Divergent arbuscular mycorrhizal fungal communities colonize roots of Pulsatilla spp. in boreal Scots pine forest and grassland soils.

•  Communities of arbuscular mycorrhizal (AM) fungi were characterized in roots of rare Pulsatilla patens and common P. pratensis native adults and seedlings grown in soils from Estonian boreal forest and grassland habitats. Since establishment of Pulsatilla species predominantly occurs in vegetation-free gaps, seedling baiting experiments were aimed at gap simulation. •  The AM fungal small subunit ribosomal RNA gene (SSU rDNA) sequences amplified from roots were subjected to denaturing gradient gel electrophoresis (DGGE), cloning, restriction fragment length polymorphism (RFLP) grouping, sequence phylogenetic and multivariate analyses. •  Nineteen identified sequence groups comprised 14 putative Glomus, two Acaulospora, two Scutellospora and one Gigaspora groupings. Four and six groupings, respectively, contained previously described species and root-derived AM fungal sequences. Sequence groups were identified in seedling roots that were more abundant in a grassland (Glomus sp. MO-G3) or a forest soil (Glomus spp. MO-G2 and MO-G5). •  Our data showed site-dependent differences in AM fungal community composition, but we failed to identify AM fungi specifically or preferentially colonizing the rare plant species.