Fungal OTU Table and Taxonomic Assignments Generated via SEED2

This dataset contains original bioinformatically processed data from fungal sequencing library using the SEED2 (v2.0.4) pipeline (Větrovský et al., 2018). The data were processed as described in Řezáčová et al. (2019) and Řezáč et al. (2021, 2025). Paired-end reads were assembled, low-quality sequences and reads shorter than 250 bp were removed, and the target regions were extracted. The sequences were then clustered into Operational Taxonomic Units (OTUs) at a 97% similarity threshold. Chimera detection was performed using USEARCH 8.1.1861. A representative sequence (most abundant in the cluster) was selected for each OTU and taxonomically assigned using BLASTn (v2.5.0+) against curated fungal reference databases. The dataset includes: OTU table: An abundance matrix of OTUs across samples. Taxonomy table: Taxonomic assignments of representative OTUs including higher-rank classification and trophic mode assignments (saprotrophic, symbiotic, pathogenic), where available. Note: This dataset represents a part of the data analyzed in the manuscript:Řezáčová, V., Šimon, T., Némethová, E., Saska, P., Mayerová, M. (2025). Soil cultivation methods rather than catch crop species enhance bacterial diversity in soil over a three-year experiment. Scientific Reports (under revision after peer review).