OprF polymorphism as a marker of ecological niche in Pseudomonas

Authors

  • Josselin Bodilis,

    Corresponding author
    1. LMDF (Laboratoire de Microbiologie Du Froid), UPRES 2123,
    2. ABISS (Atelier de Biologie, Informatique, Statistique et Sociolinguistinque) and
    3. Flanders Interuniversity Institute of Biotechnology, Laboratory of Microbial Interactions, Vrije Universiteit Brussel, 1050 Brussels, Belgium.
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  • Mickaël Hedde,

    1. Laboratoire ECODIV (Etude et COmpréhension de la bioDIVersité), UPRES 1293, Université de Rouen, 76821 Mont Saint Aignan, France.
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  • Nicole Orange,

    1. LMDF (Laboratoire de Microbiologie Du Froid), UPRES 2123,
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  • Sylvie Barray

    1. LMDF (Laboratoire de Microbiologie Du Froid), UPRES 2123,
    2. ABISS (Atelier de Biologie, Informatique, Statistique et Sociolinguistinque) and
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*E-mail josselin.bodilis@univ-rouen.fr; Tel. (+33) 235 1467 78; Fax (+33) 235 1466 88.

Summary

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.

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