Skip to main content

Thank you for visiting You are using a browser version with limited support for CSS. To obtain the best experience, we recommend you use a more up to date browser (or turn off compatibility mode in Internet Explorer). In the meantime, to ensure continued support, we are displaying the site without styles and JavaScript.

Soil biodiversity supports the delivery of multiple ecosystem functions in urban greenspaces


While the contribution of biodiversity to supporting multiple ecosystem functions is well established in natural ecosystems, the relationship of the above- and below-ground diversity with ecosystem multifunctionality remains virtually unknown in urban greenspaces. Here we conducted a standardized survey of urban greenspaces from 56 municipalities across six continents, aiming to investigate the relationships of plant and soil biodiversity (diversity of bacteria, fungi, protists and invertebrates, and metagenomics-based functional diversity) with 18 surrogates of ecosystem functions from nine ecosystem services. We found that soil biodiversity across biomes was significantly and positively correlated with multiple dimensions of ecosystem functions, and contributed to key ecosystem services such as microbially driven carbon pools, organic matter decomposition, plant productivity, nutrient cycling, water regulation, plant–soil mutualism, plant pathogen control and antibiotic resistance regulation. Plant diversity only indirectly influenced multifunctionality in urban greenspaces via changes in soil conditions that were associated with soil biodiversity. These findings were maintained after controlling for climate, spatial context, soil properties, vegetation and management practices. This study provides solid evidence that conserving soil biodiversity in urban greenspaces is key to supporting multiple dimensions of ecosystem functioning, which is critical for the sustainability of urban ecosystems and human wellbeing.

This is a preview of subscription content, access via your institution

Access options

Rent or buy this article

Get just this article for as long as you need it


Prices may be subject to local taxes which are calculated during checkout

Fig. 1: The distribution of soil sampling locations in urban greenspaces.
Fig. 2: Soil biodiversity drives multiple ecosystem functions in urban greenspaces.
Fig. 3: Relationships between soil biodiversity and multi-threshold ecosystem functioning.
Fig. 4: Relationships between soil biodiversity and independent dimensions of ecosystem functioning.
Fig. 5: Contribution of soil biodiversity to ecosystem functions in urban greenspaces.
Fig. 6: Relationships between the diversity of soil microbial traits and ecosystem multifunctionality.

Data availability

Soil biodiversity, plant diversity and ecosystem functioning data from urban greenspaces are publicly available at figshare: (ref. 64).

Code availability

Code for statistical analyses is available at


  1. Griggs, D. et al. Sustainable development goals for people and planet. Nature 495, 305–307 (2013).

    Article  CAS  Google Scholar 

  2. Charlop-Powers, Z. et al. Urban park soil microbiomes are a rich reservoir of natural product biosynthetic diversity. Proc. Natl Acad. Sci. USA 113, 14811 (2016).

    Article  CAS  Google Scholar 

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

    Article  CAS  Google Scholar 

  4. Martínez, J. L. Antibiotics and antibiotic resistance genes in natural environments. Science 321, 365–367 (2008).

    Article  Google Scholar 

  5. Forsberg, K. J. et al. The shared antibiotic resistome of soil bacteria and human pathogens. Science 337, 1107–1111 (2012).

    Article  CAS  Google Scholar 

  6. Byrnes, J. E. K. et al. Investigating the relationship between biodiversity and ecosystem multifunctionality: challenges and solutions. Methods Ecol. Evolution 5, 111–124 (2014).

    Article  Google Scholar 

  7. Gamfeldt, L. & Roger, F. Revisiting the biodiversity–ecosystem multifunctionality relationship. Nat. Ecol. Evolution 1, 0168 (2017).

    Article  Google Scholar 

  8. Lefcheck, J. S. et al. Biodiversity enhances ecosystem multifunctionality across trophic levels and habitats. Nat. Commun. 6, 6936 (2015).

    Article  CAS  Google Scholar 

  9. Zavaleta, E. S. et al. Sustaining multiple ecosystem functions in grassland communities requires higher biodiversity. Proc. Natl Acad. Sci. USA 107, 1443 (2010).

    Article  CAS  Google Scholar 

  10. Delgado-Baquerizo, M. et al. Microbial diversity drives multifunctionality in terrestrial ecosystems. Nat. Commun. 7, 10541 (2016).

    Article  CAS  Google Scholar 

  11. Wagg, C. et al. Soil biodiversity and soil community composition determine ecosystem multifunctionality. Proc. Natl Acad. Sci. USA 111, 5266 (2014).

    Article  CAS  Google Scholar 

  12. van der Heijden, M. G. A. et al. Mycorrhizal fungal diversity determines plant biodiversity, ecosystem variability and productivity. Nature 396, 69–72 (1998).

    Article  Google Scholar 

  13. Delgado-Baquerizo, M. et al. Multiple elements of soil biodiversity drive ecosystem functions across biomes. Nat. Ecol. Evol. 4, 210–220 (2020).

    Article  Google Scholar 

  14. Ramirez, K. S. et al. Biogeographic patterns in below-ground diversity in New York City’s Central Park are similar to those observed globally. Proc. R. Soc. B 281, 20141988 (2014).

    Article  Google Scholar 

  15. Schittko, C. et al. Biodiversity maintains soil multifunctionality and soil organic carbon in novel urban ecosystems. J. Ecol. (2022).

  16. Maestre, F. T. et al. Plant species richness and ecosystem multifunctionality in global drylands. Science 335, 214–218 (2012).

    Article  CAS  Google Scholar 

  17. Jing, X. et al. The links between ecosystem multifunctionality and above-and belowground biodiversity are mediated by climate. Nat. Commun. 6, 1–8 (2015).

    Article  Google Scholar 

  18. Kadowaki, K. et al. Mycorrhizal fungi mediate the direction and strength of plant–soil feedbacks differently between arbuscular mycorrhizal and ectomycorrhizal communities. Commun. Biol. 1, 196 (2018).

    Article  Google Scholar 

  19. Soliveres, S. et al. Biodiversity at multiple trophic levels is needed for ecosystem multifunctionality. Nature 536, 456–459 (2016).

    Article  CAS  Google Scholar 

  20. Berman, J. J. in Taxonomic Guide to Infectious Diseases (ed. Berman, J. J.) 37–47 (Academic Press, 2012).

  21. Berman, J. J. in Taxonomic Guide to Infectious Diseases (ed. Berman, J. J.) 25–31 (Academic Press, 2012).

  22. Busse, H.-J. in Methods in Microbiology (eds Rainey, F. & Oren. A.) Vol. 38, 239–259 (Academic Press, 2011).

  23. van den Hoogen, J. et al. Soil nematode abundance and functional group composition at a global scale. Nature 572, 194–198 (2019).

    Article  Google Scholar 

  24. van Bergeijk, D. A. et al. Ecology and genomics of Actinobacteria: new concepts for natural product discovery. Nat. Rev. Microbiol. 18, 546–558 (2020).

    Article  Google Scholar 

  25. Orellana, L. H. et al. Verrucomicrobiota are specialist consumers of sulfated methyl pentoses during diatom blooms. ISME J. 16, 630–641 (2022).

    Article  CAS  Google Scholar 

  26. Fincker, M. et al. Metabolic strategies of marine subseafloor Chloroflexi inferred from genome reconstructions. Environ. Microbiol. 22, 3188–3204 (2020).

    Article  CAS  Google Scholar 

  27. Stralis-Pavese, N. et al. Analysis of methanotroph community composition using a pmoA-based microbial diagnostic microarray. Nat. Protoc. 6, 609–624 (2011).

    Article  CAS  Google Scholar 

  28. Berube, P. M. et al. Physiology and evolution of nitrate acquisition in Prochlorococcus. ISME J. 9, 1195–1207 (2015).

    Article  CAS  Google Scholar 

  29. Liang, J.-L. et al. Novel phosphate-solubilizing bacteria enhance soil phosphorus cycling following ecological restoration of land degraded by mining. ISME J. 14, 1600–1613 (2020).

    Article  CAS  Google Scholar 

  30. Hättenschwiler, S. & Gasser, P. Soil animals alter plant litter diversity effects on decomposition. Proc. Natl Acad. Sci. USA 102, 1519 (2005).

    Article  Google Scholar 

  31. Erktan, A. et al. The physical structure of soil: determinant and consequence of trophic interactions. Soil Biol. Biochem. 148, 107876 (2020).

    Article  CAS  Google Scholar 

  32. Grime, J. P. Benefits of plant diversity to ecosystems: immediate, filter and founder effects. J. Ecol. 86, 902–910 (1998).

    Article  Google Scholar 

  33. Barberán, A. et al. Why are some microbes more ubiquitous than others? Predicting the habitat breadth of soil bacteria. Ecol. Lett. 17, 794–802 (2014).

    Article  Google Scholar 

  34. Chen, Q. L. et al. Rare microbial taxa as the major drivers of ecosystem multifunctionality in long-term fertilized soils. Soil Biol. Biochem. 141, 107686 (2020).

    Article  CAS  Google Scholar 

  35. Zhang, Z. et al. Rare species-driven diversity-ecosystem multifunctionality relationships are promoted by stochastic community assembly. mBio. mBio. 13, e00449–22 (2022).

    Article  Google Scholar 

  36. Domínguez-García, V. et al. Unveiling dimensions of stability in complex ecological networks. Proc. Natl Acad. Sci. USA 116, 25714 (2019).

    Article  Google Scholar 

  37. Zhang, L. et al. Signal beyond nutrient, fructose, exuded by an arbuscular mycorrhizal fungus triggers phytate mineralization by a phosphate solubilizing bacterium. ISME J. 12, 2339–2351 (2018).

    Article  CAS  Google Scholar 

  38. Couturier, M. et al. Lytic xylan oxidases from wood-decay fungi unlock biomass degradation. Nat. Chem. Biol. 14, 306–310 (2018).

    Article  CAS  Google Scholar 

  39. Steinberg, G. et al. A lipophilic cation protects crops against fungal pathogens by multiple modes of action. Nat. Commun. 11, 1608 (2020).

    Article  CAS  Google Scholar 

  40. Johnston, A. S. A. & Sibly, R. M. The influence of soil communities on the temperature sensitivity of soil respiration. Nat. Ecol. Evol. 2, 1597–1602 (2018).

    Article  Google Scholar 

  41. Watson, C. J. et al. Ecological and economic benefits of low-intensity urban lawn management. J. Appl. Ecol. 57, 436–446 (2020).

    Article  Google Scholar 

  42. Williams, N. S. G. et al. A conceptual framework for predicting the effects of urban environments on floras. J. Ecol. 97, 4–9 (2009).

    Article  Google Scholar 

  43. Trabucco, A. & Zomer, R. Global Aridity Index and Potential Evapotranspiration (ET0) Climate Database v2 (figshare, 2019);

  44. Kettler, T. A. et al. Simplifed method for soil particle-size determination to accompany soil-quality analyses. Soil Sci. Soc. Am. J. 65, 849–852 (2001).

    Article  CAS  Google Scholar 

  45. Delgado-Baquerizo, M. et al. Changes in belowground biodiversity during ecosystem development. Proc. Natl Acad. Sci. USA 116, 6891 (2019).

    Article  CAS  Google Scholar 

  46. Ramirez, K. S. et al. Biogeographic patterns in below-ground diversity in New York City’s Central Park are similar to those observed globally. Proc. Biol. Sci. 281, 22 (2014).

    Google Scholar 

  47. Callahan, B. J. et al. DADA2: high-resolution sample inference from Illumina amplicon data. Nat. Methods 13, 581–583 (2016).

    Article  CAS  Google Scholar 

  48. Tedersoo, L. et al. Regional-scale in-depth analysis of soil fungal diversity reveals strong pH and plant species effects in Northern Europe. Front. Microbiol. 11, 1953 (2020).

    Article  Google Scholar 

  49. Bastida, F. et al. Microbiological degradation index of soils in a semiarid climate. Soil Biol. Biochem. 38, 3463–3473 (2006).

    Article  CAS  Google Scholar 

  50. Lugato, E. et al. Different climate sensitivity of particulate and mineral-associated soil organic matter. Nat. Geosci. 14, 295–300 (2021).

    Article  CAS  Google Scholar 

  51. Delgado-Baquerizo, M. et al. The influence of soil age on ecosystem structure and function across biomes. Nat. Commun. 11, 4721 (2020).

    Article  CAS  Google Scholar 

  52. Frostegård, Å. et al. Use and misuse of PLFA measurements in soils. Soil Biol. Biochem. 43, 1621–1625 (2011).

    Article  Google Scholar 

  53. Olsson, P. A. et al. The use of phospholipid and neutral lipid fatty acids to estimate biomass of arbuscular mycorrhizal fungi in soil. Mycol. Res. 99, 623–629 (1995).

    Article  CAS  Google Scholar 

  54. Campbell, C. D. et al. A rapid microtiter plate method to measure carbon dioxide evolved from carbon substrate amendments so as to determine the physiological profiles of soil microbial communities by using whole soil. Appl. Environ. Microbiol. 69, 3593–3599 (2003).

    Article  CAS  Google Scholar 

  55. Bell, C. W. et al. High-throughput fluorometric measurement of potential soil extracellular enzyme activities. J. Vis. Exp. 15, e50961 (2013).

    Google Scholar 

  56. Nguyen, N. H. et al. FUNGuild: an open annotation tool for parsing fungal community datasets by ecological guild. Fungal Ecol. 20, 241–248 (2016).

    Article  Google Scholar 

  57. Fierer, N. et al. Cross-biome metagenomic analyses of soil microbial communities and their functional attributes. Proc. Natl Acad. Sci. USA 109, 21390–21395 (2012).

    Article  CAS  Google Scholar 

  58. Fierer, N. et al. Reconstructing the microbial diversity and function of pre-agricultural tallgrass prairie soils in the United States. Science 342, 621–624 (2013).

    Article  CAS  Google Scholar 

  59. Buchfink, B., Reuter, K. & Drost, H. G. Sensitive protein alignments at tree-of-life scale using DIAMOND. Nat. Methods 18, 366–368 (2021).

    Article  CAS  Google Scholar 

  60. Manning, P. et al. Redefining ecosystem multifunctionality. Nat. Ecol. Evolution 2, 427–436 (2018).

    Article  Google Scholar 

  61. Legendre, P. & Legendre, L. Interpretation of Ecological Structures Numerical Ecology 3rd English edn (Elsevier Science BV, 2012).

  62. Grace, J. B. Structural Equation Modeling and Natural Systems (Cambridge University Press, 2006).

  63. Subramanian, S. et al. Persistent gut microbiota immaturity in malnourished Bangladeshi children. Nature 510, 417 (2014).

    Article  CAS  Google Scholar 

  64. Fan, K. et al. Soil biodiversity supports the delivery of multiple ecosystem functions in urban greenspaces. figshare (2022).

Download references


We thank the researchers involved in the MUSGONET project for collection of field data and soil samples. This study was supported by a 2019 Leonardo Grant for Researchers and Cultural Creators, BBVA Foundation (URBANFUN), and by the BES grant agreement number LRB17\1019 (MUSGONET). M.D.-B. acknowledges support from the Spanish Ministry of Science and Innovation for the I+D+i project PID2020-115813RA-I00 funded by MCIN/AEI/10.13039/501100011033. M.D.-B. is also supported by a project of the Fondo Europeo de Desarrollo Regional (FEDER) and the Consejería de Transformación Económica, Industria, Conocimiento y Universidades of the Junta de Andalucía (FEDER Andalucía 2014-2020 Objetivo temático ‘01—Refuerzo de la investigación, el desarrollo tecnológico y la innovación’) associated with the research project P20_00879 (ANDABIOMA). H.C. was supported by the Strategic Priority Research Program of Chinese Academy of Sciences (XDA28020202), National Key R&D Program of China (2022YFD1500202) and the National Natural Science Foundation of China (91951109, 42230511, 92251305). K.F. was supported by Young Elite Scientist Sponsorship Program by CAST (2021QNRC001) and China Postdoctoral Science Foundation (2021M703302). F.D.A. and S.A. were supported by ANID FONDECYT 11180538 and 1170995. J.P.V. was supported by SERB (SIR/2022/000626, EEQ/2021/001083), DST (DST/INT/SL/P-31/2021) and Banaras Hindu University, IoE (6031) incentives grant for plant-microbe interaction and soil microbiome research. T.G. and T.U.N were supported by the Slovenian Research Agency grants P4-0107, J4-3098 and J4-4547.

Author information

Authors and Affiliations



M.D.-B. developed the original idea and designed the research with discussion with H.Chu. and K.F. M.D.-B. coordinated all field and laboratory operations. K.F., M.D.-B. and H.Chu. analysed data. Field data were collected by M.D.-B., D.J.E., Y.-R.L., B.S., A.R.B., J.L.B.-P., J.G.I., T.P.M., C.S., P.T., E.Z., J.P.V., L.W., J.W., T.G., A.M., M.B., G.F.P.-B., T.U.N., A.L.T., X.-Q.Z., F.B., M.D.-L, J.D., A. Rodríguez., X.Z., F.D.A., S.A., C.P., J.J.G., J.-T.W., H.-W.H., J.-Z.H., W.S., H.Cui., T.Y., L.T. and A. Rey. The manuscript was written by K.F., M.D.-B. and H.Chu., with contributions from all co-authors.

Corresponding authors

Correspondence to Haiyan Chu or Manuel Delgado-Baquerizo.

Ethics declarations

Competing interests

The authors declare no competing interests.

Peer review

Peer review information

Nature Ecology & Evolution thanks María Gómez Brandón and the other, anonymous, reviewer(s) for their contribution to the peer review of this work. Peer reviewer reports are available.

Additional information

Publisher’s note Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.

Extended data

Extended Data Fig. 1 Location of the 27 urban greenspaces selected for shotgun sequencing analyses.

Location of the 27 urban greenspaces selected for shotgun sequencing analyses and covering the entire biogeographical range in Fig. 1.

Extended Data Fig. 2 Ordinary least squares linear regression between plant diversity and the multiple dimensions of ecosystem functions.

Ordinary least squares linear regression between plant diversity and the multiple dimensions of ecosystem functions, n = 56 study sites.

Extended Data Fig. 3 Conceptual model investigating the direct and indirect linkages between soil biodiversity and ecosystem function.

Conceptual model investigating the direct and indirect linkages between soil biodiversity and ecosystem function. (a) A priori structural equation modeling (SEM) metamodel aimed to evaluate the link between soil biodiversity and ecosystem multifunctionality after controlling for key ecological predictors such as space, climate, and soil and plant attributes. (b) Explanations for each association link priori structural equation modeling metamodel.

Extended Data Fig. 4 Random forest model detects soil biota that are accurately predictive of ecosystem multifunctionality in urban greenspaces across the globe.

Random forest model detects soil biota that are accurately predictive of ecosystem multifunctionality in urban greenspaces across the globe. The result of predicting ecosystem multifunctionality in urban greenspaces across the globe using the random forest (RF) models for the soil biota of the selected groups (bacteria, fungi, protists, and invertebrates). Heat maps of the relative abundance of the 77 indicative soil biota and ecosystem multifunctionality. Statistical analysis was performed using two-sided spearman correlations; P values were adjusted by Benjamini Hochberg false discovery correction, and indicated by asterisks, ‘*’ represents Benjamini Hochberg-adjusted 0.01 < P ≤ 0.05; ‘**’ represents Benjamini Hochberg-adjusted P ≤ 0.01; n = 56 study sites.

Extended Data Fig. 5 Random forest model detects soil genes that are accurately predictive of ecosystem multifunctionality in urban greenspaces across the globe.

Random forest model detects soil genes that are accurately predictive of ecosystem multifunctionality in urban greenspaces across the globe. (a) Random forest model detects 159 genes in contributing to the ecosystem multifunctionality in urban greenspaces across the globe. (b) Ordinary least squares linear regression between multifunctionality and the proportion of the selected nutrient cycling associated genes: methane monooxygenase subunit A encoding (pmoA) gene, ferredoxin-nitrate reductase encoding (narB) gene, alkaline phosphatase D encoding (phoD) gene, and sulfate adenylyltransferase subunit 2 encoding (cysD) gene; n = 27 study sites.

Supplementary information

Supplementary Information

This pdf file includes: Supplementary Figs. 1–5, Tables 1–11 and references.

Reporting Summary.

Peer Review File.

Rights and permissions

Springer Nature or its licensor (e.g. a society or other partner) holds exclusive rights to this article under a publishing agreement with the author(s) or other rightsholder(s); author self-archiving of the accepted manuscript version of this article is solely governed by the terms of such publishing agreement and applicable law.

Reprints and Permissions

About this article

Verify currency and authenticity via CrossMark

Cite this article

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

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI:

This article is cited by


Quick links

Nature Briefing

Sign up for the Nature Briefing newsletter — what matters in science, free to your inbox daily.

Get the most important science stories of the day, free in your inbox. Sign up for Nature Briefing