phlD-based genetic diversity and detection of genotypes of 2,4-diacetylphloroglucinol-producing Pseudomonas fluorescens.

Diversity within a worldwide collection of 2,4-diacetylphloroglucinol-producing Pseudomonas fluorescens strains was assessed by sequencing the phlD gene. Phylogenetic analyses based on the phlD sequences of 70 isolates supported the previous classification into 18 BOX-PCR genotypes (A-Q and T). Exploiting polymorphisms within the sequence of phlD, we designed and used allele-specific PCR primers with a PCR-based dilution endpoint assay to quantify the population sizes of A-, B-, D-, K-, L- and P-genotype strains grown individually or in pairs in vitro, in the rhizosphere of wheat and in bulk soil. Except for P. fluorescens Q8r1-96, which strongly inhibited the growth of P. fluorescens Q2-87, inhibition between pairs of strains grown in vitro did not affect the accuracy of the method. The allele-specific primer-based technique is a rapid method for studies of the interactions between genotypes of 2,4-diacetylphloroglucinol producers in natural environments.

[1]  B. Landa,et al.  Enrichment and genotypic diversity of phlD-containing fluorescent Pseudomonas spp. in two soils after a century of wheat and flax monoculture. , 2006, FEMS microbiology ecology.

[2]  R. Edema,et al.  Distribution and Biocontrol Potential of phlD(+) Pseudomonads in Corn and Soybean Fields. , 2005, Phytopathology.

[3]  J. Raaijmakers,et al.  Assessment of Genotypic Diversity of Antibiotic-Producing Pseudomonas Species in the Rhizosphere by Denaturing Gradient Gel Electrophoresis , 2005, Applied and Environmental Microbiology.

[4]  A. Boronin,et al.  Antagonistic activity among 2,4-diacetylphloroglucinol-producing fluorescent Pseudomonas spp. , 2005, FEMS microbiology letters.

[5]  L. Thomashow,et al.  Pseudomonas Fluorescens UP61 Isolated From Birdsfoot Trefoil Rhizosphere Produces Multiple Antibiotics and Exerts a Broad Spectrum of Biocontrol Activity , 2004, European Journal of Plant Pathology.

[6]  M. Mazzola,et al.  Wheat Cultivar-Specific Selection of 2,4-Diacetylphloroglucinol-Producing Fluorescent Pseudomonas Species from Resident Soil Populations , 2004, Microbial Ecology.

[7]  L. Cui,et al.  Antibacterial activity of 2,4-diacetylphloroglucinol produced by Pseudomonas sp. AMSN isolated from a marine alga, against vancomycin-resistant Staphylococcus aureus. , 2003, International journal of antimicrobial agents.

[8]  E. Boutet,et al.  Induced systemic resistance in Arabidopsis thaliana in response to root inoculation with Pseudomonas fluorescens CHA0. , 2003, Molecular plant-microbe interactions : MPMI.

[9]  J. T. de Souza,et al.  Effect of 2,4-diacetylphloroglucinol on pythium: cellular responses and variation in sensitivity among propagules and species. , 2003, Phytopathology.

[10]  B. Landa,et al.  Interactions Between Strains of 2,4-Diacetylphloroglucinol-Producing Pseudomonas fluorescens in the Rhizosphere of Wheat. , 2003, Phytopathology.

[11]  M. Bosco,et al.  Genetic diversity of phlD gene from 2,4-diacetylphloroglucinol-producing Pseudomonas spp. strains from the maize rhizosphere. , 2003, FEMS microbiology letters.

[12]  F. Rezzonico,et al.  Effect of Stress on the Ability of a phlA-Based Quantitative Competitive PCR Assay To Monitor Biocontrol Strain Pseudomonas fluorescens CHA0 , 2003, Applied and Environmental Microbiology.

[13]  Y. Kamei,et al.  Lysis of methicillin-resistant Staphylococcus aureus by 2,4-diacetylphloroglucinol produced by Pseudomonas sp. AMSN isolated from a marine alga. , 2003, International journal of antimicrobial agents.

[14]  J. T. de Souza,et al.  Frequency, Diversity, and Activity of 2,4-Diacetylphloroglucinol-Producing Fluorescent Pseudomonas spp. in Dutch Take-all Decline Soils. , 2003, Phytopathology.

[15]  B. Landa,et al.  Identification of Differences in Genome Content among phlD-Positive Pseudomonas fluorescens Strains by Using PCR-Based Subtractive Hybridization , 2002, Applied and Environmental Microbiology.

[16]  B. Landa,et al.  Differential Ability of Genotypes of 2,4-Diacetylphloroglucinol-Producing Pseudomonas fluorescens Strains To Colonize the Roots of Pea Plants , 2002, Applied and Environmental Microbiology.

[17]  B. Landa,et al.  Comparison of Three Methods for Monitoring Populations of Different Genotypes of 2,4-Diacetylphloroglucinol-Producing Pseudomonas fluorescens in the Rhizosphere. , 2002, Phytopathology.

[18]  B. M. Gardener,et al.  Microbial populations responsible for specific soil suppressiveness to plant pathogens. , 2002, Annual review of phytopathology.

[19]  E. Green.  Allele-specific oligonucleotide PCR. , 2002, Methods in molecular biology.

[20]  M. Zala,et al.  Cosmopolitan distribution of phlD-containing dicotyledonous crop-associated biocontrol pseudomonads of worldwide origin , 2001 .

[21]  O. Nybroe,et al.  A panel of Tn7-based vectors for insertion of the gfp marker gene or for delivery of cloned DNA into Gram-negative bacteria at a neutral chromosomal site. , 2001, Journal of microbiological methods.

[22]  D. Weller,et al.  Exploiting Genotypic Diversity of 2,4-Diacetylphloroglucinol-Producing Pseudomonas spp.: Characterization of Superior Root-Colonizing P. fluorescensStrain Q8r1-96 , 2001, Applied and Environmental Microbiology.

[23]  G. Défago,et al.  Polymorphism of the polyketide synthase gene phID in biocontrol fluorescent pseudomonads producing 2,4-diacetylphloroglucinol and comparison of PhID with plant polyketide synthases. , 2001, Molecular plant-microbe interactions : MPMI.

[24]  L. Thomashow,et al.  Genetic Diversity of phlD from 2,4-Diacetylphloroglucinol-Producing Fluorescent Pseudomonas spp. , 2001, Phytopathology.

[25]  B. Lugtenberg,et al.  Molecular determinants of rhizosphere colonization by Pseudomonas. , 2001, Annual review of phytopathology.

[26]  B. M. Gardener,et al.  A rapid polymerase chain reaction-based assay characterizing rhizosphere populations of 2,4-diacetylphloroglucinol-producing bacteria. , 2001, Phytopathology.

[27]  R. S. Shmookler Reis,et al.  Discrimination of primer 3'-nucleotide mismatch by taq DNA polymerase during polymerase chain reaction. , 2000, Analytical biochemistry.

[28]  S. Kalloger,et al.  Genotypic and Phenotypic Diversity of phlD-ContainingPseudomonas Strains Isolated from the Rhizosphere of Wheat , 2000, Applied and Environmental Microbiology.

[29]  R. Fani,et al.  Frequency and Biodiversity of 2,4-Diacetylphloroglucinol-Producing Bacteria Isolated from the Maize Rhizosphere at Different Stages of Plant Growth , 2000, Applied and Environmental Microbiology.

[30]  L. Thomashow,et al.  Identification and Characterization of a Gene Cluster for Synthesis of the Polyketide Antibiotic 2,4-Diacetylphloroglucinol from Pseudomonas fluorescens Q2-87 , 1999, Journal of bacteriology.

[31]  F. Noya,et al.  Fluorescent Pseudomonas spp. as biocontrol agents against forage legume root pathogenic fungi , 1998 .

[32]  D. Weller,et al.  Natural plant protection by 2,4-diacetylphloroglucinol-producing Pseudomonas spp. in take-all decline soils , 1998 .

[33]  B. Duffy,et al.  Zinc Improves Biocontrol of Fusarium Crown and Root Rot of Tomato by Pseudomonas fluorescens and Represses the Production of Pathogen Metabolites Inhibitory to Bacterial Antibiotic Biosynthesis. , 1997, Phytopathology.

[34]  Thomas L. Madden,et al.  Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. , 1997, Nucleic acids research.

[35]  F. O'Gara,et al.  Ecological interaction of a biocontrol Pseudomonas fluorescens strain producing 2,4-diacetylphloroglucinol with the soft rot potato pathogen Erwinia carotovora subsp. atroseptica , 1997 .

[36]  F. O'Gara,et al.  Role of 2,4-Diacetylphloroglucinol in the Interactions of the Biocontrol Pseudomonad Strain F113 with the Potato Cyst Nematode Globodera rostochiensis , 1997, Applied and environmental microbiology.

[37]  Levin,et al.  Allelopathy in Spatially Distributed Populations , 1997, Journal of theoretical biology.

[38]  L. Thomashow,et al.  Frequency of Antibiotic-Producing Pseudomonas spp. in Natural Environments , 1997, Applied and environmental microbiology.

[39]  L. Thomashow,et al.  Quantification of 2,4-Diacetylphloroglucinol Produced by Fluorescent Pseudomonas spp. In Vitro and in the Rhizosphere of Wheat , 1997, Applied and environmental microbiology.

[40]  C. Keel,et al.  Conservation of the 2,4-diacetylphloroglucinol biosynthesis locus among fluorescent Pseudomonas strains from diverse geographic locations , 1996, Applied and environmental microbiology.

[41]  L. Thomashow,et al.  Current Concepts in the Use of Introduced Bacteria for Biological Disease Control: Mechanisms and Antifungal Metabolites , 1996 .

[42]  C. Keel,et al.  Amplification of the housekeeping sigma factor in Pseudomonas fluorescens CHA0 enhances antibiotic production and improves biocontrol abilities , 1995, Journal of bacteriology.

[43]  F. O'Gara,et al.  Exploitation of gene(s) involved in 2,4-diacetylphloroglucinol biosynthesis to confer a new biocontrol capability to a Pseudomonas strain , 1992, Applied and Environmental Microbiology.

[44]  F. O'Gara,et al.  Isolation of 2,4-Diacetylphloroglucinol from a Fluorescent Pseudomonad and Investigation of Physiological Parameters Influencing Its Production , 1992, Applied and environmental microbiology.

[45]  C. Keel,et al.  Suppression of root diseases by Pseudomonas fluorescens CHA0 - importance of the bacterial seconday metabolite 2,4-diacetylphloroglucinol , 1992 .

[46]  D. Weller,et al.  Genetic analysis of the antifungal activity of a soilborne Pseudomonas aureofaciens strain , 1991, Applied and environmental microbiology.

[47]  Laurence V. Madden,et al.  Introduction to Plant Disease Epidemiology , 1990 .

[48]  G. Défago,et al.  Naturally occurring fluorescent pseudomonads involved in suppression of black root rot of tobacco , 1986 .

[49]  R. Cook,et al.  Suppression of take-all of wheat by seed treatments with fluorescent pseudomonads. , 1983 .

[50]  C. R. Howell.  Control of rhizoctonia solani on cotton seedlings with Pseudomonas fluorescens and with an antibiotic produced by the bacterium. , 1979 .

[51]  King Eo,et al.  Two simple media for the demonstration of pyocyanin and fluorescin. , 1954 .

[52]  E. King,et al.  Two simple media for the demonstration of pyocyanin and fluorescin. , 1954, The Journal of laboratory and clinical medicine.