Molecular-based strategies to exploit Pseudomonas biocontrol strains for environmental biotechnology applications

FEMS Microbiology Ecology

Volumn 56, Issue 2, 2006, Pages 167-177

  Mark, Genevieve L ^a   Morrissey, John P ^a   Higgins, P ^a   O'Gara, Fergal ^a  

^a UNIVERSITY COLLEGE CORK   (Ireland)

Author keywords

Biocontrol; Genomics; Plant microbe interactions

Indexed keywords

AGRICULTURE; ALTERNATIVE AGRICULTURE; BACTERIUM; BIOCONTROL AGENT; FUNGUS; MICROBIAL ACTIVITY; RHIZOSPHERE; RISK ASSESSMENT;

BACILLUS; BACTERIAL GENOME; BACTERIAL STRAIN; BENEFICIAL ORGANISM; BIOLOGICAL CONTROL AGENT; BIOSAFETY; BIOTECHNOLOGY; CONFERENCE PAPER; ENVIRONMENTAL MANAGEMENT; EUROPEAN UNION; GENE SEQUENCE; GENOMICS; MARKETING; MICROARRAY ANALYSIS; MICROCHIP ANALYSIS; MOLECULAR BIOLOGY; NONHUMAN; PLANT MICROORGANISM INTERACTION; PRIORITY JOURNAL; PROTEOMICS; PSEUDOMONAS; PSEUDOMONAS FLUORESCENS; REGISTRATION; RHIZOSPHERE; RISK ASSESSMENT; SUSTAINABLE AGRICULTURE; THEORY-PRACTICE RELATIONSHIP; TRANSCRIPTOMICS; TRICHODERMA; UNITED STATES;

BIOTECHNOLOGY; CROPS, AGRICULTURAL; ECOSYSTEM; GENETIC ENGINEERING; MARKETING; PEST CONTROL, BIOLOGICAL; PSEUDOMONAS; RISK ASSESSMENT; SIGNAL TRANSDUCTION; SOIL MICROBIOLOGY;

EURASIA; EUROPE; NORTH AMERICA; UNITED STATES;

BACILLUS (BACTERIUM); BACTERIA (MICROORGANISMS); FUNGI; PSEUDOMONAS; PSEUDOMONAS FLUORESCENS; TRICHODERMA;

EID: 33646013910     PISSN: 01686496     EISSN: 15746941     Source Type: Journal    
DOI: 10.1111/j.1574-6941.2006.00056.x     Document Type: Conference Paper

References (80)

1. 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.
2. 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. 150 2443 2450.
3. Ampe F Kiss E Sabourdy F Batut J 2003 Transcriptome analysis of Sinorhizobium meliloti during symbiosis. Genome Biol 4 15 21.
4. Bakker PA Glandorf DC Viebahn M Ouwens TW Smit E Leeflang PK Wernars K Thomashow LS Thomas-Oates JE van Loon LC 2002 Effects of Pseudomonas putida modified to produce phenazine-1-carboxylic acid and 2,4-diacetylphloroglucinol on the microflora of field grown wheat. Antonie Van Leeuwenhoek 81 617 624.
5. Barea JM Andrade G Bianciotto V Dowling D Lohrke S Bonfante P O'Gara F Azcon-Aguilar C 1998 Impact on arbuscular mycorrhiza formation of Pseudomonas strains used as inoculants for biocontrol of soil-borne fungal plant pathogens. 64 2304 2307.
6. Barnett J Toman J Fisher F Long S 2004 A dual-genome Symbiosis Chip for coordinate study of signal exchange and development in a prokaryote-host interaction. Proc Natl Acad Sci 101 16636 16641.
7. Berges H Lauber E Liebe C Batut J Kahn D de Bruijn FJ Ampe F 2003 Development of Sinorhizobium meliloti pilot macroarrays for transcriptome analysis. Appl Environ Microbiol 69 1214 1219.
8. Bestel-Corre G Dumas-Gaudot E Gianinazzi S 2003 Proteomics as a tool to monitor plant-microbe endosymbioses in the rhizosphere mycorrhiza. 14 1 10.
9. Beyler M Keel C Michaux P Haas D 1999 Enhanced production of indole-3-acetic acid by a genetically modified strain of Pseudomonas fluorescens CHA0 affects root growth of cucumber, but does not improve protection of the plant against Pythium root rot. FEMS Microbiol Ecol 28 225 233.
10. Bloemberg GV Lugtenberg BJ 2001 Molecular basis of plant growth promotion and biocontrol by rhizobacteria. Curr Opin Plant Biol 4 343 350.
11. Buell CR Joardar V Lindeberg M et al 2003 The complete genome sequence of the Arabidopsis and tomato pathogen Pseudomonas syringae pv. tomato DC3000. Proc Natl Acad Sci USA 100 10181 10186.
12. Chet I Inbar J 1994 Biological control of fungal pathogens. Appl Biochem Biotechnol 48 37 43.
13. Chin-A-Woeng TF Bloemberg GV Mulders IH Dekkers LC Lugtenberg BJ 2000 Root colonization by phenazine-1-carboxamide-producing bacterium Pseudomonas chlororaphis PCL1391 is essential for biocontrol of tomato foot and root rot. Mol Plant Microbe Interact 13 1340 1345.
14. Corbell N Loper JE 1995 A global regulator of secondary metabolite production in Pseudomonas fluorescens Pf-5. J Bacteriol 177 6230 6236.
15. 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 146 537 543.
16. Delany IR Walsh UF Ross I Fenton AM Corkery DM O'Gara F 2001 Enhancing the biocontrol efficacy of Pseudomonas fluorescens F113 by altering the regulation and production of 2,4-diacetylphloroglucinol. Plant Soil 232 195 205.
17. Duffy BK Defago G 1999 Environmental factors modulating antibiotic and siderophore biosynthesis by Pseudomonas fluorescens biocontrol strains. Appl Environ Microbiol 65 2429 2438.
18. Dunne C Delany I Fenton A O'Gara F 1996 Mechanisms involved in biocontrol by microbial inoculants. Agronomie 16 721 729.
19. Fenton AM Stephens PM Crowley J O'Callaghan M O'Gara F 1992 Exploitation of gene(s) involved in 2,4-diacetylphloroglucinol biosynthesis to confer a new biocontrol capability to a Pseudomonas strain. Appl Environ Microbiol 58 3873 3878.
20. Girlanda M Perotto S Moenne-Loccoz Y Bergero R Lazzari A Défago G Bonfante P Luppi AM 2001 Impact of biocontrol Pseudomonas fluorescens CHA0 and a genetically modified derivative on the diversity of culturable fungi in the cucumber rhizosphere. Appl Environ Microbiol 67 1851 1864.
21. Glandorf DC Verheggen P Jansen T et al 2001 Effect of genetically modified Pseudomonas putida WCS358r on the fungal rhizosphere microflora of field-grown wheat. Appl Environ Microbiol 67 3371 3378.
22. Gough C Galera C Vasse J Webster G Cocking EC Denarie J 1997 Specific flavonoids promote intercellular root colonization of Arabidopsis thaliana by Azorhizobium caulinodans ORS571. Mol Plant Microbe Interact 10 560 570.
23. Haas D Blumer C Keel C 2000 Biocontrol ability of fluorescent pseudomonads genetically dissected importance of positive feedback regulation. Curr Opin Biotechnol 11 290 297.
24. Keel C Schnider U Maurhofer M Viossard C Laville J Burger U Wirthner P Haas D Defago G 1992 Suppression of root diseases by Pseudomonas fluorescens CHA0 importance of the bacterial secondary metabolite 2,4-diacetylphloroglucinol. Mol Plant Microbe Interact 5 4 13.
25. Kowalchuk GA Buma DS de Boer W Klinkhamer PG van Veen JA 2002 Effects of above-ground plant species composition and diversity on the diversity of soil-borne microorganisms. Antonie Van Leeuwenhoek 81 509 520.
26. Kuiper I Bloemberg GV Noreen S Thomas-Oates JE Lugtenberg BJ 2001 Increased uptake of putrescine in the rhizosphere inhibits competitive root colonization by Pseudomonas fluorescens strain WCS365. Mol Plant Microbe Interact 14 1096 1104.
27. 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.
28. Landa BB Mavrodi OV Raaijmakers JM McSpadden Gardener BB Thomashow LS Weller DM 2002 Differential ability of genotypes of 2,4-diacetylphloroglucinol-producing Pseudomonas fluorescens strains to colonize the roots of pea plants. Appl Environ Microbiol 68 3226 3237.
29. van Loon LC Bakker PAHM Pieterse CMJ 1998 Systemic resistance induced by rhizosphere bacteria. Annu Rev Phytopathol 35 453 483.
30. de Lorenzo V 2001 The potential for genetically modified bacteria to break down toxic pollutants in the environment. EMBO Rep 2 357 359.
31. Lowe AM Beattie DT Deresiewics RL 1998 Identification of novel staphylococcal virulence genes by in vivo expression technology. Mol Microbiol 27 967 976.
32. Mark GL Cassells AC 1996 Genotype-dependence in the interaction between Glomus fistulosum, Phytophthora fragariae and the wild strawberry (Fragaria vesca). Plant Soil 185 233 239.
33. Mark GL Morrissey JP O'Gara F 2003 Designing improved GM bacteria for application in environmental biotechnology. Ecological Impact of GMO Dissemination in Agro-Ecosystems [Proceedings of OECD Workshop, Grossrussbach, Austria] Lelley T Balázs E Tepfer M eds), pp. 11 24. Facultas Verlags und Buchhandels AG Vienna.
34. Mark GL Dow TM Kiely P et al 2006 Elucidation of molecular interactions in the rhizosphere directed by transcriptome profiling of bacterial responses to root exudates. Proc Natl Acad Sci USA 71 1818 1825.
35. Moënne-Loccoz Y Powell J Higgins P McCarthy J O'Gara F 1998 An investigation of the impact of biocontrol Pseudomonas fluorescens F113 on the growth of sugarbeet and the performance of subsequent clover-Rhizobium symbiosis. Appl Soil Ecol 7 225 237.
36. Moënne-Loccoz Y Tichy H-V O'Donnell A Simon R O'Gara F 2001 Impact of 2,4-diacetylphloroglucinol-producing biocontrol strain Pseudomonas fluorescens F113 on intraspecific diversity of resident culturable fluorescent pseudomonads associated with the roots of field-grown sugar beet seedlings. 67 3418 3425.
37. Montesinos E 2003 Development, registration and commercialisation of microbial pesticides for plant protection. Int Microbiol 6 245 252.
38. Morris AC Djordjevic MA 2001 Proteome analysis of cultivar-specific interactions between Rhizobium leguminosarumbiovar trifolii and subterranean clover cultivar Woogenellup. Electrophoresis 22 586 598.
39. Morrissey JP Walsh UF O'Donnell A Moenne-Loccoz Y O'Gara F 2002 Exploitation of genetically modified inoculants for industrial ecology applications. Antonie Van Leeuwenhoek 81 599 606.
40. Morrissey JP Abbas A Mark L Cullinane M O'Gara F 2004a Biosynthesis of antifungal metabolites by biocontrol strains of Pseudomonas. The Pseudomonads Vol. III Ramos JL ed), pp. 635 670. Kluwer Press Dordrecht.
41. Morrissey JP Dow JM Mark GL O'Gara F 2004b Are microbes at the root of a solution to world food production? EMBO Rep 5 922 926.
42. Mutch LA Young JP 2004 Diversity and specificity of Rhizobium leguminosarum biovar viciae on wild and cultivated legumes. Mol Ecol 13 2435 2444.
43. Natsch A Keel C Hebecker N Laasik E Defago G 1998 Impact of Pseudomonas fluorescens strain CHAO and a derivative with improved biocontrol activity on the culturable resident bacterial community on cucumber roots. FEMS Microbiol Ecol 27 365 380.
44. 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.
45. Nelson KE Weinel C Paulsen IT et al 2002 Complete genome sequence and comparative analysis of the metabolically versatile Pseudomonas putida KT2440. Environ Microbiol 4 799 808.
46. Niemann S Keel C Puhler A Selbitschka W 1997 Biocontrol strain Pseudomonas fluorescens CHA0 and its genetically modified derivative with enhanced biocontrol capability exert comparable effects on the structure of a Sinorhizobium meliloti population in gnotobiotic systems. Biol Fertil Soils 25 240 244.
47. Ochsner UA Wilderman PJ Vasil AI Vasil ML 2002 GeneChip expression analysis of the iron starvation response in Pseudomonas aeruginosa identification of novel pyoverdine biosynthesis genes. Mol Microbiol 45 1277 1287.
48. Palma M Worgall S Quadri LE 2003 Transcriptome analysis of the Pseudomonas aeruginosa response to iron. Arch Microbiol 180 374 379.
49. Palma M DeLuca D Worgall S Quadri LE 2004 Transcriptome analysis of the response of Pseudomonas aeruginosa to hydrogen peroxide. J Bacteriol 186 248 252.
50. Paulsen IT Press CM Ravel J et al 2005 Complete genome sequence of the plant commensal Pseudomonas fluorescens Pf-5. Nat Biotech 23 873 878.
51. Press MC Phoenix GK 2005 Impacts of parasitic plants on natural communities. New Phytol 166 737 751.
52. Preston GM Bertrand N Rainey PB 2001 Type III secretion in plant growth-promoting Pseudomonas fluorescens SBW25. Mol Microbiol 41 999 1014.
53. Pühler A Arlat M Becker A Göttfert 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.
54. Raaijmakers JM Vlami M de Souza JT 2002 Antibiotic production by bacterial biocontrol agents. Antonie Van Leeuwenhoek 81 537 547.
55. Rainey PB 1999 Adaptation of Pseudomonas fluorescens to the plant rhizosphere. Environ Microbiol 1 243 57.
56. Rediers H Rainey PB Vanderleyden J De Mot R 2005 Unraveling the secret lives of bacteria use of in vivo expression technology and differential fluorescence induction promoter traps as tools for exploring niche-specific gene expression. Microbiol Mol Biol Rev 69 217 261.
57. Resca R Basaglia M Poggiolini S et al 2001 An integrated approach for the evaluation of biological control of the complex Polymyxa betae/Beet Necrotic Yellow Vein Virus, by means of seed inoculants. 232 215 226.
58. Salunkhe P Topfer T Buer J Tummler B 2005 Genome-wide transcriptional profiling of the steady-state response of Pseudomonas aeruginosa to hydrogen peroxide. J Bacteriol 187 2565 2572.
59. 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.
60. 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.
61. 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.
62. Sessitsch A Reiter B Berg G 2004 Endophytic bacterial communities of field-grown potato plants and their plant-growth-promoting and antagonistic abilities. Can J Microbiol/Rev Can Microbiol 50 239 249.
63. Shaukat SS Siddiqui IA 2003 Impact of biocontrol agents Pseudomonas fluorescens CHA0 and its genetically modified derivatives on the diversity of culturable fungi in the rhizosphere of mungbean. J Appl Microbiol 95 1039 1048.
64. 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.
65. Simons M van der Bij AJ Brand I de Weger LA Wijffelman CA Lugtenberg BJ 1996 Gnotobiotic system for studying rhizosphere colonization by plant growth-promoting Pseudomonas bacteria. Mol Plant Microbe Interact 9 600 607.
66. 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.
67. Stover CK Pham XO Erwin AL et al 2000 Complete genome sequence of Pseudomonas aeruginosa PA01, an opportunistic pathogen. Nature 406 959 964.
68. Vandenkoornhuyse P Ridgway KP Watson IJ Fitter AH Young JP 2003 Co-existing grass species have distinctive arbuscular mycorrhizal communities. Mol Ecol 12 3085 3095.
69. Viebahn M Glandorf DC Ouwens TW Smit E Leeflang P Wernars K Thomashow LS van Loon LC Bakker PA 2003 Repeated introduction of genetically modified Pseudomonas putida WCS358r without intensified effects on the indigenous microflora of field-grown wheat. Appl Environ Microbiol 69 3110 3118.
70. Walker TS Bais HP Deziel E Schweizer HP Rahme LG Fall R Vivanco JM 2004 Pseudomonas aeruginosa-plant root interactions. Pathogenicity, biofilm formation, and root exudation. Plant Physiol 134 320 331.
71. Walsh U O'Gara F Economidis I Hogan S 2000 Harnessing the Potential of Genetically Modified Microorganisms and Plants. European Commission (Brochure) Brussels.
72. Walsh UF Morrissey JP O'Gara F 2001a Pseudomonas for biocontrol of phytopathogens from functional genomics to commercial exploitation. Curr Opin Biotechnol 12 289 295.
73. Walsh UF Morrissey JP O'Gara F 2001b Pseudomonas for biocontrol of phytopathogens: from functional genomics to commercial exploitation. Curr Opin Biotechnol 12 289 295.
74. Walsh UF Moënne-Loccoz Y Tichy HV Gardner A Corkery DM Lohrke S O'Gara F 2003 Residual impact of the biocontrol inoculant Pseudomonas fluorescens F113 on the resident population of rhizobia nodulating a red clover rotation crop. 45 145 155.
75. Wang J Mushegian A Lory S Jin S 1996 Large-scale isolation of candidate virulence genes of Pseudomonas aeruginosa by in vivo selection. Proc Natl Acad Sci USA 93 10434 10439.
76. Wieland G Neumann R Backhaus H 2001 Variation of microbial communities in soil, rhizosphere, and rhizoplane in response to crop species, soil type, and crop development. Appl Environ Microbiol 67 5849 5854.
77. 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.
78. Wolfgang MC Jyot J Goodman AL Ramphal R Lory S 2004 Pseudomonas aeruginosa regulates flagellin expression as part of a global response to airway fluid from cystic fibrosis patients. Proc Natl Acad Sci USA 101 6664 6668.
79. Yang CH Crowley DE 2000 Rhizosphere microbial community structure in relation to root location and plant iron nutritional status. Appl Environ Microbiol 66 345 351.
80. Young GM Miller VL 1997 Identification of novel chromosomal loci affecting Yersinia enterocolitica pathogenesis. Mol Microbiol 25 319 328.