Global Standardised Soil Eukaryome Dataset (GloSED)

Dataset description

The GloSED dataset is a metabarcoding-based dataset encompassing the entire spectrum of soil eukaryotes collected and analysed using standardized protocols.

Key characteristics

- Sampling sites: 4,147 globally distributed locations across 121 countries  
- Taxonomic scope: Complete soil eukaryome including fungi, protists, animals, and plants  
- Operational taxonomic units: 988,824 curated OTUs  
- Sequencing technology: PacBio long-read sequencing of full-length ITS  

Data collection and processing

- Standardized sampling design: 50x50 m plots  
- Soil cores: 40 cores per plot (5 cm diameter x 5 cm depth), pooled by volume  
- DNA extraction: PowerMax Soil DNA Isolation kit (Qiagen) with FavorPrep cleanup  
- Primers: universal eukaryotic primers ITS9mun/ITS4ngsUni  
- Processing: NextITS v.1.0.0 workflow (DOI: 10.5281/zenodo.15074882)  
- Taxonomic annotation: EUKARYOME v.1.9.4 database (DOI: 10.1093/database/baae043)  

 
Data files and formats

Core data

- `GloSED__OTU_sequences.fasta.gz`: Quality-filtered representative sequences for all OTUs, FASTA format  
- `GloSED__OTU_table.tsv.zip`: Sample-by-OTU abundance matrix (TSV format)  
- `GloSED__Taxonomy.tsv.zip`: Complete taxonomic annotations with UNITE-based species hypotheses (TSV format)  

- `GloSED__OTU_table.parquet`: Columnar format of abundance data for efficient querying (Parquet format)  
- `GloSED__Taxonomy.parquet`: Columnar format of taxonomic data (Parquet format)  

- `GloSED__phyloseq.RData`: phyloseq object for R-based analyses  
- `GloSED__BIOM.biom`: BIOM v.2.1 format compatible with QIIME2  

Metadata files

- `GloSED__Sample_metadata.xlsx`: Sample metadata  
- `DRI.json`: Data Reuse Information tag with ORCID identifiers  
- `DRI.csv`: Tabular format mapping accession IDs 

- `Contributors.xlsx`: List of contributors

Related resources

• Raw sequence data:
  • European Nucleotide Archive (ENA) project: PRJEB103811
  • Sample accessions: ERS27941879 - ERS27946063  
  • Sequence accessions: ERR15957609 - ERR15964175
• Bioinformatics pipeline: NextITS
• Reference databases: EUKARYOME, UNITE