Global Spore Sampling Project: a global, standardized dataset of airborne fungal DNA
Citation
Abrego N, Ovaskainen O, Furneaux B, Babiy U, Bao T, Bässler C, Bazzano G, Bondarchuk S, Bonebrake T, Brennan G, Bret-Harte S, Cagnolo L, Cameron E, Chapurlat E, Creer S, D’Acqui L, de Vere N, Desprez-Loustau M, Dongmo M, Fisher B, Flores de Jesus M, Gilbert G, Griffith G, Gritsuk A, Gross A, Grudd H, Halme P, Hanna R, Hansen J, Hansen L, Hardwick B, Hebert P, Hegbe A, Hill S, Hogg I, Hultman J, Hyde K, Hynson N, Ivanova N, Jacobsen I, Karisto P, Kerdraon D, Knorre A, Krisai-Greilhuber I, Kurhinen J, Kuzmina M, Lecomte E, Lecomte N, Loaiza V, Lundin E, Meire A, Mešić A, Miettinen O, Monkhause N, Mortimer P, Müller J, Nilsson R H, Nonti P, Nordén B, Nordén J, Palorinne I, Pätsi S, Paz C, Pellikka P, Pereira D, Petch G, Pitkänen J, Popa F, Potter C, Purhonen J, Rafiq A, Raharinjanahary D, Rakos N, Rathnayaka A, Raundrup K, Rebriev Y, Rikkinen J, Rogers H, Rogovsky A, Roslin T, Rozhkov Y, Runnel K, Saarto A, Savchenko A, Schlegel M, Schmidt N, Seibold S, Skjøth C, Somervuo P, Stengel E, Sutyrina S, Syvänperä I, Tedersoo L, Timm J, Tipton L, Toju H, Uscka-Perzanowska M, van der Bank F H, van der Bank M, Vandenbrink B, Ventura S, Vignisson S, Wang X, Weisser W, Wijesinghe S, Wright S J, Yang C, Yorou N, Young A, Yu D, Zakharov E (2025). Global Spore Sampling Project: a global, standardized dataset of airborne fungal DNA. University of Jyväskylä - Department of Biological and Environmental Sciences. Occurrence dataset https://doi.org/10.15468/psyfjq accessed via GBIF.org on 2025-10-13.Description
Novel methods for sampling and characterizing biodiversity hold great promise for re-evaluating patterns of life across the planet. The sampling of airborne spores with a cyclone sampler, and the sequencing of their DNA, have been suggested as an efficient and well-calibrated tool for surveying fungal diversity across various environments. These data originate from the Global Spore Sampling Project, comprising 2,768 samples collected during two years at 47 outdoor locations across the world. Each sample represents fungal DNA extracted from 24 m3 of air. We applied a conservative bioinformatics pipeline that filtered out sequences that did not show strong evidence of representing a fungal species. The pipeline yielded 27,954 species-level operational taxonomic units (OTUs). Each OTU is accompanied by a probabilistic taxonomic classification, validated through comparison with expert evaluations. To examine the potential of the data for ecological analyses, we partitioned the variation in species distributions into spatial and seasonal components, showing a strong effect of the annual mean temperature on community composition.
[This dataset was processed using the GBIF Metabarcoding Data Toolkit.]
Sampling Description
Study Extent
A globally distributed network of 47 sampling sites collecting two 24-hr air samples per week over one to two years.Sampling
Each sampling site was equipped with a cyclone sampler (Burkard Cyclone Sampler for Field Operation, Burkard Manufacturing Co Ltd; http://burkard.co.uk/product/cyclone-sampler-for-field-operation). The sampling sites represent varying climatic zones and altitudes. Most sampling sites were located in natural environments, with a few in urban settings.Method steps
- Air DNA samples were acquired using cyclone samplers placed at ground level to ensure free airflow through the sampler. The cyclone sampler orientates itself in the direction of the wind and collects all particles from the air with a single reverse flow cyclone. The sampler collects particles with size >1 μm from the air directly into a sampling tube, including spores, pollen, bacteria, and small insects. The sampler's average air throughput is 16.5 liters per minute for a total of 23,800 liters during each 24-h sampling period. Sterile 1.5 ml Eppendorf vials were used as sampling tubes. After sampling, the vial was removed from the cyclone sampler, the lid was closed, and the vials were labeled with the site code and week number. Likewise, the time and duration of the sampling, as well as notes about the presence of rainwater or larger objects (e.g., arthropods), were recorded. Every week, two 24-h samples (henceforth called Sample A and Sample B) were collected from each site. To avoid contamination, gloves were used while handling the samples or the device. Sampling teams were instructed to clean the cyclone part of the device monthly with water and soap and to rinse it with ethanol, or to sterilize it with dry-heat, chlorine or UV when such equipment was available.
- The samples were stored at −20°C until they were shipped to the University of Helsinki, Finland. Shipping was at room temperature as the shipping time was relatively short and refrigerated transport would be costly. In Helsinki, visible arthropods were removed from the samples. To avoid losing fungal spores attached to the arthropod bodies, their surface was rinsed by adding sterile water into the sample tube and vortexing. After washing, the arthropods were removed with sterile tweezers. Samples with rainwater were dried in a freeze drier (24 h, −80°C, 0.57 mbar) covered with a porous Parafilm to avoid cross-contamination between samples. After drying, all samples were sent to the University of Guelph, Canada, for DNA extraction and sequencing.
- Upon receipt, each sample tube was accessioned and assigned a unique Process ID. DNA extraction followed Ivanova et al. (2008) with minor modifications. Two hundred seventy microlitre of ILB (700 mM GuSCN, 30 mM EDTA pH 8.0, 30 mM Tris–HCl pH 8.0, 0.5% Triton® X-100, 5% Tween-20) with 30 μl Proteinase K (20 mg/ml) was added to each collection tube before it was gently rotated to wash spores off the tube walls and lid, and the tube was then centrifuged at 11,000 g for 5 s. The resultant pellet was re-suspended by gentle pipetting, and the entire volume was transferred to a Lysing Matrix A tube (MP-BIO). Tissue was ground in a TissueLyser (Qiagen) for 2 min at 28 Hz. Samples were then incubated for 1 h at 56°C, followed by 1 h at 65°C. Lysates were transferred to a MN block containing 600 μl of 5M GuSCN Binding Buffer (5 M GuSCN, 16.66 mM EDTA pH 8.0, 8.33 mM Tris–HCl pH 6.4, 3.33% Triton® X-100), and the entire volume was transferred in two equal aliquots of 350 μl (each followed by centrifugation at 5,000 xg) onto AcroPrep 96 Filter Plates with 3.0 μm glass fiber media/0.2 μm Bio-Inert membrane, followed by two washes with WB buffer (60% ethanol, 50 mM NaCl, 10 mM Tris–HCl pH 7.4, 0.5 mM EDTA pH 8.0). DNA was eluted in 45 μl of 10 mM Tris-HCl pH 8.0.
Taxonomic Coverages
Fungi
-
Fungirank: kingdom
Geographic Coverages
Global
Bibliographic Citations
- Ovaskainen, Otso, et al. "Global Spore Sampling Project: A global, standardized dataset of airborne fungal DNA." Scientific data 11.1 (2024): 561. - DOI:https://doi.org/10.1038/s41597-024-03410-0
- Abrego, Nerea, et al. "Give me a sample of air and I will tell which species are found from your region: Molecular identification of fungi from airborne spore samples." Molecular ecology resources 18.3 (2018): 511-524. - DOI:https://doi.org/10.1111/1755-0998.12755
- Ovaskainen, Otso, et al. "Monitoring fungal communities with the global spore sampling project." Frontiers in Ecology and Evolution 7 (2020): 511. - DOI:https://doi.org/10.3389/fevo.2019.00511
- Abrego, Nerea, et al. "Airborne DNA reveals predictable spatial and seasonal dynamics of fungi." Nature 631.8022 (2024): 835-842. - DOI:https://doi.org/10.1038/s41586-024-07658-9
Contacts
Nerea Abregooriginator
position: Associate professor
University of Jyväskylä
Survontie 9
Jyväskylä
Central Finland
FI
Telephone: 358505052640
email: nerea.n.abrego-antia@jyu.fi
userId: http://orcid.org/0000-0001-6347-6127
Otso Ovaskainen
originator
position: Academy professor
University of Jyväskylä
Survontie 9
Jyväskylä
Central Finland
FI
Telephone: 358503092795
email: otso.t.ovaskainen@jyu.fi
userId: http://orcid.org/0000-0001-9750-4421
Brendan Furneaux
originator
position: Postdoctoral Researcher
University of Jyväskylä
Survontie 9
Jyväskylä
Central Finland
FI
Telephone: 358469225077
email: brendan.r.furneaux@jyu.fi
userId: http://orcid.org/0000-0003-3522-7363
Ulyana Babiy
originator
Wrangel Island State Nature Reserve
Pevek
RU
Tan Bao
originator
Department of Biological Sciences, MacEwan University
Edmonton
CA
Claus Bässler
originator
Goethe-University Frankfurt, Faculty of Biological Sciences, Institute for Ecology,Evolution and Diversity,Conservation Biology
D- 60438
Frankfurt am Main
DE
Gisela Bazzano
originator
Universidad Nacional de Còrdoba, Facultad de Ciencias Exactas Físicas y Naturales,Centro de Zoología Aplicada
Córdoba
AR
Svetlana Bondarchuk
originator
Sikhote-Alin State Nature Biosphere Reserve named after K. G. Abramov
44 Partizanskaya Str. 692150
Primorsky krai
RU
Timothy Bonebrake
originator
School of Biological Sciences, The University of Hong Kong
Hong Kong SAR
CN
Georgina Brennan
originator
CSIC,Institute of Marine Sciences, Passeig Marítim de la Barceloneta
37-49 ES08003
Barcelona
ES
Syndonia Bret-Harte
originator
Institute of Arctic Biology, University of Alaska
Fairbanks
US
Luciano Cagnolo
originator
Consejo de Investigaciones Científicas y Técnicas (CONICET), Instituto Multidisciplinario de Biología Vegetal
Córdoba
AR
Erin Cameron
originator
Department of Environmental Science, Saint Mary’s University
923 Robie St. B3H 3C3
Halifax
CA
Elodie Chapurlat
originator
Department of Ecology, Swedish University of Agricultural Sciences (SLU)
Uppsala
SE
Simon Creer
originator
Molecular Ecology and Evolution at Bangor (MEEB), School of Environmental and Natural Sciences, Bangor University, Environment Centre Wales
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Luigi D’Acqui
originator
Research Institute on Terrestrial Ecosystems - IRET, National Research Council - CNR
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IT
Natasha de Vere
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Natural History Museum of Denmark, University of Copenhagen
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København K
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INRAE, BIOGECO
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Michel Dongmo
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School of Biological Sciences, The University of Hong Kong
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Entomology, California Academy of Sciences
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Miguel Flores de Jesus
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Legado das Águas, Reserva Votorantin
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Environmental Studies Department, University of California
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Department of Life Sciences, Aberystwyth University
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Anna Gritsuk
originator
Sikhote-Alin State Nature Biosphere Reserve named after K. G. Abramov
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Andrin Gross
originator
Research Unit Biodiversity and Conservation Biology, SwissFungi, Swiss Federal Research Institute WSL
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Håkan Grudd
originator
Swedish Polar Research Secretariat, Abisko Scientific Research Station
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Panu Halme
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Department of Biological and Environmental Science, University of Jyväskylä
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Center for Tropical Research, Congo Basin Institute, University of California Los Angeles (UCLA)
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Department of Ecoscience, Aarhus University
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Roskilde
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Canadian High Arctic Research Station, Polar Knowledge Canada
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Centre for Biodiversity Genomics, University of Guelph
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Research Unit in Tropical Mycology and Plant-Soil Fungi Interactions, Faculty of Agronomy, University of Parakou
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Natural History Museum, Zoology, University of New England
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Department of Microbiology, University of Helsinki
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Kevin Hyde
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Center of Excellence in Fungal Research, Mae Fah Luang University
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TH
Nicole Hynson
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Pacific Biosciences Research Center, University of Hawaii at Manoa
Honolulu
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Natalia Ivanova
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Centre for Biodiversity Genomics, University of Guelph
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Greenland Institute of Natural Resources
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Plant Pathology Group, Institute of Integrative Biology
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Department of Ecology, Swedish University of Agricultural Sciences (SLU)
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Science Department, National Park Krasnoyarsk Stolby
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Department of Botany and Biodiversity Research, University of Vienna
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Organismal and Evolutionary Biology Research Programme, Faculty of Biological and Environmental Sciences, University of Helsinki
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Centre for Biodiversity Genomics, University of Guelph
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Centre d’études nordiques and Canada Research Chair in Polar and Boreal Ecology, Department of Biology
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Department of Evolutionary Biology and Environmental Sciences, University of Zürich
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Swedish Polar Research Secretariat, Abisko Scientific Research Station
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Laboratory for Biological Diversity, Rudjer Boskovic Institute
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Finnish Museum of Natural History, University of Helsinki
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Centre for Biodiversity Genomics, University of Guelph
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Centre for Mountain Futures, Kunming Institute of Botany, Chinese Academy of Sciences
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Field Station Fabrikschleichach, Department of Animal Ecology and Tropical Biology (Zoology III), Julius Maximilians University Würzburg
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Department of Biological and Environmental Sciences, Gothenburg Global Biodiversity Centre, University of Gothenburg
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Research Unit in Tropical Mycology and Plant-Soil Fungi Interactions, Faculty of Agronomy, University of Parakou
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Norwegian Institute for Nature Research (NINA)
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Norwegian Institute for Nature Research (NINA)
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Department of Agricultural Sciences, University of Helsinki
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The Biodiversity Unit of the University of Turku
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Department of Biodiversity,Institute of Biosciences, São Paulo State University
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Department of Geosciences and Geography, Faculty of Science,University of Helsinki
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Plant Pathology Group, Institute of Integrative Biology
Zurich
CH
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School of Science and the Environment, University of Worcester
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Worcester
GB
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Natural Resources Institute Finland
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Department of Ecosystem Monitoring, Research & Conservation, Black Forest National Park
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Department of Life Sciences, Aberystwyth University
GB
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Department of Biological and Environmental Science, University of Jyväskylä
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Abdullah Rafiq
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Molecular Ecology and Evolution at Bangor (MEEB), School of Environmental and Natural Sciences, Bangor University, Environment Centre Wales
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Madagascar Biodiversity Center, Parc Botanique et Zoologique de Tsimbazaza
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Swedish Polar Research Secretariat, Abisko Scientific Research Station
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Center of Excellence in Fungal Research, Mae Fah Luang University
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TH
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Greenland Institute of Natural Resources
Kivioq 2, P.O. Box 57 03900
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Southern Scientific Center of the Russian Academy of Sciences
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Organismal and Evolutionary Biology Research Programme, Faculty of Biological and Environmental Sciences, University of Helsinki
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Department of Ecology, Swedish University of Agricultural Sciences (SLU)
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Science Department, National Park Krasnoyarsk Stolby
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Organismal and Evolutionary Biology Research Programme, Faculty of Biological and Environmental Sciences, University of Helsinki
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State Nature Reserve Olekminsky,Olekminsk
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Mycology and Microbiology Center, University of Tartu
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The Biodiversity Unit of the University of Turku
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originator
Institute of Ecology and Earth Sciences, University of Tartu
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originator
Research Unit Biodiversity and Conservation Biology, SwissFungi, Swiss Federal Research Institute WSL
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Niels Schmidt
originator
Department of Ecoscience, Aarhus University
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TUD Dresden University of Technology, Forest Zoology
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School of Science and the Environment, University of Worcester
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Organismal and Evolutionary Biology Research Programme, Faculty of Biological and Environmental Sciences, University of Helsinki
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Field Station Fabrikschleichach, Department of Animal Ecology and Tropical Biology (Zoology III), Julius Maximilians University Würzburg
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DE
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originator
Sikhote-Alin State Nature Biosphere Reserve named after K. G. Abramov
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originator
The Biodiversity Unit of the University of Turku
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originator
Mycology and Microbiology Center, University of Tartu
Tartu
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originator
Institute of Arctic Biology, University of Alaska
Fairbanks
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originator
School of Natural Science and Mathematics, Chaminade University of Honolulu
Honolulu
US
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originator
Laboratory of Ecosystems and Coevolution, Graduate School of Biostudies, Kyoto University
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Kyoto
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Department of Ecology, Swedish University of Agricultural Sciences (SLU)
Uppsala
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originator
African Centre for DNA Barcoding (ACDB), University of Johannesburg
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originator
African Centre for DNA Barcoding (ACDB), University of Johannesburg
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originator
Canadian High Arctic Research Station, Polar Knowledge Canada
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originator
Research Institute on Terrestrial Ecosystems - IRET, National Research Council - CNR
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originator
Sudurnes Science and Learning Center
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originator
State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences
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originator
Technical University of Munich, Terrestrial Ecology Research Group, Department of Life Science Systems, School of Life Sciences
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Freising
DE
Subodini Wijesinghe
originator
Center of Excellence in Fungal Research, Mae Fah Luang University
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TH
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originator
Smithsonian Tropical Research Institute
Apartado 0843–03092
Balboa
PA
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originator
State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences
Kunming
CN
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originator
Research Unit in Tropical Mycology and Plant-Soil Fungi Interactions, Faculty of Agronomy, University of Parakou
BP 123
Parakou
BJ
Amanda Young
originator
Institute of Arctic Biology, University of Alaska
Fairbanks
US
Douglas Yu
originator
State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences
Kunming
CN
Evgeny Zakharov
originator
Centre for Biodiversity Genomics, University of Guelph
N1G 2W1
Guelph
CA
Brendan Furneaux
administrative point of contact
position: Postdoctoral Researcher
University of Jyväskylä
Survontie 9
Jyväskylä
Central Finland
FI
Telephone: +358469225077
email: brendan.r.furneaux@jyu.fi
userId: http://orcid.org/0000-0003-3522-7363