Chloroflexota

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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.[2] 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) and Actinomycetota (high-G+C gram-positives).

History

Script error: No such module "Labelled list hatnote". 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.[3]

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",[4][5] which was temporarily renamed as "Chloroflexi" in Volume One of Bergey's Manual of Systematic Bacteriology.[6]

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.[6] 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,[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 Chloroflexota 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]

16S rRNA based LTP_10_2024[13][14][15] 120 marker proteins based GTDB release 10-RS226[16][17][18]

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Taxonomy

Genus "Candidatus Caldibacter" corrig. Spieck et al. 2020
Genus "Candidatus Chlorotrichoides" corrig. Oren et al. 2020 ["Candidatus Chlorothrix" Klappenbach & Pierson 2004 non Dyar 1921 non Berger-Perrot 1982[19]]
Genus "Candidatus Nitrocaldera" Spieck et al. 2020
Genus "Candidatus Nitrotheca" Spieck et al. 2020
Class "Bathosphaeria" Mehrshad et al. 2018

  • Order "Bathosphaerales" Mehrshad et al. 2018
    • Family "Bathosphaeraceae" Mehrshad et al. 2018
      • Genus ?"Candidatus Bathosphaera" Mehrshad et al. 2018 (JG30-KF-CM66)

Class "Martimicrobia" Williams et al. 2024

  • Order "Martimicrobiales" Williams et al. 2024
    • Family "Martimicrobiaceae" Williams et al. 2024

Class "Poriflexia" Mehrshad et al. 2018

  • Genus ?"Candidatus Poriflexus" Kogawa et al. 2022

Class "Spiritibacteria" Williams et al. 2024

  • Order "Spiritibacterales" Williams et al. 2024
    • Family "Spiritibacteraceae" Williams et al. 2024

Class "Tarhunnaeia" Williams et al. 2024

  • Order "Tarhunnaeales" Williams et al. 2024
    • Family "Tarhunnaeaceae" Williams et al. 2024
      • Genus ?"Candidatus Sutekhia" Williams et al. 2024
      • Genus ?"Candidatus Tarhunnaea" Williams et al. 2024

Class "Uliximicrobia" Williams et al. 2024

  • Order "Uliximicrobiales" Williams et al. 2024
    • Family "Uliximicrobiaceae" Williams et al. 2024

Class "Umbricyclopia" Mehrshad et al. 2018

  • Order "Umbricyclopales" Mehrshad et al. 2018
    • Family "Umbricyclopaceae" Mehrshad et al. 2018
      • Genus ?"Candidatus Umbricyclops" Mehrshad et al. 2018 (TK10)

Class "Limnocylindria" Mehrshad et al. 2018

  • Order "Limnocylindrales" Mehrshad et al. 2018
    • Family "Limnocylindraceae" Mehrshad et al. 2018 (SL56)

Class Ktedonobacteria Cavaletti et al. 2007 emend. Yabe et al. 2010

  • Order Thermogemmatisporales Yabe et al. 2011
  • Order Ktedonobacterales Cavaletti et al. 2007

Class Thermomicrobiia Oren, Parte & Garrity 2016

Class Chloroflexia Gupta et al. 2013

Class Tepidiformia Kochetkova et al. 2020

  • Order Tepidiformales Kochetkova et al. 2020
    • Family Tepidiformaceae Kochetkova et al. 2020

Class Dehalococcoidia Löffler et al. 2013

  • Order Dehalococcoidales Löffler et al. 2013
  • Order "Lucifugimonadales" Lim et al. 2023
    • Family "Lucifugimonadaceae" Lim et al. 2023
      • Genus "Candidatus Lucifugimonas" Lim et al. 2023 [SAR202; UBA1151]
  • Order "Australimonadales" Prabhu et al. 2024
    • Family "Australimonadaceae" Prabhu et al. 2024
  • Order "Monstramariales" Landry et al. 2017 [SAR202 group III; UBA3495]
    • Family "Monstramariaceae" Landry et al. 2017

Class Ardenticatenia Kawaichi et al. 2013

  • Order Ardenticatenales Kawaichi et al. 2013
    • Family Ardenticatenaceae Kawaichi et al. 2013
  • Order "Epilineales" Petriglieri et al. 2023
    • Family "Epilineaceae" Petriglieri et al. 2023
      • Genus "Candidatus Avedoeria" Petriglieri et al. 2023
      • Genus "Candidatus Epilinea" Petriglieri et al. 2023

Class "Caldilineia" Oren, Parte & Garrity 2016 ex Cavalier-Smith 2020

  • Order Caldilineales Yamada et al. 2006
    • Family "Amarolineaceae" Andersen et al. 2019
      • Genus "Candidatus Amarolinea" Andersen et al. 2019
    • Family Caldilineaceae Yamada et al. 2006

Class Thermoflexia Dodsworth et al. 2014

  • Order Thermoflexales Dodsworth et al. 2014
    • Family "Roseilineaceae" Ward et al. 2021
    • Family Thermoflexaceae Dodsworth et al. 2014

Class "Thermofontia" corrig. Ward et al. 2018

  • Order "Phototrophicales" Zheng et al. 2022
    • Family "Phototrophicaceae" Zheng et al. 2022

Class "Anaerolineia" Oren, Parte & Garrity 2016

  • Genus ?"Candidatus Defluviifilum" Nierychlo et al. 2019
  • Family "Profundisolitariaceae" Mehrshad et al. 2018
  • Order "Promineifilales" Chuvochina et al. 2023
    • Family "Promineifilaceae" Chuvochina et al. 2023
  • Order Aggregatilineales Nakahara et al. 2019
    • Family Aggregatilineaceae Nakahara et al. 2019
  • Order Anaerolineales Yamada et al. 2006

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),[26] meaning "greenish-yellow," and the Latin masculine passive perfect participle flexus (of flecto),[27] meaning "bent."[6] 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."[28]

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.

See also

References

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  1. ^ Page Module:Citation/CS1/styles.css has no content.Oren A, Garrity GM (2021). "Valid publication of the names of forty-two phyla of prokaryotes". Int J Syst Evol Microbiol. 71 (10): 5056. doi:10.1099/ijsem.0.005056. PMID 34694987. S2CID 239887308.
  2. ^ Page Module:Citation/CS1/styles.css has no content.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.
  3. ^ Page Module:Citation/CS1/styles.css has no content.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. Vol. 2A (2nd ed.). New York: Springer. p. 304. ISBN 978-0-387-24143-2. British Library no. GBA561951.
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  7. ^ Page Module:Citation/CS1/styles.css has no content.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. ^ Page Module:Citation/CS1/styles.css has no content.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.
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