1. Isolation and identification ofPseudomonas syringaefacilitated by a PCR targeting the wholeP. syringaegroup
- Author
-
Mohamed Barakat, Cindy E. Morris, Odile Berge, Caroline Guilbaud, Philippe Ortet, Unité de Pathologie Végétale (PV), Institut National de la Recherche Agronomique (INRA), Institut de Biosciences et Biotechnologies d'Aix-Marseille (ex-IBEB) (BIAM), Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS)-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA), Commissariat à l'énergie atomique et aux énergies alternatives (CEA), Berge, Odile, Direction de Recherche Fondamentale (CEA) (DRF (CEA)), and Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS)
- Subjects
[SDV.SA]Life Sciences [q-bio]/Agricultural sciences ,0106 biological sciences ,0301 basic medicine ,Biodiversité et Ecologie ,Pseudomonas syringae ,Polymerase Chain Reaction ,01 natural sciences ,Applied Microbiology and Biotechnology ,Genome ,law.invention ,structure de la population ,chemistry.chemical_compound ,bactérie de l'environnement ,diversité microbienne ,law ,Polymerase chain reaction ,P. syringae identification ,Ecology ,biology ,Pseudomonas ,Isolation (microbiology) ,Biological Evolution ,Agricultural sciences ,environmental pathogen ,méthode de détection ,Phenotype ,Identification (biology) ,détection pcr ,mise au point de test ,specific PCR ,DNA, Bacterial ,identification spécifique ,Phytopathology and phytopharmacy ,PCR-assisted detection ,Microbiology ,Biodiversity and Ecology ,03 medical and health sciences ,Rivers ,P. syringae diversity ,population structure ,DNA Primers ,Plant Diseases ,bactérie phytopathogène ,écologie microbienne ,Base Sequence ,Sequence Analysis, DNA ,biology.organism_classification ,Phytopathologie et phytopharmacie ,[SDV.BV.PEP]Life Sciences [q-bio]/Vegetal Biology/Phytopathology and phytopharmacy ,Molecular Typing ,030104 developmental biology ,chemistry ,[SDE.BE]Environmental Sciences/Biodiversity and Ecology ,Sciences agricoles ,DNA ,Bacteria ,010606 plant biology & botany - Abstract
International audience; We present a reliable PCR-based method to avoid the biases related to identification based on the conventional phenotypes currently used in the identification of Pseudomonas syringae sensu lato, a ubiquitous environmental bacterium including plant pathogens. We identified a DNA target suitable for this purpose by applying a comparative genomic pipeline to Pseudomonas genomes. We designed primers and developed PCR conditions that led to a clean and strong PCR product from 97% of the 185 strains of P. syringae strains tested and gave a clear negative result for the 31 non-P. syringae strains tested. The sensitivity of standard PCR was determined with pure strains to be 10(6) bacteria mL(-1) or 0.4 ng of DNA μL(-1). Sensitivity could be improved with the touchdown method. The new PCR-assisted isolation of P. syringae was efficient when deployed on an environmental sample of river water as compared to the isolation based on phenotypes. This innovation eliminates the need for extensive expertise in isolating P. syringae colonies, was simpler, faster and very reliable. It will facilitate discovery of more diversity of P. syringae and research on emergence, dispersion, and evolution to understand the varied functions of this environmental bacterium.
- Published
- 2015
- Full Text
- View/download PDF