resistant to gamma irradiation of about 5,000 Gy, doses sufficient to eliminate most other microorganisms. The radiation
resistance of Deinococcus could be linked to the presence of a
mechanism specific (and very effective) for DNA repair (Cox
and Battista 2005). These bacteria have a special envelope
with a thick Gram-positive wall and in addition, an outer
membrane, and an outer layer of S protein.
The Thermales, with one family, Thermaceae, combine
several genera including genus Thermus isolated from hot
springs (70–90
C) which gave the thermostable DNA
polymerase used for PCR, an enzyme that represents an
annual market of 300 million dollars. This genus comprises
bacteria in short filaments or rods, hyperthermophilic,
chemoorganotrophic, and aerobic, with certain strains that
are capable of using nitrate as electron acceptor under anaerobic conditions. The members of this phylum contain ornithine in their cell wall.
The Phylum Chloroflexi
This phylum contains Gram-negative photosynthetic
anoxygenic bacteria (also called phototrophic green
nonsulfur bacteria) formed of multicellular filaments living
in microbial mats or in the water in hot environments anoxic
and exposed to light, often in hot springs. Class Chloroflexi
with order Chloroflexales contains Chloroflexaceae families
(genera Chloroflexus, Chloronema) and Oscillochloridaceae
(genus Oscillochloris). This class includes bacteria which
contain bacteriochlorophyll c and carotenoids present in
structures attached to the cytoplasmic membrane, the
chlorosomes (cf. Sect. 3.3.4, Fig. 3.27), and the genus
Heliothrix that contains bacteriochlorophyll a with no apparent membrane structures. These bacteria perform
anoxygenic photosynthesis and use organic compounds in
photoorganotrophic metabolism, and they can fix CO 2 by
the pathway called hydroxypropionate cycle (cf. Sect. 3.4.1,
Fig. 3.34). In this class, there are also many nonphotosynthetic species grouped in order Herpetosiphonales.
Classes of Anaerolineae (Anaerolinea) and Caldilineae
(Caldilinea) include many genera and species of filamentous
bacteria isolated from anaerobic fermenters. Other nonphotosynthetic bacteria are also present in this group and
have been detected so far by genetic analysis. These bacteria
are in the majority inhabitants of environments contaminated
by organic pollutants and metal, whether in soils or aquatic
environments.
The Phylum Nitrospirae
With a single order (Nitrospirales) and one family
(Nitrospiraceae), this phylum includes bacteria belonging
to genera quite different, consisting of spiral or curved
rods, Gram-negative. These microorganisms are aerobic
chemolithotrophic nitrifiers (Nitrospira), iron-oxidizers
(Leptospirillum), anaerobic chemoorganotrophic sulfate
reducers, and thermophilic microbes (Thermodesulfovibrio) or
microbes with magnetic iron inclusions (“Magnetobacterium”
Fig. 14.46), mostly isolated from terrestrial and marine aquatic
environments.
6.6.2.2 The Phylum B 10 Synergistetes
This phylum is Gram-negative, anaerobic, chemo- and fermentative organotrophic isolated from animals (rumen,
genus Synergists) or man (genus Jonquetella). These bacteria are involved in anaerobic digestion operation in the
rumen of animals and the human intestinal flora.
6.6.2.3 The Phylum Cyanobacteria B11
(Figs. 6.12 and 6.13)
This phylum consists of Gram-negative bacteria, performing
oxygenic photosynthesis with photosystems I and II inserted
in membrane systems (thylakoids) and producing oxygen
(cf. Sect. 3.3.4, Fig. 3.28). This bacterial group would be
considered as the ancestors of chloroplasts (cf. Sects. 3.3.4,
4.3.1, and 5.4.3). They form a group of bacteria of varied
forms ranging from unicellular to multicellular filamentous
and colonial types (Figs. 6.12 and 6.13). They contain chlorophyll, carotenoids, and phycobilins or biliproteins, giving
them a dark blue-green pigmentation. Some cyanobacteria
have the divinyl chlorophyll. They are present in surface
waters as well as all kinds of wet surfaces exposed to light
where their photosynthetic capacity gives them a competitive advantage. Many kinds of cyanobacteria fixing
dinitrogen, including filamentous genera Anabaena and Nostoc and a proportion of them lives in symbiosis with Fungi
(lichens) or with Viridiplantae (Cycas, Azolla). Some species of cyanobacteria in algal blooms can produce
enterotoxic, hepatotoxic, or neurotoxic cyanotoxins that
cause poisoning, which are sometimes fatal like microcystin
in Microcystis spp. (Box 15.2). Cyanobacteria use the Calvin
cycle for CO 2 fixation. For many years, cyanobacteria have
been considered algae (hence the name blue-green algae)
due to their ability to perform oxygenic photosynthesis.
Their phylogenetic positioning has allowed classifying
them as members of the domain Bacteria where they form
a major phylum organized into five subsections. Classification within cyanobacteria is problematic because of their
membership to the bacterial and botanical systematic
codes. Numerous discussions between botanists and
bacteriologists are still underway to harmonize the classification of cyanobacteria in both systematic codes.
Subsection 1 (Chroococcales): it relates unicellular
cyanobacteria that can form clusters of cells such as
Microcystis, Synechococcus, Cyanobium, Cyanothece,
and Gloeothece.
Subsection 2 (Pleurocapsales): it includes cyanobacteria
forming colonial structures and small spherical structures
6 Taxonomy and Phylogeny of Prokaryotes
177
resistance of Deinococcus could be linked to the presence of a
mechanism specific (and very effective) for DNA repair (Cox
and Battista 2005). These bacteria have a special envelope
with a thick Gram-positive wall and in addition, an outer
membrane, and an outer layer of S protein.
The Thermales, with one family, Thermaceae, combine
several genera including genus Thermus isolated from hot
springs (70–90
C) which gave the thermostable DNA
polymerase used for PCR, an enzyme that represents an
annual market of 300 million dollars. This genus comprises
bacteria in short filaments or rods, hyperthermophilic,
chemoorganotrophic, and aerobic, with certain strains that
are capable of using nitrate as electron acceptor under anaerobic conditions. The members of this phylum contain ornithine in their cell wall.
The Phylum Chloroflexi
This phylum contains Gram-negative photosynthetic
anoxygenic bacteria (also called phototrophic green
nonsulfur bacteria) formed of multicellular filaments living
in microbial mats or in the water in hot environments anoxic
and exposed to light, often in hot springs. Class Chloroflexi
with order Chloroflexales contains Chloroflexaceae families
(genera Chloroflexus, Chloronema) and Oscillochloridaceae
(genus Oscillochloris). This class includes bacteria which
contain bacteriochlorophyll c and carotenoids present in
structures attached to the cytoplasmic membrane, the
chlorosomes (cf. Sect. 3.3.4, Fig. 3.27), and the genus
Heliothrix that contains bacteriochlorophyll a with no apparent membrane structures. These bacteria perform
anoxygenic photosynthesis and use organic compounds in
photoorganotrophic metabolism, and they can fix CO 2 by
the pathway called hydroxypropionate cycle (cf. Sect. 3.4.1,
Fig. 3.34). In this class, there are also many nonphotosynthetic species grouped in order Herpetosiphonales.
Classes of Anaerolineae (Anaerolinea) and Caldilineae
(Caldilinea) include many genera and species of filamentous
bacteria isolated from anaerobic fermenters. Other nonphotosynthetic bacteria are also present in this group and
have been detected so far by genetic analysis. These bacteria
are in the majority inhabitants of environments contaminated
by organic pollutants and metal, whether in soils or aquatic
environments.
The Phylum Nitrospirae
With a single order (Nitrospirales) and one family
(Nitrospiraceae), this phylum includes bacteria belonging
to genera quite different, consisting of spiral or curved
rods, Gram-negative. These microorganisms are aerobic
chemolithotrophic nitrifiers (Nitrospira), iron-oxidizers
(Leptospirillum), anaerobic chemoorganotrophic sulfate
reducers, and thermophilic microbes (Thermodesulfovibrio) or
microbes with magnetic iron inclusions (“Magnetobacterium”
Fig. 14.46), mostly isolated from terrestrial and marine aquatic
environments.
6.6.2.2 The Phylum B 10 Synergistetes
This phylum is Gram-negative, anaerobic, chemo- and fermentative organotrophic isolated from animals (rumen,
genus Synergists) or man (genus Jonquetella). These bacteria are involved in anaerobic digestion operation in the
rumen of animals and the human intestinal flora.
6.6.2.3 The Phylum Cyanobacteria B11
(Figs. 6.12 and 6.13)
This phylum consists of Gram-negative bacteria, performing
oxygenic photosynthesis with photosystems I and II inserted
in membrane systems (thylakoids) and producing oxygen
(cf. Sect. 3.3.4, Fig. 3.28). This bacterial group would be
considered as the ancestors of chloroplasts (cf. Sects. 3.3.4,
4.3.1, and 5.4.3). They form a group of bacteria of varied
forms ranging from unicellular to multicellular filamentous
and colonial types (Figs. 6.12 and 6.13). They contain chlorophyll, carotenoids, and phycobilins or biliproteins, giving
them a dark blue-green pigmentation. Some cyanobacteria
have the divinyl chlorophyll. They are present in surface
waters as well as all kinds of wet surfaces exposed to light
where their photosynthetic capacity gives them a competitive advantage. Many kinds of cyanobacteria fixing
dinitrogen, including filamentous genera Anabaena and Nostoc and a proportion of them lives in symbiosis with Fungi
(lichens) or with Viridiplantae (Cycas, Azolla). Some species of cyanobacteria in algal blooms can produce
enterotoxic, hepatotoxic, or neurotoxic cyanotoxins that
cause poisoning, which are sometimes fatal like microcystin
in Microcystis spp. (Box 15.2). Cyanobacteria use the Calvin
cycle for CO 2 fixation. For many years, cyanobacteria have
been considered algae (hence the name blue-green algae)
due to their ability to perform oxygenic photosynthesis.
Their phylogenetic positioning has allowed classifying
them as members of the domain Bacteria where they form
a major phylum organized into five subsections. Classification within cyanobacteria is problematic because of their
membership to the bacterial and botanical systematic
codes. Numerous discussions between botanists and
bacteriologists are still underway to harmonize the classification of cyanobacteria in both systematic codes.
Subsection 1 (Chroococcales): it relates unicellular
cyanobacteria that can form clusters of cells such as
Microcystis, Synechococcus, Cyanobium, Cyanothece,
and Gloeothece.
Subsection 2 (Pleurocapsales): it includes cyanobacteria
forming colonial structures and small spherical structures
6 Taxonomy and Phylogeny of Prokaryotes
177