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Appl. Environ. Microbiol., Sep 1995, 3400-3406, Vol 61, No. 9
Copyright © 1995, American Society for Microbiology

Comparison of Phenotypical and Molecular Methods for the Identification of Bacterial Strains Isolated from a Deep Subsurface Environment

V Boivin-Jahns, A Bianchi, R Ruimy, J Garcin, S Daumas and R Christen
Centre National de la Recherche Scientifique and Station Zoologique, Observatoire Oceanologique, Universite Paris 6, 06230 Villefranche sur mer, Microbiologie Marine, Centre National de la Recherche Scientifique, UPR 223, Campus de Luminy, 13288 Marseille Cedex 9, and Societe GRAM SA, 13856 Aix en Provence Cedex 3, France

Seventy-four bacterial strains were freshly isolated from a mine gallery. Using these bacteria, we have investigated how a molecular identification based on the analysis of small subunit rDNA sequences would compare in terms of precision and reliability to a more classical comparison of phenotypical descriptions (100 morphological and physiological traits). Our data clearly showed that a phylogenetic analysis of small subunit rDNA sequences is more efficient than classical phenotypic methods for the identification of bacterial strains freshly isolated from a natural environment, because occurrences of misidentification are very much decreased by this method. The lack of rDNA sequences for many described species is probably the major cause of a few failures in molecular identification, as the completeness of the database of small subunit rDNA sequences holds much importance in the degree of uncertainty in such identifications.

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