Plant and Soil

, Volume 365, Issue 1–2, pp 183–199 | Cite as

Combining ecophysiological and microbial ecological approaches to study the relationship between Medicago truncatula genotypes and their associated rhizosphere bacterial communities

  • A. Zancarini
  • C. Mougel
  • S. Terrat
  • C. Salon
  • N. Munier-Jolain
Regular Article

Abstract

Background and aims

To assess how plant genotype and rhizosphere bacterial communities may interact, the genetic structure and diversity of bacterial communities in the rhizosphere soil of different Medicago truncatula genotypes were studied in relation to the plant carbon and nitrogen nutrition at the whole plant level.

Methods

The genetic structure and diversity of plant-associated rhizosphere bacterial communities was analysed by Automated Ribosomal Intergenic Spacer Analysis and 454-pyrosequencing. In parallel, the carbon and nitrogen nutrition of the plants was estimated by a phenotypic description at both structural level (growth) and functional level (using carbon and nitrogen isotope labeling and an ecophysiological framework).

Results

An early effect of the plant genotype was observed on the rhizosphere bacterial communities, while few significant differences were detected at the plant structural phenotypic level. However, at a functional level, the different Medicago truncatula genotypes could be distinguished by their different nutritional strategies. Moreover, a comparison analysis showed that ecophysiological profiles of the different Medicago truncatula genotypes were correlated to the genetic structure and the diversity of the rhizosphere bacterial communities.

Conclusions

The exploration of the genetic structure and diversity of rhizosphere bacterial communities combined with an ecophysiological approach is an innovative way to progress in our knowledge of plant-microbe interactions in the rhizosphere.

Keywords

Bacterial communities Diversity Genetic structure Medicago truncatula Nutrition Rhizosphere 

Supplementary material

11104_2012_1364_MOESM1_ESM.pptx (74 kb)
ESM 1(PPTX 73 kb)
11104_2012_1364_MOESM2_ESM.docx (17 kb)
ESM 2(DOCX 17 kb)

References

  1. Acosta-Martinez V, Dowd S, Sun Y, Allen V (2008) Tag-encoded pyrosequencing analysis of bacterial diversity in a single soil type as affected by management and land use. Soil Biol Biochem 40:2762–2770CrossRefGoogle Scholar
  2. Andreote FD, de Araujo WL, de Azevedo JL, van Elsas JD, da Rocha UN, van Overbeek LS (2009) Endophytic colonization of potato (Solanum tuberosum L.) by a novel competent bacterial endophyte, pseudomonas putida strain P9, and its effect on associated bacterial communities. Appl Environ Microbiol 75:3396–3406PubMedCrossRefGoogle Scholar
  3. Bais HP, Weir TL, Perry LG, Gilroy S, Vivanco JM (2006) The role of root exudates in rhizosphere interations with plants and other organisms. Annu Rev Plant Biol 57:233–266PubMedCrossRefGoogle Scholar
  4. Behnke A, Engel M, Christen R, Nebel M, Klein RR, Stoeck T (2011) Depicting more accurate pictures of protistan community complexity using pyrosequencing of hypervariable SSU rRNA gene regions. Environ Microbiol 13:340–349PubMedCrossRefGoogle Scholar
  5. Brooks PD, Stark JM, McInteer BB, Preston T (1989) Diffusion method to prepare soil extracts for automated N-15 analysis. Soil Sci Soc Am J 53:1707–1711CrossRefGoogle Scholar
  6. Brouwer R (1983) Functional equilibrium - sense or nonsense. Neth J Agric Sci 31:335–348Google Scholar
  7. Buee M, De Boer W, Martin F, van Overbeek L, Jurkevitch E (2009) The rhizosphere zoo: an overview of plant-associated communities of microorganisms, including phages, bacteria, archaea, and fungi, and of some of their structuring factors. Plant Soil 321:189–212CrossRefGoogle Scholar
  8. Chenu K (2004) Variabilité phénotypique de l’architecture de la rosette d’Arabidopsis thaliana en réponse au rayonnement: analyse et modélisation de la réponse de différents génotypes. Université Montpellier 2, Montpellier, FranceGoogle Scholar
  9. Cole JR, Wang Q, Cardenas E, Fish J, Chai B, Farris RJ, Kulam-Syed-Mohideen AS, McGarrell DM, Marsh T, Garrity GM, Tiedje JM (2009) The ribosomal database project: improved alignments and new tools for rRNA analysis. Nucleic Acids Res 37:D141–D145PubMedCrossRefGoogle Scholar
  10. da Rocha UN, van Overbeek L, van Elsas JD (2009) Exploration of hitherto-uncultured bacteria from the rhizosphere. FEMS Microbiol Ecol 69:313–328PubMedCrossRefGoogle Scholar
  11. Dalmastri C, Chiarini L, Cantale C, Bevivino A, Tabacchioni S (1999) Soil type and maize cultivar affect the genetic diversity of maize root-associated Burkholderia cepacia populations. Microb Ecol 38:273–284PubMedCrossRefGoogle Scholar
  12. Doledec S, Chessel D (1994) Co-inertia analysis - an alternative method for studying species environment relationships. Freshw Biol 31:277–294CrossRefGoogle Scholar
  13. Dray S, Chessel D, Thioulouse J (2003) Co-inertia analysis and the linking of ecological data tables. Ecology 84:3078–3089CrossRefGoogle Scholar
  14. Dunfield KE, Germida JJ (2003) Seasonal changes in the rhizosphere microbial communities associated with field-grown genetically modified canola (Brassica napus). Appl Environ Microbiol 69:7310–7318PubMedCrossRefGoogle Scholar
  15. Farrar JF, Jones DL (2000) The control of carbon acquisition by roots. New Phytol 147:43–53CrossRefGoogle Scholar
  16. Fierer N, Bradford MA, Jackson RB (2007) Toward an ecological classification of soil bacteria. Ecology 88:1354–1364PubMedCrossRefGoogle Scholar
  17. Fisher MM, Triplett EW (1999) Automated approach for ribosomal intergenic spacer analysis of microbial diversity and its application to freshwater bacterial communities. Appl Environ Microbiol 65:4630–4636PubMedGoogle Scholar
  18. Franche C, Lindstrom K, Elmerich C (2009) Nitrogen-fixing bacteria associated with leguminous and non-leguminous plants. Plant Soil 321:35–59CrossRefGoogle Scholar
  19. Harrison MJ (1999) Molecular and cellular aspects of the arbuscular mycorrhizal symbiosis. Annu Rev Plant Physiol Plant Mol Biol 50:361–389PubMedCrossRefGoogle Scholar
  20. Hartmann A, Schmid M, van Tuinen D, Berg G (2009) Plant-driven selection of microbes. Plant Soil 321:235–257CrossRefGoogle Scholar
  21. Jensen ES, Hauggaard-Nielsen H (2003) How can increased use of biological N-2 fixation in agriculture benefit the environment? Plant Soil 252:177–186CrossRefGoogle Scholar
  22. Jeudy C, Ruffel S, Freixes S, Tillard P, Santoni AL, Morel S, Journet EP, Duc G, Gojon A, Lepetit M, Salon C (2010) Adaptation of Medicago truncatula to nitrogen limitation is modulated via local and systemic nodule developmental responses. New Phytol 185:817–828PubMedCrossRefGoogle Scholar
  23. Jones DL, Nguyen C, Finlay RD (2009a) Carbon flow in the rhizosphere: carbon trading at the soil-root interface. Plant Soil 321:5–33CrossRefGoogle Scholar
  24. Jones RT, Robeson MS, Lauber CL, Hamady M, Knight R, Fierer N (2009b) A comprehensive survey of soil acidobacterial diversity using pyrosequencing and clone library analyses. ISME J 3:442–453PubMedCrossRefGoogle Scholar
  25. Kunin V, Engelbrektson A, Ochman H, Hugenholtz P (2010) Wrinkles in the rare biosphere: pyrosequencing errors can lead to artificial inflation of diversity estimates. Environ Microbiol 12:118–123PubMedCrossRefGoogle Scholar
  26. Lambers H, Mougel C, Jaillard B, Hinsinger P (2009) Plant-microbe-soil interactions in the rhizosphere: an evolutionary perspective. Plant Soil 321:83–115CrossRefGoogle Scholar
  27. Lemaire G, van Oosterom E, Jeuffroy MH, Gastal F, Massignam A (2008) Crop species present different qualitative types of response to N deficiency during their vegetative growth. Field Crop Res 105:253–265CrossRefGoogle Scholar
  28. Marschner H (1995) Mineral nutrition of higher plants. Academic, LondonGoogle Scholar
  29. Mathieu O (2005) Application du traçage isotopique 15N à l’étude du protoxyde d’azote (N2O), gaz à effet de serre produit par l’acitivité microbienn des sols. Quantification des flux et approche spaciale au terrain. Université Bourgogne, Dijon, FranceGoogle Scholar
  30. Mazzola M, Funnell DL, Raaijmakers JM (2004) Wheat cultivar-specific selection of 2,4-diacetylphloroglucinol-producing fluorescent Pseudomonas species from resident soil populations. Microb Ecol 48:338–348PubMedCrossRefGoogle Scholar
  31. Micallef SA, Shiaris MP, Colon-Carmona A (2009) Influence of Arabidopsis thaliana accessions on rhizobacterial communities and natural variation in root exudates. J Exp Bot 60:1729–1742PubMedCrossRefGoogle Scholar
  32. Minchin FR, Summerfield RJ, Hadley P, Roberts EH, Rawsthorne S (1981) Carbon and nitrogen nutrition of nodulated roots of grain legumes. Plant Cell Environ 4:5–26CrossRefGoogle Scholar
  33. Moreau D (2007) Réponse du développement et de la croissance de Medicago truncatula aux facteurs environnementaux: contribution à l’élaboration d’outils de phénotypage pour l’analyse de la variabilité génétique associée à la nutrition azotée. Université Bourgogne, Dijon, FranceGoogle Scholar
  34. Moreau D, Salon C, Munier-Jolain N (2006) Using a standard framework for the phenotypic analysis of Medicago truncatula: an effective method for characterizing the plant material used for functional genomics approaches. Plant Cell Environ 29:1087–1098PubMedCrossRefGoogle Scholar
  35. Moreau D, Voisin AS, Salon C, Munier-Jolain N (2008) The model symbiotic association between Medicago truncatula cv. Jemalong and Rhizobium meliloti strain 2011 leads to N-stressed plants when symbiotic N-2 fixation is the main N source for plant growth. J Exp Bot 59:3509–3522PubMedCrossRefGoogle Scholar
  36. Moreau D, Burstin J, Aubert G, Huguet T, Ben C, Prosperi JM, Salon C, Munier-Jolain N (2012) Using a physiological framework for improving the detection of quantitative trait loci related to nitrogen nutrition in Medicago truncatula. Theor Appl Genet 124:755–768PubMedCrossRefGoogle Scholar
  37. Mougel C, Offre P, Ranjard L, Corberand T, Gamalero E, Robin C, Lemanceau P (2006) Dynamic of the genetic structure of bacterial and fungal communities at different developmental stages of Medicago truncatula Gaertn. cv. Jemalong line J5. New Phytol 170:165–175PubMedCrossRefGoogle Scholar
  38. Munier-Jolain N, Carrouée B (2003) Considering pea in sustainable agriculture: agricultural and environmental arguments. Cahiers Agricultures 12:111–120Google Scholar
  39. Nemecek T, von Richthofen JS, Dubois G, Casta P, Charles R, Pahl H (2008) Environmental impacts of introducing grain legumes into European crop rotations. Eur J Agron 28:380–393CrossRefGoogle Scholar
  40. Nguyen C (2003) Rhizodeposition of organic C by plants: mechanisms and controls. Agronomie 23:375–396CrossRefGoogle Scholar
  41. Normand P, Ponsonnet C, Nesme X, Neyra M, Simonet P (1996) ITS analysis of prokaryotes. In: Akkermans DL, Van Elsas JD, De Bruijn EI (eds) Molecular microbial ecology manual. Kluwer, Amsterdam, pp 1–12Google Scholar
  42. Offre P, Pivato B, Siblot S, Gamalero E, Corberand T, Lemanceau P, Mougel C (2007) Identification of bacterial groups preferentially associated with mycorrhizal roots of Medicago truncatula. Appl Environ Microbiol 73:913–921PubMedCrossRefGoogle Scholar
  43. Oldroyd GED, Downie JM (2008) Coordinating nodule morphogenesis with rhizobial infection in legumes. Annu Rev Plant Biol 59:519–546PubMedCrossRefGoogle Scholar
  44. Paffetti D, Scotti C, Gnocchi S, Fancelli S, Bazzicalupo M (1996) Genetic diversity of an Italian Rhizobium meliloti population from different Medicago sativa varieties. Appl Environ Microbiol 62:2279–2285PubMedGoogle Scholar
  45. Parra-Colmenares A, Kahn ML (2005) Determination of nitrogen fixation effectiveness in selected Medicago truncatula isolates by measuring nitrogen isotope incorporation into pheophytin. Plant Soil 270:159–168CrossRefGoogle Scholar
  46. Pawlowski J, Christen R, Lecroq B, Bachar D, Shahbazkia HR, Amaral-Zettler L, Guillou L (2011) Eukaryotic richness in the abyss: insights from pyrotag sequencing. PLoS One 6:e18169PubMedCrossRefGoogle Scholar
  47. Raaijmakers JM, Paulitz TC, Steinberg C, Alabouvette C, Moenne-Loccoz Y (2009) The rhizosphere: a playground and battlefield for soilborne pathogens and beneficial microorganisms. Plant Soil 321:341–361CrossRefGoogle Scholar
  48. Ranjard L, Poly F, Nazaret S (2000) Monitoring complex bacterial communities using culture-independent molecular techniques: application to soil environment. Res Microbiol 151:167–177PubMedCrossRefGoogle Scholar
  49. Ranjard L, Poly F, Lata JC, Mougel C, Thioulouse J, Nazaret S (2001) Characterization of bacterial and fungal soil communities by automated ribosomal intergenic spacer analysis fingerprints: biological and methodological variability. Appl Environ Microbiol 67:4479–4487PubMedCrossRefGoogle Scholar
  50. 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 5:1111–1120PubMedCrossRefGoogle Scholar
  51. Reeder J, Knight R (2009) The ‘rare biosphere’: a reality check. Nat Methods 6:636–637PubMedCrossRefGoogle Scholar
  52. Richardson AE, Barea JM, McNeill AM, Prigent-Combaret C (2009) Acquisition of phosphorus and nitrogen in the rhizosphere and plant growth promotion by microorganisms. Plant Soil 321:305–339CrossRefGoogle Scholar
  53. Roesch LF, Fulthorpe RR, Riva A, Casella G, Hadwin AK, Kent AD, Daroub SH, Camargo FA, Farmerie WG, Triplett EW (2007) Pyrosequencing enumerates and contrasts soil microbial diversity. ISME J 1:283–290PubMedGoogle Scholar
  54. Ronfort J, Bataillon T, Santoni S, Delalande M, David JL, Prosperi JM (2006) Microsatellite diversity and broad scale geographic structure in a model legume: building a set of nested core collection for studying naturally occurring variation in Medicago truncatula. Bmc Plant Biology 6Google Scholar
  55. Salon C, Voisin AS, Delfosse O, Mary B (2010) Methodologies for measuring symbiotic nitrogen fixation in the field. In: Munier-Jolain N, Biarnes V, Chaillet I, Lecoeur J, Jeuffroy MH (eds) Physiology of the pea crop. CRC Press, Editions Quae, Versailles, pp 83–87Google Scholar
  56. Singh BK, Millard P, Whiteley AS, Murrell JC (2004) Unravelling rhizosphere-microbial interactions: opportunities and limitations. Trends Microbiol 12:386–393PubMedCrossRefGoogle Scholar
  57. Stevenson BS, Eichorst SA, Wertz JT, Schmidt TM, Breznak JA (2004) New strategies for cultivation and detection of previously uncultured microbes. Appl Environ Microbiol 70:4748–4755PubMedCrossRefGoogle Scholar
  58. Terrat S, Christen R, Dequiedt S, Lelievre M, Nowak V, Regnier T, Bachar D, Plassart P, Wincker P, Jolivet C, Bispo A, Lemanceau P, Maron PA, Mougel C, Ranjard L (2011) Molecular biomass and metataxogenomic assessment of soil microbial communities as influenced by soil DNA extraction procedure. Microb BiotechnolGoogle Scholar
  59. Thioulouse J, Dray S (2007) Interactive multivariate data analysis in R with the ade4 and ade4TkGUI packages. J Stat Softw 22:1–14Google Scholar
  60. van Overbeek L, van Elsas JD (2008) Effects of plant genotype and growth stage on the structure of bacterial communities associated with potato (Solanum tuberosum L.). FEMS Microbiol Ecol 64:283–296PubMedCrossRefGoogle Scholar
  61. Voisin AS, Salon C, Jeudy C, Warembourg FR (2003) Root and nodule growth in Pisum sativum L. in relation to photosynthesis: analysis using C-13-labelling. Ann Bot 92:557–563PubMedCrossRefGoogle Scholar

Copyright information

© Springer Science+Business Media B.V. 2012

Authors and Affiliations

  • A. Zancarini
    • 1
  • C. Mougel
    • 1
  • S. Terrat
    • 1
  • C. Salon
    • 1
  • N. Munier-Jolain
    • 1
  1. 1.INRA, UMR1347 AgroécologieDijonFrance

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