Comparison of three typing methods for evaluating the diversity of pseudomonas fluorescens in the rhizosphere

Pseudomonads are of significant environmental importance as the members including plant and animal/human pathogens, xenobiotic degraders, plant growth promoters and biocontrol agents. Three typing methods were evaluated, utilising 143 strains of fluorescent pseudomonads isolated from maize-oat-alfalfa-alfalfa rotation plots in Canada, to assess their usefulness as tools to study the microbial community diversity. The methods used were repetitive element sequence-based PCR (rep-PCR) utilising BOX and Enterobacterial Repetitive Intergenic Consensus (ERIC) primers, another new PCR method using an engineered polymerase and 10-nucleotide miniprimers expands the scope of detectable sequences beyond those detected by standard methods using longer primers and Taq polymerase. Cluster analysis of the results clearly demonstrated the groups can be divided into two big clusters in line with the morphological variation. Rep-PCR proved to be highly discriminatory, interesting tools for the delineation or genotyping of bacterial species. We concluded that a combination of Box-, Eric- and Miniprimer-PCR results is a rapid and reliable alternative for discrimination among P. fluorescens isolates, contributing to epidemiological studies. © 2011 Academie Journals Inc.