Novel T-RFLP method to investigate six main groups of 2,4-diacetylphloroglucinol-producing pseudomonads in environmental samples

Journal of Microbiological Methods

Volumn 84, Issue 3, 2011, Pages 379-387

  von Felten, Andreas ^a   Meyer, Joana Beatrice ^a   Défago, Geneviève ^a   Maurhofer, Monika ^a  

^a ETH ZURICH   (Switzerland)

Author keywords

2,4 diacetylphloroglucinol; Biocontrol pseudomonads; DGGE; Rhizospher; T RFLP

Indexed keywords

2,4 DIACETYLPHLOROGLUCINOL; PHLOROGLUCINOL DERIVATIVE; RESTRICTION ENDONUCLEASE; UNCLASSIFIED DRUG;

ARTICLE; BACTERIAL GENE; BACTERIAL STRAIN; BACTERIUM CULTURE; BACTERIUM DETECTION; COLONY FORMING UNIT; CONTROLLED STUDY; DENATURING GRADIENT GEL ELECTROPHORESIS; ENVIRONMENT; GENE AMPLIFICATION; GREENHOUSE; MAIZE; NONHUMAN; NUCLEOTIDE SEQUENCE; PHLD GENE; PLANT ROOT; PRIORITY JOURNAL; PSEUDOMONAD; PSEUDOMONAS FLUORESCENS; RESTRICTION FRAGMENT LENGTH POLYMORPHISM; RHIZOSPHERE; WHEAT;

BACTERIAL PROTEINS; BACTERIOLOGICAL TECHNIQUES; ELECTROPHORESIS, POLYACRYLAMIDE GEL; ENVIRONMENTAL MICROBIOLOGY; NUCLEIC ACID DENATURATION; PHLOROGLUCINOL; POLYMORPHISM, RESTRICTION FRAGMENT LENGTH; PSEUDOMONAS; RHIZOSPHERE; TRITICUM; ZEA MAYS;

PSEUDOMONAS FLUORESCENS; PSEUDOMONAS FLUORESCENS GROUP; TRITICUM AESTIVUM; ZEA MAYS;

EID: 79951813795     PISSN: 01677012     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.mimet.2010.11.012     Document Type: Article

References (40)

1. Bergsma-Vlami M., Prins M.E., Staats M., Raaijmakers J.M. Assessment of genotypic diversity of antibiotic-producing Pseudomonas species in the rhizosphere by denaturing gradient gel electrophoresis. Appl. Environ. Microbiol. 2005, 71:993-1003.
2. Briones A.M., Reichardt W. Estimating microbial population counts by 'most probable number' using Microsoft Excel (R). J. Microbiol. Meth. 1999, 35:157-161.
3. De La Fuente L., Thomashow L., Weller D., Bajsa N., Quagliotto L., Chernin L., Arias A. Pseudomonas fluorescens UP61 isolated from birdsfoot trefoil rhizosphere produces multiple antibiotics and exerts a broad spectrum of biocontrol activity. Eur. J. Plant Pathol. 2004, 110:671-681.
4. De La Fuente L., Mavrodi D.V., Landa B.B., Thomashow L.S., Weller D.M. PhlD-based genetic diversity and detection of genotypes of 2, 4-diacetylphloroglucinol-producing Pseudomonas fluorescens. FEMS Microbiol. Ecol. 2006, 56:64-78.
5. De Souza J.T., Weller D.M., Raaijmakers J.M. Frequency, diversity, and activity of 2, 4-diacetylphloroglucinol-producing fluorescent Pseudomonas spp. in Dutch take-all decline soils. Phytopathology 2003, 93:54-63.
6. Fenton A.M., Stephens P.M., Crowley J., O'Callaghan M., O'Gara F. Exploitation of genes involved in 2, 4-diacetylphloroglucinol biosynthesis to confer a new biocontrol capability to a Pseudomonas strain. Appl. Environ. Microbiol. 1992, 58:3873-3878.
7. Frapolli M., Défago G., Moënne-Loccoz Y. Multilocus sequence analysis of biocontrol fluorescent Pseudomonas spp. producing the antifungal compound 2, 4-diacetylphloroglucinol. Environ. Microbiol. 2007, 9:1939-1955.
8. Frapolli M., Moënne-Loccoz Y., Meyer J., Défago G. A new DGGE protocol targeting 2, 4-diacetylphloroglucinol biosynthetic gene phlD from phylogenetically contrasted biocontrol pseudomonads for assessment of disease-suppressive soils. FEMS Microbiol. Ecol. 2008, 64:468-481.
9. Fuchs J., Défago G. Protection of cucumber plants against black root rot caused by Phomopsis sclerotioides with rhizobacteria. IOBC/WPRS Bulletin 1991, 14:57-62. C. Keel, B. Koller, G. Défago (Eds.).
10. Haas D., Défago G. Biological control of soil-borne pathogens by fluorescent pseudomonads. Nat. Rev. Microbiol. 2005, 3:307-319.
11. Hahn M., Wilhelm J., Pingoud A. Influence of fluorophor dye labels on the migration behavior of polymerase chain reaction - amplified short tandem repeats during denaturing capillary electrophoresis. Electrophoresis 2001, 22:2691-2700.
12. Harrison L.A., Letendre L., Kovacevich P., Pierson E., Weller D. Purification of an antibiotic effective against Gaeumannomyces graminis var tritici produced by a biocontrol agent, Pseudomonas aureofaciens. Soil Biol. Biochem. 1993, 25:215-221.
13. Howell C.R., Stipanovic R.D. Suppression of Pythium ultimum-induced damping-off of cotton seedlings by Pseudomonas fluorescens and its antibiotic, pyoluteorin. Phytopathology 1980, 70:712-715.
14. Kaplan C.W., Kitts C.L. Variation between observed and true Terminal Restriction Fragment length is dependent on true TRF length and purine content. J. Microbiol. Meth. 2003, 54:121-125.
15. Keel C., Schnider U., Maurhofer M., Voisard C., Laville J., Burger U., Wirthner P., Haas D., Défago G. Suppression of root diseases by Pseudomonas fluorescens CHA0: importance of the bacterial secondary metabolite 2, 4-diacetylphloroglucinol. Mol. Plant-Microbe Interact. 1992, 5:4-13.
16. Keel C., Weller D.M., Natsch A., Défago G., Cook R.J., Thomashow L.S. Conservation of the 2, 4-diacetylphloroglucinol biosynthesis locus among fluorescent Pseudomonas strains from diverse geographic locations. Appl. Environ. Microbiol. 1996, 62:552-563.
17. King E.O., Ward M.K., Raney D.E. Two simple media for the demonstration of pyocyanin and fluorescin. J. Lab. Clin. Med. 1954, 44:301-307.
18. Landa B.B., Mavrodi O.V., Schroeder K.L., Allende-Molar R., Weller D.M. Enrichment and genotypic diversity of phlD-containing fluorescent Pseudomonas spp. in two soils after a century of wheat and flax monoculture. Fems Microbiol. Ecology 2006, 55:351-368.
19. Levy E., Gough F.J., Berlin K.D., Guiana P.W., Smith J.T. Inhibition of Septoria tritici and other phytopatogenic fungi and bacteria by Pseudomonas fluorescens and its antibiotics. Plant Pathol. 1992, 41:335-341.
20. Marsh T.L. Culture-independent microbial community analysis with terminal restriction fragment length polymorphism. Environ. Microbiol. 2005, 397:308-329.
21. Mavrodi O.V., Gardener B.B.M., Mavrodi D.V., Bonsall R.F., Weller D.M., Thomashow L.S. Genetic diversity of phlD from 2, 4-diacetylphloroglucinol-producing fluorescent Pseudomonas spp. Phytopathology 2001, 91:35-43.
22. McSpadden Gardener B.B., Schroeder K.L., Kalloger S.E., Raaijmakers J.M., Thomashow L.S., Weller D.M. Genotypic and phenotypic diversity of phlD-containing Pseudomonas strains isolated from the rhizosphere of wheat. Appl. Environ. Microbiol. 2000, 66:1939-1946.
23. McSpadden Gardener B.B., Mavrodi D.V., Thomashow L.S., Weller D.M. A rapid polymerase chain reaction-based assay characterizing rhizosphere populations of 2, 4-diacetylphloroglucinol-producing bacteria. Phytopathology 2001, 91:44-54.
24. Moeseneder M.M., Arrieta J.M., Muyzer G., Winter C., Herndl G.J. Optimization of terminal-restriction fragment length polymorphism analysis for complex marine bacterioplankton communities and comparison with denaturing gradient gel electrophoresis. Appl. Environ. Microbiol. 1999, 65:3518-3525.
25. Nocker A., Burr M., Camper A.K. Genotypic microbial community profiling: a critical technical review. Microb. Ecol. 2007, 54:276-289.
26. Nunan N., Daniell T.J., Singh B.K., Papert A., McNicol J.W., Prosser J.I. Links between plant and rhizoplane bacterial communities in grassland soils, characterized using molecular techniques. Appl. Environ. Microbiol. 2005, 71:6784-6792.
27. Picard C., Di Cello F., Ventura M., Fani R., Guckert A. Frequency and biodiversity of 2, 4-diacetylphloroglucinol-producing bacteria isolated from the maize rhizosphere at different stages of plant growth. Appl. Environ. Microbiol. 2000, 66:948-955.
28. Raaijmakers J.M., Weller D.M. Natural plant protection by 2, 4-diacetylphloroglucinol-producing Pseudomonas spp. in take-all decline soils. Mol. Plant-Microbe Interact. 1998, 11:144-152.
29. Ramette A., Moenne-Loccoz Y., Defago G. Polymorphism of the polyketide synthase gene phlD in biocontrol fluorescent pseudomonads producing 2, 4-diacetylphloroglucinol and comparison of PhlD with plant polyketide synthases. Mol. Plant-Microbe Interact. 2001, 14:639-652.
30. Ramette A., Moënne-Loccoz Y., Défago G. Prevalence of fluorescent pseudomonads producing antifungal phloroglucinols and/or hydrogen cyanide in soils naturally suppressive or conducive to tobacco black root rot. FEMS Microbiol. Ecol. 2003, 44:35-43.
31. Schutte U.M.E., Abdo Z., Bent S.J., Shyu C., Williams C.J., Pierson J.D., Forney L.J. Advances in the use of terminal restriction fragment length polymorphism (T-RFLP) analysis of 16S rRNA genes to characterize microbial communities. Appl. Microbiol. Biotechnol. 2008, 80:365-380.
32. Shanahan P., O'Sullivan D.J., Simpson P., Glennon J.D., O'Gara F. Isolation of 2, 4-diacetylphloroglucinol from a fluorescent Pseudomonad and investigation of physiological parameters influencing its production. Appl. Environ. Microbiol. 1992, 58:353-358.
33. Stutz E.W., Défago G., Kern H. Naturally occurring fluorescent pseudomonads involved in suppression of black root rot of tobacco. Phytopathology 1986, 76:181-185.
34. Thomashow L.S., Weller D.M. Current concepts in the use of introduced bacteria for biological disease control: mechanisms and antifungal metabolites of special interest. Chapman and Hall 1995, 1:187-235. New York, USA. G. Stacey, N. Keen (Eds.).
35. Tu O., Knott T., Marsh M., Bechtol K., Harris D., Barker D., Bashkin J. The influence of fluorescent dye structure on the electrophoretic mobility of end-labeled DNA. Nucl. Acids Res. 1998, 26:2797-2802.
36. Vincent M.N., Harrison L.A., Brackin J.M., Kovacevich P.A., Mukerji P., Weller D.M., Pierson E.A. Genetic analysis of the antifungal activity of a soilborne Pseudomonas aureofaciens strain. Appl. Environ. Microbiol. 1991, 57:2928-2934.
37. Von Felten A., Defago G., Maurhofer M. Quantification of Pseudomonas fluorescens strains F113, CHA0 and Pf153 in the rhizosphere of maize by strain-specific real-time PCR unaffected by the variability of DNA extraction efficiency. J. Microbiol. Meth. 2010, 81:108-115.
38. Wang C.X., Ramette A., Punjasamarnwong P., Zala M., Natsch A., Moenne-Loccoz Y., Defago G. Cosmopolitan distribution of phlD-containing dicotyledonous crop-associated biocontrol pseudomonads of worldwide origin. FEMS Microbiol. Ecol. 2001, 37:105-116.
39. Weller D.M., Raaijmakers J.M., Gardener B.B.M., Thomashow L.S. Microbial populations responsible for specific soil suppressiveness to plant pathogens. Annu. Rev. Phytopathol. 2002, 40:309-348.
40. Weller D.M., Landa B.B., Mavrodi O.V., Schroeder K.L., De La Fuente L., Blouin Bankhead S., Allende Molar R., Bonsall R.F., Mavrodi D.V., Thomashow L.S. Role of 2, 4-diacetylphloroglucinol-producing fluorescent Pseudomonas spp. in the defense of plant roots. Plant Biol. 2007, 9:4-20.