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1. 20 years of bibliometric data illustrates a lack of concordance between journal impact factor and fungal species discovery in systematic mycology

Author

R. Henrik Nilsson, Arnold Tobias Jansson, Christian Wurzbacher, Sten Anslan, Pauline Belford, Natàlia Corcoll, Alexandra Dombrowski, Masoomeh Ghobad-Nejhad, Mikael Gustavsson, Daniela Gómez-Martínez, Faheema Kalsoom Khan, Maryia Khomich, Charlotte Lennartsdotter, David Lund, Breyten Van Der Merwe, Vladimir Mikryukov, Marko Peterson, Teresita M. Porter, Sergei Põlme, Alice Retter, Marisol Sanchez-Garcia, Sten Svantesson, Patrik Svedberg, Duong Vu, Martin Ryberg, Kessy Abarenkov, and Erik Kristiansson

Subjects
Botany, QK1-989
Abstract

Journal impact factors were devised to qualify and compare university library holdings but are frequently repurposed for use in ranking applications, research papers, and even individual applicants in mycology and beyond. The widely held assumption that mycological studies published in journals with high impact factors add more to systematic mycology than studies published in journals without high impact factors nevertheless lacks evidential underpinning. The present study uses the species hypothesis system of the UNITE database for molecular identification of fungi and other eukaryotes to trace the publication history and impact factor of sequences uncovering new fungal species hypotheses. The data show that journal impact factors are poor predictors of discovery potential in systematic mycology. There is no clear relationship between journal impact factor and the discovery of new species hypotheses for the years 2000–2021. On the contrary, we found journals with low, and even no, impact factor to account for substantial parts of the species hypothesis landscape, often discovering new fungal taxa that are only later picked up by journals with high impact factors. Funding agencies and hiring committees that insist on upholding journal impact factors as a central funding and recruitment criterion in systematic mycology should consider using indicators such as research quality, productivity, outreach activities, review services for scientific journals, and teaching ability directly rather than using publication in high impact factor journals as a proxy for these indicators.

Published
2024
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3. Towards a unified paradigm for sequence-based identification of Fungi

Author

R. Henrik Nilsson, Gareth W. Griffith, Ave Suija, Urmas Kõljalg, James A. Scott, Thomas D. Bruns, Margarita Dueñas, M. Teresa Telleria, D. Lee Taylor, Robert Lücking, Michael Weiss, Tiia Drenkhan, María P. Martín, Leho Tedersoo, Kabir G. Peay, Tony M. Callaghan, Kessy Abarenkov, Ursula Eberhardt, Ellen Larsson, Paul M. Kirk, Irja Saar, Nhu H. Nguyen, Mohammad Bahram, Martin Hartmann, Andy F. S. Taylor, Tine Grebenc, Johan Bengtsson-Palme, Marko Peterson, Ursula Peintner, Karl-Henrik Larsson, Jane Oja, Arthur Schüßler, Scott T. Bates, Lauri Saag, Carolina Senés, Brian Douglas, Tuula Niskanen, Matthew E. Smith, Björn D. Lindahl, P. Brandon Matheny, Kadri Põldmaa, Petr Kohout, North European Forest Mycologists (Denmark), and Estonian Research Council

Subjects
0106 biological sciences, Microbial diversity, Bioinformatics, mycorrhiza, Computational biology, Biology, Barcode, 01 natural sciences, DNA barcoding, law.invention, 03 medical and health sciences, Annotation, Type (biology), law, DNK barcoding, DNA, Ribosomal Spacer, Genetics, DNA Barcoding, Taxonomic, Internal transcribed spacer, forest ecology, DNA, Fungal, FORESTRY, Ecology, Evolution, Behavior and Systematics, Phylogeny, 030304 developmental biology, Sequence (medicine), 0303 health sciences, Internet, glive, Fungi, 15. Life on land, Accession number (bioinformatics), udc:574.1, bioinformatika, Ecological genomics, ekološka genomika, mikrobna pestrost, Identification (biology), Databases, Nucleic Acid, 010606 plant biology & botany
Abstract

Kõljalg, Urmas et al., The nuclear ribosomal internal transcribed spacer (ITS) region is the formal fungal barcode and in most cases the marker of choice for the exploration of fungal diversity in environmental samples. Two problems are particularly acute in the pursuit of satisfactory taxonomic assignment of newly generated ITS sequences: (i) the lack of an inclusive, reliable public reference data set and (ii) the lack of means to refer to fungal species, for which no Latin name is available in a standardized stable way. Here, we report on progress in these regards through further development of the UNITE database (http://unite.ut.ee) for molecular identification of fungi. All fungal species represented by at least two ITS sequences in the international nucleotide sequence databases are now given a unique, stable name of the accession number type (e.g. Hymenoscyphus pseudoalbidus|GU586904|SH133781.05FU), and their taxonomic and ecological annotations were corrected as far as possible through a distributed, third-party annotation effort. We introduce the term ‘species hypothesis’ (SH) for the taxa discovered in clustering on different similarity thresholds (97–99%). An automatically or manually designated sequence is chosen to represent each such SH. These reference sequences are released (http://unite.ut.ee/repository.php) for use by the scientific community in, for example, local sequence similarity searches and in the QIIME pipeline. The system and the data will be updated automatically as the number of public fungal ITS sequences grows. We invite everybody in the position to improve the annotation or metadata associated with their particular fungal lineages of expertise to do so through the new Web-based sequence management system in UNITE., The North European Forest Mycologists network is acknowledged for support. Urmas Kõljalg and Kessy Abarenkov are supported by the Estonian Research Council grant no 8235.

Published
2017

4. Fungal biogeography. Global diversity and geography of soil fungi

Author

Leho, Tedersoo, Mohammad, Bahram, Sergei, Põlme, Urmas, Kõljalg, Nourou S, Yorou, Ravi, Wijesundera, Luis, Villarreal Ruiz, Aída M, Vasco-Palacios, Pham Quang, Thu, Ave, Suija, Matthew E, Smith, Cathy, Sharp, Erki, Saluveer, Alessandro, Saitta, Miguel, Rosas, Taavi, Riit, David, Ratkowsky, Karin, Pritsch, Kadri, Põldmaa, Meike, Piepenbring, Cherdchai, Phosri, Marko, Peterson, Kaarin, Parts, Kadri, Pärtel, Eveli, Otsing, Eduardo, Nouhra, André L, Njouonkou, R Henrik, Nilsson, Luis N, Morgado, Jordan, Mayor, Tom W, May, Luiza, Majuakim, D Jean, Lodge, Su See, Lee, Karl-Henrik, Larsson, Petr, Kohout, Kentaro, Hosaka, Indrek, Hiiesalu, Terry W, Henkel, Helery, Harend, Liang-dong, Guo, Alina, Greslebin, Gwen, Grelet, Jozsef, Geml, Genevieve, Gates, William, Dunstan, Chris, Dunk, Rein, Drenkhan, John, Dearnaley, André, De Kesel, Tan, Dang, Xin, Chen, Franz, Buegger, Francis Q, Brearley, Gregory, Bonito, Sten, Anslan, Sandra, Abell, and Kessy, Abarenkov

Subjects
Soil, Geography, Fungi, DNA Barcoding, Taxonomic, Forests, Grassland, Tundra, Soil Microbiology
Abstract

Fungi play major roles in ecosystem processes, but the determinants of fungal diversity and biogeographic patterns remain poorly understood. Using DNA metabarcoding data from hundreds of globally distributed soil samples, we demonstrate that fungal richness is decoupled from plant diversity. The plant-to-fungus richness ratio declines exponentially toward the poles. Climatic factors, followed by edaphic and spatial variables, constitute the best predictors of fungal richness and community composition at the global scale. Fungi show similar latitudinal diversity gradients to other organisms, with several notable exceptions. These findings advance our understanding of global fungal diversity patterns and permit integration of fungi into a general macroecological framework.

Published
2014

5. Global diversity and geography of soil fungi

Author

Leho Tedersoo, Mohammad Bahram, Sergei Põlme, Urmas gKõljal, Nourou S. Yorou, Ravi Wijesundera, Luis Villarreal Ruiz, Aída M, Vasco-Palacios, Pham Quang Thu, Ave Suija, Matthew E. Smith, Sharp, Cathy, Erki Saluveer, Alessandro Saitta, Miguel Rosas, Taavi Riit, David Ratkowsky, Karin Pritsch, Kadri Põldmaa, Meike Piepenbring, Cherdchai Phosri, Marko Peterson, Kaarin Parts, Kadri Pärtel, Eveli Otsing, Eduardo Nouhra, André L. Njouonkou, R. Henrik Nilsson, Luis N. Morgado, Jordan Mayor, Tom W. May, Luiza Majuakim, D. Jean Lodge, Su, See Lee, Karl-Henrik Larsson, Petr Kohout, Kentaro, Hosaka, Indrek Hiiesalu, Terry W. Henkel, Helery Harend, Guo, Liang-dong, Alina Greslebin, Gwen Grelet, Jozsef Geml, Genevieve Gates, Dunstan, William, Dunk, Chris, Rein Drenkhan, Dearnaley, John, André De Kesel, Tan Dang, Xin Chen, Franz Buegger, Brearley, Francis Q., Bonito, Gregory, Sten Anslan, Abell, Sandra, Kessy Abarenkov, Leho Tedersoo, Mohammad Bahram, Sergei Põlme, Urmas gKõljal, Nourou S. Yorou, Ravi Wijesundera, Luis Villarreal Ruiz, Aída M, Vasco-Palacios, Pham Quang Thu, Ave Suija, Matthew E. Smith, Sharp, Cathy, Erki Saluveer, Alessandro Saitta, Miguel Rosas, Taavi Riit, David Ratkowsky, Karin Pritsch, Kadri Põldmaa, Meike Piepenbring, Cherdchai Phosri, Marko Peterson, Kaarin Parts, Kadri Pärtel, Eveli Otsing, Eduardo Nouhra, André L. Njouonkou, R. Henrik Nilsson, Luis N. Morgado, Jordan Mayor, Tom W. May, Luiza Majuakim, D. Jean Lodge, Su, See Lee, Karl-Henrik Larsson, Petr Kohout, Kentaro, Hosaka, Indrek Hiiesalu, Terry W. Henkel, Helery Harend, Guo, Liang-dong, Alina Greslebin, Gwen Grelet, Jozsef Geml, Genevieve Gates, Dunstan, William, Dunk, Chris, Rein Drenkhan, Dearnaley, John, André De Kesel, Tan Dang, Xin Chen, Franz Buegger, Brearley, Francis Q., Bonito, Gregory, Sten Anslan, Abell, Sandra, and Kessy Abarenkov

Abstract

Fungi play major roles in ecosystem processes, but the determinants of fungal diversity and biogeographic patterns remain poorly understood. Using DNA metabarcoding data from hundreds of globally distributed soil samples, we demonstrate that fungal richness is decoupled from plant diversity. The plant-to-fungus richness ratio declines exponentially toward the poles. Climatic factors, followed by edaphic and spatial variables, constitute the best predictors of fungal richness and community composition at the global scale. Fungi show similar latitudinal diversity gradients to other organisms, with several notable exceptions. These findings advance our understanding of global fungal diversity patterns and permit integration of fungi into a general macroecological framework.

Published
2014

6. Global diversity and geography of soil fungi

Author

R. Henrik Nilsson, Luis Villarreal Ruiz, Sandra E. Abell, Helery Harend, André Ledoux Njouonkou, Sergei Põlme, Luiza Majuakim, Jordan R. Mayor, Karin Pritsch, Kentaro Hosaka, Gregory Bonito, Rein Drenkhan, Cherdchai Phosri, John Dearnaley, Tan Dang, Nourou S. Yorou, József Geml, Su S ee Lee, Xin Chen, D. Jean Lodge, Leho Tedersoo, Kessy Abarenkov, Francis Q. Brearley, Miguel Rosas, Meike Piepenbring, Alessandro Saitta, Marko Peterson, Urmas Kõljalg, Eveli Otsing, Kadri Põldmaa, Sten Anslan, Terry W. Henkel, Franz Buegger, Genevieve Gates, Karl-Henrik Larsson, Cathy Sharp, Taavi Riit, Aída M. Vasco-Palacios, Luis N. Morgado, Eduardo Nouhra, Matthew E. Smith, Ravi L. C. Wijesundera, Chris W. Dunk, Ave Suija, André De Kesel, Gwen Grelet, Kaarin Parts, Liang-Dong Guo, Tom W. May, Pham Q uang Thu, Erki Saluveer, Petr Kohout, Kadri Pärtel, W. Dunstan, Alina Greslebin, Indrek Hiiesalu, Mohammad Bahram, David A. Ratkowsky, Tedersoo, L, Bahram, M, Põlme, S, Kõljalg, U, Yorou, NS, Wijesundera, R, Villareal Ruiz, L, Vasco-Palacios, AM, Quang Thu, P, Suija, A, Smith, ME, Sharp, C, Saluveer, E, Saitta, A, Rosas, M, Riit, T, Ratkowsky, D, Pritsch, K, Põldma, K, Piepenbring, M, Phosri, C, Peterson, M, Parts, K, Pärtel, K, Otsing, E, Nouhra, E, Njouonkou, A L, Nilsson, RH, Morgado, LN, Mayor, J, May, TW, Majuakim, L, Lodge, DJ, Lee, SS, Larsson, K-H, Kohout, P, Hosaka, K, Hiiesalu, I, Henkel, TW, Harend, H, Guo, L-d, Greslebin, A, Grelet, G, Geml, J, Gates, G, Dunstan, W, Dunk, C, Drenkhan, R, Dearnaley, J, De Kesel, A, Dang, T, Chen, X, Buegger, F, Brearley, F Q, Bonito, G, Anslan, S, Abell, S, and Abarenkov, K

Subjects
media_common.quotation_subject, Biodiversity, DIVERSITY, fungi, diversity, Biology, PHYLOGEOGRAPHY, Ciencias Biológicas, METABARCODING, Ecosystem, Macroecology, media_common, Multidisciplinary, Ecology, Settore BIO/02 - Botanica Sistematica, fungi, FUNGI, Global change, Edaphic, Ecología, Species richness, Micología, Soil microbiology, human activities, CIENCIAS NATURALES Y EXACTAS, Diversity (politics)
Abstract

Fungi play integral roles in soil nutrient cycling, but the determinants of fungal diversity and biogeographic patterns of key functional groups remain poorly understood. By using pyrosequencing data from hundreds of globally distributed soil samples, we demonstrated fungal diversity that expands upon the taxonomic and molecular diversity recorded so far. Except for ectomycorrhizal symbionts, fungal functional group richness was unrelated to plant diversity and plant-to-fungus richness ratio declined exponentially towards the poles. Climatic factors, followed by edaphic and spatial variables, constituted the best predictors of fungal richness and community composition at the global scale. Fungi follow general biogeographic patterns and latitudinal diversity gradients with several exceptions. Fil: Tedersoo, Leho. University Of Tartu.; Estonia Fil: Bahram, Mohammad. University Of Tartu.; Estonia Fil: Põlme, Sergei. University Of Tartu.; Estonia Fil: Kõljalg, Urmas. University Of Tartu.; Estonia Fil: Yorou, Nourou. Université de Parakou. Faculté d′Agronomie; Benín Fil: Nouhra, Eduardo Ramon. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Córdoba. Instituto Multidisciplinario de Biología Vegetal. Universidad Nacional de Córdoba. Facultad de Ciencias Exactas Físicas y Naturales. Instituto Multidisciplinario de Biología Vegetal; Argentina Fil: Greslebin, Alina Gabriela. Universidad Nacional de la Patagonia; Argentina Fil: Kohout, Petr. University Of Tartu.; Estonia Fil: Hosaka, Kentaro. National Museum of Nature and Science. Department of Botany; Japón Fil: Hiiesalu, Indrek. University Of Tartu.; Estonia Fil: Henkel, Terry W.. Humboldt State University. Department of Biological Sciences; Estados Unidos Fil: Harend, Helery. University Of Tartu.; Estonia Fil: Guo, Liang-dong. Chinese Academy of Sciences. Institute of Microbiology. State Key Laboratory of Mycology; China Fil: Geml, József. Fil: Grelet, Gwen. Landcare Research. Ecosystems and Global Change Team; Nueva Zelanda Fil: Gates, Genevieve. Tasmanian Institute of Agriculture; Australia Fil: Dunstan, William. Murdoch University. School of Veterinary and Life Sciences; Australia Fil: Dunk, Chris. Swedish University of Agricultural Sciences. Department of Forest Ecology and Management; Suecia Fil: Drenkhan, Rein. Estonian University of Life Sciences. Institute of Forestry and Rural Engineering; Estonia Fil: Dearnaley, John. University of Southern Queensland. Faculty of Health, Engineering and Sciences; Australia Fil: De Kesel, André. Botanic Garden Meise; Bélgica Fil: Dang,Tan. Vietnamese Academy of Forest Sciences; Vietnam Fil: Chen, Xin. Zhejiag University. College of Life Sciences; China Fil: Buegger, Franz. Helmholtz Zentrum München. Institute of Soil Ecology; Alemania Fil: Brearley, Francis Q.. Manchester Metropolitan University. School of Science and the Environment; Reino Unido Fil: Bonito, Gregory. Royal Botanic Gardens Melbourne; Australia Fil: Anslan, Sten. University Of Tartu.; Estonia Fil: Abell, Sandra. James Cook University. School of Marine and Tropical Biology; Australia Fil: Abarenkov, Kessy. University Of Tartu.; Estonia

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