Global Spore Sampling Project: a global, standardized dataset of airborne fungal DNA

https://ipt.gbif.org/resource?r=tim-spores Global Spore Sampling Project: a global, standardized dataset of airborne fungal DNA Nerea Abrego University of Jyväskylä Associate professor

Survontie 9 Jyväskylä Central Finland FI

358505052640 nerea.n.abrego-antia@jyu.fi 0000-0001-6347-6127 Otso Ovaskainen University of Jyväskylä Academy professor

Survontie 9 Jyväskylä Central Finland FI

358503092795 otso.t.ovaskainen@jyu.fi 0000-0001-9750-4421 Brendan Furneaux University of Jyväskylä Postdoctoral Researcher

Survontie 9 Jyväskylä Central Finland FI

358469225077 brendan.r.furneaux@jyu.fi 0000-0003-3522-7363 Ulyana Babiy Wrangel Island State Nature Reserve

Pevek RU

Tan Bao Department of Biological Sciences, MacEwan University

Edmonton CA

Claus Bässler Goethe-University Frankfurt, Faculty of Biological Sciences, Institute for Ecology,Evolution and Diversity,Conservation Biology

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Gisela Bazzano Universidad Nacional de Còrdoba, Facultad de Ciencias Exactas Físicas y Naturales,Centro de Zoología Aplicada

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2025-07-08 eng 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.] metabarcoding DNA MDT N/A Occurrence GBIF Dataset Type Vocabulary: http://rs.gbif.org/vocabulary/gbif/dataset_type_2015-07-10.xml This work is licensed under a http://creativecommons.org/licenses/by/4.0/legalcode. https://zenodo.org/records/11125610 Global -178.48333 151.64079 78.92446 -32.72686 2018-05-07 2021-01-24 Fungi kingdom Fungi daily Brendan Furneaux University of Jyväskylä Postdoctoral Researcher

Survontie 9 Jyväskylä Central Finland FI

+358469225077 brendan.r.furneaux@jyu.fi 0000-0003-3522-7363 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. A globally distributed network of 47 sampling sites collecting two 24-hr air samples per week over one to two years. 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. Global Spore Sampling Project Nerea Abrego 0000-0001-6347-6127 PRINCIPAL_INVESTIGATOR Otso Ovaskainen 0000-0001-9750-4421 AUTHOR Brendan Furneaux 0000-0003-3522-7363 AUTHOR This study was supported by funding from Academy of Finland (grant no. 336212, 345110, 322266, 335354), the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (grant agreement No 856506; ERC-synergy project LIFEPLAN), EU Horizon 2020 project INTERACT, under grant agreements no. 730938 and 871120, Jane and Aatos Erkko Foundation, Research Council of Norway through its Centres of Excellence Funding Scheme (223257), Estonian Research Council (grant no. PRG1170, PRG632), FORMAS (grant no. 215-2011-498, 226-2014-1109), Polar Knowledge Canada, Natural Sciences and Engineering Research Council of Canada (NSERC Discovery grant to NL), Bruce McDonald, Natural Environment Research Council (NERC) U.K. (grant no. NE/N001710/1, NE/N002431/1), BBSRC (grant no. BB/L012286/1), Novo Nordisk Foundation (Project ID NNF22OC0071701), Austrian ministry of Science (the ABOL-HRSM project), municipality of Vienna (division Environmental protection), the Southern Scientific Centre RAS (project no. 122020100332-8), the Croatian Science Foundation under the project FunMed (grant no. HRZZ-IP-2022-10-5219), the US National Science Foundation (grant no. DEB-1655896, DEB-1655076, DEB-1932467), the Pepper-Giberson Chair Fund, the National Science Foundation of China (grant no. 41761144055, 41771063), Dirigibile Italia Station, Institute of Polar Science (ISP) - National Research Council (CNR), São Paulo Research Foundation (FAPESP 2016/25197-0) and Legado das Águas-Brazil, Hong Kong’s Research Grants Council (General Research Fund 17118317), the Norwegian Institute for Nature Research (NINA), the Canada Research Chair program, the International Institute of Tropical Agriculture, the Mushroom Research Foundation (MRF), Thailand, the Swedish Research Council’s support (grant no. 4.3-2021-00164) to SITES and Abisko Scientific Research Station, the Danish Environmental Protection Agency, and the Italian National Biodiversity Future Center (MUR-PNRR, Mission 4.2. Investment 1.4, Project CN00000033). 2025-07-08T10:24:35.000+00:00 dataset Ovaskainen, Otso, et al. "Global Spore Sampling Project: A global, standardized dataset of airborne fungal DNA." Scientific data 11.1 (2024): 561. 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. Ovaskainen, Otso, et al. "Monitoring fungal communities with the global spore sampling project." Frontiers in Ecology and Evolution 7 (2020): 511. Abrego, Nerea, et al. "Airborne DNA reveals predictable spatial and seasonal dynamics of fungi." Nature 631.8022 (2024): 835-842.