associated with bacteriochlorophylls. In fact this phylum
gathers a large number of lineages related to these photosynthetic pigments (hence, the purple pigmentation characteristic). Similarly, the so-called Gram-positive bacteria (testing
positive for Gram stain) form two distinct bacterial phyla (i.
e., the Firmicutes and Actinobacteria); this indicates that
they are not specifically related to each other. In fact, only
two phyla, the Spirochetes and the Cyanobacteria, were
found to have been properly defined on the basis of phenotypic traits, meaning a spiral shape and the ability to achieve
an oxygenic photosynthesis, respectively. This was a disappointment for those who believed that the use of molecular
markers would allow discerning evolutionary traits
associated with each phylum, which is not the case. An
analogy can be made between the major phylogenetic groups
and neighborhoods within large cities; knowing the large
group to which a given microorganism belongs does not
reveal much of its physiology and its characteristics, rather
it may give some indications. An analogy can be made with
the fact of belonging to a city neighborhood: it tells little
about the personal characteristics of individuals who live
there, and at most, it indicates membership in the area.
This underlies the great plasticity of phenotypic and physiological features within high taxonomic groups.
In 1990, Woese and collaborators (1990) proposed a
definition of each of the three domains of life:
1. The Eucarya from the Greek adjective “eu” meaning true
and the Greek name “Karyon” signifying kernel include
organisms with cells carrying genetic information in linear chromosomes enveloped by a nuclear membrane
(core), containing eukaryotic-type ribosomes, and
surrounded by a phospholipid bilayer (cf. Sect. 3.1.2)
that consists of a glycerol core attached to two fatty acid
molecules by ester bonds.
2. The Bacteria (from the Greek name “bakterios” meaning
stick) denote cells with an prokaryotic-type organization
(pro “Karyon” that does not have a true nucleus)
surrounded by a phospholipids bilayer (cf. Sect. 3.1.1),
consisting of a glycerol molecule attached to two
molecules of fatty acid by ester bonds and which contain
bacterial-type ribosomes.
3. The Archaea from the Greek adjective “arkeos” meaning
ancient, primitive, group cells with archaeal-type ribosomes,
having a prokaryotic-type organization, and surrounded by
either a phospholipid bilayer mainly made of phospholipids
consisting of a glycerol molecule attached to two molecules
of isoprenoid by ether bonds or a phospholipid monolayer
consisting of two glycerol molecules connected together by
two isoprenoid chains (cf. Sect. 4.1.10, Fig. 4.5).
6.6.1 Domain Archaea
6.6.1.1 The Discovery of Archaea
The domain Archaea has been revealed by Carl R. Woese
and George E. Fox who analyzed the oligonucleotide
profiles derived from the digestion of the RNA component
of small ribosomal subunits (16S for prokaryotes/18S for
eukaryotes) (Woese 2007). Briefly, the 16S (or 18S) rRNAs
of each organism are extracted and digested with different
restriction enzymes (including the RNase T1). Digestion
products are then subjected to bidirectional electrophoresis
to build migration profiles (also called oligonucleotide
catalogs) specific to each organism. The pairwise comparison of these catalogs (via Sokal and Michener index calculation) allows quantifying the similarities between rRNA
profiles and thus studying and classifying the corresponding
organisms. In their seminal study, Woese and Fox analyzed
the rRNAs from the cytoplasm of various eukaryotes and
prokaryotes (including methanogens), mitochondria and
chloroplast. The results were surprising. As expected, the
eukaryotes and prokaryotes rRNA sequences appeared very
different from each other. However, a similar difference was
observed between the prokaryotic 16S rRNA sequences,
which form two distinct and distantly related groups. This
means that at the genetic level, 16S rRNA sequences from
two prokaryotes displaying strong phenotypic similarities
can be more different than the 18S rRNA sequences from
Homo sapiens and a plant or even than the 18S rRNA from
Homo sapiens and the 16S rRNA from E. coli. These results
have profoundly changed our view of the living world, by
shifting from a eukaryote/prokaryote dichotomy to a tripartite divide. This divide was rapidly confirmed by subsequent
phylogenetic analyses. At that time, the first group of
prokaryotes gathered a wide variety of bacteria, while the
second corresponded to methanogenic bacteria (i.e., carrying
out the biosynthesis of methane). The former was named
Eubacteria (eu ¼ true) and the latter Archaebacteria
(archaea ¼ old) by Carl Woese. The name Archaebacteria
reflects the widespread belief at the time that
methanogenesis could have been one of the earliest
metabolisms on Earth. Accordingly, present-day
methanogens (and thus Archaebacteria) would have
conserved this ancestral metabolism. Contradicting this
hypothesis, Archaebacteria were rapidly enriched with new
members, most of them being non-methanogens: the
thermoacidophilic Thermoplasma that were formerly classified with Mycoplasma because like the latter they are devoid
of cell wall; the Halobacteria which are extreme halophiles;
the Sulfolobales, another group of thermoacidophiles; and
6 Taxonomy and Phylogeny of Prokaryotes
161
gathers a large number of lineages related to these photosynthetic pigments (hence, the purple pigmentation characteristic). Similarly, the so-called Gram-positive bacteria (testing
positive for Gram stain) form two distinct bacterial phyla (i.
e., the Firmicutes and Actinobacteria); this indicates that
they are not specifically related to each other. In fact, only
two phyla, the Spirochetes and the Cyanobacteria, were
found to have been properly defined on the basis of phenotypic traits, meaning a spiral shape and the ability to achieve
an oxygenic photosynthesis, respectively. This was a disappointment for those who believed that the use of molecular
markers would allow discerning evolutionary traits
associated with each phylum, which is not the case. An
analogy can be made between the major phylogenetic groups
and neighborhoods within large cities; knowing the large
group to which a given microorganism belongs does not
reveal much of its physiology and its characteristics, rather
it may give some indications. An analogy can be made with
the fact of belonging to a city neighborhood: it tells little
about the personal characteristics of individuals who live
there, and at most, it indicates membership in the area.
This underlies the great plasticity of phenotypic and physiological features within high taxonomic groups.
In 1990, Woese and collaborators (1990) proposed a
definition of each of the three domains of life:
1. The Eucarya from the Greek adjective “eu” meaning true
and the Greek name “Karyon” signifying kernel include
organisms with cells carrying genetic information in linear chromosomes enveloped by a nuclear membrane
(core), containing eukaryotic-type ribosomes, and
surrounded by a phospholipid bilayer (cf. Sect. 3.1.2)
that consists of a glycerol core attached to two fatty acid
molecules by ester bonds.
2. The Bacteria (from the Greek name “bakterios” meaning
stick) denote cells with an prokaryotic-type organization
(pro “Karyon” that does not have a true nucleus)
surrounded by a phospholipids bilayer (cf. Sect. 3.1.1),
consisting of a glycerol molecule attached to two
molecules of fatty acid by ester bonds and which contain
bacterial-type ribosomes.
3. The Archaea from the Greek adjective “arkeos” meaning
ancient, primitive, group cells with archaeal-type ribosomes,
having a prokaryotic-type organization, and surrounded by
either a phospholipid bilayer mainly made of phospholipids
consisting of a glycerol molecule attached to two molecules
of isoprenoid by ether bonds or a phospholipid monolayer
consisting of two glycerol molecules connected together by
two isoprenoid chains (cf. Sect. 4.1.10, Fig. 4.5).
6.6.1 Domain Archaea
6.6.1.1 The Discovery of Archaea
The domain Archaea has been revealed by Carl R. Woese
and George E. Fox who analyzed the oligonucleotide
profiles derived from the digestion of the RNA component
of small ribosomal subunits (16S for prokaryotes/18S for
eukaryotes) (Woese 2007). Briefly, the 16S (or 18S) rRNAs
of each organism are extracted and digested with different
restriction enzymes (including the RNase T1). Digestion
products are then subjected to bidirectional electrophoresis
to build migration profiles (also called oligonucleotide
catalogs) specific to each organism. The pairwise comparison of these catalogs (via Sokal and Michener index calculation) allows quantifying the similarities between rRNA
profiles and thus studying and classifying the corresponding
organisms. In their seminal study, Woese and Fox analyzed
the rRNAs from the cytoplasm of various eukaryotes and
prokaryotes (including methanogens), mitochondria and
chloroplast. The results were surprising. As expected, the
eukaryotes and prokaryotes rRNA sequences appeared very
different from each other. However, a similar difference was
observed between the prokaryotic 16S rRNA sequences,
which form two distinct and distantly related groups. This
means that at the genetic level, 16S rRNA sequences from
two prokaryotes displaying strong phenotypic similarities
can be more different than the 18S rRNA sequences from
Homo sapiens and a plant or even than the 18S rRNA from
Homo sapiens and the 16S rRNA from E. coli. These results
have profoundly changed our view of the living world, by
shifting from a eukaryote/prokaryote dichotomy to a tripartite divide. This divide was rapidly confirmed by subsequent
phylogenetic analyses. At that time, the first group of
prokaryotes gathered a wide variety of bacteria, while the
second corresponded to methanogenic bacteria (i.e., carrying
out the biosynthesis of methane). The former was named
Eubacteria (eu ¼ true) and the latter Archaebacteria
(archaea ¼ old) by Carl Woese. The name Archaebacteria
reflects the widespread belief at the time that
methanogenesis could have been one of the earliest
metabolisms on Earth. Accordingly, present-day
methanogens (and thus Archaebacteria) would have
conserved this ancestral metabolism. Contradicting this
hypothesis, Archaebacteria were rapidly enriched with new
members, most of them being non-methanogens: the
thermoacidophilic Thermoplasma that were formerly classified with Mycoplasma because like the latter they are devoid
of cell wall; the Halobacteria which are extreme halophiles;
the Sulfolobales, another group of thermoacidophiles; and
6 Taxonomy and Phylogeny of Prokaryotes
161