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

Otso Ovaskainen; Nerea Abrego; Brendan Furneaux; Bess Hardwick; Panu Somervuo; Isabella Palorinne; Nigel R. Andrew; Ulyana V. Babiy; Tan Bao; Gisela Bazzano; Svetlana N. Bondarchuk; Timothy C. Bonebrake; Georgina L. Brennan; Syndonia Bret-Harte; Claus Bässler; Luciano Cagnolo; Erin K. Cameron; Elodie Chapurlat; Simon Creer; Luigi P. D’Acqui; Natasha de Vere; Marie Laure Desprez-Loustau; Michel A.K. Dongmo; Ida B. Dyrholm Jacobsen; Brian L. Fisher; Miguel Flores de Jesus; Gregory S. Gilbert; Gareth W. Griffith; Anna A. Gritsuk; Andrin Gross; Håkan Grudd; Panu Halme; Rachid Hanna; Jannik Hansen; Lars Holst Hansen; Apollon D.M.T. Hegbe; Sarah Hill; Ian D. Hogg; Jenni Hultman; Kevin D. Hyde; Nicole A. Hynson; Natalia Ivanova; Petteri Karisto; Deirdre Kerdraon; Anastasia Knorre; Irmgard Krisai-Greilhuber; Juri Kurhinen; Masha Kuzmina; Nicolas Lecomte; Erin Lecomte; Viviana Loaiza; Erik Lundin; Alexander Meire; Armin Mešić; Otto Miettinen; Norman Monkhause; Peter Mortimer; Jörg Müller; R. Henrik Nilsson; Puani Yannick C. Nonti; Jenni Nordén; Björn Nordén; Claudia Paz; Petri Pellikka; Danilo Pereira; Geoff Petch; Juha Matti Pitkänen; Flavius Popa; Caitlin Potter; Jenna Purhonen; Sanna Pätsi; Abdullah Rafiq; Dimby Raharinjanahary; Niklas Rakos; Achala R. Rathnayaka; Katrine Raundrup; Yury A. Rebriev; Jouko Rikkinen; Hanna M.K. Rogers; Andrey Rogovsky; Yuri Rozhkov; Kadri Runnel; Annika Saarto; Anton Savchenko; Markus Schlegel; Niels Martin Schmidt; Sebastian Seibold; Carsten Skjøth; Elisa Stengel; Svetlana V. Sutyrina; Ilkka Syvänperä; Leho Tedersoo; Jebidiah Timm; Laura Tipton; Hirokazu Toju; Maria Uscka-Perzanowska; Michelle van der Bank; F. Herman van der Bank; Bryan Vandenbrink; Stefano Ventura; Solvi R. Vignisson; Xiaoyang Wang; Wolfgang W. Weisser; Subodini N. Wijesinghe; S. Joseph Wright; Chunyan Yang; Nourou S. Yorou; Amanda Young; Douglas W. Yu; Evgeny V. Zakharov; Paul D.N. Hebert; Tomas Roslin

doi:10.1038/s41597-024-03410-0

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

Otso Ovaskainen (Corresponding author)
, Nerea Abrego
, Brendan Furneaux
, Bess Hardwick
, Panu Somervuo
, Isabella Palorinne
, Nigel R. Andrew
, Ulyana V. Babiy
, Tan Bao
, Gisela Bazzano
, Svetlana N. Bondarchuk
, Timothy C. Bonebrake
, Georgina L. Brennan
, Syndonia Bret-Harte
, Claus Bässler
, Luciano Cagnolo
, Erin K. Cameron
, Elodie Chapurlat
, Simon Creer
, Luigi P. D’Acqui

Natasha de Vere, Marie Laure Desprez-Loustau, Michel A.K. Dongmo, Ida B. Dyrholm Jacobsen, Brian L. Fisher, Miguel Flores de Jesus, Gregory S. Gilbert, Gareth W. Griffith, Anna A. Gritsuk, Andrin Gross, Håkan Grudd, Panu Halme, Rachid Hanna, Jannik Hansen, Lars Holst Hansen, Apollon D.M.T. Hegbe, Sarah Hill, Ian D. Hogg, Jenni Hultman, Kevin D. Hyde, Nicole A. Hynson, Natalia Ivanova, Petteri Karisto, Deirdre Kerdraon, Anastasia Knorre, Irmgard Krisai-Greilhuber, Juri Kurhinen, Masha Kuzmina, Nicolas Lecomte, Erin Lecomte, Viviana Loaiza, Erik Lundin, Alexander Meire, Armin Mešić, Otto Miettinen, Norman Monkhause, Peter Mortimer, Jörg Müller, R. Henrik Nilsson, Puani Yannick C. Nonti, Jenni Nordén, Björn Nordén, Claudia Paz, Petri Pellikka, Danilo Pereira, Geoff Petch, Juha Matti Pitkänen, Flavius Popa, Caitlin Potter, Jenna Purhonen, Sanna Pätsi, Abdullah Rafiq, Dimby Raharinjanahary, Niklas Rakos, Achala R. Rathnayaka, Katrine Raundrup, Yury A. Rebriev, Jouko Rikkinen, Hanna M.K. Rogers, Andrey Rogovsky, Yuri Rozhkov, Kadri Runnel, Annika Saarto, Anton Savchenko, Markus Schlegel, Niels Martin Schmidt, Sebastian Seibold, Carsten Skjøth, Elisa Stengel, Svetlana V. Sutyrina, Ilkka Syvänperä, Leho Tedersoo, Jebidiah Timm, Laura Tipton, Hirokazu Toju, Maria Uscka-Perzanowska, Michelle van der Bank, F. Herman van der Bank, Bryan Vandenbrink, Stefano Ventura, Solvi R. Vignisson, Xiaoyang Wang, Wolfgang W. Weisser, Subodini N. Wijesinghe, S. Joseph Wright, Chunyan Yang, Nourou S. Yorou, Amanda Young, Douglas W. Yu, Evgeny V. Zakharov, Paul D.N. Hebert, Tomas Roslin

Department of Botany and Biodiversity Research

Publications: Contribution to journal › Article › Peer Reviewed

Abstract

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. Here we present data originating 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.

Original language	English
Article number	561
Number of pages	17
Journal	Scientific Data
Volume	11
Issue number	1
DOIs	https://doi.org/10.1038/s41597-024-03410-0
Publication status	Published - 30 May 2024

Funding

We acknowledge Hanna Aho, Julian Frietsch, Tuomas Kankaanp\u00E4\u00E4, Janne Koskinen, Terrance McDermott, Evgeniy Meyke, Mwadime Mjomba, Pascal A. Niklaus, T\u00E4he Helk Rosenvald, Gilles Saint-Jean, Mikko Tiusanen, Helena Wirta, Veronika Zengerer, and several UCSC students for their contributions in data sampling and for many kinds of technical assistance. 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\u2019s 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), S\u00E3o Paulo Research Foundation (FAPESP 2016/25197-0) and Legado das \u00C1guas-Brazil, Hong Kong\u2019s 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\u2019s 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).

Austrian Fields of Science 2012

106024 Mycology

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10.1038/s41597-024-03410-0Licence: CC BY 4.0

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Ovaskainen, O., Abrego, N., Furneaux, B., Hardwick, B., Somervuo, P., Palorinne, I., Andrew, N. R., Babiy, U. V., Bao, T., Bazzano, G., Bondarchuk, S. N., Bonebrake, T. C., Brennan, G. L., Bret-Harte, S., Bässler, C., Cagnolo, L., Cameron, E. K., Chapurlat, E., Creer, S., ... Roslin, T. (2024). Global Spore Sampling Project: A global, standardized dataset of airborne fungal DNA. Scientific Data, 11(1), Article 561. https://doi.org/10.1038/s41597-024-03410-0

@article{b078be5b67d04234aed158c4fbe1c30b,

title = "Global Spore Sampling Project: A global, standardized dataset of airborne fungal DNA",

abstract = "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. Here we present data originating 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.",

author = "Otso Ovaskainen and Nerea Abrego and Brendan Furneaux and Bess Hardwick and Panu Somervuo and Isabella Palorinne and Andrew, \{Nigel R.\} and Babiy, \{Ulyana V.\} and Tan Bao and Gisela Bazzano and Bondarchuk, \{Svetlana N.\} and Bonebrake, \{Timothy C.\} and Brennan, \{Georgina L.\} and Syndonia Bret-Harte and Claus B{\"a}ssler and Luciano Cagnolo and Cameron, \{Erin K.\} and Elodie Chapurlat and Simon Creer and D{\textquoteright}Acqui, \{Luigi P.\} and \{de Vere\}, Natasha and Desprez-Loustau, \{Marie Laure\} and Dongmo, \{Michel A.K.\} and \{Dyrholm Jacobsen\}, \{Ida B.\} and Fisher, \{Brian L.\} and \{Flores de Jesus\}, Miguel and Gilbert, \{Gregory S.\} and Griffith, \{Gareth W.\} and Gritsuk, \{Anna A.\} and Andrin Gross and H{\aa}kan Grudd and Panu Halme and Rachid Hanna and Jannik Hansen and Hansen, \{Lars Holst\} and Hegbe, \{Apollon D.M.T.\} and Sarah Hill and Hogg, \{Ian D.\} and Jenni Hultman and Hyde, \{Kevin D.\} and Hynson, \{Nicole A.\} and Natalia Ivanova and Petteri Karisto and Deirdre Kerdraon and Anastasia Knorre and Irmgard Krisai-Greilhuber and Juri Kurhinen and Masha Kuzmina and Nicolas Lecomte and Erin Lecomte and Viviana Loaiza and Erik Lundin and Alexander Meire and Armin Me{\v s}i{\'c} and Otto Miettinen and Norman Monkhause and Peter Mortimer and J{\"o}rg M{\"u}ller and Nilsson, \{R. Henrik\} and Nonti, \{Puani Yannick C.\} and Jenni Nord{\'e}n and Bj{\"o}rn Nord{\'e}n and Claudia Paz and Petri Pellikka and Danilo Pereira and Geoff Petch and Pitk{\"a}nen, \{Juha Matti\} and Flavius Popa and Caitlin Potter and Jenna Purhonen and Sanna P{\"a}tsi and Abdullah Rafiq and Dimby Raharinjanahary and Niklas Rakos and Rathnayaka, \{Achala R.\} and Katrine Raundrup and Rebriev, \{Yury A.\} and Jouko Rikkinen and Rogers, \{Hanna M.K.\} and Andrey Rogovsky and Yuri Rozhkov and Kadri Runnel and Annika Saarto and Anton Savchenko and Markus Schlegel and Schmidt, \{Niels Martin\} and Sebastian Seibold and Carsten Skj{\o}th and Elisa Stengel and Sutyrina, \{Svetlana V.\} and Ilkka Syv{\"a}nper{\"a} and Leho Tedersoo and Jebidiah Timm and Laura Tipton and Hirokazu Toju and Maria Uscka-Perzanowska and \{van der Bank\}, Michelle and \{Herman van der Bank\}, F. and Bryan Vandenbrink and Stefano Ventura and Vignisson, \{Solvi R.\} and Xiaoyang Wang and Weisser, \{Wolfgang W.\} and Wijesinghe, \{Subodini N.\} and \{Joseph Wright\}, S. and Chunyan Yang and Yorou, \{Nourou S.\} and Amanda Young and Yu, \{Douglas W.\} and Zakharov, \{Evgeny V.\} and Hebert, \{Paul D.N.\} and Tomas Roslin",

note = "Publisher Copyright: {\textcopyright} The Author(s) 2024.",

year = "2024",

month = may,

day = "30",

doi = "10.1038/s41597-024-03410-0",

language = "English",

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issn = "2052-4463",

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Ovaskainen, O, Abrego, N, Furneaux, B, Hardwick, B, Somervuo, P, Palorinne, I, Andrew, NR, Babiy, UV, Bao, T, Bazzano, G, Bondarchuk, SN, Bonebrake, TC, Brennan, GL, Bret-Harte, S, Bässler, C, Cagnolo, L, Cameron, EK, Chapurlat, E, Creer, S, D’Acqui, LP, de Vere, N, Desprez-Loustau, ML, Dongmo, MAK, Dyrholm Jacobsen, IB, Fisher, BL, Flores de Jesus, M, Gilbert, GS, Griffith, GW, Gritsuk, AA, Gross, A, Grudd, H, Halme, P, Hanna, R, Hansen, J, Hansen, LH, Hegbe, ADMT, Hill, S, Hogg, ID, Hultman, J, Hyde, KD, Hynson, NA, Ivanova, N, Karisto, P, Kerdraon, D, Knorre, A, Krisai-Greilhuber, I, Kurhinen, J, Kuzmina, M, Lecomte, N, Lecomte, E, Loaiza, V, Lundin, E, Meire, A, Mešić, A, Miettinen, O, Monkhause, N, Mortimer, P, Müller, J, Nilsson, RH, Nonti, PYC, Nordén, J, Nordén, B, Paz, C, Pellikka, P, Pereira, D, Petch, G, Pitkänen, JM, Popa, F, Potter, C, Purhonen, J, Pätsi, S, Rafiq, A, Raharinjanahary, D, Rakos, N, Rathnayaka, AR, Raundrup, K, Rebriev, YA, Rikkinen, J, Rogers, HMK, Rogovsky, A, Rozhkov, Y, Runnel, K, Saarto, A, Savchenko, A, Schlegel, M, Schmidt, NM, Seibold, S, Skjøth, C, Stengel, E, Sutyrina, SV, Syvänperä, I, Tedersoo, L, Timm, J, Tipton, L, Toju, H, Uscka-Perzanowska, M, van der Bank, M, Herman van der Bank, F, Vandenbrink, B, Ventura, S, Vignisson, SR, Wang, X, Weisser, WW, Wijesinghe, SN, Joseph Wright, S, Yang, C, Yorou, NS, Young, A, Yu, DW, Zakharov, EV, Hebert, PDN & Roslin, T 2024, 'Global Spore Sampling Project: A global, standardized dataset of airborne fungal DNA', Scientific Data, vol. 11, no. 1, 561. https://doi.org/10.1038/s41597-024-03410-0

TY - JOUR

T1 - Global Spore Sampling Project

T2 - A global, standardized dataset of airborne fungal DNA

AU - Ovaskainen, Otso

AU - Abrego, Nerea

AU - Furneaux, Brendan

AU - Hardwick, Bess

AU - Somervuo, Panu

AU - Palorinne, Isabella

AU - Andrew, Nigel R.

AU - Babiy, Ulyana V.

AU - Bao, Tan

AU - Bazzano, Gisela

AU - Bondarchuk, Svetlana N.

AU - Bonebrake, Timothy C.

AU - Brennan, Georgina L.

AU - Bret-Harte, Syndonia

AU - Bässler, Claus

AU - Cagnolo, Luciano

AU - Cameron, Erin K.

AU - Chapurlat, Elodie

AU - Creer, Simon

AU - D’Acqui, Luigi P.

AU - de Vere, Natasha

AU - Desprez-Loustau, Marie Laure

AU - Dongmo, Michel A.K.

AU - Dyrholm Jacobsen, Ida B.

AU - Fisher, Brian L.

AU - Flores de Jesus, Miguel

AU - Gilbert, Gregory S.

AU - Griffith, Gareth W.

AU - Gritsuk, Anna A.

AU - Gross, Andrin

AU - Grudd, Håkan

AU - Halme, Panu

AU - Hanna, Rachid

AU - Hansen, Jannik

AU - Hansen, Lars Holst

AU - Hegbe, Apollon D.M.T.

AU - Hill, Sarah

AU - Hogg, Ian D.

AU - Hultman, Jenni

AU - Hyde, Kevin D.

AU - Hynson, Nicole A.

AU - Ivanova, Natalia

AU - Karisto, Petteri

AU - Kerdraon, Deirdre

AU - Knorre, Anastasia

AU - Krisai-Greilhuber, Irmgard

AU - Kurhinen, Juri

AU - Kuzmina, Masha

AU - Lecomte, Nicolas

AU - Lecomte, Erin

AU - Loaiza, Viviana

AU - Lundin, Erik

AU - Meire, Alexander

AU - Mešić, Armin

AU - Miettinen, Otto

AU - Monkhause, Norman

AU - Mortimer, Peter

AU - Müller, Jörg

AU - Nilsson, R. Henrik

AU - Nonti, Puani Yannick C.

AU - Nordén, Jenni

AU - Nordén, Björn

AU - Paz, Claudia

AU - Pellikka, Petri

AU - Pereira, Danilo

AU - Petch, Geoff

AU - Pitkänen, Juha Matti

AU - Popa, Flavius

AU - Potter, Caitlin

AU - Purhonen, Jenna

AU - Pätsi, Sanna

AU - Rafiq, Abdullah

AU - Raharinjanahary, Dimby

AU - Rakos, Niklas

AU - Rathnayaka, Achala R.

AU - Raundrup, Katrine

AU - Rebriev, Yury A.

AU - Rikkinen, Jouko

AU - Rogers, Hanna M.K.

AU - Rogovsky, Andrey

AU - Rozhkov, Yuri

AU - Runnel, Kadri

AU - Saarto, Annika

AU - Savchenko, Anton

AU - Schlegel, Markus

AU - Schmidt, Niels Martin

AU - Seibold, Sebastian

AU - Skjøth, Carsten

AU - Stengel, Elisa

AU - Sutyrina, Svetlana V.

AU - Syvänperä, Ilkka

AU - Tedersoo, Leho

AU - Timm, Jebidiah

AU - Tipton, Laura

AU - Toju, Hirokazu

AU - Uscka-Perzanowska, Maria

AU - van der Bank, Michelle

AU - Herman van der Bank, F.

AU - Vandenbrink, Bryan

AU - Ventura, Stefano

AU - Vignisson, Solvi R.

AU - Wang, Xiaoyang

AU - Weisser, Wolfgang W.

AU - Wijesinghe, Subodini N.

AU - Joseph Wright, S.

AU - Yang, Chunyan

AU - Yorou, Nourou S.

AU - Young, Amanda

AU - Yu, Douglas W.

AU - Zakharov, Evgeny V.

AU - Hebert, Paul D.N.

AU - Roslin, Tomas

PY - 2024/5/30

Y1 - 2024/5/30

N2 - 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. Here we present data originating 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.

AB - 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. Here we present data originating 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.

UR - https://www.scopus.com/pages/publications/85194993972

U2 - 10.1038/s41597-024-03410-0

DO - 10.1038/s41597-024-03410-0

M3 - Article

C2 - 38816458

AN - SCOPUS:85194993972

SN - 2052-4463

VL - 11

JO - Scientific Data

JF - Scientific Data

IS - 1

M1 - 561

ER -

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

Abstract

Funding

Austrian Fields of Science 2012

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