Linking soil bacterial diversity to ecosystem multifunctionality using backward-elimination boosted trees analysis



Background, aim, and scope

There is increasing evidence of linkages between biodiversity and ecosystem functions. Recent interests on this topic have expanded from an individual-function perspective to a multifunction perspective. This study aims to explore the soil bacterial diversity–multifunctionality relationship.

Materials and methods

Soil bacterial diversity was determined using culture-independent molecular techniques. Bacterial taxa groups with positive effects on certain ecosystem functions were identified by aggregated boosted tree analysis with a prediction-error-based backward-elimination criterion. Soil bacterial diversity–multifunctionality relationship was examined by exploring the relationship between the number of ecosystem functions and the number of soil bacterial taxa.


More ecosystem functions would require greater numbers of bacterial taxa, which can be explained potentially using the multifunctional complementarity mechanism. Furthermore, a power law equation, OTU N  = OTU1(N) T , was firstly proposed to describe the observed positive relationship between the soil bacterial diversity and the ecosystem multifunctionality, where OTU N is the number of operational taxonomic units (OTUs) required by N functions, while OTU1 is the average number of species required for one function, and T is the average turnover rate of OTU across functions.


The number of ecosystem functions would decrease with the loss of soil bacterial diversity. This biodiversity–multifunctionality relationship has an important implication for comprehensively understanding the risk of bacterial diversity loss in relation to the ecosystem functions.


Bacterial diversity Belowground ecosystem Boosted tree analysis Ecosystem multifunctionality Microorganisms Soils 



This research was jointly supported by the Chinese Academy of Sciences (KZCX2-YW-408, KZCX1-YW-0603), the Natural Science Foundation of China (40871129), and the Australian Research Council. The assistances of the staff at the Australian and Chinese sites for soil sampling and data collecting are sincerely appreciated.


  1. Balvanera P, Pfisterer AB, Buchmann N, He J-S, Nakashizuka T, Raffaelli D, Schmid B (2006) Quantifying the evidence for biodiversity effects on ecosystem functioning and services. Ecol Lett 9:1146–1156CrossRefGoogle Scholar
  2. Bell T, Ager D, Song J-I, Newman JA, Thompson IP, Lilley AK, van der Gast CJ (2005a) Larger islands house more bacterial taxa. Science 308:1884CrossRefGoogle Scholar
  3. Bell T, Newman JA, Silverman BW, Turner SL, Lilley AK (2005b) The contribution of species richness and composition to bacterial services. Nature 436:1157–1160CrossRefGoogle Scholar
  4. Cardinale BJ, Srivastava DS, Duffy JE, Wright JP, Downing AL, Sankaran M, Jouseau C (2006) Effects of biodiversity on the functioning of trophic groups and ecosystems. Nature 443:989–992CrossRefGoogle Scholar
  5. Chen CR, Xu ZH, Hughes J (2002) Effects of nitrogen fertilization on soil nitrogen pools and microbial properties in a hoop pine (Araucaria cunninghamii) plantation in southeast Queensland, Australia. Biol Fert Soils 36:276–283CrossRefGoogle Scholar
  6. Chen CR, Xu ZH, Mathers NJ (2004) Soil carbon pools in adjacent natural and plantation forests of subtropical Australia. Soil Sci Soc Am J 68:282–291Google Scholar
  7. Choi I-G, Kim S-H (2007) Global extent of horizontal gene transfer. Proc Natl Acad Sci USA 104:4489–4494CrossRefGoogle Scholar
  8. De'ath G (2007) Boosted trees for ecological modeling and prediction. Ecology 88:243–251CrossRefGoogle Scholar
  9. Gamfeldt L, Hillebrand H, Jonsson PR (2008) Multiple functions increase the importance of biodiversity for overall ecosystem functioning. Ecology 89:1223–1231CrossRefGoogle Scholar
  10. Gans J, Wolinsky M, Dunbar J (2005) Computational improvements reveal great bacterial diversity and high metal toxicity in soil. Science 309:1387–1390CrossRefGoogle Scholar
  11. Ge Y, He J-Z, Zhu Y-G, Zhang J-B, Xu ZH, Zhang L-M, Zheng Y-M (2008a) Differences in soil bacterial diversity: driven by contemporary disturbances or historical contingencies? ISME J 2:254–264CrossRefGoogle Scholar
  12. Ge Y, Zhang J-B, Zhang L-M, Yang M, He J-Z (2008b) Long-term fertilization regimes affect bacterial community structure and diversity of an agricultural soil in northern China. J Soils Sediment 8:43–50CrossRefGoogle Scholar
  13. Ge Y, Chen CR, Xu ZH, Eldridge SM, Chan KY, He Y, He J-Z (2009) Carbon/nitrogen ratio as a major factor for predicting the effects of organic wastes on soil bacterial communities assessed by DNA-based molecular techniques. Environ Sci Pollut Res . doi: 10.1007/s11356-009-0185-6 Google Scholar
  14. He J-Z, Xu ZH, Hughes J (2006) Molecular bacterial diversity of a forest soil under residue management regimes in subtropical Australia. Fems Microbiol Ecol 55:38–47CrossRefGoogle Scholar
  15. He J-Z, Shen J-P, Zhang L-M, Zhu Y-G, Zheng Y-M, Xu M-G, Di H-J (2007) Quantitative analyses of the abundance and composition of ammonia-oxidizing bacteria and ammonia-oxidizing archaea of a Chinese upland red soil under long-term fertilization practices. Environ Microbiol 9:2364–2374CrossRefGoogle Scholar
  16. Hector A, Bagchi R (2007) Biodiversity and ecosystem multifunctionality. Nature 448:188–190CrossRefGoogle Scholar
  17. Kareiva P, Watts S, McDonald R, Boucher T (2007) Domesticated nature: shaping landscapes and ecosystems for human welfare. Science 316:1866–1869CrossRefGoogle Scholar
  18. Loreau M (1998) Biodiversity and ecosystem functioning: a mechanistic model. Proc Natl Acad Sci USA 95:5632–5636CrossRefGoogle Scholar
  19. Loreau M, Hector A (2001) Partitioning selection and complementarity in biodiversity experiments. Nature 412:72–76CrossRefGoogle Scholar
  20. Loreau M, Naeem S, Inchausti P, Bengtsson J, Grime JP, Hector A, Hooper DU, Huston MA, Raffaelli D, Schmid B, Tilman D, Wardle DA (2001) Biodiversity and ecosystem functioning: current knowledge and future challenges. Science 294:804–808CrossRefGoogle Scholar
  21. Madsen EL (2005) Identifying microorganisms responsible for ecologically significant biogeochemical processes. Nat Rev Microbiol 3:439–446CrossRefGoogle Scholar
  22. Muyzer G, de Waal E, Uitterlinden A (1993) Profiling of complex microbial populations by denaturing gradient gel electrophoresis analysis of polymerase chain reaction-amplified genes coding for 16S rRNA. Appl Environ Microbiol 59:695–700Google Scholar
  23. Naeem S, Li S (1997) Biodiversity enhances ecosystem reliability. Nature 390:507–509CrossRefGoogle Scholar
  24. Naeem S, Thompson LJ, Lawler SP, Lawton JH, Woodfin RM (1994) Declining biodiversity can alter the performance of ecosystems. Nature 368:734–737CrossRefGoogle Scholar
  25. Prosser JI, Bohannan BJM, Curtis TP, Ellis RJ, Firestone MK, Freckleton RP, Green JL, Green LE, Killham K, Lennon JJ, Osborn AM, Solan M, van der Gast CJ, Young JPW (2007) The role of ecological theory in microbial ecology. Nat Rev Microbiol 5:384–392CrossRefGoogle Scholar
  26. Reche I, Pulido-Villena E, Morales-Baquero R, Casamayor EO (2005) Does ecosystem size determine aquatic bacterial richness? Ecology 86:1715–1722CrossRefGoogle Scholar
  27. Srivastava DS, Vellend M (2005) Biodiversity-ecosystem function research: is it relevant to conservation? Annu Rev Ecol Evol S 36:267–294CrossRefGoogle Scholar
  28. Thomas CM, Nielsen KM (2005) Mechanisms of, and barriers to, horizontal gene transfer between bacteria. Nat Rev Microbiol 3:711–721CrossRefGoogle Scholar
  29. Tilman D, Lehman CL, Thomson KT (1997) Plant diversity and ecosystem productivity: theoretical considerations. Proc Natl Acad Sci USA 94:1857–1861CrossRefGoogle Scholar
  30. Venables WN, Ripley BD (2002) Modern applied statistics with S. Springer, BerlinGoogle Scholar
  31. Worm B, Barbier EB, Beaumont N, Duffy JE, Folke C, Halpern BS, Jackson JBC, Lotze HK, Micheli F, Palumbi SR, Sala E, Selkoe KA, Stachowicz JJ, Watson R (2006) Impacts of biodiversity loss on ocean ecosystem services. Science 314:787–790CrossRefGoogle Scholar
  32. Xu ZH, Chen CR (2006) Fingerprinting global climate change and forest management within rhizosphere carbon and nutrient cycling processes. Environ Sci Pollut Res 13:293–298CrossRefGoogle Scholar
  33. Yin B, Crowley D, Sparovek G, De Melo WJ, Borneman J (2000) Bacterial functional redundancy along a soil reclamation gradient. Appl Environ Microbiol 66:4361–4365CrossRefGoogle Scholar
  34. Yu Z, Morrison M (2004) Comparisons of different hypervariable regions of rrs genes for use in fingerprinting of microbial communities by PCR-denaturing gradient gel electrophoresis. Appl Environ Microbiol 70:4800–4806CrossRefGoogle Scholar

Copyright information

© Springer-Verlag 2009

Authors and Affiliations

  • Ji-Zheng He
    • 1
  • Yuan Ge
    • 1
  • Zhihong Xu
    • 2
  • Chengrong Chen
    • 2
  1. 1.State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-environmental SciencesChinese Academy of SciencesBeijingChina
  2. 2.Center for Forestry and Horticultural Research and School of Biomolecular and Physical SciencesGriffith UniversityNathanAustralia

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