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Fossil-fuel-dependent scenarios could lead to a significant decline of global plant-beneficial bacteria abundance in soils by 2100

Nature Food volume 4, pages 996–1006 (2023)Cite this article

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Abstract

Exploiting the potential benefits of plant-associated microbes represents a sustainable approach to enhancing crop productivity. Plant-beneficial bacteria (PBB) provide multiple benefits to plants. However, the biogeography and community structure remain largely unknown. Here we constructed a PBB database to couple microbial taxonomy with their plant-beneficial traits and analysed the global atlas of potential PBB from 4,245 soil samples. We show that the diversity of PBB peaks in low-latitude regions, following a strong latitudinal diversity gradient. The distribution of potential PBB was primarily governed by environmental filtering, which was mainly determined by local climate. Our projections showed that fossil-fuel-dependent future scenarios would lead to a significant decline of potential PBB by 2100, especially biocontrol agents (−1.03%) and stress resistance bacteria (−0.61%), which may potentially threaten global food production and (agro)ecosystem services.

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Fig. 1: Taxonomy of PBB in global soils.
Fig. 2: Global biogeographical distribution of PBB.
Fig. 3: Factors affecting the global distribution of PBB.
Fig. 4: Predicted future changes in PBB.

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Data availability

All raw data used in the current study, including the PBB database, sample metadata, climate data and species-abundance dataset, are publicly available in Figshare (https://doi.org/10.6084/m9.figshare.22274866). The taxonomy information of bacteria is available in the Silva database (https://www.arb-silva.de/). The current and future climate data are available in WorldClim2 (https://www.worldclim.org/). The soil property data are available in the Harmonized World Soil Database (https://www.fao.org/soils-portal/soil-survey). Source data are provided with this paper.

Code availability

Most numerical analyses included in this article do not have an associated code. Used codes are available in Figshare (https://doi.org/10.6084/m9.figshare.22274866).

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Acknowledgements

This study was supported by the National Key R&D Program of China (2022YFA0912501 to J.J.), Fundamental Research Funds for the Central Universities (KYZZ2023003 to J.J.; KYQN2023027 to P.L.; XUEKEN2022003 to B.W.), the National Natural Science Foundation of China (42207349 to P.L.; 41977056 to B.W.; 42107336 to L.L.), the Jiangsu Funding Program for Excellent Postdoctoral Talent (2022ZB331 to P.L.), the Natural Science Foundation of Jiangsu Province (BK20221005 to P.L.), the China Postdoctoral Science Foundation (2022M711653 to P.L.), the grants from DOB Ecology and the Bernina Foundation to T.W.C., and the financial support provided by the USDA National Institute of Food and Agriculture and Hatch Appropriations under Project PEN04732 and Accession number 7000239 to F.D.-A.

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Author notes

  1. These authors contributed equally: Pengfa Li, Leho Tedersoo.

Authors and Affiliations

  1. Department of Microbiology, College of Life Sciences, Nanjing Agricultural University, Key Laboratory of Agricultural and Environmental Microbiology, Ministry of Agriculture and Rural Affairs, Nanjing, China

    Pengfa Li, Lu Kuang, Ting Li, Baozhan Wang & Jiandong Jiang

  2. State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, China

    Pengfa Li, Meng Wu, Yuji Jiang, Lu Luan & Zhongpei Li

  3. Mycology and Microbiology Center, University of Tartu, Tartu, Estonia

    Leho Tedersoo & Mohammad Bahram

  4. Institute of Integrative Biology, ETH Zürich, Zürich, Switzerland

    Thomas W. Crowther

  5. School of Life Sciences, University of Essex, Colchester, UK

    Alex J. Dumbrell

  6. Department of Plant Science and Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA, USA

    Francisco Dini-Andreote

  7. Department of Biological Sciences, Alabama State University, Montgomery, AL, USA

    Muhammad Saleem

  8. Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, Amsterdam, Netherlands

    Franciska T. de Vries

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Contributions

J.J. and B.W. designed the framework. P.L., M.W., Y.J., L.L. and Z.L. collected the samples. P.L., L.K., T.L. and M.B. performed the data analysis. P.L., L.T., T.W.C., A.J.D., F.D.-A., M.B., L.L., M.S., F.T.d.V. and J.J. wrote the paper. All authors discussed the results and commented on the manuscript.

Corresponding authors

Correspondence to Baozhan Wang or Jiandong Jiang.

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The authors declare no competing interests.

Peer review

Peer review information

Nature Food thanks Massimiliano Cardinale, Eleonora Egidi and Joshua Ladau for their contribution to the peer review of this work.

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Supplementary information

Supplementary Information

Supplementary Figs. 1–12 and Tables 1–3.

Reporting Summary

Supplementary Data 1

PBB database.

Supplementary Data 2

Comprehensive list of phytopathogenic bacteria.

Supplementary Data 3

Combined database and R script.

Source data

Source Data Fig. 1

Full PBB database.

Source Data Fig. 2

Source data of biogeographical pattern analyses.

Source Data Fig. 3

Source data of driving force analyses.

Source Data Fig. 4

Source data of future change analyses.

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Li, P., Tedersoo, L., Crowther, T.W. et al. Fossil-fuel-dependent scenarios could lead to a significant decline of global plant-beneficial bacteria abundance in soils by 2100. Nat Food 4, 996–1006 (2023). https://doi.org/10.1038/s43016-023-00869-9

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