Research is being undertaken by several universities into the effects of glyphosate on soil biota. Concerned consumers are being told it now stays in the soil for a number of years even if applied only once.
Doing my own research into this subject I found that there is an increase of soil activity, especially an increase of fungi after an application. However there is a decrease in bacteria. The university research also says that the increase in fungi in the soil is leading to rot in a number of crop species. An interesting article and to read further on this:
Pesticide Effects on Soil Biology by Jill Clapperton from the Conservation Agriculture Alliance of Australia & New Zealand
A.S.F. Araújo, R.T.R. Monteiro & R.B. Abarkeli, 2003, Effect of glyphosate on the microbial activity of two Brazilian soils, Chemosphere 52: 799-804
(Extract from Sustainable Gardening Australia – eclippings)