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 , which uses halogenated organics (such as the toxic chlorinated ethenes and polychlorinated biphenyls) as electron acceptors.

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[]

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 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]

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 " Klappenbach & Pierson 2004^[17]

• Species "Candidatus " Klappenbach & Pierson 2004

Class Dodsworth et al. 2014

• Order Dodsworth et al. 2014
  • Family Dodsworth et al. 2014
    • Genus Dodsworth et al. 2014
      • Species Dodsworth et al. 2014

Class Dehalococcoidia Löffler et al. 2013 ["Dehalococcoidetes" Hugenholtz & Stackebrandt 2004]

• Order Löffler et al. 2013
  • Family Löffler et al. 2013
    • Genus Dehalococcoides Löffler et al. 2013 ["Dehalococcoides" Maymo-Gatell et al. 1997]
      • Species 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 Yamada et al. 2006

• Order Yamada et al. 2006
  • Family Anaerolineaceae Yamada et al. 2006
    • Genus "Thermanaerothrix" ♠ Gregoire et al. 2011^[18]
      • Species "" ♠ Gregoire et al. 2011
    • Genus "Brevefilum" ♠ McIlroy et al. 2017
      • Species "" ♠ McIlroy et al. 2017
    • Genus "Candidatus " ♠ Thiel et al. 2016
      • Species "Candidatus " ♠ Thiel et al. 2016
    • Genus Thermomarinilinea Nunoura et al. 2013
      • Species 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 Yamada et al. 2007^[16]
    • Genus Flexilinea Sun et al. 2015
      • Species 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 Yamada et al. 2007
    • Genus Ornatilinea Podosokorskaya et al. 2013
      • Species Podosokorskaya et al. 2013
    • Genus Pelolinea Imachi et al. 2014
      • Species Imachi et al. 2014

Class Kawaichi et al. 2013

• Order Kawaichi et al. 2013
  • Family Kawaichi et al. 2013
    • Genus "Candidatus " ♠ McIlroy et al. 2016
      • Species "Candidatus " ♠ McIlroy et al. 2016
    • Genus Ardenticatena Kawaichi et al. 2013
      • Species Kawaichi et al. 2013

Class Yamada et al. 2006

• Order Yamada et al. 2006
  • Family Yamada et al. 2006
    • Genus Kale et al. 2013
      • Species Kale et al. 2013
    • Genus Caldilinea Sekiguchi et al. 2003
      • Species C. aerophila Sekiguchi et al. 2003^[15] (type sp.)
      • Species Grégoire et al. 2011^[19]

Class Cavaletti et al. 2007 emend. Yabe et al. 2010 ["Ktedobacteria" (sic) Cavaletti et al. 2006]

• Order Yabe et al. 2011
  • Family Yabe et al. 2011
    • Genus Yabe et al. 2011^[20]
      • Species Yabe et al. 2011^[20]
      • Species King & King 2014
      • Species Yabe et al. 2011^[20] (type sp.)
• Order Cavaletti et al. 2007 ["Ktedobacterales" (sic) Cavaletti et al. 2006]
  • Family Cavaletti et al. 2007 ["Ktedobacteraceae" (sic) Cavaletti et al. 2006]
    • Genus Yabe et al. 2017
      • Species Yabe et al. 2017
    • Genus corrig. Cavaletti et al. 2007 ["Ktedobacter" (sic) Cavaletti et al. 2006]
      • Species corrig. Cavaletti et al. 2007^[21] ["Ktedobacter (sic) racemifer" Cavaletti et al. 2006]
  • Family Yabe et al. 2010
    • Genus Yabe et al. 2010^[22]
      • Species Yabe et al. 2010
      • Species Yabe, Sakai & Yokota 2016

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

• Genus "" ♠ Botero et al. 2004^[23]
  • Species "" ♠ Botero et al. 2004
• Order Sphaerobacterales Stackebrandt et al. 1997
  • Family Sphaerobacteraceae Stackebrandt et al. 1997
    • Genus Sorokin et al. 2014 ["Nitrolancetus" Sorokin et al. 2012]
      • Species 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 Garrity and Holt 2002
  • Family Garrity and Holt 2002
    • Genus King & King 2014
      • Species Houghton et al. 2015
      • Species King & King 2014
    • Genus Jackson et al. 1973^[25]
      • Species King & King 2014
      • Species Jackson et al. 1973

Class Gupta et al. 2013

• Order Cole et al. 2013
  • Family Cole et al. 2013
    • Genus Cole et al. 2013
      • Species 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 Holt & Lewin 1968^[26] ["Herpetosiphon giganteus"]
      • Species Lewin 1970^[27][28] ["Lewinella geysericola" non "Phormidium geysericola" Copeland 1936; "Herpetosiphon geysericolus" (sic) Lewin 1970]
• Order Chloroflexales Gupta et al. 2013
  • Genus "" ♠ Wu et al. 2002^[29]
    • Species "" ♠ Wu et al. 2002
  • Suborder Gupta et al. 2013
    • Family Gupta et al. 2013
      • Genus "" ♠ Kohno et al. 2002
        • Species "" ♠ Kohno et al. 2002
      • Genus ♦ 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 Gupta et al. 2013
    • Family Gupta et al. 2013
      • Genus Candidatus Thiel et al. 2016
        • Species Candidatus 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 Gupta et al. 2013
      • Genus Candidatus Gorlenko et al. 2014
        • Species Candidatus Gorlenko et al. 2014
      • Genus ♪ Dubinina & Gorlenko 1975
        • Species ♪ Dubinina & Gorlenko 1975
      • Genus Gorlenko & Pivovarova 1989 emend. Keppen et al. 2000
        • Species ♪ Gorlenko & Pivovarova 1989(type sp.)
        • Species ♦ (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[]