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Chloroflexota

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Chloroflexota
Scientific classificationEdit this classification
Domain: Bacteria
Clade: Terrabacteria
Phylum: Chloroflexota
Garrity and Holt 2021[1]
Classes
Synonyms
  • "Chlorobacteria"Cavalier-Smith2006
  • "Chloroflexi"Garrity and Holt 2001
  • "Eobacteria"Cavalier-Smith 2002
  • "Chloroflexota"Whitman et al. 2018
  • "Chloroflexaeota"Oren et al. 2015
  • ThermomicrobiotaOren & Garrity 2021

TheChloroflexotaare aphylumofbacteriacontaining isolates with a diversity of phenotypes, including members that areaerobicthermophiles,which use oxygen and grow well in high temperatures; anoxygenicphototrophs,which use light forphotosynthesis(green non-sulfur bacteria); andanaerobichalorespirers,which uses halogenated organics (such as the toxic chlorinatedethenesandpolychlorinated biphenyls) as electron acceptors.

The members of the phylumChloroflexotaaremonoderms(that is, have one cell membrane with no outer membrane), but they stain mostly gram-negative.[2]Many well-studied phyla of bacteria aredidermsand staingram-negative,whereas well-known monoderms that stain Gram-positive includeFirmicutes(orBacillota) (low G+Cgram-positives),Actinomycetota(high-G+C gram-positives) andDeinococcota(gram-positive diderms with thick peptidoglycan).

History[edit]

See also:Bacterial taxonomyandBacterial phyla

The taxon name was created in the 2001 edition of Volume 1 ofBergey's Manual of Systematic Bacteriologyand is the Latin plural of the nameChloroflexus,the name of thetypegenus of the phylum, acommon practice.[3]

In 1987,Carl Woese,regarded as one of the forerunner of the molecular phylogeny revolution, divided Eubacteria into 11 divisions based on16S ribosomal RNA(SSU) sequences and grouped the generaChloroflexus,HerpetosiphonandThermomicrobiuminto 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 (seeBacterial 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 wasDehalogenimonas 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 RNAidentity, 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 noconserved signature indelswere 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 Chloroflexisensu strictoshould 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[edit]

The currently accepted taxonomy is based on theList of Prokaryotic names with Standing in Nomenclature(LPSN)[11]andNational Center for Biotechnology Information(NCBI).[12]

16S rRNA basedLTP_08_2023[13][14][15] 120 marker proteins basedGTDB08-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"

"CaAquidulcis"

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[edit]

Genus "CandidatusCaldibacter"corrig. Spieck et al. 2020
Genus "CandidatusChlorotrichoides"corrig. Oren et al. 2020[ "CandidatusChlorothrix"Klappenbach & Pierson 2004 non Dyar 1921 non Berger-Perrot 1982[22]]
Genus "CandidatusNitrocaldera"Spieck et al. 2020
Genus "CandidatusNitrotheca"Spieck et al. 2020
Genus "CandidatusPoriflexus"Kogawa et al. 2022
Class "Limnocylindria"Mehrshad et al. 2018

ClassKtedonobacteriaCavaletti et al. 2007 emend. Yabe et al. 2010

Class "Umbricyclopia"Mehrshad et al. 2018

Class "Bathosphaeria"Mehrshad et al. 2018

ClassTepidiformiaKochetkova et al. 2020

ClassDehalococcoidiaLöffler et al. 2013

Class "Thermofontia"corrig. Ward et al. 2018

ClassArdenticateniaKawaichi et al. 2013

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

ClassThermoflexiaDodsworth et al. 2014

Class "Anaerolineia"Oren, Parte & Garrity 2016

ClassThermomicrobiiaOren, 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

ClassChloroflexiaGupta et al. 2013

Etymology[edit]

The nameChloroflexiis a Neolatin nominative case masculine plural ofChloroflexus,which is the name of the first genus described. The noun is a combination of the Greek adjectivechloros, -a, on (χλωρός, -ά, -όν),[27]meaning "greenish-yellow," and the Latin masculine passive perfect participleflexus(offlecto),[28]meaning "bent."[6]The etymology is unrelated tochlorine,an element that was discovered in 1810 bySir Humphry Davyand named after its pale green colour. Another phylum with the same root isChlorobiota,whereas "Cyanobacteria"has the rootcyanos(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[edit]

References[edit]

  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.PMID34694987.S2CID239887308.
  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.PMID20637628.
  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.ISBN978-0-387-24143-2.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.PMC373105.PMID2439888.
  6. ^abcDon 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.ISBN978-0-387-24143-2.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.PMID15545432.
  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.PMID9171062.
  9. ^abMoe, 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.PMID19625421.
  10. ^abcdGupta, 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.PMID22903492.S2CID17656551.
  11. ^J.P. Euzéby."Chloroflexi".List of Prokaryotic names with Standing in Nomenclature(LPSN).Retrieved2018-07-20.
  12. ^Sayers; et al."Chloroflexi".National Center for Biotechnology Information(NCBI) taxonomy database.Retrieved2014-03-20.
  13. ^"The LTP".Retrieved20 November2023.
  14. ^"LTP_all tree in newick format".Retrieved20 November2023.
  15. ^"LTP_08_2023 Release Notes"(PDF).Retrieved20 November2023.
  16. ^"GTDB release 08-RS214".Genome Taxonomy Database.Retrieved10 May2023.
  17. ^"bac120_r214.sp_label".Genome Taxonomy Database.Retrieved10 May2023.
  18. ^"Taxon History".Genome Taxonomy Database.Retrieved10 May2023.
  19. ^abcdeYamada, T.; Sekiguchi, Y.; Hanada, S.; Imachi, H.; Ohashi, A.; Harada, H.; Kamagata, Y. (2006)."Anaerolinea thermolimosasp. nov.,Levilinea saccharolyticagen. nov., sp. nov. AndLeptolinea tardivitalisgen. 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.PMID16738111.
  20. ^Sekiguchi, Y.; Yamada, T.; Hanada, S.; Ohashi, A.; Harada, H.; Kamagata, Y. (2003)."Anaerolinea thermophilagen. nov., sp. nov. AndCaldilinea aerophilagen. 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.PMID14657113.
  21. ^abcYamada, T.; Imachi, H.; Ohashi, A.; Harada, H.; Hanada, S.; Kamagata, Y.; Sekiguchi, Y. (2007)."Bellilinea caldifistulaegen. nov., sp. nov. AndLongilinea arvoryzaegen. 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.PMID17911301.
  22. ^Klappenbach, J. A.; Pierson, B. K. (2004). "Phylogenetic and physiological characterization of a filamentous anoxygenic photoautotrophic bacterium'CandidatusChlorothrix halophila'Gen. Nov., sp. Nov., recovered from hypersaline microbial mats ".Archives of Microbiology.181(1): 17–25.doi:10.1007/s00203-003-0615-7.PMID14655000.S2CID23854988.
  23. ^Yabe, S.; Aiba, Y.; Sakai, Y.; Hazaka, M.; Yokota, A. (2010)."Thermogemmatispora onikobensisgen. nov., sp. nov. AndThermogemmatispora foliorumsp. 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.PMID20495028.
  24. ^Yabe, S.; Aiba, Y.; Sakai, Y.; Hazaka, M.; Yokota, A. (2009)."Thermosporothrix hazakensisgen. 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.PMID19767365.
  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 ofThermanaerothrix daxensisgen. 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.PMID21621938.
  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.PMC126686.PMID11823222.
  27. ^χλωρός.Liddell, Henry George;Scott, Robert;A Greek–English Lexiconat thePerseus Project
  28. ^Lewis & Short...
  29. ^κύανος.Liddell, Henry George;Scott, Robert;A Greek–English Lexiconat thePerseus Project
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