Many plants leak chemical compounds into the soil through their roots. There are concerns that transgenic plants may leak different compounds than conventional plants do, as an unintended consequence of their changed DNA. Speculation that this may be happening leads to concern about whether the communities of micro-organisms living near transgenic plants may be affected. The interaction between plants and soil micro-organisms is very complex, with the micro-organisms that live around plant roots also leaking chemical compounds into the soil. Much more research must be done before we understand the relationships that occur between micro-organisms and conventional crops. Attempts to discover whether transgenic plants are changing the soil environment, and whether they are changing it in good ways or bad ways, are hindered by our lack of basic scientific knowledge.

A few studies have attempted to describe conditions in soils where transgenic crops are grown. A Canadian study (Dunfield and Germida, 2001), tested the soils around four transgenic and four conventional canola varieties. Some differences were associated with whether the crop being grown was transgenic or conventional. Other soil characteristics were similar regardless of the crop type, and some differences were not associated with the crop type. An analysis of fatty acids that are associated with certain kinds of soil micro-organisms indicated that transgenic plant roots might harbor higher levels of certain micro-organisms, but further research is essential to determine whether this is true.