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Urbanization increases the complexity of soil microbial interaction networks

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Abstract

Urbanization reshapes soil ecosystems, yet its impacts on the composition and interactions of soil microbial communities remain insufficiently understood. Here, we use high-throughput sequencing to profile bacteria, fungi, and protists across four representative habitat types of different urbanization level—campuses, roadside greenbelts, suburban unmanaged lands, and concrete pavements in four Chinese cities spanning a broad latitudes (Changchun, Beijing, Hangzhou, Haikou). Vegetated habitats consistently structure microbial communities, whereas concrete pavements form a distinct disturbed habitat with the lowest microbial richness. Bacterial richness is highest in campuses and roadside greenbelts, while fungal and protistan richness peaks in suburban unmanaged lands. Despite regional variation, communities under similar vegetation types show convergent compositions, jointly shaped by regional climate and land-use intensity. Bacterial assemblages are more sensitive to environmental variation than fungi and protists. Proteobacteria dominate bacteria communities, whereas fungal and protistan communities display marked habitat specificity. Co-occurrence networks complexity peaks in roadside greenbelts, remains stable in suburban unmanaged lands and collapses significantly in concrete pavements. Microbial diversity patterns are strongly associated with temperature, soil pH, and latitude. Together, these results demonstrate that environmental conditions and urbanization intensity drive the biogeography and interaction patterns of soil microbiomes, providing insights for ecological restoration and urban green-space management.

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Data availability

The raw sequencing data are available in the NCBI Sequence Read Archive (SRA) (http://trace.ncbi.nlm.nih.gov/Traces/sra/) under accession number PRJNA1309871 for roadside greenbelts, PRJNA1309878 for suburban unmanaged lands, PRJNA1309853 for concrete pavements, and PRJNA1309333 for urban campus. Processed data and analysis inputs are available in the Zenodo repository at https://doi.org/10.5281/zenodo.1881998271 and https://doi.org/10.5281/zenodo.1910416472. In addition, Supplementary Data 1 contains environmental, climatic, microbial diversity, and urbanization-related variables used in this study. Supplementary Data 2 contains OTU abundance matrices of bacterial, fungal, and protistan communities with taxonomic annotations. Supplementary Data 3 provides the source data underlying all figures and charts in the main manuscript. Any remaining information can be obtained from the corresponding author upon reasonable request.

Code availability

All custom R scripts used for data processing, statistical analyses, microbial network construction, and structural equation modelling in this study are publicly available on Zenodo at https://doi.org/10.5281/zenodo.18819982. Analyses were performed in R (v4.3.0), using packages including vegan, randomForest, ggplot2, igraph, piecewiseSEM, dplyr, and ggpubr. No restrictions apply to the access or use of the code.

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Acknowledgements

We thank the National Key R & D Program of China (2023YFF1304600) for funding support.

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Authors and Affiliations

  1. Ministry of Education Key Laboratory for Ecology of Tropical Islands, Key Laboratory of Tropical Animal and Plant Ecology of Hainan Province, College of Life Sciences, Hainan Normal University, Haikou, China

    Xin Liu, Guixiang Li, Mingzhao Han, Peng Li & Wei Liang

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  1. Xin Liu
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Contributions

X.L.: Formal analysis, investigation, methodology, visualization, writing-original draft. G.L.: Investigation, methodology. M.H.: Investigation, methodology. P.L.: Conceptualization, data curation, supervision, visualization, validation, writing-review & editing. W.L.: Conceptualization, supervision, writing-review & editing.

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Communications Biology thanks Nikolaos Pechlivanis and Rashid Nazir for their contribution to the peer review of this work. Primary Handling Editors: Usman Irshad and Rupali Sathe.

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Liu, X., Li, G., Han, M. et al. Urbanization increases the complexity of soil microbial interaction networks.
Commun Biol (2026). https://doi.org/10.1038/s42003-026-09997-x

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