I can not access this peer reviewed study, but the author is a scientist with the USDA's Agricultural Research Service.
Here is the abstract:"Current crop production relies heavily on transgenic, glyphosate-resistant (GR) cultivars. Widespread cultivation of transgenic crops has received considerable attention. Impacts of glyphosate on rhizosphere microorganisms and activities are reviewed based on published and new data from long-term field projects documenting effects of glyphosate applied to GR soybean and maize. Field studies conducted in Missouri, U.S.A. during 1997–2007 assessed effects of glyphosate applied to GR soybean and maize on root colonization and soil populations of Fusarium and selected rhizosphere bacteria. Frequency of root-colonizing Fusarium increased significantly after glyphosate application during growing seasons in each year at all sites. Roots of GR soybean and maize treated with glyphosate were heavily colonized by Fusarium compared to non-GR or GR cultivars not treated with glyphosate. Microbial groups and functions affected by glyphosate included Mn transformation and plant availability; phytopathogen–antagonistic bacterial interactions; and reduction in nodulation. Root-exuded glyphosate may serve as a nutrient source for fungi and stimulate propagule germination. The specific microbial indicator groups and processes were sensitive to impacts of GR crops and are part of an evolving framework in developing polyphasic microbial analyses for complete assessment of GR technology that is more reliable than single techniques or general microbial assays."
Perhaps someone here is a member and can access the full report?
Dr. Kremer, or I guess I should just say Kremer, is observing degradation of soils where Roundup is used. Superweeds, resistant to roundup, are a more important problem according to his boss at Agricultural Research Service, Michael Shannon. But Mr. Shannon acknowledges that soil degradation is also a concern.
"Michael McNeill, who has a Ph.D. in quantitative genetics and plant pathology from Iowa State University, advises large-scale corn and soy farmers on weed control and soil fertility. He's observing trends in the field that are consistent with Kremer's research. Here's Boulder Weekly:
McNeill explains that glyphosate is a chelating agent, which means it clamps onto molecules that are valuable to a plant, like iron, calcium, manganese, and zinc.…The farmers' increased use of Roundup is actually harming their crops, according to McNeill, because it is killing micronutrients in the soil that they need, a development that has been documented in several scientific papers by the nation's leading experts in the field. For example, he says, harmful fungi and parasites like fusarium, phytopthora and pythium are on the rise as a result of the poison, while beneficial fungi and other organisms that help plants reduce minerals to a usable state are on the decline. He explains that the overuse of glyphosate means that oxidizing agents are on the rise, creating oxides that plants can't use, leading to lower yields and higher susceptibility to disease."
Link
I do not care for the reporting, but these scientists are suggesting that roundup is not good for the soil. It's possibly choking off the nutrients and agents that break down the nutrients the plants require by attaching to the nutrients themselves.
Perhaps someone can find a peer reviewed study that refutes this study?