OprF polymorphism as a marker of ecological niche in Pseudomonas

Abstract

OprF is the major outer-membrane protein of Pseudomonas sensu stricto (rRNA group I). In addition to playing a role as porin, membrane structural protein and root adhesion, this pleiotropic protein shows a length polymorphism corresponding to two types of OprF, termed OprF type 1 and OprF type 2. In a previous work, all the P. fluorescens isolated from bulk soil (non-rhizospheric) were shown to possess oprF type 1, while all the clinical P. fluorescens isolates and most rhizospheric strains corresponded to type 2. In this study, we further investigated the relation between the OprF polymorphism and the ecological niche by developing a culture-independent approach (a ratio polymerase chain reaction) to measure the percentage of each oprF type in environmental DNA samples, including two different soils and three different cultured plants (flax, wheat and grassland). Although the proportions of oprF type 2 between rhizospheric samples were quite variable, they were always very significantly higher (P<0.001) than the proportions of oprF type 2 of the adjacent bulk soil where the vast majority of oprF (>95%) corresponded to type 1. We discuss the potential applications of this ecological fingerprint in an agronomic and taxonomic point of view.

Evidence for Selective Bacterial Community Structuring in the Freshwater Sponge Ephydatia fluviatilis

“…The 16S rRNA gene has been found to poorly resolve Pseudomonas spp. phylogeny [49,50], and alternative protocols for the analysis of their diversity and function have been suggested [51][52][53]. Because of their well-reported secondary metabolite production capacity in terrestrial ecosystems [24,54,55], typical symbiotic lifestyle, amenability to cultivation and documented retrieval from freshwater sponges [45], further studies combining alternative molecular tools and culturing might help in gaining novel insights into the occurrence, degree of specificity and potential roles of Pseudomonas species in Spongiliidae.…”

Pseudomonas spp. isolates with high phosphate-mobilizing potential and root colonization properties from agricultural bulk soils under no-till management

“…The taxonomic identity of the isolates was determined by sequencing the conserved 16S rDNA gene and the Pseudomonas-specific marker gene oprF (Bodilis et al 2006). The 16S rDNA gene was amplified by polymerase chain reaction (PCR) with primers P0 and P6 (Picard et al 2000), and the oprF gene was amplified with primers oprF-FW2 and oprF-Rev2, as described elsewhere (Agaras et al 2011).…”

Glycerophospholipid synthesis and functions in Pseudomonas

“…Thus, the utilization of antibiotics uncommonly used in clinical practice, such as polymyxins like colistin, is recommended (Gunderson et al, 2003;Sabuda et al, 2008). Bacteria of the P. fluorescens lineage are found preferentially in soil and in association with plants (Bodilis et al, 2006;Loper et al, 2012). Members of the P. putida group show an adaptation to various ecological niches and are characterized by their adaptation to grow in soils and sediments contaminated with high concentrations of heavy metals and organic contaminants (Hachicho et al, 2014;Heipieper et al, 1996;Ramos et al, 1997;Wu et al, 2011).…”

“…Recently, strains of P. syringae, virulent on diverse species of crop plants, were isolated from epilithic biofilms of rivers (Morris et al, 2007) and clouds at several kilometers altitude (Amato et al, 2007) outside the zones of agricultural production (Morris et al, 2008). Bacteria of the P. fluorescens group commonly found in soil (Bodilis et al, 2006) and water (Janek et al, 2010) are also able to develop in air Kondakova et al, 2014). Some of P. fluorescens group members, adapted to the human temperature are members of the skin microbiota or behave as opportunistic pathogens (Chapalain et al, 2008).…”