concepts that have been developed and used by the author and his colleagues to study the potential effects of genetically engineered microorganisms (GEMs) introduced, deliberately or accidently, into soil on microbemediated ecological processes in soil. The potential impacts of GEMs on the structure and function of natural environments into which the GEMs are introduced is the 'bottom-line' aspect in the concern about the survival of, and genetic transfer by, GEMs in these habitats. If a GEM survives in the habitat into which it is introduced, does the job for which it was designed, and even if the novel gene(s) is transferred to indigenous microbes, there should be little cause for concern unless the novel gene(s), either in the introduced GEM or in an indigenous recipient(s), results in some unexpected impacts on the environment.