The Phylum Lentisphaerae
In this phylum, the class Lentisphaeria includes two orders,
order Lentisphaerales (Lentisphaeraceae family, genus
Lentisphaera) with a single marine species isolated in
Oregon (Lentisphaera araneosa) composed of Gramnegative spherical cells, chemoorganotrophs, and aerobic
cocci, producing a transparent exopolymer, and order
Victivallales with a single species corresponding to
Victivallis vadensis, Gram-negative chemoorganotrophic
anaerobic cocci isolated from feces.
The Phylum Dictyoglomi
This phylum (Dictyoglomales order, Dictyoglomaceae family) includes thermophilic bacteria and fermentative obligate
anaerobes (genus Dictyoglomus).
The Phylum Caldiserica
With the order Caldisericales and the family Caldisericaceae,
it comprises a single species, Caldisericum exile, isolated
from a hot spring in Japan, consisting of multicellular
filaments with a common envelope, motile by a polar flagellum, anaerobic and chemoheterotrophic, realizing anaerobic
respirations with sulfur compounds such as thiosulfate, sulfite,
and elemental sulfur as electron acceptors.
The Phylum Elusimicrobia
This phylum (order of Elusimicrobiales, family of
Elusimicrobiaceae) comprises a single species in a single
genus Elusimicrobium corresponding to pleomorphic rods,
nonmotile, Gram-negative, anaerobic, fermentative, isolated
from the intestinal tract of the larva Pachnoda ephippiata
which feeds on humus.
The Phylum Armatimonadetes
This phylum includes two classes. Class Armatimonadia
(order Armatimonadales, family Armatimonadaceae)
consists of one genus, Armatimonas, formed of sticks to
ovoid cells, nonmotile, Gram-negative, aerobic, chemoorganotrophic, isolated from the rhizoplane of an aquatic plant,
Phragmites australis, in a freshwater lake in Japan. Class
Chthonomonadetes (order Chthonomonadales, family
Chthonomonadaceae) includes a genus, Chthonomona,
corresponding to Gram-negative, aerobic, chemoorganotrophs, moderately thermophilic and acidophilic isolated
from geothermal soils in New Zealand.
6.6.2.6 The Major Phyla of Gram-Positive Bacteria
The Phylum Firmicutes
It corresponds to the Gram-positive bacteria with low G + C
% (GC% DNA in <50 %), but there are some exceptions
with high G + C percentages (e.g., Symbiobacterium with a
GC% as high as 69 %) (Fig. 6.3). The characteristic of
having a thick peptidoglycan wall which gives its name to
the taxon is shared with the Actinobacteria, which had
resulted in many authors grouping into a category called
“Gram-positive,” a position which was reexamined on
sequence analysis of many genes.
This group of microorganisms has a striking character,
which is its ability to produce heat-resistant spores.
Consisting of aerobic or anaerobic bacteria, it includes
well-known taxa such as Bacillus subtilis, the model soil
organism, or Bacillus anthracis, responsible of anthrax
which has earned it a great reputation since biological
weapons programs were announced in the 1990s. This
group also contains bacteria that produce toxins such as the
highly virulent Clostridium botulinum, the botulism agent
that also contains microorganisms used in several biological
weapons programs, or Clostridium tetani, the tetanus agent.
In this group is also found Desulfotomaculum, a sporeforming sulfate-reducing bacterium. These spore-forming
bacteria are found in two classes that constitute the phylum.
The class Clostridia contains three orders of chemoorganotrophic anaerobic fermentative bacteria. The order
Clostridiales is composed of eight families. The family
Clostridiaceae contains the genera Clostridium and Acetonoma
(Fig. 6.15b, c), Sporobacter (Fig. 6.15i), Anaerobacter, etc.
These are bacteria that live in soil and anoxic sediments,
manures, and composts where they carry out fermentations.
Among Clostridium, spore-forming bacteria, some are
pathogens, producing toxins (botulism, tetanus). The families
Lachnospiraceae (Anaerophilum, Butyrivibrio, Coprococcus),
Peptostreptococcaceae (Peptostreptococcus), Eubacteriaceae
(Eubacterium), and Peptococcaceae (Peptococcus, Desulfotomaculum (Fig. 6.15f), etc.) involve bacteria, cocci, or rods,
obligately fermentative or sulfate-reducing bacteria, living in
sediments, manure, anoxic sludges of organic-rich wastewater
treatment plants, and feces. The family Heliobacteriaceae
(Heliobacterium, Heliobacillus) corresponds to the phototrophic
bacteria with bacteriochlorophyll g performing anoxygenic
photosynthesis in photoorganotrophy (cf. Sect. 3.3.4). The
families Acidaminococcaceae (Acidaminococcus, Sporomusa)
and Syntrophomonadaceae (Syntrophomonas, Anaerobaculum)
contain anaerobic cocci or rods developed by fermentation or
syntrophy in the rumen or intestinal flora as well as in fermenters
or anoxic organic sediments. The order Thermoanaerobacteriales with the family Thermoanaerobacteriaceae
(Thermoanaerobacterium; Thermoanaerobacter, Fig. 6.15d)
and the order Haloanaerobiales with the families Haloanaerobiaceae (Haloanaerobium, Fig. 6.15g; Halothermothrix,
Fig. 6.15l) and Halobacteroidaceae (Halobacteroides,
Haloanaerobacter) group fermentative bacteria living in
sediments, or isolated from thermophilic or halophilic composts
or fermenters, some of the bacteria being moderate halophiles or
hyperhalophiles (Haloanaerobiales).
6 Taxonomy and Phylogeny of Prokaryotes
185
In this phylum, the class Lentisphaeria includes two orders,
order Lentisphaerales (Lentisphaeraceae family, genus
Lentisphaera) with a single marine species isolated in
Oregon (Lentisphaera araneosa) composed of Gramnegative spherical cells, chemoorganotrophs, and aerobic
cocci, producing a transparent exopolymer, and order
Victivallales with a single species corresponding to
Victivallis vadensis, Gram-negative chemoorganotrophic
anaerobic cocci isolated from feces.
The Phylum Dictyoglomi
This phylum (Dictyoglomales order, Dictyoglomaceae family) includes thermophilic bacteria and fermentative obligate
anaerobes (genus Dictyoglomus).
The Phylum Caldiserica
With the order Caldisericales and the family Caldisericaceae,
it comprises a single species, Caldisericum exile, isolated
from a hot spring in Japan, consisting of multicellular
filaments with a common envelope, motile by a polar flagellum, anaerobic and chemoheterotrophic, realizing anaerobic
respirations with sulfur compounds such as thiosulfate, sulfite,
and elemental sulfur as electron acceptors.
The Phylum Elusimicrobia
This phylum (order of Elusimicrobiales, family of
Elusimicrobiaceae) comprises a single species in a single
genus Elusimicrobium corresponding to pleomorphic rods,
nonmotile, Gram-negative, anaerobic, fermentative, isolated
from the intestinal tract of the larva Pachnoda ephippiata
which feeds on humus.
The Phylum Armatimonadetes
This phylum includes two classes. Class Armatimonadia
(order Armatimonadales, family Armatimonadaceae)
consists of one genus, Armatimonas, formed of sticks to
ovoid cells, nonmotile, Gram-negative, aerobic, chemoorganotrophic, isolated from the rhizoplane of an aquatic plant,
Phragmites australis, in a freshwater lake in Japan. Class
Chthonomonadetes (order Chthonomonadales, family
Chthonomonadaceae) includes a genus, Chthonomona,
corresponding to Gram-negative, aerobic, chemoorganotrophs, moderately thermophilic and acidophilic isolated
from geothermal soils in New Zealand.
6.6.2.6 The Major Phyla of Gram-Positive Bacteria
The Phylum Firmicutes
It corresponds to the Gram-positive bacteria with low G + C
% (GC% DNA in <50 %), but there are some exceptions
with high G + C percentages (e.g., Symbiobacterium with a
GC% as high as 69 %) (Fig. 6.3). The characteristic of
having a thick peptidoglycan wall which gives its name to
the taxon is shared with the Actinobacteria, which had
resulted in many authors grouping into a category called
“Gram-positive,” a position which was reexamined on
sequence analysis of many genes.
This group of microorganisms has a striking character,
which is its ability to produce heat-resistant spores.
Consisting of aerobic or anaerobic bacteria, it includes
well-known taxa such as Bacillus subtilis, the model soil
organism, or Bacillus anthracis, responsible of anthrax
which has earned it a great reputation since biological
weapons programs were announced in the 1990s. This
group also contains bacteria that produce toxins such as the
highly virulent Clostridium botulinum, the botulism agent
that also contains microorganisms used in several biological
weapons programs, or Clostridium tetani, the tetanus agent.
In this group is also found Desulfotomaculum, a sporeforming sulfate-reducing bacterium. These spore-forming
bacteria are found in two classes that constitute the phylum.
The class Clostridia contains three orders of chemoorganotrophic anaerobic fermentative bacteria. The order
Clostridiales is composed of eight families. The family
Clostridiaceae contains the genera Clostridium and Acetonoma
(Fig. 6.15b, c), Sporobacter (Fig. 6.15i), Anaerobacter, etc.
These are bacteria that live in soil and anoxic sediments,
manures, and composts where they carry out fermentations.
Among Clostridium, spore-forming bacteria, some are
pathogens, producing toxins (botulism, tetanus). The families
Lachnospiraceae (Anaerophilum, Butyrivibrio, Coprococcus),
Peptostreptococcaceae (Peptostreptococcus), Eubacteriaceae
(Eubacterium), and Peptococcaceae (Peptococcus, Desulfotomaculum (Fig. 6.15f), etc.) involve bacteria, cocci, or rods,
obligately fermentative or sulfate-reducing bacteria, living in
sediments, manure, anoxic sludges of organic-rich wastewater
treatment plants, and feces. The family Heliobacteriaceae
(Heliobacterium, Heliobacillus) corresponds to the phototrophic
bacteria with bacteriochlorophyll g performing anoxygenic
photosynthesis in photoorganotrophy (cf. Sect. 3.3.4). The
families Acidaminococcaceae (Acidaminococcus, Sporomusa)
and Syntrophomonadaceae (Syntrophomonas, Anaerobaculum)
contain anaerobic cocci or rods developed by fermentation or
syntrophy in the rumen or intestinal flora as well as in fermenters
or anoxic organic sediments. The order Thermoanaerobacteriales with the family Thermoanaerobacteriaceae
(Thermoanaerobacterium; Thermoanaerobacter, Fig. 6.15d)
and the order Haloanaerobiales with the families Haloanaerobiaceae (Haloanaerobium, Fig. 6.15g; Halothermothrix,
Fig. 6.15l) and Halobacteroidaceae (Halobacteroides,
Haloanaerobacter) group fermentative bacteria living in
sediments, or isolated from thermophilic or halophilic composts
or fermenters, some of the bacteria being moderate halophiles or
hyperhalophiles (Haloanaerobiales).
6 Taxonomy and Phylogeny of Prokaryotes
185