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Chloroflexota

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.

Chloroflexota
Scientific classification Edit this classification
Domain: Bacteria
Clade: Terrabacteria
Phylum: Chloroflexota
Garrity and Holt 2021[1]
Classes
Synonyms
  • "Chlorobacteria" Cavalier-Smith 2006
  • "Chloroflexi" Garrity and Holt 2001
  • "Eobacteria" Cavalier-Smith 2002
  • "Chloroflexota" Whitman et al. 2018
  • "Chloroflexaeota" Oren et al. 2015
  • Thermomicrobiota Oren & Garrity 2021

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), Actinomycetota (high-G+C gram-positives) and Deinococcota (gram-positive diderms with thick peptidoglycan).

History

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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.[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

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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_08_2023[13][14][15] 120 marker proteins based GTDB 08-RS214 (28th April 2023).[16][17][18]
"Caldilineia"
Caldilineales
Caldilineaceae
Ktedonobacteria
Thermogemmatisporales
Thermogemmatisporaceae

Thermogemmatispora

Ktedonobacteriales
Thermosporotrichaceae

Thermosporothrix

Ktedonobacteraceae

Ktedonobacter

Ktedonosporobacteraceae

Ktedonosporobacter

Reticulibacteraceae

Reticulibacter

Dictyobacteraceae
Thermoflexia
Thermoflexales
Thermoflexaceae

Thermoflexus

"Thermomicrobiia"
Chloroflexia
Kallotenuales
Kallotenuaceae

Kallotenue

Herpetosiphonales
Herpetosiphonaceae

Herpetosiphon

Chloroflexales
Roseiflexaceae

Roseiflexus

Chloroflexaceae
"Limnocylindria"
"Limnocylindrales"
"Limnocylindraceae"

"Ca Aquidulcis"

Ktedonobacteria
"Caldilineia"
⊞
⊟
Ardenticatenales
Ardenticatenaceae

Ardenticatena

"Caldilineidae"
Caldilineales
Caldilineaceae
"Anaerolineidae"
J036
"Roseilineaceae"

"Ca. Roseilinea"

Thermoflexales
Thermoflexaceae

Thermoflexus

"Promineofilales"
"Promineofilaceae"

"Ca. Promineifilum"

Chloroflexia
"Thermobaculales"
"Thermobaculaceae"

Thermobaculum

Thermomicrobiales
Chloroflexales
Herpetosiphonaceae

Herpetosiphon

Roseiflexaceae
Chloroflexaceae

Taxonomy

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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[22]]
Genus "Candidatus Nitrocaldera" Spieck et al. 2020
Genus "Candidatus Nitrotheca" Spieck et al. 2020
Genus "Candidatus Poriflexus" Kogawa et al. 2022
Class "Limnocylindria" Mehrshad et al. 2018

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

Class "Umbricyclopia" Mehrshad et al. 2018

Class "Bathosphaeria" Mehrshad et al. 2018

Class Tepidiformia Kochetkova et al. 2020

Class Dehalococcoidia Löffler et al. 2013

Class "Thermofontia" corrig. Ward et al. 2018

Class Ardenticatenia Kawaichi et al. 2013

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

Class Thermoflexia Dodsworth et al. 2014

Class "Anaerolineia" Oren, Parte & Garrity 2016

Class Thermomicrobiia Oren, Parte & Garrity 2016

Class "Spiritibacteria" Williams et al. 2024

Class "Martimicrobia" Williams et al. 2024

Class "Tarhunnaeia" Williams et al. 2024

Class "Uliximicrobia" Williams et al. 2024

Class Chloroflexia Gupta et al. 2013

Etymology

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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),[27] meaning "greenish-yellow," and the Latin masculine passive perfect participle flexus (of flecto),[28] 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."[29]

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

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References

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  1. ^ 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. ^ 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. ^ 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.
  4. ^ Holland L. (22 May 1990). "Woese,Carl in the forefront of bacterial evolution revolution". Scientist. 4 (10).
  5. ^ 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.
  6. ^ 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. Vol. 2A (2nd ed.). New York: Springer. p. 304. ISBN 978-0-387-24143-2. British Library no. GBA561951.
  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. S2CID 17656551.
  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. ^ "The LTP". Retrieved 20 November 2023.
  14. ^ "LTP_all tree in newick format". Retrieved 20 November 2023.
  15. ^ "LTP_08_2023 Release Notes" (PDF). Retrieved 20 November 2023.
  16. ^ "GTDB release 08-RS214". Genome Taxonomy Database. Retrieved 10 May 2023.
  17. ^ "bac120_r214.sp_label". Genome Taxonomy Database. Retrieved 10 May 2023.
  18. ^ "Taxon History". Genome Taxonomy Database. Retrieved 10 May 2023.
  19. ^ a b c d e 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.
  20. ^ 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.
  21. ^ a b c 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.
  22. ^ 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. S2CID 23854988.
  23. ^ 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.
  24. ^ 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.
  25. ^ 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.
  26. ^ 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. Bibcode:2002ApEnM..68..807W. doi:10.1128/AEM.68.2.807-812.2002. PMC 126686. PMID 11823222.
  27. ^ χλωρός. Liddell, Henry George; Scott, Robert; A Greek–English Lexicon at the Perseus Project
  28. ^ Lewis & Short...
  29. ^ κύανος. Liddell, Henry George; Scott, Robert; A Greek–English Lexicon at the Perseus Project
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