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Climate warming accelerates temporal scaling of grassland soil microbial biodiversity

Nature Ecology & Evolution volume 3, pages 612–619 (2019)Cite this article

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Abstract

Determining the temporal scaling of biodiversity, typically described as species–time relationships (STRs), in the face of global climate change is a central issue in ecology because it is fundamental to biodiversity preservation and ecosystem management. However, whether and how climate change affects microbial STRs remains unclear, mainly due to the scarcity of long-term experimental data. Here, we examine the STRs and phylogenetic–time relationships (PTRs) of soil bacteria and fungi in a long-term multifactorial global change experiment with warming (+3 °C), half precipitation (−50%), double precipitation (+100%) and clipping (annual plant biomass removal). Soil bacteria and fungi all exhibited strong STRs and PTRs across the 12 experimental conditions. Strikingly, warming accelerated the bacterial and fungal STR and PTR exponents (that is, the w values), yielding significantly (P < 0.001) higher temporal scaling rates. While the STRs and PTRs were significantly shifted by altered precipitation, clipping and their combinations, warming played the predominant role. In addition, comparison with the previous literature revealed that soil bacteria and fungi had considerably higher overall temporal scaling rates (w = 0.39–0.64) than those of plants and animals (w = 0.21–0.38). Our results on warming-enhanced temporal scaling of microbial biodiversity suggest that the strategies of soil biodiversity preservation and ecosystem management may need to be adjusted in a warmer world.

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Fig. 1: STR and PTR of bacteria and fungi under warming (red) and control (blue) treatment conditions.
Fig. 2: Effect size (Cohen’s d) of all single and combined treatments.
Fig. 3: Changes in STR ws and PTR wp in major common phyla under different treatments.
Fig. 4: Comparison of STR and PTR exponents in micro- and macroorganisms.

References

  1. Chase, J. M. Stochastic community assembly causes higher biodiversity in more productive environments. Science 328, 1388–1391 (2010).

    Article  CAS  PubMed  Google Scholar 

  2. Morlon, H. et al. Spatial patterns of phylogenetic diversity. Ecol. Lett. 14, 141–149 (2011).

    Article  PubMed  PubMed Central  Google Scholar 

  3. Rosenzweig, M. L. Species Diversity in Space and Time (Cambridge Univ. Press, 1995).

  4. Zhou, J., Kang, S., Schadt, C. W. & Garten, C. T. Jr. Spatial scaling of functional gene diversity across various microbial taxa. Proc. Natl Acad. Sci. USA 105, 7768–7773 (2008).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  5. Lawton, J. H. Are there general laws in ecology? Oikos 84, 177–192 (1999).

    Article  Google Scholar 

  6. Green, J. & Bohannan, B. J. Spatial scaling of microbial biodiversity. Trends Ecol. Evol. 21, 501–507 (2006).

    Article  PubMed  Google Scholar 

  7. Storch, D., Keil, P. & Jetz, W. Universal species–area and endemics–area relationships at continental scales. Nature 488, 78–81 (2012).

    Article  CAS  PubMed  Google Scholar 

  8. Sheik, C. S. et al. Effect of warming and drought on grassland microbial communities. ISME J. 5, 1692–1700 (2011).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  9. Guilhaumon, F., Gimenez, O., Gaston, K. J. & Mouillot, D. Taxonomic and regional uncertainty in species–area relationships and the identification of richness hotspots. Proc. Natl Acad. Sci. USA 105, 15458–15463 (2008).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  10. Horner-Devine, M. C., Lage, M., Hughes, J. B. & Bohannan, B. J. A taxa–area relationship for bacteria. Nature 432, 750–753 (2004).

    Article  CAS  PubMed  Google Scholar 

  11. Shade, A., Caporaso, J. G., Handelsman, J., Knight, R. & Fierer, N. A meta-analysis of changes in bacterial and archaeal communities with time. ISME J. 7, 1493–1506 (2013).

    Article  PubMed  PubMed Central  Google Scholar 

  12. Chen, L. X. et al. Comparative metagenomic and metatranscriptomic analyses of microbial communities in acid mine drainage. ISME J. 9, 1579–1592 (2015).

    Article  PubMed  Google Scholar 

  13. van der Gast, C. J., Ager, D. & Lilley, A. K. Temporal scaling of bacterial taxa is influenced by both stochastic and deterministic ecological factors. Environ. Microbiol. 10, 1411–1418 (2008).

    Article  PubMed  Google Scholar 

  14. Deng, Y. et al. Spatial scaling of forest soil microbial communities across a temperature gradient. Environ. Microbiol. 20, 3504–3513 (2018).

    Article  PubMed  Google Scholar 

  15. Preston, F. W. Time and space and the variation of species. Ecology 41, 611–627 (1960).

    Article  Google Scholar 

  16. Adler, P. B. & Lauenroth, W. K. The power of time: spatiotemporal scaling of species diversity. Ecol. Lett. 6, 749–756 (2003).

    Article  Google Scholar 

  17. White, E P. et al. A comparison of the species–time relationship across ecosystems and taxonomic groups. Oikos 112, 185–195 (2006).

    Article  Google Scholar 

  18. Carey, S., Ostling, A., Harte, J. & del Moral, R. Impact of curve construction and community dynamics on the species–time relationship. Ecology 88, 2145–2153 (2007).

    Article  PubMed  Google Scholar 

  19. Swenson, N. G. et al. Species–time–area and phylogenetic–time–area relationships in tropical tree communities. Ecol. Evol. 3, 1173–1183 (2013).

    Article  PubMed  PubMed Central  Google Scholar 

  20. Devictor, V. et al. Spatial mismatch and congruence between taxonomic, phylogenetic and functional diversity: the need for integrative conservation strategies in a changing world. Ecol. Lett. 13, 1030–1040 (2010).

    PubMed  Google Scholar 

  21. Winter, M. et al. Plant extinctions and introductions lead to phylogenetic and taxonomic homogenization of the European flora. Proc. Natl Acad. Sci. USA 106, 21721–21725 (2009).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  22. Srivastava, D. S., Cadotte, M. W., MacDonald, A. A. M., Marushia, R. G. & Mirotchnick, N. Phylogenetic diversity and the functioning of ecosystems. Ecol. Lett. 15, 637–648 (2012).

    Article  PubMed  Google Scholar 

  23. Jabot, F. & Chave, J. Inferring the parameters of the neutral theory of biodiversity using phylogenetic information and implications for tropical forests. Ecol. Lett. 12, 239–248 (2009).

    Article  PubMed  Google Scholar 

  24. IPCC Climate Change 2013: The Physical Science Basis—Findings and Lessons Learned (eds. Stocker, T. F. et al.) (Cambridge Univ. Press, 2013).

  25. Bellard, C., Bertelsmeier, C., Leadley, P., Thuiller, W. & Courchamp, F. Impacts of climate change on the future of biodiversity. Ecol. Lett. 15, 365–377 (2012).

    Article  PubMed  PubMed Central  Google Scholar 

  26. Moss, R. H. et al. The next generation of scenarios for climate change research and assessment. Nature 463, 747–756 (2010).

    Article  CAS  PubMed  Google Scholar 

  27. Bebber, D. P., Ramotowski, M. A. T. & Gurr, S. J. Crop pests and pathogens move polewards in a warming world. Nat. Clim. Change 3, 985–988 (2013).

    Article  Google Scholar 

  28. Xue, K. et al. Tundra soil carbon is vulnerable to rapid microbial decomposition under climate warming. Nat. Clim. Change 6, 595–600 (2016).

    Article  CAS  Google Scholar 

  29. Brown, J. H., Gillooly, J. F., Allen, A. P., Savage, V. M. & West, G. B. Toward a metabolic theory of ecology. Ecology 85, 1771–1789 (2004).

    Article  Google Scholar 

  30. Zhou, J. et al. Temperature mediates continental-scale diversity of microbes in forest soils. Nat. Commun. 7, 12083 (2016).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  31. Zhao, L. et al. Soil organic carbon and total nitrogen pools in permafrost zones of the Qinghai-Tibetan Plateau. Sci. Rep. 8, 3656 (2018).

    Article  PubMed  PubMed Central  Google Scholar 

  32. Guo, X. et al. Climate warming leads to divergent succession of grassland microbial communities. Nat. Clim. Change 8, 813–818 (2018).

    Article  Google Scholar 

  33. Zhou, J. et al. Stochasticity, succession, and environmental perturbations in a fluidic ecosystem. Proc. Natl Acad. Sci. USA 111, E836–E845 (2014).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  34. Xu, X., Sherry, R. A., Niu, S., Li, D. & Luo, Y. Net primary productivity and rain‐use efficiency as affected by warming, altered precipitation, and clipping in a mixed‐grass prairie. Glob. Change Biol. 19, 2753–2764 (2013).

    Article  Google Scholar 

  35. Shi, Z. et al. Successional change in species composition alters climate sensitivity of grassland productivity. Glob. Change Biol. 24, 4993–5003 (2018).

    Article  Google Scholar 

  36. Xu, X. et al. Unchanged carbon balance driven by equivalent responses of production and respiration to climate change in a mixed-grass prairie. Glob. Change Biol. 22, 1857–1866 (2016).

    Article  Google Scholar 

  37. Bardgett, R. D., Bowman, W. D., Kaufmann, R. & Schmidt, S. K. A temporal approach to linking aboveground and belowground ecology. Trends Ecol. Evol. 20, 634–641 (2005).

    Article  PubMed  Google Scholar 

  38. Tscherko, D., Hammesfahr, U., Zeltner, G., Kandeler, E. & Böcker, R. Plant succession and rhizosphere microbial communities in a recently deglaciated alpine terrain. Basic Appl. Ecol. 6, 367–383 (2005).

    Article  CAS  Google Scholar 

  39. Shaw, M. R. et al. Grassland responses to global environmental changes suppressed by elevated CO2. Science 298, 1987–1990 (2002).

    Article  CAS  PubMed  Google Scholar 

  40. Zhou, X., Sherry, R. A., An, Y., Wallace, L. L. & Luo, Y. Main and interactive effects of warming, clipping, and doubled precipitation on soil CO2 efflux in a grassland ecosystem. Global Biogeochem. Cycles 20 https://doi.org/10.1029/2005GB002526 (2006).

  41. Zavaleta, E. S., Shaw, M. R., Chiariello, N. R., Mooney, H. A. & Field, C. B. Additive effects of simulated climate changes, elevated CO2, and nitrogen deposition on grassland diversity. Proc. Natl Acad. Sci. USA 100, 7650–7654 (2003).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  42. Zhou, J. et al. Microbial mediation of carbon-cycle feedbacks to climate warming. Nat. Clim. Change 2, 106–110 (2012).

    Article  CAS  Google Scholar 

  43. Fierer, N., Bradford, M. A. & Jackson, R. B. Toward an ecological classification of soil bacteria. Ecology 88, 1354–1364 (2007).

    Article  PubMed  Google Scholar 

  44. Blois, J. L., Williams, J. W., Fitzpatrick, M. C., Jackson, S. T. & Ferrier, S. Space can substitute for time in predicting climate-change effects on biodiversity. Proc. Natl Acad. Sci. USA 110, 9374–9379 (2013).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  45. Li, D., Zhou, X., Wu, L., Zhou, J. & Luo, Y. Contrasting responses of heterotrophic and autotrophic respiration to experimental warming in a winter annual-dominated prairie. Glob. Change Biol. 19, 3553–3564 (2013).

    Google Scholar 

  46. Yahdjian, L. & Sala, O. E. A rainout shelter design for intercepting different amounts of rainfall. Oecologia 133, 95–101 (2002).

    Article  PubMed  Google Scholar 

  47. Zhou, J., Bruns, M. A. & Tiedje, J. M. DNA recovery from soils of diverse composition. Appl. Environ. Microbiol. 62, 316–322 (1996).

    CAS  PubMed  PubMed Central  Google Scholar 

  48. Wu, L. et al. Phasing amplicon sequencing on Illumina Miseq for robust environmental microbial community analysis. BMC Microbiol. 15, 125 (2015).

    Article  PubMed  PubMed Central  Google Scholar 

  49. Peiffer, J. A. et al. Diversity and heritability of the maize rhizosphere microbiome under field conditions. Proc. Natl Acad. Sci. USA 110, 6548–6553 (2013).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  50. Caporaso, J. G. et al. Ultra-high-throughput microbial community analysis on the Illumina HiSeq and MiSeq platforms. ISME J. 6, 1621–1624 (2012).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  51. Giardine, B. et al. Galaxy: a platform for interactive large-scale genome analysis. Genome Res. 15, 1451–1455 (2005).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  52. Kong, Y. Btrim: a fast, lightweight adapter and quality trimming program for next-generation sequencing technologies. Genomics 98, 152–153 (2011).

    Article  CAS  PubMed  Google Scholar 

  53. Magoč, T. & Salzberg, S. L. FLASH: fast length adjustment of short reads to improve genome assemblies. Bioinformatics 27, 2957–2963 (2011).

    Article  PubMed  PubMed Central  Google Scholar 

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

    Article  CAS  PubMed  Google Scholar 

  55. DeSantis, T. Z. et al. Greengenes, a chimera-checked 16S rRNA gene database and workbench compatible with ARB. Appl. Environ. Microbiol. 72, 5069–5072 (2006).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  56. Wang, Q., Garrity, G. M., Tiedje, J. M. & Cole, J. R. Naive Bayesian classifier for rapid assignment of rRNA sequences into the new bacterial taxonomy. Appl. Environ. Microbiol. 73, 5261–5267 (2007).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  57. Price, M. N., Dehal, P. S. & Arkin, A. P. FastTree 2—approximately maximum-likelihood trees for large alignments. PLoS ONE 5, e9490 (2010).

    PubMed  PubMed Central  Google Scholar 

  58. Kembel, S. W. et al. Picante: R tools for integrating phylogenies and ecology. Bioinformatics 26, 1463–1464 (2010).

    Article  CAS  PubMed  Google Scholar 

  59. Martiny, J. B., Eisen, J. A., Penn, K., Allison, S. D. & Horner-Devine, M. C. Drivers of bacterial β-diversity depend on spatial scale. Proc. Natl Acad. Sci. USA 108, 7850–7854 (2011).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  60. Deng, Y. et al. Elevated carbon dioxide accelerates the spatial turnover of soil microbial communities. Glob. Change Biol. 22, 957–964 (2016).

    Article  Google Scholar 

  61. R Core Team. R: a language and environment for statistical computing (R Foundation for Statistical Computing, 2013).

  62. Stackebrandt, E. et al. Report of the ad hoc committee for the re-evaluation of the species definition in bacteriology. Int. J. Syst. Evol. Microbiol. 52, 1043–1047 (2002).

    CAS  PubMed  Google Scholar 

  63. Gevers, D. et al. Re-evaluating prokaryotic species. Nat. Rev. Microbiol. 3, 733–739 (2005).

    Article  CAS  PubMed  Google Scholar 

  64. Fierer, N. & Lennon, J. T. The generation and maintenance of diversity in microbial communities. Am. J. Bot. 98, 439–448 (2011).

    Article  PubMed  Google Scholar 

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Acknowledgements

We thank numerous former laboratory members for their help in maintaining the experimental site. This work is supported by the US Department of Energy, Office of Science, Genomic Science Program under award nos. DE-SC0004601 and DE-SC0010715, the National Science Foundation of China (award no. 41430856) and the Office of the Vice President for Research at the University of Oklahoma. X.G., X.Z. and Q.G. were generously supported by the China Scholarship Council (award no. 201406370046, 201306370141 and 201506210136).

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Author notes

  1. These authors contributed equally: Xue Guo, Xishu Zhou, Lauren Hale.

Authors and Affiliations

  1. Key Laboratory of Biometallurgy of Ministry of Education, School of Minerals Processing and Bioengineering, Central South University, Changsha, China

    Xue Guo, Xishu Zhou, Guanzhou Qiu & Xueduan Liu

  2. Institute for Environmental Genomics, University of Oklahoma, Norman, OK, USA

    Xue Guo, Xishu Zhou, Lauren Hale, Mengting Yuan, Daliang Ning, Jiajie Feng, Zhou Shi, Zhenxin Li, Bin Feng, Qun Gao, Linwei Wu, Weiling Shi, Aifen Zhou, Ying Fu, Liyou Wu, Zhili He, Joy D. Van Nostrand & Jizhong Zhou

  3. Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK, USA

    Xue Guo, Xishu Zhou, Lauren Hale, Mengting Yuan, Daliang Ning, Jiajie Feng, Zhou Shi, Zhenxin Li, Bin Feng, Qun Gao, Linwei Wu, Weiling Shi, Aifen Zhou, Ying Fu, Liyou Wu, Zhili He, Joy D. Van Nostrand, Yiqi Luo & Jizhong Zhou

  4. State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing, China

    Xue Guo, Qun Gao, Linwei Wu, Yunfeng Yang & Jizhong Zhou

  5. Water Management Research Unit, SJVASC, USDA-ARS, Parlier, CA, USA

    Lauren Hale

  6. Department of Environmental Science, Policy, and Management, University of California, Berkeley, CA, USA

    Mengting Yuan

  7. Center for Ecosystem Science and Society, Department of Biological Sciences, Northern Arizona University, Flagstaff, AZ, USA

    Yiqi Luo

  8. Department of Earth System Science, Tsinghua University, Beijing, China

    Yiqi Luo

  9. Center for Microbial Ecology, Michigan State University, East Lansing, MI, USA

    James M. Tiedje

  10. School of Civil Engineering and Environmental Sciences, University of Oklahoma, Norman, OK, USA

    Jizhong Zhou

  11. Earth and Environmental Sciences, Lawrence Berkeley National Laboratory, Berkeley, CA, USA

    Jizhong Zhou

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  1. Xue Guo
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Contributions

All authors contributed intellectual input and assistance to this study. The original concept and experimental strategy were developed by J.Z., Y.L. and J.M.T. Field management was carried out by M.Y., J.F., B.F., X.Z., A.Z., L.H., Z.L., Liyou Wu and J.D.V.N. Collection sampling, DNA preparation and MiSeq sequencing analysis were carried out by X.Z., X.G., J.F., M.Y., Y.F. and L.H. Soil chemical analysis was carried out by X.Z., X.G. and M.Y. Various statistical analyses were carried by X.G., Z.S., D.N., Linwei Wu, W.S. and Q.G. Assistance in data interpretation was provided by G.Q., X.L., Z.H. and Y.Y. All data analysis and integration were guided by J.Z. The paper was written by J.Z. and X.G. with help from J.M.T. and D.N. Because of their contributions in terms of site management, and data collection, analysis and/or integration over the last 6 years, X.G., X.Z. and L.H. were listed as co-first authors.

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Correspondence to Jizhong Zhou.

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Guo, X., Zhou, X., Hale, L. et al. Climate warming accelerates temporal scaling of grassland soil microbial biodiversity. Nat Ecol Evol 3, 612–619 (2019). https://doi.org/10.1038/s41559-019-0848-8

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