Rapid identification of Pseudomonas spp. from Aquatic samples using terminal restriction fragment length Polymorphism analysis

The genus Pseudomonas includes several species with an important biotechnological potential. Here we present a molecular approach for the analysis of the diversity of Pseudomonas spp. in aquatic samples based on the amplification of 16S rDNAs using taxon-specific primers, followed by multienzymatic restrictions and subsequent screening of terminal restriction fragments using capillary electrophoresis. This method, tested on seawater, groundwater and aquatic sediments, allows the identification of Pseudomonas spp. in samples, in which culture-based approaches failed in identifying their presence. The diversity of Pseudomonas spp. was very high in all samples investigated, with values higher than those reported in previous studies. The method was intercalibrated with Pseudomonas sp. isolates and allowed the distinction of different isolates. The possibility of identifying the taxonomic affiliation of the different isolates was tested with an "in silico" computer-assisted analysis (TAP terminal restriction fragment length polymorphisms). © 2008, Wiley Periodicals, Inc.