La taxonomie bactérienne moderne : revue des techniques — application à la caractérisation des bactéries nodulant les légumineuses (BNL)

Abstract

Taxonomy is the science that studies the relationships between organisms. It comprises classification, nomenclature, and identification. Modern bacterial taxonomy is polyphasic. This means that it is based on several molecular techniques, each one retrieving the information at different cellular levels (proteins, fatty acids, DNA...). The obtained results are combined and analysed to reach a "consensus taxonomy" of a microorganism. Until 1970, a small number of classification techniques were available for microbiologists (mainly phenotypic characterization was performed: a legume species nodulation ability for a Rhizobium, for example). With the development of techniques based on polymerase chain reaction for characterization, the bacterial taxonomy has undergone great changes. In particular, the classification of the legume nodulating bacteria has been repeatedly modified over the last 20 years. We present here a review of the currently used molecular techniques in bacterial characterization, with examples of application of these techniques for the study of the legume nodulating bacteria.

Genome and pan-genome analysis to classify emerging bacteria

“…Currently, prokaryote taxonomy relies on polyphasic combinations of phenotypic properties (pathogenesis, morphology, environmental and culture conditions), chemotaxonomic properties (chemical composition of cellular components) and genotypic properties [11, 90], including DNA-DNA hybridization (DDH), DNA G + C content [91] and 16S rRNA sequence similarity [12, 92] The application of molecular hybridization methods provides a genomic definition of the bacterial species, taking into account the similarity rate and the thermal stability of the hybrids obtained by the DNAs of two bacterial isolates. Isolates belonging to the same species are characterized by homologies of their DNA, which result in hybridization percentages greater than or equal to 70%, and stability of the hybrids formed below 5 °C [93–95].…”

Phenotypic and Genotypic Diversity of Microsymbionts Nodulating Medicago sativa (L.) in the Algerian Sahara

“…The development of polyphasic taxonomy (phenotypic, genotypic and phylogenetic characteristics) and the use of 16S rRNA as a taxonomic marker has led to many changes in the taxonomy of rhizobia (Zakhia and de Lajudie, 2006). A highly conserved gene like 16S rRNA is not suitable for the discrimination of closely related Sinorhizobium (or Ensifer) species (Martens et al, 2007).…”

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“…The development of polyphasic taxonomy (phenotypic, genotypic and phylogenetic characteristics) and the use of 16S rRNA as a taxonomic marker has led to many changes in the taxonomy of rhizobia (Zakhia and de Lajudie, 2006). A highly conserved gene like 16S rRNA is not suitable for the discrimination of closely related Sinorhizobium (or Ensifer) species (Martens et al, 2007).…”