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Exploiting New Systems-Based Strategies to Elucidate Plant-Bacterial Interactions in the Rhizosphere

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Abstract

The rhizosphere is the site of intense interactions between plant, bacterial, and fungal partners. In plant-bacterial interactions, signal molecules exuded by the plant affect both primary initiation and subsequent behavior of the bacteria in complex beneficial associations such as biocontrol. However, despite this general acceptance that plant-root exudates have an effect on the resident bacterial populations, very little is still known about the influence of these signals on bacterial gene expression and the roles of genes found to have altered expression in plant-microbial interactions. Analysis of the rhizospheric communities incorporating both established techniques, and recently developed “omic technologies” can now facilitate investigations into the molecular basis underpinning the establishment of beneficial plant-microbial interactomes in the rhizosphere. The understanding of these signaling processes, and the functions they regulate, is fundamental to understanding the basis of beneficial microbial–plant interactions, to overcoming existing limitations, and to designing improved strategies for the development of novel Pseudomonas biocontrol strains.

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References

  1. Abbas, A, McGuire, JE, Crowley, D, Baysse, C, Dow, M, O'Gara, F (2004) The putative permease PhlE of Pseudomonas fluorescens F113 has a role in 2,4-diacetylphloroglucinol resistance and in general stress tolerance. Microbiology 150: 2443–2450

    Article  PubMed  CAS  Google Scholar 

  2. Abbas, A, Morrissey, JP, Marquez, PC, Sheehan, MM, Delany, IR, O'Gara, F (2002) Characterization of interactions between the transcriptional repressor PhlF and its binding site at the phlA promoter in Pseudomonas fluorescens F113. J Bacteriol 184: 3008–3016

    Article  PubMed  CAS  Google Scholar 

  3. Achouak, W, Conrod, S, Cohen, V, Heulin, T (2004) Phenotypic variation of Pseudomonas brassicacearum as a plant root-colonization strategy. Mol Plant Microb Interact 17: 872–879

    Article  CAS  Google Scholar 

  4. Allen, J, Davey, HM, Broadhurst, D, Heald, JK, Rowland, JJ, Oliver, SG, Kell, DB (2003) High-throughput classification of yeast mutants for functional genomics using metabolic footprinting. Nat Biotechnol 21: 692–696

    Article  PubMed  CAS  Google Scholar 

  5. Artursson, V, Jansson, JK (2003) Use of bromodeoxyuridine immunocapture to identify active bacteria associated with arbuscular mycorrhizal hyphae. Appl Environ Microbiol 69: 6208 – 6215

    Article  PubMed  CAS  Google Scholar 

  6. Barnett, MJ, Toman, CJ, Fisher, RF, Long, SR (2004) A dual-genome Symbiosis Chip for coordinate study of signal exchange and development in a prokaryote–host interaction. Proc Natl Acad Sci USA 101: 16636–16641

    Article  PubMed  CAS  Google Scholar 

  7. Bestel-Corre, G, Dumas-Gaudot, E, Poinsot, V, Dieu, M, Dierick, JF, van, TD, Remacle, J, Gianinazzi-Pearson, V,Gianinazzi, S (2002) Proteome analysis and identification of symbiosis-related proteins from Medicago truncatula Gaertn. by two-dimensional electrophoresis and mass spectrometry. Electrophoresis 23: 122–137

    Article  PubMed  CAS  Google Scholar 

  8. Bloemberg, GV, O'Toole, GA, Lugtenberg, BJ, Kolter, R (1997) Green fluorescent protein as a marker for Pseudomonas spp. Appl Environ Microbiol 63: 4543–4551

    PubMed  CAS  Google Scholar 

  9. Buell, CR, Joardar, V, Lindeberg, M, Selengut, J, Paulsen, IT, Gwinn, ML, Dodson, RJ, Deboy, RT, Durkin, AS, Kolonay, JF, Madupu, R, Daugherty, S, Brinkac, L, Beanan, MJ, Haft, DH, Nelson, WC, Davidsen, T, Zafar, N, Zhou, L, Liu, J, Yuan, Q, Khouri, H, Fedorova, N, Tran, B, Russell, D, Berry, K, Utterback, T, Van Aken, SE, Feldblyum, TV, D’Ascenzo, M, Deng, WL, Ramos, AR, Alfano, JR, Cartinhour, S, Chatterjee, AK, Delaney, TP, Lazarowitz, SG, Martin, GB, Schneider, DJ, Tang, X, Bender, CL, White, O, Fraser, CM, Collmer, A (2003) The complete genome sequence of the Arabidopsis and tomato pathogen Pseudomonas syringae pv. tomato DC3000. Proc Natl Acad Sci USA 100: 10181–10186

    Article  PubMed  CAS  Google Scholar 

  10. Cook, RJ, Thomashow, LS, Weller, DM, Fujimoto, D, Mazzola, M, Bangera, G, Kim, DS (1995) Molecular mechanisms of defense by rhizobacteria against root disease. Proc Natl Acad Sci USA 92: 4197–4201

    Article  PubMed  CAS  Google Scholar 

  11. Delany, I, Sheehan, MM, Fenton, A, Bardin, S, Aarons, S, O'Gara, F (2000) Regulation of production of the antifungal metabolite 2,4-diacetylphloroglucinol in Pseudomonas fluorescens F113: genetic analysis of phlF as a transcriptional repressor. Microbiology 146(Pt 2): 537–543

    PubMed  CAS  Google Scholar 

  12. Dumas-Gaudot, E, Amiour, N, Weidmann, S, Bestel-Corre, G, Valot, B, Lenogu, S, Gianinazzi-Pearson, V, Gianinazzi, S (2004) A technical trick for studying proteomics in parallel to transcriptomics in symbiotic root–fungus interactions. Proteomics 4: 451–453

    Article  PubMed  CAS  Google Scholar 

  13. Gage, DJ (2002) Analysis of infection thread development using Gfp- and DsRed-expressing Sinorhizobium meliloti. J Bacteriol 184: 7042–7046

    Article  PubMed  CAS  Google Scholar 

  14. Gage, DJ, Bobo, T, Long, SR (1996) Use of green fluorescent protein to visualize the early events of symbiosis between Rhizobium meliloti and alfalfa (Medicago sativa). J Bacteriol 178: 7159–7166

    PubMed  CAS  Google Scholar 

  15. Germaine, K, Keogh, E, Garcia-Cabellos, G, Borremans, B, van der Lelie, D, Barac, T, Oeyen, L, Vangronsveld, J, Porteus-Moore, F, Moore, ERB, Campblee, CD, Ryan, D, Dowling, DN (2004) Colonisation of poplar trees by gfp expressing bacterial endophytes. FEMS Microbiol Ecol 48: 109–118

    Article  CAS  Google Scholar 

  16. Giddings, G, Allison, G, Brooks, D, Carter, A (2000) Transgenic plants as factories for biopharmaceuticals. Nat Biotechnol 18: 1151–1155

    Article  PubMed  CAS  Google Scholar 

  17. Griffiths, RI, Manefield, M, Ostle, N, McNamara, N, O'Donnell, AG, Bailey, MJ, Whiteley, AS (2004) 13CO2 pulse labelling of plants in tandem with stable isotope probing: methodological considerations for examining microbial function in the rhizosphere. J Microbiol Methods 58: 119–129

    Article  PubMed  CAS  Google Scholar 

  18. Gygi, SP, Rochon, Y, Franza, BR, Aebersold, R (1999) Correlation between protein and mRNA abundance in yeast. Mol Cell Biol 19: 1720–3170

    PubMed  CAS  Google Scholar 

  19. Humphery-Smith, I, Cordwell, SJ, Blackstock, WP (1997) Proteome research: complementarity and limitations with respect to the RNA and DNA worlds. Electrophoresis 18: 1217–1242

    Article  PubMed  CAS  Google Scholar 

  20. Ivanova, PT, Cerda, BA, Horn, DM, Cohen, JS, McLafferty, FW, Brown, HA (2001) Electrospray ionization mass spectrometry analysis of changes in phospholipids in RBL-2H3 mastocytoma cells during degranulation. Proc Natl Acad Sci USA 98: 7152–7157

    Article  PubMed  CAS  Google Scholar 

  21. Jeon, CO, Park, W, Padmanabhan, P, DeRito, C, Snape, JR, Madsen, EL (2003) Discovery of a bacterium, with distinctive dioxygenase, that is responsible for in situ biodegradation in contaminated sediment. Proc Natl Acad Sci USA 100: 13591–13596

    Article  PubMed  CAS  Google Scholar 

  22. Kim, ST, Cho, KS, Jang, YS, Kang, KY (2001) Two-dimensional electrophoretic analysis of rice proteins by polyethylene glycol fractionation for protein arrays. Electrophoresis 22: 2103–2109

    Article  PubMed  CAS  Google Scholar 

  23. Kim, ST, Cho, KS, Yu, S, Kim, SG, Hong, JC, Han, CD, Bae, DW, Nam, MH, Kang, KY (2003) Proteomic analysis of differentially expressed proteins induced by rice blast fungus and elicitor in suspension-cultured rice cells. Proteomics 3: 2368–2378

    Article  PubMed  CAS  Google Scholar 

  24. Kuske, CR, Ticknor, LO, Miller, ME, Dunbar, JM, Davis, JA, Barns, SM, Belnap, J (2002) Comparison of soil bacterial communities in rhizospheres of three plant species and the interspaces in an arid grassland. Appl Environ Microbiol 68: 1854–1863

    Article  PubMed  CAS  Google Scholar 

  25. Loy, A, Schultz, C, Lucker, S, Schopfer-Wendels, A, Stoecker, K, Baranyi, C, Lehner, A, Wagner, M (2004) 16S rRNA gene-based oligonucleotide microarray for environmental monitoring of the betaproteobacterial order Rhodocyclales. Appl Environ Microbiol 71.3: 1373–1386

    Google Scholar 

  26. Lueders, T, Manefield, M, Friedrich, MW (2004) Enhanced sensitivity of DNA- and rRNA-based stable isotope probing by fractionation and quantitative analysis of isopycnic centrifugation gradients. Environ Microbiol 6: 73–78

    Article  PubMed  CAS  Google Scholar 

  27. Lueders, T, Pommerenke, B, Friedrich, MW (2004) Stable-isotope probing of microorganisms thriving at thermodynamic limits: syntrophic propionate oxidation in flooded soil. Appl Environ Microbiol 70: 5778–5786

    Article  PubMed  CAS  Google Scholar 

  28. Lueders, T, Wagner, B, Claus, P, Friedrich, MW (2004) Stable isotope probing of rRNA and DNA reveals a dynamic methylotroph community and trophic interactions with fungi and protozoa in oxic rice field soil. Environ Microbiol 6: 60–72

    Article  PubMed  CAS  Google Scholar 

  29. Maier, W, Schmidt, J, Nimitz, M, Wray, V, Strack, D (2000) Secondary products in mycorrhizal roots of tobacco and tomato. Phytochemistry 54: 473–479

    Article  PubMed  CAS  Google Scholar 

  30. Maleck, K, Levine, A, Eulgem, T, Morgan, A, Schmid, J, Lawton, KA, Dangl, JL, Dietrich, RA (2000) The transcriptome of Arabidopsis thaliana during systemic acquired resistance. Nat Genet 26: 403–410

    Article  PubMed  CAS  Google Scholar 

  31. Manefield, M, Whiteley, AS, Griffiths, RI, Bailey, MJ (2002) RNA stable isotope probing, a novel means of linking microbial community function to phylogeny. Appl Environ Microbiol 68: 5367–5373

    Article  PubMed  CAS  Google Scholar 

  32. Mark, GL, Dow, JM, Kiely, PD, Higgins, H, Haynes, J, Baysse, C, Abbas, A, Foley, T, Franks, A, Morrissey, J, O'Gara, F (2005) Transcriptome profiling of bacterial responses to root exudates identifies novel genes involved in microbe–plant interactions. Proc Natl Acad Sci USA 102(48): 17454–17459

    Article  PubMed  CAS  Google Scholar 

  33. Morris, AC, Djordjevic, MA (2001) Proteome analysis of cultivar-specific interactions between Rhizobium leguminosarum biovar trifolii and subterranean clover cultivar Woogenellup. Electrophoresis 22: 586–598

    Article  PubMed  CAS  Google Scholar 

  34. Morrissey, JP, Dow, JM, Mark, LG, O'Gara, F (2004) Are microbes at the root of a solution to world food production? EMBO Reports 5: 922–926

    Article  PubMed  CAS  Google Scholar 

  35. Larrainzar, E, O'Gara, F, Morrissey, JP (2005) Applications of autofluorescent proteins for in situ studies in microbial ecology. Annu Rev Microbiol 59: 257–277

    Article  PubMed  CAS  Google Scholar 

  36. Muyzer, G (1999) DGGE/TGGE a method for identifying genes from natural ecosystems. Curr Opin Microbiol 2: 317–322

    Article  PubMed  CAS  Google Scholar 

  37. Narasimhan, K, Basheer, C, Bajic, VB, Swarup, S (2003) Enhancement of plant–microbe interactions using a rhizosphere metabolomics-driven approach and its application in the removal of polychlorinated biphenyls. Plant Physiol 132: 146–153

    Article  PubMed  CAS  Google Scholar 

  38. Ndimba, BK, Chivasa, S, Hamilton, JM, Simon, WJ, Slabas, AR (2003) Proteomic analysis of changes in the extracellular matrix of Arabidopsis cell suspension cultures induced by fungal elicitors. Proteomics 3: 1047–1059

    Article  PubMed  CAS  Google Scholar 

  39. Nelson, KE, Weinel, C, Paulsen, IT, Dodson, RJ, Hilbert, H, Martins dos Santos, VA, Fouts, DE, Gill, SR, Pop, M, Holmes, M, Brinkac, L, Beanan, M, DeBoy, RT, Daugherty, S, Kolonay, J, Madupu, R, Nelson, W, White, O, Peterson, J, Khouri, H, Hance, I, Chris Lee, P, Holtzapple, E, Scanlan, D, Tran, K, Moazzez, A, Utterback, T, Rizzo, M, Lee, K, Kosack, D, Moestl, D, Wedler, H, Lauber, J, Stjepandic, D, Hoheisel, J, Straetz, M, Heim, S, Kiewitz, C, Eisen, JA, Timmis, KN, Dusterhoft, A, Tummler, B, Fraser, CM (2002) Complete genome sequence and comparative analysis of the metabolically versatile Pseudomonas putida KT2440. Environ Microbiol 4: 799 –808

    Article  PubMed  CAS  Google Scholar 

  40. Normander, B, Hendriksen, NB, Nybroe, O (1999) Green fluorescent protein-marked Pseudomonas fluorescens: localization, viability, and activity in the natural barley rhizosphere. Appl Environ Microbiol 65: 4646–4651

    PubMed  CAS  Google Scholar 

  41. Oliver, SG, Winson, MK, Kell, DB, Baganz, F (1998) Systematic functional analysis of the yeast genome. Trends Biotechnol 16: 373–378

    Article  PubMed  CAS  Google Scholar 

  42. Palma, M, Worgall, S, Quadri, LE (2003) Transcriptome analysis of the Pseudomonas aeruginosa response to iron. Arch Microbiol 180: 374–379

    Article  PubMed  CAS  Google Scholar 

  43. Peck, SC, Nuhse, TS, Hess, D, Iglesias, A, Meins, F, Boller, T (2001) Directed proteomics identifies a plant-specific protein rapidly phosphorylated in response to bacterial and fungal elicitors. Plant Cell 13: 1467–1475

    Article  PubMed  CAS  Google Scholar 

  44. Puhler, A, Arlat, M, Becker, A, Gottfert, M, Morrissey, JP, O'Gara, F (2004) What can bacterial genome research teach us about bacteria–plant interactions? Curr Opin Plant Biol 7: 137–147

    Article  PubMed  CAS  Google Scholar 

  45. Raamsdonk, LM, Teusink, B, Broadhurst, D, Zhang, N, Hayes, A, Walsh, MC, Berden, JA, Brindle, KM, Kell, DB, Rowland, JJ, Westerhoff, HV, van Dam, K, Oliver, SG (2001) A functional genomics strategy that uses metabolome data to reveal the phenotype of silent mutations. Nat Biotechnol 19: 45–50

    Article  PubMed  CAS  Google Scholar 

  46. Radajewski, S, Ineson, P, Parekh, NR, Murrell, JC (2000) Stable-isotope probing as a tool in microbial ecology. Nature 403: 646–649

    Article  PubMed  CAS  Google Scholar 

  47. Rainey, PB (1999) Adaptation of Pseudomonas fluorescens to the plant rhizosphere. Environ Microbiol 1: 243–257

    Article  PubMed  CAS  Google Scholar 

  48. Ramos, C, Molbak, L, Molin, S (2000) Bacterial activity in the rhizosphere analyzed at the single-cell level by monitoring ribosome contents and synthesis rates. Appl Environ Microbiol 66: 801–809

    Article  PubMed  CAS  Google Scholar 

  49. Ramos, HJ, Roncato-Maccari, LD, Souza, EM, Soares-Ramos, JR, Hungria, M, Pedrosa, FO (2002) Monitoring Azospirillum–wheat interactions using the gfp and gusA genes constitutively expressed from a new broad-host range vector. J Biotechnol 97: 243–252

    Article  PubMed  CAS  Google Scholar 

  50. Scheideler, M, Schlaich, NL, Fellenberg, K, Beissbarth, T, Hauser, NC, Vingron, M, Slusarenko, AJ, Hoheisel, JD (2002) Monitoring the switch from housekeeping to pathogen defense metabolism in Arabidopsis thaliana using cDNA arrays. J Biol Chem 277: 10555–10561

    Article  PubMed  CAS  Google Scholar 

  51. Schena, M, Heller, RA, Theriault, TP, Konrad, K, Lachenmeier, E, Davis, RW (1998) Microarrays: biotechnology's discovery platform for functional genomics. Trends Biotechnol 16: 301–306

    Article  PubMed  CAS  Google Scholar 

  52. Schenk, PM, Kazan, K, Wilson, I, Anderson, JP, Richmond, T, Somerville, SC, Manners, JM (2000) Coordinated plant defense responses in Arabidopsis revealed by microarray analysis. Proc Natl Acad Sci USA 97: 11655–11660

    Article  PubMed  CAS  Google Scholar 

  53. Schuster, M, Lostroh, CP, Ogi, T, Greenberg, EP (2003) Identification, timing, and signal specificity of Pseudomonas aeruginosa quorum-controlled genes: a transcriptome analysis. J Bacteriol 185: 2066–2079

    Article  PubMed  CAS  Google Scholar 

  54. Silby, MW, Levy, SB (2004) Use of in vivo expression technology to identify genes important in growth and survival of Pseudomonas fluorescens Pf0-1 in soil: discovery of expressed sequences with novel genetic organization. J Bacteriol 186: 7411–7419

    Article  PubMed  CAS  Google Scholar 

  55. Smalla, K, Wieland, G, Buchner, A, Zock, A, Parzy, J, Kaiser, S, Roskot, N, Heuer, H, Berg, G (2001) Bulk and rhizosphere soil bacterial communities studied by denaturing gradient gel electrophoresis: plant-dependent enrichment and seasonal shifts revealed. Appl Environ Microbiol 67: 4742–4751

    Article  PubMed  CAS  Google Scholar 

  56. Stover, CK, Pham, XQ, Erwin, AL, Mizoguchi, SD, Warrener, P, Hickey, MJ, Brinkman, FS, Hufnagle, WO, Kowalik, DJ, Lagrou, M, Garber, RL, Goltry, L, Tolentino, E, Westbrock-Wadman, S, Yuan, Y, Brody, LL, Coulter, SN, Folger, KR, Kas, A, Larbig, K, Lim, R, Smith, K, Spencer, D, Wong, GK, Wu, Z, Paulsen, IT, Reizer, J, Saier, MH, Hancock, RE, Lory, S, Olson, MV (2000) Complete genome sequence of Pseudomonas aeruginosa PA01, an opportunistic pathogen. Nature 406: 959–964

    Article  PubMed  CAS  Google Scholar 

  57. Sweeney P (2005) The influence of plant varieties and P. fluorescens F113, on the diversity of ecologically significant bacterial communities in the rhizosphere. MSc thesis, University College Cork, Ireland

  58. Thomas MAaK, R (2004) Genomics for the ecological toolbox. Trends Ecol Evol 19: 439–445

    Article  Google Scholar 

  59. Tombolini, R, Unge, A, Davy, ME, de Bruijn, FJ, Jansson, J (1997) Flow cytometric and microscopic analysis of GFP-tagged Pseudomonas fluorescens bacteria. FEMS Microbiol Ecol 22: 17–28

    Article  CAS  Google Scholar 

  60. Tombolini, R, van der Gaag, DJ, Gerhardson, B, Jansson, JK (1999) Colonization pattern of the biocontrol strain Pseudomonas chlororaphis MA 342 on barley seeds visualized by using green fluorescent protein. Appl Environ Microbiol 65: 3674–3680

    PubMed  CAS  Google Scholar 

  61. Unge, A, Jansson, J (2001) Monitoring population size, activity, and distribution of gfp-luxAB-tagged Pseudomonas fluorescens SBW25 during colonization of wheat. Microb Ecol 41: 290–300

    PubMed  CAS  Google Scholar 

  62. Urbanczyk-Wochniak, E, Luedemann, A, Kopka, J, Selbig, J, Roessner-Tunali, U, Willmitzer, L, Fernie, AR (2003) Parallel analysis of transcript and metabolic profiles: a new approach in systems biology. EMBO Rep 4: 989–993

    Article  PubMed  CAS  Google Scholar 

  63. van Loon, LC, Bakker, PA, Pieterse, CM (1998) Systemic resistance induced by rhizosphere bacteria. Annu Rev Phytopathol 36: 453–483

    Article  PubMed  Google Scholar 

  64. van Mispelaar, VG, Tas, AC, Smilde, AK, Schoenmakers, PJ, van Asten, AC (2003) Quantitative analysis of target components by comprehensive two-dimensional gas chromatography. J Chromatogr A 1019: 15–29

    Article  PubMed  CAS  Google Scholar 

  65. Villacieros, M, Power, B, Sanchez-Contreras, M, Lloret, J, Oruezabal, RI, Martin, M, Fernandez-Piñas, F, Bonilla, I, Whelan, C, Dowling, DN, Rivilla, R (2003) Colonization behaviour of Pseudomonas fluorescens and Sinorhizobium meliloti in the alfalfa (Medicago sativa) rhizosphere. Plant Soil 251(1): 47–54

    Article  CAS  Google Scholar 

  66. Walsh, UF, Morrissey, JP, O'Gara, F (2001) Pseudomonas for biocontrol of phytopathogens: from functional genomics to commercial exploitation. Curr Opin Biotechnol 12: 289–295

    Article  PubMed  CAS  Google Scholar 

  67. Weckwerth, W (2003) Metabolomics in systems biology. Annu Rev Plant Biol 54: 669–689

    Article  PubMed  CAS  Google Scholar 

  68. Wilkins, MR, Sanchez, JC, Gooley, AA, Appel, RD, Humphery-Smith, I, Hochstrasser, DF, Williams, KL (1996) Progress with proteome projects: why all proteins expressed by a genome should be identified and how to do it. Biotechnol Genet Eng Rev 13: 19–50

    PubMed  CAS  Google Scholar 

  69. Yu, J, Hu, S, Wang, J, Wong, GK, Li, S, Liu, B, Deng, Y, Dai, L, Zhou, Y, Zhang, X, Cao, M, Liu, J, Sun, J, Tang, J, Chen, Y, Huang, X, Lin, W, Ye, C, Tong, W, Cong, L, Geng, J, Han, Y, Li, L, Li, W, Hu, G, Li, J, Liu, Z, Qi, Q, Li, T, Wang, X, Lu, H, Wu, T, Zhu, M, Ni, P, Han, H, Dong, W, Ren, X, Feng, X, Cui, P, Li, X, Wang, H, Xu, X, Zhai, W, Xu, Z, Zhang, J, He, S, Xu, J, Zhang, K, Zheng, X, Dong, J, Zeng, W, Tao, L, Ye, J, Tan, J, Chen, X, He, J, Liu, D, Tian, W, Tian, C, Xia, H, Bao, Q, Li, G, Gao, H, Cao, T, Zhao, W, Li, P, Chen, W, Zhang, Y, Hu, J, Liu, S, Yang, J, Zhang, G, Xiong, Y, Li, Z, Mao, L, Zhou, C, Zhu, Z, Chen, R, Hao, B, Zheng, W, Chen, S, Guo, W, Tao, M, Zhu, L, Yuan, L, Yang, H (2002) A draft sequence of the rice genome (Oryza sativa L. ssp. indica). Science 296: 79–92

    Article  PubMed  CAS  Google Scholar 

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Acknowledgments

We acknowledge Abdelhamid Abbas, Maeve Cullinane, Max Dow, and Pat Higgins for useful advice and discussions. We acknowledge the IMPACT, ECO-SAFE GM-RHIZO, and PSEUDOMICS EU-consortia for fruitful discussion and valuable scientific comment. Research in the authors' laboratories is supported in part by grants awarded by the European Union: BIO4-CT96-0027 (IMPACT 11), QLK3-CT-2000-31759 (ECO-SAFE) QLK3-2001-00101 (GM-RHIZO), QLRT-2001-00914 (PSEUDOMICS); The Higher Education Authority of Ireland (PRTI2, PRTI3); Enterprise Ireland, SC/02/517, SC/02/0420, and Science Foundation of Ireland (04/BR/B0597; 02/IN.1/B1261).

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  1. Biomerit Research Centre, Department of Microbiology, National University of Ireland (UCC), Cork, Ireland

    P. D. Kiely, J. M. Haynes, C. H. Higgins, A. Franks, G. L. Mark, J. P. Morrissey & F. O'Gara

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Kiely, P.D., Haynes, J.M., Higgins, C.H. et al. Exploiting New Systems-Based Strategies to Elucidate Plant-Bacterial Interactions in the Rhizosphere. Microb Ecol 51, 257–266 (2006). https://doi.org/10.1007/s00248-006-9019-y

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