Nelson, A. G., Quideau, S., Frick, B., Niziol, D., Clapperton, J. and Spaner, D. 2011. Spring wheat genotypes differentially alter soil microbial communities and wheat breadmaking quality in organic and conventional systems. Can. J. Plant Sci. 91: 485-495. Wheat (Triticum aestivum L.) cultivars may have differential effects on soil microbial communities and the breadmaking quality of harvested grain. We conducted a field study comparing five Canadian spring wheat cultivars grown under organic and conventional management systems for yield, breadmaking quality and soil phospholipid fatty acid (PLFA) profile. Organic yields (2.74 t ha^-1) were roughly half of conventional yields (5.02 t ha^-1), but protein levels were higher in the organic system than the conventional system (16.6 vs. 15.3%, respectively). Soil microbial diversity measures were significantly higher in the organic system compared with the conventional system, including PLFA richness (31 vs. 27 unique PLFAs per sample, respectively) and PLFA diversity (Shannon diversity indexes of 2.90 and 2.73, respectively). Diversity measures were positively correlated with weed seed yield in the organic system (0.44<r<0.55), indicating that the presence of weeds played some role in increased microbial diversity. The use of composted dairy manure in the organic system may also have contributed to differences between the microbial communities in the organic and conventional systems. In the conventional system, the most recent wheat cultivar, AC Superb, had higher levels of mycorrhizal fungi in the soil (1.97%) than the other cultivars (1.32-1.43). Our results suggest that breeding efforts in conventionally managed environments may have resulted in cultivating mycorrhizal dependence in that environment. Cropping systems that include a diversity of plants, such as polycultures, may increase soil microbial diversity.