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Liang Q, Mod HK, Luo S, Ma B, Yang K, Chen B, Qi W, Zhao Z, Du G, Guisan A, Ma X, Le Roux X. Taxonomic and functional biogeographies of soil bacterial communities across the Tibet plateau are better explained by abiotic conditions than distance and plant community composition. Mol Ecol 2023. [PMID: 37060060 DOI: 10.1111/mec.16952] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Revised: 03/26/2023] [Accepted: 03/29/2023] [Indexed: 04/16/2023]
Abstract
The processes governing soil bacteria biogeography are still not fully understood. It remains unknown how the importance of environmental filtering and dispersal differs between bacterial taxonomic and functional biogeography, and whether their importance is scale-dependent. We sampled soils across the Tibet plateau, with distances among plots ranging from 20 m to 1550 km. Taxonomic composition of bacterial community was characterized by 16S amplicon sequencing and functional community composition by qPCR targeting 9 functional groups involved in N dynamics. Factors representing climate, soil and plant community were measured to assess different facets of environmental dissimilarity. Both bacterial taxonomic and functional dissimilarities were more related to abiotic dissimilarity than biotic (vegetation) dissimilarity or distance. Taxonomic dissimilarity was mostly explained by differences in soil pH and mean annual temperature (MAT), while functional dissimilarity was linked to differences in soil N and P availabilities and N:P ratio. Soil pH and MAT remained the main determinants of taxonomic dissimilarity across spatial scales. In contrast, the explanatory variables of N-related functional dissimilarity varied across the scales, with soil moisture and organic matter having the highest role across short distances (<~330 km), and available P, N:P ratio and distance being important over long distances (>~660 km). Our results demonstrate how biodiversity dimension (taxonomic versus functional aspects) and spatial scale influence the factors driving soil bacterial biogeography.
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Affiliation(s)
- Qingqing Liang
- School of Life Sciences, Lanzhou University, Lanzhou, China
| | - Heidi K Mod
- Department of Geosciences and Geography, University of Helsinki, Helsinki, Finland
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland
| | - Shuaiwei Luo
- College of Ecology, Lanzhou University, Lanzhou, China
| | - Beibei Ma
- School of Life Sciences, Lanzhou University, Lanzhou, China
| | - Kena Yang
- School of Life Sciences, Lanzhou University, Lanzhou, China
| | - Beibei Chen
- School of Life Sciences, Lanzhou University, Lanzhou, China
| | - Wei Qi
- College of Ecology, Lanzhou University, Lanzhou, China
| | - Zhigang Zhao
- College of Ecology, Lanzhou University, Lanzhou, China
| | - Guozhen Du
- College of Ecology, Lanzhou University, Lanzhou, China
| | - Antoine Guisan
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland
- Institute of Earth Surface Dynamics, University of Lausanne, Lausanne, Switzerland
| | - Xiaojun Ma
- School of Life Sciences, Lanzhou University, Lanzhou, China
| | - Xavier Le Roux
- INRAE, Université de Lyon, Université Lyon 1, CNRS, vetAgroSup, UMR 1418 INRAE, UMR 5557 CNRS, Ecologie Microbienne LEM, Villeurbanne, France
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Mod HK, Buri A, Yashiro E, Guex N, Malard L, Pinto-Figueroa E, Pagni M, Niculita-Hirzel H, van der Meer JR, Guisan A. Predicting spatial patterns of soil bacteria under current and future environmental conditions. ISME J 2021; 15:2547-2560. [PMID: 33712699 PMCID: PMC8397778 DOI: 10.1038/s41396-021-00947-5] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/18/2020] [Revised: 02/16/2021] [Accepted: 02/19/2021] [Indexed: 02/01/2023]
Abstract
Soil bacteria are largely missing from future biodiversity assessments hindering comprehensive forecasts of ecosystem changes. Soil bacterial communities are expected to be more strongly driven by pH and less by other edaphic and climatic factors. Thus, alkalinisation or acidification along with climate change may influence soil bacteria, with subsequent influences for example on nutrient cycling and vegetation. Future forecasts of soil bacteria are therefore needed. We applied species distribution modelling (SDM) to quantify the roles of environmental factors in governing spatial abundance distribution of soil bacterial OTUs and to predict how future changes in these factors may change bacterial communities in a temperate mountain area. Models indicated that factors related to soil (especially pH), climate and/or topography explain and predict part of the abundance distribution of most OTUs. This supports the expectations that microorganisms have specific environmental requirements (i.e., niches/envelopes) and that they should accordingly respond to environmental changes. Our predictions indicate a stronger role of pH over other predictors (e.g. climate) in governing distributions of bacteria, yet the predicted future changes in bacteria communities are smaller than their current variation across space. The extent of bacterial community change predictions varies as a function of elevation, but in general, deviations from neutral soil pH are expected to decrease abundances and diversity of bacteria. Our findings highlight the need to account for edaphic changes, along with climate changes, in future forecasts of soil bacteria.
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Affiliation(s)
- Heidi K Mod
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland.
- Department of Geosciences and Geography, University of Helsinki, Helsinki, Finland.
| | - Aline Buri
- Institute of Earth Surface Dynamics, University of Lausanne, Lausanne, Switzerland
| | - Erika Yashiro
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland
- Department of Fundamental Microbiology, University of Lausanne, Lausanne, Switzerland
| | - Nicolas Guex
- Bioinformatics Competence Center, University of Lausanne, Lausanne, Switzerland
- Vital-IT, SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Lucie Malard
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland
| | | | - Marco Pagni
- Vital-IT, SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Hélène Niculita-Hirzel
- Department of Occupational Health and Environment, Center for Primary Care and Public Health (Unisanté), University of Lausanne, Lausanne, Switzerland
| | | | - Antoine Guisan
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland
- Institute of Earth Surface Dynamics, University of Lausanne, Lausanne, Switzerland
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Mazel F, Malard L, Niculita-Hirzel H, Yashiro E, Mod HK, Mitchell EAD, Singer D, Buri A, Pinto E, Guex N, Lara E, Guisan A. Soil protist function varies with elevation in the Swiss Alps. Environ Microbiol 2021; 24:1689-1702. [PMID: 34347350 PMCID: PMC9290697 DOI: 10.1111/1462-2920.15686] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2021] [Revised: 07/06/2021] [Accepted: 07/25/2021] [Indexed: 11/29/2022]
Abstract
Protists are abundant and play key trophic functions in soil. Documenting how their trophic contributions vary across large environmental gradients is essential to understand and predict how biogeochemical cycles will be impacted by global changes. Here, using amplicon sequencing of environmental DNA in open habitat soil from 161 locations spanning 2600 m of elevation in the Swiss Alps (from 400 to 3000 m), we found that, over the whole study area, soils are dominated by consumers, followed by parasites and phototrophs. In contrast, the proportion of these groups in local communities shows large variations in relation to elevation. While there is, on average, three times more consumers than parasites at low elevation (400–1000 m), this ratio increases to 12 at high elevation (2000–3000 m). This suggests that the decrease in protist host biomass and diversity toward mountains tops impact protist functional composition. Furthermore, the taxonomic composition of protists that infect animals was related to elevation while that of protists that infect plants or of protist consumers was related to soil pH. This study provides a first step to document and understand how soil protist functions vary along the elevational gradient.
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Affiliation(s)
- Florent Mazel
- Department of Ecology and Evolution, University of Lausanne, Lausanne, 1015, Switzerland
| | - Lucie Malard
- Department of Ecology and Evolution, University of Lausanne, Lausanne, 1015, Switzerland
| | - Hélène Niculita-Hirzel
- Department of Occupational Health and Environment, Center for Primary Care and Public Health (Unisanté), University of Lausanne, Epalinges, CH-1066, Switzerland
| | - Erika Yashiro
- Center for Microbial Communities, Section of Biotechnology, Aalborg University, Aalborg, Denmark
| | - Heidi K Mod
- Department of Geosciences and Geography, University of Helsinki, Helsinki, Finland
| | - Edward A D Mitchell
- Laboratory of Soil Biodiversity, Institute of Biology, University of Neuchâtel, Rue Emile-Argand 11, Neuchâtel, CH-2000, Switzerland.,Jardin Botanique de Neuchâtel, Chemin du Perthuis-du-Sault 58, Neuchâtel, CH-2000, Switzerland
| | - David Singer
- Laboratory of Soil Biodiversity, Institute of Biology, University of Neuchâtel, Rue Emile-Argand 11, Neuchâtel, CH-2000, Switzerland.,UMR CNRS 6112 LPG-BIAF, Université d'Angers, Angers Cedex 1, France
| | - Aline Buri
- Institute of Earth Surface Dynamics, University of Lausanne, Lausanne, 1015, Switzerland
| | - Eric Pinto
- Terrabiom Association, Dörflistrasse 32, Oberrieden, Zürich, 8942, Switzerland
| | - Nicolas Guex
- Bioinformatics Competence Center, University of Lausanne, Lausanne, Switzerland
| | - Enrique Lara
- Real Jardín Botánico, CSIC, Plaza de Murillo 2, Madrid, 28014, Spain
| | - Antoine Guisan
- Department of Ecology and Evolution, University of Lausanne, Lausanne, 1015, Switzerland.,Institute of Earth Surface Dynamics, University of Lausanne, Lausanne, 1015, Switzerland
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Mod HK, Scherrer D, Di Cola V, Broennimann O, Blandenier Q, Breiner FT, Buri A, Goudet J, Guex N, Lara E, Mitchell EAD, Niculita‐Hirzel H, Pagni M, Pellissier L, Pinto‐Figueroa E, Sanders IR, Schmidt BR, Seppey CVW, Singer D, Ursenbacher S, Yashiro E, van der Meer JR, Guisan A. Greater topoclimatic control of above- versus below-ground communities. Glob Chang Biol 2020; 26:6715-6728. [PMID: 32866994 PMCID: PMC7756268 DOI: 10.1111/gcb.15330] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/03/2020] [Revised: 06/04/2020] [Accepted: 08/04/2020] [Indexed: 06/11/2023]
Abstract
Assessing the degree to which climate explains the spatial distributions of different taxonomic and functional groups is essential for anticipating the effects of climate change on ecosystems. Most effort so far has focused on above-ground organisms, which offer only a partial view on the response of biodiversity to environmental gradients. Here including both above- and below-ground organisms, we quantified the degree of topoclimatic control on the occurrence patterns of >1,500 taxa and phylotypes along a c. 3,000 m elevation gradient, by fitting species distribution models. Higher model performances for animals and plants than for soil microbes (fungi, bacteria and protists) suggest that the direct influence of topoclimate is stronger on above-ground species than on below-ground microorganisms. Accordingly, direct climate change effects are predicted to be stronger for above-ground than for below-ground taxa, whereas factors expressing local soil microclimate and geochemistry are likely more important to explain and forecast the occurrence patterns of soil microbiota. Detailed mapping and future scenarios of soil microclimate and microhabitats, together with comparative studies of interacting and ecologically dependent above- and below-ground biota, are thus needed to understand and realistically forecast the future distribution of ecosystems.
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Affiliation(s)
- Heidi K. Mod
- Department of Ecology and EvolutionUniversity of LausanneLausanneSwitzerland
- Department of Geosciences and GeographyUniversity of HelsinkiHelsinkiFinland
| | - Daniel Scherrer
- Department of Ecology and EvolutionUniversity of LausanneLausanneSwitzerland
- Swiss Federal Institute for Forest, Snow and Landscape Research WSLBirmensdorfSwitzerland
| | - Valeria Di Cola
- Department of Ecology and EvolutionUniversity of LausanneLausanneSwitzerland
| | - Olivier Broennimann
- Department of Ecology and EvolutionUniversity of LausanneLausanneSwitzerland
- Institute of Earth Surface DynamicsUniversity of LausanneLausanneSwitzerland
| | - Quentin Blandenier
- Laboratory of Soil BiodiversityInstitute of BiologyUniversity of NeuchâtelNeuchâtelSwitzerland
- Real Jardín BotánicoCSICMadridSpain
| | - Frank T. Breiner
- Department of Ecology and EvolutionUniversity of LausanneLausanneSwitzerland
| | - Aline Buri
- Institute of Earth Surface DynamicsUniversity of LausanneLausanneSwitzerland
| | - Jérôme Goudet
- Department of Ecology and EvolutionUniversity of LausanneLausanneSwitzerland
- Swiss Institute of BioinformaticsUniversity of LausanneLausanneSwitzerland
| | - Nicolas Guex
- Bioinformatics Competence CenterUniversity of LausanneLausanneSwitzerland
- Vital‐IT GroupSwiss Institute of BioinformaticsLausanneSwitzerland
| | | | - Edward A. D. Mitchell
- Laboratory of Soil BiodiversityInstitute of BiologyUniversity of NeuchâtelNeuchâtelSwitzerland
- Jardin Botanique de NeuchâtelNeuchâtelSwitzerland
| | - Hélène Niculita‐Hirzel
- Department of Occupational Health and EnvironmentCenter for Primary Care and Public Health (Unisanté)University of LausanneLausanneSwitzerland
| | - Marco Pagni
- Vital‐IT GroupSwiss Institute of BioinformaticsLausanneSwitzerland
| | - Loïc Pellissier
- Swiss Federal Institute for Forest, Snow and Landscape Research WSLBirmensdorfSwitzerland
- Landscape EcologyDepartment of Environmental Systems ScienceETH ZürichZürichSwitzerland
| | | | - Ian R. Sanders
- Department of Ecology and EvolutionUniversity of LausanneLausanneSwitzerland
| | - Benedikt R. Schmidt
- Info Fauna KarchNeuchâtelSwitzerland
- Department of Evolutionary Biology and Environmental StudiesUniversity of ZurichZurichSwitzerland
| | | | - David Singer
- Laboratory of Soil BiodiversityInstitute of BiologyUniversity of NeuchâtelNeuchâtelSwitzerland
- Department of ZoologyInstitute of BiosciencesUniversity of São PauloSão PauloBrazil
| | - Sylvain Ursenbacher
- Info Fauna KarchNeuchâtelSwitzerland
- Department of Environmental SciencesSection of Conservation BiologyUniversity of BaselBaselSwitzerland
| | - Erika Yashiro
- Department of Ecology and EvolutionUniversity of LausanneLausanneSwitzerland
- Department of Fundamental MicrobiologyUniversity of LausanneLausanneSwitzerland
| | - Jan R. van der Meer
- Department of Fundamental MicrobiologyUniversity of LausanneLausanneSwitzerland
| | - Antoine Guisan
- Department of Ecology and EvolutionUniversity of LausanneLausanneSwitzerland
- Institute of Earth Surface DynamicsUniversity of LausanneLausanneSwitzerland
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5
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Affiliation(s)
- Daniel Scherrer
- Department of Ecology and Evolution University of Lausanne Biophore Lausanne Switzerland
- Swiss Federal Institute for Forest, Snow and Landscape Research WSL, Forest Dynamics Birmensdorf Switzerland
| | - Heidi K. Mod
- Department of Ecology and Evolution University of Lausanne Biophore Lausanne Switzerland
- Department of Geosciences and Geography University of Helsinki Helsinki Finland
| | - Antoine Guisan
- Department of Ecology and Evolution University of Lausanne Biophore Lausanne Switzerland
- Institute of Earth Surface Dynamics University of Lausanne Géopolis Lausanne Switzerland
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6
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Norberg A, Abrego N, Blanchet FG, Adler FR, Anderson BJ, Anttila J, Araújo MB, Dallas T, Dunson D, Elith J, Foster SD, Fox R, Franklin J, Godsoe W, Guisan A, O'Hara B, Hill NA, Holt RD, Hui FKC, Husby M, Kålås JA, Lehikoinen A, Luoto M, Mod HK, Newell G, Renner I, Roslin T, Soininen J, Thuiller W, Vanhatalo J, Warton D, White M, Zimmermann NE, Gravel D, Ovaskainen O. A comprehensive evaluation of predictive performance of 33 species distribution models at species and community levels. ECOL MONOGR 2019. [DOI: 10.1002/ecm.1370] [Citation(s) in RCA: 169] [Impact Index Per Article: 33.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Anna Norberg
- Organismal and Evolutionary Biology Research Programme University of Helsinki P.O. Box 65 Helsinki FI‐00014 Finland
| | - Nerea Abrego
- Department of Biology Centre for Biodiversity Dynamics Norwegian University of Science and Technology Trondheim N‐7491 Norway
- Department of Agricultural Sciences University of Helsinki P.O. Box 27 Helsinki FI‐00014 Finland
| | - F. Guillaume Blanchet
- Département de Biologie Université de Sherbrooke 2500 boulevard de l'Université Sherbrooke Quebec J1K 2R1 Canada
| | - Frederick R. Adler
- Department of Mathematics University of Utah 155 South 1400 East Salt Lake City Utah 84112 USA
- School of Biological Sciences University of Utah 257 South 1400 East Salt Lake City Utah 84112 USA
| | | | - Jani Anttila
- Organismal and Evolutionary Biology Research Programme University of Helsinki P.O. Box 65 Helsinki FI‐00014 Finland
| | - Miguel B. Araújo
- Departmento de Biogeografía y Cambio Global Museo Nacional de Ciencias Naturales Consejo Superior de Investigaciones Científicas (CSIC) Calle José Gutiérrez Abascal 2 Madrid 28006 Spain
- Rui Nabeiro Biodiversity Chair Universidade de Évora Largo dos Colegiais Evora 7000 Portugal
- Center for Macroecology, Evolution and Climate Natural History Museum of Denmark University of Copenhagen Copenhagen 2100 Denmark
| | - Tad Dallas
- Organismal and Evolutionary Biology Research Programme University of Helsinki P.O. Box 65 Helsinki FI‐00014 Finland
| | - David Dunson
- Department of Statistical Science Duke University P.O. Box 90251 Durham North Carolina 27708 USA
| | - Jane Elith
- School of BioSciences University of Melbourne Parkville Victoria 3010 Australia
| | - Scott D. Foster
- Commonwealth Scientific and Industrial Research Organisation (CSIRO) Hobart Tasmania Australia
| | - Richard Fox
- Butterfly Conservation Manor Yard, East Lulworth Wareham BH20 5QP United Kingdom
| | - Janet Franklin
- Department of Botany and Plant Sciences University of California Riverside California 92521 USA
| | - William Godsoe
- Bio‐Protection Research Centre Lincoln University P.O. Box 85084 Lincoln 7647 New Zealand
| | - Antoine Guisan
- Department of Ecology and Evolution (DEE) University of Lausanne, Biophore Lausanne CH‐1015 Switzerland
- Institute of Earth Surface Dynamics (IDYST) University of Lausanne, Geopolis Lausanne CH‐1015 Switzerland
| | - Bob O'Hara
- Department of Mathematical Sciences Norwegian University of Science and Technology Trondheim N‐7491 Norway
| | - Nicole A. Hill
- Institute for Marine and Antarctic Studies University of Tasmania Private Bag 49 Hobart Tasmania 7001 Australia
| | - Robert D. Holt
- Department of Biology The University of Florida Gainesville Florida 32611 USA
| | - Francis K. C. Hui
- Mathematical Sciences Institute The Australian National University Acton Australian Capital Territory 2601 Australia
| | - Magne Husby
- Nord University Røstad Levanger 7600 Norway
- BirdLife Norway Sandgata 30B Trondheim 7012 Norway
| | - John Atle Kålås
- Norwegian Institute for Nature Research P.O. Box 5685, Torgarden Trondheim NO‐7485 Norway
| | - Aleksi Lehikoinen
- The Helsinki Lab of Ornithology Finnish Museum of Natural History University of Helsinki P.O. Box 17 Helsinki FI‐00014 Finland
| | - Miska Luoto
- Department of Geosciences and Geography University of Helsinki P.O. Box 64 Helsinki 00014 Finland
| | - Heidi K. Mod
- Institute of Earth Surface Dynamics (IDYST) University of Lausanne, Geopolis Lausanne CH‐1015 Switzerland
| | - Graeme Newell
- Biodiversity Division Department of Environment, Land, Water & Planning Arthur Rylah Institute for Environmental Research 123 Brown Street Heidelberg Victoria 3084 Australia
| | - Ian Renner
- School of Mathematical and Physical Sciences The University of Newcastle University Drive Callaghan New South Wales 2308 Australia
| | - Tomas Roslin
- Department of Agricultural Sciences University of Helsinki P.O. Box 27 Helsinki FI‐00014 Finland
- Department of Ecology Swedish University of Agricultural Sciences Box 7044 Uppsala 750 07 Sweden
| | - Janne Soininen
- Department of Geosciences and Geography University of Helsinki P.O. Box 64 Helsinki 00014 Finland
| | - Wilfried Thuiller
- CNRS LECA Laboratoire d’Écologie Alpine University Grenoble Alpes Grenoble F‐38000 France
| | - Jarno Vanhatalo
- Organismal and Evolutionary Biology Research Programme University of Helsinki P.O. Box 65 Helsinki FI‐00014 Finland
| | - David Warton
- School of Mathematics and Statistics Evolution & Ecology Research Centre University of New South Wales Sydney New South Wales 2052 Australia
| | - Matt White
- Biodiversity Division Department of Environment, Land, Water & Planning Arthur Rylah Institute for Environmental Research 123 Brown Street Heidelberg Victoria 3084 Australia
| | - Niklaus E. Zimmermann
- Dynamic Macroecology Swiss Federal Research Institute WSL Zuercherstrasse 111 Birmensdorf CH‐8903 Switzerland
| | - Dominique Gravel
- Département de Biologie Université de Sherbrooke 2500 boulevard de l'Université Sherbrooke Quebec J1K 2R1 Canada
| | - Otso Ovaskainen
- Organismal and Evolutionary Biology Research Programme University of Helsinki P.O. Box 65 Helsinki FI‐00014 Finland
- Department of Biology Centre for Biodiversity Dynamics Norwegian University of Science and Technology Trondheim N‐7491 Norway
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