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Disruption of the oak tree microbiome with urbanization

Nature Cities volume 2, pages 958–968 (2025) Cite this article

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Abstract

The tree microbiome, the community of bacteria and fungi that live in and on trees, is a critical determinant of tree and ecosystem functioning, but human-caused disturbances can disrupt natural microbe–tree relationships. Here we show that urbanization shifts the structure and composition of the oak tree microbiome, reducing mutualistic root and leaf symbionts and increasing decomposers and pathogens, including those relevant to plant, animal and human health. These shifts correlate with urban stressors such as heat, drought and atmospheric aerosol deposition. Urban tree microbiomes also show altered biogeochemical cycling capabilities, with higher potential for nitrogen loss through greenhouse gas (N2O) production and reduced capacity for methane consumption relative to rural trees. Urbanization reduces overall tree microbiome diversity, particularly among non-pathogenic microbes, potentially diminishing the ecological and health benefits of environmental microbiomes in cities.

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Fig. 1: Urbanization impacts key functional groups within the tree microbiome.
The alternative text for this image may have been generated using AI.
Fig. 2: The impact of urbanization on animal and zoonotic pathogen loads within the tree microbiome.
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Fig. 3: Urbanization shifted biogeochemical cycling and cycling potential of soil microbiomes.
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Fig. 4: The effect of urbanization on the diversity of fungal and bacterial communities in leaves and belowground.
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Data availability

Raw amplicon sequence data can be accessed with the NCBI BioProject accession PRJNA1297772. Associated metadata can be found at the Environmental Data Initiative (https://doi.org/10.6073/pasta/8a62a159a839e8a33e10b787f2edd5d1).

Code availability

All data analysis scripts are publicly available via Github at https://github.com/k-atherton/M-BUDS.

Change history

  • 29 January 2026

    In the version of this article initially published, thanks in the Acknowledgements to the W.M. Keck Foundation for an award (CRM:0132339) to J.M.B., L.R.H. and P.H.T. was missing and is now included in the HTML and PDF versions of the article.

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Acknowledgements

We thank the Boston Parks and Recreation Department, Arnold Arboretum of Harvard University, Harvard Forest, Massachusetts Department of Conservation and Recreation, Massachusetts Department of Environmental Protection, the Massachusetts Department of Transportation, Massachusetts Audubon Society, National Grid, cities of Newton and Lexington, MA, and all landowners for allowing research on their properties. We thank the Design, Automation, Manufacturing and Processes (DAMP) lab at Boston University for PCR amplification of many DNA extracts. We are grateful for assistance in leaf collections from the UNE sites from J. Rindy and from the Harvard Forest Biomass Inventory Plots from B. Munger and T. Whitby and help with soil processing from D. Moyer, R. Miller and C. Bagnani. We further thank members of the Bhatnagar, Templer and Hutyra labs for their assistance in the laboratory, field and data analysis and edits on earlier drafts of this manuscript from members of Bhatnagar, Templer and Hutyra Labs. This study was financially supported in part by the Boston University URBAN Program awards to K.F.A., the Boston University Microbiome Initiative Accelerator Program and an Initiative on Cities grant to K.F.A. and J.M.B.; W.M. Keck Foundation award (CRM:0132339) to J.M.B., L.R.H. and P.H.T., United States Department of Agriculture and National Institute of Food and Agriculture grant to P.H.T. and L.R.H. (USDA NIFA 67003-26615), DOE BER award DE-SC0020403, a Patricia McLellan Leavitt Research Award, a start-up fund from Boston University and Boston University’s internal Peter Paul Professorship fund to J.M.B. Research reported in this publication was supported by the National Institute of General Medical Sciences of the National Institutes of Health under award numbers T32GM150533 and T32GM100842. Support was also provided by a National Science Foundation Research Traineeship (NRT) grant to Boston University (DGE 1735087). The content is solely the responsibility of the authors and does not necessarily represent the official views of the National Institutes of Health.

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Authors and Affiliations

  1. Bioinformatics Graduate Program, Boston University, Boston, MA, USA

    Kathryn F. Atherton

  2. Department of Biology, Boston University, Boston, MA, USA

    Kathryn F. Atherton, Chikae Tatsumi, Isabelle Frenette, David Heaton, Pamela H. Templer & Jennifer M. Bhatnagar

  3. Department of Earth and Environment, Boston University, Boston, MA, USA

    Ian A. Smith & Lucy R. Hutyra

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Contributions

K.F.A., I.A.S., L.R.H., P.H.T. and J.M.B. designed research; K.F.A., I.F., D.H. and J.M.B. performed research; K.F.A., C.T., I.A.S. and J.M.B. analyzed research; and K.F.A., C.T. and J.M.B. wrote the paper.

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Atherton, K.F., Tatsumi, C., Frenette, I. et al. Disruption of the oak tree microbiome with urbanization. Nat Cities 2, 958–968 (2025). https://doi.org/10.1038/s44284-025-00322-x

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