Phylogenetic Relationships Between Environmental and Clinical Isolates of Pseudomonas fluorescens and Related Species Deduced from 16S rRNA Gene and OprF Protein Sequences

https://doi.org/10.1078/0723-2020-00253Get rights and content

Summary

The major surface protein of the genus Pseudomonas, OprF, is a non-specific porin that plays an important role in maintenance of cell shape, in growth in a low osmolarity environment, and in adhesion to various supports. The objectives of our study were (i) to carry out a comparative analysis of phylogenies obtained from the OprF protein and from the 16S rRNA gene in 41 isolates from various sources (water, soil, milk and the hospital) and (ii) to investigate the physiological characteristics correlated with the phylogeny of OprF. We report here an important incongruence between the phylogenies of the 16S rRNA gene and the OprF protein. Phylogenetic analysis of 16S rRNA genes grouped Pseudomonas fluorescens isolates into one cluster (termed fluorescens r-cluster) whilst the phylogeny of the OprF protein divided Pseudomonas fluorescens isolates into two quite distinct clusters (termed fluorescens 1 o-cluster and fluorescens 2 o-cluster) that may be related to the original habitat of the strain. The fluorescens 1 o-cluster contained the majority of non-rhizospheric soil isolates, while the fluorescens 2 o-cluster contained all our clinical isolates and most of the rhizospheric isolates (which are fixed to the roots). In order to check this correlation, we studied two physiological characteristics: the range of growth temperature and the capacity for non-specific adhesion to polystyrene. The temperature range study for strains did not explain the existence of the two o-clusters but it did confirm the capacity of certain P. fluorescens strains to grow at 37 °C. The adhesion capacities of the isolates in the two o-clusters seems to be correlated with ecological niche.

References (0)

Cited by (42)

  • A cultivation-independent PCR-RFLP assay targeting oprF gene for detection and identification of Pseudomonas spp. in samples from fibrocystic pediatric patients

    2015, Journal of Microbiological Methods
    Citation Excerpt :

    We have already tested the utility of the oprF gene, encoding a non-specific outer membrane porin, to specifically monitor Pseudomonas populations in soil and plant root samples (Agaras et al., 2012). Although oprF is conserved in the genus Pseudomonas, its sequence shows enough diversity to be used as a genetic marker to explore its allelic variation among different species (Bodilis and Barray, 2006; Bodilis et al., 2004; Bodilis et al., 2006). Based on this, we have developed a PCR-RFLP protocol targeting the oprF gene that allows species level differentiation in environmental pseudomonad isolates (Agaras et al., 2012).

  • Occurrence of multi-antibiotic resistant Pseudomonas spp. in drinking water produced from karstic hydrosystems

    2014, Science of the Total Environment
    Citation Excerpt :

    E. coli and Pseudomonas spp. densities were investigated, and the antibiotic resistance of the Pseudomonas isolates was determined. The Pseudomonas spp. isolated in the drinking water reservoir were identified at the species level or related species level by sequencing the rpoD and oprF genes (Bodilis et al., 2004, 2011; Mulet et al., 2009). In order to evaluate potential resistance transferability, we carried out a preliminary investigation into the possible presence of plasmids by transformation assays.

  • Evaluation of oprI and oprL genes as molecular markers for the genus Pseudomonas and their use in studying the biodiversity of a small Belgian River

    2013, Research in Microbiology
    Citation Excerpt :

    Based on sequencing of conserved housekeeping genes, including 16S rRNA, gacA, gyrB, recA, rpoB and rpoD, different intrageneric clusters, lineages and groups have been described (Anzai et al., 2000; de Souza et al., 2003; Hilario et al., 2004; Moore et al., 1996; Tayeb et al., 2005; Yamamoto et al., 2000). In addition, outer membrane proteins such as lipoproteins OprI, peptidoglycan-associated OprL and the non-specific porin OprF, have also been used as taxonomic tools (Bodilis et al., 2004; De Vos et al., 1997, 1998; Jaffe et al., 2001; Pirnay et al., 2000, 2002). OprF is a structural protein (Rawling et al., 1998).

  • Specific enumeration and analysis of the community structure of culturable pseudomonads in agricultural soils under no-till management in Argentina

    2012, Applied Soil Ecology
    Citation Excerpt :

    To meet these goals, we rely on specific detection methods. For pseudomonads, three genes have been utilized for phylogenetic diversity studies at the genus levels: 16S rDNA, gacA and oprF (Bodilis et al., 2004; de Souza et al., 2003; Pesaro and Widmer, 2006). gacA encodes the cognate transcriptional regulator of the membrane associated sensor protein GacS.

View all citing articles on Scopus
View full text