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

• Published in: FEMS microbiology ecology Vol. 56; no. 1; pp. 64 - 78
• Main Authors: De La Fuente, Leonardo, Mavrodi, Dmitri V., Landa, Blanca B., Thomashow, Linda S., Weller, David M.
• Format: Journal Article
• Language: English
• Published: Oxford, UK Blackwell Publishing Ltd 01-04-2006; Blackwell Science Ltd; Oxford University Press
• Subjects: 2,4‐diacetylphloroglucinol; Alleles; allele‐specific PCR; Base Sequence; biological control; Colony Count, Microbial; Dilution; DNA, Bacterial - chemistry; DNA, Bacterial - genetics; Ecology; Gene sequencing; Genetic diversity; Genetic Variation; Genotype; Genotypes; Microbiology; Natural environment; phlD; PhlD gene; Phloroglucinol - analogs & derivatives; Phloroglucinol - metabolism; Phylogeny; Polymerase Chain Reaction; Pseudomonas; Pseudomonas fluorescens; Pseudomonas fluorescens - genetics; Pseudomonas fluorescens - growth & development; Pseudomonas fluorescens - metabolism; Rhizosphere; rhizosphere colonization; Sequence Alignment; Sequence Analysis, DNA; Soil Microbiology; Strains (organisms); Wheat; biological control; rhizosphere colonization; 2,4-diacetylphloroglucinol; allele-specific PCR
• ISSN: 0168-6496; 1574-6941
• DOI: 10.1111/j.1574-6941.2006.00074.x

Abstract
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.