Systematic and Evolution of Microorganisms:
General Concepts
5
Charles-Franc ¸ois Boudouresque, Pierre Caumette, Jean-Claude Bertrand,
Philippe Normand, and Te ´lesphore Sime-Ngando
Abstract
The diversity of metabolic activities is a characteristic of the microbial world. This
enormous diversity needs to be structured in order to be understood, and as a result,
taxonomy and systematics are constantly changing since the beginning of the history of
microbiology and particularly today with the introduction in the last 20 years of phylogeny
as the core of systematics. The history of concepts in systematics and classification is
presented. Classification is the science of ordering microorganism groups (taxa) based on
their interrelationships. Taxonomy is the discipline that defines the principles and laws
of classification. Nomenclature is the science of defining and naming the taxonomic
categories (species, genera, families, orders, classes, divisions, phyla, kingdoms, domains),
according to their hierarchical rank. In this way, different schools of classification and
bacterial systematics were developed in the twentieth century. Today, there is an international
consensus based on the classification of the Bergey’s Manual revisited with the concepts of
phylogeny. Through this classification, the concept of the prokaryotic world organization has
evolved. From the idea of a kingdom of prokaryotes, the concept of three domains in the
organization of life supported by phylogenetic trees is fully accepted today. Among these
three domains, two are prokaryotic: Bacteria and Archaea. In this chapter, the role of
horizontal gene transfers in the evolution of life is discussed. The origin of eukaryotes with
the primary, secondary, and tertiary endosymbioses is also presented. This allows to improve
or to transform the concept of the tree of life from phylogeny to full genome study.
C.-F. Boudouresque* (*) J.-C. Bertrand
Institut Me ´diterrane ´en d’Oce ´anologie (MIO), UM 110, CNRS 7294
IRD 235, Universite ´ de Toulon, Aix-Marseille Universite ´,
Campus de Luminy, 13288 Marseille Cedex 9, France
e-mail: charles.boudouresque@mio.osupytheas.fr; Jean-Claude.
bertrand@univ-amu.fr
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
P. Normand
Microbial Ecology Center, UMR CNRS 5557 / USC INRA 1364,
Universite ´ Lyon 1, 69622 Villeurbanne, France
e-mail: philippe.normand@univ-lyon1.fr
T. Sime-Ngando
Laboratoire Microorganismes: Ge ´nome et Environnement (LMGE),
UMR CNRS 6023, Universite ´ Blaise Pascal, Clermont Universite ´, B.P.
80026, 63171 Aube `re Cedex, France
e-mail: telesphore.sime-ngando@univ-bpclermont.fr
* Chapter Coordinator
J.-C. Bertrand et al. (eds.), Environmental Microbiology: Fundamentals and Applications: Microbial Ecology,
DOI 10.1007/978-94-017-9118-2_5, # Springer Science+Business Media Dordrecht 2015
107
General Concepts
5
Charles-Franc ¸ois Boudouresque, Pierre Caumette, Jean-Claude Bertrand,
Philippe Normand, and Te ´lesphore Sime-Ngando
Abstract
The diversity of metabolic activities is a characteristic of the microbial world. This
enormous diversity needs to be structured in order to be understood, and as a result,
taxonomy and systematics are constantly changing since the beginning of the history of
microbiology and particularly today with the introduction in the last 20 years of phylogeny
as the core of systematics. The history of concepts in systematics and classification is
presented. Classification is the science of ordering microorganism groups (taxa) based on
their interrelationships. Taxonomy is the discipline that defines the principles and laws
of classification. Nomenclature is the science of defining and naming the taxonomic
categories (species, genera, families, orders, classes, divisions, phyla, kingdoms, domains),
according to their hierarchical rank. In this way, different schools of classification and
bacterial systematics were developed in the twentieth century. Today, there is an international
consensus based on the classification of the Bergey’s Manual revisited with the concepts of
phylogeny. Through this classification, the concept of the prokaryotic world organization has
evolved. From the idea of a kingdom of prokaryotes, the concept of three domains in the
organization of life supported by phylogenetic trees is fully accepted today. Among these
three domains, two are prokaryotic: Bacteria and Archaea. In this chapter, the role of
horizontal gene transfers in the evolution of life is discussed. The origin of eukaryotes with
the primary, secondary, and tertiary endosymbioses is also presented. This allows to improve
or to transform the concept of the tree of life from phylogeny to full genome study.
C.-F. Boudouresque* (*) J.-C. Bertrand
Institut Me ´diterrane ´en d’Oce ´anologie (MIO), UM 110, CNRS 7294
IRD 235, Universite ´ de Toulon, Aix-Marseille Universite ´,
Campus de Luminy, 13288 Marseille Cedex 9, France
e-mail: charles.boudouresque@mio.osupytheas.fr; Jean-Claude.
bertrand@univ-amu.fr
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
P. Normand
Microbial Ecology Center, UMR CNRS 5557 / USC INRA 1364,
Universite ´ Lyon 1, 69622 Villeurbanne, France
e-mail: philippe.normand@univ-lyon1.fr
T. Sime-Ngando
Laboratoire Microorganismes: Ge ´nome et Environnement (LMGE),
UMR CNRS 6023, Universite ´ Blaise Pascal, Clermont Universite ´, B.P.
80026, 63171 Aube `re Cedex, France
e-mail: telesphore.sime-ngando@univ-bpclermont.fr
* Chapter Coordinator
J.-C. Bertrand et al. (eds.), Environmental Microbiology: Fundamentals and Applications: Microbial Ecology,
DOI 10.1007/978-94-017-9118-2_5, # Springer Science+Business Media Dordrecht 2015
107