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The production of tree seedlings in forest nurseries and their use in the replanting of clear-cut forest sites is a common practice in the temperate and boreal forests of Europe. Although conifers dominate on replanted sites, in recent years, deciduous tree species have received more attention due to their often-higher resilience to abiotic and biotic stress factors. The aim of the present study was to assess the belowground fungal communities of bare-root cultivated seedlings of  Alnus glutinosa ,  Betula pendula ,  Pinus sylvestris ,  Picea abies  and  Quercus robur  in order to gain a better understanding of the associated fungi and oomycetes, and their potential effects on the seedling performance in forest nurseries and after outplanting. The study sites were at the seven largest bare-root forest nurseries in Lithuania. The sampling included the roots and adjacent soil of 2–3 year old healthy-looking seedlings. Following the isolation of the DNA from the individual root and soil samples, these were amplified using ITS rRNA as a marker, and subjected to high-throughput PacBio sequencing. The results showed the presence of 161,302 high-quality sequences, representing 2003 fungal and oomycete taxa. The most common fungi were  Malassezia restricta  (6.7% of all of the high-quality sequences),  Wilcoxina mikolae  (5.0%),  Pustularia  sp. 3993_4 (4.6%), and  Fusarium oxysporum  (3.5%). The most common oomycetes were  Pythium ultimum  var.  ultimum  (0.6%),  Pythium heterothallicum  (0.3%),  Pythium spiculum  (0.3%), and  Pythium sylvaticum  (0.2%). The coniferous tree species ( P. abies  and  P. sylvestris ) generally showed a higher richness of fungal taxa and a rather distinct fungal community composition compared to the deciduous tree species ( A. glutinosa ,  B. pendula,  and  Q. robur ). The results demonstrated that the seedling roots and the rhizosphere soil in forest nurseries support a high richness of fungal taxa. The seedling roots were primarily inhabited by saprotrophic and mycorrhizal fungi, while fungal pathogens and oomycetes were less abundant, showing that the cultivation practices used in forest nurseries secured both the production of high-quality planting stock and disease control.

DNA-Metabarcoding of Belowground Fungal Communities in Bare-Root Forest Nurseries: Focus on Different Tree Species