in collection. This approach which has been used for decades
and applied to the study of pathogenic bacteria and bacteria
from the environment has led to the definition of a set of
rules. Prokaryotic taxonomy has been based on a series of
morphological and increasingly of biochemical criteria in
the different editions of books of bacterial systematics.
Early taxonomic schemes were based on dichotomous
keys similar to those used for botanical books with a priority
given to radiative autotrophy (photosynthesis), the existence
of a thick wall capable of withholding a dye (Gram stain),
the presence of survival structures (“spores”), etc. Morphological criteria have later been supplemented by physiological criteria.
Besides characterization of microorganisms, classification, nomenclature, and identification are the three main
areas of systematics.
Classification is the science of ordering microorganism
groups (taxa) based on their interrelationships. The term
classification is used not only for the method but also for
the resulting system. Taxonomy is the study which 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. It helps to provide internationally
recognized microorganism names correctly and place them
in the classification as belonging to specific and defined
groups (taxa). These names are controlled and regulated by
international codes of nomenclature, whether for prokaryotic
(bacterial nomenclature) or eukaryotic (plant nomenclature,
which includes the “fungi,” and animal nomenclature which
includes the “protozoa”). When a microorganism is rigorously characterized and classified, it is assigned a name that
corresponds to the genus and species in which it is included.
Each isolated microorganism strain is defined by its genus
name followed by the species name and finally the code of
the isolated strain.
Identification is a set of procedures used to determine
whether an unknown microorganism belongs or not to a
taxonomic group already described. If it shows enough
differences with taxa of the same hierarchical level, it can
be described and named as a new taxon.
Classification and identification are dependent on data for
characterization of microorganisms. They are constantly
changing based on scientific advances in data acquisition
and characterization methods.
Nomenclature, by giving the correct names for taxa (classification) or unknown strains (identification), connects the
two approaches and, in the same way, is constantly evolving
to maintain coherence. A Nomenclatural Committee (“International Committee on Systematics of Prokaryotes” ICSP:
www.the-icsp.org/) was created to resolve conflicts, express
opinions, and standardize practices internationally. ICSP is
responsible for regularly updating the International Code of
Nomenclature of Bacteria,
2 which concerns Bacteria and
Archaea.
5.1.3.2 Different Schools of Classification
of Prokaryotes
Meanwhile, schools of classification and bacterial systematic were developed in the twentieth century. The French
school, at the Institut Pasteur, proposed a hierarchical classification taking into account not only the morphological and
physiological criteria but also criteria of pathogenicity. It
was essentially a classification of pathogenic bacteria with
dichotomous identification keys to quickly orient the diagnosis of species of pathogenic bacteria. This classification
led to the “Treaty of bacterial systematics of Pre ´vot” (Traite ´
de Syste ´matique bacte ´rienne de Pre ´vot), the name of the
French microbiologist who was the first to propose such a
classification in 1961. At the same time, a second classification was proposed by the Russian school of microbiology. It
took into account the environmental bacteria in a classification very close to the plant systematics.
Today, there is an international consensus based on the
classification of Bergey. It was proposed in 1923 by the
American microbiologist D. H. Bergey (1860–1937) who
was the coordinator of a committee of classification of bacteria set up under the authority of the American Society of
Microbiologists in 1917. This classification has been adopted
internationally for greater consistency with the systematic and
bacterial nomenclature. The committee (“Bergey’s trust”)
was subsequently extended to the international community
and consists today of microbial taxonomists from different
countries. It manages the classification and systematics of
prokaryotes and regularly provides an updated systematics
book based on new knowledge about prokaryotes. This is
the “Bergey’s Manual for Systematic Bacteriology”; the latest
edition (2002–2012) was used for the present work. In this
latest edition, each chapter written by one or several experts
contains the elements necessary for the identification of
prokaryotes. In this edition, many concepts used in molecular
biology from gene sequencing of 16S ribosomal RNA and
genomic studies were introduced in order to try to combine
the genotypic data with the phenotypic characteristics for
each species described. The main change in recent years has
been the need to change the taxa so as to be more consistent
with the phylogeny, which led to many large changes at all
taxonomic levels.
2 http://www.ncbi.nlm.nih.gov/books/bv.fcgi?call¼bv.View.
ShowTOC&rid¼icnb.TOC&depth¼2)
5 Systematic and Evolution of Microorganisms: General Concepts
113
and applied to the study of pathogenic bacteria and bacteria
from the environment has led to the definition of a set of
rules. Prokaryotic taxonomy has been based on a series of
morphological and increasingly of biochemical criteria in
the different editions of books of bacterial systematics.
Early taxonomic schemes were based on dichotomous
keys similar to those used for botanical books with a priority
given to radiative autotrophy (photosynthesis), the existence
of a thick wall capable of withholding a dye (Gram stain),
the presence of survival structures (“spores”), etc. Morphological criteria have later been supplemented by physiological criteria.
Besides characterization of microorganisms, classification, nomenclature, and identification are the three main
areas of systematics.
Classification is the science of ordering microorganism
groups (taxa) based on their interrelationships. The term
classification is used not only for the method but also for
the resulting system. Taxonomy is the study which 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. It helps to provide internationally
recognized microorganism names correctly and place them
in the classification as belonging to specific and defined
groups (taxa). These names are controlled and regulated by
international codes of nomenclature, whether for prokaryotic
(bacterial nomenclature) or eukaryotic (plant nomenclature,
which includes the “fungi,” and animal nomenclature which
includes the “protozoa”). When a microorganism is rigorously characterized and classified, it is assigned a name that
corresponds to the genus and species in which it is included.
Each isolated microorganism strain is defined by its genus
name followed by the species name and finally the code of
the isolated strain.
Identification is a set of procedures used to determine
whether an unknown microorganism belongs or not to a
taxonomic group already described. If it shows enough
differences with taxa of the same hierarchical level, it can
be described and named as a new taxon.
Classification and identification are dependent on data for
characterization of microorganisms. They are constantly
changing based on scientific advances in data acquisition
and characterization methods.
Nomenclature, by giving the correct names for taxa (classification) or unknown strains (identification), connects the
two approaches and, in the same way, is constantly evolving
to maintain coherence. A Nomenclatural Committee (“International Committee on Systematics of Prokaryotes” ICSP:
www.the-icsp.org/) was created to resolve conflicts, express
opinions, and standardize practices internationally. ICSP is
responsible for regularly updating the International Code of
Nomenclature of Bacteria,
2 which concerns Bacteria and
Archaea.
5.1.3.2 Different Schools of Classification
of Prokaryotes
Meanwhile, schools of classification and bacterial systematic were developed in the twentieth century. The French
school, at the Institut Pasteur, proposed a hierarchical classification taking into account not only the morphological and
physiological criteria but also criteria of pathogenicity. It
was essentially a classification of pathogenic bacteria with
dichotomous identification keys to quickly orient the diagnosis of species of pathogenic bacteria. This classification
led to the “Treaty of bacterial systematics of Pre ´vot” (Traite ´
de Syste ´matique bacte ´rienne de Pre ´vot), the name of the
French microbiologist who was the first to propose such a
classification in 1961. At the same time, a second classification was proposed by the Russian school of microbiology. It
took into account the environmental bacteria in a classification very close to the plant systematics.
Today, there is an international consensus based on the
classification of Bergey. It was proposed in 1923 by the
American microbiologist D. H. Bergey (1860–1937) who
was the coordinator of a committee of classification of bacteria set up under the authority of the American Society of
Microbiologists in 1917. This classification has been adopted
internationally for greater consistency with the systematic and
bacterial nomenclature. The committee (“Bergey’s trust”)
was subsequently extended to the international community
and consists today of microbial taxonomists from different
countries. It manages the classification and systematics of
prokaryotes and regularly provides an updated systematics
book based on new knowledge about prokaryotes. This is
the “Bergey’s Manual for Systematic Bacteriology”; the latest
edition (2002–2012) was used for the present work. In this
latest edition, each chapter written by one or several experts
contains the elements necessary for the identification of
prokaryotes. In this edition, many concepts used in molecular
biology from gene sequencing of 16S ribosomal RNA and
genomic studies were introduced in order to try to combine
the genotypic data with the phenotypic characteristics for
each species described. The main change in recent years has
been the need to change the taxa so as to be more consistent
with the phylogeny, which led to many large changes at all
taxonomic levels.
2 http://www.ncbi.nlm.nih.gov/books/bv.fcgi?call¼bv.View.
ShowTOC&rid¼icnb.TOC&depth¼2)
5 Systematic and Evolution of Microorganisms: General Concepts
113