Understanding and managing soil biodiversity: a major challenge in agroecology

详细信息    查看全文

• 作者：Philippe Lemanceau (1)
  Pierre-Alain Maron (1)
  Sylvie Mazurier (1)
  Christophe Mougel (2)
  Barbara Pivato (1)
  Pierre Plassart (1)
  Lionel Ranjard (1)
  C茅cile Revellin (1)
  Vincent Tardy (1)
  Daniel Wipf (3)
  
  1. INRA ; UMR 1347 Agro茅cologie ; 17 rue Sully ; BP 86510 ; F-21065 ; Dijon cedex ; France
  2. INRA ; UMR 1349 IGEPP BP35327 ; F-35653 ; Le Rheu cedex ; France
  3. Universit茅 de Bourgogne ; UMR 1347 Agro茅cologie ; 17 rue Sully ; BP 86510 ; 21065 ; Dijon cedex ; France
  
• 关键词：Agroecology ; Biodiversity ; Microbial communities ; Plant growth and heath ; Soil biology ; Soil fertility
• 刊名：Agronomy for Sustainable Development
• 出版年：2015
• 出版时间：January 2015
• 年：2015
• 卷：35
• 期：1
• 页码：67-81
• 全文大小：2,323 KB
• 参考文献：1. B氓氓th E, Anderson TH (2003) Comparisons of soil fungal/bacterial ratios in a pH gradient using physiological and PLFA-based techniques. Soil Biol Biochem 35:955鈥?63. doi:10.1016/S0038-0717(03)00154-8 38-0717(03)00154-8" target="_blank" title="It opens in new window">CrossRef
  2. Balvanera P, Pfisterer AB, Buchmann N, He JS, Nakashizuka T, Raffaelli D, Schmid B (2006) Quantifying the evidence for biodiversity effects on ecosystem functioning and services. Ecol Lett 9:1146鈥?156. doi:10.1111/j.1461-0248.2006.00963.x 3.x" target="_blank" title="It opens in new window">CrossRef
  3. Baslam M, Pascual L, Sanchez-Dial M, Erro J, Garcia-Mina JM, Goicoechea N (2011) Improvement of nutritional quality of greenhouse-grown lettuce by arbuscular mycorrhizal fungi is conditioned by the source of phosphorus nutrition. J Agric Food Chem 59:11129鈥?1140. doi:10.1021/jf202445y CrossRef
  4. Bates ST, Berg-Lyons D, Caporaso JG, Walters WA, Knight R, Fierer N (2011) Examining the global distribution of dominant archaeal populations in soil. ISME J 5:908鈥?17. doi:10.1038/ismej.2010.171 38/ismej.2010.171" target="_blank" title="It opens in new window">CrossRef
  5. Bispo A, Grand C, Galsomies L (2009) Le programme ADEME 鈥淏ioindicateurs de qualit茅 des sols鈥? 脡tude Gest Sols 16:145鈥?58
  6. Bulgarelli D, Rott M, Schlaeppi K, van Themaat EVL, Ahmadinejad N, Assenza F, Rauf P, Huettel B, Reinhardt R, Schmelzer E, Peplies J, Gloeckner FO, Amann R, Eickhorst T, Schulze-Lefert P (2012) Revealing structure and assembly cues for / Arabidopsis root inhabiting bacterial microbiota. Nature 488:91鈥?5. doi:10.1038/nature11336 38/nature11336" target="_blank" title="It opens in new window">CrossRef
  7. Catroux G, Hartmann A, Revellin C (2001) Trends in rhizobial inoculant production and use. Plant Soil 230:21鈥?0 3/A:1004777115628" target="_blank" title="It opens in new window">CrossRef
  8. Cook RJ, Thomashow LS, Weller DM, Fujimoto D, Mazzola M, Bangera G, Kim D (1995) Molecular mechanisms of defense by rhizobacteria against root disease. Proc Natl Acad Sci U S A 92:4197鈥?201 3/pnas.92.10.4197" target="_blank" title="It opens in new window">CrossRef
  9. Copetta A, Lingua G, Berta G (2006) Effects of three AM fungi on growth, distribution of glandular hairs, and essential oil production in / Ocimum basilicum L. var. / Genovese. Mycorrhiza 16:485鈥?94. doi:10.1007/s00572-006-0065-6 CrossRef
  10. Dequiedt S, Thioulouse J, Jolivet C, Saby NPA, Lelievre M, Maron PA, Martin MP, Chemidlin-Pr茅vost-Bour茅 N, Toutain B, Arrouays D, Lemanceau P, Ranjard L (2009) Biogeographical patterns of soil bacterial communities. Environ Microbiol Rep 1:251鈥?55. doi:10.1111/j.1758-2229.2009.00040.x CrossRef
  11. Dequiedt S, Saby NPA, Lelievre M, Jolivet C, Thioulouse J, Toutain B, Arrouays D, Bispo A, Lemanceau P, Ranjard L (2011) Biogeographical patterns of soil molecular microbial biomass as influenced by soil characteristics and management. Glob Ecol Biogeogr 20:641鈥?52. doi:10.1111/j.1466-8238.2010.00628.x 38.2010.00628.x" target="_blank" title="It opens in new window">CrossRef
  12. Fierer N, Jackson RB (2006) The diversity and biogeography of soil bacterial communities. Proc Natl Acad Sci U S A 103:626鈥?31. doi:10.1073/pnas.0507535103 3/pnas.0507535103" target="_blank" title="It opens in new window">CrossRef
  13. Fontaine S, Henault C, Aamor A, Bdioui N, Bloor JMG, Maire V, Mary B, Revaillot S, Maron PA (2011) Fungi mediate long term sequestration of carbon and nitrogen in soil through their priming effect. Soil Biol Biochem 43:86鈥?6. doi:10.1016/j.soilbio.2010.09.017 CrossRef
  14. Friesen M, Porter SS, Stark SC, von Wettberg EJ, Sachc JL, Martinez-Romero E (2011) Microbially mediated plant functional traits. Annu Rev Ecol Evol Syst 42:23鈥?6. doi:10.1146/annurev-ecolsys-102710-145039 39" target="_blank" title="It opens in new window">CrossRef
  15. Gardi C, Montanarella L, Arrouays D, Bispo A, Lemanceau P, Jolivet C, Mulder C, Ranjard L, Roembke J, Rutgers M, Menta C (2009) Soil biodiversity monitoring in Europe: ongoing activities and challenges. Eur J Soil Sci 60:807鈥?19. doi:10.1111/j.1365-2389.2009.01177.x 365-2389.2009.01177.x" target="_blank" title="It opens in new window">CrossRef
  16. Gianinazzi S, Gollotte A, Binet MA, van Tuinen D, Redecker D, Wipf D (2010) Agroecology: the key role of arbuscular mycorrhizas in ecosystem services. Mycorrhiza 20:519鈥?30. doi:10.1007/s00572-010-0333-3 333-3" target="_blank" title="It opens in new window">CrossRef
  17. Girvan MS, Campbell CD, Killham K, Prosser JI, Glover LA (2005) Bacterial diversity promoted community structure stability and functional resilience after perturbation. Environ Microbiol 7:301鈥?13. doi:10.1111/j.1462-2920.2005.00695.x CrossRef
  18. Gobat JM, Aragno M, Matthey W, Bally R (2010) Le sol vivant. Bases de p茅dologie, Biologie des sols, 3e 茅dition revue et augment茅e. Presses Polytechniques et Universitaires Romandes, Lausanne
  19. Griffiths BS, Philippot L (2013) Insights into the resistance and resilience of the soil microbial community. FEMS Microbiol Rev 37:112鈥?29. doi:10.1111/j.1574-6976.2012.00343.x
  20. Griffiths BS, Ritz K, Bardgett RD, Cook R, Christensen S, Ekelund F, Sorensen SJ, Baath E, Bloem J, de Ruiter PC, Dolfing J, Nicolardot B (2000) Ecosystem response of pasture soil communities to fumigation-induced microbial diversity reductions: an examination of the biodiversity-ecosystem function relationship. Oikos 90:279鈥?94 34/j.1600-0706.2000.900208.x" target="_blank" title="It opens in new window">CrossRef
  21. Griffiths RI, Thomson B, James P, Bell T, Bailey M, Whiteley AS (2011) The bacterial biogeography of British soils. Environ Microbiol 13:1642鈥?654. doi:10.1111/j.1462-2920.2011.02480.x CrossRef
  22. Henault C, Revellin C (2011) Inoculants of leguminous crops for mitigating soil emissions of the greenhouse gas nitrous oxide. Plant Soil 346:289鈥?96. doi:10.1007/s11104-011-0820-0 CrossRef
  23. Herridge DF, Peoples MB, Boddey RM (2008) Global inputs of biological nitrogen fixation in agricultural systems. Plant Soil 311:1鈥?8. doi:10.1007/s11104-008-9668-3 3" target="_blank" title="It opens in new window">CrossRef
  24. Horwath WR, Paul EA (1994) Microbial biomass. In: Weaver RW (ed) Methods of soil analysis, SSSA book series 5. Soil Sci Soc Am Inc, Madison, pp 727鈥?52
  25. Horz HP, Barbrook A, Field CB, Bohannan BJM (2004) Ammoniaoxidizing bacteria respond to multifactorial global change. Proc Natl Acad Sci U S A 101:15136鈥?5141. doi:10.1073/pnas.0406616101 3/pnas.0406616101" target="_blank" title="It opens in new window">CrossRef
  26. INRA (2010) Document d鈥檕rientation INRA 2010鈥?020, une science pour l鈥檌mpact. INRA, Paris
  27. ISO Standard 11063 (2009) Soil quality鈥攎ethod to directly extract DNA from soil samples. ISO, Gen猫ve
  28. Johnson MJ, Lee KY, Scow KM (2003) DNA fingerprinting reveals links among agricultural crops, soil properties, and the composition of soil microbial communities. Geoderma 114:279鈥?03. doi:10.1016/S0016-7061(03)00045-4 3)00045-4" target="_blank" title="It opens in new window">CrossRef
  29. Jones RT, Robeson MS, Lauber CL, Hamady M, Knight R, Fierer N (2009) A comprehensive survey of soil acidobacterial diversity using pyrosequencing and clone library analyses. ISME J 3:442鈥?53. doi:10.1038/ismej.2008.127 38/ismej.2008.127" target="_blank" title="It opens in new window">CrossRef
  30. Lambert H, Mougel C, Jaillard B, Hinsinger P (2009) Plant-microbe-soil interactions in the rhizosphere: an evolutionary perspective. Plant Soil 321:83鈥?15. doi:10.1007/s11104-009-0042-x CrossRef
  31. Lata JC, Guillaume K, Degrange V, Abbadie L, Lensi R (2000) Relationships between root density of the African grass / Hyparrhenia diplandra and nitrification at the decimetric scale: an inhibition-stimulation balance hypothesis. Proc Biol Sci 267:595鈥?00. doi:10.1098/rspb.2000.1043 3" target="_blank" title="It opens in new window">CrossRef
  32. Lata JC, Degrange V, Raynaud X, Maron PA, Lensi R, Abbadie L (2004) Grass populations control nitrification in savanna soils. Funct Ecol 18:605鈥?11. doi:10.1111/j.0269-8463.2004.00880.x 3.2004.00880.x" target="_blank" title="It opens in new window">CrossRef
  33. Lawes JB, Gilbert JH, Warington R (1882) On the amount and composition of the rain and drainage water collected at Rothamsted. Clowes, London. Originally published in J Royal Agr Soc Eng XVII 1881:241鈥?79, 311鈥?50; XVIII 1882:1鈥?1
  34. Leckie SE, Prescott CE, Grayston SJ, Neufeld JD, Mohn WW (2004) Comparison of chloroform fumigation extraction, phospholipid fatty acid, and DNA methods to determine microbial biomass in forest humus. Soil Biol Biochem 36:529鈥?32. doi:10.1016/j.soilbio.2003.10.014 3.10.014" target="_blank" title="It opens in new window">CrossRef
  35. Lejon DPH, Chaussod R, Ranger J, Ranjard L (2005) Microbial community structure and density under different tree species in an acid forest soil (Morvan, France). Microb Ecol 50:614鈥?25. doi:10.1007/s00248-005-5130-8 30-8" target="_blank" title="It opens in new window">CrossRef
  36. Lejon DPH, Sebastia J, Lamy I, Nowak V, Chaussod R, Ranjard L (2007) Microbial density and genetic structure in two agricultural soils submitted to various organic managements. Microb Ecol 53:650鈥?53. doi:10.1007/s00248-006-9145-6 CrossRef
  37. Lemanceau P (2011) EcoFINDERS characterizes biodiversity and functions of soils in Europe 23 partners in 10 European countries and China. Biofutur 326:56鈥?8
  38. Lindstrom K, Murwira M, Willems A, Altier N (2010) The biodiversity of beneficial microbe-host mutualism: the case of rhizobia. Res Microbiol 161:453鈥?63. doi:10.1016/j.resmic.2010.05.005 CrossRef
  39. Loreau M (2000) Biodiversity and ecosystem functioning: recent theoretical advances. Oikos 91:3鈥?7. doi:10.1034/j.1600-0706.2000.910101.x 34/j.1600-0706.2000.910101.x" target="_blank" title="It opens in new window">CrossRef
  40. Lundberg DS, Lebeis SL, Paredes SH, Yourstone S, Gehring J, Malfatti S, Tremblay J, Engelbrektson A, Kunin V, Rio TGD, Edgar RC, Eickhorst T, Ley RE, Hugenholtz P, Tringe SG, Dangl JL (2012) Defining the core / Arabidopsis thaliana root microbiome. Nature 488:86鈥?0. doi:10.1038/nature11237 38/nature11237" target="_blank" title="It opens in new window">CrossRef
  41. Manter DK, Delgado JA, Holm DG, Stong RA (2010) Pyrosequencing reveals a highly diverse and cultivar-specific bacterial endophyte community in potato roots. Microb Ecol 60:157鈥?66. doi:10.1007/s00248-010-9658-x CrossRef
  42. Maron PA, Ranjard L, Mougel C, Lemanceau P (2007) Metaproteomics: a new approach for studying functional microbial ecology. Microb Ecol 53:486鈥?93. doi:10.1007/s00248-006-9196-8 CrossRef
  43. Maron PA, Mougel C, Ranjard L (2011) Soil microbial diversity: spatial overview, driving factors and functional interest. C R Acad Sci Biol 334:403鈥?11. doi:10.1016/j.crvi.2010.12.003
  44. Marstorp H, Guan X, Gong P (2000) Relationship between dsDNA, chloroformlabile C and ergosterol in soils of different organic matter contents and pH. Soil Biol Biochem 32:879鈥?82 38-0717(99)00210-2" target="_blank" title="It opens in new window">CrossRef
  45. Mavrodi OV, Mavrodi DV, Thomashow LS, Weller DM (2007) Quantification of 2,4 diacetylphloroglucinol-producing / Pseudomonas fluorescens strains in the plant rhizosphere by real-time PCR. Appl Environ Microbiol 73:5531鈥?538. doi:10.1128/AEM.00925-07 CrossRef
  46. Mougel C, Maron PA, Philippot L, Ranjard L, Lemanceau P (2011) Translation of metagenomics agroecosystems in ecological services. Biofutur 319:44鈥?7
  47. Naeem S, Li S (1997) Biodiversity enhances ecosystem reliability. Nature 390:507鈥?09. doi:10.1038/37348 38/37348" target="_blank" title="It opens in new window">CrossRef
  48. Nguyen C (2003) Rhizodeposition of organic C by plants: mechanism and controls. Agronomie 23:375鈥?96. doi:10.1051/agro:2003011 3011" target="_blank" title="It opens in new window">CrossRef
  49. Nicolardot B, Bouziri L, Bastian F, Ranjard L (2007) A microcosm experiment to evaluate the influence of location and quality of plant residues on residue decomposition and genetic structure of soil microbial communities. Soil Biol Biochem 39:1631鈥?644. doi:10.1016/j.soilbio.2007.01.012 CrossRef
  50. Peres G, Vandenbulcke F, Guernion M, Hedde M, Beguiristain T, Douay F, Houot S, Piron D, Richard A, Bispo A, Grand C, Galsomies L, Cluzeau D (2011) Earthworm indicators as tools for soil monitoring, characterization and risk assessment. An example from the national Bioindicator programme (France). Pedobiologia 54:S77鈥揝87. doi:10.1016/j.pedobi.2011.09.015 CrossRef
  51. Petric I, Philippot L, Abbate C, Bispo A, Chesnot T, Hallin S, Laval K, Lebeau T, Lemanceau P, Leyval C, Lindstr枚m K, Pandard P, Romero E, Sarr A, Schloter M, Simonet P, Smalla K, Wilke BM, Martin-Laurent F (2011) Inter-laboratory evaluation of the ISO standard 11063 鈥淪oil quality鈥攎ethod to directly extract DNA from soil samples鈥? J Microbiol Meth 84:454鈥?60. doi:10.1016/j.mimet.2011.01.016 CrossRef
  52. Philippot L (2002) Denitrifying genes in bacterial and archaeal genomes. Biochim Biophys Acta 1577:355鈥?76. doi:10.1016/S0167-4781(02)00420-7 CrossRef
  53. Philippot L, Hallin S (2011) Towards food, feed and energy crops mitigating climate change. Trends Plant Sci 16:476鈥?80. doi:10.1016/j.tplants.2011.05.00 CrossRef
  54. Philippot L, Abbate C, Bispo A, Chesnot T, Hallin S, Lemanceau P, Lindstr枚m K, Pandard P, Romero E, Schloter M, Simonet P, Smalla K, Wilke BM, Petric I, Martin-Laurent F (2010) Soil microbial diversity: an ISO standard for soil DNA extraction. J Soils Sediments 10:1344鈥?345. doi:10.1007/s11368-010-0265-8 368-010-0265-8" target="_blank" title="It opens in new window">CrossRef
  55. Philippot L, Raaijmakers JM, Lemanceau P, van der Putten WH (2013a) Going back to the roots: the microbial ecology of the rhizosphere. Nat Rev Microbiol 11:789鈥?99. doi:10.1038/nrmicro3109 38/nrmicro3109" target="_blank" title="It opens in new window">CrossRef
  56. Philippot L, Spor A, Henault C, Bru D, Bizouard F, Jones CM, Sarr A, Maron PA (2013b) Loss in microbial diversity affects nitrogen cycling in soil. ISME J 7:1609鈥?619. doi:10.1038/ismej.2013.34 38/ismej.2013.34" target="_blank" title="It opens in new window">CrossRef
  57. Plassart P, Terrat S, Thomson B, Griffiths R, Dequiedt S, Lelievre M, Regnier T, Nowak V, Bailey M, Lemanceau P, Bispo A, Chabbi A, Maron PA, Mougel C, Ranjard L (2012) Evaluation of the ISO standard 11063 DNA extraction procedure for assessing soil microbial abundance and community structure. PLoS One 7:e44279. doi:10.1371/journal.pone.0044279 371/journal.pone.0044279" target="_blank" title="It opens in new window">CrossRef
  58. Raaijmakers JM, Weller DM, Thomashow LS (1997) Frequency of antibiotic-producing / Pseudomonas spp. in natural environments. Appl Environ Microbiol 63:881鈥?87
  59. Rajendhran J, Gunasekaran P (2008) Strategies for accessing soil metagenome for desired applications. Biotechnol Adv 26:576鈥?90. doi:10.1016/j.biotechadv.2008.08.002 CrossRef
  60. Ranjard L, Richaume AS (2001) Quantitative and qualitative microscale distribution of bacteria in soil. Res Microbiol 152:707鈥?16 3-2508(01)01251-7" target="_blank" title="It opens in new window">CrossRef
  61. Ranjard L, Lejon DPH, Mougel C, Schehrer L, Merdinoglu D, Chaussod R (2003) Sampling strategy in molecular microbial ecology: influence of soil sample size on DNA fingerprinting analysis of fungal and bacterial communities. Environ Microbiol 5:1111鈥?120. doi:10.1046/j.1462-2920.2003.00521.x 3.00521.x" target="_blank" title="It opens in new window">CrossRef
  62. Ranjard L, Echairi A, Nowak V, Lejon DPH, Noua茂m R, Chaussod R (2006) Field and microcosm experiments to evaluate the effects of agricultural copper treatment on the density and genetic structure of microbial communities in two different soils. FEMS Microbiol Ecol 58:303鈥?15. doi:10.1111/j.1574-6941.2006.00157.x CrossRef
  63. Ranjard L, Dequiedt S, Lelievre M, Maron PA, Mougel C, Morin F, Lemanceau P (2009) Platform GenoSol: a new tool for conserving and exploring soil microbial diversity. Environ Microbiol Rep 1:97鈥?9. doi:10.1111/j.1758-2229.2009.00023.x 3.x" target="_blank" title="It opens in new window">CrossRef
  64. Ranjard L, Dequiedt S, Jolivet C, Saby NPA, Thioulouse J, Harmand J, Loisel P, Rapaport A, Fall S, Simonet P, Joffre R, Chemidlin-Pr茅vost Bour茅 N, Maron PA, Mougel C, Martin MP, Toutain B, Arrouays D, Lemanceau P (2010) Biogeography of soil microbial communities: a review and a description of the ongoing French National Initiative. Agron Sustain Dev 30:359鈥?65. doi:10.1051/agro/2009033 33" target="_blank" title="It opens in new window">CrossRef
  65. Redecker D, Raab P (2006) Phylogeny of the Glomeromycota (arbuscular mycorrhizal fungi): recent developments and new gene markers. Mycologia 98:885鈥?95. doi:10.3852/mycologia.98.6.885 3852/mycologia.98.6.885" target="_blank" title="It opens in new window">CrossRef
  66. Redecker D, Kodner R, Graham LE (2000) Glomalean fungi from the Ordovician. Science 289:1920鈥?921. doi:10.1126/science.289.5486.1920 CrossRef
  67. Rutgers M, Schouten AJ, Bloem J, van Eekeren N, de Goede RGM, Akkerhuis GAJM, van der Wal A, Mulder C, Brussaard L, Breure AM (2009) Biological measurements in a nationwide soil monitoring network. Eur J Soil Sci 60:820鈥?32. doi:10.1111/j.1365-2389.2009.01163.x 365-2389.2009.01163.x" target="_blank" title="It opens in new window">CrossRef
  68. Schloss PD, Handelsman J (2003) Biotechnological prospects from metagenomics. Curr Opin Biotechnol 14:303鈥?10. doi:10.1016/S0958-1669(03)00067-3 3)00067-3" target="_blank" title="It opens in new window">CrossRef
  69. Smith SE, Read DJ (2008) Mycorrhizal symbiosis, 3rd edn. Academic, San Diego
  70. Smith KP, Handelsman J, Goodman RM (1999) Genetic basis in plants for interactions with disease-suppressive bacteria. Proc Natl Acad Sci U S A 96:4786鈥?790. doi:10.1073/pnas.96.9.4786 3/pnas.96.9.4786" target="_blank" title="It opens in new window">CrossRef
  71. Sprent JI (2008) 60 Ma of legume nodulation. What鈥檚 new? What鈥檚 changing? J Exp Bot 59:1081鈥?084. doi:10.1093/jxb/erm286 3/jxb/erm286" target="_blank" title="It opens in new window">CrossRef
  72. Subbarao GV, Nakahara K, Hurtado MP, Ono H, Moreta DE, Salcedo AF, Yoshihashi AT, Ishikawa T, Ishitani M, Ohnishi-Kameyama M, Yoshida M, Rondon M et al (2009) Evidence for biological nitrification inhibition in / Brachiaria pastures. Proc Natl Acad Sci U S A 106:17302鈥?7307. doi:10.1073/pnas.0903694106 3/pnas.0903694106" target="_blank" title="It opens in new window">CrossRef
  73. Tardy V, Mathieu O, Leveque J, Terrat V, Chabbi A, Lemanceau P, Ranjard L, Maron PA (2014) Stability of soil microbial structure and activity depends on microbial diversity. Environ Microbiol Rep 6:173鈥?83. doi:10.1111/1758-2229.12126 CrossRef
  74. Tilman D, Wedin D, Knops J (1996) Productivity and sustainability influenced by biodiversity in grassland ecosystems. Nature 379:718鈥?20. doi:10.1038/379718a0 38/379718a0" target="_blank" title="It opens in new window">CrossRef
  75. Tilman D, Knops J, Wedin D, Reich P, Ritchie M, Siemann E (1997) The influence of functional diversity and composition on ecosystem processes. Science 277:1300鈥?302. doi:10.1126/science.277.5330.1300 330.1300" target="_blank" title="It opens in new window">CrossRef
  76. Torsvik V, 脴vre氓s L (2002) Microbial diversity and function in soil: from genes to ecosystems. Curr Opin Microbiol 5:240鈥?45 369-5274(02)00324-7" target="_blank" title="It opens in new window">CrossRef
  77. Van der Heijden MGA, Klironomos JN, Ursic M, Moutoglis P, Streitwolf-Engel R, Boller T, Wiemken A, Sanders IR (1998) Mycorrhizal fungal diversity determines plant biodiversity, ecosystem variability and productivity. Nature 396:69鈥?2. doi:10.1038/23932 38/23932" target="_blank" title="It opens in new window">CrossRef
  78. Vance ED, Brookes PC, Jenkinson DS (1987) An extraction method for measuring soil microbial biomass C. Soil Biol Biochem 19:703鈥?07 38-0717(87)90052-6" target="_blank" title="It opens in new window">CrossRef
  79. Vogel TM, Simonet P, Jansson JK, Hirsch PR, Tiedje JM, van Elsas JD, Bailey MJ, Nalin R, Philippot L (2009) TerraGenome: a consortium for the sequencing of a soil metagenome. Nat Rev Microbiol 7:252. doi:10.1038/nrmicro2119
  80. Weller DM, Raaijmakers JM, Gardener BB, Thomashow LS (2002) Microbial populations responsible for specific soil suppressiveness to plant pathogens. Annu Rev Phytopathol 40:309鈥?48. doi:10.1146/annurev.phyto.40.030402.110010 30402.110010" target="_blank" title="It opens in new window">CrossRef
  81. Werner D, Newton WE (2005) Nitrogen fixation in agriculture, forestry, ecology and the environment. Kluwer, Dordrecht 3544-6" target="_blank" title="It opens in new window">CrossRef
  82. Yachi S, Loreau M (1999) Biodiversity and ecosystem productivity in a fluctuating environment: the insurance hypothesis. Proc Natl Acad Sci U S A 96:1463鈥?468. doi:10.1073/pnas.96.4.1463 3/pnas.96.4.1463" target="_blank" title="It opens in new window">CrossRef
  83. Zancarini A, Mougel C, Terrat S, Salon C, Munier-Jolain N (2013a) Combining ecophysiological and microbial ecological approaches to study the relationship between / Medicago truncatula genotypes and their associated rhizosphere bacterial communities. Plant Soil 365:183鈥?99. doi:10.1007/s11104-012-1364-7 364-7" target="_blank" title="It opens in new window">CrossRef
  84. Zancarini A, L茅pinay C, Burstin J, Duc G, Lemanceau P, Moreau D, Munier-Jolain N, Pivato B, Rigaud T, Salon C, Mougel C (2013b) Combining molecular microbial ecology with ecophysiology and plant genetics for a better understanding of plant-microbial communities interactions in the rhizosphere. Chapter 7. In: de Bruijn FJ (ed) Molecular microbial ecology of the rhizosphere. Wiley, Hoboken, pp 69鈥?6 CrossRef
  
• 刊物主题：Agriculture; Soil Science & Conservation; Sustainable Development;
• 出版者：Springer Paris
• ISSN：1773-0155

文摘

Soils are living environments in which particularly abundant and diverse microbiome and fauna are evolving. The resulting biological functioning has a direct impact not only on soil fertility but also on a series of ecosystems services. Thus, microbial communities are involved in geochemical cycles in which microbial enzymes catalyse the different steps. Modulation of the corresponding activities is essential as these affect plant growth and environmental quality. In general, biodiversity affects both the productivity and stability of agroecosystems. It is therefore of paramount importance to take soil biodiversity and biological functioning into account when designing cropping systems and evaluating their impacts. The progress achieved in soil microbiology in recent years now makes it possible to propose analyses of soil biology, as has been feasible for many years for soil physicochemistry. These analyses obviously require the use of standardized procedures for soil sampling, measuring the abundance and diversity of the microbial communities, as well as the identification of bioindicators. Similarly, referential systems need to be established to interpret these analyses and diagnose the biological status of soils, and, more especially, to determine whether the obtained values are within the range of variations normal for a given soil type and land use. Great progress to standardize such procedures and establish referential systems has been achieved during large-scale research programmes carried out to characterize biodiversity on national and European scales. These diagnostic elements need to be accompanied by recommendations. The aim of ongoing research is thus to propose aids for decision-making, based on the results of biological analyses, so attempts can be made to monitor and manage biodiversity to satisfy soil fertility requirements and ensure the ecosystem services expected of soils.