{"key":"341e5878-1075-40ac-bc52-b0fd7f693cb7","installationKey":"d0e2b9a9-8496-4959-8cba-a7fea22537eb","publishingOrganizationKey":"a8b02799-6e2e-4084-a9e5-86c5917b75f1","doi":"10.15468/rb47qz","version":"1.2","external":false,"numConstituents":0,"type":"OCCURRENCE","subtype":"OBSERVATION","title":"The first environmental DNA-based inventory of soil fungal diversity in Ukraine - ITS-based occurrences","description":"\n            This dataset presents the first national-scale, DNA metabarcoding-based record of soil fungal communities in Ukraine, compiled following FAIR data principles. It is derived from 225 topsoil samples collected across accessible regions of Ukraine (June–November 2023), spanning five ecoregions including Carpathian montane forests, mixed forests, forest-steppe, and Pontic steppe habitats. Soil DNA was amplified using universal fungal-specific primers (ITS3/ITS4) targeting the internal transcribed spacer (ITS2) rRNA gene region, sequenced on an Illumina NextSeq 2000 platform, and resolved into Operational Taxonomic Units (OTUs) using QIIME2. We assigned taxonomy folowing two-step approach. First, we automatically assigned taxonomy using scikit-learn Naїve Bayes classifier with RESCRIPt tool tained against UNITE reference dataset (v10). Then, to control quality of taxonomic accuracy, 3366 OTU was manually checked by six taxonomic experts by manually pairwise alignement against reference databases using Mycobank and NCBI Nucleotide BLAST web tools. Occurrence records are provided for 14,029 OTUs belonging to Kingdom Fungi, alongside its reference sequences. This dataset extends the area of Europe densely covered by soil eDNA sampling more than 800 km eastward and represents the first unified, national-scale eDNA characterization of soil fungal diversity in Ukraine. By adhering to contemporary biodiversity data standards, it supports advanced spatial analyses, diversity hotspot identification, and evidence-based planning for post-war ecological restoration. The structured, standards-compliant format is intended to facilitate reuse by a broad range of stakeholders — including local communities, protected area managers, environmental agencies and NGOs, and researchers — regardless of their prior expertise with soil microbiome data.[This dataset follows up SSU-based occurrence dataset https://doi.org/10.15468/yp9p4v and was processed using the GBIF Metabarcoding Data Toolkit.]\n        ","language":"eng","citation":{"text":"Prylutskyi O, Akulov O, Zinenko O, Fomenko M, Usichenko A, Khodosovtsev A, Kapets N, Kuzemko A, Borovyk D, Lavrinenko K, Novikov A, Moysiyenko I, Grebenschykov V, Prydiuk M, Miskova O, Viter S, Prylutska A, Brusentsova N, Viunnyk V, Protsenko Y, Bohoslavets O, Malaniuk V, Makarenko Y, Zykova M, Haidash O, Yakovliev M, Vlashchenko A, Chorney I, Dmytrash-Vatseba I, Zinchenko M, Skobel N, Chusova O, Shevchyk V, Zghonnyk M, Bronskov O, Bronskova O, Tolstyak N, Kharkova O (2026). The first environmental DNA-based inventory of soil fungal diversity in Ukraine - ITS-based occurrences. Version 1.2. Falz-Fein Biosphere Reserve \"Askania Nova\". Occurrence dataset https://doi.org/10.15468/rb47qz accessed via GBIF.org on 2026-10-16.","citationProvidedBySource":false},"contactsCitation":[{"key":7633959,"abbreviatedName":"Prylutskyi O","firstName":"Oleh","lastName":"Prylutskyi","roles":["ORIGINATOR","METADATA_AUTHOR"],"userId":["https://orcid.org/0000-0001-5730-517X"]},{"key":7633960,"abbreviatedName":"Akulov O","firstName":"Olexander","lastName":"Akulov","roles":["ORIGINATOR"],"userId":["https://orcid.org/0000-0002-8191-3957"]},{"key":7633961,"abbreviatedName":"Zinenko O","firstName":"Oleksandr","lastName":"Zinenko","roles":["ORIGINATOR"],"userId":["https://orcid.org/0000-0001-5228-9940"]},{"key":7633962,"abbreviatedName":"Fomenko M","firstName":"Mykhailo","lastName":"Fomenko","roles":["ORIGINATOR"],"userId":["https://orcid.org/0000-0002-5095-7252"]},{"key":7633963,"abbreviatedName":"Usichenko 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Sampling was a single, non-repeated campaign (not a recurring time series).","sampling":"Soil fungal communities were surveyed at 225 sites across mainland Ukraine using a standardized plot-based protocol. At each site, a 900 m² (30 × 30 m) plot was established in natural habitat, avoiding populated areas, croplands, and infrastructure. Within each plot, nine soil cores were collected in a grid arrangement after removing the surface litter layer, then pooled and homogenized in the field to capture local fungal diversity while accounting for spatial heterogeneity. Samples were dried using silica gel and stored at room temperature until processing. DNA was extracted from each sample and used to amplify two fungal marker regions: the ITS2 region (targeting the broader fungal community) and the SSU rDNA region (targeting arbuscular mycorrhizal fungi specifically). Amplicons were sequenced on an Illumina platform and processed bioinformatically to generate taxonomically resolved fungal community data for each site.","qualityControl":"To control quality of taxonomic accuracy, 3366 OTU was manually checked by six taxonomic experts following three-step approach. First, the consolidated OTU sequences generated by VSEARCH were manually pairwise aligned against reference databases using Mycobank and NCBI Nucleotide BLAST web tools. For Mycobank, we opted to FunCBS (https://wi.knaw.nl), UNITE (https://unite.ut.ee/),  refseqITS (https://www.ncbi.nlm.nih.gov/refseq/targetedloci/),  MIRRI (http://catalog.mirri.org) as reference database. For NCBI, we applied BLASTn algorithm for somewhat similar sequences (Altschul et al., 1997). At second step, the most probable consensus identification for each OTU at reliable taxonomic level were manually selected. Finally, in case of disagreement in identification, the sequences were aligned by an independent taxonomic expert to resolve a conflict. To track automatic (made solely by bioinformatics pipeline) and curated (made by human experts) identificatons, we added a field “indetifiedBy” recorded the identification source (either “automated” or the names of experts).","methodSteps":["Field sampling. At each of 225 sites, a 900 m² plot was established following removal of coarse surface litter. Nine soil cores (5 cm diameter, 10 cm depth) were collected per plot in a grid design, then pooled and homogenized in the field for a minimum of two minutes to produce one composite sample per site. Samples were dried with silica gel and stored dry at room temperature; a 200 mg subsample was reserved for molecular analysis and the remainder retained for physicochemical assessment.","DNA extraction and QC. Nucleic acids were extracted from 200 mg soil subsamples using the DNeasy PowerSoil Pro Kit (Qiagen). Extraction yield was spot-checked on a subset of ten samples via microspectrophotometry, with all falling within an acceptable concentration range; remaining samples were not individually quantified. No laboratory extraction negative control was included; low-abundance OTUs (below 1% of reads) were instead filtered post-sequencing as a quality control step. Extracted DNA was shipped to the Scripps Research Institute (USA) for amplification and sequencing.","PCR amplification. Two markers were amplified using a two-step PCR protocol: the fungal ITS2 region (primers ITS3/ITS4) for general fungal community profiling, and the SSU rDNA region (primers WANDA/AML2) targeting arbuscular mycorrhizal fungi.","Sequencing. Indexed amplicon libraries were sequenced on an Illumina NextSeq 2000 platform using 2 × 300 bp paired-end chemistry. Raw read quality was assessed with MultiQC.","Bioinformatic processing. Reads were processed using the LotuS2 pipeline for quality filtering and dereplication. ITS2 sequences were clustered into OTUs at 97% similarity using VSEARCH. SSU sequences were instead denoised into ASVs using DADA2, following standard practice for higher-resolution AM fungal detection. Taxonomy for SSU sequences was assigned using BLASTn against MaajAM database. Fot ITS, taxonomic assignment folowed two-step approach. First, we automatically assigned taxonomy using scikit-learn Naїve Bayes classifier with RESCRIPt tool tained against UNITE reference dataset (v10). Then, to control quality of taxonomic accuracy, 3366 OTU was manually checked by six taxonomic experts by manually pairwise alignement against reference databases using Mycobank and NCBI Nucleotide BLAST web tools."]},"countryCoverage":[],"collections":[],"dataDescriptions":[],"dataLanguage":"eng","pubDate":"2026-10-02T00:00:00.000+00:00","maintenanceUpdateFrequency":"AS_NEEDED","maintenanceDescription":"","license":"http://creativecommons.org/licenses/by/4.0/legalcode","dwca":{"coreType":"http://rs.tdwg.org/dwc/terms/Occurrence","extensions":["http://rs.gbif.org/terms/1.0/DNADerivedData"],"modified":"2026-10-02T13:57:37.413+00:00"},"category":["eDNA"],"approximateCounts":{"occurrenceCount":178631}}