1932

Abstract

Soils represent a significant reservoir of biological diversity that underpins a broad range of key processes and moderate ecosystem service provision. Our understanding of the role that soil organisms play in ecosystems is still developing, but the increased investigation into biodiversity-ecosystem functioning relationships in soils over the past couple of decades has provided insights that have greatly enhanced our ability to sustainably manage soil biodiversity. In this review, we synthesize emerging knowledge of soil biodiversity as a natural resource that supports the functioning of terrestrial ecosystems and their delivery of ecosystem services. We explore how environmental changes alter soil biodiversity and how this in turn can affect ecosystem processes as well as resistance and resilience to environmental changes. We then discuss ways to include soil biodiversity in management strategies for sustainable production and biodiversity conservation. We conclude by highlighting key research challenges to further improve our knowledge of soil biodiversity and its management.

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/content/journals/10.1146/annurev-environ-102014-021257
2015-11-04
2024-12-26
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Literature Cited

  1. Brussaard L, Behan-Pelletier VM, Bignell DE, Brown VK, Didden W. 1.  et al. 1997. Biodiversity and ecosystem functioning in soil. Ambio 26:563–70 [Google Scholar]
  2. Bardgett RD, van der Putten WH. 2.  2014. Belowground biodiversity and ecosystem functioning. Nature 515:505–11 [Google Scholar]
  3. Swift MJ, Heal OW, Anderson JM. 3.  1979. Decomposition in Terrestrial Ecosystems. Berkeley, CA: Univ. Calif. Press [Google Scholar]
  4. Bardgett RD, Usher MB, Hopkins DW. 4.  2005. Biological Diversity and Function in Soil. Cambridge, UK: Cambridge Univ. Press [Google Scholar]
  5. Nielsen UN, Ayres E, Wall DH, Bardgett RD. 5.  2011. Soil biodiversity and carbon cycling: a synthesis of studies examining diversity-function relationships. Eur. J. Soil Sci. 62:105–16 [Google Scholar]
  6. Barrios E. 6.  2007. Soil biota, ecosystem services and land productivity. Ecol. Econ. 64:269–85 [Google Scholar]
  7. Dominati E, Patterson M, Mackay A. 7.  2010. A framework for classifying and quantifying the natural capital and ecosystem services of soils. Ecol. Econ. 69:1858–68 [Google Scholar]
  8. Bissett A, Brown MV, Siciliano SD, Thrall PH. 8.  2013. Microbial community responses to anthropogenically induced environmental change: towards a systems approach. Ecol. Lett. 16:128–39 [Google Scholar]
  9. Bardgett RD, Wardle DA. 9.  2010. Aboveground-Belowground Linkages: Biotic Interactions, Ecosystem Processes, and Global Change Oxford, UK: Oxford Univ. Press [Google Scholar]
  10. van der Putten WH, Bardgett RD, Bever JD, Bezemer TM, Casper BB. 10.  et al. 2013. Plant-soil feedbacks: the past, the present and the future challenges. J. Ecol. 101:265–76 [Google Scholar]
  11. Decaëns T. 11.  2010. Macroecological patterns in soil communities. Glob. Ecol. Biogeogr. 19:287–302 [Google Scholar]
  12. Foley JA, Defries R, Asner GP, Barford C, Bonan G. 12.  et al. 2005. Global consequences of land use. Science 309:570–74 [Google Scholar]
  13. Galloway JN, Townsend AR, Erisman JW, Bekunda M, Cai ZC. 13.  et al. 2008. Transformation of the nitrogen cycle: recent trends, questions and potential solutions. Science 320:889–92 [Google Scholar]
  14. 14. Millenn. Ecosyst. Assess. 2005. Ecosystems and Human Well-being: Current State and Trends. 1 Findings of the Condition and Trends Working Group Washington, DC: Island [Google Scholar]
  15. Bridges EM, Oldeman LR. 15.  1999. Global assessment of human-induced soil degradation. Arid Soil Res. Rehabil. 13:319–25 [Google Scholar]
  16. Reynolds JF, Smith DM, Lambin EF, Turner BL 2nd, Mortimore M. 16.  et al. 2007. Global desertification: building a science for dryland development. Science 316:847–51 [Google Scholar]
  17. Peñuelas J, Sardans J, Rivas-Ubach, Janssens IA. 17.  2012. The human-induced imbalance between C, N and P in Earth's life system. Glob. Change Biol. 18:3–6 [Google Scholar]
  18. Wardle DA, Bardgett RD, Callaway RM, van der Putten W. 18.  2011. Terrestrial ecosystem responses to species gains and losses. Science 332:1273–77 [Google Scholar]
  19. Wall DH, Bardgett RD, Behan-Pelletier V, Herrick JE, Jones H. 19.  et al. 2012. Soil Ecology and Ecosystem Services Oxford, UK: Oxford Univ. Press [Google Scholar]
  20. Crotty FV, Adl SM, Blackshaw RP, Murray PJ. 20.  2013. Measuring soil protist respiration and ingestion rates using stable isotopes. Soil Biol. Biochem. 57:919–21 [Google Scholar]
  21. Griffiths RI, Thomson BC, James P, Bell T, Bailey M, Whiteley AS. 21.  2011. The bacterial biogeography of British soils. Environ. Microbiol. 13:1642–54 [Google Scholar]
  22. Ferguson BA, Dreisbach TA, Parks CG, Filip GM, Schmitt CL. 22.  2003. Coarse-scale population structure of pathogenic Armillaria species in a mixed-conifer forest in the Blue Mountains of northeast Oregon. Can. J. For. Res. 33:612–23 [Google Scholar]
  23. Wardle DA. 23.  2006. The influence of biotic interactions on soil biodiversity. Ecol. Lett. 9:870–86 [Google Scholar]
  24. Fierer N, Strickland MS, Liptzin D, Bradford MA, Cleveland CC. 24.  2009. Global patterns in belowground communities. Ecol. Lett. 12:1238–49 [Google Scholar]
  25. Roesch LF, Fulthorpe RR, Riva A, Casella G, Hadwin AKM. 25.  et al. 2007. Pyrosequencing enumerates and contrasts soil microbial diversity. ISME J. 1:283–90 [Google Scholar]
  26. Lauber CL, Hamady M, Knight R, Fierer N. 26.  2009. Pyrosequencing-based assessment of soil pH as a predictor of soil bacterial community structure at the continental scale. Appl. Environ. Microbiol. 75:5115–20 [Google Scholar]
  27. Tedersoo L, Bahram M, Põlme S, Kõljalg U, Yorou NS. 27.  et al. 2014. Global diversity and geography of soil fungi. Science 346:6213 [Google Scholar]
  28. Bates ST, Berg-Lyons D, Caporaso JG, Walters WA, Knight R, Fierer N. 28.  2011. Examining the global distribution of dominant archaeal populations in soil. ISME J. 5:908–17 [Google Scholar]
  29. Bates ST, Clemente JC, Flores GE, Walters WA, Parfrey LW. 29.  et al. 2013. Global biogeography of highly diverse protistan communities in soil. ISME J. 7:652–59 [Google Scholar]
  30. Nielsen UN, Ayres E, Wall DH, Li G, Bardgett RD. 30.  et al. 2014. Global-scale patterns of soil nematode assemblage structure in relation to climate and ecosystem properties. Glob. Ecol. Biogeogr. 23:968–78 [Google Scholar]
  31. Bignell DE, Eggleton P. 31.  2000. Termites in ecosystems. Termites: Evolution, Sociality, Symbiosis, Ecology T Abe, DE Bignell, M Higashi 363–87 Dordrecth, Neth.: Kluwer Acad. [Google Scholar]
  32. Ettema CH, Wardle DA. 32.  2002. Spatial soil ecology. Trends Ecol. Evol. 17:177–83 [Google Scholar]
  33. Bardgett RD. 33.  2002. Causes and consequences of biological diversity in soil. Zoology 105:367–74 [Google Scholar]
  34. Beare MH, Coleman DS, Crossley DA Jr, Hendrix PF, Odum EP. 34.  1995. A hierarchical approach to evaluating the significance of soil biodiversity to biogeochemical cycling. Plant Soil 170:5–22 [Google Scholar]
  35. Nielsen UN, Osler GHR, Campbell CD, Burslem DFRP, van der Wal R. 35.  2012. Predictors of fine-scale spatial variation in soil mite and microbe community composition differ between biotic groups and habitats. Pedobiologia 55:83–91 [Google Scholar]
  36. Nielsen UN, Osler GHR, Campbell CD, Burslem DFRP, van der Wal R. 36.  2010. The influence of vegetation type, soil properties and precipitation on the composition of soil mite and microbial communities at the landscape scale. J. Biogeogr. 37:1317–28 [Google Scholar]
  37. Wu T, Ayres E, Bardgett RD, Wall DH, Garey JR. 37.  2011. Molecular study of worldwide distribution and diversity of soil animals. PNAS 108:17720–25 [Google Scholar]
  38. Ramirez KS, Leff JW, Barberán A, Bates ST, Betley J. 38.  et al. 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 [Google Scholar]
  39. Powers JS, Montgomery RA, Adair EC, Brearley FQ, DeWalt SJ. 39.  et al. 2009. Decomposition in tropical forests: a pan-tropical study of the effects of litter type, litter placement and mesofaunal exclusion across a precipitation gradient. J. Ecol. 97:801–11 [Google Scholar]
  40. Cornwell WK, Cornelissen JHC, Amatangelo K, Dorrepaal E, Eviner VT. 40.  et al. 2008. Plant species traits are the predominant control on litter decomposition rates within biomes worldwide. Ecol. Lett. 11:1065–71 [Google Scholar]
  41. Gessner MO, Swan CM, Dang CK, McKie BG, Bardgett RD. 41.  et al. 2010. Diversity meets decomposition. Trends Ecol. Evol. 25:372–80 [Google Scholar]
  42. Ulyshen MD. 42.  2014. Wood decomposition as influenced by invertebrates. Biol. Rev. doi: 10.1111/brv.12158. In press [Google Scholar]
  43. Six J, Frey SD, Thiet RK, Batten KM. 43.  2006. Bacterial and fungal contributions to C-sequestration in agroecosystems. Soil Sci. Soc. Am. J. 70:555–69 [Google Scholar]
  44. van der Heijden MGA, Bardgett RD, van Straalen NM. 44.  2008. The unseen majority: soil microbes as drivers of plant diversity and productivity in terrestrial ecosystems. Ecol. Lett. 11:296–310 [Google Scholar]
  45. Leininger S, Urich T, Schloter M, Schwark L, Qi J. 45.  et al. 2006. Archaea predominate among ammonia-oxidizing prokaryotes in soils. Nature 442:806–9 [Google Scholar]
  46. Philippot L, Raaijmakers JM, Lemanceau P, van der Putten W. 46.  2013. Going back to the roots: the microbial ecology of the rhizosphere. Nat. Rev. Microbiol. 11:789–99 [Google Scholar]
  47. De Deyn GB, Raaijmakers CE, Zoomer HR, Berg MP, de Ruiter PC. 47.  et al. 2003. Soil invertebrate fauna enhances grassland succession and diversity. Science 422:711–13 [Google Scholar]
  48. Klironomos JN. 48.  2002. Feedback with soil biota contributes to plant rarity and invasiveness in communities. Nature 417:67–70 [Google Scholar]
  49. Cleveland CC, Townsend AR, Schimel DS, Fisher H, Howarth RW. 49.  et al. 1999. Global patterns of terrestrial biological nitrogen (N-2) fixation in natural ecosystems. Glob. Biogeochem. Cycles 13:623–45 [Google Scholar]
  50. Soler Gamborena R, Bezemer TM, van der Putten WH, Vet LEM, Harvey JA. 50.  2005. Root herbivore effects on above-ground herbivore, parasitoid and hyperparasitoid performance via changes in plant quality. J. Anim. Ecol. 74:1121–34 [Google Scholar]
  51. Staley JT, Mortimer SR, Morecroft MD, Brown VK, Masters GJ. 51.  2007. Summer drought alters plant-mediated competition between foliar- and root-feeding insects. Glob. Change Biol. 13:866–77 [Google Scholar]
  52. Bardgett RD, Streeter T, Bol R. 52.  2003. Soil microbes compete effectively with plants for organic nitrogen inputs to temperate grasslands. Ecology 84:1277–87 [Google Scholar]
  53. Kucey RMN. 53.  1983. Phosphate solubilizing bacteria and fungi in various cultivated and virgin Alberta soils. Can. J. Soil Sci. 63:671–78 [Google Scholar]
  54. Landeweert R, Hoffland E, Finlay RD, Kuyper TW, van Breemen N. 54.  2001. Linking plants to rocks: ectomycorrhizal fungi mobilize nutrients from minerals. Trends Ecol. Evol. 16:248–54 [Google Scholar]
  55. García-Palacios P, Maestre FT, Kattge J, Wall DH. 55.  2013. Climate and litter quality differently modulate the effects of soil fauna on litter decomposition across biomes. Ecol. Lett. 16:1045–53 [Google Scholar]
  56. Mikola J, Bardgett RD, Hedlund K. 56.  2002. Biodiversity, ecosystem functioning and soil decomposer food webs. Biodiversity and Ecosystem Functioning: Synthesis and Perspectives M Loreau, S Naeem, P Inchausti 169–80 Oxford, UK: Oxford Univ. Press [Google Scholar]
  57. Hunt HW, Wall DH. 57.  2002. Modelling the effects of loss of soil biodiversity on ecosystem function. Glob. Change Biol. 8:33–50 [Google Scholar]
  58. Caron D, Worden AZ, Countway PD, Demir E, Heidelberg KB. 58.  2009. Protists are microbes too: a perspective. ISME J. 3:4–12 [Google Scholar]
  59. van Groeningen JW, Lubbers IM, Vos HMJ, Brown GG, De Deyn GB, van Groeningen KJ. 59.  2014. Earthworms increase plant production: a meta-analysis. Sci. Rep. 4:6365 [Google Scholar]
  60. He Z, Xu M, Deng Y, Kang S, Kellogg L. 60.  et al. 2010. Metagenomic analysis reveals a marked divergence in the structure of belowground microbial communities at elevated CO2. Ecol. Lett. 13:564–75 [Google Scholar]
  61. Luo C, Rodriguez-R LM, Johnston ER, Wu L, Cheng L. 61.  et al. 2014. Soil microbial community responses to a decade of warming as revealed by comparative metagenomics. Appl. Environ. Microbiol. 80:1777–86 [Google Scholar]
  62. Mackelprang R, Waldrop MP, DeAngelis KM, David MM, Chavarria KL. 62.  et al. 2011. Metagenomic analysis of a permafrost microbial community reveals a rapid response to thaw. Nature 480:368–71 [Google Scholar]
  63. Carvalhais LC, Dennis PG, Tyson GW, Schenk PM. 63.  2012. Application of metatranscriptomics to soil environments. J. Microbiol. Methods 91:246–51 [Google Scholar]
  64. Allison SD, Martiny JBH. 64.  2008. Resistance, resilience, and redundancy in microbial communities. PNAS 105:11512–19 [Google Scholar]
  65. Fierer N, Leff JW, Adams BJ, Nielsen UN, Bates ST. 65.  et al. 2012. Cross-biome metagenomic analyses of soil microbial communities and their functional attributes. PNAS 109:21390–95 [Google Scholar]
  66. Tringe SG, von Mering C, Kobayashi A, Salamov AA, Chen K. 66.  2005. Comparative metagenomics of microbial communities. Science 308:554–57 [Google Scholar]
  67. Bryant JA, Stewart FJ, Eppley JM, DeLong EF. 67.  2012. Microbial community phylogenetic and trait diversity declines with depth in a marine oxygen minimum zone. Ecology 93:1659–73 [Google Scholar]
  68. Petchey OL, Gaston KJ. 68.  2002. Functional diversity (FD), species richness and community composition. Ecol. Lett. 5:402–11 [Google Scholar]
  69. Ridder B. 69.  2008. Questioning the ecosystem services argument for biodiversity conservation. Biodivers. Conserv. 17:781–90 [Google Scholar]
  70. Wagg C, Bendera SF, Widmerc F, van der MGA. 70.  2014. Soil biodiversity and soil community composition determine ecosystem multifunctionality. PNAS 111:5266–70 [Google Scholar]
  71. Burke C, Steinberg P, Rusch D, Kjelleberg S, Thomas T. 71.  2011. Bacterial community assembly based on functional genes rather than species. PNAS 108:14288–93 [Google Scholar]
  72. Wohl DL, Arora S, Gladstone JR. 72.  2004. Functional redundancy supports biodiversity and ecosystem function in a closed and constant environment. Ecology 85:1534–40 [Google Scholar]
  73. Singh BK, Quince C, Macdonald CA, Khachane A, Thomas N. 73.  et al. 2014. Loss of microbial diversity in soils is coincident with reductions in some specialized functions. Environ. Microbiol. 16:2408–20 [Google Scholar]
  74. Bowen JL, Ward BB, Morrison HG, Hobbie JE, Valiela I. 74.  et al. 2011. Microbial community composition in sediments resists perturbation by nutrient enrichment. ISME J. 5:1540–48 [Google Scholar]
  75. Bradford MA, Wood SA, Bardgett RD, Black HIJ, Bonkowski M. 75.  et al. 2014. Discontinuity in the responses of ecosystem processes and multifunctionality to altered soil community composition. PNAS 111:14478–83 [Google Scholar]
  76. Heemsbergen DA, Berg MP, Loreau M, van Hal JR, Faber JH, Verhoef HA. 76.  2004. Biodiversity effects on soil processes explained by interspecific functional dissimilarity. Science 306:1019–20 [Google Scholar]
  77. Kitz F, Steinwandter M, Traugott M, Seeber J. 77.  2015. Increased decomposer diversity accelerates and potentially stabilises litter decomposition. Soil Biol. Biochem. 83:138–41 [Google Scholar]
  78. Tardy V, Mathieu O, Lévêque J, Terrat S, Chabbi A. 78.  et al. 2014. Stability of soil microbial structure and activity depends on microbial diversity. Environ. Microbiol. Rep. 6:173–83 [Google Scholar]
  79. Girvan MS, Campbell CD, Killham K, Prosser JI, Glover LA. 79.  2005. Bacterial diversity promotes community stability and functional resilience after perturbation. Environ. Microbiol. 7:301–13 [Google Scholar]
  80. Griffiths BS, Philippot L. 80.  2012. Insights into the resistance and resilience of the soil microbial community. FEMS Microbiol. Rev. 37:112–29 [Google Scholar]
  81. Pereira EIP, Chung H, Scow KM, Six J. 81.  2013. Microbial communities and soil structure are affected by reduced precipitation, but not by elevated carbon dioxide. Soil Sci. Soc. Am. J. 77:482–88 [Google Scholar]
  82. Susilo FX, Neutel AM, van Noordwijk M, Hairiah K, Brown G, Swift MJ. 82.  2004. Soil biodiversity and food webs. Below-Ground Interactions in Tropical Agroecosystems: Concepts and Models with Multiple Plant Components M van Noordwijk, G Cadisch, CK Ong 285–302 Wallingford, UK: CABI Publ. [Google Scholar]
  83. Ceulemans T, Merckx R, Hens M, Honnay O. 83.  2011. A trait-based analysis of the role of phosphorus versus nitrogen enrichment in plant species loss across north-west European grasslands. J. Appl. Ecol. 48:1155–63 [Google Scholar]
  84. Latz E, Eisenhauer N, Rall BC, Allan E, Roscher C. 84.  et al. 2011. Plant diversity improves protection against soil-borne pathogens by fostering antagonistic bacterial communities. J. Ecol. 100:597–604 [Google Scholar]
  85. Sánches-Moreno S, Ferris H. 85.  2007. Suppressive services of the soil food web: effects of environmental management. Agric. Ecosyst. Environ. 119:75–87 [Google Scholar]
  86. Frey SD, Lee J, Melillo JM, Six J. 86.  2013. The temperature response of soil microbial growth efficiency and its feedback to climate. Nat. Clim. Change 3:395–98 [Google Scholar]
  87. García-Palacios P, Vandegehuchte ML, Shaw EA, Dam M, Post KH. 87.  et al. 2015. Are there links between responses of soil microbes and ecosystem functioning to elevated CO2, N deposition and warming? A global perspective. Glob. Change Biol. 21:1590–600 [Google Scholar]
  88. 88. IPCC 2013. Climate Change 2013: The Physical Science Basis. Summary for Policymakers. Contribution of Working Group I to the Fifth Assessment Report of the Intergovernmental Panel on Climate Change TF Stocker, D Qin, G-K Plattner, M Tignor, SK Allen, et al. 3–29 Cambridge, UK/New York: Cambridge Univ. Press [Google Scholar]
  89. Blankinship JC, Niklaus PA, Hungate BA. 89.  2011. A meta-analysis of responses of soil biota to global change. Oecologia 165:553–65 [Google Scholar]
  90. Sylvain ZA, Wall DH, Cherwin KL, Peters DP, Reichmann LG, Sala OE. 90.  2014. Soil animal responses to moisture availability are largely scale, not ecosystem dependent: insight from a cross-site study. Glob. Change Biol. 20:2631–43 [Google Scholar]
  91. Geisen S, Bandow C, Römbke J, Bonkowski M. 91.  2014. Soil water availability strongly alters the community composition of protists. Pedobiologia 57:205–13 [Google Scholar]
  92. Nielsen UN, Ball B. 92.  2015. Impacts of altered precipitation regimes on soil communities and biogeochemistry in arid and semi-arid ecosystems. Glob. Change Biol. 21:1407–21 [Google Scholar]
  93. Bouskill NJ, Lim HC, Borglin S, Salve R, Wood TE. 93.  et al. 2013. Pre-exposure to drought increases the resistance of tropical forest soil bacterial communities to extended drought. ISME J. 7:284–94 [Google Scholar]
  94. Evans SE, Wallenstein MD. 94.  2014. Climate change alters ecological strategies of soil biota. Ecol. Lett. 17:155–64 [Google Scholar]
  95. Briones MJI, Ineson P, Heinemeyer A. 95.  2007. Predicting potential impacts of climate change on the geographical distribution of enchytraeids: a meta-analysis approach. Glob. Change Biol. 13:2252–69 [Google Scholar]
  96. de Vries FT, Liiri M, Bjørnlund L, Bowker MA, Christensen S. 96.  et al. 2012. Land use alters the resistance and resilience of soil food webs to drought. Nat. Clim. Change 2:276–80 [Google Scholar]
  97. Six J. 97.  2012. Fungal friends against drought. Nat. Clim. Change 2:234–35 [Google Scholar]
  98. Drigo B, Kowalchuk GA, van Veen JA. 98.  2008. Climate change goes underground: effects of elevated atmospheric CO2 on microbial community structure and activities in the rhizosphere. Biol. Fertil Soils 44:667–79 [Google Scholar]
  99. Johnson SN, Nielsen UN. 99.  2012. Foraging in the dark—chemically mediated host plant location by belowground insect herbivores. J. Chem. Ecol. 38:604–14 [Google Scholar]
  100. Ainsworth EA, Long SP. 100.  2005. What have we learned from 15 years of free-air CO2 enrichment (FACE)? A meta-analytic review of the responses of photosynthesis, canopy properties and plant production to rising CO2. New Phytol. 165:351–72 [Google Scholar]
  101. Eisenhauer N, Cesarz S, Koller R, Worm K, Reich PB. 101.  2012. Global change belowground: impacts of elevated CO2, nitrogen and summer drought on soil food webs and biodiversity. Glob. Change Biol. 18:435–47 [Google Scholar]
  102. Treseder KK. 102.  2008. Nitrogen additions and microbial biomass: a meta-analysis of ecosystem studies. Ecol. Lett. 11:1111–20 [Google Scholar]
  103. Berthrong ST, Yeager CM, Gallegos-Graves L, Steven B, Eichorst SA. 103.  et al. 2014. Nitrogen fertilization has a stronger effect on soil nitrogen-fixing bacterial communities than elevated atmospheric CO2. Appl. Environ. Microbiol. 80:3103–12 [Google Scholar]
  104. Kiers ET, Palmer TM, Ives AR, Bruno JF, Bronstein JL. 104.  2010. Mutualisms in a changing world: an evolutionary perspective. Ecol. Lett. 13:1459–74 [Google Scholar]
  105. Lau JA, Bowling EJ, Gentry LE, Glasser PA, Monarch EA. 105.  et al. 2012. Direct and interactive effects of light and nutrients on the legume-rhizobia mutualism. Acta Oecol. 39:80–86 [Google Scholar]
  106. Antunes PM, Lehmann A, Hart MM, Baumecker M, Rillig MC. 106.  2012. Long-term effects of soil nutrient deficiency on arbuscular mycorrhizal communities. Funct. Ecol. 26:532–40 [Google Scholar]
  107. Johnson PTJ, Townsend AR, Cleveland CC, Glibert PM, Howarth RW. 107.  et al. 2010. Linking environmental nutrient enrichment and disease emergence in humans and wildlife. Ecol. Appl. 20:16–29 [Google Scholar]
  108. Postma-Blaauw MB, de Goede RGM, Bloem J, Faber JH, Brussaard L. 108.  2010. Soil biota community structure and abundance under agricultural intensification and extensification. Ecology 91:460–73 [Google Scholar]
  109. Tsiafouli MA, Thébault E, Sgardelis SP, de Ruiter PC, van der Putten WH. 109.  et al. 2015. Intensive agriculture reduces soil biodiversity across Europe. Glob. Change Biol. 21:973–85 [Google Scholar]
  110. de Vries FT, Hoffland E, van Eekeren N, Brussaard L, Bloem J. 110.  2006. Fungal/bacterial ratios in grasslands with contrasting nitrogen management. Soil Biol. Biochem. 38:2092–103 [Google Scholar]
  111. Liiri M, Häsa M, Haimi J, Setälä H. 111.  2012. History of land-use intensity can modify the relationship between functional complexity of the soil fauna and soil ecosystem services—a microcosm study. Appl. Soil Ecol. 55:53–61 [Google Scholar]
  112. Bünemann EK, Schwenke GD, Van Zwieten L. 112.  2006. Impact of agricultural inputs on soil organisms: a review. Soil Res. 44:379–406 [Google Scholar]
  113. Hussain S, Siddique T, Saleem M, Arshad M, Khalid A, Donald LS. 113.  2009. Impact of pesticides on soil microbial diversity, enzymes, and biochemical reactions. Adv. Agron. 102:159–200 [Google Scholar]
  114. Richter ED. 114.  2002. Acute human pesticide poisonings. Encyclopedia of Pest Management D Pimentel 3–6 Boca Raton, FL: CRC Press [Google Scholar]
  115. Cassman KG, Dobermann A, Walters DT. 115.  2002. Agroecosystems, nitrogen-use efficiency, and nitrogen management. Ambio 31:132–40 [Google Scholar]
  116. Smith KP, Handelsman J, Goodman RM. 116.  1999. Genetic basis in plants for interactions with disease-suppressive bacteria. PNAS 96:4786–90 [Google Scholar]
  117. Germida JJ, Siciliano SD. 117.  2001. Taxonomic diversity of bacteria associated with the roots of modern, recent and ancient wheat cultivars. Biol. Fertil Soils 33:410–15 [Google Scholar]
  118. Foster D, Swanson F, Aber J, Burke I, Brokaw N. 118.  et al. 2003. The importance of land-use legacies to ecology and conservation. Bioscience 53:77–88 [Google Scholar]
  119. Crowther TW, Maynard DS, Leff JW, Oldfield EE, McCulley RL. 119.  et al. 2014. Predicting the responsiveness of soil biodiversity to deforestation: a cross-biome study. Glob. Change Biol. 20:2983–94 [Google Scholar]
  120. Engelkes T, Morrien E, Verhoeven KJF, Bezemer TM, Biere A. 120.  et al. 2008. Successful range-expanding plants experience less above-ground and below-ground enemy impact. Nature 456:946–48 [Google Scholar]
  121. van der Putten WH, Kowalchuk GA, Brinkman EP, Doodeman GTA, van der Kaaij RM. 121.  et al. 2007. Soil feedback of exotic savanna grass relates to pathogen absence and mycorrhizal selectivity. Ecology 88:978–88 [Google Scholar]
  122. Hale AN, Tonsor SJ, Kalisz S. 122.  2011. Testing the mutualism disruption hypothesis: physiological mechanisms for invasion of intact perennial plant communities. Ecosphere 2:110 [Google Scholar]
  123. Mangla S, Inderjit, Callaway RM. 123.  2008. Exotic invasive plant accumulates native soil pathogens which inhibit native plants. J. Ecol. 96:58–67 [Google Scholar]
  124. Porter SS, Stanton ML, Rice KJ. 124.  2011. Mutualism and adaptive divergence: co-invasion of a heterogeneous grassland by an exotic legume-rhizobium symbiosis. PLOS ONE 6:e27935 [Google Scholar]
  125. Bohlen PJ, Scheu S, Hale CM, McLean MA, Migge S. 125.  et al. 2004. Non-native invasive earthworms as agents of change in northern temperate forests. Front. Ecol. Environ. 2:427–35 [Google Scholar]
  126. Palm C, Blanco-Canqui H, DeClerk F, Gatere L, Grace P. 126.  2014. Conservation agriculture and ecosystem services: an overview. Agric. Ecosyst. Environ. 187:87–104 [Google Scholar]
  127. Powlson DS, Stirling CM, Jat ML, Gerard BG, Palm CA. 127.  et al. 2014. Limited potential for no-till agriculture for climate change mitigation. Nat. Clim. Change 4:678–83 [Google Scholar]
  128. Pittelkow CM, Liang X, Linquist BA, van Groenigen KJ, Lee J. 128.  et al. 2015. Productivity limits and potentials of the principles of conservation agriculture. Nature 517:365–68 [Google Scholar]
  129. Ceja-Navarro JA, Rivera-Orduña FN, Patiño-Zúñiga L, Vila-Sanjurjo A, Crossa J. 129.  et al. 2010. Phylogenetic and multivariate analyses to determine the effects of different tillage and residue management practices on soil bacterial communities. Appl. Environ. Microbiol. 76:3685–91 [Google Scholar]
  130. Simpson RT, Frey SD, Six J, Thiet RK. 130.  2004. Preferential accumulation of microbial carbon in aggregate structures of no-tillage soils. Soil Sci. Soc. Am. J. 68:1249–55 [Google Scholar]
  131. Jansa J, Wiemken A, Frossard E. 131.  2006. The effects of agricultural practices on arbuscular mycorrhizal fungi. Function of Soils for Human Societies and the Environment Special Publ. 266, ed. E Frossard, WEH Blum, BP Warkentin 89–115 London, UK: Geol. Soc. [Google Scholar]
  132. Birkhofer K, Bezemer TM, Bloem J, Bonkowski M, Christensen S. 132.  et al. 2008. Long-term organic farming fosters below and aboveground biota: implications for soil quality biological control and productivity. Soil Biol. Biochem. 40:2297–308 [Google Scholar]
  133. Reganold JP, Andrews PK, Reeve JR, Carpenter-Boggs L, Schadt CW. 133.  et al. 2010. Fruit and soil quality of organic and conventional strawberry agroecosystems. PLOS ONE 5:e12346 [Google Scholar]
  134. Bell LW, Sparling B, Tenuta M, Entz MH. 134.  2012. Soil profile carbon and nutrient stocks under long-term conventional and organic crop and alfalfa-crop rotations and re-established grassland. Agric. Ecosyst. Environ. 158:156–63 [Google Scholar]
  135. Williams A, Hedlund K. 135.  2013. Indicators of soil ecosystem services in conventional and organic arable fields along a gradient of landscape heterogeneity in southern Sweden. Appl. Soil Ecol. 65:1–7 [Google Scholar]
  136. de Vries FT, Thébault E, Liiri M, Birkhofer K, Tsiafouli MA. 136.  et al. 2013. Soil food web properties explain ecosystem services across European land use systems. PNAS 110:14296–301 [Google Scholar]
  137. Coleman-Derr D, Tringe SG. 137.  2014. Building the crops of tomorrow: advantages of symbiont-based approaches to improving abiotic stress tolerance. Front. Microbiol. 5:283 [Google Scholar]
  138. Rodriguez RJ, Henson J, Van Volkenburgh E, Hoy M, Wright L. 138.  et al. 2008. Stress tolerance in plants via habitat-adapted symbiosis. ISME J. 2:404–16 [Google Scholar]
  139. Thiele-Bruhn S, Bloem J, de Vries FT, Kalbitz K, Wagg C. 139.  2012. Linking soil biodiversity and agricultural soil management. Curr. Opin. Environ. Sustain. 4:523–28 [Google Scholar]
  140. Kong AYY, Six J. 140.  2012. Microbial community assimilation of cover crop rhizodeposition within soil microenvironments in alternative and conventional cropping systems. Plant Soil 356:315–30 [Google Scholar]
  141. Fonte SJ, Barrios E, Six J. 141.  2010. Earthworms, soil fertility and aggregate-associated soil organic matter dynamics in the Quesungual agroforestry ecosystem. Geoderma 155:320–28 [Google Scholar]
  142. Benayas JMR, Newton AC, Diaz A, Bullock JM. 142.  2009. Enhancement of biodiversity and ecosystem services by ecological restoration: a meta-analysis. Science 325:1121–24 [Google Scholar]
  143. Glassman SI, Casper BB. 143.  2012. Biotic contexts alter metal sequestration and AMF effects on plant growth in soils polluted with heavy metals. Ecology 93:1550–59 [Google Scholar]
  144. Boyer S, Wratten SD. 144.  2010. The potential of earthworms to restore ecosystem services after opencast mining—a review. Basic Appl. Ecol. 11:196–203 [Google Scholar]
  145. Wall DH, Bardgett RD, Kelly E. 145.  2010. Biodiversity in the dark. Nat. Geosci. 3:297–98 [Google Scholar]
  146. Schmitz OJ, Raymond PA, Estes JA, Kurz WA, Holtgrieve GW. 146.  et al. 2014. Animating the carbon cycle. Ecosystems 17:344–59 [Google Scholar]
  147. Dirzo R, Young HS, Galetti M, Ceballos G, Isaac NJB, Collen B. 147.  2014. Defaunation in the Anthropocene. Science 345:401–6 [Google Scholar]
  148. Dykhuizen DE. 148.  1998. Santa Rosalia revisited: Why are there so many species of bacteria?. Antonie van Leeuwenhoek 73:25–33 [Google Scholar]
  149. Torsvik V, Øvreås L, Thingstad TF. 149.  2002. Prokaryotic diversity—magnitude, dynamics, and controlling factors. Science 296:1064–66 [Google Scholar]
  150. Blackwell M. 150.  2011. The Fungi: 1, 2, 3…5.1 million species?. Am. J. Bot. 98:426–38 [Google Scholar]
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