The NYT has an interesting article on how Glyphosate (Round Up) affects the soil. We home gardeners do not use Round Up to the extent that GMO corn and soy farmers use it, so this article should be viewed from that perspective, but it's got some facts (which Monsanto does not deny) on what Glyphosate does to the soil in farmland. I do use Round Up (selectively, rarely, and carefully, with a paintbrush, not spray) on certain weeds that simply cannot be controlled by pulling.

'the plants� roots systems rely on a complex system of bacteria, fungi and minerals in the soil. The combination, in the right balance, helps protect the crops from diseases and improves photosynthesis.

In some studies, scientists have found that a big selling point for the pesticide � that it binds tightly to minerals in the soil, like calcium, boron and manganese, thus preventing runoff � also means it competes with plants for those nutrients. Other research indicates that glyphosate can alter the mix of bacteria and fungi that interact with plant root systems, making them more susceptible to parasites and pathogens. '"

Unfortunately, gardenweb rejects my link to the article for some reason, but you can google it up with

"nyt misgivings about how weedkiller affects the soil"