Chloroflexota Garrity & Holt, 2021
- Dataset
- English Wikipedia - Species Pages
- Rank
- PHYLUM
Classification
- phylum
- Chloroflexota
Abstract
The Chloroflexota 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 electron acceptors. The members of the phylum Chloroflexota are monoderms (that is, have one cell membrane with no outer membrane), but they stain mostly gram-negative. Many well-studied phyla of bacteria are diderms and stain gram-negative, whereas well-known monoderms that stain Gram-positive include Firmicutes (or Bacillota) (low G+C gram-positives), Actinomycetota (high-G+C gram-positives) and Deinococcota (gram-positive diderms with thick peptidoglycan).
Etymology
The name Chloroflexi is a Neolatin nominative case masculine plural of Chloroflexus, which is 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),Lewis & Short... meaning "bent." The etymology is unrelated to chlorine, an element that was discovered in 1810 by Sir Humphry Davy and named after its pale green colour. Another phylum with the same root is Chlorobiota, 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 Chloroflexota, and in fact many genera beginning with "Chloro-" or ending in "-chloris" are either cyanobacteria or chlorobi.
History
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 one of 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. Chloroflexota being a deep branching phylum (see Bacterial phyla), it was considered in Volume One of Bergey's Manual of Systematic Bacteriology to include a single class with the same name. Since 2001, however, new classes have been created thanks to newly discovered species, and the phylum Chloroflexi is now divided into several classes. "Dehalococcoidetes" is a placeholder name given by Hugenholtz & Stackebrandt, 2004, after "Dehalococcoides ethenogenes" a species partially described in 1997. 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 ribosomal RNA identity, meaning that they could fall in different families or even orders. Recent phylogenetic analysis of the Chloroflexota 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 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). The phylogeny is based on 16S rRNA-based LTP release 132 by The All-Species Living Tree Project
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., they are not cultivated or cannot be sustained in culture for more than a few serial passages.
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., they are not cultivated or cannot be sustained in culture for more than a few serial passages.
Taxonomy
Genus "Candidatus Chlorothrix" Klappenbach & Pierson 2004
Species "Candidatus Chlorothrix halophila" Klappenbach & Pierson 2004
Class Thermoflexia Dodsworth et al. 2014
Order Thermoflexales Dodsworth et al. 2014 Family Thermoflexaceae Dodsworth et al. 2014 Genus Thermoflexus Dodsworth et al. 2014 Species Thermoflexus hugenholtzii Dodsworth et al. 2014
Class Dehalococcoidia Löffler et al. 2013 ["Dehalococcoidetes" Hugenholtz & Stackebrandt 2004]
Order Dehalococcoidales Löffler et al. 2013 Family Dehalococcoidaceae Löffler et al. 2013 Genus Dehalococcoides Löffler et al. 2013 ["Dehalococcoides" Maymo-Gatell et al. 1997] Species Dehalococcoides mccartyi Löffler et al. 2013 ["Dehalococcoides ethenogenes" Maymo-Gatell et al. 1997] Genus Dehalogenimonas Moe et al. 2009 Species D. alkenigignens Bowmann et al. 2013 Species D. formicexedens Key et al. 2017 Species D. lykanthroporepellens Moe et al. 2009 (type sp.)
Class Anaerolineae Yamada et al. 2006
Order Anaerolineales Yamada et al. 2006 Family Anaerolineaceae Yamada et al. 2006 Genus "Thermanaerothrix" ♠ Gregoire et al. 2011 Species "Thermanaerothrix daxensis" ♠ Gregoire et al. 2011 Genus "Brevefilum" ♠ McIlroy et al. 2017 Species "Brevefilum fermentans" ♠ McIlroy et al. 2017 Genus "Candidatus Roseilinea" ♠ Thiel et al. 2016 Species "Candidatus Roseilinea gracile" ♠ Thiel et al. 2016 Genus Thermomarinilinea Nunoura et al. 2013 Species Thermomarinilinea lacunifontana Nunoura et al. 2013 Genus Anaerolinea Sekiguchi et al. 2003 emend. Yamada et al. 2006 Species A. thermolimosa Yamada et al. 2006 Species A. thermophila Sekiguchi et al. 2003 (type sp.) Genus Bellilinea Yamada et al. 2007 Species Bellilinea caldifistulae Yamada et al. 2007 Genus Flexilinea Sun et al. 2015 Species Flexilinea flocculi Sun et al. 2015 Genus Levilinea Yamada et al. 2006 Species Levilinea saccharolytica Yamada et al. 2006 Genus Leptolinea Yamada et al. 2006 Species Leptolinea tardivitalis Yamada et al. 2006 Genus Longilinea Yamada et al. 2007 Species Longilinea arvoryzae Yamada et al. 2007 Genus Ornatilinea Podosokorskaya et al. 2013 Species Ornatilinea apprima Podosokorskaya et al. 2013 Genus Pelolinea Imachi et al. 2014 Species Pelolinea submarina Imachi et al. 2014
Class Ardenticatenia Kawaichi et al. 2013
Order Ardenticatenales Kawaichi et al. 2013 Family Ardenticatenaceae Kawaichi et al. 2013 Genus "Candidatus Promineofilum" ♠ McIlroy et al. 2016 Species "Candidatus Promineofilum breve" ♠ McIlroy et al. 2016 Genus Ardenticatena Kawaichi et al. 2013 Species Ardenticatena maritima Kawaichi et al. 2013
Class Caldilineae Yamada et al. 2006
Order Caldilineales Yamada et al. 2006 Family Caldilineaceae Yamada et al. 2006 Genus Litorilinea Kale et al. 2013 Species Litorilinea aerophila Kale et al. 2013 Genus Caldilinea Sekiguchi et al. 2003 Species C. aerophila Sekiguchi et al. 2003 (type sp.) Species C. tarbellica Grégoire et al. 2011
Class Ktedonobacteria Cavaletti et al. 2007 emend. Yabe et al. 2010 ["Ktedobacteria" (sic) Cavaletti et al. 2006]
Order Thermogemmatisporales Yabe et al. 2011 Family Thermogemmatisporaceae Yabe et al. 2011 Genus Thermogemmatispora Yabe et al. 2011 Species T. foliorum Yabe et al. 2011 Species T. carboxidivorans King & King 2014 Species T. onikobensis Yabe et al. 2011 (type sp.) Order Ktedonobacterales Cavaletti et al. 2007 ["Ktedobacterales" (sic) Cavaletti et al. 2006] Family Ktedonobacteriaceae Cavaletti et al. 2007 ["Ktedobacteraceae" (sic) Cavaletti et al. 2006] Genus Dictyobacter Yabe et al. 2017 Species Dictyobacter aurantiacus Yabe et al. 2017 Genus Ktedonobacter corrig. Cavaletti et al. 2007 ["Ktedobacter" (sic) Cavaletti et al. 2006] Species Ktedonobacter racemifer corrig. Cavaletti et al. 2007 ["Ktedobacter (sic) racemifer" Cavaletti et al. 2006] Family Thermosporotrichaceae Yabe et al. 2010 Genus Thermosporothrix Yabe et al. 2010 Species T. hazakensis Yabe et al. 2010 Species T. narukonensis Yabe, Sakai & Yokota 2016
Class Chloroflexia Gupta et al. 2013
Order Kallotenuales Cole et al. 2013 Family Kallotenuaceae Cole et al. 2013 Genus Kallotenue Cole et al. 2013 Species Kallotenue papyrolyticum Cole et al. 2013 Order Herpetosiphonales Gupta et al. 2013 ["Herpetosiphonales" Castenholz 2001] Family Herpetosiphonaceae Gupta et al. 2013 ["Herpetosiphonaceae" Castenholz 2001] Genus Herpetosiphon Holt & Lewin 1968 Species H. aurantiacus Holt & Lewin 1968 ["Herpetosiphon giganteus"] Species H. geysericola Lewin 1970 ["Lewinella geysericola" non "Phormidium geysericola" Copeland 1936; "Herpetosiphon geysericolus" (sic) Lewin 1970] Order Chloroflexales Gupta et al. 2013 Genus "Dehalobium" ♠ Wu et al. 2002 Species "Dehalobium chlorocoercia" ♠ Wu et al. 2002 Suborder Roseiflexineae Gupta et al. 2013 Family Roseiflexaceae Gupta et al. 2013 Genus "Kouleothrix" ♠ Kohno et al. 2002 Species "Kouleothrix aurantiaca" ♠ Kohno et al. 2002 Genus Heliothrix ♦ Pierson et al. 1986 Species Heliothrix oregonensis ♦ Pierson et al. 1986 Genus Roseiflexus Hanada et al. 2002 Species Roseiflexus castenholzii Hanada et al. 2002 Suborder Chloroflexineae Gupta et al. 2013 Family Chloroflexaceae Gupta et al. 2013 Genus Candidatus Chloranaerofilum Thiel et al. 2016 Species Candidatus Chloranaerofilum corporosum Thiel et al. 2016 Genus Chloroflexus Pierson & Castenholz 1974 Species C. aggregans Hanada et al. 1995 Species C. aurantiacus Pierson & Castenholz 1974 (type sp.) Species C. islandicus Gaisin et al. 2017 Family Oscillochloridaceae Gupta et al. 2013 Genus Candidatus Chloroploca Gorlenko et al. 2014 Species Candidatus Chloroploca asiatica Gorlenko et al. 2014 Genus Chloronema ♪ Dubinina & Gorlenko 1975 Species Chloronema giganteum ♪ Dubinina & Gorlenko 1975 Genus Oscillochloris Gorlenko & Pivovarova 1989 emend. Keppen et al. 2000 Species O. chrysea ♪ Gorlenko & Pivovarova 1989(type sp.) Species O. trichoides ♦ (ex Szafer) Gorlenko & Korotkov 1989 emend. Keppen et al. 2000 ["Oscillatoria trichoides" (Szafer) Lauterborn 1915]
Species "Candidatus Chlorothrix halophila" Klappenbach & Pierson 2004
Class Thermoflexia Dodsworth et al. 2014
Order Thermoflexales Dodsworth et al. 2014 Family Thermoflexaceae Dodsworth et al. 2014 Genus Thermoflexus Dodsworth et al. 2014 Species Thermoflexus hugenholtzii Dodsworth et al. 2014
Class Dehalococcoidia Löffler et al. 2013 ["Dehalococcoidetes" Hugenholtz & Stackebrandt 2004]
Order Dehalococcoidales Löffler et al. 2013 Family Dehalococcoidaceae Löffler et al. 2013 Genus Dehalococcoides Löffler et al. 2013 ["Dehalococcoides" Maymo-Gatell et al. 1997] Species Dehalococcoides mccartyi Löffler et al. 2013 ["Dehalococcoides ethenogenes" Maymo-Gatell et al. 1997] Genus Dehalogenimonas Moe et al. 2009 Species D. alkenigignens Bowmann et al. 2013 Species D. formicexedens Key et al. 2017 Species D. lykanthroporepellens Moe et al. 2009 (type sp.)
Class Anaerolineae Yamada et al. 2006
Order Anaerolineales Yamada et al. 2006 Family Anaerolineaceae Yamada et al. 2006 Genus "Thermanaerothrix" ♠ Gregoire et al. 2011 Species "Thermanaerothrix daxensis" ♠ Gregoire et al. 2011 Genus "Brevefilum" ♠ McIlroy et al. 2017 Species "Brevefilum fermentans" ♠ McIlroy et al. 2017 Genus "Candidatus Roseilinea" ♠ Thiel et al. 2016 Species "Candidatus Roseilinea gracile" ♠ Thiel et al. 2016 Genus Thermomarinilinea Nunoura et al. 2013 Species Thermomarinilinea lacunifontana Nunoura et al. 2013 Genus Anaerolinea Sekiguchi et al. 2003 emend. Yamada et al. 2006 Species A. thermolimosa Yamada et al. 2006 Species A. thermophila Sekiguchi et al. 2003 (type sp.) Genus Bellilinea Yamada et al. 2007 Species Bellilinea caldifistulae Yamada et al. 2007 Genus Flexilinea Sun et al. 2015 Species Flexilinea flocculi Sun et al. 2015 Genus Levilinea Yamada et al. 2006 Species Levilinea saccharolytica Yamada et al. 2006 Genus Leptolinea Yamada et al. 2006 Species Leptolinea tardivitalis Yamada et al. 2006 Genus Longilinea Yamada et al. 2007 Species Longilinea arvoryzae Yamada et al. 2007 Genus Ornatilinea Podosokorskaya et al. 2013 Species Ornatilinea apprima Podosokorskaya et al. 2013 Genus Pelolinea Imachi et al. 2014 Species Pelolinea submarina Imachi et al. 2014
Class Ardenticatenia Kawaichi et al. 2013
Order Ardenticatenales Kawaichi et al. 2013 Family Ardenticatenaceae Kawaichi et al. 2013 Genus "Candidatus Promineofilum" ♠ McIlroy et al. 2016 Species "Candidatus Promineofilum breve" ♠ McIlroy et al. 2016 Genus Ardenticatena Kawaichi et al. 2013 Species Ardenticatena maritima Kawaichi et al. 2013
Class Caldilineae Yamada et al. 2006
Order Caldilineales Yamada et al. 2006 Family Caldilineaceae Yamada et al. 2006 Genus Litorilinea Kale et al. 2013 Species Litorilinea aerophila Kale et al. 2013 Genus Caldilinea Sekiguchi et al. 2003 Species C. aerophila Sekiguchi et al. 2003 (type sp.) Species C. tarbellica Grégoire et al. 2011
Class Ktedonobacteria Cavaletti et al. 2007 emend. Yabe et al. 2010 ["Ktedobacteria" (sic) Cavaletti et al. 2006]
Order Thermogemmatisporales Yabe et al. 2011 Family Thermogemmatisporaceae Yabe et al. 2011 Genus Thermogemmatispora Yabe et al. 2011 Species T. foliorum Yabe et al. 2011 Species T. carboxidivorans King & King 2014 Species T. onikobensis Yabe et al. 2011 (type sp.) Order Ktedonobacterales Cavaletti et al. 2007 ["Ktedobacterales" (sic) Cavaletti et al. 2006] Family Ktedonobacteriaceae Cavaletti et al. 2007 ["Ktedobacteraceae" (sic) Cavaletti et al. 2006] Genus Dictyobacter Yabe et al. 2017 Species Dictyobacter aurantiacus Yabe et al. 2017 Genus Ktedonobacter corrig. Cavaletti et al. 2007 ["Ktedobacter" (sic) Cavaletti et al. 2006] Species Ktedonobacter racemifer corrig. Cavaletti et al. 2007 ["Ktedobacter (sic) racemifer" Cavaletti et al. 2006] Family Thermosporotrichaceae Yabe et al. 2010 Genus Thermosporothrix Yabe et al. 2010 Species T. hazakensis Yabe et al. 2010 Species T. narukonensis Yabe, Sakai & Yokota 2016
Class Chloroflexia Gupta et al. 2013
Order Kallotenuales Cole et al. 2013 Family Kallotenuaceae Cole et al. 2013 Genus Kallotenue Cole et al. 2013 Species Kallotenue papyrolyticum Cole et al. 2013 Order Herpetosiphonales Gupta et al. 2013 ["Herpetosiphonales" Castenholz 2001] Family Herpetosiphonaceae Gupta et al. 2013 ["Herpetosiphonaceae" Castenholz 2001] Genus Herpetosiphon Holt & Lewin 1968 Species H. aurantiacus Holt & Lewin 1968 ["Herpetosiphon giganteus"] Species H. geysericola Lewin 1970 ["Lewinella geysericola" non "Phormidium geysericola" Copeland 1936; "Herpetosiphon geysericolus" (sic) Lewin 1970] Order Chloroflexales Gupta et al. 2013 Genus "Dehalobium" ♠ Wu et al. 2002 Species "Dehalobium chlorocoercia" ♠ Wu et al. 2002 Suborder Roseiflexineae Gupta et al. 2013 Family Roseiflexaceae Gupta et al. 2013 Genus "Kouleothrix" ♠ Kohno et al. 2002 Species "Kouleothrix aurantiaca" ♠ Kohno et al. 2002 Genus Heliothrix ♦ Pierson et al. 1986 Species Heliothrix oregonensis ♦ Pierson et al. 1986 Genus Roseiflexus Hanada et al. 2002 Species Roseiflexus castenholzii Hanada et al. 2002 Suborder Chloroflexineae Gupta et al. 2013 Family Chloroflexaceae Gupta et al. 2013 Genus Candidatus Chloranaerofilum Thiel et al. 2016 Species Candidatus Chloranaerofilum corporosum Thiel et al. 2016 Genus Chloroflexus Pierson & Castenholz 1974 Species C. aggregans Hanada et al. 1995 Species C. aurantiacus Pierson & Castenholz 1974 (type sp.) Species C. islandicus Gaisin et al. 2017 Family Oscillochloridaceae Gupta et al. 2013 Genus Candidatus Chloroploca Gorlenko et al. 2014 Species Candidatus Chloroploca asiatica Gorlenko et al. 2014 Genus Chloronema ♪ Dubinina & Gorlenko 1975 Species Chloronema giganteum ♪ Dubinina & Gorlenko 1975 Genus Oscillochloris Gorlenko & Pivovarova 1989 emend. Keppen et al. 2000 Species O. chrysea ♪ Gorlenko & Pivovarova 1989(type sp.) Species O. trichoides ♦ (ex Szafer) Gorlenko & Korotkov 1989 emend. Keppen et al. 2000 ["Oscillatoria trichoides" (Szafer) Lauterborn 1915]