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

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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.

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References

  • Anderson JM, Ingram JSI, Eds. 1993. Tropical soil biology and fertility: a handbook of methods, 2nd ed. Wallingford: CAB International.

    Google Scholar 

  • Archer E. 2016. rfPermute, estimate permutation p-values for random forest importance metrics. R package version 1.5.2.

  • Bodelier PLE. 2011. Toward understanding, managing, and protecting microbial ecosystems. Front Microbiol 2:80.

    Article  PubMed  PubMed Central  Google Scholar 

  • Breiman L. 2001. Random For Mach Learn 45:5–32.

    Article  Google Scholar 

  • 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.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • 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.

    Article  CAS  PubMed  Google Scholar 

  • 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.

    Article  Google Scholar 

  • 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.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • 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.

    Article  Google Scholar 

  • 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.

    Article  CAS  PubMed  Google Scholar 

  • 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.

    Article  CAS  Google Scholar 

  • 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.

  • 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.

    Article  Google Scholar 

  • Dirzo R, Young HS, Galetti M, Ceballos G, Isaac NJB et al. 2014. Defaunation in the Anthropocene. Science 345:401–6.

    Article  CAS  PubMed  Google Scholar 

  • Edgar RC. 2013. UPARSE: highly accurate OTU sequences from microbial amplicon reads. Nat Methods 10:996–8.

    Article  CAS  PubMed  Google Scholar 

  • Edgar RC, Haas BJ, Clemente JC, Quince C, Knight R. 2011. UCHIME improves sensitivity and speed of chimera detection. Bioinformatics 27:2194–200.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • 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.

    Article  PubMed  Google Scholar 

  • Fierer N, Jackson RB. 2006. The diversity and biogeography of soil bacterial communities. Proc Natl Acad Sci USA 103:626–31.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • 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.

    Article  PubMed  PubMed Central  Google Scholar 

  • Fierer N. 2017. Embracing the unknown: disentangling the complexities of the soil microbiome. Nat Rev Microbiol 15:579–90.

    Article  CAS  PubMed  Google Scholar 

  • Gotelli NJ, Colwell RK. 2001. Quantifying biodiversity: procedures and pitfalls in the measurement and comparison of species richness. Ecol Lett 4:379–91.

    Article  Google Scholar 

  • Grace JB. 2006. Structural equation modelling and natural systems. Cambridge: Cambridge University Press.

    Book  Google Scholar 

  • 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.

    Article  PubMed  Google Scholar 

  • 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.

    Article  Google Scholar 

  • 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.

    Article  Google Scholar 

  • 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.

    Article  CAS  PubMed  Google Scholar 

  • 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.

    Article  PubMed  Google Scholar 

  • 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.

    Article  CAS  Google Scholar 

  • Kuhn M, Weston S, Keefer C, Coulter N. 2016. Cubist: rule- and instance-based regression modeling. R package version 0.0.19.

  • Laliberté E, Zemunik G, Turner BL. 2014. Environmental filtering explains variation in plant diversity along resource gradients. Science 345:1602–5.

    Article  CAS  PubMed  Google Scholar 

  • 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.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • 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.

    CAS  PubMed  PubMed Central  Google Scholar 

  • 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.

    Article  PubMed  Google Scholar 

  • 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.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • 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.

    Article  PubMed  Google Scholar 

  • Quinlan JR. 1993. C4.5: Programs for machine learning. San Mateo, CA: Morgan Kaufmann Publishers.

    Google Scholar 

  • 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.

    Article  PubMed  PubMed Central  Google Scholar 

  • 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.

    Article  PubMed  PubMed Central  Google Scholar 

  • 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.

    Article  CAS  PubMed  Google Scholar 

  • 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.

    Article  CAS  Google Scholar 

  • 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.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • 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.

    Article  CAS  Google Scholar 

  • 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 

  • 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 

  • 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.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • 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.

    Article  CAS  Google Scholar 

  • 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.

    Article  Google Scholar 

  • 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.

    Article  PubMed  Google Scholar 

  • Wieder WR, Bonan GB, Allison SD. 2013. Global soil carbon projections are improved by modelling microbial processes. Nat Clim Change 3:909–12.

    Article  CAS  Google Scholar 

  • Wilkinson DM. 1999. The disturbing history of intermediate disturbance. Oikos 84(1):145–7.

    Article  Google Scholar 

  • 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.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • 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.

    Article  Google Scholar 

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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.

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Authors and Affiliations

  1. Cooperative Institute for Research in Environmental Sciences, University of Colorado, Boulder, Colorado, 80309, USA

    Manuel Delgado-Baquerizo

  2. Departamento de Biología y Geología, Física y Química Inorgánica, Escuela Superior de Ciencias Experimentales y Tecnología, Universidad Rey Juan Carlos, Calle Tulipán Sin Número, 28933, Móstoles, Spain

    Manuel Delgado-Baquerizo

  3. Centre for Ecosystem Science, School of Biological, Earth and Environmental Sciences, University of New South Wales, Sydney, New South Wales, 2052, Australia

    David J. Eldridge

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Correspondence to Manuel Delgado-Baquerizo.

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Author Contributions

M.D-B. designed this study. M.D-B. and D.J.E. were involved in the collection of the soils used in this study. M.D-B. conducted statistical modeling. The manuscript was written by M.D-B and edited by D.J.E.

Data Accessibility

All data used in this study are publicly available in Figshare (https://figshare.com/s/82a2d3f5d38ace925492; https://doi.org/10.6084/m9.figshare.5611321).

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Delgado-Baquerizo, M., Eldridge, D.J. Cross-Biome Drivers of Soil Bacterial Alpha Diversity on a Worldwide Scale. Ecosystems 22, 1220–1231 (2019). https://doi.org/10.1007/s10021-018-0333-2

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