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Unforeseen high continental-scale soil microbiome homogenization in urban greenspaces

Nature Cities volume 2, pages 759–769 (2025)Cite this article

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Abstract

Soils in urban greenspaces often support higher microbial richness but with more homogenous communities than in natural ecosystems. However, it is not known how urbanization impacts the diversity and homogeneity of soil communities in urban greenspaces compared with other highly managed ecosystems such as farmlands. Here we conducted a continental-scale study spanning 13 cities and four land uses (city parks, residential areas, and adjacent forests and farmlands) in China. We found that urban ecosystems consistently support higher local soil bacterial, protist and fungal (but not metazoan) richness than farmlands and forests. This elevated richness was closely related to higher pH in urban ecosystem soils. Urban greenspaces also supported more homogenous soil communities than farmlands. The results indicate that urbanization drives biotic homogenization and increases synchronous responses to environmental stressors in urban greenspaces at a continental scale. Our findings have important implications for managing soil ecosystem resilience and functional diversity in cities of the future.

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Fig. 1: Study sites and design.
Fig. 2: Alpha and beta diversities of soil organisms.
Fig. 3: Diversity accumulation curves in different land-use types (relative to forests).
Fig. 4: Soil biodiversity–environment relationships in different land uses.
Fig. 5: Biodiversity drivers of different soil biota in different land uses.

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Data availability

The data that support the findings of this study are available in the NCBI Sequence Read Archive (SRA; Bioproject ID PRJNA1114439) and via figshare at https://doi.org/10.6084/m9.figshare.26122408.v1.

Code availability

Core scripts have been archived in figshare (https://doi.org/10.6084/m9.figshare.27928692).

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Acknowledgements

X.S. acknowledges support from the National Natural Science Foundation of China (no. 32361143523), the National Key Research and Development Program of China (no. 2023YFF1304600) and the International Partnership Program of Chinese Academy of Sciences (no. 322GJHZ2022028FN). Y.-G.Z. acknowledges support from the National Natural Science Foundation of China (no. 42021005) and the Ningbo S&T project (no. 2021-DST-004). M.D.-B. acknowledges support from TED2021-130908B-C41/AEI/10.13039/501100011033/Unión Europea NextGenerationEU/PRTR and from the Spanish Ministry of Science and Innovation for the I+D+i project PID2020-115813RA-I00 funded by MCIN/AEI/10.13039/501100011033. N.E. acknowledges the support of iDiv, which is funded by the German Research Foundation (DFG-FZT 118, 202548816), as well as by the DFG (Ei 862/29-1; Ei 862/31-1). We gratefully acknowledge S. Díaz from the Universidad Nacional de Córdoba for her valuable comments on our manuscript, and Z. Qiao, H. Shangguan, Q. Yan, D. Yu, Y. Zhang, B. Wang, X. Liu, T. Chen and other colleagues in the Urban Soil Ecology (USE) laboratory of the Institute of Urban Environment, Chinese Academy of Sciences, for their contributions to the fieldwork, DNA extraction and environmental data collection.

Author information

Authors and Affiliations

  1. State Key Laboratory of Regional and Urban Ecology, Ningbo Observation and Research Station, Fujian Key Laboratory of Watershed Ecology, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen, China

    Xin Sun, Haifeng Yao, Zhipeng Li & Yong-Guan Zhu

  2. Zhejiang Key Laboratory of Urban Environmental Processes and Pollution Control, CAS Haixi Industrial Technology Innovation Center in Beilun, Ningbo, China

    Xin Sun, Haifeng Yao, Zhipeng Li & Yong-Guan Zhu

  3. University of Chinese Academy of Sciences, Beijing, China

    Xin Sun, Haifeng Yao & Yong-Guan Zhu

  4. The Aerobiome Innovation and Research Hub, College of Science and Engineering, Flinders University, Bedford Park, South Australia, Australia

    Xin Sun, Jake M. Robinson & Martin F. Breed

  5. College of Science and Engineering, Flinders University, Bedford Park, South Australia, Australia

    Jake M. Robinson & Martin F. Breed

  6. Laboratorio de Biodiversidad y Funcionamiento Ecosistémico, Instituto de Recursos Naturales y Agrobiología de Sevilla (IRNAS). Consejo Superior de Investigaciones Científicas (CSIC), Sevilla, Spain

    Manuel Delgado-Baquerizo

  7. Senckenberg Museum of Natural History Görlitz, Görlitz, Germany

    Anton Potapov

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

    Anton Potapov & Nico Eisenhauer

  9. International Institute Zittau, TUD Dresden University of Technology, Zittau, Germany

    Anton Potapov

  10. State Key Laboratory of Vegetation Structure, Function and Construction (VegLab), Ministry of Education Key Laboratory of Earth Surface Processes, and College of Urban and Environmental Sciences, Peking University, Beijing, China

    Biao Zhu

  11. A.N. Severtsov Institute of Ecology and Evolution, Russian Academy of Sciences, Moscow, Russia

    Alexei V. Tiunov

  12. International Ecosystem Management Partnership, United Nations Environment Programme, Beijing, China

    Linxiu Zhang

  13. Center for Chinese Agricultural Policy, Institute of Geographic Sciences and Natural Resources Research, Chinese Academy of Sciences, Beijing, China

    Linxiu Zhang

  14. School of Geographical Sciences, University of Nottingham Ningbo China, Ningbo, China

    Faith Ka Shun Chan

  15. Water@Leeds and School of Geography, University of Leeds, Leeds, UK

    Faith Ka Shun Chan

  16. Department of Renewable Resources, University of Alberta, Edmonton, Alberta, Canada

    Scott X. Chang

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

    Nico Eisenhauer

  18. J.F. Blumenbach Institute of Zoology and Anthropology, University of Goettingen, Goettingen, Germany

    Stefan Scheu

  19. Centre of Biodiversity and Sustainable Land Use, University of Goettingen, Goettingen, Germany

    Stefan Scheu

Authors
  1. Xin Sun
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  2. Jake M. Robinson
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Contributions

X.S. was responsible for designing, securing funding, supervising and performing research. X.S., J.M.R. and Z.L. contributed significantly to writing, editing, reviewing and overseeing all figures and text in the manuscript. M.D.-B., A.P., S.X.C., M.F.B., N.E., S.S. and Y.-G.Z. acted as senior authors, providing contributions in editing, conceptual input and manuscript review. Other co-authors were involved in editing, reviewing and graphic designing.

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Correspondence to Xin Sun, Jake M. Robinson or Zhipeng Li.

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Sun, X., Robinson, J.M., Delgado-Baquerizo, M. et al. Unforeseen high continental-scale soil microbiome homogenization in urban greenspaces. Nat Cities 2, 759–769 (2025). https://doi.org/10.1038/s44284-025-00294-y

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