| Summary: | In European forests, the Scots pine (<i>Pinus sylvestris</i> L.) most often regenerates on clearcuts, following mechanical site preparation. Both of these silvicultural treatments (the removal of trees and preparation) have an impact on soil properties, and on the mycorrhizal fungi associated with the roots of seedlings. We therefore compared assemblages of mycorrhizal fungi associating with natural-regeneration pine seedlings growing on a clearcut, in relation to six types of microsite created using three mechanical site-preparation tools, i.e., a double-mouldboard forest plough (creating furrow and ridge), an active single-disc plough (establishing another type of furrow and ridge), and a forest mill—developing strips, as well as a non-mechanical site preparation control. A total of 46 taxa of mycorrhizal fungi were detected, with <i>Wilcoxina mikolae</i> being the most abundant species (relative abundance—79.8%), and the one occurring most frequently (96.8%). Other abundant mycorrhizal fungi were <i>Thelephora terrestris</i> (3.8%), <i>Tylospora asterophora</i> (3.2%), <i>Hyaloscypha bicolor</i> (2.2%), and <i>Cenococcum geophilum</i> (1.7%). The roots of seedlings growing in the non-mechanical site preparation control were characterised by a significantly greater presence of mycorrhizal root tips, compared with the roots of seedlings growing at other microsites. The highest percentage of non-mycorrhizal root tips was present on pines growing on the two types of ridge: the microsites which characterized the highest levels of mineral nutrients. Communities of mycorrhizal fungi differed between microsites. The five microsites: both types of furrow, forest plough ridge, forest mill strip, and non-mechanical site preparation control, were not found to differ from each other, but did differ from the active plough ridge treatment. The highest diversity of mycorrhizal fungi (Shannon–Wiener and Simpson indexes) was in the non-mechanical site preparation control. Any method of mechanical site preparation in the clearcut decreases the level of root mycorrhization and the biodiversity of mycorrhizal fungi. The least suitable method from the point of view of mycorrhizal fungal communities is the use of an active plough.
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