Chloroflexi (phylum)

For relation to other phyla, see Bacterial phyla.

For the class, see Chloroflexi (class).

Chloroflexi
Scientific classification
Domain:	Bacteria
Phylum:	Chloroflexi (Garrity and Holt 2001) Hugenholtz and Stackebrandt 2004
Classes
Class Thermoflexia Dodsworth et al. 2014 Order Thermoflexales Dodsworth et al. 2014 Family Thermoflexaceae Dodsworth et al. 2014 Class Dehalococcoidia Löffler et al. 2013 Order Dehalococcoidales Löffler et al. 2013 Family Dehalococcoidaceae Löffler et al. 2013 Class Anaerolineae Yamada et al. 2006 Order Anaerolineales Yamada et al. 2006 Family Anaerolineaceae Yamada et al. 2006 Class Ardenticatenia Kawaichi et al. 2013 Order Ardenticatenales Kawaichi et al. 2013 Family Ardenticatenaceae Kawaichi et al. 2013 Class Caldilineae Yamada et al. 2006 Order Caldilineales Yamada et al. 2006 Family Caldilineaceae Yamada et al. 2006 Class Ktedonobacteria Cavaletti et al. 2007 emend. Yabe et al. 2010 Order Thermogemmatisporales Yabe et al. 2011 Family Thermogemmatisporaceae Yabe et al. 2011 Order Ktedonobacterales Cavaletti et al. 2007 Family Ktedonobacteriaceae Cavaletti et al. 2007 Family Thermosporotrichaceae Yabe et al. 2010 Class Thermomicrobia Garrity and Holt 2002 emend. Hugenholtz and Stackebrandt 2004 Order Thermomicrobiales Garrity and Holt 2002 Family Thermomicrobiaceae Garrity and Holt 2002 Order Sphaerobacterales Stackebrandt et al. 1997 Family Sphaerobacteraceae Stackebrandt et al. 1997 Class Chloroflexia Gupta et al. 2013 Order Kallotenuales Cole et al. 2013 Family Kallotenuaceae Cole et al. 2013 Order Herpetosiphonales Gupta et al. 2013 Family Herpetosiphonaceae Gupta et al. 2013 Order Chloroflexales Gupta et al. 2013 Suborder Chloroflexineae Gupta et al. 2013 Family Chloroflexaceae Gupta et al. 2013 Family Oscillochloridaceae Gupta et al. 2013 Suborder Roseiflexineae Gupta et al. 2013 Family Roseiflexaceae Gupta et al. 2013
Synonyms
Chlorobacteria Cavalier-Smith, 1992

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 (green non-sulfur bacteria), 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, but stain mostly Gram negative.

History

See also: Bacterial taxonomy and Bacterial phyla

The taxon name was created in the 2001 edition of Volume 1 of Bergey's Manual of Systematic Bacteriology and is the Latin plural of the name Chloroflexus, the name of the type genus of the phylum, a common practice.

In 1987, Carl Woese, 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 Chloroflexi. Since 2001 however, new classes have been created thanks to newly discovered species, therefore currently the phylum Chloroflexi is divided into:

• Chloroflexi Gupta et al. 2012
• 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", 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.

Recent phylogenetic analysis of the Chloroflexi has found very weak support for the grouping together of the different classes currently part of the phylum. The six classes that make up the phylum did not consistently form a well-supported monophyletic clade in phylogenetic trees based on concatenated sequences for large datasets of proteins and no conserved signature indels were identified that were uniquely shared by the entire phylum. However, the classes "Chloroflexi" and Thermomicrobia were found to group together consistently by both the usual phylogenetic means and the identification of shared conserved signature indels in the 50S ribosomal protein L19 and the enzyme UDP-glucose 4-epimerase. It has been suggested that the phylum Chloroflexi "sensu stricto" should comprise only the classes Chloroflexi and Thermomicrobia, and the other four classes ("Dehalococcoidetes," Anaerolineae, Caldilineae and Ktedonobacteria) may represent one or more independent phyla branching in the neighborhood of the Chloroflexi.

Phylogeny

The currently accepted taxonomy is based on the List of Prokaryotic names with Standing in Nomenclature (LPSN) and National Center for Biotechnology Information (NCBI) and the phylogeny is based on 16S rRNA-based LTP release 115 by 'The All-Species Living Tree' Project.

Kouleothrix aurantiaca ♠ Kohno et al. 2002 Candidatus Chlorothrix halophila Thermoflexus hugenholtzii Dodsworth et al. 2014 Dehalococcoidaceae Dehalococcoides mccartyi Löffler et al. 2013 Dehalogenimonas D. alkenigignens Bowman et al. 2013 D. lykanthroporepellens Moe et al. 2009 (type sp.) Caldilineaceae Litorilinea aerophila Kale et al. 2013 Caldilinea C. aerophila (type sp.) C. tarbellica Ardenticatena maritima Kawaichi et al. 2013 Anaerolineaceae ?Thermanaerothrix daxensis ♠ A. thermolimosa A. thermophila (type sp.) Ornatilinea apprima Podosokorskaya et al. 2013 Pelolinea submarina Imachi et al. 2014 Bellilinea caldifistulae Levilinea saccharolytica Leptolinea tardivitalis Longilinea arvoryzae Ktedonobacteria Ktedonobacteriales Ktedonobacter racemifer corrig. Thermosporothrix hazakensis Thermogemmatispora T. foliorum T. carboxidivorans King & King 2014 T. onikobensis (type sp.) Thermomicrobia ?Thermobaculum terrenum ♠ Sphaerobacteraceae Nitrolancetus hollandicus ♠ Sorokin et al. 2012 Sphaerobacter thermophilus Thermomicrobiaceae Thermorudis peleae King & King 2014 Thermomicrobium T. carboxidum King & King 2014 T. roseum Chloroflexia Kallotenue papyrolyticum Cole et al. 2013 Herpetosiphon H. aurantiacus (type sp.) H. geysericola Chloroflexales ?Dehalobium chlorocoercia ♠ Roseiflexaceae Heliothrix oregonensis Roseiflexus castenholzii Chloroflexineae Chloroflexus C. aggregans C. aurantiacus (type sp.) Oscillochloridaceae Candidatus Chloroploca asiatica Gorlenko et al. 2014 Chloronema giganteum ♪ Dubinina and Gorlenko 1975 Oscillochloris O. chrysea ♪ Gorlenko and Pivovarova 1989 (type sp.) O. trichoides (ex Szafer) Gorlenko and Korotkov 1989 emend. Keppen et al. 2000

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.

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 phylum 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.