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Green Non Sulfur Bacteria

Chloroflexi

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.

Most bacteria, in terms of diversity, are diderms and stain gram-negative, notable exceptions being Bacillota (low G+C gram-positives), Actinomycetota (high-G+C gram-positives) and Deinococcota (gram-positive diderms with thick peptidoglycan). In contrast, the members of the phylum Chloroflexota are monoderms, but stain mostly gram-negative.[2]

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.[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] The phylogeny is based on 16S rRNA-based LTP release 132 by The All-Species Living Tree Project[13]

       

Thermoflexus hugenholtzii Dodsworth et al. 2014

    Dehalococcoidaceae

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

              Caldilineaceae

Litorilinea aerophila Kale et al. 2013

Caldilinea

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

   

C. tarbellica Grégoire et al. 2011

        Ardenticatenaceae

Ardenticatena maritima Kawaichi et al. 2013

Anaerolineaceae

Thermomarinilinea lacunifontana Nunoura et al. 2013

    Anaerolinea

A. thermolimosa Yamada et al. 2006[14]

   

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

       

Flexilinea flocculi Sun et al. 2015

     

Ornatilinea apprima Podosokorskaya et al. 2013

     

Levilinea saccharolytica Yamada et al. 2006[14]

       

Bellilinea caldifistulae Yamada et al. 2007

   

Pelolinea submarina Imachi et al. 2014

       

Leptolinea tardivitalis Yamada et al. 2006[14]

   

Longilinea arvoryzae Yamada et al. 2007[16]

                          Ktedonobacteria Thermogemmatispora

T. foliorum Yabe et al. 2011

     

T. carboxidivorans King & King 2014

   

T. onikobensis Yabe et al. 2011 (type sp.)

      Ktedonobacteriales Ktedonobacteraceae

Dictyobacter aurantiacus Yabe et al. 2017

   

Ktedonobacter racemifer corrig. Cavaletti et al. 2007

    Thermosporothrix

T. hazakensis Yabe et al. 2010

   

T. narukonensis Yabe, Sakai & Yokota 2016

         

Thermomicrobiota

    Chloroflexia Herpetosiphon

H. aurantiacus Holt & Lewin 1968

   

H. geysericola Lewin 1970

      Kallotenuaceae

Kallotenue papyrolyticum Cole et al. 2013

Chloroflexales Roseiflexaceae

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 Chlorothrix" Klappenbach & Pierson 2004[17]

Class Thermoflexia Dodsworth et al. 2014

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

Class Anaerolineae Yamada et al. 2006

Class Ardenticatenia Kawaichi et al. 2013

Class Caldilineae Yamada et al. 2006

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

Class Chloroflexia Gupta et al. 2013

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),[31] meaning "greenish-yellow," and the Latin masculine passive perfect participle flexus (of flecto),[32] 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."[33]

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.

References

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  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. S2CID 23854988.
  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.
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  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.
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  31. ^ χλωρός. Liddell, Henry George; Scott, Robert; A Greek–English Lexicon at the Perseus Project
  32. ^ Lewis & Short...
  33. ^ κύανος. Liddell, Henry George; Scott, Robert; A Greek–English Lexicon at the Perseus Project
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Chloroflexota: Brief Summary

provided by wikipedia EN

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.

Most bacteria, in terms of diversity, are diderms and stain gram-negative, notable exceptions being Bacillota (low G+C gram-positives), Actinomycetota (high-G+C gram-positives) and Deinococcota (gram-positive diderms with thick peptidoglycan). In contrast, the members of the phylum Chloroflexota are monoderms, but stain mostly gram-negative.

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