Skip to main content

Thank you for visiting nature.com. 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.

  • Article
  • Published:

The proportion of soil-borne pathogens increases with warming at the global scale

Nature Climate Change volume 10, pages 550–554 (2020)Cite this article

Subjects

Abstract

Understanding the present and future distribution of soil-borne plant pathogens is critical to supporting food and fibre production in a warmer world. Using data from a global field survey and a nine-year field experiment, we show that warmer temperatures increase the relative abundance of soil-borne potential fungal plant pathogens. Moreover, we provide a global atlas of these organisms along with future distribution projections under different climate change and land-use scenarios. These projections show an overall increase in the relative abundance of potential plant pathogens worldwide. This work advances our understanding of the global distribution of potential fungal plant pathogens and their sensitivity to ongoing climate and land-use changes, which is fundamental to reduce their incidence and impacts on terrestrial ecosystems globally.

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

Access options

Buy this article

  • Purchase on Springer Link
  • Instant access to full article PDF
Buy now

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

Fig. 1: Relative abundance, identity and ecological preferences of potential plant pathogens worldwide.
Fig. 2: Temperature is positively associated with the relative abundance of potential plant pathogens at the genus level.
Fig. 3: Experimental evidence that warming increases the relative and total abundance of potential plant pathogens.
Fig. 4: Current relative abundance and temporal projections (2050) of potential plant pathogens across the globe.

Similar content being viewed by others

Data availability

The data associated with the global field survey and the field experiment are publicly available in Figshare57.

Code availability

Most numerical analyses included in this article do not have an associated code. Used codes are available in Figshare57.

References

  1. Barford E. Crop pests advancing with global warming. Nature https://doi.org/10.1038/nature.2013.13644 (2013).

  2. Newbery, F. et al. Modelling impacts of climate change on arable crop diseases: progress, challenges and applications. Curr. Opin. Plant Biol. 32, 101–109 (2016).

    Google Scholar 

  3. Tollefson, J. IPCC says limiting global warming to 1.5 °C will require drastic action. Nature 562, 172–173 (2018).

    CAS  Google Scholar 

  4. Chakraborty, S. & Newton, A. C. Climate change, plant diseases and food security. Plant Pathol. 60, 2–14 (2011).

    Google Scholar 

  5. Moore, D. et al. 21st Century Guidebook to Fungi (Cambridge Univ. Press, 2011).

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

    Google Scholar 

  7. Parry, D. W. et al. Fusarium ear blight (scab) in small grain cereals—a review. Plant Pathol. 44, 207–238 (1993).

    Google Scholar 

  8. Qiu, Z. et al. New frontiers in agriculture productivity: optimised microbial inoculants and in situ microbiome engineering. Biotechnol. Adv. 37, 107371 (2019).

    Google Scholar 

  9. Tedersoo, L. et al. Global diversity and geography of soil fungi. Science 346, 1256688 (2014).

    Google Scholar 

  10. Asner, G. P. et al. Grazing systems, ecosystem responses, and global change. Annu. Rev. Environ. Resour. 29, 261–299 (2004).

    Google Scholar 

  11. Maestre, F. T. et al. Structure and functioning of dryland ecosystems in a changing world. Annu. Rev. Environ. Resour. 47, 215–237 (2016).

    Google Scholar 

  12. IPCC Climate Change 2013: The Physical Science Basis (eds Stocker, T. F. et al.) (Cambridge Univ. Press, 2013).

  13. Oliverio, A. M. et al. Identifying the microbial taxa that consistently respond to soil warming across time and space. Glob. Change Biol. 23, 2117–2129 (2017).

    Google Scholar 

  14. Bebber, D. P. et al. The global spread of crop pests and pathogens. Glob. Ecol. Biogeogr. 23, 1398–1407 (2013).

    Google Scholar 

  15. Egidi, E. et al. A few Ascomycota taxa dominate soil fungal communities worldwide. Nat. Commun. 10, 2369 (2019).

    Google Scholar 

  16. De Guevara, M. L. et al. The ‘PhenoBox’, a flexible, automated, open‐source plant phenotyping solution. New Phytol. 219, 808–823 (2018).

    Google Scholar 

  17. Guiot, J. & Wolfgang Cramer, W. Mediterranean warming fast, deserts may spread in Europe. Science 354, 465–468 (2016).

    CAS  Google Scholar 

  18. Dean, R. et al. The top 10 fungal pathogens in molecular plant pathology. Mol. Plant Pathol. 13, 414–430 (2012).

    Google Scholar 

  19. Agrios, G. N. Plant Pathology (Academic, 2005).

  20. IPCC Special Report on Land Use, Land-Use Change and Forestry (Cambridge Univ. Press, 2000).

  21. Bell, T. & Tylianakis, J. M. Microbes in the Anthropocene: spillover of agriculturally selected bacteria and their impact on natural ecosystems. Proc. Biol. Sci. 283, 20160896 (2016).

    Google Scholar 

  22. Caliz, J. et al. A long-term survey unveils strong seasonal patterns in the airborne microbiome coupled to general and regional atmospheric circulations. Proc. Natl Acad. Sci. USA 115, 12229–12234 (2018).

    CAS  Google Scholar 

  23. Barberan, A. et al. Continental-scale distributions of dust-associated bacteria and fungi. Proc. Natl Acad. Sci. USA 112, 5756–5761 (2015).

    CAS  Google Scholar 

  24. Sugden, A. M. Warming, crops, and insect pests. Science 361, 888–889 (2018).

    Google Scholar 

  25. Borrelli, P. et al. An assessment of the global impact of 21st century land use change on soil erosion. Nat. Commun. 8, 2013 (2017).

    Google Scholar 

  26. Panagos, P. et al. The new assessment of soil loss by water erosion in Europe. Environ. Sci. Policy 54, 438 (2015).

    Google Scholar 

  27. World Population Prospects 2019: Highlights (United Nations Department of Economic and Social Affairs, Population Division, 2019).

  28. Delgado-Baquerizo, M. et al. A global atlas of the dominant bacteria found in soil. Science 325, 320–325 (2018).

    Google Scholar 

  29. Steidinger, B. S. et al. Climatic controls of decomposition drive the global biogeography of forest–tree symbioses. Nature 569, 404–408 (2019).

    CAS  Google Scholar 

  30. Köhl, J. et al. Epidemiology of dark leaf spot caused by Alternaria brassicicola and A. brassicae in organic seed production of cauliflower. Plant Pathol. 59, 358–367 (2010).

    Google Scholar 

  31. Hijmans, R. J. et al. Very high resolution interpolated climate surfaces for global land areas. Int. J. Clim. 25, 1965–1978 (2005).

    Google Scholar 

  32. Filipponi, F. et al. Global MODIS fraction of green vegetation cover for monitoring abrupt and gradual vegetation changes. Remote Sens. 10, 653 (2018).

    Google Scholar 

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

    CAS  Google Scholar 

  34. Anderson, J. M. & Ingram, J. S. I. (eds) Tropical Soil Biology and Fertility: A Handbook of Methods 2nd edn (CABI, 1993).

  35. Grace, J. B. Structural Equation Modeling Natural Systems (Cambridge Univ. Press, 2006).

  36. Schermelleh-Engel, K. et al. Evaluating the fit of structural equation models: tests of significance and descriptive goodness-of-fit measures. Methods Psychol. Res. 8, 23–74 (2003).

    Google Scholar 

  37. Klaus B. & Strimmer K. Estimation of (Local) False Discovery Rates and Higher Criticism. R package ‘drtool’ version 1.2.15 (2015); https://cran.r-project.org/

  38. Monteleoni, C. et al. Tracking climate models. Stat. Anal. Data Min. 4, 372–392 (2011).

    Google Scholar 

  39. Hempel, S. et al. A trend-preserving bias correction—the ISI–MIP approach. Earth Syst. Dyn. 4, 219–236 (2013).

    Google Scholar 

  40. Lawrence, D. M. et al. The land use model intercomparison project (LUMIP) contribution to CMIP6: rationale and experimental design. Geosci. Model Dev. 9, 2973–2998 (2016).

    Google Scholar 

  41. Kim, H. et al. A protocol for an intercomparison of biodiversity and ecosystem services models using harmonized land-use and climate scenarios. Geosci. Model Dev. 11, 4537–4562 (2018).

    Google Scholar 

  42. Dufresne, J.-L. et al. Climate change projections using the IPSL-CM5 Earth System Model: from CMIP3 to CMIP5. Clim. Dyn. 40, 2123–2165 (2013).

    Google Scholar 

  43. Hurtt, G. C. et al. Harmonization of land-use scenarios for the period 1500–2100: 600 years of global gridded annual land-use transitions, wood harvest, and resulting secondary lands. Clim. Change 109, 117 (2011).

    Google Scholar 

  44. Popp, A. et al. Land-use futures in the shared socio-economic pathways. Glob. Environ. Change 42, 331–345 (2017).

    Google Scholar 

  45. O’Neill, B. C. et al. A new scenario framework for climate change research: the concept of shared socioeconomic pathways. Clim. Change 122, 387–400 (2014).

    Google Scholar 

  46. USGS EROS Archive. Digital Elevation - Global Multi-resolution Terrain Elevation Data 2010 (GMTED2010) (USGS, 2010); https://www.usgs.gov/centers/eros/science/usgs-eros-archive-digital-elevation-global-multi-resolution-terrain-elevation

  47. Maestre F. T. et al. in Biological Soil Crusts: An Organizing Principle in Drylands (eds Weber, Büdel, B. and Belnap, J.) 407–425 (Springer, 2016).

  48. Bowker, M. A. et al. Biological soil crusts (biocrusts) as a model system in community, landscape and ecosystem ecology. Biodivers. Conserv. 23, 1619–1637 (2014).

    Google Scholar 

  49. Castillo-Monroy, A. P. et al. Biological soil crusts modulate nitrogen availability in semi-arid ecosystems: insights from a Mediterranean grassland. Plant Soil 333, 21–34 (2010).

    CAS  Google Scholar 

  50. Maestre, F. T. et al. Changes in biocrust cover drive carbon cycle responses to climate change in drylands. Glob. Change Biol. 19, 3835–3847 (2013).

    Google Scholar 

  51. De Castro, M. et al. Evaluación Preliminar de los Impactos en España por Efecto del Cambio Climático (Ministerio Medio Ambiente, 2005).

  52. Edgar, R. C. Search and clustering orders of magnitude faster than BLAST. Bioinformatics 26, 2460–2461 (2010).

    CAS  Google Scholar 

  53. Edgar, R. C. UNOISE2: improved error-correction for Illumina 16S and ITS amplicon sequencing. Preprint at https://doi.org/10.1101/081257 (2016).

  54. Kõljalg, U. et al. UNITE: a database providing web-based methods for the molecular identification of ectomycorrhizal fungi. New Phytol. 166, 1063–1068 (2005).

    Google Scholar 

  55. Geiser, D. M. et al. One fungus, one name: defining the genus Fusarium in a scientifically robust way that preserves longstanding use. Phytopathology 103, 400–408 (2013).

    Google Scholar 

  56. Kulik, T. et al. Quantification of Alternaria, Cladosporium, Fusarium and Penicillium verrucosum in conventional and organic grains by qPCR. J. Phytopathol. 163, 522–528 (2015).

    Google Scholar 

  57. Delgado-Baquerizo, M. et al. The Proportion of Soil-borne Pathogens Increases with Warming at the Global Scale https://doi.org/10.6084/m9.figshare.11484747 (2020).

Download references

Acknowledgements

This project received funding from the European Union’s Horizon 2020 research and innovation programme under the Marie Sklodowska-Curie grant agreement No 702057 and the European Research Council (ERC) grant agreements no. 242658 (BIOCOM) and no. 647038 (BIODESERT). We thank R. D. Bardgett, N. Fierer, A. Benavent-González and D. J. Eldridge for their original contributions to the global survey, and V. Ochoa, C. Escolar, P. Alonso, B. Gozalo and S. Ochoa for maintaining the warming experiment and for their help with laboratory analyses. We also thank M.S. Martin for revising the English of the manuscript. M.D.-B. is supported by a Ramón y Cajal grant from the Spanish Government (agreement no. RYC2018-025483-I) and a MUSGONET grant (LRA17\1193) from the British Ecological Society. F.T.M. also acknowledges funding from Generalitat Valenciana (CIDEGENT/2018/041) and from sDiv, the synthesis centre of the German Centre for Integrative Biodiversity Research Halle–Jena–Leipzig (iDiv). Work on microbial distribution and colonization in the B.K.S. laboratory is funded by the Australian Research Council (DP190103714). B.K.S. also acknowledges a research award by the Humboldt Foundation. C.A.G. and N.E. acknowledge support from iDiv, funded by the German Research Foundation (DFG FZT118) through flexpool proposals 34600850 and 34600844. N.E. also acknowledges support from the ERC under the European Union’s Horizon 2020 research and innovation programme (grant agreement no. 677232).

Author information

Authors and Affiliations

  1. Departamento de Sistemas Físicos, Químicos y Naturales, Universidad Pablo de Olavide, Sevilla, Spain

    Manuel Delgado-Baquerizo

  2. German Centre for Integrative Biodiversity Research (iDiv) Halle–Jena–Leipzig, Leipzig, Germany

    Carlos A. Guerra & Nico Eisenhauer

  3. Institute of Biology, Martin-Luther University Halle–Wittenberg, Halle (Saale), Germany

    Carlos A. Guerra

  4. Departamento de Biología y Geología, Física y Química Inorgánica, Escuela Superior de Ciencias Experimentales y Tecnología, Universidad Rey Juan Carlos, Móstoles, Spain

    Concha Cano-Díaz

  5. Global Centre for Land-Based Innovation, Western Sydney University, Penrith, New South Wales, Australia

    Eleonora Egidi, Jun-Tao Wang & Brajesh K. Singh

  6. Hawkesbury Institute for the Environment, Western Sydney University, Penrith, New South Wales, Australia

    Eleonora Egidi, Jun-Tao Wang & Brajesh K. Singh

  7. State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China

    Jun-Tao Wang

  8. Institute of Biology, Leipzig University, Leipzig, Germany

    Nico Eisenhauer

  9. Instituto Multidisciplinar para el Estudio del Medio ‘Ramón Margalef’, Universidad de Alicante, Alicante, Spain

    Fernando T. Maestre

  10. Departamento de Ecología, Universidad de Alicante, Alicante, Spain

    Fernando T. Maestre

Authors
  1. Manuel Delgado-Baquerizo
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Carlos A. Guerra
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Concha Cano-Díaz
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Eleonora Egidi
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. Jun-Tao Wang
    View author publications

    You can also search for this author in PubMed Google Scholar

  6. Nico Eisenhauer
    View author publications

    You can also search for this author in PubMed Google Scholar

  7. Brajesh K. Singh
    View author publications

    You can also search for this author in PubMed Google Scholar

  8. Fernando T. Maestre
    View author publications

    You can also search for this author in PubMed Google Scholar

Contributions

M.D.-B. developed the original idea of the analyses presented in the manuscript. M.D.-B, F.T.M. and B.K.S. led the global survey. F.T.M. designed the field warming experiment and has maintained it over the years. Lab analyses were done by M.D.-B., C.C.-D., E.E., F.T.M. and B.K.S. Bioinformatic analyses were done by B.K.S., J.-T.W. and E.E. Statistical modelling, mapping and data interpretations were done by C.A.G., N.E. and M.D.-B. The manuscript was written by M.D.-B. with contributions from all the co-authors.

Corresponding author

Correspondence to Manuel Delgado-Baquerizo.

Ethics declarations

Competing interests

The authors declare no competing interests.

Additional information

Peer review information Nature Climate Change thanks Leho Tedersoo and the other, anonymous, reviewer(s) for their contribution to the peer review of this work.

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

Supplementary information

Supplementary Information

Supplementary Appendices 1 and 2, Figs. 1–12 and Tables 1–10.

Reporting Summary

Supplementary Data 1

Rights and permissions

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Delgado-Baquerizo, M., Guerra, C.A., Cano-Díaz, C. et al. The proportion of soil-borne pathogens increases with warming at the global scale. Nat. Clim. Chang. 10, 550–554 (2020). https://doi.org/10.1038/s41558-020-0759-3

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1038/s41558-020-0759-3

This article is cited by

Search

Advanced search

Quick links

Nature Briefing Anthropocene

Sign up for the Nature Briefing: Anthropocene newsletter — what matters in anthropocene research, free to your inbox weekly.

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