Chloroflexi (phylum)

Chloroflexi (phylum)

Chloroflexi
Scientific classification
Domain: Bacteria
Phylum: Chloroflexi
(Garrity and Holt 2001) Hugenholtz and Stackebrandt 2004
Classes

Class Dehalococcoidia Löffler et al. 2013

Class Anaerolineae Yamada et al. 2006

Class Caldilineae Yamada et al. 2006

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

Class Thermomicrobia Garrity and Holt 2002 emend. Hugenholtz and Stackebrandt 2004

Class Chloroflexia Gupta et al. 2013

Synonyms

Chlorobacteria

The Chloroflexi or Chlorobacteria, known colloquially as Green non-sulfur bacteria, are a polychlorinated biphenyls) as energy sources.

Whereas most Bacteria, in terms of diversity, are diderms and stain Gram negative with the exception of the Firmicutes (low CG Gram positives), Actinobacteria (high CG gram positives) and the Deinococcus-Thermus group (Gram positive, but diderms with thick peptidoglycan), the members of the phylum Chloroflexi are monoderms and stain mostly Gram negative.[1]

Contents

  • History 1
  • Phylogeny 2
  • Etymology 3
  • References 4

History

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 Thermomicrobium into the "Green non-sulfur bacteria and relatives",[2][3] which was temporarily renamed as "Chloroflexi" in Volume One of Bergey's Manual of Systematic Bacteriology.[4]

Being a deep branching phylum (cf. Bacterial phyla) its classification was analysed in Volume One of Bergey's Manual of Systematic Bacteriology and included a single class with the same name, the class Chloroflexi.[4] Since 2001 however, new classes have been created thanks to newly discovered species, therefore currently the phylum Chloroflexi is divided into:[5]

  • 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

Regarding the class "Dehalococcoidetes", the placeholder name was given by Hugenholtz & Stackebrandt, 2004,[6] after "Dehalococcoides ethenogenes" a partially described species in 1997,[7] whereas the first species fully described was Dehalogenimonas lykanthroporepellens by Moe et al. 2009,[8] 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 identity, meaning that they could fall in different families or even orders.[8]

Recent phylogenetic analysis of the Chloroflexi has found very weak support for the grouping together of the different classes currently part of the phylum.[9] The six classes that make up the phylum did not consistently form a well-supported monophyletic 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.[9] 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.[9] 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.[9]

Phylogeny

The currently accepted taxonomy is based on the List of Prokaryotic names with Standing in Nomenclature (LPSN) [10] and National Center for Biotechnology Information (NCBI)[11] and the phylogeny is based on 16S rRNA-based LTP release 115 by 'The All-Species Living Tree' Project [12]



Kouleothrix aurantiacaKohno et al. 2002


Candidatus Chlorothrix halophila [13]


Dehalococcoidaceae

Dehalococcoides mccartyi Löffler et al. 2013

Dehalogenimonas

D. alkenigignens Bowman et al. 2013


D. lykanthroporepellens Moe et al. 2009 (type sp.)




Caldilineaceae

Litorilinea aerophila Kale et al. 2013

Caldilinea

C. aerophila [14] (type sp.)


C. tarbellica [15]



Anaerolineaceae

?Thermanaerothrix daxensis[16]



A. thermolimosa [17]


A. thermophila [14] (type sp.)




Ornatilinea apprima Podosokorskaya et al. 2013




Bellilinea caldifistulae [18]


Levilinea saccharolytica [17]




Leptolinea tardivitalis [17]


Longilinea arvoryzae [18]








  Ktedonobacteria
  Thermogemmatispora

T. foliorum [19]


T. onikobensis [19] (type sp.)


Ktedonobacteriales

Ktedonobacter racemifer corrig.[20]


Thermosporothrix hazakensis [21]




Thermomicrobia

?Thermobaculum terrenum[22]


Thermomicrobium roseum [23]

Sphaerobacteraceae

Nitrolancetus hollandicusSorokin et al. 2012


Sphaerobacter thermophilus [24]



Chloroflexia
Herpetosiphon

H. aurantiacus [25] (type sp.)


H. geysericola [26][27]


Chloroflexales

?Dehalobium chlorocoercia[28]

Roseiflexaceae

Heliothrix oregonensis [29]


Roseiflexus castenholzii [30]


Chloroflexineae
Chloroflexus

C. aggregans [31]


C. aurantiacus [32] (type sp.)


Oscillochloridaceae

Chloronema giganteumDubinina and Gorlenko 1975

Oscillochloris

O. chryseaGorlenko and Pivovarova 1989 (type sp.)


O. trichoides (ex Szafer) Gorlenko and Korotkov 1989 emend. Keppen et al. 2000









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. not cultivated or can not be sustained in culture for more than a few serial passages.

Etymology

The name "Chloroflexi" is a Neolatin nominative case masculine plural of "Chloroflexus", which the name of the first genus described. The noun is a combination of the Greek adjective chloros, -a, on (χλωρός, -ά, -όν)[33] meaning "greenish-yellow" and the Latin masculine passive perfect participle flexus (of flecto)[34] meaning "bent" to mean "a green bending".[4] It should be therefore noted that the etymology is not due to chlorine, an element (dephlogisticated muriatic acid air) which was confirmed as such 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"[35]

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.  
  2. ^ Holland L. (22 May 1990). "Woese,Carl in the forefront of bacterial evolution revolution". scientist 4 (10). 
  3. ^ Woese, C. R. (1987). "Bacterial evolution". Microbiological reviews 51 (2): 221–271.  
  4. ^ 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.  
  5. ^ Bacterial classification entry in  ]
  6. ^ 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.  
  7. ^ 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.  
  8. ^ 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.  
  9. ^ 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.  
  10. ^ J.P. Euzéby. "Chloroflexi".  
  11. ^ Sayers et al. "Chloroflexi".  
  12. ^  
  13. ^ 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.  
  14. ^ a b 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.  
  15. ^ 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.  
  16. ^ 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.  
  17. ^ a b c 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.  
  18. ^ a b 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.  
  19. ^ a b 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.  
  20. ^ 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.  
  21. ^ 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.  
  22. ^ 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.  
  23. ^ 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.  
  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.  
  25. ^ 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.  
  26. ^ Copeland, J. J. (1936). "Yellowstone Thermal Myxophyceae". Annals of the New York Academy of Sciences 36: 4.  
  27. ^ Lewin, R. A. (1970). "NewHerpetosiphonspecies (Flexibacterales)". Canadian Journal of Microbiology 16 (6): 517–520.  
  28. ^ 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.  
  29. ^ 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.  
  30. ^ 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.  
  31. ^ 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.  
  32. ^ 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.  
  33. ^ χλωρός. Liddell, Henry George; Scott, Robert; A Greek–English Lexicon at the Perseus Project
  34. ^ Lewis & Short...
  35. ^ κύανος. Liddell, Henry George; Scott, Robert; A Greek–English Lexicon at the Perseus Project