Chloroflexi (phylum)

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 electron acceptors.

For relation to other phyla, see Bacterial phyla. For the class, see Chloroflexi (class).

Chloroflexi
Scientific classification
Domain:	Bacteria
(unranked):	Terrabacteria
Phylum:	Chloroflexi (Garrity and Holt 2002) Hugenholtz and Stackebrandt 2004
Classes
Thermoflexia Dehalococcoidia Anaerolineae Ardenticatenia Caldilineae Ktedonobacteria Thermomicrobia Chloroflexia
Synonyms
"Chlorobacteria" Cavalier-Smith, 1992 Chloroflexaeota Oren et al. 2015 Thermomicrobaeota Oren et al. 2015

Most bacteria, in terms of diversity, are diderms and stain gram-negative, notable exceptions being Firmicutes (low G+C gram-positives), Actinobacteria (high-G+C gram-positives) and the Deinococcus–Thermus group (gram-positive diderms with thick peptidoglycan). In contrast, the members of the phylum Chloroflexi are monoderms, but stain mostly gram-negative.[1]

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.[2]

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",[3][4] which was temporarily renamed as "Chloroflexi" in Volume One of Bergey's Manual of Systematic Bacteriology.[5]

Chloroflexi 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, the class Chloroflexi.[5] Since 2001, however, new classes have been created thanks to newly discovered species, and the phylum Chloroflexi is now divided as follows:[6]

• 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

"Dehalococcoidetes" is a placeholder name given by Hugenholtz & Stackebrandt, 2004,[7] after "Dehalococcoides ethenogenes" a species partially described in 1997.[8] The first species fully described was Dehalogenimonas lykanthroporepellens, by Moe et al. 2009,[9] 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.[9]

Recent phylogenetic analysis of the Chloroflexi has found very weak support for the grouping together of the different classes currently part of the phylum.[10] 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.[10] 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.[10] 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.[10]

Phylogeny

The currently accepted taxonomy is based on the List of Prokaryotic names with Standing in Nomenclature (LPSN)[11] and National Center for Biotechnology Information (NCBI).[12] The phylogeny is based on 16S rRNA-based LTP release 132 by The All-Species Living Tree Project[13]

Thermoflexus hugenholtzii Dodsworth et al. 2014     Dehalococcoidaceae   Dehalococcoides Löffler et al. 2013   Dehalogenimonas   D. lykanthroporepellens Moe et al. 2009 (type sp.)       D. alkenigignens Bowman et al. 2013     D. formicexedens Key et al. 2017               Caldilineaceae   Litorilinea aerophila Kale et al. 2013   Caldilinea   C. aerophila Sekiguchi et al. 2003 (type sp.)     C. tarbellica Grégoire et al. 2011         Ardenticatenaceae Ardenticatena maritima Kawaichi et al. 2013   Anaerolineaceae   Thermomarinilinea lacunifontana Nunoura et al. 2013     Anaerolinea   A. thermolimosa Yamada et al. 2006[14]     A. thermophila Sekiguchi et al. 2003[15] (type sp.)         Flexilinea flocculi Sun et al. 2015       Ornatilinea apprima Podosokorskaya et al. 2013       Levilinea saccharolytica Yamada et al. 2006[14]         Bellilinea caldifistulae Yamada et al. 2007     Pelolinea submarina Imachi et al. 2014         Leptolinea tardivitalis Yamada et al. 2006[14]     Longilinea arvoryzae Yamada et al. 2007[16]                           Ktedonobacteria Thermogemmatispora   T. foliorum Yabe et al. 2011       T. carboxidivorans King & King 2014     T. onikobensis Yabe et al. 2011 (type sp.)       Ktedonobacteriales Ktedonobacteraceae   Dictyobacter aurantiacus Yabe et al. 2017     Ktedonobacter racemifer corrig. Cavaletti et al. 2007     Thermosporothrix   T. hazakensis Yabe et al. 2010     T. narukonensis Yabe, Sakai & Yokota 2016         Thermomicrobia Sphaerobacteraceae   Nitrolancea hollandica Sorokin et al. 2014     Sphaerobacter thermophilus Demharter et al. 1989     Thermomicrobiaceae Thermorudis   T. peleae King & King 2014     T. pharmacophila Houghton et al. 2015     Thermomicrobium   T. carboxidum King & King 2014     T. roseum Jackson et al. 1973           Chloroflexia Herpetosiphon   H. aurantiacus Holt & Lewin 1968     H. geysericola Lewin 1970       Kallotenuaceae Kallotenue papyrolyticum Cole et al. 2013   Chloroflexales Roseiflexaceae Roseiflexus castenholzii Hanada et al. 2002   Chloroflexus   C. aurantiacus Pierson & Castenholz 1974       C. aggregans Hanada et al. 1995     C. islandicus Gaisin et al. 2017

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[17]

• 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[18]
      • 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[14]
      • Species A. thermophila Sekiguchi et al. 2003[15] (type sp.)
    • Genus Bellilinea Yamada et al. 2007[16]
      • Species Bellilinea caldifistulae Yamada et al. 2007[16]
    • Genus Flexilinea Sun et al. 2015
      • Species Flexilinea flocculi Sun et al. 2015
    • Genus Levilinea Yamada et al. 2006[14]
      • Species Levilinea saccharolytica Yamada et al. 2006
    • Genus Leptolinea Yamada et al. 2006[14]
      • Species Leptolinea tardivitalis Yamada et al. 2006
    • Genus Longilinea Yamada et al. 2007[16]
      • 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[15] (type sp.)
      • Species C. tarbellica Grégoire et al. 2011[19]

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[20]
      • Species T. foliorum Yabe et al. 2011[20]
      • Species T. carboxidivorans King & King 2014
      • Species T. onikobensis Yabe et al. 2011[20] (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[21] ["Ktedobacter (sic) racemifer" Cavaletti et al. 2006]
  • Family Thermosporotrichaceae Yabe et al. 2010
    • Genus Thermosporothrix Yabe et al. 2010[22]
      • Species T. hazakensis Yabe et al. 2010
      • Species T. narukonensis Yabe, Sakai & Yokota 2016

Class Thermomicrobia Garrity and Holt 2002 emend. Hugenholtz and Stackebrandt 2004

• Genus "Thermobaculum" ♠ Botero et al. 2004[23]
  • Species "Thermobaculum terrenum" ♠ Botero et al. 2004
• Order Sphaerobacterales Stackebrandt et al. 1997
  • Family Sphaerobacteraceae Stackebrandt et al. 1997
    • Genus Nitrolancea Sorokin et al. 2014 ["Nitrolancetus" Sorokin et al. 2012]
      • Species Nitrolancea hollandica Sorokin et al. 2014 ["Nitrolancetus hollandicus" Sorokin et al. 2012]
    • Genus Sphaerobacter Demharter et al. 1989
      • Species Sphaerobacter thermophilus Demharter et al. 1989[24]
• Order Thermomicrobiales Garrity and Holt 2002
  • Family Thermomicrobiaceae Garrity and Holt 2002
    • Genus Thermorudis King & King 2014
      • Species T. pharmacophila Houghton et al. 2015
      • Species T. peleae King & King 2014
    • Genus Thermomicrobium Jackson et al. 1973[25]
      • Species T. carboxidum King & King 2014
      • Species T. roseum Jackson et al. 1973

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[26] ["Herpetosiphon giganteus"]
      • Species H. geysericola Lewin 1970[27][28] ["Lewinella geysericola" non "Phormidium geysericola" Copeland 1936; "Herpetosiphon geysericolus" (sic) Lewin 1970]
• Order Chloroflexales Gupta et al. 2013
  • Genus "Dehalobium" ♠ Wu et al. 2002[29]
    • 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[30]
      • Genus Roseiflexus Hanada et al. 2002
        • Species Roseiflexus castenholzii Hanada et al. 2002[31]
  • 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[32]
        • Species C. aurantiacus Pierson & Castenholz 1974[33] (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]

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)[34], meaning "greenish-yellow," and the Latin masculine passive perfect participle flexus (of flecto)[35], meaning "bent."[5] 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 Chlorobi, whereas Cyanobacteria has the root cyanos (κύανος), meaning "blue-green."[36]

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.

References

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34. χλωρός. Liddell, Henry George; Scott, Robert; A Greek–English Lexicon at the Perseus Project
35. Lewis & Short...
36. κύανος. Liddell, Henry George; Scott, Robert; A Greek–English Lexicon at the Perseus Project