Abstract
Fungi are highly important biotic components of terrestrial ecosystems, but we still have a very limited understanding about their diversity and distribution. This data article releases a global soil fungal dataset of the Global Soil Mycobiome consortium (GSMc) to boost further research in fungal diversity, biogeography and macroecology. The dataset comprises 722,682 fungal operational taxonomic units (OTUs) derived from PacBio sequencing of full-length ITS and 18S-V9 variable regions from 3200 plots in 108 countries on all continents. The plots are supplied with geographical and edaphic metadata. The OTUs are taxonomically and functionally assigned to guilds and other functional groups. The entire dataset has been corrected by excluding chimeras, index-switch artefacts and potential contamination. The dataset is more inclusive in terms of geographical breadth and phylogenetic diversity of fungi than previously published data. The GSMc dataset is available over the PlutoF repository.
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Data availability
The GSMc OTU-by-sample dataset is available from the PlutoF data repository (https://doi.org/10.15156/BIO/2263453) in six files: information file, OTU matrix in spreadsheet format, sample metadata (equivalent to Table S1), taxonomic and functional description of OTUs, OTU sequences in FASTA format, as well as data in Biological Observation Matrix (BIOM) format. Representative sequences of identical sequences per sample will be available from the UNITE database.
Code availability
The scripts used for the bioinformatic analysis are available at GitHub: https://github.com/Mycology-Microbiology-Center/GSMc
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Acknowledgements
We Thank Liis Tiirmann for assistance during manuscript preparation and multiple students for assistance in sample and metadata collection. We also thank two anonymous referees for their constructive suggestions.
Funding
The bulk of this work was supported by the Estonian Science Foundation (Grant Nos. PRG632, PSG136, MOBTP198, PUT1170), Norway-Baltic EEA financial mechanism (Grant No. EMP442), RSF19-14-00038, DSFP-2021 and Novo Nordisk Fonden (Silva Nova).
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Supplementary file1 (XLSX 688 KB)
Table S1 Metadata of plots. Only the 3200 plots with available data are indicated.
Supplementary file2 (XLSX 13 KB)
Table S2 Sequences of barcodes and forward and reverse primers used in the current study.
Supplementary file3 (XLSX 18 KB)
Table S3 Taxon-specific e-value thresholds used for taxonomic assignments of OTUs with BLAST.
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Item S1 Sampling protocol.
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Tedersoo, L., Mikryukov, V., Anslan, S. et al. The Global Soil Mycobiome consortium dataset for boosting fungal diversity research. Fungal Diversity 111, 573–588 (2021). https://doi.org/10.1007/s13225-021-00493-7
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DOI: https://doi.org/10.1007/s13225-021-00493-7