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Chloroflexi
Scientific classification
Domain:
(unranked):
Phylum:
Chloroflexi

(Garrity and Holt 2002) Hugenholtz and Stackebrandt 2004
Classes
Synonyms
  • "Chlorobacteria" Cavalier-Smith, 1992
  • Chloroflexaeota Oren et al. 2015
  • Thermomicrobaeota Oren et al. 2015

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]

Dodsworth et al. 2014

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

Kale et al. 2013

Caldilinea

C. aerophila Sekiguchi et al. 2003 (type sp.)

Grégoire et al. 2011

Kawaichi et al. 2013

Anaerolineaceae

Nunoura et al. 2013

Anaerolinea

A. thermolimosa Yamada et al. 2006[14]

A. thermophila Sekiguchi et al. 2003[15] (type sp.)

Sun et al. 2015

Podosokorskaya et al. 2013

Levilinea saccharolytica Yamada et al. 2006[14]

Yamada et al. 2007

Imachi et al. 2014

Leptolinea tardivitalis Yamada et al. 2006[14]

Yamada et al. 2007[16]

Yabe et al. 2011

King & King 2014

Yabe et al. 2011 (type sp.)

Yabe et al. 2017

corrig. Cavaletti et al. 2007

Yabe et al. 2010

Yabe, Sakai & Yokota 2016

Thermomicrobia
Sphaerobacteraceae

Sorokin et al. 2014

Sphaerobacter thermophilus Demharter et al. 1989

King & King 2014

Houghton et al. 2015

King & King 2014

Jackson et al. 1973

Herpetosiphon

Holt & Lewin 1968

Lewin 1970

Cole et al. 2013

Chloroflexales

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 " 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]

Class Yamada et al. 2006

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

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
  • 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
    • Suborder Gupta et al. 2013
      • Family Gupta et al. 2013
      • 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

  1. ^ Sutcliffe, I. C. (2010). "A phylum level perspective on bacterial cell envelope architecture". Trends in Microbiology. 18 (10): 464–470. doi:10.1016/j.tim.2010.06.005. PMID 20637628.
  2. ^ Don J. Brenner; Noel R. Krieg; James T. Staley (July 26, 2005) [1984(Williams & Wilkins)]. George M. Garrity (ed.). Introductory Essays. Bergey's Manual of Systematic Bacteriology. 2A (2nd ed.). New York: Springer. p. 304. ISBN 978-0-387-24143-2. British Library no. GBA561951.
  3. ^ Holland L. (22 May 1990). "Woese,Carl in the forefront of bacterial evolution revolution". Scientist. 4 (10).
  4. ^ Woese, C. R. (1987). "Bacterial evolution". Microbiological Reviews. 51 (2): 221–271. doi:10.1128/MMBR.51.2.221-271.1987. PMC 373105. PMID 2439888.
  5. ^ a b c Don J. Brenner; Noel R. Krieg; James T. Staley (July 26, 2005) [1984(Williams & Wilkins)]. George M. Garrity (ed.). Introductory Essays. Bergey's Manual of Systematic Bacteriology. 2A (2nd ed.). New York: Springer. p. 304. ISBN 978-0-387-24143-2. British Library no. GBA561951.
  6. ^ Bacterial classification entry in LPSN [Euzéby, J.P. (1997). "List of Bacterial Names with Standing in Nomenclature: a folder available on the Internet". International Journal of Systematic and Evolutionary Microbiology. 47 (2): 590–2. doi:10.1099/00207713-47-2-590. PMID 9103655.]
  7. ^ Hugenholtz, P.; Stackebrandt, E. (2004). "Reclassification of Sphaerobacter thermophilus from the subclass Sphaerobacteridae in the phylum Actinobacteria to the class Thermomicrobia (emended description) in the phylum Chloroflexi (emended description)". International Journal of Systematic and Evolutionary Microbiology. 54 (6): 2049–2051. doi:10.1099/ijs.0.03028-0. PMID 15545432.
  8. ^ Maymo-Gatell, X.; Chien, Y.; Gossett, J. M.; Zinder, S. H. (1997). "Isolation of a Bacterium That Reductively Dechlorinates Tetrachloroethene to Ethene". Science. 276 (5318): 1568–1571. doi:10.1126/science.276.5318.1568. PMID 9171062.
  9. ^ a b Moe, W. M.; Yan, J.; Nobre, M. F.; Da Costa, M. S.; Rainey, F. A. (2009). "Dehalogenimonas lykanthroporepellens gen. Nov., sp. Nov., a reductively dehalogenating bacterium isolated from chlorinated solvent-contaminated groundwater". International Journal of Systematic and Evolutionary Microbiology. 59 (11): 2692–2697. doi:10.1099/ijs.0.011502-0. PMID 19625421.
  10. ^ a b c d Gupta, R. S.; Chander, P.; George, S. (2012). "Phylogenetic framework and molecular signatures for the class Chloroflexi and its different clades; proposal for division of the class Chloroflexi class. Nov. Into the suborder Chloroflexineae subord. Nov., consisting of the emended family Oscillochloridaceae and the family Chloroflexaceae fam. Nov., and the suborder Roseiflexineae subord. Nov., containing the family Roseiflexaceae fam. Nov". Antonie van Leeuwenhoek. 103 (1): 99–119. doi:10.1007/s10482-012-9790-3. PMID 22903492.
  11. ^ J.P. Euzéby. "Chloroflexi". List of Prokaryotic names with Standing in Nomenclature (LPSN). Retrieved 2018-07-20.
  12. ^ Sayers; et al. "Chloroflexi". National Center for Biotechnology Information (NCBI) taxonomy database. Retrieved 2014-03-20.
  13. ^ "16S rRNA-based LTP release 132 (full tree)". All-Species Living Tree Project. Silva Comprehensive Ribosomal RNA Database. Retrieved 2018-07-20.
  14. ^ a b c d e f Yamada, T.; Sekiguchi, Y.; Hanada, S.; Imachi, H.; Ohashi, A.; Harada, H.; Kamagata, Y. (2006). "Anaerolinea thermolimosa sp. nov., Levilinea saccharolytica gen. nov., sp. nov. And Leptolinea tardivitalis gen. nov., sp. nov., novel filamentous anaerobes, and description of the new classes Anaerolineae classis nov. And Caldilineae classis nov. In the bacterial phylum Chloroflexi". International Journal of Systematic and Evolutionary Microbiology. 56 (6): 1331–1340. doi:10.1099/ijs.0.64169-0. PMID 16738111.
  15. ^ a b c Sekiguchi, Y.; Yamada, T.; Hanada, S.; Ohashi, A.; Harada, H.; Kamagata, Y. (2003). "Anaerolinea thermophila gen. nov., sp. nov. And Caldilinea aerophila gen. nov., sp. nov., novel filamentous thermophiles that represent a previously uncultured lineage of the domain Bacteria at the subphylum level". International Journal of Systematic and Evolutionary Microbiology. 53 (6): 1843–1851. doi:10.1099/ijs.0.02699-0. PMID 14657113.
  16. ^ a b c d Yamada, T.; Imachi, H.; Ohashi, A.; Harada, H.; Hanada, S.; Kamagata, Y.; Sekiguchi, Y. (2007). "Bellilinea caldifistulae gen. nov., sp. nov. And Longilinea arvoryzae gen. nov., sp. nov., strictly anaerobic, filamentous bacteria of the phylum Chloroflexi isolated from methanogenic propionate-degrading consortia". International Journal of Systematic and Evolutionary Microbiology. 57 (10): 2299–2306. doi:10.1099/ijs.0.65098-0. PMID 17911301.
  17. ^ Klappenbach, J. A.; Pierson, B. K. (2004). "Phylogenetic and physiological characterization of a filamentous anoxygenic photoautotrophic bacterium 'Candidatus Chlorothrix halophila' Gen. Nov., sp. Nov., recovered from hypersaline microbial mats". Archives of Microbiology. 181 (1): 17–25. doi:10.1007/s00203-003-0615-7. PMID 14655000.
  18. ^ Grégoire, P.; Fardeau, M. L.; Joseph, M.; Guasco, S.; Hamaide, F.; Biasutti, S.; Michotey, V. R.; Bonin, P.; Ollivier, B. (2011). "Isolation and characterization of Thermanaerothrix daxensis gen. nov., sp. nov., a thermophilic anaerobic bacterium pertaining to the phylum "Chloroflexi", isolated from a deep hot aquifer in the Aquitaine Basin". Systematic and Applied Microbiology. 34 (7): 494–497. doi:10.1016/j.syapm.2011.02.004. PMID 21621938.
  19. ^ Gregoire, P.; Bohli, M.; Cayol, J. -L.; Joseph, M.; Guasco, S.; Dubourg, K.; Cambar, J.; Michotey, V.; Bonin, P.; Fardeau, M. -L.; Ollivier, B. (2010). "Caldilinea tarbellica sp. nov., a filamentous, thermophilic, anaerobic bacterium isolated from a deep hot aquifer in the Aquitaine Basin". International Journal of Systematic and Evolutionary Microbiology. 61 (6): 1436–1441. doi:10.1099/ijs.0.025676-0. PMID 20584812.
  20. ^ a b c Yabe, S.; Aiba, Y.; Sakai, Y.; Hazaka, M.; Yokota, A. (2010). "Thermogemmatispora onikobensis gen. nov., sp. nov. And Thermogemmatispora foliorum sp. nov., isolated from fallen leaves on geothermal soils, and description of Thermogemmatisporaceae fam. Nov. And Thermogemmatisporales ord. Nov. Within the class Ktedonobacteria". International Journal of Systematic and Evolutionary Microbiology. 61 (4): 903–910. doi:10.1099/ijs.0.024877-0. PMID 20495028.
  21. ^ Cavaletti, L.; Monciardini, P.; Bamonte, R.; Schumann, P.; Rohde, M.; Sosio, M.; Donadio, S. (2006). "New Lineage of Filamentous, Spore-Forming, Gram-Positive Bacteria from Soil". Applied and Environmental Microbiology. 72 (6): 4360–4369. doi:10.1128/AEM.00132-06. PMC 1489649. PMID 16751552.
  22. ^ Yabe, S.; Aiba, Y.; Sakai, Y.; Hazaka, M.; Yokota, A. (2009). "Thermosporothrix hazakensis gen. nov., sp. nov., isolated from compost, description of Thermosporotrichaceae fam. Nov. Within the class Ktedonobacteria Cavaletti et al. 2007 and emended description of the class Ktedonobacteria". International Journal of Systematic and Evolutionary Microbiology. 60 (8): 1794–1801. doi:10.1099/ijs.0.018069-0. PMID 19767365.
  23. ^ Botero, L. M.; Brown, K. B.; Brumefield, S.; Burr, M.; Castenholz, R. W.; Young, M.; McDermott, T. R. (2004). "Thermobaculum terrenum gen. nov., sp. nov.: A non-phototrophic gram-positive thermophile representing an environmental clone group related to the Chloroflexi (green non-sulfur bacteria) and Thermomicrobia". Archives of Microbiology. 181 (4): 269–277. doi:10.1007/s00203-004-0647-7. PMID 14745485.
  24. ^ Demharter, W.; Hensel, R.; Smida, J.; Stackebrandt, E. (1989). "Sphaerobacter thermophilus gen. nov., sp. nov. A Deeply Rooting Member of the Actinomycetes Subdivision Isolated from Thermophilically Treated Sewage Sludge". Systematic and Applied Microbiology. 11 (3): 261–266. doi:10.1016/S0723-2020(89)80023-2.
  25. ^ Jackson, T. J.; Ramaley, R. F.; Meinschein, W. G. (1973). "Thermomicrobium, a New Genus of Extremely Thermophilic Bacteria". International Journal of Systematic Bacteriology. 23: 28–36. doi:10.1099/00207713-23-1-28.
  26. ^ Holt, J. G.; Lewin, R. A. (1968). "Herpetosiphon aurantiacus gen. Et sp. N., a new filamentous gliding organism". Journal of Bacteriology. 95 (6): 2407–2408. doi:10.1128/JB.95.6.2407-2408.1968. PMC 315177. PMID 5669912.
  27. ^ Copeland, J. J. (1936). "Yellowstone Thermal Myxophyceae". Annals of the New York Academy of Sciences. 36: 4–223. doi:10.1111/j.1749-6632.1936.tb56976.x.
  28. ^ Lewin, R. A. (1970). "New Herpetosiphon species (Flexibacterales)". Canadian Journal of Microbiology. 16 (6): 517–520. doi:10.1139/m70-087. PMID 5423287.
  29. ^ Wu, Q.; Watts, J. E. M.; Sowers, K. R.; May, H. D. (2002). "Identification of a Bacterium That Specifically Catalyzes the Reductive Dechlorination of Polychlorinated Biphenyls with Doubly Flanked Chlorines". Applied and Environmental Microbiology. 68 (2): 807–812. doi:10.1128/AEM.68.2.807-812.2002. PMC 126686. PMID 11823222.
  30. ^ Pierson, B. K.; Giovannoni, S. J.; Stahl, D. A.; Castenholz, R. W. (1985). "Heliothrix oregonensis, gen. Nov., sp. Nov., a phototrophic filamentous gliding bacterium containing bacteriochlorophyll a". Archives of Microbiology. 142 (2): 164–167. doi:10.1007/BF00447061. PMID 2412519.
  31. ^ Hanada, S.; Takaichi, S.; Matsuura, K.; Nakamura, K. (2002). "Roseiflexus castenholzii gen. nov., sp. nov., a thermophilic, filamentous, photosynthetic bacterium that lacks chlorosomes". International Journal of Systematic and Evolutionary Microbiology. 52 (Pt 1): 187–193. doi:10.1099/00207713-52-1-187. PMID 11837302.
  32. ^ Hanada, S.; Hiraishi, A.; Shimada, K.; Matsuura, K. (1995). "Chloroflexus aggregans sp. nov., a Filamentous Phototrophic Bacterium Which Forms Dense Cell Aggregates by Active Gliding Movement". International Journal of Systematic Bacteriology. 45 (4): 676–681. doi:10.1099/00207713-45-4-676. PMID 7547286.
  33. ^ Pierson, B. K.; Castenholz, R. W. (1974). "A phototrophic gliding filamentous bacterium of hot springs, Chloroflexus aurantiacus, gen. And sp. Nov". Archives of Microbiology. 100 (1): 5–24. doi:10.1007/BF00446302. PMID 4374148.
  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

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