Charles-François Boudouresque, Pierre Caumette, Jean-Claude Bertrand, Philippe Normand, Télesphore Sime-Ngando
Russian Université de Toulon, Aix-Marseille Université, Institut Méditerranéen d’Océanologie (MIO), UM 110, CNRS 7294 IRD 235, Cedex 9.
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.
Keywords: Endosymbiosis; Hierarchical classification; History of systematics; Life domains; Microbial classification; Microbial systematics; Nomenclature codes; Phylogeny; Tree of life