The impact of fallowing on the genetic structure of arbuscular mycorrhizal fungi (AMF) was studied by hierarchical sampling of spores from four plots in a fallow and a cultivated field.

A nested multiplex PCR approach was used to assign the spores to genotypes. Variable introns of the two protein-coding genes GmFOX2 and GmTOR2 were used as co-dominant genetic markers together with the large subunit (LSU) rDNA. The gene diversity and genetic structure of Glomus mosseae, Glomus geosporum and Glomus caledonium were compared within and between the fields.

Spores of G. caledonium and G. geosporum were more abundant in the cultivated field, whereas G. mosseae was more frequent in the fallow field. The number of genotypes was not different between the two fields.

Analysis of gene diversity of G. caledonium in the fallow field indicated that a larger part of the heterogeneity could be attributed to variation between plots rather than subplots, suggesting that the lack of soil cultivation resulted in more heterogeneous population genetic structures. Analyses of haplotype networks of the fungi suggested a subdivision of G. mosseae haplotypes between the two fields, whereas no such division was seen in G. geosporum and G. caledonium. The results show that agricultural practices differently affect both the abundance and the population structure of different AMF species.