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The trade-off between microbial functionality and evolutionary flexibility under urbanization

Nature Cities (2026)Cite this article

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Abstract

Urban parks, situated between cities and nature, act as ecological buffers and provide unique niches for soil microbial communities. However, it remains unclear how urbanization affects the functional diversity and evolutionary potential of microbial communities. Here, to address this, we conducted a large-scale field survey across 54 urban park and forest sites in the Pearl River Delta, one of the most rapidly urbanizing regions. Urban parks exhibited higher bacterial and archaeal alpha diversity, biomass, and functional genes related to nutrient cycling compared with forests. These differences were driven by nutrient enrichment and soil pH changes. Microbial genomic analysis revealed a trade-off between short-term ecological functionality and long-term evolvability. Urban parks enhanced immediate functionality but reduced genomic size and evolutionary flexibility, suggesting that urbanization pushes microbial communities toward functional specialization at the expense of adaptive capacity. In contrast, forest soils maintained higher genomic diversity, supporting resilience to environmental changes. These findings highlight the importance of integrating ecological and genomic approaches to predict ecosystem service sustainability in urbanizing areas.

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Fig. 1: Sampling sites and microbial profiles.
Fig. 2: Profiles of microbial functional genes involved in nutrient cycles.
Fig. 3: Profiles of MMF and their influencing factors.
Fig. 4: Metagenome-assembled genomes from UPs and NFs.
Fig. 5: Comparative microbial genomic variation between natural forest and urban park environments.

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Data availability

The data underlying this article are available via the China National Center for Bioinformation at https://www.cncb.ac.cn/ and can be accessed with accession numbers PRJCA049581 (metagenomic). The data that support the findings of this study are available from the corresponding authors upon request.

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Acknowledgements

This study was jointly funded by the National Natural Science Foundation of China (grant number 42477132 to S.-Y.-D.Z.), the NSFC-Guangdong Joint Fund (grant number U25A20764) and the Science and Technology Program of Guangdong (numbers 2024B1212080005 and 2024B1212070012).

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Author notes

  1. These authors contributed equally: Shu-Yi-Dan Zhou, Chaotang Lei.

Authors and Affiliations

  1. Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China

    Shu-Yi-Dan Zhou, Chaotang Lei, Xu Li, Han Sheng & Juxiu Liu

  2. National Ecological Science Data Center Guangdong Branch, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China

    Shu-Yi-Dan Zhou, Chaotang Lei, Xu Li, Han Sheng & Juxiu Liu

  3. Institute for Advanced Study, Shaoxing University, Shaoxing, People’s Republic of China

    Qi Zhang

  4. Hawkesbury Institute for the Environment, Western Sydney University, Hawkesbury Campus, Richmond, Victoria, Australia

    David T. Tissue

  5. Global Ecology Unit CREAF-CSIC-UAB, CSIC, Barcelona, Spain

    Josep Peñuelas

  6. CREAF, Barcelona, Spain

    Josep Peñuelas

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Contributions

S.-Y.-D.Z. conceived and designed the research. C.L., X.L. and H.S. performed the sampling and experiments. S.-Y.-D.Z. and C.L. analyzed the data and prepared the figures. S.-Y.-D.Z. wrote the draft paper. S.-Y.-D.Z., C.L., Q.Z., D.T.T., J.P. and J.L. revised the paper. S.-Y.-D.Z. and J.L. received funding. All authors read and approved the paper.

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Correspondence to Shu-Yi-Dan Zhou or Juxiu Liu.

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Nature Cities thanks Colin T. Bates, Jessica Cuartero and the other, anonymous, reviewer(s) for their contribution to the peer review of this work.

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Supplementary information

Supplementary Information (download PDF )

Supplementary notes, Table 1 and Figs. 1–9.

Supplementary Table 1 (download XLSX )

Urban development indicators and soil physicochemical properties between urban park forests and natural forest areas.

Supplementary Table 2 (download XLSX )

Microbial community diversity in urban forest parks and natural forests.

Supplementary Table 3 (download XLSX )

Ecological niche width between urban park forests and natural forest areas.

Supplementary Table 4 (download XLSX )

Overview of 208 MAGs recovered from metagenomic assemblies of urban forest parks and natural forests.

Supplementary Table 5 (download XLSX )

Genomic genetic variation diversity of soil microbiomes in urban forest parks and natural forests.

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Zhou, SYD., Lei, C., Li, X. et al. The trade-off between microbial functionality and evolutionary flexibility under urbanization. Nat Cities (2026). https://doi.org/10.1038/s44284-026-00412-4

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