Application of PCR primer sets for detection of Pseudomonas sp. functional genes in the plant rhizosphere

Jong-Shik Kim, Pauline M. Mele, David E. Crowley

Department of Environmental Sciences, University of California, Riverside, USA.
Department of Primary Industries, Rutherglen, Australia.

DOI: 10.4236/jacen.2013.21002                

Abstract

Plant growth promoting pseudomonads play an important role in disease suppression and there is considerable interest in development of bio-marker genes that can be used to monitor these bacteria in agricultural soils. Here, we report the application ofa PCR primer sets targeting genes encoding the main antibiotic groups. Distribution of the genes was variably distributed across type strains of 28 species with no phylogenetic groupingfor the detected antibioticsgenes, phlD for 2,4-diacetylphloroglucinol (2,4-DAPG) and phzCD for phenazine-1-carboxylic acid or hcnBC for hydrogen cyanide production. Analysis of field soils showed that primer sets for phlD and phzCD detected these genes in a fallowed neutral pH soil following wheat production, but that the copy numbers were below the detection limits in bulk soils having an acidic pH. In contrast, PCR products for the phzCD, pltc and hcnBc genes were detectable in mature root zones following plantingwith wheat. The ability to rapidly characterize populations of antibiotics producers using specific primer sets will improve our ability to assess the impacts of management practices on the functional traits of Pseudomonas spp. populations in agricultural soils.

Keywords

PGPR (Plant Growth-Promoting Rhizosphere); Pseudomonas; PCR; 16S rDNA; Plant-Microbe Interactions

Conflicts of Interest

The authors declare no conflicts of interest.

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