Farm system management affects community structure of arbuscular mycorrhizal fungi

• AMF community structure differed under organic versus conventional farm management.
• AMF community structure was also affected by farm location.
• Abundance of individualAMF isolates was affected by farm management. AMF isolates was affected by farm management.
• This research supports that certain AMF taxa have a global distribution.

Arbuscular mycorrhizal fungi (AMF) are considered to play a pivotal role in organic farming systems as they are known to enhance plant phosphorus (P) uptake from soils low in plant-available P. However, the structure and therefore function of AMF communities may be altered depending on environment and management conditions. Polymerase chain reaction-denaturing gradient gel electrophoresis (PCR-DGGE) and quantitative real-time PCR (qPCR) were used to explore AMF community structure in soils from perennial forages (Medicago sativa—Phleum pratense) on three pairs of long-term (>20 yr) organic and conventional dairy farm soils in Ontario, Canada. There were no significant differences in DGGE band numbers (indicative of species richness) among organic and conventionally managed soils. Analysis of Similarity revealed significant differences in AMF community composition with both farming system management and farm pair location having significant effects (R = 0.71 and 0.91, respectively, P < 0.0001 for both). Real-time qPCR indicated greater abundance of Funneliformis mosseae under conventional management (P = 0.036), while organic management tended to support greater abundance of Claroideoglomus claroideum (P = 0.067). Such a compositional shift in AMF communities could have consequences for the growth and P-use efficiency of their host. The results of this study highlight that the structure of AMF community assemblages are co-determined by both local environmental conditions and farming system management, and importantly, demonstrate for the first time differences between organic and conventional management in dairy farm soils from mixed perennial forages.