[en] Advances in high-throughput DNA sequencing technologies have accelerated research on aquatic microorganisms, their diversity, and ecological functions. This has also significantly advanced research on fungi that shape aquatic ecosystems and food webs. Here, we present the FunAqua dataset, which describes global fungal biodiversity in aquatic ecosystems based on eukaryotic long-read metabarcoding data from 1,076 sediment and 1,299 filtered water samples collected across 1,452 sampling sites in 87 countries. We targeted the internal transcribed spacer (ITS) region. In total, 50,152 fungal OTUs were recorded. The sequencing data is accompanied by comprehensive sample metadata, including physicochemical data of water and sediments. The FunAqua dataset provides a new resource for analysing and better understanding the biodiversity of fungi in different types of aquatic habitats across biogeographical regions. The dataset described in this data paper will be periodically updated with additional metabarcoding data.
Research Center/Unit :
FOCUS - Freshwater and OCeanic science Unit of reSearch - ULiège
Disciplines :
Aquatic sciences & oceanology
Author, co-author :
Prins, V.
Tedersoo, L.
Mikryukov, V.
Paiste, P.
Sepp, M.
Grossart, H.
Kisand, V.
Laas, A.
Tammert, H.
Abarenkov, Kessy
Agan, A.
Agasild, H.
Agha, R.
Alatalo, J.
Alvarez-Manjarrez, J.
Ameryk, A.
Anderson, J.
Anslan, S.
Antão-Geraldes, A.
Antosiak, A.
Funck, J. Arce
Arias-Real, R.
Ariyan, M.
Bahram, M.
Bansal, S.
Bao, R.
Beck, S.
Bernotas, P.
Berry, N.
Bertilsson, S.
Birnbaum, C.
Bonk, M.
Borges, Alberto ; Université de Liège - ULiège > Freshwater and OCeanic science Unit of reSearch (FOCUS)
Grossart H-P et al. Fungi in aquatic ecosystems Nat. Rev. Microbiol. 2019 17 339 354 10.1038/s41579-019-0175-8 30872817
Kagami M de Bruin A Ibelings BW Van Donk E Parasitic chytrids: their effects on phytoplankton communities and food-web dynamics Hydrobiologia 2007 578 113 129 2007HyBio.578.113K 10.1007/s10750-006-0438-z
Gulis, V., Su, R. & Kuehn, K. A. Fungal Decomposers in Freshwater Environments. in The Structure and Function of Aquatic Microbial Communities (ed. Hurst, C. J.) 121–155, https://doi.org/10.1007/978-3-030-16775-2_5 (Springer International Publishing, Cham, 2019).
Marins JFde Carrenho R Arbuscular mycorrhizal fungi and dark septate fungi in plants associated with aquatic environments Acta Bot. Bras. 2017 31 295 308 10.1590/0102-33062016abb0296
Thüs, H., Aptroot, A. & Seaward, M. R. D. Freshwater lichens. in Freshwater Fungi: and Fungal-like Organisms (eds. Jones, E. B. G., Hyde, K. D. & Pang, K.-L.) 333–358 (De Gruyter, 2014).
Grossart H-P Rojas-Jimenez K Aquatic fungi: targeting the forgotten in microbial ecology Curr. Opin. Microbiol. 2016 31 140 145 10.1016/j.mib.2016.03.016 27078576
Grossart H-P Wurzbacher C James TY Kagami M Discovery of dark matter fungi in aquatic ecosystems demands a reappraisal of the phylogeny and ecology of zoosporic fungi Fungal Ecol. 2016 19 28 38 10.1016/j.funeco.2015.06.004
Malosso, E. & Schoenlein-Crusius, I. H. An insight into the study methods of aquatic fungi. in Freshwater Mycology (eds. Bandh, S. A. & Shafi, S.) 229–246, https://doi.org/10.1016/B978-0-323-91232-7.00014-3 (Elsevier, 2022).
Franco-Duarte, R., Fernandes, I., Gulis, V., Cássio, F. & Pascoal, C. ITS rDNA Barcodes Clarify Molecular Diversity of Aquatic Hyphomycetes. Microorganisms 10, https://doi.org/10.3390/microorganisms10081569 (2022).
Jones EBG et al. An online resource for marine fungi Fungal Divers. 2019 96 347 433 10.1007/s13225-019-00426-5
Calabon M et al. an online platform for the taxonomic classification of freshwater fungi Asian J. Mycol. 2020 3 419 445 10.5943/ajom/3/1/14 www.freshwaterfungi.org10.5943/ajom/3/1/14
Van den Wyngaert S et al. ParAquaSeq, a Database of Ecologically Annotated rRNA Sequences Covering Zoosporic Parasites Infecting Aquatic Primary Producers in Natural and Industrial Systems Mol. Ecol. Resour. 2025 25 e14099 10.1111/1755-0998.14099 40087979 12225711
Panzer K et al. Identification of Habitat-Specific Biomes of Aquatic Fungal Communities Using a Comprehensive Nearly Full-Length 18S rRNA Dataset Enriched with Contextual Data PLOS ONE 2015 10 e0134377 10.1371/journal.pone.0134377 26226014 4520555
Tedersoo L Anslan S Towards PacBio-based pan-eukaryote metabarcoding using full-length ITS sequences Environ. Microbiol. Rep. 2019 11 659 668 10.1111/1758-2229.12776 31219680
Schoch CL et al. Nuclear ribosomal internal transcribed spacer (ITS) region as a universal DNA barcode marker for Fungi. Proc. Natl. Acad. Sci. 2012 109 6241 6246 2012PNAS.109.6241S 10.1073/pnas.1117018109 22454494 3341068
Tedersoo, L. et al. EUKARYOME: the rRNA gene reference database for identification of all eukaryotes. Database2024, https://doi.org/10.1093/database/baae043 (2024).
Panksep K Tedersoo L Tammert H Laas A Kisand V Sampling protocol for aquatic fungi from marine, river and lake water and sediment 2023 10.5281/zenodo.7875536 Zenodo
Panksep, K., Kisand, V., Tammert, H., Laas, A. & Tedersoo, L. FunAqua sampling protocol: standardized methods for fungal diversity assessment in aquatic ecosystems. https://doi.org/10.5281/zenodo.17750254 (2025).
Longmire, J. L., Maltbie, M., Baker, R. J. & Texas Tech University. Museum. Use of ‘Lysis Buffer’ in DNA Isolation and Its Implication for Museum Collections. (Lubbock, TX.: Museum of Texas Tech University, 1997).
Bruce, K. et al. A practical guide to DNA-based methods for biodiversity assessment. Adv. Books1, https://doi.org/10.3897/ab.e68634 (2021).
Tedersoo L et al. The Global Soil Mycobiome consortium dataset for boosting fungal diversity research Fungal Divers. 2021 111 573 588 10.1007/s13225-021-00493-7
Mikryukov V Anslan S Tedersoo L NextITS: a pipeline for metabarcoding eukaryotes with full-length ITS sequenced with PacBio 2025 10.5281/zenodo.15074882 Zenodo
Di Tommaso P et al. Nextflow enables reproducible computational workflows Nat. Biotechnol. 2017 35 316 319 10.1038/nbt.3820 28398311
Kurtzer, G. M., Sochat, V. & Bauer, M. W. Singularity: Scientific containers for mobility of compute. PLOS ONE 12, https://doi.org/10.1371/journal.pone.0177459 (2017).
Martin M Cutadapt removes adapter sequences from high-throughput sequencing reads EMBnet.journal 2011 17 10 12 10.14806/ej.17.1.200
Bengtsson-Palme J et al. Improved software detection and extraction of ITS1 and ITS2 from ribosomal ITS sequences of fungi and other eukaryotes for analysis of environmental sequencing data Methods Ecol. Evol. 2013 4 914 919 10.1111/2041-210X.12073
Nilsson RH et al. A Comprehensive, Automatically Updated Fungal ITS Sequence Dataset for Reference-Based Chimera Control in Environmental Sequencing Efforts Microbes Environ. 2015 30 145 150 10.1264/jsme2.ME14121 25786896 4462924 110.1264/jsme2.ME14121
Rognes, T., Flouri, T., Nichols, B., Quince, C. & Mahé, F. VSEARCH: a versatile open source tool for metagenomics. PeerJ 4, https://doi.org/10.7717/peerj.2584 (2016).
Edgar, R. C. UNCROSS2: identification of cross-talk in 16S rRNA OTU tables. 400762 Preprint at https://doi.org/10.1101/400762 (2018).
Edgar, R. C. UNOISE2: improved error-correction for Illumina 16S and ITS amplicon sequencing. 081257 Preprint at https://doi.org/10.1101/081257 (2016).
Hansen, H. P. & Koroleff, F. Determination of nutrients. in Methods of Seawater Analysis 159–228, https://doi.org/10.1002/9783527613984.ch10 (John Wiley & Sons, Ltd, 1999).
International Organization for Standardization. ISO 6878:2004. Water quality — Determination of phosphorus — Ammonium molybdate spectrometric method. Edition 2. (2004).
APHA, AWWA, and WEF. Standards Methods for the Examination of Water and Wastewater (1999).
International Organization for Standardization. ISO 11905-1:1997. (1997).
U.S. EPA. Method 3051A (SW-846): Microwave Assisted Acid Digestion of Sediments, Sludges, and Oils (2007).
Prins V FunAqua Consortium Panksep K FunAqua dataset of global fungal biodiversity in aquatic ecosystems 2026 10.5281/zenodo.20509884 Zenodo
ENA European Nucleotide Archive. https://identifiers.org/ena.embl:PRJEB104083 (2025).
Wieczorek, J. et al. Darwin Core: An Evolving Community-Developed Biodiversity Data Standard. PLOS ONE7, https://doi.org/10.1371/journal.pone.0029715 (2012).
Yilmaz P et al. Minimum information about a marker gene sequence (MIMARKS) and minimum information about any (x) sequence (MIxS) specifications Nat. Biotechnol. 2011 29 415 420 10.1038/nbt.1823 21552244 3367316
Abarenkov K et al. PlutoF—a Web Based Workbench for Ecological and Taxonomic Research, with an Online Implementation for Fungal ITS Sequences Evol. Bioinforma. Online 2010 6 189 196 10.4137/EBO.S6271
Duarte, S., Cássio, F., Pascoal, C. & Bärlocher, F. Taxa-area relationship of aquatic fungi on deciduous leaves. PLOS ONE 12, https://doi.org/10.1371/journal.pone.0181545 (2017).
Lepère, C. et al. Diversity, spatial distribution and activity of fungi in freshwater ecosystems. PeerJ7, https://doi.org/10.7717/peerj.6247 (2019).
Kettner MT Rojas-Jimenez K Oberbeckmann S Labrenz M Grossart H-P Microplastics alter composition of fungal communities in aquatic ecosystems Environ. Microbiol. 2017 19 4447 4459 10.1111/1462-2920.13891 28805294
Niskanen T et al. Pushing the Frontiers of Biodiversity Research: Unveiling the Global Diversity, Distribution, and Conservation of Fungi Annu. Rev. Environ. Resour. 2023 48 149 176 10.1146/annurev-environ-112621-090937
Hug LA et al. A roadmap for equitable reuse of public microbiome data Nat. Microbiol. 2025 10 2384 2395 10.1038/s41564-025-02116-2 41006832
