Chloroflexi (phylum)

Chloroflexi
Chloroflexus
Scientific classification
Domain:	Bacteria
Phylum:	Chloroflexi (Garrity and Holt 2001) Hugenholtz and Stackebrandt 2004
Classes
Anaerolineae "Chloroflexi" "Dehalococcoidetes" Ktedonobacteria Thermomicrobia
Synonyms
Chlorobacteria

The Chloroflexi or Chlorobacteria 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, and anaerobic halorespirers, which uses halogenated organics (such as the toxic chlorinated ethenes and 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]

For relation to other phyla, see Bacterial phyla.

History

See also: Bacterial taxonomy and bacterial phyla

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 Cloroflexi.^[4] Since 2001 however, new classes have been created thanks to newly discovered species, therefore currently the phylum Chloroflexi is divided into:^[5]

• "Chloroflexi" (Garrity & Holt, 2001)
• 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]

Taxonomy

See also: Bacterial taxonomy

The currently accepted taxonomy is as follows:^[5]

Class Anaerolineae

• Order Anaerolineales
  • Family Anaerolineaceae
    • Genus Anaerolinea Sekiguchi et al. 2003 emend. Yamada et al. 2006
      • A. thermolimosa Yamada et al. 2006
      • A. thermophila Sekiguchi et al. 2003
    • Genus Bellilinea Yamada et al. 2007
      • Bellilinea caldifistulae Yamada et al. 2007
    • Genus Leptolinea Yamada et al. 2006
      • Leptolinea tardivitalis Yamada et al. 2006
    • Genus Levilinea Yamada et al. 2006
      • Levilinea saccharolytica Yamada et al. 2006
    • Genus Longilinea Yamada et al. 2007
      • Longilinea arvoryzae Yamada et al. 2007
• Order Caldilineales
  • Family Caldilineaceae
    • Genus Caldilinea Sekiguchi et al. 2003
      • C. aerophila Sekiguchi et al. 2003
      • C. tarbellica Gregoire et al. 2010

Class Caldilineae

• Order Caldilineales
  • Family Caldilineaceae
    • Genus Caldilinea

Class "Chloroflexi (class)"

• Order "Chloroflexales"
  • Family "Chloroflexaceae"
    • Genera: Chloroflexus, Chloronema, Heliothrix, Roseiflexus
  • Family Oscillochloridaceae
    • Genus Oscillochloris
• Order "Herpetosiphonales"
  • Family "Herpetosiphonaceae"
    • Genus Herpetosiphon

• Class "Dehalococcoidetes"
  • Order not defined (would be "Dehalococcoidetales" or "Dehalogenimonadales")
    • Family not defined (would be "Dehalogenimonadaceae")
      • Genus Dehalogenimonas
  • Order not defined (would be "Dehalococcoidetales" or "Dehalogenimonadales")
    • Family not defined (would be "Dehalococcoidetaceae")
      • Genus "Dehalococcoides"

Class Ktedonobacteria

• Order Ktedonobacterales
  • Family Ktedonobacteraceae
    • Genus Ktedonobacter Cavaletti et al. 2007
      • Ktedonobacter racemifer Cavaletti et al. 2007
  • Family Thermosporotrichaceae
    • Genus Thermosporothrix Yabe et al. 2010
      • Thermosporothrix hazakensis Yabe et al. 2010
• Order Thermogemmatisporales
  • Family Thermogemmatisporaceae
    • Genus Thermogemmatispora Yabe et al. 2010
      • T. foliorum Yabe et al. 2010
      • T. onikobensis Yabe et al. 2010

Class Thermomicrobia

• Order Thermomicrobiales
  • Family Thermomicrobiaceae
    • Genus Thermomicrobium
• Order Sphaerobacterales
  • Family Sphaerobacteraceae
    • Genus Sphaerobacter

Additionally, there are several strains which have not been fully described, these include Candidatus "Chlorothrix halophila" and "Dehalococcoides ethenogenes".^[9]

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)^[10] meaning "greenish-yellow" and the Latin masculine passive perfect participle flexus (of flecto)^[11] 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 phyla with the same root is Chlorobi, whereas Cyanobacteria has the root cyanos (κύανος) meaning "blue-green"^[12]

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. doi:10.1016/j.tim.2010.06.005. PMID 20637628.  edit
2. ^ Holland L. (22). "Woese,Carl in the forefront of bacterial evolution revolution". scientist 4 (10). 
3. ^ Woese, CR (1987). "Bacterial evolution". Microbiological reviews 51 (2): 221–71. PMC 373105. PMID 2439888. http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=373105.  edit
4. ^ ^{a b c} George M. Garrity, ed (July 26, 2005) [1984(Williams & Wilkins)]. Introductory Essays. Bergey's Manual of Systematic Bacteriology. 2A (2nd ed.). New York: Springer. pp. 304. ISBN 978-0-387-24143-2. British Library no. GBA561951. http://www.springer.com/life+sciences/book/978-0-387-24143-2. 
5. ^ ^{a b} Bacterial classification entry in LPSN [Euzéby, J.P. (1997). "List of Bacterial Names with Standing in Nomenclature: a folder available on the Internet". Int J Syst Bacteriol 47 (2): 590-2. doi:10.1099/00207713-47-2-590. ISSN 0020-7713. PMID 9103655. http://ijs.sgmjournals.org/cgi/reprint/47/2/590. ]
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. doi:10.1099/ijs.0.03028-0. PMID 15545432.  edit
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. doi:10.1126/science.276.5318.1568. PMID 9171062.  edit
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. doi:10.1099/ijs.0.011502-0.  edit
9. ^ See the NCBI webpage on Chloroflexi. Data extracted from the "NCBI taxonomy resources". National Center for Biotechnology Information. http://www.ncbi.nlm.nih.gov/Taxonomy/taxonomyhome.html/index.cgi. Retrieved 2011-06-05. 
10. ^ χλωρός. Liddell, Henry George; Scott, Robert; A Greek–English Lexicon at Perseus Project
11. ^ Lewis & Short...
12. ^ κύανος. Liddell, Henry George; Scott, Robert; A Greek–English Lexicon at Perseus Project