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Landscape effects on global soil pathogenic fungal diversity across spatial scales

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Abstract

Growing evidence has shown that, apart from local environmental factors, changes in landscape-level factors by accelerated land-use change can also shape soil pathogenic fungal diversity. However, the global representativeness of such patterns remains unclear. Here, we assess how pathogenic fungal diversity in 511 soil samples worldwide responds to landscape factors, including landscape complexity index based on eight landscape metrics and quantity of different land cover types across six spatial scales (i.e., surrounding landscape, 250 m to 10,000 m radii from the sampling coordinate). We find that while soil variables explain over half of the variance, pathogenic fungal alpha diversity increases with landscape complexity and crop cover proportion, but decreases with grass and tree cover proportion, together explaining 23.4% of the total variance. Landscape factors have weaker impacts on beta diversity, explaining 13.0% of the variance. Across spatial scales, grassland ecosystems exhibit increasingly stronger responses to landscape variables compared to forest ecosystems. Landscape factors have a higher relative contribution to root-associated fungi than leaf/fruit/seed-associated fungi. Our results emphasize the importance of local factors and the complementary role of landscape patterns in shaping global soil pathogenic fungal distributions, highlighting scale-dependent effects across ecosystems and fungal functional groups.

Data availability

The raw sequencing data generated in this study have been deposited in the NCBI Sequence Read Archive (SRA) under accession code PRJNA1045969. The source data underlying all figures are available on Figshare at https://doi.org/10.6084/m9.figshare.26377660.v5. All other data supporting the findings of this study are provided in the Supplementary Information.

Code availability

The code that support the findings of this study are openly available on figshare at https://doi.org/10.6084/m9.figshare.26377660.v5.

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Acknowledgements

We thank all the people who helped in sampling and experiment processes and volunteering researchers from the networks of ILTER (https://www.ilter.network) and eLTER (https://elter-ri.eu). We also thank all the landowners for the access to their lands. We thank JiaJia Liu for his contribution to the research idea and manuscript revision, as well as supporting Y.L. for participation in the iSBio project. We thank Yuanyuan Huang, Shengen Liu for advice on data analysis. We acknowledge funding from the German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig of the German Research Foundation (FZT118, 202548816), and from The Swedish Research Council for Environment, Agricultural sciences and Spatial Planning (Formas, grant no. 2020-02339). Sequencing was financed by the German Research Foundation (DFG, BU 941/32-1 | EI 862/27-1 | HE 8266/4-1 | KU 1367/14-1 | WE 6579/2-1 to F.B., N.E., A.H.-B., K.Kü., C.-E.W.). Sequence data analysis was performed at the High-Performance Computing (HPC) Cluster EVE, a joint effort of both the Helmholtz Centre for Environmental Research-UFZ and the German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, whose administrators are thanked for excellent support. Moreover, we acknowledge support by the DFG grants EI 862/29-1 and EI 862/31-1 (to N.E.). Y.L. acknowledges funding from China Scholarship Council (202106100117). F.T.M. acknowledges support by the King Abdullah University of Science and Technology (KAUST) and the KAUST Climate and Livability Initiative. G.W. acknowledges financial support by the Austrian National Science Fund (FWF, grant no. P31669). A.G. acknowledges Fondecyt 1201643 & FB210006 & ICN2021_044. Zs.K. acknowledges the MATE Research Excellence Program MATE-K/1011–32/2024). M.B. acknowledges the Scientific Grant Agency VEGA (Grant No. 2/0045/22). K.L. acknowledges support to the H.J. Andrews Experimental Forest and Long Term Ecological Research (LTER) program under NSF grant LTER8 DEB-2025755. A.S.F.A. acknowledges CNPq-Brazil for his Fellowship of Research (grant 301755/2022-1). Funding was provided by CNPq-Brazil (Grant No. 304636/2022-3) to A.C. A.P. and M.C. acknowledge that this work has benefited from the equipment and framework of the COMP-HUB and COMP-R Initiatives, funded by the ‘Departments of Excellence’ program of the Italian Ministry for University and Research (MIUR, 2018-2022 and MUR, 2023-2027). L.v.d.B., R.C. and R.M. thank Conaf (Chile) and Comunidad Agricola Quebrada de Talca (Chile), and were supported by DFG (Priority Program SPP-1803 ‘EarthShape: Earth Surface Shaping by Biota’, TI 338/14-1 and BA 3843/6-1). L.v.d.B. thanks additional support from ANID PIA/ACT 210038. A.I.S. acknowledges the FCT—Foundation for Science and Technology, I.P. through the individual project CEECIND/00962/2017 (DOI: 10.54499/CEECIND/00962/2017/CP1459/CT0008), for the financial support to CESAM under the project/grant UID/50006 + LA/P/0094/2020 (doi.org/10.54499/LA/P/0094/2020). A.R.G. and R.L.M. are grateful to CNPq-Brazil (PELD—Grant No. 441610/2016-1) for supporting this study. H.J. and F.Z. thank the Galapagos National Park Directorate and the Ecuadorian Ministry of Environment, Water and Ecological Transition for their support and for issuing permit numbers MAE-DNB-CM-2016-0043 and 006-2021-EXP-CM-FAU-DBI/MAAE. This publication is contribution number 2664 of the Charles Darwin Foundation for the Galapagos Islands. P.P. was supported by the long-term research development project RVO 67985939 (Czech Academy of Sciences). S.M.T.-T. was supported by an Australian Research Council DECRA Fellowship (DE210101029). I.D. thanks UNILEVER and EKATERRA for sponsoring tea bags. I.F. acknowledges support by Scientific Council of the University of Nyíregyháza. T.M.U. was supported through the Nucleu Program as part of the 2022–2027 National Research, Development and Innovation Plan, funded by MCID, project no. PN23020401, contract no. 7N/03.01.2023. C.A.G. was funded by the Portuguese Foundation for Science and Technology, as part of Project SoilRecon (PTDC/BIA-CBI/2340/2020). Q.P. thanks the Walloon forest service (Service Public de Wallonie-Département de la Nature et des Forêts) for its financial support to the installation and maintenance of the FORBIO-Gedinne site through the 5-year research programme ‘Accord-cadre de recherches et de vulgarisation forestières’. A.St. and P.B.R. acknowledge the National Science Foundation, Biological Integration Institutes grant NSF-DBI-2021898. I.O. and K.Kr. were supported by the Estonian Research Council grant PRG916. C.B. and H.C.S. were supported by projects AdaptForGrazing (02/C05-i03/2021.PPRR-C05-i03-I-000035), SustInAfrica (EU H2020 R&I GA 861924), and Portuguese National Funds through ‘Fundação para a Ciência e Tecnologia’ (FCT) within the cE3c Unit funding (DOI:10.54499/UIDB/00329/2020). G.G. was supported by the grant DEB 0620910, 1831952 and 2425484 from the National Science Foundation as part of the Luquillo LTER. The U.S. Forest Service (Department of Agriculture) and University of Puerto Rico gave additional support. P.F. was supported by the Swedish Research Council FORMAS (2020-01100). S.L. was supported by the Integrated Monitoring Programme contract 221-22-006 financed by the Swedish Environmental Protection Agency. Financial support was provided by the EU Horizon 2020 project eLTER PLUS (grant 871128) to P.H. M.Di. receives financial support from the Swiss Federal Office of the Environment. S.K.-R. was supported by Novo Nordisk Foundation grant NNF20OC0059948. P.D.T. was supported by the GreenMount project (PN-IV-P2-2.1-TE-2023-0726), funded by UEFISCDI Romania. S.E.V. was supported by an Australian Research Council Linkage project, LP190100844. H.K. and K.H. were supported by the Grant-in-Aid for Scientific Research (B) (17H03835 to H.K. and 19H02999 to K.H.) from Japan Society for the Promotion of Science. C.C. was supported by the Long-Term Ecological Research project (2006–2025), Ministry of Agriculture, Taiwan. R.G.G. was supported by a grant (PR3/23-30823) from Complutense University. U.H. and M.Frei. received financial support by the German Research Foundation (DFG) Infrastructure Priority Program 1374 “Biodiversity-Exploratories” (HA 4597/6-4). H.B. and S.T. acknowledge the support by the BEF-China platform and the Deutsche Forschungsgemeinschaft (DFG, German Research Foundation)—35758305 (FOR891); 319936945 (GRK2324).

Author information

Authors and Affiliations

  1. College of Chemistry and Life Science, Suzhou University of Science and Technology, Suzhou, China

    Yawen Lu

  2. German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Leipzig, Germany

    Yawen Lu, Nico Eisenhauer, Guillaume Patoine, Kirsten Küsel, François Buscot, Helge Bruelheide, Rafaella Canessa, Martin Schädler, Stefan Trogisch & Carlos A. Guerra

  3. MOE Key Laboratory for Biodiversity Science and Ecological Engineering, Institute of Biodiversity Science, School of Life Sciences, Fudan University, Shanghai, China

    Yawen Lu

  4. Institute of Biology, Leipzig University, Leipzig, Germany

    Nico Eisenhauer & Guillaume Patoine

  5. Institute of Ecology, College of Urban and Environmental Sciences, Key Laboratory for Earth Surface Processes of the Ministry of Education, Peking University, Beijing, China

    Ying Chen

  6. Swammerdam Institute for Life Sciences, University of Amsterdam, Amsterdam, The Netherlands

    Anna Heintz-Buschart

  7. Institute of Biodiversity, Ecology and Evolution, Aquatic Geomicrobiology, Friedrich Schiller University, Jena, Germany

    Kirsten Küsel & Carl-Eric Wegner

  8. Cluster of Excellence Balance of the Microverse, Friedrich Schiller University Jena, Jena, Germany

    Kirsten Küsel

  9. Bioinorganic Chemistry, Biomics Group, Heinrich Heine University, Düsseldorf, Germany

    Carl-Eric Wegner

  10. Department of Soil Ecology, Helmholtz Centre for Environmental Research-UFZ, Halle (Saale), Germany

    François Buscot & Qicheng Bei

  11. State Key Laboratory of Herbage Improvement and Grassland Agro-Ecosystems & College of Ecology, Lanzhou University, Lanzhou, China

    Xiang Liu

  12. Soil Microbial Ecology Group, Agricultural Science Center, Federal University of Piaui, Teresina, PI, Brazil

    Ademir S. F. Araujo

  13. Swiss Federal Institute for Forest, Snow and Landscape Research WSL, Birmensdorf, Switzerland

    Beat Frey, Markus Didion, Ika Djukic & Marcus Schaub

  14. Environmental Sciences and Engineering, Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology, Thuwal, Kingdom of Saudi Arabia

    Fernando T. Maestre

  15. Earth Systems Research Center, University of New Hampshire, Durham, NH, USA

    Matthew Vadeboncoeur

  16. Plant Ecology Group, Department of Biology, University of Tübingen, Tübingen, Germany

    Liesbeth van den Brink

  17. ECOBIOSIS, Department of Botany, University of Concepcion, Concepcion, Chile

    Liesbeth van den Brink

  18. UCLouvain—Earth and Life Institute, Louvain-la-Neuve, Belgium

    Quentin Ponette

  19. Universität Innsbruck, Institut für Ökologie, Innsbruck, Austria

    Georg Wohlfahrt

  20. Facultad de Ciencias Biológicas, P. Universidad Catolica de Chile, Alameda 340, Santiago & Instituto de Ecología y Biodiversidad (IEB), Santiago, Chile

    Aurora Gaxiola

  21. cE3c-Center for Ecology, Evolution and Environmental Changes & CHANGE – Global Change and Sustainability Institute, Faculdade de Ciências, Universidade de Lisboa, Lisboa, Portugal

    Cristina Branquinho & Helena Cristina Serrano

  22. Northwest German Forest Research Institute, Göttingen, Germany

    Henning Meesenburg & Markus Wagner

  23. Nakagawa Experimental Forest, Field Science Center for Northern Biosphere, Hokkaido University, Otoineppu, Hokkaido, Japan

    Karibu Fukuzawa

  24. Rubenstein School of Environment and Natural Resources, Aiken Center, 81 Carrigan Drive, University of Vermont, Burlington, VT, USA

    E. Carol Adair

  25. BioSense Institute, University of Novi Sad, Novi Sad, Serbia

    Andrijana Andrić & Dušanka Vujanović

  26. Institute of Forest Ecology, Slovak Academy of Sciences, Zvolen, Slovakia

    Milan Barna

  27. Institute of Biology/Geobotany and Botanical Garden, Martin Luther University Halle-Wittenberg, Halle (Saale), Germany

    Helge Bruelheide & Stefan Trogisch

  28. Departamento de Ecologia, Universidade Federal do Rio Grande do Norte, Natal, RN, Brazil

    Adriano Caliman

  29. Institute of Biology, Martin Luther University Halle-Wittenberg, Halle (Saale), Germany

    Rafaella Canessa

  30. Ecological Plant Geography, University of Marburg, Marburg, Germany

    Rafaella Canessa

  31. Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parma, Italy

    Michele Carbognani, Alessandro Petraglia & Marcello Tomaselli

  32. Department of Biological, Geological, and Environmental Sciences, University of Bologna, Bologna, Italy

    Roberto Cazzolla Gatti

  33. Taiwan Agricultural Research Institute, MOA, Taichung, Taiwan

    Chiling Chen

  34. Terrestrial Ecology Section, Department of Biology, University of Copenhagen, Copenhagen, Denmark

    Casper T. Christiansen

  35. Université de Lorraine, CNRS, LIEC, Metz, France

    Michaël Danger & Florence Maunoury-Danger

  36. Altai State University, Barnaul, Russia

    Evgeny A. Davydov

  37. Department of Biological Sciences, Boise State University, Boise, ID, USA

    Marie-Anne de Graaff

  38. Meteo-France/CNRS, Toulouse, France

    Christine Delire

  39. Maiella National Park, Sulmona, Italy

    Valter Di Cecco & Luciano Di Martino

  40. Bioclimatology, University of Göttingen, Göttingen, Germany

    Simon Drollinger

  41. Kyushu University Forest, Kyushu University, Ashoro, Hokkaido, Japan

    Tsutomu Enoki

  42. Institute of Environmental Science, University of Nyíregyháza, Nyíregyháza, Hungary

    István Fekete

  43. Department of Forest Mycology and Plant Pathology, Uppsala BioCenter, Swedish University of Agricultural Sciences, Uppsala, Sweden

    Petra Fransson

  44. Institute of Landscape Ecology, University of Münster, Münster, Germany

    Martin Freitag & Ute Hamer

  45. Department of Community Ecology, Helmholtz Centre for Environmental Research-UFZ, Halle (Saale), Germany

    Mark Frenzel & Martin Schädler

  46. Botany Unit, Department of Pharmacology, Pharmacognosy and Botany, Complutense University, Madrid, Spain

    Rosario G. Gavilán

  47. Faculty of Geosciences, Geography and Astronomy, Geoecology Group, University of Vienna, Vienna, Austria

    Stephan Glatzel

  48. Forest Research Institute-Bulgarian Academy of Sciences, Sofia, Bulgaria

    Maria Glushkova

  49. USDA Forest Service, International Institute of Tropical Forestry, San Juan, Puerto Rico

    Grizelle González

  50. Institute of Biodiversity and Sustainability, Federal University of Rio de Janeiro, Macaé, Rio de Janeiro, Brazil

    Anderson da R. Gripp & Rodrigo L. Martins

  51. Department of River Ecology and Conservation, Senckenberg Research Institute and Natural History Museum Frankfurt, Gelnhausen, Germany

    Peter Haase

  52. Faculty of Biology, University of Duisburg-Essen, Essen, Germany

    Peter Haase

  53. Kyushu University Forest, Kyushu University, Sasaguri-machi, Fukuoka, Japan

    Takuo Hishi

  54. Department of Ecosystem Studies, The University of Tokyo, Bunkyo-ku, Tokyo, Japan

    Tsutom Hiura

  55. Department of Zoology, University of Veteinary Medicine Budapest, Budapest, István utca 2., Hungary

    Elisabeth Hornung

  56. Department of Biological Environment, Akita Prefectural University, Akita, Japan

    Kazuhiko Hoshizaki

  57. Charles Darwin Research Station, Charles Darwin Foundation, Santa Cruz, Galapagos, Ecuador

    Heinke Jäger

  58. Pyrenean Institute of Ecology (IPE, CSIC), Jaca, Spain

    Juan J. Jiménez

  59. Department of Biological Sciences, Boise State University, Boise, ID, USA

    Megan J. Kelly-Slatten

  60. Department of Geosciences and Natural Resource Management, University of Copenhagen, Copenhagen, Denmark

    Sebastian Kepfer-Rojas

  61. Department of Agro-Environmental Studies, Hungarian University of Agriculture and Life Sciences, Gödöllő, Hungary

    Zsolt Kotroczó

  62. Institute of Ecology and Earth Sciences, University of Tartu, Tartu, Estonia

    Kaie Kriiska & Ivika Ostonen

  63. Graduate School of Agriculture, Kyoto University, Kitashirakawa Oiwake, Sakyo, Kyoto, Japan

    Hiroko Kurokawa

  64. Department of Crop and Soil Sciences, Oregon State University, Corvallis, OR, USA

    Kate Lajtha

  65. Faculty of Biological and Environmental Sciences, Lammi Biological Station, University of Helsinki, Lammi, Finland

    John Loehr

  66. Department of Aquatic Sciences and Assessment, Swedish University of Agricultural Sciences, Uppsala, Sweden

    Stefan Löfgren

  67. Département des Sciences de l’Environnement, Université du Québec à Trois-Rivières, Trois-Rivières, QC, Canada

    Vincent Maire

  68. Institute of Biology, Faculty of Medicine and Life Sciences, University of Latvia, Riga, Latvia

    Inara Melece

  69. Instituto Universitario de Investigación en el Olivar y el Aceite de Oliva, Universidad de Jaén, Jaén, Spain

    Victoria Ochoa

  70. Centre for Forest Research, Université du Québec à Montréal, MontréalQC, QC, Canada

    Alain Paquette

  71. Ontario Ministry of Natural Resources, Sault Ste. Marie ON, ON, Canada

    William C. Parker

  72. Instituto Nacional de Tecnología Agropecuaria (INTA), Universidad Nacional de la Patagonia Austral (UNPA)-CONICET, Río Gallegos, Santa Cruz, Argentina

    Pablo Luis Peri

  73. Department of Geosciences, University of Tübingen, Tübingen, Germany

    Rebecca Mast

  74. Department of Vegetation Ecology, Institute of Botany, Czech Academy of Sciences, Průhonice, Czech Republic

    Petr Petřík

  75. Faculty of Environmental Sciences, Czech University of Life Sciences, Prague, Czech Republic

    Petr Petřík

  76. A. Borza Botanic Garden, Babeș-Bolyai University, Cluj-Napoca, Romania

    Mihai Pușcaș & Pavel Dan Turtureanu

  77. Centre for Systems Biology, Biodiversity and Bioresources (3B), Babeș-Bolyai University, Cluj-Napoca, Romania

    Mihai Pușcaș & Pavel Dan Turtureanu

  78. Emil G. Racoviță Institute, Babeș-Bolyai University, Cluj-Napoca, Romania

    Mihai Pușcaș & Pavel Dan Turtureanu

  79. Department Computational Hydrosystems, Helmholtz Centre for Environmental Research (UFZ), Leipzig, Germany

    Corinna Rebmann

  80. Department of Forest Resources, University of Minnesota, St. Paul, MN, USA

    Peter B. Reich & Artur Stefanski

  81. Hawkesbury Institute for the Environment, Western Sydney University, Penrith, NSW, Australia

    Peter B. Reich

  82. Institute for Global Change Biology and School for Environment and Sustainability, University of Michigan, Ann Arbor, MI, USA

    Peter B. Reich

  83. Institute of Biology, Freie Universität Berlin, Berlin, Germany

    Matthias C. Rillig

  84. Berlin-Brandenburg Institute of Advanced Biodiversity Research (BBIB), Berlin, Germany

    Matthias C. Rillig

  85. Department of Conservation Biology & Social-Ecological Systems, Helmholtz Centre for Environmental Research-UFZ, Leipzig, Germany

    Anja Schmidt

  86. Universität Innsbruck, Institut für Ökologie, Sternwartestr. 15/Technikerstrasse 25, Innsbruck, Austria

    Julia Seeber

  87. Institute for Alpine Environment, Eurac Research, Bozen/Bolzano, Italy

    Julia Seeber

  88. ECOMARE, CESAM—Centre for Environmental and Marine Studies, Department of Biology, University of Aveiro, Aveiro, Portugal

    Ana I. Sousa

  89. JFB Institute of Zoology and Anthropology, University of Göttingen, Göttingen, Germany

    Stefan Scheu

  90. Centre of Biodiversity and Sustainable Land Use, University of Göttingen, Götingen, Germany

    Stefan Scheu

  91. College of Natural Resources, University of Wisconsin, Stevens Point, WI, USA

    Artur Stefanski

  92. Institute for Soil Sciences, HUN-REN Centre for Agricultural Research, Budapest, Herman Ottó út 15, Hungary

    Zsolt Tóth

  93. Centre for Nature Positive Solutions, Biology Department, School of Science, RMIT University, Melbourne, VIC, Australia

    Stacey M. Trevathan-Tackett

  94. Institute of Biological Research Cluj, National Institute of Research and Development for Biological Sciences, Cluj-Napoca, Romania

    Tudor M. Ursu

  95. School of Life and Environmental Sciences, Deakin University, Burwood, VIC, Australia

    Susanna E. Venn

  96. Research Institute for Nature and Forest (INBO), Geraardsbergen, Belgium

    Arne Verstraeten

  97. Forest Research Institute Malaysia (FRIM), Kepong, Selangor, Malaysia

    Jeyanny Vijayanathan

  98. Department of Crop Production Ecology, Swedish University of Agricultural Sciences, Uppsala, Sweden

    Martin Weih

  99. BOKU University, Institute of Soil Research, Department of Ecosystem Management, Climate and Biodiversity, Vienna, Austria

    Franz Zehetner

  100. Galapagos National Park Directorate, Puerto Ayora, Galapagos, Ecuador

    Franz Zehetner

  101. Universidade de Coimbra, Departamento de Geografia, Colégio São Jerónimo, Coimbra, Portugal

    Carlos A. Guerra

Authors

  1. Yawen Lu
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  2. Nico Eisenhauer
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  3. Guillaume Patoine
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Contributions

Y.L., N.E., G.P., A.H.-B., K.Kü., C.-E.W., F.B., and C.A.G. conceived and designed the study. Y.L., X.L., Y.C., and C.A.G. performed the data analyses. Y.L. wrote the first draft of the manuscript with support by C.A.G. and N.E., and all authors contributed greatly to the final manuscript. N.E., G.P., A.H.-B., K.Kü., C.-E.W., F.B., Q.B., M.C.R., and S.S. worked on laboratorial analyses and data compiling. Site coordination and soil sampling were contributed by A.S.F.A., B.F., F.T.M., M.V., L.v.d.B., Q.P., M.Di., G.W., A.G., C.B., H.M., K.F., E.C.A., A.A., M.B., H.B., A.C., R.C., M.C., R.C.G., C.C., C.T.C., M.Da., E.A.D., M.-A.d.G., C.D., V.D.C., L.D.M., I.D., S.D., T.E., I.F., P.F., M.Frei., M.Fren., R.G.G., S.G., M.G., G.G., A.R.G., P.H., U.H., T.His., T.Hiu., E.H., K.H., H.J., J.J.J., M.J.K.-S., S.K.-R., Zs.K., K.Kr., H.K., K.L., J.L., S.L., V.M., R.L.M., F.M.-D., I.M., V.O., I.O., A.P., W.C.P., P.L.P., R.M., A.P., P.P., M.P., C.R., P.B.R., M.C.R., M.Schä., M.Scha., A.Sc., J.S., H.C.S., A.I.S., S.S., A.St., M.T., Z.T., S.M.T.-T., S.T., P.D.T., T.M.U., S.E.V., A.V., J.V., D.V., M.Wa., M.We., and F.Z.

Corresponding authors

Correspondence to
Yawen Lu or Carlos A. Guerra.

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Lu, Y., Eisenhauer, N., Patoine, G. et al. Landscape effects on global soil pathogenic fungal diversity across spatial scales.
Nat Commun (2026). https://doi.org/10.1038/s41467-025-67929-5

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