Theodorou, P. The effects of urbanisation on ecological interactions. Curr. Opin. Insect Sci. 52, 100922 (2022).


Google Scholar
 

Sol, D. et al. The worldwide impact of urbanisation on avian functional diversity. Ecol. Lett. 23, 962–972 (2020).


Google Scholar
 

Fenoglio, M. S., Calviño, A., González, E., Salvo, A. & Videla, M. Urbanisation drivers and underlying mechanisms of terrestrial insect diversity loss in cities. Ecol. Entomol. 46, 757–771 (2021).


Google Scholar
 

Gong et al. Climate and edaphic factors drive soil nematode diversity and community composition in urban ecosystems. Soil Biol. Biochem. 180, 109010 (2023).


Google Scholar
 

Urban, M. C. et al. Interactions between climate change and urbanization will shape the future of biodiversity. Nat. Clim. Change 14, 436–447 (2024).


Google Scholar
 

Nelson, A. E. & Forbes, A. A. Urban land use decouples plant-herbivore-parasitoid interactions at multiple spatial scales. PLoS ONE 9, e102127 (2014).


Google Scholar
 

Li, Z. P. et al. Land use decouples parasite–metazoan host biodiversity associations in soils across subtropical and temperate zones in China. Global Ecol. Biogeogr. 32, 2164–2176 (2023).


Google Scholar
 

Kim, S. W. & Brown, R. D. Urban heat island (UHI) intensity and magnitude estimations: a systematic literature review. Sci. Total Environ. 779, 146389 (2021).


Google Scholar
 

Robinson, J. M., Cameron, R. & Parker, B. The effects of anthropogenic sound and artificial light exposure on microbiomes: ecological and public health implications. Front. Ecol. Evol. 9, 662588 (2021).


Google Scholar
 

Groffman, P. M. et al. Ecological homogenization of residential macrosystems. Nat. Ecol. Evol. 1, 0191 (2017).


Google Scholar
 

Mahtta, R. et al. Urban land expansion: the role of population and economic growth for 300+ cities. npj Urban Sustain. 2, 5 (2022).


Google Scholar
 

O’Riordan, R., Davies, J., Stevens, C., Quinton, J. N. & Boyko, C. The ecosystem services of urban soils: a review. Geoderma 395, 115076 (2021).


Google Scholar
 

Fan, K. et al. Soil biodiversity supports the delivery of multiple ecosystem functions in urban greenspaces. Nat. Ecol. Evol. 7, 113–126 (2023).


Google Scholar
 

Jouquet, P. et al. Above-ground earthworm casts affect water runoff and soil erosion in Northern Vietnam. Catena 74, 13–21 (2008).


Google Scholar
 

Kakeh, J. et al. Biocrust islands enhance infiltration, and reduce runoff and sediment yield on a heavily salinized dryland soil. Geoderma 404, 115329 (2021).


Google Scholar
 

Das, N. & Chandran, P. Microbial degradation of petroleum hydrocarbon contaminants: an overview. Biotechnol. Res. Int. 2011, 941810 (2011).


Google Scholar
 

Sun, X. et al. Harnessing soil biodiversity to promote human health in cities. npj Urban Sustain. 3, 5 (2023).


Google Scholar
 

Delgado-Baquerizo, M. et al. Biogenic factors explain soil carbon in paired urban and natural ecosystems worldwide. Nat. Clim. Change 13, 450–455 (2023).


Google Scholar
 

Rawlins, B. G., Harris, J., Price, S. & Bartlett, M. A review of climate change impacts on urban soil functions with examples and policy insights from England, UK. Soil Use Manag. 31, 46–61 (2015).


Google Scholar
 

Delgado-Baquerizo, M. et al. Global homogenization of the structure and function in the soil microbiome of urban greenspaces. Sci. Adv. 7, eabg5809 (2021).


Google Scholar
 

Whitehead, J., Roy, J., Hempel, S. & Rillig, M. C. Soil microbial communities shift along an urban gradient in Berlin, Germany. Front. Microbiol. 13, 972052 (2022).

Bock, H. W. et al. Soil animal communities demonstrate simplification without homogenization along an urban gradient. Ecol. Appl. 34, e3039 (2024).


Google Scholar
 

Peng, Z. et al. Land conversion to agriculture induces taxonomic homogenization of soil microbial communities globally. Nat. Commun. 15, 3624 (2024).


Google Scholar
 

Valencia, E. et al. Synchrony matters more than species richness in plant community stability at a global scale. Proc. Natl Acad. Sci. USA 117, 24345–24351 (2020).


Google Scholar
 

Christel, A. et al. Urban land uses shape soil microbial abundance and diversity. Sci. Total Environ. 883, 163455 (2023).


Google Scholar
 

Szabó, B. et al. Urbanization decreases species richness, and increases abundance in dry climates whereas decreases in wet climates: a global meta-analysis. Sci. Total Environ. 859, 160145 (2023).


Google Scholar
 

Liu, L. et al. Urbanization reduces soil microbial network complexity and stability in the megacity of Shanghai. Sci. Total Environ. 893, 164915 (2023).


Google Scholar
 

Zhou, J. et al. Urbanization increases stochasticity and reduces the ecological stability of microbial communities in amphibian hosts. Front. Microbiol. 13, 1108662 (2023).


Google Scholar
 

Classen, A. T. et al. Direct and indirect effects of climate change on soil microbial and soil microbial‐plant interactions: What lies ahead? Ecosphere 6, 130 (2015).


Google Scholar
 

Maher, R. L., Rice, M. M., McMinds, R., Burkepile, D. E. & Vega Thurber, R. Multiple stressors interact primarily through antagonism to drive changes in the coral microbiome. Sci. Rep. 9, 6834 (2019).


Google Scholar
 

Ferguson, R. M. et al. The ecological impacts of multiple environmental stressors on coastal biofilm bacteria. Global Change Biol. 27, 3166–3178 (2021).


Google Scholar
 

Belay, A. M., Selassie, Y. G., Tsegaye, E. A., Meshesha, D. T. & Addis, H. K. Soil pH mapping as a function of land use, elevation, and rainfall in the lake tana basin, northwestern of ethiopia. Agrosyst. Geosci. Environ. 6, e20420 (2023).


Google Scholar
 

Liu, J. et al. Soil pH rather than nutrients drive changes in microbial community following long-term fertilization in acidic Ultisols of southern China. J. Soils Sediments 18, 1853–1864 (2018).


Google Scholar
 

Barnett, S. E., Youngblut, N. D. & Buckley, D. H. Soil characteristics and land-use drive bacterial community assembly patterns. FEMS Microbiol. Ecol. 96, fiz194 (2020).


Google Scholar
 

Rate, A. W. in Urban Soils 63–84 (Springer, 2022).

Marcacci, G. et al. Taxonomic and functional homogenization of farmland birds along an urbanization gradient in a tropical megacity. Global Change Biol. 27, 4980–4994 (2021).


Google Scholar
 

Li, Z. P. et al. Colonization ability and uniformity of resources and environmental factors determine biological homogenization of soil protists in human land-use systems. Global Change Biol. 30, e17411 (2024).


Google Scholar
 

Amossé, J. et al. Patterns of earthworm, enchytraeid and nematode diversity and community structure in urban soils of different ages. Eur. J. Soil Biol. 73, 46–58 (2016).


Google Scholar
 

Phillips, H. R. P. et al. Global change and their environmental stressors have a significant impact on soil biodiversity—a meta-analysis. iScience 27, 110540 (2024).


Google Scholar
 

Epp Schmidt, D. J. et al. Urbanization erodes ectomycorrhizal fungal diversity and may cause microbial communities to converge. Nat. Ecol. Evol. 1, 0123 (2017).


Google Scholar
 

Oliverio, A. M. et al. The global-scale distributions of soil protists and their contributions to belowground systems. Sci. Adv. 6, eaax8787 (2020).


Google Scholar
 

Phillips, H. R. et al. Global distribution of earthworm diversity. Science 366, 480–485 (2019).


Google Scholar
 

Bang, C. et al. Metaorganisms in extreme environments: do microbes play a role in organismal adaptation? Zoology 127, 1–19 (2018).


Google Scholar
 

Larsen, S. et al. Climatic effects on the synchrony and stability of temperate headwater invertebrates over four decades. Global Change Biol. 30, e17017 (2024).


Google Scholar
 

Tougeron, K., Brodeur, J., Le Lann, C. & van Baaren, J. How climate change affects the seasonal ecology of insect parasitoids. Ecol. Entomol. 45, 167–181 (2020).


Google Scholar
 

Caruso, T., Melecis, V., Kagainis, U. & Bolger, T. Population asynchrony alone does not explain stability in species‐rich soil animal assemblages: the stabilizing role of forest age on oribatid mite communities. J. Anim. Ecol. 89, 1520–1531 (2020).


Google Scholar
 

Kharouba, H. M. et al. Global shifts in the phenological synchrony of species interactions over recent decades. Proc. Natl Acad. Sci. USA 115, 5211–5216 (2018).


Google Scholar
 

Lai, K. Y. et al. Nexus between residential air pollution and physiological stress is moderated by greenness. Nat. Cities 1, 225–237 (2024).


Google Scholar
 

Luo, S. et al. Impact of socioeconomic factors on soil-borne animal pathogenic fungi in urban greenspaces. Nat. Cities 1, 406–412 (2024).


Google Scholar
 

Biddle, J. F., Fitz-Gibbon, S., Schuster, S. C., Brenchley, J. E. & House, C. H. Metagenomic signatures of the Peru Margin subseafloor biosphere show a genetically distinct environment. Proc. Natl Acad. Sci. USA 105, 10583–10588 (2008).


Google Scholar
 

Stoeck, T. et al. Multiple marker parallel tag environmental DNA sequencing reveals a highly complex eukaryotic community in marine anoxic water. Mol. Ecol. 19, 21–31 (2010).


Google Scholar
 

Adams, R. I., Miletto, M., Taylor, J. W. & Bruns, T. D. Dispersal in microbes: fungi in indoor air are dominated by outdoor air and show dispersal limitation at short distances. ISME J. 7, 1262–1273 (2013).


Google Scholar
 

White, T. J., Bruns, T., Lee, S. J. W. T. & Taylor, J. Amplification and direct sequencing of fungal ribosomal RNA genes for phylogenetics. In PCR Protocols: A Guide to Methods and Applications 315–322 (Academic Press, 1990).

Fan, L. et al. Microbiota comparison of Pacific white shrimp intestine and sediment at freshwater and marine cultured environment. Sci. Total Environ. https://doi.org/10.1016/j.scitotenv.2018.12.069 (2019).

Caporaso, J. G. et al. QIIME allows analysis of high-throughput community sequencing data. Nat. Methods 7, 335–336 (2010).


Google Scholar
 

Edgar, R. C. UPARSE: highly accurate OTU sequences from microbial amplicon reads. Nat. Methods 10, 996–998 (2013).


Google Scholar
 

Edgar, R. C., Haas, B. J., Clemente, J. C., Quince, C. & Knight, R. UCHIME improves sensitivity and speed of chimera detection. Bioinformatics 27, 2194–2200 (2011).


Google Scholar
 

Guillou, L. et al. The Protist Ribosomal Reference database (PR2): a catalog of unicellular eukaryote small sub-unit rRNA sequences with curated taxonomy. Nucleic Acids Res. 41, D597–D604 (2013).


Google Scholar
 

Quast, C. et al. The SILVA ribosomal RNA gene database project: improved data processing and web-based tools. Nucleic Acids Res. 41, D590–D596 (2012).


Google Scholar
 

Nilsson, R. H. et al. The UNITE database for molecular identification of fungi: handling dark taxa and parallel taxonomic classifications. Nucleic Acids Res. 47, D259–D264 (2019).


Google Scholar
 

R Core Team. R: a language and environment for statistical computing (R Foundation for Statistical Computing, 2018); https://www.R-project.org/

Allan, E. et al. Interannual variation in land-use intensity enhances grassland multidiversity. Proc. Natl Acad. Sci. USA 111, 308–313 (2014).


Google Scholar
 

Jurburg, S. D., Keil, P., Singh, B. K. & Chase, J. M. All together now: limitations and recommendations for the simultaneous analysis of all eukaryotic soil sequences. Mol. Ecol. Resour. 21, 1759–1771 (2021).


Google Scholar
 

Oliverio, A. M., Gan, H., Wickings, K. & Fierer, N. A DNA metabarcoding approach to characterize soil arthropod communities. Soil Biol. Biochem. 125, 37–43 (2018).


Google Scholar
 

Bates, D., Mächler, M., Bolker, B. & Walker, S. Fitting linear mixed-effects models using lme4. J. Stat. Softw. 67, 1–48 (2015).


Google Scholar
 

Kuznetsova, A., Brockhoff, P. B. & Christensen, R. H. B. lmerTest package: tests in linear mixed effects models. J. Stat. Softw. 82, 1–26 (2017).


Google Scholar
 

Oksanen, J. et al. vegan: Community Ecology Package. R package version 2.5-7 https://cran.r-project.org/web/packages/vegan/index.html (2020).

Lefcheck, J. S. piecewiseSEM: Piecewise structural equation modeling in R for ecology, evolution, and systematics. Methods Ecol. Evol. https://doi.org/10.1111/2041-210X.12512 (2016).

Lenth, R. emmeans: Estimated Marginal Means, aka Least-Squares Means version 1.11.2 https://cran.r-project.org/package=emmeans (2019).