Biology:Chloroflexia

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Short description: Class of bacteria

Chloroflexia
Scientific classification e
Domain: Bacteria
Phylum: Chloroflexota
Class: Chloroflexia
corrig. Gupta et al. 2013
Orders
Synonyms
  • "Chloroflexia" Castenholz 2001
  • "Chlorobacteria" Cavalier-Smith 2002
  • "Chloroflexi" Gupta et al. 2013

The Chloroflexia are a class of bacteria in the phylum Chloroflexota. Chloroflexia are typically filamentous, and can move about through bacterial gliding. It is named after the order Chloroflexales.[1]

Etymology

The name "Chloroflexi" is a Neolatin plural of "Chloroflexus", which is the name of the first genus described. The noun is a combination of the Greek chloros (χλωρός)[2] meaning "greenish-yellow" and the Latin flexus (of flecto)[3] meaning "bent" to mean "a green bending".[4] The name is not due to chlorine, an element confirmed as such in 1810 by Sir Humphry Davy and named after its pale green colour.

Taxonomy and molecular signatures

The Chloroflexia class is a group of deep branching photosynthetic bacteria (with the exception of Herpetosiphon and Kallotenue species) that currently consist of three orders: Chloroflexales, Herpetosiphonales, and Kallotenuales.[1][5][6][7][8] The Herpetosiphonales and Kallotenuales each consist of a single genus within its own family, Herpetosiphonaceae (Herpetosiphon) and Kallotenuaceae (Kallotenue), respectively, whereas the Chloroflexales are more phylogenetically diverse.[1][5][7]

Microscopic distinguishing characteristics

Members of the phylum Chloroflexota are monoderms and stain mostly Gram negative, whereas most bacteria species are diderms and stain Gram negative, with the Gram positive exceptions of the Bacillota (low GC Gram positives), Actinomycetota (high GC, Gram positives), and the Deinococcota (Gram positive, diderms with thick peptidoglycan).[9][10][11]

Genetic distinguishing characteristics

Comparative genomic analysis has recently refined the taxonomy of the class Chloroflexia, dividing the Chloroflexales into the suborder Chloroflexineae consisting of the families Oscillachloridaceae and Chloroflexaceae, and the suborder Roseiflexineae containing family Roseiflexaceae.[1] The revised taxonomy was based on the identification of a number of conserved signature indels (CSIs) which serve as highly reliable molecular markers of shared ancestry.[12][13][14][15]

Physiological distinguishing characteristics

Additional support for the division of the Chloroflexales into two suborders is the observed differences in physiological characteristics where each suborder is characterized by distinct carotenoids, quinones, and fatty acid profiles that are consistently absent in the other suborder.[1][16][17]

In addition to demarcating taxonomic ranks, CSIs may play a role in the unique characteristics of members within the clade: In particular, a four-amino-acid insert in the protein pyruvate flavodoxin/ferredoxin oxidoreductase, a protein which plays important roles in photosynthetic organisms, has been found exclusively among all members in the genus Chloroflexus, and is thought to play an important functional role.[18][19]

Additional work has been done using CSIs to demarcate the phylogenetic position of Chloroflexia relative to other photosynthetic groups such as the Cyanobacteria.[20] Chloroflexia shares a number of CSIs with Chlorobiota in the chlorophyll-synthesizing proteins. As the two lineages are not otherwise closely related, the interpretation is that the CSIs are the result of a horizontal gene transfer event between the two. Chloroflexia in turn acquired these proteins by another HGT from a "Clade C" marine cyanobacteria.[21]

Phylogeny

16S rRNA based LTP_08_2023[22][23][24] 120 marker proteins based GTDB 07-RS207[25][26][27]
 
"Thermomicrobiia"
Sphaerobacterales
Sphaerobacteraceae
 

Nitrolancea

 
 

Sphaerobacter

 
 
 
Thermomicrobiales
Thermomicrobiaceae
 

Thermalbibacter

 
 
 

Thermomicrobium

 
 

Thermorudis

 
 
 
 
 
Chloroflexia
 
Kallotenuales
Kallotenuaceae

Kallotenue

 
 
 
 
Herpetosiphonales
Herpetosiphonaceae

Herpetosiphon

 
 
Chloroflexales
Roseiflexaceae

Roseiflexus

 
Chloroflexaceae
 

Heliothrix

 
 
 

Oscillochloris

 
 

Chloroflexus

 
 
 
 
 
 
 
Chloroflexia
 
"Thermobaculales"
"Thermobaculaceae"

Thermobaculum

 
 
Thermomicrobiales
Thermomicrobiaceae
 
 

Nitrolancea

 
 

Sphaerobacter

 
 
 
 

Thermomicrobium

 
 

Thermorudis

 
 
 
 
 
 
Chloroflexales
 
Herpetosiphonaceae

Herpetosiphon

 
 
 
Roseiflexaceae
 

"Kouleothrix"

 
 

Roseiflexus

 
 
Chloroflexaceae
 

Chloroflexus

 
 
 

Oscillochloris

 
 
 

"Ca. Chloroploca"

 
 

"Ca. Viridilinea"

 
 
 
 
 
 
 
 

Taxonomy

The currently accepted taxonomy is as follows:[1][5][28]

Class Chloroflexia Gupta et al. 2013

  • Genus "Dehalobium" Wu et al. 2002[29]
  • Genus "Candidatus Lithoflexus" Saghai et al. 2020
  • Genus "Candidatus Sarcinithrix" Nierychlo et al. 2019
  • Order "Thermobaculales"
    • Family "Thermobaculaceae"
      • Genus "Thermobaculum" Botero et al. 2004
  • Order Kallotenuales Cole et al. 2013
    • Family Kallotenuaceae Cole et al. 2013
      • Genus Kallotenue Cole et al. 2013
  • Order Herpetosiphonales Gupta et al. 2013
    • Family Herpetosiphonaceae Gupta et al. 2013
      • Genus "Candidatus Anthektikosiphon" Ward, Fischer & McGlynn 2020
      • Genus Herpetosiphon Holt & Lewin 1968 [Flavilitoribacter García-López et al. 2020]
  • Order Chloroflexales Gupta et al. 2013
    • Suborder Roseiflexineae Gupta et al. 2013
      • Family Roseiflexaceae Gupta et al. 2013 ["Kouleotrichaceae" Mehrshad et al. 2018]
        • Genus "Kouleothrix" Kohno et al. 2002
        • Genus Heliothrix Pierson et al. 1986
        • Genus Roseiflexus Hanada et al. 2002
    • Suborder Chloroflexineae Gupta et al. 2013
      • Family Chloroflexaceae Gupta et al. 2013
        • Genus Candidatus Chloranaerofilum Thiel et al. 2016
        • Genus Chloroflexus Pierson & Castenholz 1974 ["Chlorocrinis"]
      • Family Oscillochloridaceae Gupta et al. 2013
        • Genus Candidatus Chloroploca Gorlenko et al. 2014
        • Genus Chloronema ♪ Dubinina & Gorlenko 1975
        • Genus Oscillochloris Gorlenko & Pivovarova 1989
        • Genus Candidatus Viridilinea Grouzdev et al. 2018

See also

References

  1. ↑ 1.0 1.1 1.2 1.3 1.4 1.5 "Phylogenetic framework and molecular signatures for the class Chloroflexia and its different clades; proposal for division of the class Chloroflexia class. nov. [corrected] 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. 2013. doi:10.1007/s10482-012-9790-3. PMID 22903492. 
  2. ↑ χλωρός. Liddell, Henry George; Scott, Robert; A Greek–English Lexicon at the Perseus Project
  3. ↑ Lewis, Charlton T. and Charles Short, A Latin Dictionary. Oxford: Clarendon Press, 1879. Online version at Perseus
  4. ↑ Brenner, Don J.; Krieg, Noel R.; James T. Staley (July 26, 2005). Garrity, George M.. ed. Bergey's Manual of Systematic Bacteriology. 2A (2nd ed.). New York: Springer (orig-pub London: Williams & Wilkins). p. 304. British Library no. GBA561951. ISBN 978-0-387-24143-2. https://www.springer.com/life+sciences/book/978-0-387-24143-2. 
  5. ↑ 5.0 5.1 5.2 "Kallotenue papyrolyticum gen. nov., sp. nov., a cellulolytic and filamentous thermophile that represents a novel lineage (Kallotenuales ord. nov., Kallotenuaceae fam. nov.) within the class Chloroflexia". Int. J. Syst. Evol. Microbiol. 63 (Part 12): 4675–82. 2013. doi:10.1099/ijs.0.053348-0. PMID 23950149. 
  6. ↑ "Evolutionary relationships among photosynthetic prokaryotes (Heliobacterium chlorum, Chloroflexus aurantiacus, cyanobacteria, Chlorobium tepidum and proteobacteria): Implications regarding the origin of photosynthesis". Mol Microbiol 32 (5): 893–906. 1999. doi:10.1046/j.1365-2958.1999.01417.x. PMID 10361294. 
  7. ↑ 7.0 7.1 "Chloroflexia". National Center for Biotechnology Information (NCBI). https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Undef&id=32061&lvl=3&p=mapview&p=has_linkout&p=blast_url&p=genome_blast&srchmode=1&keep=1&unlock. Retrieved 2016-10-25. 
  8. ↑ "List of new names and new combinations previously effectively, but not validly, published". Int. J. Syst. Evol. Microbiol. 63: 1577–1580. 2013. doi:10.1099/ijs.0.052571-0. 
  9. ↑ 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. 
  10. ↑ "Comparative proteome analysis of Acidaminococcus intestini supports a relationship between outer membrane biogenesis in Negativicutes and Proteobacteria". Arch. Microbiol. 196 (4): 307–310. 2014. doi:10.1007/s00203-014-0964-4. PMID 24535491. http://nrl.northumbria.ac.uk/16439/1/AOMI-D-14-00009.pdf. 
  11. ↑ "Evolutionary relationships among photosynthetic bacteria". Photosynth Res 76 (1–3): 173–183. 2003. doi:10.1023/A:1024999314839. PMID 16228576. http://ovidsp.ovid.com/ovidweb.cgi?T=JS&PAGE=linkout&SEARCH=16228576.ui. 
  12. ↑ Gupta, R.S. (2016). "Impact of genomics on the understanding of microbial evolution and classification: The importance of Darwin's views on classification". FEMS Microbiol. Rev. 40 (4): 520–553. doi:10.1093/femsre/fuw011. PMID 27279642. 
  13. ↑ Gupta, R.S. (1998). "Protein phylogenies and signature sequences: A reappraisal of evolutionary relationships among archaebacteria, eubacteria, and eukaryotes". Microbiology and Molecular Biology Reviews 62 (4): 1435–1491. doi:10.1128/MMBR.62.4.1435-1491.1998. PMID 9841678. 
  14. ↑ Rokas, A.; Holland, P.W. (2000). "Rare genomic changes as a tool for phylogenetics". Trends in Ecology & Evolution 15 (11): 454–459. doi:10.1016/S0169-5347(00)01967-4. PMID 11050348. 
  15. ↑ Gupta, R.S.; Griffiths, E. (2002). "Critical issues in bacterial phylogeny". Theoretical Population Biology 61 (4): 423–434. doi:10.1006/tpbi.2002.1589. PMID 12167362. 
  16. ↑ Hanada, S.; Pierson, B.K. (2006). The Prokaryotes: A handbook on the biology of bacteria. New York: Springer. pp. 815–842. 
  17. ↑ Pierson, B.K.; Castenholz, R.W. (1992). The Prokaryotes. New York: Springer. pp. 3754–3775. 
  18. ↑ "Molecular signatures for the main phyla of photosynthetic bacteria and their subgroups". Photosynth. Res. 104 (2–3): 357–372. 2010. doi:10.1007/s11120-010-9553-9. PMID 20414806. 
  19. ↑ Stolz, F.M.; Hansmann, I. (1990). "An MspI RFLP detected by probe pFMS76 D20S23 isolated from a flow-sorted chromosome 20-specific DNA library". Nucleic Acids Research 18 (7): 1929. doi:10.1093/nar/18.7.1929. PMID 1692410. 
  20. ↑ "Novel insights into the origin and diversification of photosynthesis based on analyses of conserved indels in the core reaction center proteins". Photosynth Res 131 (2): 159–171. 2016. doi:10.1007/s11120-016-0307-1. PMID 27638319. 
  21. ↑ "Origin and spread of photosynthesis based upon conserved sequence features in key bacteriochlorophyll biosynthesis proteins". Mol Biol Evol 29 (11): 3397–412. 2012. doi:10.1093/molbev/mss145. PMID 22628531. 
  22. ↑ "The LTP". https://imedea.uib-csic.es/mmg/ltp/#LTP. 
  23. ↑ "LTP_all tree in newick format". https://imedea.uib-csic.es/mmg/ltp/wp-content/uploads/ltp/LTP_all_08_2023.ntree. 
  24. ↑ "LTP_08_2023 Release Notes". https://imedea.uib-csic.es/mmg/ltp/wp-content/uploads/ltp/LTP_08_2023_release_notes.pdf. 
  25. ↑ "GTDB release 07-RS207". https://gtdb.ecogenomic.org/about#4%7C. 
  26. ↑ "bac120_r207.sp_labels". https://data.gtdb.ecogenomic.org/releases/release207/207.0/auxillary_files/bac120_r207.sp_labels.tree. 
  27. ↑ "Taxon History". https://gtdb.ecogenomic.org/taxon_history/. 
  28. ↑ Classification of Chloroflexi 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 (Microbiology Society) 47 (2): 590–2. doi:10.1099/00207713-47-2-590. ISSN 0020-7713. PMID 9103655. https://ijs.microbiologyresearch.org/content/journal/ijsem/10.1099/00207713-47-2-590. Retrieved 2019-02-23. ]
  29. ↑ 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. doi:10.1128/AEM.68.2.807-812.2002. PMID 11823222. 


Further reading

External links

External links

Wikidata ☰ Q15732012 entry



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