Saproxylic fungal communities in fine woody debris in boreal forests of Oulanka, Finland, assessed by DNA metabarcoding

This work elucidates community development patterns of saproxylic fungi in undisturbed boreal forests, exploring how environment and forest management practices influence fungal diversity in decaying wood. Sterilized wooden pins were placed in the topsoil layer and were subjected to natural microbial colonization with subsequent periodic extraction; fungal colonization was monitored across three different forest ecosystems near Oulanka Research Station, Kuusamo, Northern Finland during 2022-2023. Oulanka Station is a regional unit of the University of Oulu located within Oulanka National Park (66.22 N, 29.19 E, 166.5 m a.s.l.), ca. 25 km south of the Arctic Circle. The station maintains an EcoClimate project which includes a plot guarded from reindeer grazing access for many years. MycoPins were placed at several local biotopes: conifer pine (Pinus sylvestris L.) dominated forest with access of reindeer (transect A), conifer pine dominated forest without access of reindeer (transect B), and a mixed, spruce (Picea abies (L.) Karst.) dominated forest with birch (Betula pendula Roth) and aspen (Populus tremula L.) (transect C). Reindeer are a keystone species in boreal forests which defines and shapes the biodiversity of major Nordic ecosystems. Cladonia spp. are lichens that are heavily consumed by reindeer and are in abundance in the protected forests and stand excluded from grazing, while suppressed in unprotected forests. Hence, reindeer grazing might have an impact on forest microbiome. Our research produced a dataset suitable for testing of several hypotheses: 1) fungal communities develop in newly available fine woody debris (FWD) and change subsequently with progression of decay; 2) diversity of saproxylic fungal guilds is different across different biotopes; 3) fungal colonization differs in hardwood FWD vs. softwood FWD. This study adopts a data model focused on operational taxonomic units (OTUs), which are defined by clusters of DNA sequences sharing a high degree of similarity and representing specific taxonomic groups. Fungal OTUs were identified using DNA metabarcoding, which analyzed fungal DNA from MycoPins undergoing decomposition across three transects over periods ranging from two weeks to one year. DNA metabarcoding included isolation of DNA from the core of MycoPins, PCR of the ITS2 fungal region using tagged primers, and subsequent high-throughput sequencing. Tagged primers were designed as follows: while the forward and reverse primers were always the same (fITS7 and ITS4), the primers were modified to include a unique nucleotide tag to create 40 unique primer pairs. A tagged fITS7-ITS4 pair was used to perform PCR for the DNA extracted from each MycoPin. A positive control was used to verify the PCR and sequencing in a form of mock fungal community (SynMock). A negative control (water) was used in the same way to exclude false-positive results. Tagged amplicons were then mixed in groups of ca 35 amplicons according to non-repeated tags into a multiplex used for sequencing. The multiplexes were sequenced using AmpliconEZ service at Genewiz (Azenta Life Sciences, New Jersey, USA) uisng Illumina MiSeq 2X 250 pair-end configuration.A taxonomy was used to classify the cluster of organisms an OTU represents. SCATA pipeline (https://scata.mykopat.slu.se/) was used to exclude low quality sequences, cluster similar sequences, and to match each OTU to the UNITE database taxonomy to primarily identify the species. For OTUs which were not matched to a UNITE reference by SCATA, a best-effort search from the NCBI database was performed. The top match from the NCBI database search was considered to be the OTUs identity.This is a raw sequence archive for the publication: Shumskaya M, et al.(2025) Progression of saproxylic fungal communities in fine woody debris in boreal forests of Oulanka, Finland, assessed by DNA metabarcoding. Biodiversity Data Journal 13: e155520. https://doi.org/10.3897/BDJ.13.e155520