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Taxonomy and Phylogeny of Prokaryotes

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Environmental Microbiology: Fundamentals and Applications

Abstract

Classification of prokaryotes is hierarchically organized into seven levels: kingdoms, phyla, classes, orders, families, genera, and species. In prokaryotes, because they reproduce by clonal fission, the species, considered as the basic unit of the biological diversity, faces several problems such as the definition of an individual. A bacterial strain can be recognized as an individual belonging to a species. However, many inconsistencies exist between phenotypic similarity levels and evolutionary relationships deduced from molecular phylogenies. Most taxonomic groups have been reconsidered through phylogenetic analysis in the 1980s, and a consensus has been reached on the need for coherence between taxonomy and phylogeny. Thus, the multiple revisions of species, genera, or higher taxonomic levels pose many complex problems that are solved gradually. Prokaryotic microorganisms correspond to two of the three domains of life: Archaea and Bacteria. Their systematics is described in the “Bergey’s Manual for Systematic Bacteriology, second edition” published in five volumes.

In the text, the Latin terms used are those accepted by the Nomenclature Committee, and the organization of the bacterial and archaeal domains is presented as they appear in the “Bergey’s Manual for Systematic Bacteriology.” They are discussed according to the recent data of the hierarchical classification of Prokaryotes.

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Notes

  1. 1.

    This is an iterative process linked to the ongoing discovery of new taxa in new environments or better explored. In 2002, for instance, a bacteria was described in which 16S rRNA gene did not hybridize with the “universal” primers commonly used.

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Websites

http://www.bacterio.cict.fr/classificationgenera.html. This site is managed by Jean Euzéby of the ENV Toulouse; it maintains bacterial taxonomy entries based on the publications validly made in journals of bacterial taxonomy.

http://www.ncbi.nlm.nih.gov/sites/entrez?db=taxonomy. This site is managed by the American NCBI. It is complementary to the first; however, it incorporates several nonvalid taxa.

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Authors and Affiliations

  1. Institut des Sciences Analytiques et de Physico-chimie pour l’Environnement et les Matériaux (IPREM), UMR CNRS 5254, Université de Pau et des Pays de l’Adour, B.P. 1155, 64013, Pau Cedex, France

    Pierre Caumette

  2. Laboratoire de Biométrie et Biologie Évolutive, UMR CNRS 5558, Université Claude Bernard Lyon 1, 69622, Villeurbanne Cedex, France

    Céline Brochier-Armanet

  3. Microbial Ecology Center, UMR CNRS 5557 / USC INRA 1364, Université Lyon 1, 69622, Villeurbanne, France

    Philippe Normand

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  1. Pierre Caumette
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  2. Céline Brochier-Armanet
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  3. Philippe Normand
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Correspondence to Pierre Caumette .

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Editors and Affiliations

  1. Université de Toulon, Aix-Marseille Université, Institut Méditerranéen d’Océanologie (MIO), UM 110, CNRS 7294 IRD 235, Cedex 9, Marseille, France

    Jean-Claude Bertrand

  2. Université de Pau et des Pays de l’Adour, Institut des Sciences Analytiques et de Physico-chimie pour l’Environnement et les Matériaux (IPREM), UM 110, CNRS 5254, Pau Cedex, France

    Pierre Caumette

  3. Observatoire Océanologique de Banyuls, Laboratoire de Biodiversité et Biotechnologie Microbiennes (LBBM), Sorbonne Universités, UPMC Univ, Paris 06, USR CNRS 3579, Banyuls-sur-Mer, France

    Philippe Lebaron

  4. Institut Méditerranéen de Biodiversité et d’Ecologie marine et continentale (IMBE), UMR-CNRS-IRD 7263, Aix-Marseille Université, Cedex 20, Marseille, France

    Robert Matheron

  5. Microbial Ecology Center, UMR CNRS 5557/USC INRA 1364, Villeubanne, France

    Philippe Normand

  6. Laboratoire Microorganismes: Génome et Environnement (LMGE), UMR CNRS 6023, Université Blaise Pascal, Clermont Université, Aubère Cedex, France

    Télesphore Sime-Ngando

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Caumette, P., Brochier-Armanet, C., Normand, P. (2015). Taxonomy and Phylogeny of Prokaryotes. In: Bertrand, JC., Caumette, P., Lebaron, P., Matheron, R., Normand, P., Sime-Ngando, T. (eds) Environmental Microbiology: Fundamentals and Applications. Springer, Dordrecht. https://doi.org/10.1007/978-94-017-9118-2_6

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