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When more research was completed, "Rahe and coworkers documented that severe root infection associated with glyphosate-treated plants was due to disruption of synthesis of plant defense compounds, or phytoalexins, through the shikimate pathway there by predisposing plants to attack by soilborne fungal pathogens (Johal and Rahe, 1988; Lévesque et al., 1987).<ref>Johal, G.S., Rahe, J.E., 1988. Glyphosate, hypersensitivity and phytoalexins accumulation in the incompatible bean anthracnose host-parasite interaction. Physiol. Mol. Plant Pathol. 32, 267-281</ref><ref>Lévesque, C.A., Rahe, J.E., Eaves, D.M., 1987. Effects of glyphosate on ''Fusarium'' spp.: its influence on root colonization of weeds, propagule density in the soil, and crop emergence. Can. J. Microbiol. 33, 354-360.</ref> Thus, infection by soilborne pathogens caused by the inability of plants to synthesize phytoalexins contributed to the overall herbicidal efficacy of glyphosate and was considered a “secondary mode of action” of glyphosate. These findings were significant because the release of glyphosate into the environment was found to have considerably more and far-reaching effects than the original notion that was limited to only the localized disruption of a specific metabolic pathway within a target plant."<ref>Preface "Glyphosate interactions with physiology, nutrition, and diseases of plants: Threat to agricultural sustainability?", European Journal of Agronomy 31 (2009) 111-113.</ref>

Once glyphosate travels to a plant's roots, it is "released into the rhizosphere," (the area immediately around the roots), "where it is immobilized at the soil matrix or microbially degraded.<ref>Tsehaye Tesfamariam, S. Bott, I. Cakmak, V. Römheld, G. Neumann, "[http://stopogm.net/webfm_send/53 Glyphosate in the rhizosphere – role of waiting times and different glyphosate binding forms in soils for phytoxicity to non-target plants]," ''European Journal of Agronomy (2009), 31:126-132.</ref> However, some of the glyphosate remains in dead plant tissues. A 2009 study found that non-target plants continue to be impacted by glyphosate toxicity up to three weeks after glyphosate application.<ref>Tsehaye Tesfamariam, S. Bott, I. Cakmak, V. Römheld, G. Neumann, "[http://stopogm.net/webfm_send/53 Glyphosate in the rhizosphere – role o If waiting times and different glyphosate binding forms in soils for phytoxicity to non-target plants]," ''European Journal of Agronomy (2009), 31:126-132.</ref>

A 2009 study examined the relationship between previous glyphosate use, tillage method (conventional, minimal, or no-till), and plant diseases caused by fungal pathogens of the genus [[Fusarium]].<ref>M.R. Fernandez, R.P. Zentner, P. Basnyat, D. Gehl, F. Selles, and Don Huber, "[http://stopogm.net/webfm_send/51 Glyphosate associations with cereal diseases caused by Fusarium spp. in the Canadian Prairies]," European Journal of Agronomy (2009), 31:133-143.</ref> The study found "a relationship between previous glyphosate use and increased ''Fusarium'' infection of spikes and subcrown internodes of wheat and barley, or ''Fusarium'' colonization of crop residues." However, the study adds, "because of the close association between noncereal crops, reduced tillage, and glyphosate use, it was not possible to completely separate the effects of these factors on ''Fusarium'' infections." (No-till or minimum till practices are often combined with herbicide use, specifically, glyphosate use. Thus, the scientists were not able to determine whether any increase or decrease in plant disease was related to tillage strategy, glyphosate use, or both.) The study recommended more research in this area.

At sub-lethal doses of glyphosate, such as the amounts a plant might be exposed to from spray drift, plants are still impacted. A study examined sunflowers treated with small amounts of glyphosate (to simulate spray drift) found:<ref>Levent Ozturk, Atilla Yazici, Selim Eker, Ozgur Gokmen, Volker Römheld, and Ismail Cakmak, "[http://research.sabanciuniv.edu/10763/1/Glyphosate_inhibition_of_ferric_reductase.pdf Glyphosate inhibition of ferric reductase activity in iron deficient sunflower roots]," ''New Phytologist'' (2008), 177:899-906.</ref>

:"In conclusion, the results presented in this study showing that glyphosate is especially inhibitory to ferric reductase complement the recently published report (Eker etal., 2006) that glyphosate exerts a strong inhibitory influence on ferric reductase activity of Fe-deficient roots and impairs the uptake and translocation of Fe in plants. These impairments could be a major reason for the increasingly observed Fe deficiency chlorosis in cropping systems associated with widespread glyphosate usage as reported for different parts of the USA (Franzen etal., 2003; Jolley etal., 2004). Such strong interference of glyphosate with root uptake and root-to-shoot transport of Fe in crop plants may represent a potential threat to human and animal nutrition because of possible reduction of Fe in edible plants parts (e.g. seed/grain)."

In other words, low doses of glyphosate equal to the amount plants are exposed to in spray drift, can result in iron deficiencies in the plants. For crops destined as animal feed or as human food, this could result in decreased dietary iron.

Several sources have found that glyphosate impacts soil microorganisms. For example:

Pesticide Interactions in Crop Production, Beneficial and Deleterious Effects. CRC Press, Inc., Boca Raton, FL, pp. 315–332.</ref><ref>C. André Lévesque and James E. Rahe, [http://www.annualreviews.org/doi/abs/10.1146/annurev.py.30.090192.003051 Herbicide Interactions with Fungal Root Pathogens, with Special Reference to Glyphosate], Annual Review of Phytopathology (1992), Vol. 30: 579-602.</ref> Levesque and Rahe (1992) showed evidence that herbicides can have a direct effect on various components of the soil microflora, such as plant pathogens, antagonists, or mycorrhizae, which can potentially increase or decrease the incidence of plant disease. Pathogens able to infect weeds can also increase their inoculum potential after weeds have been sprayed with herbicides, which could subsequently affect host crops."<ref>M.R. Fernandez, R.P. Zentner, P. Basnyat, D. Gehl, F. Selles, and Don Huber, "[http://stopogm.net/webfm_send/51 Glyphosate associations with cereal diseases caused by Fusarium spp. in the Canadian Prairies]," European Journal of Agronomy (2009), 31:133-143.</ref>

Although glyphosate is highly soluble in water, its tendency to bond to soils makes it unlikely to leach into groundwater or runoff "significantly." (Studies have found about 1%-2% of glyphosate may runoff in rainfall after glyphosate is applied.<ref>John P. Giesy, Stuard Dobson, and Keith R. Solomon, 2000, "[http://www.colby.edu/biology/BI402B/Giesy%20et%20al%202000.pdf Ecotoxicological Risk Assessment for Roundup Herbicide]," Rev Environ Contam Toxicol 167:35-120.</ref>)

Glyphosate can reach the soil by washing off the foliage of plants, via spray drift, by exudation from the roots of treated plants, or by the decomposition of treated plants. However, "risks of glyphosate toxicity to non-target organisms in soils are generally considered as marginal,since glyphosate is almost instantaneously inactivated by adsorption to clay minerals and cationic binding sites of the soil matrix (Piccoloetal.,1992;Dong-Meietal.,2004), while glyphosate in the soil solution is prone to rapid microbial degradation (Giesy et al., 2000)."<ref>Tsehaye Tesfamariam, S. Bott, I. Cakmak, V. Römheld, G. Neumann, "[http://stopogm.net/webfm_send/53 Glyphosate in the rhizosphere – role of waiting times and different glyphosate binding forms in soils for phytoxicity to non-target plants]," ''European Journal of Agronomy (2009), 31:126-132.</ref><ref>John P. Giesy, Stuard Dobson, and Keith R. Solomon, 2000, "[http://www.colby.edu/biology/BI402B/Giesy%20et%20al%202000.pdf Ecotoxicological Risk Assessment for Roundup Herbicide]," Rev Environ Contam Toxicol 167:35-120.</ref> In other words, glyphosate residues in the soil are not considered hazardous as it either breaks down quickly or binds to minerals that make it no longer a threat to plants. Glyphosate that biodegrades usually breaks down into carbon dioxide and ammonium (NH4+).<ref>John P. Giesy, Stuard Dobson, and Keith R. Solomon, 2000, "[http://www.colby.edu/biology/BI402B/Giesy%20et%20al%202000.pdf Ecotoxicological Risk Assessment for Roundup Herbicide]," Rev Environ Contam Toxicol 167:35-120.</ref> In an analysis of 47 studies, 50% of glyphosate broke down in the soil in time periods ranging from 1.2 days to 197.3 days. The arithmetic mean amount of time was 32 days and the geometric mean was 17 days.<ref>John P. Giesy, Stuard Dobson, and Keith R. Solomon, 2000, "[http://www.colby.edu/biology/BI402B/Giesy%20et%20al%202000.pdf Ecotoxicological Risk Assessment for Roundup Herbicide]," Rev Environ Contam Toxicol 167:35-120.</ref>

Although glyphosate is mostly broken down by microbes or bound to the soil, a 2009 study found that "the root tissue of glyphosate-treated weeds represents a storage pool for glyphosate."<ref>Tsehaye Tesfamariam, S. Bott, I. Cakmak, V. Römheld, G. Neumann, "[http://stopogm.net/webfm_send/53 Glyphosate in the rhizosphere – role of waiting times and different glyphosate binding forms in soils for phytoxicity to non-target plants]," ''European Journal of Agronomy (2009), 31:126-132.</ref>

Although most glyphosate applied to soil does not run off into waterways, sometimes glyphosate is applied to aquatic environments directly. In flowing water, it is dissipated via "tributary dilution, dispersion, and loss through processes such as absorption to suspended particulate matter or sediments and microbial degradation."<ref>John P. Giesy, Stuard Dobson, and Keith R. Solomon, 2000, "[http://www.colby.edu/biology/BI402B/Giesy%20et%20al%202000.pdf Ecotoxicological Risk Assessment for Roundup Herbicide]," Rev Environ Contam Toxicol 167:35-120.</ref> The half-life of glyphosate in water has been estimated to be from 7 to 14 days.<ref>John P. Giesy, Stuard Dobson, and Keith R. Solomon, 2000, "[http://www.colby.edu/biology/BI402B/Giesy%20et%20al%202000.pdf Ecotoxicological Risk Assessment for Roundup Herbicide]," Rev Environ Contam Toxicol 167:35-120.</ref>