evolutionary point of view, it would be close to the
Chlorobi phylum.
The Phylum Chlorobi
Class Chlorobia contains one order (Chlorobiales) and a
single family (Chlorobiaceae) with several genera
(Chlorobium, Chloroherpeton, Pelodyction, etc.). This phylum corresponds to anoxygenic phototrophic green sulfuroxidizing bacteria, containing bacteriochlorophyll c, d, or
e in chlorosomes, structures attached to the inner layer of the
cytoplasmic membrane. These bacteria use sulfur
compounds as electron donors during anoxygenic photosynthesis (cf. Sect. 3.3.4, Fig. 3.29). From an evolutionary point
of view, it would be close to the phylum Bacteroidetes.
6.6.2.5 The Major Phyla of Gram-Positive Bacteria
The Phylum Acidobacteria
It is composed of chemoorganotrophic bacteria commonly
found in soils and sediments but of which very few
representatives have been grown. Besides order Acidobacteriales represented by a family (Acidobacteriaceae), it
contains, in addition to the genus Acidobacterium which
corresponds to one of many taxa revealed as a result of direct
in situ sequencing programs from soils, homoacetogenic bacteria (Holophaga), and iron-reducing bacteria (Geothrix).
The Phylum Chlamydiae
It contains chemoorganotrophic bacteria, obligatory intracellular parasites, and pathogens; it is constituted by one order
(the Chlamydiales) containing four families: Chlamydiaceae
(Chlamydia) responsible for lungs or urogenital infections,
Parachlamydiaceae
(Parachlamydia),
Simkaniaceae
(Simkania), and Waddliaceae (Waddlia). It is close to the
phyla Planctomycetes and Verrucomicrobia [super phylum
PVC (Planctomycetes/Verrucomicrobia/Chlamydiae)].
The Phylum Planctomycetes
This phylum, close to Chlamydiae and Verrucomicrobia
(super phylum PVC), is formed by budding bacteria, unicellular or filamentous devoid of peptidoglycan, which was
initially classified with Fungi. With the order
Planctomycetales and one family Planctomycetaceae
(Planctomyces, Gemmata, Pirellula, etc.), it consists of specific bacteria with internal membranes that keep DNA
isolated from the cytoplasm. From the representatives of
this family, the anaerobic oxidation of ammonia reaction
(Anammox) was discovered, a reaction that takes place in
a special membrane compartment (anammoxosome,
Figs. 14.32 and 14.33).
The Phylum Verrucomicrobia
It includes two classes, Verrumicrobiae and Opitutae. The
first class, with order Verrucomicrobiales and family
Verrucomicrobiaceae (Verrucomicrobium), consists of
unusual bacteria abundant in soil microbial communities
but of which very few representatives have been isolated.
The second class, with two orders, Opitutales and
Puniceicoccales, includes Gram-negative chemoorganotrophic cocci, aerobic or fermentative, isolated from
marine environments, hot springs, or paddy fields. This
phylum would be close to phyla Planctomycetes and
Chlamydiae (constituting together the PVC super phylum).
The Phylum Spirochaetes
It contains bacteria with a particular cell morphology: where
cells are long, flexuous, and much spiraled. They are all
motile by means of an axial filament. These are aerobic or
anaerobic inhabitants of soils and aquatic environments. The
spirochaetes are grouped in a single order, Spirochaetales,
divided into three families. The family Spirochaetaceae
contains pathogenic bacteria such as the well-known Treponema pallidum (agent of syphilis), Borrelia (relapsing agents
transmitted by vectors such as ticks or lice and responsible
for Lyme disease, relapsing fever or hemorrhagic fevers in
animals and men), and many spirochetes (Spirochaeta,
Cristispira) living under aerobic or anaerobic conditions in
soils or aquatic sediments (Fig. 6.10f). Serpulinaceae family
with genus Serpulina and the family Leptospiraceae with
Leptospira consist of strict aerobic bacteria, the two families
containing parasitic agents, pathogens of the oral cavity or
causing kidney disease, and intestinal or liver infections in
animals and man.
The Phylum Fibrobacteres
This phylum consists of one order, Fibrobacterales with the
family
Fibrobacteraceae
containing
one
genus
(Fibrobacter) corresponding to anaerobic chemoorganotrophic fermentative bacteria, some of which live in the
digestive tract of animals and can degrade cellulose.
The Phylum Fusobacteria
Composed of one order, Fusobacteriales, with one family,
Fusobacteriaceae, the phylum Fusobacteria contains obligate
anaerobic bacteria commonly found in the oral cavity and in
the intestines of animals, such as the genera Fusobacterium,
Leptotrichia, and Streptobacillus, some of which are exclusively responsible for ENT infections and angina.
The Phylum Gemmatimonadetes
It includes a single order, Gemmatimonadales, with one family and one genus (Gemmatimonadaceae: Gemmatimonas) in
which one species was isolated from a laboratory reactor,
Gemmatimonas aurantiaca. It is a Gram-negative, motile,
aerobic, and chemoorganotrophic bacterium that can divide
by binary fission or budding.
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P. Caumette et al.
Chlorobi phylum.
The Phylum Chlorobi
Class Chlorobia contains one order (Chlorobiales) and a
single family (Chlorobiaceae) with several genera
(Chlorobium, Chloroherpeton, Pelodyction, etc.). This phylum corresponds to anoxygenic phototrophic green sulfuroxidizing bacteria, containing bacteriochlorophyll c, d, or
e in chlorosomes, structures attached to the inner layer of the
cytoplasmic membrane. These bacteria use sulfur
compounds as electron donors during anoxygenic photosynthesis (cf. Sect. 3.3.4, Fig. 3.29). From an evolutionary point
of view, it would be close to the phylum Bacteroidetes.
6.6.2.5 The Major Phyla of Gram-Positive Bacteria
The Phylum Acidobacteria
It is composed of chemoorganotrophic bacteria commonly
found in soils and sediments but of which very few
representatives have been grown. Besides order Acidobacteriales represented by a family (Acidobacteriaceae), it
contains, in addition to the genus Acidobacterium which
corresponds to one of many taxa revealed as a result of direct
in situ sequencing programs from soils, homoacetogenic bacteria (Holophaga), and iron-reducing bacteria (Geothrix).
The Phylum Chlamydiae
It contains chemoorganotrophic bacteria, obligatory intracellular parasites, and pathogens; it is constituted by one order
(the Chlamydiales) containing four families: Chlamydiaceae
(Chlamydia) responsible for lungs or urogenital infections,
Parachlamydiaceae
(Parachlamydia),
Simkaniaceae
(Simkania), and Waddliaceae (Waddlia). It is close to the
phyla Planctomycetes and Verrucomicrobia [super phylum
PVC (Planctomycetes/Verrucomicrobia/Chlamydiae)].
The Phylum Planctomycetes
This phylum, close to Chlamydiae and Verrucomicrobia
(super phylum PVC), is formed by budding bacteria, unicellular or filamentous devoid of peptidoglycan, which was
initially classified with Fungi. With the order
Planctomycetales and one family Planctomycetaceae
(Planctomyces, Gemmata, Pirellula, etc.), it consists of specific bacteria with internal membranes that keep DNA
isolated from the cytoplasm. From the representatives of
this family, the anaerobic oxidation of ammonia reaction
(Anammox) was discovered, a reaction that takes place in
a special membrane compartment (anammoxosome,
Figs. 14.32 and 14.33).
The Phylum Verrucomicrobia
It includes two classes, Verrumicrobiae and Opitutae. The
first class, with order Verrucomicrobiales and family
Verrucomicrobiaceae (Verrucomicrobium), consists of
unusual bacteria abundant in soil microbial communities
but of which very few representatives have been isolated.
The second class, with two orders, Opitutales and
Puniceicoccales, includes Gram-negative chemoorganotrophic cocci, aerobic or fermentative, isolated from
marine environments, hot springs, or paddy fields. This
phylum would be close to phyla Planctomycetes and
Chlamydiae (constituting together the PVC super phylum).
The Phylum Spirochaetes
It contains bacteria with a particular cell morphology: where
cells are long, flexuous, and much spiraled. They are all
motile by means of an axial filament. These are aerobic or
anaerobic inhabitants of soils and aquatic environments. The
spirochaetes are grouped in a single order, Spirochaetales,
divided into three families. The family Spirochaetaceae
contains pathogenic bacteria such as the well-known Treponema pallidum (agent of syphilis), Borrelia (relapsing agents
transmitted by vectors such as ticks or lice and responsible
for Lyme disease, relapsing fever or hemorrhagic fevers in
animals and men), and many spirochetes (Spirochaeta,
Cristispira) living under aerobic or anaerobic conditions in
soils or aquatic sediments (Fig. 6.10f). Serpulinaceae family
with genus Serpulina and the family Leptospiraceae with
Leptospira consist of strict aerobic bacteria, the two families
containing parasitic agents, pathogens of the oral cavity or
causing kidney disease, and intestinal or liver infections in
animals and man.
The Phylum Fibrobacteres
This phylum consists of one order, Fibrobacterales with the
family
Fibrobacteraceae
containing
one
genus
(Fibrobacter) corresponding to anaerobic chemoorganotrophic fermentative bacteria, some of which live in the
digestive tract of animals and can degrade cellulose.
The Phylum Fusobacteria
Composed of one order, Fusobacteriales, with one family,
Fusobacteriaceae, the phylum Fusobacteria contains obligate
anaerobic bacteria commonly found in the oral cavity and in
the intestines of animals, such as the genera Fusobacterium,
Leptotrichia, and Streptobacillus, some of which are exclusively responsible for ENT infections and angina.
The Phylum Gemmatimonadetes
It includes a single order, Gemmatimonadales, with one family and one genus (Gemmatimonadaceae: Gemmatimonas) in
which one species was isolated from a laboratory reactor,
Gemmatimonas aurantiaca. It is a Gram-negative, motile,
aerobic, and chemoorganotrophic bacterium that can divide
by binary fission or budding.
184
P. Caumette et al.