ARS | Publication request: Population structure and diversity of phenazine-1-carboxylic acid producing fluorescent pseudomonas spp. from dryland cereal fields of central Washington State (U.S.)

Submitted to: Microbial Ecology
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: January 20, 2012
Publication Date: March 2, 2012
Citation: Parejko, J.A., Mavrodi, D.V., Mavrodi, O.V., Weller, D.M., Thomashow, L.S. 2012. Population structure and diversity of phenazine-1-carboxylic acid producing fluorescent pseudomonas spp. from dryland cereal fields of central Washington State (U.S.). Microbial Ecology. 64:226-241.

Interpretive Summary: Certain strains of beneficial bacteria that grow on roots produce phenazine antibiotics that protect crop plants against a wide variety of fungal pathogens. In 2007 and 2008 we isolated 412 phenazine-producing (Phz+) strains from roots of wheat and barley grown in the low-precipitation region (less than 350 mm annual precipitation) of central Washington State. As a first step towards determining the contribution of these strains to plant health and productivity, a variety of genetic and biochemical tests were performed to determine the relationships of these isolates to each other, to other bacteria, and to the model biological control strain 2-79. Based on results of genomic fingerprinting analysis the new isolates, as well as the model strain 2-79, were assigned to 31 distinct groups separated into four clusters. DNA sequence analysis indicated that all of the isolates are related to Pseudomonas fluorescens group of related species and that the phenazine genes of most of the strains are similar to those of strain 2-79. However, there was considerable diversity among the isolates in their ability to grow under a variety of conditions and in their ability to produce the phenazine antibiotic. Collectively, the results of this study reveal greater diversity among phenazine producers than has previously been reported and provide a foundation for further analysis of these new strains.

Technical Abstract: Certain strains of the rhizosphere bacterium Pseudomonas fluorescens contain the phenazine biosynthesis operon (phzABCEDF) and produce redox-active phenazine antibiotics that suppress a wide variety of soilborne plant pathogens. In 2007 and 2008 we isolated 412 phenazine-producing (Phz+) fluorescent Pseudomonas strains from roots of dryland wheat and barley grown in the low-precipitation region (< 350 mm annual precipitation) of central Washington State. Based on results of BOX-PCR genomic fingerprinting analysis these isolates, as well as the model biocontrol Phz+ strain P. fluorescens 2-79, were assigned to 31 distinct genotypes separated into four clusters. All of the isolates exhibited high 16S rDNA sequence similarity to members of the P. fluorescens species complex including P. orientalis, P. gessardii, P. libanensis, and P. synxantha. Further recA-based sequence analyses revealed that the majority of new Phz+ isolates (386 of 413) form a clade distinctly separated from P. fluorescens 2-79. Analysis of phzF alleles, however, revealed that the majority of those isolates (280 of 386) carried phenazine biosynthesis genes highly similar to those of P. fluorescens 2-79. phzF-based analyses also revealed that phenazine genes were under purifying selection and showed evidence of intra-cluster recombination. Phenotypic analyses using Biolog substrate utilization and observations of PCA production showed considerable variability amongst members of all four clusters. In summary, this study revealed a genotypically and phenotypically diverse group of phenazine producers with a population structure not seen before in indigenous rhizosphere-inhabiting Phz+ Pseudomonas spp.