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Chloroflexi (phylum)
Encyclopedia
The Chloroflexi or Chlorobacteria are a phylum
of bacteria
containing isolates with a diversity of phenotypes including members that are aerobic thermophiles, which use oxygen and grow well in high temperatures, anoxygenic phototrophs, which use light for photosynthesis, and anaerobic halorespirers, which uses halogenated organics (such as the toxic chlorinated ethenes and polychlorinated biphenyls) as energy sources.
Whereas most Bacteria, in terms of diversity, are diderms and stain Gram negative with the exception of the Firmicutes
(low CG Gram positives), Actinobacteria
(high CG gram positives) and the Deinococcus-Thermus group (Gram positive, but diderms with thick peptidoglycan), the members of the phylum Chloroflexi are monoderms and stain mostly Gram negative.
, regarded as the forerunner of the molecular phylogeny revolution, divided Eubacteria into 11 divisions based on 16S ribosomal RNA
(SSU) sequences and grouped the genera Chloroflexus, Herpetosiphon
and Thermomicrobium into the "Green non-sulfur bacteria and relatives", which was temporarily renamed as "Chloroflexi" in Volume One of Bergey's Manual of Systematic Bacteriology.
Being a deep branching phylum (cf. Bacterial phyla
) its classification was analysed in Volume One of Bergey's Manual of Systematic Bacteriology and included a single class with the same name, the class Cloroflexi. Since 2001 however, new classes have been created thanks to newly discovered species, therefore currently the phylum Chloroflexi is divided into:
Regarding the class "Dehalococcoidetes
", the placeholder name was given by Hugenholtz & Stackebrandt, 2004, after "Dehalococcoides ethenogenes" a partially described species in 1997, whereas the first species fully described was Dehalogenimonas lykanthroporepellens by Moe et al. 2009, but in the description of that species the class was not made official nor were families or orders laid out as the two species share only 90% 16S identity, meaning that they could fall in different families or even orders.
Notes:
♠ Strains found at the National Center for Biotechnology Information
(NCBI) but not listed in the List of Prokaryotic names with Standing in Nomenclature (LSPN).
♪ Prokaryotes where no pure (axenic) cultures are isolated or available, i. e. not cultivated or can not be sustained in culture for more than a few serial passages.
Unlike some other phyla, there is no theme root in the name of genera of Chloroflexi and in fact many genera beginning with "Chloro-" or ending in "-chloris" are either cyanobacteria or chlorobi.
Phylum
In biology, a phylum The term was coined by Georges Cuvier from Greek φῦλον phylon, "race, stock," related to φυλή phyle, "tribe, clan." is a taxonomic rank below kingdom and above class. "Phylum" is equivalent to the botanical term division....
of bacteria
Bacteria
Bacteria are a large domain of prokaryotic microorganisms. Typically a few micrometres in length, bacteria have a wide range of shapes, ranging from spheres to rods and spirals...
containing isolates with a diversity of phenotypes including members that are aerobic thermophiles, which use oxygen and grow well in high temperatures, anoxygenic phototrophs, which use light for photosynthesis, and anaerobic halorespirers, which uses halogenated organics (such as the toxic chlorinated ethenes and polychlorinated biphenyls) as energy sources.
Whereas most Bacteria, in terms of diversity, are diderms and stain Gram negative with the exception of the Firmicutes
Firmicutes
The Firmicutes are a phylum of bacteria, most of which have Gram-positive cell wall structure. A few, however, such as Megasphaera, Pectinatus, Selenomonas and Zymophilus, have a porous pseudo-outer-membrane that causes them to stain Gram-negative...
(low CG Gram positives), Actinobacteria
Actinobacteria
Actinobacteria are a group of Gram-positive bacteria with high guanine and cytosine content. They can be terrestrial or aquatic. Actinobacteria is one of the dominant phyla of the bacteria....
(high CG gram positives) and the Deinococcus-Thermus group (Gram positive, but diderms with thick peptidoglycan), the members of the phylum Chloroflexi are monoderms and stain mostly Gram negative.
History
In 1987, Carl WoeseCarl Woese
Carl Richard Woese is an American microbiologist and physicist. Woese is famous for defining the Archaea in 1977 by phylogenetic taxonomy of 16S ribosomal RNA, a technique pioneered by Woese and which is now standard practice. He was also the originator of the RNA world hypothesis in 1977,...
, regarded as the forerunner of the molecular phylogeny revolution, divided Eubacteria into 11 divisions based on 16S ribosomal RNA
16S ribosomal RNA
16S ribosomal RNA is a component of the 30S subunit of prokaryotic ribosomes. It is approximately 1.5kb in length...
(SSU) sequences and grouped the genera Chloroflexus, Herpetosiphon
Herpetosiphon
Herpetosiphon is a genus of bacteria in the family Herpetosiphonaceae....
and Thermomicrobium into the "Green non-sulfur bacteria and relatives", which was temporarily renamed as "Chloroflexi" in Volume One of Bergey's Manual of Systematic Bacteriology.
Being a deep branching phylum (cf. Bacterial phyla
Bacterial phyla
The bacterial phyla are the major lineages of the domain Bacteria.In the scientific classification established by Carl von Linné, each bacterial strain has to be assigned to a species , which is a lower level of a hierarchy of ranks...
) its classification was analysed in Volume One of Bergey's Manual of Systematic Bacteriology and included a single class with the same name, the class Cloroflexi. Since 2001 however, new classes have been created thanks to newly discovered species, therefore currently the phylum Chloroflexi is divided into:
- "Chloroflexi" (Garrity & Holt, 2001)
- Thermomicrobia (Hugenholtz & Stackebrandt, 2004)
- "Dehalococcoidetes" (Hugenholtz & Stackebrandt, 2004)
- Anaerolineae (Yamada et al., 2006)
- Caldilineae (Yamada et al., 2006)
- Ktedonobacteria (Cavaletti et al. 2007 emend. Yabe et al. 2010)
Regarding the class "Dehalococcoidetes
Dehalococcoidetes
"Dehalococcoides" is a class of "Chloroflexi", a phylum of Bacteria. It is also known as the DHC group.The name "Dehalococcoidetes" is a placeholder name given by Hugenholtz and Stackebrandt, 2004, after "Dehalococcoides ethenogenes" a partially described species in 1997, whereas the first species...
", the placeholder name was given by Hugenholtz & Stackebrandt, 2004, after "Dehalococcoides ethenogenes" a partially described species in 1997, whereas the first species fully described was Dehalogenimonas lykanthroporepellens by Moe et al. 2009, but in the description of that species the class was not made official nor were families or orders laid out as the two species share only 90% 16S identity, meaning that they could fall in different families or even orders.
Phylogeny
The currently accepted taxonomy is based on the List of Prokaryotic names with Standing in Nomenclature (LSPN) and the phylogeny is based on 16S rRNA-based LTP release 106 by The All-Species Living Tree ProjectNotes:
♠ Strains found at the National Center for Biotechnology Information
National Center for Biotechnology Information
The National Center for Biotechnology Information is part of the United States National Library of Medicine , a branch of the National Institutes of Health. The NCBI is located in Bethesda, Maryland and was founded in 1988 through legislation sponsored by Senator Claude Pepper...
(NCBI) but not listed in the List of Prokaryotic names with Standing in Nomenclature (LSPN).
♪ Prokaryotes where no pure (axenic) cultures are isolated or available, i. e. not cultivated or can not be sustained in culture for more than a few serial passages.
Etymology
The name "Chloroflexi" is a Neolatin nominative case masculine plural of "Chloroflexus", which the name of the first genus described. The noun is a combination of the Greek adjective chloros, -a, on (χλωρός, -ά, -όν) meaning "greenish-yellow" and the Latin masculine passive perfect participle flexus (of flecto) meaning "bent" to mean "a green bending". It should be therefore noted that the etymology is not due to chlorine, an element (dephlogisticated muriatic acid air) which was confirmed as such in 1810 by Sir Humphry Davy and named after its pale green colour. Another phyla with the same root is Chlorobi, whereas Cyanobacteria has the root cyanos (κύανος) meaning "blue-green"Unlike some other phyla, there is no theme root in the name of genera of Chloroflexi and in fact many genera beginning with "Chloro-" or ending in "-chloris" are either cyanobacteria or chlorobi.