Taxonomy and Phylogeny of Prokaryotes
6
Pierre Caumette, Ce ´line Brochier-Armanet, and Philippe Normand
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.
Keywords
16S RNA homology Archaea Bacteria Bacterial taxonomy Dendrogram DNA/DNA
hybridization Domains G + C% Genotypic criteria Phenotypic criteria Phylogenetic
tree Phyla Systematics of prokaryotes
6.1
The Concept of Species in Prokaryotes
and Its Evolution
Classification of prokaryotes has long been based on the
same hierarchical systems on which Linnaeus (Linnaeus
1753) based his nomenclatural system applied initially to
plants and animals. These classifications are hierarchically
organized into seven levels: kingdoms*, phyla*, classes*,
orders*, families*, genera*, and species*. In the kingdoms
corresponding to the animal and the plant worlds, a robust
classification has been established. Its success depends in
part on the definition of a species that has been proposed for
eukaryotes: a species is a group of individuals who have the
ability to reproduce and yield fecund offspring and share
P. Caumette* (*)
Institut des Sciences Analytiques et de Physico-chimie pour
l’Environnement et les Mate ´riaux (IPREM), UMR CNRS 5254,
Universite ´ de Pau et des Pays de l’Adour, B.P. 1155,
64013 Pau Cedex, France
e-mail: pierre.caumette@univ-pau.fr
C. Brochier-Armanet
Laboratoire de Biome ´trie et Biologie E ´ volutive, UMR CNRS 5558,
Universite ´ Claude Bernard Lyon 1, 69622 Villeurbanne Cedex, France
e-mail: Celine.brochier-armanet@univ-lyon1.fr
P. Normand
Microbial Ecology Center, UMR CNRS 5557 / USC INRA 1364,
Universite ´ Lyon 1, 69622 Villeurbanne, France
e-mail: philippe.normand@univ-lyon1.fr
* Chapter Coordinator
J.-C. Bertrand et al. (eds.), Environmental Microbiology: Fundamentals and Applications: Microbial Ecology,
DOI 10.1007/978-94-017-9118-2_6, # Springer Science+Business Media Dordrecht 2015
145
6
Pierre Caumette, Ce ´line Brochier-Armanet, and Philippe Normand
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.
Keywords
16S RNA homology Archaea Bacteria Bacterial taxonomy Dendrogram DNA/DNA
hybridization Domains G + C% Genotypic criteria Phenotypic criteria Phylogenetic
tree Phyla Systematics of prokaryotes
6.1
The Concept of Species in Prokaryotes
and Its Evolution
Classification of prokaryotes has long been based on the
same hierarchical systems on which Linnaeus (Linnaeus
1753) based his nomenclatural system applied initially to
plants and animals. These classifications are hierarchically
organized into seven levels: kingdoms*, phyla*, classes*,
orders*, families*, genera*, and species*. In the kingdoms
corresponding to the animal and the plant worlds, a robust
classification has been established. Its success depends in
part on the definition of a species that has been proposed for
eukaryotes: a species is a group of individuals who have the
ability to reproduce and yield fecund offspring and share
P. Caumette* (*)
Institut des Sciences Analytiques et de Physico-chimie pour
l’Environnement et les Mate ´riaux (IPREM), UMR CNRS 5254,
Universite ´ de Pau et des Pays de l’Adour, B.P. 1155,
64013 Pau Cedex, France
e-mail: pierre.caumette@univ-pau.fr
C. Brochier-Armanet
Laboratoire de Biome ´trie et Biologie E ´ volutive, UMR CNRS 5558,
Universite ´ Claude Bernard Lyon 1, 69622 Villeurbanne Cedex, France
e-mail: Celine.brochier-armanet@univ-lyon1.fr
P. Normand
Microbial Ecology Center, UMR CNRS 5557 / USC INRA 1364,
Universite ´ Lyon 1, 69622 Villeurbanne, France
e-mail: philippe.normand@univ-lyon1.fr
* Chapter Coordinator
J.-C. Bertrand et al. (eds.), Environmental Microbiology: Fundamentals and Applications: Microbial Ecology,
DOI 10.1007/978-94-017-9118-2_6, # Springer Science+Business Media Dordrecht 2015
145