Advertisement

Ecosystems

pp 1–12 | Cite as

Cross-Biome Drivers of Soil Bacterial Alpha Diversity on a Worldwide Scale

  • Manuel Delgado-Baquerizo
  • David J. Eldridge
Article

Abstract

We lack a defined suite of attributes that allow us to universally predict the distribution of bacterial diversity across and within globally distributed biomes. Using data from a global survey, including 237 locations and multiple environmental predictors, we found that only ultraviolet light, forest environments, soil carbon and pH can be considered as significant and globally consistent predictors of soil bacterial diversity, valid within and across biomes (arid, temperate and continental). Bacterial diversity always peaked in grasslands, with moderate-to-low carbon and ultraviolet light levels, and high soil pH. Using these environmental data, we generated the first global predictive map of the distribution of soil bacterial diversity. Our work helps to identify a unique set of environmental attributes for universally predicting the distribution of soil bacterial diversity. This knowledge is key to help predict changes in ecosystem functioning and the provision of essential services under changing environments.

Keywords

α-diversity terrestrial ecosystems arid continental temperate cross-biome 

Notes

Acknowledgements

This project has received funding from the European Union’s Horizon 2020 research and innovation programme under the Marie Sklodowska-Curie Grant agreement No 702057.

Compliance with Ethical Standards

Conflict of interest

The authors declare no conflict of interest.

Supplementary material

10021_2018_333_MOESM1_ESM.doc (5 mb)
Supplementary material 1 (DOC 5156 kb)

References

  1. Anderson JM, Ingram JSI, Eds. 1993. Tropical soil biology and fertility: a handbook of methods, 2nd ed. Wallingford: CAB International.Google Scholar
  2. Archer E. 2016. rfPermute, estimate permutation p-values for random forest importance metrics. R package version 1.5.2.Google Scholar
  3. Bodelier PLE. 2011. Toward understanding, managing, and protecting microbial ecosystems. Front Microbiol 2:80.CrossRefGoogle Scholar
  4. Breiman L. 2001. Random For Mach Learn 45:5–32.CrossRefGoogle Scholar
  5. Caporaso JG, Kuczynski J, Stombaugh J, Bittinger K, Bushman FD, Costello EK et al. 2010. QIIME allows analysis of high-throughput community sequencing data. Nat Methods 7:335–6.CrossRefGoogle Scholar
  6. Cardinale BJ, Emmett Duffy J, Gonzalez A, Hooper DU, Perrins C, Venail P et al. 2012. Biodiversity loss and its impact on humanity. Nature 486:59–67.CrossRefGoogle Scholar
  7. Crowther TW, Maynard DS, Leff JW, Oldfield EE, McCulley RL, Fierer N et al. 2014. Explaining the vulnerability of soil biodiversity to deforestation: a cross-biome study. Glob Change Biol 20:2983–94.CrossRefGoogle Scholar
  8. Delgado-Baquerizo M, Maestre FT, Reich PB, Jeffries TC, Gaitan JJ, Encinar D et al. 2016a. Microbial diversity drives multifunctionality in terrestrial ecosystems. Nat Commun 7:10541.CrossRefGoogle Scholar
  9. Delgado-Baquerizo M, Maestre FT, Reich PB, Trivedi P, Osanai Y, Liu Y-R et al. 2016b. Carbon content and climate variability drive global soil bacterial diversity patterns. Ecol Monogr 86:373–80.CrossRefGoogle Scholar
  10. Delgado-Baquerizo M, Reich PB, Khachane AN, Campbell CD, Thomas N, Freitag T et al. 2017. It is elemental: soil nutrient stoichiometry drives bacterial diversity. Environ Microbiol 19:1176–88.CrossRefGoogle Scholar
  11. Delgado-Baquerizo M, Oliverio AM, Brewer TE, Benavent-González A, Eldridge DJ, Bardgett RD et al. 2018a. A global atlas of the dominant bacteria found in soil. Science 19:320–5.CrossRefGoogle Scholar
  12. Delgado-Baquerizo M, Reith F, Dennis PG, Hamonts K, Powell JR, Young A, Singh BK, Bissett A. 2018b. Ecological drivers of soil microbial diversity and soil biological networks in the Southern Hemisphere. Ecology (in press).  https://doi.org/10.1002/ecy.2137.
  13. Delgado-Baquerizo M, Giaramida L, Reich PB, Khachane AN, Hamonts K, Edwards C, Lawton L, Singh BK. 2016c. Lack of functional redundancy in the relationship between microbial diversity and ecosystem functioning. J Ecol 104:936–46.CrossRefGoogle Scholar
  14. Dirzo R, Young HS, Galetti M, Ceballos G, Isaac NJB et al. 2014. Defaunation in the Anthropocene. Science 345:401–6.CrossRefGoogle Scholar
  15. Edgar RC. 2013. UPARSE: highly accurate OTU sequences from microbial amplicon reads. Nat Methods 10:996–8.CrossRefGoogle Scholar
  16. Edgar RC, Haas BJ, Clemente JC, Quince C, Knight R. 2011. UCHIME improves sensitivity and speed of chimera detection. Bioinformatics 27:2194–200.CrossRefGoogle Scholar
  17. Eldridge DJ, Delgado-Baquerizo M, Travers SK, Val J, Oliver I, Hamonts K et al. 2017. Competition drives the response of soil microbial diversity to increased grazing by vertebrate herbivores. Ecology 98:1922–31.CrossRefGoogle Scholar
  18. Fierer N, Jackson RB. 2006. The diversity and biogeography of soil bacterial communities. Proc Natl Acad Sci USA 103:626–31.CrossRefGoogle Scholar
  19. Fierer N, Leff JW, Adams BJ, Nielsen UN, Bates ST, Lauber CL et al. 2012. Cross-biome metagenomic analyses of soil microbial communities and their functional attributes. Proc Natl Acad Sci USA 109:21390–5.CrossRefGoogle Scholar
  20. Fierer N. 2017. Embracing the unknown: disentangling the complexities of the soil microbiome. Nat Rev Microbiol 15:579–90.CrossRefGoogle Scholar
  21. Gotelli NJ, Colwell RK. 2001. Quantifying biodiversity: procedures and pitfalls in the measurement and comparison of species richness. Ecol Lett 4:379–91.CrossRefGoogle Scholar
  22. Grace JB. 2006. Structural equation modelling and natural systems. Cambridge: Cambridge University Press.CrossRefGoogle Scholar
  23. Hendershot JN, Read QD, Henning JA, Sanders NJ, Classen AT. 2017. Consistently inconsistent drivers of microbial diversity and abundance at macroecological scales. Ecology 98:1757–63.CrossRefGoogle Scholar
  24. Hijmans RJ, Cameron SE, Parra JL, Jones PG, Jarvis A. 2005. Very high resolution interpolated climate surfaces for global land areas. Int J Clim 25:1965–78.CrossRefGoogle Scholar
  25. Hooper DU, Chapin FS, Ewel JJ, Hector A, Inchausti P, Lavorel S et al. 2005. Effects of biodiversity on ecosystem functioning: a consensus of current knowledge. Ecol Monogr 75:3–35.CrossRefGoogle Scholar
  26. Isbell F, Colgano V, Hector A, Connelly J, Harpole WS, Reich PB et al. 2011. High plant diversity is needed to maintain ecosystem services. Nature 477:199–202.  https://doi.org/10.1038/nature10282.CrossRefPubMedGoogle Scholar
  27. Jing X, Sanders NJ, Shi Y, Chu H, Classen AT, Zhao K et al. 2015. The links between ecosystem multifunctionality and above- and belowground biodiversity are mediated by climate. Nat Commun 6:8159.CrossRefGoogle Scholar
  28. Kettler TA, Doran JW, Gilbert TL. 2001. Simplified method for soil particle-size determination to accompany soil-quality analyses. Soil Sci Soc Am J 65:849–52.CrossRefGoogle Scholar
  29. Kuhn M, Weston S, Keefer C, Coulter N. 2016. Cubist: rule- and instance-based regression modeling. R package version 0.0.19.Google Scholar
  30. Laliberté E, Zemunik G, Turner BL. 2014. Environmental filtering explains variation in plant diversity along resource gradients. Science 345:1602–5.CrossRefGoogle Scholar
  31. Lauber CL, Hamady M, Knight R, Fierer N. 2009. Pyrosequencing-based assessment of soil pH as a predictor of soil bacterial community structure at the continental scale. Appl Environ Microbiol 75:5111–20.CrossRefGoogle Scholar
  32. Maestre FT, Delgado-Baquerizo M, Jeffries TC, Eldridge DJ, Ochoa V, Gozalo B et al. 2015. Increasing aridity reduces soil microbial diversity and abundance in global drylands. Proc Natl Acad Sci USA 112:15684–9.PubMedGoogle Scholar
  33. Pettorelli N, Vik JO, Mysterud A, Gaillard JM, Tucker CJ, Stenseth NC. 2005. Using the satellite-derived NDVI to assess ecological responses to environmental change. Trends Ecol Evol 20:503–10.CrossRefGoogle Scholar
  34. Philippot L, Spor A, Hénault C, Bru D, Bizouard F, Jones CM et al. 2013. Loss in microbial diversity affects nitrogen cycling in soil. ISME J 7:1609–19.CrossRefGoogle Scholar
  35. Prober SM, Leff JW, Bates ST, Borer ET, Firn J, Harpole WS et al. 2015. Plant diversity predicts beta but not alpha diversity of soil microbes across grasslands worldwide. Ecol Lett 18:85–95.CrossRefGoogle Scholar
  36. Quinlan JR. 1993. C4.5: Programs for machine learning. San Mateo, CA: Morgan Kaufmann Publishers.Google Scholar
  37. Ramirez KS, Leff JW, Barberán A, Bates ST, Betley J, Crowther TW. 2014. 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.CrossRefGoogle Scholar
  38. Ranjan K, Paula FS, Mueller RC, Jesus EC, Cenciani K, Bohannan BJM et al. 2015. Forest-to-pasture conversion increases the diversity of the phylum Verrucomicrobia in Amazon rainforest soils. Front Microbiol 6:779.CrossRefGoogle Scholar
  39. Reich PB, Tilman D, Isbell F, Mueller K, Hobbie SE, Flynn DF, Eisenhauer N. 2012. Impacts of biodiversity loss escalate through time as redundancy fades. Science 336(6081):589–92.  https://doi.org/10.1126/science.1217909.CrossRefPubMedGoogle Scholar
  40. Rousk J, Brookes PC, Baath E. 2010. The microbial PLFA composition as affected by pH in an arable soil. Soil Biol Biochem 42:516–20.CrossRefGoogle Scholar
  41. Roux S, Enault F, Robin A, Ravet V, Personnic S, Theil S et al. 2012. Assessing the diversity and specificity of two freshwater viral communities through metagenomics. PLoS ONE 7:e33641.CrossRefGoogle Scholar
  42. Santos AL, Gomes NC, Henriques I, Almeida A, Correia A, Cunha Â. 2012. Contribution of reactive oxygen species to UV-B-induced damage in bacteria. J Photochem Photobiol B 117:40–6.  https://doi.org/10.1016/j.jphotobiol.2012.08.016.CrossRefGoogle Scholar
  43. Schermelleh-Engel K, Moosbrugger H, Muller H. 2003. Evaluating the fit of structural equation models, tests of significance descriptive goodness-of-fit measures. Methods Psychol Res Online 8:23–74.Google Scholar
  44. Szoboszlay M, Dohrmann AB, Poeplau C, Don A, Tebbe CC. 2017. Impact of land-use change and soil organic carbon quality on microbial diversity in soils across Europe. FEMS Microbiol Ecol 1:93.Google Scholar
  45. Terrat S, Horrigue W, Dequietd S, Saby NPA, Lelièvre M, Nowak V et al. 2017. Mapping and predictive variations of soil bacterial richness across France. PLoS ONE 12:e0186766.CrossRefGoogle Scholar
  46. Thompson LR, Sanders JG, McDonald D, Amir A, Ladau J, Locey KJ et al. 2017. A communal catalogue reveals Earth’s multiscale microbial diversity. Nature 23:457–63.Google Scholar
  47. Tilman D, Balzer C, Hill J, Befort BL. 2011. Global food demand and the sustainable intensification of agriculture. Proc Natl Acad Sci USA 13:20260–4.CrossRefGoogle Scholar
  48. Waldrop MP, Zak DR, Blackwood CB, Curtis CD, Tilman D. 2006. Resource availability controls fungal diversity across a plant diversity gradient. Ecol Lett 9:1127–35.CrossRefGoogle Scholar
  49. Wieder WR, Bonan GB, Allison SD. 2013. Global soil carbon projections are improved by modelling microbial processes. Nat Clim Change 3:909–12.CrossRefGoogle Scholar
  50. Wilkinson DM. 1999. The disturbing history of intermediate disturbance. Oikos 84(1):145–7.CrossRefGoogle Scholar
  51. Zhou J, Deng Y, Shen L, Wen C, Yan Q, Ning D et al. 2016. Temperature mediates continental-scale diversity of microbes in forest soils. Nat Commun 7:12083.CrossRefGoogle Scholar
  52. Zomer RJ, Trabucco A, Bossio DA, Verchot LV. 2008. Climate change mitigation: a spatial analysis of global land suitability for clean development mechanism afforestation and reforestation. Agric Ecosyst Environ 126:67–80.CrossRefGoogle Scholar

Copyright information

© Springer Science+Business Media, LLC, part of Springer Nature 2018

Authors and Affiliations

  1. 1.Cooperative Institute for Research in Environmental SciencesUniversity of ColoradoBoulderUSA
  2. 2.Departamento de Biología y Geología, Física y Química Inorgánica, Escuela Superior de Ciencias Experimentales y TecnologíaUniversidad Rey Juan CarlosMóstolesSpain
  3. 3.Centre for Ecosystem Science, School of Biological, Earth and Environmental SciencesUniversity of New South WalesSydneyAustralia

Personalised recommendations