Global homogenization of the structure and function in the soil microbiome of urban greenspaces
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2021
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American Association for the Advancement of Science
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Abstract
The structure and function of the soil microbiome of urban greenspaces remain largely undetermined. We conducted a global field survey in urban greenspaces and neighboring natural ecosystems across 56 cities from six continents, and found that urban soils are important hotspots for soil bacterial, protist and functional gene diversity, but support highly homogenized microbial communities worldwide. Urban greenspaces had a greater proportion of fast-growing bacteria, algae, amoebae, and fungal pathogens, but a lower proportion of ectomycorrhizal fungi than natural ecosystems. These urban ecosystems also showed higher proportions of genes associated with human pathogens, greenhouse gas emissions, faster nutrient cycling, and more intense abiotic stress than natural environments. City affluence, management practices, and climate were fundamental drivers of urban soil communities. Our work paves the way toward a more comprehensive global-scale perspective on urban greenspaces, which is integral to managing the health of these ecosystems and the well-being of human populations.
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Acknowledgments
We would like to thank C. Walsh and R. Ochoa-Hueso for advice on bioinformatics and statistical analyses. We also thank M. Martin for revising the English of the manuscript. In addition, we thank J. Owojori for connecting us with our sampling collaborator in Nigeria, A. R. Bamigboye. Funding: M.D.-B. and this project were supported by a 2019 Leonardo Grant for Researchers and Cultural Creators, BBVA Foundation (URBANFUN) and by the BES grant agreement no. LRB17\1019 (MUSGONET). M.D.-B. is also supported by a Ramón y Cajal grant from the Spanish Ministry of Science and Innovation (RYC2018-025483-I). N.F. was supported by grants from the U.S. National Science Foundation (DEB1556090 and DEB1542653). L.T. acknowledges support from Norway-Baltic collaboration grant EMP442 and Estonian Science Foundation grant PRG632. B.K.S. acknowledges a research award by the Humboldt Foundation and funding from the Australian Research Council (DP190103714). F.A. is supported by ANID FONDECYT 11180538 and 1170995. S.A. is funded by ANID FONDECYT 1170995 and ANID ANILLO ACT192027. F.B. and J.L.M. acknowledge support from the Spanish Ministry and FEDER funds for the project AGL2017-85755-R, the i-LINK+ 2018 (LINKA20069) from CSIC, as well as funds from “Fundación Séneca” from Murcia Province (19896/GERM/15). C.P. acknowledges support from the Spanish State Plan for Scientific and Technical Research and Innovation (2013–2016), award reference AGL201675762-R (AEI/FEDER, UE). M.B. acknowledges support from a Juan de la Cierva Formación grant from the Spanish Ministry of Economy and Competitiveness (FJCI-2018-036520-I). T.P.M. would like to acknowledge contributions from the National Research Foundation of South Africa and cities involved in the South African survey. Slovenian coauthors were supported by the research project J4-1766 “Methodology approaches in genome-based diversity and ecological plasticity study of truffles from their natural distribution areas” and the Research Program in Forest Biology, Ecology, and Technology (P4-0107) of the Slovenian Research Agency. J.D. and A. Rey acknowledge support from the FCT (IF/00950/2014 and SFRH/BDP/108913/2015, respectively), as well as from the MCTES, FSE, UE, and the CFE (UIDB/04004/2020) research unit financed by FCT/MCTES through national funds (PIDDAC). J.P.V. acknowledges financial support from SERB (Science and Engineering Research Board) (EEQ/2017/000775) India. J.-Z.H. and H.-W.H. are financially supported by Australian Research Council (DP170101628). The BBVA Foundation accepts no responsibility for the opinions, statements, and contents included in the project and/or the results thereof, which are entirely the responsibility of the authors. Author contributions: M.D.-B. developed the original idea of the analyses presented in the manuscript and coordinated all field and laboratory operations. Field data were collected by M.D.-B., D.J.E., Y.-R.L., 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., M.B., G.F.P.-B., T.U.N., A.L.T., X.-Q.Z., J.D., A. Rodriguez, X.Z., F.A., S.A., C.P., and A. Rey. Laboratory analyses were done by M.D.-B., N.F., H.-W.H., J.-Z.H., F.B., J.L.M., and L.T. Bioinformatic analyses were done by N.F., B.S., J.-T.W., B.K.S., and C.C.-D. Statistical analyses were done by M.D.-B. The manuscript was written by M.D.-B. and edited by N.F. and D.J.E., with contributions from all coauthors. Competing interests: The authors declare that they have no competing interests. Data and materials availability: All data needed to evaluate the conclusions in the paper are present in the paper and/or the Supplementary Materials. The data associated with this study can be found in the following: https://figshare.com/s/529c98609cd88e78e1a3; DOI: 10.6084/m9.figshare.12930986.