many functional and morphological characteristics. This
definition of species based on the “interfertility” criterion,
which aims to be universal, is not applicable to prokaryotes
because they reproduce by clonal reproduction*. However,
the species is considered as the basic unit of biological
diversity, and its definition should be unambiguous and
strong. In relation to this, the systematic of prokaryotes
faces several problems such as the definition of an individual* and the definition of a species without being able to rely
on the criterion of interfertility.
For years, the species concept in prokaryotes was based
on morphological and physiological criteria (morphologic
and physiologic are very seldom used) that have proven not
to be really effective. Today molecular biology provides
new tools to strengthen the concept of species replacing
interfertility criteria and proposing quantitative criteria
(Box 6.1). Thus, strains of prokaryotes for which hybridization of genomic DNA considered pairwise reaches 70 %
are considered as belonging to the same species (Wayne
et al. 1987). Other taxonomic levels are left to the discretion
of the researchers and the consideration of a set of rules
(priority, uniqueness, consistency, etc.). However, it is
important to remember that the goal of this approach is to
provide a solid framework in which the defined taxa*,
must be, inasmuch as possible, “natural” and “consistent”
(i.e., reflecting relationships between microorganisms),
which is not always possible. Also, Stackebrandt and Goebel
(1994) have suggested an equivalence between the classical
definition of a species based on the labor-intensive and
delicate genomic hybridization* technique and an identification technique most commonly used in recent years. This
approach is based on the comparison of genes encoding
RNA of the small subunit of the ribosome (16S rRNA). By
this method, which is being reevaluated (Stackebrandt and
Ebers 2006), two strains are considered as not belonging to
the same species if their 16S rRNA sequences have a similarity below a threshold currently set at 97 %.
Box 6.1: The Species Concept Paradox
Xavier Nesme
Species and speciation are constant topics of discussion
in biology. In prokaryotes, this issue is particularly
crucial at the time of metagenomics, which generates
large volumes of nucleotide sequences from a variety of
X. Nesme
Laboratoire d’e ´cologie microbienne, UMR 5557 Universite ´
Claude Bernard Lyon 1, Villeurbanne Cedex, France
(continued)
Box 6.1 (continued)
strains, species, genera, etc., that should be classified
and ranked automatically with maximum biological
sense. However, the bacterial species is paradoxically
both well definable and lacking a consensual concept
that would highlight the causes and biological
consequences that this definition covers.
Bacterial Species Versus Eukaryotic Species
The bacterial species is defined simply on a technical
basis by measuring the reassociation rate (“relative
binding ratio” or RBR) of the genomic DNA of pairs
of bacterial strains. For its part, the species in
eukaryotes has benefited from profound reflections
that led to the biological species concept (“biological
species concept” or BSC), which highlights the role of
the sexual isolation of species with, as a result, the
containment of gene flow and therefore of genetic
innovations to a given species.
The genomic definition of bacterial species (Wayne
et al. 1987) is as follows:
“The bacterial species includes strains with both a
relative DNA reassociation % superior to 70 % and
5
C or less ΔTm; the two must be considered.”
The biological species concept (BSC) in eukaryotes
(Mayr 1942) is as follows:
“Species are groups of actually or potentially
interbreeding populations, which are reproductively
isolated from other such groups.”
A simply operational definition of the species in
bacteria corresponds to a biological species concept in
eukaryotes: Are they the same thing? Can a biological
concept be associated to the definition of bacterial
species?
The genomic basis of the definition of a bacterial
species was confirmed in 2002 by the International
Committee of the definition of bacterial species,
because since its publication in 1987, this definition
proved operational in most lineages of prokaryotes
(Stackebrandt et al. 2002). This definition, based on a
rigorous physical measurement, has greatly reduced
taxonomists’ strifes about what should or not be
grouped in the same species. This is unfortunately
not the case for other taxonomic levels, especially
the genus that do not currently have a definition as
consensual, with as consequences technical and regulatory debates where purely scientific arguments are
sometimes rare to find.
However, the same committee requested that alternative methods to RBR be proposed to define the
(continued)
146
P. Caumette et al.
definition of species based on the “interfertility” criterion,
which aims to be universal, is not applicable to prokaryotes
because they reproduce by clonal reproduction*. However,
the species is considered as the basic unit of biological
diversity, and its definition should be unambiguous and
strong. In relation to this, the systematic of prokaryotes
faces several problems such as the definition of an individual* and the definition of a species without being able to rely
on the criterion of interfertility.
For years, the species concept in prokaryotes was based
on morphological and physiological criteria (morphologic
and physiologic are very seldom used) that have proven not
to be really effective. Today molecular biology provides
new tools to strengthen the concept of species replacing
interfertility criteria and proposing quantitative criteria
(Box 6.1). Thus, strains of prokaryotes for which hybridization of genomic DNA considered pairwise reaches 70 %
are considered as belonging to the same species (Wayne
et al. 1987). Other taxonomic levels are left to the discretion
of the researchers and the consideration of a set of rules
(priority, uniqueness, consistency, etc.). However, it is
important to remember that the goal of this approach is to
provide a solid framework in which the defined taxa*,
must be, inasmuch as possible, “natural” and “consistent”
(i.e., reflecting relationships between microorganisms),
which is not always possible. Also, Stackebrandt and Goebel
(1994) have suggested an equivalence between the classical
definition of a species based on the labor-intensive and
delicate genomic hybridization* technique and an identification technique most commonly used in recent years. This
approach is based on the comparison of genes encoding
RNA of the small subunit of the ribosome (16S rRNA). By
this method, which is being reevaluated (Stackebrandt and
Ebers 2006), two strains are considered as not belonging to
the same species if their 16S rRNA sequences have a similarity below a threshold currently set at 97 %.
Box 6.1: The Species Concept Paradox
Xavier Nesme
Species and speciation are constant topics of discussion
in biology. In prokaryotes, this issue is particularly
crucial at the time of metagenomics, which generates
large volumes of nucleotide sequences from a variety of
X. Nesme
Laboratoire d’e ´cologie microbienne, UMR 5557 Universite ´
Claude Bernard Lyon 1, Villeurbanne Cedex, France
(continued)
Box 6.1 (continued)
strains, species, genera, etc., that should be classified
and ranked automatically with maximum biological
sense. However, the bacterial species is paradoxically
both well definable and lacking a consensual concept
that would highlight the causes and biological
consequences that this definition covers.
Bacterial Species Versus Eukaryotic Species
The bacterial species is defined simply on a technical
basis by measuring the reassociation rate (“relative
binding ratio” or RBR) of the genomic DNA of pairs
of bacterial strains. For its part, the species in
eukaryotes has benefited from profound reflections
that led to the biological species concept (“biological
species concept” or BSC), which highlights the role of
the sexual isolation of species with, as a result, the
containment of gene flow and therefore of genetic
innovations to a given species.
The genomic definition of bacterial species (Wayne
et al. 1987) is as follows:
“The bacterial species includes strains with both a
relative DNA reassociation % superior to 70 % and
5
C or less ΔTm; the two must be considered.”
The biological species concept (BSC) in eukaryotes
(Mayr 1942) is as follows:
“Species are groups of actually or potentially
interbreeding populations, which are reproductively
isolated from other such groups.”
A simply operational definition of the species in
bacteria corresponds to a biological species concept in
eukaryotes: Are they the same thing? Can a biological
concept be associated to the definition of bacterial
species?
The genomic basis of the definition of a bacterial
species was confirmed in 2002 by the International
Committee of the definition of bacterial species,
because since its publication in 1987, this definition
proved operational in most lineages of prokaryotes
(Stackebrandt et al. 2002). This definition, based on a
rigorous physical measurement, has greatly reduced
taxonomists’ strifes about what should or not be
grouped in the same species. This is unfortunately
not the case for other taxonomic levels, especially
the genus that do not currently have a definition as
consensual, with as consequences technical and regulatory debates where purely scientific arguments are
sometimes rare to find.
However, the same committee requested that alternative methods to RBR be proposed to define the
(continued)
146
P. Caumette et al.